Starting phenix.real_space_refine
on Sat Aug 23 11:27:21 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9n71_49081/08_2025/9n71_49081.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9n71_49081/08_2025/9n71_49081.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.2
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/9n71_49081/08_2025/9n71_49081.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9n71_49081/08_2025/9n71_49081.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/9n71_49081/08_2025/9n71_49081.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9n71_49081/08_2025/9n71_49081.map"
  }
  resolution = 3.2
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.008 sd=   0.159
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      36      5.16       5
     C    7410      2.51       5
     N    1980      2.21       5
     O    2352      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 18 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 11778
  Number of models: 1
  Model: ""
    Number of chains: 1
    Chain: "B"
      Number of atoms: 1963
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 264, 1963
          Classifications: {'peptide': 264}
          Incomplete info: {'truncation_to_alanine': 1}
          Link IDs: {'PTRANS': 7, 'TRANS': 256}
          Unresolved non-hydrogen bonds: 3
          Unresolved non-hydrogen angles: 3
          Unresolved non-hydrogen dihedrals: 3
  Restraints were copied for chains:
    A, C, D, E, F
  Time building chain proxies: 1.55, per 1000 atoms: 0.13
  Number of scatterers: 11778
  At special positions: 0
  Unit cell: (150.537, 131.043, 61.731, 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      36     16.00
     O    2352      8.00
     N    1980      7.00
     C    7410      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: 0.79
  Conformation dependent library (CDL) restraints added in 557.5 milliseconds
  
  Enol-peptide restraints added in 715.3 nanoseconds
  

  3144 Ramachandran restraints generated.
    1572 Oldfield, 0 Emsley, 1572 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2892

