Starting phenix.real_space_refine on Wed Aug 27 03:05:35 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9flp_50537/08_2025/9flp_50537.cif Found real_map, /net/cci-nas-00/data/ceres_data/9flp_50537/08_2025/9flp_50537.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9flp_50537/08_2025/9flp_50537.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9flp_50537/08_2025/9flp_50537.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9flp_50537/08_2025/9flp_50537.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9flp_50537/08_2025/9flp_50537.map" } resolution = 3.8 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.001 sd= 0.097 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 210 5.16 5 C 27755 2.51 5 N 7364 2.21 5 O 9772 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 21 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 45101 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 6443 Number of conformers: 1 Conformer: "" Number of residues, atoms: 912, 6443 Classifications: {'peptide': 912} Link IDs: {'PTRANS': 63, 'TRANS': 848} Restraints were copied for chains: B, C, D, E, F, G Time building chain proxies: 7.84, per 1000 atoms: 0.17 Number of scatterers: 45101 At special positions: 0 Unit cell: (95.424, 95.424, 475.416, 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 210 16.00 O 9772 8.00 N 7364 7.00 C 27755 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=70, symmetry=0 Simple disulfide: pdb=" SG CYS A1413 " - pdb=" SG CYS A1551 " distance=2.03 Simple disulfide: pdb=" SG CYS A1497 " - pdb=" SG CYS A1634 " distance=2.04 Simple disulfide: pdb=" SG CYS A1577 " - pdb=" SG CYS A1716 " distance=2.03 Simple disulfide: pdb=" SG CYS A1661 " - pdb=" SG CYS A1800 " distance=2.03 Simple disulfide: pdb=" SG CYS A1743 " - pdb=" SG CYS A1883 " distance=2.03 Simple disulfide: pdb=" SG CYS A1828 " - pdb=" SG CYS A1965 " distance=2.04 Simple disulfide: pdb=" SG CYS A1910 " - pdb=" SG CYS A2049 " distance=2.04 Simple disulfide: pdb=" SG CYS A1992 " - pdb=" SG CYS A2132 " distance=2.03 Simple disulfide: pdb=" SG CYS A2077 " - pdb=" SG CYS A2214 " distance=2.03 Simple disulfide: pdb=" SG CYS A2159 " - pdb=" SG CYS A2298 " distance=2.03 Simple disulfide: pdb=" SG CYS B1413 " - pdb=" SG CYS B1551 " distance=2.03 Simple disulfide: pdb=" SG CYS C1413 " - pdb=" SG CYS C1551 " distance=2.03 Simple disulfide: pdb=" SG CYS D1413 " - pdb=" SG CYS D1551 " distance=2.03 Simple disulfide: pdb=" SG CYS E1413 " - pdb=" SG CYS E1551 " distance=2.03 Simple disulfide: pdb=" SG CYS F1413 " - pdb=" SG CYS F1551 " distance=2.03 Simple disulfide: pdb=" SG CYS G1413 " - pdb=" SG CYS G1551 " distance=2.03 Simple disulfide: pdb=" SG CYS B1497 " - pdb=" SG CYS B1634 " distance=2.04 Simple disulfide: pdb=" SG CYS C1497 " - pdb=" SG CYS C1634 " distance=2.04 Simple disulfide: pdb=" SG CYS D1497 " - pdb=" SG CYS D1634 " distance=2.04 Simple disulfide: pdb=" SG CYS E1497 " - pdb=" SG CYS E1634 " distance=2.04 Simple disulfide: pdb=" SG CYS F1497 " - pdb=" SG CYS F1634 " distance=2.04 Simple disulfide: pdb=" SG CYS G1497 " - pdb=" SG CYS G1634 " distance=2.04 Simple disulfide: pdb=" SG CYS B1577 " - pdb=" SG CYS B1716 " distance=2.03 Simple disulfide: pdb=" SG CYS C1577 " - pdb=" SG CYS C1716 " distance=2.03 Simple disulfide: pdb=" SG CYS D1577 " - pdb=" SG CYS D1716 " distance=2.03 Simple disulfide: pdb=" SG CYS E1577 " - pdb=" SG CYS E1716 " distance=2.03 Simple disulfide: pdb=" SG CYS F1577 " - pdb=" SG CYS F1716 " distance=2.03 Simple disulfide: pdb=" SG CYS G1577 " - pdb=" SG CYS G1716 " distance=2.03 Simple disulfide: pdb=" SG CYS B1661 " - pdb=" SG CYS B1800 " distance=2.03 Simple disulfide: pdb=" SG CYS C1661 " - pdb=" SG CYS C1800 " distance=2.03 Simple disulfide: pdb=" SG CYS D1661 " - pdb=" SG CYS D1800 " distance=2.03 Simple disulfide: pdb=" SG CYS E1661 " - pdb=" SG CYS E1800 " distance=2.03 Simple disulfide: pdb=" SG CYS F1661 " - pdb=" SG CYS F1800 " distance=2.03 Simple disulfide: pdb=" SG CYS G1661 " - pdb=" SG CYS G1800 " distance=2.03 Simple disulfide: pdb=" SG CYS B1743 " - pdb=" SG CYS B1883 " distance=2.03 Simple disulfide: pdb=" SG CYS C1743 " - pdb=" SG CYS C1883 " distance=2.03 Simple disulfide: pdb=" SG CYS D1743 " - pdb=" SG CYS D1883 " distance=2.03 Simple disulfide: pdb=" SG CYS E1743 " - pdb=" SG CYS E1883 " distance=2.03 Simple disulfide: pdb=" SG CYS F1743 " - pdb=" SG CYS F1883 " distance=2.03 Simple disulfide: pdb=" SG CYS G1743 " - pdb=" SG CYS G1883 " distance=2.03 Simple disulfide: pdb=" SG CYS B1828 " - pdb=" SG CYS B1965 " distance=2.04 Simple disulfide: pdb=" SG CYS C1828 " - pdb=" SG CYS C1965 " distance=2.04 Simple disulfide: pdb=" SG CYS D1828 " - pdb=" SG CYS D1965 " distance=2.04 Simple disulfide: pdb=" SG CYS E1828 " - pdb=" SG CYS E1965 " distance=2.04 Simple disulfide: pdb=" SG CYS F1828 " - pdb=" SG CYS F1965 " distance=2.04 Simple disulfide: pdb=" SG CYS G1828 " - pdb=" SG CYS G1965 " distance=2.04 Simple disulfide: pdb=" SG CYS B1910 " - pdb=" SG CYS B2049 " distance=2.04 Simple disulfide: pdb=" SG CYS C1910 " - pdb=" SG CYS C2049 " distance=2.04 Simple disulfide: pdb=" SG CYS D1910 " - pdb=" SG CYS D2049 " distance=2.04 Simple disulfide: pdb=" SG CYS E1910 " - pdb=" SG CYS E2049 " distance=2.04 Simple disulfide: pdb=" SG CYS F1910 " - pdb=" SG CYS F2049 " distance=2.04 Simple disulfide: pdb=" SG CYS G1910 " - pdb=" SG CYS G2049 " distance=2.04 Simple disulfide: pdb=" SG CYS B1992 " - pdb=" SG CYS B2132 " distance=2.03 Simple disulfide: pdb=" SG CYS C1992 " - pdb=" SG CYS C2132 " distance=2.03 Simple disulfide: pdb=" SG CYS D1992 " - pdb=" SG CYS D2132 " distance=2.03 Simple disulfide: pdb=" SG CYS E1992 " - pdb=" SG CYS E2132 " distance=2.03 Simple disulfide: pdb=" SG CYS F1992 " - pdb=" SG CYS F2132 " distance=2.03 Simple disulfide: pdb=" SG CYS G1992 " - pdb=" SG CYS G2132 " distance=2.03 Simple disulfide: pdb=" SG CYS B2077 " - pdb=" SG CYS B2214 " distance=2.03 Simple disulfide: pdb=" SG CYS C2077 " - pdb=" SG CYS C2214 " distance=2.03 Simple disulfide: pdb=" SG CYS D2077 " - pdb=" SG CYS D2214 " distance=2.03 Simple disulfide: pdb=" SG CYS E2077 " - pdb=" SG CYS E2214 " distance=2.03 Simple disulfide: pdb=" SG CYS F2077 " - pdb=" SG CYS F2214 " distance=2.03 Simple disulfide: pdb=" SG CYS G2077 " - pdb=" SG CYS G2214 " distance=2.03 Simple disulfide: pdb=" SG CYS B2159 " - pdb=" SG CYS B2298 " distance=2.03 Simple disulfide: pdb=" SG CYS C2159 " - pdb=" SG CYS C2298 " distance=2.03 Simple disulfide: pdb=" SG CYS D2159 " - pdb=" SG CYS D2298 " distance=2.03 Simple disulfide: pdb=" SG CYS E2159 " - pdb=" SG CYS E2298 " distance=2.03 Simple disulfide: pdb=" SG CYS F2159 " - pdb=" SG CYS F2298 " distance=2.03 Simple disulfide: pdb=" SG CYS G2159 " - pdb=" SG CYS G2298 " distance=2.03 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: 4.32 Conformation dependent library (CDL) restraints added in 2.0 seconds Enol-peptide restraints added in 715.3 nanoseconds 12740 Ramachandran restraints generated. 6370 Oldfield, 0 Emsley, 6370 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 11774 Finding SS restraints... Secondary structure from input PDB file: 56 helices and 189 sheets defined 4.1% alpha, 37.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.89 Creating SS restraints... Processing helix chain 'A' and resid 1454 through 1457 Processing helix chain 'A' and resid 1534 through 1538 Processing helix chain 'A' and resid 1618 through 1622 Processing helix chain 'A' and resid 1699 through 1703 Processing helix chain 'A' and resid 1931 through 1933 No H-bonds generated for 'chain 'A' and resid 1931 through 1933' Processing helix chain 'A' and resid 1948 through 1952 Processing helix chain 'A' and resid 2099 through 2103 removed outlier: 3.776A pdb=" N THR A2102 " --> pdb=" O ASP A2099 " (cutoff:3.500A) removed outlier: 4.091A pdb=" N SER A2103 " --> pdb=" O ALA A2100 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 2099 through 2103' Processing helix chain 'A' and resid 2197 through 2201 Processing helix chain 'B' and resid 1454 through 1457 Processing helix chain 'B' and resid 1534 through 1538 Processing helix chain 'B' and resid 1618 through 1622 Processing helix chain 'B' and resid 1699 through 1703 Processing helix chain 'B' and resid 1931 through 1933 No H-bonds generated for 'chain 'B' and resid 1931 through 1933' Processing helix chain 'B' and resid 1948 through 1952 Processing helix chain 'B' and resid 2099 through 2103 removed outlier: 3.776A pdb=" N THR B2102 " --> pdb=" O ASP B2099 " (cutoff:3.500A) removed outlier: 4.090A pdb=" N SER B2103 " --> pdb=" O ALA B2100 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 2099 through 2103' Processing helix chain 'B' and resid 2197 through 2201 Processing helix chain 'C' and resid 1454 through 1457 Processing helix chain 'C' and resid 1534 through 1538 Processing helix chain 'C' and resid 1618 through 1622 Processing helix chain 'C' and resid 1699 through 1703 Processing helix chain 'C' and resid 1931 through 1933 No H-bonds generated for 'chain 'C' and resid 1931 through 1933' Processing helix chain 'C' and resid 1948 through 1952 Processing helix chain 'C' and resid 2099 through 2103 removed outlier: 3.776A pdb=" N THR C2102 " --> pdb=" O ASP C2099 " (cutoff:3.500A) removed outlier: 4.091A pdb=" N SER C2103 " --> pdb=" O ALA C2100 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 2099 through 2103' Processing helix chain 'C' and resid 2197 through 2201 Processing helix chain 'D' and resid 1454 through 1457 Processing helix chain 'D' and resid 1534 through 1538 Processing helix chain 'D' and resid 1618 through 1622 Processing helix chain 'D' and resid 1699 through 1703 Processing helix chain 'D' and resid 1931 through 1933 No H-bonds generated for 'chain 'D' and resid 1931 through 1933' Processing helix chain 'D' and resid 1948 through 1952 Processing helix chain 'D' and resid 2099 through 2103 removed outlier: 3.776A pdb=" N THR D2102 " --> pdb=" O ASP D2099 " (cutoff:3.500A) removed outlier: 4.090A pdb=" N SER D2103 " --> pdb=" O ALA D2100 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 2099 through 2103' Processing helix chain 'D' and resid 2197 through 2201 Processing helix chain 'E' and resid 1454 through 1457 Processing helix chain 'E' and resid 1534 through 1538 Processing helix chain 'E' and resid 1618 through 1622 Processing helix chain 'E' and resid 1699 through 1703 Processing helix chain 'E' and resid 1931 through 1933 No H-bonds generated for 'chain 'E' and resid 1931 through 1933' Processing helix chain 'E' and resid 1948 through 1952 Processing helix chain 'E' and resid 2099 through 2103 removed outlier: 3.776A pdb=" N THR E2102 " --> pdb=" O ASP E2099 " (cutoff:3.500A) removed outlier: 4.090A pdb=" N SER E2103 " --> pdb=" O ALA E2100 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 2099 through 2103' Processing helix chain 'E' and resid 2197 through 2201 Processing helix chain 'F' and resid 1454 through 1457 Processing helix chain 'F' and resid 1534 through 1538 Processing helix chain 'F' and resid 1618 through 1622 Processing helix chain 'F' and resid 1699 through 1703 Processing helix chain 'F' and resid 1931 through 1933 No H-bonds generated for 'chain 'F' and resid 1931 through 1933' Processing helix chain 'F' and resid 1948 through 1952 Processing helix chain 'F' and resid 2099 through 2103 removed outlier: 3.776A pdb=" N THR F2102 " --> pdb=" O ASP F2099 " (cutoff:3.500A) removed outlier: 4.091A pdb=" N SER F2103 " --> pdb=" O ALA F2100 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 2099 through 2103' Processing helix chain 'F' and resid 2197 through 2201 Processing helix chain 'G' and resid 1454 through 1457 Processing helix chain 'G' and resid 1534 through 1538 Processing helix chain 'G' and resid 1618 through 1622 Processing helix chain 'G' and resid 1699 through 1703 Processing helix chain 'G' and resid 1931 through 1933 No H-bonds generated for 'chain 'G' and resid 1931 through 1933' Processing helix chain 'G' and resid 1948 through 1952 Processing helix chain 'G' and resid 2099 through 2103 removed outlier: 3.777A pdb=" N THR G2102 " --> pdb=" O ASP G2099 " (cutoff:3.500A) removed outlier: 4.091A pdb=" N SER G2103 " --> pdb=" O ALA G2100 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 2099 through 2103' Processing helix chain 'G' and resid 2197 through 2201 Processing sheet with id=AA1, first strand: chain 'A' and resid 1406 through 1408 Processing sheet with id=AA2, first strand: chain 'A' and resid 1412 through 1413 removed outlier: 6.619A pdb=" N ILE A1412 " --> pdb=" O ASN A1483 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N ALA A1443 " --> pdb=" O TRP A1432 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 1412 through 1413 removed outlier: 6.619A pdb=" N ILE A1412 " --> pdb=" O ASN A1483 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 1492 through 1493 Processing sheet with id=AA5, first strand: chain 'A' and resid 1521 through 1523 Processing sheet with id=AA6, first strand: chain 'A' and resid 1576 through 1577 removed outlier: 6.736A pdb=" N VAL A1576 " --> pdb=" O ARG A1646 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'A' and resid 1582 through 1585 Processing sheet with id=AA8, first strand: chain 'A' and resid 1603 through 1607 Processing sheet with id=AA9, first strand: chain 'A' and resid 1603 through 1607 Processing sheet with id=AB1, first strand: chain 'A' and resid 1658 through 1661 removed outlier: 6.892A pdb=" N PHE A1658 " --> pdb=" O THR A1726 " (cutoff:3.500A) removed outlier: 7.949A pdb=" N ASN A1728 " --> pdb=" O PHE A1658 " (cutoff:3.500A) removed outlier: 6.872A pdb=" N VAL A1660 " --> pdb=" O ASN A1728 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 1737 through 1738 Processing sheet with id=AB3, first strand: chain 'A' and resid 1741 through 1743 removed outlier: 7.103A pdb=" N ILE A1742 " --> pdb=" O ASN A1813 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 1821 through 1823 Processing sheet with id=AB5, first strand: chain 'A' and resid 1827 through 1828 removed outlier: 6.588A pdb=" N VAL A1827 " --> pdb=" O TYR A1895 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB5 Processing sheet with id=AB6, first