Starting phenix.real_space_refine
on Fri Feb 14 19:31:23 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7k9l_22754/02_2025/7k9l_22754.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7k9l_22754/02_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_22754/02_2025/7k9l_22754.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7k9l_22754/02_2025/7k9l_22754.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7k9l_22754/02_2025/7k9l_22754.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7k9l_22754/02_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-5592/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: 5.31, 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: 2.68
  Conformation dependent library (CDL) restraints added in 1.4 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: 1.23
  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: 3.25

  Time building geometry restraints manager: 3.14 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:             3.050
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.380
  Check model and map are aligned:         0.080
  Set scattering table:                    0.100
  Process input model:                     24.940
  Find NCS groups from input model:        0.210
  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:2.840
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   31.630
-------------------------------------------------------------------------------
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= 0.482
  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 

*********************** 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  : 0.296 
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: 0.1787
  time to fit residues: 32.2628
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  : 0.295 
-------------------------------------------------------------------------------
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 = 38)----------------|
| r_work = 0.2846 r_free = 0.2846 target = 0.074663 restraints weight = 5968.868|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.2900 r_free = 0.2900 target = 0.077746 restraints weight = 3810.883|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.2943 r_free = 0.2943 target = 0.080102 restraints weight = 2667.481|
|-----------------------------------------------------------------------------|
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= 0.359
  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 D 295 
 HIS   0.009   0.002   HIS A 219 
 PHE   0.023   0.003   PHE C  93 
 TYR   0.013   0.002   TYR C 327 
 ARG   0.006   0.001   ARG D 257 

*********************** 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  : 0.318 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: D    7 LEU cc_start: 0.9029 (mt) cc_final: 0.8399 (mt)
REVERT: D   14 GLU cc_start: 0.8871 (mp0) cc_final: 0.8587 (mm-30)
REVERT: D   61 LEU cc_start: 0.8859 (mt) cc_final: 0.8100 (mp)
REVERT: D   72 CYS cc_start: 0.8919 (m) cc_final: 0.8713 (m)
REVERT: D   79 PHE cc_start: 0.8048 (t80) cc_final: 0.7798 (t80)
REVERT: D  104 VAL cc_start: 0.8720 (t) cc_final: 0.8399 (t)
REVERT: D  138 LYS cc_start: 0.8491 (tptt) cc_final: 0.7908 (ttmt)
REVERT: D  178 GLN cc_start: 0.9044 (mt0) cc_final: 0.8765 (mt0)
REVERT: D  195 ASP cc_start: 0.8886 (p0) cc_final: 0.8039 (t0)
REVERT: D  248 ILE cc_start: 0.9512 (mt) cc_final: 0.9279 (tt)
REVERT: D  284 ASN cc_start: 0.8184 (t0) cc_final: 0.7484 (t0)
REVERT: D  305 LEU cc_start: 0.9396 (tp) cc_final: 0.9078 (tp)
REVERT: D  313 TRP cc_start: 0.8032 (t60) cc_final: 0.6638 (t60)
REVERT: D  326 GLU cc_start: 0.9133 (mm-30) cc_final: 0.8612 (mm-30)
REVERT: D  329 LYS cc_start: 0.8848 (mttp) cc_final: 0.8236 (mttm)
REVERT: D  332 LEU cc_start: 0.8492 (tp) cc_final: 0.8187 (pp)
  outliers start: 4
  outliers final: 1
  residues processed: 131
  average time/residue: 0.1649
  time to fit residues: 25.0511
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  : 0.353 
-------------------------------------------------------------------------------
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:    6.9990
   chunk 93 optimal weight:    0.5980
   chunk 60 optimal weight:    0.9980
   chunk 22 optimal weight:    8.9990
   chunk 35 optimal weight:    4.9990
   chunk 112 optimal weight:    6.9990
   chunk 95 optimal weight:    1.9990
   chunk 77 optimal weight:    5.9990
   chunk 76 optimal weight:    0.0060
   chunk 2 optimal weight:    0.9980
   overall best weight:    0.9198
-------------------------------------------------------------------------------
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 = 0.104553 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.2999 r_free = 0.2999 target = 0.082378 restraints weight = 5526.258|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3055 r_free = 0.3055 target = 0.085670 restraints weight = 3579.027|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3098 r_free = 0.3098 target = 0.088228 restraints weight = 2519.391|
|-----------------------------------------------------------------------------|
r_work (final): 0.3084
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7863
moved from start:          0.4519