  Finding SS restraints...
    Secondary structure from input PDB file:
      30 helices and 12 sheets defined
      12.5% alpha, 41.7% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.42
  Creating SS restraints...
    Processing helix  chain 'B' and resid 27 through 31
      removed outlier: 4.245A  pdb=" N   LEU B  31 " --> pdb=" O   ALA B  28 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 32 through 37
    Processing helix  chain 'B' and resid 83 through 91
    Processing helix  chain 'B' and resid 94 through 98
      removed outlier: 3.842A  pdb=" N   THR B  97 " --> pdb=" O   ALA B  94 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 248 through 255
    Processing helix  chain 'A' and resid 27 through 31
      removed outlier: 4.245A  pdb=" N   LEU A  31 " --> pdb=" O   ALA A  28 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 32 through 37
    Processing helix  chain 'A' and resid 83 through 91
    Processing helix  chain 'A' and resid 94 through 98
      removed outlier: 3.843A  pdb=" N   THR A  97 " --> pdb=" O   ALA A  94 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 248 through 255
    Processing helix  chain 'C' and resid 27 through 31
      removed outlier: 4.245A  pdb=" N   LEU C  31 " --> pdb=" O   ALA C  28 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 32 through 37
    Processing helix  chain 'C' and resid 83 through 91
    Processing helix  chain 'C' and resid 94 through 98
      removed outlier: 3.842A  pdb=" N   THR C  97 " --> pdb=" O   ALA C  94 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 248 through 255
    Processing helix  chain 'D' and resid 27 through 31
      removed outlier: 4.246A  pdb=" N   LEU D  31 " --> pdb=" O   ALA D  28 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 32 through 37
    Processing helix  chain 'D' and resid 83 through 91
    Processing helix  chain 'D' and resid 94 through 98
      removed outlier: 3.843A  pdb=" N   THR D  97 " --> pdb=" O   ALA D  94 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 248 through 255
    Processing helix  chain 'E' and resid 27 through 31
      removed outlier: 4.246A  pdb=" N   LEU E  31 " --> pdb=" O   ALA E  28 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 32 through 37
    Processing helix  chain 'E' and resid 83 through 91
    Processing helix  chain 'E' and resid 94 through 98
      removed outlier: 3.842A  pdb=" N   THR E  97 " --> pdb=" O   ALA E  94 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 248 through 255
    Processing helix  chain 'F' and resid 27 through 31
      removed outlier: 4.245A  pdb=" N   LEU F  31 " --> pdb=" O   ALA F  28 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 32 through 37
    Processing helix  chain 'F' and resid 83 through 91
    Processing helix  chain 'F' and resid 94 through 98
      removed outlier: 3.842A  pdb=" N   THR F  97 " --> pdb=" O   ALA F  94 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 248 through 255
    Processing sheet with id=AA1, first strand: chain 'B' and resid 19 through 23
      removed outlier: 6.523A  pdb=" N   PHE B 194 " --> pdb=" O   LYS B 214 " (cutoff:3.500A)
      removed outlier: 4.040A  pdb=" N   LYS B 214 " --> pdb=" O   PHE B 194 " (cutoff:3.500A)
      removed outlier: 3.559A  pdb=" N   PHE B 261 " --> pdb=" O   ILE B 211 " (cutoff:3.500A)
      removed outlier: 4.297A  pdb=" N   TRP D 133 " --> pdb=" O   SER D 177 " (cutoff:3.500A)
      removed outlier: 6.877A  pdb=" N   THR D 159 " --> pdb=" O   ASP D 151 " (cutoff:3.500A)
      removed outlier: 4.661A  pdb=" N   ILE D 153 " --> pdb=" O   THR D 157 " (cutoff:3.500A)
      removed outlier: 6.826A  pdb=" N   THR D 157 " --> pdb=" O   ILE D 153 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'D' and resid 107 through 108
      removed outlier: 3.559A  pdb=" N   PHE B 261 " --> pdb=" O   ILE B 211 " (cutoff:3.500A)
      removed outlier: 5.091A  pdb=" N   TRP B  73 " --> pdb=" O   ALA B 239 " (cutoff:3.500A)
      removed outlier: 5.588A  pdb=" N   THR B  63 " --> pdb=" O   GLN B  57 " (cutoff:3.500A)
      removed outlier: 6.598A  pdb=" N   GLN B  57 " --> pdb=" O   THR B  63 " (cutoff:3.500A)
      removed outlier: 3.766A  pdb=" N   HIS B  65 " --> pdb=" O   LEU B  55 " (cutoff:3.500A)
      removed outlier: 6.428A  pdb=" N   THR B  51 " --> pdb=" O   THR B  69 " (cutoff:3.500A)
      removed outlier: 4.329A  pdb=" N   ASP B  71 " --> pdb=" O   ASP B  49 " (cutoff:3.500A)
      removed outlier: 6.534A  pdb=" N   ASP B  49 " --> pdb=" O   ASP B  71 " (cutoff:3.500A)
      removed outlier: 4.229A  pdb=" N   TRP B  73 " --> pdb=" O   ALA B  47 " (cutoff:3.500A)
      removed outlier: 6.588A  pdb=" N   ALA B  47 " --> pdb=" O   TRP B  73 " (cutoff:3.500A)
      removed outlier: 4.352A  pdb=" N   ILE B  75 " --> pdb=" O   ALA B  45 " (cutoff:3.500A)
      removed outlier: 6.728A  pdb=" N   ALA B  45 " --> pdb=" O   ILE B  75 " (cutoff:3.500A)
      removed outlier: 4.118A  pdb=" N   GLY B  77 " --> pdb=" O   ASN B  43 " (cutoff:3.500A)
      removed outlier: 6.983A  pdb=" N   ASN B  43 " --> pdb=" O   GLY B  77 " (cutoff:3.500A)
      removed outlier: 6.868A  pdb=" N   GLY B  79 " --> pdb=" O   PHE B  41 " (cutoff:3.500A)
      removed outlier: 7.030A  pdb=" N   PHE B  41 " --> pdb=" O   GLY B  79 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'B' and resid 107 through 108
      removed outlier: 3.558A  pdb=" N   PHE E 261 " --> pdb=" O   ILE E 211 " (cutoff:3.500A)
      removed outlier: 5.090A  pdb=" N   TRP E  73 " --> pdb=" O   ALA E 239 " (cutoff:3.500A)
      removed outlier: 5.587A  pdb=" N   THR E  63 " --> pdb=" O   GLN E  57 " (cutoff:3.500A)
      removed outlier: 6.597A  pdb=" N   GLN E  57 " --> pdb=" O   THR E  63 " (cutoff:3.500A)
      removed outlier: 3.766A  pdb=" N   HIS E  65 " --> pdb=" O   LEU E  55 " (cutoff:3.500A)
      removed outlier: 6.427A  pdb=" N   THR E  51 " --> pdb=" O   THR E  69 " (cutoff:3.500A)
      removed outlier: 4.330A  pdb=" N   ASP E  71 " --> pdb=" O   ASP E  49 " (cutoff:3.500A)
      removed outlier: 6.535A  pdb=" N   ASP E  49 " --> pdb=" O   ASP E  71 " (cutoff:3.500A)
      removed outlier: 4.230A  pdb=" N   TRP E  73 " --> pdb=" O   ALA E  47 " (cutoff:3.500A)
      removed outlier: 6.588A  pdb=" N   ALA E  47 " --> pdb=" O   TRP E  73 " (cutoff:3.500A)
      removed outlier: 4.352A  pdb=" N   ILE E  75 " --> pdb=" O   ALA E  45 " (cutoff:3.500A)
      removed outlier: 6.728A  pdb=" N   ALA E  45 " --> pdb=" O   ILE E  75 " (cutoff:3.500A)
      removed outlier: 4.117A  pdb=" N   GLY E  77 " --> pdb=" O   ASN E  43 " (cutoff:3.500A)
      removed outlier: 6.984A  pdb=" N   ASN E  43 " --> pdb=" O   GLY E  77 " (cutoff:3.500A)
      removed outlier: 6.868A  pdb=" N   GLY E  79 " --> pdb=" O   PHE E  41 " (cutoff:3.500A)
      removed outlier: 7.028A  pdb=" N   PHE E  41 " --> pdb=" O   GLY E  79 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'B' and resid 119 through 121
      removed outlier: 6.826A  pdb=" N   THR B 157 " --> pdb=" O   ILE B 153 " (cutoff:3.500A)
      removed outlier: 4.662A  pdb=" N   ILE B 153 " --> pdb=" O   THR B 157 " (cutoff:3.500A)
      removed outlier: 6.877A  pdb=" N   THR B 159 " --> pdb=" O   ASP B 151 " (cutoff:3.500A)
      removed outlier: 4.297A  pdb=" N   TRP B 133 " --> pdb=" O   SER B 177 " (cutoff:3.500A)
      removed outlier: 3.558A  pdb=" N   PHE E 261 " --> pdb=" O   ILE E 211 " (cutoff:3.500A)
      removed outlier: 4.041A  pdb=" N   LYS E 214 " --> pdb=" O   PHE E 194 " (cutoff:3.500A)
      removed outlier: 6.523A  pdb=" N   PHE E 194 " --> pdb=" O   LYS E 214 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'A' and resid 19 through 23
      removed outlier: 6.522A  pdb=" N   PHE A 194 " --> pdb=" O   LYS A 214 " (cutoff:3.500A)
      removed outlier: 4.041A  pdb=" N   LYS A 214 " --> pdb=" O   PHE A 194 " (cutoff:3.500A)
      removed outlier: 3.558A  pdb=" N   PHE A 261 " --> pdb=" O   ILE A 211 " (cutoff:3.500A)
      removed outlier: 4.296A  pdb=" N   TRP E 133 " --> pdb=" O   SER E 177 " (cutoff:3.500A)
      removed outlier: 6.877A  pdb=" N   THR E 159 " --> pdb=" O   ASP E 151 " (cutoff:3.500A)
      removed outlier: 4.661A  pdb=" N   ILE E 153 " --> pdb=" O   THR E 157 " (cutoff:3.500A)
      removed outlier: 6.826A  pdb=" N   THR E 157 " --> pdb=" O   ILE E 153 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'E' and resid 107 through 108
      removed outlier: 3.558A  pdb=" N   PHE A 261 " --> pdb=" O   ILE A 211 " (cutoff:3.500A)
      removed outlier: 5.090A  pdb=" N   TRP A  73 " --> pdb=" O   ALA A 239 " (cutoff:3.500A)
      removed outlier: 5.587A  pdb=" N   THR A  63 " --> pdb=" O   GLN A  57 " (cutoff:3.500A)
      removed outlier: 6.597A  pdb=" N   GLN A  57 " --> pdb=" O   THR A  63 " (cutoff:3.500A)
      removed outlier: 3.766A  pdb=" N   HIS A  65 " --> pdb=" O   LEU A  55 " (cutoff:3.500A)
      removed outlier: 6.428A  pdb=" N   THR A  51 " --> pdb=" O   THR A  69 " (cutoff:3.500A)
      removed outlier: 4.330A  pdb=" N   ASP A  71 " --> pdb=" O   ASP A  49 " (cutoff:3.500A)
      removed outlier: 6.534A  pdb=" N   ASP A  49 " --> pdb=" O   ASP A  71 " (cutoff:3.500A)
      removed outlier: 4.229A  pdb=" N   TRP A  73 " --> pdb=" O   ALA A  47 " (cutoff:3.500A)
      removed outlier: 6.587A  pdb=" N   ALA A  47 " --> pdb=" O   TRP A  73 " (cutoff:3.500A)
      removed outlier: 4.353A  pdb=" N   ILE A  75 " --> pdb=" O   ALA A  45 " (cutoff:3.500A)
      removed outlier: 6.727A  pdb=" N   ALA A  45 " --> pdb=" O   ILE A  75 " (cutoff:3.500A)
      removed outlier: 4.117A  pdb=" N   GLY A  77 " --> pdb=" O   ASN A  43 " (cutoff:3.500A)
      removed outlier: 6.985A  pdb=" N   ASN A  43 " --> pdb=" O   GLY A  77 " (cutoff:3.500A)
      removed outlier: 6.867A  pdb=" N   GLY A  79 " --> pdb=" O   PHE A  41 " (cutoff:3.500A)
      removed outlier: 7.029A  pdb=" N   PHE A  41 " --> pdb=" O   GLY A  79 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'A' and resid 107 through 108
      removed outlier: 3.559A  pdb=" N   PHE C 261 " --> pdb=" O   ILE C 211 " (cutoff:3.500A)
      removed outlier: 5.091A  pdb=" N   TRP C  73 " --> pdb=" O   ALA C 239 " (cutoff:3.500A)
      removed outlier: 5.587A  pdb=" N   THR C  63 " --> pdb=" O   GLN C  57 " (cutoff:3.500A)
      removed outlier: 6.597A  pdb=" N   GLN C  57 " --> pdb=" O   THR C  63 " (cutoff:3.500A)
      removed outlier: 3.766A  pdb=" N   HIS C  65 " --> pdb=" O   LEU C  55 " (cutoff:3.500A)
      removed outlier: 6.428A  pdb=" N   THR C  51 " --> pdb=" O   THR C  69 " (cutoff:3.500A)
      removed outlier: 4.330A  pdb=" N   ASP C  71 " --> pdb=" O   ASP C  49 " (cutoff:3.500A)
      removed outlier: 6.534A  pdb=" N   ASP C  49 " --> pdb=" O   ASP C  71 " (cutoff:3.500A)
      removed outlier: 4.230A  pdb=" N   TRP C  73 " --> pdb=" O   ALA C  47 " (cutoff:3.500A)
      removed outlier: 6.588A  pdb=" N   ALA C  47 " --> pdb=" O   TRP C  73 " (cutoff:3.500A)
      removed outlier: 4.352A  pdb=" N   ILE C  75 " --> pdb=" O   ALA C  45 " (cutoff:3.500A)
      removed outlier: 6.728A  pdb=" N   ALA C  45 " --> pdb=" O   ILE C  75 " (cutoff:3.500A)
      removed outlier: 4.118A  pdb=" N   GLY C  77 " --> pdb=" O   ASN C  43 " (cutoff:3.500A)
      removed outlier: 6.983A  pdb=" N   ASN C  43 " --> pdb=" O   GLY C  77 " (cutoff:3.500A)
      removed outlier: 6.868A  pdb=" N   GLY C  79 " --> pdb=" O   PHE C  41 " (cutoff:3.500A)
      removed outlier: 7.029A  pdb=" N   PHE C  41 " --> pdb=" O   GLY C  79 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'A' and resid 119 through 121
      removed outlier: 6.826A  pdb=" N   THR A 157 " --> pdb=" O   ILE A 153 " (cutoff:3.500A)
      removed outlier: 4.661A  pdb=" N   ILE A 153 " --> pdb=" O   THR A 157 " (cutoff:3.500A)
      removed outlier: 6.877A  pdb=" N   THR A 159 " --> pdb=" O   ASP A 151 " (cutoff:3.500A)
      removed outlier: 4.297A  pdb=" N   TRP A 133 " --> pdb=" O   SER A 177 " (cutoff:3.500A)
      removed outlier: 3.559A  pdb=" N   PHE C 261 " --> pdb=" O   ILE C 211 " (cutoff:3.500A)
      removed outlier: 4.041A  pdb=" N   LYS C 214 " --> pdb=" O   PHE C 194 " (cutoff:3.500A)
      removed outlier: 6.522A  pdb=" N   PHE C 194 " --> pdb=" O   LYS C 214 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'C' and resid 107 through 108
      removed outlier: 3.558A  pdb=" N   PHE F 261 " --> pdb=" O   ILE F 211 " (cutoff:3.500A)
      removed outlier: 5.090A  pdb=" N   TRP F  73 " --> pdb=" O   ALA F 239 " (cutoff:3.500A)
      removed outlier: 5.587A  pdb=" N   THR F  63 " --> pdb=" O   GLN F  57 " (cutoff:3.500A)
      removed outlier: 6.597A  pdb=" N   GLN F  57 " --> pdb=" O   THR F  63 " (cutoff:3.500A)
      removed outlier: 3.766A  pdb=" N   HIS F  65 " --> pdb=" O   LEU F  55 " (cutoff:3.500A)
      removed outlier: 6.427A  pdb=" N   THR F  51 " --> pdb=" O   THR F  69 " (cutoff:3.500A)
      removed outlier: 4.330A  pdb=" N   ASP F  71 " --> pdb=" O   ASP F  49 " (cutoff:3.500A)
      removed outlier: 6.534A  pdb=" N   ASP F  49 " --> pdb=" O   ASP F  71 " (cutoff:3.500A)
      removed outlier: 4.230A  pdb=" N   TRP F  73 " --> pdb=" O   ALA F  47 " (cutoff:3.500A)
      removed outlier: 6.588A  pdb=" N   ALA F  47 " --> pdb=" O   TRP F  73 " (cutoff:3.500A)
      removed outlier: 4.352A  pdb=" N   ILE F  75 " --> pdb=" O   ALA F  45 " (cutoff:3.500A)
      removed outlier: 6.728A  pdb=" N   ALA F  45 " --> pdb=" O   ILE F  75 " (cutoff:3.500A)
      removed outlier: 4.117A  pdb=" N   GLY F  77 " --> pdb=" O   ASN F  43 " (cutoff:3.500A)
      removed outlier: 6.984A  pdb=" N   ASN F  43 " --> pdb=" O   GLY F  77 " (cutoff:3.500A)
      removed outlier: 6.868A  pdb=" N   GLY F  79 " --> pdb=" O   PHE F  41 " (cutoff:3.500A)
      removed outlier: 7.029A  pdb=" N   PHE F  41 " --> pdb=" O   GLY F  79 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'C' and resid 119 through 121
      removed outlier: 6.826A  pdb=" N   THR C 157 " --> pdb=" O   ILE C 153 " (cutoff:3.500A)
      removed outlier: 4.662A  pdb=" N   ILE C 153 " --> pdb=" O   THR C 157 " (cutoff:3.500A)
      removed outlier: 6.877A  pdb=" N   THR C 159 " --> pdb=" O   ASP C 151 " (cutoff:3.500A)
      removed outlier: 4.297A  pdb=" N   TRP C 133 " --> pdb=" O   SER C 177 " (cutoff:3.500A)
      removed outlier: 3.558A  pdb=" N   PHE F 261 " --> pdb=" O   ILE F 211 " (cutoff:3.500A)
      removed outlier: 4.041A  pdb=" N   LYS F 214 " --> pdb=" O   PHE F 194 " (cutoff:3.500A)
      removed outlier: 6.522A  pdb=" N   PHE F 194 " --> pdb=" O   LYS F 214 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'D' and resid 19 through 23
      removed outlier: 6.522A  pdb=" N   PHE D 194 " --> pdb=" O   LYS D 214 " (cutoff:3.500A)
      removed outlier: 4.041A  pdb=" N   LYS D 214 " --> pdb=" O   PHE D 194 " (cutoff:3.500A)
      removed outlier: 3.558A  pdb=" N   PHE D 261 " --> pdb=" O   ILE D 211 " (cutoff:3.500A)
      removed outlier: 4.297A  pdb=" N   TRP F 133 " --> pdb=" O   SER F 177 " (cutoff:3.500A)
      removed outlier: 6.878A  pdb=" N   THR F 159 " --> pdb=" O   ASP F 151 " (cutoff:3.500A)
      removed outlier: 4.661A  pdb=" N   ILE F 153 " --> pdb=" O   THR F 157 " (cutoff:3.500A)
      removed outlier: 6.826A  pdb=" N   THR F 157 " --> pdb=" O   ILE F 153 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'F' and resid 107 through 108
      removed outlier: 3.558A  pdb=" N   PHE D 261 " --> pdb=" O   ILE D 211 " (cutoff:3.500A)
      removed outlier: 5.090A  pdb=" N   TRP D  73 " --> pdb=" O   ALA D 239 " (cutoff:3.500A)
      removed outlier: 5.587A  pdb=" N   THR D  63 " --> pdb=" O   GLN D  57 " (cutoff:3.500A)
      removed outlier: 6.597A  pdb=" N   GLN D  57 " --> pdb=" O   THR D  63 " (cutoff:3.500A)
      removed outlier: 3.766A  pdb=" N   HIS D  65 " --> pdb=" O   LEU D  55 " (cutoff:3.500A)
      removed outlier: 6.427A  pdb=" N   THR D  51 " --> pdb=" O   THR D  69 " (cutoff:3.500A)
      removed outlier: 4.330A  pdb=" N   ASP D  71 " --> pdb=" O   ASP D  49 " (cutoff:3.500A)
      removed outlier: 6.533A  pdb=" N   ASP D  49 " --> pdb=" O   ASP D  71 " (cutoff:3.500A)
      removed outlier: 4.230A  pdb=" N   TRP D  73 " --> pdb=" O   ALA D  47 " (cutoff:3.500A)
      removed outlier: 6.588A  pdb=" N   ALA D  47 " --> pdb=" O   TRP D  73 " (cutoff:3.500A)
      removed outlier: 4.353A  pdb=" N   ILE D  75 " --> pdb=" O   ALA D  45 " (cutoff:3.500A)
      removed outlier: 6.727A  pdb=" N   ALA D  45 " --> pdb=" O   ILE D  75 " (cutoff:3.500A)
      removed outlier: 4.118A  pdb=" N   GLY D  77 " --> pdb=" O   ASN D  43 " (cutoff:3.500A)
      removed outlier: 6.984A  pdb=" N   ASN D  43 " --> pdb=" O   GLY D  77 " (cutoff:3.500A)
      removed outlier: 6.868A  pdb=" N   GLY D  79 " --> pdb=" O   PHE D  41 " (cutoff:3.500A)
      removed outlier: 7.029A  pdb=" N   PHE D  41 " --> pdb=" O   GLY D  79 " (cutoff:3.500A)