strand: chain 'A' and resid 1856 through 1858 removed outlier: 6.609A pdb=" N TRP A1847 " --> pdb=" O PHE A1857 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 1856 through 1858 removed outlier: 6.609A pdb=" N TRP A1847 " --> pdb=" O PHE A1857 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 1907 through 1910 removed outlier: 6.872A pdb=" N PHE A1907 " --> pdb=" O THR A1975 " (cutoff:3.500A) removed outlier: 7.947A pdb=" N ASN A1977 " --> pdb=" O PHE A1907 " (cutoff:3.500A) removed outlier: 6.845A pdb=" N VAL A1909 " --> pdb=" O ASN A1977 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N SER A1925 " --> pdb=" O VAL A1960 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'A' and resid 1986 through 1987 Processing sheet with id=AC1, first strand: chain 'A' and resid 1990 through 1992 removed outlier: 7.196A pdb=" N ILE A1991 " --> pdb=" O ASN A2062 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'A' and resid 2076 through 2077 removed outlier: 6.341A pdb=" N VAL A2076 " --> pdb=" O TYR A2144 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC2 Processing sheet with id=AC3, first strand: chain 'A' and resid 2082 through 2083 Processing sheet with id=AC4, first strand: chain 'A' and resid 2105 through 2107 removed outlier: 6.491A pdb=" N TRP A2096 " --> pdb=" O PHE A2106 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'A' and resid 2105 through 2107 removed outlier: 6.491A pdb=" N TRP A2096 " --> pdb=" O PHE A2106 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'A' and resid 2156 through 2159 removed outlier: 6.890A pdb=" N PHE A2156 " --> pdb=" O THR A2224 " (cutoff:3.500A) removed outlier: 8.164A pdb=" N ASN A2226 " --> pdb=" O PHE A2156 " (cutoff:3.500A) removed outlier: 6.860A pdb=" N VAL A2158 " --> pdb=" O ASN A2226 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'A' and resid 2235 through 2236 Processing sheet with id=AC8, first strand: chain 'A' and resid 2240 through 2241 removed outlier: 6.909A pdb=" N ILE A2240 " --> pdb=" O ASN A2311 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC8 Processing sheet with id=AC9, first strand: chain 'A' and resid 2266 through 2269 Processing sheet with id=AD1, first strand: chain 'B' and resid 1406 through 1408 Processing sheet with id=AD2, first strand: chain 'B' and resid 1412 through 1413 removed outlier: 6.619A pdb=" N ILE B1412 " --> pdb=" O ASN B1483 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N ALA B1443 " --> pdb=" O TRP B1432 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 1412 through 1413 removed outlier: 6.619A pdb=" N ILE B1412 " --> pdb=" O ASN B1483 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'B' and resid 1492 through 1493 Processing sheet with id=AD5, first strand: chain 'B' and resid 1521 through 1523 Processing sheet with id=AD6, first strand: chain 'B' and resid 1576 through 1577 removed outlier: 6.735A pdb=" N VAL B1576 " --> pdb=" O ARG B1646 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD6 Processing sheet with id=AD7, first strand: chain 'B' and resid 1582 through 1585 Processing sheet with id=AD8, first strand: chain 'B' and resid 1603 through 1607 Processing sheet with id=AD9, first strand: chain 'B' and resid 1603 through 1607 Processing sheet with id=AE1, first strand: chain 'B' and resid 1658 through 1661 removed outlier: 6.892A pdb=" N PHE B1658 " --> pdb=" O THR B1726 " (cutoff:3.500A) removed outlier: 7.949A pdb=" N ASN B1728 " --> pdb=" O PHE B1658 " (cutoff:3.500A) removed outlier: 6.872A pdb=" N VAL B1660 " --> pdb=" O ASN B1728 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'B' and resid 1737 through 1738 Processing sheet with id=AE3, first strand: chain 'B' and resid 1741 through 1743 removed outlier: 7.104A pdb=" N ILE B1742 " --> pdb=" O ASN B1813 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'B' and resid 1821 through 1823 Processing sheet with id=AE5, first strand: chain 'B' and resid 1827 through 1828 removed outlier: 6.587A pdb=" N VAL B1827 " --> pdb=" O TYR B1895 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE5 Processing sheet with id=AE6, first strand: chain 'B' and resid 1856 through 1858 removed outlier: 6.609A pdb=" N TRP B1847 " --> pdb=" O PHE B1857 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'B' and resid 1856 through 1858 removed outlier: 6.609A pdb=" N TRP B1847 " --> pdb=" O PHE B1857 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'B' and resid 1907 through 1910 removed outlier: 6.871A pdb=" N PHE B1907 " --> pdb=" O THR B1975 " (cutoff:3.500A) removed outlier: 7.947A pdb=" N ASN B1977 " --> pdb=" O PHE B1907 " (cutoff:3.500A) removed outlier: 6.845A pdb=" N VAL B1909 " --> pdb=" O ASN B1977 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N SER B1925 " --> pdb=" O VAL B1960 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'B' and resid 1986 through 1987 Processing sheet with id=AF1, first strand: chain 'B' and resid 1990 through 1992 removed outlier: 7.196A pdb=" N ILE B1991 " --> pdb=" O ASN B2062 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'B' and resid 2076 through 2077 removed outlier: 6.342A pdb=" N VAL B2076 " --> pdb=" O TYR B2144 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF2 Processing sheet with id=AF3, first strand: chain 'B' and resid 2082 through 2083 Processing sheet with id=AF4, first strand: chain 'B' and resid 2105 through 2107 removed outlier: 6.491A pdb=" N TRP B2096 " --> pdb=" O PHE B2106 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'B' and resid 2105 through 2107 removed outlier: 6.491A pdb=" N TRP B2096 " --> pdb=" O PHE B2106 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'B' and resid 2156 through 2159 removed outlier: 6.890A pdb=" N PHE B2156 " --> pdb=" O THR B2224 " (cutoff:3.500A) removed outlier: 8.164A pdb=" N ASN B2226 " --> pdb=" O PHE B2156 " (cutoff:3.500A) removed outlier: 6.859A pdb=" N VAL B2158 " --> pdb=" O ASN B2226 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'B' and resid 2235 through 2236 Processing sheet with id=AF8, first strand: chain 'B' and resid 2240 through 2241 removed outlier: 6.908A pdb=" N ILE B2240 " --> pdb=" O ASN B2311 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF8 Processing sheet with id=AF9, first strand: chain 'B' and resid 2266 through 2269 Processing sheet with id=AG1, first strand: chain 'C' and resid 1406 through 1408 Processing sheet with id=AG2, first strand: chain 'C' and resid 1412 through 1413 removed outlier: 6.619A pdb=" N ILE C1412 " --> pdb=" O ASN C1483 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N ALA C1443 " --> pdb=" O TRP C1432 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'C' and resid 1412 through 1413 removed outlier: 6.619A pdb=" N ILE C1412 " --> pdb=" O ASN C1483 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'C' and resid 1492 through 1493 Processing sheet with id=AG5, first strand: chain 'C' and resid 1521 through 1523 Processing sheet with id=AG6, first strand: chain 'C' and resid 1576 through 1577 removed outlier: 6.735A pdb=" N VAL C1576 " --> pdb=" O ARG C1646 " (cutoff:3.500A) No H-bonds generated for sheet with id=AG6 Processing sheet with id=AG7, first strand: chain 'C' and resid 1582 through 1585 Processing sheet with id=AG8, first strand: chain 'C' and resid 1603 through 1607 Processing sheet with id=AG9, first strand: chain 'C' and resid 1603 through 1607 Processing sheet with id=AH1, first strand: chain 'C' and resid 1658 through 1661 removed outlier: 6.891A pdb=" N PHE C1658 " --> pdb=" O THR C1726 " (cutoff:3.500A) removed outlier: 7.948A pdb=" N ASN C1728 " --> pdb=" O PHE C1658 " (cutoff:3.500A) removed outlier: 6.873A pdb=" N VAL C1660 " --> pdb=" O ASN C1728 " (cutoff:3.500A) Processing sheet with id=AH2, first strand: chain 'C' and resid 1737 through 1738 Processing sheet with id=AH3, first strand: chain 'C' and resid 1741 through 1743 removed outlier: 7.103A pdb=" N ILE C1742 " --> pdb=" O ASN C1813 " (cutoff:3.500A) Processing sheet with id=AH4, first strand: chain 'C' and resid 1821 through 1823 Processing sheet with id=AH5, first strand: chain 'C' and resid 1827 through 1828 removed outlier: 6.587A pdb=" N VAL C1827 " --> pdb=" O TYR C1895 " (cutoff:3.500A) No H-bonds generated for sheet with id=AH5 Processing sheet with id=AH6, first strand: chain 'C' and resid 1856 through 1858 removed outlier: 6.610A pdb=" N TRP C1847 " --> pdb=" O PHE C1857 " (cutoff:3.500A) Processing sheet with id=AH7, first strand: chain 'C' and resid 1856 through 1858 removed outlier: 6.610A pdb=" N TRP C1847 " --> pdb=" O PHE C1857 " (cutoff:3.500A) Processing sheet with id=AH8, first strand: chain 'C' and resid 1907 through 1910 removed outlier: 6.872A pdb=" N PHE C1907 " --> pdb=" O THR C1975 " (cutoff:3.500A) removed outlier: 7.947A pdb=" N ASN C1977 " --> pdb=" O PHE C1907 " (cutoff:3.500A) removed outlier: 6.846A pdb=" N VAL C1909 " --> pdb=" O ASN C1977 " (cutoff:3.500A) Processing sheet with id=AH9, first strand: chain 'C' and resid 1986 through 1987 Processing sheet with id=AI1, first strand: chain 'C' and resid 1990 through 1992 removed outlier: 7.196A pdb=" N ILE C1991 " --> pdb=" O ASN C2062 " (cutoff:3.500A) Processing sheet with id=AI2, first strand: chain 'C' and resid 2076 through 2077 removed outlier: 6.341A pdb=" N VAL C2076 " --> pdb=" O TYR C2144 " (cutoff:3.500A) No H-bonds generated for sheet with id=AI2 Processing sheet with id=AI3, first strand: chain 'C' and resid 2082 through 2083 Processing sheet with id=AI4, first strand: chain 'C' and resid 2105 through 2107 removed outlier: 6.490A pdb=" N TRP C2096 " --> pdb=" O PHE C2106 " (cutoff:3.500A) Processing sheet with id=AI5, first strand: chain 'C' and resid 2105 through 2107 removed outlier: 6.490A pdb=" N TRP C2096 " --> pdb=" O PHE C2106 " (cutoff:3.500A) Processing sheet with id=AI6, first strand: chain 'C' and resid 2156 through 2159 removed outlier: 6.891A pdb=" N PHE C2156 " --> pdb=" O THR C2224 " (cutoff:3.500A) removed outlier: 8.165A pdb=" N ASN C2226 " --> pdb=" O PHE C2156 " (cutoff:3.500A) removed outlier: 6.860A pdb=" N VAL C2158 " --> pdb=" O ASN C2226 " (cutoff:3.500A) Processing sheet with id=AI7, first strand: chain 'C' and resid 2235 through 2236 Processing sheet with id=AI8, first strand: chain 'C' and resid 2240 through 2241 removed outlier: 6.909A pdb=" N ILE C2240 " --> pdb=" O ASN C2311 " (cutoff:3.500A) No H-bonds generated for sheet with id=AI8 Processing sheet with id=AI9, first strand: chain 'C' and resid 2266 through 2269 Processing sheet with id=AJ1, first strand: chain 'D' and resid 1406 through 1408 Processing sheet with id=AJ2, first strand: chain 'D' and resid 1412 through 1413 removed outlier: 6.622A pdb=" N ILE D1412 " --> pdb=" O ASN D1483 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N ALA D1443 " --> pdb=" O TRP D1432 " (cutoff:3.500A) Processing sheet with id=AJ3, first strand: chain 'D' and resid 1412 through 1413 removed outlier: 6.622A pdb=" N ILE D1412 " --> pdb=" O ASN D1483 " (cutoff:3.500A) Processing sheet with id=AJ4, first strand: chain 'D' and resid 1492 through 1493 Processing sheet with id=AJ5, first strand: chain 'D' and resid 1521 through 1523 Processing sheet with id=AJ6, first strand: chain 'D' and resid 1576 through 1577 removed outlier: 6.736A pdb=" N VAL D1576 " --> pdb=" O ARG D1646 " (cutoff:3.500A) No H-bonds generated for sheet with id=AJ6 Processing sheet with id=AJ7, first strand: chain 'D' and resid 1582 through 1585 Processing sheet with id=AJ8, first strand: chain 'D' and resid 1603 through 1607 Processing sheet with id=AJ9, first strand: chain 'D' and resid 1603 through 1607 Processing sheet with id=AK1, first strand: chain 'D' and resid 1658 through 1661 removed outlier: 6.892A pdb=" N PHE D1658 " --> pdb=" O THR D1726 " (cutoff:3.500A) removed outlier: 7.949A pdb=" N ASN D1728 " --> pdb=" O PHE D1658 " (cutoff:3.500A) removed outlier: 6.872A pdb=" N VAL D1660 " --> pdb=" O ASN D1728 " (cutoff:3.500A) Processing sheet with id=AK2, first strand: chain 'D' and resid 1737 through 1738 Processing sheet with id=AK3, first strand: chain 'D' and resid 1741 through 1743 removed outlier: 7.104A pdb=" N ILE D1742 " --> pdb=" O ASN D1813 " (cutoff:3.500A) Processing sheet with id=AK4, first strand: chain 'D' and resid 1821 through 1823 Processing sheet with id=AK5, first strand: chain 'D' and resid 1827 through 1828 removed outlier: 6.587A pdb=" N VAL D1827 " --> pdb=" O TYR D1895 " (cutoff:3.500A) No H-bonds generated for sheet with id=AK5 Processing sheet with id=AK6, first strand: chain 'D' and resid 1856 through 1858 removed outlier: 6.610A pdb=" N TRP D1847 " --> pdb=" O PHE D1857 " (cutoff:3.500A) Processing sheet with id=AK7, first strand: chain 'D' and resid 1856 through 1858 removed outlier: 6.610A pdb=" N TRP D1847 " --> pdb=" O PHE D1857 " (cutoff:3.500A) Processing sheet with id=AK8, first strand: chain 'D' and resid 1907 through 1910 removed outlier: 6.872A pdb=" N PHE D1907 " --> pdb=" O THR D1975 " (cutoff:3.500A) removed outlier: 7.947A pdb=" N ASN D1977 " --> pdb=" O PHE D1907 " (cutoff:3.500A) removed outlier: 6.845A pdb=" N VAL D1909 " --> pdb=" O ASN D1977 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N SER D1925 " --> pdb=" O VAL D1960 " (cutoff:3.500A) Processing sheet with id=AK9, first strand: chain 'D' and resid 1986 through 1987 Processing sheet with id=AL1, first strand: chain 'D' and resid 1990 through 1992 removed outlier: 7.196A pdb=" N ILE D1991 " --> pdb=" O ASN D2062 " (cutoff:3.500A) Processing sheet with id=AL2, first strand: chain 'D' and resid 2076 through 2077 removed outlier: 6.341A pdb=" N VAL D2076 " --> pdb=" O TYR D2144 " (cutoff:3.500A) No H-bonds generated for sheet with id=AL2 Processing sheet with id=AL3, first strand: chain 'D' and resid 2082 through 2083 Processing sheet with id=AL4, first strand: chain 'D' and resid 2105 through 2107 removed outlier: 6.491A pdb=" N TRP D2096 " --> pdb=" O PHE D2106 " (cutoff:3.500A) Processing sheet with id=AL5, first strand: chain 'D' and resid 2105 through 2107 removed outlier: 6.491A pdb=" N TRP D2096 " --> pdb=" O PHE D2106 " (cutoff:3.500A) Processing sheet with id=AL6, first strand: chain 'D' and resid 2156 through 2159 removed outlier: 6.890A