Starting phenix.real_space_refine
on Sat Nov 16 22:52:14 2024 by dcliebschner
===============================================================================

Processing files:
-------------------------------------------------------------------------------

  Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9cv6_45956/11_2024/9cv6_45956.cif
  Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9cv6_45956/11_2024/9cv6_45956.map

Processing PHIL parameters:
-------------------------------------------------------------------------------

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.12
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9cv6_45956/11_2024/9cv6_45956.map"
    default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9cv6_45956/11_2024/9cv6_45956.map"
    model {
      file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9cv6_45956/11_2024/9cv6_45956.cif"
    }
    default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9cv6_45956/11_2024/9cv6_45956.cif"
  }
  resolution = 3.12
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


Starting job
===============================================================================
-------------------------------------------------------------------------------
Citation:
*********
Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams
PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography.
Acta Cryst. D74:531-544.

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.010
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      44      5.16       5
     C    7586      2.51       5
     N    2146      2.21       5
     O    2254      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 6 residue(s): 0.04s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/chem_data/mon_lib"
  Total number of atoms: 12030
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "A"
      Number of atoms: 6015
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 760, 6015
          Classifications: {'peptide': 760}
          Link IDs: {'PTRANS': 36, 'TRANS': 723}
          Chain breaks: 1
    Chain: "B"
      Number of atoms: 6015
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 760, 6015
          Classifications: {'peptide': 760}
          Link IDs: {'PTRANS': 36, 'TRANS': 723}
          Chain breaks: 1
  Time building chain proxies: 8.19, per 1000 atoms: 0.68
  Number of scatterers: 12030
  At special positions: 0
  Unit cell: (123.061, 172.64, 112.437, 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      44     16.00
     O    2254      8.00
     N    2146      7.00
     C    7586      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 2.85
  Conformation dependent library (CDL) restraints added in 1.6 seconds
  

  3024 Ramachandran restraints generated.
    1512 Oldfield, 0 Emsley, 1512 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2824