    396 hydrogen bonds defined for protein.
    1062 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: 1.86

  Time building geometry restraints manager: 1.12 seconds

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

  Histogram of bond lengths:
        1.22 -     1.34: 3934
        1.34 -     1.46: 1590
        1.46 -     1.57: 6380
        1.57 -     1.69: 0
        1.69 -     1.81: 60
  Bond restraints: 11964
  Sorted by residual:
  bond pdb=" N   ARG B 106 "
       pdb=" CA  ARG B 106 "
    ideal  model  delta    sigma   weight residual
    1.457  1.501 -0.043 1.29e-02 6.01e+03 1.13e+01
  bond pdb=" N   ARG C 106 "
       pdb=" CA  ARG C 106 "
    ideal  model  delta    sigma   weight residual
    1.457  1.501 -0.043 1.29e-02 6.01e+03 1.13e+01
  bond pdb=" N   ARG F 104 "
       pdb=" CA  ARG F 104 "
    ideal  model  delta    sigma   weight residual
    1.456  1.497 -0.041 1.21e-02 6.83e+03 1.13e+01
  bond pdb=" N   ARG E 104 "
       pdb=" CA  ARG E 104 "
    ideal  model  delta    sigma   weight residual
    1.456  1.497 -0.041 1.21e-02 6.83e+03 1.13e+01
  bond pdb=" N   ARG A 104 "
       pdb=" CA  ARG A 104 "
    ideal  model  delta    sigma   weight residual
    1.456  1.497 -0.041 1.21e-02 6.83e+03 1.13e+01
  ... (remaining 11959 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.47: 15485
        1.47 -     2.94: 620
        2.94 -     4.41: 167
        4.41 -     5.88: 30
        5.88 -     7.35: 6
  Bond angle restraints: 16308
  Sorted by residual:
  angle pdb=" N   THR C 105 "
        pdb=" CA  THR C 105 "
        pdb=" C   THR C 105 "
      ideal   model   delta    sigma   weight residual
     111.07  118.42   -7.35 1.07e+00 8.73e-01 4.71e+01
  angle pdb=" N   THR A 105 "
        pdb=" CA  THR A 105 "
        pdb=" C   THR A 105 "
      ideal   model   delta    sigma   weight residual
     111.07  118.41   -7.34 1.07e+00 8.73e-01 4.70e+01
  angle pdb=" N   THR D 105 "
        pdb=" CA  THR D 105 "
        pdb=" C   THR D 105 "
      ideal   model   delta    sigma   weight residual
     111.07  118.41   -7.34 1.07e+00 8.73e-01 4.70e+01
  angle pdb=" N   THR B 105 "
        pdb=" CA  THR B 105 "
        pdb=" C   THR B 105 "
      ideal   model   delta    sigma   weight residual
     111.07  118.40   -7.33 1.07e+00 8.73e-01 4.69e+01
  angle pdb=" N   THR F 105 "
        pdb=" CA  THR F 105 "
        pdb=" C   THR F 105 "
      ideal   model   delta    sigma   weight residual
     111.07  118.38   -7.31 1.07e+00 8.73e-01 4.67e+01
  ... (remaining 16303 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    18.00: 6254
       18.00 -    36.00: 622
       36.00 -    54.00: 162
       54.00 -    72.00: 12
       72.00 -    90.00: 18
  Dihedral angle restraints: 7068
    sinusoidal: 2538
      harmonic: 4530
  Sorted by residual:
  dihedral pdb=" CA  ASP A 250 "
           pdb=" CB  ASP A 250 "
           pdb=" CG  ASP A 250 "
           pdb=" OD1 ASP A 250 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -30.00  -82.21   52.21     1      2.00e+01 2.50e-03 9.29e+00
  dihedral pdb=" CA  ASP D 250 "
           pdb=" CB  ASP D 250 "
           pdb=" CG  ASP D 250 "
           pdb=" OD1 ASP D 250 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -30.00  -82.21   52.21     1      2.00e+01 2.50e-03 9.29e+00
  dihedral pdb=" CA  ASP E 250 "
           pdb=" CB  ASP E 250 "
           pdb=" CG  ASP E 250 "
           pdb=" OD1 ASP E 250 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -30.00  -82.16   52.16     1      2.00e+01 2.50e-03 9.28e+00
  ... (remaining 7065 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.059: 1600
       0.059 -    0.118: 258
       0.118 -    0.177: 73
       0.177 -    0.236: 13
       0.236 -    0.295: 6
  Chirality restraints: 1950
  Sorted by residual:
  chirality pdb=" CA  THR C 105 "
            pdb=" N   THR C 105 "
            pdb=" C   THR C 105 "
            pdb=" CB  THR C 105 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.53    2.23    0.29 2.00e-01 2.50e+01 2.17e+00
  chirality pdb=" CA  THR B 105 "
            pdb=" N   THR B 105 "
            pdb=" C   THR B 105 "
            pdb=" CB  THR B 105 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.53    2.23    0.29 2.00e-01 2.50e+01 2.16e+00
  chirality pdb=" CA  THR E 105 "
            pdb=" N   THR E 105 "
            pdb=" C   THR E 105 "
            pdb=" CB  THR E 105 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.53    2.23    0.29 2.00e-01 2.50e+01 2.14e+00
  ... (remaining 1947 not shown)

  Planarity restraints: 2124
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ASN D  83 "   -0.024 5.00e-02 4.00e+02   3.67e-02 2.16e+00
        pdb=" N   PRO D  84 "    0.064 5.00e-02 4.00e+02
        pdb=" CA  PRO D  84 "   -0.019 5.00e-02 4.00e+02
        pdb=" CD  PRO D  84 "   -0.021 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ASN A  83 "    0.024 5.00e-02 4.00e+02   3.67e-02 2.16e+00
        pdb=" N   PRO A  84 "   -0.064 5.00e-02 4.00e+02
        pdb=" CA  PRO A  84 "    0.019 5.00e-02 4.00e+02
        pdb=" CD  PRO A  84 "    0.021 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ASN B  83 "   -0.024 5.00e-02 4.00e+02   3.67e-02 2.16e+00
        pdb=" N   PRO B  84 "    0.064 5.00e-02 4.00e+02
        pdb=" CA  PRO B  84 "   -0.019 5.00e-02 4.00e+02
        pdb=" CD  PRO B  84 "   -0.021 5.00e-02 4.00e+02
  ... (remaining 2121 not shown)

  Histogram of nonbonded interaction distances:
        2.29 -     2.81: 3079
        2.81 -     3.33: 8820
        3.33 -     3.85: 17968
        3.85 -     4.38: 20690
        4.38 -     4.90: 40298
  Nonbonded interactions: 90855
  Sorted by model distance:
  nonbonded pdb=" OG1 THR E 155 "
            pdb=" N   ASN E 156 "
     model   vdw
     2.287 3.120
  nonbonded pdb=" OG1 THR B 155 "
            pdb=" N   ASN B 156 "
     model   vdw
     2.288 3.120
  nonbonded pdb=" OG1 THR C 155 "
            pdb=" N   ASN C 156 "
     model   vdw
     2.288 3.120
  nonbonded pdb=" OG1 THR F 155 "
            pdb=" N   ASN F 156 "
     model   vdw
     2.288 3.120
  nonbonded pdb=" OG1 THR D 155 "
            pdb=" N   ASN D 156 "
     model   vdw
     2.288 3.120
  ... (remaining 90850 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.04
Found NCS groups:
ncs_group {
  reference = chain 'B'
  selection = chain 'A'
  selection = chain 'C'
  selection = chain 'D'
  selection = chain 'E'
  selection = chain 'F'
}

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:             2.670
  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:          0.160
  Check model and map are aligned:         0.040
  Set scattering table:                    0.030
  Process input model:                     9.870
  Find NCS groups from input model:        0.100
  Set up NCS constraints:                  0.010
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.010
  Load rotamer database and sin/cos tables:1.020
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   13.920
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8751
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      :  0.005   0.046  11964  Z= 0.309
  Angle     :  0.723   7.345  16308  Z= 0.502
  Chirality :  0.053   0.295   1950
  Planarity :  0.003   0.037   2124
  Dihedral  : 15.885  89.996   4176
  Min Nonbonded Distance : 2.287

Molprobity Statistics.
  All-atom Clashscore : 4.53
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.29 %
    Favored  : 97.71 %
  Rotamer:
    Outliers :  0.48 %
    Allowed  : 19.71 %
    Favored  : 79.81 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.53 (0.20), residues: 1572
  helix: -0.88 (0.40), residues: 144
  sheet:  1.46 (0.21), residues: 624
  loop : -1.86 (0.17), residues: 804

