Starting phenix.real_space_refine on Thu Dec 26 16:54:42 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9flp_50537/12_2024/9flp_50537.cif Found real_map, /net/cci-nas-00/data/ceres_data/9flp_50537/12_2024/9flp_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/9flp_50537/12_2024/9flp_50537.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9flp_50537/12_2024/9flp_50537.map" model { file = "/net/cci-nas-00/data/ceres_data/9flp_50537/12_2024/9flp_50537.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9flp_50537/12_2024/9flp_50537.cif" } resolution = 3.8 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.001 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): 0.11s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/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: C, B, E, D, G, F Time building chain proxies: 18.14, per 1000 atoms: 0.40 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=10, 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 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: 10.93 Conformation dependent library (CDL) restraints added in 6.4 seconds 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: 14.47 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: 42.21 Time building geometry restraints manager: 12.63 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: 26369 17.88 - 35.75: 564 35.75 - 53.63: 116 53.63 - 71.50: 43 71.50 - 89.38: 14 Dihedral angle restraints: 27106 sinusoidal: 8752 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 27103 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: 74 2.22 - 2.89: 20912 2.89 - 3.56: 61540 3.56 - 4.23: 107761 4.23 - 4.90: 172285 Nonbonded interactions: 362572 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 362567 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain '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: 9.130 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.070 Extract box with map and model: 1.490 Check model and map are aligned: 0.310 Set scattering table: 0.450 Process input model: 124.090 Find NCS groups from input model: 1.810 Set up NCS constraints: 0.200 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:2.860 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 140.420 ------------------------------------------------------------------------------- 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 46053 Z= 1.118 Angle : 1.532 13.397 63749 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 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 TRP 0.050 0.009 TRP F1598 PHE 0.032 0.006 PHE E2156 TYR 0.055 0.006 TYR F2034 ARG 0.005 0.001 ARG F1564 *********************** 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 : 5.170 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: 0.7677 (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: 0.5255 time to fit residues: 272.1988 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 : 5.222 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 637 random chunks: chunk 537 optimal weight: 2.9990 chunk 482 optimal weight: 0.9980 chunk 267 optimal weight: 1.9990 chunk 164 optimal weight: 1.9990 chunk 325 optimal weight: 0.5980 chunk 257 optimal weight: 2.9990 chunk 499 optimal weight: 0.9980 chunk 193 optimal weight: 0.9980 chunk 303 optimal weight: 0.9980 chunk 371 optimal weight: 0.9990 chunk 578 optimal weight: 5.9990 overall best weight: 0.9180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1446 GLN A1683 ASN A1856 GLN A2237 ASN B1446 GLN B1683 ASN B1856 GLN B1973 GLN B2237 ASN C1446 GLN C1683 ASN C1856 GLN C2237 ASN D1683 ASN D1856 GLN D2237 ASN E1446 GLN E1683 ASN E1856 GLN E2237 ASN F1446 GLN F1683 ASN F1856 GLN F2237 ASN G1446 GLN G1683 ASN G1856 GLN G2237 ASN Total number of N/Q/H flips: 28 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8360 moved from start: 0.1850 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.067 46053 Z= 0.248 Angle : 0.647 8.215 63749 Z= 0.348 Chirality : 0.048 0.197 7952 Planarity : 0.005 0.048 8393 Dihedral : 5.326 22.723 6615 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 5.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.43 % Favored : 98.57 % Rotamer: Outliers : 0.65 % Allowed : 3.88 % Favored : 95.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.94 (0.10), residues: 6370 helix: None (None), residues: 0 sheet: 0.93 (0.10), residues: 2639 loop : 0.52 (0.10), residues: 3731 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP C2177 PHE 0.013 0.002 PHE G1857 TYR 0.025 0.002 TYR F2034 ARG 0.004 0.001 ARG C1564 *********************** 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 167 residues out of total 5201 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 133 time to evaluate : 4.625 Fit side-chains REVERT: A 1438 LEU cc_start: 0.7661 (mt) cc_final: 0.7420 (mt) REVERT: B 1480 VAL cc_start: 0.7780 (t) cc_final: 0.7527 (p) REVERT: B 1496 LEU cc_start: 0.8463 (OUTLIER) cc_final: 0.8127 (tt) REVERT: B 1857 PHE cc_start: 0.8048 (t80) cc_final: 0.7668 (t80) REVERT: B 1999 MET cc_start: 0.8958 (mtp) cc_final: 0.8757 (mtm) REVERT: B 2051 SER cc_start: 0.8874 (p) cc_final: 0.8629 (t) REVERT: C 1438 LEU cc_start: 0.7605 (OUTLIER) cc_final: 0.7260 (mt) REVERT: C 1480 VAL cc_start: 0.7731 (t) cc_final: 0.7494 (p) REVERT: D 1438 LEU cc_start: 0.7432 (mt) cc_final: 0.7064 (mt) REVERT: D 1496 LEU cc_start: 0.8061 (OUTLIER) cc_final: 0.7671 (tt) REVERT: D 1533 SER cc_start: 0.9085 (t) cc_final: 0.8559 (p) REVERT: D 2034 TYR cc_start: 0.9009 (t80) cc_final: 0.8550 (t80) REVERT: E 1480 VAL cc_start: 0.7687 (t) cc_final: 0.7387 (p) REVERT: E 1519 ASN cc_start: 0.8991 (OUTLIER) cc_final: 0.8711 (t0) REVERT: F 1438 LEU cc_start: 0.7765 (mt) cc_final: 0.7429 (mt) REVERT: F 2061 ILE cc_start: 0.9126 (mt) cc_final: 0.8704 (pt) REVERT: F 2248 MET cc_start: 0.8312 (mtp) cc_final: 0.7832 (mtp) REVERT: G 1480 VAL cc_start: 0.7497 (t) cc_final: 0.7276 (p) outliers start: 34 outliers final: 13 residues processed: 161 average time/residue: 0.4974 time to fit residues: 150.0886 Evaluate side-chains 101 residues out of total 5201 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 84 time to evaluate : 5.033 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 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 1570 ILE Chi-restraints excluded: chain F residue 1963 ASN Chi-restraints excluded: chain F residue 2253 THR 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 321 optimal weight: 3.9990 chunk 179 optimal weight: 6.9990 chunk 481 optimal weight: 3.9990 chunk 393 optimal weight: 6.9990 chunk 159 optimal weight: 1.9990 chunk 579 optimal weight: 2.9990 chunk 626 optimal weight: 0.8980 chunk 516 optimal weight: 0.9990 chunk 574 optimal weight: 1.9990 chunk 197 optimal weight: 2.9990 chunk 464 optimal weight: 0.7980 overall best weight: 1.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B1765 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1951 ASN ** C1765 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D1446 GLN D1951 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: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8501 moved from start: 0.3022 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.066 46053 Z= 0.294 Angle : 0.595 13.525 63749 Z= 0.312 Chirality : 0.046 0.232 7952 Planarity : 0.005 0.053 8393 Dihedral : 4.744 27.284 6615 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 5.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.75 % Favored : 97.25 % Rotamer: Outliers : 1.21 % Allowed : 4.61 % Favored : 94.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.68 (0.10), residues: 6370 helix: None (None), residues: 0 sheet: 0.77 (0.09), residues: 2569 loop : 0.32 (0.10), residues: 3801 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP G2177 PHE 0.022 0.002 PHE A2106 TYR 0.029 0.002 TYR F2034 ARG 0.008 0.001 ARG B1564 *********************** 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 156 residues out of total 5201 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 93 time to evaluate : 4.880 Fit side-chains REVERT: A 1438 LEU cc_start: 0.8405 (mt) cc_final: 0.8143 (mt) REVERT: A 2248 MET cc_start: 0.8324 (OUTLIER) cc_final: 0.8102 (mtp) REVERT: B 1421 MET cc_start: 0.7549 (mtp) cc_final: 0.6548 (ttt) REVERT: B 1480 VAL cc_start: 0.7860 (t) cc_final: 0.7585 (p) REVERT: C 1963 ASN cc_start: 0.8278 (OUTLIER) cc_final: 0.7608 (p0) REVERT: D 1438 LEU cc_start: 0.7868 (mt) cc_final: 0.7594 (mt) REVERT: D 1496 LEU cc_start: 0.8297 (OUTLIER) cc_final: 0.8061 (tt) REVERT: D 2034 TYR cc_start: 0.9080 (t80) cc_final: 0.8813 (t80) REVERT: E 1405 MET cc_start: 0.8375 (mmt) cc_final: 0.8121 (mmt) REVERT: E 2060 GLU cc_start: 0.8351 (mt-10) cc_final: 0.7925 (pm20) REVERT: F 1421 MET cc_start: 0.7610 (mtp) cc_final: 0.6446 (ttt) REVERT: F 1438 LEU cc_start: 0.8272 (mt) cc_final: 0.8052 (mt) REVERT: F 2034 TYR cc_start: 0.8671 (t80) cc_final: 0.8422 (t80) REVERT: F 2248 MET cc_start: 0.8286 (mtp) cc_final: 0.7968 (mtt) REVERT: G 2034 TYR cc_start: 0.9084 (t80) cc_final: 0.8764 (t80) outliers start: 63 outliers final: 31 residues processed: 146 average time/residue: 0.5041 time to fit residues: 138.3277 Evaluate side-chains 108 residues out of total 5201 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 74 time to evaluate : 4.925 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1480 VAL Chi-restraints excluded: chain A residue 1570 ILE 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 2248 MET Chi-restraints excluded: chain A residue 2253 THR Chi-restraints excluded: chain B residue 2197 THR Chi-restraints excluded: chain B residue 2253 THR Chi-restraints excluded: chain C residue 1496 LEU Chi-restraints excluded: chain C residue 1963 ASN 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 1768 ASP 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 1924 SER Chi-restraints excluded: chain E residue 1963 ASN Chi-restraints excluded: chain E residue 2197 THR 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 1987 THR 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 1987 THR 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 572 optimal weight: 3.9990 chunk 435 optimal weight: 3.9990 chunk 300 optimal weight: 0.3980 chunk 64 optimal weight: 1.9990 chunk 276 optimal weight: 3.9990 chunk 389 optimal weight: 0.6980 chunk 581 optimal weight: 1.9990 chunk 615 optimal weight: 3.9990 chunk 303 optimal weight: 0.8980 chunk 551 optimal weight: 4.9990 chunk 165 optimal weight: 2.9990 overall best weight: 1.1984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1765 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1951 ASN ** C1765 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E1765 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E1951 ASN ** G1765 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G2189 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8520 moved from start: 0.3355 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 46053 Z= 0.247 Angle : 0.544 7.770 63749 Z= 0.282 Chirality : 0.045 0.188 7952 Planarity : 0.005 0.055 8393 Dihedral : 4.503 23.400 6615 Min Nonbonded Distance : 2.540 Molprobity Statistics. All-atom Clashscore : 5.