pdb=" N PHE D2156 " --> pdb=" O THR D2224 " (cutoff:3.500A) removed outlier: 8.164A pdb=" N ASN D2226 " --> pdb=" O PHE D2156 " (cutoff:3.500A) removed outlier: 6.860A pdb=" N VAL D2158 " --> pdb=" O ASN D2226 " (cutoff:3.500A) Processing sheet with id=AL7, first strand: chain 'D' and resid 2235 through 2236 Processing sheet with id=AL8, first strand: chain 'D' and resid 2240 through 2241 removed outlier: 6.909A pdb=" N ILE D2240 " --> pdb=" O ASN D2311 " (cutoff:3.500A) No H-bonds generated for sheet with id=AL8 Processing sheet with id=AL9, first strand: chain 'D' and resid 2266 through 2269 Processing sheet with id=AM1, first strand: chain 'E' and resid 1406 through 1408 Processing sheet with id=AM2, first strand: chain 'E' and resid 1412 through 1413 removed outlier: 6.620A pdb=" N ILE E1412 " --> pdb=" O ASN E1483 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N ALA E1443 " --> pdb=" O TRP E1432 " (cutoff:3.500A) Processing sheet with id=AM3, first strand: chain 'E' and resid 1412 through 1413 removed outlier: 6.620A pdb=" N ILE E1412 " --> pdb=" O ASN E1483 " (cutoff:3.500A) Processing sheet with id=AM4, first strand: chain 'E' and resid 1492 through 1493 Processing sheet with id=AM5, first strand: chain 'E' and resid 1521 through 1523 Processing sheet with id=AM6, first strand: chain 'E' and resid 1576 through 1577 removed outlier: 6.736A pdb=" N VAL E1576 " --> pdb=" O ARG E1646 " (cutoff:3.500A) No H-bonds generated for sheet with id=AM6 Processing sheet with id=AM7, first strand: chain 'E' and resid 1582 through 1585 Processing sheet with id=AM8, first strand: chain 'E' and resid 1603 through 1607 Processing sheet with id=AM9, first strand: chain 'E' and resid 1603 through 1607 Processing sheet with id=AN1, first strand: chain 'E' and resid 1658 through 1661 removed outlier: 6.892A pdb=" N PHE E1658 " --> pdb=" O THR E1726 " (cutoff:3.500A) removed outlier: 7.949A pdb=" N ASN E1728 " --> pdb=" O PHE E1658 " (cutoff:3.500A) removed outlier: 6.872A pdb=" N VAL E1660 " --> pdb=" O ASN E1728 " (cutoff:3.500A) Processing sheet with id=AN2, first strand: chain 'E' and resid 1737 through 1738 Processing sheet with id=AN3, first strand: chain 'E' and resid 1741 through 1743 removed outlier: 7.103A pdb=" N ILE E1742 " --> pdb=" O ASN E1813 " (cutoff:3.500A) Processing sheet with id=AN4, first strand: chain 'E' and resid 1821 through 1823 Processing sheet with id=AN5, first strand: chain 'E' and resid 1827 through 1828 removed outlier: 6.587A pdb=" N VAL E1827 " --> pdb=" O TYR E1895 " (cutoff:3.500A) No H-bonds generated for sheet with id=AN5 Processing sheet with id=AN6, first strand: chain 'E' and resid 1856 through 1858 removed outlier: 6.609A pdb=" N TRP E1847 " --> pdb=" O PHE E1857 " (cutoff:3.500A) Processing sheet with id=AN7, first strand: chain 'E' and resid 1856 through 1858 removed outlier: 6.609A pdb=" N TRP E1847 " --> pdb=" O PHE E1857 " (cutoff:3.500A) Processing sheet with id=AN8, first strand: chain 'E' and resid 1907 through 1910 removed outlier: 6.871A pdb=" N PHE E1907 " --> pdb=" O THR E1975 " (cutoff:3.500A) removed outlier: 7.947A pdb=" N ASN E1977 " --> pdb=" O PHE E1907 " (cutoff:3.500A) removed outlier: 6.845A pdb=" N VAL E1909 " --> pdb=" O ASN E1977 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N SER E1925 " --> pdb=" O VAL E1960 " (cutoff:3.500A) Processing sheet with id=AN9, first strand: chain 'E' and resid 1986 through 1987 Processing sheet with id=AO1, first strand: chain 'E' and resid 1990 through 1992 removed outlier: 7.197A pdb=" N ILE E1991 " --> pdb=" O ASN E2062 " (cutoff:3.500A) Processing sheet with id=AO2, first strand: chain 'E' and resid 2076 through 2077 removed outlier: 6.342A pdb=" N VAL E2076 " --> pdb=" O TYR E2144 " (cutoff:3.500A) No H-bonds generated for sheet with id=AO2 Processing sheet with id=AO3, first strand: chain 'E' and resid 2082 through 2083 Processing sheet with id=AO4, first strand: chain 'E' and resid 2105 through 2107 removed outlier: 6.491A pdb=" N TRP E2096 " --> pdb=" O PHE E2106 " (cutoff:3.500A) Processing sheet with id=AO5, first strand: chain 'E' and resid 2105 through 2107 removed outlier: 6.491A pdb=" N TRP E2096 " --> pdb=" O PHE E2106 " (cutoff:3.500A) Processing sheet with id=AO6, first strand: chain 'E' and resid 2156 through 2159 removed outlier: 6.890A pdb=" N PHE E2156 " --> pdb=" O THR E2224 " (cutoff:3.500A) removed outlier: 8.164A pdb=" N ASN E2226 " --> pdb=" O PHE E2156 " (cutoff:3.500A) removed outlier: 6.860A pdb=" N VAL E2158 " --> pdb=" O ASN E2226 " (cutoff:3.500A) Processing sheet with id=AO7, first strand: chain 'E' and resid 2235 through 2236 Processing sheet with id=AO8, first strand: chain 'E' and resid 2240 through 2241 removed outlier: 6.909A pdb=" N ILE E2240 " --> pdb=" O ASN E2311 " (cutoff:3.500A) No H-bonds generated for sheet with id=AO8 Processing sheet with id=AO9, first strand: chain 'E' and resid 2266 through 2269 Processing sheet with id=AP1, first strand: chain 'F' and resid 1406 through 1408 Processing sheet with id=AP2, first strand: chain 'F' and resid 1412 through 1413 removed outlier: 6.621A pdb=" N ILE F1412 " --> pdb=" O ASN F1483 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N ALA F1443 " --> pdb=" O TRP F1432 " (cutoff:3.500A) Processing sheet with id=AP3, first strand: chain 'F' and resid 1412 through 1413 removed outlier: 6.621A pdb=" N ILE F1412 " --> pdb=" O ASN F1483 " (cutoff:3.500A) Processing sheet with id=AP4, first strand: chain 'F' and resid 1492 through 1493 Processing sheet with id=AP5, first strand: chain 'F' and resid 1521 through 1523 Processing sheet with id=AP6, first strand: chain 'F' and resid 1576 through 1577 removed outlier: 6.735A pdb=" N VAL F1576 " --> pdb=" O ARG F1646 " (cutoff:3.500A) No H-bonds generated for sheet with id=AP6 Processing sheet with id=AP7, first strand: chain 'F' and resid 1582 through 1585 Processing sheet with id=AP8, first strand: chain 'F' and resid 1603 through 1607 Processing sheet with id=AP9, first strand: chain 'F' and resid 1603 through 1607 Processing sheet with id=AQ1, first strand: chain 'F' and resid 1658 through 1661 removed outlier: 6.891A pdb=" N PHE F1658 " --> pdb=" O THR F1726 " (cutoff:3.500A) removed outlier: 7.949A pdb=" N ASN F1728 " --> pdb=" O PHE F1658 " (cutoff:3.500A) removed outlier: 6.872A pdb=" N VAL F1660 " --> pdb=" O ASN F1728 " (cutoff:3.500A) Processing sheet with id=AQ2, first strand: chain 'F' and resid 1737 through 1738 Processing sheet with id=AQ3, first strand: chain 'F' and resid 1741 through 1743 removed outlier: 7.103A pdb=" N ILE F1742 " --> pdb=" O ASN F1813 " (cutoff:3.500A) Processing sheet with id=AQ4, first strand: chain 'F' and resid 1821 through 1823 Processing sheet with id=AQ5, first strand: chain 'F' and resid 1827 through 1828 removed outlier: 6.588A pdb=" N VAL F1827 " --> pdb=" O TYR F1895 " (cutoff:3.500A) No H-bonds generated for sheet with id=AQ5 Processing sheet with id=AQ6, first strand: chain 'F' and resid 1856 through 1858 removed outlier: 6.609A pdb=" N TRP F1847 " --> pdb=" O PHE F1857 " (cutoff:3.500A) Processing sheet with id=AQ7, first strand: chain 'F' and resid 1856 through 1858 removed outlier: 6.609A pdb=" N TRP F1847 " --> pdb=" O PHE F1857 " (cutoff:3.500A) Processing sheet with id=AQ8, first strand: chain 'F' and resid 1907 through 1910 removed outlier: 6.871A pdb=" N PHE F1907 " --> pdb=" O THR F1975 " (cutoff:3.500A) removed outlier: 7.947A pdb=" N ASN F1977 " --> pdb=" O PHE F1907 " (cutoff:3.500A) removed outlier: 6.845A pdb=" N VAL F1909 " --> pdb=" O ASN F1977 " (cutoff:3.500A) Processing sheet with id=AQ9, first strand: chain 'F' and resid 1986 through 1987 Processing sheet with id=AR1, first strand: chain 'F' and resid 1990 through 1992 removed outlier: 7.195A pdb=" N ILE F1991 " --> pdb=" O ASN F2062 " (cutoff:3.500A) Processing sheet with id=AR2, first strand: chain 'F' and resid 2076 through 2077 removed outlier: 6.342A pdb=" N VAL F2076 " --> pdb=" O TYR F2144 " (cutoff:3.500A) No H-bonds generated for sheet with id=AR2 Processing sheet with id=AR3, first strand: chain 'F' and resid 2082 through 2083 Processing sheet with id=AR4, first strand: chain 'F' and resid 2105 through 2107 removed outlier: 6.490A pdb=" N TRP F2096 " --> pdb=" O PHE F2106 " (cutoff:3.500A) Processing sheet with id=AR5, first strand: chain 'F' and resid 2105 through 2107 removed outlier: 6.490A pdb=" N TRP F2096 " --> pdb=" O PHE F2106 " (cutoff:3.500A) Processing sheet with id=AR6, first strand: chain 'F' and resid 2156 through 2159 removed outlier: 6.890A pdb=" N PHE F2156 " --> pdb=" O THR F2224 " (cutoff:3.500A) removed outlier: 8.164A pdb=" N ASN F2226 " --> pdb=" O PHE F2156 " (cutoff:3.500A) removed outlier: 6.860A pdb=" N VAL F2158 " --> pdb=" O ASN F2226 " (cutoff:3.500A) Processing sheet with id=AR7, first strand: chain 'F' and resid 2235 through 2236 Processing sheet with id=AR8, first strand: chain 'F' and resid 2240 through 2241 removed outlier: 6.908A pdb=" N ILE F2240 " --> pdb=" O ASN F2311 " (cutoff:3.500A) No H-bonds generated for sheet with id=AR8 Processing sheet with id=AR9, first strand: chain 'F' and resid 2266 through 2269 Processing sheet with id=AS1, first strand: chain 'G' and resid 1406 through 1408 Processing sheet with id=AS2, first strand: chain 'G' and resid 1412 through 1413 removed outlier: 6.620A pdb=" N ILE G1412 " --> pdb=" O ASN G1483 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N ALA G1443 " --> pdb=" O TRP G1432 " (cutoff:3.500A) Processing sheet with id=AS3, first strand: chain 'G' and resid 1412 through 1413 removed outlier: 6.620A pdb=" N ILE G1412 " --> pdb=" O ASN G1483 " (cutoff:3.500A) Processing sheet with id=AS4, first strand: chain 'G' and resid 1492 through 1493 Processing sheet with id=AS5, first strand: chain 'G' and resid 1521 through 1523 Processing sheet with id=AS6, first strand: chain 'G' and resid 1576 through 1577 removed outlier: 6.735A pdb=" N VAL G1576 " --> pdb=" O ARG G1646 " (cutoff:3.500A) No H-bonds generated for sheet with id=AS6 Processing sheet with id=AS7, first strand: chain 'G' and resid 1582 through 1585 Processing sheet with id=AS8, first strand: chain 'G' and resid 1603 through 1607 Processing sheet with id=AS9, first strand: chain 'G' and resid 1603 through 1607 Processing sheet with id=AT1, first strand: chain 'G' and resid 1658 through 1661 removed outlier: 6.892A pdb=" N PHE G1658 " --> pdb=" O THR G1726 " (cutoff:3.500A) removed outlier: 7.948A pdb=" N ASN G1728 " --> pdb=" O PHE G1658 " (cutoff:3.500A) removed outlier: 6.872A pdb=" N VAL G1660 " --> pdb=" O ASN G1728 " (cutoff:3.500A) Processing sheet with id=AT2, first strand: chain 'G' and resid 1737 through 1738 Processing sheet with id=AT3, first strand: chain 'G' and resid 1741 through 1743 removed outlier: 7.103A pdb=" N ILE G1742 " --> pdb=" O ASN G1813 " (cutoff:3.500A) Processing sheet with id=AT4, first strand: chain 'G' and resid 1821 through 1823 Processing sheet with id=AT5, first strand: chain 'G' and resid 1827 through 1828 removed outlier: 6.588A pdb=" N VAL G1827 " --> pdb=" O TYR G1895 " (cutoff:3.500A) No H-bonds generated for sheet with id=AT5 Processing sheet with id=AT6, first strand: chain 'G' and resid 1856 through 1858 removed outlier: 6.609A pdb=" N TRP G1847 " --> pdb=" O PHE G1857 " (cutoff:3.500A) Processing sheet with id=AT7, first strand: chain 'G' and resid 1856 through 1858 removed outlier: 6.609A pdb=" N TRP G1847 " --> pdb=" O PHE G1857 " (cutoff:3.500A) Processing sheet with id=AT8, first strand: chain 'G' and resid 1907 through 1910 removed outlier: 6.872A pdb=" N PHE G1907 " --> pdb=" O THR G1975 " (cutoff:3.500A) removed outlier: 7.947A pdb=" N ASN G1977 " --> pdb=" O PHE G1907 " (cutoff:3.500A) removed outlier: 6.845A pdb=" N VAL G1909 " --> pdb=" O ASN G1977 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N SER G1925 " --> pdb=" O VAL G1960 " (cutoff:3.500A) Processing sheet with id=AT9, first strand: chain 'G' and resid 1986 through 1987 Processing sheet with id=AU1, first strand: chain 'G' and resid 1990 through 1992 removed outlier: 7.197A pdb=" N ILE G1991 " --> pdb=" O ASN G2062 " (cutoff:3.500A) Processing sheet with id=AU2, first strand: chain 'G' and resid 2076 through 2077 removed outlier: 6.342A pdb=" N VAL G2076 " --> pdb=" O TYR G2144 " (cutoff:3.500A) No H-bonds generated for sheet with id=AU2 Processing sheet with id=AU3, first strand: chain 'G' and resid 2082 through 2083 Processing sheet with id=AU4, first strand: chain 'G' and resid 2105 through 2107 removed outlier: 6.491A pdb=" N TRP G2096 " --> pdb=" O PHE G2106 " (cutoff:3.500A) Processing sheet with id=AU5, first strand: chain 'G' and resid 2105 through 2107 removed outlier: 6.491A pdb=" N TRP G2096 " --> pdb=" O PHE G2106 " (cutoff:3.500A) Processing sheet with id=AU6, first strand: chain 'G' and resid 2156 through 2159 removed outlier: 6.890A pdb=" N PHE G2156 " --> pdb=" O THR G2224 " (cutoff:3.500A) removed outlier: 8.164A pdb=" N ASN G2226 " --> pdb=" O PHE G2156 " (cutoff:3.500A) removed outlier: 6.859A pdb=" N VAL G2158 " --> pdb=" O ASN G2226 " (cutoff:3.500A) Processing sheet with id=AU7, first strand: chain 'G' and resid 2235 through 2236 Processing sheet with id=AU8, first strand: chain 'G' and resid 2240 through 2241 removed outlier: 6.909A pdb=" N ILE G2240 " --> pdb=" O ASN G2311 " (cutoff:3.500A) No H-bonds generated for sheet with id=AU8 Processing sheet with id=AU9, first strand: chain 'G' and resid 2266 through 2269 1703 hydrogen bonds defined for protein. 