Starting phenix.real_space_refine on Sun Sep 29 03:08:14 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6odi_20020/09_2024/6odi_20020_neut.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6odi_20020/09_2024/6odi_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 { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6odi_20020/09_2024/6odi_20020.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6odi_20020/09_2024/6odi_20020.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6odi_20020/09_2024/6odi_20020_neut.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6odi_20020/09_2024/6odi_20020_neut.cif" } resolution = 3.8 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.004 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): 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib" Total number of atoms: 20902 Number of models: 1 Model: "" Number of chains: 1 Chain: "c" 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: b, e, d, g, f, i, h, k, j, m, l, o, n Time building chain proxies: 7.20, per 1000 atoms: 0.34 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: 5.12 Conformation dependent library (CDL) restraints added in 2.9 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: 3.11 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: 6.80 Time building geometry restraints manager: 6.00 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: 0.00 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: 16.570 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: 0.000 Extract box with map and model: 0.000 Check model and map are aligned: 0.000 Set scattering table: 0.000 Process input model: 41.940 Find NCS groups from input model: 0.740 Set up NCS constraints: 0.090 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:2.770 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 62.110 ------------------------------------------------------------------------------- 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= 0.512 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -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 TRP 0.003 0.001 TRP e1723 HIS 0.001 0.000 HIS h1793 PHE 0.020 0.003 PHE o1810 TYR 0.016 0.002 TYR k1695 ARG 0.002 0.001 ARG d1754 *********************** 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 fitting. rotamer outliers: 98 poor density : 774 time to evaluate : 2.418 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: 0.9448 (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: 0.8040 (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: 0.7207 (mmt) REVERT: e 1734 LYS cc_start: 0.6521 (ttpt) cc_final: 0.6049 (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: 0.8114 (pt0) REVERT: e 1783 GLU cc_start: 0.7468 (pm20) cc_final: 0.6822 (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: 0.7245 (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: 0.7721 (m-30) REVERT: e 1894 LYS cc_start: 0.9091 (ptmt) cc_final: 0.8620 (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: 0.7105 (tpt) REVERT: f 1734 LYS cc_start: 0.6782 (ttpt) cc_final: 0.6427 (ttpt) REVERT: f 1737 LYS cc_start: 0.8782 (mtmm) cc_final: 0.8244 (mtpp) REVERT: f 1739 TYR cc_start: 0.8887 (m-80) cc_final: 0.7926 (m-80) REVERT: f 1742 TYR cc_start: 0.8281 (p90) cc_final: 0.7779 (p90) REVERT: f 1766 ASP cc_start: 0.9060 (m-30) cc_final: 0.8616 (m-30) REVERT: f 1776 GLN cc_start: 0.8396 (pt0) cc_final: 0.8174 (pt0) REVERT: f 1780 MET cc_start: 0.7963 (tpt) cc_final: 0.7694 (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: 0.7661 (tpp) REVERT: g 1870 TYR cc_start: 0.8344 (m-80) cc_final: 0.8051 (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: 0.9065 (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: 0.2943 time to fit residues: 388.2298 Evaluate side-chains 670 residues out of total 2338 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 630 time to evaluate : 2.500 ------------------------------------------------------------------------------- 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 224 optimal weight: 3.9990 chunk 201 optimal weight: 4.9990 chunk 111 optimal weight: 1.9990 chunk 68 optimal weight: 5.9990 chunk 135 optimal weight: 1.9990 chunk 107 optimal weight: 0.9990 chunk 208 optimal weight: 0.2980 chunk 80 optimal weight: 0.2980 chunk 126 optimal weight: 4.9990 chunk 155 optimal weight: 7.9990 chunk 241 optimal weight: 0.4980 overall best weight: 0.8184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: b1907 GLN c1907 GLN d1680 GLN e1793 HIS e1907 GLN f1793 HIS f1907 GLN g1907 GLN h1907 GLN i1907 GLN j1907 GLN k1907 GLN l1907 GLN m1907 GLN n1907 GLN o1907 GLN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8150 moved from start: 0.2321 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 21238 Z= 0.207 Angle : 0.669 8.674 28784 Z= 0.353 Chirality : 0.050 0.160 3486 Planarity : 0.005 0.044 3612 Dihedral : 7.247 45.850 2923 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 10.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.32 % Favored : 90.68 % Rotamer: Outliers : 3.55 % Allowed : 18.78 % Favored : 77.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.53 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.75 (0.15), residues: 2716 helix: -4.33 (0.15), residues: 406 sheet: -2.28 (0.17), residues: 812 loop : -2.01 (0.15), residues: 1498 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP f1723 HIS 0.003 0.001 HIS e1793 PHE 0.019 0.002 PHE h1810 TYR 0.026 0.002 TYR h1695 ARG 0.003 0.000 ARG l1797 *********************** 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 751 residues out of total 2338 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 83 poor density : 668 time to evaluate : 2.719 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 1729 MET cc_start: 0.7272 (ptm) cc_final: 0.6419 (mmt) REVERT: b 1734 LYS cc_start: 0.6642 (ttpt) cc_final: 0.6110 (pttt) REVERT: b 1737 LYS cc_start: 0.7906 (mptt) cc_final: 0.7692 (mptt) REVERT: b 1783 GLU cc_start: 0.7792 (pm20) cc_final: 0.7392 (pm20) REVERT: b 1795 MET cc_start: 0.7677 (ptm) cc_final: 0.7240 (ptt) REVERT: b 1886 ASP cc_start: 0.8621 (t0) cc_final: 0.8417 (t70) REVERT: b 1902 ASP cc_start: 0.8762 (t0) cc_final: 0.8101 (t70) REVERT: c 1710 LEU cc_start: 0.8531 (OUTLIER) cc_final: 0.8054 (pp) REVERT: c 1729 MET cc_start: 0.7765 (ptm) cc_final: 0.6397 (mmm) REVERT: c 1734 LYS cc_start: 0.6948 (ttpt) cc_final: 0.6724 (ttpp) REVERT: c 1742 TYR cc_start: 0.8551 (p90) cc_final: 0.8147 (p90) REVERT: c 1885 ILE cc_start: 0.9262 (mm) cc_final: 0.9054 (mm) REVERT: c 1902 ASP cc_start: 0.8723 (t0) cc_final: 0.8109 (t70) REVERT: d 1710 LEU cc_start: 0.8437 (OUTLIER) cc_final: 0.7591 (pp) REVERT: d 1729 MET cc_start: 0.8230 (ptm) cc_final: 0.7178 (mmt) REVERT: d 1739 TYR cc_start: 0.8670 (m-80) cc_final: 0.8341 (m-80) REVERT: d 1752 MET cc_start: 0.9161 (ppp) cc_final: 0.8356 (ptt) REVERT: d 1766 ASP cc_start: 0.8790 (m-30) cc_final: 0.8454 (m-30) REVERT: d 1774 ASN cc_start: 0.8654 (p0) cc_final: 0.8438 (p0) REVERT: d 1800 PHE cc_start: 0.8030 (m-80) cc_final: 0.7483 (m-80) REVERT: d 1857 GLN cc_start: 0.8768 (tp-100) cc_final: 0.8444 (tp40) REVERT: d 1897 ASN cc_start: 0.9255 (t0) cc_final: 0.8980 (t0) REVERT: e 1707 ASP cc_start: 0.7484 (p0) cc_final: 0.7036 (p0) REVERT: e 1729 MET cc_start: 0.8771 (ptm) cc_final: 0.6768 (mmm) REVERT: e 1734 LYS cc_start: 0.6236 (ttpt) cc_final: 0.5879 (pttp) REVERT: e 1752 MET cc_start: 0.8917 (ppp) cc_final: 0.8700 (ptt) REVERT: e 1783 GLU cc_start: 0.8019 (pm20) cc_final: 0.7683 (pm20) REVERT: e 1795 MET cc_start: 0.7594 (ptm) cc_final: 0.7288 (ptp) REVERT: e 1810 PHE cc_start: 0.7236 (p90) cc_final: 0.6945 (p90) REVERT: e 1870 TYR cc_start: 0.8225 (m-80) cc_final: 0.7868 (m-80) REVERT: e 1902 ASP cc_start: 0.8708 (t0) cc_final: 0.8353 (t70) REVERT: f 1707 ASP cc_start: 0.7839 (t0) cc_final: 0.7582 (t0) REVERT: f 1729 MET cc_start: 0.8219 (ptm) cc_final: 0.7106 (mmt) REVERT: f 1737 LYS cc_start: 0.8682 (mtmm) cc_final: 0.8070 (mtpp) REVERT: f 1739 TYR cc_start: 0.8617 (m-80) cc_final: 0.8031 (m-80) REVERT: f 1742 TYR cc_start: 0.8374 (p90) cc_final: 0.7782 (p90) REVERT: f 1766 ASP cc_start: 0.9048 (m-30) cc_final: 0.8730 (m-30) REVERT: f 1780 MET cc_start: 0.7981 (tpt) cc_final: 0.7710 (tpp) REVERT: f 1783 GLU cc_start: 0.8347 (pm20) cc_final: 0.7920 (pm20) REVERT: f 1854 MET cc_start: 0.8231 (mtt) cc_final: 0.7794 (ttt) REVERT: f 1857 GLN cc_start: 0.9070 (tp-100) cc_final: 0.8353 (tp40) REVERT: f 1858 ILE cc_start: 0.9219 (tp) cc_final: 0.8969 (mp) REVERT: f 1861 GLN cc_start: 0.8981 (mp-120) cc_final: 0.8545 (mp10) REVERT: f 1882 MET cc_start: 0.8817 (mmm) cc_final: 0.8587 (mmm) REVERT: f 1897 ASN cc_start: 0.9238 (t0) cc_final: 0.8892 (t0) REVERT: g 1729 MET cc_start: 0.8384 (ptm) cc_final: 0.7037 (tpt) REVERT: g 1752 MET cc_start: 0.8708 (ppp) cc_final: 0.8223 (ptt) REVERT: g 1766 ASP cc_start: 0.8497 (m-30) cc_final: 0.8129 (m-30) REVERT: g 1780 MET cc_start: 0.8458 (tpt) cc_final: 0.8101 (tpp) REVERT: g 1870 TYR cc_start: 0.8418 (m-80) cc_final: 0.8122 (m-80) REVERT: g 1885 ILE cc_start: 0.9376 (mm) cc_final: 0.9134 (mm) REVERT: g 1894 LYS cc_start: 0.8650 (ptmt) cc_final: 0.8262 (pttm) REVERT: h 1729 MET cc_start: 0.8394 (ptm) cc_final: 0.7354 (tpt) REVERT: h 1731 LEU cc_start: 0.9169 (mm) cc_final: 0.8943 (mp) REVERT: h 1872 ASN cc_start: 0.7967 (m110) cc_final: 0.7623 (m-40) REVERT: h 1886 ASP cc_start: 0.7293 (p0) cc_final: 0.6126 (p0) REVERT: h 1895 ILE cc_start: 0.8894 (mp) cc_final: 0.8390 (tp) REVERT: i 1706 VAL cc_start: 0.9153 (t) cc_final: 0.8927 (t) REVERT: i 1707 ASP cc_start: 0.8314 (p0) cc_final: 0.7496 (p0) REVERT: i 1729 MET cc_start: 0.8343 (ptm) cc_final: 0.7149 (tpt) REVERT: i 1734 LYS cc_start: 0.6805 (ttpt) cc_final: 0.6590 (pttm) REVERT: i 1742 TYR cc_start: 0.8649 (p90) cc_final: 0.8003 (p90) REVERT: i 1752 MET cc_start: 0.8839 (ppp) cc_final: 0.8027 (ppp) REVERT: i 1766 ASP cc_start: 0.8584 (m-30) cc_final: 0.8120 (m-30) REVERT: i 1810 PHE cc_start: 0.7561 (p90) cc_final: 0.6786 (p90) REVERT: i 1853 GLN cc_start: 0.7783 (pp30) cc_final: 0.7493 (pp30) REVERT: i 1857 GLN cc_start: 0.9013 (tp-100) cc_final: 0.8301 (tp40) REVERT: i 1861 GLN cc_start: 0.8844 (mp-120) cc_final: 0.8587 (mp10) REVERT: i 1902 ASP cc_start: 0.8459 (t0) cc_final: 0.7937 (t70) REVERT: j 1699 GLU cc_start: 0.6579 (pt0) cc_final: 0.6152 (pm20) REVERT: j 1729 MET cc_start: 0.8655 (ptm) cc_final: 0.7079 (mmt) REVERT: j 1734 LYS cc_start: 0.7144 (ttpt) cc_final: 0.6476 (pttp) REVERT: j 1752 MET cc_start: 0.9076 (ppp) cc_final: 0.8264 (ptt) REVERT: j 1756 MET cc_start: 0.9064 (tpp) cc_final: 0.7980 (tpt) REVERT: j 1780 MET cc_start: 0.8230 (tpt) cc_final: 0.7668 (tpp) REVERT: j 1783 GLU cc_start: 0.8266 (pm20) cc_final: 0.7949 (pm20) REVERT: j 1795 MET cc_start: 0.7562 (ptp) cc_final: 0.7236 (ptt) REVERT: j 1870 TYR cc_start: 0.8128 (m-80) cc_final: 0.7855 (m-80) REVERT: k 1680 GLN cc_start: 0.8190 (mt0) cc_final: 0.7979 (mt0) REVERT: k 1710 LEU cc_start: 0.8830 (OUTLIER) cc_final: 0.8071 (pp) REVERT: k 1729 MET cc_start: 0.8957 (ptm) cc_final: 0.7690 (mmt) REVERT: k 1739 TYR cc_start: 0.8841 (m-80) cc_final: 0.8559 (m-80) REVERT: k 1752 MET cc_start: 0.9087 (ppp) cc_final: 0.8680 (ptt) REVERT: k 1766 ASP cc_start: 0.8808 (m-30) cc_final: 0.8532 (m-30) REVERT: k 1855 SER cc_start: 0.9320 (OUTLIER) cc_final: 0.9008 (t) REVERT: k 1857 GLN cc_start: 0.8730 (tp-100) cc_final: 0.8309 (tp40) REVERT: k 1897 ASN cc_start: 0.9170 (t0) cc_final: 0.8969 (t0) REVERT: l 1729 MET cc_start: 0.8444 (ptm) cc_final: 0.7254 (tpt) REVERT: l 1734 LYS cc_start: 0.6736 (ttpt) cc_final: 0.6173 (pttt) REVERT: l 1737 LYS cc_start: 0.8521 (mtmm) cc_final: 0.8267 (mtpp) REVERT: l 1742 TYR cc_start: 0.8280 (p90) cc_final: 0.8052 (p90) REVERT: l 1800 PHE cc_start: 0.8026 (m-80) cc_final: 0.7537 (m-80) REVERT: l 1857 GLN cc_start: 0.8951 (mm-40) cc_final: 0.8284 (tp40) REVERT: l 1861 GLN cc_start: 0.8928 (mp10) cc_final: 0.8425 (mp10) REVERT: l 1885 ILE cc_start: 0.9122 (mm) cc_final: 0.8627 (mm) REVERT: l 1897 ASN cc_start: 0.9185 (t0) cc_final: 0.8930 (t0) REVERT: l 1898 LYS cc_start: 0.9008 (tptp) cc_final: 0.8645 (tptp) REVERT: l 1903 GLU cc_start: 0.3696 (tt0) cc_final: 0.3368 (tt0) REVERT: m 1710 LEU cc_start: 0.8490 (OUTLIER) cc_final: 0.7818 (pp) REVERT: m 1729 MET cc_start: 0.8594 (ptm) cc_final: 0.7599 (tpt) REVERT: m 1736 THR cc_start: 0.9230 (OUTLIER) cc_final: 0.8973 (t) REVERT: m 1857 GLN cc_start: 0.8861 (tp40) cc_final: 0.8202 (tp40) REVERT: m 1861 GLN cc_start: 0.8620 (mp-120) cc_final: 0.8083 (mp10) REVERT: m 1875 ASP cc_start: 0.7795 (m-30) cc_final: 0.7577 (m-30) REVERT: m 1884 ASP cc_start: 0.8429 (m-30) cc_final: 0.8142 (m-30) REVERT: m 1895 ILE cc_start: 0.9109 (mp) cc_final: 0.8663 (tp) REVERT: n 1729 MET cc_start: 0.8151 (ptm) cc_final: 0.6605 (mmm) REVERT: n 1752 MET cc_start: 0.8545 (ppp) cc_final: 0.8043 (ptt) REVERT: n 1756 MET cc_start: 0.8685 (tpp) cc_final: 0.7082 (tpp) REVERT: n 1766 ASP cc_start: 0.8461 (m-30) cc_final: 0.8207 (m-30) REVERT: n 1789 TYR cc_start: 0.7165 (t80) cc_final: 0.6913 (m-10) REVERT: n 1810 PHE cc_start: 0.6716 (p90) cc_final: 0.6516 (p90) REVERT: n 1880 LEU cc_start: 0.9446 (mt) cc_final: 0.9243 (mt) REVERT: n 1894 LYS cc_start: 0.8967 (ptmt) cc_final: 0.8545 (pttm) REVERT: n 1902 ASP cc_start: 0.8648 (t0) cc_final: 0.8422 (t70) REVERT: o 1710 LEU cc_start: 0.9183 (OUTLIER) cc_final: 0.8724 (pp) REVERT: o 1729 MET cc_start: 0.8275 (ptm) cc_final: 0.6808 (mmt) REVERT: o 1736 THR cc_start: 0.9304 (OUTLIER) cc_final: 0.9036 (t) REVERT: o 1741 ASN cc_start: 0.8941 (p0) cc_final: 0.8725 (p0) REVERT: o 1752 MET cc_start: 0.9262 (ppp) cc_final: 0.8861 (ppp) REVERT: o 1783 GLU cc_start: 0.8210 (pm20) cc_final: 0.7438 (pm20) REVERT: o 1795 MET cc_start: 0.7567 (ptm) cc_final: 0.7146 (ptp) REVERT: o 1810 PHE cc_start: 0.7052 (p90) cc_final: 0.6815 (p90) REVERT: o 1870 TYR cc_start: 0.8429 (m-80) cc_final: 0.8026 (m-10) REVERT: o 1897 ASN cc_start: 0.9289 (t0) cc_final: 0.8903 (t0) REVERT: o 1902 ASP cc_start: 0.8308 (t0) cc_final: 0.8036 (t70) outliers start: 83 outliers final: 49 residues processed: 724 average time/residue: 0.2741 time to fit residues: 319.9712 Evaluate side-chains 674 residues out of total 2338 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 617 time to evaluate : 2.948 ------------------------------------------------------------------------------- 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 h residue 1795 MET 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 j residue 1854 MET Chi-restraints excluded: chain k residue 1698 ILE Chi-restraints excluded: chain k residue 1710 LEU 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 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 Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 266 random chunks: chunk 134 optimal weight: 0.2980 chunk 74 optimal weight: 2.9990 chunk 201 optimal weight: 0.7980 chunk 164 optimal weight: 5.9990 chunk 66 optimal weight: 0.8980 chunk 241 optimal weight: 9.9990 chunk 261 optimal weight: 2.9990 chunk 215 optimal weight: 5.9990 chunk 239 optimal weight: 3.9990 chunk 82 optimal weight: 4.9990 chunk 194 optimal weight: 0.7980 overall best weight: 1.1582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: d1680 GLN d1793 HIS d1907 GLN k1793 HIS o1793 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8198 moved from start: 0.3105 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 21238 Z= 0.234 Angle : 0.644 9.647 28784 Z= 0.338 Chirality : 0.049 0.173 3486 Planarity : 0.004 0.039 3612 Dihedral : 6.465 42.242 2896 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 11.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.05 % Favored : 88.95 % Rotamer: Outliers : 5.09 % Allowed : 19.46 % Favored : 75.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.53 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.47 (0.15), residues: 2716 helix: -4.14 (0.17), residues: 392 sheet: -2.20 (0.17), residues: 826 loop : -1.77 (0.16), residues: 1498 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP d1723 HIS 0.002 0.001 HIS f1793 PHE 0.020 0.002 PHE h1810 TYR 0.026 0.002 TYR h1695 ARG 0.002 0.000 ARG o1754 *********************** 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 771 residues out of total 2338 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 119 poor density : 652 time to evaluate : 2.710 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: b 1689 THR cc_start: 0.9523 (OUTLIER) cc_final: 0.9128 (t) REVERT: b 1715 SER cc_start: 0.9374 (t) cc_final: 0.8967 (m) REVERT: b 1729 MET cc_start: 0.8343 (ptm) cc_final: 0.6659 (mmt) REVERT: b 1734 LYS cc_start: 0.6619 (ttpt) cc_final: 0.6233 (pttt) REVERT: b 1752 MET cc_start: 0.9029 (ppp) cc_final: 0.8542 (ptt) REVERT: b 1783 GLU cc_start: 0.8058 (pm20) cc_final: 0.7706 (pm20) REVERT: b 1795 MET cc_start: 0.7534 (ptm) cc_final: 0.6969 (ptt) REVERT: b 1886 ASP cc_start: 0.8799 (t0) cc_final: 0.8589 (t70) REVERT: b 1902 ASP cc_start: 0.8792 (t0) cc_final: 0.8202 (t70) REVERT: c 1729 MET cc_start: 0.7978 (ptm) cc_final: 0.6571 (mmm) REVERT: c 1742 TYR cc_start: 0.8523 (p90) cc_final: 0.8114 (p90) REVERT: c 1795 MET cc_start: 0.7742 (OUTLIER) cc_final: 0.7258 (ptm) REVERT: c 1885 ILE cc_start: 0.9197 (mm) cc_final: 0.8882 (mm) REVERT: c 1886 ASP cc_start: 0.7819 (t0) cc_final: 0.7343 (t0) REVERT: c 1902 ASP cc_start: 0.8724 (t0) cc_final: 0.8150 (t70) REVERT: d 1710 LEU cc_start: 0.8630 (OUTLIER) cc_final: 0.8334 (pp) REVERT: d 1715 SER cc_start: 0.9527 (t) cc_final: 0.9267 (m) REVERT: d 1729 MET cc_start: 0.8342 (ptm) cc_final: 0.7268 (mmt) REVERT: d 1739 TYR cc_start: 0.8725 (m-80) cc_final: 0.8422 (m-80) REVERT: d 1752 MET cc_start: 0.9234 (ppp) cc_final: 0.8744 (ptt) REVERT: d 1766 ASP cc_start: 0.8794 (m-30) cc_final: 0.8482 (m-30) REVERT: d 1774 ASN cc_start: 0.8701 (p0) cc_final: 0.8368 (p0) REVERT: d 1857 GLN cc_start: 0.8756 (tp-100) cc_final: 0.8328 (tp40) REVERT: d 1876 SER cc_start: 0.9387 (OUTLIER) cc_final: 0.8842 (m) REVERT: d 1886 ASP cc_start: 0.8340 (t0) cc_final: 0.8051 (t0) REVERT: d 1897 ASN cc_start: 0.9313 (t0) cc_final: 0.9099 (t0) REVERT: e 1729 MET cc_start: 0.8824 (ptm) cc_final: 0.7080 (mmt) REVERT: e 1734 LYS cc_start: 0.6947 (ttpt) cc_final: 0.6289 (pttp) REVERT: e 1756 MET cc_start: 0.8845 (tpp) cc_final: 0.8566 (tpt) REVERT: e 1783 GLU cc_start: 0.8028 (pm20) cc_final: 0.7755 (pm20) REVERT: e 1795 MET cc_start: 0.7550 (ptm) cc_final: 0.7278 (ptp) REVERT: e 1810 PHE cc_start: 0.7209 (p90) cc_final: 0.6905 (p90) REVERT: e 1870 TYR cc_start: 0.8177 (m-80) cc_final: 0.7809 (m-80) REVERT: e 1882 MET cc_start: 0.8547 (mmt) cc_final: 0.8298 (mmm) REVERT: e 1886 ASP cc_start: 0.8358 (t0) cc_final: 0.8111 (t0) REVERT: e 1894 LYS cc_start: 0.8936 (ptmt) cc_final: 0.8512 (pttm) REVERT: e 1902 ASP cc_start: 0.8708 (t0) cc_final: 0.8358 (t70) REVERT: f 1707 ASP cc_start: 0.8391 (t0) cc_final: 0.7620 (t0) REVERT: f 1709 THR cc_start: 0.9089 (p) cc_final: 0.8850 (p) REVERT: f 1729 MET cc_start: 0.8118 (ptm) cc_final: 0.7042 (tpt) REVERT: f 1734 LYS cc_start: 0.6793 (ttpt) cc_final: 0.6566 (ttpt) REVERT: f 1737 LYS cc_start: 0.8750 (mtmm) cc_final: 0.8051 (mtpp) REVERT: f 1739 TYR cc_start: 0.8650 (m-80) cc_final: 0.7959 (m-80) REVERT: f 1742 TYR cc_start: 0.8464 (p90) cc_final: 0.7716 (p90) REVERT: f 1766 ASP cc_start: 0.9043 (m-30) cc_final: 0.8741 (m-30) REVERT: f 1780 MET cc_start: 0.8111 (tpt) cc_final: 0.7817 (tpp) REVERT: f 1783 GLU cc_start: 0.8370 (pm20) cc_final: 0.7879 (pm20) REVERT: f 1857 GLN cc_start: 0.9099 (tp-100) cc_final: 0.8283 (tp40) REVERT: f 1861 GLN cc_start: 0.8995 (mp-120) cc_final: 0.8479 (mp10) REVERT: f 1882 MET cc_start: 0.8841 (mmm) cc_final: 0.8633 (mmm) REVERT: f 1886 ASP cc_start: 0.8472 (t0) cc_final: 0.8250 (t0) REVERT: f 1897 ASN cc_start: 0.9163 (t0) cc_final: 0.8934 (t0) REVERT: g 1699 GLU cc_start: 0.7011 (pt0) cc_final: 0.6797 (pt0) REVERT: g 1721 ASP cc_start: 0.6589 (p0) cc_final: 0.6380 (p0) REVERT: g 1729 MET cc_start: 0.8329 (ptm) cc_final: 0.6987 (mmt) REVERT: g 1752 MET cc_start: 0.8937 (ppp) cc_final: 0.7940 (ptt) REVERT: g 1766 ASP cc_start: 0.8583 (m-30) cc_final: 0.8337 (m-30) REVERT: g 1780 MET cc_start: 0.8500 (tpt) cc_final: 0.8167 (tpp) REVERT: g 1885 ILE cc_start: 0.9404 (mm) cc_final: 0.9157 (mm) REVERT: g 1894 LYS cc_start: 0.8703 (ptmt) cc_final: 0.8310 (pttm) REVERT: g 1897 ASN cc_start: 0.9064 (t0) cc_final: 0.8786 (t0) REVERT: g 1898 LYS cc_start: 0.8634 (tptp) cc_final: 0.8433 (tptp) REVERT: g 1903 GLU cc_start: 0.4129 (tt0) cc_final: 0.3821 (tt0) REVERT: h 1707 ASP cc_start: 0.7881 (p0) cc_final: 0.7613 (p0) REVERT: h 1729 MET cc_start: 0.8300 (ptm) cc_final: 0.7232 (tpt) REVERT: h 1795 MET cc_start: 0.8210 (ptm) cc_final: 0.7716 (ptm) REVERT: h 1872 ASN cc_start: 0.8154 (m110) cc_final: 0.7848 (m-40) REVERT: h 1886 ASP cc_start: 0.7869 (p0) cc_final: 0.7485 (p0) REVERT: i 1707 ASP cc_start: 0.8182 (p0) cc_final: 0.7291 (p0) REVERT: i 1729 MET cc_start: 0.8247 (ptm) cc_final: 0.6998 (tpt) REVERT: i 1734 LYS cc_start: 0.6822 (ttpt) cc_final: 0.6477 (pttm) REVERT: i 1742 TYR cc_start: 0.8572 (p90) cc_final: 0.7707 (p90) REVERT: i 1752 MET cc_start: 0.8872 (ppp) cc_final: 0.8188 (ppp) REVERT: i 1756 MET cc_start: 0.8939 (tpt) cc_final: 0.8581 (tpt) REVERT: i 1766 ASP cc_start: 0.8614 (m-30) cc_final: 0.8141 (m-30) REVERT: i 1810 PHE cc_start: 0.7618 (p90) cc_final: 0.6941 (p90) REVERT: i 1857 GLN cc_start: 0.9088 (tp-100) cc_final: 0.8412 (tp40) REVERT: i 1861 GLN cc_start: 0.8924 (mp-120) cc_final: 0.8709 (mp10) REVERT: i 1902 ASP cc_start: 0.8673 (t0) cc_final: 0.8251 (t70) REVERT: j 1699 GLU cc_start: 0.6587 (pt0) cc_final: 0.6194 (pm20) REVERT: j 1707 ASP cc_start: 0.7932 (p0) cc_final: 0.7408 (p0) REVERT: j 1729 MET cc_start: 0.8750 (ptm) cc_final: 0.7345 (mmt) REVERT: j 1734 LYS cc_start: 0.7166 (ttpt) cc_final: 0.6627 (pttp) REVERT: j 1752 MET cc_start: 0.9127 (ppp) cc_final: 0.8655 (ppp) REVERT: j 1780 MET cc_start: 0.8353 (tpt) cc_final: 0.7864 (tpp) REVERT: j 1783 GLU cc_start: 0.8183 (pm20) cc_final: 0.7879 (pm20) REVERT: j 1795 MET cc_start: 0.7606 (ptp) cc_final: 0.7299 (ptt) REVERT: j 1870 TYR cc_start: 0.8147 (m-80) cc_final: 0.7864 (m-80) REVERT: k 1710 LEU cc_start: 0.8896 (OUTLIER) cc_final: 0.8621 (pp) REVERT: k 1715 SER cc_start: 0.9601 (t) cc_final: 0.9396 (m) REVERT: k 1729 MET cc_start: 0.8231 (ptm) cc_final: 0.7130 (mmt) REVERT: k 1739 TYR cc_start: 0.8799 (m-80) cc_final: 0.8591 (m-80) REVERT: k 1752 MET cc_start: 0.9190 (ppp) cc_final: 0.8796 (ptt) REVERT: k 1766 ASP cc_start: 0.8799 (m-30) cc_final: 0.8536 (m-30) REVERT: k 1783 GLU cc_start: 0.8444 (pm20) cc_final: 0.8194 (pm20) REVERT: k 1857 GLN cc_start: 0.8802 (tp-100) cc_final: 0.8336 (tp40) REVERT: k 1897 ASN cc_start: 0.9179 (t0) cc_final: 0.8971 (t0) REVERT: l 1729 MET cc_start: 0.8449 (ptm) cc_final: 0.7175 (mmm) REVERT: l 1737 LYS cc_start: 0.8626 (mtmm) cc_final: 0.8364 (mtpp) REVERT: l 1742 TYR cc_start: 0.8452 (p90) cc_final: 0.8071 (p90) REVERT: l 1780 MET cc_start: 0.8201 (tpt) cc_final: 0.7728 (tpp) REVERT: l 1857 GLN cc_start: 0.8922 (mm-40) cc_final: 0.8312 (tp40) REVERT: l 1861 GLN cc_start: 0.8963 (mp10) cc_final: 0.8429 (mp10) REVERT: l 1885 ILE cc_start: 0.9154 (mm) cc_final: 0.8670 (mm) REVERT: l 1897 ASN cc_start: 0.9171 (t0) cc_final: 0.8924 (t0) REVERT: l 1898 LYS cc_start: 0.8783 (tptp) cc_final: 0.8465 (tptp) REVERT: l 1903 GLU cc_start: 0.3143 (tt0) cc_final: 0.2811 (tt0) REVERT: m 1710 LEU cc_start: 0.8559 (OUTLIER) cc_final: 0.7946 (pp) REVERT: m 1729 MET cc_start: 0.8531 (ptm) cc_final: 0.7694 (tpt) REVERT: m 1736 THR cc_start: 0.9249 (OUTLIER) cc_final: 0.8779 (t) REVERT: m 1752 MET cc_start: 0.9219 (ppp) cc_final: 0.8827 (ppp) REVERT: m 1857 GLN cc_start: 0.9013 (tp40) cc_final: 0.8160 (tp-100) REVERT: m 1861 GLN cc_start: 0.8729 (mp-120) cc_final: 0.8123 (mp10) REVERT: m 1875 ASP cc_start: 0.7704 (m-30) cc_final: 0.7493 (m-30) REVERT: m 1886 ASP cc_start: 0.7805 (t0) cc_final: 0.7417 (t0) REVERT: n 1729 MET cc_start: 0.8235 (ptm) cc_final: 0.6788 (mmt) REVERT: n 1752 MET cc_start: 0.8552 (ppp) cc_final: 0.8197 (ptt) REVERT: n 1766 ASP cc_start: 0.8449 (m-30) cc_final: 0.8202 (m-30) REVERT: n 1810 PHE cc_start: 0.6833 (p90) cc_final: 0.6565 (p90) REVERT: n 1894 LYS cc_start: 0.8944 (ptmt) cc_final: 0.8515 (pttm) REVERT: o 1729 MET cc_start: 0.8425 (ptm) cc_final: 0.6964 (mmt) REVERT: o 1736 THR cc_start: 0.9334 (OUTLIER) cc_final: 0.9064 (t) REVERT: o 1741 ASN cc_start: 0.8855 (p0) cc_final: 0.8596 (p0) REVERT: o 1752 MET cc_start: 0.9272 (ppp) cc_final: 0.8798 (ppp) REVERT: o 1783 GLU cc_start: 0.8327 (pm20) cc_final: 0.7432 (pm20) REVERT: o 1795 MET cc_start: 0.7605 (ptm) cc_final: 0.7127 (ptt) REVERT: o 1810 PHE cc_start: 0.7080 (p90) cc_final: 0.6873 (p90) REVERT: o 1870 TYR cc_start: 0.8462 (m-80) cc_final: 0.8102 (m-10) outliers start: 119 outliers final: 67 residues processed: 751 average time/residue: 0.2752 time to fit residues: 331.7045 Evaluate side-chains 676 residues out of total 2338 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 75 poor density : 601 time to evaluate : 2.420 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain b residue 1678 VAL Chi-restraints excluded: chain b residue 1689 THR Chi-restraints excluded: chain b residue 1698 ILE Chi-restraints excluded: chain b residue 1755 LEU Chi-restraints excluded: chain b residue 1781 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 1736 THR Chi-restraints excluded: chain c residue 1776 GLN 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 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 1876 SER 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 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 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 1710 LEU Chi-restraints excluded: chain h residue 1715 SER Chi-restraints excluded: chain h residue 1730 ILE 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 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 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 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 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 1706 VAL 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 1873 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 266 random chunks: chunk 239 optimal weight: 3.9990 chunk 181 optimal weight: 1.9990 chunk 125 optimal weight: 2.9990 chunk 26 optimal weight: 1.9990 chunk 115 optimal weight: 0.8980 chunk 162 optimal weight: 7.9990 chunk 242 optimal weight: 7.9990 chunk 257 optimal weight: 4.9990 chunk 126 optimal weight: 0.5980 chunk 230 optimal weight: 2.9990 chunk 69 optimal weight: 0.9980 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: b1793 HIS k1680 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8232 moved from start: 0.3540 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 21238 Z= 0.246 Angle : 0.660 13.165 28784 Z= 0.339 Chirality : 0.050 0.163 3486 Planarity : 0.004 0.037 3612 Dihedral : 6.154 34.960 2889 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 10.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.94 % Favored : 89.06 % Rotamer: Outliers : 5.56 % Allowed : 20.44 % Favored : 73.