Starting phenix.real_space_refine
on Thu Jul  2 22:09:37 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7k9l_22754/07_2026/7k9l_22754.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7k9l_22754/07_2026/7k9l_22754.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=4.9
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/7k9l_22754/07_2026/7k9l_22754.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7k9l_22754/07_2026/7k9l_22754.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/7k9l_22754/07_2026/7k9l_22754.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7k9l_22754/07_2026/7k9l_22754.map"
  }
  resolution = 4.9
  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=   0.000 sd=   0.004
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 4
    Type Number    sf(0)   Gaussians
     S      44      5.16       5
     C    6588      2.51       5
     N    1860      2.21       5
     O    1980      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 40 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib"
  Total number of atoms: 10472
  Number of models: 1
  Model: ""
    Number of chains: 1
    Chain: "B"
      Number of atoms: 2618
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 343, 2618
          Classifications: {'peptide': 343}
          Link IDs: {'PCIS': 1, 'PTRANS': 17, 'TRANS': 324}
  Restraints were copied for chains:
    A, C, D
  Time building chain proxies: 2.12, per 1000 atoms: 0.20
  Number of scatterers: 10472
  At special positions: 0
  Unit cell: (97.37, 80.99, 106.47, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     S      44     16.00
     O    1980      8.00
     N    1860      7.00
     C    6588      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: 1.01
  Conformation dependent library (CDL) restraints added in 330.2 milliseconds
  

  2728 Ramachandran restraints generated.
    1364 Oldfield, 0 Emsley, 1364 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2520

