Starting phenix.real_space_refine
on Mon Jul 28 18:00:38 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7k9l_22754/07_2025/7k9l_22754.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7k9l_22754/07_2025/7k9l_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 {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7k9l_22754/07_2025/7k9l_22754.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7k9l_22754/07_2025/7k9l_22754.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7k9l_22754/07_2025/7k9l_22754.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7k9l_22754/07_2025/7k9l_22754.cif"
  }
  resolution = 4.9
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.004
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): 0.03s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib"
  Total number of atoms: 10472
  Number of models: 1
  Model: ""
    Number of chains: 1
    Chain: "A"
      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:
    C, B, D
  Time building chain proxies: 5.29, per 1000 atoms: 0.51
  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: 2.56
  Conformation dependent library (CDL) restraints added in 1.3 seconds
  

  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: 1.35
  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: 3.06

  Time building geometry restraints manager: 3.00 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: 0.08
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'C'
  selection = chain 'B'
  selection = chain 'D'
}

Set up NCS constraints
  Number of NCS constrained groups: 1
  pdb_interpretation.ncs_group {
  reference = chain 'A'
  selection = chain 'C'
  selection = chain 'B'
  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:             2.530
  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:             0.020
  Extract box with map and model:          0.440
  Check model and map are aligned:         0.080
  Set scattering table:                    0.120
  Process input model:                     25.640
  Find NCS groups from input model:        0.220
  Set up NCS constraints:                  0.020
  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:2.940
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   32.010
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7921
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 : 9.45
  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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.98 (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
 TRP   0.015   0.003   TRP A 295 
 HIS   0.007   0.002   HIS B 219 
 PHE   0.013   0.003   PHE C  93 
 TYR   0.021   0.004   TYR B  58 
 ARG   0.009   0.001   ARG D  42 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.18368 (  564)
  hydrogen bonds       : angle       7.27086 ( 1632)
  covalent geometry    : bond        0.00733 (10672)
  covalent geometry    : angle       1.18906 (14464)

*********************** 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
  165 residues out of total 278 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 154
  time to evaluate  : 0.291 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   12 LYS cc_start: 0.8999 (mttt) cc_final: 0.8664 (mmtp)
REVERT: A   21 ARG cc_start: 0.8944 (mtm-85) cc_final: 0.8633 (mtp85)
REVERT: A   61 LEU cc_start: 0.8986 (mt) cc_final: 0.8585 (mt)
REVERT: A   81 GLU cc_start: 0.9243 (OUTLIER) cc_final: 0.8786 (pp20)
REVERT: A   89 ASP cc_start: 0.6687 (OUTLIER) cc_final: 0.6445 (p0)
REVERT: A  104 VAL cc_start: 0.8846 (t) cc_final: 0.8534 (t)
REVERT: A  113 VAL cc_start: 0.9303 (t) cc_final: 0.8977 (t)
REVERT: A  115 LEU cc_start: 0.9133 (mt) cc_final: 0.8883 (mm)
REVERT: A  122 THR cc_start: 0.8325 (t) cc_final: 0.7883 (t)
REVERT: A  144 PHE cc_start: 0.8375 (p90) cc_final: 0.8166 (p90)
REVERT: A  149 CYS cc_start: 0.8233 (p) cc_final: 0.7731 (t)
REVERT: A  152 LYS cc_start: 0.8278 (pttp) cc_final: 0.7948 (pttp)
REVERT: A  178 GLN cc_start: 0.9144 (mt0) cc_final: 0.8876 (mt0)
REVERT: A  191 LEU cc_start: 0.9175 (OUTLIER) cc_final: 0.8884 (tp)
REVERT: A  199 LYS cc_start: 0.9384 (mtmm) cc_final: 0.8929 (mmmt)
REVERT: A  203 TYR cc_start: 0.8758 (t80) cc_final: 0.8533 (t80)
REVERT: A  242 LYS cc_start: 0.8842 (mmtt) cc_final: 0.8628 (tttm)
REVERT: A  247 GLU cc_start: 0.9286 (mt-10) cc_final: 0.8740 (mt-10)
REVERT: A  254 THR cc_start: 0.8950 (p) cc_final: 0.8730 (t)
REVERT: A  282 ASN cc_start: 0.9117 (m-40) cc_final: 0.8915 (m-40)
REVERT: A  284 ASN cc_start: 0.8287 (t0) cc_final: 0.7532 (t0)
REVERT: A  291 LEU cc_start: 0.8450 (mt) cc_final: 0.8099 (tp)
REVERT: A  292 LEU cc_start: 0.8655 (mm) cc_final: 0.8436 (mm)
REVERT: A  305 LEU cc_start: 0.9363 (tp) cc_final: 0.9052 (tp)
REVERT: A  310 LEU cc_start: 0.9112 (tp) cc_final: 0.8849 (mt)
REVERT: A  313 TRP cc_start: 0.7413 (t60) cc_final: 0.6422 (t60)
  outliers start: 11
  outliers final: 3
  residues processed: 158
  average time/residue: 0.1917
  time to fit residues: 34.4806
Evaluate side-chains
  116 residues out of total 278 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 110
  time to evaluate  : 0.320 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 136
   random chunks:
   chunk 114 optimal weight:    5.9990
   chunk 103 optimal weight:    5.9990
   chunk 57 optimal weight:    4.9990
   chunk 35 optimal weight:    6.9990
   chunk 69 optimal weight:    5.9990
   chunk 55 optimal weight:    3.9990
   chunk 106 optimal weight:    9.9990
   chunk 41 optimal weight:   10.0000
   chunk 64 optimal weight:    5.9990
   chunk 79 optimal weight:    0.0870
   chunk 123 optimal weight:    3.9990
   overall best weight:    3.8166
-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

Flipped N/Q/H residues before XYZ refinement:
D  60 GLN
D 119 ASN
D 125 GLN
D 237 HIS
D 284 ASN
D 287 ASN
** D 306 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
D 324 GLN

Total number of N/Q/H flips: 7

-------------------------------------------------------------------------------
Update NCS operators
********************
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3204 r_free = 0.3204 target = 0.095587 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.2846 r_free = 0.2846 target = 0.074647 restraints weight = 5968.873|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.2900 r_free = 0.2900 target = 0.077726 restraints weight = 3822.174|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.2943 r_free = 0.2943 target = 0.080082 restraints weight = 2672.523|
|-----------------------------------------------------------------------------|
r_work (final): 0.2936
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8021
moved from start:          0.3649