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.53 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.35 (0.15), residues: 2716 helix: -3.96 (0.18), residues: 392 sheet: -2.13 (0.17), residues: 826 loop : -1.71 (0.16), residues: 1498 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP g1723 HIS 0.003 0.001 HIS d1793 PHE 0.022 0.002 PHE h1759 TYR 0.025 0.002 TYR h1695 ARG 0.001 0.000 ARG j1754 *********************** 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 769 residues out of total 2338 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 130 poor density : 639 time to evaluate : 2.403 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 1689 THR cc_start: 0.9550 (OUTLIER) cc_final: 0.9223 (t) REVERT: b 1715 SER cc_start: 0.9260 (t) cc_final: 0.8980 (m) REVERT: b 1729 MET cc_start: 0.8251 (ptm) cc_final: 0.6272 (mmt) REVERT: b 1734 LYS cc_start: 0.6759 (ttpt) cc_final: 0.6345 (pttt) REVERT: b 1752 MET cc_start: 0.9206 (ppp) cc_final: 0.8440 (ptt) REVERT: b 1781 LEU cc_start: 0.6590 (OUTLIER) cc_final: 0.6149 (tt) REVERT: b 1783 GLU cc_start: 0.8149 (pm20) cc_final: 0.7874 (pm20) REVERT: b 1791 ASN cc_start: 0.8699 (t0) cc_final: 0.8494 (t0) REVERT: b 1795 MET cc_start: 0.7305 (ptm) cc_final: 0.7093 (ptt) REVERT: b 1886 ASP cc_start: 0.8842 (t0) cc_final: 0.8556 (t70) REVERT: b 1902 ASP cc_start: 0.8843 (t0) cc_final: 0.8295 (t70) REVERT: c 1729 MET cc_start: 0.8068 (ptm) cc_final: 0.6696 (mmm) REVERT: c 1742 TYR cc_start: 0.8514 (p90) cc_final: 0.7950 (p90) REVERT: c 1853 GLN cc_start: 0.8276 (pp30) cc_final: 0.8032 (pp30) REVERT: c 1885 ILE cc_start: 0.9227 (mm) cc_final: 0.8892 (mm) REVERT: c 1886 ASP cc_start: 0.7986 (t0) cc_final: 0.7683 (t0) REVERT: c 1902 ASP cc_start: 0.8721 (t0) cc_final: 0.8051 (t0) REVERT: d 1710 LEU cc_start: 0.8784 (OUTLIER) cc_final: 0.8469 (pp) REVERT: d 1729 MET cc_start: 0.8356 (ptm) cc_final: 0.7192 (mmt) REVERT: d 1739 TYR cc_start: 0.8799 (m-80) cc_final: 0.8483 (m-80) REVERT: d 1752 MET cc_start: 0.9194 (ppp) cc_final: 0.8782 (ptt) REVERT: d 1766 ASP cc_start: 0.8777 (m-30) cc_final: 0.8497 (m-30) REVERT: d 1774 ASN cc_start: 0.8736 (p0) cc_final: 0.8433 (p0) REVERT: d 1857 GLN cc_start: 0.8762 (tp-100) cc_final: 0.8253 (tp40) REVERT: d 1876 SER cc_start: 0.9218 (OUTLIER) cc_final: 0.8947 (p) REVERT: d 1886 ASP cc_start: 0.8388 (t0) cc_final: 0.8141 (t70) REVERT: e 1729 MET cc_start: 0.8798 (ptm) cc_final: 0.7093 (mmt) REVERT: e 1734 LYS cc_start: 0.7118 (ttpt) cc_final: 0.6540 (pttp) REVERT: e 1739 TYR cc_start: 0.8195 (m-80) cc_final: 0.7956 (m-10) REVERT: e 1780 MET cc_start: 0.8327 (tpt) cc_final: 0.8013 (tpp) REVERT: e 1783 GLU cc_start: 0.8098 (pm20) cc_final: 0.7843 (pm20) REVERT: e 1810 PHE cc_start: 0.7157 (p90) cc_final: 0.6858 (p90) REVERT: e 1886 ASP cc_start: 0.8465 (t0) cc_final: 0.8132 (t0) REVERT: e 1894 LYS cc_start: 0.8936 (ptmt) cc_final: 0.8529 (pttm) REVERT: e 1902 ASP cc_start: 0.8746 (t0) cc_final: 0.8427 (t70) REVERT: f 1707 ASP cc_start: 0.8378 (t0) cc_final: 0.7625 (t0) REVERT: f 1709 THR cc_start: 0.9123 (p) cc_final: 0.8805 (p) REVERT: f 1729 MET cc_start: 0.8076 (ptm) cc_final: 0.7212 (tpt) REVERT: f 1734 LYS cc_start: 0.6823 (ttpt) cc_final: 0.6577 (ttpt) REVERT: f 1737 LYS cc_start: 0.8721 (mtmm) cc_final: 0.8008 (mtpp) REVERT: f 1739 TYR cc_start: 0.8688 (m-80) cc_final: 0.7907 (m-80) REVERT: f 1742 TYR cc_start: 0.8492 (p90) cc_final: 0.7886 (p90) REVERT: f 1752 MET cc_start: 0.8786 (ppp) cc_final: 0.8130 (ppp) REVERT: f 1766 ASP cc_start: 0.8971 (m-30) cc_final: 0.8591 (m-30) REVERT: f 1780 MET cc_start: 0.8148 (tpt) cc_final: 0.7783 (tpp) REVERT: f 1783 GLU cc_start: 0.8342 (pm20) cc_final: 0.7802 (pm20) REVERT: f 1857 GLN cc_start: 0.9118 (tp-100) cc_final: 0.8578 (tp40) REVERT: f 1897 ASN cc_start: 0.9235 (t0) cc_final: 0.8996 (t0) REVERT: g 1729 MET cc_start: 0.8297 (ptm) cc_final: 0.6969 (mmt) REVERT: g 1752 MET cc_start: 0.8939 (ppp) cc_final: 0.8047 (ptt) REVERT: g 1766 ASP cc_start: 0.8424 (m-30) cc_final: 0.8202 (m-30) REVERT: g 1885 ILE cc_start: 0.9455 (mm) cc_final: 0.9188 (mm) REVERT: g 1894 LYS cc_start: 0.8691 (ptmt) cc_final: 0.8338 (pttm) REVERT: h 1729 MET cc_start: 0.8207 (ptm) cc_final: 0.6930 (tpt) REVERT: h 1870 TYR cc_start: 0.8218 (m-10) cc_final: 0.7990 (m-10) REVERT: h 1886 ASP cc_start: 0.8041 (p0) cc_final: 0.7442 (p0) REVERT: h 1903 GLU cc_start: 0.3753 (tt0) cc_final: 0.3142 (mt-10) REVERT: i 1707 ASP cc_start: 0.8163 (p0) cc_final: 0.7315 (p0) REVERT: i 1729 MET cc_start: 0.8276 (ptm) cc_final: 0.7221 (tpt) REVERT: i 1734 LYS cc_start: 0.6709 (ttpt) cc_final: 0.6476 (pttt) REVERT: i 1742 TYR cc_start: 0.8533 (p90) cc_final: 0.7713 (p90) REVERT: i 1752 MET cc_start: 0.8882 (ppp) cc_final: 0.8095 (ppp) REVERT: i 1756 MET cc_start: 0.8948 (tpt) cc_final: 0.8569 (tpt) REVERT: i 1766 ASP cc_start: 0.8701 (m-30) cc_final: 0.8239 (m-30) REVERT: i 1810 PHE cc_start: 0.7688 (p90) cc_final: 0.6996 (p90) REVERT: i 1857 GLN cc_start: 0.9155 (tp-100) cc_final: 0.8584 (tp40) REVERT: i 1902 ASP cc_start: 0.8751 (t0) cc_final: 0.8344 (t70) REVERT: j 1699 GLU cc_start: 0.6161 (pt0) cc_final: 0.5622 (pm20) REVERT: j 1729 MET cc_start: 0.8761 (ptm) cc_final: 0.7416 (mmt) REVERT: j 1734 LYS cc_start: 0.7199 (ttpt) cc_final: 0.6497 (pttp) REVERT: j 1752 MET cc_start: 0.9145 (ppp) cc_final: 0.8665 (ppp) REVERT: j 1780 MET cc_start: 0.8400 (tpt) cc_final: 0.7912 (tpp) REVERT: j 1783 GLU cc_start: 0.8208 (pm20) cc_final: 0.7870 (pm20) REVERT: j 1854 MET cc_start: 0.7958 (ttm) cc_final: 0.6932 (pmm) REVERT: j 1870 TYR cc_start: 0.8187 (m-80) cc_final: 0.7898 (m-80) REVERT: j 1902 ASP cc_start: 0.8311 (t70) cc_final: 0.7805 (t70) REVERT: k 1710 LEU cc_start: 0.8927 (OUTLIER) cc_final: 0.8654 (pp) REVERT: k 1715 SER cc_start: 0.9567 (t) cc_final: 0.9358 (m) REVERT: k 1729 MET cc_start: 0.8293 (ptm) cc_final: 0.7166 (mmt) REVERT: k 1752 MET cc_start: 0.9177 (ppp) cc_final: 0.8752 (ptt) REVERT: k 1766 ASP cc_start: 0.8776 (m-30) cc_final: 0.8510 (m-30) REVERT: k 1789 TYR cc_start: 0.7857 (t80) cc_final: 0.7502 (m-10) REVERT: k 1857 GLN cc_start: 0.8728 (tp-100) cc_final: 0.8303 (tp40) REVERT: l 1707 ASP cc_start: 0.8132 (t0) cc_final: 0.7323 (t0) REVERT: l 1729 MET cc_start: 0.8445 (ptm) cc_final: 0.7170 (mmm) REVERT: l 1737 LYS cc_start: 0.8654 (mtmm) cc_final: 0.8381 (mtpp) REVERT: l 1742 TYR cc_start: 0.8409 (p90) cc_final: 0.7990 (p90) REVERT: l 1743 GLN cc_start: 0.7781 (mm-40) cc_final: 0.7483 (mm-40) REVERT: l 1861 GLN cc_start: 0.8855 (mp10) cc_final: 0.8558 (mp10) REVERT: l 1885 ILE cc_start: 0.9198 (mm) cc_final: 0.8727 (mm) REVERT: l 1897 ASN cc_start: 0.9199 (t0) cc_final: 0.8948 (t0) REVERT: l 1898 LYS cc_start: 0.8655 (tptp) cc_final: 0.8350 (tptp) REVERT: l 1903 GLU cc_start: 0.4550 (tt0) cc_final: 0.4329 (tt0) REVERT: m 1729 MET cc_start: 0.8408 (ptm) cc_final: 0.7374 (tpt) REVERT: m 1736 THR cc_start: 0.9232 (OUTLIER) cc_final: 0.8933 (t) REVERT: m 1752 MET cc_start: 0.9321 (ppp) cc_final: 0.8810 (ppp) REVERT: m 1783 GLU cc_start: 0.8441 (pm20) cc_final: 0.8169 (pm20) REVERT: m 1857 GLN cc_start: 0.9032 (tp40) cc_final: 0.8227 (tp-100) REVERT: m 1861 GLN cc_start: 0.8783 (mp-120) cc_final: 0.8414 (mp10) REVERT: n 1729 MET cc_start: 0.8285 (ptm) cc_final: 0.6871 (mmt) REVERT: n 1752 MET cc_start: 0.8648 (ppp) cc_final: 0.8226 (ptt) REVERT: n 1886 ASP cc_start: 0.8583 (t0) cc_final: 0.8339 (t0) REVERT: n 1894 LYS cc_start: 0.8898 (ptmt) cc_final: 0.8473 (pttm) REVERT: o 1729 MET cc_start: 0.7693 (ptm) cc_final: 0.6625 (mmt) REVERT: o 1736 THR cc_start: 0.9364 (OUTLIER) cc_final: 0.9126 (t) REVERT: o 1752 MET cc_start: 0.9259 (ppp) cc_final: 0.8917 (ppp) REVERT: o 1780 MET cc_start: 0.8195 (tpp) cc_final: 0.7961 (tpp) REVERT: o 1783 GLU cc_start: 0.8333 (pm20) cc_final: 0.7519 (pm20) REVERT: o 1795 MET cc_start: 0.7540 (ptm) cc_final: 0.7158 (ptt) REVERT: o 1810 PHE cc_start: 0.7142 (p90) cc_final: 0.6912 (p90) REVERT: o 1870 TYR cc_start: 0.8504 (m-80) cc_final: 0.8080 (m-10) outliers start: 130 outliers final: 85 residues processed: 744 average time/residue: 0.2760 time to fit residues: 330.6882 Evaluate side-chains 680 residues out of total 2338 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 92 poor density : 588 time to evaluate : 2.536 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain b residue 1689 THR Chi-restraints excluded: chain b residue 1698 ILE Chi-restraints excluded: chain b residue 1700 ILE Chi-restraints excluded: chain b residue 1755 LEU Chi-restraints excluded: chain b residue 1781 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 1736 THR Chi-restraints excluded: chain c residue 1755 LEU 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 1790 VAL Chi-restraints excluded: chain d residue 1876 SER Chi-restraints excluded: chain d residue 1883 ASP Chi-restraints excluded: chain e residue 1683 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 1790 VAL Chi-restraints excluded: chain f residue 1879 ILE Chi-restraints excluded: chain g residue 1790 VAL Chi-restraints excluded: chain g residue 1865 ILE Chi-restraints excluded: chain h residue 1700 ILE Chi-restraints excluded: chain h residue 1715 SER Chi-restraints excluded: chain h residue 1730 ILE Chi-restraints excluded: chain h residue 1738 VAL Chi-restraints excluded: chain h residue 1755 LEU 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 1790 VAL 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 1715 SER 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 1776 GLN Chi-restraints excluded: chain m residue 1790 VAL 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 1698 ILE Chi-restraints excluded: chain n residue 1710 LEU Chi-restraints excluded: chain n residue 1733 ASP 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 1698 ILE 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 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 1883 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 266 random chunks: chunk 214 optimal weight: 0.9990 chunk 145 optimal weight: 5.9990 chunk 3 optimal weight: 5.9990 chunk 191 optimal weight: 2.9990 chunk 106 optimal weight: 4.9990 chunk 219 optimal weight: 4.9990 chunk 177 optimal weight: 3.9990 chunk 0 optimal weight: 5.9990 chunk 131 optimal weight: 0.6980 chunk 230 optimal weight: 0.4980 chunk 64 optimal weight: 3.9990 overall best weight: 1.8386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: c1793 HIS c1897 ASN d1680 GLN g1897 ASN k1680 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8283 moved from start: 0.3948 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.057 21238 Z= 0.314 Angle : 0.709 13.983 28784 Z= 0.362 Chirality : 0.051 0.170 3486 Planarity : 0.004 0.037 3612 Dihedral : 6.354 36.449 2885 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 10.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.27 % Favored : 88.73 % Rotamer: Outliers : 6.29 % Allowed : 21.17 % Favored : 72.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.53 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.99 (0.16), residues: 2716 helix: -3.86 (0.18), residues: 392 sheet: -2.15 (0.19), residues: 672 loop : -1.38 (0.15), residues: 1652 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP b1723 HIS 0.003 0.001 HIS k1793 PHE 0.022 0.002 PHE h1759 TYR 0.028 0.002 TYR h1695 ARG 0.003 0.000 ARG b1754 *********************** 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 766 residues out of total 2338 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 147 poor density : 619 time to evaluate : 2.366 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: b 1689 THR cc_start: 0.9592 (OUTLIER) cc_final: 0.9307 (t) REVERT: b 1710 LEU cc_start: 0.9036 (OUTLIER) cc_final: 0.8588 (pp) REVERT: b 1715 SER cc_start: 0.9167 (t) cc_final: 0.8826 (m) REVERT: b 1729 MET cc_start: 0.8329 (ptm) cc_final: 0.6361 (mmt) REVERT: b 1734 LYS cc_start: 0.7009 (ttpt) cc_final: 0.6612 (pttt) REVERT: b 1752 MET cc_start: 0.9253 (ppp) cc_final: 0.8989 (ppp) REVERT: b 1781 LEU cc_start: 0.7288 (OUTLIER) cc_final: 0.6989 (tt) REVERT: b 1783 GLU cc_start: 0.8306 (pm20) cc_final: 0.8012 (pm20) REVERT: b 1886 ASP cc_start: 0.8575 (t0) cc_final: 0.8300 (t70) REVERT: b 1902 ASP cc_start: 0.8869 (t0) cc_final: 0.8428 (t70) REVERT: c 1729 MET cc_start: 0.8444 (ptm) cc_final: 0.7070 (mmm) REVERT: c 1742 TYR cc_start: 0.8560 (p90) cc_final: 0.7989 (p90) REVERT: c 1885 ILE cc_start: 0.9298 (mm) cc_final: 0.8970 (mm) REVERT: c 1886 ASP cc_start: 0.8222 (t0) cc_final: 0.7688 (t0) REVERT: c 1902 ASP cc_start: 0.8812 (t0) cc_final: 0.8321 (t70) REVERT: c 1903 GLU cc_start: 0.7691 (tm-30) cc_final: 0.7229 (tm-30) REVERT: d 1729 MET cc_start: 0.8360 (ptm) cc_final: 0.7223 (mmt) REVERT: d 1752 MET cc_start: 0.9216 (ppp) cc_final: 0.8788 (ptt) REVERT: d 1766 ASP cc_start: 0.8810 (m-30) cc_final: 0.8547 (m-30) REVERT: d 1857 GLN cc_start: 0.8821 (tp-100) cc_final: 0.8388 (tp40) REVERT: e 1729 MET cc_start: 0.8795 (ptm) cc_final: 0.7291 (mmt) REVERT: e 1734 LYS cc_start: 0.7223 (ttpt) cc_final: 0.6590 (pttp) REVERT: e 1742 TYR cc_start: 0.8419 (p90) cc_final: 0.8083 (p90) REVERT: e 1780 MET cc_start: 0.8396 (tpt) cc_final: 0.8024 (tpp) REVERT: e 1783 GLU cc_start: 0.8257 (pm20) cc_final: 0.7951 (pm20) REVERT: e 1810 PHE cc_start: 0.7179 (p90) cc_final: 0.6838 (p90) REVERT: e 1886 ASP cc_start: 0.8592 (t0) cc_final: 0.8067 (t0) REVERT: e 1894 LYS cc_start: 0.8805 (ptmt) cc_final: 0.8461 (pttm) REVERT: e 1902 ASP cc_start: 0.8834 (t0) cc_final: 0.8520 (t70) REVERT: f 1707 ASP cc_start: 0.8275 (t0) cc_final: 0.7645 (t0) REVERT: f 1709 THR cc_start: 0.9137 (p) cc_final: 