  Finding SS restraints...
    Secondary structure from input PDB file:
      60 helices and 8 sheets defined
      56.0% alpha, 13.4% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.30
  Creating SS restraints...
    Processing helix  chain 'B' and resid 8 through 23
    Processing helix  chain 'B' and resid 35 through 47
    Processing helix  chain 'B' and resid 51 through 64
    Processing helix  chain 'B' and resid 66 through 70
    Processing helix  chain 'B' and resid 79 through 84
      removed outlier: 3.592A  pdb=" N   LEU B  83 " --> pdb=" O   PHE B  79 " (cutoff:3.500A)
      removed outlier: 4.222A  pdb=" N   TYR B  84 " --> pdb=" O   HIS B  80 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 79 through 84'
    Processing helix  chain 'B' and resid 92 through 100
      removed outlier: 3.866A  pdb=" N   LYS B 100 " --> pdb=" O   VAL B  96 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 129 through 140
    Processing helix  chain 'B' and resid 159 through 181
      removed outlier: 3.870A  pdb=" N   ASN B 180 " --> pdb=" O   ILE B 176 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 197 through 219
      removed outlier: 3.620A  pdb=" N   CYS B 201 " --> pdb=" O   ASP B 197 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 222 through 225
    Processing helix  chain 'B' and resid 244 through 258
    Processing helix  chain 'B' and resid 275 through 288
      removed outlier: 4.094A  pdb=" N   SER B 280 " --> pdb=" O   GLU B 276 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 302 through 314
      removed outlier: 3.738A  pdb=" N   GLN B 306 " --> pdb=" O   GLY B 302 " (cutoff:3.500A)
      removed outlier: 5.639A  pdb=" N   SER B 308 " --> pdb=" O   ALA B 304 " (cutoff:3.500A)
      removed outlier: 5.053A  pdb=" N   ALA B 309 " --> pdb=" O   LEU B 305 " (cutoff:3.500A)
      removed outlier: 3.702A  pdb=" N   GLY B 314 " --> pdb=" O   LEU B 310 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 316 through 318
      No H-bonds generated for 'chain 'B' and resid 316 through 318'
    Processing helix  chain 'B' and resid 319 through 340
    Processing helix  chain 'A' and resid 8 through 23
    Processing helix  chain 'A' and resid 35 through 47
    Processing helix  chain 'A' and resid 51 through 64
    Processing helix  chain 'A' and resid 66 through 70
    Processing helix  chain 'A' and resid 79 through 84
      removed outlier: 3.593A  pdb=" N   LEU A  83 " --> pdb=" O   PHE A  79 " (cutoff:3.500A)
      removed outlier: 4.221A  pdb=" N   TYR A  84 " --> pdb=" O   HIS A  80 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 79 through 84'
    Processing helix  chain 'A' and resid 92 through 100
      removed outlier: 3.865A  pdb=" N   LYS A 100 " --> pdb=" O   VAL A  96 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 129 through 140
    Processing helix  chain 'A' and resid 159 through 181
      removed outlier: 3.870A  pdb=" N   ASN A 180 " --> pdb=" O   ILE A 176 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 197 through 219
      removed outlier: 3.619A  pdb=" N   CYS A 201 " --> pdb=" O   ASP A 197 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 222 through 225
    Processing helix  chain 'A' and resid 244 through 258
    Processing helix  chain 'A' and resid 275 through 288
      removed outlier: 4.093A  pdb=" N   SER A 280 " --> pdb=" O   GLU A 276 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 302 through 314
      removed outlier: 3.740A  pdb=" N   GLN A 306 " --> pdb=" O   GLY A 302 " (cutoff:3.500A)
      removed outlier: 5.639A  pdb=" N   SER A 308 " --> pdb=" O   ALA A 304 " (cutoff:3.500A)
      removed outlier: 5.053A  pdb=" N   ALA A 309 " --> pdb=" O   LEU A 305 " (cutoff:3.500A)
      removed outlier: 3.702A  pdb=" N   GLY A 314 " --> pdb=" O   LEU A 310 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 316 through 318
      No H-bonds generated for 'chain 'A' and resid 316 through 318'
    Processing helix  chain 'A' and resid 319 through 340
    Processing helix  chain 'C' and resid 8 through 23
    Processing helix  chain 'C' and resid 35 through 47
    Processing helix  chain 'C' and resid 51 through 64
    Processing helix  chain 'C' and resid 66 through 70
    Processing helix  chain 'C' and resid 79 through 84
      removed outlier: 3.593A  pdb=" N   LEU C  83 " --> pdb=" O   PHE C  79 " (cutoff:3.500A)
      removed outlier: 4.221A  pdb=" N   TYR C  84 " --> pdb=" O   HIS C  80 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'C' and resid 79 through 84'
    Processing helix  chain 'C' and resid 92 through 100
      removed outlier: 3.867A  pdb=" N   LYS C 100 " --> pdb=" O   VAL C  96 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 129 through 140
    Processing helix  chain 'C' and resid 159 through 181
      removed outlier: 3.870A  pdb=" N   ASN C 180 " --> pdb=" O   ILE C 176 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 197 through 219
      removed outlier: 3.620A  pdb=" N   CYS C 201 " --> pdb=" O   ASP C 197 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 222 through 225
    Processing helix  chain 'C' and resid 244 through 258
    Processing helix  chain 'C' and resid 275 through 288
      removed outlier: 4.093A  pdb=" N   SER C 280 " --> pdb=" O   GLU C 276 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 302 through 314
      removed outlier: 3.738A  pdb=" N   GLN C 306 " --> pdb=" O   GLY C 302 " (cutoff:3.500A)
      removed outlier: 5.639A  pdb=" N   SER C 308 " --> pdb=" O   ALA C 304 " (cutoff:3.500A)
      removed outlier: 5.053A  pdb=" N   ALA C 309 " --> pdb=" O   LEU C 305 " (cutoff:3.500A)
      removed outlier: 3.702A  pdb=" N   GLY C 314 " --> pdb=" O   LEU C 310 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 316 through 318
      No H-bonds generated for 'chain 'C' and resid 316 through 318'
    Processing helix  chain 'C' and resid 319 through 340
    Processing helix  chain 'D' and resid 8 through 23
    Processing helix  chain 'D' and resid 35 through 47
    Processing helix  chain 'D' and resid 51 through 64
    Processing helix  chain 'D' and resid 66 through 70
    Processing helix  chain 'D' and resid 79 through 84
      removed outlier: 3.593A  pdb=" N   LEU D  83 " --> pdb=" O   PHE D  79 " (cutoff:3.500A)
      removed outlier: 4.221A  pdb=" N   TYR D  84 " --> pdb=" O   HIS D  80 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'D' and resid 79 through 84'
    Processing helix  chain 'D' and resid 92 through 100
      removed outlier: 3.866A  pdb=" N   LYS D 100 " --> pdb=" O   VAL D  96 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 129 through 140
    Processing helix  chain 'D' and resid 159 through 181
      removed outlier: 3.870A  pdb=" N   ASN D 180 " --> pdb=" O   ILE D 176 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 197 through 219
      removed outlier: 3.621A  pdb=" N   CYS D 201 " --> pdb=" O   ASP D 197 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 222 through 225
    Processing helix  chain 'D' and resid 244 through 258
    Processing helix  chain 'D' and resid 275 through 288
      removed outlier: 4.094A  pdb=" N   SER D 280 " --> pdb=" O   GLU D 276 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 302 through 314
      removed outlier: 3.739A  pdb=" N   GLN D 306 " --> pdb=" O   GLY D 302 " (cutoff:3.500A)
      removed outlier: 5.639A  pdb=" N   SER D 308 " --> pdb=" O   ALA D 304 " (cutoff:3.500A)
      removed outlier: 5.054A  pdb=" N   ALA D 309 " --> pdb=" O   LEU D 305 " (cutoff:3.500A)
      removed outlier: 3.703A  pdb=" N   GLY D 314 " --> pdb=" O   LEU D 310 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 316 through 318
      No H-bonds generated for 'chain 'D' and resid 316 through 318'
    Processing helix  chain 'D' and resid 319 through 340
    Processing sheet with id=AA1, first strand: chain 'B' and resid 28 through 32
      removed outlier: 6.147A  pdb=" N   GLY B  28 " --> pdb=" O   GLY B  75 " (cutoff:3.500A)
      removed outlier: 7.909A  pdb=" N   ILE B  77 " --> pdb=" O   GLY B  28 " (cutoff:3.500A)
      removed outlier: 6.819A  pdb=" N   LEU B  30 " --> pdb=" O   ILE B  77 " (cutoff:3.500A)
      removed outlier: 7.017A  pdb=" N   GLY B  74 " --> pdb=" O   VAL B 103 " (cutoff:3.500A)
      removed outlier: 7.738A  pdb=" N   GLY B 105 " --> pdb=" O   GLY B  74 " (cutoff:3.500A)
      removed outlier: 6.204A  pdb=" N   VAL B  76 " --> pdb=" O   GLY B 105 " (cutoff:3.500A)
      removed outlier: 7.437A  pdb=" N   LYS B 107 " --> pdb=" O   VAL B  76 " (cutoff:3.500A)
      removed outlier: 6.827A  pdb=" N   LEU B  78 " --> pdb=" O   LYS B 107 " (cutoff:3.500A)
      removed outlier: 7.218A  pdb=" N   VAL B 104 " --> pdb=" O   ASP B 143 " (cutoff:3.500A)
      removed outlier: 5.642A  pdb=" N   ALA B 145 " --> pdb=" O   VAL B 104 " (cutoff:3.500A)
      removed outlier: 5.872A  pdb=" N   ILE B 106 " --> pdb=" O   ALA B 145 " (cutoff:3.500A)
      removed outlier: 5.806A  pdb=" N   TRP B 147 " --> pdb=" O   ILE B 106 " (cutoff:3.500A)
      removed outlier: 4.302A  pdb=" N   TRP B 147 " --> pdb=" O   ILE B 185 " (cutoff:3.500A)
      removed outlier: 3.907A  pdb=" N   GLU B 187 " --> pdb=" O   TRP B 147 " (cutoff:3.500A)
      removed outlier: 6.149A  pdb=" N   LEU B 228 " --> pdb=" O   THR B 268 " (cutoff:3.500A)
      removed outlier: 3.629A  pdb=" N   ALA B  31 " --> pdb=" O   TYR B 301 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'B' and resid 112 through 114
    Processing sheet with id=AA3, first strand: chain 'A' and resid 28 through 32
      removed outlier: 6.147A  pdb=" N   GLY A  28 " --> pdb=" O   GLY A  75 " (cutoff:3.500A)
      removed outlier: 7.910A  pdb=" N   ILE A  77 " --> pdb=" O   GLY A  28 " (cutoff:3.500A)
      removed outlier: 6.818A  pdb=" N   LEU A  30 " --> pdb=" O   ILE A  77 " (cutoff:3.500A)
      removed outlier: 7.017A  pdb=" N   GLY A  74 " --> pdb=" O   VAL A 103 " (cutoff:3.500A)
      removed outlier: 7.739A  pdb=" N   GLY A 105 " --> pdb=" O   GLY A  74 " (cutoff:3.500A)
      removed outlier: 6.204A  pdb=" N   VAL A  76 " --> pdb=" O   GLY A 105 " (cutoff:3.500A)
      removed outlier: 7.437A  pdb=" N   LYS A 107 " --> pdb=" O   VAL A  76 " (cutoff:3.500A)
      removed outlier: 6.827A  pdb=" N   LEU A  78 " --> pdb=" O   LYS A 107 " (cutoff:3.500A)
      removed outlier: 7.218A  pdb=" N   VAL A 104 " --> pdb=" O   ASP A 143 " (cutoff:3.500A)
      removed outlier: 5.642A  pdb=" N   ALA A 145 " --> pdb=" O   VAL A 104 " (cutoff:3.500A)
      removed outlier: 5.873A  pdb=" N   ILE A 106 " --> pdb=" O   ALA A 145 " (cutoff:3.500A)
      removed outlier: 5.806A  pdb=" N   TRP A 147 " --> pdb=" O   ILE A 106 " (cutoff:3.500A)
      removed outlier: 4.303A  pdb=" N   TRP A 147 " --> pdb=" O   ILE A 185 " (cutoff:3.500A)
      removed outlier: 3.906A  pdb=" N   GLU A 187 " --> pdb=" O   TRP A 147 " (cutoff:3.500A)
      removed outlier: 6.150A  pdb=" N   LEU A 228 " --> pdb=" O   THR A 268 " (cutoff:3.500A)
      removed outlier: 3.629A  pdb=" N   ALA A  31 " --> pdb=" O   TYR A 301 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 112 through 114
    Processing sheet with id=AA5, first strand: chain 'C' and resid 28 through 32
      removed outlier: 6.148A  pdb=" N   GLY C  28 " --> pdb=" O   GLY C  75 " (cutoff:3.500A)
      removed outlier: 7.910A  pdb=" N   ILE C  77 " --> pdb=" O   GLY C  28 " (cutoff:3.500A)
      removed outlier: 6.819A  pdb=" N   LEU C  30 " --> pdb=" O   ILE C  77 " (cutoff:3.500A)
      removed outlier: 7.018A  pdb=" N   GLY C  74 " --> pdb=" O   VAL C 103 " (cutoff:3.500A)
      removed outlier: 7.738A  pdb=" N   GLY C 105 " --> pdb=" O   GLY C  74 " (cutoff:3.500A)
      removed outlier: 6.204A  pdb=" N   VAL C  76 " --> pdb=" O   GLY C 105 " (cutoff:3.500A)
      removed outlier: 7.438A  pdb=" N   LYS C 107 " --> pdb=" O   VAL C  76 " (cutoff:3.500A)
      removed outlier: 6.827A  pdb=" N   LEU C  78 " --> pdb=" O   LYS C 107 " (cutoff:3.500A)
      removed outlier: 7.218A  pdb=" N   VAL C 104 " --> pdb=" O   ASP C 143 " (cutoff:3.500A)
      removed outlier: 5.642A  pdb=" N   ALA C 145 " --> pdb=" O   VAL C 104 " (cutoff:3.500A)
      removed outlier: 5.872A  pdb=" N   ILE C 106 " --> pdb=" O   ALA C 145 " (cutoff:3.500A)
      removed outlier: 5.806A  pdb=" N   TRP C 147 " --> pdb=" O   ILE C 106 " (cutoff:3.500A)
      removed outlier: 4.302A  pdb=" N   TRP C 147 " --> pdb=" O   ILE C 185 " (cutoff:3.500A)
      removed outlier: 3.906A  pdb=" N   GLU C 187 " --> pdb=" O   TRP C 147 " (cutoff:3.500A)
      removed outlier: 6.150A  pdb=" N   LEU C 228 " --> pdb=" O   THR C 268 " (cutoff:3.500A)
      removed outlier: 3.629A  pdb=" N   ALA C  31 " --> pdb=" O   TYR C 301 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'C' and resid 112 through 114
    Processing sheet with id=AA7, first strand: chain 'D' and resid 28 through 32
      removed outlier: 6.148A  pdb=" N   GLY D  28 " --> pdb=" O   GLY D  75 " (cutoff:3.500A)
      removed outlier: 7.910A  pdb=" N   ILE D  77 " --> pdb=" O   GLY D  28 " (cutoff:3.500A)
      removed outlier: 6.818A  pdb=" N   LEU D  30 " --> pdb=" O   ILE D  77 " (cutoff:3.500A)
      removed outlier: 7.018A  pdb=" N   GLY D  74 " --> pdb=" O   VAL D 103 " (cutoff:3.500A)
      removed outlier: 7.738A  pdb=" N   GLY D 105 " --> pdb=" O   GLY D  74 " (cutoff:3.500A)
      removed outlier: 6.205A  pdb=" N   VAL D  76 " --> pdb=" O   GLY D 105 " (cutoff:3.500A)
      removed outlier: 7.437A  pdb=" N   LYS D 107 " --> pdb=" O   VAL D  76 " (cutoff:3.500A)
      removed outlier: 6.827A  pdb=" N   LEU D  78 " --> pdb=" O   LYS D 107 " (cutoff:3.500A)
      removed outlier: 7.218A  pdb=" N   VAL D 104 " --> pdb=" O   ASP D 143 " (cutoff:3.500A)
      removed outlier: 5.642A  pdb=" N   ALA D 145 " --> pdb=" O   VAL D 104 " (cutoff:3.500A)
      removed outlier: 5.872A  pdb=" N   ILE D 106 " --> pdb=" O   ALA D 145 " (cutoff:3.500A)
      removed outlier: 5.806A  pdb=" N   TRP D 147 " --> pdb=" O   ILE D 106 " (cutoff:3.500A)
      removed outlier: 4.302A  pdb=" N   TRP D 147 " --> pdb=" O   ILE D 185 " (cutoff:3.500A)
      removed outlier: 3.907A  pdb=" N   GLU D 187 " --> pdb=" O   TRP D 147 " (cutoff:3.500A)
      removed outlier: 6.150A  pdb=" N   LEU D 228 " --> pdb=" O   THR D 268 " (cutoff:3.500A)
      removed outlier: 3.629A  pdb=" N   ALA D  31 " --> pdb=" O   TYR D 301 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'D' and resid 112 through 114

    564 hydrogen bonds defined for protein.
    1632 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: 1.72