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.31 % Favored : 97.69 % Rotamer: Outliers : 1.44 % Allowed : 5.27 % Favored : 93.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.79 (0.10), residues: 6370 helix: None (None), residues: 0 sheet: 0.78 (0.09), residues: 2597 loop : 0.46 (0.10), residues: 3773 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP G2177 PHE 0.015 0.001 PHE A2106 TYR 0.019 0.001 TYR F2034 ARG 0.004 0.000 ARG G1564 *********************** 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 161 residues out of total 5201 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 86 time to evaluate : 4.966 Fit side-chains REVERT: A 1421 MET cc_start: 0.7872 (mmm) cc_final: 0.7592 (mmm) REVERT: A 1438 LEU cc_start: 0.8388 (mt) cc_final: 0.8134 (mt) REVERT: B 1421 MET cc_start: 0.7594 (mtp) cc_final: 0.7027 (ttt) REVERT: B 1480 VAL cc_start: 0.7604 (t) cc_final: 0.7329 (p) REVERT: B 1496 LEU cc_start: 0.8609 (OUTLIER) cc_final: 0.8304 (tt) REVERT: B 1985 MET cc_start: 0.8741 (ttm) cc_final: 0.8509 (ttm) REVERT: C 1963 ASN cc_start: 0.8259 (OUTLIER) cc_final: 0.7522 (p0) REVERT: C 2034 TYR cc_start: 0.9075 (t80) cc_final: 0.8852 (t80) REVERT: D 1438 LEU cc_start: 0.7835 (mt) cc_final: 0.7559 (mt) REVERT: E 1405 MET cc_start: 0.8393 (mmt) cc_final: 0.8142 (mmt) REVERT: E 2060 GLU cc_start: 0.8371 (mt-10) cc_final: 0.7975 (pm20) REVERT: F 1421 MET cc_start: 0.7477 (mtp) cc_final: 0.6145 (ttt) REVERT: F 1438 LEU cc_start: 0.8231 (mt) cc_final: 0.8021 (mt) REVERT: F 2248 MET cc_start: 0.8459 (mtp) cc_final: 0.8212 (mtp) REVERT: G 2034 TYR cc_start: 0.9118 (t80) cc_final: 0.8825 (t80) outliers start: 75 outliers final: 35 residues processed: 152 average time/residue: 0.4801 time to fit residues: 137.8529 Evaluate side-chains 109 residues out of total 5201 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 72 time to evaluate : 4.415 ------------------------------------------------------------------------------- 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 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 1987 THR Chi-restraints excluded: chain B residue 2253 THR Chi-restraints excluded: chain B residue 2313 ILE Chi-restraints excluded: chain C residue 1438 LEU Chi-restraints excluded: chain C residue 1496 LEU Chi-restraints excluded: chain C residue 1795 VAL Chi-restraints excluded: chain C residue 1963 ASN 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 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 2238 SER 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 1570 ILE Chi-restraints excluded: chain F residue 1795 VAL Chi-restraints excluded: chain F residue 1963 ASN 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 1563 GLU Chi-restraints excluded: chain G residue 2197 THR 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 512 optimal weight: 2.9990 chunk 349 optimal weight: 0.8980 chunk 8 optimal weight: 0.2980 chunk 458 optimal weight: 3.9990 chunk 254 optimal weight: 2.9990 chunk 525 optimal weight: 0.7980 chunk 425 optimal weight: 0.8980 chunk 0 optimal weight: 10.0000 chunk 314 optimal weight: 3.9990 chunk 552 optimal weight: 6.9990 chunk 155 optimal weight: 5.9990 overall best weight: 1.1782 ------------------------------------------------------------------------------- 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** C1951 ASN ** E1765 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G1765 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G2189 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8537 moved from start: 0.3641 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 46053 Z= 0.242 Angle : 0.531 7.593 63749 Z= 0.273 Chirality : 0.045 0.154 7952 Planarity : 0.005 0.053 8393 Dihedral : 4.352 26.448 6615 Min Nonbonded Distance : 2.569 Molprobity Statistics. All-atom Clashscore : 5.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.90 % Favored : 97.10 % Rotamer: Outliers : 1.50 % Allowed : 5.92 % Favored : 92.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.86 (0.10), residues: 6370 helix: None (None), residues: 0 sheet: 0.76 (0.09), residues: 2632 loop : 0.56 (0.10), residues: 3738 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP G2177 PHE 0.017 0.001 PHE A2106 TYR 0.029 0.001 TYR F2034 ARG 0.003 0.001 ARG B1564 *********************** 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 165 residues out of total 5201 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 87 time to evaluate : 4.914 Fit side-chains revert: symmetry clash REVERT: A 1438 LEU cc_start: 0.8414 (mt) cc_final: 0.8166 (mt) REVERT: B 1421 MET cc_start: 0.7648 (mtp) cc_final: 0.6910 (ttt) REVERT: B 1496 LEU cc_start: 0.8601 (OUTLIER) cc_final: 0.8312 (tt) REVERT: B 1710 VAL cc_start: 0.9127 (OUTLIER) cc_final: 0.8921 (t) REVERT: B 1985 MET cc_start: 0.8677 (ttm) cc_final: 0.8418 (ttm) REVERT: B 2248 MET