Starting phenix.real_space_refine on Thu Mar 5 09:31:42 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6odi_20020/03_2026/6odi_20020_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/6odi_20020/03_2026/6odi_20020.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/6odi_20020/03_2026/6odi_20020_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6odi_20020/03_2026/6odi_20020_neut.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6odi_20020/03_2026/6odi_20020.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6odi_20020/03_2026/6odi_20020.map" } resolution = 3.8 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= 0.004 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 126 5.16 5 C 13426 2.51 5 N 3374 2.21 5 O 3976 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 56 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 20902 Number of models: 1 Model: "" Number of chains: 1 Chain: "b" Number of atoms: 1493 Number of conformers: 1 Conformer: "" Number of residues, atoms: 198, 1493 Classifications: {'peptide': 198} Link IDs: {'CIS': 1, 'PTRANS': 8, 'TRANS': 188} Chain breaks: 1 Restraints were copied for chains: c, d, e, f, g, h, i, j, k, l, m, n, o Time building chain proxies: 2.02, per 1000 atoms: 0.10 Number of scatterers: 20902 At special positions: 0 Unit cell: (195.16, 195.16, 109.88, 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 126 16.00 O 3976 8.00 N 3374 7.00 C 13426 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.64 Conformation dependent library (CDL) restraints added in 1.0 seconds 5432 Ramachandran restraints generated. 2716 Oldfield, 0 Emsley, 2716 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5068 Finding SS restraints... Secondary structure from input PDB file: 84 helices and 61 sheets defined 19.2% alpha, 15.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.71 Creating SS restraints... Processing helix chain 'b' and resid 1687 through 1691 removed outlier: 3.725A pdb=" N PHE b1690 " --> pdb=" O ASP b1687 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N VAL b1691 " --> pdb=" O PRO b1688 " (cutoff:3.500A) No H-bonds generated for 'chain 'b' and resid 1687 through 1691' Processing helix chain 'b' and resid 1793 through 1798 Processing helix chain 'b' and resid 1801 through 1806 Processing helix chain 'b' and resid 1807 through 1809 No H-bonds generated for 'chain 'b' and resid 1807 through 1809' Processing helix chain 'b' and resid 1852 through 1863 removed outlier: 3.684A pdb=" N ASN b1856 " --> pdb=" O ALA b1852 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N GLY b1860 " --> pdb=" O ASN b1856 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N GLN b1861 " --> pdb=" O GLN b1857 " (cutoff:3.500A) Processing helix chain 'b' and resid 1899 through 1904 Processing helix chain 'c' and resid 1687 through 1691 removed outlier: 3.724A pdb=" N PHE c1690 " --> pdb=" O ASP c1687 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N VAL c1691 " --> pdb=" O PRO c1688 " (cutoff:3.500A) No H-bonds generated for 'chain 'c' and resid 1687 through 1691' Processing helix chain 'c' and resid 1793 through 1798 Processing helix chain 'c' and resid 1801 through 1806 Processing helix chain 'c' and resid 1807 through 1809 No H-bonds generated for 'chain 'c' and resid 1807 through 1809' Processing helix chain 'c' and resid 1852 through 1863 removed outlier: 3.684A pdb=" N ASN c1856 " --> pdb=" O ALA c1852 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N GLY c1860 " --> pdb=" O ASN c1856 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N GLN c1861 " --> pdb=" O GLN c1857 " (cutoff:3.500A) Processing helix chain 'c' and resid 1899 through 1904 Processing helix chain 'd' and resid 1687 through 1691 removed outlier: 3.724A pdb=" N PHE d1690 " --> pdb=" O ASP d1687 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N VAL d1691 " --> pdb=" O PRO d1688 " (cutoff:3.500A) No H-bonds generated for 'chain 'd' and resid 1687 through 1691' Processing helix chain 'd' and resid 1793 through 1798 Processing helix chain 'd' and resid 1801 through 1806 Processing helix chain 'd' and resid 1807 through 1809 No H-bonds generated for 'chain 'd' and resid 1807 through 1809' Processing helix chain 'd' and resid 1852 through 1863 removed outlier: 3.685A pdb=" N ASN d1856 " --> pdb=" O ALA d1852 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N GLY d1860 " --> pdb=" O ASN d1856 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N GLN d1861 " --> pdb=" O GLN d1857 " (cutoff:3.500A) Processing helix chain 'd' and resid 1899 through 1904 Processing helix chain 'e' and resid 1687 through 1691 removed outlier: 3.725A pdb=" N PHE e1690 " --> pdb=" O ASP e1687 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N VAL e1691 " --> pdb=" O PRO e1688 " (cutoff:3.500A) No H-bonds generated for 'chain 'e' and resid 1687 through 1691' Processing helix chain 'e' and resid 1793 through 1798 Processing helix chain 'e' and resid 1801 through 1806 Processing helix chain 'e' and resid 1807 through 1809 No H-bonds generated for 'chain 'e' and resid 1807 through 1809' Processing helix chain 'e' and resid 1852 through 1863 removed outlier: 3.684A pdb=" N ASN e1856 " --> pdb=" O ALA e1852 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N GLY e1860 " --> pdb=" O ASN e1856 " (cutoff:3.500A) removed outlier: 3.978A pdb=" N GLN e1861 " --> pdb=" O GLN e1857 " (cutoff:3.500A) Processing helix chain 'e' and resid 1899 through 1904 Processing helix chain 'f' and resid 1687 through 1691 removed outlier: 3.724A pdb=" N PHE f1690 " --> pdb=" O ASP f1687 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N VAL f1691 " --> pdb=" O PRO f1688 " (cutoff:3.500A) No H-bonds generated for 'chain 'f' and resid 1687 through 1691' Processing helix chain 'f' and resid 1793 through 1798 Processing helix chain 'f' and resid 1801 through 1806 Processing helix chain 'f' and resid 1807 through 1809 No H-bonds generated for 'chain 'f' and resid 1807 through 1809' Processing helix chain 'f' and resid 1852 through 1863 removed outlier: 3.684A pdb=" N ASN f1856 " --> pdb=" O ALA f1852 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N GLY f1860 " --> pdb=" O ASN f1856 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N GLN f1861 " --> pdb=" O GLN f1857 " (cutoff:3.500A) Processing helix chain 'f' and resid 1899 through 1904 Processing helix chain 'g' and resid 1687 through 1691 removed outlier: 3.724A pdb=" N PHE g1690 " --> pdb=" O ASP g1687 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N VAL g1691 " --> pdb=" O PRO g1688 " (cutoff:3.500A) No H-bonds generated for 'chain 'g' and resid 1687 through 1691' Processing helix chain 'g' and resid 1793 through 1798 Processing helix chain 'g' and resid 1801 through 1806 Processing helix chain 'g' and resid 1807 through 1809 No H-bonds generated for 'chain 'g' and resid 1807 through 1809' Processing helix chain 'g' and resid 1852 through 1863 removed outlier: 3.685A pdb=" N ASN g1856 " --> pdb=" O ALA g1852 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N GLY g1860 " --> pdb=" O ASN g1856 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N GLN g1861 " --> pdb=" O GLN g1857 " (cutoff:3.500A) Processing helix chain 'g' and resid 1899 through 1904 Processing helix chain 'h' and resid 1687 through 1691 removed outlier: 3.724A pdb=" N PHE h1690 " --> pdb=" O ASP h1687 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N VAL h1691 " --> pdb=" O PRO h1688 " (cutoff:3.500A) No H-bonds generated for 'chain 'h' and resid 1687 through 1691' Processing helix chain 'h' and resid 1793 through 1798 Processing helix chain 'h' and resid 1801 through 1806 Processing helix chain 'h' and resid 1807 through 1809 No H-bonds generated for 'chain 'h' and resid 1807 through 1809' Processing helix chain 'h' and resid 1852 through 1863 removed outlier: 3.685A pdb=" N ASN h1856 " --> pdb=" O ALA h1852 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N GLY h1860 " --> pdb=" O ASN h1856 " (cutoff:3.500A) removed outlier: 3.978A pdb=" N GLN h1861 " --> pdb=" O GLN h1857 " (cutoff:3.500A) Processing helix chain 'h' and resid 1899 through 1904 Processing helix chain 'i' and resid 1687 through 1691 removed outlier: 3.724A pdb=" N PHE i1690 " --> pdb=" O ASP i1687 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N VAL i1691 " --> pdb=" O PRO i1688 " (cutoff:3.500A) No H-bonds generated for 'chain 'i' and resid 1687 through 1691' Processing helix chain 'i' and resid 1793 through 1798 Processing helix chain 'i' and resid 1801 through 1806 Processing helix chain 'i' and resid 1807 through 1809 No H-bonds generated for 'chain 'i' and resid 1807 through 1809' Processing helix chain 'i' and resid 1852 through 1863 removed outlier: 3.685A pdb=" N ASN i1856 " --> pdb=" O ALA i1852 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N GLY i1860 " --> pdb=" O ASN i1856 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N GLN i1861 " --> pdb=" O GLN i1857 " (cutoff:3.500A) Processing helix chain 'i' and resid 1899 through 1904 Processing helix chain 'j' and resid 1687 through 1691 removed outlier: 3.725A pdb=" N PHE j1690 " --> pdb=" O ASP j1687 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N VAL j1691 " --> pdb=" O PRO j1688 " (cutoff:3.500A) No H-bonds generated for 'chain 'j' and resid 1687 through 1691' Processing helix chain 'j' and resid 1793 through 1798 Processing helix chain 'j' and resid 1801 through 1806 Processing helix chain 'j' and resid 1807 through 1809 No H-bonds generated for 'chain 'j' and resid 1807 through 1809' Processing helix chain 'j' and resid 1852 through 1863 removed outlier: 3.685A pdb=" N ASN j1856 " --> pdb=" O ALA j1852 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N GLY j1860 " --> pdb=" O ASN j1856 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N GLN j1861 " --> pdb=" O GLN j1857 " (cutoff:3.500A) Processing helix chain 'j' and resid 1899 through 1904 Processing helix chain 'k' and resid 1687 through 1691 removed outlier: 3.724A pdb=" N PHE k1690 " --> pdb=" O ASP k1687 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N VAL k1691 " --> pdb=" O PRO k1688 " (cutoff:3.500A) No H-bonds generated for 'chain 'k' and resid 1687 through 1691' Processing helix chain 'k' and resid 1793 through 1798 Processing helix chain 'k' and resid 1801 through 1806 Processing helix chain 'k' and resid 1807 through 1809 No H-bonds generated for 'chain 'k' and resid 1807 through 1809' Processing helix chain 'k' and resid 1852 through 1863 removed outlier: 3.684A pdb=" N ASN k1856 " --> pdb=" O ALA k1852 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N GLY k1860 " --> pdb=" O ASN k1856 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N GLN k1861 " --> pdb=" O GLN k1857 " (cutoff:3.500A) Processing helix chain 'k' and resid 1899 through 1904 Processing helix chain 'l' and resid 1687 through 1691 removed outlier: 3.724A pdb=" N PHE l1690 " --> pdb=" O ASP l1687 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N VAL l1691 " --> pdb=" O PRO l1688 " (cutoff:3.500A) No H-bonds generated for 'chain 'l' and resid 1687 through 1691' Processing helix chain 'l' and resid 1793 through 1798 Processing helix chain 'l' and resid 1801 through 1806 Processing helix chain 'l' and resid 1807 through 1809 No H-bonds generated for 'chain 'l' and resid 1807 through 1809' Processing helix chain 'l' and resid 1852 through 1863 removed outlier: 3.685A pdb=" N ASN l1856 " --> pdb=" O ALA l1852 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N GLY l1860 " --> pdb=" O ASN l1856 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N GLN l1861 " --> pdb=" O GLN l1857 " (cutoff:3.500A) Processing helix chain 'l' and resid 1899 through 1904 Processing helix chain 'm' and resid 1687 through 1691 removed outlier: 3.724A pdb=" N PHE m1690 " --> pdb=" O ASP m1687 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N VAL m1691 " --> pdb=" O PRO m1688 " (cutoff:3.500A) No H-bonds generated for 'chain 'm' and resid 1687 through 1691' Processing helix chain 'm' and resid 1793 through 1798 Processing helix chain 'm' and resid 1801 through 1806 Processing helix chain 'm' and resid 1807 through 1809 No H-bonds generated for 'chain 'm' and resid 1807 through 1809' Processing helix chain 'm' and resid 1852 through 1863 removed outlier: 3.685A pdb=" N ASN m1856 " --> pdb=" O ALA m1852 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N GLY m1860 " --> pdb=" O ASN m1856 " (cutoff:3.500A) removed outlier: 3.978A pdb=" N GLN m1861 " --> pdb=" O GLN m1857 " (cutoff:3.500A) Processing helix chain 'm' and resid 1899 through 1904 Processing helix chain 'n' and resid 1687 through 1691 removed outlier: 3.723A pdb=" N PHE n1690 " --> pdb=" O ASP n1687 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N VAL n1691 " --> pdb=" O PRO n1688 " (cutoff:3.500A) No H-bonds generated for 'chain 'n' and resid 1687 through 1691' Processing helix chain 'n' and resid 1793 through 1798 Processing helix chain 'n' and resid 1801 through 1806 Processing helix chain 'n' and resid 1807 through 1809 No H-bonds generated for 'chain 'n' and resid 1807 through 1809' Processing helix chain 'n' and resid 1852 through 1863 removed outlier: 3.684A pdb=" N ASN n1856 " --> pdb=" O ALA n1852 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N GLY n1860 " --> pdb=" O ASN n1856 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N GLN n1861 " --> pdb=" O GLN n1857 " (cutoff:3.500A) Processing helix chain 'n' and resid 1899 through 1904 Processing helix chain 'o' and resid 1687 through 1691 removed outlier: 3.724A pdb=" N PHE o1690 " --> pdb=" O ASP o1687 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N VAL o1691 " --> pdb=" O PRO o1688 " (cutoff:3.500A) No H-bonds generated for 'chain 'o' and resid 1687 through 1691' Processing helix chain 'o' and resid 1793 through 1798 Processing helix chain 'o' and resid 1801 through 1806 Processing helix chain 'o' and resid 1807 through 1809 No H-bonds generated for 'chain 'o' and resid 1807 through 1809' Processing helix chain 'o' and resid 1852 through 1863 removed outlier: 3.685A pdb=" N ASN o1856 " --> pdb=" O ALA o1852 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N GLY o1860 " --> pdb=" O ASN o1856 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N GLN o1861 " --> pdb=" O GLN o1857 " (cutoff:3.500A) Processing helix chain 'o' and resid 1899 through 1904 Processing sheet with id=AA1, first strand: chain 'b' and resid 1679 through 1680 removed outlier: 6.726A pdb=" N LYS b1679 " --> pdb=" O ASP c1886 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'b' and resid 1682 through 1683 removed outlier: 5.112A pdb=" N PHE c1759 " --> pdb=" O ASN c1741 " (cutoff:3.500A) removed outlier: 6.583A pdb=" N ASN c1741 " --> pdb=" O PHE c1759 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N LYS c1761 " --> pdb=" O TYR c1739 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'b' and resid 1697 through 1698 Processing sheet with id=AA4, first strand: chain 'b' and resid 1701 through 1702 removed outlier: 3.594A pdb=" N LYS b1761 " --> pdb=" O TYR b1739 " (cutoff:3.500A) removed outlier: 6.583A pdb=" N ASN b1741 " --> pdb=" O PHE b1759 " (cutoff:3.500A) removed outlier: 5.112A pdb=" N PHE b1759 " --> pdb=" O ASN b1741 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'b' and resid 1754 through 1755 Processing sheet with id=AA6, first strand: chain 'b' and resid 1789 through 1791 Processing sheet with id=AA7, first strand: chain 'b' and resid 1885 through 1886 Processing sheet with id=AA8, first strand: chain 'c' and resid 1679 through 1680 removed outlier: 6.218A pdb=" N LYS c1679 " --> pdb=" O ASP d1886 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'c' and resid 1682 through 1683 removed outlier: 5.113A pdb=" N PHE d1759 " --> pdb=" O ASN d1741 " (cutoff:3.500A) removed outlier: 6.582A pdb=" N ASN d1741 " --> pdb=" O PHE d1759 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N LYS d1761 " --> pdb=" O TYR d1739 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'c' and resid 1697 through 1698 Processing sheet with id=AB2, first strand: chain 'c' and resid 1754 through 1755 Processing sheet with id=AB3, first strand: chain 'c' and resid 1789 through 1791 Processing sheet with id=AB4, first strand: chain 'd' and resid 1682 through 1683 removed outlier: 5.113A pdb=" N PHE e1759 " --> pdb=" O ASN e1741 " (cutoff:3.500A) removed outlier: 6.582A pdb=" N ASN e1741 " --> pdb=" O PHE e1759 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N LYS e1761 " --> pdb=" O TYR e1739 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'd' and resid 1697 through 1698 Processing sheet with id=AB6, first strand: chain 'd' and resid 1754 through 1755 Processing sheet with id=AB7, first strand: chain 'd' and resid 1789 through 1791 Processing sheet with id=AB8, first strand: chain 'e' and resid 1679 through 1680 removed outlier: 6.704A pdb=" N LYS e1679 " --> pdb=" O ASP f1886 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB8 Processing sheet with id=AB9, first strand: chain 'e' and resid 1682 through 1683 removed outlier: 5.112A pdb=" N PHE f1759 " --> pdb=" O ASN f1741 " (cutoff:3.500A) removed outlier: 6.582A pdb=" N ASN f1741 " --> pdb=" O PHE f1759 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N LYS f1761 " --> pdb=" O TYR f1739 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'e' and resid 1697 through 1698 Processing sheet with id=AC2, first strand: chain 'e' and resid 1754 through 1755 Processing sheet with id=AC3, first strand: chain 'e' and resid 1789 through 1791 Processing sheet with id=AC4, first strand: chain 'f' and resid 1682 through 1683 removed outlier: 5.112A pdb=" N PHE g1759 " --> pdb=" O ASN g1741 " (cutoff:3.500A) removed outlier: 6.582A pdb=" N ASN g1741 " --> pdb=" O PHE g1759 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N LYS g1761 " --> pdb=" O TYR g1739 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'f' and resid 1697 through 1698 Processing sheet with id=AC6, first strand: chain 'f' and resid 1754 through 1755 Processing sheet with id=AC7, first strand: chain 'f' and resid 1789 through 1791 Processing sheet with id=AC8, first strand: chain 'g' and resid 1682 through 1683 removed outlier: 3.552A pdb=" N PHE g1682 " --> pdb=" O ILE h1769 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N ILE h1769 " --> pdb=" O PHE g1682 " (cutoff:3.500A) removed outlier: 5.113A pdb=" N PHE h1759 " --> pdb=" O ASN h1741 " (cutoff:3.500A) removed outlier: 6.582A pdb=" N ASN h1741 " --> pdb=" O PHE h1759 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N LYS h1761 " --> pdb=" O TYR h1739 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'g' and resid 1697 through 1698 Processing sheet with id=AD1, first strand: chain 'g' and resid 1754 through 1755 Processing sheet with id=AD2, first strand: chain 'g' and resid 1789 through 1791 Processing sheet with id=AD3, first strand: chain 'h' and resid 1682 through 1683 removed outlier: 3.821A pdb=" N PHE h1682 " --> pdb=" O ILE m1769 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N ILE m1769 " --> pdb=" O PHE h1682 " (cutoff:3.500A) removed outlier: 5.112A pdb=" N PHE m1759 " --> pdb=" O ASN m1741 " (cutoff:3.500A) removed outlier: 6.583A pdb=" N ASN m1741 " --> pdb=" O PHE m1759 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N LYS m1761 " --> pdb=" O TYR m1739 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'h' and resid 1697 through 1698 Processing sheet with id=AD5, first strand: chain 'h' and resid 1754 through 1755 Processing sheet with id=AD6, first strand: chain 'h' and resid 1789 through 1791 Processing sheet with id=AD7, first strand: chain 'i' and resid 1682 through 1683 removed outlier: 5.112A pdb=" N PHE n1759 " --> pdb=" O ASN n1741 " (cutoff:3.500A) removed outlier: 6.582A pdb=" N ASN n1741 " --> pdb=" O PHE n1759 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N LYS n1761 " --> pdb=" O TYR n1739 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'i' and resid 1697 through 1698 Processing sheet with id=AD9, first strand: chain 'i' and resid 1701 through 1702 removed outlier: 3.594A pdb=" N LYS i1761 " --> pdb=" O TYR i1739 " (cutoff:3.500A) removed outlier: 6.582A pdb=" N ASN i1741 " --> pdb=" O PHE i1759 " (cutoff:3.500A) removed outlier: 5.112A pdb=" N PHE i1759 " --> pdb=" O ASN i1741 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'i' and resid 1754 through 1755 Processing sheet with id=AE2, first strand: chain 'i' and resid 1789 through 1791 Processing sheet with id=AE3, first strand: chain 'j' and resid 1697 through 1698 Processing sheet with id=AE4, first strand: chain 'j' and resid 1701 through 1702 removed outlier: 3.594A pdb=" N LYS j1761 " --> pdb=" O TYR j1739 " (cutoff:3.500A) removed outlier: 6.582A pdb=" N ASN j1741 " --> pdb=" O PHE j1759 " (cutoff:3.500A) removed outlier: 5.113A pdb=" N PHE j1759 " --> pdb=" O ASN j1741 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'j' and resid 1754 through 1755 Processing sheet with id=AE6, first strand: chain 'j' and resid 1789 through 1791 Processing sheet with id=AE7, first strand: chain 'k' and resid 1697 through 1698 Processing sheet with id=AE8, first strand: chain 'k' and resid 1701 through 1702 removed outlier: 3.594A pdb=" N LYS k1761 " --> pdb=" O TYR k1739 " (cutoff:3.500A) removed outlier: 6.583A pdb=" N ASN k1741 " --> pdb=" O PHE k1759 " (cutoff:3.500A) removed outlier: 5.112A pdb=" N PHE k1759 " --> pdb=" O ASN k1741 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N ILE k1769 " --> pdb=" O PHE l1682 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N PHE l1682 " --> pdb=" O ILE k1769 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'k' and resid 1754 through 1755 Processing sheet with id=AF1, first strand: chain 'k' and resid 1789 through 1791 Processing sheet with id=AF2, first strand: chain 'l' and resid 1697 through 1698 Processing sheet with id=AF3, first strand: chain 'l' and resid 1701 through 1702 removed outlier: 3.594A pdb=" N LYS l1761 " --> pdb=" O TYR l1739 " (cutoff:3.500A) removed outlier: 6.582A pdb=" N ASN l1741 " --> pdb=" O PHE l1759 " (cutoff:3.500A) removed outlier: 5.111A pdb=" N PHE l1759 " --> pdb=" O ASN l1741 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'l' and resid 1754 through 1755 Processing sheet with id=AF5, first strand: chain 'l' and resid 1789 through 1791 Processing sheet with id=AF6, first strand: chain 'm' and resid 1697 through 1698 Processing sheet with id=AF7, first strand: chain 'm' and resid 1754 through 1755 Processing sheet with id=AF8, first strand: chain 'm' and resid 1789 through 1791 Processing sheet with id=AF9, first strand: chain 'n' and resid 1679 through 1680 removed outlier: 6.442A pdb=" N LYS n1679 " --> pdb=" O ASP o1886 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF9 Processing sheet with id=AG1, first strand: chain 'n' and resid 1682 through 1683 removed outlier: 5.113A pdb=" N PHE o1759 " --> pdb=" O ASN o1741 " (cutoff:3.500A) removed outlier: 6.582A pdb=" N ASN o1741 " --> pdb=" O PHE o1759 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N LYS o1761 " --> pdb=" O TYR o1739 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'n' and resid 1697 through 1698 Processing sheet with id=AG3, first strand: chain 'n' and resid 1754 through 1755 Processing sheet with id=AG4, first strand: chain 'n' and resid 1789 through 1791 Processing sheet with id=AG5, first strand: chain 'o' and resid 1697 through 1698 Processing sheet with id=AG6, first strand: chain 'o' and resid 1754 through 1755 Processing sheet with id=AG7, first strand: chain 'o' and resid 1789 through 1791 499 hydrogen bonds defined for protein. 