  Time building geometry restraints manager: 1.23 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: 3395
        1.34 -     1.45: 1572
        1.45 -     1.57: 5645
        1.57 -     1.69: 4
        1.69 -     1.81: 56
  Bond restraints: 10672
  Sorted by residual:
  bond pdb=" C   HIS A 220 "
       pdb=" N   ILE A 221 "
    ideal  model  delta    sigma   weight residual
    1.334  1.305  0.029 1.29e-02 6.01e+03 5.11e+00
  bond pdb=" C   HIS C 220 "
       pdb=" N   ILE C 221 "
    ideal  model  delta    sigma   weight residual
    1.334  1.305  0.029 1.29e-02 6.01e+03 4.88e+00
  bond pdb=" C   HIS B 220 "
       pdb=" N   ILE B 221 "
    ideal  model  delta    sigma   weight residual
    1.334  1.306  0.028 1.29e-02 6.01e+03 4.79e+00
  bond pdb=" C   HIS D 220 "
       pdb=" N   ILE D 221 "
    ideal  model  delta    sigma   weight residual
    1.334  1.306  0.028 1.29e-02 6.01e+03 4.67e+00
  bond pdb=" CB  GLU B  52 "
       pdb=" CG  GLU B  52 "
    ideal  model  delta    sigma   weight residual
    1.520  1.580 -0.060 3.00e-02 1.11e+03 4.05e+00
  ... (remaining 10667 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     3.58: 14241
        3.58 -     7.16: 191
        7.16 -    10.74: 20
       10.74 -    14.32: 4
       14.32 -    17.90: 8
  Bond angle restraints: 14464
  Sorted by residual:
  angle pdb=" CA  LEU A 320 "
        pdb=" CB  LEU A 320 "
        pdb=" CG  LEU A 320 "
      ideal   model   delta    sigma   weight residual
     116.30  134.20  -17.90 3.50e+00 8.16e-02 2.62e+01
  angle pdb=" CA  LEU B 320 "
        pdb=" CB  LEU B 320 "
        pdb=" CG  LEU B 320 "
      ideal   model   delta    sigma   weight residual
     116.30  134.20  -17.90 3.50e+00 8.16e-02 2.62e+01
  angle pdb=" CA  LEU C 320 "
        pdb=" CB  LEU C 320 "
        pdb=" CG  LEU C 320 "
      ideal   model   delta    sigma   weight residual
     116.30  134.19  -17.89 3.50e+00 8.16e-02 2.61e+01
  angle pdb=" CA  LEU D 320 "
        pdb=" CB  LEU D 320 "
        pdb=" CG  LEU D 320 "
      ideal   model   delta    sigma   weight residual
     116.30  134.18  -17.88 3.50e+00 8.16e-02 2.61e+01
  angle pdb=" CA  LEU A  78 "
        pdb=" CB  LEU A  78 "
        pdb=" CG  LEU A  78 "
      ideal   model   delta    sigma   weight residual
     116.30  132.68  -16.38 3.50e+00 8.16e-02 2.19e+01
  ... (remaining 14459 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.34: 5843
       17.34 -    34.68: 485
       34.68 -    52.03: 112
       52.03 -    69.37: 48
       69.37 -    86.71: 16
  Dihedral angle restraints: 6504
    sinusoidal: 2572
      harmonic: 3932
  Sorted by residual:
  dihedral pdb=" CA  ASN A 319 "
           pdb=" C   ASN A 319 "
           pdb=" N   LEU A 320 "
           pdb=" CA  LEU A 320 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -150.93  -29.07     0      5.00e+00 4.00e-02 3.38e+01
  dihedral pdb=" CA  ASN B 319 "
           pdb=" C   ASN B 319 "
           pdb=" N   LEU B 320 "
           pdb=" CA  LEU B 320 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -150.94  -29.06     0      5.00e+00 4.00e-02 3.38e+01
  dihedral pdb=" CA  ASN D 319 "
           pdb=" C   ASN D 319 "
           pdb=" N   LEU D 320 "
           pdb=" CA  LEU D 320 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -150.94  -29.06     0      5.00e+00 4.00e-02 3.38e+01
  ... (remaining 6501 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.080: 1372
       0.080 -    0.159: 223
       0.159 -    0.239: 35
       0.239 -    0.318: 10
       0.318 -    0.398: 4
  Chirality restraints: 1644
  Sorted by residual:
  chirality pdb=" CB  THR C 205 "
            pdb=" CA  THR C 205 "
            pdb=" OG1 THR C 205 "
            pdb=" CG2 THR C 205 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.55    2.15    0.40 2.00e-01 2.50e+01 3.96e+00
  chirality pdb=" CB  THR D 205 "
            pdb=" CA  THR D 205 "
            pdb=" OG1 THR D 205 "
            pdb=" CG2 THR D 205 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.55    2.15    0.40 2.00e-01 2.50e+01 3.94e+00
  chirality pdb=" CB  THR B 205 "
            pdb=" CA  THR B 205 "
            pdb=" OG1 THR B 205 "
            pdb=" CG2 THR B 205 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.55    2.16    0.40 2.00e-01 2.50e+01 3.92e+00
  ... (remaining 1641 not shown)

  Planarity restraints: 1880
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  LYS B 329 "    0.016 2.00e-02 2.50e+03   3.14e-02 9.84e+00
        pdb=" C   LYS B 329 "   -0.054 2.00e-02 2.50e+03
        pdb=" O   LYS B 329 "    0.021 2.00e-02 2.50e+03
        pdb=" N   ARG B 330 "    0.018 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  LYS C 329 "    0.016 2.00e-02 2.50e+03   3.14e-02 9.83e+00
        pdb=" C   LYS C 329 "   -0.054 2.00e-02 2.50e+03
        pdb=" O   LYS C 329 "    0.021 2.00e-02 2.50e+03
        pdb=" N   ARG C 330 "    0.018 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  LYS D 329 "   -0.016 2.00e-02 2.50e+03   3.13e-02 9.80e+00
        pdb=" C   LYS D 329 "    0.054 2.00e-02 2.50e+03
        pdb=" O   LYS D 329 "   -0.020 2.00e-02 2.50e+03
        pdb=" N   ARG D 330 "   -0.018 2.00e-02 2.50e+03
  ... (remaining 1877 not shown)

  Histogram of nonbonded interaction distances:
        2.25 -     2.78: 2647
        2.78 -     3.31: 10217
        3.31 -     3.84: 18354
        3.84 -     4.37: 20655
        4.37 -     4.90: 34745
  Nonbonded interactions: 86618
  Sorted by model distance:
  nonbonded pdb=" O   PHE B 269 "
            pdb=" OG  SER B 300 "
     model   vdw
     2.254 3.040
  nonbonded pdb=" O   PHE D 269 "
            pdb=" OG  SER D 300 "
     model   vdw
     2.255 3.040
  nonbonded pdb=" O   PHE C 269 "
            pdb=" OG  SER C 300 "
     model   vdw
     2.255 3.040
  nonbonded pdb=" O   PHE A 269 "
            pdb=" OG  SER A 300 "
     model   vdw
     2.255 3.040
  nonbonded pdb=" O   GLN A  60 "
            pdb=" OG1 THR A  64 "
     model   vdw
     2.272 3.040
  ... (remaining 86613 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: 0.03
Found NCS groups:
ncs_group {
  reference = chain 'B'
  selection = chain 'A'
  selection = chain 'C'
  selection = chain 'D'
}

Set up NCS constraints
  Number of NCS constrained groups: 1
  pdb_interpretation.ncs_group {
  reference = chain 'B'
  selection = chain 'A'
  selection = chain 'C'
  selection = chain 'D'
}
Set refine NCS operators
  NCS operators will be refined.
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             1.770
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.270
  Check model and map are aligned:         0.040
  Set scattering table:                    0.030
  Process input model:                     10.470
  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:             0.000
  Load rotamer database and sin/cos tables:0.990
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   13.680
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7840
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      :  0.007   0.065  10672  Z= 0.348
  Angle     :  1.189  17.902  14464  Z= 0.639
  Chirality :  0.066   0.398   1644
  Planarity :  0.008   0.048   1880
  Dihedral  : 15.276  86.709   3984
  Min Nonbonded Distance : 2.254

Molprobity Statistics.
  All-atom Clashscore : 9.21
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.52 %
    Favored  : 96.48 %
  Rotamer:
    Outliers :  3.96 %
    Allowed  : 10.79 %
    Favored  : 85.25 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.56 %
    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 are not related in a simple way.
  whole: -1.98 (0.19), residues: 1364
  helix: -0.95 (0.16), residues: 652
  sheet: -2.05 (0.33), residues: 196
  loop : -1.22 (0.24), residues: 516

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.001   ARG D  42 
 TYR   0.021   0.004   TYR B  58 
 PHE   0.013   0.003   PHE C  93 
 TRP   0.015   0.003   TRP A 295 
 HIS   0.007   0.002   HIS B 219 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00733 /  0.35 (10672)
  covalent geometry    : angle       1.18906 /  0.64 (14464)
  hydrogen bonds       : bond        0.18368 / 12.68 (  564)
  hydrogen bonds       : angle       7.27086 /  5.10 ( 1632)