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG B 104 
 TYR   0.011   0.001   TYR B 252 
 PHE   0.010   0.001   PHE B 261 
 TRP   0.004   0.001   TRP F 133 
 HIS   0.002   0.001   HIS A  36 

Details of bonding type rmsd
  covalent geometry    : bond        0.00455 (11964)
  covalent geometry    : angle       0.72302 (16308)
  hydrogen bonds       : bond        0.21579 (  354)
  hydrogen bonds       : angle       8.93854 ( 1062)

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

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

  3144 Ramachandran restraints generated.
    1572 Oldfield, 0 Emsley, 1572 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3144 Ramachandran restraints generated.
    1572 Oldfield, 0 Emsley, 1572 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  200 residues out of total 1254 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 194
  time to evaluate  : 0.481 
Fit side-chains
REVERT: B   88 MET cc_start: 0.9179 (mtp) cc_final: 0.8911 (mtm)
REVERT: A  228 THR cc_start: 0.8773 (p) cc_final: 0.8548 (p)
REVERT: A  245 LYS cc_start: 0.8860 (ptpp) cc_final: 0.8490 (mmtm)
REVERT: C   88 MET cc_start: 0.9155 (mtp) cc_final: 0.8901 (mtm)
REVERT: D  228 THR cc_start: 0.8820 (p) cc_final: 0.8591 (p)
REVERT: D  245 LYS cc_start: 0.8852 (ptpp) cc_final: 0.8495 (mmtm)
REVERT: E  161 ASP cc_start: 0.8162 (p0) cc_final: 0.7773 (p0)
REVERT: F  161 ASP cc_start: 0.8172 (p0) cc_final: 0.7908 (p0)
  outliers start: 6
  outliers final: 0
  residues processed: 194
  average time/residue: 0.1104
  time to fit residues: 30.3082
Evaluate side-chains
  165 residues out of total 1254 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 165
  time to evaluate  : 0.316 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 156
   random chunks:
   chunk 98 optimal weight:    1.9990
   chunk 107 optimal weight:    6.9990
   chunk 10 optimal weight:    9.9990
   chunk 66 optimal weight:    6.9990
   chunk 130 optimal weight:    4.9990
   chunk 124 optimal weight:    2.9990
   chunk 103 optimal weight:    3.9990
   chunk 77 optimal weight:    6.9990
   chunk 122 optimal weight:    7.9990
   chunk 91 optimal weight:   10.0000
   chunk 149 optimal weight:    0.8980
   overall best weight:    2.9788

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

Flipped N/Q/H residues before XYZ refinement:
B 144 ASN
B 255 HIS
A 144 ASN
A 255 HIS
C 144 ASN
C 255 HIS
D 144 ASN
D 255 HIS
E 144 ASN
E 255 HIS
F 144 ASN
F 255 HIS

Total number of N/Q/H flips: 12

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3224 r_free = 0.3224 target = 0.113571 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.2835 r_free = 0.2835 target = 0.086248 restraints weight = 13903.854|
|-----------------------------------------------------------------------------|
r_work (start): 0.2702 rms_B_bonded: 1.86
r_work: 0.2579 rms_B_bonded: 2.20 restraints_weight: 0.5000
r_work: 0.2441 rms_B_bonded: 3.56 restraints_weight: 0.2500
r_work (final): 0.2441
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8838
moved from start:          0.1353

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.033  11964  Z= 0.207
  Angle     :  0.545   5.555  16308  Z= 0.291
  Chirality :  0.048   0.164   1950
  Planarity :  0.004   0.048   2124
  Dihedral  :  4.031  13.178   1668
  Min Nonbonded Distance : 2.532

Molprobity Statistics.
  All-atom Clashscore : 2.13
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.97 %
    Favored  : 98.03 %
  Rotamer:
    Outliers :  2.72 %
    Allowed  : 17.87 %
    Favored  : 79.41 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.35 (0.20), residues: 1572
  helix: -0.43 (0.43), residues: 144
  sheet:  1.46 (0.21), residues: 612
  loop : -1.65 (0.18), residues: 816

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.001   ARG B 104 
 TYR   0.015   0.002   TYR C 252 
 PHE   0.014   0.002   PHE A 261 
 TRP   0.006   0.001   TRP B  73 
 HIS   0.003   0.001   HIS E 255 

Details of bonding type rmsd
  covalent geometry    : bond        0.00523 (11964)
  covalent geometry    : angle       0.54514 (16308)
  hydrogen bonds       : bond        0.04427 (  354)
  hydrogen bonds       : angle       5.74985 ( 1062)

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

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

  3144 Ramachandran restraints generated.
    1572 Oldfield, 0 Emsley, 1572 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3144 Ramachandran restraints generated.
    1572 Oldfield, 0 Emsley, 1572 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  201 residues out of total 1254 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 167
  time to evaluate  : 0.536 
Fit side-chains
REVERT: B   21 MET cc_start: 0.9292 (mtt) cc_final: 0.9070 (mtt)
REVERT: B   88 MET cc_start: 0.9185 (mtp) cc_final: 0.8945 (mtm)
REVERT: C   21 MET cc_start: 0.9297 (mtt) cc_final: 0.9071 (mtt)
REVERT: C   88 MET cc_start: 0.9180 (mtp) cc_final: 0.8944 (mtm)
  outliers start: 34
  outliers final: 31
  residues processed: 181
  average time/residue: 0.1297
  time to fit residues: 32.3552
Evaluate side-chains
  190 residues out of total 1254 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 159
  time to evaluate  : 0.454 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   59 VAL
Chi-restraints excluded: chain B residue  144 ASN
Chi-restraints excluded: chain B residue  178 THR
Chi-restraints excluded: chain B residue  222 ASN
Chi-restraints excluded: chain B residue  223 LEU
Chi-restraints excluded: chain B residue  228 THR
Chi-restraints excluded: chain A residue   59 VAL
Chi-restraints excluded: chain A residue  178 THR
Chi-restraints excluded: chain A residue  222 ASN
Chi-restraints excluded: chain A residue  223 LEU
Chi-restraints excluded: chain A residue  228 THR
Chi-restraints excluded: chain C residue   59 VAL
Chi-restraints excluded: chain C residue  144 ASN
Chi-restraints excluded: chain C residue  178 THR
Chi-restraints excluded: chain C residue  222 ASN
Chi-restraints excluded: chain C residue  223 LEU
Chi-restraints excluded: chain C residue  228 THR
Chi-restraints excluded: chain D residue   59 VAL
Chi-restraints excluded: chain D residue  178 THR
Chi-restraints excluded: chain D residue  222 ASN
Chi-restraints excluded: chain D residue  223 LEU
Chi-restraints excluded: chain D residue  228 THR
Chi-restraints excluded: chain E residue   59 VAL
Chi-restraints excluded: chain E residue  212 VAL
Chi-restraints excluded: chain E residue  222 ASN
Chi-restraints excluded: chain E residue  228 THR
Chi-restraints excluded: chain F residue   59 VAL
Chi-restraints excluded: chain F residue  178 THR
Chi-restraints excluded: chain F residue  212 VAL
Chi-restraints excluded: chain F residue  222 ASN
Chi-restraints excluded: chain F residue  228 THR
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 156
   random chunks:
   chunk 60 optimal weight:    0.7980
   chunk 18 optimal weight:    0.0370
   chunk 95 optimal weight:   10.0000
   chunk 41 optimal weight:    8.9990
   chunk 125 optimal weight:    3.9990
   chunk 138 optimal weight:    3.9990
   chunk 25 optimal weight:    6.9990
   chunk 139 optimal weight:    2.9990
   chunk 123 optimal weight:    0.9990
   chunk 133 optimal weight:    6.9990
   chunk 92 optimal weight:    9.9990
   overall best weight:    1.7664

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

Flipped N/Q/H residues before XYZ refinement:
B 143 ASN
B 144 ASN
C 143 ASN
C 144 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3228 r_free = 0.3228 target = 0.113515 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.2835 r_free = 0.2835 target = 0.085771 restraints weight = 13904.779|
|-----------------------------------------------------------------------------|
r_work (start): 0.2818 rms_B_bonded: 1.92
r_work: 0.2692 rms_B_bonded: 2.26 restraints_weight: 0.5000
r_work: 0.2552 rms_B_bonded: 3.68 restraints_weight: 0.2500
r_work (final): 0.2552
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8796
moved from start:          0.1506

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.021  11964  Z= 0.133
  Angle     :  0.468   4.084  16308  Z= 0.254
  Chirality :  0.045   0.161   1950
  Planarity :  0.004   0.053   2124
  Dihedral  :  3.813  12.101   1668
  Min Nonbonded Distance : 2.584

Molprobity Statistics.
  All-atom Clashscore : 2.56
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.91 %
    Favored  : 98.09 %
  Rotamer:
    Outliers :  2.00 %
    Allowed  : 18.91 %
    Favored  : 79.09 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.34 (0.20), residues: 1572
  helix: -0.40 (0.44), residues: 144
  sheet:  1.53 (0.21), residues: 612
  loop : -1.71 (0.18), residues: 816

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B 106 
 TYR   0.010   0.001   TYR B 252 
 PHE   0.014   0.001   PHE E 261 
 TRP   0.003   0.001   TRP A 133 
 HIS   0.002   0.001   HIS A 255 

Details of bonding type rmsd
  covalent geometry    : bond        0.00329 (11964)
  covalent geometry    : angle       0.46824 (16308)
  hydrogen bonds       : bond        0.03558 (  354)
  hydrogen bonds       : angle       5.47775 ( 1062)