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.045  10672  Z= 0.209
  Angle     :  0.657   8.934  14464  Z= 0.325
  Chirality :  0.043   0.131   1644
  Planarity :  0.005   0.051   1880
  Dihedral  :  5.029  18.427   1472
  Min Nonbonded Distance : 2.531

Molprobity Statistics.
  All-atom Clashscore : 13.82
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.93 %
    Favored  : 97.07 %
  Rotamer:
    Outliers :  0.36 %
    Allowed  :  3.96 %
    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:  0.16 (0.22), residues: 1364
  helix:  0.94 (0.19), residues: 696
  sheet: -1.28 (0.35), residues: 200
  loop : -0.33 (0.28), residues: 468

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.020   0.002   TRP C 295 
 HIS   0.007   0.001   HIS C 219 
 PHE   0.009   0.001   PHE A 144 
 TYR   0.012   0.001   TYR A 203 
 ARG   0.006   0.001   ARG A  42 

*********************** 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
  127 residues out of total 278 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 126
  time to evaluate  : 0.273 
Fit side-chains
   revert: symmetry clash
REVERT: D    7 LEU cc_start: 0.8974 (mt) cc_final: 0.8757 (mt)
REVERT: D   12 LYS cc_start: 0.9071 (mttt) cc_final: 0.8733 (mmtp)
REVERT: D  138 LYS cc_start: 0.8381 (tptt) cc_final: 0.7777 (ttmt)
REVERT: D  229 LYS cc_start: 0.8149 (tttp) cc_final: 0.7761 (tptp)
REVERT: D  276 GLU cc_start: 0.7869 (pm20) cc_final: 0.7092 (pm20)
REVERT: D  277 GLU cc_start: 0.8967 (mm-30) cc_final: 0.8145 (mm-30)
REVERT: D  282 ASN cc_start: 0.9144 (m-40) cc_final: 0.8806 (m-40)
REVERT: D  283 LEU cc_start: 0.9311 (tp) cc_final: 0.9097 (tp)
REVERT: D  284 ASN cc_start: 0.8145 (t0) cc_final: 0.7908 (m-40)
REVERT: D  293 LYS cc_start: 0.8777 (pptt) cc_final: 0.8568 (pptt)
REVERT: D  303 ARG cc_start: 0.8663 (ttm-80) cc_final: 0.8366 (ttm-80)
REVERT: D  305 LEU cc_start: 0.9390 (tp) cc_final: 0.8992 (tp)
REVERT: D  311 LYS cc_start: 0.8850 (ttpt) cc_final: 0.8625 (pttm)
REVERT: D  325 GLU cc_start: 0.9120 (tp30) cc_final: 0.8658 (tp30)
REVERT: D  326 GLU cc_start: 0.9140 (mm-30) cc_final: 0.8788 (mm-30)
REVERT: D  329 LYS cc_start: 0.8782 (mttp) cc_final: 0.8323 (mttm)
REVERT: D  332 LEU cc_start: 0.8398 (tp) cc_final: 0.8073 (pp)
REVERT: D  336 LEU cc_start: 0.8895 (mt) cc_final: 0.8683 (mt)
  outliers start: 1
  outliers final: 0
  residues processed: 127
  average time/residue: 0.1460
  time to fit residues: 21.6937
Evaluate side-chains
  98 residues out of total 278 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 98
  time to evaluate  : 0.285 
-------------------------------------------------------------------------------
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:    0.0070
   chunk 106 optimal weight:    9.9990
   chunk 117 optimal weight:   20.0000
   chunk 110 optimal weight:    0.0980
   chunk 74 optimal weight:    0.7980
   chunk 67 optimal weight:    6.9990
   chunk 111 optimal weight:    5.9990
   chunk 96 optimal weight:    0.7980
   chunk 11 optimal weight:    4.9990
   chunk 103 optimal weight:    5.9990
   chunk 68 optimal weight:    7.9990
   overall best weight:    1.3400
-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