3822 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: 17.91 Time building geometry restraints manager: 5.69 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.34: 14895 1.34 - 1.46: 11897 1.46 - 1.59: 18995 1.59 - 1.72: 0 1.72 - 1.84: 266 Bond restraints: 46053 Sorted by residual: bond pdb=" CA TYR B2144 " pdb=" C TYR B2144 " ideal model delta sigma weight residual 1.528 1.479 0.049 1.11e-02 8.12e+03 1.97e+01 bond pdb=" CA TYR G2144 " pdb=" C TYR G2144 " ideal model delta sigma weight residual 1.528 1.479 0.049 1.11e-02 8.12e+03 1.95e+01 bond pdb=" CA TYR A2144 " pdb=" C TYR A2144 " ideal model delta sigma weight residual 1.528 1.480 0.049 1.11e-02 8.12e+03 1.93e+01 bond pdb=" CA TYR E2144 " pdb=" C TYR E2144 " ideal model delta sigma weight residual 1.528 1.480 0.049 1.11e-02 8.12e+03 1.93e+01 bond pdb=" CA TYR C2144 " pdb=" C TYR C2144 " ideal model delta sigma weight residual 1.528 1.480 0.049 1.11e-02 8.12e+03 1.92e+01 ... (remaining 46048 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.68: 58641 2.68 - 5.36: 4608 5.36 - 8.04: 387 8.04 - 10.72: 92 10.72 - 13.40: 21 Bond angle restraints: 63749 Sorted by residual: angle pdb=" N TYR F2097 " pdb=" CA TYR F2097 " pdb=" CB TYR F2097 " ideal model delta sigma weight residual 111.37 97.97 13.40 1.82e+00 3.02e-01 5.42e+01 angle pdb=" N TYR G2097 " pdb=" CA TYR G2097 " pdb=" CB TYR G2097 " ideal model delta sigma weight residual 111.37 97.97 13.40 1.82e+00 3.02e-01 5.42e+01 angle pdb=" N TYR D2097 " pdb=" CA TYR D2097 " pdb=" CB TYR D2097 " ideal model delta sigma weight residual 111.37 97.99 13.38 1.82e+00 3.02e-01 5.40e+01 angle pdb=" N TYR C2097 " pdb=" CA TYR C2097 " pdb=" CB TYR C2097 " ideal model delta sigma weight residual 111.37 97.99 13.38 1.82e+00 3.02e-01 5.40e+01 angle pdb=" N TYR E2097 " pdb=" CA TYR E2097 " pdb=" CB TYR E2097 " ideal model delta sigma weight residual 111.37 97.99 13.38 1.82e+00 3.02e-01 5.40e+01 ... (remaining 63744 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.88: 26453 17.88 - 35.75: 630 35.75 - 53.63: 140 53.63 - 71.50: 49 71.50 - 89.38: 14 Dihedral angle restraints: 27286 sinusoidal: 8932 harmonic: 18354 Sorted by residual: dihedral pdb=" CD ARG G1564 " pdb=" NE ARG G1564 " pdb=" CZ ARG G1564 " pdb=" NH1 ARG G1564 " ideal model delta sinusoidal sigma weight residual 0.00 70.75 -70.75 1 1.00e+01 1.00e-02 6.44e+01 dihedral pdb=" CD ARG F1564 " pdb=" NE ARG F1564 " pdb=" CZ ARG F1564 " pdb=" NH1 ARG F1564 " ideal model delta sinusoidal sigma weight residual 0.00 70.75 -70.75 1 1.00e+01 1.00e-02 6.43e+01 dihedral pdb=" CD ARG D1564 " pdb=" NE ARG D1564 " pdb=" CZ ARG D1564 " pdb=" NH1 ARG D1564 " ideal model delta sinusoidal sigma weight residual 0.00 70.74 -70.74 1 1.00e+01 1.00e-02 6.43e+01 ... (remaining 27283 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.052: 4682 0.052 - 0.104: 2253 0.104 - 0.156: 695 0.156 - 0.208: 251 0.208 - 0.259: 71 Chirality restraints: 7952 Sorted by residual: chirality pdb=" CA VAL B1422 " pdb=" N VAL B1422 " pdb=" C VAL B1422 " pdb=" CB VAL B1422 " both_signs ideal model delta sigma weight residual False 2.44 2.70 -0.26 2.00e-01 2.50e+01 1.68e+00 chirality pdb=" CA VAL E1422 " pdb=" N VAL E1422 " pdb=" C VAL E1422 " pdb=" CB VAL E1422 " both_signs ideal model delta sigma weight residual False 2.44 2.70 -0.26 2.00e-01 2.50e+01 1.67e+00 chirality pdb=" CA VAL D1422 " pdb=" N VAL D1422 " pdb=" C VAL D1422 " pdb=" CB VAL D1422 " both_signs ideal model delta sigma weight residual False 2.44 2.70 -0.26 2.00e-01 2.50e+01 1.66e+00 ... (remaining 7949 not shown) Planarity restraints: 8393 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG C1564 " 1.014 9.50e-02 1.11e+02 4.54e-01 1.25e+02 pdb=" NE ARG C1564 " -0.060 2.00e-02 2.50e+03 pdb=" CZ ARG C1564 " -0.016 2.00e-02 2.50e+03 pdb=" NH1 ARG C1564 " 0.008 2.00e-02 2.50e+03 pdb=" NH2 ARG C1564 " 0.023 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG A1564 " 1.014 9.50e-02 1.11e+02 4.54e-01 1.25e+02 pdb=" NE ARG A1564 " -0.060 2.00e-02 2.50e+03 pdb=" CZ ARG A1564 " -0.016 2.00e-02 2.50e+03 pdb=" NH1 ARG A1564 " 0.008 2.00e-02 2.50e+03 pdb=" NH2 ARG A1564 " 0.023 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG G1564 " 1.014 9.50e-02 1.11e+02 4.54e-01 1.25e+02 pdb=" NE ARG G1564 " -0.059 2.00e-02 2.50e+03 pdb=" CZ ARG G1564 " -0.016 2.00e-02 2.50e+03 pdb=" NH1 ARG G1564 " 0.008 2.00e-02 2.50e+03 pdb=" NH2 ARG G1564 " 0.023 2.00e-02 2.50e+03 ... (remaining 8390 not shown) Histogram of nonbonded interaction distances: 1.55 - 2.22: 14 2.22 - 2.89: 20906 2.89 - 3.56: 61426 3.56 - 4.23: 107761 4.23 - 4.90: 172285 Nonbonded interactions: 362392 Sorted by model distance: nonbonded pdb=" SD MET B1405 " pdb=" OH TYR C1433 " model vdw 1.546 3.400 nonbonded pdb=" SD MET D1405 " pdb=" OH TYR E1433 " model vdw 1.547 3.400 nonbonded pdb=" SD MET C1405 " pdb=" OH TYR D1433 " model vdw 1.568 3.400 nonbonded pdb=" OH TYR A1433 " pdb=" SD MET G1405 " model vdw 1.584 3.400 nonbonded pdb=" SD MET A1405 " pdb=" OH TYR B1433 " model vdw 1.586 3.400 ... (remaining 362387 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: 0.16 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' } 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: 14.080 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.030 Construct map_model_manager: 0.060 Extract box with map and model: 0.570 Check model and map are aligned: 0.140 Set scattering table: 0.130 Process input model: 50.060 Find NCS groups from input model: 0.560 Set up NCS constraints: 0.150 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.240 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 67.030 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8262 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 : 0.017 0.120 46123 Z= 0.870 Angle : 1.534 13.397 63889 Z= 0.995 Chirality : 0.070 0.259 7952 Planarity : 0.015 0.454 8393 Dihedral : 9.131 89.380 15302 Min Nonbonded Distance : 1.546 Molprobity Statistics. All-atom Clashscore : 6.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.54 % Favored : 98.46 % Rotamer: Outliers : 0.00 % Allowed : 0.81 % Favored : 99.19 % Cbeta Deviations : 0.71 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.95 (0.10), residues: 6370 helix: None (None), residues: 0 sheet: 1.12 (0.10), residues: 2555 loop : 0.38 (0.10), residues: 3815 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG F1564 TYR 0.055 0.006 TYR F2034 PHE 0.032 0.006 PHE E2156 TRP 0.050 0.009 TRP F1598 Details of bonding type rmsd covalent geometry : bond 0.01664 (46053) covalent geometry : angle 1.53204 (63749) SS BOND : bond 0.00431 ( 70) SS BOND : angle 2.32134 ( 140) hydrogen bonds : bond 0.16487 ( 1479) hydrogen bonds : angle 8.96083 ( 3822) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12740 Ramachandran restraints generated. 6370 Oldfield, 0 Emsley, 6370 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12740 Ramachandran restraints generated. 6370 Oldfield, 0 Emsley, 6370 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 291 residues out of total 5201 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 291 time to evaluate : 1.593 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 1438 LEU cc_start: 0.7453 (mt) cc_final: 0.7225 (mt) REVERT: A 1480 VAL cc_start: 0.7912 (t) cc_final: 0.7676 (p) REVERT: A 1736 MET cc_start: 0.8581 (ttm) cc_final: 0.8240 (ttp) REVERT: A 1944 ILE cc_start: 0.8811 (mt) cc_final: 0.8577 (mm) REVERT: A 1985 MET cc_start: 0.8454 (ttm) cc_final: 0.7911 (ttm) REVERT: A 2034 TYR cc_start: 0.8725 (t80) cc_final: 0.8423 (t80) REVERT: A 2051 SER cc_start: 0.8413 (p) cc_final: 0.8142 (t) REVERT: A 2076 VAL cc_start: 0.8666 (t) cc_final: 0.8304 (p) REVERT: B 1480 VAL cc_start: 0.7539 (t) cc_final: 0.7254 (p) REVERT: B 1857 PHE cc_start: 0.7845 (t80) cc_final: 0.7386 (t80) REVERT: B 1985 MET cc_start: 0.8532 (ttm) cc_final: 0.8098 (ttm) REVERT: B 2051 SER cc_start: 0.8722 (p) cc_final: 0.8521 (t) REVERT: C 1480 VAL cc_start: 0.7651 (t) cc_final: 0.7388 (p) REVERT: C 1664 ASP cc_start: 0.8401 (t0) cc_final: 0.7732 (m-30) REVERT: D 1480 VAL cc_start: 0.8262 (t) cc_final: 0.8053 (p) REVERT: D 2034 TYR cc_start: 0.8888 (t80) cc_final: 0.8665 (t80) REVERT: D 2076 VAL cc_start: 0.8602 (t) cc_final: 0.8284 (p) REVERT: E 1480 VAL cc_start: 0.7446 (t) cc_final: 0.7182 (p) REVERT: E 2034 TYR cc_start: 0.8650 (t80) cc_final: 0.8388 (t80) REVERT: E 2076 VAL cc_start: 0.8942 (t) cc_final: 0.8462 (m) REVERT: F 1480 VAL cc_start: 0.8250 (t) cc_final: 0.8038 (p) REVERT: F 1662 GLU cc_start: 0.8492 (mt-10) cc_final: 0.8197 (mt-10) REVERT: F 1874 PHE cc_start: 0.9211 (m-80) cc_final: 0.8843 (m-80) REVERT: F 2061 ILE cc_start: 0.9391 (mt) cc_final: 0.9087 (pt) REVERT: F 2248 MET cc_start: 0.8235 (mtp) cc_final: 0.7469 (mtp) REVERT: G 1480 VAL cc_start: 0.7620 (t) cc_final: 0.7365 (p) REVERT: G 2034 TYR cc_start: 0.8843 (t80) cc_final: 0.8527 (t80) REVERT: G 2061 ILE cc_start: 0.9403 (mt) cc_final: 0.8976 (mt) REVERT: G 2248 MET cc_start: 0.8218 (mtp) cc_final: 0.7691 (mtt) outliers start: 0 outliers final: 0 residues processed: 291 average time/residue: 0.2089 time to fit residues: 108.4639 Evaluate side-chains 108 residues out of total 5201 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 108 time to evaluate : 1.027 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 637 random chunks: chunk 394 optimal weight: 0.9980 chunk 430 optimal weight: 4.9990 chunk 41 optimal weight: 0.9990 chunk 265 optimal weight: 4.9990 chunk 523 optimal weight: 2.9990 chunk 497 optimal weight: 0.7980 chunk 414 optimal weight: 8.9990 chunk 310 optimal weight: 0.6980 chunk 488 optimal weight: 0.6980 chunk 366 optimal weight: 1.9990 chunk 597 optimal weight: 0.7980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1446 GLN A1856 GLN A2237 ASN B1446 GLN B1856 GLN B1973 GLN B2237 ASN C1446 GLN C1683 ASN C1856 GLN C2237 ASN D1856 GLN D2237 ASN E1446 GLN E1856 GLN E2237 ASN F1446 GLN F1856 GLN F2237 ASN G1446 GLN G1856 GLN G2237 ASN Total number of N/Q/H flips: 22 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3186 r_free = 0.3186 target = 0.076087 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2894 r_free = 0.2894 target = 0.062941 restraints weight = 135089.928| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.2938 r_free = 0.2938 target = 0.064802 restraints weight = 60924.201| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.2965 r_free = 0.2965 target = 0.066007 restraints weight = 34532.114| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.2983 r_free = 0.2983 target = 0.066795 restraints weight = 22576.656| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.2994 r_free = 0.2994 target = 0.067306 restraints weight = 16292.843| |-----------------------------------------------------------------------------| r_work (final): 0.2948 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8443 moved from start: 0.1920 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 46123 Z= 0.173 Angle : 0.639 7.959 63889 Z= 0.343 Chirality : 0.047 0.213 7952 Planarity : 0.005 0.055 8393 Dihedral : 5.225 22.453 6615 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 6.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.44 % Favored : 98.56 % Rotamer: Outliers : 0.85 % Allowed : 3.83 % Favored : 95.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.94 (0.10), residues: 6370 helix: None (None), residues: 0 sheet: 0.93 (0.10), residues: 2639 loop : 0.51 (0.10), residues: 3731 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A1564 TYR 0.026 0.002 TYR F2034 PHE 0.016 0.001 PHE G1857 TRP 0.017 0.003 TRP C2177 Details of bonding type rmsd covalent geometry : bond 0.00352 (46053) covalent geometry : angle 0.63679 (63749) SS BOND : bond 0.00469 ( 70) SS BOND : angle 1.20862 ( 140) hydrogen bonds : bond 0.04443 ( 1479) hydrogen bonds : angle 6.75494 ( 3822) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12740 Ramachandran restraints generated. 6370 Oldfield, 0 Emsley, 6370 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12740 Ramachandran restraints generated. 6370 Oldfield, 0 Emsley, 6370 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 183 residues out of total 5201 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 139 time to evaluate : 1.883 Fit side-chains REVERT: A 1438 LEU cc_start: 0.7606 (mt) cc_final: 0.7394 (mt) REVERT: A 1519 ASN cc_start: 0.9031 (OUTLIER) cc_final: 0.8785 (t0) REVERT: B 1496 LEU cc_start: 0.8747 (OUTLIER) cc_final: 0.8440 (tt) REVERT: B 1857 PHE cc_start: 0.8042 (t80) cc_final: 0.7685 (t80) REVERT: B 2051 SER cc_start: 0.8854 (p) cc_final: 0.8614 (t) REVERT: C 1438 LEU cc_start: 0.8103 (OUTLIER) cc_final: 0.7813 (mt) REVERT: C 1480 VAL cc_start: 0.8026 (t) cc_final: 0.7720 (p) REVERT: D 1438 LEU cc_start: 0.7288 (mt) cc_final: 0.6946 (mt) REVERT: D 1496 LEU cc_start: 0.8304 (OUTLIER) cc_final: 0.7939 (tt) REVERT: D 1519 ASN cc_start: 0.8997 (OUTLIER) cc_final: 0.8435 (t0) REVERT: D 1533 SER cc_start: 0.8959 (t) cc_final: 0.8664 (p) REVERT: D 2034 TYR cc_start: 0.9150 (t80) cc_final: 0.8691 (t80) REVERT: E 1480 VAL cc_start: 0.7964 (t) cc_final: 0.7663 (p) REVERT: E 1519 ASN cc_start: 0.8898 (OUTLIER) cc_final: 0.8587 (t0) REVERT: F 1438 LEU cc_start: 0.7786 (mt) cc_final: 0.7457 (mt) REVERT: F 1519 ASN cc_start: 0.9130 (OUTLIER) cc_final: 0.8685 (t0) REVERT: F 2248 MET cc_start: 0.8155 (mtp) cc_final: 0.7744 (mtt) REVERT: G 1519 ASN cc_start: 0.9133 (OUTLIER) cc_final: 0.8410 (t0) outliers start: 44 outliers final: 16 residues processed: 177 average time/residue: 0.2024 time to fit residues: 66.8202 Evaluate side-chains 105 residues out of total 5201 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 81 time to evaluate : 1.866 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1519 ASN Chi-restraints excluded: chain A residue 1570 ILE Chi-restraints excluded: chain A residue 2061 ILE Chi-restraints excluded: chain A residue 2253 THR Chi-restraints excluded: chain B residue 1496 LEU Chi-restraints excluded: chain B residue 2049 CYS Chi-restraints excluded: chain B residue 2253 THR Chi-restraints excluded: chain C residue 1438 LEU Chi-restraints excluded: chain C residue 1963 ASN Chi-restraints excluded: chain C residue 2253 THR Chi-restraints excluded: chain D residue 1496 LEU Chi-restraints excluded: chain D residue 1519 ASN Chi-restraints excluded: chain D residue 1944 ILE Chi-restraints excluded: chain D residue 1963 ASN Chi-restraints excluded: chain D residue 2253 THR Chi-restraints excluded: chain E residue 1519 ASN Chi-restraints excluded: chain E residue 1963 ASN Chi-restraints excluded: chain F residue 1519 ASN Chi-restraints excluded: chain F residue 1570 ILE Chi-restraints excluded: chain F residue 1841 SER Chi-restraints excluded: chain F residue 1963 ASN Chi-restraints excluded: chain F residue 2253 THR Chi-restraints excluded: chain G residue 1519 ASN Chi-restraints excluded: chain G residue 1963 ASN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 637 random chunks: chunk 351 optimal weight: 0.8980 chunk 537 optimal weight: 0.9980 chunk 240 optimal weight: 3.9990 chunk 461 optimal weight: 7.9990 chunk 322 optimal weight: 1.9990 chunk 160 optimal weight: 0.6980 chunk 470 optimal weight: 3.9990 chunk 632 optimal weight: 10.0000 chunk 543 optimal weight: 9.9990 chunk 199 optimal weight: 3.9990 chunk 280 optimal weight: 2.9990 overall best weight: 1.5184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1765 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1951 ASN ** B1765 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1951 ASN ** C1765 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1951 ASN D1446 GLN D1447 ASN D1951 ASN E1683 ASN ** E1765 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F1683 ASN ** F1765 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G1683 ASN ** G1765 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3085 r_free = 0.3085 target = 0.070674 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.2784 r_free = 0.2784 target = 0.057922 restraints weight = 139086.780| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.2827 r_free = 0.2827 target = 0.059624 restraints weight = 62701.969| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.2855 r_free = 0.2855 target = 0.060734 restraints weight = 35525.278| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.2872 r_free = 0.2872 target = 0.061452 restraints weight = 23231.843| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.2884 r_free = 0.2884 target = 0.061939 restraints weight = 16956.398| |-----------------------------------------------------------------------------| r_work (final): 0.2837 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8597 moved from start: 0.2985 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 46123 Z= 0.219 Angle : 0.611 8.312 63889 Z= 0.324 Chirality : 0.046 0.206 7952 Planarity : 0.005 0.056 8393 Dihedral : 4.813 29.214 6615 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 5.