  Finding SS restraints...
    Secondary structure from input PDB file:
      65 helices and 14 sheets defined
      53.2% alpha, 13.4% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 1.62
  Creating SS restraints...
    Processing helix  chain 'A' and resid 1624 through 1635
    Processing helix  chain 'A' and resid 1638 through 1640
      No H-bonds generated for 'chain 'A' and resid 1638 through 1640'
    Processing helix  chain 'A' and resid 1641 through 1661
      removed outlier: 4.129A  pdb=" N   MET A1645 " --> pdb=" O   ASP A1641 " (cutoff:3.500A)
      removed outlier: 3.917A  pdb=" N   PHE A1646 " --> pdb=" O   ILE A1642 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1728 through 1732
    Processing helix  chain 'A' and resid 1734 through 1751
      removed outlier: 3.754A  pdb=" N   VAL A1740 " --> pdb=" O   GLN A1736 " (cutoff:3.500A)
      removed outlier: 3.611A  pdb=" N   TYR A1741 " --> pdb=" O   GLU A1737 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1769 through 1774
      removed outlier: 3.788A  pdb=" N   LYS A1773 " --> pdb=" O   ALA A1769 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1796 through 1804
      removed outlier: 3.636A  pdb=" N   LYS A1802 " --> pdb=" O   GLU A1798 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1835 through 1856
      removed outlier: 4.153A  pdb=" N   LEU A1839 " --> pdb=" O   GLY A1835 " (cutoff:3.500A)
      removed outlier: 3.753A  pdb=" N   ASP A1841 " --> pdb=" O   GLU A1837 " (cutoff:3.500A)
      removed outlier: 3.583A  pdb=" N   GLY A1843 " --> pdb=" O   LEU A1839 " (cutoff:3.500A)
      removed outlier: 3.632A  pdb=" N   LEU A1844 " --> pdb=" O   ARG A1840 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1868 through 1878
      removed outlier: 3.545A  pdb=" N   TYR A1872 " --> pdb=" O   GLY A1868 " (cutoff:3.500A)
      removed outlier: 3.503A  pdb=" N   HIS A1878 " --> pdb=" O   VAL A1874 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1892 through 1901
    Processing helix  chain 'A' and resid 1907 through 1913
      removed outlier: 4.167A  pdb=" N   LEU A1911 " --> pdb=" O   SER A1907 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1913 through 1921
      removed outlier: 4.316A  pdb=" N   HIS A1919 " --> pdb=" O   GLN A1915 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1929 through 1944
      removed outlier: 3.912A  pdb=" N   PHE A1943 " --> pdb=" O   ARG A1939 " (cutoff:3.500A)
      removed outlier: 3.957A  pdb=" N   VAL A1944 " --> pdb=" O   TRP A1940 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1975 through 1981
      removed outlier: 4.068A  pdb=" N   MET A1979 " --> pdb=" O   ASP A1975 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 2054 through 2071
      removed outlier: 3.645A  pdb=" N   GLU A2071 " --> pdb=" O   ASP A2067 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 2087 through 2093
    Processing helix  chain 'A' and resid 2094 through 2108
      removed outlier: 3.674A  pdb=" N   PHE A2098 " --> pdb=" O   GLN A2094 " (cutoff:3.500A)
      removed outlier: 3.666A  pdb=" N   ILE A2102 " --> pdb=" O   PHE A2098 " (cutoff:3.500A)
      removed outlier: 3.836A  pdb=" N   VAL A2103 " --> pdb=" O   GLY A2099 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 2125 through 2132
      removed outlier: 4.006A  pdb=" N   ALA A2129 " --> pdb=" O   GLY A2125 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 2133 through 2136
    Processing helix  chain 'A' and resid 2154 through 2163
    Processing helix  chain 'A' and resid 2164 through 2176
    Processing helix  chain 'A' and resid 2176 through 2196
    Processing helix  chain 'A' and resid 2220 through 2235
      removed outlier: 3.567A  pdb=" N   ARG A2224 " --> pdb=" O   GLU A2220 " (cutoff:3.500A)
      removed outlier: 3.512A  pdb=" N   LYS A2235 " --> pdb=" O   LEU A2231 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 2238 through 2244
    Processing helix  chain 'A' and resid 2244 through 2258
    Processing helix  chain 'A' and resid 2261 through 2268
      removed outlier: 3.642A  pdb=" N   MET A2265 " --> pdb=" O   THR A2261 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 2279 through 2305
      removed outlier: 3.725A  pdb=" N   LEU A2283 " --> pdb=" O   ASP A2279 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 2312 through 2328
      removed outlier: 3.668A  pdb=" N   ALA A2316 " --> pdb=" O   GLN A2312 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 2334 through 2339
    Processing helix  chain 'A' and resid 2341 through 2353
      removed outlier: 3.934A  pdb=" N   GLY A2352 " --> pdb=" O   GLU A2348 " (cutoff:3.500A)
      removed outlier: 3.801A  pdb=" N   ASP A2353 " --> pdb=" O   ALA A2349 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 2356 through 2380
      removed outlier: 3.634A  pdb=" N   ARG A2360 " --> pdb=" O   SER A2356 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 2382 through 2396
      removed outlier: 3.612A  pdb=" N   SER A2387 " --> pdb=" O   PRO A2383 " (cutoff:3.500A)
      removed outlier: 3.743A  pdb=" N   GLU A2388 " --> pdb=" O   SER A2384 " (cutoff:3.500A)
      removed outlier: 3.621A  pdb=" N   LEU A2396 " --> pdb=" O   LYS A2392 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 1624 through 1635
    Processing helix  chain 'B' and resid 1638 through 1640
      No H-bonds generated for 'chain 'B' and resid 1638 through 1640'
    Processing helix  chain 'B' and resid 1641 through 1661
      removed outlier: 4.112A  pdb=" N   MET B1645 " --> pdb=" O   ASP B1641 " (cutoff:3.500A)
      removed outlier: 3.991A  pdb=" N   PHE B1646 " --> pdb=" O   ILE B1642 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 1728 through 1732
    Processing helix  chain 'B' and resid 1734 through 1751
    Processing helix  chain 'B' and resid 1769 through 1776
      removed outlier: 3.635A  pdb=" N   LYS B1773 " --> pdb=" O   ALA B1769 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 1796 through 1804
      removed outlier: 3.579A  pdb=" N   LYS B1802 " --> pdb=" O   GLU B1798 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 1835 through 1856
      removed outlier: 4.146A  pdb=" N   LEU B1839 " --> pdb=" O   GLY B1835 " (cutoff:3.500A)
      removed outlier: 3.561A  pdb=" N   GLY B1843 " --> pdb=" O   LEU B1839 " (cutoff:3.500A)
      removed outlier: 3.582A  pdb=" N   LEU B1844 " --> pdb=" O   ARG B1840 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 1868 through 1878
      removed outlier: 3.532A  pdb=" N   TYR B1872 " --> pdb=" O   GLY B1868 " (cutoff:3.500A)
      removed outlier: 3.511A  pdb=" N   HIS B1878 " --> pdb=" O   VAL B1874 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 1892 through 1901
    Processing helix  chain 'B' and resid 1908 through 1913
    Processing helix  chain 'B' and resid 1913 through 1921
      removed outlier: 4.377A  pdb=" N   HIS B1919 " --> pdb=" O   GLN B1915 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 1929 through 1944
      removed outlier: 3.941A  pdb=" N   PHE B1943 " --> pdb=" O   ARG B1939 " (cutoff:3.500A)
      removed outlier: 3.960A  pdb=" N   VAL B1944 " --> pdb=" O   TRP B1940 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 1975 through 1981
      removed outlier: 4.157A  pdb=" N   MET B1979 " --> pdb=" O   ASP B1975 " (cutoff:3.500A)
      removed outlier: 3.629A  pdb=" N   LEU B1980 " --> pdb=" O   PRO B1976 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 2054 through 2071
      removed outlier: 3.619A  pdb=" N   GLU B2071 " --> pdb=" O   ASP B2067 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 2087 through 2093
    Processing helix  chain 'B' and resid 2094 through 2108
      removed outlier: 3.610A  pdb=" N   PHE B2098 " --> pdb=" O   GLN B2094 " (cutoff:3.500A)
      removed outlier: 3.632A  pdb=" N   GLU B2101 " --> pdb=" O   LYS B2097 " (cutoff:3.500A)
      removed outlier: 3.950A  pdb=" N   ILE B2102 " --> pdb=" O   PHE B2098 " (cutoff:3.500A)
      removed outlier: 4.017A  pdb=" N   VAL B2103 " --> pdb=" O   GLY B2099 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 2125 through 2132
      removed outlier: 3.998A  pdb=" N   ALA B2129 " --> pdb=" O   GLY B2125 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 2133 through 2136
    Processing helix  chain 'B' and resid 2154 through 2163
    Processing helix  chain 'B' and resid 2164 through 2176
    Processing helix  chain 'B' and resid 2176 through 2196
    Processing helix  chain 'B' and resid 2217 through 2219
      No H-bonds generated for 'chain 'B' and resid 2217 through 2219'
    Processing helix  chain 'B' and resid 2220 through 2235
      removed outlier: 3.774A  pdb=" N   ARG B2224 " --> pdb=" O   GLU B2220 " (cutoff:3.500A)