Flipped N/Q/H residues before XYZ refinement:
B  44 GLN
B 287 ASN
** 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 = 0.3361 r_free = 0.3361 target = 0.105677 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3022 r_free = 0.3022 target = 0.083799 restraints weight = 5742.542|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3079 r_free = 0.3079 target = 0.087241 restraints weight = 3735.404|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3121 r_free = 0.3121 target = 0.089864 restraints weight = 2629.089|
|-----------------------------------------------------------------------------|
r_work (final): 0.3115
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7887
moved from start:          0.5087

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= 0.205
  Angle     :  0.601   7.517  14464  Z= 0.302
  Chirality :  0.041   0.137   1644
  Planarity :  0.005   0.053   1880
  Dihedral  :  4.755  16.641   1472
  Min Nonbonded Distance : 2.545

Molprobity Statistics.
  All-atom Clashscore : 15.86
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.11 %
    Favored  : 95.89 %
  Rotamer:
    Outliers :  0.36 %
    Allowed  :  2.88 %
    Favored  : 96.76 %
  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:  0.42 (0.22), residues: 1364
  helix:  1.23 (0.19), residues: 700
  sheet: -1.30 (0.34), residues: 200
  loop : -0.29 (0.29), residues: 464

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.023   0.002   TRP C 295 
 HIS   0.005   0.001   HIS D 219 
 PHE   0.010   0.002   PHE D 144 
 TYR   0.012   0.001   TYR C 213 
 ARG   0.005   0.001   ARG C  42 

*********************** 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
  126 residues out of total 278 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 125
  time to evaluate  : 0.285 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   14 GLU cc_start: 0.8938 (mp0) cc_final: 0.8607 (mm-30)
REVERT: B   30 LEU cc_start: 0.8244 (tt) cc_final: 0.7833 (tp)
REVERT: B   99 SER cc_start: 0.8800 (p) cc_final: 0.8557 (p)
REVERT: B  128 ASP cc_start: 0.8416 (t0) cc_final: 0.8199 (t70)
REVERT: B  138 LYS cc_start: 0.8416 (tptt) cc_final: 0.7845 (ttmt)
REVERT: B  140 ASP cc_start: 0.8574 (m-30) cc_final: 0.8298 (m-30)
REVERT: B  191 LEU cc_start: 0.9486 (tp) cc_final: 0.9275 (tp)
REVERT: B  195 ASP cc_start: 0.8937 (p0) cc_final: 0.8298 (t0)
REVERT: B  214 LYS cc_start: 0.9264 (tmtt) cc_final: 0.8757 (tppt)
REVERT: B  247 GLU cc_start: 0.9147 (mt-10) cc_final: 0.8688 (mt-10)
REVERT: B  250 MET cc_start: 0.9125 (ttp) cc_final: 0.8911 (tpp)
REVERT: B  276 GLU cc_start: 0.7958 (pm20) cc_final: 0.7715 (pm20)
REVERT: B  282 ASN cc_start: 0.9059 (m-40) cc_final: 0.8799 (m-40)
REVERT: B  283 LEU cc_start: 0.9242 (tp) cc_final: 0.9008 (tp)
REVERT: B  305 LEU cc_start: 0.9341 (tp) cc_final: 0.8541 (tp)
REVERT: B  332 LEU cc_start: 0.8368 (tp) cc_final: 0.8064 (pp)
  outliers start: 1
  outliers final: 0
  residues processed: 125
  average time/residue: 0.1530
  time to fit residues: 22.5185
Evaluate side-chains
  101 residues out of total 278 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 101
  time to evaluate  : 0.288 
-------------------------------------------------------------------------------
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:    2.9990
   chunk 122 optimal weight:    0.8980
   chunk 8 optimal weight:    0.0040
   chunk 63 optimal weight:    4.9990
   chunk 135 optimal weight:    6.9990
   chunk 134 optimal weight:    6.9990
   chunk 66 optimal weight:    7.9990
   chunk 9 optimal weight:    6.9990
   chunk 52 optimal weight:    0.9980
   chunk 123 optimal weight:    3.9990
   chunk 14 optimal weight:    3.9990
   overall best weight:    1.7796
-------------------------------------------------------------------------------
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 ** both conformations clash, **PLEASE CHECK MANUALLY**
B 334 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
Update NCS operators
********************
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3366 r_free = 0.3366 target = 0.105986 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3028 r_free = 0.3028 target = 0.084169 restraints weight = 5713.890|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3084 r_free = 0.3084 target = 0.087619 restraints weight = 3710.318|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3125 r_free = 0.3125 target = 0.090181 restraints weight = 2614.567|
|-----------------------------------------------------------------------------|
r_work (final): 0.3123
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7884
moved from start:          0.5450