1170 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.05 Time building geometry restraints manager: 2.25 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: 6591 1.34 - 1.46: 3852 1.46 - 1.57: 10543 1.57 - 1.69: 0 1.69 - 1.81: 252 Bond restraints: 21238 Sorted by residual: bond pdb=" N THR l1813 " pdb=" CA THR l1813 " ideal model delta sigma weight residual 1.457 1.483 -0.026 1.29e-02 6.01e+03 4.06e+00 bond pdb=" N THR e1813 " pdb=" CA THR e1813 " ideal model delta sigma weight residual 1.457 1.483 -0.026 1.29e-02 6.01e+03 4.04e+00 bond pdb=" N THR k1813 " pdb=" CA THR k1813 " ideal model delta sigma weight residual 1.457 1.483 -0.026 1.29e-02 6.01e+03 4.00e+00 bond pdb=" N THR d1813 " pdb=" CA THR d1813 " ideal model delta sigma weight residual 1.457 1.483 -0.026 1.29e-02 6.01e+03 4.00e+00 bond pdb=" N THR o1813 " pdb=" CA THR o1813 " ideal model delta sigma weight residual 1.457 1.483 -0.026 1.29e-02 6.01e+03 3.97e+00 ... (remaining 21233 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.84: 27070 1.84 - 3.67: 1449 3.67 - 5.51: 167 5.51 - 7.35: 68 7.35 - 9.18: 30 Bond angle restraints: 28784 Sorted by residual: angle pdb=" C GLN b1812 " pdb=" N THR b1813 " pdb=" CA THR b1813 " ideal model delta sigma weight residual 121.54 129.45 -7.91 1.91e+00 2.74e-01 1.71e+01 angle pdb=" C GLN c1812 " pdb=" N THR c1813 " pdb=" CA THR c1813 " ideal model delta sigma weight residual 121.54 129.43 -7.89 1.91e+00 2.74e-01 1.71e+01 angle pdb=" C GLN k1812 " pdb=" N THR k1813 " pdb=" CA THR k1813 " ideal model delta sigma weight residual 121.54 129.43 -7.89 1.91e+00 2.74e-01 1.71e+01 angle pdb=" C GLN f1812 " pdb=" N THR f1813 " pdb=" CA THR f1813 " ideal model delta sigma weight residual 121.54 129.42 -7.88 1.91e+00 2.74e-01 1.70e+01 angle pdb=" C GLN j1812 " pdb=" N THR j1813 " pdb=" CA THR j1813 " ideal model delta sigma weight residual 121.54 129.40 -7.86 1.91e+00 2.74e-01 1.69e+01 ... (remaining 28779 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.00: 11574 18.00 - 35.99: 1026 35.99 - 53.99: 112 53.99 - 71.98: 70 71.98 - 89.98: 28 Dihedral angle restraints: 12810 sinusoidal: 4914 harmonic: 7896 Sorted by residual: dihedral pdb=" CA ALA c1719 " pdb=" C ALA c1719 " pdb=" N LYS c1720 " pdb=" CA LYS c1720 " ideal model delta harmonic sigma weight residual -180.00 -140.58 -39.42 0 5.00e+00 4.00e-02 6.22e+01 dihedral pdb=" CA ALA n1719 " pdb=" C ALA n1719 " pdb=" N LYS n1720 " pdb=" CA LYS n1720 " ideal model delta harmonic sigma weight residual -180.00 -140.58 -39.42 0 5.00e+00 4.00e-02 6.21e+01 dihedral pdb=" CA ALA o1719 " pdb=" C ALA o1719 " pdb=" N LYS o1720 " pdb=" CA LYS o1720 " ideal model delta harmonic sigma weight residual -180.00 -140.61 -39.39 0 5.00e+00 4.00e-02 6.21e+01 ... (remaining 12807 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.055: 2122 0.055 - 0.109: 1013 0.109 - 0.164: 288 0.164 - 0.218: 49 0.218 - 0.273: 14 Chirality restraints: 3486 Sorted by residual: chirality pdb=" CB ILE j1865 " pdb=" CA ILE j1865 " pdb=" CG1 ILE j1865 " pdb=" CG2 ILE j1865 " both_signs ideal model delta sigma weight residual False 2.64 2.37 0.27 2.00e-01 2.50e+01 1.86e+00 chirality pdb=" CB ILE f1865 " pdb=" CA ILE f1865 " pdb=" CG1 ILE f1865 " pdb=" CG2 ILE f1865 " both_signs ideal model delta sigma weight residual False 2.64 2.37 0.27 2.00e-01 2.50e+01 1.85e+00 chirality pdb=" CB ILE o1865 " pdb=" CA ILE o1865 " pdb=" CG1 ILE o1865 " pdb=" CG2 ILE o1865 " both_signs ideal model delta sigma weight residual False 2.64 2.37 0.27 2.00e-01 2.50e+01 1.85e+00 ... (remaining 3483 not shown) Planarity restraints: 3612 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ALA m1719 " 0.013 2.00e-02 2.50e+03 2.59e-02 6.72e+00 pdb=" C ALA m1719 " -0.045 2.00e-02 2.50e+03 pdb=" O ALA m1719 " 0.017 2.00e-02 2.50e+03 pdb=" N LYS m1720 " 0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ALA n1719 " 0.013 2.00e-02 2.50e+03 2.58e-02 6.66e+00 pdb=" C ALA n1719 " -0.045 2.00e-02 2.50e+03 pdb=" O ALA n1719 " 0.017 2.00e-02 2.50e+03 pdb=" N LYS n1720 " 0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ALA k1719 " 0.013 2.00e-02 2.50e+03 2.57e-02 6.63e+00 pdb=" C ALA k1719 " -0.045 2.00e-02 2.50e+03 pdb=" O ALA k1719 " 0.017 2.00e-02 2.50e+03 pdb=" N LYS k1720 " 0.015 2.00e-02 2.50e+03 ... (remaining 3609 not shown) Histogram of nonbonded interaction distances: 2.41 - 2.90: 8880 2.90 - 3.40: 20150 3.40 - 3.90: 32761 3.90 - 4.40: 37153 4.40 - 4.90: 60937 Nonbonded interactions: 159881 Sorted by model distance: nonbonded pdb=" N ASP b1707 " pdb=" OD1 ASP b1707 " model vdw 2.406 3.120 nonbonded pdb=" N ASP i1707 " pdb=" OD1 ASP i1707 " model vdw 2.406 3.120 nonbonded pdb=" N ASP h1707 " pdb=" OD1 ASP h1707 " model vdw 2.406 3.120 nonbonded pdb=" N ASP o1707 " pdb=" OD1 ASP o1707 " model vdw 2.406 3.120 nonbonded pdb=" N ASP e1707 " pdb=" OD1 ASP e1707 " model vdw 2.406 3.120 ... (remaining 159876 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: 0.04 Found NCS groups: ncs_group { reference = chain 'b' selection = chain 'c' selection = chain 'd' selection = chain 'e' selection = chain 'f' selection = chain 'g' selection = chain 'h' selection = chain 'i' selection = chain 'j' selection = chain 'k' selection = chain 'l' selection = chain 'm' selection = chain 'n' selection = chain 'o' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as 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: 8.480 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.280 Check model and map are aligned: 0.060 Set scattering table: 0.070 Process input model: 15.270 Find NCS groups from input model: 0.140 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.130 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.480 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8149 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 : 0.008 0.053 21238 Z= 0.353 Angle : 0.980 9.184 28784 Z= 0.530 Chirality : 0.067 0.273 3486 Planarity : 0.007 0.055 3612 Dihedral : 14.952 89.981 7742 Min Nonbonded Distance : 2.406 Molprobity Statistics. All-atom Clashscore : 7.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.76 % Favored : 90.24 % Rotamer: Outliers : 4.19 % Allowed : 13.77 % Favored : 82.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.53 % Twisted Proline : 0.00 % Twisted General : 0.53 % 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: -4.06 (0.13), residues: 2716 helix: -4.84 (0.10), residues: 392 sheet: -2.43 (0.22), residues: 448 loop : -2.41 (0.12), residues: 1876 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.001 ARG d1754 TYR 0.016 0.002 TYR k1695 PHE 0.020 0.003 PHE o1810 TRP 0.003 0.001 TRP e1723 HIS 0.001 0.000 HIS h1793 Details of bonding type rmsd covalent geometry : bond 0.00786 (21238) covalent geometry : angle 0.98021 (28784) hydrogen bonds : bond 0.17207 ( 499) hydrogen bonds : angle 9.64009 ( 1170) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5432 Ramachandran restraints generated. 2716 Oldfield, 0 Emsley, 2716 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5432 Ramachandran restraints generated. 2716 Oldfield, 0 Emsley, 2716 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 872 residues out of total 2338 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 98 poor density : 774 time to evaluate : 0.696 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: b 1699 GLU cc_start: 0.8073 (pt0) cc_final: 0.7585 (pt0) REVERT: b 1729 MET cc_start: 0.7460 (ptm) cc_final: 0.6816 (mmt) REVERT: b 1734 LYS cc_start: 0.6412 (ttpt) cc_final: 0.5854 (pttt) REVERT: b 1739 TYR cc_start: 0.8735 (m-80) cc_final: 0.8457 (m-80) REVERT: b 1795 MET cc_start: 0.7140 (ptm) cc_final: 0.6866 (ptt) REVERT: b 1902 ASP cc_start: 0.8757 (OUTLIER) cc_final: 0.8232 (t70) REVERT: c 1706 VAL cc_start: 0.9447 (t) cc_final: 0.9191 (t) REVERT: c 1710 LEU cc_start: 0.8513 (OUTLIER) cc_final: 0.7649 (pp) REVERT: c 1729 MET cc_start: 0.7886 (ptm) cc_final: 0.6313 (mmm) REVERT: c 1734 LYS cc_start: 0.7045 (ttpt) cc_final: 0.6765 (ttpp) REVERT: c 1885 ILE cc_start: 0.9314 (mm) cc_final: 0.8849 (mm) REVERT: c 1902 ASP cc_start: 0.8706 (OUTLIER) cc_final: 0.8049 (t70) REVERT: d 1710 LEU cc_start: 0.8769 (OUTLIER) cc_final: 0.7837 (pp) REVERT: d 1729 MET cc_start: 0.8204 (ptm) cc_final: 0.7059 (mmt) REVERT: d 1734 LYS cc_start: 0.7237 (ttpt) cc_final: 0.6892 (ttpp) REVERT: d 1737 LYS cc_start: 0.8486 (mtmm) cc_final: 0.8075 (mmmm) REVERT: d 1766 ASP cc_start: 0.8774 (m-30) cc_final: 0.8317 (m-30) REVERT: d 1776 GLN cc_start: 0.8417 (pt0) cc_final: 0.8041 (pt0) REVERT: d 1800 PHE cc_start: 0.8433 (m-80) cc_final: 0.7815 (m-80) REVERT: d 1857 GLN cc_start: 0.8739 (tp-100) cc_final: 0.8322 (tp40) REVERT: d 1897 ASN cc_start: 0.9416 (t0) cc_final: 0.9151 (t0) REVERT: e 1729 MET cc_start: 0.8978 (ptm) cc_final: 0.7205 (mmt) REVERT: e 1734 LYS cc_start: 0.6521 (ttpt) cc_final: 0.6048 (ttpt) REVERT: e 1736 THR cc_start: 0.9228 (OUTLIER) cc_final: 0.9018 (t) REVERT: e 1741 ASN cc_start: 0.9017 (p0) cc_final: 0.8798 (p0) REVERT: e 1742 TYR cc_start: 0.8564 (p90) cc_final: 0.8133 (p90) REVERT: e 1776 GLN cc_start: 0.8494 (pt0) cc_final: 0.8115 (pt0) REVERT: e 1783 GLU cc_start: 0.7468 (pm20) cc_final: 0.6821 (pm20) REVERT: e 1795 MET cc_start: 0.7956 (ptm) cc_final: 0.7717 (ptm) REVERT: e 1810 PHE cc_start: 0.7516 (p90) cc_final: 0.7244 (p90) REVERT: e 1870 TYR cc_start: 0.8351 (m-80) cc_final: 0.7943 (m-80) REVERT: e 1883 ASP cc_start: 0.7943 (m-30) cc_final: 0.7722 (m-30) REVERT: e 1894 LYS cc_start: 0.9091 (ptmt) cc_final: 0.8621 (pttm) REVERT: e 1902 ASP cc_start: 0.8540 (OUTLIER) cc_final: 0.8332 (t0) REVERT: f 1729 MET cc_start: 0.8493 (ptm) cc_final: 0.7106 (tpt) REVERT: f 1734 LYS cc_start: 0.6782 (ttpt) cc_final: 0.6428 (ttpt) REVERT: f 1737 LYS cc_start: 0.8782 (mtmm) cc_final: 0.8256 (mtpp) REVERT: f 1739 TYR cc_start: 0.8887 (m-80) cc_final: 0.7910 (m-80) REVERT: f 1742 TYR cc_start: 0.8281 (p90) cc_final: 0.7778 (p90) REVERT: f 1766 ASP cc_start: 0.9060 (m-30) cc_final: 0.8614 (m-30) REVERT: f 1776 GLN cc_start: 0.8396 (pt0) cc_final: 0.8173 (pt0) REVERT: f 1780 MET cc_start: 0.7963 (tpt) cc_final: 0.7692 (tpp) REVERT: f 1795 MET cc_start: 0.7786 (ptm) cc_final: 0.7561 (ptp) REVERT: f 1857 GLN cc_start: 0.9149 (tp-100) cc_final: 0.8426 (tp40) REVERT: f 1858 ILE cc_start: 0.9322 (tp) cc_final: 0.8966 (mt) REVERT: f 1861 GLN cc_start: 0.9006 (mp-120) cc_final: 0.8608 (mp10) REVERT: f 1869 PHE cc_start: 0.9058 (t80) cc_final: 0.8809 (t80) REVERT: f 1897 ASN cc_start: 0.9258 (t0) cc_final: 0.8976 (t0) REVERT: g 1724 ASN cc_start: 0.9400 (p0) cc_final: 0.9129 (p0) REVERT: g 1726 ASN cc_start: 0.9283 (p0) cc_final: 0.9040 (p0) REVERT: g 1729 MET cc_start: 0.8499 (ptm) cc_final: 0.7125 (tpt) REVERT: g 1734 LYS cc_start: 0.7318 (ttpt) cc_final: 0.7052 (ttpt) REVERT: g 1768 VAL cc_start: 0.9149 (t) cc_final: 0.8945 (t) REVERT: g 1780 MET cc_start: 0.8127 (tpt) cc_final: 0.7660 (tpp) REVERT: g 1870 TYR cc_start: 0.8344 (m-80) cc_final: 0.8050 (m-80) REVERT: g 1885 ILE cc_start: 0.9355 (mm) cc_final: 0.8965 (mm) REVERT: h 1723 TRP cc_start: 0.8403 (m100) cc_final: 0.8053 (m100) REVERT: h 1729 MET cc_start: 0.7679 (ptm) cc_final: 0.6930 (tpt) REVERT: h 1794 PHE cc_start: 0.8938 (m-10) cc_final: 0.8716 (m-10) REVERT: h 1895 ILE cc_start: 0.8724 (mp) cc_final: 0.8470 (tp) REVERT: i 1706 VAL cc_start: 0.9072 (t) cc_final: 0.8872 (t) REVERT: i 1707 ASP cc_start: 0.8414 (p0) cc_final: 0.7807 (p0) REVERT: i 1729 MET cc_start: 0.8329 (ptm) cc_final: 0.6931 (tpt) REVERT: i 1734 LYS cc_start: 0.7042 (ttpt) cc_final: 0.6762 (pttm) REVERT: i 1766 ASP cc_start: 0.8569 (m-30) cc_final: 0.8037 (m-30) REVERT: i 1774 ASN cc_start: 0.8875 (p0) cc_final: 0.8644 (p0) REVERT: i 1810 PHE cc_start: 0.7513 (p90) cc_final: 0.6862 (p90) REVERT: i 1857 GLN cc_start: 0.8998 (tp-100) cc_final: 0.8500 (tp40) REVERT: i 1861 GLN cc_start: 0.8693 (mp-120) cc_final: 0.8458 (mp10) REVERT: i 1882 MET cc_start: 0.8561 (mmt) cc_final: 0.8298 (mmm) REVERT: i 1900 VAL cc_start: 0.9473 (p) cc_final: 0.9221 (p) REVERT: i 1902 ASP cc_start: 0.8733 (OUTLIER) cc_final: 0.8427 (t70) REVERT: j 1729 MET cc_start: 0.8824 (ptm) cc_final: 0.7236 (mmt) REVERT: j 1734 LYS cc_start: 0.7428 (ttpt) cc_final: 0.6837 (pttp) REVERT: j 1739 TYR cc_start: 0.9015 (m-80) cc_final: 0.8423 (m-80) REVERT: j 1741 ASN cc_start: 0.8997 (p0) cc_final: 0.8647 (p0) REVERT: j 1752 MET cc_start: 0.8956 (ppp) cc_final: 0.8622 (ppp) REVERT: j 1783 GLU cc_start: 0.7997 (pm20) cc_final: 0.7419 (pm20) REVERT: j 1857 GLN cc_start: 0.8976 (tp-100) cc_final: 0.8752 (tp-100) REVERT: j 1870 TYR cc_start: 0.8265 (m-80) cc_final: 0.8024 (m-80) REVERT: j 1894 LYS cc_start: 0.8872 (ptmt) cc_final: 0.8392 (pttm) REVERT: k 1710 LEU cc_start: 0.8971 (OUTLIER) cc_final: 0.8671 (pt) REVERT: k 1729 MET cc_start: 0.8018 (ptm) cc_final: 0.6954 (mmt) REVERT: k 1741 ASN cc_start: 0.8920 (p0) cc_final: 0.8698 (p0) REVERT: k 1743 GLN cc_start: 0.8735 (mm-40) cc_final: 0.8518 (mm-40) REVERT: k 1766 ASP cc_start: 0.8874 (m-30) cc_final: 0.8460 (m-30) REVERT: k 1776 GLN cc_start: 0.8501 (pt0) cc_final: 0.8058 (pt0) REVERT: k 1800 PHE cc_start: 0.8349 (m-80) cc_final: 0.7857 (m-80) REVERT: k 1857 GLN cc_start: 0.8791 (tp-100) cc_final: 0.8438 (tp40) REVERT: k 1897 ASN cc_start: 0.9370 (t0) cc_final: 0.9064 (t0) REVERT: l 1710 LEU cc_start: 0.8992 (OUTLIER) cc_final: 0.8703 (mp) REVERT: l 1729 MET cc_start: 0.8544 (ptm) cc_final: 0.7408 (tpt) REVERT: l 1734 LYS cc_start: 0.6818 (ttpt) cc_final: 0.6316 (pttt) REVERT: l 1742 TYR cc_start: 0.8261 (p90) cc_final: 0.7897 (p90) REVERT: l 1776 GLN cc_start: 0.8513 (pt0) cc_final: 0.8253 (pt0) REVERT: l 1780 MET cc_start: 0.7737 (tpt) cc_final: 0.7440 (tpp) REVERT: l 1791 ASN cc_start: 0.8550 (t0) cc_final: 0.8268 (t0) REVERT: l 1795 MET cc_start: 0.7477 (ptm) cc_final: 0.7125 (ptp) REVERT: l 1897 ASN cc_start: 0.9289 (t0) cc_final: 0.8971 (t0) REVERT: l 1898 LYS cc_start: 0.9073 (tptp) cc_final: 0.8767 (tptp) REVERT: m 1710 LEU cc_start: 0.8549 (OUTLIER) cc_final: 0.7751 (pp) REVERT: m 1729 MET cc_start: 0.8562 (ptm) cc_final: 0.7292 (tpt) REVERT: m 1731 LEU cc_start: 0.9144 (mt) cc_final: 0.8866 (mm) REVERT: m 1736 THR cc_start: 0.9403 (OUTLIER) cc_final: 0.9139 (t) REVERT: m 1776 GLN cc_start: 0.8128 (pt0) cc_final: 0.7893 (pt0) REVERT: m 1810 PHE cc_start: 0.7409 (p90) cc_final: 0.7132 (p90) REVERT: m 1861 GLN cc_start: 0.8597 (mp-120) cc_final: 0.8287 (mp10) REVERT: m 1875 ASP cc_start: 0.8071 (m-30) cc_final: 0.7817 (m-30) REVERT: m 1884 ASP cc_start: 0.8446 (m-30) cc_final: 0.8215 (m-30) REVERT: n 1729 MET cc_start: 0.8465 (ptm) cc_final: 0.6801 (mmt) REVERT: n 1766 ASP cc_start: 0.8482 (m-30) cc_final: 0.8278 (m-30) REVERT: n 1787 ASP cc_start: 0.7909 (p0) cc_final: 0.7661 (p0) REVERT: n 1789 TYR cc_start: 0.7160 (t80) cc_final: 0.6936 (m-10) REVERT: n 1795 MET cc_start: 0.7237 (ptm) cc_final: 0.6999 (ptm) REVERT: n 1810 PHE cc_start: 0.6896 (p90) cc_final: 0.6584 (p90) REVERT: n 1894 LYS cc_start: 0.9115 (ptmt) cc_final: 0.8695 (pttm) REVERT: n 1902 ASP cc_start: 0.8679 (OUTLIER) cc_final: 0.8287 (t70) REVERT: n 1903 GLU cc_start: 0.4740 (tt0) cc_final: 0.4469 (tt0) REVERT: o 1699 GLU cc_start: 0.7667 (pt0) cc_final: 0.7435 (pt0) REVERT: o 1706 VAL cc_start: 0.9337 (t) cc_final: 0.9130 (t) REVERT: o 1710 LEU cc_start: 0.9250 (OUTLIER) cc_final: 0.8764 (pp) REVERT: o 1729 MET cc_start: 0.7644 (ptm) cc_final: 0.6435 (mmt) REVERT: o 1752 MET cc_start: 0.9176 (ppp) cc_final: 0.8892 (ppp) REVERT: o 1783 GLU cc_start: 0.7964 (pm20) cc_final: 0.6868 (pm20) REVERT: o 1787 ASP cc_start: 0.7997 (p0) cc_final: 0.7741 (p0) REVERT: o 1795 MET cc_start: 0.7793 (ptm) cc_final: 0.7536 (ptp) REVERT: o 1857 GLN cc_start: 0.8946 (tp-100) cc_final: 0.8582 (tp-100) REVERT: o 1870 TYR cc_start: 0.8439 (m-80) cc_final: 0.8055 (m-10) REVERT: o 1902 ASP cc_start: 0.8399 (OUTLIER) cc_final: 0.8089 (t70) outliers start: 98 outliers final: 26 residues processed: 840 average time/residue: 0.1344 time to fit residues: 179.6927 Evaluate side-chains 670 residues out of total 2338 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 630 time to evaluate : 0.815 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain b residue 1855 SER Chi-restraints excluded: chain b residue 1879 ILE Chi-restraints excluded: chain b residue 1902 ASP Chi-restraints excluded: chain c residue 1710 LEU Chi-restraints excluded: chain c residue 1736 THR Chi-restraints excluded: chain c residue 1879 ILE Chi-restraints excluded: chain c residue 1902 ASP Chi-restraints excluded: chain d residue 1710 LEU Chi-restraints excluded: chain d residue 1855 SER Chi-restraints excluded: chain e residue 1710 LEU Chi-restraints excluded: chain e residue 1736 THR Chi-restraints excluded: chain e residue 1902 ASP Chi-restraints excluded: chain f residue 1710 LEU Chi-restraints excluded: chain f residue 1879 ILE Chi-restraints excluded: chain g residue 1710 LEU Chi-restraints excluded: chain g residue 1855 SER Chi-restraints excluded: chain h residue 1698 ILE Chi-restraints excluded: chain h residue 1710 LEU Chi-restraints excluded: chain h residue 1855 SER Chi-restraints excluded: chain i residue 1710 LEU Chi-restraints excluded: chain i residue 1855 SER Chi-restraints excluded: chain i residue 1879 ILE Chi-restraints excluded: chain i residue 1902 ASP Chi-restraints excluded: chain j residue 1710 LEU Chi-restraints excluded: chain j residue 1855 SER Chi-restraints excluded: chain k residue 1710 LEU Chi-restraints excluded: chain k residue 1855 SER Chi-restraints excluded: chain l residue 1710 LEU Chi-restraints excluded: chain l residue 1736 THR Chi-restraints excluded: chain l residue 1879 ILE Chi-restraints excluded: chain m residue 1698 ILE Chi-restraints excluded: chain m residue 1710 LEU Chi-restraints excluded: chain m residue 1736 THR Chi-restraints excluded: chain m residue 1855 SER Chi-restraints excluded: chain n residue 1710 LEU Chi-restraints excluded: chain n residue 1855 SER Chi-restraints excluded: chain n residue 1902 ASP Chi-restraints excluded: chain o residue 1698 ILE Chi-restraints excluded: chain o residue 1710 LEU Chi-restraints excluded: chain o residue 1902 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 266 random chunks: chunk 197 optimal weight: 4.9990 chunk 215 optimal weight: 0.9990 chunk 20 optimal weight: 3.9990 chunk 132 optimal weight: 0.2980 chunk 261 optimal weight: 3.9990 chunk 248 optimal weight: 1.9990 chunk 207 optimal weight: 0.5980 chunk 155 optimal weight: 7.9990 chunk 244 optimal weight: 0.7980 chunk 183 optimal weight: 0.9990 chunk 111 optimal weight: 1.9990 overall best weight: 0.7384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: d1680 GLN e1793 HIS f1793 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3349 r_free = 0.3349 target = 0.100819 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3164 r_free = 0.3164 target = 0.090415 restraints weight = 47062.830| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3201 r_free = 0.3201 target = 0.092498 restraints weight = 22828.773| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3223 r_free = 0.3223 target = 0.093756 restraints weight = 13139.667| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 45)----------------| | r_work = 0.3237 r_free = 0.3237 target = 0.094554 restraints weight = 8657.924| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3245 r_free = 0.3245 target = 0.095019 restraints weight = 6413.646| |-----------------------------------------------------------------------------| r_work (final): 0.3242 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8132 moved from start: 0.2317 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 21238 Z= 0.134 Angle : 0.660 8.496 28784 Z= 0.348 Chirality : 0.050 0.154 3486 Planarity : 0.005 0.044 3612 Dihedral : 7.179 45.511 2923 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 10.93 Ramachandran Plot: Outliers : 0.15 % Allowed : 8.91 % Favored : 90.94 % Rotamer: Outliers : 3.51 % Allowed : 19.33 % Favored : 77.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.53 % 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: -3.75 (0.15), residues: 2716 helix: -4.33 (0.15), residues: 406 sheet: -2.29 (0.17), residues: 812 loop : -2.01 (0.15), residues: 1498 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG l1797 TYR 0.026 0.002 TYR h1695 PHE 0.019 0.002 PHE h1810 TRP 0.008 0.001 TRP f1723 HIS 0.003 0.001 HIS e1793 Details of bonding type rmsd covalent geometry : bond 0.00296 (21238) covalent geometry : angle 0.65980 (28784) hydrogen bonds : bond 0.03343 ( 499) hydrogen bonds : angle 7.39805 ( 1170) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5432 Ramachandran restraints generated. 2716 Oldfield, 0 Emsley, 2716 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5432 Ramachandran restraints generated. 