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

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

  2728 Ramachandran restraints generated.
    1364 Oldfield, 0 Emsley, 1364 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2728 Ramachandran restraints generated.
    1364 Oldfield, 0 Emsley, 1364 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Update NCS operators
********************
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  163 residues out of total 278 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 152
  time to evaluate  : 0.103 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: B    7 LEU cc_start: 0.9205 (mt) cc_final: 0.8958 (mt)
REVERT: B   11 GLN cc_start: 0.9279 (mt0) cc_final: 0.9078 (mt0)
REVERT: B   12 LYS cc_start: 0.8899 (mttt) cc_final: 0.8450 (mmtp)
REVERT: B   61 LEU cc_start: 0.9116 (mt) cc_final: 0.8858 (mt)
REVERT: B   81 GLU cc_start: 0.9142 (OUTLIER) cc_final: 0.8747 (tm-30)
REVERT: B  104 VAL cc_start: 0.8517 (t) cc_final: 0.8260 (t)
REVERT: B  122 THR cc_start: 0.7989 (t) cc_final: 0.7603 (t)
REVERT: B  144 PHE cc_start: 0.8330 (p90) cc_final: 0.7925 (p90)
REVERT: B  149 CYS cc_start: 0.8554 (p) cc_final: 0.7978 (t)
REVERT: B  152 LYS cc_start: 0.8379 (pttp) cc_final: 0.8027 (pttp)
REVERT: B  178 GLN cc_start: 0.8979 (mt0) cc_final: 0.8572 (mt0)
REVERT: B  191 LEU cc_start: 0.8986 (OUTLIER) cc_final: 0.8774 (tp)
REVERT: B  199 LYS cc_start: 0.9345 (mtmm) cc_final: 0.8875 (mmmt)
REVERT: B  241 GLN cc_start: 0.8287 (mp10) cc_final: 0.8083 (mp10)
REVERT: B  247 GLU cc_start: 0.9312 (mt-10) cc_final: 0.8765 (mt-10)
REVERT: B  248 ILE cc_start: 0.9122 (mt) cc_final: 0.8826 (tt)
REVERT: B  254 THR cc_start: 0.8856 (p) cc_final: 0.8626 (t)
REVERT: B  276 GLU cc_start: 0.8821 (OUTLIER) cc_final: 0.8302 (mt-10)
REVERT: B  284 ASN cc_start: 0.8222 (t0) cc_final: 0.7351 (t0)
REVERT: B  305 LEU cc_start: 0.9474 (tp) cc_final: 0.9082 (tp)
REVERT: B  313 TRP cc_start: 0.7668 (t60) cc_final: 0.6634 (t60)
  outliers start: 11
  outliers final: 3
  residues processed: 157
  average time/residue: 0.0582
  time to fit residues: 10.7144
Evaluate side-chains
  118 residues out of total 278 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 112
  time to evaluate  : 0.071 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 136
   random chunks:
   chunk 98 optimal weight:    3.9990
   chunk 107 optimal weight:    2.9990
   chunk 10 optimal weight:    6.9990
   chunk 66 optimal weight:    8.9990
   chunk 130 optimal weight:    0.0980
   chunk 124 optimal weight:    0.9990
   chunk 103 optimal weight:    6.9990
   chunk 77 optimal weight:    3.9990
   chunk 122 optimal weight:    2.9990
   chunk 91 optimal weight:    0.0060
   chunk 55 optimal weight:    3.9990
   overall best weight:    1.4202
-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
B 119 ASN
B 156 HIS
B 168 ASN
B 245 HIS
B 284 ASN
B 324 GLN
B 334 ASN
B 339 GLN

Total number of N/Q/H flips: 8

-------------------------------------------------------------------------------
Update NCS operators
********************
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3229 r_free = 0.3229 target = 0.098797 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.2906 r_free = 0.2906 target = 0.078390 restraints weight = 5723.432|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.2961 r_free = 0.2961 target = 0.081698 restraints weight = 3531.016|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3001 r_free = 0.3001 target = 0.084140 restraints weight = 2405.725|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.3031 r_free = 0.3031 target = 0.085983 restraints weight = 1758.106|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.3053 r_free = 0.3053 target = 0.087371 restraints weight = 1353.260|
|-----------------------------------------------------------------------------|
r_work (final): 0.3045
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7822
moved from start:          0.3285

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032  10672  Z= 0.158
  Angle     :  0.670   7.572  14464  Z= 0.342
  Chirality :  0.044   0.136   1644
  Planarity :  0.005   0.047   1880
  Dihedral  :  5.109  17.408   1472
  Min Nonbonded Distance : 2.608

Molprobity Statistics.
  All-atom Clashscore : 12.82
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.64 %
    Favored  : 97.36 %
  Rotamer:
    Outliers :  0.72 %
    Allowed  :  3.96 %
    Favored  : 95.32 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.56 %
    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 are not related in a simple way.
  whole: -0.06 (0.22), residues: 1364
  helix:  0.92 (0.19), residues: 664
  sheet: -1.56 (0.35), residues: 200
  loop : -0.54 (0.27), residues: 500

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG C  42 
 TYR   0.018   0.002   TYR D  58 
 PHE   0.019   0.003   PHE D  93 
 TRP   0.011   0.002   TRP A 295 
 HIS   0.009   0.001   HIS B 219 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00348 /  0.16 (10672)
  covalent geometry    : angle       0.67028 /  0.34 (14464)
  hydrogen bonds       : bond        0.04189 /  2.88 (  564)
  hydrogen bonds       : angle       4.80873 /  3.38 ( 1632)

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

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

  2728 Ramachandran restraints generated.
    1364 Oldfield, 0 Emsley, 1364 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2728 Ramachandran restraints generated.
    1364 Oldfield, 0 Emsley, 1364 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Update NCS operators
********************
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  142 residues out of total 278 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 140
  time to evaluate  : 0.104 
Fit side-chains
   revert: symmetry clash
REVERT: A    7 LEU cc_start: 0.8935 (mt) cc_final: 0.8048 (mt)
REVERT: A   11 GLN cc_start: 0.9553 (mt0) cc_final: 0.9349 (mt0)
REVERT: A   12 LYS cc_start: 0.9235 (mttt) cc_final: 0.8848 (mmtp)
REVERT: A   61 LEU cc_start: 0.8753 (OUTLIER) cc_final: 0.8256 (mp)
REVERT: A  104 VAL cc_start: 0.8757 (t) cc_final: 0.8475 (t)
REVERT: A  115 LEU cc_start: 0.8285 (mm) cc_final: 0.8067 (mm)
REVERT: A  178 GLN cc_start: 0.9048 (mt0) cc_final: 0.8760 (mt0)
REVERT: A  199 LYS cc_start: 0.9232 (mtmm) cc_final: 0.8992 (mmmt)
REVERT: A  202 GLN cc_start: 0.9049 (pp30) cc_final: 0.8718 (pp30)
REVERT: A  229 LYS cc_start: 0.8154 (tttm) cc_final: 0.7650 (tptp)
REVERT: A  245 HIS cc_start: 0.7990 (m90) cc_final: 0.7482 (p-80)
REVERT: A  247 GLU cc_start: 0.9151 (mt-10) cc_final: 0.8677 (mt-10)
REVERT: A  248 ILE cc_start: 0.9145 (mt) cc_final: 0.8818 (tt)
REVERT: A  282 ASN cc_start: 0.9287 (m-40) cc_final: 0.9024 (m-40)
REVERT: A  284 ASN cc_start: 0.8198 (t0) cc_final: 0.7460 (m110)
REVERT: A  291 LEU cc_start: 0.7935 (mm) cc_final: 0.7243 (tp)
REVERT: A  292 LEU cc_start: 0.8540 (mm) cc_final: 0.8328 (mm)
REVERT: A  305 LEU cc_start: 0.9294 (tp) cc_final: 0.8940 (tp)
REVERT: A  313 TRP cc_start: 0.7984 (t60) cc_final: 0.6777 (t60)
REVERT: A  332 LEU cc_start: 0.8552 (tp) cc_final: 0.8342 (pp)
  outliers start: 2
  outliers final: 0
  residues processed: 141
  average time/residue: 0.0606
  time to fit residues: 10.1102
Evaluate side-chains
  101 residues out of total 278 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 100
  time to evaluate  : 0.091 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 136
   random chunks:
   chunk 86 optimal weight:    2.9990
   chunk 131 optimal weight:    0.0010
   chunk 3 optimal weight:    8.9990
   chunk 41 optimal weight:   10.0000
   chunk 126 optimal weight:    3.9990
   chunk 5 optimal weight:    3.9990
   chunk 66 optimal weight:    6.9990
   chunk 84 optimal weight:    3.9990
   chunk 35 optimal weight:    5.9990
   chunk 88 optimal weight:    0.9980
   chunk 25 optimal weight:    1.9990
   overall best weight:    1.9992
-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A  60 GLN
A 119 ASN
A 219 HIS
A 237 HIS
A 284 ASN
A 324 GLN
A 334 ASN

Total number of N/Q/H flips: 7

-------------------------------------------------------------------------------
Update NCS operators
********************
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3284 r_free = 0.3284 target = 0.101506 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.2946 r_free = 0.2946 target = 0.079301 restraints weight = 5753.312|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3003 r_free = 0.3003 target = 0.082637 restraints weight = 3721.506|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3045 r_free = 0.3045 target = 0.085199 restraints weight = 2613.760|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 27)----------------|
| r_work = 0.3075 r_free = 0.3075 target = 0.087065 restraints weight = 1948.628|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 38)----------------|
| r_work = 0.3098 r_free = 0.3098 target = 0.088600 restraints weight = 1528.610|
|-----------------------------------------------------------------------------|
r_work (final): 0.3088
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7815
moved from start:          0.4468

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.052  10672  Z= 0.172
  Angle     :  0.672   8.250  14464  Z= 0.339
  Chirality :  0.043   0.129   1644
  Planarity :  0.007   0.105   1880
  Dihedral  :  5.606  29.215   1472
  Min Nonbonded Distance : 2.448

Molprobity Statistics.
  All-atom Clashscore : 17.00
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.81 %
    Favored  : 96.19 %
  Rotamer:
    Outliers :  0.36 %
    Allowed  :  5.76 %
    Favored  : 93.88 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.56 %
    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 are not related in a simple way.
  whole:  0.60 (0.23), residues: 1364
  helix:  1.45 (0.19), residues: 700
  sheet: -1.26 (0.36), residues: 200
  loop : -0.32 (0.29), residues: 464

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.022   0.001   ARG D 257 
 TYR   0.013   0.002   TYR A 203 
 PHE   0.009   0.001   PHE C 144 
 TRP   0.018   0.002   TRP D 295 
 HIS   0.004   0.001   HIS B 237 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00387 /  0.17 (10672)
  covalent geometry    : angle       0.67159 /  0.34 (14464)
  hydrogen bonds       : bond        0.03861 /  2.63 (  564)
  hydrogen bonds       : angle       4.70306 /  3.33 ( 1632)