0.8792 (p) REVERT: f 1729 MET cc_start: 0.8050 (ptm) cc_final: 0.6980 (tpt) REVERT: f 1737 LYS cc_start: 0.8766 (mtmm) cc_final: 0.7991 (mtpp) REVERT: f 1742 TYR cc_start: 0.8612 (p90) cc_final: 0.8010 (p90) REVERT: f 1752 MET cc_start: 0.8925 (ppp) cc_final: 0.8206 (ppp) REVERT: f 1766 ASP cc_start: 0.9108 (m-30) cc_final: 0.8660 (m-30) REVERT: f 1783 GLU cc_start: 0.8360 (pm20) cc_final: 0.7902 (pm20) REVERT: f 1857 GLN cc_start: 0.9152 (tp-100) cc_final: 0.8553 (tp40) REVERT: f 1861 GLN cc_start: 0.8980 (mp10) cc_final: 0.8540 (mp10) REVERT: f 1863 MET cc_start: 0.9094 (tpp) cc_final: 0.8884 (tpp) REVERT: f 1886 ASP cc_start: 0.8359 (t0) cc_final: 0.8115 (t0) REVERT: f 1902 ASP cc_start: 0.8631 (t70) cc_final: 0.7892 (t70) REVERT: g 1729 MET cc_start: 0.8316 (ptm) cc_final: 0.6939 (mmt) REVERT: g 1752 MET cc_start: 0.8987 (ppp) cc_final: 0.8284 (ptt) REVERT: g 1766 ASP cc_start: 0.8455 (m-30) cc_final: 0.8212 (m-30) REVERT: g 1810 PHE cc_start: 0.7701 (p90) cc_final: 0.7324 (p90) REVERT: g 1885 ILE cc_start: 0.9520 (mm) cc_final: 0.9279 (mm) REVERT: g 1894 LYS cc_start: 0.8727 (ptmt) cc_final: 0.8373 (pttm) REVERT: h 1729 MET cc_start: 0.7591 (ptm) cc_final: 0.6657 (tpt) REVERT: h 1736 THR cc_start: 0.9330 (OUTLIER) cc_final: 0.9085 (t) REVERT: h 1752 MET cc_start: 0.9137 (ppp) cc_final: 0.8700 (ppp) REVERT: h 1776 GLN cc_start: 0.8060 (OUTLIER) cc_final: 0.7621 (tt0) REVERT: h 1886 ASP cc_start: 0.8081 (p0) cc_final: 0.7450 (p0) REVERT: h 1903 GLU cc_start: 0.3769 (tt0) cc_final: 0.3161 (mt-10) REVERT: i 1707 ASP cc_start: 0.8271 (p0) cc_final: 0.7339 (p0) REVERT: i 1729 MET cc_start: 0.8269 (ptm) cc_final: 0.7242 (tpt) REVERT: i 1737 LYS cc_start: 0.8789 (OUTLIER) cc_final: 0.8580 (mptt) REVERT: i 1742 TYR cc_start: 0.8646 (p90) cc_final: 0.7712 (p90) REVERT: i 1752 MET cc_start: 0.8909 (ppp) cc_final: 0.7900 (ppp) REVERT: i 1756 MET cc_start: 0.8986 (tpt) cc_final: 0.8594 (tpt) REVERT: i 1766 ASP cc_start: 0.8717 (m-30) cc_final: 0.8289 (m-30) REVERT: i 1810 PHE cc_start: 0.8082 (p90) cc_final: 0.7222 (p90) REVERT: i 1857 GLN cc_start: 0.9191 (tp-100) cc_final: 0.8678 (tp40) REVERT: i 1897 ASN cc_start: 0.8792 (t0) cc_final: 0.8333 (t0) REVERT: i 1902 ASP cc_start: 0.8992 (t0) cc_final: 0.8574 (t70) REVERT: j 1729 MET cc_start: 0.8746 (ptm) cc_final: 0.7304 (mmt) REVERT: j 1752 MET cc_start: 0.9177 (ppp) cc_final: 0.8683 (ppp) REVERT: j 1780 MET cc_start: 0.8481 (tpt) cc_final: 0.8093 (tpp) REVERT: j 1783 GLU cc_start: 0.8314 (pm20) cc_final: 0.8049 (pm20) REVERT: j 1870 TYR cc_start: 0.8256 (m-80) cc_final: 0.7947 (m-80) REVERT: j 1902 ASP cc_start: 0.8451 (t70) cc_final: 0.7930 (t70) REVERT: k 1729 MET cc_start: 0.8320 (ptm) cc_final: 0.7170 (mmt) REVERT: k 1737 LYS cc_start: 0.8755 (mtmm) cc_final: 0.8288 (mtpp) REVERT: k 1752 MET cc_start: 0.9174 (ppp) cc_final: 0.8593 (ptt) REVERT: k 1766 ASP cc_start: 0.8792 (m-30) cc_final: 0.8524 (m-30) REVERT: k 1857 GLN cc_start: 0.8801 (tp-100) cc_final: 0.8350 (tp40) REVERT: l 1729 MET cc_start: 0.8124 (ptm) cc_final: 0.6919 (mmm) REVERT: l 1737 LYS cc_start: 0.8646 (mtmm) cc_final: 0.8394 (mtpp) REVERT: l 1742 TYR cc_start: 0.8501 (p90) cc_final: 0.7666 (p90) REVERT: l 1752 MET cc_start: 0.9085 (ppp) cc_final: 0.8409 (ppp) REVERT: l 1780 MET cc_start: 0.8605 (tpt) cc_final: 0.8145 (tpp) REVERT: l 1861 GLN cc_start: 0.8914 (mp10) cc_final: 0.8582 (mp10) REVERT: l 1885 ILE cc_start: 0.9230 (mm) cc_final: 0.8985 (mm) REVERT: l 1897 ASN cc_start: 0.9034 (t0) cc_final: 0.8828 (t0) REVERT: l 1898 LYS cc_start: 0.8625 (tptp) cc_final: 0.8338 (tptp) REVERT: l 1903 GLU cc_start: 0.4605 (tt0) cc_final: 0.4370 (tt0) REVERT: m 1729 MET cc_start: 0.8501 (ptm) cc_final: 0.7283 (tpt) REVERT: m 1736 THR cc_start: 0.9278 (OUTLIER) cc_final: 0.8847 (t) REVERT: m 1752 MET cc_start: 0.9169 (ppp) cc_final: 0.8793 (ppp) REVERT: m 1783 GLU cc_start: 0.8453 (pm20) cc_final: 0.8179 (pm20) REVERT: m 1857 GLN cc_start: 0.8990 (tp40) cc_final: 0.8201 (tp-100) REVERT: m 1861 GLN cc_start: 0.8853 (mp-120) cc_final: 0.8456 (mp10) REVERT: m 1886 ASP cc_start: 0.8207 (t0) cc_final: 0.7623 (t0) REVERT: n 1729 MET cc_start: 0.8313 (ptm) cc_final: 0.6881 (mmt) REVERT: n 1742 TYR cc_start: 0.8570 (p90) cc_final: 0.7398 (p90) REVERT: n 1752 MET cc_start: 0.8720 (ppp) cc_final: 0.8165 (ptt) REVERT: n 1894 LYS cc_start: 0.8809 (ptmt) cc_final: 0.8495 (pttm) REVERT: o 1729 MET cc_start: 0.7797 (ptm) cc_final: 0.6648 (mmt) REVERT: o 1736 THR cc_start: 0.9435 (OUTLIER) cc_final: 0.9196 (t) REVERT: o 1752 MET cc_start: 0.9268 (ppp) cc_final: 0.8900 (ppp) REVERT: o 1780 MET cc_start: 0.8198 (tpp) cc_final: 0.7834 (mmm) REVERT: o 1783 GLU cc_start: 0.8392 (pm20) cc_final: 0.7466 (pm20) REVERT: o 1795 MET cc_start: 0.7717 (ptm) cc_final: 0.7494 (ptm) REVERT: o 1810 PHE cc_start: 0.7258 (p90) cc_final: 0.6984 (p90) REVERT: o 1870 TYR cc_start: 0.8508 (m-80) cc_final: 0.8086 (m-10) REVERT: o 1886 ASP cc_start: 0.8110 (t0) cc_final: 0.7864 (t0) outliers start: 147 outliers final: 104 residues processed: 737 average time/residue: 0.2783 time to fit residues: 329.2066 Evaluate side-chains 702 residues out of total 2338 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 112 poor density : 590 time to evaluate : 2.412 ------------------------------------------------------------------------------- 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 1698 ILE Chi-restraints excluded: chain b residue 1700 ILE Chi-restraints excluded: chain b residue 1709 THR Chi-restraints excluded: chain b residue 1710 LEU Chi-restraints excluded: chain b residue 1755 LEU Chi-restraints excluded: chain b residue 1781 LEU Chi-restraints excluded: chain b residue 1790 VAL Chi-restraints excluded: chain b residue 1873 GLU 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 1795 MET Chi-restraints excluded: chain c residue 1856 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 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 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 g residue 1755 LEU Chi-restraints excluded: chain g residue 1790 VAL Chi-restraints excluded: chain g residue 1865 ILE 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 1730 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 1776 GLN 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 1737 LYS 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 j residue 1857 GLN 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 1790 VAL Chi-restraints excluded: chain k residue 1811 LEU Chi-restraints excluded: chain k residue 1854 MET 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 1683 ILE Chi-restraints excluded: chain l residue 1703 THR Chi-restraints excluded: chain l residue 1736 THR Chi-restraints excluded: chain l residue 1776 GLN 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 1700 ILE Chi-restraints excluded: chain m residue 1707 ASP 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 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 1883 ASP Chi-restraints excluded: chain o residue 1698 ILE 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 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 Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 266 random chunks: chunk 86 optimal weight: 4.9990 chunk 231 optimal weight: 0.9990 chunk 50 optimal weight: 0.7980 chunk 150 optimal weight: 3.9990 chunk 63 optimal weight: 5.9990 chunk 257 optimal weight: 0.8980 chunk 213 optimal weight: 0.6980 chunk 119 optimal weight: 0.9980 chunk 21 optimal weight: 10.0000 chunk 85 optimal weight: 0.8980 chunk 135 optimal weight: 0.8980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** c1853 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** d1680 GLN g1897 ASN k1680 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8236 moved from start: 0.4187 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 21238 Z= 0.208 Angle : 0.657 11.129 28784 Z= 0.338 Chirality : 0.049 0.166 3486 Planarity : 0.004 0.037 3612 Dihedral : 5.895 35.265 2885 Min Nonbonded Distance : 2.547 Molprobity Statistics. All-atom Clashscore : 10.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.01 % Favored : 89.99 % Rotamer: Outliers : 5.90 % Allowed : 22.46 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.07 (0.16), residues: 2716 helix: -3.59 (0.19), residues: 406 sheet: -1.99 (0.18), residues: 812 loop : -1.52 (0.16), residues: 1498 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP e1723 HIS 0.002 0.000 HIS i1793 PHE 0.027 0.001 PHE n1810 TYR 0.022 0.002 TYR h1695 ARG 0.002 0.000 ARG g1754 *********************** 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 743 residues out of total 2338 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 138 poor density : 605 time to evaluate : 2.562 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: b 1710 LEU cc_start: 0.9112 (OUTLIER) cc_final: 0.8648 (pp) REVERT: b 1715 SER cc_start: 0.9074 (t) cc_final: 0.8812 (m) REVERT: b 1729 MET cc_start: 0.8142 (ptm) cc_final: 0.6812 (mmt) REVERT: b 1734 LYS cc_start: 0.6793 (ttpt) cc_final: 0.6364 (pttm) REVERT: b 1752 MET cc_start: 0.9145 (ppp) cc_final: 0.8421 (ppp) REVERT: b 1781 LEU cc_start: 0.7089 (OUTLIER) cc_final: 0.6869 (tt) REVERT: b 1783 GLU cc_start: 0.8150 (pm20) cc_final: 0.7899 (pm20) REVERT: b 1857 GLN cc_start: 0.8968 (tp-100) cc_final: 0.8635 (tp40) REVERT: b 1886 ASP cc_start: 0.8469 (t0) cc_final: 0.8054 (t70) REVERT: b 1902 ASP cc_start: 0.8850 (t0) cc_final: 0.8411 (t70) REVERT: c 1715 SER cc_start: 0.9267 (t) cc_final: 0.8988 (m) REVERT: c 1729 MET cc_start: 0.8407 (ptm) cc_final: 0.7084 (mmm) REVERT: c 1742 TYR cc_start: 0.8462 (p90) cc_final: 0.7757 (p90) REVERT: c 1862 LEU cc_start: 0.9269 (OUTLIER) cc_final: 0.8933 (mt) REVERT: c 1885 ILE cc_start: 0.9280 (mm) cc_final: 0.8949 (mm) REVERT: c 1886 ASP cc_start: 0.8072 (t0) cc_final: 0.7641 (t0) REVERT: c 1902 ASP cc_start: 0.8817 (t0) cc_final: 0.8312 (t70) REVERT: c 1903 GLU cc_start: 0.7618 (tm-30) cc_final: 0.7190 (tm-30) REVERT: d 1729 MET cc_start: 0.8350 (ptm) cc_final: 0.7213 (mmt) REVERT: d 1737 LYS cc_start: 0.8651 (mtmm) cc_final: 0.8216 (mtpt) REVERT: d 1752 MET cc_start: 0.9162 (ppp) cc_final: 0.8684 (ptt) REVERT: d 1766 ASP cc_start: 0.8751 (m-30) cc_final: 0.8494 (m-30) REVERT: d 1857 GLN cc_start: 0.8782 (tp-100) cc_final: 0.8284 (tp40) REVERT: d 1861 GLN cc_start: 0.8748 (mp10) cc_final: 0.8421 (mp10) REVERT: d 1886 ASP cc_start: 0.8200 (t0) cc_final: 0.7928 (t0) REVERT: e 1707 ASP cc_start: 0.7992 (p0) cc_final: 0.7613 (p0) REVERT: e 1729 MET cc_start: 0.8767 (ptm) cc_final: 0.7315 (mmt) REVERT: e 1734 LYS cc_start: 0.7090 (ttpt) cc_final: 0.6393 (pttp) REVERT: e 1783 GLU cc_start: 0.8279 (pm20) cc_final: 0.8031 (pm20) REVERT: e 1810 PHE cc_start: 0.7039 (p90) cc_final: 0.6769 (p90) REVERT: e 1886 ASP cc_start: 0.8515 (t0) cc_final: 0.8047 (t0) REVERT: e 1894 LYS cc_start: 0.8759 (ptmt) cc_final: 0.8439 (pttm) REVERT: e 1902 ASP cc_start: 0.8809 (t0) cc_final: 0.8498 (t70) REVERT: f 1707 ASP cc_start: 0.8273 (t0) cc_final: 0.7619 (t0) REVERT: f 1709 THR cc_start: 0.9173 (p) cc_final: 0.8801 (p) REVERT: f 1729 MET cc_start: 0.8054 (ptm) cc_final: 0.7007 (tpt) REVERT: f 1737 LYS cc_start: 0.8800 (mtmm) cc_final: 0.8066 (mtpp) REVERT: f 1739 TYR cc_start: 0.8689 (m-80) cc_final: 0.7734 (m-80) REVERT: f 1742 TYR cc_start: 0.8463 (p90) cc_final: 0.7754 (p90) REVERT: f 1752 MET cc_start: 0.8842 (ppp) cc_final: 0.8167 (ppp) REVERT: f 1766 ASP cc_start: 0.8917 (m-30) cc_final: 0.8490 (m-30) REVERT: f 1776 GLN cc_start: 0.7826 (tt0) cc_final: 0.7184 (tm-30) REVERT: f 1783 GLU cc_start: 0.8402 (pm20) cc_final: 0.8185 (pm20) REVERT: f 1857 GLN cc_start: 0.9096 (tp-100) cc_final: 0.8489 (tp40) REVERT: f 1861 GLN cc_start: 0.8948 (mp10) cc_final: 0.8462 (mp10) REVERT: f 1863 MET cc_start: 0.8907 (tpp) cc_final: 0.8690 (tpp) REVERT: f 1886 ASP cc_start: 0.8411 (t0) cc_final: 0.8101 (t0) REVERT: f 1902 ASP cc_start: 0.8560 (t70) cc_final: 0.7819 (t70) REVERT: g 1729 MET cc_start: 0.8290 (ptm) cc_final: 0.6913 (mmt) REVERT: g 1737 LYS cc_start: 0.8795 (mtmm) cc_final: 0.8093 (mtpp) REVERT: g 1752 MET cc_start: 0.8913 (ppp) cc_final: 0.8025 (ptt) REVERT: g 1766 ASP cc_start: 0.8428 (m-30) cc_final: 0.8186 (m-30) REVERT: g 1780 MET cc_start: 0.8213 (tpt) cc_final: 0.7842 (tpp) REVERT: g 1885 ILE cc_start: 0.9503 (mm) cc_final: 0.9132 (mm) REVERT: g 1894 LYS cc_start: 0.8652 (ptmt) cc_final: 0.8289 (pttm) REVERT: h 1729 MET cc_start: 0.7536 (ptm) cc_final: 0.6626 (tpt) REVERT: h 1736 THR cc_start: 0.9312 (OUTLIER) cc_final: 0.9090 (t) REVERT: h 1752 MET cc_start: 0.9141 (ppp) cc_final: 0.8207 (ppp) REVERT: h 1870 TYR cc_start: 0.8289 (m-10) cc_final: 0.7978 (m-10) REVERT: h 1886 ASP cc_start: 0.8034 (p0) cc_final: 0.7771 (p0) REVERT: h 1903 GLU cc_start: 0.4364 (tt0) cc_final: 0.3864 (mt-10) REVERT: i 1707 ASP cc_start: 0.7843 (p0) cc_final: 0.7009 (p0) REVERT: i 1729 MET cc_start: 0.8304 (ptm) cc_final: 0.7265 (tpt) REVERT: i 1742 TYR cc_start: 0.8502 (p90) cc_final: 0.7703 (p90) REVERT: i 1752 MET cc_start: 0.8841 (ppp) cc_final: 0.8012 (ppp) REVERT: i 1756 MET cc_start: 0.8985 (tpt) cc_final: 0.8576 (tpt) REVERT: i 1780 MET cc_start: 0.7985 (mmm) cc_final: 0.7784 (mmm) REVERT: i 1810 PHE cc_start: 0.8022 (p90) cc_final: 0.7248 (p90) REVERT: i 1857 GLN cc_start: 0.9207 (tp-100) cc_final: 0.8540 (tp40) REVERT: i 1861 GLN cc_start: 0.8837 (mp10) cc_final: 0.8444 (mp10) REVERT: i 1886 ASP cc_start: 0.8316 (t0) cc_final: 0.8089 (t0) REVERT: i 1902 ASP cc_start: 0.8730 (t0) cc_final: 0.8337 (t70) REVERT: j 1707 ASP cc_start: 0.7583 (p0) cc_final: 0.7012 (p0) REVERT: j 