2716 Oldfield, 0 Emsley, 2716 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 752 residues out of total 2338 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 670 time to evaluate : 0.825 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: symmetry clash REVERT: b 1729 MET cc_start: 0.7218 (ptm) cc_final: 0.6411 (mmt) REVERT: b 1734 LYS cc_start: 0.6624 (ttpt) cc_final: 0.6093 (pttt) REVERT: b 1737 LYS cc_start: 0.7915 (mptt) cc_final: 0.7705 (mptt) REVERT: b 1752 MET cc_start: 0.8711 (ppp) cc_final: 0.8469 (ptt) REVERT: b 1783 GLU cc_start: 0.7680 (pm20) cc_final: 0.7355 (pm20) REVERT: b 1795 MET cc_start: 0.7566 (ptm) cc_final: 0.7146 (ptt) REVERT: b 1853 GLN cc_start: 0.7718 (pp30) cc_final: 0.7404 (tm-30) REVERT: b 1857 GLN cc_start: 0.8980 (tp40) cc_final: 0.8767 (tp-100) REVERT: b 1886 ASP cc_start: 0.8519 (t0) cc_final: 0.8232 (t0) REVERT: b 1902 ASP cc_start: 0.8638 (t0) cc_final: 0.8027 (t70) REVERT: c 1710 LEU cc_start: 0.8568 (OUTLIER) cc_final: 0.8091 (pp) REVERT: c 1729 MET cc_start: 0.7724 (ptm) cc_final: 0.6487 (mmm) REVERT: c 1734 LYS cc_start: 0.6940 (ttpt) cc_final: 0.6715 (ttpp) REVERT: c 1742 TYR cc_start: 0.8557 (p90) cc_final: 0.8173 (p90) REVERT: c 1902 ASP cc_start: 0.8510 (t0) cc_final: 0.7981 (t70) REVERT: d 1710 LEU cc_start: 0.8495 (OUTLIER) cc_final: 0.7629 (pp) REVERT: d 1729 MET cc_start: 0.8204 (ptm) cc_final: 0.7244 (mmt) REVERT: d 1742 TYR cc_start: 0.8488 (p90) cc_final: 0.8225 (p90) REVERT: d 1752 MET cc_start: 0.9135 (ppp) cc_final: 0.8622 (ptt) REVERT: d 1766 ASP cc_start: 0.8682 (m-30) cc_final: 0.8333 (m-30) REVERT: d 1774 ASN cc_start: 0.8640 (p0) cc_final: 0.8430 (p0) REVERT: d 1800 PHE cc_start: 0.8038 (m-80) cc_final: 0.7579 (m-80) REVERT: d 1857 GLN cc_start: 0.8648 (tp-100) cc_final: 0.8371 (tp40) REVERT: d 1897 ASN cc_start: 0.9115 (t0) cc_final: 0.8895 (t0) REVERT: e 1707 ASP cc_start: 0.7416 (p0) cc_final: 0.6939 (p0) REVERT: e 1729 MET cc_start: 0.8719 (ptm) cc_final: 0.6793 (mmm) REVERT: e 1734 LYS cc_start: 0.6213 (ttpt) cc_final: 0.5853 (pttp) REVERT: e 1752 MET cc_start: 0.8903 (ppp) cc_final: 0.8612 (ptt) REVERT: e 1783 GLU cc_start: 0.7928 (pm20) cc_final: 0.7537 (pm20) REVERT: e 1795 MET cc_start: 0.7487 (ptm) cc_final: 0.7190 (ptp) REVERT: e 1810 PHE cc_start: 0.7181 (p90) cc_final: 0.6883 (p90) REVERT: e 1870 TYR cc_start: 0.8063 (m-80) cc_final: 0.7744 (m-80) REVERT: e 1902 ASP cc_start: 0.8497 (t0) cc_final: 0.8184 (t70) REVERT: f 1707 ASP cc_start: 0.7848 (t0) cc_final: 0.7584 (t0) REVERT: f 1729 MET cc_start: 0.8212 (ptm) cc_final: 0.7151 (mmt) REVERT: f 1737 LYS cc_start: 0.8679 (mtmm) cc_final: 0.8093 (mtpp) REVERT: f 1739 TYR cc_start: 0.8570 (m-80) cc_final: 0.7967 (m-80) REVERT: f 1742 TYR cc_start: 0.8376 (p90) cc_final: 0.7818 (p90) REVERT: f 1766 ASP cc_start: 0.8969 (m-30) cc_final: 0.8614 (m-30) REVERT: f 1854 MET cc_start: 0.8113 (mtt) cc_final: 0.7692 (ttt) REVERT: f 1857 GLN cc_start: 0.9011 (tp-100) cc_final: 0.8333 (tp40) REVERT: f 1858 ILE cc_start: 0.9269 (tp) cc_final: 0.9006 (mp) REVERT: f 1861 GLN cc_start: 0.8925 (mp-120) cc_final: 0.8495 (mp10) REVERT: f 1882 MET cc_start: 0.8773 (mmm) cc_final: 0.8570 (mmm) REVERT: f 1897 ASN cc_start: 0.9071 (t0) cc_final: 0.8815 (t0) REVERT: g 1709 THR cc_start: 0.8704 (p) cc_final: 0.8481 (m) REVERT: g 1729 MET cc_start: 0.8372 (ptm) cc_final: 0.7058 (tpt) REVERT: g 1752 MET cc_start: 0.8675 (ppp) cc_final: 0.8141 (ptt) REVERT: g 1766 ASP cc_start: 0.8370 (m-30) cc_final: 0.8009 (m-30) REVERT: g 1780 MET cc_start: 0.8414 (tpt) cc_final: 0.8074 (tpp) REVERT: g 1870 TYR cc_start: 0.8302 (m-80) cc_final: 0.7982 (m-80) REVERT: g 1885 ILE cc_start: 0.9333 (mm) cc_final: 0.9089 (mm) REVERT: g 1894 LYS cc_start: 0.8586 (ptmt) cc_final: 0.8228 (pttm) REVERT: h 1729 MET cc_start: 0.8314 (ptm) cc_final: 0.7388 (tpt) REVERT: h 1731 LEU cc_start: 0.9153 (mm) cc_final: 0.8946 (mp) REVERT: h 1756 MET cc_start: 0.8592 (tpp) cc_final: 0.8251 (tpt) REVERT: h 1872 ASN cc_start: 0.7889 (m110) cc_final: 0.7598 (m-40) REVERT: h 1886 ASP cc_start: 0.7296 (p0) cc_final: 0.6045 (p0) REVERT: h 1895 ILE cc_start: 0.8915 (mp) cc_final: 0.8428 (tp) REVERT: i 1706 VAL cc_start: 0.9144 (t) cc_final: 0.8914 (t) REVERT: i 1707 ASP cc_start: 0.8392 (p0) cc_final: 0.7677 (p0) REVERT: i 1729 MET cc_start: 0.8316 (ptm) cc_final: 0.7202 (tpt) REVERT: i 1742 TYR cc_start: 0.8608 (p90) cc_final: 0.7979 (p90) REVERT: i 1752 MET cc_start: 0.8822 (ppp) cc_final: 0.8101 (ppp) REVERT: i 1766 ASP cc_start: 0.8474 (m-30) cc_final: 0.8009 (m-30) REVERT: i 1810 PHE cc_start: 0.7529 (p90) cc_final: 0.6749 (p90) REVERT: i 1853 GLN cc_start: 0.7813 (pp30) cc_final: 0.7522 (pp30) REVERT: i 1857 GLN cc_start: 0.8942 (tp-100) cc_final: 0.8266 (tp40) REVERT: i 1861 GLN cc_start: 0.8792 (mp-120) cc_final: 0.8528 (mp10) REVERT: i 1902 ASP cc_start: 0.8098 (t0) cc_final: 0.7730 (t70) REVERT: j 1699 GLU cc_start: 0.6533 (pt0) cc_final: 0.6116 (pm20) REVERT: j 1729 MET cc_start: 0.8632 (ptm) cc_final: 0.7080 (mmt) REVERT: j 1734 LYS cc_start: 0.7139 (ttpt) cc_final: 0.6493 (pttp) REVERT: j 1752 MET cc_start: 0.9068 (ppp) cc_final: 0.8195 (ptt) REVERT: j 1756 MET cc_start: 0.8996 (tpp) cc_final: 0.7964 (tpt) REVERT: j 1780 MET cc_start: 0.8186 (tpt) cc_final: 0.7643 (tpp) REVERT: j 1783 GLU cc_start: 0.8191 (pm20) cc_final: 0.7971 (pm20) REVERT: j 1795 MET cc_start: 0.7508 (ptp) cc_final: 0.7211 (ptt) REVERT: j 1870 TYR cc_start: 0.8015 (m-80) cc_final: 0.7739 (m-80) REVERT: k 1680 GLN cc_start: 0.8086 (mt0) cc_final: 0.7876 (mt0) REVERT: k 1710 LEU cc_start: 0.8893 (OUTLIER) cc_final: 0.8103 (pp) REVERT: k 1729 MET cc_start: 0.8898 (ptm) cc_final: 0.7731 (mmt) REVERT: k 1739 TYR cc_start: 0.8769 (m-80) cc_final: 0.8516 (m-80) REVERT: k 1752 MET cc_start: 0.9063 (ppp) cc_final: 0.8596 (ptt) REVERT: k 1766 ASP cc_start: 0.8685 (m-30) cc_final: 0.8417 (m-30) REVERT: k 1780 MET cc_start: 0.8460 (tpt) cc_final: 0.8253 (tpt) REVERT: k 1857 GLN cc_start: 0.8670 (tp-100) cc_final: 0.8263 (tp40) REVERT: l 1729 MET cc_start: 0.8422 (ptm) cc_final: 0.7355 (tpt) REVERT: l 1734 LYS cc_start: 0.6733 (ttpt) cc_final: 0.6155 (pttt) REVERT: l 1737 LYS cc_start: 0.8517 (mtmm) cc_final: 0.8315 (mtpp) REVERT: l 1800 PHE cc_start: 0.8049 (m-80) cc_final: 0.7608 (m-80) REVERT: l 1857 GLN cc_start: 0.8860 (mm-40) cc_final: 0.8223 (tp40) REVERT: l 1861 GLN cc_start: 0.8849 (mp10) cc_final: 0.8390 (mp10) REVERT: l 1897 ASN cc_start: 0.9073 (t0) cc_final: 0.8861 (t0) REVERT: l 1898 LYS cc_start: 0.8894 (tptp) cc_final: 0.8557 (tptp) REVERT: l 1903 GLU cc_start: 0.3698 (tt0) cc_final: 0.3346 (tt0) REVERT: m 1710 LEU cc_start: 0.8535 (OUTLIER) cc_final: 0.7863 (pp) REVERT: m 1729 MET cc_start: 0.8577 (ptm) cc_final: 0.7653 (tpt) REVERT: m 1736 THR cc_start: 0.9191 (OUTLIER) cc_final: 0.8947 (t) REVERT: m 1756 MET cc_start: 0.8541 (tpp) cc_final: 0.8313 (tpt) REVERT: m 1857 GLN cc_start: 0.8796 (tp40) cc_final: 0.8151 (tp40) REVERT: m 1861 GLN cc_start: 0.8536 (mp-120) cc_final: 0.8018 (mp10) REVERT: m 1875 ASP cc_start: 0.7749 (m-30) cc_final: 0.7530 (m-30) REVERT: m 1884 ASP cc_start: 0.8305 (m-30) cc_final: 0.8027 (m-30) REVERT: m 1895 ILE cc_start: 0.9130 (mp) cc_final: 0.8691 (tp) REVERT: n 1729 MET cc_start: 0.8107 (ptm) cc_final: 0.6653 (mmm) REVERT: n 1752 MET cc_start: 0.8539 (ppp) cc_final: 0.7948 (ptt) REVERT: n 1756 MET cc_start: 0.8623 (tpp) cc_final: 0.6780 (tpp) REVERT: n 1766 ASP cc_start: 0.8391 (m-30) cc_final: 0.8137 (m-30) REVERT: n 1880 LEU cc_start: 0.9441 (mt) cc_final: 0.9215 (mt) REVERT: n 1894 LYS cc_start: 0.8925 (ptmt) cc_final: 0.8521 (pttm) REVERT: n 1902 ASP cc_start: 0.8392 (t0) cc_final: 0.8191 (t70) REVERT: o 1706 VAL cc_start: 0.9281 (t) cc_final: 0.9078 (t) REVERT: o 1710 LEU cc_start: 0.9191 (OUTLIER) cc_final: 0.8724 (pp) REVERT: o 1729 MET cc_start: 0.8205 (ptm) cc_final: 0.6850 (mmt) REVERT: o 1736 THR cc_start: 0.9283 (OUTLIER) cc_final: 0.9025 (t) REVERT: o 1752 MET cc_start: 0.9250 (ppp) cc_final: 0.8894 (ppp) REVERT: o 1756 MET cc_start: 0.8916 (tpp) cc_final: 0.8685 (tpt) REVERT: o 1783 GLU cc_start: 0.8140 (pm20) cc_final: 0.7470 (pm20) REVERT: o 1795 MET cc_start: 0.7525 (ptm) cc_final: 0.7124 (ptp) REVERT: o 1810 PHE cc_start: 0.7022 (p90) cc_final: 0.6795 (p90) REVERT: o 1870 TYR cc_start: 0.8324 (m-80) cc_final: 0.7953 (m-10) REVERT: o 1897 ASN cc_start: 0.9154 (t0) cc_final: 0.8827 (t0) REVERT: o 1903 GLU cc_start: 0.4372 (OUTLIER) cc_final: 0.4114 (tt0) outliers start: 82 outliers final: 47 residues processed: 724 average time/residue: 0.1265 time to fit residues: 150.1917 Evaluate side-chains 670 residues out of total 2338 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 615 time to evaluate : 0.797 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain b residue 1790 VAL Chi-restraints excluded: chain b residue 1879 ILE Chi-restraints excluded: chain c residue 1683 ILE Chi-restraints excluded: chain c residue 1710 LEU Chi-restraints excluded: chain c residue 1736 THR Chi-restraints excluded: chain c residue 1795 MET Chi-restraints excluded: chain c residue 1879 ILE Chi-restraints excluded: chain d residue 1698 ILE Chi-restraints excluded: chain d residue 1700 ILE Chi-restraints excluded: chain d residue 1710 LEU Chi-restraints excluded: chain d residue 1790 VAL Chi-restraints excluded: chain d residue 1883 ASP Chi-restraints excluded: chain e residue 1683 ILE Chi-restraints excluded: chain e residue 1700 ILE Chi-restraints excluded: chain e residue 1710 LEU Chi-restraints excluded: chain f residue 1698 ILE Chi-restraints excluded: chain f residue 1700 ILE Chi-restraints excluded: chain f residue 1710 LEU Chi-restraints excluded: chain f residue 1713 ILE Chi-restraints excluded: chain f residue 1855 SER Chi-restraints excluded: chain f residue 1879 ILE Chi-restraints excluded: chain f residue 1883 ASP Chi-restraints excluded: chain g residue 1710 LEU Chi-restraints excluded: chain g residue 1733 ASP Chi-restraints excluded: chain h residue 1698 ILE Chi-restraints excluded: chain h residue 1700 ILE Chi-restraints excluded: chain h residue 1702 LEU Chi-restraints excluded: chain h residue 1710 LEU Chi-restraints excluded: chain h residue 1733 ASP Chi-restraints excluded: chain i residue 1683 ILE Chi-restraints excluded: chain i residue 1700 ILE Chi-restraints excluded: chain i residue 1710 LEU Chi-restraints excluded: chain i residue 1879 ILE Chi-restraints excluded: chain j residue 1700 ILE Chi-restraints excluded: chain j residue 1710 LEU Chi-restraints excluded: chain j residue 1790 VAL Chi-restraints excluded: chain k residue 1698 ILE Chi-restraints excluded: chain k residue 1710 LEU Chi-restraints excluded: chain k residue 1883 ASP Chi-restraints excluded: chain l residue 1683 ILE Chi-restraints excluded: chain l residue 1715 SER Chi-restraints excluded: chain l residue 1736 THR Chi-restraints excluded: chain l residue 1879 ILE Chi-restraints excluded: chain m residue 1700 ILE Chi-restraints excluded: chain m residue 1710 LEU Chi-restraints excluded: chain m residue 1715 SER Chi-restraints excluded: chain m residue 1736 THR Chi-restraints excluded: chain m residue 1883 ASP Chi-restraints excluded: chain n residue 1698 ILE Chi-restraints excluded: chain n residue 1710 LEU Chi-restraints excluded: chain o residue 1710 LEU Chi-restraints excluded: chain o residue 1733 ASP Chi-restraints excluded: chain o residue 1736 THR Chi-restraints excluded: chain o residue 1873 GLU Chi-restraints excluded: chain o residue 1903 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 266 random chunks: chunk 247 optimal weight: 0.9980 chunk 192 optimal weight: 1.9990 chunk 24 optimal weight: 0.4980 chunk 15 optimal weight: 0.9980 chunk 32 optimal weight: 0.2980 chunk 121 optimal weight: 3.9990 chunk 19 optimal weight: 5.9990 chunk 92 optimal weight: 4.9990 chunk 232 optimal weight: 0.0770 chunk 202 optimal weight: 4.9990 chunk 4 optimal weight: 0.7980 overall best weight: 0.5338 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: d1680 GLN d1793 HIS k1793 HIS l1793 HIS o1793 HIS o1907 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3363 r_free = 0.3363 target = 0.101731 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3179 r_free = 0.3179 target = 0.091304 restraints weight = 47033.674| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3216 r_free = 0.3216 target = 0.093406 restraints weight = 22978.281| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.3237 r_free = 0.3237 target = 0.094680 restraints weight = 13268.986| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3252 r_free = 0.3252 target = 0.095489 restraints weight = 8752.511| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3261 r_free = 0.3261 target = 0.095998 restraints weight = 6471.152| |-----------------------------------------------------------------------------| r_work (final): 0.3259 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8122 moved from start: 0.3096 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 21238 Z= 0.117 Angle : 0.617 14.030 28784 Z= 0.324 Chirality : 0.049 0.156 3486 Planarity : 0.004 0.039 3612 Dihedral : 6.128 39.318 2895 Min Nonbonded Distance : 2.574 Molprobity Statistics. All-atom Clashscore : 10.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.05 % Favored : 89.95 % Rotamer: Outliers : 4.83 % Allowed : 19.42 % Favored : 75.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.53 % 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: -3.41 (0.15), residues: 2716 helix: -4.02 (0.18), residues: 392 sheet: -2.17 (0.17), residues: 826 loop : -1.75 (0.16), residues: 1498 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG d1754 TYR 0.025 0.001 TYR h1695 PHE 0.032 0.002 PHE n1810 TRP 0.007 0.001 TRP e1723 HIS 0.002 0.001 HIS f1793 Details of bonding type rmsd covalent geometry : bond 0.00268 (21238) covalent geometry : angle 0.61698 (28784) hydrogen bonds : bond 0.02998 ( 499) hydrogen bonds : angle 6.96426 ( 1170) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5432 Ramachandran restraints generated. 2716 Oldfield, 0 Emsley, 2716 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5432 Ramachandran restraints generated. 2716 Oldfield, 0 Emsley, 2716 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 773 residues out of total 2338 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 113 poor density : 660 time to evaluate : 0.777 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: b 1715 SER cc_start: 0.9395 (t) cc_final: 0.8926 (m) REVERT: b 1729 MET cc_start: 0.8129 (ptm) cc_final: 0.6641 (mmt) REVERT: b 1734 LYS cc_start: 0.6503 (ttpt) cc_final: 0.6031 (pttt) REVERT: b 1752 MET cc_start: 0.8914 (ppp) cc_final: 0.8398 (ptt) REVERT: b 1783 GLU cc_start: 0.7803 (pm20) cc_final: 0.7522 (pm20) REVERT: b 1795 MET cc_start: 0.7483 (ptm) cc_final: 0.6883 (ptt) REVERT: b 1857 GLN cc_start: 0.8933 (tp40) cc_final: 0.8626 (tp-100) REVERT: b 1886 ASP cc_start: 0.8519 (t0) cc_final: 0.7867 (t0) REVERT: b 1902 ASP cc_start: 0.8610 (t0) cc_final: 0.8077 (t70) REVERT: c 1710 LEU cc_start: 0.8631 (OUTLIER) cc_final: 0.8183 (pp) REVERT: c 1729 MET cc_start: 0.7969 (ptm) cc_final: 0.6511 (mmm) REVERT: c 1734 LYS cc_start: 0.6823 (ttpt) cc_final: 0.6617 (ttpp) REVERT: c 1739 TYR cc_start: 0.8656 (m-80) cc_final: 0.8425 (m-80) REVERT: c 1742 TYR cc_start: 0.8516 (p90) cc_final: 0.8046 (p90) REVERT: c 1795 MET cc_start: 0.7534 (OUTLIER) cc_final: 0.7078 (ptm) REVERT: c 1902 ASP cc_start: 0.8455 (t0) cc_final: 0.7969 (t0) REVERT: d 1710 LEU cc_start: 0.8590 (OUTLIER) cc_final: 0.7721 (pp) REVERT: d 1729 MET cc_start: 0.8256 (ptm) cc_final: 0.7297 (mmt) REVERT: d 1752 MET cc_start: 0.9135 (ppp) cc_final: 0.8606 (ptt) REVERT: d 1766 ASP cc_start: 0.8652 (m-30) cc_final: 0.8298 (m-30) REVERT: d 1774 ASN cc_start: 0.8738 (p0) cc_final: 0.8449 (p0) REVERT: d 1795 MET cc_start: 0.7815 (ptm) cc_final: 0.7553 (ptt) REVERT: d 1857 GLN cc_start: 0.8633 (tp-100) cc_final: 0.8382 (tp40) REVERT: e 1729 MET cc_start: 0.8717 (ptm) cc_final: 0.7079 (mmt) REVERT: e 1734 LYS cc_start: 0.5997 (ttpt) cc_final: 0.5657 (pttp) REVERT: e 1752 MET cc_start: 0.8837 (ppp) cc_final: 0.8593 (ptt) REVERT: e 1756 MET cc_start: 0.8751 (tpp) cc_final: 0.8503 (tpt) REVERT: e 1783 GLU cc_start: 0.7910 (pm20) cc_final: 0.7531 (pm20) REVERT: e 1795 MET cc_start: 0.7397 (ptm) cc_final: 0.7159 (ptp) REVERT: e 1810 PHE cc_start: 0.7099 (p90) cc_final: 0.6842 (p90) REVERT: e 1870 TYR cc_start: 0.7959 (m-80) cc_final: 0.7523 (m-80) REVERT: e 1886 ASP cc_start: 0.8236 (t0) cc_final: 0.7972 (t0) REVERT: e 1894 LYS cc_start: 0.8911 (ptmt) cc_final: 0.8515 (pttm) REVERT: e 1902 ASP cc_start: 0.8519 (t0) cc_final: 0.8243 (t70) REVERT: f 1707 ASP cc_start: 0.8323 (t0) cc_final: 0.7535 (t0) REVERT: f 1709 THR cc_start: 0.9048 (p) cc_final: 0.8781 (p) REVERT: f 1729 MET cc_start: 0.8106 (ptm) cc_final: 0.7091 (tpt) REVERT: f 1737 LYS cc_start: 0.8718 (mtmm) cc_final: 0.8096 (mtpp) REVERT: f 1739 TYR cc_start: 0.8395 (m-80) cc_final: 0.7843 (m-80) REVERT: f 1742 TYR cc_start: 0.8367 (p90) cc_final: 0.7732 (p90) REVERT: f 1857 GLN cc_start: 0.9030 (tp-100) cc_final: 0.8241 (tp40) REVERT: f 1861 GLN cc_start: 0.8911 (mp-120) cc_final: 0.8401 (mp10) REVERT: g 1709 THR cc_start: 0.8684 (p) cc_final: 0.8453 (m) REVERT: g 1729 MET cc_start: 0.8286 (ptm) cc_final: 0.7005 (mmt) REVERT: g 1752 MET cc_start: 0.8820 (ppp) cc_final: 0.8050 (ptt) REVERT: g 1766 ASP cc_start: 0.8515 (m-30) cc_final: 0.8211 (m-30) REVERT: g 1885 ILE cc_start: 0.9321 (mm) cc_final: 0.9058 (mm) REVERT: g 1894 LYS cc_start: 0.8612 (ptmt) cc_final: 0.8249 (pttm) REVERT: h 1687 ASP cc_start: 0.8795 (t0) cc_final: 0.8496 (t0) REVERT: h 1707 ASP cc_start: 0.7608 (p0) cc_final: 0.7378 (p0) REVERT: h 1729 MET cc_start: 0.8201 (ptm) cc_final: 0.7406 (tpt) REVERT: h 1731 LEU cc_start: 0.9188 (mm) cc_final: 0.8943 (mp) REVERT: h 1872 ASN cc_start: 0.7889 (m110) cc_final: 0.7641 (m-40) REVERT: h 1886 ASP cc_start: 0.7684 (p0) cc_final: 0.7034 (p0) REVERT: h 1895 ILE cc_start: 0.9083 (mp) cc_final: 0.8606 (tp) REVERT: i 1707 ASP cc_start: 0.8138 (p0) cc_final: 0.7435 (p0) REVERT: i 1729 MET cc_start: 0.8331 (ptm) cc_final: 0.7192 (tpt) REVERT: i 1742 TYR cc_start: 0.8526 (p90) cc_final: 0.7735 (p90) REVERT: i 1752 MET cc_start: 0.8789 (ppp) cc_final: 0.8127 (ppp) REVERT: i 1756 MET cc_start: 0.8783 (tpt) cc_final: 0.8561 (tpt) REVERT: i 1766 ASP cc_start: 0.8444 (m-30) cc_final: 0.7973 (m-30) REVERT: i 1810 PHE cc_start: 0.7511 (p90) cc_final: 0.6836 (p90) REVERT: i 1857 GLN cc_start: 0.8982 (tp-100) cc_final: 0.8373 (tp40) REVERT: i 1861 GLN cc_start: 0.8850 (mp-120) cc_final: 0.8649 (mp10) REVERT: i 1902 ASP cc_start: 0.8270 (t0) cc_final: 0.7960 (t70) REVERT: j 1707 ASP cc_start: 0.7672 (p0) cc_final: 0.7202 (p0) REVERT: j 1729 MET cc_start: 0.8623 (ptm) cc_final: 0.7209 (mmt) REVERT: j 1734 LYS cc_start: 0.6885 (ttpt) cc_final: 0.6363 (pttp) REVERT: j 1752 MET cc_start: 0.9063 (ppp) cc_final: 0.8637 (ppp) REVERT: j 1780 MET cc_start: 0.8173 (tpt) cc_final: 0.7680 (tpp) REVERT: j 1783 GLU cc_start: 0.8071 (pm20) cc_final: 0.7844 (pm20) REVERT: j 1795 MET cc_start: 0.7528 (ptp) cc_final: 0.7186 (ptt) REVERT: j 1854 MET cc_start: 0.7918 (OUTLIER) cc_final: 0.7627 (ttm) REVERT: j 1870 TYR cc_start: 0.7951 (m-80) cc_final: 0.7652 (m-80) REVERT: k 1710 LEU cc_start: 0.8758 (OUTLIER) cc_final: 0.8437 (pp) REVERT: k 1715 SER cc_start: 0.9593 (t) cc_final: 0.9304 (m) REVERT: k 1729 MET cc_start: 0.8846 (ptm) cc_final: 0.7579 (mmt) REVERT: k 1739 TYR cc_start: 0.8633 (m-80) cc_final: 0.8415 (m-80) REVERT: k 1752 MET cc_start: 0.9080 (ppp) cc_final: 0.8585 (ptt) REVERT: k 1766 ASP cc_start: 0.8650 (m-30) cc_final: 0.8393 (m-30) REVERT: k 1783 GLU cc_start: 0.8375 (pm20) cc_final: 0.8140 (pm20) REVERT: k 1855 SER cc_start: 0.9310 (OUTLIER) cc_final: 0.8856 (t) REVERT: k 1857 GLN cc_start: 0.8776 (tp-100) cc_final: 0.8353 (tp40) REVERT: l 1729 MET cc_start: 0.8395 (ptm) cc_final: 0.7394 (tpt) REVERT: l 1742 TYR cc_start: 0.8560 (p90) cc_final: 0.8221 (p90) REVERT: l 1752 MET cc_start: 0.8705 (ppp) cc_final: 0.7987 (ppp) REVERT: l 1857 GLN cc_start: 0.8993 (mm-40) cc_final: 0.8450 (tp40) REVERT: l 1861 GLN cc_start: 0.8779 (mp10) cc_final: 0.8365 (mp10) REVERT: l 1897 ASN cc_start: 0.8991 (t0) cc_final: 0.8678 (t0) REVERT: l 1898 LYS cc_start: 0.8586 (tptp) cc_final: 0.8256 (tptp) REVERT: l 1903 GLU cc_start: 0.4286 (tt0) cc_final: 0.3947 (tt0) REVERT: m 1710 LEU cc_start: 0.8605 (OUTLIER) cc_final: 0.8025 (pp) REVERT: m 1729 MET cc_start: 0.8453 (ptm) cc_final: 0.7662 (tpt) REVERT: m 1736 THR cc_start: 0.9200 (OUTLIER) cc_final: 0.8755 (t) REVERT: m 1752 MET cc_start: 0.9033 (ppp) cc_final: 0.8827 (ppp) REVERT: m 1857 GLN cc_start: 0.8881 (tp40) cc_final: 0.7854 (tp-100) REVERT: m 1861 GLN cc_start: 0.8568 (mp-120) cc_final: 0.7803 (mp10) REVERT: m 1886 ASP cc_start: 0.7523 (t0) cc_final: 0.7166 (t0) REVERT: n 1729 MET cc_start: 0.8129 (ptm) cc_final: 0.6823 (mmt) REVERT: n 1752 MET cc_start: 0.8563 (ppp) cc_final: 0.7936 (ptt) REVERT: n 1766 ASP cc_start: 0.8342 (m-30) cc_final: 0.8091 (m-30) REVERT: n 1894 LYS cc_start: 0.8901 (ptmt) cc_final: 0.8469 (pttm) REVERT: o 1729 MET cc_start: 0.8209 (ptm) cc_final: 0.6940 (mmt) REVERT: o 1736 THR cc_start: 0.9234 (OUTLIER) cc_final: 0.8958 (t) REVERT: o 1752 MET cc_start: 0.9220 (ppp) cc_final: 0.8729 (ppp) REVERT: o 1757 ILE cc_start: 0.9544 (mt) cc_final: 0.9327 (pt) REVERT: o 1783 GLU cc_start: 0.8123 (pm20) cc_final: 0.7387 (pm20) REVERT: o 1795 MET cc_start: 0.7474 (ptm) cc_final: 0.6921 (ptt) REVERT: o 1810 PHE cc_start: 0.6940 (p90) cc_final: 0.6733 (p90) REVERT: o 1857 GLN cc_start: 0.8920 (mm-40) cc_final: 0.8643 (tp-100) REVERT: o 1870 TYR cc_start: 0.8305 (m-80) cc_final: 0.8000 (m-10) REVERT: o 1897 ASN cc_start: 0.9120 (t0) cc_final: 0.8772 (t0) REVERT: o 1903 GLU cc_start: 0.5866 (OUTLIER) cc_final: 0.5629 (tt0) outliers start: 113 outliers final: 58 residues processed: 746 average time/residue: 0.1276 time to fit residues: 155.5155 Evaluate side-chains 668 residues out of total 2338 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 600 time to evaluate : 0.782 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain b residue 1698 ILE Chi-restraints excluded: chain b residue 1755 LEU Chi-restraints excluded: chain b residue 1769 ILE Chi-restraints excluded: chain c residue 1683 ILE Chi-restraints excluded: chain c residue 1710 LEU Chi-restraints excluded: chain c residue 1736 THR Chi-restraints excluded: chain c residue 1790 VAL Chi-restraints excluded: chain c residue 1795 MET Chi-restraints excluded: chain c residue 1879 ILE Chi-restraints excluded: chain d residue 1700 ILE Chi-restraints excluded: chain d residue 1710 LEU Chi-restraints