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

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

  2728 Ramachandran restraints generated.
    1364 Oldfield, 0 Emsley, 1364 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2728 Ramachandran restraints generated.
    1364 Oldfield, 0 Emsley, 1364 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Update NCS operators
********************
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  122 residues out of total 278 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 121
  time to evaluate  : 0.096 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: D    7 LEU cc_start: 0.8894 (mt) cc_final: 0.8686 (mt)
REVERT: D   11 GLN cc_start: 0.9522 (mt0) cc_final: 0.9287 (mt0)
REVERT: D   12 LYS cc_start: 0.9152 (mttt) cc_final: 0.8615 (mmtp)
REVERT: D   61 LEU cc_start: 0.9018 (mt) cc_final: 0.8715 (mt)
REVERT: D   80 HIS cc_start: 0.8708 (t-170) cc_final: 0.8401 (t70)
REVERT: D  138 LYS cc_start: 0.8386 (tptt) cc_final: 0.7923 (tttt)
REVERT: D  152 LYS cc_start: 0.8211 (ptpp) cc_final: 0.7953 (pttp)
REVERT: D  245 HIS cc_start: 0.8524 (m90) cc_final: 0.8035 (p-80)
REVERT: D  247 GLU cc_start: 0.9177 (mt-10) cc_final: 0.8647 (mt-10)
REVERT: D  248 ILE cc_start: 0.9500 (mt) cc_final: 0.9263 (tt)
REVERT: D  276 GLU cc_start: 0.8098 (pm20) cc_final: 0.7565 (pm20)
REVERT: D  282 ASN cc_start: 0.9146 (m-40) cc_final: 0.8718 (m-40)
REVERT: D  283 LEU cc_start: 0.9214 (tp) cc_final: 0.8963 (tp)
REVERT: D  291 LEU cc_start: 0.8082 (mm) cc_final: 0.7734 (tp)
REVERT: D  332 LEU cc_start: 0.8463 (tp) cc_final: 0.8177 (tp)
  outliers start: 1
  outliers final: 0
  residues processed: 121
  average time/residue: 0.0604
  time to fit residues: 8.5894
Evaluate side-chains
  89 residues out of total 278 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 89
  time to evaluate  : 0.082 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 136
   random chunks:
   chunk 77 optimal weight:    0.8980
   chunk 7 optimal weight:    7.9990
   chunk 81 optimal weight:    0.9990
   chunk 29 optimal weight:    0.9980
   chunk 33 optimal weight:    6.9990
   chunk 135 optimal weight:    5.9990
   chunk 46 optimal weight:    4.9990
   chunk 106 optimal weight:    0.4980
   chunk 65 optimal weight:    8.9990
   chunk 3 optimal weight:   10.0000
   chunk 93 optimal weight:    3.9990
   overall best weight:    1.4784
-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
D  44 GLN
D  60 GLN
D  80 HIS
D 119 ASN
D 334 ASN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
Update NCS operators
********************
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3331 r_free = 0.3331 target = 0.104815 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.2995 r_free = 0.2995 target = 0.082502 restraints weight = 5689.929|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3049 r_free = 0.3049 target = 0.085961 restraints weight = 3733.945|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.3091 r_free = 0.3091 target = 0.088675 restraints weight = 2641.896|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 32)----------------|
| r_work = 0.3123 r_free = 0.3123 target = 0.090831 restraints weight = 1966.902|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3146 r_free = 0.3146 target = 0.092348 restraints weight = 1520.731|
|-----------------------------------------------------------------------------|
r_work (final): 0.3131
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7766
moved from start:          0.5044

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033  10672  Z= 0.139
  Angle     :  0.636   7.687  14464  Z= 0.322
  Chirality :  0.043   0.148   1644
  Planarity :  0.005   0.056   1880
  Dihedral  :  5.250  28.220   1472
  Min Nonbonded Distance : 2.506

Molprobity Statistics.
  All-atom Clashscore : 15.48
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.81 %
    Favored  : 96.19 %
  Rotamer:
    Outliers :  0.36 %
    Allowed  :  4.68 %
    Favored  : 94.96 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.56 %
    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 are not related in a simple way.
  whole:  0.77 (0.23), residues: 1364
  helix:  1.71 (0.19), residues: 700
  sheet: -1.27 (0.34), residues: 200
  loop : -0.42 (0.29), residues: 464

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG B 257 
 TYR   0.013   0.001   TYR D 203 
 PHE   0.010   0.002   PHE A  93 
 TRP   0.020   0.002   TRP C 295 
 HIS   0.003   0.001   HIS B 219 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00320 /  0.14 (10672)
  covalent geometry    : angle       0.63647 /  0.32 (14464)
  hydrogen bonds       : bond        0.03517 /  2.42 (  564)
  hydrogen bonds       : angle       4.57193 /  3.24 ( 1632)

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

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

  2728 Ramachandran restraints generated.
    1364 Oldfield, 0 Emsley, 1364 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2728 Ramachandran restraints generated.
    1364 Oldfield, 0 Emsley, 1364 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Update NCS operators
********************
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  127 residues out of total 278 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 126
  time to evaluate  : 0.109 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: D    7 LEU cc_start: 0.8847 (mt) cc_final: 0.8624 (mt)
REVERT: D   10 GLU cc_start: 0.9240 (pm20) cc_final: 0.8838 (mp0)
REVERT: D   11 GLN cc_start: 0.9520 (mt0) cc_final: 0.9253 (mt0)
REVERT: D   12 LYS cc_start: 0.9085 (mttt) cc_final: 0.8607 (mmtp)
REVERT: D   61 LEU cc_start: 0.8987 (mt) cc_final: 0.8647 (mt)
REVERT: D  138 LYS cc_start: 0.8398 (tptt) cc_final: 0.7911 (ttmt)
REVERT: D  140 ASP cc_start: 0.8939 (m-30) cc_final: 0.8686 (m-30)
REVERT: D  152 LYS cc_start: 0.8161 (ptpp) cc_final: 0.7790 (pttm)
REVERT: D  195 ASP cc_start: 0.8786 (p0) cc_final: 0.8237 (t0)
REVERT: D  245 HIS cc_start: 0.8640 (m90) cc_final: 0.8207 (p-80)
REVERT: D  246 GLU cc_start: 0.9584 (mp0) cc_final: 0.9285 (pm20)
REVERT: D  276 GLU cc_start: 0.8183 (pm20) cc_final: 0.7674 (pm20)
REVERT: D  282 ASN cc_start: 0.9102 (m-40) cc_final: 0.8742 (m-40)
REVERT: D  291 LEU cc_start: 0.8146 (mm) cc_final: 0.7846 (tp)
REVERT: D  293 LYS cc_start: 0.8753 (pptt) cc_final: 0.8447 (pptt)
REVERT: D  313 TRP cc_start: 0.8020 (t60) cc_final: 0.7387 (t60)
REVERT: D  332 LEU cc_start: 0.8453 (tp) cc_final: 0.8164 (tp)
  outliers start: 1
  outliers final: 1
  residues processed: 127
  average time/residue: 0.0553
  time to fit residues: 8.4067
Evaluate side-chains
  93 residues out of total 278 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 92
  time to evaluate  : 0.100 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 136
   random chunks:
   chunk 104 optimal weight:    3.9990
   chunk 32 optimal weight:    6.9990
   chunk 33 optimal weight:    6.9990
   chunk 99 optimal weight:    5.9990
   chunk 94 optimal weight:    6.9990
   chunk 135 optimal weight:    6.9990
   chunk 50 optimal weight:    4.9990
   chunk 52 optimal weight:    0.0970
   chunk 91 optimal weight:    1.9990
   chunk 57 optimal weight:    4.9990
   chunk 127 optimal weight:    3.9990
   overall best weight:    3.0186
-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
Update NCS operators
********************
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3285 r_free = 0.3285 target = 0.100734 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.2938 r_free = 0.2938 target = 0.079339 restraints weight = 5880.233|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 19)----------------|
| r_work = 0.2994 r_free = 0.2994 target = 0.082599 restraints weight = 3878.161|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 22)----------------|
| r_work = 0.3037 r_free = 0.3037 target = 0.085107 restraints weight = 2766.125|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 31)----------------|
| r_work = 0.3067 r_free = 0.3067 target = 0.086968 restraints weight = 2080.673|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.3091 r_free = 0.3091 target = 0.088432 restraints weight = 1639.446|
|-----------------------------------------------------------------------------|
r_work (final): 0.3094
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7896
moved from start:          0.5467

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.077  10672  Z= 0.202
  Angle     :  0.676   6.358  14464  Z= 0.347
  Chirality :  0.043   0.162   1644
  Planarity :  0.006   0.058   1880
  Dihedral  :  5.355  26.574   1472
  Min Nonbonded Distance : 2.547

Molprobity Statistics.
  All-atom Clashscore : 18.14
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.99 %
    Favored  : 95.01 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  3.60 %
    Favored  : 96.40 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.56 %
    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 are not related in a simple way.
  whole:  0.58 (0.23), residues: 1364
  helix:  1.51 (0.19), residues: 696
  sheet: -0.97 (0.35), residues: 192
  loop : -0.64 (0.29), residues: 476

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.013   0.001   ARG B 257 
 TYR   0.010   0.002   TYR B 203 
 PHE   0.007   0.002   PHE A 144 
 TRP   0.017   0.002   TRP C 295 
 HIS   0.005   0.001   HIS D 196 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00456 /  0.20 (10672)
  covalent geometry    : angle       0.67642 /  0.35 (14464)
  hydrogen bonds       : bond        0.03896 /  2.66 (  564)
  hydrogen bonds       : angle       4.66133 /  3.29 ( 1632)