      removed outlier: 3.835A  pdb=" N   GLU B2225 " --> pdb=" O   THR B2221 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 2238 through 2244
    Processing helix  chain 'B' and resid 2244 through 2258
    Processing helix  chain 'B' and resid 2261 through 2268
      removed outlier: 3.699A  pdb=" N   MET B2265 " --> pdb=" O   THR B2261 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 2279 through 2306
      removed outlier: 3.659A  pdb=" N   LEU B2283 " --> pdb=" O   ASP B2279 " (cutoff:3.500A)
      removed outlier: 3.721A  pdb=" N   GLU B2296 " --> pdb=" O   LEU B2292 " (cutoff:3.500A)
      removed outlier: 3.704A  pdb=" N   LYS B2306 " --> pdb=" O   GLN B2302 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 2312 through 2328
      removed outlier: 3.674A  pdb=" N   ALA B2316 " --> pdb=" O   GLN B2312 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 2333 through 2337
      removed outlier: 3.772A  pdb=" N   TRP B2336 " --> pdb=" O   SER B2333 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 2339 through 2353
      removed outlier: 3.622A  pdb=" N   VAL B2343 " --> pdb=" O   ASP B2339 " (cutoff:3.500A)
      removed outlier: 4.135A  pdb=" N   GLY B2352 " --> pdb=" O   GLU B2348 " (cutoff:3.500A)
      removed outlier: 3.798A  pdb=" N   ASP B2353 " --> pdb=" O   ALA B2349 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 2356 through 2380
      removed outlier: 3.660A  pdb=" N   ARG B2360 " --> pdb=" O   SER B2356 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 2382 through 2396
      removed outlier: 3.542A  pdb=" N   SER B2387 " --> pdb=" O   PRO B2383 " (cutoff:3.500A)
      removed outlier: 3.710A  pdb=" N   GLU B2388 " --> pdb=" O   SER B2384 " (cutoff:3.500A)
      removed outlier: 3.593A  pdb=" N   LEU B2396 " --> pdb=" O   LYS B2392 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 1687 through 1690
      removed outlier: 4.525A  pdb=" N   ALA A1703 " --> pdb=" O   LEU A1677 " (cutoff:3.500A)
      removed outlier: 8.029A  pdb=" N   VAL A1679 " --> pdb=" O   MET A1701 " (cutoff:3.500A)
      removed outlier: 11.147A  pdb=" N   MET A1701 " --> pdb=" O   VAL A1679 " (cutoff:3.500A)
      removed outlier: 8.701A  pdb=" N   ILE A1756 " --> pdb=" O   ASP A1718 " (cutoff:3.500A)
      removed outlier: 6.355A  pdb=" N   VAL A1720 " --> pdb=" O   ILE A1756 " (cutoff:3.500A)
      removed outlier: 7.887A  pdb=" N   ILE A1758 " --> pdb=" O   VAL A1720 " (cutoff:3.500A)
      removed outlier: 6.728A  pdb=" N   ILE A1722 " --> pdb=" O   ILE A1758 " (cutoff:3.500A)
      removed outlier: 6.398A  pdb=" N   VAL A1880 " --> pdb=" O   ALA A1925 " (cutoff:3.500A)
      removed outlier: 7.707A  pdb=" N   ALA A1927 " --> pdb=" O   VAL A1880 " (cutoff:3.500A)
      removed outlier: 6.198A  pdb=" N   GLN A1882 " --> pdb=" O   ALA A1927 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 1777 through 1780
      removed outlier: 6.480A  pdb=" N   ASN A1777 " --> pdb=" O   LEU A1793 " (cutoff:3.500A)
      removed outlier: 4.681A  pdb=" N   LEU A1793 " --> pdb=" O   ASN A1777 " (cutoff:3.500A)
      removed outlier: 6.791A  pdb=" N   ALA A1779 " --> pdb=" O   LYS A1791 " (cutoff:3.500A)
      removed outlier: 16.388A  pdb=" N   LYS A1791 " --> pdb=" O   ASP A1826 " (cutoff:3.500A)
      removed outlier: 12.225A  pdb=" N   ASP A1826 " --> pdb=" O   LYS A1791 " (cutoff:3.500A)
      removed outlier: 5.528A  pdb=" N   LEU A1793 " --> pdb=" O   ILE A1824 " (cutoff:3.500A)
      removed outlier: 3.672A  pdb=" N   ASP A1816 " --> pdb=" O   GLU A1819 " (cutoff:3.500A)
      removed outlier: 6.611A  pdb=" N   LYS A1810 " --> pdb=" O   THR A1825 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 1866 through 1867
      removed outlier: 5.940A  pdb=" N   ALA A1866 " --> pdb=" O   ILE A1889 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA3
    Processing sheet with id=AA4, first strand: chain 'A' and resid 1996 through 1997
      removed outlier: 7.587A  pdb=" N   MET A2076 " --> pdb=" O   PRO A2017 " (cutoff:3.500A)
      removed outlier: 6.031A  pdb=" N   GLY A2019 " --> pdb=" O   MET A2076 " (cutoff:3.500A)
      removed outlier: 7.383A  pdb=" N   PHE A2078 " --> pdb=" O   GLY A2019 " (cutoff:3.500A)
      removed outlier: 6.547A  pdb=" N   ILE A2021 " --> pdb=" O   PHE A2078 " (cutoff:3.500A)
      removed outlier: 6.514A  pdb=" N   ILE A2075 " --> pdb=" O   LEU A2114 " (cutoff:3.500A)
      removed outlier: 7.683A  pdb=" N   TYR A2116 " --> pdb=" O   ILE A2075 " (cutoff:3.500A)
      removed outlier: 6.086A  pdb=" N   ILE A2077 " --> pdb=" O   TYR A2116 " (cutoff:3.500A)
      removed outlier: 4.219A  pdb=" N   GLU A2273 " --> pdb=" O   MET A2142 " (cutoff:3.500A)
      removed outlier: 3.617A  pdb=" N   ALA A2144 " --> pdb=" O   GLU A2273 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'A' and resid 2028 through 2032
    Processing sheet with id=AA6, first strand: chain 'A' and resid 2052 through 2053
      removed outlier: 3.703A  pdb=" N   TRP A2053 " --> pdb=" O   GLY A2083 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA6
    Processing sheet with id=AA7, first strand: chain 'A' and resid 2122 through 2124
      removed outlier: 3.537A  pdb=" N   GLY A2151 " --> pdb=" O   LEU A2123 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'B' and resid 1687 through 1690
      removed outlier: 4.544A  pdb=" N   ALA B1703 " --> pdb=" O   LEU B1677 " (cutoff:3.500A)
      removed outlier: 8.008A  pdb=" N   VAL B1679 " --> pdb=" O   MET B1701 " (cutoff:3.500A)
      removed outlier: 11.176A  pdb=" N   MET B1701 " --> pdb=" O   VAL B1679 " (cutoff:3.500A)
      removed outlier: 8.666A  pdb=" N   ILE B1756 " --> pdb=" O   ASP B1718 " (cutoff:3.500A)
      removed outlier: 6.290A  pdb=" N   VAL B1720 " --> pdb=" O   ILE B1756 " (cutoff:3.500A)
      removed outlier: 7.974A  pdb=" N   ILE B1758 " --> pdb=" O   VAL B1720 " (cutoff:3.500A)
      removed outlier: 6.779A  pdb=" N   ILE B1722 " --> pdb=" O   ILE B1758 " (cutoff:3.500A)
      removed outlier: 6.389A  pdb=" N   VAL B1880 " --> pdb=" O   ALA B1925 " (cutoff:3.500A)
      removed outlier: 7.674A  pdb=" N   ALA B1927 " --> pdb=" O   VAL B1880 " (cutoff:3.500A)
      removed outlier: 6.161A  pdb=" N   GLN B1882 " --> pdb=" O   ALA B1927 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'B' and resid 1777 through 1780
      removed outlier: 6.633A  pdb=" N   ASN B1777 " --> pdb=" O   LEU B1793 " (cutoff:3.500A)
      removed outlier: 4.861A  pdb=" N   LEU B1793 " --> pdb=" O   ASN B1777 " (cutoff:3.500A)
      removed outlier: 6.826A  pdb=" N   ALA B1779 " --> pdb=" O   LYS B1791 " (cutoff:3.500A)
      removed outlier: 16.272A  pdb=" N   LYS B1791 " --> pdb=" O   ASP B1826 " (cutoff:3.500A)
      removed outlier: 12.266A  pdb=" N   ASP B1826 " --> pdb=" O   LYS B1791 " (cutoff:3.500A)
      removed outlier: 5.566A  pdb=" N   LEU B1793 " --> pdb=" O   ILE B1824 " (cutoff:3.500A)
      removed outlier: 3.640A  pdb=" N   ASP B1816 " --> pdb=" O   GLU B1819 " (cutoff:3.500A)
      removed outlier: 6.581A  pdb=" N   LYS B1810 " --> pdb=" O   THR B1825 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'B' and resid 1866 through 1867
      removed outlier: 5.987A  pdb=" N   ALA B1866 " --> pdb=" O   ILE B1889 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AB1
    Processing sheet with id=AB2, first strand: chain 'B' and resid 1996 through 1997
      removed outlier: 7.578A  pdb=" N   MET B2076 " --> pdb=" O   PRO B2017 " (cutoff:3.500A)
      removed outlier: 6.068A  pdb=" N   GLY B2019 " --> pdb=" O   MET B2076 " (cutoff:3.500A)
      removed outlier: 7.425A  pdb=" N   PHE B2078 " --> pdb=" O   GLY B2019 " (cutoff:3.500A)
      removed outlier: 6.623A  pdb=" N   ILE B2021 " --> pdb=" O   PHE B2078 " (cutoff:3.500A)
      removed outlier: 6.518A  pdb=" N   ILE B2075 " --> pdb=" O   LEU B2114 " (cutoff:3.500A)
      removed outlier: 7.696A  pdb=" N   TYR B2116 " --> pdb=" O   ILE B2075 " (cutoff:3.500A)
      removed outlier: 6.080A  pdb=" N   ILE B2077 " --> pdb=" O   TYR B2116 " (cutoff:3.500A)
      removed outlier: 4.230A  pdb=" N   GLU B2273 " --> pdb=" O   MET B2142 " (cutoff:3.500A)
      removed outlier: 3.627A  pdb=" N   ALA B2144 " --> pdb=" O   GLU B2273 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'B' and resid 2028 through 2032
    Processing sheet with id=AB4, first strand: chain 'B' and resid 2052 through 2053
      removed outlier: 3.546A  pdb=" N   TRP B2053 " --> pdb=" O   GLY B2083 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AB4
    Processing sheet with id=AB5, first strand: chain 'B' and resid 2122 through 2124
      removed outlier: 3.564A  pdb=" N   GLY B2151 " --> pdb=" O   LEU B2123 " (cutoff:3.500A)