1729 MET cc_start: 0.8733 (ptm) cc_final: 0.7342 (mmt) REVERT: j 1737 LYS cc_start: 0.8902 (mtmm) cc_final: 0.8514 (mmmm) REVERT: j 1752 MET cc_start: 0.9144 (ppp) cc_final: 0.8669 (ppp) REVERT: j 1756 MET cc_start: 0.9177 (tpt) cc_final: 0.8845 (tpt) REVERT: j 1776 GLN cc_start: 0.8219 (tt0) cc_final: 0.7714 (tt0) REVERT: j 1780 MET cc_start: 0.8409 (tpt) cc_final: 0.7841 (tpp) REVERT: j 1783 GLU cc_start: 0.8333 (pm20) cc_final: 0.8002 (pm20) REVERT: j 1870 TYR cc_start: 0.8204 (m-80) cc_final: 0.7889 (m-80) REVERT: j 1894 LYS cc_start: 0.8854 (ptmt) cc_final: 0.8573 (pttm) REVERT: j 1902 ASP cc_start: 0.8519 (t70) cc_final: 0.8029 (t70) REVERT: k 1715 SER cc_start: 0.9530 (t) cc_final: 0.9326 (m) REVERT: k 1729 MET cc_start: 0.8309 (ptm) cc_final: 0.7166 (mmt) REVERT: k 1752 MET cc_start: 0.9081 (ppp) cc_final: 0.8703 (ptt) REVERT: k 1766 ASP cc_start: 0.8747 (m-30) cc_final: 0.8502 (m-30) REVERT: k 1789 TYR cc_start: 0.7798 (t80) cc_final: 0.7503 (m-10) REVERT: k 1857 GLN cc_start: 0.8658 (tp-100) cc_final: 0.8219 (tp40) REVERT: k 1886 ASP cc_start: 0.8245 (t0) cc_final: 0.8020 (t0) REVERT: l 1707 ASP cc_start: 0.7960 (t0) cc_final: 0.7112 (t0) REVERT: l 1729 MET cc_start: 0.8079 (ptm) cc_final: 0.6898 (mmm) REVERT: l 1737 LYS cc_start: 0.8637 (mtmm) cc_final: 0.8403 (mtpp) REVERT: l 1742 TYR cc_start: 0.8278 (p90) cc_final: 0.7697 (p90) REVERT: l 1743 GLN cc_start: 0.7742 (mm-40) cc_final: 0.7540 (mm-40) REVERT: l 1780 MET cc_start: 0.8549 (tpt) cc_final: 0.8228 (tpp) REVERT: l 1861 GLN cc_start: 0.8861 (mp10) cc_final: 0.8531 (mp10) REVERT: l 1885 ILE cc_start: 0.9178 (mm) cc_final: 0.8899 (mm) REVERT: l 1898 LYS cc_start: 0.8634 (tptp) cc_final: 0.8305 (tptp) REVERT: m 1729 MET cc_start: 0.8482 (ptm) cc_final: 0.7305 (tpt) REVERT: m 1736 THR cc_start: 0.9231 (OUTLIER) cc_final: 0.8803 (t) REVERT: m 1752 MET cc_start: 0.9188 (ppp) cc_final: 0.8836 (ppp) REVERT: m 1783 GLU cc_start: 0.8452 (pm20) cc_final: 0.8135 (pm20) REVERT: m 1857 GLN cc_start: 0.9005 (tp40) cc_final: 0.8293 (tp-100) REVERT: m 1861 GLN cc_start: 0.8870 (mp-120) cc_final: 0.8432 (mp10) REVERT: n 1707 ASP cc_start: 0.8211 (p0) cc_final: 0.7894 (p0) REVERT: n 1729 MET cc_start: 0.8292 (ptm) cc_final: 0.6882 (mmt) REVERT: n 1752 MET cc_start: 0.8715 (ppp) cc_final: 0.8108 (ptt) REVERT: n 1886 ASP cc_start: 0.8308 (t0) cc_final: 0.8044 (t0) REVERT: n 1894 LYS cc_start: 0.8760 (ptmt) cc_final: 0.8482 (pttm) REVERT: o 1729 MET cc_start: 0.7769 (ptm) cc_final: 0.6640 (mmt) REVERT: o 1736 THR cc_start: 0.9391 (OUTLIER) cc_final: 0.9172 (t) REVERT: o 1752 MET cc_start: 0.9240 (ppp) cc_final: 0.8878 (ppp) REVERT: o 1781 LEU cc_start: 0.9152 (tt) cc_final: 0.8938 (tt) REVERT: o 1783 GLU cc_start: 0.8403 (pm20) cc_final: 0.7472 (pm20) REVERT: o 1795 MET cc_start: 0.7688 (ptm) cc_final: 0.7411 (ptt) REVERT: o 1853 GLN cc_start: 0.8010 (pp30) cc_final: 0.7786 (pp30) REVERT: o 1870 TYR cc_start: 0.8527 (m-80) cc_final: 0.8122 (m-10) REVERT: o 1886 ASP cc_start: 0.8074 (t0) cc_final: 0.7804 (t0) outliers start: 138 outliers final: 99 residues processed: 708 average time/residue: 0.2790 time to fit residues: 315.0489 Evaluate side-chains 691 residues out of total 2338 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 105 poor density : 586 time to evaluate : 2.407 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain b residue 1683 ILE Chi-restraints excluded: chain b residue 1699 GLU Chi-restraints excluded: chain b residue 1700 ILE Chi-restraints excluded: chain b residue 1710 LEU Chi-restraints excluded: chain b residue 1755 LEU Chi-restraints excluded: chain b residue 1781 LEU Chi-restraints excluded: chain b residue 1811 LEU Chi-restraints excluded: chain b residue 1873 GLU 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 1795 MET Chi-restraints excluded: chain c residue 1862 LEU Chi-restraints excluded: chain c residue 1876 SER 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 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 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 f residue 1896 THR Chi-restraints excluded: chain g residue 1700 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 1883 ASP Chi-restraints excluded: chain h residue 1700 ILE Chi-restraints excluded: chain h residue 1715 SER Chi-restraints excluded: chain h residue 1730 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 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 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 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 1790 VAL Chi-restraints excluded: chain k residue 1811 LEU Chi-restraints excluded: chain k residue 1854 MET 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 1715 SER Chi-restraints excluded: chain l residue 1736 THR Chi-restraints excluded: chain l residue 1776 GLN 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 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 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 1683 ILE Chi-restraints excluded: chain o residue 1700 ILE Chi-restraints excluded: chain o residue 1736 THR Chi-restraints excluded: chain o residue 1755 LEU Chi-restraints excluded: chain o residue 1760 THR Chi-restraints excluded: chain o residue 1790 VAL Chi-restraints excluded: chain o residue 1811 LEU Chi-restraints excluded: chain o residue 1873 GLU Chi-restraints excluded: chain o residue 1883 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 266 random chunks: chunk 248 optimal weight: 2.9990 chunk 29 optimal weight: 6.9990 chunk 146 optimal weight: 0.9990 chunk 187 optimal weight: 2.9990 chunk 145 optimal weight: 0.7980 chunk 216 optimal weight: 0.9980 chunk 143 optimal weight: 5.9990 chunk 256 optimal weight: 4.9990 chunk 160 optimal weight: 0.8980 chunk 156 optimal weight: 1.9990 chunk 118 optimal weight: 0.8980 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: b1864 ASN g1897 ASN k1680 GLN l1897 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8236 moved from start: 0.4376 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= 0.216 Angle : 0.666 14.534 28784 Z= 0.342 Chirality : 0.049 0.166 3486 Planarity : 0.004 0.037 3612 Dihedral : 5.766 35.062 2885 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 10.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.82 % Favored : 89.18 % Rotamer: Outliers : 5.73 % Allowed : 22.97 % Favored : 71.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.53 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.97 (0.16), residues: 2716 helix: -3.42 (0.20), residues: 392 sheet: -1.93 (0.18), residues: 812 loop : -1.52 (0.16), residues: 1512 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP g1723 HIS 0.002 0.000 HIS l1793 PHE 0.034 0.001 PHE n1810 TYR 0.021 0.001 TYR h1695 ARG 0.002 0.000 ARG g1754 *********************** 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 734 residues out of total 2338 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 134 poor density : 600 time to evaluate : 2.512 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: b 1689 THR cc_start: 0.9603 (OUTLIER) cc_final: 0.9333 (t) REVERT: b 1710 LEU cc_start: 0.9102 (OUTLIER) cc_final: 0.8575 (pp) REVERT: b 1729 MET cc_start: 0.8147 (ptm) cc_final: 0.6770 (mmt) REVERT: b 1734 LYS cc_start: 0.6792 (ttpt) cc_final: 0.6384 (pttm) REVERT: b 1737 LYS cc_start: 0.8153 (mptt) cc_final: 0.7574 (mmmm) REVERT: b 1752 MET cc_start: 0.9188 (ppp) cc_final: 0.8437 (ppp) REVERT: b 1780 MET cc_start: 0.7514 (tpp) cc_final: 0.5814 (tmm) REVERT: b 1857 GLN cc_start: 0.8934 (tp-100) cc_final: 0.8573 (tp40) REVERT: b 1886 ASP cc_start: 0.8455 (t0) cc_final: 0.8025 (t70) REVERT: b 1902 ASP cc_start: 0.8796 (t0) cc_final: 0.8389 (t70) REVERT: c 1715 SER cc_start: 0.9218 (t) cc_final: 0.8964 (m) REVERT: c 1729 MET cc_start: 0.8415 (ptm) cc_final: 0.7084 (mmm) REVERT: c 1737 LYS cc_start: 0.7598 (mptt) cc_final: 0.7392 (mmtt) REVERT: c 1742 TYR cc_start: 0.8497 (p90) cc_final: 0.7815 (p90) REVERT: c 1795 MET cc_start: 0.7698 (OUTLIER) cc_final: 0.7291 (ptm) REVERT: c 1854 MET cc_start: 0.8876 (tpp) cc_final: 0.8627 (mmm) REVERT: c 1885 ILE cc_start: 0.9292 (mm) cc_final: 0.8967 (mm) REVERT: c 1886 ASP cc_start: 0.8053 (t0) cc_final: 0.7597 (t0) REVERT: c 1902 ASP cc_start: 0.8791 (t0) cc_final: 0.8322 (t70) REVERT: d 1707 ASP cc_start: 0.8101 (t0) cc_final: 0.7882 (t0) REVERT: d 1729 MET cc_start: 0.8347 (ptm) cc_final: 0.7216 (mmt) REVERT: d 1737 LYS cc_start: 0.8716 (mtmm) cc_final: 0.8251 (mtpt) REVERT: d 1752 MET cc_start: 0.9125 (ppp) cc_final: 0.8358 (ptt) REVERT: d 1766 ASP cc_start: 0.8744 (m-30) cc_final: 0.8495 (m-30) REVERT: d 1776 GLN cc_start: 0.8025 (tt0) cc_final: 0.7778 (tt0) REVERT: d 1795 MET cc_start: 0.8140 (ptm) cc_final: 0.7862 (ptm) REVERT: d 1857 GLN cc_start: 0.8718 (tp-100) cc_final: 0.8181 (tp40) REVERT: d 1861 GLN cc_start: 0.8734 (mp10) cc_final: 0.8336 (mp10) REVERT: d 1897 ASN cc_start: 0.9083 (t0) cc_final: 0.8518 (t0) REVERT: e 1707 ASP cc_start: 0.7814 (p0) cc_final: 0.7341 (p0) REVERT: e 1729 MET cc_start: 0.8764 (ptm) cc_final: 0.7318 (mmt) REVERT: e 1734 LYS cc_start: 0.6987 (ttpt) cc_final: 0.6322 (pttp) REVERT: e 1752 MET cc_start: 0.9041 (ppp) cc_final: 0.8520 (ppp) REVERT: e 1780 MET cc_start: 0.8355 (tpt) cc_final: 0.7874 (tpp) REVERT: e 1783 GLU cc_start: 0.8299 (pm20) cc_final: 0.8022 (pm20) REVERT: e 1810 PHE cc_start: 0.7046 (p90) cc_final: 0.6727 (p90) REVERT: e 1884 ASP cc_start: 0.8169 (m-30) cc_final: 0.7940 (m-30) REVERT: e 1886 ASP cc_start: 0.8500 (t0) cc_final: 0.8049 (t0) REVERT: e 1894 LYS cc_start: 0.8756 (ptmt) cc_final: 0.8456 (pttm) REVERT: e 1902 ASP cc_start: 0.8823 (t0) cc_final: 0.8519 (t70) REVERT: f 1707 ASP cc_start: 0.8179 (t0) cc_final: 0.7608 (t0) REVERT: f 1709 THR cc_start: 0.9181 (p) cc_final: 0.8860 (p) REVERT: f 1729 MET cc_start: 0.8028 (ptm) cc_final: 0.6995 (tpt) REVERT: f 1734 LYS cc_start: 0.6841 (ttpt) cc_final: 0.6549 (ttpt) REVERT: f 1737 LYS cc_start: 0.8798 (mtmm) cc_final: 0.8027 (mtpp) REVERT: f 1739 TYR cc_start: 0.8699 (m-80) cc_final: 0.7809 (m-80) REVERT: f 1742 TYR cc_start: 0.8483 (p90) cc_final: 0.7775 (p90) REVERT: f 1766 ASP cc_start: 0.8931 (m-30) cc_final: 0.8487 (m-30) REVERT: f 1776 GLN cc_start: 0.7882 (tt0) cc_final: 0.7169 (tm-30) REVERT: f 1857 GLN cc_start: 0.9067 (tp-100) cc_final: 0.8461 (tp40) REVERT: f 1861 GLN cc_start: 0.8931 (mp10) cc_final: 0.8437 (mp10) REVERT: f 1886 ASP cc_start: 0.8424 (t0) cc_final: 0.8109 (t0) REVERT: f 1902 ASP cc_start: 0.8493 (t70) cc_final: 0.7730 (t70) REVERT: g 1729 MET cc_start: 0.8295 (ptm) cc_final: 0.6896 (mmt) REVERT: g 1885 ILE cc_start: 0.9487 (mm) cc_final: 0.9092 (mm) REVERT: g 1894 LYS cc_start: 0.8643 (ptmt) cc_final: 0.8281 (pttm) REVERT: h 1729 MET cc_start: 0.7574 (ptm) cc_final: 0.6622 (tpt) REVERT: h 1736 THR cc_start: 0.9335 (OUTLIER) cc_final: 0.9094 (t) REVERT: h 1752 MET cc_start: 0.9070 (ppp) cc_final: 0.8397 (ppp) REVERT: h 1783 GLU cc_start: 0.8510 (pm20) cc_final: 0.8144 (pm20) REVERT: h 1791 ASN cc_start: 0.8929 (t0) cc_final: 0.8447 (t0) REVERT: h 1870 TYR cc_start: 0.8270 (m-10) cc_final: 0.7970 (m-10) REVERT: h 1886 ASP cc_start: 0.8013 (p0) cc_final: 0.7794 (p0) REVERT: h 1903 GLU cc_start: 0.4503 (tt0) cc_final: 0.3766 (mt-10) REVERT: i 1707 ASP cc_start: 0.7954 (p0) cc_final: 0.7231 (p0) REVERT: i 1729 MET cc_start: 0.8252 (ptm) cc_final: 0.7283 (tpt) REVERT: i 1742 TYR cc_start: 0.8612 (p90) cc_final: 0.7961 (p90) REVERT: i 1752 MET cc_start: 0.8852 (ppp) cc_final: 0.8350 (ppp) REVERT: i 1756 MET cc_start: 0.8964 (tpt) cc_final: 0.8608 (tpt) REVERT: i 1766 ASP cc_start: 0.8724 (m-30) cc_final: 0.8163 (m-30) REVERT: i 1780 MET cc_start: 0.8072 (mmm) cc_final: 0.7742 (mmm) REVERT: i 1810 PHE cc_start: 0.8028 (p90) cc_final: 0.7312 (p90) REVERT: i 1857 GLN cc_start: 0.9136 (tp-100) cc_final: 0.8623 (tp40) REVERT: i 1861 GLN cc_start: 0.8849 (mp10) cc_final: 0.8456 (mp10) REVERT: i 1886 ASP cc_start: 0.8330 (t0) cc_final: 0.8090 (t0) REVERT: i 1902 ASP cc_start: 0.8689 (t0) cc_final: 0.8332 (t70) REVERT: j 1707 ASP cc_start: 0.7790 (p0) cc_final: 0.7244 (p0) REVERT: j 1729 MET cc_start: 0.8731 (ptm) cc_final: 0.7341 (mmt) REVERT: j 1737 LYS cc_start: 0.8892 (mtmm) cc_final: 0.8527 (mmmm) REVERT: j 1752 MET cc_start: 0.9200 (ppp) cc_final: 0.8733 (ppp) REVERT: j 1756 MET cc_start: 0.9253 (tpt) cc_final: 0.8927 (tpt) REVERT: j 1776 GLN cc_start: 0.8200 (tt0) cc_final: 0.7674 (tt0) REVERT: j 1780 MET cc_start: 0.8394 (tpt) cc_final: 0.7884 (tpp) REVERT: j 1783 GLU cc_start: 0.8377 (pm20) cc_final: 0.8025 (pm20) REVERT: j 1870 TYR cc_start: 0.8160 (m-80) cc_final: 0.7843 (m-80) REVERT: j 1894 LYS cc_start: 0.8852 (ptmt) cc_final: 0.8586 (pttm) REVERT: j 1902 ASP cc_start: 0.8547 (t70) cc_final: 0.8064 (t70) REVERT: k 1729 MET cc_start: 0.8316 (ptm) cc_final: 0.7170 (mmt) REVERT: k 1737 LYS cc_start: 0.8703 (mtmm) cc_final: 0.8196 (mtpp) REVERT: k 1752 MET cc_start: 0.9038 (ppp) cc_final: 0.8463 (ppp) REVERT: k 1766 ASP cc_start: 0.8742 (m-30) cc_final: 0.8470 (m-30) REVERT: k 1789 TYR cc_start: 0.7785 (t80) cc_final: 0.7510 (m-10) REVERT: k 1857 GLN cc_start: 0.8591 (tp-100) cc_final: 0.8190 (tp40) REVERT: l 1729 MET cc_start: 0.8086 (ptm) cc_final: 0.6897 (mmm) REVERT: l 1737 LYS cc_start: 0.8765 (mtmm) cc_final: 0.8497 (mtpp) REVERT: l 1742 TYR cc_start: 0.8427 (p90) cc_final: 0.7714 (p90) REVERT: l 1752 MET cc_start: 0.9071 (ppp) cc_final: 0.8343 (ppp) REVERT: l 1780 MET cc_start: 0.8552 (tpt) cc_final: 0.8205 (tpp) REVERT: l 1795 MET cc_start: 0.7504 (ptm) cc_final: 0.7246 (ptm) REVERT: l 1861 GLN cc_start: 0.8862 (mp10) cc_final: 0.8462 (mp10) REVERT: l 1885 ILE cc_start: 0.9177 (mm) cc_final: 0.8946 (mm) REVERT: l 1898 LYS cc_start: 0.8578 (tptp) cc_final: 0.8286 (tptp) REVERT: m 1729 MET cc_start: 0.8495 (ptm) cc_final: 0.7247 (tpt) REVERT: m 1736 THR cc_start: 0.9207 (OUTLIER) cc_final: 0.8673 (t) REVERT: m 1752 MET cc_start: 0.9214 (ppp) cc_final: 0.8834 (ppp) REVERT: m 1783 GLU cc_start: 0.8464 (pm20) cc_final: 0.8152 (pm20) REVERT: m 1857 GLN cc_start: 0.9062 (tp40) cc_final: 0.8327 (tp-100) REVERT: m 1861 GLN cc_start: 0.8878 (mp-120) cc_final: 0.8445 (mp10) REVERT: m 1886 ASP cc_start: 0.7698 (t0) cc_final: 0.7277 (t0) REVERT: m 1888 SER cc_start: 0.8716 (p) cc_final: 0.8439 (m) REVERT: n 1707 ASP cc_start: 0.7811 (p0) cc_final: 0.7555 (p0) REVERT: n 1729 MET cc_start: 0.8297 (ptm) cc_final: 0.6901 (mmt) REVERT: n 1752 MET cc_start: 0.8726 (ppp) cc_final: 0.8171 (ptt) REVERT: n 1894 LYS cc_start: 0.8766 (ptmt) cc_final: 0.8501 (pttm) REVERT: o 1729 MET cc_start: 0.7642 (ptm) cc_final: 0.6567 (mmt) REVERT: o 1736 THR cc_start: 0.9404 (OUTLIER) cc_final: 0.9143 (t) REVERT: o 1752 MET cc_start: 0.9229 (ppp) cc_final: 0.8908 (ppp) REVERT: o 1783 GLU cc_start: 0.8415 (pm20) cc_final: 0.7473 (pm20) REVERT: o 1795 MET cc_start: 0.7700 (ptm) cc_final: 0.7491 (ptm) REVERT: o 1870 TYR cc_start: 0.8504 (m-80) cc_final: 0.8082 (m-10) REVERT: o 1886 ASP cc_start: 0.8020 (t0) cc_final: 0.7718 (t0) REVERT: o 1902 ASP cc_start: 0.8046 (t70) cc_final: 0.7643 (t70) outliers start: 134 outliers final: 102 residues processed: 697 average time/residue: 0.2822 time to fit residues: 314.6495 Evaluate side-chains 688 residues out of total 2338 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 108 poor density : 580 time to evaluate : 2.425 ------------------------------------------------------------------------------- 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 1710 LEU Chi-restraints excluded: chain b residue 1755 LEU Chi-restraints excluded: chain b residue 1811 LEU Chi-restraints excluded: chain b residue 1873 GLU 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 1795 MET Chi-restraints excluded: chain c residue 1856 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 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 1755 LEU Chi-restraints excluded: chain e residue 1790 VAL Chi-restraints excluded: chain e residue 1795 MET 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 1756 MET 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 1700 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 1883 ASP Chi-restraints excluded: chain h residue 1700 ILE Chi-restraints excluded: chain h residue 1715 SER Chi-restraints excluded: chain h residue 1730 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 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 1755 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 1790 VAL Chi-restraints excluded: chain k residue 1811 LEU Chi-restraints excluded: chain k residue 1854 MET 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 1683 ILE Chi-restraints excluded: chain l residue 1703 THR Chi-restraints excluded: chain l residue 1736 THR Chi-restraints excluded: chain l residue 1776 GLN 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 1700 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 1811 LEU Chi-restraints excluded: chain m residue 1865 ILE Chi-restraints excluded: chain n residue 1683 ILE Chi-restraints excluded: chain n residue 1698 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 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 1683 ILE 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 1760 THR 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 158 optimal weight: 0.6980 chunk 102 optimal weight: 0.9980 chunk 153 optimal weight: 0.8980 chunk 77 optimal weight: 0.3980 chunk 50 optimal weight: 4.9990 chunk 49 optimal weight: 1.9990 chunk 162 optimal weight: 6.9990 chunk 174 optimal weight: 3.9990 chunk 126 optimal weight: 4.9990 chunk 23 optimal weight: 0.4980 chunk 201 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: g1897 ASN k1680 GLN ** m1776 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** n1743 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8216 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 0.038 21238 Z= 0.200 Angle : 0.665 13.353 28784 Z= 0.340 Chirality : 0.048 0.168 3486 Planarity : 0.004 0.039 3612 Dihedral : 5.577 34.873 2885 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 10.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.94 % Favored : 90.06 % Rotamer: Outliers : 5.47 % Allowed : 23.61 % Favored : 70.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.53 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.92 (0.16), residues: 2716 helix: -3.48 (0.21), residues: 392 sheet: -1.88 (0.18), residues: 826 loop : -1.44 (0.16), residues: 1498 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP g1723 HIS 0.002 0.000 HIS l1793 PHE 0.030 0.001 PHE n1810 TYR 0.019 0.001 TYR h1695 ARG 0.001 0.000 ARG g1754 *********************** 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 707 residues out of total 2338 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 128 poor density : 579 time to evaluate : 2.490 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: b 1689 THR cc_start: 0.9589 (OUTLIER) cc_final: 0.9352 (t) REVERT: b 1710 LEU cc_start: 0.9043 (OUTLIER) cc_final: 0.8500 (pp) REVERT: b 1729 MET cc_start: 0.8150 (ptm) cc_final: 0.6791 (mmt) REVERT: b 1734 LYS cc_start: 0.6784 (ttpt) cc_final: 0.6353 (pttm) REVERT: b 1737 LYS cc_start: 0.8142 (mptt) cc_final: 0.7568 (mmmm) REVERT: b 1752 MET cc_start: 0.9155 (ppp) cc_final: 0.8379 (ppp) REVERT: b 1780 MET cc_start: 0.7151 (tpp) cc_final: 0.5467 (tmm) REVERT: b 1783 GLU cc_start: 0.8050 (pm20) cc_final: 0.7646 (pm20) REVERT: b 1857 GLN cc_start: 0.8979 (tp-100) cc_final: 0.8550 (tp40) REVERT: b 1886 ASP cc_start: 0.8419 (t0) cc_final: 0.7916 (t70) REVERT: b 1902 ASP cc_start: 0.8777 (t0) cc_final: 0.8397 (t70) REVERT: c 1715 SER cc_start: 0.9121 (t) cc_final: 0.8858 (m) REVERT: c 1729 MET cc_start: 0.8390 (ptm) cc_final: 0.7103 (mmm) REVERT: c 1742 TYR cc_start: 0.8443 (p90) cc_final: 0.7691 (p90) REVERT: c 1752 MET cc_start: 0.9073 (ppp) cc_final: 0.8330 (ppp) REVERT: c 1756 MET cc_start: 0.8799 (tpt) cc_final: 0.8283 (tpt) REVERT: c 1795 MET cc_start: 0.7576 (OUTLIER) cc_final: 0.7121 (ptm) REVERT: c 1854 MET cc_start: 0.8931 (tpp) cc_final: 0.8727 (mmm) REVERT: c 1885 ILE cc_start: 0.9272 (mm) cc_final: 0.8963 (mm) REVERT: c 1886 ASP cc_start: 0.8050 (t0) cc_final: 0.7550 (t0) REVERT: c 1902 ASP cc_start: 0.8792 (t0) cc_final: 0.8341 (t70) REVERT: d 1710 LEU cc_start: 0.8763 (OUTLIER) cc_final: 0.8517 (pp) REVERT: d 1729 MET cc_start: 0.8345 (ptm) cc_final: 0.7222 (mmt) REVERT: d 1737 LYS cc_start: 0.8385 (mtmm) cc_final: 0.7918 (mtpt) REVERT: d 1752 MET cc_start: 0.8808 (ppp) cc_final: 0.8322 (ppp) REVERT: d 1766 ASP cc_start: 0.8727 (m-30) cc_final: 0.8468 (m-30) REVERT: d 1776 GLN cc_start: 0.7999 (tt0) cc_final: 0.7728 (tt0) REVERT: d 1789 TYR cc_start: 0.7847 (t80) cc_final: 0.7228 (m-10) REVERT: d 1795 MET cc_start: 0.8166 (ptm) cc_final: 0.7948 (ptm) REVERT: d 1857 GLN cc_start: 0.8812 (tp-100) cc_final: 0.8308 (tp40) REVERT: d 1861 GLN cc_start: 0.8736 (mp10) cc_final: 0.8339 (mp10) REVERT: d 1886 ASP cc_start: 0.8141 (t0) cc_final: 0.7885 (t0) REVERT: e 1707 ASP cc_start: 0.7620 (p0) cc_final: 0.7182 (p0) REVERT: e 1729 MET cc_start: 0.8747 (ptm) cc_final: 0.7327 (mmt) REVERT: e 1734 LYS cc_start: 0.6906 (ttpt) cc_final: 0.6229 (pttp) REVERT: e 1780 MET cc_start: 0.8258 (tpt) cc_final: 0.7753 (tpp) REVERT: e 1783 GLU cc_start: 0.8275 (pm20) cc_final: 0.7967 (pm20) REVERT: e 1810 PHE cc_start: 0.6950 (p90) cc_final: 0.6710 (p90) REVERT: e 1886 ASP cc_start: 0.8485 (t0) cc_final: 0.8216 (t0) REVERT: e 1894 LYS cc_start: 0.8746 (ptmt) cc_final: 0.8476 (pttm) REVERT: e 1902 ASP cc_start: 0.8879 (t0) cc_final: 0.8600 (t70) REVERT: f 1707 ASP cc_start: 0.8159 (t0) cc_final: 0.7494 (t0) REVERT: f 1709 THR cc_start: 0.9209 (p) cc_final: 0.8845 (p) REVERT: f 1729 MET cc_start: 0.8048 (ptm) cc_final: 0.7158 (tpt) REVERT: f 1734 LYS cc_start: 0.6760 (ttpt) cc_final: 0.6467 (ttpt) REVERT: f 1737 LYS cc_start: 0.8813 (mtmm) cc_final: 0.8053 (mtpp) REVERT: f 1739 TYR cc_start: 0.8638 (m-80) cc_final: 0.7759 (m-80) REVERT: f 1742 TYR cc_start: 0.8560 (p90) cc_final: 0.7779 (p90) REVERT: f 1766 ASP cc_start: 0.8869 (m-30) cc_final: 0.8565 (m-30) REVERT: f 1776 GLN cc_start: 0.7826 (tt0) cc_final: 0.7139 (tm-30) REVERT: f 1857 GLN cc_start: 0.9075 (tp-100) cc_final: 0.8375 (tp40) REVERT: f 1861 GLN cc_start: 0.8902 (mp10) cc_final: 0.8366 (mp10) REVERT: f 1886 ASP cc_start: 0.8424 (t0) cc_final: 0.8115 (t0) REVERT: f 1902 ASP cc_start: 0.8487 (t70) cc_final: 0.7738 (t70) REVERT: g 1729 MET cc_start: 0.8286 (ptm) cc_final: 0.6905 (mmt) REVERT: g 1776 GLN cc_start: 0.8102 (tt0) cc_final: 0.7900 (tt0) REVERT: g 1894 LYS cc_start: 0.8624 (ptmt) cc_final: 0.8325 (pttm) REVERT: h 1729 MET cc_start: 0.7564 (ptm) cc_final: 0.6547 (mmt) REVERT: h 1736 THR cc_start: 0.9316 (OUTLIER) cc_final: 0.9086 (t) REVERT: h 1752 MET cc_start: 0.8999 (ppp) cc_final: 0.8429 (ppp) REVERT: h 1791 ASN cc_start: 0.8893 (t0) cc_final: 0.8418 (t0) REVERT: h 1870 TYR cc_start: 0.8233 (m-10) cc_final: 0.7988 (m-10) REVERT: h 1886 ASP cc_start: 0.8002 (p0) cc_final: 0.7660 (p0) REVERT: h 1903 GLU cc_start: 0.5578 (tt0) cc_final: 0.4614 (mt-10) REVERT: i 1707 ASP cc_start: 0.7923 (p0) cc_final: 0.7277 (p0) REVERT: i 1729 MET cc_start: 0.8267 (ptm) cc_final: 0.7299 (tpt) REVERT: i 1742 TYR cc_start: 0.8609 (p90) cc_final: 0.7911 (p90) REVERT: i 1752 MET cc_start: 0.8863 (ppp) cc_final: 0.8338 (ppp) REVERT: i 1780 MET cc_start: 0.8044 (mmm) cc_final: 0.7772 (mmm) REVERT: i 1783 GLU cc_start: 0.8282 (pm20) cc_final: 0.8035 (pm20) REVERT: i 1810 PHE cc_start: 0.7989 (p90) cc_final: 0.7341 (p90) REVERT: i 1857 GLN cc_start: 0.9294 (tp-100) cc_final: 0.8582 (tp40) REVERT: i 1861 GLN cc_start: 0.8912 (mp10) cc_final: 0.8561 (mp10) REVERT: i 1882 MET cc_start: 0.8569 (mmm) cc_final: 0.8236 (mmm) REVERT: i 1886 ASP cc_start: 0.8387 (t0) cc_final: 0.8125 (t0) REVERT: i 1894 LYS cc_start: 0.8777 (ptmt) cc_final: 0.8374 (pttm) REVERT: i 1902 ASP cc_start: 0.8686 (t0) cc_final: 0.8270 (t70) REVERT: j 1707 ASP cc_start: 0.7738 (p0) cc_final: 0.7207 (p0) REVERT: j 1729 MET cc_start: 0.8718 (ptm) cc_final: 0.7354 (mmt) REVERT: j 1737 LYS cc_start: 0.8882 (mtmm) cc_final: 0.8455 (mmmm) REVERT: j 1752 MET cc_start: 0.9112 (ppp) cc_final: 0.8674 (ppp) REVERT: j 1756 MET cc_start: 0.9188 (tpt) cc_final: 0.8895 (tpt) REVERT: j 1776 GLN cc_start: 0.8190 (tt0) cc_final: 0.7637 (tt0) REVERT: j 1780 MET cc_start: 0.8379 (tpt) cc_final: 0.7873 (tpp) REVERT: j 1783 GLU cc_start: 0.8365 (pm20) cc_final: 0.8003 (pm20) REVERT: j 1789 TYR cc_start: 0.7661 (t80) cc_final: 0.7410 (m-10) REVERT: j 1870 TYR cc_start: 0.8144 (m-80) cc_final: 0.7830 (m-80) REVERT: j 1894 LYS cc_start: 0.8849 (ptmt) cc_final: 0.8559 (pttm) REVERT: j 1902 ASP cc_start: 0.8562 (t70) cc_final: 0.8076 (t70) REVERT: k 1729 MET cc_start: 0.8308 (ptm) cc_final: 0.7185 (mmt) REVERT: k 1737 LYS cc_start: 0.8708 (mtmm) cc_final: 0.8213 (mtpt) REVERT: k 1752 MET cc_start: 0.8946 (ppp) cc_final: 0.8368 (ppp) REVERT: k 1766 ASP cc_start: 0.8737 (m-30) cc_final: 0.8468 (m-30) REVERT: k 1780 MET cc_start: 0.8067 (mmm) cc_final: 0.7645 (mmm) REVERT: k 1789 TYR cc_start: 0.7825 (t80) cc_final: 0.7397 (m-10) REVERT: k 1857 GLN cc_start: 0.8663 (tp-100) cc_final: 0.8340 (tp40) REVERT: k 1886 ASP cc_start: 0.8152 (t0) cc_final: 0.7938 (t0) REVERT: l 1707 ASP cc_start: 0.7901 (t0) cc_final: 0.7198 (t0) REVERT: l 1729 MET cc_start: 0.8354 (ptm) cc_final: 0.7200 (mmm) REVERT: l 1734 LYS cc_start: 0.6698 (ttpt) cc_final: 0.6208 (pttm) REVERT: l 1737 LYS cc_start: 0.8763 (mtmm) cc_final: 0.8499 (mtpp) REVERT: l 1742 TYR cc_start: 0.8462 (p90) cc_final: 0.7759 (p90) REVERT: l 1752 MET cc_start: 0.9058 (ppp) cc_final: 0.8311 (ppp) REVERT: l 1795 MET cc_start: 0.7513 (ptm) cc_final: 0.7250 (ptm) REVERT: l 1861 GLN cc_start: 0.8798 (mp10) cc_final: 0.8418 (mp10) REVERT: l 1897 ASN cc_start: 0.8764 (t0) cc_final: 0.8519 (t0) REVERT: l 1898 LYS cc_start: 0.8557 (tptp) cc_final: 0.8318 (tptp) REVERT: m 1729 MET cc_start: 0.8482 (ptm) cc_final: 0.7218 (mmt) REVERT: m 1736 THR cc_start: 0.9169 (OUTLIER) cc_final: 0.8652 (t) REVERT: m 1752 MET cc_start: 0.9296 (ppp) cc_final: 0.8948 (ppp) REVERT: m 1783 GLU cc_start: 0.8486 (pm20) cc_final: 0.8221 (pm20) REVERT: m 1857 GLN cc_start: 0.9053 (tp40) cc_final: 0.8415 (tp-100) REVERT: m 1861 GLN cc_start: 0.8878 (mp-120) cc_final: 0.8427 (mp10) REVERT: n 1707 ASP cc_start: 0.7824 (p0) cc_final: 0.7434 (p0) REVERT: n 1729 MET cc_start: 0.8293 (ptm) cc_final: 0.6898 (mmt) REVERT: n 1752 MET cc_start: 0.8727 (ppp) cc_final: 0.8159 (ptt) REVERT: n 1781 LEU cc_start: 0.7872 (mt) cc_final: 0.7390 (tt) REVERT: n 1858 ILE cc_start: 0.9397 (OUTLIER) cc_final: 0.9144 (mp) REVERT: n 1886 ASP cc_start: 0.8047 (t0) cc_final: 0.7755 (t0) REVERT: n 1894 LYS cc_start: 0.8747 (ptmt) cc_final: 0.8498 (pttm) REVERT: o 1729 MET cc_start: 0.7779 (ptm) cc_final: 0.6714 (mmt) REVERT: o 1736 THR cc_start: 0.9378 (OUTLIER) cc_final: 0.9144 (t) REVERT: o 1752 MET cc_start: 0.9190 (ppp) cc_final: 0.8944 (ppp) REVERT: o 1783 GLU cc_start: 0.8305 (pm20) cc_final: 0.7446 (pm20) REVERT: o 1795 MET cc_start: 0.7707 (ptm) cc_final: 0.7501 (ptm) REVERT: o 1870 TYR cc_start: 0.8501 (m-80) cc_final: 0.8071 (m-10) REVERT: o 1886 ASP cc_start: 0.8019 (t0) cc_final: 0.7628 (t0) REVERT: o 1902 ASP cc_start: 0.8070 (t70) cc_final: 0.7638 (t70) outliers start: 128 outliers final: 93 residues processed: 677 average time/residue: 0.2799 time to fit residues: 304.4365 Evaluate side-chains 671 residues out of total 2338 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 101 poor density : 570 time to evaluate : 2.363 ------------------------------------------------------------------------------- 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 1710 LEU Chi-restraints excluded: chain b residue 1811 LEU Chi-restraints excluded: chain b residue 1873 GLU 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 1795 MET Chi-restraints excluded: chain c residue 1879 ILE Chi-restraints excluded: chain c residue 1896 THR 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 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 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 1700 ILE 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 1715 SER Chi-restraints excluded: chain h residue 1730 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 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 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 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 1790 VAL Chi-restraints excluded: chain k residue 1811 LEU 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 1683 ILE Chi-restraints excluded: chain l residue 1736 THR Chi-restraints excluded: chain l residue 1776 GLN 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 n residue 1683 ILE Chi-restraints excluded: chain n residue 1698 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 1858 ILE Chi-restraints excluded: chain n residue 1865 ILE Chi-restraints excluded: chain n residue 1883 ASP Chi-restraints excluded: chain o residue 1683 ILE Chi-restraints excluded: chain o residue 1698 ILE 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 1760 THR 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 233 optimal weight: 2.9990 chunk 245 optimal weight: 4.9990 chunk 224 optimal weight: 0.0970 chunk 238 optimal weight: 5.9990 chunk 143 optimal weight: 2.9990 chunk 104 optimal weight: 0.8980 chunk 187 optimal weight: 1.9990 chunk 73 optimal weight: 2.9990 chunk 215 optimal weight: 2.9990 chunk 225 optimal weight: 4.9990 chunk 156 optimal weight: 2.9990 overall best weight: 1.7984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: d1680 GLN k1680 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8287 moved from start: 0.4604 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 21238 Z= 0.318 Angle : 0.747 12.180 28784 Z= 0.380 Chirality : 0.051 0.181 3486 Planarity : 0.004 0.038 3612 Dihedral : 6.053 36.870 2885 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 11.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.56 % Favored : 88.44 % Rotamer: Outliers : 5.13 % Allowed : 24.08 % Favored : 70.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.53 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.58 (0.16), residues: 2716 helix: -3.74 (0.18), residues: 364 sheet: -1.74 (0.21), residues: 602 loop : -1.23 (0.15), residues: 1750 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP g1723 HIS 0.002 0.001 HIS l1793 PHE 0.030 0.002 PHE n1810 TYR 0.022 0.002 TYR h1695 ARG 0.004 0.001 ARG c1754 *********************** 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 706 residues out of total 2338 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 120 poor density : 586 time to evaluate : 2.585 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: b 1689 THR cc_start: 0.9606 (OUTLIER) cc_final: 0.9363 (t) REVERT: b 1729 MET cc_start: 0.8090 (ptm) cc_final: 0.6674 (mmt) REVERT: b 1734 LYS cc_start: 0.7066 (ttpt) cc_final: 0.6752 (ttpt) REVERT: b 1739 TYR cc_start: 0.8986 (m-80) cc_final: 0.8756 (m-80) REVERT: b 1752 MET cc_start: 0.9183 (ppp) cc_final: 0.8365 (ppp) REVERT: b 1756 MET cc_start: 0.8582 (tpt) cc_final: 0.8221 (tpt) REVERT: b 1780 MET cc_start: 0.7631 (tpp) cc_final: 0.5839 (tmm) REVERT: b 1783 GLU cc_start: 0.8234 (pm20) cc_final: 0.7433 (pm20) REVERT: b 1857 GLN cc_start: 0.8997 (tp-100) cc_final: 0.8562 (tp40) REVERT: b 1886 ASP cc_start: 0.8424 (t0) cc_final: 0.8088 (t70) REVERT: b 1902 ASP cc_start: 0.8806 (t0) cc_final: 0.8497 (t70) REVERT: c 1715 SER cc_start: 0.9156 (t) cc_final: 0.8861 (m) REVERT: c 1729 MET cc_start: 0.8429 (ptm) cc_final: 0.7104 (mmm) REVERT: c 1742 TYR cc_start: 0.8576 (p90) cc_final: 0.7768 (p90) REVERT: c 1810 PHE cc_start: 0.8242 (p90) cc_final: 0.7747 (p90) REVERT: c 1862 LEU cc_start: 0.9009 (OUTLIER) cc_final: 0.8785 (mt) REVERT: c 1885 ILE cc_start: 0.9303 (mm) cc_final: 0.8969 (mm) REVERT: c 1886 ASP cc_start: 0.7946 (t0) cc_final: 0.7634 (t0) REVERT: c 1902 ASP cc_start: 0.8825 (t0) cc_final: 0.8405 (t70) REVERT: d 1707 ASP cc_start: 0.8074 (t0) cc_final: 0.7720 (t0) REVERT: d 1729 MET cc_start: 0.8359 (ptm) cc_final: 0.7247 (mmt) REVERT: d 1752 MET cc_start: 0.9105 (ppp) cc_final: 0.8636 (ptt) REVERT: d 1766 ASP cc_start: 0.8691 (m-30) cc_final: 0.8447 (m-30) REVERT: d 1854 MET cc_start: 0.8714 (mmm) cc_final: 0.8317 (mmm) REVERT: d 1857 GLN cc_start: 0.8844 (tp-100) cc_final: 0.8242 (tp40) REVERT: d 1861 GLN cc_start: 0.8806 (mp10) cc_final: 0.8418 (mp10) REVERT: d 1886 ASP cc_start: 0.8195 (t0) cc_final: 0.7972 (t0) REVERT: e 1707 ASP cc_start: 0.8017 (p0) cc_final: 0.7537 (p0) REVERT: e 1729 MET cc_start: 0.8785 (ptm) cc_final: 0.7291 (mmt) REVERT: e 1734 LYS cc_start: 0.7141 (ttpt) cc_final: 0.6908 (ttpt) REVERT: e 1780 MET cc_start: 0.8455 (tpt) cc_final: 0.7913 (tpp) REVERT: e 1783 GLU cc_start: 0.8365 (pm20) cc_final: 0.8061 (pm20) REVERT: e 1810 PHE cc_start: 0.7072 (p90) cc_final: 0.6725 (p90) REVERT: e 1882 MET cc_start: 0.8597 (mmm) cc_final: 0.8274 (mmt) REVERT: e 1884 ASP cc_start: 0.8217 (m-30) cc_final: 0.7990 (m-30) REVERT: e 1886 ASP cc_start: 0.8600 (t0) cc_final: 0.8259 (t0) REVERT: e 1894 LYS cc_start: 0.8801 (ptmt) cc_final: 0.8524 (pttm) REVERT: e 1902 ASP cc_start: 0.8898 (t0) cc_final: 0.8605 (t70) REVERT: f 1707 ASP cc_start: 0.8133 (t0) cc_final: 0.7546 (t0) REVERT: f 1709 THR cc_start: 0.9166 (p) cc_final: 0.8758 (p) REVERT: f 1729 MET cc_start: 0.8007 (ptm) cc_final: 0.6962 (tpt) REVERT: f 1734 LYS cc_start: 0.7041 (ttpt) cc_final: 0.6767 (ttpt) REVERT: f 1737 LYS cc_start: 0.8811 (mtmm) cc_final: 0.8017 (mtpp) REVERT: f 1742 TYR cc_start: 0.8642 (p90) cc_final: 0.7977 (p90) REVERT: f 1766 ASP cc_start: 0.8959 (m-30) cc_final: 0.8536 (m-30) REVERT: f 1776 GLN cc_start: 0.7789 (tt0) cc_final: 0.7137 (tm-30) REVERT: f 1857 GLN cc_start: 0.9073 (tp-100) cc_final: 0.8438 (tp40) REVERT: f 1861 GLN cc_start: 0.8923 (mp10) cc_final: 0.8416 (mp10) REVERT: f 1902 ASP cc_start: 0.8594 (t70) cc_final: 0.7867 (t70) REVERT: g 1729 MET cc_start: 0.8345 (ptm) cc_final: 0.6896 (mmt) REVERT: g 1776 GLN cc_start: 0.8071 (tt0) cc_final: 0.7864 (tt0) REVERT: g 1885 ILE cc_start: 0.9438 (mm) cc_final: 0.9113 (mm) REVERT: g 1894 LYS cc_start: 0.8640 (ptmt) cc_final: 0.8356 (pttm) REVERT: h 1729 MET cc_start: 0.7673 (ptm) cc_final: 0.6562 (mmt) REVERT: h 1752 MET cc_start: 0.9162 (ppp) cc_final: 0.8749 (ppp) REVERT: h 1791 ASN cc_start: 0.8658 (t0) cc_final: 0.8203 (t0) REVERT: h 1870 TYR cc_start: 0.8284 (m-10) cc_final: 0.7958 (m-10) REVERT: h 1886 ASP cc_start: 0.8070 (p0) cc_final: 0.7861 (p0) REVERT: h 1903 GLU cc_start: 0.5071 (tt0) cc_final: 0.4664 (tt0) REVERT: i 1707 ASP cc_start: 0.8085 (p0) cc_final: 0.7436 (p0) REVERT: i 1729 MET cc_start: 0.8219 (ptm) cc_final: 0.7047 (tpt) REVERT: i 1742 TYR cc_start: 0.8669 (p90) cc_final: 0.8055 (p90) REVERT: i 1752 MET cc_start: 0.8890 (ppp) cc_final: 0.8328 (ppp) REVERT: i 1783 GLU cc_start: 0.8314 (pm20) cc_final: 0.8058 (pm20) REVERT: i 1810 PHE cc_start: 0.8062 (p90) cc_final: 0.7357 (p90) REVERT: i 1857 GLN cc_start: 0.9216 (tp-100) cc_final: 0.8717 (tp40) REVERT: i 1861 GLN cc_start: 0.8935 (mp10) cc_final: 0.8562 (mp10) REVERT: i 1894 LYS cc_start: 0.8745 (ptmt) cc_final: 0.8405 (pttm) REVERT: i 1902 ASP cc_start: 0.8847 (t0) cc_final: 0.8509 (t70) REVERT: j 1687 ASP cc_start: 0.8850 (t0) cc_final: 0.8240 (t0) REVERT: j 1726 ASN cc_start: 0.9021 (p0) cc_final: 0.8815 (p0) REVERT: j 1729 MET cc_start: 0.8765 (ptm) cc_final: 0.7333 (mmt) REVERT: j 1737 LYS cc_start: 0.8882 (mtmm) cc_final: 0.8521 (mmmm) REVERT: j 1752 MET cc_start: 0.9190 (ppp) cc_final: 0.8710 (ppp) REVERT: j 1756 MET cc_start: 0.9268 (tpt) cc_final: 0.8942 (tpt) REVERT: j 1776 GLN cc_start: 0.8264 (tt0) cc_final: 0.7753 (tt0) REVERT: j 1783 GLU cc_start: 0.8477 (pm20) cc_final: 0.8210 (pm20) REVERT: j 1870 TYR cc_start: 0.8227 (m-80) cc_final: 0.7898 (m-80) REVERT: j 1894 LYS cc_start: 0.8851 (ptmt) cc_final: 0.8595 (pttm) REVERT: j 1897 ASN cc_start: 0.8819 (t0) cc_final: 0.8481 (t0) REVERT: j 1902 ASP cc_start: 0.8540 (t70) cc_final: 0.8097 (t70) REVERT: k 1729 MET cc_start: 0.8328 (ptm) cc_final: 0.7177 (mmt) REVERT: k 1752 MET cc_start: 0.9121 (ppp) cc_final: 0.8758 (ptt) REVERT: k 1766 ASP cc_start: 0.8761 (m-30) cc_final: 0.8507 (m-30) REVERT: k 1789 TYR cc_start: 0.7889 (t80) cc_final: 0.7437 (m-10) REVERT: k 1857 GLN cc_start: 0.8753 (tp-100) cc_final: 0.8222 (tp40) REVERT: k 1861 GLN cc_start: 0.8828 (mp10) cc_final: 0.8497 (mp10) REVERT: k 1886 ASP cc_start: 0.8291 (t0) cc_final: 0.8049 (t0) REVERT: l 1729 MET cc_start: 0.8113 (ptm) cc_final: 0.6898 (mmm) REVERT: l 1737 LYS cc_start: 0.8771 (mtmm) cc_final: 0.8519 (mtpp) REVERT: l 1742 TYR cc_start: 0.8561 (p90) cc_final: 0.7956 (p90) REVERT: l 1780 MET cc_start: 0.8670 (tpt) cc_final: 0.8310 (tpp) REVERT: l 1795 MET cc_start: 0.7615 (ptm) cc_final: 0.7342 (ptm) REVERT: l 1861 GLN cc_start: 0.8822 (mp10) cc_final: 0.8420 (mp10) REVERT: l 1897 ASN cc_start: 0.8861 (t0) cc_final: 0.8595 (t0) REVERT: l 1898 LYS cc_start: 0.8571 (tptp) cc_final: 0.8341 (tptp) REVERT: m 1729 MET cc_start: 0.8508 (ptm) cc_final: 0.7147 (mmt) REVERT: m 1736 THR cc_start: 0.9354 (OUTLIER) cc_final: 0.8947 (t) REVERT: m 1752 MET cc_start: 0.9152 (ppp) cc_final: 0.8697 (ppp) REVERT: m 1783 GLU cc_start: 0.8520 (pm20) cc_final: 0.8272 (pm20) REVERT: m 1857 GLN cc_start: 0.9116 (tp40) cc_final: 0.8455 (tp-100) REVERT: m 1861 GLN cc_start: 0.8889 (mp-120) cc_final: 0.8427 (mp10) REVERT: m 1886 ASP cc_start: 0.7991 (t0) cc_final: 0.7592 (t0) REVERT: n 1687 ASP cc_start: 0.9061 (t70) cc_final: 0.8828 (t0) REVERT: n 1707 ASP cc_start: 0.8021 (p0) cc_final: 0.7486 (p0) REVERT: n 1729 MET cc_start: 0.8322 (ptm) cc_final: 0.6937 (mmt) REVERT: n 1742 TYR cc_start: 0.8510 (p90) cc_final: 0.7487 (p90) REVERT: n 1752 MET cc_start: 0.8785 (ppp) cc_final: 0.8215 (ptt) REVERT: n 1756 MET cc_start: 0.8792 (tpt) cc_final: 0.8332 (tpp) REVERT: n 1781 LEU cc_start: 0.8835 (mt) cc_final: 0.8186 (tt) REVERT: n 1870 TYR cc_start: 0.8189 (m-10) cc_final: 0.7836 (m-10) REVERT: n 1894 LYS cc_start: 0.8871 (ptmt) cc_final: 0.8574 (pttm) REVERT: o 1729 MET cc_start: 0.7694 (ptm) cc_final: 0.6572 (mmt) REVERT: o 1736 THR cc_start: 0.9443 (OUTLIER) cc_final: 0.9192 (t) REVERT: o 1752 MET cc_start: 0.9265 (ppp) cc_final: 0.8903 (ppp) REVERT: o 1783 GLU cc_start: 0.8442 (pm20) cc_final: 0.7529 (pm20) REVERT: o 1795 MET cc_start: 0.7820 (ptm) cc_final: 0.7605 (ptm) REVERT: o 1870 TYR cc_start: 0.8535 (m-80) cc_final: 0.8108 (m-10) REVERT: o 1886 ASP cc_start: 0.8083 (t0) cc_final: 0.7735 (t0) REVERT: o 1902 ASP cc_start: 0.8039 (t70) cc_final: 0.7633 (t70) outliers start: 120 outliers final: 101 residues processed: 681 average time/residue: 0.2836 time to fit residues: 307.1747 Evaluate side-chains 680 residues out of total 2338 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 105 poor density : 575 time to evaluate : 2.383 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 b residue 1811 LEU Chi-restraints excluded: chain b residue 1873 GLU 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 1795 MET Chi-restraints excluded: chain c residue 1862 LEU Chi-restraints excluded: chain c residue 1879 ILE Chi-restraints excluded: chain c residue 1896 THR 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 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 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 1700 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 1730 ILE 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 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 1790 VAL Chi-restraints excluded: chain k residue 1811 LEU 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 1683 ILE Chi-restraints excluded: chain l residue 1703 THR Chi-restraints excluded: chain l residue 1736 THR Chi-restraints excluded: chain l residue 1776 GLN 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 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 1873 GLU Chi-restraints excluded: chain n residue 1683 ILE Chi-restraints excluded: chain n residue 1698 ILE Chi-restraints excluded: chain n residue 1700 ILE Chi-restraints excluded: chain n residue 1755 LEU Chi-restraints excluded: chain n residue 1865 ILE Chi-restraints excluded: chain n residue 1883 ASP Chi-restraints excluded: chain o residue 1683 ILE Chi-restraints excluded: chain o residue 1698 ILE Chi-restraints excluded: chain o residue 1700 ILE Chi-restraints excluded: chain o residue 1736 THR Chi-restraints excluded: chain o residue 1755 LEU Chi-restraints excluded: chain o residue 1760 THR 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 252 optimal weight: 0.5980 chunk 154 optimal weight: 0.8980 chunk 119 optimal weight: 0.8980 chunk 175 optimal weight: 2.9990 chunk 265 optimal weight: 1.9990 chunk 243 optimal weight: 5.9990 chunk 211 optimal weight: 2.9990 chunk 21 optimal weight: 0.7980 chunk 163 optimal weight: 1.9990 chunk 129 optimal weight: 0.3980 chunk 167 optimal weight: 2.