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

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

  2728 Ramachandran restraints generated.
    1364 Oldfield, 0 Emsley, 1364 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2728 Ramachandran restraints generated.
    1364 Oldfield, 0 Emsley, 1364 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Update NCS operators
********************
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  118 residues out of total 278 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 118
  time to evaluate  : 0.080 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: D   11 GLN cc_start: 0.9550 (mt0) cc_final: 0.9323 (mt0)
REVERT: D   12 LYS cc_start: 0.9172 (mttt) cc_final: 0.8711 (mmtp)
REVERT: D  138 LYS cc_start: 0.8517 (tptt) cc_final: 0.7952 (ttmt)
REVERT: D  140 ASP cc_start: 0.8996 (m-30) cc_final: 0.8781 (m-30)
REVERT: D  152 LYS cc_start: 0.8159 (ptpp) cc_final: 0.7722 (pttm)
REVERT: D  195 ASP cc_start: 0.8897 (p0) cc_final: 0.8201 (t0)
REVERT: D  246 GLU cc_start: 0.9548 (mp0) cc_final: 0.9198 (pm20)
REVERT: D  270 LEU cc_start: 0.8656 (mm) cc_final: 0.8444 (mm)
REVERT: D  276 GLU cc_start: 0.8337 (pm20) cc_final: 0.7959 (pm20)
REVERT: D  282 ASN cc_start: 0.9026 (m-40) cc_final: 0.8748 (m-40)
REVERT: D  291 LEU cc_start: 0.8204 (mm) cc_final: 0.7931 (tp)
REVERT: D  293 LYS cc_start: 0.8676 (pptt) cc_final: 0.8279 (pptt)
REVERT: D  325 GLU cc_start: 0.9167 (mm-30) cc_final: 0.8824 (tp30)
REVERT: D  332 LEU cc_start: 0.8375 (tp) cc_final: 0.8040 (tp)
  outliers start: 0
  outliers final: 0
  residues processed: 118
  average time/residue: 0.0593
  time to fit residues: 8.3348
Evaluate side-chains
  87 residues out of total 278 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 87
  time to evaluate  : 0.100 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 136
   random chunks:
   chunk 22 optimal weight:    2.9990
   chunk 89 optimal weight:    3.9990
   chunk 2 optimal weight:    0.3980
   chunk 123 optimal weight:    3.9990
   chunk 75 optimal weight:    1.9990
   chunk 99 optimal weight:    0.9980
   chunk 113 optimal weight:    0.3980
   chunk 126 optimal weight:    0.9980
   chunk 91 optimal weight:    0.0570
   chunk 122 optimal weight:    1.9990
   chunk 129 optimal weight:    0.0870
   overall best weight:    0.3876
-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
D  44 GLN
** D  60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
D 219 HIS
D 334 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
Update NCS operators
********************
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3392 r_free = 0.3392 target = 0.109676 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3074 r_free = 0.3074 target = 0.087312 restraints weight = 5443.262|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3132 r_free = 0.3132 target = 0.091155 restraints weight = 3448.457|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3177 r_free = 0.3177 target = 0.094010 restraints weight = 2375.906|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3208 r_free = 0.3208 target = 0.096099 restraints weight = 1741.782|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 35)----------------|
| r_work = 0.3232 r_free = 0.3232 target = 0.097783 restraints weight = 1345.610|
|-----------------------------------------------------------------------------|
r_work (final): 0.3224
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7701
moved from start:          0.5746

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.046  10672  Z= 0.126
  Angle     :  0.665   8.769  14464  Z= 0.323
  Chirality :  0.044   0.173   1644
  Planarity :  0.006   0.076   1880
  Dihedral  :  5.135  26.656   1472
  Min Nonbonded Distance : 2.472

Molprobity Statistics.
  All-atom Clashscore : 13.15
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.64 %
    Favored  : 97.36 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.16 %
    Favored  : 97.84 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.56 %
    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 are not related in a simple way.
  whole:  0.78 (0.23), residues: 1364
  helix:  1.62 (0.20), residues: 704
  sheet: -1.23 (0.34), residues: 172
  loop : -0.34 (0.29), residues: 488

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG D  42 
 TYR   0.008   0.001   TYR A 327 
 PHE   0.010   0.001   PHE D 144 
 TRP   0.010   0.002   TRP A 295 
 HIS   0.006   0.001   HIS D 219 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00280 /  0.13 (10672)
  covalent geometry    : angle       0.66526 /  0.32 (14464)
  hydrogen bonds       : bond        0.03267 /  2.25 (  564)
  hydrogen bonds       : angle       4.31751 /  3.04 ( 1632)

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

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

  2728 Ramachandran restraints generated.
    1364 Oldfield, 0 Emsley, 1364 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2728 Ramachandran restraints generated.
    1364 Oldfield, 0 Emsley, 1364 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Update NCS operators
********************
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  128 residues out of total 278 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 128
  time to evaluate  : 0.121 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: D   12 LYS cc_start: 0.9031 (mttt) cc_final: 0.8610 (mmtp)
REVERT: D   30 LEU cc_start: 0.8011 (tp) cc_final: 0.7808 (tp)
REVERT: D   61 LEU cc_start: 0.8857 (mt) cc_final: 0.8448 (mt)
REVERT: D  138 LYS cc_start: 0.8426 (tptt) cc_final: 0.7976 (ttmt)
REVERT: D  140 ASP cc_start: 0.8988 (m-30) cc_final: 0.8742 (m-30)
REVERT: D  152 LYS cc_start: 0.8036 (ptpp) cc_final: 0.7805 (pttm)
REVERT: D  195 ASP cc_start: 0.8856 (p0) cc_final: 0.8262 (t0)
REVERT: D  229 LYS cc_start: 0.7817 (tttp) cc_final: 0.7548 (tptm)
REVERT: D  276 GLU cc_start: 0.8261 (pm20) cc_final: 0.8043 (pm20)
REVERT: D  282 ASN cc_start: 0.9068 (m-40) cc_final: 0.8644 (m-40)
REVERT: D  283 LEU cc_start: 0.9287 (tp) cc_final: 0.9079 (tp)
REVERT: D  291 LEU cc_start: 0.8195 (mm) cc_final: 0.7967 (tp)
REVERT: D  293 LYS cc_start: 0.8631 (pptt) cc_final: 0.8296 (pptt)
REVERT: D  313 TRP cc_start: 0.8004 (t60) cc_final: 0.7110 (t60)
REVERT: D  325 GLU cc_start: 0.9182 (mm-30) cc_final: 0.8756 (tp30)
REVERT: D  332 LEU cc_start: 0.8531 (tp) cc_final: 0.8157 (pp)
  outliers start: 0
  outliers final: 0
  residues processed: 128
  average time/residue: 0.0554
  time to fit residues: 8.4624
Evaluate side-chains
  95 residues out of total 278 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 95
  time to evaluate  : 0.095 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 136
   random chunks:
   chunk 49 optimal weight:   10.0000
   chunk 7 optimal weight:    4.9990
   chunk 53 optimal weight:    6.9990
   chunk 69 optimal weight:    5.9990
   chunk 37 optimal weight:    7.9990
   chunk 26 optimal weight:    0.0570
   chunk 38 optimal weight:    2.9990
   chunk 90 optimal weight:    2.9990
   chunk 30 optimal weight:    3.9990
   chunk 2 optimal weight:    3.9990
   chunk 20 optimal weight:    0.9980
   overall best weight:    2.2104
-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
D  60 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Update NCS operators
********************
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3316 r_free = 0.3316 target = 0.103627 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.2963 r_free = 0.2963 target = 0.080849 restraints weight = 5611.408|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3018 r_free = 0.3018 target = 0.084260 restraints weight = 3682.192|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3060 r_free = 0.3060 target = 0.086865 restraints weight = 2620.899|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 36)----------------|
| r_work = 0.3094 r_free = 0.3094 target = 0.088868 restraints weight = 1977.576|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 24)----------------|
| r_work = 0.3119 r_free = 0.3119 target = 0.090380 restraints weight = 1559.792|
|-----------------------------------------------------------------------------|
r_work (final): 0.3107
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7820
moved from start:          0.5951

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.039  10672  Z= 0.164
  Angle     :  0.661   7.929  14464  Z= 0.332
  Chirality :  0.043   0.132   1644
  Planarity :  0.007   0.098   1880
  Dihedral  :  5.222  23.431   1472
  Min Nonbonded Distance : 2.567

Molprobity Statistics.
  All-atom Clashscore : 14.81
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.11 %
    Favored  : 95.89 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.44 %
    Favored  : 98.56 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.56 %
    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 are not related in a simple way.
  whole:  0.57 (0.23), residues: 1364
  helix:  1.47 (0.19), residues: 708
  sheet: -1.13 (0.32), residues: 192
  loop : -0.56 (0.29), residues: 464

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.001   ARG B 257 
 TYR   0.013   0.002   TYR A 213 
 PHE   0.019   0.002   PHE A 299 
 TRP   0.008   0.002   TRP A 295 
 HIS   0.004   0.001   HIS A  80 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00358 /  0.16 (10672)
  covalent geometry    : angle       0.66070 /  0.33 (14464)
  hydrogen bonds       : bond        0.03490 /  2.39 (  564)
  hydrogen bonds       : angle       4.59712 /  3.23 ( 1632)