    594 hydrogen bonds defined for protein.
    1731 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: 4.49

  Time building geometry restraints manager: 3.28 seconds

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.

  Histogram of bond lengths:
        1.23 -     1.34: 4046
        1.34 -     1.46: 1942
        1.46 -     1.57: 6206
        1.57 -     1.69: 0
        1.69 -     1.81: 76
  Bond restraints: 12270
  Sorted by residual:
  bond pdb=" C   ILE B1642 "
       pdb=" N   PRO B1643 "
    ideal  model  delta    sigma   weight residual
    1.335  1.364 -0.028 1.36e-02 5.41e+03 4.38e+00
  bond pdb=" C   ILE A1642 "
       pdb=" N   PRO A1643 "
    ideal  model  delta    sigma   weight residual
    1.335  1.363 -0.028 1.36e-02 5.41e+03 4.15e+00
  bond pdb=" C   SER A2245 "
       pdb=" N   PRO A2246 "
    ideal  model  delta    sigma   weight residual
    1.336  1.359 -0.023 1.23e-02 6.61e+03 3.63e+00
  bond pdb=" N   ALA A1984 "
       pdb=" CA  ALA A1984 "
    ideal  model  delta    sigma   weight residual
    1.459  1.480 -0.021 1.15e-02 7.56e+03 3.44e+00
  bond pdb=" C   SER B2245 "
       pdb=" N   PRO B2246 "
    ideal  model  delta    sigma   weight residual
    1.336  1.358 -0.022 1.20e-02 6.94e+03 3.35e+00
  ... (remaining 12265 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.89: 15971
        1.89 -     3.78: 541
        3.78 -     5.67: 86
        5.67 -     7.56: 26
        7.56 -     9.45: 10
  Bond angle restraints: 16634
  Sorted by residual:
  angle pdb=" N   ILE A1828 "
        pdb=" CA  ILE A1828 "
        pdb=" C   ILE A1828 "
      ideal   model   delta    sigma   weight residual
     108.96  103.28    5.68 1.42e+00 4.96e-01 1.60e+01
  angle pdb=" C   ILE A1998 "
        pdb=" CA  ILE A1998 "
        pdb=" CB  ILE A1998 "
      ideal   model   delta    sigma   weight residual
     111.71  115.05   -3.34 8.50e-01 1.38e+00 1.55e+01
  angle pdb=" CA  ILE A1998 "
        pdb=" C   ILE A1998 "
        pdb=" N   MET A1999 "
      ideal   model   delta    sigma   weight residual
     117.37  120.14   -2.77 7.40e-01 1.83e+00 1.40e+01
  angle pdb=" CB  ARG B2224 "
        pdb=" CG  ARG B2224 "
        pdb=" CD  ARG B2224 "
      ideal   model   delta    sigma   weight residual
     111.30  119.84   -8.54 2.30e+00 1.89e-01 1.38e+01
  angle pdb=" C   GLU A1997 "
        pdb=" N   ILE A1998 "
        pdb=" CA  ILE A1998 "
      ideal   model   delta    sigma   weight residual
     122.97  119.38    3.59 9.80e-01 1.04e+00 1.34e+01
  ... (remaining 16629 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    14.34: 6749
       14.34 -    28.67: 532
       28.67 -    43.01: 131
       43.01 -    57.35: 26
       57.35 -    71.68: 2
  Dihedral angle restraints: 7440
    sinusoidal: 3052
      harmonic: 4388
  Sorted by residual:
  dihedral pdb=" CA  THR B2236 "
           pdb=" C   THR B2236 "
           pdb=" N   ALA B2237 "
           pdb=" CA  ALA B2237 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  157.68   22.32     0      5.00e+00 4.00e-02 1.99e+01
  dihedral pdb=" CA  THR A2236 "
           pdb=" C   THR A2236 "
           pdb=" N   ALA A2237 "
           pdb=" CA  ALA A2237 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  158.11   21.89     0      5.00e+00 4.00e-02 1.92e+01
  dihedral pdb=" CA  VAL B2052 "
           pdb=" C   VAL B2052 "
           pdb=" N   TRP B2053 "
           pdb=" CA  TRP B2053 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  160.18   19.82     0      5.00e+00 4.00e-02 1.57e+01
  ... (remaining 7437 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.057: 1395
       0.057 -    0.115: 338
       0.115 -    0.172: 86
       0.172 -    0.229: 9
       0.229 -    0.286: 2
  Chirality restraints: 1830
  Sorted by residual:
  chirality pdb=" CB  ILE A2247 "
            pdb=" CA  ILE A2247 "
            pdb=" CG1 ILE A2247 "
            pdb=" CG2 ILE A2247 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.36    0.29 2.00e-01 2.50e+01 2.05e+00
  chirality pdb=" CB  ILE B2247 "
            pdb=" CA  ILE B2247 "
            pdb=" CG1 ILE B2247 "
            pdb=" CG2 ILE B2247 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.37    0.27 2.00e-01 2.50e+01 1.85e+00
  chirality pdb=" CA  ILE A1828 "
            pdb=" N   ILE A1828 "
            pdb=" C   ILE A1828 "
            pdb=" CB  ILE A1828 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.66   -0.23 2.00e-01 2.50e+01 1.31e+00
  ... (remaining 1827 not shown)

  Planarity restraints: 2186
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ASP B2132 "   -0.062 5.00e-02 4.00e+02   9.38e-02 1.41e+01
        pdb=" N   PRO B2133 "    0.162 5.00e-02 4.00e+02
        pdb=" CA  PRO B2133 "   -0.050 5.00e-02 4.00e+02
        pdb=" CD  PRO B2133 "   -0.051 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ASP A2132 "    0.054 5.00e-02 4.00e+02   8.22e-02 1.08e+01
        pdb=" N   PRO A2133 "   -0.142 5.00e-02 4.00e+02
        pdb=" CA  PRO A2133 "    0.043 5.00e-02 4.00e+02
        pdb=" CD  PRO A2133 "    0.045 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  VAL B1650 "    0.015 2.00e-02 2.50e+03   2.93e-02 8.58e+00
        pdb=" C   VAL B1650 "   -0.051 2.00e-02 2.50e+03
        pdb=" O   VAL B1650 "    0.019 2.00e-02 2.50e+03
        pdb=" N   GLU B1651 "    0.017 2.00e-02 2.50e+03
  ... (remaining 2183 not shown)

  Histogram of nonbonded interaction distances:
        2.31 -     2.83: 3455
        2.83 -     3.35: 10360
        3.35 -     3.87: 19124
        3.87 -     4.38: 23297
        4.38 -     4.90: 39520
  Nonbonded interactions: 95756
  Sorted by model distance:
  nonbonded pdb=" OG  SER A1759 "
            pdb=" OD1 ASN A1761 "
     model   vdw
     2.314 3.040
  nonbonded pdb=" OD1 ASP B1991 "
            pdb=" NH2 ARG B2281 "
     model   vdw
     2.352 3.120
  nonbonded pdb=" O   PRO B1960 "
            pdb=" NH1 ARG B2281 "
     model   vdw
     2.365 3.120
  nonbonded pdb=" OD1 ASP A1991 "
            pdb=" NH2 ARG A2281 "
     model   vdw
     2.366 3.120
  nonbonded pdb=" OG  SER B1759 "
            pdb=" OD1 ASN B1761 "
     model   vdw
     2.381 3.040
  ... (remaining 95751 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'
}