excluded: chain d residue 1883 ASP Chi-restraints excluded: chain e residue 1683 ILE Chi-restraints excluded: chain e residue 1700 ILE Chi-restraints excluded: chain e residue 1710 LEU Chi-restraints excluded: chain e residue 1790 VAL Chi-restraints excluded: chain f residue 1710 LEU Chi-restraints excluded: chain f residue 1713 ILE Chi-restraints excluded: chain f residue 1755 LEU Chi-restraints excluded: chain f residue 1790 VAL Chi-restraints excluded: chain f residue 1879 ILE Chi-restraints excluded: chain f residue 1883 ASP Chi-restraints excluded: chain g residue 1683 ILE Chi-restraints excluded: chain g residue 1710 LEU Chi-restraints excluded: chain g residue 1790 VAL Chi-restraints excluded: chain g residue 1865 ILE Chi-restraints excluded: chain g residue 1883 ASP Chi-restraints excluded: chain h residue 1700 ILE Chi-restraints excluded: chain h residue 1702 LEU Chi-restraints excluded: chain h residue 1710 LEU Chi-restraints excluded: chain h residue 1715 SER Chi-restraints excluded: chain h residue 1738 VAL Chi-restraints excluded: chain i residue 1683 ILE Chi-restraints excluded: chain i residue 1698 ILE Chi-restraints excluded: chain i residue 1700 ILE Chi-restraints excluded: chain i residue 1710 LEU Chi-restraints excluded: chain i residue 1755 LEU Chi-restraints excluded: chain i residue 1790 VAL Chi-restraints excluded: chain i residue 1879 ILE Chi-restraints excluded: chain j residue 1700 ILE Chi-restraints excluded: chain j residue 1710 LEU Chi-restraints excluded: chain j residue 1755 LEU Chi-restraints excluded: chain j residue 1854 MET Chi-restraints excluded: chain k residue 1700 ILE Chi-restraints excluded: chain k residue 1710 LEU Chi-restraints excluded: chain k residue 1790 VAL Chi-restraints excluded: chain k residue 1855 SER Chi-restraints excluded: chain k residue 1883 ASP Chi-restraints excluded: chain l residue 1683 ILE Chi-restraints excluded: chain l residue 1736 THR Chi-restraints excluded: chain l residue 1790 VAL Chi-restraints excluded: chain l residue 1879 ILE Chi-restraints excluded: chain m residue 1710 LEU Chi-restraints excluded: chain m residue 1736 THR Chi-restraints excluded: chain m residue 1790 VAL Chi-restraints excluded: chain m residue 1883 ASP Chi-restraints excluded: chain n residue 1683 ILE Chi-restraints excluded: chain n residue 1710 LEU Chi-restraints excluded: chain n residue 1755 LEU Chi-restraints excluded: chain n residue 1790 VAL Chi-restraints excluded: chain n residue 1865 ILE Chi-restraints excluded: chain n residue 1883 ASP Chi-restraints excluded: chain o residue 1736 THR Chi-restraints excluded: chain o residue 1755 LEU Chi-restraints excluded: chain o residue 1790 VAL Chi-restraints excluded: chain o residue 1865 ILE Chi-restraints excluded: chain o residue 1873 GLU Chi-restraints excluded: chain o residue 1903 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 266 random chunks: chunk 7 optimal weight: 0.0970 chunk 104 optimal weight: 0.8980 chunk 197 optimal weight: 1.9990 chunk 256 optimal weight: 0.0370 chunk 103 optimal weight: 1.9990 chunk 189 optimal weight: 4.9990 chunk 52 optimal weight: 4.9990 chunk 225 optimal weight: 2.9990 chunk 79 optimal weight: 4.9990 chunk 161 optimal weight: 2.9990 chunk 99 optimal weight: 0.9980 overall best weight: 0.8058 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: d1680 GLN d1907 GLN f1907 GLN g1907 GLN h1907 GLN i1907 GLN j1907 GLN k1680 GLN k1907 GLN m1907 GLN n1907 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3266 r_free = 0.3266 target = 0.096909 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3093 r_free = 0.3093 target = 0.087059 restraints weight = 49158.720| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3125 r_free = 0.3125 target = 0.088861 restraints weight = 25323.236| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3144 r_free = 0.3144 target = 0.089947 restraints weight = 15103.189| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3157 r_free = 0.3157 target = 0.090655 restraints weight = 10203.268| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3163 r_free = 0.3163 target = 0.091029 restraints weight = 7668.324| |-----------------------------------------------------------------------------| r_work (final): 0.3156 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8171 moved from start: 0.3535 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 21238 Z= 0.132 Angle : 0.627 13.221 28784 Z= 0.324 Chirality : 0.049 0.175 3486 Planarity : 0.004 0.037 3612 Dihedral : 5.796 32.748 2889 Min Nonbonded Distance : 2.569 Molprobity Statistics. All-atom Clashscore : 10.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.20 % Favored : 89.80 % Rotamer: Outliers : 5.05 % Allowed : 21.43 % Favored : 73.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.53 % 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: -3.15 (0.15), residues: 2716 helix: -3.79 (0.19), residues: 392 sheet: -2.02 (0.17), residues: 812 loop : -1.59 (0.16), residues: 1512 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG f1797 TYR 0.025 0.001 TYR h1695 PHE 0.021 0.002 PHE n1810 TRP 0.005 0.001 TRP c1723 HIS 0.004 0.001 HIS l1793 Details of bonding type rmsd covalent geometry : bond 0.00300 (21238) covalent geometry : angle 0.62696 (28784) hydrogen bonds : bond 0.03080 ( 499) hydrogen bonds : angle 6.70258 ( 1170) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5432 Ramachandran restraints generated. 2716 Oldfield, 0 Emsley, 2716 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5432 Ramachandran restraints generated. 2716 Oldfield, 0 Emsley, 2716 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 738 residues out of total 2338 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 118 poor density : 620 time to evaluate : 0.777 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: b 1689 THR cc_start: 0.9500 (OUTLIER) cc_final: 0.9105 (t) REVERT: b 1715 SER cc_start: 0.9225 (t) cc_final: 0.8903 (m) REVERT: b 1729 MET cc_start: 0.8116 (ptm) cc_final: 0.6341 (mmt) REVERT: b 1734 LYS cc_start: 0.6527 (ttpt) cc_final: 0.6095 (pttm) REVERT: b 1752 MET cc_start: 0.8946 (ppp) cc_final: 0.8274 (ptt) REVERT: b 1795 MET cc_start: 0.7204 (ptm) cc_final: 0.6979 (ptt) REVERT: b 1857 GLN cc_start: 0.9039 (tp40) cc_final: 0.8800 (tp-100) REVERT: b 1886 ASP cc_start: 0.8553 (t0) cc_final: 0.7912 (t0) REVERT: b 1902 ASP cc_start: 0.8585 (t0) cc_final: 0.8120 (t70) REVERT: c 1710 LEU cc_start: 0.8734 (OUTLIER) cc_final: 0.8442 (pp) REVERT: c 1729 MET cc_start: 0.7953 (ptm) cc_final: 0.6724 (mmm) REVERT: c 1742 TYR cc_start: 0.8602 (p90) cc_final: 0.8003 (p90) REVERT: c 1756 MET cc_start: 0.8230 (tpt) cc_final: 0.7575 (tpt) REVERT: c 1862 LEU cc_start: 0.8999 (OUTLIER) cc_final: 0.8738 (mt) REVERT: c 1902 ASP cc_start: 0.8462 (t0) cc_final: 0.7954 (t0) REVERT: d 1710 LEU cc_start: 0.8608 (OUTLIER) cc_final: 0.8203 (pp) REVERT: d 1729 MET cc_start: 0.8265 (ptm) cc_final: 0.7427 (mmt) REVERT: d 1752 MET cc_start: 0.9137 (ppp) cc_final: 0.8548 (ptt) REVERT: d 1766 ASP cc_start: 0.8535 (m-30) cc_final: 0.8196 (m-30) REVERT: d 1857 GLN cc_start: 0.8689 (tp-100) cc_final: 0.8259 (tp40) REVERT: d 1886 ASP cc_start: 0.7993 (t0) cc_final: 0.7699 (t0) REVERT: e 1707 ASP cc_start: 0.7495 (p0) cc_final: 0.7049 (p0) REVERT: e 1729 MET cc_start: 0.8708 (ptm) cc_final: 0.7230 (mmt) REVERT: e 1734 LYS cc_start: 0.6189 (ttpt) cc_final: 0.5914 (pttp) REVERT: e 1752 MET cc_start: 0.8836 (ppp) cc_final: 0.8592 (ptt) REVERT: e 1783 GLU cc_start: 0.7757 (pm20) cc_final: 0.7372 (pm20) REVERT: e 1810 PHE cc_start: 0.7052 (p90) cc_final: 0.6798 (p90) REVERT: e 1870 TYR cc_start: 0.7945 (m-80) cc_final: 0.7507 (m-80) REVERT: e 1894 LYS cc_start: 0.8885 (ptmt) cc_final: 0.8637 (pttm) REVERT: e 1902 ASP cc_start: 0.8498 (t0) cc_final: 0.8261 (t70) REVERT: f 1707 ASP cc_start: 0.8163 (t0) cc_final: 0.7613 (t0) REVERT: f 1709 THR cc_start: 0.9079 (p) cc_final: 0.8747 (p) REVERT: f 1729 MET cc_start: 0.8071 (ptm) cc_final: 0.7313 (tpt) REVERT: f 1737 LYS cc_start: 0.8708 (mtmm) cc_final: 0.8049 (mtpp) REVERT: f 1739 TYR cc_start: 0.8448 (m-80) cc_final: 0.7904 (m-80) REVERT: f 1742 TYR cc_start: 0.8444 (p90) cc_final: 0.7781 (p90) REVERT: f 1752 MET cc_start: 0.8674 (ppp) cc_final: 0.8221 (ppp) REVERT: f 1857 GLN cc_start: 0.9060 (tp-100) cc_final: 0.8500 (tp40) REVERT: f 1886 ASP cc_start: 0.8186 (t0) cc_final: 0.7822 (t0) REVERT: f 1897 ASN cc_start: 0.8802 (t0) cc_final: 0.8585 (t0) REVERT: g 1699 GLU cc_start: 0.7176 (pt0) cc_final: 0.6882 (pt0) REVERT: g 1729 MET cc_start: 0.8237 (ptm) cc_final: 0.7046 (mmt) REVERT: g 1752 MET cc_start: 0.8811 (ppp) cc_final: 0.7651 (ptt) REVERT: g 1863 MET cc_start: 0.8613 (mmm) cc_final: 0.8352 (mmm) REVERT: g 1885 ILE cc_start: 0.9358 (mm) cc_final: 0.8954 (mm) REVERT: g 1894 LYS cc_start: 0.8646 (ptmt) cc_final: 0.8297 (pttm) REVERT: g 1897 ASN cc_start: 0.8810 (t0) cc_final: 0.8481 (t0) REVERT: h 1729 MET cc_start: 0.8056 (ptm) cc_final: 0.7082 (tpt) REVERT: h 1752 MET cc_start: 0.8277 (ppp) cc_final: 0.7435 (ppp) REVERT: h 1886 ASP cc_start: 0.7739 (p0) cc_final: 0.6933 (p0) REVERT: h 1903 GLU cc_start: 0.3797 (tt0) cc_final: 0.3170 (mt-10) REVERT: i 1707 ASP cc_start: 0.8061 (p0) cc_final: 0.7427 (p0) REVERT: i 1729 MET cc_start: 0.8204 (ptm) cc_final: 0.7173 (tpt) REVERT: i 1742 TYR cc_start: 0.8537 (p90) cc_final: 0.7714 (p90) REVERT: i 1752 MET cc_start: 0.8818 (ppp) cc_final: 0.8188 (ppp) REVERT: i 1756 MET cc_start: 0.8734 (tpt) cc_final: 0.8513 (tpt) REVERT: i 1766 ASP cc_start: 0.8426 (m-30) cc_final: 0.7950 (m-30) REVERT: i 1810 PHE cc_start: 0.7544 (p90) cc_final: 0.6902 (p90) REVERT: i 1857 GLN cc_start: 0.9069 (tp-100) cc_final: 0.8729 (tp40) REVERT: i 1902 ASP cc_start: 0.8431 (t0) cc_final: 0.8175 (t70) REVERT: j 1707 ASP cc_start: 0.7697 (p0) cc_final: 0.7200 (p0) REVERT: j 1729 MET cc_start: 0.8625 (ptm) cc_final: 0.7360 (mmt) REVERT: j 1734 LYS cc_start: 0.7038 (ttpt) cc_final: 0.6523 (pttp) REVERT: j 1752 MET cc_start: 0.9127 (ppp) cc_final: 0.8726 (ppp) REVERT: j 1780 MET cc_start: 0.8172 (tpt) cc_final: 0.7693 (tpp) REVERT: j 1783 GLU cc_start: 0.7995 (pm20) cc_final: 0.7791 (pm20) REVERT: j 1870 TYR cc_start: 0.7950 (m-80) cc_final: 0.7657 (m-80) REVERT: k 1710 LEU cc_start: 0.8986 (OUTLIER) cc_final: 0.8667 (pp) REVERT: k 1715 SER cc_start: 0.9569 (t) cc_final: 0.9278 (m) REVERT: k 1729 MET cc_start: 0.8212 (ptm) cc_final: 0.7425 (mmt) REVERT: k 1739 TYR cc_start: 0.8559 (m-80) cc_final: 0.8346 (m-80) REVERT: k 1752 MET cc_start: 0.9058 (ppp) cc_final: 0.8475 (ptt) REVERT: k 1766 ASP cc_start: 0.8592 (m-30) cc_final: 0.8292 (m-30) REVERT: k 1780 MET cc_start: 0.8387 (OUTLIER) cc_final: 0.7937 (tpp) REVERT: k 1783 GLU cc_start: 0.8386 (pm20) cc_final: 0.8158 (pm20) REVERT: k 1857 GLN cc_start: 0.8834 (tp-100) cc_final: 0.8384 (tp40) REVERT: l 1729 MET cc_start: 0.8386 (ptm) cc_final: 0.7358 (mmm) REVERT: l 1742 TYR cc_start: 0.8706 (p90) cc_final: 0.8321 (p90) REVERT: l 1743 GLN cc_start: 0.7540 (mm-40) cc_final: 0.7263 (mm-40) REVERT: l 1752 MET cc_start: 0.8800 (ppp) cc_final: 0.8126 (ppp) REVERT: l 1756 MET cc_start: 0.8522 (tpt) cc_final: 0.8293 (tpt) REVERT: l 1857 GLN cc_start: 0.8858 (mm-40) cc_final: 0.8558 (tp40) REVERT: l 1885 ILE cc_start: 0.9054 (mm) cc_final: 0.8794 (mm) REVERT: l 1897 ASN cc_start: 0.9053 (t0) cc_final: 0.8798 (t0) REVERT: l 1898 LYS cc_start: 0.8425 (tptp) cc_final: 0.8131 (tptp) REVERT: l 1903 GLU cc_start: 0.4651 (tt0) cc_final: 0.4437 (tt0) REVERT: m 1710 LEU cc_start: 0.8650 (OUTLIER) cc_final: 0.7971 (pp) REVERT: m 1729 MET cc_start: 0.8484 (ptm) cc_final: 0.7805 (tpt) REVERT: m 1736 THR cc_start: 0.9218 (OUTLIER) cc_final: 0.8922 (t) REVERT: m 1752 MET cc_start: 0.9139 (ppp) cc_final: 0.8811 (ppp) REVERT: m 1857 GLN cc_start: 0.8920 (tp40) cc_final: 0.8112 (tp-100) REVERT: m 1861 GLN cc_start: 0.8582 (mp-120) cc_final: 0.8005 (mp10) REVERT: n 1707 ASP cc_start: 0.8146 (p0) cc_final: 0.7656 (p0) REVERT: n 1729 MET cc_start: 0.8168 (ptm) cc_final: 0.6918 (mmt) REVERT: n 1752 MET cc_start: 0.8537 (ppp) cc_final: 0.7982 (ptt) REVERT: n 1766 ASP cc_start: 0.8077 (m-30) cc_final: 0.7848 (m-30) REVERT: n 1894 LYS cc_start: 0.8855 (ptmt) cc_final: 0.8386 (pttm) REVERT: o 1729 MET cc_start: 0.8161 (ptm) cc_final: 0.6960 (mmt) REVERT: o 1736 THR cc_start: 0.9289 (OUTLIER) cc_final: 0.9057 (t) REVERT: o 1752 MET cc_start: 0.9216 (ppp) cc_final: 0.8932 (ppp) REVERT: o 1756 MET cc_start: 0.8517 (tpt) cc_final: 0.8250 (tpt) REVERT: o 1783 GLU cc_start: 0.8126 (pm20) cc_final: 0.7416 (pm20) REVERT: o 1795 MET cc_start: 0.7489 (ptm) cc_final: 0.7112 (ptt) REVERT: o 1857 GLN cc_start: 0.9090 (mm-40) cc_final: 0.8815 (tp-100) REVERT: o 1870 TYR cc_start: 0.8288 (m-80) cc_final: 0.7980 (m-10) REVERT: o 1897 ASN cc_start: 0.9059 (t0) cc_final: 0.8733 (t0) outliers start: 118 outliers final: 79 residues processed: 713 average time/residue: 0.1249 time to fit residues: 145.8798 Evaluate side-chains 688 residues out of total 2338 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 600 time to evaluate : 0.815 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain b residue 1689 THR Chi-restraints excluded: chain b residue 1700 ILE Chi-restraints excluded: chain b residue 1755 LEU Chi-restraints excluded: chain b residue 1769 ILE Chi-restraints excluded: chain b residue 1790 VAL Chi-restraints excluded: chain c residue 1683 ILE Chi-restraints excluded: chain c residue 1710 LEU Chi-restraints excluded: chain c residue 1736 THR Chi-restraints excluded: chain c residue 1755 LEU Chi-restraints excluded: chain c residue 1790 VAL Chi-restraints excluded: chain c residue 1862 LEU Chi-restraints excluded: chain c residue 1879 ILE Chi-restraints excluded: chain d residue 1700 ILE Chi-restraints excluded: chain d residue 1710 LEU Chi-restraints excluded: chain d residue 1755 LEU Chi-restraints excluded: chain d residue 1790 VAL Chi-restraints excluded: chain d residue 1811 LEU Chi-restraints excluded: chain d residue 1883 ASP Chi-restraints excluded: chain d residue 1902 ASP Chi-restraints excluded: chain e residue 1683 ILE Chi-restraints excluded: chain e residue 1710 LEU Chi-restraints excluded: chain e residue 1790 VAL Chi-restraints excluded: chain e residue 1865 ILE Chi-restraints excluded: chain f residue 1678 VAL Chi-restraints excluded: chain f residue 1698 ILE Chi-restraints excluded: chain f residue 1700 ILE Chi-restraints excluded: chain f residue 1710 LEU Chi-restraints excluded: chain f residue 1713 ILE Chi-restraints excluded: chain f residue 1790 VAL Chi-restraints excluded: chain f residue 1879 ILE Chi-restraints excluded: chain g residue 1683 ILE Chi-restraints excluded: chain g residue 1710 LEU Chi-restraints excluded: chain g residue 1790 VAL Chi-restraints excluded: chain g residue 1865 ILE Chi-restraints excluded: chain g residue 1879 ILE Chi-restraints excluded: chain g residue 1883 ASP Chi-restraints excluded: chain h residue 1700 ILE Chi-restraints excluded: chain h residue 1702 LEU Chi-restraints excluded: chain h residue 1710 LEU Chi-restraints excluded: chain h residue 1715 SER Chi-restraints excluded: chain h residue 1738 VAL Chi-restraints excluded: chain h residue 1795 MET Chi-restraints excluded: chain i residue 1678 VAL Chi-restraints excluded: chain i residue 1683 ILE Chi-restraints excluded: chain i residue 1698 ILE Chi-restraints excluded: chain i residue 1700 ILE Chi-restraints excluded: chain i residue 1710 LEU Chi-restraints excluded: chain i residue 1755 LEU Chi-restraints excluded: chain i residue 1790 VAL Chi-restraints excluded: chain i residue 1879 ILE Chi-restraints excluded: chain j residue 1683 ILE Chi-restraints excluded: chain j residue 1700 ILE Chi-restraints excluded: chain j residue 1710 LEU Chi-restraints excluded: chain j residue 1755 LEU Chi-restraints excluded: chain j residue 1790 VAL Chi-restraints excluded: chain k residue 1700 ILE Chi-restraints excluded: chain k residue 1710 LEU Chi-restraints excluded: chain k residue 1755 LEU Chi-restraints excluded: chain k residue 1780 MET Chi-restraints excluded: chain k residue 1790 VAL Chi-restraints excluded: chain k residue 1811 LEU Chi-restraints excluded: chain k residue 1883 ASP Chi-restraints excluded: chain l residue 1683 ILE Chi-restraints excluded: chain l residue 1710 LEU Chi-restraints excluded: chain l residue 1736 THR Chi-restraints excluded: chain l residue 1790 VAL Chi-restraints excluded: chain l residue 1879 ILE Chi-restraints excluded: chain m residue 1698 ILE Chi-restraints excluded: chain m residue 1700 ILE Chi-restraints excluded: chain m residue 1710 LEU Chi-restraints excluded: chain m residue 1736 THR Chi-restraints excluded: chain m residue 1738 VAL Chi-restraints excluded: chain m residue 1755 LEU Chi-restraints excluded: chain m residue 1790 VAL Chi-restraints excluded: chain m residue 1873 GLU Chi-restraints excluded: chain m residue 1883 ASP Chi-restraints excluded: chain n residue 1683 ILE Chi-restraints excluded: chain n residue 1710 LEU Chi-restraints excluded: chain n residue 1755 LEU Chi-restraints excluded: chain n residue 1790 VAL Chi-restraints excluded: chain n residue 1865 ILE Chi-restraints excluded: chain n residue 1883 ASP Chi-restraints excluded: chain o residue 1700 ILE Chi-restraints excluded: chain o residue 1710 LEU Chi-restraints excluded: chain o residue 1736 THR Chi-restraints excluded: chain o residue 1741 ASN Chi-restraints excluded: chain o residue 1790 VAL Chi-restraints excluded: chain o residue 1873 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 266 random chunks: chunk 148 optimal weight: 0.6980 chunk 73 optimal weight: 4.9990 chunk 133 optimal weight: 5.9990 chunk 171 optimal weight: 0.2980 chunk 104 optimal weight: 4.9990 chunk 184 optimal weight: 6.9990 chunk 188 optimal weight: 3.9990 chunk 195 optimal weight: 0.9990 chunk 189 optimal weight: 2.9990 chunk 236 optimal weight: 0.9980 chunk 221 optimal weight: 5.9990 overall best weight: 1.1984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: c1897 ASN c1907 GLN d1680 GLN e1907 GLN k1680 GLN l1907 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3242 r_free = 0.3242 target = 0.095465 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3066 r_free = 0.3066 target = 0.085462 restraints weight = 49152.459| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3099 r_free = 0.3099 target = 0.087296 restraints weight = 24992.807| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3119 r_free = 0.3119 target = 0.088428 restraints weight = 14859.301| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3131 r_free = 0.3131 target = 0.089135 restraints weight = 9954.381| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3139 r_free = 0.3139 target = 0.089571 restraints weight = 7456.149| |-----------------------------------------------------------------------------| r_work (final): 0.3125 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8213 moved from start: 0.3833 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 21238 Z= 0.157 Angle : 0.656 14.250 28784 Z= 0.337 Chirality : 0.049 0.161 3486 Planarity : 0.004 0.036 3612 Dihedral : 5.869 33.722 2889 Min Nonbonded Distance : 2.552 Molprobity Statistics. All-atom Clashscore : 10.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.82 % Favored : 89.18 % Rotamer: Outliers : 5.69 % Allowed : 21.51 % Favored : 72.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.53 % 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: -3.07 (0.15), residues: 2716 helix: -3.73 (0.19), residues: 392 sheet: -1.91 (0.18), residues: 798 loop : -1.57 (0.16), residues: 1526 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG c1754 TYR 0.024 0.001 TYR h1695 PHE 0.020 0.002 PHE n1810 TRP 0.005 0.001 TRP b1723 HIS 0.002 0.000 HIS d1793 Details of bonding type rmsd covalent geometry : bond 0.00361 (21238) covalent geometry : angle 0.65641 (28784) hydrogen bonds : bond 0.03246 ( 499) hydrogen bonds : angle 6.61643 ( 1170) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5432 Ramachandran restraints generated. 2716 Oldfield, 0 Emsley, 2716 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5432 Ramachandran restraints generated. 