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.72 % Favored : 97.28 % Rotamer: Outliers : 1.02 % Allowed : 5.13 % Favored : 93.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.72 (0.10), residues: 6370 helix: None (None), residues: 0 sheet: 0.82 (0.10), residues: 2555 loop : 0.33 (0.10), residues: 3815 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B1564 TYR 0.017 0.002 TYR F1430 PHE 0.024 0.002 PHE A2106 TRP 0.018 0.002 TRP G2177 Details of bonding type rmsd covalent geometry : bond 0.00492 (46053) covalent geometry : angle 0.60905 (63749) SS BOND : bond 0.00196 ( 70) SS BOND : angle 1.19791 ( 140) hydrogen bonds : bond 0.04345 ( 1479) hydrogen bonds : angle 6.01448 ( 3822) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12740 Ramachandran restraints generated. 6370 Oldfield, 0 Emsley, 6370 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12740 Ramachandran restraints generated. 6370 Oldfield, 0 Emsley, 6370 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 5201 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 88 time to evaluate : 1.614 Fit side-chains REVERT: A 1438 LEU cc_start: 0.8321 (mt) cc_final: 0.8103 (mt) REVERT: B 1999 MET cc_start: 0.8831 (mtm) cc_final: 0.8439 (mtm) REVERT: C 2034 TYR cc_start: 0.8938 (t80) cc_final: 0.8695 (t80) REVERT: D 1438 LEU cc_start: 0.7737 (mt) cc_final: 0.7490 (mt) REVERT: D 2034 TYR cc_start: 0.9215 (t80) cc_final: 0.8927 (t80) REVERT: E 1405 MET cc_start: 0.8608 (mmt) cc_final: 0.8308 (mmt) REVERT: F 1421 MET cc_start: 0.7384 (mtp) cc_final: 0.5924 (ttt) REVERT: F 1438 LEU cc_start: 0.8126 (mt) cc_final: 0.7912 (mt) REVERT: F 2248 MET cc_start: 0.8145 (mtp) cc_final: 0.7856 (mtt) outliers start: 53 outliers final: 34 residues processed: 134 average time/residue: 0.2057 time to fit residues: 51.8278 Evaluate side-chains 106 residues out of total 5201 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 72 time to evaluate : 2.261 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1424 THR Chi-restraints excluded: chain A residue 1496 LEU Chi-restraints excluded: chain A residue 2061 ILE Chi-restraints excluded: chain A residue 2069 SER Chi-restraints excluded: chain A residue 2253 THR Chi-restraints excluded: chain B residue 1424 THR Chi-restraints excluded: chain B residue 2253 THR Chi-restraints excluded: chain B residue 2313 ILE Chi-restraints excluded: chain C residue 1496 LEU Chi-restraints excluded: chain C residue 2061 ILE Chi-restraints excluded: chain C residue 2253 THR Chi-restraints excluded: chain C residue 2313 ILE Chi-restraints excluded: chain D residue 1736 MET Chi-restraints excluded: chain D residue 1768 ASP Chi-restraints excluded: chain D residue 1963 ASN Chi-restraints excluded: chain D residue 2049 CYS Chi-restraints excluded: chain D residue 2197 THR Chi-restraints excluded: chain D residue 2253 THR Chi-restraints excluded: chain E residue 1496 LEU Chi-restraints excluded: chain E residue 1736 MET Chi-restraints excluded: chain E residue 1924 SER Chi-restraints excluded: chain E residue 1963 ASN Chi-restraints excluded: chain E residue 2238 SER Chi-restraints excluded: chain E residue 2253 THR Chi-restraints excluded: chain F residue 1496 LEU Chi-restraints excluded: chain F residue 1570 ILE Chi-restraints excluded: chain F residue 1841 SER Chi-restraints excluded: chain F residue 2197 THR Chi-restraints excluded: chain F residue 2238 SER Chi-restraints excluded: chain F residue 2253 THR Chi-restraints excluded: chain F residue 2313 ILE Chi-restraints excluded: chain G residue 1496 LEU Chi-restraints excluded: chain G residue 1795 VAL Chi-restraints excluded: chain G residue 2069 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 637 random chunks: chunk 588 optimal weight: 0.9990 chunk 628 optimal weight: 0.9990 chunk 399 optimal weight: 2.9990 chunk 446 optimal weight: 0.0270 chunk 11 optimal weight: 1.9990 chunk 247 optimal weight: 4.9990 chunk 524 optimal weight: 3.9990 chunk 76 optimal weight: 3.9990 chunk 465 optimal weight: 3.9990 chunk 127 optimal weight: 0.8980 chunk 240 optimal weight: 0.8980 overall best weight: 0.7642 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1765 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1932 ASN B1951 ASN ** C1765 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1932 ASN C1951 ASN D1447 ASN ** E1765 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E1951 ASN ** G1765 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3109 r_free = 0.3109 target = 0.071416 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2813 r_free = 0.2813 target = 0.058677 restraints weight = 137798.544| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.2856 r_free = 0.2856 target = 0.060411 restraints weight = 61947.160| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.2883 r_free = 0.2883 target = 0.061548 restraints weight = 34903.879| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.2901 r_free = 0.2901 target = 0.062282 restraints weight = 22681.039| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.2913 r_free = 0.2913 target = 0.062769 restraints weight = 16485.915| |-----------------------------------------------------------------------------| r_work (final): 0.2863 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8568 moved from start: 0.3266 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 46123 Z= 0.117 Angle : 0.527 7.423 63889 Z= 0.272 Chirality : 0.045 0.193 7952 Planarity : 0.005 0.058 8393 Dihedral : 4.397 22.662 6615 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 4.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.14 % Favored : 97.86 % Rotamer: Outliers : 1.27 % Allowed : 5.36 % Favored : 93.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.90 (0.10), residues: 6370 helix: None (None), residues: 0 sheet: 0.88 (0.10), residues: 2555 loop : 0.52 (0.10), residues: 3815 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG G1564 TYR 0.026 0.001 TYR F2034 PHE 0.013 0.001 PHE C1857 TRP 0.016 0.002 TRP G2177 Details of bonding type rmsd covalent geometry : bond 0.00258 (46053) covalent geometry : angle 0.52536 (63749) SS BOND : bond 0.00104 ( 70) SS BOND : angle 0.96174 ( 140) hydrogen bonds : bond 0.03396 ( 1479) hydrogen bonds : angle 5.64501 ( 3822) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12740 Ramachandran restraints generated. 6370 Oldfield, 0 Emsley, 6370 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12740 Ramachandran restraints generated. 6370 Oldfield, 0 Emsley, 6370 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 5201 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 85 time to evaluate : 1.662 Fit side-chains REVERT: A 1438 LEU cc_start: 0.8203 (mt) cc_final: 0.7987 (mt) REVERT: B 1421 MET cc_start: 0.7305 (mtp) cc_final: 0.6871 (ttt) REVERT: B 1496 LEU cc_start: 0.8817 (OUTLIER) cc_final: 0.8518 (tt) REVERT: B 1999 MET cc_start: 0.8858 (mtm) cc_final: 0.8473 (mtm) REVERT: D 1438 LEU cc_start: 0.7600 (mt) cc_final: 0.7380 (mt) REVERT: D 1496 LEU cc_start: 0.8619 (OUTLIER) cc_final: 0.8342 (tt) REVERT: E 1405 MET cc_start: 0.8551 (mmt) cc_final: 0.8266 (mmt) REVERT: F 1421 MET cc_start: 0.7114 (mtp) cc_final: 0.5981 (ttt) outliers start: 66 outliers final: 30 residues processed: 146 average time/residue: 0.1893 time to fit residues: 52.0538 Evaluate side-chains 103 residues out of total 5201 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 71 time to evaluate : 1.470 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1496 LEU Chi-restraints excluded: chain A residue 1987 THR Chi-restraints excluded: chain A residue 2061 ILE Chi-restraints excluded: chain A residue 2069 SER Chi-restraints excluded: chain A residue 2253 THR Chi-restraints excluded: chain B residue 1496 LEU Chi-restraints excluded: chain B residue 2049 CYS Chi-restraints excluded: chain B residue 2253 THR Chi-restraints excluded: chain B residue 2313 ILE Chi-restraints excluded: chain C residue 1496 LEU Chi-restraints excluded: chain C residue 2061 ILE Chi-restraints excluded: chain C residue 2253 THR Chi-restraints excluded: chain C residue 2313 ILE Chi-restraints excluded: chain D residue 1496 LEU Chi-restraints excluded: chain D residue 1736 MET Chi-restraints excluded: chain D residue 1963 ASN Chi-restraints excluded: chain D residue 2253 THR Chi-restraints excluded: chain E residue 1496 LEU Chi-restraints excluded: chain E residue 1924 SER Chi-restraints excluded: chain E residue 1963 ASN Chi-restraints excluded: chain E residue 2248 MET Chi-restraints excluded: chain E residue 2253 THR Chi-restraints excluded: chain F residue 1496 LEU Chi-restraints excluded: chain F residue 1795 VAL Chi-restraints excluded: chain F residue 1841 SER Chi-restraints excluded: chain F residue 1963 ASN Chi-restraints excluded: chain F residue 1987 THR Chi-restraints excluded: chain F residue 2253 THR Chi-restraints excluded: chain F residue 2313 ILE Chi-restraints excluded: chain G residue 1496 LEU Chi-restraints excluded: chain G residue 1924 SER Chi-restraints excluded: chain G residue 2253 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 637 random chunks: chunk 343 optimal weight: 0.7980 chunk 367 optimal weight: 0.5980 chunk 230 optimal weight: 3.9990 chunk 477 optimal weight: 2.9990 chunk 127 optimal weight: 1.9990 chunk 300 optimal weight: 3.9990 chunk 81 optimal weight: 4.9990 chunk 305 optimal weight: 5.9990 chunk 172 optimal weight: 6.9990 chunk 404 optimal weight: 6.9990 chunk 113 optimal weight: 4.9990 overall best weight: 2.0786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1765 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1765 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1932 ASN B1951 ASN ** C1765 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1932 ASN C1951 ASN D1447 ASN ** E1765 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F1765 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G1765 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3053 r_free = 0.3053 target = 0.068973 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2752 r_free = 0.2752 target = 0.056363 restraints weight = 140325.999| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.2793 r_free = 0.2793 target = 0.057999 restraints weight = 63453.431| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.2819 r_free = 0.2819 target = 0.059061 restraints weight = 36384.409| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.2837 r_free = 0.2837 target = 0.059767 restraints weight = 23966.659| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.2849 r_free = 0.2849 target = 0.060257 restraints weight = 17584.996| |-----------------------------------------------------------------------------| r_work (final): 0.2797 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8657 moved from start: 0.3626 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.075 46123 Z= 0.267 Angle : 0.607 8.050 63889 Z= 0.315 Chirality : 0.046 0.173 7952 Planarity : 0.005 0.058 8393 Dihedral : 4.693 26.414 6615 Min Nonbonded Distance : 2.569 Molprobity Statistics. All-atom Clashscore : 5.79 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.22 % Favored : 96.77 % Rotamer: Outliers : 1.56 % Allowed : 6.11 % Favored : 92.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.58 (0.10), residues: 6370 helix: None (None), residues: 0 sheet: 0.68 (0.09), residues: 2653 loop : 0.27 (0.10), residues: 3717 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG F2260 TYR 0.029 0.002 TYR F2034 PHE 0.025 0.002 PHE A2106 TRP 0.015 0.002 TRP A1432 Details of bonding type rmsd covalent geometry : bond 0.00603 (46053) covalent geometry : angle 0.60580 (63749) SS BOND : bond 0.00304 ( 70) SS BOND : angle 1.12538 ( 140) hydrogen bonds : bond 0.04120 ( 1479) hydrogen bonds : angle 5.73283 ( 3822) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12740 Ramachandran restraints generated. 6370 Oldfield, 0 Emsley, 6370 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12740 Ramachandran restraints generated. 