cc_start: 0.8531 (ptm) cc_final: 0.8235 (ptm) REVERT: C 1422 VAL cc_start: 0.7259 (OUTLIER) cc_final: 0.6831 (t) REVERT: C 1438 LEU cc_start: 0.7655 (OUTLIER) cc_final: 0.7450 (mt) REVERT: C 1963 ASN cc_start: 0.8260 (OUTLIER) cc_final: 0.7505 (p0) REVERT: D 1438 LEU cc_start: 0.7827 (mt) cc_final: 0.7566 (mt) REVERT: D 1441 LEU cc_start: 0.9016 (OUTLIER) cc_final: 0.8462 (tp) REVERT: E 1405 MET cc_start: 0.8393 (mmt) cc_final: 0.8038 (mmt) REVERT: E 1441 LEU cc_start: 0.9050 (OUTLIER) cc_final: 0.8741 (tp) REVERT: E 1662 GLU cc_start: 0.8311 (mt-10) cc_final: 0.8005 (mt-10) REVERT: E 1811 GLU cc_start: 0.8689 (mt-10) cc_final: 0.7770 (pm20) REVERT: E 2060 GLU cc_start: 0.8379 (mt-10) cc_final: 0.8010 (pm20) REVERT: F 1421 MET cc_start: 0.7365 (mtp) cc_final: 0.6505 (ttt) REVERT: F 1438 LEU cc_start: 0.8211 (mt) cc_final: 0.7987 (mt) REVERT: F 2234 MET cc_start: 0.8236 (ttp) cc_final: 0.7829 (ttp) REVERT: F 2248 MET cc_start: 0.8613 (mtp) cc_final: 0.8220 (mtp) REVERT: G 1405 MET cc_start: 0.8397 (mmt) cc_final: 0.8171 (mmt) REVERT: G 2034 TYR cc_start: 0.9158 (t80) cc_final: 0.8890 (t80) REVERT: G 2248 MET cc_start: 0.9122 (ptm) cc_final: 0.8528 (ptm) outliers start: 78 outliers final: 48 residues processed: 158 average time/residue: 0.4908 time to fit residues: 144.4386 Evaluate side-chains 133 residues out of total 5201 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 78 time to evaluate : 4.904 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 1627 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 2253 THR Chi-restraints excluded: chain B residue 1496 LEU Chi-restraints excluded: chain B residue 1710 VAL 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 1422 VAL Chi-restraints excluded: chain C residue 1438 LEU Chi-restraints excluded: chain C residue 1496 LEU Chi-restraints excluded: chain C residue 1963 ASN 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 1441 LEU Chi-restraints excluded: chain D residue 1512 ILE 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 1944 ILE 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 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 2248 MET Chi-restraints excluded: chain E residue 2253 THR 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 1710 VAL 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 1496 LEU Chi-restraints excluded: chain G residue 1795 VAL Chi-restraints excluded: chain G residue 1924 SER 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 637 random chunks: chunk 207 optimal weight: 2.9990 chunk 554 optimal weight: 0.5980 chunk 121 optimal weight: 2.9990 chunk 361 optimal weight: 0.9980 chunk 151 optimal weight: 2.9990 chunk 616 optimal weight: 2.9990 chunk 511 optimal weight: 0.8980 chunk 285 optimal weight: 0.9980 chunk 51 optimal weight: 3.9990 chunk 203 optimal weight: 3.9990 chunk 323 optimal weight: 5.9990 overall best weight: 1.2982 ------------------------------------------------------------------------------- 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** ** G2189 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8553 moved from start: 0.3855 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 46053 Z= 0.261 Angle : 0.535 7.790 63749 Z= 0.275 Chirality : 0.045 0.154 7952 Planarity : 0.005 0.052 8393 Dihedral : 4.327 19.144 6615 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 5.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.72 % Favored : 97.28 % Rotamer: Outliers : 1.52 % Allowed : 6.59 % Favored : 91.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.85 (0.10), residues: 6370 helix: None (None), residues: 0 sheet: 0.78 (0.09), residues: 2653 loop : 0.53 (0.11), residues: 3717 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP G2177 PHE 0.016 0.001 PHE A2106 TYR 0.023 0.001 TYR F2034 ARG 0.005 0.000 ARG E1564 *********************** 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 161 residues out of total 5201 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 82 time to evaluate : 5.421 Fit side-chains revert: symmetry clash REVERT: A 1438 LEU cc_start: 0.8410 (mt) cc_final: 0.8176 (mt) REVERT: B 1421 MET cc_start: 0.7765 (mtp) cc_final: 0.7017 (ttt) REVERT: B 1496 LEU cc_start: 0.8615 (OUTLIER) cc_final: 0.8338 (tt) REVERT: B 1710 VAL cc_start: 0.9102 (OUTLIER) cc_final: 0.8897 (t) REVERT: B 1985 MET cc_start: 0.8633 (ttm) cc_final: 0.8390 (ttm) REVERT: B 1999 MET cc_start: 0.8646 (mtm) cc_final: 0.8415 (mtm) REVERT: C 1422 VAL cc_start: 0.7439 (OUTLIER) cc_final: 0.7189 (t) REVERT: C 1438 LEU cc_start: 0.7579 (OUTLIER) cc_final: 0.6921 (mt) REVERT: C 1963 ASN cc_start: 0.8256 (OUTLIER) cc_final: 0.7491 (p0) REVERT: D 1438 LEU cc_start: 0.7942 (mt) cc_final: 0.7682 (mt) REVERT: E 1405 MET cc_start: 0.8549 (mmt) cc_final: 0.8257 (mmt) REVERT: E 1662 GLU cc_start: 0.8328 (mt-10) cc_final: 0.8000 (mt-10) REVERT: E 1811 GLU cc_start: 0.8739 (mt-10) cc_final: 0.7799 (pm20) REVERT: E 2060 GLU cc_start: 0.8379 (mt-10) cc_final: 0.7941 (pm20) REVERT: F 1421 MET cc_start: 0.8129 (mtp) cc_final: 0.7408 (ttt) REVERT: F 1438 LEU cc_start: 0.8265 (mt) cc_final: 0.8062 (mt) REVERT: F 2234 MET cc_start: 0.8508 (ttp) cc_final: 0.8020 (ttp) REVERT: F 2248 MET cc_start: 0.8650 (mtp) cc_final: 0.8279 (mtp) REVERT: G 1405 MET cc_start: 0.8394 (mmt) cc_final: 0.8126 (mmt) REVERT: G 1441 LEU cc_start: 0.8907 (OUTLIER) cc_final: 