2716 Oldfield, 0 Emsley, 2716 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 748 residues out of total 2338 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 133 poor density : 615 time to evaluate : 0.826 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: b 1689 THR cc_start: 0.9527 (OUTLIER) cc_final: 0.9194 (t) REVERT: b 1729 MET cc_start: 0.8190 (ptm) cc_final: 0.6351 (mmt) REVERT: b 1734 LYS cc_start: 0.6815 (ttpt) cc_final: 0.6385 (pttt) REVERT: b 1752 MET cc_start: 0.9077 (ppp) cc_final: 0.8278 (ptt) REVERT: b 1795 MET cc_start: 0.7173 (ptm) cc_final: 0.6948 (ptt) REVERT: b 1857 GLN cc_start: 0.9058 (tp40) cc_final: 0.8764 (tp-100) REVERT: b 1886 ASP cc_start: 0.8580 (t0) cc_final: 0.8353 (t70) REVERT: b 1902 ASP cc_start: 0.8592 (t0) cc_final: 0.8213 (t70) REVERT: c 1729 MET cc_start: 0.8022 (ptm) cc_final: 0.6814 (mmm) REVERT: c 1742 TYR cc_start: 0.8492 (p90) cc_final: 0.7934 (p90) REVERT: c 1862 LEU cc_start: 0.9030 (OUTLIER) cc_final: 0.8736 (mt) REVERT: c 1886 ASP cc_start: 0.7821 (t0) cc_final: 0.7475 (t0) REVERT: c 1902 ASP cc_start: 0.8649 (t0) cc_final: 0.8171 (t0) REVERT: d 1710 LEU cc_start: 0.8866 (OUTLIER) cc_final: 0.8495 (pp) REVERT: d 1729 MET cc_start: 0.8276 (ptm) cc_final: 0.7324 (mmt) REVERT: d 1737 LYS cc_start: 0.8822 (mtmm) cc_final: 0.8340 (mtpt) REVERT: d 1752 MET cc_start: 0.9113 (ppp) cc_final: 0.8457 (ptt) REVERT: d 1766 ASP cc_start: 0.8571 (m-30) cc_final: 0.8274 (m-30) REVERT: d 1857 GLN cc_start: 0.8787 (tp-100) cc_final: 0.8377 (tp40) REVERT: d 1886 ASP cc_start: 0.7955 (t0) cc_final: 0.7682 (t0) REVERT: e 1729 MET cc_start: 0.8726 (ptm) cc_final: 0.7224 (mmt) REVERT: e 1734 LYS cc_start: 0.6961 (ttpt) cc_final: 0.6075 (pttp) REVERT: e 1752 MET cc_start: 0.8901 (ppp) cc_final: 0.8377 (ptt) REVERT: e 1783 GLU cc_start: 0.8127 (pm20) cc_final: 0.7866 (pm20) REVERT: e 1810 PHE cc_start: 0.7036 (p90) cc_final: 0.6795 (p90) REVERT: e 1870 TYR cc_start: 0.8009 (m-80) cc_final: 0.7648 (m-80) REVERT: e 1902 ASP cc_start: 0.8548 (t0) cc_final: 0.8324 (t70) REVERT: f 1707 ASP cc_start: 0.8173 (t0) cc_final: 0.7628 (t0) REVERT: f 1709 THR cc_start: 0.9108 (p) cc_final: 0.8754 (p) REVERT: f 1729 MET cc_start: 0.8005 (ptm) cc_final: 0.7098 (tpt) REVERT: f 1737 LYS cc_start: 0.8732 (mtmm) cc_final: 0.8066 (mtpp) REVERT: f 1739 TYR cc_start: 0.8596 (m-80) cc_final: 0.7869 (m-80) REVERT: f 1742 TYR cc_start: 0.8464 (p90) cc_final: 0.7812 (p90) REVERT: f 1752 MET cc_start: 0.8781 (ppp) cc_final: 0.8223 (ppp) REVERT: f 1756 MET cc_start: 0.8546 (tpt) cc_final: 0.8264 (tpt) REVERT: f 1857 GLN cc_start: 0.9067 (tp-100) cc_final: 0.8489 (tp40) REVERT: f 1861 GLN cc_start: 0.8846 (mp10) cc_final: 0.8454 (mp10) REVERT: f 1897 ASN cc_start: 0.8795 (t0) cc_final: 0.8570 (t0) REVERT: g 1729 MET cc_start: 0.8287 (ptm) cc_final: 0.7033 (mmt) REVERT: g 1737 LYS cc_start: 0.8797 (mtmm) cc_final: 0.8120 (mtpp) REVERT: g 1752 MET cc_start: 0.8862 (ppp) cc_final: 0.7832 (ptt) REVERT: g 1885 ILE cc_start: 0.9383 (mm) cc_final: 0.9128 (mm) REVERT: g 1894 LYS cc_start: 0.8630 (ptmt) cc_final: 0.8319 (pttm) REVERT: h 1702 LEU cc_start: 0.9206 (OUTLIER) cc_final: 0.9006 (mp) REVERT: h 1729 MET cc_start: 0.8116 (ptm) cc_final: 0.7070 (tpt) REVERT: h 1736 THR cc_start: 0.9131 (OUTLIER) cc_final: 0.8910 (t) REVERT: h 1752 MET cc_start: 0.8530 (ppp) cc_final: 0.7749 (ppp) REVERT: h 1776 GLN cc_start: 0.8109 (pt0) cc_final: 0.7755 (tt0) REVERT: h 1886 ASP cc_start: 0.7760 (p0) cc_final: 0.7443 (p0) REVERT: h 1903 GLU cc_start: 0.3878 (tt0) cc_final: 0.3238 (mt-10) REVERT: i 1707 ASP cc_start: 0.7895 (p0) cc_final: 0.7350 (p0) REVERT: i 1729 MET cc_start: 0.8255 (ptm) cc_final: 0.7332 (tpt) REVERT: i 1742 TYR cc_start: 0.8531 (p90) cc_final: 0.7756 (p90) REVERT: i 1752 MET cc_start: 0.8857 (ppp) cc_final: 0.8215 (ppp) REVERT: i 1810 PHE cc_start: 0.7853 (p90) cc_final: 0.7024 (p90) REVERT: i 1857 GLN cc_start: 0.9132 (tp-100) cc_final: 0.8314 (tp40) REVERT: i 1861 GLN cc_start: 0.8747 (mp10) cc_final: 0.8288 (mp10) REVERT: i 1897 ASN cc_start: 0.8504 (t0) cc_final: 0.8303 (t0) REVERT: i 1902 ASP cc_start: 0.8459 (t0) cc_final: 0.8186 (t70) REVERT: j 1707 ASP cc_start: 0.7738 (p0) cc_final: 0.7184 (p0) REVERT: j 1729 MET cc_start: 0.8692 (ptm) cc_final: 0.7463 (mmt) REVERT: j 1752 MET cc_start: 0.9179 (ppp) cc_final: 0.8764 (ppp) REVERT: j 1780 MET cc_start: 0.8231 (tpt) cc_final: 0.7833 (tpp) REVERT: j 1783 GLU cc_start: 0.8124 (pm20) cc_final: 0.7836 (pm20) REVERT: j 1870 TYR cc_start: 0.8003 (m-80) cc_final: 0.7700 (m-80) REVERT: j 1902 ASP cc_start: 0.8220 (t70) cc_final: 0.7783 (t70) REVERT: k 1710 LEU cc_start: 0.9024 (OUTLIER) cc_final: 0.8741 (pp) REVERT: k 1715 SER cc_start: 0.9579 (t) cc_final: 0.9377 (m) REVERT: k 1729 MET cc_start: 0.8276 (ptm) cc_final: 0.7300 (mmt) REVERT: k 1752 MET cc_start: 0.9056 (ppp) cc_final: 0.8421 (ptt) REVERT: k 1766 ASP cc_start: 0.8607 (m-30) cc_final: 0.8294 (m-30) REVERT: k 1780 MET cc_start: 0.8378 (OUTLIER) cc_final: 0.7994 (tpp) REVERT: k 1783 GLU cc_start: 0.8429 (pm20) cc_final: 0.8207 (pm20) REVERT: k 1857 GLN cc_start: 0.8829 (tp-100) cc_final: 0.8330 (tp40) REVERT: l 1729 MET cc_start: 0.8409 (ptm) cc_final: 0.7341 (mmm) REVERT: l 1742 TYR cc_start: 0.8749 (p90) cc_final: 0.8404 (p90) REVERT: l 1743 GLN cc_start: 0.7866 (mm-40) cc_final: 0.7593 (mm-40) REVERT: l 1752 MET cc_start: 0.8818 (ppp) cc_final: 0.8138 (ppp) REVERT: l 1756 MET cc_start: 0.8439 (tpt) cc_final: 0.8005 (tpt) REVERT: l 1780 MET cc_start: 0.8299 (tpt) cc_final: 0.8054 (tpp) REVERT: l 1857 GLN cc_start: 0.8846 (mm-40) cc_final: 0.8366 (tp40) REVERT: l 1861 GLN cc_start: 0.8592 (mp10) cc_final: 0.8111 (mp10) REVERT: l 1885 ILE cc_start: 0.9139 (mm) cc_final: 0.8897 (mm) REVERT: l 1898 LYS cc_start: 0.8541 (tptp) cc_final: 0.8313 (tptp) REVERT: l 1903 GLU cc_start: 0.4658 (tt0) cc_final: 0.4426 (tt0) REVERT: m 1729 MET cc_start: 0.8342 (ptm) cc_final: 0.7502 (tpt) REVERT: m 1736 THR cc_start: 0.9250 (OUTLIER) cc_final: 0.8798 (t) REVERT: m 1752 MET cc_start: 0.9197 (ppp) cc_final: 0.8861 (ppp) REVERT: m 1857 GLN cc_start: 0.8955 (tp40) cc_final: 0.8246 (tp-100) REVERT: m 1861 GLN cc_start: 0.8647 (mp-120) cc_final: 0.8273 (mp10) REVERT: n 1707 ASP cc_start: 0.8107 (p0) cc_final: 0.7587 (p0) REVERT: n 1729 MET cc_start: 0.8222 (ptm) cc_final: 0.6965 (mmt) REVERT: n 1752 MET cc_start: 0.8627 (ppp) cc_final: 0.8082 (ptt) REVERT: n 1894 LYS cc_start: 0.8889 (ptmt) cc_final: 0.8435 (pttm) REVERT: o 1699 GLU cc_start: 0.6288 (pt0) cc_final: 0.6016 (pm20) REVERT: o 1729 MET cc_start: 0.7608 (ptm) cc_final: 0.6642 (mmt) REVERT: o 1736 THR cc_start: 0.9335 (OUTLIER) cc_final: 0.9134 (t) REVERT: o 1752 MET cc_start: 0.9215 (ppp) cc_final: 0.8899 (ppp) REVERT: o 1781 LEU cc_start: 0.8606 (tt) cc_final: 0.8349 (tt) REVERT: o 1783 GLU cc_start: 0.8202 (pm20) cc_final: 0.7467 (pm20) REVERT: o 1795 MET cc_start: 0.7446 (ptm) cc_final: 0.7074 (ptt) REVERT: o 1870 TYR cc_start: 0.8284 (m-80) cc_final: 0.7964 (m-10) REVERT: o 1897 ASN cc_start: 0.9065 (t0) cc_final: 0.8708 (t0) outliers start: 133 outliers final: 91 residues processed: 720 average time/residue: 0.1262 time to fit residues: 149.2645 Evaluate side-chains 696 residues out of total 2338 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 100 poor density : 596 time to evaluate : 0.732 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain b residue 1683 ILE Chi-restraints excluded: chain b residue 1689 THR Chi-restraints excluded: chain b residue 1700 ILE Chi-restraints excluded: chain b residue 1755 LEU Chi-restraints excluded: chain b residue 1790 VAL Chi-restraints excluded: chain c residue 1683 ILE Chi-restraints excluded: chain c residue 1710 LEU Chi-restraints excluded: chain c residue 1715 SER Chi-restraints excluded: chain c residue 1736 THR Chi-restraints excluded: chain c residue 1755 LEU Chi-restraints excluded: chain c residue 1790 VAL Chi-restraints excluded: chain c residue 1862 LEU Chi-restraints excluded: chain c residue 1879 ILE Chi-restraints excluded: chain d residue 1700 ILE Chi-restraints excluded: chain d residue 1710 LEU Chi-restraints excluded: chain d residue 1755 LEU Chi-restraints excluded: chain d residue 1790 VAL Chi-restraints excluded: chain d residue 1811 LEU Chi-restraints excluded: chain d residue 1883 ASP Chi-restraints excluded: chain e residue 1683 ILE Chi-restraints excluded: chain e residue 1700 ILE Chi-restraints excluded: chain e residue 1710 LEU Chi-restraints excluded: chain e residue 1755 LEU Chi-restraints excluded: chain e residue 1790 VAL Chi-restraints excluded: chain e residue 1865 ILE Chi-restraints excluded: chain f residue 1678 VAL Chi-restraints excluded: chain f residue 1698 ILE Chi-restraints excluded: chain f residue 1700 ILE Chi-restraints excluded: chain f residue 1710 LEU Chi-restraints excluded: chain f residue 1713 ILE Chi-restraints excluded: chain f residue 1755 LEU Chi-restraints excluded: chain f residue 1790 VAL Chi-restraints excluded: chain f residue 1879 ILE Chi-restraints excluded: chain g residue 1683 ILE Chi-restraints excluded: chain g residue 1755 LEU Chi-restraints excluded: chain g residue 1790 VAL Chi-restraints excluded: chain g residue 1865 ILE Chi-restraints excluded: chain g residue 1879 ILE Chi-restraints excluded: chain g residue 1883 ASP Chi-restraints excluded: chain h residue 1700 ILE Chi-restraints excluded: chain h residue 1702 LEU Chi-restraints excluded: chain h residue 1715 SER Chi-restraints excluded: chain h residue 1736 THR Chi-restraints excluded: chain h residue 1738 VAL Chi-restraints excluded: chain h residue 1755 LEU Chi-restraints excluded: chain h residue 1795 MET Chi-restraints excluded: chain h residue 1872 ASN Chi-restraints excluded: chain i residue 1678 VAL Chi-restraints excluded: chain i residue 1683 ILE Chi-restraints excluded: chain i residue 1698 ILE Chi-restraints excluded: chain i residue 1700 ILE Chi-restraints excluded: chain i residue 1710 LEU Chi-restraints excluded: chain i residue 1755 LEU Chi-restraints excluded: chain i residue 1790 VAL Chi-restraints excluded: chain i residue 1879 ILE Chi-restraints excluded: chain j residue 1683 ILE Chi-restraints excluded: chain j residue 1700 ILE Chi-restraints excluded: chain j residue 1710 LEU Chi-restraints excluded: chain j residue 1755 LEU Chi-restraints excluded: chain j residue 1790 VAL Chi-restraints excluded: chain k residue 1700 ILE Chi-restraints excluded: chain k residue 1710 LEU Chi-restraints excluded: chain k residue 1755 LEU Chi-restraints excluded: chain k residue 1780 MET Chi-restraints excluded: chain k residue 1790 VAL Chi-restraints excluded: chain k residue 1811 LEU Chi-restraints excluded: chain k residue 1855 SER Chi-restraints excluded: chain k residue 1883 ASP Chi-restraints excluded: chain l residue 1678 VAL Chi-restraints excluded: chain l residue 1683 ILE Chi-restraints excluded: chain l residue 1710 LEU Chi-restraints excluded: chain l residue 1736 THR Chi-restraints excluded: chain l residue 1790 VAL Chi-restraints excluded: chain l residue 1863 MET Chi-restraints excluded: chain l residue 1879 ILE Chi-restraints excluded: chain m residue 1698 ILE Chi-restraints excluded: chain m residue 1710 LEU Chi-restraints excluded: chain m residue 1736 THR Chi-restraints excluded: chain m residue 1738 VAL Chi-restraints excluded: chain m residue 1755 LEU Chi-restraints excluded: chain m residue 1790 VAL Chi-restraints excluded: chain m residue 1811 LEU Chi-restraints excluded: chain m residue 1865 ILE Chi-restraints excluded: chain m residue 1883 ASP Chi-restraints excluded: chain n residue 1683 ILE Chi-restraints excluded: chain n residue 1698 ILE Chi-restraints excluded: chain n residue 1710 LEU Chi-restraints excluded: chain n residue 1755 LEU Chi-restraints excluded: chain n residue 1790 VAL Chi-restraints excluded: chain n residue 1865 ILE Chi-restraints excluded: chain n residue 1873 GLU Chi-restraints excluded: chain n residue 1883 ASP Chi-restraints excluded: chain o residue 1700 ILE Chi-restraints excluded: chain o residue 1706 VAL Chi-restraints excluded: chain o residue 1736 THR Chi-restraints excluded: chain o residue 1741 ASN Chi-restraints excluded: chain o residue 1755 LEU Chi-restraints excluded: chain o residue 1790 VAL Chi-restraints excluded: chain o residue 1811 LEU Chi-restraints excluded: chain o residue 1873 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 266 random chunks: chunk 5 optimal weight: 0.3980 chunk 55 optimal weight: 3.9990 chunk 245 optimal weight: 2.9990 chunk 25 optimal weight: 0.8980 chunk 68 optimal weight: 0.0670 chunk 101 optimal weight: 1.9990 chunk 211 optimal weight: 1.9990 chunk 19 optimal weight: 2.9990 chunk 234 optimal weight: 4.9990 chunk 198 optimal weight: 0.4980 chunk 148 optimal weight: 0.9990 overall best weight: 0.5720 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: d1680 GLN ** d1853 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** g1897 ASN j1776 GLN k1680 GLN l1793 HIS l1897 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3269 r_free = 0.3269 target = 0.097125 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3077 r_free = 0.3077 target = 0.086328 restraints weight = 47821.833| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3111 r_free = 0.3111 target = 0.088272 restraints weight = 24491.599| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3132 r_free = 0.3132 target = 0.089445 restraints weight = 14641.317| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3146 r_free = 0.3146 target = 0.090201 restraints weight = 9918.491| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3154 r_free = 0.3154 target = 0.090616 restraints weight = 7487.862| |-----------------------------------------------------------------------------| r_work (final): 0.3151 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8182 moved from start: 0.4150 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 21238 Z= 0.122 Angle : 0.635 14.108 28784 Z= 0.328 Chirality : 0.048 0.161 3486 Planarity : 0.004 0.038 3612 Dihedral : 5.533 33.070 2885 Min Nonbonded Distance : 2.544 Molprobity Statistics. All-atom Clashscore : 10.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.90 % Favored : 90.10 % Rotamer: Outliers : 5.09 % Allowed : 22.54 % Favored : 72.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.53 % 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: -2.93 (0.16), residues: 2716 helix: -3.64 (0.20), residues: 392 sheet: -1.86 (0.18), residues: 798 loop : -1.45 (0.16), residues: 1526 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG f1754 TYR 0.022 0.001 TYR h1695 PHE 0.018 0.001 PHE n1810 TRP 0.004 0.001 TRP g1723 HIS 0.003 0.001 HIS i1793 Details of bonding type rmsd covalent geometry : bond 0.00280 (21238) covalent geometry : angle 0.63535 (28784) hydrogen bonds : bond 0.03039 ( 499) hydrogen bonds : angle 6.54746 ( 1170) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5432 Ramachandran restraints generated. 2716 Oldfield, 0 Emsley, 2716 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5432 Ramachandran restraints generated. 2716 Oldfield, 0 Emsley, 2716 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 726 residues out of total 2338 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 119 poor density : 607 time to evaluate : 0.786 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: b 1729 MET cc_start: 0.8233 (ptm) cc_final: 0.6434 (mmt) REVERT: b 1734 LYS cc_start: 0.6743 (ttpt) cc_final: 0.6295 (pttt) REVERT: b 1739 TYR cc_start: 0.8951 (m-80) cc_final: 0.8676 (m-80) REVERT: b 1752 MET cc_start: 0.9034 (ppp) cc_final: 0.8176 (ptt) REVERT: b 1781 LEU cc_start: 0.9248 (tt) cc_final: 0.8828 (mm) REVERT: b 1857 GLN cc_start: 0.9075 (tp40) cc_final: 0.8748 (tp-100) REVERT: b 1886 ASP cc_start: 0.8315 (t0) cc_final: 0.8045 (t70) REVERT: b 1902 ASP cc_start: 0.8650 (t0) cc_final: 0.8235 (t70) REVERT: c 1707 ASP cc_start: 0.7658 (t0) cc_final: 0.7260 (t0) REVERT: c 1729 MET cc_start: 0.8028 (ptm) cc_final: 0.6814 (mmm) REVERT: c 1734 LYS cc_start: 0.5715 (ttpp) cc_final: 0.5193 (pttt) REVERT: c 1742 TYR cc_start: 0.8410 (p90) cc_final: 0.7735 (p90) REVERT: c 1752 MET cc_start: 0.8977 (ppp) cc_final: 0.8380 (ppp) REVERT: c 1780 MET cc_start: 0.7547 (mmp) cc_final: 0.7061 (mmm) REVERT: c 1862 LEU cc_start: 0.8931 (OUTLIER) cc_final: 0.8639 (mt) REVERT: c 1886 ASP cc_start: 0.7792 (t0) cc_final: 0.7443 (t0) REVERT: c 1902 ASP cc_start: 0.8626 (t0) cc_final: 0.8122 (t0) REVERT: d 1710 LEU cc_start: 0.8733 (OUTLIER) cc_final: 0.8470 (pp) REVERT: d 1729 MET cc_start: 0.8272 (ptm) cc_final: 0.7416 (mmt) REVERT: d 1752 MET cc_start: 0.9105 (ppp) cc_final: 0.8389 (ptt) REVERT: d 1766 ASP cc_start: 0.8573 (m-30) cc_final: 0.8265 (m-30) REVERT: d 1857 GLN cc_start: 0.8796 (tp-100) cc_final: 0.8402 (tp40) REVERT: d 1861 GLN cc_start: 0.8687 (mp10) cc_final: 0.8419 (mp10) REVERT: e 1707 ASP cc_start: 0.7556 (p0) cc_final: 0.7151 (p0) REVERT: e 1729 MET cc_start: 0.8721 (ptm) cc_final: 0.7227 (mmt) REVERT: e 1734 LYS cc_start: 0.6753 (ttpt) cc_final: 0.5902 (pttp) REVERT: e 1752 MET cc_start: 0.8873 (ppp) cc_final: 0.8358 (ptt) REVERT: e 1783 GLU cc_start: 0.7858 (pm20) cc_final: 0.7603 (pm20) REVERT: e 1800 PHE cc_start: 0.7390 (m-80) cc_final: 0.7083 (m-80) REVERT: e 1810 PHE cc_start: 0.6950 (p90) cc_final: 0.6701 (p90) REVERT: e 1870 TYR cc_start: 0.8002 (m-80) cc_final: 0.7515 (m-80) REVERT: e 1902 ASP cc_start: 0.8592 (t0) cc_final: 0.8346 (t70) REVERT: f 1707 ASP cc_start: 0.8125 (t0) cc_final: 0.7528 (t0) REVERT: f 1709 THR cc_start: 0.9132 (p) cc_final: 0.8753 (p) REVERT: f 1729 MET cc_start: 0.8021 (ptm) cc_final: 0.7066 (tpt) REVERT: f 1737 LYS cc_start: 0.8765 (mtmm) cc_final: 0.8055 (mtpp) REVERT: f 1739 TYR cc_start: 0.8499 (m-80) cc_final: 0.7853 (m-80) REVERT: f 1742 TYR cc_start: 0.8317 (p90) cc_final: 0.7632 (p90) REVERT: f 1752 MET cc_start: 0.8813 (ppp) cc_final: 0.8268 (ppp) REVERT: f 1756 MET cc_start: 0.8300 (tpt) cc_final: 0.7567 (tpt) REVERT: f 1857 GLN cc_start: 0.9032 (tp-100) cc_final: 0.8489 (tp40) REVERT: f 1861 GLN cc_start: 0.8874 (mp10) cc_final: 0.8425 (mp10) REVERT: f 1863 MET cc_start: 0.8752 (tpp) cc_final: 0.8443 (tpp) REVERT: f 1886 ASP cc_start: 0.8093 (t0) cc_final: 0.7778 (t0) REVERT: f 1897 ASN cc_start: 0.8792 (t0) cc_final: 0.8557 (t0) REVERT: f 1902 ASP cc_start: 0.8105 (t70) cc_final: 0.7350 (t70) REVERT: g 1729 MET cc_start: 0.8232 (ptm) cc_final: 0.6981 (mmt) REVERT: g 1752 MET cc_start: 0.8872 (ppp) cc_final: 0.7723 (ptt) REVERT: g 1878 LYS cc_start: 0.9136 (mmtp) cc_final: 0.8855 (mmtt) REVERT: g 1885 ILE cc_start: 0.9409 (mm) cc_final: 0.9075 (mm) REVERT: g 1894 LYS cc_start: 0.8632 (ptmt) cc_final: 0.8309 (pttm) REVERT: h 1729 MET cc_start: 0.7430 (ptm) cc_final: 0.6700 (tpt) REVERT: h 1736 THR cc_start: 0.9104 (OUTLIER) cc_final: 0.8874 (t) REVERT: h 1752 MET cc_start: 0.8541 (ppp) cc_final: 0.7757 (ppp) REVERT: h 1776 GLN cc_start: 0.8052 (pt0) cc_final: 0.7729 (tt0) REVERT: h 1886 ASP cc_start: 0.7795 (p0) cc_final: 0.7499 (p0) REVERT: h 1903 GLU cc_start: 0.3861 (tt0) cc_final: 0.3131 (mt-10) REVERT: i 1707 ASP cc_start: 0.7880 (p0) cc_final: 0.7378 (p0) REVERT: i 1729 MET cc_start: 0.8220 (ptm) cc_final: 0.7343 (tpt) REVERT: i 1742 TYR cc_start: 0.8711 (p90) cc_final: 0.8122 (p90) REVERT: i 1752 MET cc_start: 0.8944 (ppp) cc_final: 0.8377 (ppp) REVERT: i 1810 PHE cc_start: 0.7819 (p90) cc_final: 0.7051 (p90) REVERT: i 1857 GLN cc_start: 0.9166 (tp-100) cc_final: 0.8318 (tp40) REVERT: i 1861 GLN cc_start: 0.8798 (mp10) cc_final: 0.8303 (mp10) REVERT: i 1886 ASP cc_start: 0.8446 (t0) cc_final: 0.8129 (t0) REVERT: i 1902 ASP cc_start: 0.8435 (t0) cc_final: 0.8145 (t70) REVERT: j 1707 ASP cc_start: 0.7653 (p0) cc_final: 0.7057 (p0) REVERT: j 1729 MET cc_start: 0.8677 (ptm) cc_final: 0.7436 (mmt) REVERT: j 1734 LYS cc_start: 0.6978 (ttpt) cc_final: 0.6453 (pttp) REVERT: j 1752 MET cc_start: 0.9197 (ppp) cc_final: 0.8769 (ppp) REVERT: j 1756 MET cc_start: 0.9132 (tpp) cc_final: 0.8200 (tpp) REVERT: j 1780 MET cc_start: 0.8316 (tpt) cc_final: 0.7821 (tpp) REVERT: j 1783 GLU cc_start: 0.8201 (pm20) cc_final: 0.7999 (pm20) REVERT: j 1870 TYR cc_start: 0.8019 (m-80) cc_final: 0.7671 (m-80) REVERT: j 1902 ASP cc_start: 0.8269 (t70) cc_final: 0.7897 (t70) REVERT: k 1710 LEU cc_start: 0.8973 (OUTLIER) cc_final: 0.8701 (pp) REVERT: k 1729 MET cc_start: 0.8275 (ptm) cc_final: 0.7263 (mmt) REVERT: k 1752 MET cc_start: 0.8938 (ppp) cc_final: 0.8102 (ptt) REVERT: k 1766 ASP cc_start: 0.8582 (m-30) cc_final: 0.8292 (m-30) REVERT: k 1780 MET cc_start: 0.8327 (OUTLIER) cc_final: 0.7901 (tpp) REVERT: k 1783 GLU cc_start: 0.8376 (pm20) cc_final: 0.8131 (pm20) REVERT: k 1857 GLN cc_start: 0.8906 (tp-100) cc_final: 0.8405 (tp40) REVERT: l 1707 ASP cc_start: 0.8109 (t0) cc_final: 0.7668 (t0) REVERT: l 1726 ASN cc_start: 0.8869 (p0) cc_final: 0.8600 (p0) REVERT: l 1729 MET cc_start: 0.8383 (ptm) cc_final: 0.7323 (mmm) REVERT: l 1742 TYR cc_start: 0.8708 (p90) cc_final: 0.8326 (p90) REVERT: l 1743 GLN cc_start: 0.7807 (mm-40) cc_final: 0.7503 (mm-40) REVERT: l 1752 MET cc_start: 0.8838 (ppp) cc_final: 0.8075 (ppp) REVERT: l 1756 MET cc_start: 0.8470 (tpt) cc_final: 0.8039 (tpt) REVERT: l 1780 MET cc_start: 0.8218 (tpt) cc_final: 0.7955 (tpp) REVERT: l 1857 GLN cc_start: 0.8839 (mm-40) cc_final: 0.8381 (tp40) REVERT: l 1861 GLN cc_start: 0.8624 (mp10) cc_final: 0.8085 (mp10) REVERT: l 1885 ILE cc_start: 0.9158 (mm) cc_final: 0.8908 (mm) REVERT: l 1886 ASP cc_start: 0.7267 (t0) cc_final: 0.7038 (t0) REVERT: l 1898 LYS cc_start: 0.8447 (tptp) cc_final: 0.8244 (tptp) REVERT: m 1729 MET cc_start: 0.8365 (ptm) cc_final: 0.7467 (tpt) REVERT: m 1736 THR cc_start: 0.9188 (OUTLIER) cc_final: 0.8847 (t) REVERT: m 1752 MET cc_start: 0.9212 (ppp) cc_final: 0.8876 (ppp) REVERT: m 1783 GLU cc_start: 0.8224 (pm20) cc_final: 0.7933 (pm20) REVERT: m 1857 GLN cc_start: 0.8992 (tp40) cc_final: 0.8205 (tp-100) REVERT: m 1861 GLN cc_start: 0.8688 (mp-120) cc_final: 0.8052 (mp10) REVERT: n 1707 ASP cc_start: 0.7900 (p0) cc_final: 0.7421 (p0) REVERT: n 1729 MET cc_start: 0.8222 (ptm) cc_final: 0.6947 (mmt) REVERT: n 1752 MET cc_start: 0.8619 (ppp) cc_final: 0.8087 (ptt) REVERT: n 1894 LYS cc_start: 0.8888 (ptmt) cc_final: 0.8401 (pttm) REVERT: o 1729 MET cc_start: 0.7601 (ptm) cc_final: 0.6633 (mmt) REVERT: o 1736 THR cc_start: 0.9319 (OUTLIER) cc_final: 0.9098 (t) REVERT: o 1741 ASN cc_start: 0.8888 (OUTLIER) cc_final: 0.8497 (p0) REVERT: o 1752 MET cc_start: 0.9206 (ppp) cc_final: 0.8885 (ppp) REVERT: o 1783 GLU cc_start: 0.8174 (pm20) cc_final: 0.7417 (pm20) REVERT: o 1795 MET cc_start: 0.7471 (ptm) cc_final: 0.7096 (ptt) REVERT: o 1870 TYR cc_start: 0.8254 (m-80) cc_final: 0.7918 (m-10) REVERT: o 1897 ASN cc_start: 0.9050 (t0) cc_final: 0.8667 (t0) outliers start: 119 outliers final: 89 residues processed: 698 average time/residue: 0.1201 time to fit residues: 137.8984 Evaluate side-chains 691 residues out of total 2338 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 97 poor density : 594 time to evaluate : 0.758 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain b residue 1683 ILE Chi-restraints excluded: chain b residue 1700 ILE Chi-restraints excluded: chain b residue 1755 LEU Chi-restraints excluded: chain b residue 1769 ILE Chi-restraints excluded: chain b residue 1790 VAL Chi-restraints excluded: chain c residue 1683 ILE Chi-restraints excluded: chain c residue 1710 LEU Chi-restraints excluded: chain c residue 1736 THR Chi-restraints excluded: chain c residue 1755 LEU Chi-restraints excluded: chain c residue 1790 VAL Chi-restraints excluded: chain c residue 1862 LEU Chi-restraints excluded: chain c residue 1879 ILE Chi-restraints excluded: chain d residue 1700 ILE Chi-restraints excluded: chain d residue 1710 LEU Chi-restraints excluded: chain d residue 1755 LEU Chi-restraints excluded: chain d residue 1790 VAL Chi-restraints excluded: chain d residue 1811 LEU Chi-restraints excluded: chain d residue 1883 ASP Chi-restraints excluded: chain e residue 1683 ILE Chi-restraints excluded: chain e residue 1700 ILE Chi-restraints excluded: chain e residue 1710 LEU Chi-restraints excluded: chain e residue 1755 LEU Chi-restraints excluded: chain e residue 1790 VAL Chi-restraints excluded: chain e residue 1865 ILE Chi-restraints excluded: chain e residue 1896 THR Chi-restraints excluded: chain f residue 1678 VAL Chi-restraints excluded: chain f residue 1698 ILE Chi-restraints excluded: chain f residue 1700 ILE Chi-restraints excluded: chain f residue 1710 LEU Chi-restraints excluded: chain f residue 1713 ILE Chi-restraints excluded: chain f residue 1755 