6370 Oldfield, 0 Emsley, 6370 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 5201 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 77 time to evaluate : 1.668 Fit side-chains REVERT: A 1464 VAL cc_start: 0.7913 (OUTLIER) cc_final: 0.7709 (p) REVERT: B 1421 MET cc_start: 0.7486 (mtp) cc_final: 0.6925 (ttt) REVERT: B 1438 LEU cc_start: 0.8274 (mt) cc_final: 0.7657 (mt) REVERT: B 1496 LEU cc_start: 0.8878 (OUTLIER) cc_final: 0.8586 (tt) REVERT: B 1999 MET cc_start: 0.8933 (mtm) cc_final: 0.8627 (mtm) REVERT: C 1422 VAL cc_start: 0.7957 (OUTLIER) cc_final: 0.7735 (t) REVERT: D 1438 LEU cc_start: 0.7854 (mt) cc_final: 0.7611 (mt) REVERT: D 1441 LEU cc_start: 0.9082 (OUTLIER) cc_final: 0.8838 (tp) REVERT: D 1496 LEU cc_start: 0.8774 (OUTLIER) cc_final: 0.8508 (tt) REVERT: D 1742 ILE cc_start: 0.8633 (OUTLIER) cc_final: 0.8269 (mt) REVERT: E 1405 MET cc_start: 0.8676 (mmt) cc_final: 0.8371 (mmt) REVERT: E 1438 LEU cc_start: 0.8120 (mt) cc_final: 0.7870 (mt) REVERT: F 1421 MET cc_start: 0.6998 (mtp) cc_final: 0.6034 (ttt) REVERT: F 1438 LEU cc_start: 0.7876 (OUTLIER) cc_final: 0.7538 (mt) REVERT: F 2234 MET cc_start: 0.8525 (ttp) cc_final: 0.8086 (ttp) REVERT: G 1438 LEU cc_start: 0.8153 (mt) cc_final: 0.7734 (mt) outliers start: 81 outliers final: 53 residues processed: 146 average time/residue: 0.1937 time to fit residues: 53.3330 Evaluate side-chains 131 residues out of total 5201 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 71 time to evaluate : 1.122 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1464 VAL Chi-restraints excluded: chain A residue 1489 VAL Chi-restraints excluded: chain A residue 1496 LEU Chi-restraints excluded: chain A residue 1987 THR Chi-restraints excluded: chain A residue 2061 ILE Chi-restraints excluded: chain A residue 2069 SER Chi-restraints excluded: chain A residue 2197 THR Chi-restraints excluded: chain A residue 2253 THR Chi-restraints excluded: chain B residue 1496 LEU Chi-restraints excluded: chain B residue 1910 CYS Chi-restraints excluded: chain B residue 1987 THR Chi-restraints excluded: chain B residue 2049 CYS Chi-restraints excluded: chain B residue 2253 THR Chi-restraints excluded: chain B residue 2313 ILE Chi-restraints excluded: chain C residue 1422 VAL Chi-restraints excluded: chain C residue 1496 LEU Chi-restraints excluded: chain C residue 1742 ILE Chi-restraints excluded: chain C residue 1795 VAL Chi-restraints excluded: chain C residue 1963 ASN Chi-restraints excluded: chain C residue 2061 ILE Chi-restraints excluded: chain C residue 2069 SER Chi-restraints excluded: chain C residue 2197 THR Chi-restraints excluded: chain C residue 2253 THR Chi-restraints excluded: chain C residue 2313 ILE Chi-restraints excluded: chain D residue 1441 LEU Chi-restraints excluded: chain D residue 1496 LEU Chi-restraints excluded: chain D residue 1593 THR Chi-restraints excluded: chain D residue 1710 VAL Chi-restraints excluded: chain D residue 1736 MET Chi-restraints excluded: chain D residue 1742 ILE Chi-restraints excluded: chain D residue 1768 ASP Chi-restraints excluded: chain D residue 1944 ILE Chi-restraints excluded: chain D residue 1963 ASN Chi-restraints excluded: chain D residue 2136 LEU Chi-restraints excluded: chain D residue 2253 THR Chi-restraints excluded: chain E residue 1496 LEU Chi-restraints excluded: chain E residue 1924 SER Chi-restraints excluded: chain E residue 1963 ASN Chi-restraints excluded: chain E residue 2238 SER Chi-restraints excluded: chain E residue 2253 THR Chi-restraints excluded: chain F residue 1438 LEU Chi-restraints excluded: chain F residue 1464 VAL Chi-restraints excluded: chain F residue 1496 LEU Chi-restraints excluded: chain F residue 1570 ILE Chi-restraints excluded: chain F residue 1795 VAL Chi-restraints excluded: chain F residue 1841 SER Chi-restraints excluded: chain F residue 1963 ASN Chi-restraints excluded: chain F residue 1987 THR Chi-restraints excluded: chain F residue 2041 LEU Chi-restraints excluded: chain F residue 2238 SER Chi-restraints excluded: chain F residue 2253 THR Chi-restraints excluded: chain F residue 2313 ILE Chi-restraints excluded: chain G residue 1496 LEU Chi-restraints excluded: chain G residue 1736 MET Chi-restraints excluded: chain G residue 1795 VAL Chi-restraints excluded: chain G residue 1924 SER Chi-restraints excluded: chain G residue 1987 THR Chi-restraints excluded: chain G residue 2069 SER Chi-restraints excluded: chain G residue 2197 THR Chi-restraints excluded: chain G residue 2253 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 637 random chunks: chunk 596 optimal weight: 7.9990 chunk 182 optimal weight: 10.9990 chunk 301 optimal weight: 2.9990 chunk 365 optimal weight: 0.1980 chunk 239 optimal weight: 1.9990 chunk 352 optimal weight: 3.9990 chunk 213 optimal weight: 0.9990 chunk 126 optimal weight: 2.9990 chunk 162 optimal weight: 3.9990 chunk 532 optimal weight: 2.9990 chunk 184 optimal weight: 0.6980 overall best weight: 1.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1765 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1765 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E1765 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G1765 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3030 r_free = 0.3030 target = 0.061457 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2729 r_free = 0.2729 target = 0.049205 restraints weight = 141246.387| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.2772 r_free = 0.2772 target = 0.050841 restraints weight = 63479.108| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.2799 r_free = 0.2799 target = 0.051913 restraints weight = 35850.015| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.2817 r_free = 0.2817 target = 0.052615 restraints weight = 23370.208| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.2828 r_free = 0.2828 target = 0.053056 restraints weight = 16983.007| |-----------------------------------------------------------------------------| r_work (final): 0.2814 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8644 moved from start: 0.3860 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 46123 Z= 0.180 Angle : 0.549 7.876 63889 Z= 0.282 Chirality : 0.045 0.212 7952 Planarity : 0.005 0.056 8393 Dihedral : 4.469 19.940 6615 Min Nonbonded Distance : 2.547 Molprobity Statistics. All-atom Clashscore : 4.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.67 % Favored : 97.33 % Rotamer: Outliers : 1.73 % Allowed : 6.50 % Favored : 91.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.65 (0.10), residues: 6370 helix: None (None), residues: 0 sheet: 0.63 (0.09), residues: 2681 loop : 0.40 (0.11), residues: 3689 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B1564 TYR 0.031 0.001 TYR F2034 PHE 0.017 0.001 PHE A2106 TRP 0.014 0.002 TRP G2177 Details of bonding type rmsd covalent geometry : bond 0.00404 (46053) covalent geometry : angle 0.54628 (63749) SS BOND : bond 0.00151 ( 70) SS BOND : angle 1.24435 ( 140) hydrogen bonds : bond 0.03626 ( 1479) hydrogen bonds : angle 5.52951 ( 3822) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12740 Ramachandran restraints generated. 6370 Oldfield, 0 Emsley, 6370 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12740 Ramachandran restraints generated. 6370 Oldfield, 0 Emsley, 6370 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 170 residues out of total 5201 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 90 poor density : 80 time to evaluate : 1.205 Fit side-chains revert: symmetry clash REVERT: A 1438 LEU cc_start: 0.7511 (OUTLIER) cc_final: 0.6992 (mt) REVERT: B 1421 MET cc_start: 0.7590 (mtp) cc_final: 0.7122 (ttt) REVERT: B 1438 LEU cc_start: 0.8227 (mt) cc_final: 0.7626 (mt) REVERT: B 1496 LEU cc_start: 0.8883 (OUTLIER) cc_final: 0.8602 (tt) REVERT: B 1710 VAL cc_start: 0.9190 (OUTLIER) cc_final: 0.8983 (t) REVERT: B 1999 MET cc_start: 0.8929 (mtm) cc_final: 0.8605 (mtm) REVERT: B 2248 MET cc_start: 0.8961 (OUTLIER) cc_final: 0.8339 (ptp) REVERT: D 1438 LEU cc_start: 0.7990 (mt) cc_final: 0.7759 (mt) REVERT: E 1405 MET cc_start: 0.8739 (mmt) cc_final: 0.8290 (mmt) REVERT: E 1438 LEU cc_start: 0.8069 (mt) cc_final: 0.7815 (mt) REVERT: E 1441 LEU cc_start: 0.9042 (OUTLIER) cc_final: 0.8788 (tp) REVERT: F 1421 MET cc_start: 0.7838 (mtp) cc_final: 0.7379 (ttt) REVERT: F 1438 LEU cc_start: 0.7714 (OUTLIER) cc_final: 0.7441 (mt) REVERT: F 1441 LEU cc_start: 0.8838 (OUTLIER) cc_final: 0.8567 (tp) REVERT: G 1405 MET cc_start: 0.8581 (mmt) cc_final: 0.8286 (mmt) REVERT: G 1441 LEU cc_start: 0.9049 (OUTLIER) cc_final: 0.8621 (tp) REVERT: G 1742 ILE cc_start: 0.8561 (OUTLIER) cc_final: 0.8186 (mt) REVERT: G 1999 MET cc_start: 0.8825 (OUTLIER) cc_final: 0.8519 (ttp) outliers start: 90 outliers final: 56 residues processed: 160 average time/residue: 0.1823 time to fit residues: 54.8496 Evaluate side-chains 139 residues out of total 5201 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 73 time to evaluate : 1.667 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1438 LEU Chi-restraints excluded: chain A residue 1496 LEU Chi-restraints excluded: chain A residue 1627 VAL Chi-restraints excluded: chain A residue 1710 VAL Chi-restraints excluded: chain A residue 1987 THR Chi-restraints excluded: chain A residue 2061 ILE Chi-restraints excluded: chain A residue 2069 SER Chi-restraints excluded: chain A residue 2248 MET Chi-restraints excluded: chain A residue 2253 THR Chi-restraints excluded: chain B residue 1496 LEU Chi-restraints excluded: chain B residue 1710 VAL Chi-restraints excluded: chain B residue 1910 CYS Chi-restraints excluded: chain B residue 1987 THR Chi-restraints excluded: chain B residue 2049 CYS Chi-restraints excluded: chain B residue 2197 THR Chi-restraints excluded: chain B residue 2248 MET Chi-restraints excluded: chain B residue 2253 THR Chi-restraints excluded: chain B residue 2313 ILE Chi-restraints excluded: chain C residue 1418 VAL Chi-restraints excluded: chain C residue 1496 LEU Chi-restraints excluded: chain C residue 1710 VAL Chi-restraints excluded: chain C residue 1742 ILE Chi-restraints excluded: chain C residue 1795 VAL Chi-restraints excluded: chain C residue 1963 ASN Chi-restraints excluded: chain C residue 2061 ILE Chi-restraints excluded: chain C residue 2193 ILE Chi-restraints excluded: chain C residue 2253 THR Chi-restraints excluded: chain C residue 2313 ILE Chi-restraints excluded: chain D residue 1627 VAL Chi-restraints excluded: chain D residue 1710 VAL Chi-restraints excluded: chain D residue 1736 MET Chi-restraints excluded: chain D residue 1768 ASP Chi-restraints excluded: chain D residue 1963 ASN Chi-restraints excluded: chain D residue 2136 LEU Chi-restraints excluded: chain D residue 2197 THR Chi-restraints excluded: chain D residue 2248 MET Chi-restraints excluded: chain D residue 2253 THR Chi-restraints excluded: chain E residue 1441 LEU Chi-restraints excluded: chain E residue 1496 LEU Chi-restraints excluded: chain E residue 1736 MET Chi-restraints excluded: chain E residue 1924 SER Chi-restraints excluded: chain E residue 1963 ASN Chi-restraints excluded: chain E residue 2238 SER Chi-restraints excluded: chain E residue 2253 THR Chi-restraints excluded: chain F residue 1438 LEU Chi-restraints excluded: chain F residue 1441 LEU Chi-restraints excluded: chain F residue 1496 LEU Chi-restraints excluded: chain F residue 1570 ILE Chi-restraints excluded: chain F residue 1710 VAL Chi-restraints excluded: chain F residue 1841 SER Chi-restraints excluded: chain F residue 1963 ASN Chi-restraints excluded: chain F residue 1987 THR Chi-restraints excluded: chain F residue 2136 LEU Chi-restraints excluded: chain F residue 2197 THR Chi-restraints excluded: chain F residue 2238 SER Chi-restraints excluded: chain F residue 2253 THR Chi-restraints excluded: chain F residue 2313 ILE Chi-restraints excluded: chain G residue 1441 LEU Chi-restraints excluded: chain G residue 1496 LEU Chi-restraints excluded: chain G residue 1742 ILE Chi-restraints excluded: chain G residue 1924 SER Chi-restraints excluded: chain G residue 1987 THR Chi-restraints excluded: chain G residue 1999 MET Chi-restraints excluded: chain G residue 2004 VAL Chi-restraints excluded: chain G residue 2197 THR Chi-restraints excluded: chain G residue 2253 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 637 random chunks: chunk 496 optimal weight: 0.9990 chunk 47 optimal weight: 1.9990 chunk 218 optimal weight: 0.8980 chunk 339 optimal weight: 1.9990 chunk 374 optimal weight: 0.8980 chunk 474 optimal weight: 0.7980 chunk 606 optimal weight: 0.9990 chunk 492 optimal weight: 4.9990 chunk 6 optimal weight: 7.9990 chunk 305 optimal weight: 0.6980 chunk 299 optimal weight: 0.9980 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1765 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1519 ASN ** C1765 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D1447 ASN ** E1765 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G1765 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3051 r_free = 0.3051 target = 0.062266 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2752 r_free = 0.2752 target = 0.049993 restraints weight = 139369.386| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.2794 r_free = 0.2794 target = 0.051643 restraints weight = 62305.507| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.2822 r_free = 0.2822 target = 0.052734 restraints weight = 35051.781| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.2840 r_free = 0.2840 target = 0.053445 restraints weight = 22778.505| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 43)----------------| | r_work = 0.2852 r_free = 0.2852 target = 0.053907 restraints weight = 16469.506| |-----------------------------------------------------------------------------| r_work (final): 0.2835 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8625 moved from start: 0.3999 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 46123 Z= 0.127 Angle : 0.517 8.094 63889 Z= 0.263 Chirality : 0.044 0.180 7952 Planarity : 0.005 0.057 8393 Dihedral : 4.213 18.356 6615 Min Nonbonded Distance : 2.575 Molprobity Statistics. All-atom Clashscore : 4.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.83 % Favored : 97.17 % Rotamer: Outliers : 1.50 % Allowed : 6.75 % Favored : 91.