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.072  10672  Z= 0.257
  Angle     :  0.755   7.537  14464  Z= 0.398
  Chirality :  0.045   0.150   1644
  Planarity :  0.009   0.134   1880
  Dihedral  :  5.657  24.908   1472
  Min Nonbonded Distance : 2.555

Molprobity Statistics.
  All-atom Clashscore : 19.08
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.23 %
    Favored  : 96.77 %
  Rotamer:
    Outliers :  1.44 %
    Allowed  :  5.76 %
    Favored  : 92.81 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.56 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.26 (0.21), residues: 1364
  helix:  0.64 (0.18), residues: 688
  sheet: -1.57 (0.32), residues: 220
  loop : -0.45 (0.28), residues: 456

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.019   0.003   TRP C 295 
 HIS   0.009   0.002   HIS C 219 
 PHE   0.023   0.003   PHE B  93 
 TYR   0.013   0.002   TYR A 327 
 ARG   0.006   0.001   ARG D 257 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04945 (  564)
  hydrogen bonds       : angle       5.23563 ( 1632)
  covalent geometry    : bond        0.00542 (10672)
  covalent geometry    : angle       0.75527 (14464)

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

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

  2046 Ramachandran restraints generated.
    1023 Oldfield, 0 Emsley, 1023 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2046 Ramachandran restraints generated.
    1023 Oldfield, 0 Emsley, 1023 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Update NCS operators
********************
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  132 residues out of total 278 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 128
  time to evaluate  : 0.294 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: D    7 LEU cc_start: 0.9030 (mt) cc_final: 0.8398 (mt)
REVERT: D   14 GLU cc_start: 0.8870 (mp0) cc_final: 0.8586 (mm-30)
REVERT: D   61 LEU cc_start: 0.8857 (mt) cc_final: 0.8099 (mp)
REVERT: D   72 CYS cc_start: 0.8921 (m) cc_final: 0.8713 (m)
REVERT: D   79 PHE cc_start: 0.8050 (t80) cc_final: 0.7798 (t80)
REVERT: D  104 VAL cc_start: 0.8721 (t) cc_final: 0.8399 (t)
REVERT: D  138 LYS cc_start: 0.8491 (tptt) cc_final: 0.7907 (ttmt)
REVERT: D  178 GLN cc_start: 0.9043 (mt0) cc_final: 0.8765 (mt0)
REVERT: D  195 ASP cc_start: 0.8887 (p0) cc_final: 0.8040 (t0)
REVERT: D  248 ILE cc_start: 0.9512 (mt) cc_final: 0.9278 (tt)
REVERT: D  284 ASN cc_start: 0.8184 (t0) cc_final: 0.7484 (t0)
REVERT: D  305 LEU cc_start: 0.9395 (tp) cc_final: 0.9077 (tp)
REVERT: D  313 TRP cc_start: 0.8037 (t60) cc_final: 0.6641 (t60)
REVERT: D  326 GLU cc_start: 0.9133 (mm-30) cc_final: 0.8611 (mm-30)
REVERT: D  329 LYS cc_start: 0.8848 (mttp) cc_final: 0.8235 (mttm)
REVERT: D  332 LEU cc_start: 0.8493 (tp) cc_final: 0.8187 (pp)
  outliers start: 4
  outliers final: 1
  residues processed: 131
  average time/residue: 0.1659
  time to fit residues: 25.1078
Evaluate side-chains
  85 residues out of total 278 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 84
  time to evaluate  : 0.315 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 136
   random chunks:
   chunk 33 optimal weight:    6.9990
   chunk 113 optimal weight:    5.9990
   chunk 93 optimal weight:    0.4980
   chunk 60 optimal weight:    0.9990
   chunk 22 optimal weight:   10.0000
   chunk 35 optimal weight:    5.9990
   chunk 112 optimal weight:    6.9990
   chunk 95 optimal weight:    1.9990
   chunk 77 optimal weight:    6.9990
   chunk 76 optimal weight:    0.6980
   chunk 2 optimal weight:    0.6980
   overall best weight:    0.9784
-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

Flipped N/Q/H residues before XYZ refinement:
D  44 GLN
D  80 HIS
D 245 HIS
D 287 ASN
D 324 GLN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
Update NCS operators
********************
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3349 r_free = 0.3349 target = 0.104644 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3004 r_free = 0.3004 target = 0.082523 restraints weight = 5524.883|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3061 r_free = 0.3061 target = 0.085844 restraints weight = 3577.934|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3104 r_free = 0.3104 target = 0.088405 restraints weight = 2514.872|
|-----------------------------------------------------------------------------|
r_work (final): 0.3097
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7909
moved from start:          0.4585

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041  10672  Z= 0.131
  Angle     :  0.651   8.090  14464  Z= 0.320
  Chirality :  0.043   0.136   1644
  Planarity :  0.005   0.052   1880
  Dihedral  :  4.995  18.046   1472
  Min Nonbonded Distance : 2.540

Molprobity Statistics.
  All-atom Clashscore : 13.58
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.93 %
    Favored  : 97.07 %
  Rotamer:
    Outliers :  0.36 %
    Allowed  :  4.32 %
    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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.16 (0.22), residues: 1364
  helix:  0.93 (0.19), residues: 700
  sheet: -1.28 (0.35), residues: 200
  loop : -0.33 (0.29), residues: 464

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.024   0.002   TRP C 295 
 HIS   0.007   0.001   HIS C 219 
 PHE   0.010   0.001   PHE C 144 
 TYR   0.012   0.001   TYR D 203 
 ARG   0.006   0.001   ARG A  42 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03726 (  564)
  hydrogen bonds       : angle       4.79886 ( 1632)
  covalent geometry    : bond        0.00302 (10672)
  covalent geometry    : angle       0.65116 (14464)