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 individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             3.770
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.520
  Check model and map are aligned:         0.090
  Set scattering table:                    0.100
  Process input model:                     31.090
  Find NCS groups from input model:        0.350
  Set up NCS constraints:                  0.060
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:3.010
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   39.000
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8399
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      :  0.004   0.066  12270  Z= 0.289
  Angle     :  0.854   9.455  16634  Z= 0.486
  Chirality :  0.055   0.286   1830
  Planarity :  0.010   0.094   2186
  Dihedral  : 11.332  71.683   4616
  Min Nonbonded Distance : 2.314

Molprobity Statistics.
  All-atom Clashscore : 3.62
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.31 %
    Favored  : 97.69 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.00 %
    Favored  : 100.00 %
  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: -1.51 (0.19), residues: 1512
  helix: -0.90 (0.17), residues: 718
  sheet:  1.37 (0.41), residues: 180
  loop : -1.78 (0.21), residues: 614

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.043   0.003   TRP B2081 
 HIS   0.011   0.002   HIS A1918 
 PHE   0.014   0.002   PHE A1733 
 TYR   0.022   0.002   TYR B1893 
 ARG   0.004   0.000   ARG B1977 

*********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  3024 Ramachandran restraints generated.
    1512 Oldfield, 0 Emsley, 1512 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3024 Ramachandran restraints generated.
    1512 Oldfield, 0 Emsley, 1512 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  222 residues out of total 1262 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 222
  time to evaluate  : 1.415 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
  outliers start: 0
  outliers final: 0
  residues processed: 222
  average time/residue: 0.3424
  time to fit residues: 99.3827
Evaluate side-chains
  122 residues out of total 1262 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 122
  time to evaluate  : 1.303 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 152
   random chunks:
   chunk 128 optimal weight:    0.8980
   chunk 115 optimal weight:    0.9980
   chunk 63 optimal weight:    2.9990
   chunk 39 optimal weight:    0.5980
   chunk 77 optimal weight:    1.9990
   chunk 61 optimal weight:    0.7980
   chunk 119 optimal weight:    0.9980
   chunk 46 optimal weight:    3.9990
   chunk 72 optimal weight:    1.9990
   chunk 88 optimal weight:    0.6980
   chunk 138 optimal weight:    0.9980
   overall best weight:    0.7980

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

Flipped N/Q/H residues before XYZ refinement:
A1724 ASN
B1724 ASN
B1761 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8528
moved from start:          0.2191

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031  12270  Z= 0.218
  Angle     :  0.574   6.961  16634  Z= 0.301
  Chirality :  0.046   0.188   1830
  Planarity :  0.006   0.065   2186
  Dihedral  :  4.560  18.186   1690
  Min Nonbonded Distance : 2.491

Molprobity Statistics.
  All-atom Clashscore : 5.50
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.98 %
    Favored  : 98.02 %
  Rotamer:
    Outliers :  0.55 %
    Allowed  :  4.36 %
    Favored  : 95.09 %
  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: -0.16 (0.21), residues: 1512
  helix:  0.52 (0.19), residues: 740
  sheet:  1.15 (0.39), residues: 200
  loop : -1.36 (0.22), residues: 572

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.001   TRP A1704 
 HIS   0.003   0.001   HIS B1918 
 PHE   0.015   0.001   PHE B2389 
 TYR   0.011   0.001   TYR B1872 
 ARG   0.006   0.000   ARG A1717 

*********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  3024 Ramachandran restraints generated.
    1512 Oldfield, 0 Emsley, 1512 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3024 Ramachandran restraints generated.
    1512 Oldfield, 0 Emsley, 1512 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  135 residues out of total 1262 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 128
  time to evaluate  : 1.530 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A 2389 PHE cc_start: 0.8110 (t80) cc_final: 0.7842 (t80)
REVERT: B 1917 MET cc_start: 0.8441 (mmt) cc_final: 0.8031 (mmt)
  outliers start: 7
  outliers final: 3
  residues processed: 132
  average time/residue: 0.3582
  time to fit residues: 62.8219
Evaluate side-chains
  111 residues out of total 1262 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 108
  time to evaluate  : 1.528 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue 1831 GLU
Chi-restraints excluded: chain A residue 2305 VAL
Chi-restraints excluded: chain B residue 2053 TRP
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 152
   random chunks:
   chunk 76 optimal weight:    4.9990
   chunk 42 optimal weight:    1.9990
   chunk 114 optimal weight:    0.6980
   chunk 93 optimal weight:    0.8980
   chunk 38 optimal weight:    1.9990
   chunk 138 optimal weight:    2.9990
   chunk 149 optimal weight:    0.6980
   chunk 123 optimal weight:    1.9990
   chunk 137 optimal weight:    0.6980
   chunk 47 optimal weight:    1.9990
   chunk 110 optimal weight:    1.9990
   overall best weight:    0.9982

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

Flipped N/Q/H residues before XYZ refinement:
A1698 ASN
A1761 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8589
moved from start:          0.2770

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.029  12270  Z= 0.244
  Angle     :  0.548   7.303  16634  Z= 0.285
  Chirality :  0.045   0.157   1830
  Planarity :  0.005   0.055   2186
  Dihedral  :  4.370  16.838   1690
  Min Nonbonded Distance : 2.441

Molprobity Statistics.
  All-atom Clashscore : 4.79
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.51 %
    Favored  : 97.49 %
  Rotamer:
    Outliers :  0.95 %
    Allowed  :  6.10 %
    Favored  : 92.95 %
  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:  0.31 (0.21), residues: 1512
  helix:  1.03 (0.20), residues: 742
  sheet:  1.02 (0.40), residues: 188
  loop : -1.14 (0.23), residues: 582

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.001   TRP A1704 
 HIS   0.002   0.001   HIS B1918 
 PHE   0.010   0.001   PHE B1776 
 TYR   0.012   0.001   TYR A2248 
 ARG   0.005   0.000   ARG A1785 

*********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  3024 Ramachandran restraints generated.
    1512 Oldfield, 0 Emsley, 1512 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3024 Ramachandran restraints generated.
    1512 Oldfield, 0 Emsley, 1512 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  123 residues out of total 1262 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 111
  time to evaluate  : 1.466 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A 1788 ARG cc_start: 0.8371 (mmt90) cc_final: 0.8145 (mtt-85)
REVERT: A 2185 ARG cc_start: 0.7074 (tpt170) cc_final: 0.6769 (tpm170)
REVERT: A 2389 PHE cc_start: 0.8231 (t80) cc_final: 0.7915 (t80)
  outliers start: 12
  outliers final: 5
  residues processed: 118
  average time/residue: 0.3486
  time to fit residues: 55.2426
Evaluate side-chains
  105 residues out of total 1262 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 100
  time to evaluate  : 1.505 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue 1831 GLU
Chi-restraints excluded: chain A residue 2053 TRP
Chi-restraints excluded: chain B residue 1825 THR
Chi-restraints excluded: chain B residue 2053 TRP
Chi-restraints excluded: chain B residue 2231 LEU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 152
   random chunks:
   chunk 136 optimal weight:    0.9980
   chunk 103 optimal weight:    1.9990
   chunk 71 optimal weight:    1.9990
   chunk 15 optimal weight:    0.8980
   chunk 65 optimal weight:    2.9990
   chunk 92 optimal weight:    2.9990
   chunk 138 optimal weight:    3.9990
   chunk 146 optimal weight:    0.7980
   chunk 72 optimal weight:    1.9990
   chunk 131 optimal weight:    0.6980
   chunk 39 optimal weight:    0.8980
   overall best weight:    0.8580