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.82 (0.10), residues: 6370 helix: None (None), residues: 0 sheet: 0.75 (0.10), residues: 2674 loop : 0.52 (0.11), residues: 3696 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG F1564 TYR 0.022 0.001 TYR F2034 PHE 0.013 0.001 PHE A2106 TRP 0.016 0.001 TRP G2177 Details of bonding type rmsd covalent geometry : bond 0.00286 (46053) covalent geometry : angle 0.51472 (63749) SS BOND : bond 0.00135 ( 70) SS BOND : angle 1.17314 ( 140) hydrogen bonds : bond 0.03292 ( 1479) hydrogen bonds : angle 5.35504 ( 3822) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12740 Ramachandran restraints generated. 6370 Oldfield, 0 Emsley, 6370 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12740 Ramachandran restraints generated. 6370 Oldfield, 0 Emsley, 6370 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 5201 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 80 time to evaluate : 1.093 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 1438 LEU cc_start: 0.7363 (OUTLIER) cc_final: 0.6838 (mt) REVERT: B 1421 MET cc_start: 0.7552 (mtp) cc_final: 0.7038 (ttt) REVERT: B 1438 LEU cc_start: 0.8202 (mt) cc_final: 0.7605 (mt) REVERT: B 1496 LEU cc_start: 0.8858 (OUTLIER) cc_final: 0.8582 (tt) REVERT: B 1710 VAL cc_start: 0.9161 (OUTLIER) cc_final: 0.8955 (t) REVERT: B 1999 MET cc_start: 0.8918 (mtm) cc_final: 0.8582 (mtm) REVERT: B 2248 MET cc_start: 0.9030 (OUTLIER) cc_final: 0.8407 (ptp) REVERT: D 1438 LEU cc_start: 0.7952 (mt) cc_final: 0.7730 (mt) REVERT: D 1742 ILE cc_start: 0.8655 (OUTLIER) cc_final: 0.8280 (mt) REVERT: E 1405 MET cc_start: 0.8733 (mmt) cc_final: 0.8287 (mmt) REVERT: E 1438 LEU cc_start: 0.8047 (mt) cc_final: 0.7789 (mt) REVERT: E 1664 ASP cc_start: 0.8755 (OUTLIER) cc_final: 0.8463 (m-30) REVERT: F 1421 MET cc_start: 0.7852 (mtp) cc_final: 0.7390 (ttt) REVERT: F 1438 LEU cc_start: 0.7667 (OUTLIER) cc_final: 0.7357 (mt) REVERT: F 2234 MET cc_start: 0.8065 (OUTLIER) cc_final: 0.7658 (ttt) REVERT: G 1405 MET cc_start: 0.8695 (mmt) cc_final: 0.8350 (mmt) REVERT: G 1441 LEU cc_start: 0.8855 (OUTLIER) cc_final: 0.8588 (tp) REVERT: G 1742 ILE cc_start: 0.8586 (OUTLIER) cc_final: 0.8217 (mt) REVERT: G 1999 MET cc_start: 0.8868 (OUTLIER) cc_final: 0.8595 (ttp) outliers start: 78 outliers final: 49 residues processed: 146 average time/residue: 0.1779 time to fit residues: 48.7479 Evaluate side-chains 135 residues out of total 5201 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 75 time to evaluate : 1.370 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1438 LEU Chi-restraints excluded: chain A residue 1480 VAL Chi-restraints excluded: chain A residue 1489 VAL Chi-restraints excluded: chain A residue 1496 LEU Chi-restraints excluded: chain A residue 1987 THR Chi-restraints excluded: chain A residue 2061 ILE Chi-restraints excluded: chain A residue 2253 THR Chi-restraints excluded: chain B residue 1496 LEU Chi-restraints excluded: chain B residue 1519 ASN Chi-restraints excluded: chain B residue 1710 VAL Chi-restraints excluded: chain B residue 1986 THR Chi-restraints excluded: chain B residue 1987 THR Chi-restraints excluded: chain B residue 2049 CYS Chi-restraints excluded: chain B residue 2248 MET Chi-restraints excluded: chain B residue 2253 THR Chi-restraints excluded: chain B residue 2313 ILE Chi-restraints excluded: chain C residue 1418 VAL Chi-restraints excluded: chain C residue 1496 LEU Chi-restraints excluded: chain C residue 1710 VAL Chi-restraints excluded: chain C residue 1795 VAL Chi-restraints excluded: chain C residue 1963 ASN Chi-restraints excluded: chain C residue 2061 ILE Chi-restraints excluded: chain C residue 2253 THR Chi-restraints excluded: chain C residue 2313 ILE Chi-restraints excluded: chain D residue 1496 LEU Chi-restraints excluded: chain D residue 1627 VAL Chi-restraints excluded: chain D residue 1710 VAL Chi-restraints excluded: chain D residue 1736 MET Chi-restraints excluded: chain D residue 1742 ILE Chi-restraints excluded: chain D residue 1768 ASP Chi-restraints excluded: chain D residue 1963 ASN Chi-restraints excluded: chain D residue 1986 THR Chi-restraints excluded: chain D residue 2136 LEU Chi-restraints excluded: chain D residue 2253 THR Chi-restraints excluded: chain E residue 1496 LEU Chi-restraints excluded: chain E residue 1664 ASP Chi-restraints excluded: chain E residue 1736 MET Chi-restraints excluded: chain E residue 1795 VAL Chi-restraints excluded: chain E residue 1963 ASN Chi-restraints excluded: chain E residue 2253 THR Chi-restraints excluded: chain F residue 1438 LEU Chi-restraints excluded: chain F residue 1496 LEU Chi-restraints excluded: chain F residue 1710 VAL Chi-restraints excluded: chain F residue 1841 SER Chi-restraints excluded: chain F residue 1963 ASN Chi-restraints excluded: chain F residue 1987 THR Chi-restraints excluded: chain F residue 2136 LEU Chi-restraints excluded: chain F residue 2234 MET Chi-restraints excluded: chain F residue 2238 SER Chi-restraints excluded: chain F residue 2253 THR Chi-restraints excluded: chain F residue 2313 ILE Chi-restraints excluded: chain G residue 1441 LEU Chi-restraints excluded: chain G residue 1496 LEU Chi-restraints excluded: chain G residue 1742 ILE Chi-restraints excluded: chain G residue 1795 VAL Chi-restraints excluded: chain G residue 1924 SER Chi-restraints excluded: chain G residue 1987 THR Chi-restraints excluded: chain G residue 1999 MET Chi-restraints excluded: chain G residue 2004 VAL Chi-restraints excluded: chain G residue 2253 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 637 random chunks: chunk 620 optimal weight: 0.7980 chunk 549 optimal weight: 5.9990 chunk 12 optimal weight: 4.9990 chunk 221 optimal weight: 0.3980 chunk 435 optimal weight: 0.0870 chunk 323 optimal weight: 3.9990 chunk 176 optimal weight: 5.9990 chunk 188 optimal weight: 8.9990 chunk 575 optimal weight: 0.0030 chunk 54 optimal weight: 0.4980 chunk 403 optimal weight: 4.9990 overall best weight: 0.3568 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1765 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1519 ASN B1932 ASN B1951 ASN ** C1765 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E1765 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3083 r_free = 0.3083 target = 0.063580 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.2786 r_free = 0.2786 target = 0.051227 restraints weight = 138779.845| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.2829 r_free = 0.2829 target = 0.052926 restraints weight = 62128.938| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.2856 r_free = 0.2856 target = 0.054039 restraints weight = 34868.326| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.2874 r_free = 0.2874 target = 0.054762 restraints weight = 22530.799| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.2886 r_free = 0.2886 target = 0.055239 restraints weight = 16283.463| |-----------------------------------------------------------------------------| r_work (final): 0.2910 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8588 moved from start: 0.4111 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 46123 Z= 0.087 Angle : 0.499 9.877 63889 Z= 0.253 Chirality : 0.044 0.156 7952 Planarity : 0.004 0.052 8393 Dihedral : 3.924 18.695 6615 Min Nonbonded Distance : 2.535 Molprobity Statistics. All-atom Clashscore : 4.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.15 % Favored : 97.85 % Rotamer: Outliers : 1.31 % Allowed : 7.13 % Favored : 91.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.07 (0.11), residues: 6370 helix: None (None), residues: 0 sheet: 0.96 (0.10), residues: 2653 loop : 0.65 (0.11), residues: 3717 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG G1564 TYR 0.019 0.001 TYR F2034 PHE 0.013 0.001 PHE C1857 TRP 0.019 0.002 TRP G2177 Details of bonding type rmsd covalent geometry : bond 0.00195 (46053) covalent geometry : angle 0.49789 (63749) SS BOND : bond 0.00119 ( 70) SS BOND : angle 0.97484 ( 140) hydrogen bonds : bond 0.02910 ( 1479) hydrogen bonds : angle 5.16681 ( 3822) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12740 Ramachandran restraints generated. 6370 Oldfield, 0 Emsley, 6370 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12740 Ramachandran restraints generated. 6370 Oldfield, 0 Emsley, 6370 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 5201 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 78 time to evaluate : 1.450 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 1421 MET cc_start: 0.7559 (mtp) cc_final: 0.7153 (ttt) REVERT: B 1496 LEU cc_start: 0.8837 (OUTLIER) cc_final: 0.8584 (tt) REVERT: B 1519 ASN cc_start: 0.8891 (OUTLIER) cc_final: 0.8610 (t0) REVERT: B 1710 VAL cc_start: 0.9107 (OUTLIER) cc_final: 0.8905 (t) REVERT: B 1999 MET cc_start: 0.8889 (mtm) cc_final: 0.8529 (mtm) REVERT: B 2248 MET cc_start: 0.9025 (ptm) cc_final: 0.8339 (ptp) REVERT: D 1438 LEU cc_start: 0.7800 (mt) cc_final: 0.7600 (mt) REVERT: E 1405 MET cc_start: 0.8721 (mmt) cc_final: 0.8390 (mmt) REVERT: F 1421 MET cc_start: 0.7914 (mtp) cc_final: 0.7432 (ttt) REVERT: F 2234 MET cc_start: 0.7843 (OUTLIER) cc_final: 0.7520 (ttt) REVERT: G 1405 MET cc_start: 0.8688 (mmt) cc_final: 0.8359 (mmt) REVERT: G 1742 ILE cc_start: 0.8679 (OUTLIER) cc_final: 0.8308 (mt) REVERT: G 1999 MET cc_start: 0.8837 (OUTLIER) cc_final: 0.8552 (ttp) outliers start: 68 outliers final: 45 residues processed: 140 average time/residue: 0.1975 time to fit residues: 51.3802 Evaluate side-chains 125 residues out of total 5201 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 74 time to evaluate : 1.675 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1496 LEU Chi-restraints excluded: chain A residue 1627 VAL Chi-restraints excluded: chain A residue 1987 THR Chi-restraints excluded: chain A residue 2061 ILE Chi-restraints excluded: chain A residue 2248 MET Chi-restraints excluded: chain A residue 2253 THR Chi-restraints excluded: chain B residue 1496 LEU Chi-restraints excluded: chain B residue 1519 ASN Chi-restraints excluded: chain B residue 1710 VAL Chi-restraints excluded: chain B residue 1986 THR Chi-restraints excluded: chain B residue 1987 THR Chi-restraints excluded: chain B residue 2253 THR Chi-restraints excluded: chain B residue 2313 ILE Chi-restraints excluded: chain C residue 1418 VAL Chi-restraints excluded: chain C residue 1496 LEU Chi-restraints excluded: chain C residue 1710 VAL Chi-restraints excluded: chain C residue 1742 ILE Chi-restraints excluded: chain C residue 1795 VAL Chi-restraints excluded: chain C residue 1963 ASN Chi-restraints excluded: chain C residue 2004 VAL Chi-restraints excluded: chain C residue 2061 ILE Chi-restraints excluded: chain C residue 2253 THR Chi-restraints excluded: chain C residue 2313 ILE Chi-restraints excluded: chain D residue 1496 LEU Chi-restraints excluded: chain D residue 1710 VAL Chi-restraints excluded: chain D residue 1736 MET Chi-restraints excluded: chain D residue 1963 ASN Chi-restraints excluded: chain D residue 1986 THR Chi-restraints excluded: chain D residue 2136 LEU Chi-restraints excluded: chain D residue 2253 THR Chi-restraints excluded: chain E residue 1496 LEU Chi-restraints excluded: chain E residue 1795 VAL Chi-restraints excluded: chain E residue 1963 ASN Chi-restraints excluded: chain E residue 2253 THR Chi-restraints excluded: chain F residue 1496 LEU Chi-restraints excluded: chain F residue 1570 ILE Chi-restraints excluded: chain F residue 1710 VAL Chi-restraints excluded: chain F residue 1841 SER Chi-restraints excluded: chain F residue 1963 ASN Chi-restraints excluded: chain F residue 1987 THR Chi-restraints excluded: chain F residue 2136 LEU Chi-restraints excluded: chain F residue 2234 MET Chi-restraints excluded: chain F residue 2238 SER Chi-restraints excluded: chain F residue 2253 THR Chi-restraints excluded: chain F residue 2313 ILE Chi-restraints excluded: chain G residue 1496 LEU Chi-restraints excluded: chain G residue 1742 ILE Chi-restraints excluded: chain G residue 1924 SER Chi-restraints excluded: chain G residue 1987 THR Chi-restraints excluded: chain G residue 1999 MET Chi-restraints excluded: chain G residue 2004 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 637 random chunks: chunk 289 optimal weight: 5.9990 chunk 265 optimal weight: 5.9990 chunk 131 optimal weight: 3.9990 chunk 397 optimal weight: 3.9990 chunk 559 optimal weight: 0.8980 chunk 465 optimal weight: 4.9990 chunk 136 optimal weight: 4.9990 chunk 577 optimal weight: 5.9990 chunk 446 optimal weight: 0.9990 chunk 382 optimal weight: 0.8980 chunk 279 optimal weight: 8.9990 overall best weight: 2.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1765 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1519 ASN ** B1765 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1932 ASN B1951 ASN ** C1765 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1765 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E1765 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F1765 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G1765 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3013 r_free = 0.3013 target = 0.060727 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2710 r_free = 0.2710 target = 0.048448 restraints weight = 142824.801| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.2752 r_free = 0.2752 target = 0.050052 restraints weight = 64715.505| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.2779 r_free = 0.2779 target = 0.051100 restraints weight = 36805.422| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.2797 r_free = 0.2797 target = 0.051798 restraints weight = 24210.853| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 21)----------------| | r_work = 0.2808 r_free = 0.2808 target = 0.052246 restraints weight = 17680.816| |-----------------------------------------------------------------------------| r_work (final): 0.2796 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8674 moved from start: 0.4225 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.072 46123 Z= 0.268 Angle : 0.601 10.112 63889 Z= 0.307 Chirality : 0.045 0.223 7952 Planarity : 0.005 0.066 8393 Dihedral : 4.419 20.258 6615 Min Nonbonded Distance : 2.411 Molprobity Statistics. All-atom Clashscore : 5.77 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.23 % Favored : 96.75 % Rotamer: Outliers : 1.25 % Allowed : 7.27 % Favored : 91.