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

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

  2046 Ramachandran restraints generated.
    1023 Oldfield, 0 Emsley, 1023 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2046 Ramachandran restraints generated.
    1023 Oldfield, 0 Emsley, 1023 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Update NCS operators
********************
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  130 residues out of total 278 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 129
  time to evaluate  : 0.282 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: D    7 LEU cc_start: 0.8877 (mt) cc_final: 0.8634 (mt)
REVERT: D   10 GLU cc_start: 0.8928 (pm20) cc_final: 0.8383 (mp0)
REVERT: D   61 LEU cc_start: 0.8905 (mt) cc_final: 0.8695 (mt)
REVERT: D  138 LYS cc_start: 0.8448 (tptt) cc_final: 0.7822 (ttmt)
REVERT: D  178 GLN cc_start: 0.8933 (mt0) cc_final: 0.8714 (mt0)
REVERT: D  229 LYS cc_start: 0.8175 (tttp) cc_final: 0.7767 (tptp)
REVERT: D  245 HIS cc_start: 0.8275 (m-70) cc_final: 0.8040 (p-80)
REVERT: D  276 GLU cc_start: 0.7911 (pm20) cc_final: 0.7418 (pm20)
REVERT: D  282 ASN cc_start: 0.9138 (m-40) cc_final: 0.8773 (m-40)
REVERT: D  283 LEU cc_start: 0.9262 (tp) cc_final: 0.8970 (tp)
REVERT: D  287 ASN cc_start: 0.9103 (OUTLIER) cc_final: 0.8890 (t0)
REVERT: D  293 LYS cc_start: 0.8775 (pptt) cc_final: 0.8540 (pptt)
REVERT: D  303 ARG cc_start: 0.8613 (ttm-80) cc_final: 0.8361 (ttm-80)
REVERT: D  305 LEU cc_start: 0.9364 (tp) cc_final: 0.8947 (tp)
REVERT: D  325 GLU cc_start: 0.9119 (tp30) cc_final: 0.8916 (tp30)
REVERT: D  332 LEU cc_start: 0.8407 (tp) cc_final: 0.8080 (pp)
  outliers start: 1
  outliers final: 0
  residues processed: 130
  average time/residue: 0.1442
  time to fit residues: 21.9867
Evaluate side-chains
  100 residues out of total 278 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 99
  time to evaluate  : 0.309 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 136
   random chunks:
   chunk 42 optimal weight:    0.3980
   chunk 106 optimal weight:    6.9990
   chunk 117 optimal weight:    9.9990
   chunk 110 optimal weight:    0.8980
   chunk 74 optimal weight:    6.9990
   chunk 67 optimal weight:    6.9990
   chunk 111 optimal weight:    6.9990
   chunk 96 optimal weight:    0.4980
   chunk 11 optimal weight:    6.9990
   chunk 103 optimal weight:    4.9990
   chunk 68 optimal weight:    8.9990
   overall best weight:    2.7584
-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

Flipped N/Q/H residues before XYZ refinement:
B  44 GLN
B 282 ASN
** B 284 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 306 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
Update NCS operators
********************
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3287 r_free = 0.3287 target = 0.100925 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.2937 r_free = 0.2937 target = 0.078972 restraints weight = 5814.529|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.2990 r_free = 0.2990 target = 0.082079 restraints weight = 3837.956|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3032 r_free = 0.3032 target = 0.084544 restraints weight = 2756.339|
|-----------------------------------------------------------------------------|
r_work (final): 0.3032
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8018
moved from start:          0.5094

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.057  10672  Z= 0.191
  Angle     :  0.663   8.770  14464  Z= 0.339
  Chirality :  0.042   0.134   1644
  Planarity :  0.005   0.056   1880
  Dihedral  :  4.927  17.810   1472
  Min Nonbonded Distance : 2.547

Molprobity Statistics.
  All-atom Clashscore : 19.46
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.11 %
    Favored  : 95.89 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  4.32 %
    Favored  : 95.68 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.56 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.11 (0.22), residues: 1364
  helix:  0.87 (0.18), residues: 700
  sheet: -0.99 (0.34), residues: 188
  loop : -0.51 (0.29), residues: 476

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.022   0.002   TRP A 295 
 HIS   0.006   0.001   HIS C 219 
 PHE   0.009   0.003   PHE D  93 
 TYR   0.014   0.002   TYR A 213 
 ARG   0.005   0.001   ARG C  42 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04101 (  564)
  hydrogen bonds       : angle       4.71256 ( 1632)
  covalent geometry    : bond        0.00427 (10672)
  covalent geometry    : angle       0.66258 (14464)

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

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

  2046 Ramachandran restraints generated.
    1023 Oldfield, 0 Emsley, 1023 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2046 Ramachandran restraints generated.
    1023 Oldfield, 0 Emsley, 1023 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  : 0.317 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   12 LYS cc_start: 0.9219 (mttt) cc_final: 0.8765 (mmtp)
REVERT: B   14 GLU cc_start: 0.8861 (mp0) cc_final: 0.8542 (mm-30)
REVERT: B   30 LEU cc_start: 0.8316 (tt) cc_final: 0.7942 (tp)
REVERT: B   61 LEU cc_start: 0.9039 (mt) cc_final: 0.8820 (mt)
REVERT: B   99 SER cc_start: 0.8833 (p) cc_final: 0.8594 (p)
REVERT: B  130 LEU cc_start: 0.8906 (mt) cc_final: 0.8649 (mp)
REVERT: B  138 LYS cc_start: 0.8467 (tptt) cc_final: 0.7793 (ttmt)
REVERT: B  195 ASP cc_start: 0.8982 (p0) cc_final: 0.8266 (t0)
REVERT: B  245 HIS cc_start: 0.8495 (m-70) cc_final: 0.8291 (p-80)
REVERT: B  246 GLU cc_start: 0.9550 (mp0) cc_final: 0.8925 (pm20)
REVERT: B  247 GLU cc_start: 0.9151 (mt-10) cc_final: 0.8669 (mt-10)
REVERT: B  250 MET cc_start: 0.9094 (ttp) cc_final: 0.8862 (tmm)
REVERT: B  276 GLU cc_start: 0.7976 (pm20) cc_final: 0.7611 (pm20)
REVERT: B  282 ASN cc_start: 0.9063 (m110) cc_final: 0.8634 (m110)
REVERT: B  283 LEU cc_start: 0.9174 (tp) cc_final: 0.8926 (tp)
REVERT: B  305 LEU cc_start: 0.9385 (tp) cc_final: 0.8592 (tp)
REVERT: B  332 LEU cc_start: 0.8403 (tp) cc_final: 0.8159 (tp)
  outliers start: 0
  outliers final: 0
  residues processed: 120
  average time/residue: 0.1708
  time to fit residues: 23.9838
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  : 0.367 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 136
   random chunks:
   chunk 58 optimal weight:    1.9990
   chunk 122 optimal weight:    2.9990
   chunk 8 optimal weight:    0.0370
   chunk 63 optimal weight:    0.0010
   chunk 135 optimal weight:    7.9990
   chunk 134 optimal weight:    3.9990
   chunk 66 optimal weight:    6.9990
   chunk 9 optimal weight:    5.9990
   chunk 52 optimal weight:    0.0870
   chunk 123 optimal weight:    4.9990
   chunk 14 optimal weight:    0.0770
   overall best weight:    0.4402
-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