LEU Chi-restraints excluded: chain f residue 1790 VAL Chi-restraints excluded: chain f residue 1879 ILE Chi-restraints excluded: chain f residue 1883 ASP Chi-restraints excluded: chain g residue 1683 ILE Chi-restraints excluded: chain g residue 1755 LEU Chi-restraints excluded: chain g residue 1790 VAL Chi-restraints excluded: chain g residue 1865 ILE Chi-restraints excluded: chain g residue 1879 ILE Chi-restraints excluded: chain h residue 1700 ILE Chi-restraints excluded: chain h residue 1715 SER Chi-restraints excluded: chain h residue 1736 THR Chi-restraints excluded: chain h residue 1738 VAL Chi-restraints excluded: chain h residue 1755 LEU Chi-restraints excluded: chain h residue 1795 MET Chi-restraints excluded: chain h residue 1872 ASN Chi-restraints excluded: chain i residue 1678 VAL Chi-restraints excluded: chain i residue 1683 ILE Chi-restraints excluded: chain i residue 1698 ILE Chi-restraints excluded: chain i residue 1700 ILE Chi-restraints excluded: chain i residue 1710 LEU Chi-restraints excluded: chain i residue 1713 ILE Chi-restraints excluded: chain i residue 1755 LEU Chi-restraints excluded: chain i residue 1790 VAL Chi-restraints excluded: chain i residue 1879 ILE Chi-restraints excluded: chain i residue 1883 ASP Chi-restraints excluded: chain j residue 1683 ILE Chi-restraints excluded: chain j residue 1700 ILE Chi-restraints excluded: chain j residue 1710 LEU Chi-restraints excluded: chain j residue 1755 LEU Chi-restraints excluded: chain j residue 1790 VAL Chi-restraints excluded: chain k residue 1700 ILE Chi-restraints excluded: chain k residue 1710 LEU Chi-restraints excluded: chain k residue 1755 LEU Chi-restraints excluded: chain k residue 1780 MET Chi-restraints excluded: chain k residue 1790 VAL Chi-restraints excluded: chain k residue 1811 LEU Chi-restraints excluded: chain k residue 1883 ASP Chi-restraints excluded: chain l residue 1678 VAL Chi-restraints excluded: chain l residue 1683 ILE Chi-restraints excluded: chain l residue 1703 THR Chi-restraints excluded: chain l residue 1710 LEU Chi-restraints excluded: chain l residue 1736 THR Chi-restraints excluded: chain l residue 1755 LEU Chi-restraints excluded: chain l residue 1790 VAL Chi-restraints excluded: chain l residue 1879 ILE Chi-restraints excluded: chain m residue 1700 ILE Chi-restraints excluded: chain m residue 1710 LEU Chi-restraints excluded: chain m residue 1736 THR Chi-restraints excluded: chain m residue 1755 LEU Chi-restraints excluded: chain m residue 1790 VAL Chi-restraints excluded: chain m residue 1811 LEU Chi-restraints excluded: chain m residue 1865 ILE Chi-restraints excluded: chain m residue 1883 ASP Chi-restraints excluded: chain n residue 1683 ILE Chi-restraints excluded: chain n residue 1710 LEU Chi-restraints excluded: chain n residue 1755 LEU Chi-restraints excluded: chain n residue 1790 VAL Chi-restraints excluded: chain n residue 1883 ASP Chi-restraints excluded: chain o residue 1700 ILE Chi-restraints excluded: chain o residue 1710 LEU Chi-restraints excluded: chain o residue 1736 THR Chi-restraints excluded: chain o residue 1741 ASN Chi-restraints excluded: chain o residue 1755 LEU Chi-restraints excluded: chain o residue 1790 VAL Chi-restraints excluded: chain o residue 1811 LEU Chi-restraints excluded: chain o residue 1873 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 266 random chunks: chunk 70 optimal weight: 0.7980 chunk 83 optimal weight: 0.9990 chunk 86 optimal weight: 0.8980 chunk 117 optimal weight: 0.9980 chunk 25 optimal weight: 3.9990 chunk 1 optimal weight: 0.3980 chunk 53 optimal weight: 6.9990 chunk 262 optimal weight: 4.9990 chunk 200 optimal weight: 9.9990 chunk 49 optimal weight: 0.3980 chunk 254 optimal weight: 3.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: d1680 GLN ** d1853 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** g1897 ASN k1680 GLN l1897 ASN n1743 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3265 r_free = 0.3265 target = 0.097034 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3070 r_free = 0.3070 target = 0.086060 restraints weight = 48165.067| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3105 r_free = 0.3105 target = 0.088011 restraints weight = 24696.847| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3127 r_free = 0.3127 target = 0.089219 restraints weight = 14753.285| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3140 r_free = 0.3140 target = 0.089937 restraints weight = 10014.933| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3147 r_free = 0.3147 target = 0.090359 restraints weight = 7645.687| |-----------------------------------------------------------------------------| r_work (final): 0.3145 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8182 moved from start: 0.4396 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 21238 Z= 0.128 Angle : 0.650 11.863 28784 Z= 0.336 Chirality : 0.049 0.240 3486 Planarity : 0.004 0.037 3612 Dihedral : 5.470 32.985 2885 Min Nonbonded Distance : 2.566 Molprobity Statistics. All-atom Clashscore : 10.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.35 % Favored : 89.65 % Rotamer: Outliers : 4.92 % Allowed : 23.44 % Favored : 71.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.53 % 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: -2.82 (0.16), residues: 2716 helix: -3.48 (0.21), residues: 392 sheet: -1.81 (0.18), residues: 798 loop : -1.37 (0.16), residues: 1526 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG c1754 TYR 0.021 0.001 TYR h1695 PHE 0.017 0.001 PHE n1810 TRP 0.005 0.001 TRP g1723 HIS 0.002 0.000 HIS i1793 Details of bonding type rmsd covalent geometry : bond 0.00297 (21238) covalent geometry : angle 0.65008 (28784) hydrogen bonds : bond 0.03075 ( 499) hydrogen bonds : angle 6.46387 ( 1170) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5432 Ramachandran restraints generated. 2716 Oldfield, 0 Emsley, 2716 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5432 Ramachandran restraints generated. 2716 Oldfield, 0 Emsley, 2716 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 718 residues out of total 2338 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 115 poor density : 603 time to evaluate : 0.802 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: b 1729 MET cc_start: 0.8262 (ptm) cc_final: 0.6491 (mmt) REVERT: b 1734 LYS cc_start: 0.6801 (ttpt) cc_final: 0.6373 (pttt) REVERT: b 1752 MET cc_start: 0.9014 (ppp) cc_final: 0.8135 (ptt) REVERT: b 1776 GLN cc_start: 0.8070 (mt0) cc_final: 0.7681 (mm-40) REVERT: b 1780 MET cc_start: 0.7418 (tpp) cc_final: 0.5933 (tmm) REVERT: b 1783 GLU cc_start: 0.8334 (pm20) cc_final: 0.7949 (pm20) REVERT: b 1857 GLN cc_start: 0.9113 (tp40) cc_final: 0.8782 (tp40) REVERT: b 1886 ASP cc_start: 0.8284 (t0) cc_final: 0.8003 (t70) REVERT: b 1902 ASP cc_start: 0.8658 (t0) cc_final: 0.8265 (t70) REVERT: c 1729 MET cc_start: 0.8338 (ptm) cc_final: 0.7161 (mmm) REVERT: c 1734 LYS cc_start: 0.5690 (ttpp) cc_final: 0.5176 (pttt) REVERT: c 1742 TYR cc_start: 0.8461 (p90) cc_final: 0.7699 (p90) REVERT: c 1752 MET cc_start: 0.8987 (ppp) cc_final: 0.8348 (ppp) REVERT: c 1776 GLN cc_start: 0.8807 (tp-100) cc_final: 0.8457 (tp-100) REVERT: c 1780 MET cc_start: 0.8075 (mmp) cc_final: 0.7413 (mmm) REVERT: c 1862 LEU cc_start: 0.8942 (OUTLIER) cc_final: 0.8703 (mt) REVERT: c 1886 ASP cc_start: 0.7855 (t0) cc_final: 0.7629 (t0) REVERT: c 1902 ASP cc_start: 0.8649 (t0) cc_final: 0.8274 (t70) REVERT: d 1710 LEU cc_start: 0.8712 (OUTLIER) cc_final: 0.8481 (pp) REVERT: d 1729 MET cc_start: 0.8275 (ptm) cc_final: 0.7432 (mmt) REVERT: d 1752 MET cc_start: 0.9126 (ppp) cc_final: 0.8400 (ptt) REVERT: d 1766 ASP cc_start: 0.8580 (m-30) cc_final: 0.8273 (m-30) REVERT: d 1776 GLN cc_start: 0.8063 (tt0) cc_final: 0.7850 (tt0) REVERT: d 1795 MET cc_start: 0.7937 (ptm) cc_final: 0.7670 (ptm) REVERT: d 1857 GLN cc_start: 0.9044 (tp-100) cc_final: 0.8606 (tp40) REVERT: d 1861 GLN cc_start: 0.8637 (mp10) cc_final: 0.8335 (mp10) REVERT: d 1886 ASP cc_start: 0.7936 (t0) cc_final: 0.7700 (t0) REVERT: e 1707 ASP cc_start: 0.7518 (p0) cc_final: 0.7042 (p0) REVERT: e 1729 MET cc_start: 0.8700 (ptm) cc_final: 0.7309 (mmt) REVERT: e 1734 LYS cc_start: 0.6770 (ttpt) cc_final: 0.5856 (pttp) REVERT: e 1752 MET cc_start: 0.8838 (ppp) cc_final: 0.8342 (ptt) REVERT: e 1756 MET cc_start: 0.8762 (tpt) cc_final: 0.8515 (tpp) REVERT: e 1800 PHE cc_start: 0.7377 (m-80) cc_final: 0.6993 (m-80) REVERT: e 1870 TYR cc_start: 0.7995 (m-80) cc_final: 0.7499 (m-80) REVERT: e 1902 ASP cc_start: 0.8595 (t0) cc_final: 0.8368 (t70) REVERT: f 1707 ASP cc_start: 0.8100 (t0) cc_final: 0.7536 (t0) REVERT: f 1709 THR cc_start: 0.9126 (p) cc_final: 0.8676 (p) REVERT: f 1729 MET cc_start: 0.7997 (ptm) cc_final: 0.7080 (tpt) REVERT: f 1737 LYS cc_start: 0.8772 (mtmm) cc_final: 0.8098 (mtpp) REVERT: f 1739 TYR cc_start: 0.8517 (m-80) cc_final: 0.7742 (m-80) REVERT: f 1742 TYR cc_start: 0.8342 (p90) cc_final: 0.7687 (p90) REVERT: f 1857 GLN cc_start: 0.9020 (tp-100) cc_final: 0.8474 (tp40) REVERT: f 1861 GLN cc_start: 0.8864 (mp10) cc_final: 0.8415 (mp10) REVERT: f 1886 ASP cc_start: 0.8180 (t0) cc_final: 0.7824 (t0) REVERT: f 1897 ASN cc_start: 0.8844 (t0) cc_final: 0.8620 (t0) REVERT: f 1902 ASP cc_start: 0.8088 (t70) cc_final: 0.7332 (t70) REVERT: g 1729 MET cc_start: 0.8246 (ptm) cc_final: 0.6986 (mmt) REVERT: g 1737 LYS cc_start: 0.8826 (mtmm) cc_final: 0.8143 (mtpp) REVERT: g 1885 ILE cc_start: 0.9425 (mm) cc_final: 0.9090 (mm) REVERT: g 1894 LYS cc_start: 0.8640 (ptmt) cc_final: 0.8332 (pttm) REVERT: h 1702 LEU cc_start: 0.9191 (OUTLIER) cc_final: 0.8974 (mp) REVERT: h 1729 MET cc_start: 0.7461 (ptm) cc_final: 0.6534 (mmt) REVERT: h 1736 THR cc_start: 0.9189 (OUTLIER) cc_final: 0.8935 (t) REVERT: h 1752 MET cc_start: 0.8677 (ppp) cc_final: 0.7991 (ppp) REVERT: h 1776 GLN cc_start: 0.8083 (pt0) cc_final: 0.7714 (tt0) REVERT: h 1781 LEU cc_start: 0.8481 (mt) cc_final: 0.8216 (mp) REVERT: h 1886 ASP cc_start: 0.7857 (p0) cc_final: 0.7598 (p0) REVERT: h 1903 GLU cc_start: 0.4734 (tt0) cc_final: 0.4014 (mt-10) REVERT: i 1696 THR cc_start: 0.9610 (t) cc_final: 0.9381 (m) REVERT: i 1707 ASP cc_start: 0.7757 (p0) cc_final: 0.7320 (p0) REVERT: i 1729 MET cc_start: 0.8197 (ptm) cc_final: 0.7388 (tpt) REVERT: i 1742 TYR cc_start: 0.8714 (p90) cc_final: 0.8077 (p90) REVERT: i 1752 MET cc_start: 0.8913 (ppp) cc_final: 0.8367 (ppp) REVERT: i 1780 MET cc_start: 0.7974 (mmm) cc_final: 0.7774 (mmm) REVERT: i 1810 PHE cc_start: 0.7818 (p90) cc_final: 0.7110 (p90) REVERT: i 1857 GLN cc_start: 0.9196 (tp-100) cc_final: 0.8540 (tp40) REVERT: i 1861 GLN cc_start: 0.8861 (mp10) cc_final: 0.8406 (mp10) REVERT: i 1886 ASP cc_start: 0.8477 (t0) cc_final: 0.8111 (t0) REVERT: i 1902 ASP cc_start: 0.8413 (t0) cc_final: 0.8144 (t70) REVERT: j 1707 ASP cc_start: 0.7636 (p0) cc_final: 0.7053 (p0) REVERT: j 1729 MET cc_start: 0.8683 (ptm) cc_final: 0.7442 (mmt) REVERT: j 1752 MET cc_start: 0.9147 (ppp) cc_final: 0.8774 (ppp) REVERT: j 1780 MET cc_start: 0.8309 (tpt) cc_final: 0.7849 (tpp) REVERT: j 1783 GLU cc_start: 0.8202 (pm20) cc_final: 0.7974 (pm20) REVERT: j 1854 MET cc_start: 0.8191 (ttt) cc_final: 0.7797 (ttt) REVERT: j 1870 TYR cc_start: 0.7976 (m-80) cc_final: 0.7606 (m-80) REVERT: j 1894 LYS cc_start: 0.8780 (ptmt) cc_final: 0.8527 (pttm) REVERT: j 1902 ASP cc_start: 0.8393 (t70) cc_final: 0.7993 (t70) REVERT: k 1710 LEU cc_start: 0.8971 (OUTLIER) cc_final: 0.8709 (pp) REVERT: k 1729 MET cc_start: 0.8296 (ptm) cc_final: 0.7279 (mmt) REVERT: k 1752 MET cc_start: 0.9030 (ppp) cc_final: 0.8486 (ppp) REVERT: k 1766 ASP cc_start: 0.8566 (m-30) cc_final: 0.8246 (m-30) REVERT: k 1783 GLU cc_start: 0.8343 (pm20) cc_final: 0.8114 (pm20) REVERT: k 1857 GLN cc_start: 0.8952 (tp-100) cc_final: 0.8419 (tp40) REVERT: l 1707 ASP cc_start: 0.8078 (t0) cc_final: 0.7515 (t0) REVERT: l 1726 ASN cc_start: 0.8934 (p0) cc_final: 0.8696 (p0) REVERT: l 1729 MET cc_start: 0.8396 (ptm) cc_final: 0.7322 (mmm) REVERT: l 1742 TYR cc_start: 0.8713 (p90) cc_final: 0.8245 (p90) REVERT: l 1743 GLN cc_start: 0.7956 (mm-40) cc_final: 0.7668 (mm-40) REVERT: l 1752 MET cc_start: 0.8887 (ppp) cc_final: 0.8113 (ppp) REVERT: l 1756 MET cc_start: 0.8524 (tpt) cc_final: 0.8176 (tpt) REVERT: l 1780 MET cc_start: 0.8255 (tpt) cc_final: 0.8002 (tpp) REVERT: l 1857 GLN cc_start: 0.8860 (mm-40) cc_final: 0.8422 (tp40) REVERT: l 1861 GLN cc_start: 0.8602 (mp10) cc_final: 0.8067 (mp10) REVERT: l 1885 ILE cc_start: 0.9157 (mm) cc_final: 0.8936 (mm) REVERT: m 1729 MET cc_start: 0.8398 (ptm) cc_final: 0.7460 (tpt) REVERT: m 1736 THR cc_start: 0.9236 (OUTLIER) cc_final: 0.8874 (t) REVERT: m 1752 MET cc_start: 0.9116 (ppp) cc_final: 0.8808 (ppp) REVERT: m 1781 LEU cc_start: 0.8943 (tt) cc_final: 0.8450 (mt) REVERT: m 1857 GLN cc_start: 0.8987 (tp40) cc_final: 0.8151 (tp-100) REVERT: m 1861 GLN cc_start: 0.8717 (mp-120) cc_final: 0.8086 (mp10) REVERT: m 1886 ASP cc_start: 0.7697 (t0) cc_final: 0.7221 (t0) REVERT: n 1707 ASP cc_start: 0.7744 (p0) cc_final: 0.7378 (p0) REVERT: n 1729 MET cc_start: 0.8221 (ptm) cc_final: 0.6968 (mmt) REVERT: n 1752 MET cc_start: 0.8635 (ppp) cc_final: 0.8099 (ptt) REVERT: n 1885 ILE cc_start: 0.9479 (mm) cc_final: 0.9222 (mm) REVERT: n 1894 LYS cc_start: 0.8873 (ptmt) cc_final: 0.8201 (pttm) REVERT: o 1729 MET cc_start: 0.7635 (ptm) cc_final: 0.6668 (mmt) REVERT: o 1736 THR cc_start: 0.9307 (OUTLIER) cc_final: 0.9056 (t) REVERT: o 1741 ASN cc_start: 0.8834 (p0) cc_final: 0.8488 (p0) REVERT: o 1752 MET cc_start: 0.9221 (ppp) cc_final: 0.8944 (ppp) REVERT: o 1783 GLU cc_start: 0.8227 (pm20) cc_final: 0.7474 (pm20) REVERT: o 1795 MET cc_start: 0.7632 (ptm) cc_final: 0.7366 (ptm) REVERT: o 1810 PHE cc_start: 0.7911 (p90) cc_final: 0.7676 (p90) REVERT: o 1870 TYR cc_start: 0.8283 (m-80) cc_final: 0.7917 (m-10) REVERT: o 1897 ASN cc_start: 0.9045 (t0) cc_final: 0.8664 (t0) outliers start: 115 outliers final: 86 residues processed: 691 average time/residue: 0.1159 time to fit residues: 132.4940 Evaluate side-chains 675 residues out of total 2338 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 93 poor density : 582 time to evaluate : 0.777 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain b residue 1683 ILE Chi-restraints excluded: chain b residue 1700 ILE Chi-restraints excluded: chain b residue 1769 ILE Chi-restraints excluded: chain b residue 1790 VAL Chi-restraints excluded: chain c residue 1683 ILE Chi-restraints excluded: chain c residue 1710 LEU Chi-restraints excluded: chain c residue 1736 THR Chi-restraints excluded: chain c residue 1755 LEU Chi-restraints excluded: chain c residue 1790 VAL Chi-restraints excluded: chain c residue 1862 LEU Chi-restraints excluded: chain c residue 1879 ILE Chi-restraints excluded: chain d residue 1700 ILE Chi-restraints excluded: chain d residue 1710 LEU Chi-restraints excluded: chain d residue 1755 LEU Chi-restraints excluded: chain d residue 1790 VAL Chi-restraints excluded: chain d residue 1811 LEU Chi-restraints excluded: chain d residue 1883 ASP Chi-restraints excluded: chain d residue 1896 THR Chi-restraints excluded: chain e residue 1683 ILE Chi-restraints excluded: chain e residue 1700 ILE Chi-restraints excluded: chain e residue 1710 LEU Chi-restraints excluded: chain e residue 1790 VAL Chi-restraints excluded: chain e residue 1865 ILE Chi-restraints excluded: chain e residue 1896 THR Chi-restraints excluded: chain f residue 1678 VAL Chi-restraints excluded: chain f residue 1698 ILE Chi-restraints excluded: chain f residue 1700 ILE Chi-restraints excluded: chain f residue 1710 LEU Chi-restraints excluded: chain f residue 1713 ILE Chi-restraints excluded: chain f residue 1790 VAL Chi-restraints excluded: chain f residue 1879 ILE Chi-restraints excluded: chain f residue 1896 THR Chi-restraints excluded: chain g residue 1683 ILE Chi-restraints excluded: chain g residue 1755 LEU Chi-restraints excluded: chain g residue 1790 VAL Chi-restraints excluded: chain g residue 1865 ILE Chi-restraints excluded: chain g residue 1879 ILE Chi-restraints excluded: chain g residue 1883 ASP Chi-restraints excluded: chain h residue 1700 ILE Chi-restraints excluded: chain h residue 1702 LEU Chi-restraints excluded: chain h residue 1715 SER Chi-restraints excluded: chain h residue 1736 THR Chi-restraints excluded: chain h residue 1738 VAL Chi-restraints excluded: chain h residue 1755 LEU Chi-restraints excluded: chain h residue 1795 MET Chi-restraints excluded: chain h residue 1872 ASN Chi-restraints excluded: chain i residue 1678 VAL Chi-restraints excluded: chain i residue 1683 ILE Chi-restraints excluded: chain i residue 1698 ILE Chi-restraints excluded: chain i residue 1700 ILE Chi-restraints excluded: chain i residue 1710 LEU Chi-restraints excluded: chain i residue 1713 ILE Chi-restraints excluded: chain i residue 1755 LEU Chi-restraints excluded: chain i residue 1790 VAL Chi-restraints excluded: chain i residue 1879 ILE Chi-restraints excluded: chain j residue 1683 ILE Chi-restraints excluded: chain j residue 1700 ILE Chi-restraints excluded: chain j residue 1710 LEU Chi-restraints excluded: chain j residue 1790 VAL Chi-restraints excluded: chain k residue 1700 ILE Chi-restraints excluded: chain k residue 1710 LEU Chi-restraints excluded: chain k residue 1755 LEU Chi-restraints excluded: chain k residue 1790 VAL Chi-restraints excluded: chain k residue 1811 LEU Chi-restraints excluded: chain k residue 1855 SER Chi-restraints excluded: chain k residue 1883 ASP Chi-restraints excluded: chain l residue 1678 VAL Chi-restraints excluded: chain l residue 1683 ILE Chi-restraints excluded: chain l residue 1703 THR Chi-restraints excluded: chain l residue 1736 THR Chi-restraints excluded: chain l residue 1755 LEU Chi-restraints excluded: chain l residue 1790 VAL Chi-restraints excluded: chain l residue 1879 ILE Chi-restraints excluded: chain m residue 1710 LEU Chi-restraints excluded: chain m residue 1736 THR Chi-restraints excluded: chain m residue 1738 VAL Chi-restraints excluded: chain m residue 1755 LEU Chi-restraints excluded: chain m residue 1790 VAL Chi-restraints excluded: chain m residue 1811 LEU Chi-restraints excluded: chain m residue 1865 ILE Chi-restraints excluded: chain m residue 1883 ASP Chi-restraints excluded: chain n residue 1683 ILE Chi-restraints excluded: chain n residue 1710 LEU Chi-restraints excluded: chain n residue 1755 LEU Chi-restraints excluded: chain n residue 1883 ASP Chi-restraints excluded: chain o residue 1700 ILE Chi-restraints excluded: chain o residue 1706 VAL Chi-restraints excluded: chain o residue 1710 LEU Chi-restraints excluded: chain o residue 1736 THR Chi-restraints excluded: chain o residue 1755 LEU Chi-restraints excluded: chain o residue 1790 VAL Chi-restraints excluded: chain o residue 1811 LEU Chi-restraints excluded: chain o residue 1873 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 266 random chunks: chunk 64 optimal weight: 0.9990 chunk 147 optimal weight: 0.9990 chunk 114 optimal weight: 4.9990 chunk 144 optimal weight: 4.9990 chunk 66 optimal weight: 0.0970 chunk 242 optimal weight: 0.9980 chunk 104 optimal weight: 6.9990 chunk 76 optimal weight: 3.9990 chunk 210 optimal weight: 0.0270 chunk 197 optimal weight: 0.2980 chunk 245 optimal weight: 4.9990 overall best weight: 0.4838 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: d1680 GLN ** d1853 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** k1680 GLN l1897 ASN ** m1776 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** n1853 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3278 r_free = 0.3278 target = 0.097736 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3089 r_free = 0.3089 target = 0.087092 restraints weight = 47520.802| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3122 r_free = 0.3122 target = 0.088943 restraints weight = 24806.873| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3142 r_free = 0.3142 target = 0.090078 restraints weight = 15017.131| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3154 r_free = 0.3154 target = 0.090756 restraints weight = 10269.156| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3162 r_free = 0.3162 target = 0.091224 restraints weight = 7922.691| |-----------------------------------------------------------------------------| r_work (final): 0.3163 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8165 moved from start: 0.4588 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 21238 Z= 0.121 Angle : 0.653 13.368 28784 Z= 0.336 Chirality : 0.049 0.161 3486 Planarity : 0.004 0.039 3612 Dihedral : 5.363 35.827 2885 Min Nonbonded Distance : 2.538 Molprobity Statistics. All-atom Clashscore : 10.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.83 % Favored : 90.17 % Rotamer: Outliers : 4.88 % Allowed : 23.52 % Favored : 71.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.53 % 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: -2.76 (0.16), residues: 2716 helix: -3.46 (0.21), residues: 392 sheet: -1.78 (0.18), residues: 798 loop : -1.32 (0.16), residues: 1526 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG e1754 TYR 0.020 0.001 TYR h1695 PHE 0.017 0.001 PHE k1810 TRP 0.005 0.001 TRP i1723 HIS 0.003 0.001 HIS j1793 Details of bonding type rmsd covalent geometry : bond 0.00282 (21238) covalent geometry : angle 0.65333 (28784) hydrogen bonds : bond 0.03015 ( 499) hydrogen bonds : angle 6.40334 ( 1170) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5432 Ramachandran restraints generated. 2716 Oldfield, 0 Emsley, 2716 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5432 Ramachandran restraints generated. 