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

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

  3144 Ramachandran restraints generated.
    1572 Oldfield, 0 Emsley, 1572 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3144 Ramachandran restraints generated.
    1572 Oldfield, 0 Emsley, 1572 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  190 residues out of total 1254 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 165
  time to evaluate  : 0.460 
Fit side-chains
REVERT: B   21 MET cc_start: 0.9296 (mtt) cc_final: 0.9084 (mtt)
REVERT: B   88 MET cc_start: 0.9158 (mtp) cc_final: 0.8941 (mtm)
REVERT: A  156 ASN cc_start: 0.8660 (m-40) cc_final: 0.8343 (t0)
REVERT: C   21 MET cc_start: 0.9303 (mtt) cc_final: 0.9090 (mtt)
REVERT: C   88 MET cc_start: 0.9163 (mtp) cc_final: 0.8946 (mtm)
REVERT: D  156 ASN cc_start: 0.8669 (m-40) cc_final: 0.8352 (t0)
REVERT: E  156 ASN cc_start: 0.8634 (m-40) cc_final: 0.8365 (t0)
REVERT: F  156 ASN cc_start: 0.8658 (m-40) cc_final: 0.8388 (t0)
  outliers start: 25
  outliers final: 13
  residues processed: 173
  average time/residue: 0.1236
  time to fit residues: 29.6853
Evaluate side-chains
  174 residues out of total 1254 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 161
  time to evaluate  : 0.409 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  178 THR
Chi-restraints excluded: chain B residue  222 ASN
Chi-restraints excluded: chain B residue  223 LEU
Chi-restraints excluded: chain A residue  178 THR
Chi-restraints excluded: chain A residue  223 LEU
Chi-restraints excluded: chain C residue  178 THR
Chi-restraints excluded: chain C residue  222 ASN
Chi-restraints excluded: chain C residue  223 LEU
Chi-restraints excluded: chain D residue  178 THR
Chi-restraints excluded: chain D residue  223 LEU
Chi-restraints excluded: chain E residue  178 THR
Chi-restraints excluded: chain E residue  222 ASN
Chi-restraints excluded: chain F residue  222 ASN
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 156
   random chunks:
   chunk 83 optimal weight:    0.3980
   chunk 89 optimal weight:    9.9990
   chunk 19 optimal weight:    6.9990
   chunk 113 optimal weight:    5.9990
   chunk 0 optimal weight:    8.9990
   chunk 38 optimal weight:    9.9990
   chunk 154 optimal weight:    3.9990
   chunk 145 optimal weight:    9.9990
   chunk 120 optimal weight:    7.9990
   chunk 86 optimal weight:    2.9990
   chunk 142 optimal weight:    9.9990
   overall best weight:    4.0788

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

Flipped N/Q/H residues before XYZ refinement:
B 143 ASN
C 143 ASN
D 236 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3197 r_free = 0.3197 target = 0.111602 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.2797 r_free = 0.2797 target = 0.083974 restraints weight = 14115.481|
|-----------------------------------------------------------------------------|
r_work (start): 0.2799 rms_B_bonded: 1.87
r_work: 0.2666 rms_B_bonded: 2.28 restraints_weight: 0.5000
r_work: 0.2526 rms_B_bonded: 3.72 restraints_weight: 0.2500
r_work (final): 0.2526
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8900
moved from start:          0.1721

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.007   0.038  11964  Z= 0.269
  Angle     :  0.571   5.041  16308  Z= 0.307
  Chirality :  0.049   0.171   1950
  Planarity :  0.005   0.056   2124
  Dihedral  :  4.336  14.670   1668
  Min Nonbonded Distance : 2.567

Molprobity Statistics.
  All-atom Clashscore : 1.62
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.67 %
    Favored  : 97.33 %
  Rotamer:
    Outliers :  3.37 %
    Allowed  : 18.91 %
    Favored  : 77.72 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.55 (0.20), residues: 1572
  helix: -0.63 (0.42), residues: 144
  sheet:  1.35 (0.21), residues: 612
  loop : -1.79 (0.18), residues: 816

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.001   ARG B 104 
 TYR   0.014   0.002   TYR E 252 
 PHE   0.017   0.002   PHE B 261 
 TRP   0.005   0.001   TRP D 133 
 HIS   0.002   0.001   HIS C  36 

Details of bonding type rmsd
  covalent geometry    : bond        0.00684 (11964)
  covalent geometry    : angle       0.57110 (16308)
  hydrogen bonds       : bond        0.04278 (  354)
  hydrogen bonds       : angle       5.62313 ( 1062)

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

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

  3144 Ramachandran restraints generated.
    1572 Oldfield, 0 Emsley, 1572 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3144 Ramachandran restraints generated.
    1572 Oldfield, 0 Emsley, 1572 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  206 residues out of total 1254 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 42
    poor density    : 164
  time to evaluate  : 0.405 
Fit side-chains
REVERT: B   88 MET cc_start: 0.9270 (mtp) cc_final: 0.9033 (mtm)
REVERT: A  156 ASN cc_start: 0.8728 (m-40) cc_final: 0.8513 (t0)
REVERT: C   88 MET cc_start: 0.9277 (mtp) cc_final: 0.9041 (mtm)
REVERT: C  156 ASN cc_start: 0.8691 (m-40) cc_final: 0.7748 (t0)
REVERT: D  156 ASN cc_start: 0.8717 (m-40) cc_final: 0.8513 (t0)
REVERT: E  156 ASN cc_start: 0.8675 (m-40) cc_final: 0.8435 (t0)
  outliers start: 42
  outliers final: 34
  residues processed: 182
  average time/residue: 0.1163
  time to fit residues: 29.7105
Evaluate side-chains
  199 residues out of total 1254 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 165
  time to evaluate  : 0.454 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   59 VAL
Chi-restraints excluded: chain B residue  178 THR
Chi-restraints excluded: chain B residue  212 VAL
Chi-restraints excluded: chain B residue  222 ASN
Chi-restraints excluded: chain B residue  223 LEU
Chi-restraints excluded: chain B residue  228 THR
Chi-restraints excluded: chain A residue   59 VAL
Chi-restraints excluded: chain A residue  178 THR
Chi-restraints excluded: chain A residue  222 ASN
Chi-restraints excluded: chain A residue  223 LEU
Chi-restraints excluded: chain A residue  228 THR
Chi-restraints excluded: chain C residue   59 VAL
Chi-restraints excluded: chain C residue  178 THR
Chi-restraints excluded: chain C residue  212 VAL
Chi-restraints excluded: chain C residue  222 ASN
Chi-restraints excluded: chain C residue  223 LEU
Chi-restraints excluded: chain C residue  228 THR
Chi-restraints excluded: chain D residue   59 VAL
Chi-restraints excluded: chain D residue  178 THR
Chi-restraints excluded: chain D residue  222 ASN
Chi-restraints excluded: chain D residue  223 LEU
Chi-restraints excluded: chain D residue  228 THR
Chi-restraints excluded: chain E residue   59 VAL
Chi-restraints excluded: chain E residue  178 THR
Chi-restraints excluded: chain E residue  212 VAL
Chi-restraints excluded: chain E residue  222 ASN
Chi-restraints excluded: chain E residue  228 THR
Chi-restraints excluded: chain E residue  263 LEU
Chi-restraints excluded: chain F residue   59 VAL
Chi-restraints excluded: chain F residue  178 THR
Chi-restraints excluded: chain F residue  212 VAL
Chi-restraints excluded: chain F residue  222 ASN
Chi-restraints excluded: chain F residue  228 THR
Chi-restraints excluded: chain F residue  263 LEU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 156
   random chunks:
   chunk 26 optimal weight:    6.9990
   chunk 4 optimal weight:    3.9990
   chunk 37 optimal weight:    4.9990
   chunk 127 optimal weight:    1.9990
   chunk 81 optimal weight:    5.9990
   chunk 154 optimal weight:    1.9990
   chunk 96 optimal weight:    5.9990
   chunk 48 optimal weight:    1.9990
   chunk 150 optimal weight:    0.9990
   chunk 93 optimal weight:    9.9990
   chunk 108 optimal weight:    1.9990
   overall best weight:    1.7990

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

Flipped N/Q/H residues before XYZ refinement:
A 143 ASN
D 143 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3223 r_free = 0.3223 target = 0.113145 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.2826 r_free = 0.2826 target = 0.085277 restraints weight = 13894.327|
|-----------------------------------------------------------------------------|
r_work (start): 0.2841 rms_B_bonded: 1.92
r_work: 0.2716 rms_B_bonded: 2.24 restraints_weight: 0.5000
r_work: 0.2578 rms_B_bonded: 3.65 restraints_weight: 0.2500
r_work (final): 0.2578
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8801
moved from start:          0.1749

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.022  11964  Z= 0.132
  Angle     :  0.455   3.576  16308  Z= 0.248
  Chirality :  0.045   0.165   1950
  Planarity :  0.004   0.057   2124
  Dihedral  :  3.869  11.970   1668
  Min Nonbonded Distance : 2.590

Molprobity Statistics.
  All-atom Clashscore : 2.48
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.04 %
    Favored  : 97.96 %
  Rotamer:
    Outliers :  3.53 %
    Allowed  : 19.55 %
    Favored  : 76.92 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.47 (0.20), residues: 1572
  helix: -0.56 (0.43), residues: 144
  sheet:  1.41 (0.21), residues: 612
  loop : -1.75 (0.18), residues: 816

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG C 106 
 TYR   0.010   0.001   TYR E 252 
 PHE   0.014   0.001   PHE E 261 
 TRP   0.002   0.001   TRP D 133 
 HIS   0.002   0.000   HIS D 255 

Details of bonding type rmsd
  covalent geometry    : bond        0.00328 (11964)
  covalent geometry    : angle       0.45548 (16308)
  hydrogen bonds       : bond        0.03266 (  354)
  hydrogen bonds       : angle       5.35432 ( 1062)

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

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

  3144 Ramachandran restraints generated.
    1572 Oldfield, 0 Emsley, 1572 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3144 Ramachandran restraints generated.
    1572 Oldfield, 0 Emsley, 1572 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  218 residues out of total 1254 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 44
    poor density    : 174
  time to evaluate  : 0.437 
Fit side-chains
REVERT: B   88 MET cc_start: 0.9175 (mtp) cc_final: 0.8959 (mtm)
REVERT: B  156 ASN cc_start: 0.8684 (m-40) cc_final: 0.7825 (t0)
REVERT: C   88 MET cc_start: 0.9176 (mtp) cc_final: 0.8961 (mtm)
REVERT: C  156 ASN cc_start: 0.8723 (m-40) cc_final: 0.7884 (t0)
REVERT: E  156 ASN cc_start: 0.8647 (m-40) cc_final: 0.8424 (t0)
REVERT: F  156 ASN cc_start: 0.8635 (OUTLIER) cc_final: 0.7945 (t0)
  outliers start: 44
  outliers final: 37
  residues processed: 193
  average time/residue: 0.1075
  time to fit residues: 29.2133
Evaluate side-chains
  207 residues out of total 1254 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 38
    poor density    : 169
  time to evaluate  : 0.295 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   59 VAL
Chi-restraints excluded: chain B residue  178 THR
Chi-restraints excluded: chain B residue  212 VAL
Chi-restraints excluded: chain B residue  222 ASN
Chi-restraints excluded: chain B residue  223 LEU
Chi-restraints excluded: chain B residue  228 THR
Chi-restraints excluded: chain B residue  263 LEU
Chi-restraints excluded: chain A residue   59 VAL
Chi-restraints excluded: chain A residue   64 VAL
Chi-restraints excluded: chain A residue  178 THR
Chi-restraints excluded: chain A residue  222 ASN
Chi-restraints excluded: chain A residue  223 LEU
Chi-restraints excluded: chain A residue  228 THR
Chi-restraints excluded: chain C residue   59 VAL
Chi-restraints excluded: chain C residue  178 THR
Chi-restraints excluded: chain C residue  222 ASN
Chi-restraints excluded: chain C residue  223 LEU
Chi-restraints excluded: chain C residue  228 THR
Chi-restraints excluded: chain C residue  263 LEU
Chi-restraints excluded: chain D residue   59 VAL
Chi-restraints excluded: chain D residue   64 VAL
Chi-restraints excluded: chain D residue  178 THR
Chi-restraints excluded: chain D residue  222 ASN
Chi-restraints excluded: chain D residue  223 LEU
Chi-restraints excluded: chain D residue  228 THR
Chi-restraints excluded: chain D residue  245 LYS
Chi-restraints excluded: chain E residue   59 VAL
Chi-restraints excluded: chain E residue  178 THR
Chi-restraints excluded: chain E residue  212 VAL
Chi-restraints excluded: chain E residue  222 ASN
Chi-restraints excluded: chain E residue  228 THR
Chi-restraints excluded: chain E residue  263 LEU
Chi-restraints excluded: chain F residue   59 VAL
Chi-restraints excluded: chain F residue  156 ASN
Chi-restraints excluded: chain F residue  212 VAL
Chi-restraints excluded: chain F residue  222 ASN
Chi-restraints excluded: chain F residue  228 THR
Chi-restraints excluded: chain F residue  263 LEU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 156
   random chunks:
   chunk 1 optimal weight:    0.6980
   chunk 10 optimal weight:    0.0870
   chunk 43 optimal weight:    0.5980
   chunk 38 optimal weight:    3.9990
   chunk 148 optimal weight:    0.2980
   chunk 143 optimal weight:    6.9990
   chunk 52 optimal weight:    5.9990
   chunk 130 optimal weight:    7.9990
   chunk 46 optimal weight:    0.7980
   chunk 3 optimal weight:    5.9990
   chunk 2 optimal weight:    1.9990
   overall best weight:    0.4958