Flipped N/Q/H residues before XYZ refinement:
B 156 HIS
B 219 HIS
** B 284 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 306 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 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 = 0.3350 r_free = 0.3350 target = 0.106162 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3030 r_free = 0.3030 target = 0.084693 restraints weight = 5563.796|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 21)----------------|
| r_work = 0.3086 r_free = 0.3086 target = 0.088275 restraints weight = 3517.046|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3130 r_free = 0.3130 target = 0.091039 restraints weight = 2458.368|
|-----------------------------------------------------------------------------|
r_work (final): 0.3112
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7777
moved from start:          0.5530

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028  10672  Z= 0.115
  Angle     :  0.625   7.177  14464  Z= 0.304
  Chirality :  0.043   0.168   1644
  Planarity :  0.005   0.058   1880
  Dihedral  :  4.612  16.754   1472
  Min Nonbonded Distance : 2.633

Molprobity Statistics.
  All-atom Clashscore : 13.77
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.52 %
    Favored  : 96.48 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.52 %
    Favored  : 97.48 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.56 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.48 (0.22), residues: 1364
  helix:  1.28 (0.19), residues: 704
  sheet: -1.03 (0.35), residues: 172
  loop : -0.48 (0.29), residues: 488

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.030   0.003   TRP A 295 
 HIS   0.007   0.001   HIS B 156 
 PHE   0.009   0.001   PHE D 144 
 TYR   0.010   0.001   TYR B 203 
 ARG   0.006   0.001   ARG A  42 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03379 (  564)
  hydrogen bonds       : angle       4.38275 ( 1632)
  covalent geometry    : bond        0.00262 (10672)
  covalent geometry    : angle       0.62520 (14464)

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

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

  2046 Ramachandran restraints generated.
    1023 Oldfield, 0 Emsley, 1023 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2046 Ramachandran restraints generated.
    1023 Oldfield, 0 Emsley, 1023 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: 0
    poor density    : 122
  time to evaluate  : 0.307 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   14 GLU cc_start: 0.9026 (mm-30) cc_final: 0.8664 (mm-30)
REVERT: B   30 LEU cc_start: 0.8180 (tt) cc_final: 0.7796 (tp)
REVERT: B   61 LEU cc_start: 0.8893 (mt) cc_final: 0.8486 (mt)
REVERT: B   79 PHE cc_start: 0.8062 (t80) cc_final: 0.7755 (t80)
REVERT: B  106 ILE cc_start: 0.8709 (tt) cc_final: 0.8488 (tt)
REVERT: B  115 LEU cc_start: 0.8065 (mm) cc_final: 0.7821 (mm)
REVERT: B  128 ASP cc_start: 0.8363 (t0) cc_final: 0.7621 (m-30)
REVERT: B  130 LEU cc_start: 0.8841 (mt) cc_final: 0.8620 (mt)
REVERT: B  138 LYS cc_start: 0.8384 (tptt) cc_final: 0.7860 (ttmt)
REVERT: B  140 ASP cc_start: 0.8671 (m-30) cc_final: 0.8444 (m-30)
REVERT: B  165 GLU cc_start: 0.8707 (tm-30) cc_final: 0.8475 (tm-30)
REVERT: B  178 GLN cc_start: 0.8745 (mt0) cc_final: 0.8528 (mt0)
REVERT: B  195 ASP cc_start: 0.8880 (p0) cc_final: 0.8302 (t0)
REVERT: B  229 LYS cc_start: 0.7887 (tttp) cc_final: 0.7525 (tptp)
REVERT: B  245 HIS cc_start: 0.8360 (m-70) cc_final: 0.7999 (p-80)
REVERT: B  246 GLU cc_start: 0.9613 (mp0) cc_final: 0.8864 (pm20)
REVERT: B  269 PHE cc_start: 0.8199 (m-80) cc_final: 0.7937 (m-10)
REVERT: B  276 GLU cc_start: 0.8085 (pm20) cc_final: 0.7693 (pm20)
REVERT: B  282 ASN cc_start: 0.9168 (m110) cc_final: 0.8824 (m110)
REVERT: B  305 LEU cc_start: 0.9390 (tp) cc_final: 0.8654 (tp)
REVERT: B  313 TRP cc_start: 0.8115 (t60) cc_final: 0.6945 (t60)
REVERT: B  332 LEU cc_start: 0.8350 (tp) cc_final: 0.8083 (pp)
  outliers start: 0
  outliers final: 0
  residues processed: 122
  average time/residue: 0.1593
  time to fit residues: 23.1491
Evaluate side-chains
  100 residues out of total 278 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 100
  time to evaluate  : 0.699 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 136
   random chunks:
   chunk 39 optimal weight:    8.9990
   chunk 36 optimal weight:    0.0670
   chunk 117 optimal weight:   20.0000
   chunk 98 optimal weight:    5.9990
   chunk 28 optimal weight:    0.8980
   chunk 17 optimal weight:    2.9990
   chunk 78 optimal weight:    0.4980
   chunk 93 optimal weight:    0.8980
   chunk 29 optimal weight:    2.9990
   chunk 127 optimal weight:    0.6980
   chunk 35 optimal weight:    6.9990
   overall best weight:    0.6118
-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

Flipped N/Q/H residues before XYZ refinement:
B  44 GLN
** B 178 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 284 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 306 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Update NCS operators
********************
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3379 r_free = 0.3379 target = 0.108209 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3049 r_free = 0.3049 target = 0.085998 restraints weight = 5621.600|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3109 r_free = 0.3109 target = 0.089606 restraints weight = 3632.442|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3151 r_free = 0.3151 target = 0.092351 restraints weight = 2554.822|
|-----------------------------------------------------------------------------|
r_work (final): 0.3136
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7818
moved from start:          0.5789