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042  10672  Z= 0.220
  Angle     :  0.613   7.109  14464  Z= 0.309
  Chirality :  0.041   0.138   1644
  Planarity :  0.005   0.059   1880
  Dihedral  :  4.730  16.867   1472
  Min Nonbonded Distance : 2.443

Molprobity Statistics.
  All-atom Clashscore : 15.67
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.81 %
    Favored  : 96.19 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  3.60 %
    Favored  : 96.40 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.56 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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:  0.35 (0.22), residues: 1364
  helix:  1.09 (0.19), residues: 704
  sheet: -1.09 (0.32), residues: 220
  loop : -0.24 (0.31), residues: 440

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.025   0.002   TRP D 295 
 HIS   0.007   0.001   HIS B 219 
 PHE   0.015   0.002   PHE D 299 
 TYR   0.012   0.001   TYR D 213 
 ARG   0.006   0.001   ARG C  42 

*********************** 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
  127 residues out of total 278 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 127
  time to evaluate  : 0.279 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B    7 LEU cc_start: 0.8882 (mt) cc_final: 0.8437 (mt)
REVERT: B   10 GLU cc_start: 0.9057 (pm20) cc_final: 0.8641 (mp0)
REVERT: B   27 LYS cc_start: 0.8374 (mmtt) cc_final: 0.8156 (mmmt)
REVERT: B   30 LEU cc_start: 0.8216 (tt) cc_final: 0.7663 (tp)
REVERT: B   79 PHE cc_start: 0.8101 (t80) cc_final: 0.7806 (t80)
REVERT: B  128 ASP cc_start: 0.8441 (t0) cc_final: 0.7661 (m-30)
REVERT: B  138 LYS cc_start: 0.8430 (tptt) cc_final: 0.7833 (ttmt)
REVERT: B  140 ASP cc_start: 0.8605 (m-30) cc_final: 0.8332 (m-30)
REVERT: B  178 GLN cc_start: 0.8859 (mt0) cc_final: 0.8593 (tp40)
REVERT: B  195 ASP cc_start: 0.8942 (p0) cc_final: 0.8282 (t0)
REVERT: B  221 ILE cc_start: 0.9103 (tp) cc_final: 0.8750 (tp)
REVERT: B  276 GLU cc_start: 0.7990 (pm20) cc_final: 0.7587 (pm20)
REVERT: B  293 LYS cc_start: 0.8893 (pptt) cc_final: 0.8613 (pptt)
REVERT: B  305 LEU cc_start: 0.9380 (tp) cc_final: 0.8689 (tp)
REVERT: B  325 GLU cc_start: 0.9059 (tp30) cc_final: 0.8746 (tp30)
REVERT: B  332 LEU cc_start: 0.8367 (tp) cc_final: 0.8151 (tp)
  outliers start: 0
  outliers final: 0
  residues processed: 127
  average time/residue: 0.1419
  time to fit residues: 21.2482
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  : 0.338 
-------------------------------------------------------------------------------
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:    5.9990
   chunk 36 optimal weight:    5.9990
   chunk 117 optimal weight:   20.0000
   chunk 98 optimal weight:    4.9990
   chunk 28 optimal weight:    1.9990
   chunk 17 optimal weight:    0.9980
   chunk 78 optimal weight:    0.8980
   chunk 93 optimal weight:    0.8980
   chunk 29 optimal weight:    4.9990
   chunk 127 optimal weight:    0.9990
   chunk 35 optimal weight:    3.9990
   overall best weight:    1.1584
-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