0.8428 (tp) REVERT: G 1710 VAL cc_start: 0.9125 (OUTLIER) cc_final: 0.8871 (t) REVERT: G 2034 TYR cc_start: 0.9141 (t80) cc_final: 0.8882 (t80) outliers start: 79 outliers final: 54 residues processed: 154 average time/residue: 0.4641 time to fit residues: 135.3424 Evaluate side-chains 138 residues out of total 5201 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 77 time to evaluate : 4.772 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 1570 ILE 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 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 2253 THR Chi-restraints excluded: chain B residue 2313 ILE Chi-restraints excluded: chain C residue 1422 VAL Chi-restraints excluded: chain C residue 1438 LEU Chi-restraints excluded: chain C residue 1496 LEU Chi-restraints excluded: chain C residue 1664 ASP 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 2193 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 1512 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 1944 ILE 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 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 1464 VAL Chi-restraints excluded: chain F residue 1496 LEU Chi-restraints excluded: chain F residue 1570 ILE 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 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 1710 VAL Chi-restraints excluded: chain G residue 1924 SER 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 594 optimal weight: 0.9980 chunk 69 optimal weight: 2.9990 chunk 351 optimal weight: 0.7980 chunk 450 optimal weight: 2.9990 chunk 348 optimal weight: 0.6980 chunk 518 optimal weight: 1.9990 chunk 344 optimal weight: 5.9990 chunk 613 optimal weight: 1.9990 chunk 384 optimal weight: 3.9990 chunk 374 optimal weight: 0.7980 chunk 283 optimal weight: 2.9990 overall best weight: 1.0582 ------------------------------------------------------------------------------- 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** D1447 ASN ** E1765 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G1765 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G2189 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8550 moved from start: 0.4040 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 46053 Z= 0.219 Angle : 0.515 7.915 63749 Z= 0.262 Chirality : 0.044 0.150 7952 Planarity : 0.005 0.052 8393 Dihedral : 4.181 24.526 6615 Min Nonbonded Distance : 2.586 Molprobity Statistics. All-atom Clashscore : 5.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.83 % Favored : 97.17 % Rotamer: Outliers : 1.40 % Allowed : 6.96 % Favored : 91.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.93 (0.11), residues: 6370 helix: None (None), residues: 0 sheet: 0.81 (0.10), residues: 2667 loop : 0.60 (0.11), residues: 3703 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP G2177 PHE 0.014 0.001 PHE A2106 TYR 0.019 0.001 TYR F2034 ARG 0.003 0.000 ARG C1564 *********************** 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 161 residues out of total 5201 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 88 time to evaluate : 4.759 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 1438 LEU cc_start: 0.8412 (mt) cc_final: 0.8192 (mt) REVERT: B 1421 MET cc_start: 0.7709 (mtp) cc_final: 0.6871 (ttt) REVERT: B 1496 LEU cc_start: 0.8661 (OUTLIER) cc_final: 0.8391 (tt) REVERT: B 1710 VAL cc_start: 0.9072 (OUTLIER) cc_final: 0.8867 (t) REVERT: B 1985 MET cc_start: 0.8586 (ttm) cc_final: 0.8316 (ttm) REVERT: B 1999 MET cc_start: 0.8659 (mtm) cc_final: 0.8400 (mtm) REVERT: C 1438 LEU cc_start: 0.8004 (OUTLIER) cc_final: 0.7334 (mt) REVERT: C 1963 ASN cc_start: 0.8179 (OUTLIER) cc_final: 0.7411 (p0) REVERT: C 2034 TYR cc_start: 0.8978 (t80) cc_final: 0.8763 (t80) REVERT: D 1438 LEU cc_start: 0.8037 (mt) cc_final: 0.7808 (mt) REVERT: D 1742 ILE cc_start: 0.8631 (OUTLIER) cc_final: 0.8329 (mt) REVERT: E 1405 MET cc_start: 0.8535 (mmt) cc_final: 0.8250 (mmt) REVERT: E 1662 GLU cc_start: 0.8316 (mt-10) cc_final: 0.7979 (mt-10) REVERT: E 1811 GLU cc_start: 0.8739 (mt-10) cc_final: 0.7942 (pm20) REVERT: E 2060 GLU cc_start: 0.8388 (mt-10) cc_final: 0.8070 (pm20) REVERT: F 1421 MET cc_start: 0.7890 (mtp) cc_final: 0.7427 (ttt) REVERT: F 1438 LEU cc_start: 0.8221 (mt) cc_final: 0.8008 (mt) REVERT: F 2234 MET cc_start: 0.8467 (ttp) cc_final: 0.8015 (ttp) REVERT: F 2248 MET cc_start: 0.8680 (mtp) cc_final: 0.8319 (mtp) REVERT: G 1405 MET cc_start: 0.8491 (mmt) cc_final: 0.8231 (mmt) REVERT: G 1441 LEU cc_start: 0.8759 (OUTLIER) cc_final: 0.8333 (tp) REVERT: G 1710 VAL cc_start: 0.9087 (OUTLIER) cc_final: 0.8838 (t) REVERT: G 2034 TYR cc_start: 0.9139 (t80) cc_final: 0.8864 (t80) outliers start: 73 outliers final: 52 residues processed: 155 average time/residue: 0.4432 time to fit residues: 128.0692 Evaluate side-chains 141 residues out of total 5201 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 82 time to evaluate : 6.256 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 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 2136 LEU Chi-restraints excluded: chain B residue 2253 THR Chi-restraints excluded: chain B residue 2313 ILE Chi-restraints excluded: chain C residue 1438 LEU 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 2193 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 1512 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 