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028  10672  Z= 0.108
  Angle     :  0.583   7.259  14464  Z= 0.289
  Chirality :  0.040   0.122   1644
  Planarity :  0.005   0.048   1880
  Dihedral  :  4.394  16.268   1472
  Min Nonbonded Distance : 2.488

Molprobity Statistics.
  All-atom Clashscore : 14.62
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.52 %
    Favored  : 96.48 %
  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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.50 (0.22), residues: 1364
  helix:  1.40 (0.19), residues: 696
  sheet: -1.24 (0.31), residues: 220
  loop : -0.37 (0.30), residues: 448

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.027   0.002   TRP D 295 
 HIS   0.004   0.001   HIS C 219 
 PHE   0.010   0.002   PHE B 144 
 TYR   0.012   0.002   TYR A 137 
 ARG   0.007   0.000   ARG A  42 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03115 (  564)
  hydrogen bonds       : angle       4.21795 ( 1632)
  covalent geometry    : bond        0.00251 (10672)
  covalent geometry    : angle       0.58286 (14464)

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

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

  2046 Ramachandran restraints generated.
    1023 Oldfield, 0 Emsley, 1023 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2046 Ramachandran restraints generated.
    1023 Oldfield, 0 Emsley, 1023 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  : 0.338 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   10 GLU cc_start: 0.9417 (pm20) cc_final: 0.9070 (pm20)
REVERT: B   12 LYS cc_start: 0.9126 (mttt) cc_final: 0.8717 (mmtp)
REVERT: B   14 GLU cc_start: 0.9073 (mm-30) cc_final: 0.8701 (mm-30)
REVERT: B   30 LEU cc_start: 0.8199 (tt) cc_final: 0.7810 (tp)
REVERT: B   61 LEU cc_start: 0.8877 (mt) cc_final: 0.8483 (mt)
REVERT: B   80 HIS cc_start: 0.8797 (t70) cc_final: 0.8539 (t70)
REVERT: B   81 GLU cc_start: 0.8940 (pp20) cc_final: 0.8577 (tm-30)
REVERT: B  115 LEU cc_start: 0.8126 (mm) cc_final: 0.7862 (mm)
REVERT: B  128 ASP cc_start: 0.8328 (t0) cc_final: 0.7593 (m-30)
REVERT: B  138 LYS cc_start: 0.8440 (tptt) cc_final: 0.7890 (ttmt)
REVERT: B  140 ASP cc_start: 0.8739 (m-30) cc_final: 0.8506 (m-30)
REVERT: B  165 GLU cc_start: 0.8707 (tm-30) cc_final: 0.8444 (tm-30)
REVERT: B  195 ASP cc_start: 0.8907 (p0) cc_final: 0.8332 (t0)
REVERT: B  246 GLU cc_start: 0.9615 (mp0) cc_final: 0.9335 (pm20)
REVERT: B  250 MET cc_start: 0.9445 (tpp) cc_final: 0.9127 (tpp)
REVERT: B  269 PHE cc_start: 0.8187 (m-80) cc_final: 0.7968 (m-10)
REVERT: B  276 GLU cc_start: 0.8085 (pm20) cc_final: 0.7766 (pm20)
REVERT: B  282 ASN cc_start: 0.9117 (m110) cc_final: 0.8768 (m110)
REVERT: B  283 LEU cc_start: 0.9322 (tp) cc_final: 0.9114 (tp)
REVERT: B  305 LEU cc_start: 0.9275 (tp) cc_final: 0.8499 (tp)
REVERT: B  313 TRP cc_start: 0.8061 (t60) cc_final: 0.7063 (t60)
REVERT: B  325 GLU cc_start: 0.9003 (tp30) cc_final: 0.8721 (tp30)
REVERT: B  332 LEU cc_start: 0.8343 (tp) cc_final: 0.8082 (pp)
  outliers start: 0
  outliers final: 0
  residues processed: 128
  average time/residue: 0.1789
  time to fit residues: 27.0429
Evaluate side-chains
  99 residues out of total 278 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 99
  time to evaluate  : 0.464 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 136
   random chunks:
   chunk 119 optimal weight:    2.9990
   chunk 124 optimal weight:    4.9990
   chunk 90 optimal weight:    5.9990
   chunk 85 optimal weight:    2.9990
   chunk 97 optimal weight:    6.9990
   chunk 0 optimal weight:    8.9990
   chunk 41 optimal weight:    0.0980
   chunk 86 optimal weight:    0.9990
   chunk 107 optimal weight:    5.9990
   chunk 25 optimal weight:    0.9980
   chunk 16 optimal weight:    5.9990
   overall best weight:    1.6186
-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

Flipped N/Q/H residues before XYZ refinement:
** B  60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 178 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 284 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 306 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 = 0.3347 r_free = 0.3347 target = 0.105711 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3017 r_free = 0.3017 target = 0.083602 restraints weight = 5864.050|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3072 r_free = 0.3072 target = 0.087016 restraints weight = 3865.103|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3111 r_free = 0.3111 target = 0.089563 restraints weight = 2745.232|
|-----------------------------------------------------------------------------|
r_work (final): 0.3105
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7938
moved from start:          0.5871

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= 0.134
  Angle     :  0.600   7.213  14464  Z= 0.299
  Chirality :  0.041   0.125   1644
  Planarity :  0.005   0.042   1880
  Dihedral  :  4.465  16.968   1472
  Min Nonbonded Distance : 2.493

Molprobity Statistics.
  All-atom Clashscore : 15.86
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.11 %
    Favored  : 95.89 %
  Rotamer:
    Outliers :  0.36 %
    Allowed  :  0.72 %
    Favored  : 98.92 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.56 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.59 (0.23), residues: 1364
  helix:  1.46 (0.19), residues: 696
  sheet: -1.24 (0.33), residues: 192
  loop : -0.38 (0.29), residues: 476