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

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

  2728 Ramachandran restraints generated.
    1364 Oldfield, 0 Emsley, 1364 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2728 Ramachandran restraints generated.
    1364 Oldfield, 0 Emsley, 1364 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Update NCS operators
********************
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  124 residues out of total 278 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 124
  time to evaluate  : 0.100 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   12 LYS cc_start: 0.9151 (mttt) cc_final: 0.8745 (mmmm)
REVERT: B   61 LEU cc_start: 0.8861 (mt) cc_final: 0.8572 (mt)
REVERT: B  130 LEU cc_start: 0.8902 (mt) cc_final: 0.8698 (mt)
REVERT: B  138 LYS cc_start: 0.8441 (tptt) cc_final: 0.7868 (ttmt)
REVERT: B  140 ASP cc_start: 0.8772 (m-30) cc_final: 0.8496 (m-30)
REVERT: B  144 PHE cc_start: 0.8633 (p90) cc_final: 0.8420 (p90)
REVERT: B  152 LYS cc_start: 0.8075 (ptpp) cc_final: 0.7832 (pttm)
REVERT: B  178 GLN cc_start: 0.8703 (mt0) cc_final: 0.8495 (mt0)
REVERT: B  195 ASP cc_start: 0.8849 (p0) cc_final: 0.8202 (t0)
REVERT: B  229 LYS cc_start: 0.7961 (tttp) cc_final: 0.7689 (tptm)
REVERT: B  276 GLU cc_start: 0.8280 (pm20) cc_final: 0.7928 (pm20)
REVERT: B  282 ASN cc_start: 0.9038 (m-40) cc_final: 0.8651 (m-40)
REVERT: B  291 LEU cc_start: 0.8279 (mm) cc_final: 0.8046 (tp)
REVERT: B  293 LYS cc_start: 0.8738 (pptt) cc_final: 0.8362 (pptt)
REVERT: B  303 ARG cc_start: 0.8680 (ttm-80) cc_final: 0.8053 (mmp80)
REVERT: B  313 TRP cc_start: 0.8108 (t60) cc_final: 0.7418 (t60)
REVERT: B  325 GLU cc_start: 0.9143 (mm-30) cc_final: 0.8728 (tp30)
REVERT: B  332 LEU cc_start: 0.8434 (tp) cc_final: 0.8084 (pp)
  outliers start: 0
  outliers final: 0
  residues processed: 124
  average time/residue: 0.0535
  time to fit residues: 7.8943
Evaluate side-chains
  90 residues out of total 278 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 90
  time to evaluate  : 0.097 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 136
   random chunks:
   chunk 53 optimal weight:    8.9990
   chunk 33 optimal weight:    8.9990
   chunk 59 optimal weight:    2.9990
   chunk 15 optimal weight:   10.0000
   chunk 56 optimal weight:    0.5980
   chunk 97 optimal weight:    1.9990
   chunk 14 optimal weight:    0.0770
   chunk 67 optimal weight:    8.9990
   chunk 114 optimal weight:    6.9990
   chunk 123 optimal weight:    3.9990
   chunk 80 optimal weight:    6.9990
   overall best weight:    1.9344
-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
B  44 GLN
B  54 ASN
B  60 GLN
B 219 HIS

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
Update NCS operators
********************
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3319 r_free = 0.3319 target = 0.103940 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.2967 r_free = 0.2967 target = 0.080822 restraints weight = 5691.755|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3023 r_free = 0.3023 target = 0.084320 restraints weight = 3731.599|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3066 r_free = 0.3066 target = 0.087024 restraints weight = 2647.842|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 32)----------------|
| r_work = 0.3097 r_free = 0.3097 target = 0.089073 restraints weight = 1992.092|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3124 r_free = 0.3124 target = 0.090761 restraints weight = 1566.070|
|-----------------------------------------------------------------------------|
r_work (final): 0.3108
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7812
moved from start:          0.6078

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037  10672  Z= 0.148
  Angle     :  0.666   8.300  14464  Z= 0.334
  Chirality :  0.043   0.137   1644
  Planarity :  0.006   0.084   1880
  Dihedral  :  5.015  20.036   1472
  Min Nonbonded Distance : 2.429

Molprobity Statistics.
  All-atom Clashscore : 15.48
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.40 %
    Favored  : 95.60 %
  Rotamer:
    Outliers :  0.36 %
    Allowed  :  1.44 %
    Favored  : 98.20 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.56 %
    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 are not related in a simple way.
  whole:  0.77 (0.23), residues: 1364
  helix:  1.64 (0.20), residues: 704
  sheet: -1.38 (0.32), residues: 200
  loop : -0.23 (0.30), residues: 460

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG A  42 
 TYR   0.013   0.002   TYR A  58 
 PHE   0.019   0.002   PHE A  79 
 TRP   0.026   0.003   TRP C 295 
 HIS   0.010   0.001   HIS B 219 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00333 /  0.15 (10672)
  covalent geometry    : angle       0.66637 /  0.33 (14464)
  hydrogen bonds       : bond        0.03487 /  2.40 (  564)
  hydrogen bonds       : angle       4.48430 /  3.17 ( 1632)

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

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

  2728 Ramachandran restraints generated.
    1364 Oldfield, 0 Emsley, 1364 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2728 Ramachandran restraints generated.
    1364 Oldfield, 0 Emsley, 1364 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Update NCS operators
********************
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  119 residues out of total 278 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 118
  time to evaluate  : 0.063 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   12 LYS cc_start: 0.9129 (mttt) cc_final: 0.8730 (mmmm)
REVERT: B   61 LEU cc_start: 0.8825 (mt) cc_final: 0.8450 (mt)
REVERT: B  115 LEU cc_start: 0.8071 (mp) cc_final: 0.7842 (mp)
REVERT: B  140 ASP cc_start: 0.8785 (m-30) cc_final: 0.8506 (m-30)
REVERT: B  144 PHE cc_start: 0.8632 (p90) cc_final: 0.8300 (p90)
REVERT: B  152 LYS cc_start: 0.8077 (ptpp) cc_final: 0.7828 (pttm)
REVERT: B  185 ILE cc_start: 0.8509 (mp) cc_final: 0.8131 (tp)
REVERT: B  195 ASP cc_start: 0.8799 (p0) cc_final: 0.8168 (t0)
REVERT: B  237 HIS cc_start: 0.8301 (t70) cc_final: 0.7921 (t70)
REVERT: B  276 GLU cc_start: 0.8180 (pm20) cc_final: 0.7848 (pm20)
REVERT: B  282 ASN cc_start: 0.9066 (m-40) cc_final: 0.8707 (m-40)
REVERT: B  293 LYS cc_start: 0.8683 (pptt) cc_final: 0.8290 (pptt)
REVERT: B  313 TRP cc_start: 0.8064 (t60) cc_final: 0.7181 (t60)
REVERT: B  325 GLU cc_start: 0.9125 (mm-30) cc_final: 0.8513 (tp30)
REVERT: B  329 LYS cc_start: 0.8940 (mttp) cc_final: 0.8346 (mttm)
REVERT: B  332 LEU cc_start: 0.8504 (tp) cc_final: 0.8148 (pp)
  outliers start: 1
  outliers final: 1
  residues processed: 118
  average time/residue: 0.0547
  time to fit residues: 7.7066
Evaluate side-chains
  89 residues out of total 278 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 88
  time to evaluate  : 0.108 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 136
   random chunks:
   chunk 35 optimal weight:    4.9990
   chunk 71 optimal weight:    7.9990
   chunk 2 optimal weight:    0.9980
   chunk 122 optimal weight:    0.9980
   chunk 78 optimal weight:    0.0020
   chunk 24 optimal weight:    1.9990
   chunk 26 optimal weight:    0.6980
   chunk 77 optimal weight:    5.9990
   chunk 23 optimal weight:    5.9990
   chunk 49 optimal weight:    9.9990
   chunk 66 optimal weight:    5.9990
   overall best weight:    0.9390
-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
Update NCS operators
********************
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3340 r_free = 0.3340 target = 0.105554 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.2989 r_free = 0.2989 target = 0.082318 restraints weight = 5725.822|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3045 r_free = 0.3045 target = 0.085822 restraints weight = 3784.913|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3089 r_free = 0.3089 target = 0.088556 restraints weight = 2710.693|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3120 r_free = 0.3120 target = 0.090604 restraints weight = 2048.333|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3145 r_free = 0.3145 target = 0.092268 restraints weight = 1619.911|
|-----------------------------------------------------------------------------|
r_work (final): 0.3128
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7755
moved from start:          0.6408

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.026  10672  Z= 0.128
  Angle     :  0.712   9.147  14464  Z= 0.349
  Chirality :  0.044   0.184   1644
  Planarity :  0.008   0.124   1880
  Dihedral  :  5.107  22.263   1472
  Min Nonbonded Distance : 2.509

Molprobity Statistics.
  All-atom Clashscore : 14.57
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.81 %
    Favored  : 96.19 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.36 %
    Favored  : 99.64 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.56 %
    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 are not related in a simple way.
  whole:  0.86 (0.23), residues: 1364
  helix:  1.73 (0.20), residues: 708
  sheet: -0.61 (0.35), residues: 172
  loop : -0.68 (0.28), residues: 484

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.014   0.001   ARG C 257 
 TYR   0.017   0.002   TYR C 213 
 PHE   0.017   0.002   PHE A  79 
 TRP   0.010   0.001   TRP C 295 
 HIS   0.001   0.000   HIS B 237 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00291 /  0.13 (10672)
  covalent geometry    : angle       0.71164 /  0.35 (14464)
  hydrogen bonds       : bond        0.03439 /  2.35 (  564)
  hydrogen bonds       : angle       4.40830 /  3.11 ( 1632)