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 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 2136 LEU 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 1963 ASN Chi-restraints excluded: chain F residue 1987 THR Chi-restraints excluded: chain F residue 2136 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 1441 LEU Chi-restraints excluded: chain G residue 1496 LEU Chi-restraints excluded: chain G residue 1710 VAL Chi-restraints excluded: chain G residue 1795 VAL Chi-restraints excluded: chain G residue 1924 SER 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 637 random chunks: chunk 379 optimal weight: 3.9990 chunk 245 optimal weight: 0.5980 chunk 366 optimal weight: 6.9990 chunk 184 optimal weight: 1.9990 chunk 120 optimal weight: 4.9990 chunk 118 optimal weight: 2.9990 chunk 390 optimal weight: 3.9990 chunk 418 optimal weight: 1.9990 chunk 303 optimal weight: 2.9990 chunk 57 optimal weight: 1.9990 chunk 482 optimal weight: 3.9990 overall best weight: 1.9188 ------------------------------------------------------------------------------- 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** D1683 ASN ** E1765 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G1765 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G2189 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8587 moved from start: 0.4213 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.042 46053 Z= 0.376 Angle : 0.583 8.205 63749 Z= 0.299 Chirality : 0.045 0.155 7952 Planarity : 0.005 0.064 8393 Dihedral : 4.531 20.454 6615 Min Nonbonded Distance : 2.560 Molprobity Statistics. All-atom Clashscore : 5.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.08 % Favored : 96.92 % Rotamer: Outliers : 1.38 % Allowed : 7.23 % Favored : 91.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.73 (0.10), residues: 6370 helix: None (None), residues: 0 sheet: 0.76 (0.10), residues: 2646 loop : 0.39 (0.11), residues: 3724 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP A1432 PHE 0.023 0.002 PHE A2106 TYR 0.022 0.002 TYR F2034 ARG 0.004 0.001 ARG A2011 *********************** 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 157 residues out of total 5201 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 85 time to evaluate : 5.164 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 1438 LEU cc_start: 0.8430 (mt) cc_final: 0.8159 (mt) REVERT: B 1421 MET cc_start: 0.7734 (mtp) cc_final: 0.6874 (ttt) REVERT: B 1438 LEU cc_start: 0.8359 (mt) cc_final: 0.7760 (mt) REVERT: B 1496 LEU cc_start: 0.8636 (OUTLIER) cc_final: 0.8342 (tt) REVERT: B 1985 MET cc_start: 0.8660 (ttm) cc_final: 0.8347 (ttm) REVERT: B 1999 MET cc_start: 0.8797 (mtm) cc_final: 0.8504 (mtm) REVERT: C 1438 LEU cc_start: 0.7653 (OUTLIER) cc_final: 0.7346 (mt) REVERT: C 1963 ASN cc_start: 0.8331 (OUTLIER) cc_final: 0.7556 (p0) REVERT: C 2034 TYR cc_start: 0.9160 (t80) cc_final: 0.8852 (t80) REVERT: D 1438 LEU cc_start: 0.8314 (mt) cc_final: 0.8075 (mt) REVERT: E 1405 MET cc_start: 0.8622 (mmt) cc_final: 0.8318 (mmt) REVERT: E 1438 LEU cc_start: 0.8253 (mt) cc_final: 0.7998 (mt) REVERT: E 1662 GLU cc_start: 0.8360 (mt-10) cc_final: 0.8028 (mt-10) REVERT: E 1811 GLU cc_start: 0.8750 (mt-10) cc_final: 0.7935 (pm20) REVERT: E 1911 GLU cc_start: 0.8759 (tt0) cc_final: 0.8149 (tt0) REVERT: E 2060 GLU cc_start: 0.8346 (mt-10) cc_final: 0.8043 (pm20) REVERT: F 1421 MET cc_start: 0.8099 (mtp) cc_final: 0.7525 (ttt) REVERT: F 2234 MET cc_start: 0.8576 (ttp) cc_final: 0.8035 (ttp) REVERT: F 2248 MET cc_start: 0.8791 (mtp) cc_final: 0.8331 (mtp) REVERT: G 1438 LEU cc_start: 0.7951 (mt) cc_final: 0.7461 (mt) REVERT: G 1441 LEU cc_start: 0.8781 (OUTLIER) cc_final: 0.8434 (tp) REVERT: G 1710 VAL cc_start: 0.9079 (OUTLIER) cc_final: 0.8823 (t) REVERT: G 1742 ILE cc_start: 0.8619 (OUTLIER) cc_final: 0.8363 (mt) REVERT: G 2034 TYR cc_start: 0.9214 (t80) cc_final: 0.8960 (t80) outliers start: 72 outliers final: 55 residues processed: 152 average time/residue: 0.4721 time to fit residues: 133.0854 Evaluate side-chains 141 residues out of total 5201 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 80 time to evaluate : 4.603 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 2253 THR Chi-restraints excluded: chain B residue 1496 LEU 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 1438 LEU Chi-restraints excluded: chain C residue 1496 LEU Chi-restraints excluded: chain C residue 1742 ILE Chi-restraints excluded: chain C residue 1963 ASN Chi-restraints excluded: chain C residue 2004 VAL 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 1496 LEU Chi-restraints excluded: chain D residue 1512 ILE 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 1944 ILE Chi-restraints excluded: chain D residue 1986 THR Chi-restraints excluded: chain D residue 2136 LEU 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 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 2041 LEU 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 1710 VAL 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 2004 VAL Chi-restraints excluded: chain G residue 2136 LEU Chi-restraints excluded: chain G residue 2197 THR Chi-restraints excluded: chain G residue 2253 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 637 random chunks: chunk 558 optimal weight: 0.6980 chunk 588 optimal weight: 0.0170 chunk 536 optimal weight: 