2716 Oldfield, 0 Emsley, 2716 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 696 residues out of total 2338 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 114 poor density : 582 time to evaluate : 0.813 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: b 1689 THR cc_start: 0.9551 (OUTLIER) cc_final: 0.9240 (t) REVERT: b 1729 MET cc_start: 0.8269 (ptm) cc_final: 0.6467 (mmt) REVERT: b 1734 LYS cc_start: 0.6812 (ttpt) cc_final: 0.6384 (pttt) REVERT: b 1752 MET cc_start: 0.8917 (ppp) cc_final: 0.8025 (ptt) REVERT: b 1780 MET cc_start: 0.7371 (tpp) cc_final: 0.5591 (tmm) REVERT: b 1783 GLU cc_start: 0.8362 (pm20) cc_final: 0.7951 (pm20) REVERT: b 1857 GLN cc_start: 0.9104 (tp40) cc_final: 0.8771 (tp40) REVERT: b 1886 ASP cc_start: 0.8226 (t0) cc_final: 0.7990 (t70) REVERT: b 1902 ASP cc_start: 0.8623 (t0) cc_final: 0.8242 (t70) REVERT: c 1707 ASP cc_start: 0.7400 (t0) cc_final: 0.7096 (t0) REVERT: c 1729 MET cc_start: 0.8315 (ptm) cc_final: 0.7181 (mmm) REVERT: c 1742 TYR cc_start: 0.8472 (p90) cc_final: 0.7725 (p90) REVERT: c 1752 MET cc_start: 0.8966 (ppp) cc_final: 0.8343 (ppp) REVERT: c 1776 GLN cc_start: 0.8777 (tp-100) cc_final: 0.8513 (tp-100) REVERT: c 1780 MET cc_start: 0.7603 (mmp) cc_final: 0.7091 (mmm) REVERT: c 1886 ASP cc_start: 0.7822 (t0) cc_final: 0.7594 (t0) REVERT: c 1902 ASP cc_start: 0.8599 (t0) cc_final: 0.8271 (t70) REVERT: d 1729 MET cc_start: 0.8271 (ptm) cc_final: 0.7421 (mmt) REVERT: d 1737 LYS cc_start: 0.8521 (mtmm) cc_final: 0.8011 (mtpp) REVERT: d 1752 MET cc_start: 0.8979 (ppp) cc_final: 0.8462 (ppp) REVERT: d 1780 MET cc_start: 0.7847 (mmm) cc_final: 0.7170 (tmm) REVERT: d 1795 MET cc_start: 0.7972 (ptm) cc_final: 0.7658 (ptm) REVERT: d 1857 GLN cc_start: 0.8893 (tp-100) cc_final: 0.8452 (tp40) REVERT: d 1861 GLN cc_start: 0.8600 (mp10) cc_final: 0.8324 (mp10) REVERT: d 1863 MET cc_start: 0.8720 (mmm) cc_final: 0.8501 (tpt) REVERT: d 1886 ASP cc_start: 0.7897 (t0) cc_final: 0.7662 (t0) REVERT: e 1707 ASP cc_start: 0.7465 (p0) cc_final: 0.7133 (p0) REVERT: e 1729 MET cc_start: 0.8698 (ptm) cc_final: 0.7398 (mmt) REVERT: e 1734 LYS cc_start: 0.6574 (ttpt) cc_final: 0.5634 (pttp) REVERT: e 1752 MET cc_start: 0.8807 (ppp) cc_final: 0.8559 (ptt) REVERT: e 1780 MET cc_start: 0.8002 (tpt) cc_final: 0.7536 (tpp) REVERT: e 1783 GLU cc_start: 0.8132 (pm20) cc_final: 0.7812 (pm20) REVERT: e 1870 TYR cc_start: 0.7952 (m-80) cc_final: 0.7524 (m-80) REVERT: e 1902 ASP cc_start: 0.8613 (t0) cc_final: 0.8385 (t70) REVERT: f 1707 ASP cc_start: 0.7971 (t0) cc_final: 0.7452 (t0) REVERT: f 1709 THR cc_start: 0.9188 (p) cc_final: 0.8764 (p) REVERT: f 1729 MET cc_start: 0.7970 (ptm) cc_final: 0.7288 (tpt) REVERT: f 1737 LYS cc_start: 0.8999 (mtmm) cc_final: 0.8436 (mtpp) REVERT: f 1739 TYR cc_start: 0.8460 (m-80) cc_final: 0.7727 (m-80) REVERT: f 1742 TYR cc_start: 0.8344 (p90) cc_final: 0.7590 (p90) REVERT: f 1752 MET cc_start: 0.8940 (ppp) cc_final: 0.8117 (ppp) REVERT: f 1857 GLN cc_start: 0.9019 (tp-100) cc_final: 0.8356 (tp40) REVERT: f 1861 GLN cc_start: 0.8811 (mp10) cc_final: 0.8324 (mp10) REVERT: f 1886 ASP cc_start: 0.8143 (t0) cc_final: 0.7758 (t0) REVERT: f 1897 ASN cc_start: 0.8772 (t0) cc_final: 0.8544 (t0) REVERT: f 1902 ASP cc_start: 0.8215 (t70) cc_final: 0.7516 (t70) REVERT: g 1729 MET cc_start: 0.8223 (ptm) cc_final: 0.6984 (mmt) REVERT: g 1737 LYS cc_start: 0.8803 (mtmm) cc_final: 0.8148 (mtpp) REVERT: g 1885 ILE cc_start: 0.9377 (mm) cc_final: 0.9032 (mm) REVERT: g 1894 LYS cc_start: 0.8594 (ptmt) cc_final: 0.8335 (pttm) REVERT: h 1729 MET cc_start: 0.7445 (ptm) cc_final: 0.6527 (mmt) REVERT: h 1736 THR cc_start: 0.9180 (OUTLIER) cc_final: 0.8929 (t) REVERT: h 1752 MET cc_start: 0.8741 (ppp) cc_final: 0.8000 (ppp) REVERT: h 1776 GLN cc_start: 0.8055 (pt0) cc_final: 0.7700 (tt0) REVERT: h 1791 ASN cc_start: 0.8904 (t0) cc_final: 0.8464 (t0) REVERT: h 1886 ASP cc_start: 0.7844 (p0) cc_final: 0.7636 (p0) REVERT: h 1903 GLU cc_start: 0.4636 (tt0) cc_final: 0.3936 (mt-10) REVERT: i 1707 ASP cc_start: 0.7860 (p0) cc_final: 0.7536 (p0) REVERT: i 1729 MET cc_start: 0.8182 (ptm) cc_final: 0.7397 (tpt) REVERT: i 1742 TYR cc_start: 0.8597 (p90) cc_final: 0.8014 (p90) REVERT: i 1752 MET cc_start: 0.8859 (ppp) cc_final: 0.8277 (ppp) REVERT: i 1776 GLN cc_start: 0.7845 (tt0) cc_final: 0.7285 (tm-30) REVERT: i 1780 MET cc_start: 0.7974 (mmm) cc_final: 0.7721 (mmm) REVERT: i 1810 PHE cc_start: 0.7882 (p90) cc_final: 0.7231 (p90) REVERT: i 1857 GLN cc_start: 0.9234 (tp-100) cc_final: 0.8640 (tp40) REVERT: i 1861 GLN cc_start: 0.8892 (mp10) cc_final: 0.8546 (mp10) REVERT: i 1902 ASP cc_start: 0.8368 (t0) cc_final: 0.8118 (t70) REVERT: j 1707 ASP cc_start: 0.7676 (p0) cc_final: 0.7078 (p0) REVERT: j 1729 MET cc_start: 0.8601 (ptm) cc_final: 0.7242 (mmt) REVERT: j 1752 MET cc_start: 0.9036 (ppp) cc_final: 0.8800 (ppp) REVERT: j 1783 GLU cc_start: 0.8179 (pm20) cc_final: 0.7956 (pm20) REVERT: j 1870 TYR cc_start: 0.7924 (m-80) cc_final: 0.7476 (m-80) REVERT: j 1894 LYS cc_start: 0.8758 (ptmt) cc_final: 0.8546 (pttm) REVERT: j 1902 ASP cc_start: 0.8308 (t70) cc_final: 0.7973 (t70) REVERT: k 1710 LEU cc_start: 0.8951 (OUTLIER) cc_final: 0.8670 (pp) REVERT: k 1729 MET cc_start: 0.8281 (ptm) cc_final: 0.7288 (mmt) REVERT: k 1752 MET cc_start: 0.8840 (ppp) cc_final: 0.8297 (ppp) REVERT: k 1766 ASP cc_start: 0.8509 (m-30) cc_final: 0.8221 (m-30) REVERT: k 1855 SER cc_start: 0.9249 (OUTLIER) cc_final: 0.9001 (t) REVERT: k 1857 GLN cc_start: 0.8919 (tp-100) cc_final: 0.8418 (tp40) REVERT: l 1707 ASP cc_start: 0.7933 (t0) cc_final: 0.7411 (t0) REVERT: l 1726 ASN cc_start: 0.8883 (p0) cc_final: 0.8653 (p0) REVERT: l 1729 MET cc_start: 0.8377 (ptm) cc_final: 0.7330 (mmm) REVERT: l 1734 LYS cc_start: 0.6743 (ttpt) cc_final: 0.6044 (pttm) REVERT: l 1742 TYR cc_start: 0.8677 (p90) cc_final: 0.8242 (p90) REVERT: l 1752 MET cc_start: 0.8858 (ppp) cc_final: 0.8220 (ppp) REVERT: l 1756 MET cc_start: 0.8494 (tpt) cc_final: 0.7725 (tpt) REVERT: l 1776 GLN cc_start: 0.8035 (tt0) cc_final: 0.7646 (tt0) REVERT: l 1780 MET cc_start: 0.8298 (tpt) cc_final: 0.8077 (tpp) REVERT: l 1857 GLN cc_start: 0.8891 (mm-40) cc_final: 0.8385 (tp40) REVERT: l 1861 GLN cc_start: 0.8579 (mp10) cc_final: 0.8022 (mp10) REVERT: l 1886 ASP cc_start: 0.7461 (t0) cc_final: 0.7222 (t0) REVERT: m 1729 MET cc_start: 0.8371 (ptm) cc_final: 0.7475 (tpt) REVERT: m 1736 THR cc_start: 0.9119 (OUTLIER) cc_final: 0.8711 (t) REVERT: m 1752 MET cc_start: 0.9198 (ppp) cc_final: 0.8908 (ppp) REVERT: m 1780 MET cc_start: 0.6957 (tpp) cc_final: 0.5549 (tmm) REVERT: m 1857 GLN cc_start: 0.9021 (tp40) cc_final: 0.8290 (tp-100) REVERT: m 1861 GLN cc_start: 0.8705 (mp-120) cc_final: 0.8099 (mp10) REVERT: n 1729 MET cc_start: 0.8205 (ptm) cc_final: 0.6975 (mmt) REVERT: n 1752 MET cc_start: 0.8607 (ppp) cc_final: 0.8045 (ptt) REVERT: n 1885 ILE cc_start: 0.9442 (mm) cc_final: 0.9180 (mm) REVERT: n 1894 LYS cc_start: 0.8949 (ptmt) cc_final: 0.8465 (pttm) REVERT: o 1729 MET cc_start: 0.7612 (ptm) cc_final: 0.6698 (mmt) REVERT: o 1736 THR cc_start: 0.9295 (OUTLIER) cc_final: 0.9042 (t) REVERT: o 1741 ASN cc_start: 0.8837 (p0) cc_final: 0.8475 (p0) REVERT: o 1752 MET cc_start: 0.9186 (ppp) cc_final: 0.8945 (ppp) REVERT: o 1757 ILE cc_start: 0.9141 (mt) cc_final: 0.8916 (tt) REVERT: o 1781 LEU cc_start: 0.8849 (tt) cc_final: 0.8610 (tt) REVERT: o 1783 GLU cc_start: 0.8220 (pm20) cc_final: 0.7483 (pm20) REVERT: o 1795 MET cc_start: 0.7601 (ptm) cc_final: 0.7314 (ptm) REVERT: o 1810 PHE cc_start: 0.7850 (p90) cc_final: 0.7646 (p90) REVERT: o 1870 TYR cc_start: 0.8245 (m-80) cc_final: 0.7857 (m-10) REVERT: o 1897 ASN cc_start: 0.8981 (t0) cc_final: 0.8623 (t0) outliers start: 114 outliers final: 89 residues processed: 668 average time/residue: 0.1194 time to fit residues: 131.8354 Evaluate side-chains 661 residues out of total 2338 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 95 poor density : 566 time to evaluate : 0.791 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain b residue 1683 ILE Chi-restraints excluded: chain b residue 1689 THR Chi-restraints excluded: chain b residue 1699 GLU Chi-restraints excluded: chain b residue 1700 ILE Chi-restraints excluded: chain b residue 1755 LEU Chi-restraints excluded: chain b residue 1769 ILE Chi-restraints excluded: chain b residue 1790 VAL Chi-restraints excluded: chain c residue 1683 ILE Chi-restraints excluded: chain c residue 1710 LEU Chi-restraints excluded: chain c residue 1736 THR Chi-restraints excluded: chain c residue 1755 LEU Chi-restraints excluded: chain c residue 1790 VAL Chi-restraints excluded: chain c residue 1879 ILE Chi-restraints excluded: chain d residue 1710 LEU Chi-restraints excluded: chain d residue 1755 LEU Chi-restraints excluded: chain d residue 1790 VAL Chi-restraints excluded: chain d residue 1811 LEU Chi-restraints excluded: chain d residue 1873 GLU Chi-restraints excluded: chain d residue 1883 ASP Chi-restraints excluded: chain d residue 1896 THR Chi-restraints excluded: chain e residue 1683 ILE Chi-restraints excluded: chain e residue 1700 ILE Chi-restraints excluded: chain e residue 1710 LEU Chi-restraints excluded: chain e residue 1790 VAL Chi-restraints excluded: chain e residue 1865 ILE Chi-restraints excluded: chain e residue 1896 THR Chi-restraints excluded: chain f residue 1678 VAL Chi-restraints excluded: chain f residue 1698 ILE Chi-restraints excluded: chain f residue 1700 ILE Chi-restraints excluded: chain f residue 1710 LEU Chi-restraints excluded: chain f residue 1713 ILE Chi-restraints excluded: chain f residue 1790 VAL Chi-restraints excluded: chain f residue 1879 ILE Chi-restraints excluded: chain f residue 1883 ASP Chi-restraints excluded: chain f residue 1896 THR Chi-restraints excluded: chain g residue 1683 ILE Chi-restraints excluded: chain g residue 1755 LEU Chi-restraints excluded: chain g residue 1790 VAL Chi-restraints excluded: chain g residue 1865 ILE Chi-restraints excluded: chain g residue 1879 ILE Chi-restraints excluded: chain h residue 1700 ILE Chi-restraints excluded: chain h residue 1715 SER Chi-restraints excluded: chain h residue 1736 THR Chi-restraints excluded: chain h residue 1738 VAL Chi-restraints excluded: chain h residue 1755 LEU Chi-restraints excluded: chain h residue 1795 MET Chi-restraints excluded: chain h residue 1872 ASN Chi-restraints excluded: chain i residue 1678 VAL Chi-restraints excluded: chain i residue 1683 ILE Chi-restraints excluded: chain i residue 1698 ILE Chi-restraints excluded: chain i residue 1700 ILE Chi-restraints excluded: chain i residue 1710 LEU Chi-restraints excluded: chain i residue 1713 ILE Chi-restraints excluded: chain i residue 1755 LEU Chi-restraints excluded: chain i residue 1790 VAL Chi-restraints excluded: chain i residue 1879 ILE Chi-restraints excluded: chain i residue 1883 ASP Chi-restraints excluded: chain j residue 1683 ILE Chi-restraints excluded: chain j residue 1700 ILE Chi-restraints excluded: chain j residue 1710 LEU Chi-restraints excluded: chain j residue 1790 VAL Chi-restraints excluded: chain j residue 1857 GLN Chi-restraints excluded: chain k residue 1700 ILE Chi-restraints excluded: chain k residue 1710 LEU Chi-restraints excluded: chain k residue 1755 LEU Chi-restraints excluded: chain k residue 1811 LEU Chi-restraints excluded: chain k residue 1855 SER Chi-restraints excluded: chain k residue 1883 ASP Chi-restraints excluded: chain k residue 1896 THR Chi-restraints excluded: chain l residue 1678 VAL Chi-restraints excluded: chain l residue 1703 THR Chi-restraints excluded: chain l residue 1736 THR Chi-restraints excluded: chain l residue 1755 LEU Chi-restraints excluded: chain l residue 1879 ILE Chi-restraints excluded: chain m residue 1700 ILE Chi-restraints excluded: chain m residue 1710 LEU Chi-restraints excluded: chain m residue 1736 THR Chi-restraints excluded: chain m residue 1755 LEU Chi-restraints excluded: chain m residue 1776 GLN Chi-restraints excluded: chain m residue 1790 VAL Chi-restraints excluded: chain m residue 1811 LEU Chi-restraints excluded: chain m residue 1865 ILE Chi-restraints excluded: chain m residue 1873 GLU Chi-restraints excluded: chain n residue 1683 ILE Chi-restraints excluded: chain n residue 1700 ILE Chi-restraints excluded: chain n residue 1710 LEU Chi-restraints excluded: chain n residue 1755 LEU Chi-restraints excluded: chain n residue 1883 ASP Chi-restraints excluded: chain o residue 1700 ILE Chi-restraints excluded: chain o residue 1710 LEU Chi-restraints excluded: chain o residue 1736 THR Chi-restraints excluded: chain o residue 1755 LEU Chi-restraints excluded: chain o residue 1790 VAL Chi-restraints excluded: chain o residue 1811 LEU Chi-restraints excluded: chain o residue 1873 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 266 random chunks: chunk 109 optimal weight: 7.9990 chunk 254 optimal weight: 0.0670 chunk 19 optimal weight: 4.9990 chunk 224 optimal weight: 4.9990 chunk 71 optimal weight: 7.9990 chunk 184 optimal weight: 0.6980 chunk 265 optimal weight: 0.0020 chunk 197 optimal weight: 0.6980 chunk 53 optimal weight: 5.9990 chunk 31 optimal weight: 2.9990 chunk 36 optimal weight: 0.7980 overall best weight: 0.4526 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: c1864 ASN d1680 GLN k1680 GLN m1776 GLN n1853 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3361 r_free = 0.3361 target = 0.101771 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3177 r_free = 0.3177 target = 0.091193 restraints weight = 46268.279| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3212 r_free = 0.3212 target = 0.093255 restraints weight = 23016.043| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3233 r_free = 0.3233 target = 0.094485 restraints weight = 13474.675| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3247 r_free = 0.3247 target = 0.095267 restraints weight = 9053.680| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3255 r_free = 0.3255 target = 0.095709 restraints weight = 6773.987| |-----------------------------------------------------------------------------| r_work (final): 0.3250 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8148 moved from start: 0.4745 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 21238 Z= 0.121 Angle : 0.662 11.467 28784 Z= 0.340 Chirality : 0.048 0.160 3486 Planarity : 0.004 0.037 3612 Dihedral : 5.220 32.520 2885 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 10.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.83 % Favored : 90.17 % Rotamer: Outliers : 4.53 % Allowed : 24.42 % Favored : 71.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.53 % 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: -2.44 (0.16), residues: 2716 helix: -3.44 (0.21), residues: 392 sheet: -1.92 (0.19), residues: 658 loop : -0.95 (0.16), residues: 1666 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG f1754 TYR 0.019 0.001 TYR h1695 PHE 0.021 0.001 PHE e1810 TRP 0.006 0.001 TRP g1723 HIS 0.004 0.001 HIS j1793 Details of bonding type rmsd covalent geometry : bond 0.00284 (21238) covalent geometry : angle 0.66186 (28784) hydrogen bonds : bond 0.02945 ( 499) hydrogen bonds : angle 6.32611 ( 1170) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5432 Ramachandran restraints generated. 2716 Oldfield, 0 Emsley, 2716 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5432 Ramachandran restraints generated. 2716 Oldfield, 0 Emsley, 2716 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 696 residues out of total 2338 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 106 poor density : 590 time to evaluate : 0.776 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: b 1689 THR cc_start: 0.9590 (OUTLIER) cc_final: 0.9317 (t) REVERT: b 1729 MET cc_start: 0.8125 (ptm) cc_final: 0.6883 (mmt) REVERT: b 1734 LYS cc_start: 0.6950 (ttpt) cc_final: 0.6505 (pttt) REVERT: b 1752 MET cc_start: 0.8929 (ppp) cc_final: 0.8378 (ppp) REVERT: b 1756 MET cc_start: 0.8343 (tpt) cc_final: 0.7948 (tpt) REVERT: b 1780 MET cc_start: 0.7294 (tpp) cc_final: 0.5586 (tmm) REVERT: b 1783 GLU cc_start: 0.8359 (pm20) cc_final: 0.7977 (pm20) REVERT: b 1857 GLN cc_start: 0.9127 (tp40) cc_final: 0.8766 (tp40) REVERT: b 1886 ASP cc_start: 0.8213 (t0) cc_final: 0.7901 (t70) REVERT: b 1902 ASP cc_start: 0.8660 (t0) cc_final: 0.8300 (t70) REVERT: c 1707 ASP cc_start: 0.7356 (t0) cc_final: 0.7019 (t0) REVERT: c 1710 LEU cc_start: 0.8547 (OUTLIER) cc_final: 0.8321 (pt) REVERT: c 1729 MET cc_start: 0.8345 (ptm) cc_final: 0.7163 (mmm) REVERT: c 1742 TYR cc_start: 0.8467 (p90) cc_final: 0.7618 (p90) REVERT: c 1752 MET cc_start: 0.8981 (ppp) cc_final: 0.8316 (ppp) REVERT: c 1780 MET cc_start: 0.7680 (mmp) cc_final: 0.7284 (mmm) REVERT: c 1886 ASP cc_start: 0.7876 (t0) cc_final: 0.7635 (t0) REVERT: c 1902 ASP cc_start: 0.8635 (t0) cc_final: 0.8296 (t70) REVERT: d 1710 LEU cc_start: 0.8768 (OUTLIER) cc_final: 0.8482 (pp) REVERT: d 1729 MET cc_start: 0.8288 (ptm) cc_final: 0.7401 (mmt) REVERT: d 1752 MET cc_start: 0.8950 (ppp) cc_final: 0.8341 (ppp) REVERT: d 1766 ASP cc_start: 0.8558 (m-30) cc_final: 0.8266 (m-30) REVERT: d 1780 MET cc_start: 0.7782 (mmm) cc_final: 0.7175 (tmm) REVERT: d 1795 MET cc_start: 0.7953 (ptm) cc_final: 0.7656 (ptm) REVERT: d 1857 GLN cc_start: 0.8895 (tp-100) cc_final: 0.8471 (tp40) REVERT: d 1861 GLN cc_start: 0.8640 (mp10) cc_final: 0.8369 (mp10) REVERT: d 1863 MET cc_start: 0.8735 (mmm) cc_final: 0.8504 (tpt) REVERT: d 1886 ASP cc_start: 0.7936 (t0) cc_final: 0.7557 (t0) REVERT: e 1707 ASP cc_start: 0.7457 (p0) cc_final: 0.6962 (p0) REVERT: e 1729 MET cc_start: 0.8707 (ptm) cc_final: 0.7376 (mmt) REVERT: e 1734 LYS cc_start: 0.6422 (ttpt) cc_final: 0.5403 (pttp) REVERT: e 1742 TYR cc_start: 0.8125 (p90) cc_final: 0.7922 (p90) REVERT: e 1752 MET cc_start: 0.8825 (ppp) cc_final: 0.8547 (ptt) REVERT: e 1776 GLN cc_start: 0.8690 (tp40) cc_final: 0.8361 (tp-100) REVERT: e 1783 GLU cc_start: 0.8140 (pm20) cc_final: 0.7703 (pm20) REVERT: e 1870 TYR cc_start: 0.7954 (m-80) cc_final: 0.7554 (m-80) REVERT: e 1902 ASP cc_start: 0.8660 (t0) cc_final: 0.8430 (t70) REVERT: f 1707 ASP cc_start: 0.7945 (t0) cc_final: 0.7286 (t0) REVERT: f 1709 THR cc_start: 0.9122 (p) cc_final: 0.8671 (p) REVERT: f 1729 MET cc_start: 0.7970 (ptm) cc_final: 0.7237 (tpt) REVERT: f 1737 LYS cc_start: 0.8880 (mtmm) cc_final: 0.8291 (mtpp) REVERT: f 1739 TYR cc_start: 0.8463 (m-80) cc_final: 0.7779 (m-80) REVERT: f 1742 TYR cc_start: 0.8325 (p90) cc_final: 0.7585 (p90) REVERT: f 1752 MET cc_start: 0.8967 (ppp) cc_final: 0.7996 (ppp) REVERT: f 1857 GLN cc_start: 0.9015 (tp-100) cc_final: 0.8310 (tp40) REVERT: f 1861 GLN cc_start: 0.8803 (mp10) cc_final: 0.8297 (mp10) REVERT: f 1886 ASP cc_start: 0.8188 (t0) cc_final: 0.7847 (t0) REVERT: f 1897 ASN cc_start: 0.8788 (t0) cc_final: 0.8554 (t0) REVERT: f 1902 ASP cc_start: 0.8313 (t70) cc_final: 0.7629 (t70) REVERT: g 1729 MET cc_start: 0.8236 (ptm) cc_final: 0.6952 (mmt) REVERT: g 1737 LYS cc_start: 0.8798 (mtmm) cc_final: 0.8114 (mtpp) REVERT: g 1752 MET cc_start: 0.8757 (ppp) cc_final: 0.7963 (ptt) REVERT: g 1781 LEU cc_start: 0.8799 (mt) cc_final: 0.8513 (tt) REVERT: g 1894 LYS cc_start: 0.8624 (ptmt) cc_final: 0.8372 (pttm) REVERT: h 1729 MET cc_start: 0.7467 (ptm) cc_final: 0.6497 (mmt) REVERT: h 1736 THR cc_start: 0.9188 (OUTLIER) cc_final: 0.8903 (t) REVERT: h 1752 MET cc_start: 0.8762 (ppp) cc_final: 0.7954 (ppp) REVERT: h 1776 GLN cc_start: 0.8081 (pt0) cc_final: 0.7699 (tt0) REVERT: h 1791 ASN cc_start: 0.8847 (t0) cc_final: 0.8387 (t0) REVERT: h 1886 ASP cc_start: 0.7913 (p0) cc_final: 0.7559 (p0) REVERT: h 1903 GLU cc_start: 0.5690 (tt0) cc_final: 0.4726 (mt-10) REVERT: i 1707 ASP cc_start: 0.7601 (p0) cc_final: 0.7267 (p0) REVERT: i 1729 MET cc_start: 0.8197 (ptm) cc_final: 0.7356 (tpt) REVERT: i 1742 TYR cc_start: 0.8561 (p90) cc_final: 0.7998 (p90) REVERT: i 1752 MET cc_start: 0.8848 (ppp) cc_final: 0.8305 (ppp) REVERT: i 1776 GLN cc_start: 0.7851 (tt0) cc_final: 0.7268 (tm-30) REVERT: i 1780 MET cc_start: 0.7940 (mmm) cc_final: 0.7636 (mmm) REVERT: i 1810 PHE cc_start: 0.7846 (p90) cc_final: 0.7241 (p90) REVERT: i 1857 GLN cc_start: 0.9212 (tp-100) cc_final: 0.8656 (tp40) REVERT: i 1861 GLN cc_start: 0.8885 (mp10) cc_final: 0.8540 (mp10) REVERT: i 1886 ASP cc_start: 0.8366 (t0) cc_final: 0.8110 (t0) REVERT: i 1902 ASP cc_start: 0.8408 (t0) cc_final: 0.8135 (t70) REVERT: j 1707 ASP cc_start: 0.7534 (p0) cc_final: 0.7064 (p0) REVERT: j 1729 MET cc_start: 0.8674 (ptm) cc_final: 0.7272 (mmt) REVERT: j 1742 TYR cc_start: 0.8634 (p90) cc_final: 0.8394 (p90) REVERT: j 1870 TYR cc_start: 0.8063 (m-80) cc_final: 0.7526 (m-80) REVERT: k 1710 LEU cc_start: 0.8923 (OUTLIER) cc_final: 0.8654 (pp) REVERT: k 1729 MET cc_start: 0.8302 (ptm) cc_final: 0.7259 (mmt) REVERT: k 1752 MET cc_start: 0.8827 (ppp) cc_final: 0.8236 (ppp) REVERT: k 1766 ASP cc_start: 0.8577 (m-30) cc_final: 0.8291 (m-30) REVERT: k 1857 GLN cc_start: 0.8889 (tp-100) cc_final: 0.8358 (tp40) REVERT: l 1707 ASP cc_start: 0.7867 (t0) cc_final: 0.7276 (t0) REVERT: l 1729 MET cc_start: 0.8393 (ptm) cc_final: 0.7275 (mmm) REVERT: l 1734 LYS cc_start: 0.6605 (ttpt) cc_final: 0.5875 (pttm) REVERT: l 1742 TYR cc_start: 0.8469 (p90) cc_final: 0.7918 (p90) REVERT: l 1752 MET cc_start: 0.8843 (ppp) cc_final: 0.8542 (ppp) REVERT: l 1857 GLN cc_start: 0.8880 (mm-40) cc_final: 0.8399 (tp40) REVERT: l 1861 GLN cc_start: 0.8592 (mp10) cc_final: 0.8018 (mp10) REVERT: m 1729 MET cc_start: 0.8408 (ptm) cc_final: 0.7408 (tpt) REVERT: m 1736 THR cc_start: 0.9098 (OUTLIER) cc_final: 0.8672 (t) REVERT: m 1752 MET cc_start: 0.9212 (ppp) cc_final: 0.8907 (ppp) REVERT: m 1780 MET cc_start: 0.6880 (tpp) cc_final: 0.5347 (tmm) REVERT: m 1857 GLN cc_start: 0.9024 (tp40) cc_final: 0.8321 (tp-100) REVERT: m 1861 GLN cc_start: 0.8745 (mp-120) cc_final: 0.8103 (mp10) REVERT: m 1886 ASP cc_start: 0.7422 (t0) cc_final: 0.6728 (t0) REVERT: n 1729 MET cc_start: 0.8226 (ptm) cc_final: 0.6931 (mmt) REVERT: n 1752 MET cc_start: 0.8582 (ppp) cc_final: 0.8022 (ptt) REVERT: n 1885 ILE cc_start: 0.9437 (mm) cc_final: 0.9200 (mm) REVERT: n 1894 LYS cc_start: 0.8974 (ptmt) cc_final: 0.8457 (pttm) REVERT: o 1726 ASN cc_start: 0.8825 (p0) cc_final: 0.8539 (p0) REVERT: o 1729 MET cc_start: 0.7631 (ptm) cc_final: 0.6662 (mmt) REVERT: o 1736 THR cc_start: 0.9276 (OUTLIER) cc_final: 0.9008 (t) REVERT: o 1741 ASN cc_start: 0.8840 (p0) cc_final: 0.8460 (p0) REVERT: o 1752 MET cc_start: 0.9180 (ppp) cc_final: 0.8964 (ppp) REVERT: o 1781 LEU cc_start: 0.8838 (tt) cc_final: 0.8595 (tt) REVERT: o 1783 GLU cc_start: 0.8175 (pm20) cc_final: 0.7409 (pm20) REVERT: o 1795 MET cc_start: 0.7636 (ptm) cc_final: 0.7312 (ptm) REVERT: o 1810 PHE cc_start: 0.7841 (p90) cc_final: 0.7640 (p90) REVERT: o 1870 TYR cc_start: 0.8320 (m-80) cc_final: 0.7882 (m-10) REVERT: o 1897 ASN cc_start: 0.9009 (t0) cc_final: 0.8649 (t0) outliers start: 106 outliers final: 87 residues processed: 668 average time/residue: 0.1123 time to fit residues: 124.5640 Evaluate side-chains 671 residues out of total 2338 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 94 poor density : 577 time to evaluate : 0.672 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain b residue 1683 ILE Chi-restraints excluded: chain b residue 1689 THR Chi-restraints excluded: chain b residue 1699 GLU Chi-restraints excluded: chain b residue 1700 ILE Chi-restraints excluded: chain b residue 1755 LEU Chi-restraints excluded: chain b residue 1769 ILE Chi-restraints excluded: chain b residue 1790 VAL Chi-restraints excluded: chain c residue 1683 ILE Chi-restraints excluded: chain c residue 1710 LEU Chi-restraints excluded: chain c residue 1715 SER Chi-restraints excluded: chain c residue 1736 THR Chi-restraints excluded: chain c residue 1755 LEU Chi-restraints excluded: chain c residue 1790 VAL Chi-restraints excluded: chain c residue 1864 ASN Chi-restraints excluded: chain c residue 1879 ILE Chi-restraints excluded: chain d residue 1700 ILE Chi-restraints excluded: chain d residue 1710 LEU Chi-restraints excluded: chain d residue 1755 LEU Chi-restraints excluded: chain d residue 1811 LEU Chi-restraints excluded: chain d residue 1865 ILE Chi-restraints excluded: chain d residue 1883 ASP Chi-restraints excluded: chain d residue 1896 THR Chi-restraints excluded: chain e residue 1683 ILE Chi-restraints excluded: chain e residue 1700 ILE Chi-restraints excluded: chain e residue 1710 LEU Chi-restraints excluded: chain e residue 1790 VAL Chi-restraints excluded: chain e residue 1865 ILE Chi-restraints excluded: chain e residue 1896 THR Chi-restraints excluded: chain f residue 1678 VAL Chi-restraints excluded: chain f residue 1698 ILE Chi-restraints excluded: chain f residue 1700 ILE Chi-restraints excluded: chain f residue 1710 LEU Chi-restraints excluded: chain f residue 1713 ILE Chi-restraints excluded: chain f residue 1790 VAL Chi-restraints excluded: chain f residue 1879 ILE Chi-restraints excluded: chain f residue 1883 ASP Chi-restraints excluded: chain f residue 1896 THR Chi-restraints excluded: chain g residue 1683 ILE Chi-restraints excluded: chain g residue 1790 VAL Chi-restraints excluded: chain g residue 1865 ILE Chi-restraints excluded: chain g residue 1879 ILE Chi-restraints excluded: chain h residue 1700 ILE Chi-restraints excluded: chain h residue 1715 SER Chi-restraints excluded: chain h residue 1736 THR Chi-restraints excluded: chain h residue 1738 VAL Chi-restraints excluded: chain h residue 1755 LEU Chi-restraints excluded: chain h residue 1795 MET Chi-restraints excluded: chain h residue 1872 ASN Chi-restraints excluded: chain h residue 1896 THR Chi-restraints excluded: chain i residue 1678 VAL Chi-restraints excluded: chain i residue 1683 ILE Chi-restraints excluded: chain i residue 1698 ILE Chi-restraints excluded: chain i residue 1700 ILE Chi-restraints excluded: chain i residue 1710 LEU Chi-restraints excluded: chain i residue 1713 ILE Chi-restraints excluded: chain i residue 1755 LEU Chi-restraints excluded: chain i residue 1790 VAL Chi-restraints excluded: chain i residue 1879 ILE Chi-restraints excluded: chain j residue 1683 ILE Chi-restraints excluded: chain j residue 1700 ILE Chi-restraints excluded: chain j residue 1710 LEU Chi-restraints excluded: chain j residue 1790 VAL Chi-restraints excluded: chain k residue 1700 ILE Chi-restraints excluded: chain k residue 1710 LEU Chi-restraints excluded: chain k residue 1755 LEU Chi-restraints excluded: chain k residue 1811 LEU Chi-restraints excluded: chain k residue 1855 SER Chi-restraints excluded: chain k residue 1883 ASP Chi-restraints excluded: chain k residue 1896 THR Chi-restraints excluded: chain l residue 1678 VAL Chi-restraints excluded: chain l residue 1703 THR Chi-restraints excluded: chain l residue 1736 THR Chi-restraints excluded: chain l residue 1755 LEU Chi-restraints excluded: chain l residue 1879 ILE Chi-restraints excluded: chain m residue 1700 ILE Chi-restraints excluded: chain m residue 1710 LEU Chi-restraints excluded: chain m residue 1736 THR Chi-restraints excluded: chain m residue 1755 LEU Chi-restraints excluded: chain m residue 1756 MET Chi-restraints excluded: chain m residue 1811 LEU Chi-restraints excluded: chain m residue 1865 ILE Chi-restraints excluded: chain m residue 1873 GLU Chi-restraints excluded: chain n residue 1683 ILE Chi-restraints excluded: chain n residue 1700 ILE Chi-restraints excluded: chain n residue 1710 LEU Chi-restraints excluded: chain n residue 1853 GLN Chi-restraints excluded: chain n residue 1883 ASP Chi-restraints excluded: chain o residue 1700 ILE Chi-restraints excluded: chain o residue 1710 LEU Chi-restraints excluded: chain o residue 1736 THR Chi-restraints excluded: chain o residue 1755 LEU Chi-restraints excluded: chain o residue 1790 VAL Chi-restraints excluded: chain o residue 1811 LEU Chi-restraints excluded: chain o residue 1873 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 266 random chunks: chunk 232 optimal weight: 2.9990 chunk 141 optimal weight: 0.9980 chunk 253 optimal weight: 3.9990 chunk 195 optimal weight: 0.0970 chunk 15 optimal weight: 0.5980 chunk 4 optimal weight: 2.9990 chunk 86 optimal weight: 7.9990 chunk 122 optimal weight: 2.9990 chunk 88 optimal weight: 2.9990 chunk 162 optimal weight: 6.9990 chunk 227 optimal weight: 0.8980 overall best weight: 1.1180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: b1793 HIS ** c1861 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** d1680 GLN k1680 GLN o1857 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3257 r_free = 0.3257 target = 0.096642 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3065 r_free = 0.3065 target = 0.085939 restraints weight = 48256.813| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3098 r_free = 0.3098 target = 0.087791 restraints weight = 25231.177| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3117 r_free = 0.3117 target = 0.088901 restraints weight = 15277.281| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3131 r_free = 0.3131 target = 0.089625 restraints weight = 10514.374| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3139 r_free = 0.3139 target = 0.090109 restraints weight = 8059.776| |-----------------------------------------------------------------------------| r_work (final): 0.3138 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8201 moved from start: 0.4768 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 21238 Z= 0.159 Angle : 0.708 11.226 28784 Z= 0.361 Chirality : 0.050 0.194 3486 Planarity : 0.004 0.041 3612 Dihedral : 5.388 33.037 2885 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 11.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.38 % Favored : 89.62 % Rotamer: Outliers : 4.32 % Allowed : 25.32 % Favored : 70.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.53 % 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: -2.71 (0.16), residues: 2716 helix: -3.41 (0.21), residues: 392 sheet: -1.75 (0.18), residues: 798 loop : -1.29 (0.16), residues: 1526 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG j1754 TYR 0.021 0.001 TYR h1695 PHE 0.023 0.002 PHE e1810 TRP 0.008 0.001 TRP g1723 HIS 0.005 0.001 HIS j1793 Details of bonding type rmsd covalent geometry : bond 0.00372 (21238) covalent geometry : angle 0.70754 (28784) hydrogen bonds : bond 0.03251 ( 499) hydrogen bonds : angle 6.29686 ( 1170) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5432 Ramachandran restraints generated. 2716 Oldfield, 0 Emsley, 2716 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5432 Ramachandran restraints generated. 2716 Oldfield, 0 Emsley, 2716 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 680 residues out of total 2338 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 101 poor density : 579 time to evaluate : 0.639 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: b 1689 THR cc_start: 0.9556 (OUTLIER) cc_final: 0.9265 (t) REVERT: b 1729 MET cc_start: 0.8113 (ptm) cc_final: 0.6911 (mmt) REVERT: b 1734 LYS cc_start: 0.7107 (ttpt) cc_final: 0.6667 (pttt) REVERT: b 1756 MET cc_start: 0.8320 (tpt) cc_final: 0.7913 (tpt) REVERT: b 1780 MET cc_start: 0.7613 (tpp) cc_final: 0.6040 (tmm) REVERT: b 1783 GLU cc_start: 0.8435 (pm20) cc_final: 0.7909 (pm20) REVERT: b 1857 GLN cc_start: 0.9136 (tp40) cc_final: 0.8761 (tp40) REVERT: b 1886 ASP cc_start: 0.8196 (t0) cc_final: 0.7983 (t70) REVERT: b 1902 ASP cc_start: 0.8610 (t0) cc_final: 0.8316 (t70) REVERT: c 1707 ASP cc_start: 0.7414 (t0) cc_final: 0.7162 (t0) REVERT: c 1710 LEU cc_start: 0.8782 (OUTLIER) cc_final: 0.8533 (pt) REVERT: c 1729 MET cc_start: 0.8358 (ptm) cc_final: 0.7204 (mmm) REVERT: c 1734 LYS cc_start: 0.5694 (ttpp) cc_final: 0.5145 (pttt) REVERT: c 1742 TYR cc_start: 0.8290 (p90) cc_final: 0.7702 (p90) REVERT: c 1752 MET cc_start: 0.9106 (ppp) cc_final: 0.8406 (ppp) REVERT: c 1780 MET cc_start: 0.8203 (mmp) cc_final: 0.7648 (mmm) REVERT: c 1886 ASP cc_start: 0.7900 (t0) cc_final: 0.7669 (t0) REVERT: c 1902 ASP cc_start: 0.8607 (t0) cc_final: 0.8292 (t70) REVERT: d 1729 MET cc_start: 0.8293 (ptm) cc_final: 0.7299 (mmt) REVERT: d 1752 MET cc_start: 0.9095 (ppp) cc_final: 0.8541 (ppp) REVERT: d 1776 GLN cc_start: 0.8028 (tt0) cc_final: 0.7736 (tm-30) REVERT: d 1780 MET cc_start: 0.8108 (mmm) cc_final: 0.7525 (tmm) REVERT: d 1795 MET cc_start: 0.7973 (ptm) cc_final: 0.7695 (ptm) REVERT: d 1857 GLN cc_start: 0.8943 (tp-100) cc_final: 0.8503 (tp40) REVERT: d 1861 GLN cc_start: 0.8620 (mp10) cc_final: 0.8393 (mp10) REVERT: d 1863 MET cc_start: 0.8750 (mmm) cc_final: 0.8506 (tpt) REVERT: e 1707 ASP cc_start: 0.7531 (p0) cc_final: 0.6963 (p0) REVERT: e 1729 MET cc_start: 0.8683 (ptm) cc_final: 0.7417 (mmt) REVERT: e 1734 LYS cc_start: 0.6906 (ttpt) cc_final: 0.5903 (pttp) REVERT: e 1742 TYR cc_start: 0.8260 (p90) cc_final: 0.8007 (p90) REVERT: e 1752 MET cc_start: 0.8892 (ppp) cc_final: 0.8608 (ptt) REVERT: e 1776 GLN cc_start: 0.8619 (tp40) cc_final: 0.8365 (tp-100) REVERT: e 1783 GLU cc_start: 0.8205 (pm20) cc_final: 0.7773 (pm20) REVERT: e 1870 TYR cc_start: 0.8011 (m-80) cc_final: 0.7505 (m-80) REVERT: e 1902 ASP cc_start: 0.8672 (t0) cc_final: 0.8452 (t70) REVERT: f 1707 ASP cc_start: 0.7946 (t0) cc_final: 0.7306 (t0) REVERT: f 1709 THR cc_start: 0.9112 (p) cc_final: 0.8639 (p) REVERT: f 1729 MET cc_start: 0.7943 (ptm) cc_final: 0.7085 (tpt) REVERT: f 1737 LYS cc_start: 0.8668 (mtmm) cc_final: 0.7972 (mtpp) REVERT: f 1739 TYR cc_start: 0.8585 (m-80) cc_final: 0.7689 (m-80) REVERT: f 1742 TYR cc_start: 0.8373 (p90) cc_final: 0.7630 (p90) REVERT: f 1857 GLN cc_start: 0.9017 (tp-100) cc_final: 0.8391 (tp40) REVERT: f 1858 ILE cc_start: 0.9333 (tp) cc_final: 0.8990 (mp) REVERT: f 1861 GLN cc_start: 0.8797 (mp10) cc_final: 0.8303 (mp10) REVERT: f 1886 ASP cc_start: 0.8256 (t0) cc_final: 0.7885 (t0) REVERT: f 1897 ASN cc_start: 0.8808 (t0) cc_final: 0.8573 (t0) REVERT: f 1902 ASP cc_start: 0.8332 (t70) cc_final: 0.7665 (t70) REVERT: g 1729 MET cc_start: 0.8258 (ptm) cc_final: 0.6995 (mmt) REVERT: g 1737 LYS cc_start: 0.8813 (mtmm) cc_final: 0.8156 (mtpp) REVERT: g 1752 MET cc_start: 0.8791 (ppp) cc_final: 0.8067 (ptt) REVERT: g 1781 LEU cc_start: 0.8977 (mt) cc_final: 0.8711 (tt) REVERT: g 1894 LYS cc_start: 0.8614 (ptmt) cc_final: 0.8364 (pttm) REVERT: h 1729 MET cc_start: 0.7478 (ptm) cc_final: 0.6553 (mmt) REVERT: h 1736 THR cc_start: 0.9266 (OUTLIER) cc_final: 0.8992 (t) REVERT: h 1752 MET cc_start: 0.8871 (ppp) cc_final: 0.8109 (ppp) REVERT: h 1791 ASN cc_start: 0.8855 (t0) cc_final: 0.8413 (t0) REVERT: h 1903 GLU cc_start: 0.4936 (tt0) cc_final: 0.4572 (tt0) REVERT: i 1707 ASP cc_start: 0.7657 (p0) cc_final: 0.7383 (p0) REVERT: i 1729 MET cc_start: 0.8169 (ptm) cc_final: 0.7217 (tpt) REVERT: i 1742 TYR cc_start: 0.8646 (p90) cc_final: 0.8168 (p90) REVERT: i 1752 MET cc_start: 0.8917 (ppp) cc_final: 0.8346 (ppp) REVERT: i 1776 GLN cc_start: 0.7855 (tt0) cc_final: 0.7276 (tm-30) REVERT: i 1810 PHE cc_start: 0.7824 (p90) cc_final: 0.7207 (p90) REVERT: i 1857 GLN cc_start: 0.9200 (tp-100) cc_final: 0.8618 (tp40) REVERT: i 1861 GLN cc_start: 0.8859 (mp10) cc_final: 0.8487 (mp10) REVERT: i 1886 ASP cc_start: 0.8453 (t0) cc_final: 0.8221 (t0) REVERT: i 1902 ASP cc_start: 0.8443 (t0) cc_final: 0.8173 (t70) REVERT: j 1707 ASP cc_start: 0.7776 (p0) cc_final: 0.7119 (p0) REVERT: j 1729 MET cc_start: 0.8630 (ptm) cc_final: 0.7336 (mmt) REVERT: j 1742 TYR cc_start: 0.8685 (p90) cc_final: 0.8422 (p90) REVERT: j 1752 MET cc_start: 0.9133 (ppp) cc_final: 0.8908 (ppp) REVERT: j 1870 TYR cc_start: 0.7972 (m-80) cc_final: 0.7593 (m-80) REVERT: k 1710 LEU cc_start: 0.8997 (OUTLIER) cc_final: 0.8751 (pp) REVERT: k 1729 MET cc_start: 0.8332 (ptm) cc_final: 0.7302 (mmt) REVERT: k 1752 MET cc_start: 0.8988 (ppp) cc_final: 0.8352 (ppp) REVERT: k 1766 ASP cc_start: 0.8557 (m-30) cc_final: 0.8255 (m-30) REVERT: k 1857 GLN cc_start: 0.8883 (tp-100) cc_final: 0.8393 (tp40) REVERT: l 1707 ASP cc_start: 0.7710 (t0) cc_final: 0.7135 (t0) REVERT: l 1729 MET cc_start: 0.8406 (ptm) cc_final: 0.7328 (mmm) REVERT: l 1734 LYS cc_start: 0.6700 (ttpt) cc_final: 0.6158 (pttm) REVERT: l 1739 TYR cc_start: 0.8410 (m-80) cc_final: 0.7934 (m-80) REVERT: l 1742 TYR cc_start: 0.8630 (p90) cc_final: 0.8099 (p90) REVERT: l 1752 MET cc_start: 0.8911 (ppp) cc_final: 0.8238 (ppp) REVERT: l 1756 MET cc_start: 0.8505 (tpt) cc_final: 0.6964 (tpt) REVERT: l 1795 MET cc_start: 0.7206 (ptm) cc_final: 0.6936 (ptm) REVERT: l 1857 GLN cc_start: 0.8900 (mm-40) cc_final: 0.8404 (tp40) REVERT: l 1861 GLN cc_start: 0.8604 (mp10) cc_final: 0.8008 (mp10) REVERT: m 1729 MET cc_start: 0.8439 (ptm) cc_final: 0.7474 (tpt) REVERT: m 1736 THR cc_start: 0.9236 (OUTLIER) cc_final: 0.8732 (t) REVERT: m 1752 MET cc_start: 0.9089 (ppp) cc_final: 0.8786 (ppp) REVERT: m 1857 GLN cc_start: 0.8992 (tp40) cc_final: 0.8299 (tp-100) REVERT: m 1861 GLN cc_start: 0.8745 (mp-120) cc_final: 0.8114 (mp10) REVERT: m 1888 SER cc_start: 0.8681 (p) cc_final: 0.8356 (m) REVERT: n 1729 MET cc_start: 0.8222 (ptm) cc_final: 0.6970 (mmt) REVERT: n 1752 MET cc_start: 0.8620 (ppp) cc_final: 0.8021 (ptt) REVERT: n 1885 ILE cc_start: 0.9460 (mm) cc_final: 0.9211 (mm) REVERT: n 1886 ASP cc_start: 0.7637 (t0) cc_final: 0.7345 (t0) REVERT: n 1894 LYS cc_start: 0.8909 (ptmt) cc_final: 0.8497 (pttm) REVERT: n 1902 ASP cc_start: 0.8416 (t70) cc_final: 0.7858 (t70) REVERT: n 1903 GLU cc_start: 0.6429 (tm-30) cc_final: 0.5948 (tt0) REVERT: o 1726 ASN cc_start: 0.8859 (p0) cc_final: 0.8596 (p0) REVERT: o 1729 MET cc_start: 0.7663 (ptm) cc_final: 0.6762 (mmt) REVERT: o 1736 THR cc_start: 0.9340 (OUTLIER) cc_final: 0.9082 (t) REVERT: o 1741 ASN cc_start: 0.8877 (p0) cc_final: 0.8506 (p0) REVERT: o 1752 MET cc_start: 0.9210 (ppp) cc_final: 0.8960 (ppp) REVERT: o 1781 LEU cc_start: 0.8917 (OUTLIER) cc_final: 0.8696 (tt) REVERT: o 1783 GLU cc_start: 0.8221 (pm20) cc_final: 0.7509 (pm20) REVERT: o 1795 MET cc_start: 0.7638 (ptm) cc_final: 0.7383 (ptm) REVERT: o 1810 PHE cc_start: 0.7919 (p90) cc_final: 0.7707 (p90) REVERT: o 1870 TYR cc_start: 0.8341 (m-80) cc_final: 0.7938 (m-10) REVERT: o 1897 ASN cc_start: 0.9073 (t0) cc_final: 0.8682 (t0) outliers start: 101 outliers final: 83 residues processed: 658 average time/residue: 0.1155 time to fit residues: 125.6667 Evaluate side-chains 655 residues out of total 2338 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 90 poor density : 565 time to evaluate : 0.846 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain b residue 1683 ILE Chi-restraints excluded: chain b residue 1689 THR Chi-restraints excluded: chain b residue 1699 GLU Chi-restraints excluded: chain b residue 1700 ILE Chi-restraints excluded: chain b residue 1755 LEU Chi-restraints excluded: chain b residue 1790 VAL Chi-restraints excluded: chain c residue 1683 ILE Chi-restraints excluded: chain c residue 1710 LEU Chi-restraints excluded: chain c residue 1715 SER Chi-restraints excluded: chain c residue 1736 THR Chi-restraints excluded: chain c residue 1755 LEU Chi-restraints excluded: chain c residue 1790 VAL Chi-restraints excluded: chain c residue 1864 ASN Chi-restraints excluded: chain c residue 1879 ILE Chi-restraints excluded: chain d residue 1700 ILE Chi-restraints excluded: chain d residue 1710 LEU Chi-restraints excluded: chain d residue 1755 LEU Chi-restraints excluded: chain d residue 1811 LEU Chi-restraints excluded: chain d residue 1883 ASP Chi-restraints excluded: chain d residue 1896 THR Chi-restraints excluded: chain e residue 1683 ILE Chi-restraints excluded: chain e residue 1700 ILE Chi-restraints excluded: chain e residue 1710 LEU Chi-restraints excluded: chain e residue 1790 VAL Chi-restraints excluded: chain e residue 1865 ILE Chi-restraints excluded: chain e residue 1896 THR Chi-restraints excluded: chain f residue 1678 VAL Chi-restraints excluded: chain f residue 1698 ILE Chi-restraints excluded: chain f residue 1700 ILE Chi-restraints excluded: chain f residue 1710 LEU Chi-restraints excluded: chain f residue 1713 ILE Chi-restraints excluded: chain f residue 1790 VAL Chi-restraints excluded: chain f residue 1879 ILE Chi-restraints excluded: chain f residue 1883 ASP Chi-restraints excluded: chain f residue 1896 THR Chi-restraints excluded: chain g residue 1683 ILE Chi-restraints excluded: chain g residue 1790 VAL Chi-restraints excluded: chain g residue 1865 ILE Chi-restraints excluded: chain g residue 1879 ILE Chi-restraints excluded: chain h residue 1700 ILE Chi-restraints excluded: chain h residue 1736 THR Chi-restraints excluded: chain h residue 1738 VAL Chi-restraints excluded: chain h residue 1755 LEU Chi-restraints excluded: chain h residue 1795 MET Chi-restraints excluded: chain h residue 1872 ASN Chi-restraints excluded: chain h residue 1896 THR Chi-restraints excluded: chain i residue 1678 VAL Chi-restraints excluded: chain i residue 1683 ILE Chi-restraints excluded: chain i residue 1698 ILE Chi-restraints excluded: chain i residue 1700 ILE Chi-restraints excluded: chain i residue 1710 LEU Chi-restraints excluded: chain i residue 1713 ILE Chi-restraints excluded: chain i residue 1790 VAL Chi-restraints excluded: chain i residue 1879 ILE Chi-restraints excluded: chain j residue 1683 ILE Chi-restraints excluded: chain j residue 1700 ILE Chi-restraints excluded: chain j residue 1710 LEU Chi-restraints excluded: chain j residue 1790 VAL Chi-restraints excluded: chain k residue 1698 ILE Chi-restraints excluded: chain k residue 1700 ILE Chi-restraints excluded: chain k residue 1710 LEU Chi-restraints excluded: chain k residue 1755 LEU Chi-restraints excluded: chain k residue 1811 LEU Chi-restraints excluded: chain k residue 1855 SER Chi-restraints excluded: chain k residue 1883 ASP Chi-restraints excluded: chain k residue 1896 THR Chi-restraints excluded: chain l residue 1678 VAL Chi-restraints excluded: chain l residue 1703 THR Chi-restraints excluded: chain l residue 1736 THR Chi-restraints excluded: chain l residue 1755 LEU Chi-restraints excluded: chain l residue 1879 ILE Chi-restraints excluded: chain m residue 1700 ILE Chi-restraints excluded: chain m residue 1710 LEU Chi-restraints excluded: chain m residue 1736 THR Chi-restraints excluded: chain m residue 1755 LEU Chi-restraints excluded: chain m residue 1811 LEU Chi-restraints excluded: chain m residue 1865 ILE Chi-restraints excluded: chain n residue 1683 ILE Chi-restraints excluded: chain n residue 1700 ILE Chi-restraints excluded: chain n residue 1710 LEU Chi-restraints excluded: chain n residue 1755 LEU Chi-restraints excluded: chain n residue 1883 ASP Chi-restraints excluded: chain n residue 1896 THR Chi-restraints excluded: chain o residue 1700 ILE Chi-restraints excluded: chain o residue 1710 LEU Chi-restraints excluded: chain o residue 1736 THR Chi-restraints excluded: chain o residue 1755 LEU Chi-restraints excluded: chain o residue 1781 LEU Chi-restraints excluded: chain o residue 1790 VAL Chi-restraints excluded: chain o residue 1811 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 266 random chunks: chunk 66 optimal weight: 0.0060 chunk 21 optimal weight: 0.9980 chunk 15 optimal weight: 0.9990 chunk 185 optimal weight: 0.5980 chunk 79 optimal weight: 3.9990 chunk 20 optimal weight: 1.9990 chunk 51 optimal weight: 5.9990 chunk 208 optimal weight: 0.6980 chunk 12 optimal weight: 1.9990 chunk 263 optimal weight: 3.9990 chunk 200 optimal weight: 3.9990 overall best weight: 0.6598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** c1861 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c1864 ASN d1680 GLN k1680 GLN k1853 GLN n1743 GLN o1857 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3271 r_free = 0.3271 target = 0.097518 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3076 r_free = 0.3076 target = 0.086523 restraints weight = 47789.709| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3110 r_free = 0.3110 target = 0.088458 restraints weight = 24510.541| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3131 r_free = 0.3131 target = 0.089632 restraints weight = 14686.501| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3144 r_free = 0.3144 target = 0.090367 restraints weight = 9999.884| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 49)----------------| | r_work = 0.3154 r_free = 0.3154 target = 0.090875 restraints weight = 7629.358| |-----------------------------------------------------------------------------| r_work (final): 0.3150 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8175 moved from start: 0.4915 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 21238 Z= 0.133 Angle : 0.692 11.063 28784 Z= 0.354 Chirality : 0.049 0.165 3486 Planarity : 0.004 0.038 3612 Dihedral : 5.284 33.170 2885 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 11.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.98 % Favored : 90.02 % Rotamer: Outliers : 3.98 % Allowed : 25.58 % Favored : 70.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.53 % 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: -2.68 (0.16), residues: 2716 helix: -3.44 (0.21), residues: 392 sheet: -1.75 (0.18), residues: 798 loop : -1.25 (0.16), residues: 1526 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG j1754 TYR 0.020 0.001 TYR h1695 PHE 0.023 0.001 PHE e1810 TRP 0.006 0.001 TRP g1723 HIS 0.004 0.001 HIS j1793 Details of bonding type rmsd covalent geometry : bond 0.00314 (21238) covalent geometry : angle 0.69192 (28784) hydrogen bonds : bond 0.03068 ( 499) hydrogen bonds : angle 6.31834 ( 1170) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3831.67 seconds wall clock time: 66 minutes 59.11 seconds (4019.11 seconds total)