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.72 (0.11), residues: 6370 helix: None (None), residues: 0 sheet: 0.77 (0.10), residues: 2660 loop : 0.36 (0.11), residues: 3710 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG F1564 TYR 0.030 0.002 TYR G1785 PHE 0.025 0.002 PHE A2106 TRP 0.014 0.002 TRP C1432 Details of bonding type rmsd covalent geometry : bond 0.00596 (46053) covalent geometry : angle 0.59764 (63749) SS BOND : bond 0.00226 ( 70) SS BOND : angle 1.49262 ( 140) hydrogen bonds : bond 0.03945 ( 1479) hydrogen bonds : angle 5.45702 ( 3822) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12740 Ramachandran restraints generated. 6370 Oldfield, 0 Emsley, 6370 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12740 Ramachandran restraints generated. 6370 Oldfield, 0 Emsley, 6370 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 5201 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 75 time to evaluate : 1.034 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 1421 MET cc_start: 0.7527 (mtp) cc_final: 0.7001 (ttt) REVERT: B 1438 LEU cc_start: 0.8202 (mt) cc_final: 0.7558 (mt) REVERT: B 1496 LEU cc_start: 0.8931 (OUTLIER) cc_final: 0.8632 (tt) REVERT: B 1710 VAL cc_start: 0.9192 (OUTLIER) cc_final: 0.8984 (t) REVERT: B 1999 MET cc_start: 0.9018 (mtm) cc_final: 0.8721 (mtm) REVERT: B 2248 MET cc_start: 0.9156 (OUTLIER) cc_final: 0.8738 (ptp) REVERT: D 1438 LEU cc_start: 0.8103 (mt) cc_final: 0.7900 (mt) REVERT: D 1742 ILE cc_start: 0.8658 (OUTLIER) cc_final: 0.8319 (mt) REVERT: E 1405 MET cc_start: 0.8786 (mmt) cc_final: 0.8440 (mmt) REVERT: F 2234 MET cc_start: 0.8021 (OUTLIER) cc_final: 0.7679 (ttt) REVERT: G 1405 MET cc_start: 0.8755 (mmt) cc_final: 0.8403 (mmt) REVERT: G 1742 ILE cc_start: 0.8617 (OUTLIER) cc_final: 0.8231 (mt) outliers start: 65 outliers final: 52 residues processed: 130 average time/residue: 0.1698 time to fit residues: 41.4632 Evaluate side-chains 131 residues out of total 5201 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 73 time to evaluate : 1.221 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1480 VAL Chi-restraints excluded: chain A residue 1496 LEU Chi-restraints excluded: chain A residue 1627 VAL Chi-restraints excluded: chain A residue 1987 THR Chi-restraints excluded: chain A residue 2061 ILE Chi-restraints excluded: chain A residue 2248 MET Chi-restraints excluded: chain A residue 2253 THR Chi-restraints excluded: chain B residue 1496 LEU Chi-restraints excluded: chain B residue 1710 VAL Chi-restraints excluded: chain B residue 1986 THR Chi-restraints excluded: chain B residue 1987 THR Chi-restraints excluded: chain B residue 2248 MET Chi-restraints excluded: chain B residue 2253 THR Chi-restraints excluded: chain B residue 2313 ILE Chi-restraints excluded: chain C residue 1418 VAL Chi-restraints excluded: chain C residue 1496 LEU Chi-restraints excluded: chain C residue 1742 ILE Chi-restraints excluded: chain C residue 1795 VAL Chi-restraints excluded: chain C residue 1963 ASN Chi-restraints excluded: chain C residue 2004 VAL Chi-restraints excluded: chain C residue 2061 ILE Chi-restraints excluded: chain C residue 2253 THR Chi-restraints excluded: chain C residue 2313 ILE Chi-restraints excluded: chain D residue 1496 LEU Chi-restraints excluded: chain D residue 1710 VAL Chi-restraints excluded: chain D residue 1736 MET Chi-restraints excluded: chain D residue 1742 ILE Chi-restraints excluded: chain D residue 1768 ASP Chi-restraints excluded: chain D residue 1944 ILE Chi-restraints excluded: chain D residue 1963 ASN Chi-restraints excluded: chain D residue 1986 THR Chi-restraints excluded: chain D residue 2136 LEU Chi-restraints excluded: chain D residue 2248 MET Chi-restraints excluded: chain D residue 2253 THR Chi-restraints excluded: chain E residue 1496 LEU Chi-restraints excluded: chain E residue 1924 SER Chi-restraints excluded: chain E residue 1963 ASN Chi-restraints excluded: chain E residue 2136 LEU Chi-restraints excluded: chain E residue 2238 SER Chi-restraints excluded: chain E residue 2253 THR Chi-restraints excluded: chain F residue 1496 LEU Chi-restraints excluded: chain F residue 1570 ILE Chi-restraints excluded: chain F residue 1710 VAL Chi-restraints excluded: chain F residue 1795 VAL Chi-restraints excluded: chain F residue 1841 SER Chi-restraints excluded: chain F residue 1963 ASN Chi-restraints excluded: chain F residue 1987 THR Chi-restraints excluded: chain F residue 2136 LEU Chi-restraints excluded: chain F residue 2197 THR Chi-restraints excluded: chain F residue 2234 MET Chi-restraints excluded: chain F residue 2238 SER Chi-restraints excluded: chain F residue 2253 THR Chi-restraints excluded: chain F residue 2313 ILE Chi-restraints excluded: chain G residue 1496 LEU Chi-restraints excluded: chain G residue 1742 ILE Chi-restraints excluded: chain G residue 1924 SER Chi-restraints excluded: chain G residue 1987 THR Chi-restraints excluded: chain G residue 2004 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 637 random chunks: chunk 220 optimal weight: 3.9990 chunk 212 optimal weight: 2.9990 chunk 361 optimal weight: 5.9990 chunk 178 optimal weight: 2.9990 chunk 88 optimal weight: 7.9990 chunk 488 optimal weight: 0.5980 chunk 299 optimal weight: 0.7980 chunk 203 optimal weight: 4.9990 chunk 228 optimal weight: 0.0370 chunk 16 optimal weight: 0.0270 chunk 563 optimal weight: 1.9990 overall best weight: 0.6918 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1765 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1932 ASN B1951 ASN ** C1765 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E1765 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3058 r_free = 0.3058 target = 0.062530 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2757 r_free = 0.2757 target = 0.050178 restraints weight = 140511.522| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.2800 r_free = 0.2800 target = 0.051840 restraints weight = 63442.798| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.2827 r_free = 0.2827 target = 0.052936 restraints weight = 35891.038| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 44)----------------| | r_work = 0.2845 r_free = 0.2845 target = 0.053651 restraints weight = 23350.170| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.2857 r_free = 0.2857 target = 0.054117 restraints weight = 16967.659| |-----------------------------------------------------------------------------| r_work (final): 0.2841 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8627 moved from start: 0.4304 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 46123 Z= 0.111 Angle : 0.510 9.513 63889 Z= 0.258 Chirality : 0.044 0.155 7952 Planarity : 0.005 0.061 8393 Dihedral : 4.080 18.228 6615 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 4.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.32 % Favored : 97.68 % Rotamer: Outliers : 0.90 % Allowed : 7.69 % Favored : 91.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.92 (0.11), residues: 6370 helix: None (None), residues: 0 sheet: 0.87 (0.10), residues: 2681 loop : 0.53 (0.11), residues: 3689 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG F1564 TYR 0.022 0.001 TYR G1785 PHE 0.012 0.001 PHE C1857 TRP 0.018 0.002 TRP G2177 Details of bonding type rmsd covalent geometry : bond 0.00255 (46053) covalent geometry : angle 0.50829 (63749) SS BOND : bond 0.00138 ( 70) SS BOND : angle 1.03385 ( 140) hydrogen bonds : bond 0.03139 ( 1479) hydrogen bonds : angle 5.23307 ( 3822) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12740 Ramachandran restraints generated. 6370 Oldfield, 0 Emsley, 6370 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12740 Ramachandran restraints generated. 6370 Oldfield, 0 Emsley, 6370 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 5201 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 80 time to evaluate : 1.670 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1736 MET cc_start: 0.8582 (ptp) cc_final: 0.8108 (ptp) REVERT: B 1421 MET cc_start: 0.7471 (mtp) cc_final: 0.6949 (ttt) REVERT: B 1438 LEU cc_start: 0.8207 (mt) cc_final: 0.7613 (mt) REVERT: B 1496 LEU cc_start: 0.8859 (OUTLIER) cc_final: 0.8603 (tt) REVERT: B 1710 VAL cc_start: 0.9077 (OUTLIER) cc_final: 0.8844 (t) REVERT: B 1999 MET cc_start: 0.8923 (mtm) cc_final: 0.8592 (mtm) REVERT: B 2248 MET cc_start: 0.9136 (OUTLIER) cc_final: 0.8747 (ptp) REVERT: E 1405 MET cc_start: 0.8773 (mmt) cc_final: 0.8411 (mmt) REVERT: E 1985 MET cc_start: 0.8024 (ttt) cc_final: 0.7474 (ttt) REVERT: F 2234 MET cc_start: 0.7884 (ptm) cc_final: 0.7607 (ttt) REVERT: G 1405 MET cc_start: 0.8692 (mmt) cc_final: 0.8353 (mmt) REVERT: G 1438 LEU cc_start: 0.7643 (OUTLIER) cc_final: 0.7399 (mt) REVERT: G 1742 ILE cc_start: 0.8634 (OUTLIER) cc_final: 0.8267 (mt) outliers start: 47 outliers final: 40 residues processed: 121 average time/residue: 0.2013 time to fit residues: 45.6099 Evaluate side-chains 123 residues out of total 5201 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 78 time to evaluate : 1.712 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1480 VAL Chi-restraints excluded: chain A residue 1496 LEU Chi-restraints excluded: chain A residue 1627 VAL Chi-restraints excluded: chain A residue 2061 ILE Chi-restraints excluded: chain A residue 2248 MET Chi-restraints excluded: chain A residue 2253 THR Chi-restraints excluded: chain B residue 1496 LEU Chi-restraints excluded: chain B residue 1710 VAL Chi-restraints excluded: chain B residue 1986 THR Chi-restraints excluded: chain B residue 1987 THR Chi-restraints excluded: chain B residue 2248 MET Chi-restraints excluded: chain B residue 2253 THR Chi-restraints excluded: chain B residue 2313 ILE Chi-restraints excluded: chain C residue 1496 LEU Chi-restraints excluded: chain C residue 1742 ILE Chi-restraints excluded: chain C residue 1795 VAL Chi-restraints excluded: chain C residue 1963 ASN Chi-restraints excluded: chain C residue 2004 VAL Chi-restraints excluded: chain C residue 2061 ILE Chi-restraints excluded: chain C residue 2253 THR Chi-restraints excluded: chain C residue 2313 ILE Chi-restraints excluded: chain D residue 1496 LEU Chi-restraints excluded: chain D residue 1710 VAL Chi-restraints excluded: chain D residue 1736 MET Chi-restraints excluded: chain D residue 1963 ASN Chi-restraints excluded: chain D residue 1986 THR Chi-restraints excluded: chain D residue 2136 LEU Chi-restraints excluded: chain D residue 2253 THR Chi-restraints excluded: chain E residue 1496 LEU Chi-restraints excluded: chain E residue 2136 LEU Chi-restraints excluded: chain E residue 2253 THR Chi-restraints excluded: chain F residue 1570 ILE Chi-restraints excluded: chain F residue 1710 VAL Chi-restraints excluded: chain F residue 1841 SER Chi-restraints excluded: chain F residue 1963 ASN Chi-restraints excluded: chain F residue 1987 THR Chi-restraints excluded: chain F residue 2136 LEU Chi-restraints excluded: chain F residue 2253 THR Chi-restraints excluded: chain F residue 2313 ILE Chi-restraints excluded: chain G residue 1438 LEU Chi-restraints excluded: chain G residue 1496 LEU Chi-restraints excluded: chain G residue 1742 ILE Chi-restraints excluded: chain G residue 1924 SER Chi-restraints excluded: chain G residue 1987 THR Chi-restraints excluded: chain G residue 2004 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 637 random chunks: chunk 542 optimal weight: 0.9980 chunk 47 optimal weight: 0.8980 chunk 344 optimal weight: 0.0570 chunk 285 optimal weight: 0.7980 chunk 438 optimal weight: 1.9990 chunk 394 optimal weight: 0.7980 chunk 200 optimal weight: 0.8980 chunk 135 optimal weight: 2.9990 chunk 407 optimal weight: 3.9990 chunk 497 optimal weight: 0.8980 chunk 388 optimal weight: 2.9990 overall best weight: 0.6898 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1765 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1765 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1765 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E1765 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F1765 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3069 r_free = 0.3069 target = 0.062993 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2768 r_free = 0.2768 target = 0.050588 restraints weight = 140228.766| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.2811 r_free = 0.2811 target = 0.052251 restraints weight = 63558.427| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.2838 r_free = 0.2838 target = 0.053343 restraints weight = 36092.864| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.2856 r_free = 0.2856 target = 0.054059 restraints weight = 23643.479| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.2868 r_free = 0.2868 target = 0.054540 restraints weight = 17196.091| |-----------------------------------------------------------------------------| r_work (final): 0.2888 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8619 moved from start: 0.4397 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 46123 Z= 0.112 Angle : 0.499 12.062 63889 Z= 0.251 Chirality : 0.044 0.147 7952 Planarity : 0.005 0.058 8393 Dihedral : 3.908 17.773 6615 Min Nonbonded Distance : 2.540 Molprobity Statistics. All-atom Clashscore : 4.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.87 % Favored : 97.13 % Rotamer: Outliers : 1.08 % Allowed : 7.65 % Favored : 91.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.02 (0.11), residues: 6370 helix: None (None), residues: 0 sheet: 0.97 (0.10), residues: 2674 loop : 0.58 (0.11), residues: 3696 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG E1564 TYR 0.020 0.001 TYR G1785 PHE 0.012 0.001 PHE A2106 TRP 0.016 0.001 TRP G2177 Details of bonding type rmsd covalent geometry : bond 0.00254 (46053) covalent geometry : angle 0.49817 (63749) SS BOND : bond 0.00143 ( 70) SS BOND : angle 0.90523 ( 140) hydrogen bonds : bond 0.02999 ( 1479) hydrogen bonds : angle 5.11695 ( 3822) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4332.17 seconds wall clock time: 77 minutes 22.03 seconds (4642.03 seconds total)