Flipped N/Q/H residues before XYZ refinement:
B  44 GLN
B  54 ASN
** B  60 GLN ** 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 = 0.3386 r_free = 0.3386 target = 0.108040 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3052 r_free = 0.3052 target = 0.085735 restraints weight = 5724.324|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3109 r_free = 0.3109 target = 0.089399 restraints weight = 3663.449|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3151 r_free = 0.3151 target = 0.092135 restraints weight = 2550.139|
|-----------------------------------------------------------------------------|
r_work (final): 0.3142
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7853
moved from start:          0.5693

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= 0.194
  Angle     :  0.620   8.223  14464  Z= 0.310
  Chirality :  0.041   0.138   1644
  Planarity :  0.005   0.047   1880
  Dihedral  :  4.617  16.437   1472
  Min Nonbonded Distance : 2.480

Molprobity Statistics.
  All-atom Clashscore : 14.15
  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:  0.34 (0.22), residues: 1364
  helix:  1.11 (0.19), residues: 704
  sheet: -1.14 (0.31), residues: 220
  loop : -0.28 (0.31), residues: 440

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.028   0.003   TRP C 295 
 HIS   0.005   0.001   HIS C 219 
 PHE   0.010   0.002   PHE C  93 
 TYR   0.010   0.001   TYR D 213 
 ARG   0.006   0.001   ARG B  42 

*********************** 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
  126 residues out of total 278 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 126
  time to evaluate  : 0.305 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B    7 LEU cc_start: 0.8928 (mt) cc_final: 0.8440 (mt)
REVERT: B   10 GLU cc_start: 0.9273 (pm20) cc_final: 0.8521 (mp0)
REVERT: B   12 LYS cc_start: 0.9149 (mttt) cc_final: 0.8686 (mtpp)
REVERT: B   14 GLU cc_start: 0.8879 (mp0) cc_final: 0.8585 (mm-30)
REVERT: B   30 LEU cc_start: 0.8155 (tt) cc_final: 0.7667 (tp)
REVERT: B   61 LEU cc_start: 0.9064 (mt) cc_final: 0.8682 (mt)
REVERT: B  128 ASP cc_start: 0.8409 (t0) cc_final: 0.7607 (m-30)
REVERT: B  138 LYS cc_start: 0.8388 (tptt) cc_final: 0.7927 (tttt)
REVERT: B  140 ASP cc_start: 0.8537 (m-30) cc_final: 0.8260 (m-30)
REVERT: B  156 HIS cc_start: 0.8535 (m90) cc_final: 0.7925 (m170)
REVERT: B  178 GLN cc_start: 0.8816 (mt0) cc_final: 0.8531 (tp40)
REVERT: B  195 ASP cc_start: 0.8972 (p0) cc_final: 0.8300 (t0)
REVERT: B  221 ILE cc_start: 0.9060 (tp) cc_final: 0.8715 (tp)
REVERT: B  229 LYS cc_start: 0.7941 (tttp) cc_final: 0.7618 (tptp)
REVERT: B  250 MET cc_start: 0.9466 (tpp) cc_final: 0.9093 (tpp)
REVERT: B  276 GLU cc_start: 0.8056 (pm20) cc_final: 0.7707 (pm20)
REVERT: B  305 LEU cc_start: 0.9356 (tp) cc_final: 0.8621 (tp)
REVERT: B  313 TRP cc_start: 0.7967 (t60) cc_final: 0.6915 (t60)
REVERT: B  325 GLU cc_start: 0.9030 (tp30) cc_final: 0.8612 (tp30)
REVERT: B  329 LYS cc_start: 0.8731 (mttp) cc_final: 0.8464 (mttt)
REVERT: B  332 LEU cc_start: 0.8417 (tp) cc_final: 0.8138 (pp)
  outliers start: 0
  outliers final: 0
  residues processed: 126
  average time/residue: 0.1431
  time to fit residues: 21.3414
Evaluate side-chains
  93 residues out of total 278 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 93
  time to evaluate  : 0.274 
-------------------------------------------------------------------------------
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:    0.2980
   chunk 124 optimal weight:    0.6980
   chunk 90 optimal weight:    0.9980
   chunk 85 optimal weight:    0.6980
   chunk 97 optimal weight:    3.9990
   chunk 0 optimal weight:    8.9990
   chunk 41 optimal weight:    9.9990
   chunk 86 optimal weight:    0.0050
   chunk 107 optimal weight:    4.9990
   chunk 25 optimal weight:    0.4980
   chunk 16 optimal weight:    5.9990
   overall best weight:    0.4394
-------------------------------------------------------------------------------
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 = 0.3429 r_free = 0.3429 target = 0.110571 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3102 r_free = 0.3102 target = 0.088413 restraints weight = 5753.006|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3161 r_free = 0.3161 target = 0.092186 restraints weight = 3704.984|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3203 r_free = 0.3203 target = 0.094954 restraints weight = 2579.410|
|-----------------------------------------------------------------------------|
r_work (final): 0.3195
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7801
moved from start:          0.6025