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: d1680 GLN ** m1776 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** n1853 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8228 moved from start: 0.4771 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 21238 Z= 0.217 Angle : 0.701 9.385 28784 Z= 0.360 Chirality : 0.049 0.165 3486 Planarity : 0.004 0.035 3612 Dihedral : 5.662 36.580 2883 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 11.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.79 % Favored : 90.21 % Rotamer: Outliers : 4.58 % Allowed : 24.89 % Favored : 70.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.53 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.75 (0.16), residues: 2716 helix: -3.35 (0.22), residues: 378 sheet: -1.58 (0.19), residues: 756 loop : -1.53 (0.15), residues: 1582 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP o1723 HIS 0.001 0.000 HIS l1793 PHE 0.029 0.001 PHE n1810 TYR 0.019 0.001 TYR h1695 ARG 0.003 0.000 ARG e1754 ********************** 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 695 residues out of total 2338 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 107 poor density : 588 time to evaluate : 2.473 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: b 1689 THR cc_start: 0.9589 (OUTLIER) cc_final: 0.9362 (t) REVERT: b 1729 MET cc_start: 0.8145 (ptm) cc_final: 0.6786 (mmt) REVERT: b 1734 LYS cc_start: 0.6898 (ttpt) cc_final: 0.6587 (ttpt) REVERT: b 1737 LYS cc_start: 0.8193 (mptt) cc_final: 0.7651 (mmmm) REVERT: b 1739 TYR cc_start: 0.8918 (m-80) cc_final: 0.8675 (m-80) REVERT: b 1752 MET cc_start: 0.9143 (ppp) cc_final: 0.8337 (ppp) REVERT: b 1780 MET cc_start: 0.7356 (tpp) cc_final: 0.5624 (tmm) REVERT: b 1781 LEU cc_start: 0.9300 (tt) cc_final: 0.8979 (mm) REVERT: b 1783 GLU cc_start: 0.8180 (pm20) cc_final: 0.7738 (pm20) REVERT: b 1857 GLN cc_start: 0.8987 (tp-100) cc_final: 0.7823 (tp40) REVERT: b 1861 GLN cc_start: 0.8843 (mm110) cc_final: 0.8628 (mp10) REVERT: b 1886 ASP cc_start: 0.8352 (t0) cc_final: 0.7932 (t70) REVERT: b 1902 ASP cc_start: 0.8766 (t0) cc_final: 0.8421 (t70) REVERT: c 1715 SER cc_start: 0.9106 (t) cc_final: 0.8879 (m) REVERT: c 1729 MET cc_start: 0.8379 (ptm) cc_final: 0.7101 (mmm) REVERT: c 1742 TYR cc_start: 0.8670 (p90) cc_final: 0.8035 (p90) REVERT: c 1752 MET cc_start: 0.9095 (ppp) cc_final: 0.8349 (ppp) REVERT: c 1810 PHE cc_start: 0.8149 (p90) cc_final: 0.7693 (p90) REVERT: c 1862 LEU cc_start: 0.9327 (OUTLIER) cc_final: 0.9044 (mt) REVERT: c 1885 ILE cc_start: 0.9236 (mm) cc_final: 0.8939 (mm) REVERT: c 1886 ASP cc_start: 0.7916 (t0) cc_final: 0.7583 (t0) REVERT: c 1902 ASP cc_start: 0.8789 (t0) cc_final: 0.8374 (t70) REVERT: d 1729 MET cc_start: 0.8357 (ptm) cc_final: 0.7233 (mmt) REVERT: d 1737 LYS cc_start: 0.8644 (mtmm) cc_final: 0.8215 (mtpt) REVERT: d 1752 MET cc_start: 0.8885 (ppp) cc_final: 0.8444 (ptt) REVERT: d 1766 ASP cc_start: 0.8690 (m-30) cc_final: 0.8427 (m-30) REVERT: d 1857 GLN cc_start: 0.8807 (tp-100) cc_final: 0.8268 (tp40) REVERT: d 1861 GLN cc_start: 0.8819 (mp10) cc_final: 0.8491 (mp10) REVERT: d 1886 ASP cc_start: 0.8149 (t0) cc_final: 0.7908 (t0) REVERT: e 1707 ASP cc_start: 0.7690 (p0) cc_final: 0.7237 (p0) REVERT: e 1729 MET cc_start: 0.8746 (ptm) cc_final: 0.7325 (mmt) REVERT: e 1734 LYS cc_start: 0.6975 (ttpt) cc_final: 0.6747 (ttpt) REVERT: e 1739 TYR cc_start: 0.8261 (m-80) cc_final: 0.8025 (m-10) REVERT: e 1752 MET cc_start: 0.9134 (ppp) cc_final: 0.8406 (ppp) REVERT: e 1780 MET cc_start: 0.8362 (tpt) cc_final: 0.7798 (tpp) REVERT: e 1783 GLU cc_start: 0.8392 (pm20) cc_final: 0.8072 (pm20) REVERT: e 1810 PHE cc_start: 0.7001 (p90) cc_final: 0.6662 (p90) REVERT: e 1882 MET cc_start: 0.8484 (mmm) cc_final: 0.8213 (mmt) REVERT: e 1886 ASP cc_start: 0.8575 (t0) cc_final: 0.8214 (t0) REVERT: e 1894 LYS cc_start: 0.8742 (ptmt) cc_final: 0.8531 (pttm) REVERT: e 1902 ASP cc_start: 0.8843 (t0) cc_final: 0.8550 (t70) REVERT: f 1707 ASP cc_start: 0.8188 (t0) cc_final: 0.7423 (t0) REVERT: f 1709 THR cc_start: 0.9182 (p) cc_final: 0.8812 (p) REVERT: f 1729 MET cc_start: 0.8058 (ptm) cc_final: 0.6971 (tpt) REVERT: f 1734 LYS cc_start: 0.6833 (ttpt) cc_final: 0.6532 (ttpt) REVERT: f 1737 LYS cc_start: 0.8778 (mtmm) cc_final: 0.8089 (mtpp) REVERT: f 1739 TYR cc_start: 0.8705 (m-80) cc_final: 0.7749 (m-80) REVERT: f 1742 TYR cc_start: 0.8513 (p90) cc_final: 0.7767 (p90) REVERT: f 1776 GLN cc_start: 0.8092 (tt0) cc_final: 0.7382 (tm-30) REVERT: f 1857 GLN cc_start: 0.9046 (tp-100) cc_final: 0.8335 (tp40) REVERT: f 1861 GLN cc_start: 0.8871 (mp10) cc_final: 0.8330 (mp10) REVERT: f 1885 ILE cc_start: 0.9536 (mm) cc_final: 0.9209 (mm) REVERT: f 1902 ASP cc_start: 0.8546 (t70) cc_final: 0.7832 (t70) REVERT: g 1729 MET cc_start: 0.8297 (ptm) cc_final: 0.6875 (mmt) REVERT: g 1742 TYR cc_start: 0.8286 (p90) cc_final: 0.8081 (p90) REVERT: g 1776 GLN cc_start: 0.7996 (tt0) cc_final: 0.7745 (tt0) REVERT: g 1885 ILE cc_start: 0.9425 (mm) cc_final: 0.9199 (mm) REVERT: g 1894 LYS cc_start: 0.8604 (ptmt) cc_final: 0.8326 (pttm) REVERT: h 1729 MET cc_start: 0.7613 (ptm) cc_final: 0.6545 (mmt) REVERT: h 1752 MET cc_start: 0.9070 (ppp) cc_final: 0.8836 (ppp) REVERT: h 1756 MET cc_start: 0.8469 (tpt) cc_final: 0.8055 (tpt) REVERT: h 1791 ASN cc_start: 0.8850 (t0) cc_final: 0.8348 (t0) REVERT: h 1870 TYR cc_start: 0.8229 (m-10) cc_final: 0.7997 (m-10) REVERT: h 1903 GLU cc_start: 0.5715 (tt0) cc_final: 0.5449 (tt0) REVERT: i 1707 ASP cc_start: 0.8042 (p0) cc_final: 0.7502 (p0) REVERT: i 1729 MET cc_start: 0.8272 (ptm) cc_final: 0.7080 (tpt) REVERT: i 1742 TYR cc_start: 0.8580 (p90) cc_final: 0.7863 (p90) REVERT: i 1752 MET cc_start: 0.8855 (ppp) cc_final: 0.8247 (ppp) REVERT: i 1756 MET cc_start: 0.8924 (tpt) cc_final: 0.8483 (tpt) REVERT: i 1781 LEU cc_start: 0.7853 (mt) cc_final: 0.7638 (tt) REVERT: i 1810 PHE cc_start: 0.7982 (p90) cc_final: 0.7332 (p90) REVERT: i 1857 GLN cc_start: 0.9191 (tp-100) cc_final: 0.8707 (tp-100) REVERT: i 1861 GLN cc_start: 0.8900 (mp10) cc_final: 0.8535 (mp10) REVERT: i 1894 LYS cc_start: 0.8812 (ptmt) cc_final: 0.8433 (pttm) REVERT: i 1902 ASP cc_start: 0.8804 (t0) cc_final: 0.8465 (t70) REVERT: j 1707 ASP cc_start: 0.7822 (p0) cc_final: 0.7277 (p0) REVERT: j 1726 ASN cc_start: 0.8961 (p0) cc_final: 0.8730 (p0) REVERT: j 1729 MET cc_start: 0.8732 (ptm) cc_final: 0.7354 (mmt) REVERT: j 1737 LYS cc_start: 0.8857 (mtmm) cc_final: 0.8507 (mmmm) REVERT: j 1752 MET cc_start: 0.9179 (ppp) cc_final: 0.8783 (ppp) REVERT: j 1776 GLN cc_start: 0.8207 (tt0) cc_final: 0.7643 (tt0) REVERT: j 1783 GLU cc_start: 0.8430 (pm20) cc_final: 0.8191 (pm20) REVERT: j 1870 TYR cc_start: 0.8148 (m-80) cc_final: 0.7815 (m-80) REVERT: j 1894 LYS cc_start: 0.8801 (ptmt) cc_final: 0.8597 (pttm) REVERT: j 1897 ASN cc_start: 0.8901 (t0) cc_final: 0.8551 (t0) REVERT: j 1902 ASP cc_start: 0.8590 (t70) cc_final: 0.8159 (t70) REVERT: k 1729 MET cc_start: 0.8309 (ptm) cc_final: 0.7167 (mmt) REVERT: k 1737 LYS cc_start: 0.8695 (mtmm) cc_final: 0.8218 (mtpt) REVERT: k 1752 MET cc_start: 0.8862 (ppp) cc_final: 0.8218 (ptt) REVERT: k 1766 ASP cc_start: 0.8744 (m-30) cc_final: 0.8491 (m-30) REVERT: k 1789 TYR cc_start: 0.7840 (t80) cc_final: 0.7367 (m-10) REVERT: k 1857 GLN cc_start: 0.8761 (tp-100) cc_final: 0.8248 (tp40) REVERT: k 1861 GLN cc_start: 0.8792 (mp10) cc_final: 0.8464 (mp10) REVERT: l 1707 ASP cc_start: 0.7938 (t0) cc_final: 0.7180 (t0) REVERT: l 1729 MET cc_start: 0.8364 (ptm) cc_final: 0.7180 (mmm) REVERT: l 1737 LYS cc_start: 0.8765 (mtmm) cc_final: 0.8485 (mtpp) REVERT: l 1742 TYR cc_start: 0.8551 (p90) cc_final: 0.7713 (p90) REVERT: l 1752 MET cc_start: 0.9051 (ppp) cc_final: 0.8546 (ppp) REVERT: l 1795 MET cc_start: 0.7563 (ptm) cc_final: 0.7308 (ptm) REVERT: l 1861 GLN cc_start: 0.8755 (mp10) cc_final: 0.8351 (mp10) REVERT: l 1897 ASN cc_start: 0.8771 (t0) cc_final: 0.8492 (t0) REVERT: m 1729 MET cc_start: 0.7919 (ptm) cc_final: 0.6859 (mmt) REVERT: m 1734 LYS cc_start: 0.6692 (ttpt) cc_final: 0.6407 (ttpt) REVERT: m 1736 THR cc_start: 0.9202 (OUTLIER) cc_final: 0.8730 (t) REVERT: m 1752 MET cc_start: 0.9227 (ppp) cc_final: 0.8623 (ppp) REVERT: m 1783 GLU cc_start: 0.8548 (pm20) cc_final: 0.8268 (pm20) REVERT: m 1857 GLN cc_start: 0.9119 (tp40) cc_final: 0.8418 (tp-100) REVERT: m 1861 GLN cc_start: 0.8849 (mp-120) cc_final: 0.8469 (mp10) REVERT: m 1886 ASP cc_start: 0.7969 (t0) cc_final: 0.7436 (t0) REVERT: n 1699 GLU cc_start: 0.6196 (pt0) cc_final: 0.5987 (pt0) REVERT: n 1707 ASP cc_start: 0.7879 (p0) cc_final: 0.7492 (p0) REVERT: n 1729 MET cc_start: 0.8287 (ptm) cc_final: 0.6914 (mmt) REVERT: n 1752 MET cc_start: 0.8730 (ppp) cc_final: 0.8116 (ptt) REVERT: n 1870 TYR cc_start: 0.8092 (m-10) cc_final: 0.7856 (m-10) REVERT: n 1886 ASP cc_start: 0.7872 (t0) cc_final: 0.7632 (t0) REVERT: n 1894 LYS cc_start: 0.8851 (ptmt) cc_final: 0.8535 (pttm) REVERT: o 1729 MET cc_start: 0.7657 (ptm) cc_final: 0.6573 (mmt) REVERT: o 1736 THR cc_start: 0.9386 (OUTLIER) cc_final: 0.9160 (t) REVERT: o 1752 MET cc_start: 0.9204 (ppp) cc_final: 0.8923 (ppp) REVERT: o 1783 GLU cc_start: 0.8286 (pm20) cc_final: 0.7466 (pm20) REVERT: o 1795 MET cc_start: 0.7851 (ptm) cc_final: 0.7606 (ptm) REVERT: o 1870 TYR cc_start: 0.8444 (m-80) cc_final: 0.8020 (m-10) REVERT: o 1886 ASP cc_start: 0.8214 (t0) cc_final: 0.7850 (t0) REVERT: o 1902 ASP cc_start: 0.8070 (t70) cc_final: 0.7651 (t70) outliers start: 107 outliers final: 90 residues processed: 668 average time/residue: 0.2984 time to fit residues: 317.2916 Evaluate side-chains 675 residues out of total 2338 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 94 poor density : 581 time to evaluate : 2.345 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 1811 LEU Chi-restraints excluded: chain b residue 1873 GLU 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 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 1760 THR 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 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 g residue 1683 ILE Chi-restraints excluded: chain g residue 1700 ILE Chi-restraints excluded: chain g residue 1790 VAL Chi-restraints excluded: chain g residue 1865 ILE Chi-restraints excluded: chain h residue 1700 ILE Chi-restraints excluded: chain h residue 1730 ILE Chi-restraints excluded: chain h residue 1738 VAL Chi-restraints excluded: chain h residue 1755 LEU 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 1883 ASP Chi-restraints excluded: chain k residue 1896 THR 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 1776 GLN 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 1873 GLU Chi-restraints excluded: chain n residue 1683 ILE Chi-restraints excluded: chain n residue 1698 ILE Chi-restraints excluded: chain n residue 1700 ILE Chi-restraints excluded: chain n residue 1755 LEU Chi-restraints excluded: chain n residue 1853 GLN Chi-restraints excluded: chain n residue 1858 ILE Chi-restraints excluded: chain n residue 1865 ILE Chi-restraints excluded: chain n residue 1883 ASP Chi-restraints excluded: chain o residue 1683 ILE Chi-restraints excluded: chain o residue 1698 ILE Chi-restraints excluded: chain o residue 1700 ILE Chi-restraints excluded: chain o residue 1736 THR Chi-restraints excluded: chain o residue 1755 LEU Chi-restraints excluded: chain o residue 1760 THR 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 224 optimal weight: 0.5980 chunk 64 optimal weight: 0.0030 chunk 194 optimal weight: 0.9980 chunk 31 optimal weight: 4.9990 chunk 58 optimal weight: 0.6980 chunk 211 optimal weight: 3.9990 chunk 88 optimal weight: 6.9990 chunk 217 optimal weight: 0.9990 chunk 26 optimal weight: 3.9990 chunk 38 optimal weight: 5.9990 chunk 185 optimal weight: 0.7980 overall best weight: 0.6190 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: d1680 GLN m1776 GLN n1853 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3305 r_free = 0.3305 target = 0.098246 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3119 r_free = 0.3119 target = 0.087764 restraints weight = 46906.259| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3156 r_free = 0.3156 target = 0.089822 restraints weight = 22689.141| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3177 r_free = 0.3177 target = 0.091052 restraints weight = 13064.863| |-----------------------------------------------------------------------------| r_work (final): 0.3171 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8235 moved from start: 0.4874 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 21238 Z= 0.209 Angle : 0.708 14.668 28784 Z= 0.360 Chirality : 0.049 0.165 3486 Planarity : 0.004 0.037 3612 Dihedral : 5.546 34.937 2883 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 10.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.49 % Favored : 89.51 % Rotamer: Outliers : 4.58 % Allowed : 25.32 % Favored : 70.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.53 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.71 (0.16), residues: 2716 helix: -3.39 (0.21), residues: 378 sheet: -1.52 (0.19), residues: 756 loop : -1.49 (0.15), residues: 1582 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP g1723 HIS 0.001 0.000 HIS l1793 PHE 0.028 0.001 PHE n1810 TYR 0.019 0.001 TYR h1695 ARG 0.002 0.000 ARG c1754 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5835.86 seconds wall clock time: 104 minutes 30.42 seconds (6270.42 seconds total)