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.027   0.003   TRP D 295 
 HIS   0.006   0.001   HIS D 219 
 PHE   0.011   0.002   PHE D 144 
 TYR   0.013   0.002   TYR B 213 
 ARG   0.005   0.000   ARG D  42 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03428 (  564)
  hydrogen bonds       : angle       4.31202 ( 1632)
  covalent geometry    : bond        0.00313 (10672)
  covalent geometry    : angle       0.59989 (14464)

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

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

  2046 Ramachandran restraints generated.
    1023 Oldfield, 0 Emsley, 1023 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2046 Ramachandran restraints generated.
    1023 Oldfield, 0 Emsley, 1023 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: 1
    poor density    : 117
  time to evaluate  : 0.320 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   12 LYS cc_start: 0.9191 (mttt) cc_final: 0.8771 (mmtp)
REVERT: B   14 GLU cc_start: 0.9062 (mm-30) cc_final: 0.8655 (mm-30)
REVERT: B   30 LEU cc_start: 0.8279 (tt) cc_final: 0.7909 (tp)
REVERT: B   61 LEU cc_start: 0.8842 (mt) cc_final: 0.8604 (mt)
REVERT: B  115 LEU cc_start: 0.8303 (mm) cc_final: 0.8044 (mp)
REVERT: B  128 ASP cc_start: 0.8341 (t0) cc_final: 0.7652 (m-30)
REVERT: B  140 ASP cc_start: 0.8779 (m-30) cc_final: 0.8557 (m-30)
REVERT: B  165 GLU cc_start: 0.8655 (tm-30) cc_final: 0.8390 (tm-30)
REVERT: B  195 ASP cc_start: 0.8901 (p0) cc_final: 0.8374 (t0)
REVERT: B  250 MET cc_start: 0.9393 (tpp) cc_final: 0.9089 (tpp)
REVERT: B  253 VAL cc_start: 0.8803 (m) cc_final: 0.8409 (m)
REVERT: B  270 LEU cc_start: 0.8587 (mm) cc_final: 0.8364 (mm)
REVERT: B  276 GLU cc_start: 0.8098 (pm20) cc_final: 0.7799 (pm20)
REVERT: B  282 ASN cc_start: 0.8985 (m110) cc_final: 0.8615 (m110)
REVERT: B  305 LEU cc_start: 0.9310 (tp) cc_final: 0.8993 (tp)
REVERT: B  313 TRP cc_start: 0.8295 (t60) cc_final: 0.7534 (t60)
REVERT: B  332 LEU cc_start: 0.8363 (tp) cc_final: 0.8162 (tp)
  outliers start: 1
  outliers final: 0
  residues processed: 118
  average time/residue: 0.1449
  time to fit residues: 20.3427
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  : 0.352 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 136
   random chunks:
   chunk 109 optimal weight:    2.9990
   chunk 35 optimal weight:    6.9990
   chunk 100 optimal weight:    2.9990
   chunk 124 optimal weight:    0.0030
   chunk 40 optimal weight:    1.9990
   chunk 88 optimal weight:    0.5980
   chunk 101 optimal weight:    6.9990
   chunk 21 optimal weight:    3.9990
   chunk 38 optimal weight:    2.9990
   chunk 103 optimal weight:    6.9990
   chunk 86 optimal weight:    0.7980
   overall best weight:    1.2794
-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

Flipped N/Q/H residues before XYZ refinement:
B  44 GLN
** B  60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 219 HIS
** B 306 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
Update NCS operators
********************
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3374 r_free = 0.3374 target = 0.107776 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3028 r_free = 0.3028 target = 0.084648 restraints weight = 5636.723|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3082 r_free = 0.3082 target = 0.088116 restraints weight = 3749.800|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3124 r_free = 0.3124 target = 0.090874 restraints weight = 2701.995|
|-----------------------------------------------------------------------------|
r_work (final): 0.3120
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7879
moved from start:          0.6047

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034  10672  Z= 0.131
  Angle     :  0.627   7.277  14464  Z= 0.310
  Chirality :  0.043   0.149   1644
  Planarity :  0.005   0.042   1880
  Dihedral  :  4.396  15.688   1472
  Min Nonbonded Distance : 2.412

Molprobity Statistics.
  All-atom Clashscore : 16.71
  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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.46 (0.22), residues: 1364
  helix:  1.40 (0.19), residues: 700
  sheet: -1.06 (0.30), residues: 220
  loop : -0.61 (0.30), residues: 444

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.035   0.003   TRP A 295 
 HIS   0.006   0.001   HIS B 219 
 PHE   0.013   0.003   PHE D  93 
 TYR   0.011   0.001   TYR A 213 
 ARG   0.008   0.000   ARG A  42 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03351 (  564)
  hydrogen bonds       : angle       4.28884 ( 1632)
  covalent geometry    : bond        0.00317 (10672)
  covalent geometry    : angle       0.62708 (14464)

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

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

  2046 Ramachandran restraints generated.
    1023 Oldfield, 0 Emsley, 1023 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2046 Ramachandran restraints generated.
    1023 Oldfield, 0 Emsley, 1023 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Update NCS operators
********************
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  115 residues out of total 278 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 115
  time to evaluate  : 0.327 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   12 LYS cc_start: 0.9130 (mttt) cc_final: 0.8732 (mmtp)
REVERT: B   14 GLU cc_start: 0.9081 (mm-30) cc_final: 0.8672 (mm-30)
REVERT: B   30 LEU cc_start: 0.8196 (tt) cc_final: 0.7866 (tp)
REVERT: B   61 LEU cc_start: 0.8815 (mt) cc_final: 0.8493 (mt)
REVERT: B  115 LEU cc_start: 0.8189 (mm) cc_final: 0.7877 (mp)
REVERT: B  128 ASP cc_start: 0.8425 (t0) cc_final: 0.7665 (m-30)
REVERT: B  140 ASP cc_start: 0.8629 (m-30) cc_final: 0.8393 (m-30)
REVERT: B  165 GLU cc_start: 0.8726 (tm-30) cc_final: 0.8461 (tm-30)
REVERT: B  178 GLN cc_start: 0.8693 (mt0) cc_final: 0.8492 (mt0)
REVERT: B  195 ASP cc_start: 0.8945 (p0) cc_final: 0.8338 (t0)
REVERT: B  229 LYS cc_start: 0.7900 (tttp) cc_final: 0.7651 (tptm)
REVERT: B  250 MET cc_start: 0.9368 (tpp) cc_final: 0.9048 (tpp)
REVERT: B  276 GLU cc_start: 0.8094 (pm20) cc_final: 0.7816 (pm20)
REVERT: B  282 ASN cc_start: 0.9001 (m110) cc_final: 0.8660 (m110)
REVERT: B  305 LEU cc_start: 0.9313 (tp) cc_final: 0.8916 (tp)
REVERT: B  313 TRP cc_start: 0.7973 (t60) cc_final: 0.7076 (t60)
  outliers start: 0
  outliers final: 0
  residues processed: 115
  average time/residue: 0.1344
  time to fit residues: 18.5148
Evaluate side-chains
  85 residues out of total 278 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 85
  time to evaluate  : 0.298 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 136
   random chunks:
   chunk 132 optimal weight:    5.9990
   chunk 101 optimal weight:    6.9990
   chunk 84 optimal weight:    4.9990
   chunk 28 optimal weight:    3.9990
   chunk 46 optimal weight:    2.9990
   chunk 118 optimal weight:    4.9990
   chunk 2 optimal weight:    0.8980
   chunk 110 optimal weight:    0.0040
   chunk 32 optimal weight:    5.9990
   chunk 115 optimal weight:    0.7980
   chunk 12 optimal weight:    0.0670
   overall best weight:    0.9532
-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