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

Flipped N/Q/H residues before XYZ refinement:
A1698 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8588
moved from start:          0.3009

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.025  12270  Z= 0.214
  Angle     :  0.516   6.018  16634  Z= 0.267
  Chirality :  0.044   0.161   1830
  Planarity :  0.005   0.052   2186
  Dihedral  :  4.242  16.400   1690
  Min Nonbonded Distance : 2.423

Molprobity Statistics.
  All-atom Clashscore : 4.83
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.38 %
    Favored  : 97.62 %
  Rotamer:
    Outliers :  0.63 %
    Allowed  :  6.74 %
    Favored  : 92.63 %
  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:  0.54 (0.22), residues: 1512
  helix:  1.26 (0.20), residues: 742
  sheet:  0.96 (0.40), residues: 188
  loop : -1.02 (0.23), residues: 582

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP B1704 
 HIS   0.002   0.001   HIS B2259 
 PHE   0.009   0.001   PHE B1776 
 TYR   0.011   0.001   TYR B2248 
 ARG   0.004   0.000   ARG A1717 

*********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  3024 Ramachandran restraints generated.
    1512 Oldfield, 0 Emsley, 1512 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3024 Ramachandran restraints generated.
    1512 Oldfield, 0 Emsley, 1512 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  118 residues out of total 1262 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 110
  time to evaluate  : 1.761 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A 2185 ARG cc_start: 0.7132 (tpt170) cc_final: 0.6843 (tpm170)
REVERT: A 2389 PHE cc_start: 0.8232 (t80) cc_final: 0.8019 (t80)
  outliers start: 8
  outliers final: 3
  residues processed: 115
  average time/residue: 0.3690
  time to fit residues: 58.0223
Evaluate side-chains
  107 residues out of total 1262 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 104
  time to evaluate  : 1.384 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue 1831 GLU
Chi-restraints excluded: chain A residue 2053 TRP
Chi-restraints excluded: chain B residue 2053 TRP
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 152
   random chunks:
   chunk 122 optimal weight:    0.9990
   chunk 83 optimal weight:    2.9990
   chunk 2 optimal weight:    0.5980
   chunk 109 optimal weight:    1.9990
   chunk 60 optimal weight:    0.4980
   chunk 125 optimal weight:    0.0970
   chunk 101 optimal weight:    4.9990
   chunk 0 optimal weight:    3.9990
   chunk 75 optimal weight:    0.8980
   chunk 131 optimal weight:    0.8980
   chunk 37 optimal weight:    1.9990
   overall best weight:    0.5978

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

Flipped N/Q/H residues before XYZ refinement:
A1698 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8569
moved from start:          0.3185

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029  12270  Z= 0.168
  Angle     :  0.487   5.850  16634  Z= 0.251
  Chirality :  0.043   0.153   1830
  Planarity :  0.004   0.049   2186
  Dihedral  :  4.092  16.427   1690
  Min Nonbonded Distance : 2.405

Molprobity Statistics.
  All-atom Clashscore : 4.92
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.58 %
    Favored  : 97.42 %
  Rotamer:
    Outliers :  0.79 %
    Allowed  :  7.92 %
    Favored  : 91.28 %
  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:  0.75 (0.22), residues: 1512
  helix:  1.43 (0.20), residues: 744
  sheet:  1.01 (0.41), residues: 188
  loop : -0.89 (0.23), residues: 580

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP B1704 
 HIS   0.002   0.000   HIS B2259 
 PHE   0.010   0.001   PHE B1776 
 TYR   0.009   0.001   TYR B2248 
 ARG   0.005   0.000   ARG A1788 

*********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  3024 Ramachandran restraints generated.
    1512 Oldfield, 0 Emsley, 1512 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3024 Ramachandran restraints generated.
    1512 Oldfield, 0 Emsley, 1512 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  120 residues out of total 1262 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 110
  time to evaluate  : 1.477 
Fit side-chains
   revert: symmetry clash
REVERT: A 2185 ARG cc_start: 0.7117 (tpt170) cc_final: 0.6835 (tpm170)
REVERT: A 2389 PHE cc_start: 0.8262 (t80) cc_final: 0.8044 (t80)
REVERT: B 1917 MET cc_start: 0.8657 (mmt) cc_final: 0.8382 (mmt)
  outliers start: 10
  outliers final: 4
  residues processed: 119
  average time/residue: 0.3352
  time to fit residues: 54.9461
Evaluate side-chains
  105 residues out of total 1262 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 101
  time to evaluate  : 1.529 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue 2053 TRP
Chi-restraints excluded: chain A residue 2379 LEU
Chi-restraints excluded: chain B residue 1825 THR
Chi-restraints excluded: chain B residue 2053 TRP
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 152
   random chunks:
   chunk 49 optimal weight:    0.9990
   chunk 132 optimal weight:    1.9990
   chunk 29 optimal weight:    1.9990
   chunk 86 optimal weight:    2.9990
   chunk 36 optimal weight:    0.6980
   chunk 147 optimal weight:    0.9990
   chunk 122 optimal weight:    2.9990
   chunk 68 optimal weight:    2.9990
   chunk 12 optimal weight:    1.9990
   chunk 48 optimal weight:    0.9980
   chunk 77 optimal weight:    0.8980
   overall best weight:    0.9184

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8600
moved from start:          0.3294

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.037  12270  Z= 0.229
  Angle     :  0.521   7.794  16634  Z= 0.268
  Chirality :  0.044   0.160   1830
  Planarity :  0.004   0.047   2186
  Dihedral  :  4.131  16.363   1690
  Min Nonbonded Distance : 2.473

Molprobity Statistics.
  All-atom Clashscore : 4.75
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.45 %
    Favored  : 97.55 %
  Rotamer:
    Outliers :  0.79 %
    Allowed  :  8.24 %
    Favored  : 90.97 %
  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 (0.22), residues: 1512
  helix:  1.40 (0.20), residues: 744
  sheet:  0.91 (0.41), residues: 188
  loop : -0.82 (0.24), residues: 580

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP A1704 
 HIS   0.002   0.001   HIS A2249 
 PHE   0.007   0.001   PHE B1776 
 TYR   0.011   0.001   TYR A2248 
 ARG   0.006   0.000   ARG A1785 