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= 0.178
  Angle     :  0.619   7.918  14464  Z= 0.302
  Chirality :  0.042   0.130   1644
  Planarity :  0.005   0.044   1880
  Dihedral  :  4.420  16.533   1472
  Min Nonbonded Distance : 2.566

Molprobity Statistics.
  All-atom Clashscore : 14.34
  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:  0.56 (0.22), residues: 1364
  helix:  1.32 (0.19), residues: 696
  sheet: -0.84 (0.30), residues: 220
  loop : -0.34 (0.30), residues: 448

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.031   0.003   TRP C 295 
 HIS   0.006   0.001   HIS B 219 
 PHE   0.009   0.002   PHE B 144 
 TYR   0.009   0.001   TYR D 203 
 ARG   0.005   0.000   ARG A  42 

*********************** 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
  120 residues out of total 278 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 119
  time to evaluate  : 0.323 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B    7 LEU cc_start: 0.8879 (mt) cc_final: 0.8355 (mt)
REVERT: B   12 LYS cc_start: 0.9133 (mttt) cc_final: 0.8655 (mtpp)
REVERT: B   14 GLU cc_start: 0.9015 (mm-30) cc_final: 0.8713 (mm-30)
REVERT: B   61 LEU cc_start: 0.8999 (mt) cc_final: 0.8589 (mt)
REVERT: B  106 ILE cc_start: 0.8759 (tt) cc_final: 0.8558 (tt)
REVERT: B  115 LEU cc_start: 0.7600 (mm) cc_final: 0.7328 (mp)
REVERT: B  128 ASP cc_start: 0.8350 (t0) cc_final: 0.7520 (m-30)
REVERT: B  130 LEU cc_start: 0.8847 (mt) cc_final: 0.8618 (mt)
REVERT: B  138 LYS cc_start: 0.8361 (tptt) cc_final: 0.7815 (tttt)
REVERT: B  140 ASP cc_start: 0.8657 (m-30) cc_final: 0.8439 (m-30)
REVERT: B  178 GLN cc_start: 0.8817 (mt0) cc_final: 0.8470 (tp40)
REVERT: B  195 ASP cc_start: 0.8852 (p0) cc_final: 0.8303 (t0)
REVERT: B  221 ILE cc_start: 0.8905 (tp) cc_final: 0.8532 (tp)
REVERT: B  232 MET cc_start: 0.8503 (mtp) cc_final: 0.7725 (mtm)
REVERT: B  250 MET cc_start: 0.9446 (tpp) cc_final: 0.9143 (tpp)
REVERT: B  269 PHE cc_start: 0.8176 (m-80) cc_final: 0.7801 (m-10)
REVERT: B  276 GLU cc_start: 0.8104 (pm20) cc_final: 0.7768 (pm20)
REVERT: B  282 ASN cc_start: 0.8854 (m110) cc_final: 0.8610 (m110)
REVERT: B  305 LEU cc_start: 0.9292 (tp) cc_final: 0.8774 (tp)
REVERT: B  313 TRP cc_start: 0.8171 (t60) cc_final: 0.6935 (t60)
REVERT: B  332 LEU cc_start: 0.8363 (tp) cc_final: 0.8079 (pp)
  outliers start: 1
  outliers final: 1
  residues processed: 120
  average time/residue: 0.1346
  time to fit residues: 19.3332
Evaluate side-chains
  91 residues out of total 278 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 90
  time to evaluate  : 0.286 
-------------------------------------------------------------------------------
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:    0.9990
   chunk 35 optimal weight:    5.9990
   chunk 100 optimal weight:    4.9990
   chunk 124 optimal weight:    0.7980
   chunk 40 optimal weight:    0.3980
   chunk 88 optimal weight:    0.9980
   chunk 101 optimal weight:    6.9990
   chunk 21 optimal weight:    4.9990
   chunk 38 optimal weight:    6.9990
   chunk 103 optimal weight:    5.9990
   chunk 86 optimal weight:    1.9990
   overall best weight:    1.0384
-------------------------------------------------------------------------------
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 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 = 0.3416 r_free = 0.3416 target = 0.109724 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3092 r_free = 0.3092 target = 0.088055 restraints weight = 5584.523|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3146 r_free = 0.3146 target = 0.091631 restraints weight = 3590.782|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3188 r_free = 0.3188 target = 0.094390 restraints weight = 2529.402|
|-----------------------------------------------------------------------------|
r_work (final): 0.3197
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7831
moved from start:          0.6187