Flipped N/Q/H residues before XYZ refinement:
B 306 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 = 0.3379 r_free = 0.3379 target = 0.107816 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3060 r_free = 0.3060 target = 0.086089 restraints weight = 5513.732|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3115 r_free = 0.3115 target = 0.089582 restraints weight = 3594.378|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3159 r_free = 0.3159 target = 0.092260 restraints weight = 2546.444|
|-----------------------------------------------------------------------------|
r_work (final): 0.3155
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7872
moved from start:          0.6167

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.027  10672  Z= 0.116
  Angle     :  0.597   7.228  14464  Z= 0.295
  Chirality :  0.042   0.130   1644
  Planarity :  0.005   0.043   1880
  Dihedral  :  4.313  16.234   1472
  Min Nonbonded Distance : 2.503

Molprobity Statistics.
  All-atom Clashscore : 14.57
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.11 %
    Favored  : 95.89 %
  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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.72 (0.23), residues: 1364
  helix:  1.67 (0.20), residues: 696
  sheet: -1.07 (0.30), residues: 220
  loop : -0.49 (0.31), residues: 448

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.035   0.003   TRP A 295 
 HIS   0.003   0.001   HIS D 219 
 PHE   0.019   0.002   PHE D 299 
 TYR   0.011   0.001   TYR D 327 
 ARG   0.008   0.000   ARG D  42 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03241 (  564)
  hydrogen bonds       : angle       4.13494 ( 1632)
  covalent geometry    : bond        0.00275 (10672)
  covalent geometry    : angle       0.59704 (14464)

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

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

  2046 Ramachandran restraints generated.
    1023 Oldfield, 0 Emsley, 1023 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2046 Ramachandran restraints generated.
    1023 Oldfield, 0 Emsley, 1023 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Update NCS operators
********************
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  115 residues out of total 278 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 114
  time to evaluate  : 0.338 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   12 LYS cc_start: 0.9137 (mttt) cc_final: 0.8727 (mmtp)
REVERT: B   14 GLU cc_start: 0.9066 (mm-30) cc_final: 0.8630 (mm-30)
REVERT: B   30 LEU cc_start: 0.8142 (tt) cc_final: 0.7608 (tp)
REVERT: B   61 LEU cc_start: 0.8804 (mt) cc_final: 0.8445 (mt)
REVERT: B  115 LEU cc_start: 0.8312 (mm) cc_final: 0.8048 (mp)
REVERT: B  128 ASP cc_start: 0.8413 (t0) cc_final: 0.7668 (m-30)
REVERT: B  140 ASP cc_start: 0.8643 (m-30) cc_final: 0.8413 (m-30)
REVERT: B  165 GLU cc_start: 0.8704 (tm-30) cc_final: 0.8314 (tm-30)
REVERT: B  195 ASP cc_start: 0.8945 (p0) cc_final: 0.8405 (t0)
REVERT: B  237 HIS cc_start: 0.8285 (t70) cc_final: 0.7897 (t70)
REVERT: B  246 GLU cc_start: 0.9589 (mp0) cc_final: 0.9306 (pm20)
REVERT: B  250 MET cc_start: 0.9344 (tpp) cc_final: 0.9051 (tpp)
REVERT: B  269 PHE cc_start: 0.8080 (m-80) cc_final: 0.7682 (m-80)
REVERT: B  276 GLU cc_start: 0.8020 (pm20) cc_final: 0.7795 (pm20)
REVERT: B  282 ASN cc_start: 0.8971 (m110) cc_final: 0.8565 (m110)
REVERT: B  305 LEU cc_start: 0.9265 (tp) cc_final: 0.8795 (tp)
REVERT: B  313 TRP cc_start: 0.8236 (t60) cc_final: 0.7093 (t60)
REVERT: B  329 LYS cc_start: 0.9088 (ptmt) cc_final: 0.8489 (ptpt)
REVERT: B  332 LEU cc_start: 0.8485 (tp) cc_final: 0.8132 (pp)
  outliers start: 1
  outliers final: 0
  residues processed: 115
  average time/residue: 0.1588
  time to fit residues: 21.7191
Evaluate side-chains
  91 residues out of total 278 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 91
  time to evaluate  : 0.304 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 136
   random chunks:
   chunk 133 optimal weight:    0.5980
   chunk 73 optimal weight:    0.8980
   chunk 106 optimal weight:    8.9990
   chunk 132 optimal weight:    4.9990
   chunk 25 optimal weight:    0.8980
   chunk 12 optimal weight:    0.0570
   chunk 74 optimal weight:    7.9990
   chunk 41 optimal weight:    0.5980
   chunk 24 optimal weight:    0.9990
   chunk 14 optimal weight:    4.9990
   chunk 98 optimal weight:    5.9990
   overall best weight:    0.6098
-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