6.9990 chunk 572 optimal weight: 2.9990 chunk 344 optimal weight: 0.9990 chunk 249 optimal weight: 2.9990 chunk 449 optimal weight: 7.9990 chunk 175 optimal weight: 3.9990 chunk 517 optimal weight: 2.9990 chunk 541 optimal weight: 6.9990 chunk 570 optimal weight: 1.9990 overall best weight: 1.3424 ------------------------------------------------------------------------------- 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** D1447 ASN ** E1765 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G1765 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G2189 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8574 moved from start: 0.4310 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 46053 Z= 0.266 Angle : 0.537 9.775 63749 Z= 0.275 Chirality : 0.045 0.212 7952 Planarity : 0.005 0.066 8393 Dihedral : 4.379 19.415 6615 Min Nonbonded Distance : 2.576 Molprobity Statistics. All-atom Clashscore : 5.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % Rotamer: Outliers : 1.38 % Allowed : 7.33 % Favored : 91.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.74 (0.11), residues: 6370 helix: None (None), residues: 0 sheet: 0.74 (0.10), residues: 2674 loop : 0.42 (0.11), residues: 3696 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP A1432 PHE 0.017 0.001 PHE A2106 TYR 0.022 0.001 TYR F2034 ARG 0.002 0.000 ARG B1564 *********************** 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 155 residues out of total 5201 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 83 time to evaluate : 3.958 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1438 LEU cc_start: 0.8418 (mt) cc_final: 0.8157 (mt) REVERT: B 1421 MET cc_start: 0.7847 (mtp) cc_final: 0.6924 (ttt) REVERT: B 1438 LEU cc_start: 0.8346 (mt) cc_final: 0.7751 (mt) REVERT: B 1496 LEU cc_start: 0.8606 (OUTLIER) cc_final: 0.8327 (tt) REVERT: B 1985 MET cc_start: 0.8607 (ttm) cc_final: 0.8331 (ttm) REVERT: B 1999 MET cc_start: 0.8788 (mtm) cc_final: 0.8532 (mtm) REVERT: C 1963 ASN cc_start: 0.8260 (OUTLIER) cc_final: 0.7489 (p0) REVERT: C 2034 TYR cc_start: 0.9130 (t80) cc_final: 0.8837 (t80) REVERT: D 1438 LEU cc_start: 0.8294 (mt) cc_final: 0.8062 (mt) REVERT: E 1405 MET cc_start: 0.8604 (mmt) cc_final: 0.8247 (mmt) REVERT: E 1438 LEU cc_start: 0.8242 (mt) cc_final: 0.7986 (mt) REVERT: E 1662 GLU cc_start: 0.8352 (mt-10) cc_final: 0.8017 (mt-10) REVERT: E 1811 GLU cc_start: 0.8747 (mt-10) cc_final: 0.7948 (pm20) REVERT: E 1911 GLU cc_start: 0.8740 (tt0) cc_final: 0.8136 (tt0) REVERT: E 2060 GLU cc_start: 0.8372 (mt-10) cc_final: 0.8082 (pm20) REVERT: E 2248 MET cc_start: 0.8935 (ptp) cc_final: 0.8311 (ptm) REVERT: F 1421 MET cc_start: 0.8129 (mtp) cc_final: 0.7531 (ttt) REVERT: F 2234 MET cc_start: 0.8545 (ttp) cc_final: 0.7987 (ttp) REVERT: F 2248 MET cc_start: 0.8785 (mtp) cc_final: 0.8333 (mtp) REVERT: G 1438 LEU cc_start: 0.7943 (mt) cc_final: 0.7456 (mt) REVERT: G 1441 LEU cc_start: 0.8785 (OUTLIER) cc_final: 0.8392 (tp) REVERT: G 1710 VAL cc_start: 0.9040 (OUTLIER) cc_final: 0.8792 (t) REVERT: G 1742 ILE cc_start: 0.8644 (OUTLIER) cc_final: 0.8372 (mt) REVERT: G 2034 TYR cc_start: 0.9184 (t80) cc_final: 0.8930 (t80) outliers start: 72 outliers final: 60 residues processed: 146 average time/residue: 0.4522 time to fit residues: 123.1899 Evaluate side-chains 147 residues out of total 5201 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 82 time to evaluate : 4.798 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 1570 ILE 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 1999 MET 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 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 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 2136 LEU 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 1496 LEU Chi-restraints excluded: chain D residue 1512 ILE 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 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 2197 THR Chi-restraints excluded: chain D residue 2248 MET Chi-restraints excluded: chain D residue 2253 THR Chi-restraints excluded: chain E residue 1422 VAL 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 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 2041 LEU 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 1710 VAL 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 2004 VAL Chi-restraints excluded: chain G residue 2136 LEU Chi-restraints excluded: chain G residue 2253 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 637 random chunks: chunk 375 optimal weight: 1.9990 chunk 605 optimal weight: 4.9990 chunk 369 optimal weight: 2.9990 chunk 287 optimal weight: 6.9990 chunk 420 optimal weight: 5.9990 chunk 634 optimal weight: 4.9990 chunk 584 optimal weight: 0.9990 chunk 505 optimal weight: 0.8980 chunk 52 optimal weight: 3.9990 chunk 390 optimal weight: 3.9990 chunk 309 optimal weight: 0.9980 overall best weight: 1.5786 ------------------------------------------------------------------------------- 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** ** G2189 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8586 moved from start: 0.4434 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 46053 Z= 0.311 Angle : 0.556 11.860 63749 Z= 0.284 Chirality : 0.045 0.175 7952 Planarity : 0.005 0.072 8393 Dihedral : 4.451 20.228 6615 Min Nonbonded Distance : 2.567 Molprobity Statistics. All-atom Clashscore : 5.