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

Flipped N/Q/H residues before XYZ refinement:
B 254 GLN
C 254 GLN
D 236 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3263 r_free = 0.3263 target = 0.116522 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.2882 r_free = 0.2882 target = 0.088916 restraints weight = 13749.187|
|-----------------------------------------------------------------------------|
r_work (start): 0.2866 rms_B_bonded: 1.92
r_work: 0.2743 rms_B_bonded: 2.27 restraints_weight: 0.5000
r_work: 0.2606 rms_B_bonded: 3.71 restraints_weight: 0.2500
r_work (final): 0.2606
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8756
moved from start:          0.1828

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.017  11964  Z= 0.069
  Angle     :  0.397   3.456  16308  Z= 0.216
  Chirality :  0.043   0.146   1950
  Planarity :  0.004   0.055   2124
  Dihedral  :  3.364  10.151   1668
  Min Nonbonded Distance : 2.580

Molprobity Statistics.
  All-atom Clashscore : 2.69
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.84 %
    Favored  : 98.16 %
  Rotamer:
    Outliers :  3.04 %
    Allowed  : 19.55 %
    Favored  : 77.40 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.20 (0.20), residues: 1572
  helix: -0.57 (0.41), residues: 144
  sheet:  1.78 (0.21), residues: 582
  loop : -1.56 (0.18), residues: 846

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG C 106 
 TYR   0.007   0.001   TYR D  82 
 PHE   0.010   0.001   PHE E 261 
 TRP   0.002   0.000   TRP B 133 
 HIS   0.002   0.000   HIS E 255 

Details of bonding type rmsd
  covalent geometry    : bond        0.00154 (11964)
  covalent geometry    : angle       0.39657 (16308)
  hydrogen bonds       : bond        0.02516 (  354)
  hydrogen bonds       : angle       5.01843 ( 1062)

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

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

  3144 Ramachandran restraints generated.
    1572 Oldfield, 0 Emsley, 1572 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3144 Ramachandran restraints generated.
    1572 Oldfield, 0 Emsley, 1572 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  206 residues out of total 1254 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 38
    poor density    : 168
  time to evaluate  : 0.459 
Fit side-chains
REVERT: B  156 ASN cc_start: 0.8668 (m-40) cc_final: 0.8198 (t0)
REVERT: C  156 ASN cc_start: 0.8673 (m-40) cc_final: 0.7879 (t0)
REVERT: E  156 ASN cc_start: 0.8632 (m-40) cc_final: 0.8415 (t0)
REVERT: F  156 ASN cc_start: 0.8703 (OUTLIER) cc_final: 0.8095 (t0)
  outliers start: 38
  outliers final: 32
  residues processed: 186
  average time/residue: 0.1166
  time to fit residues: 30.5577
Evaluate side-chains
  202 residues out of total 1254 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 169
  time to evaluate  : 0.400 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   59 VAL
Chi-restraints excluded: chain B residue  178 THR
Chi-restraints excluded: chain B residue  212 VAL
Chi-restraints excluded: chain B residue  222 ASN
Chi-restraints excluded: chain B residue  228 THR
Chi-restraints excluded: chain B residue  263 LEU
Chi-restraints excluded: chain A residue   59 VAL
Chi-restraints excluded: chain A residue   64 VAL
Chi-restraints excluded: chain A residue  178 THR
Chi-restraints excluded: chain A residue  222 ASN
Chi-restraints excluded: chain A residue  228 THR
Chi-restraints excluded: chain C residue   59 VAL
Chi-restraints excluded: chain C residue  178 THR
Chi-restraints excluded: chain C residue  222 ASN
Chi-restraints excluded: chain C residue  228 THR
Chi-restraints excluded: chain C residue  263 LEU
Chi-restraints excluded: chain D residue   59 VAL
Chi-restraints excluded: chain D residue   64 VAL
Chi-restraints excluded: chain D residue  178 THR
Chi-restraints excluded: chain D residue  222 ASN
Chi-restraints excluded: chain D residue  228 THR
Chi-restraints excluded: chain E residue   59 VAL
Chi-restraints excluded: chain E residue  178 THR
Chi-restraints excluded: chain E residue  212 VAL
Chi-restraints excluded: chain E residue  222 ASN
Chi-restraints excluded: chain E residue  228 THR
Chi-restraints excluded: chain E residue  263 LEU
Chi-restraints excluded: chain F residue   59 VAL
Chi-restraints excluded: chain F residue  156 ASN
Chi-restraints excluded: chain F residue  212 VAL
Chi-restraints excluded: chain F residue  222 ASN
Chi-restraints excluded: chain F residue  228 THR
Chi-restraints excluded: chain F residue  263 LEU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 156
   random chunks:
   chunk 71 optimal weight:    7.9990
   chunk 8 optimal weight:    1.9990
   chunk 50 optimal weight:    6.9990
   chunk 133 optimal weight:    7.9990
   chunk 151 optimal weight:    3.9990
   chunk 84 optimal weight:    8.9990
   chunk 128 optimal weight:    6.9990
   chunk 56 optimal weight:    5.9990
   chunk 42 optimal weight:    8.9990
   chunk 53 optimal weight:    6.9990
   chunk 82 optimal weight:    3.9990
   overall best weight:    4.5990

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

Flipped N/Q/H residues before XYZ refinement:
B 254 GLN
A 236 GLN
C 254 GLN
D 143 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3161 r_free = 0.3161 target = 0.108797 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.2756 r_free = 0.2756 target = 0.080993 restraints weight = 14012.622|
|-----------------------------------------------------------------------------|
r_work (start): 0.2633 rms_B_bonded: 1.93
r_work: 0.2511 rms_B_bonded: 2.25 restraints_weight: 0.5000
r_work: 0.2370 rms_B_bonded: 3.65 restraints_weight: 0.2500
r_work (final): 0.2370
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8876
moved from start:          0.1953

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.008   0.041  11964  Z= 0.302
  Angle     :  0.583   5.147  16308  Z= 0.314
  Chirality :  0.050   0.177   1950
  Planarity :  0.005   0.056   2124
  Dihedral  :  4.329  13.667   1668
  Min Nonbonded Distance : 2.532

Molprobity Statistics.
  All-atom Clashscore : 1.58
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.42 %
    Favored  : 97.58 %
  Rotamer:
    Outliers :  3.37 %
    Allowed  : 20.35 %
    Favored  : 76.28 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.47 (0.20), residues: 1572
  helix: -0.70 (0.41), residues: 144
  sheet:  1.52 (0.21), residues: 552
  loop : -1.58 (0.18), residues: 876

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.001   ARG B  85 
 TYR   0.024   0.002   TYR A  82 
 PHE   0.018   0.002   PHE B 261 
 TRP   0.006   0.002   TRP D 133 
 HIS   0.003   0.001   HIS C  36 

Details of bonding type rmsd
  covalent geometry    : bond        0.00767 (11964)
  covalent geometry    : angle       0.58347 (16308)
  hydrogen bonds       : bond        0.04274 (  354)
  hydrogen bonds       : angle       5.48135 ( 1062)

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

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

  3144 Ramachandran restraints generated.
    1572 Oldfield, 0 Emsley, 1572 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3144 Ramachandran restraints generated.
    1572 Oldfield, 0 Emsley, 1572 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  211 residues out of total 1254 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 42
    poor density    : 169
  time to evaluate  : 0.528 
Fit side-chains
REVERT: B  156 ASN cc_start: 0.8682 (m-40) cc_final: 0.7808 (t0)
REVERT: B  244 ARG cc_start: 0.8432 (mtm110) cc_final: 0.8162 (mtt90)
REVERT: A   82 TYR cc_start: 0.9334 (m-80) cc_final: 0.9053 (m-80)
REVERT: A   88 MET cc_start: 0.9242 (mtp) cc_final: 0.9007 (mtm)
REVERT: C  156 ASN cc_start: 0.8712 (m-40) cc_final: 0.7851 (t0)
REVERT: D   82 TYR cc_start: 0.9335 (m-80) cc_final: 0.9049 (m-80)
REVERT: D   88 MET cc_start: 0.9240 (mtp) cc_final: 0.9006 (mtm)
  outliers start: 42
  outliers final: 38
  residues processed: 187
  average time/residue: 0.1242
  time to fit residues: 32.5309
Evaluate side-chains
  210 residues out of total 1254 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 38
    poor density    : 172
  time to evaluate  : 0.457 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   59 VAL
Chi-restraints excluded: chain B residue  178 THR
Chi-restraints excluded: chain B residue  212 VAL
Chi-restraints excluded: chain B residue  222 ASN
Chi-restraints excluded: chain B residue  223 LEU
Chi-restraints excluded: chain B residue  228 THR
Chi-restraints excluded: chain B residue  263 LEU
Chi-restraints excluded: chain A residue   59 VAL
Chi-restraints excluded: chain A residue   64 VAL
Chi-restraints excluded: chain A residue  178 THR
Chi-restraints excluded: chain A residue  222 ASN
Chi-restraints excluded: chain A residue  223 LEU
Chi-restraints excluded: chain A residue  228 THR
Chi-restraints excluded: chain C residue   59 VAL
Chi-restraints excluded: chain C residue  178 THR
Chi-restraints excluded: chain C residue  212 VAL
Chi-restraints excluded: chain C residue  222 ASN
Chi-restraints excluded: chain C residue  223 LEU
Chi-restraints excluded: chain C residue  228 THR
Chi-restraints excluded: chain C residue  263 LEU
Chi-restraints excluded: chain D residue   59 VAL
Chi-restraints excluded: chain D residue   64 VAL
Chi-restraints excluded: chain D residue  178 THR
Chi-restraints excluded: chain D residue  222 ASN
Chi-restraints excluded: chain D residue  223 LEU
Chi-restraints excluded: chain D residue  228 THR
Chi-restraints excluded: chain E residue   59 VAL
Chi-restraints excluded: chain E residue  178 THR
Chi-restraints excluded: chain E residue  212 VAL
Chi-restraints excluded: chain E residue  222 ASN
Chi-restraints excluded: chain E residue  228 THR
Chi-restraints excluded: chain E residue  263 LEU
Chi-restraints excluded: chain F residue   59 VAL
Chi-restraints excluded: chain F residue  178 THR
Chi-restraints excluded: chain F residue  212 VAL
Chi-restraints excluded: chain F residue  222 ASN
Chi-restraints excluded: chain F residue  228 THR
Chi-restraints excluded: chain F residue  263 LEU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 156
   random chunks:
   chunk 129 optimal weight:    4.9990
   chunk 138 optimal weight:    1.9990
   chunk 18 optimal weight:    2.9990
   chunk 88 optimal weight:   10.0000
   chunk 106 optimal weight:    1.9990
   chunk 14 optimal weight:    2.9990
   chunk 4 optimal weight:    0.9980
   chunk 34 optimal weight:    0.9990
   chunk 90 optimal weight:    7.9990
   chunk 10 optimal weight:    6.9990
   chunk 12 optimal weight:    9.9990
   overall best weight:    1.7988