Flipped N/Q/H residues before XYZ refinement:
B  54 ASN
B 219 HIS
** B 306 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
Update NCS operators
********************
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3408 r_free = 0.3408 target = 0.109916 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3099 r_free = 0.3099 target = 0.088299 restraints weight = 5232.621|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3153 r_free = 0.3153 target = 0.091861 restraints weight = 3423.698|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3195 r_free = 0.3195 target = 0.094562 restraints weight = 2419.108|
|-----------------------------------------------------------------------------|
r_work (final): 0.3191
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7831
moved from start:          0.6344

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030  10672  Z= 0.116
  Angle     :  0.633   7.821  14464  Z= 0.306
  Chirality :  0.042   0.129   1644
  Planarity :  0.004   0.044   1880
  Dihedral  :  4.275  15.487   1472
  Min Nonbonded Distance : 2.513

Molprobity Statistics.
  All-atom Clashscore : 14.24
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.52 %
    Favored  : 96.48 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.72 %
    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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.54 (0.23), residues: 1364
  helix:  1.56 (0.19), residues: 700
  sheet: -1.07 (0.30), residues: 220
  loop : -0.73 (0.30), residues: 444

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.037   0.003   TRP C 295 
 HIS   0.008   0.001   HIS B 219 
 PHE   0.029   0.003   PHE C 299 
 TYR   0.008   0.001   TYR D 203 
 ARG   0.002   0.000   ARG C  55 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03107 (  564)
  hydrogen bonds       : angle       4.11309 ( 1632)
  covalent geometry    : bond        0.00280 (10672)
  covalent geometry    : angle       0.63262 (14464)

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

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

  2046 Ramachandran restraints generated.
    1023 Oldfield, 0 Emsley, 1023 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2046 Ramachandran restraints generated.
    1023 Oldfield, 0 Emsley, 1023 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: 0
    poor density    : 119
  time to evaluate  : 0.337 
Fit side-chains
   revert: symmetry clash
REVERT: B   12 LYS cc_start: 0.9110 (mttt) cc_final: 0.8695 (mmtp)
REVERT: B   14 GLU cc_start: 0.9075 (mm-30) cc_final: 0.8649 (mm-30)
REVERT: B   61 LEU cc_start: 0.8758 (mt) cc_final: 0.8393 (mt)
REVERT: B   72 CYS cc_start: 0.8946 (m) cc_final: 0.8672 (m)
REVERT: B  115 LEU cc_start: 0.8277 (mm) cc_final: 0.8038 (mp)
REVERT: B  128 ASP cc_start: 0.8418 (t0) cc_final: 0.7667 (m-30)
REVERT: B  140 ASP cc_start: 0.8622 (m-30) cc_final: 0.8397 (m-30)
REVERT: B  165 GLU cc_start: 0.8726 (tm-30) cc_final: 0.8340 (tm-30)
REVERT: B  195 ASP cc_start: 0.8933 (p0) cc_final: 0.8406 (t0)
REVERT: B  237 HIS cc_start: 0.8360 (t70) cc_final: 0.8014 (t70)
REVERT: B  246 GLU cc_start: 0.9572 (mp0) cc_final: 0.9263 (pm20)
REVERT: B  250 MET cc_start: 0.9356 (tpp) cc_final: 0.9129 (tpp)
REVERT: B  269 PHE cc_start: 0.8049 (m-80) cc_final: 0.7631 (m-80)
REVERT: B  270 LEU cc_start: 0.8366 (mm) cc_final: 0.8111 (mm)
REVERT: B  282 ASN cc_start: 0.8923 (m110) cc_final: 0.8691 (m110)
REVERT: B  305 LEU cc_start: 0.9260 (tp) cc_final: 0.8790 (tp)
REVERT: B  313 TRP cc_start: 0.8018 (t60) cc_final: 0.7151 (t60)
REVERT: B  329 LYS cc_start: 0.8953 (ptmt) cc_final: 0.8277 (ptmt)
REVERT: B  332 LEU cc_start: 0.8552 (tp) cc_final: 0.8196 (pp)
  outliers start: 0
  outliers final: 0
  residues processed: 119
  average time/residue: 0.1423
  time to fit residues: 20.2944
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  : 0.399 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 136
   random chunks:
   chunk 12 optimal weight:    0.0070
   chunk 135 optimal weight:    5.9990
   chunk 125 optimal weight:    5.9990
   chunk 95 optimal weight:    0.3980
   chunk 66 optimal weight:    2.9990
   chunk 114 optimal weight:    0.0070
   chunk 119 optimal weight:    1.9990
   chunk 80 optimal weight:    0.7980
   chunk 68 optimal weight:    9.9990
   chunk 5 optimal weight:    0.8980
   chunk 91 optimal weight:    0.0970
   overall best weight:    0.2614
-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

Flipped N/Q/H residues before XYZ refinement:
B 282 ASN
B 306 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
Update NCS operators
********************
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3454 r_free = 0.3454 target = 0.112378 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3136 r_free = 0.3136 target = 0.090963 restraints weight = 5356.370|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 25)----------------|
| r_work = 0.3194 r_free = 0.3194 target = 0.094702 restraints weight = 3395.557|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3238 r_free = 0.3238 target = 0.097500 restraints weight = 2353.360|
|-----------------------------------------------------------------------------|
r_work (final): 0.3231
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7791
moved from start:          0.6564

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= 0.120
  Angle     :  0.636   7.032  14464  Z= 0.312
  Chirality :  0.042   0.130   1644
  Planarity :  0.005   0.044   1880
  Dihedral  :  4.389  21.659   1472
  Min Nonbonded Distance : 2.454

Molprobity Statistics.
  All-atom Clashscore : 13.58
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.81 %
    Favored  : 96.19 %
  Rotamer:
    Outliers :  0.36 %
    Allowed  :  0.00 %
    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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.64 (0.23), residues: 1364
  helix:  1.63 (0.19), residues: 696
  sheet: -1.09 (0.30), residues: 220
  loop : -0.59 (0.30), residues: 448

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.036   0.003   TRP A 295 
 HIS   0.002   0.000   HIS C 220 
 PHE   0.023   0.003   PHE A 299 
 TYR   0.007   0.001   TYR A 203 
 ARG   0.003   0.000   ARG B  42 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02956 (  564)
  hydrogen bonds       : angle       4.10334 ( 1632)
  covalent geometry    : bond        0.00282 (10672)
  covalent geometry    : angle       0.63595 (14464)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3033.27 seconds
wall clock time: 57 minutes 27.70 seconds (3447.70 seconds total)