*********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  3024 Ramachandran restraints generated.
    1512 Oldfield, 0 Emsley, 1512 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3024 Ramachandran restraints generated.
    1512 Oldfield, 0 Emsley, 1512 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  113 residues out of total 1262 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 103
  time to evaluate  : 1.536 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A 2091 MET cc_start: 0.9402 (tpp) cc_final: 0.9191 (mmm)
REVERT: A 2185 ARG cc_start: 0.7143 (tpt170) cc_final: 0.6849 (tpm170)
REVERT: B 1917 MET cc_start: 0.8734 (mmt) cc_final: 0.8445 (mmt)
  outliers start: 10
  outliers final: 8
  residues processed: 111
  average time/residue: 0.3326
  time to fit residues: 49.6046
Evaluate side-chains
  107 residues out of total 1262 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 99
  time to evaluate  : 1.460 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue 1831 GLU
Chi-restraints excluded: chain A residue 2053 TRP
Chi-restraints excluded: chain A residue 2093 GLU
Chi-restraints excluded: chain A residue 2379 LEU
Chi-restraints excluded: chain A residue 2390 ILE
Chi-restraints excluded: chain B residue 1825 THR
Chi-restraints excluded: chain B residue 2053 TRP
Chi-restraints excluded: chain B residue 2093 GLU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 152
   random chunks:
   chunk 141 optimal weight:    0.6980
   chunk 16 optimal weight:    4.9990
   chunk 83 optimal weight:    0.9990
   chunk 107 optimal weight:    1.9990
   chunk 123 optimal weight:    2.9990
   chunk 82 optimal weight:    3.9990
   chunk 146 optimal weight:    1.9990
   chunk 91 optimal weight:    0.5980
   chunk 89 optimal weight:    0.8980
   chunk 67 optimal weight:    3.9990
   chunk 90 optimal weight:    1.9990
   overall best weight:    1.0384

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8615
moved from start:          0.3395

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.040  12270  Z= 0.250
  Angle     :  0.531   6.627  16634  Z= 0.274
  Chirality :  0.045   0.175   1830
  Planarity :  0.004   0.048   2186
  Dihedral  :  4.171  16.228   1690
  Min Nonbonded Distance : 2.412

Molprobity Statistics.
  All-atom Clashscore : 4.58
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.71 %
    Favored  : 97.29 %
  Rotamer:
    Outliers :  0.95 %
    Allowed  :  7.92 %
    Favored  : 91.13 %
  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:  0.75 (0.22), residues: 1512
  helix:  1.42 (0.20), residues: 744
  sheet:  0.76 (0.41), residues: 188
  loop : -0.78 (0.24), residues: 580

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP A1704 
 HIS   0.003   0.001   HIS A2249 
 PHE   0.007   0.001   PHE B1776 
 TYR   0.013   0.001   TYR B2248 
 ARG   0.006   0.000   ARG A2391 

*********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  3024 Ramachandran restraints generated.
    1512 Oldfield, 0 Emsley, 1512 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3024 Ramachandran restraints generated.
    1512 Oldfield, 0 Emsley, 1512 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  115 residues out of total 1262 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 103
  time to evaluate  : 1.496 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A 2091 MET cc_start: 0.9415 (tpp) cc_final: 0.9191 (mmm)
REVERT: A 2185 ARG cc_start: 0.7147 (tpt170) cc_final: 0.6842 (tpm170)
REVERT: B 1917 MET cc_start: 0.8740 (mmt) cc_final: 0.8503 (mmt)
  outliers start: 12
  outliers final: 10
  residues processed: 111
  average time/residue: 0.3600
  time to fit residues: 53.4015
Evaluate side-chains
  107 residues out of total 1262 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 97
  time to evaluate  : 1.353 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue 1831 GLU
Chi-restraints excluded: chain A residue 1951 THR
Chi-restraints excluded: chain A residue 2053 TRP
Chi-restraints excluded: chain A residue 2093 GLU
Chi-restraints excluded: chain A residue 2379 LEU
Chi-restraints excluded: chain B residue 1825 THR
Chi-restraints excluded: chain B residue 1951 THR
Chi-restraints excluded: chain B residue 2053 TRP
Chi-restraints excluded: chain B residue 2093 GLU
Chi-restraints excluded: chain B residue 2231 LEU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 152
   random chunks:
   chunk 58 optimal weight:    0.8980
   chunk 87 optimal weight:    2.9990
   chunk 44 optimal weight:    0.8980
   chunk 28 optimal weight:    2.9990
   chunk 93 optimal weight:    0.6980
   chunk 99 optimal weight:    2.9990
   chunk 72 optimal weight:    1.9990
   chunk 13 optimal weight:    1.9990
   chunk 115 optimal weight:    1.9990
   chunk 133 optimal weight:    9.9990
   chunk 140 optimal weight:    0.6980
   overall best weight:    1.0382

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8618
moved from start:          0.3459

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.037  12270  Z= 0.252
  Angle     :  0.548   8.943  16634  Z= 0.283
  Chirality :  0.045   0.161   1830
  Planarity :  0.004   0.047   2186
  Dihedral  :  4.183  17.619   1690
  Min Nonbonded Distance : 2.438

Molprobity Statistics.
  All-atom Clashscore : 4.71
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.65 %
    Favored  : 97.35 %
  Rotamer:
    Outliers :  0.87 %
    Allowed  :  8.40 %
    Favored  : 90.73 %
  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:  0.84 (0.22), residues: 1512
  helix:  1.53 (0.20), residues: 730
  sheet:  0.74 (0.41), residues: 188
  loop : -0.72 (0.24), residues: 594

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP B1704 
 HIS   0.003   0.001   HIS B2249 
 PHE   0.011   0.001   PHE B2389 
 TYR   0.012   0.001   TYR B2248 
 ARG   0.008   0.000   ARG B2391 

*********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  3024 Ramachandran restraints generated.
    1512 Oldfield, 0 Emsley, 1512 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3024 Ramachandran restraints generated.
    1512 Oldfield, 0 Emsley, 1512 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  109 residues out of total 1262 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 98
  time to evaluate  : 1.441 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A 1785 ARG cc_start: 0.7657 (ttp-110) cc_final: 0.7421 (ttp-110)
REVERT: A 2091 MET cc_start: 0.9419 (tpp) cc_final: 0.9197 (mmm)
REVERT: A 2185 ARG cc_start: 0.7127 (tpt170) cc_final: 0.6820 (tpm170)
REVERT: B 1917 MET cc_start: 0.8744 (mmt) cc_final: 0.8530 (mmt)
  outliers start: 11
  outliers final: 10
  residues processed: 106
  average time/residue: 0.3515
  time to fit residues: 50.1159
Evaluate side-chains
  107 residues out of total 1262 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 97
  time to evaluate  : 1.450 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue 1831 GLU
Chi-restraints excluded: chain A residue 1951 THR
Chi-restraints excluded: chain A residue 2053 TRP
Chi-restraints excluded: chain A residue 2093 GLU
Chi-restraints excluded: chain A residue 2379 LEU
Chi-restraints excluded: chain B residue 1825 THR
Chi-restraints excluded: chain B residue 1951 THR
Chi-restraints excluded: chain B residue 2053 TRP
Chi-restraints excluded: chain B residue 2093 GLU
Chi-restraints excluded: chain B residue 2231 LEU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 152
   random chunks:
   chunk 128 optimal weight:    0.6980
   chunk 136 optimal weight:    1.9990
   chunk 140 optimal weight:    0.8980
   chunk 82 optimal weight:    4.9990
   chunk 59 optimal weight:    0.7980
   chunk 107 optimal weight:    1.9990
   chunk 41 optimal weight:    0.5980
   chunk 123 optimal weight:    0.5980
   chunk 129 optimal weight:    5.9990
   chunk 89 optimal weight:    0.4980
   chunk 144 optimal weight:    0.7980
   overall best weight:    0.6380