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

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

  2728 Ramachandran restraints generated.
    1364 Oldfield, 0 Emsley, 1364 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2728 Ramachandran restraints generated.
    1364 Oldfield, 0 Emsley, 1364 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Update NCS operators
********************
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  120 residues out of total 278 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 120
  time to evaluate  : 0.099 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   12 LYS cc_start: 0.9089 (mttt) cc_final: 0.8689 (mmmm)
REVERT: B   44 GLN cc_start: 0.9299 (tp40) cc_final: 0.9098 (tp-100)
REVERT: B  140 ASP cc_start: 0.8759 (m-30) cc_final: 0.8515 (m-30)
REVERT: B  144 PHE cc_start: 0.8645 (p90) cc_final: 0.8326 (p90)
REVERT: B  152 LYS cc_start: 0.8008 (ptpp) cc_final: 0.7775 (pttm)
REVERT: B  155 GLU cc_start: 0.8745 (pt0) cc_final: 0.8326 (pt0)
REVERT: B  185 ILE cc_start: 0.8464 (mp) cc_final: 0.8102 (tp)
REVERT: B  195 ASP cc_start: 0.8848 (p0) cc_final: 0.8274 (t0)
REVERT: B  237 HIS cc_start: 0.8338 (t70) cc_final: 0.7946 (t70)
REVERT: B  270 LEU cc_start: 0.8693 (mm) cc_final: 0.8436 (mm)
REVERT: B  276 GLU cc_start: 0.8217 (pm20) cc_final: 0.7879 (pm20)
REVERT: B  282 ASN cc_start: 0.9014 (m-40) cc_final: 0.8659 (m-40)
REVERT: B  293 LYS cc_start: 0.8607 (pptt) cc_final: 0.8225 (pptt)
REVERT: B  313 TRP cc_start: 0.7980 (t60) cc_final: 0.7075 (t60)
REVERT: B  325 GLU cc_start: 0.9113 (mm-30) cc_final: 0.8582 (tp30)
REVERT: B  329 LYS cc_start: 0.8903 (mttp) cc_final: 0.8569 (mtpt)
REVERT: B  332 LEU cc_start: 0.8525 (tp) cc_final: 0.8154 (pp)
  outliers start: 0
  outliers final: 0
  residues processed: 120
  average time/residue: 0.0628
  time to fit residues: 8.8947
Evaluate side-chains
  89 residues out of total 278 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 89
  time to evaluate  : 0.099 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 136
   random chunks:
   chunk 5 optimal weight:    1.9990
   chunk 18 optimal weight:    0.7980
   chunk 93 optimal weight:    4.9990
   chunk 14 optimal weight:    0.0030
   chunk 126 optimal weight:    3.9990
   chunk 96 optimal weight:    0.1980
   chunk 16 optimal weight:    2.9990
   chunk 25 optimal weight:    4.9990
   chunk 86 optimal weight:    4.9990
   chunk 135 optimal weight:    7.9990
   chunk 0 optimal weight:    9.9990
   overall best weight:    1.1994
-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
B 219 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Update NCS operators
********************
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3359 r_free = 0.3359 target = 0.107423 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3015 r_free = 0.3015 target = 0.084475 restraints weight = 5715.233|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 22)----------------|
| r_work = 0.3071 r_free = 0.3071 target = 0.087934 restraints weight = 3774.768|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3114 r_free = 0.3114 target = 0.090576 restraints weight = 2720.657|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 34)----------------|
| r_work = 0.3145 r_free = 0.3145 target = 0.092646 restraints weight = 2050.656|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 32)----------------|
| r_work = 0.3168 r_free = 0.3168 target = 0.094124 restraints weight = 1613.820|
|-----------------------------------------------------------------------------|
r_work (final): 0.3148
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7761
moved from start:          0.6492

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031  10672  Z= 0.137
  Angle     :  0.750  10.262  14464  Z= 0.359
  Chirality :  0.044   0.152   1644
  Planarity :  0.007   0.103   1880
  Dihedral  :  4.985  20.195   1472
  Min Nonbonded Distance : 2.521

Molprobity Statistics.
  All-atom Clashscore : 15.90
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.69 %
    Favored  : 95.31 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.36 %
    Favored  : 99.64 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.56 %
    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 are not related in a simple way.
  whole:  0.83 (0.23), residues: 1364
  helix:  1.75 (0.20), residues: 708
  sheet: -0.73 (0.34), residues: 172
  loop : -0.72 (0.28), residues: 484

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.015   0.001   ARG C 257 
 TYR   0.011   0.002   TYR C  58 
 PHE   0.017   0.002   PHE B  79 
 TRP   0.015   0.002   TRP A 295 
 HIS   0.008   0.001   HIS B 219 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00315 /  0.14 (10672)
  covalent geometry    : angle       0.75002 /  0.36 (14464)
  hydrogen bonds       : bond        0.03413 /  2.33 (  564)
  hydrogen bonds       : angle       4.33252 /  3.05 ( 1632)

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

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

  2728 Ramachandran restraints generated.
    1364 Oldfield, 0 Emsley, 1364 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2728 Ramachandran restraints generated.
    1364 Oldfield, 0 Emsley, 1364 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Update NCS operators
********************
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  118 residues out of total 278 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 118
  time to evaluate  : 0.066 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B    7 LEU cc_start: 0.8797 (mt) cc_final: 0.8034 (mt)
REVERT: B   12 LYS cc_start: 0.9100 (mttt) cc_final: 0.8812 (mmmm)
REVERT: B   79 PHE cc_start: 0.8207 (t80) cc_final: 0.7639 (t80)
REVERT: B  115 LEU cc_start: 0.8081 (mp) cc_final: 0.7748 (mp)
REVERT: B  140 ASP cc_start: 0.8776 (m-30) cc_final: 0.8526 (m-30)
REVERT: B  144 PHE cc_start: 0.8657 (p90) cc_final: 0.8343 (p90)
REVERT: B  152 LYS cc_start: 0.8019 (ptpp) cc_final: 0.7761 (pttm)
REVERT: B  185 ILE cc_start: 0.8475 (mp) cc_final: 0.8076 (tp)
REVERT: B  195 ASP cc_start: 0.8851 (p0) cc_final: 0.8302 (t0)
REVERT: B  214 LYS cc_start: 0.9252 (tmtt) cc_final: 0.8707 (tppt)
REVERT: B  237 HIS cc_start: 0.8252 (t70) cc_final: 0.7855 (t70)
REVERT: B  246 GLU cc_start: 0.9549 (mp0) cc_final: 0.9343 (pm20)
REVERT: B  250 MET cc_start: 0.8726 (tmm) cc_final: 0.8424 (tpp)
REVERT: B  270 LEU cc_start: 0.8660 (mm) cc_final: 0.8378 (mm)
REVERT: B  276 GLU cc_start: 0.8342 (pm20) cc_final: 0.7992 (pm20)
REVERT: B  282 ASN cc_start: 0.8952 (m-40) cc_final: 0.8606 (m-40)
REVERT: B  293 LYS cc_start: 0.8503 (pptt) cc_final: 0.8069 (pptt)
REVERT: B  299 PHE cc_start: 0.9159 (p90) cc_final: 0.8930 (p90)
REVERT: B  313 TRP cc_start: 0.8073 (t60) cc_final: 0.7216 (t60)
REVERT: B  325 GLU cc_start: 0.9064 (mm-30) cc_final: 0.8500 (tp30)
REVERT: B  329 LYS cc_start: 0.8897 (mttp) cc_final: 0.8510 (mttt)
REVERT: B  332 LEU cc_start: 0.8514 (tp) cc_final: 0.8140 (pp)
  outliers start: 0
  outliers final: 0
  residues processed: 118
  average time/residue: 0.0623
  time to fit residues: 8.5791
Evaluate side-chains
  88 residues out of total 278 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 88
  time to evaluate  : 0.102 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 136
   random chunks:
   chunk 5 optimal weight:    2.9990
   chunk 75 optimal weight:    9.9990
   chunk 42 optimal weight:    4.9990
   chunk 124 optimal weight:    1.9990
   chunk 41 optimal weight:    7.9990
   chunk 89 optimal weight:    3.9990
   chunk 77 optimal weight:    5.9990
   chunk 122 optimal weight:    0.7980
   chunk 3 optimal weight:    8.9990
   chunk 22 optimal weight:    0.9980
   chunk 29 optimal weight:    0.5980
   overall best weight:    1.4784
-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
B  60 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Update NCS operators
********************
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3365 r_free = 0.3365 target = 0.107694 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3017 r_free = 0.3017 target = 0.084160 restraints weight = 5649.764|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3076 r_free = 0.3076 target = 0.087682 restraints weight = 3677.369|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3121 r_free = 0.3121 target = 0.090455 restraints weight = 2641.760|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.3153 r_free = 0.3153 target = 0.092562 restraints weight = 1989.040|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3174 r_free = 0.3174 target = 0.093903 restraints weight = 1565.124|
|-----------------------------------------------------------------------------|
r_work (final): 0.3151
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7808
moved from start:          0.6681

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.055  10672  Z= 0.145
  Angle     :  0.731   9.388  14464  Z= 0.362
  Chirality :  0.044   0.174   1644
  Planarity :  0.007   0.123   1880
  Dihedral  :  5.071  22.373   1472
  Min Nonbonded Distance : 2.543

Molprobity Statistics.
  All-atom Clashscore : 16.95
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.99 %
    Favored  : 95.01 %
  Rotamer:
    Outliers :  0.36 %
    Allowed  :  0.36 %
    Favored  : 99.28 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.56 %
    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 are not related in a simple way.
  whole:  0.75 (0.23), residues: 1364
  helix:  1.72 (0.20), residues: 708
  sheet: -1.04 (0.32), residues: 200
  loop : -0.64 (0.30), residues: 456

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.011   0.001   ARG B 257 
 TYR   0.011   0.002   TYR C  58 
 PHE   0.017   0.002   PHE C  79 
 TRP   0.009   0.002   TRP D 295 
 HIS   0.004   0.001   HIS A 219 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00337 /  0.15 (10672)
  covalent geometry    : angle       0.73106 /  0.36 (14464)
  hydrogen bonds       : bond        0.03582 /  2.43 (  564)
  hydrogen bonds       : angle       4.48441 /  3.17 ( 1632)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1021.59 seconds
wall clock time: 18 minutes 52.54 seconds (1132.54 seconds total)