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.31 % Favored : 96.69 % Rotamer: Outliers : 1.27 % Allowed : 7.46 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.67 (0.11), residues: 6370 helix: None (None), residues: 0 sheet: 0.71 (0.10), residues: 2660 loop : 0.36 (0.11), residues: 3710 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP E1432 PHE 0.021 0.002 PHE A2106 TYR 0.021 0.001 TYR F2034 ARG 0.002 0.000 ARG B1564 ********************** 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 151 residues out of total 5201 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 85 time to evaluate : 5.021 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1438 LEU cc_start: 0.8479 (mt) cc_final: 0.8223 (mt) REVERT: B 1421 MET cc_start: 0.7927 (mtp) cc_final: 0.6852 (ttt) REVERT: B 1438 LEU cc_start: 0.8445 (mt) cc_final: 0.7867 (mt) REVERT: B 1496 LEU cc_start: 0.8602 (OUTLIER) cc_final: 0.8325 (tt) REVERT: B 1985 MET cc_start: 0.8622 (ttm) cc_final: 0.8339 (ttm) REVERT: B 1999 MET cc_start: 0.8812 (mtm) cc_final: 0.8575 (mtm) REVERT: C 1963 ASN cc_start: 0.8289 (OUTLIER) cc_final: 0.7525 (p0) REVERT: C 2034 TYR cc_start: 0.9159 (t80) cc_final: 0.8846 (t80) REVERT: D 1438 LEU cc_start: 0.8414 (mt) cc_final: 0.8191 (mp) REVERT: E 1438 LEU cc_start: 0.8337 (mt) cc_final: 0.8080 (mt) REVERT: E 1811 GLU cc_start: 0.8770 (mt-10) cc_final: 0.8011 (pm20) REVERT: E 1911 GLU cc_start: 0.8762 (tt0) cc_final: 0.8174 (tt0) REVERT: E 2060 GLU cc_start: 0.8393 (mt-10) cc_final: 0.8091 (pm20) REVERT: E 2248 MET cc_start: 0.8891 (ptp) cc_final: 0.8182 (ptm) REVERT: F 1421 MET cc_start: 0.8359 (mtp) cc_final: 0.7817 (ttt) REVERT: F 2234 MET cc_start: 0.8532 (ttp) cc_final: 0.7951 (ttp) REVERT: F 2248 MET cc_start: 0.8870 (mtp) cc_final: 0.8416 (mtp) REVERT: G 1438 LEU cc_start: 0.8029 (mt) cc_final: 0.7731 (mt) REVERT: G 1441 LEU cc_start: 0.8805 (OUTLIER) cc_final: 0.8431 (tp) REVERT: G 1710 VAL cc_start: 0.9022 (OUTLIER) cc_final: 0.8777 (t) REVERT: G 1742 ILE cc_start: 0.8595 (OUTLIER) cc_final: 0.8360 (mt) REVERT: G 2034 TYR cc_start: 0.9217 (t80) cc_final: 0.8958 (t80) outliers start: 66 outliers final: 60 residues processed: 145 average time/residue: 0.4177 time to fit residues: 113.6658 Evaluate side-chains 145 residues out of total 5201 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 80 time to evaluate : 3.755 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 1570 ILE 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 1999 MET 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 1820 SER 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 1496 LEU Chi-restraints excluded: chain C residue 1664 ASP 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 2136 LEU 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 1496 LEU Chi-restraints excluded: chain D residue 1512 ILE 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 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 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 2041 LEU 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 1710 VAL 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 2004 VAL Chi-restraints excluded: chain G residue 2136 LEU Chi-restraints excluded: chain G residue 2253 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 637 random chunks: chunk 401 optimal weight: 0.4980 chunk 538 optimal weight: 2.9990 chunk 154 optimal weight: 0.9990 chunk 465 optimal weight: 0.7980 chunk 74 optimal weight: 0.7980 chunk 140 optimal weight: 1.9990 chunk 506 optimal weight: 1.9990 chunk 211 optimal weight: 3.9990 chunk 519 optimal weight: 1.9990 chunk 64 optimal weight: 5.9990 chunk 93 optimal weight: 0.8980 overall best weight: 0.7982 ------------------------------------------------------------------------------- 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** ** G2189 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 = 0.069499 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2770 r_free = 0.2770 target = 0.057017 restraints weight = 144550.291| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.2811 r_free = 0.2811 target = 0.058618 restraints weight = 64739.043| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.2836 r_free = 0.2836 target = 0.059655 restraints weight = 36823.876| |-----------------------------------------------------------------------------| r_work (final): 0.2786 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8673 moved from start: 0.4496 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 46053 Z= 0.180 Angle : 0.504 7.546 63749 Z= 0.256 Chirality : 0.044 0.149 7952 Planarity : 0.005 0.065 8393 Dihedral : 4.159 18.183 6615 Min Nonbonded Distance : 2.576 Molprobity Statistics. All-atom Clashscore : 4.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.56 % Favored : 97.44 % Rotamer: Outliers : 1.13 % Allowed : 7.65 % Favored : 91.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.88 (0.11), residues: 6370 helix: None (None), residues: 0 sheet: 0.85 (0.10), residues: 2674 loop : 0.50 (0.11), residues: 3696 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP A1432 PHE 0.012 0.001 PHE C1857 TYR 0.021 0.001 TYR F2034 ARG 0.001 0.000 ARG E1564 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5612.73 seconds wall clock time: 105 minutes 52.64 seconds (6352.64 seconds total)