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

Flipped N/Q/H residues before XYZ refinement:
B 254 GLN
A 143 ASN
C 254 GLN
D 143 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3215 r_free = 0.3215 target = 0.112722 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.2819 r_free = 0.2819 target = 0.084975 restraints weight = 13823.564|
|-----------------------------------------------------------------------------|
r_work (start): 0.2834 rms_B_bonded: 1.91
r_work: 0.2709 rms_B_bonded: 2.24 restraints_weight: 0.5000
r_work: 0.2569 rms_B_bonded: 3.65 restraints_weight: 0.2500
r_work (final): 0.2569
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8806
moved from start:          0.1940

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.022  11964  Z= 0.131
  Angle     :  0.454   3.316  16308  Z= 0.248
  Chirality :  0.045   0.166   1950
  Planarity :  0.004   0.057   2124
  Dihedral  :  3.876  11.384   1668
  Min Nonbonded Distance : 2.544

Molprobity Statistics.
  All-atom Clashscore : 2.18
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.97 %
    Favored  : 98.03 %
  Rotamer:
    Outliers :  3.21 %
    Allowed  : 20.59 %
    Favored  : 76.20 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.29 (0.20), residues: 1572
  helix: -0.60 (0.41), residues: 144
  sheet:  1.82 (0.22), residues: 522
  loop : -1.47 (0.18), residues: 906

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B 104 
 TYR   0.015   0.001   TYR A  82 
 PHE   0.014   0.001   PHE C 261 
 TRP   0.002   0.000   TRP B  73 
 HIS   0.002   0.001   HIS A 255 

Details of bonding type rmsd
  covalent geometry    : bond        0.00326 (11964)
  covalent geometry    : angle       0.45446 (16308)
  hydrogen bonds       : bond        0.03190 (  354)
  hydrogen bonds       : angle       5.24790 ( 1062)

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

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

  3144 Ramachandran restraints generated.
    1572 Oldfield, 0 Emsley, 1572 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3144 Ramachandran restraints generated.
    1572 Oldfield, 0 Emsley, 1572 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  214 residues out of total 1254 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 40
    poor density    : 174
  time to evaluate  : 0.440 
Fit side-chains
REVERT: B  156 ASN cc_start: 0.8644 (m-40) cc_final: 0.7822 (t0)
REVERT: A   82 TYR cc_start: 0.9293 (m-80) cc_final: 0.9034 (m-80)
REVERT: C  156 ASN cc_start: 0.8686 (m-40) cc_final: 0.7848 (t0)
REVERT: D   82 TYR cc_start: 0.9300 (m-80) cc_final: 0.9042 (m-80)
REVERT: E  106 ARG cc_start: 0.8495 (mtt-85) cc_final: 0.8272 (ttt180)
REVERT: E  172 ASP cc_start: 0.8396 (m-30) cc_final: 0.8146 (m-30)
REVERT: F  106 ARG cc_start: 0.8501 (mtt-85) cc_final: 0.8279 (ttt180)
REVERT: F  172 ASP cc_start: 0.8397 (m-30) cc_final: 0.8145 (m-30)
  outliers start: 40
  outliers final: 38
  residues processed: 192
  average time/residue: 0.1198
  time to fit residues: 32.0511
Evaluate side-chains
  212 residues out of total 1254 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 38
    poor density    : 174
  time to evaluate  : 0.451 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   59 VAL
Chi-restraints excluded: chain B residue  178 THR
Chi-restraints excluded: chain B residue  222 ASN
Chi-restraints excluded: chain B residue  228 THR
Chi-restraints excluded: chain B residue  263 LEU
Chi-restraints excluded: chain A residue   59 VAL
Chi-restraints excluded: chain A residue   64 VAL
Chi-restraints excluded: chain A residue  140 LEU
Chi-restraints excluded: chain A residue  178 THR
Chi-restraints excluded: chain A residue  222 ASN
Chi-restraints excluded: chain A residue  223 LEU
Chi-restraints excluded: chain A residue  228 THR
Chi-restraints excluded: chain C residue   59 VAL
Chi-restraints excluded: chain C residue  178 THR
Chi-restraints excluded: chain C residue  222 ASN
Chi-restraints excluded: chain C residue  228 THR
Chi-restraints excluded: chain C residue  263 LEU
Chi-restraints excluded: chain D residue   59 VAL
Chi-restraints excluded: chain D residue   64 VAL
Chi-restraints excluded: chain D residue  108 VAL
Chi-restraints excluded: chain D residue  140 LEU
Chi-restraints excluded: chain D residue  178 THR
Chi-restraints excluded: chain D residue  222 ASN
Chi-restraints excluded: chain D residue  223 LEU
Chi-restraints excluded: chain D residue  228 THR
Chi-restraints excluded: chain D residue  245 LYS
Chi-restraints excluded: chain E residue   59 VAL
Chi-restraints excluded: chain E residue  178 THR
Chi-restraints excluded: chain E residue  212 VAL
Chi-restraints excluded: chain E residue  222 ASN
Chi-restraints excluded: chain E residue  228 THR
Chi-restraints excluded: chain E residue  263 LEU
Chi-restraints excluded: chain F residue   59 VAL
Chi-restraints excluded: chain F residue  178 THR
Chi-restraints excluded: chain F residue  212 VAL
Chi-restraints excluded: chain F residue  222 ASN
Chi-restraints excluded: chain F residue  228 THR
Chi-restraints excluded: chain F residue  263 LEU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 156
   random chunks:
   chunk 87 optimal weight:    1.9990
   chunk 28 optimal weight:    3.9990
   chunk 140 optimal weight:   10.0000
   chunk 153 optimal weight:    6.9990
   chunk 33 optimal weight:    4.9990
   chunk 148 optimal weight:    4.9990
   chunk 34 optimal weight:    0.8980
   chunk 124 optimal weight:    4.9990
   chunk 64 optimal weight:   10.0000
   chunk 56 optimal weight:    4.9990
   chunk 31 optimal weight:    0.0570
   overall best weight:    2.3904

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

Flipped N/Q/H residues before XYZ refinement:
B 254 GLN
A 143 ASN
C 254 GLN
D 143 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3176 r_free = 0.3176 target = 0.110063 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.2775 r_free = 0.2775 target = 0.082253 restraints weight = 13822.056|
|-----------------------------------------------------------------------------|
r_work (start): 0.2643 rms_B_bonded: 1.92
r_work: 0.2522 rms_B_bonded: 2.24 restraints_weight: 0.5000
r_work: 0.2384 rms_B_bonded: 3.62 restraints_weight: 0.2500
r_work (final): 0.2384
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8821
moved from start:          0.1968

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.026  11964  Z= 0.165
  Angle     :  0.480   4.112  16308  Z= 0.261
  Chirality :  0.046   0.167   1950
  Planarity :  0.004   0.056   2124
  Dihedral  :  3.982  11.693   1668
  Min Nonbonded Distance : 2.542

Molprobity Statistics.
  All-atom Clashscore : 2.01
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.42 %
    Favored  : 97.58 %
  Rotamer:
    Outliers :  3.53 %
    Allowed  : 20.27 %
    Favored  : 76.20 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.32 (0.20), residues: 1572
  helix: -0.61 (0.41), residues: 144
  sheet:  1.78 (0.22), residues: 522
  loop : -1.47 (0.18), residues: 906

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B 104 
 TYR   0.017   0.001   TYR A  82 
 PHE   0.016   0.001   PHE C 261 
 TRP   0.003   0.001   TRP C  73 
 HIS   0.002   0.001   HIS A 255 

Details of bonding type rmsd
  covalent geometry    : bond        0.00416 (11964)
  covalent geometry    : angle       0.47984 (16308)
  hydrogen bonds       : bond        0.03454 (  354)
  hydrogen bonds       : angle       5.29033 ( 1062)