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8588
moved from start:          0.3494

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031  12270  Z= 0.178
  Angle     :  0.516   7.773  16634  Z= 0.265
  Chirality :  0.044   0.153   1830
  Planarity :  0.004   0.047   2186
  Dihedral  :  4.075  17.986   1690
  Min Nonbonded Distance : 2.471

Molprobity Statistics.
  All-atom Clashscore : 4.58
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.58 %
    Favored  : 97.42 %
  Rotamer:
    Outliers :  0.87 %
    Allowed  :  8.32 %
    Favored  : 90.81 %
  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:  0.90 (0.22), residues: 1512
  helix:  1.59 (0.20), residues: 730
  sheet:  0.84 (0.41), residues: 188
  loop : -0.71 (0.24), residues: 594

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.001   TRP A1704 
 HIS   0.002   0.000   HIS A2249 
 PHE   0.013   0.001   PHE B2389 
 TYR   0.010   0.001   TYR A2248 
 ARG   0.009   0.000   ARG B2391 

*********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  3024 Ramachandran restraints generated.
    1512 Oldfield, 0 Emsley, 1512 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3024 Ramachandran restraints generated.
    1512 Oldfield, 0 Emsley, 1512 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  109 residues out of total 1262 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 98
  time to evaluate  : 1.517 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A 2091 MET cc_start: 0.9411 (tpp) cc_final: 0.9203 (mmm)
REVERT: A 2185 ARG cc_start: 0.7113 (tpt170) cc_final: 0.6805 (tpm170)
  outliers start: 11
  outliers final: 9
  residues processed: 107
  average time/residue: 0.3586
  time to fit residues: 51.9231
Evaluate side-chains
  103 residues out of total 1262 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 94
  time to evaluate  : 1.341 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue 1951 THR
Chi-restraints excluded: chain A residue 2053 TRP
Chi-restraints excluded: chain A residue 2093 GLU
Chi-restraints excluded: chain A residue 2390 ILE
Chi-restraints excluded: chain B residue 1825 THR
Chi-restraints excluded: chain B residue 1951 THR
Chi-restraints excluded: chain B residue 2053 TRP
Chi-restraints excluded: chain B residue 2093 GLU
Chi-restraints excluded: chain B residue 2231 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 152
   random chunks:
   chunk 88 optimal weight:    0.6980
   chunk 68 optimal weight:    2.9990
   chunk 100 optimal weight:    4.9990
   chunk 151 optimal weight:    6.9990
   chunk 139 optimal weight:    0.5980
   chunk 120 optimal weight:    1.9990
   chunk 12 optimal weight:    0.6980
   chunk 93 optimal weight:    0.5980
   chunk 73 optimal weight:    0.7980
   chunk 95 optimal weight:    3.9990
   chunk 128 optimal weight:    0.8980
   overall best weight:    0.6780

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8588
moved from start:          0.3529

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032  12270  Z= 0.187
  Angle     :  0.520   7.962  16634  Z= 0.266
  Chirality :  0.044   0.157   1830
  Planarity :  0.004   0.056   2186
  Dihedral  :  4.059  17.844   1690
  Min Nonbonded Distance : 2.493

Molprobity Statistics.
  All-atom Clashscore : 4.33
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.65 %
    Favored  : 97.35 %
  Rotamer:
    Outliers :  0.71 %
    Allowed  :  8.40 %
    Favored  : 90.89 %
  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:  0.91 (0.22), residues: 1512
  helix:  1.57 (0.20), residues: 730
  sheet:  0.84 (0.41), residues: 188
  loop : -0.67 (0.24), residues: 594

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP B1704 
 HIS   0.002   0.001   HIS B2249 
 PHE   0.008   0.001   PHE B1776 
 TYR   0.011   0.001   TYR B2248 
 ARG   0.014   0.000   ARG B2391 

********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  3024 Ramachandran restraints generated.
    1512 Oldfield, 0 Emsley, 1512 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3024 Ramachandran restraints generated.
    1512 Oldfield, 0 Emsley, 1512 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  104 residues out of total 1262 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 95
  time to evaluate  : 1.473 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A 2091 MET cc_start: 0.9414 (tpp) cc_final: 0.9192 (mmm)
REVERT: A 2185 ARG cc_start: 0.7151 (tpt170) cc_final: 0.6846 (tpm170)
  outliers start: 9
  outliers final: 9
  residues processed: 103
  average time/residue: 0.3411
  time to fit residues: 47.4834
Evaluate side-chains
  103 residues out of total 1262 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 94
  time to evaluate  : 1.414 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue 1831 GLU
Chi-restraints excluded: chain A residue 1951 THR
Chi-restraints excluded: chain A residue 2053 TRP
Chi-restraints excluded: chain A residue 2093 GLU
Chi-restraints excluded: chain A residue 2390 ILE
Chi-restraints excluded: chain B residue 1825 THR
Chi-restraints excluded: chain B residue 1951 THR
Chi-restraints excluded: chain B residue 2053 TRP
Chi-restraints excluded: chain B residue 2093 GLU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 152
   random chunks:
   chunk 36 optimal weight:    2.9990
   chunk 111 optimal weight:    0.0770
   chunk 17 optimal weight:    2.9990
   chunk 33 optimal weight:    1.9990
   chunk 120 optimal weight:    1.9990
   chunk 50 optimal weight:    0.8980
   chunk 124 optimal weight:    0.6980
   chunk 15 optimal weight:    1.9990
   chunk 22 optimal weight:    0.5980
   chunk 106 optimal weight:    3.9990
   chunk 6 optimal weight:    6.9990
   overall best weight:    0.8540

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

Flipped N/Q/H residues before XYZ refinement:
A1698 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3426 r_free = 0.3426 target = 0.093872 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3042 r_free = 0.3042 target = 0.071943 restraints weight = 23699.535|
|-----------------------------------------------------------------------------|
r_work (start): 0.3123 rms_B_bonded: 2.73
r_work: 0.2987 rms_B_bonded: 3.04 restraints_weight: 0.5000
r_work: 0.2853 rms_B_bonded: 4.93 restraints_weight: 0.2500
r_work (final): 0.2853
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8657
moved from start:          0.3562

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034  12270  Z= 0.216
  Angle     :  0.532   8.174  16634  Z= 0.273
  Chirality :  0.044   0.156   1830
  Planarity :  0.004   0.057   2186
  Dihedral  :  4.094  17.588   1690
  Min Nonbonded Distance : 2.499

Molprobity Statistics.
  All-atom Clashscore : 4.29
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.58 %
    Favored  : 97.42 %
  Rotamer:
    Outliers :  0.71 %
    Allowed  :  8.48 %
    Favored  : 90.81 %
  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 (0.22), residues: 1512
  helix:  1.54 (0.20), residues: 730
  sheet:  0.79 (0.41), residues: 188
  loop : -0.66 (0.24), residues: 594

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP A1704 
 HIS   0.002   0.001   HIS A2249 
 PHE   0.008   0.001   PHE B1776 
 TYR   0.011   0.001   TYR A2248 
 ARG   0.013   0.000   ARG B2391 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2868.24 seconds
wall clock time: 63 minutes 49.41 seconds (3829.41 seconds total)