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

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

  3144 Ramachandran restraints generated.
    1572 Oldfield, 0 Emsley, 1572 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3144 Ramachandran restraints generated.
    1572 Oldfield, 0 Emsley, 1572 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  220 residues out of total 1254 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 44
    poor density    : 176
  time to evaluate  : 0.556 
Fit side-chains
REVERT: B  156 ASN cc_start: 0.8625 (m-40) cc_final: 0.7795 (t0)
REVERT: A   82 TYR cc_start: 0.9323 (m-80) cc_final: 0.9030 (m-80)
REVERT: C  156 ASN cc_start: 0.8670 (m-40) cc_final: 0.7828 (t0)
REVERT: D   82 TYR cc_start: 0.9328 (m-80) cc_final: 0.9031 (m-80)
REVERT: E  106 ARG cc_start: 0.8524 (mtt-85) cc_final: 0.8264 (ttt180)
REVERT: F  106 ARG cc_start: 0.8535 (mtt-85) cc_final: 0.8268 (ttt180)
  outliers start: 44
  outliers final: 41
  residues processed: 194
  average time/residue: 0.1203
  time to fit residues: 32.5628
Evaluate side-chains
  215 residues out of total 1254 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 41
    poor density    : 174
  time to evaluate  : 0.466 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   59 VAL
Chi-restraints excluded: chain B residue  178 THR
Chi-restraints excluded: chain B residue  222 ASN
Chi-restraints excluded: chain B residue  228 THR
Chi-restraints excluded: chain B residue  263 LEU
Chi-restraints excluded: chain A residue   59 VAL
Chi-restraints excluded: chain A residue   64 VAL
Chi-restraints excluded: chain A residue  108 VAL
Chi-restraints excluded: chain A residue  140 LEU
Chi-restraints excluded: chain A residue  178 THR
Chi-restraints excluded: chain A residue  222 ASN
Chi-restraints excluded: chain A residue  223 LEU
Chi-restraints excluded: chain A residue  228 THR
Chi-restraints excluded: chain C residue   59 VAL
Chi-restraints excluded: chain C residue  178 THR
Chi-restraints excluded: chain C residue  222 ASN
Chi-restraints excluded: chain C residue  228 THR
Chi-restraints excluded: chain C residue  263 LEU
Chi-restraints excluded: chain D residue   59 VAL
Chi-restraints excluded: chain D residue   64 VAL
Chi-restraints excluded: chain D residue  108 VAL
Chi-restraints excluded: chain D residue  140 LEU
Chi-restraints excluded: chain D residue  178 THR
Chi-restraints excluded: chain D residue  222 ASN
Chi-restraints excluded: chain D residue  223 LEU
Chi-restraints excluded: chain D residue  228 THR
Chi-restraints excluded: chain D residue  245 LYS
Chi-restraints excluded: chain E residue   59 VAL
Chi-restraints excluded: chain E residue  140 LEU
Chi-restraints excluded: chain E residue  178 THR
Chi-restraints excluded: chain E residue  212 VAL
Chi-restraints excluded: chain E residue  222 ASN
Chi-restraints excluded: chain E residue  228 THR
Chi-restraints excluded: chain E residue  263 LEU
Chi-restraints excluded: chain F residue   59 VAL
Chi-restraints excluded: chain F residue  140 LEU
Chi-restraints excluded: chain F residue  178 THR
Chi-restraints excluded: chain F residue  212 VAL
Chi-restraints excluded: chain F residue  222 ASN
Chi-restraints excluded: chain F residue  228 THR
Chi-restraints excluded: chain F residue  263 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 156
   random chunks:
   chunk 19 optimal weight:    5.9990
   chunk 138 optimal weight:    4.9990
   chunk 153 optimal weight:    0.0050
   chunk 26 optimal weight:    7.9990
   chunk 50 optimal weight:    7.9990
   chunk 118 optimal weight:    7.9990
   chunk 39 optimal weight:    9.9990
   chunk 29 optimal weight:    2.9990
   chunk 31 optimal weight:    0.0770
   chunk 101 optimal weight:    0.8980
   chunk 41 optimal weight:    9.9990
   overall best weight:    1.7956

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

Flipped N/Q/H residues before XYZ refinement:
B 254 GLN
C 254 GLN
D 143 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3217 r_free = 0.3217 target = 0.112842 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.2822 r_free = 0.2822 target = 0.085113 restraints weight = 13848.463|
|-----------------------------------------------------------------------------|
r_work (start): 0.2681 rms_B_bonded: 1.91
r_work: 0.2561 rms_B_bonded: 2.24 restraints_weight: 0.5000
r_work: 0.2421 rms_B_bonded: 3.67 restraints_weight: 0.2500
r_work (final): 0.2421
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8830
moved from start:          0.1973

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.022  11964  Z= 0.131
  Angle     :  0.451   3.410  16308  Z= 0.246
  Chirality :  0.045   0.166   1950
  Planarity :  0.004   0.056   2124
  Dihedral  :  3.826  11.025   1668
  Min Nonbonded Distance : 2.541

Molprobity Statistics.
  All-atom Clashscore : 2.22
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.91 %
    Favored  : 98.09 %
  Rotamer:
    Outliers :  3.45 %
    Allowed  : 20.51 %
    Favored  : 76.04 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.26 (0.20), residues: 1572
  helix: -0.56 (0.42), residues: 144
  sheet:  1.83 (0.22), residues: 522
  loop : -1.44 (0.18), residues: 906

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG F 106 
 TYR   0.015   0.001   TYR A  82 
 PHE   0.015   0.001   PHE C 261 
 TRP   0.002   0.001   TRP B  73 
 HIS   0.002   0.001   HIS D 255 

Details of bonding type rmsd
  covalent geometry    : bond        0.00325 (11964)
  covalent geometry    : angle       0.45124 (16308)
  hydrogen bonds       : bond        0.03163 (  354)
  hydrogen bonds       : angle       5.20124 ( 1062)

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

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

  3144 Ramachandran restraints generated.
    1572 Oldfield, 0 Emsley, 1572 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3144 Ramachandran restraints generated.
    1572 Oldfield, 0 Emsley, 1572 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  217 residues out of total 1254 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 43
    poor density    : 174
  time to evaluate  : 0.418 
Fit side-chains
REVERT: B  156 ASN cc_start: 0.8637 (m-40) cc_final: 0.7828 (t0)
REVERT: A   82 TYR cc_start: 0.9312 (m-80) cc_final: 0.9033 (m-80)
REVERT: C  156 ASN cc_start: 0.8664 (m-40) cc_final: 0.7827 (t0)
REVERT: D   82 TYR cc_start: 0.9319 (m-80) cc_final: 0.9042 (m-80)
REVERT: E  172 ASP cc_start: 0.8386 (m-30) cc_final: 0.8150 (m-30)
REVERT: F  172 ASP cc_start: 0.8386 (m-30) cc_final: 0.8148 (m-30)
  outliers start: 43
  outliers final: 42
  residues processed: 192
  average time/residue: 0.1006
  time to fit residues: 27.2933
Evaluate side-chains
  216 residues out of total 1254 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 42
    poor density    : 174
  time to evaluate  : 0.462 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   59 VAL
Chi-restraints excluded: chain B residue  178 THR
Chi-restraints excluded: chain B residue  222 ASN
Chi-restraints excluded: chain B residue  237 MET
Chi-restraints excluded: chain B residue  263 LEU
Chi-restraints excluded: chain A residue   59 VAL
Chi-restraints excluded: chain A residue   64 VAL
Chi-restraints excluded: chain A residue  108 VAL
Chi-restraints excluded: chain A residue  140 LEU
Chi-restraints excluded: chain A residue  178 THR
Chi-restraints excluded: chain A residue  222 ASN
Chi-restraints excluded: chain A residue  223 LEU
Chi-restraints excluded: chain A residue  228 THR
Chi-restraints excluded: chain A residue  245 LYS
Chi-restraints excluded: chain C residue   59 VAL
Chi-restraints excluded: chain C residue  178 THR
Chi-restraints excluded: chain C residue  222 ASN
Chi-restraints excluded: chain C residue  228 THR
Chi-restraints excluded: chain C residue  237 MET
Chi-restraints excluded: chain C residue  263 LEU
Chi-restraints excluded: chain D residue   59 VAL
Chi-restraints excluded: chain D residue   64 VAL
Chi-restraints excluded: chain D residue  108 VAL
Chi-restraints excluded: chain D residue  140 LEU
Chi-restraints excluded: chain D residue  178 THR
Chi-restraints excluded: chain D residue  222 ASN
Chi-restraints excluded: chain D residue  223 LEU
Chi-restraints excluded: chain D residue  228 THR
Chi-restraints excluded: chain D residue  245 LYS
Chi-restraints excluded: chain E residue   59 VAL
Chi-restraints excluded: chain E residue  178 THR
Chi-restraints excluded: chain E residue  212 VAL
Chi-restraints excluded: chain E residue  222 ASN
Chi-restraints excluded: chain E residue  228 THR
Chi-restraints excluded: chain E residue  263 LEU
Chi-restraints excluded: chain F residue   59 VAL
Chi-restraints excluded: chain F residue  140 LEU
Chi-restraints excluded: chain F residue  178 THR
Chi-restraints excluded: chain F residue  212 VAL
Chi-restraints excluded: chain F residue  222 ASN
Chi-restraints excluded: chain F residue  228 THR
Chi-restraints excluded: chain F residue  263 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 156
   random chunks:
   chunk 77 optimal weight:    5.9990
   chunk 86 optimal weight:    0.7980
   chunk 149 optimal weight:    3.9990
   chunk 19 optimal weight:    5.9990
   chunk 4 optimal weight:    4.9990
   chunk 48 optimal weight:    7.9990
   chunk 118 optimal weight:    3.9990
   chunk 65 optimal weight:    7.9990
   chunk 42 optimal weight:    3.9990
   chunk 52 optimal weight:    7.9990
   chunk 25 optimal weight:    4.9990
   overall best weight:    3.5588

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

Flipped N/Q/H residues before XYZ refinement:
B 254 GLN
A 143 ASN
C 254 GLN
D 143 ASN
D 236 GLN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3187 r_free = 0.3187 target = 0.110612 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.2784 r_free = 0.2784 target = 0.082804 restraints weight = 13895.395|
|-----------------------------------------------------------------------------|
r_work (start): 0.2760 rms_B_bonded: 1.92
r_work: 0.2637 rms_B_bonded: 2.23 restraints_weight: 0.5000
r_work: 0.2499 rms_B_bonded: 3.61 restraints_weight: 0.2500
r_work (final): 0.2499
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8839
moved from start:          0.2028

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.034  11964  Z= 0.236
  Angle     :  0.533   4.754  16308  Z= 0.289
  Chirality :  0.048   0.173   1950
  Planarity :  0.005   0.056   2124
  Dihedral  :  4.221  12.861   1668
  Min Nonbonded Distance : 2.538

Molprobity Statistics.
  All-atom Clashscore : 1.88
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.54 %
    Favored  : 97.46 %
  Rotamer:
    Outliers :  3.45 %
    Allowed  : 20.67 %
    Favored  : 75.88 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.48 (0.20), residues: 1572
  helix: -0.63 (0.41), residues: 144
  sheet:  1.48 (0.21), residues: 552
  loop : -1.57 (0.18), residues: 876

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.001   ARG F 104 
 TYR   0.018   0.002   TYR A  82 
 PHE   0.018   0.002   PHE C 261 
 TRP   0.005   0.001   TRP B  73 
 HIS   0.002   0.001   HIS C  36 

Details of bonding type rmsd
  covalent geometry    : bond        0.00598 (11964)
  covalent geometry    : angle       0.53350 (16308)
  hydrogen bonds       : bond        0.03904 (  354)
  hydrogen bonds       : angle       5.40747 ( 1062)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2608.97 seconds
wall clock time: 45 minutes 21.47 seconds (2721.47 seconds total)