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.025  10672  Z= 0.195
  Angle     :  0.642   8.187  14464  Z= 0.318
  Chirality :  0.041   0.120   1644
  Planarity :  0.005   0.042   1880
  Dihedral  :  4.416  16.692   1472
  Min Nonbonded Distance : 2.417

Molprobity Statistics.
  All-atom Clashscore : 15.29
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.81 %
    Favored  : 96.19 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.08 %
    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:  0.32 (0.22), residues: 1364
  helix:  1.23 (0.19), residues: 700
  sheet: -1.08 (0.29), residues: 220
  loop : -0.59 (0.30), residues: 444

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.036   0.003   TRP C 295 
 HIS   0.007   0.001   HIS B 219 
 PHE   0.020   0.002   PHE D  79 
 TYR   0.010   0.002   TYR B 137 
 ARG   0.008   0.001   ARG D  42 

*********************** 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
  119 residues out of total 278 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 119
  time to evaluate  : 0.313 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B    7 LEU cc_start: 0.8800 (mt) cc_final: 0.7907 (mt)
REVERT: B   12 LYS cc_start: 0.9129 (mttt) cc_final: 0.8665 (mtpp)
REVERT: B   14 GLU cc_start: 0.9029 (mm-30) cc_final: 0.8731 (mm-30)
REVERT: B   30 LEU cc_start: 0.7466 (tt) cc_final: 0.7060 (mt)
REVERT: B   61 LEU cc_start: 0.8963 (mt) cc_final: 0.8561 (mt)
REVERT: B   72 CYS cc_start: 0.8912 (m) cc_final: 0.8668 (m)
REVERT: B   80 HIS cc_start: 0.8753 (t70) cc_final: 0.8527 (t70)
REVERT: B  115 LEU cc_start: 0.7780 (mm) cc_final: 0.7543 (mp)
REVERT: B  128 ASP cc_start: 0.8363 (t0) cc_final: 0.7524 (m-30)
REVERT: B  130 LEU cc_start: 0.8880 (mt) cc_final: 0.8650 (mt)
REVERT: B  138 LYS cc_start: 0.8449 (tptt) cc_final: 0.7818 (ttmt)
REVERT: B  140 ASP cc_start: 0.8710 (m-30) cc_final: 0.8481 (m-30)
REVERT: B  178 GLN cc_start: 0.8814 (mt0) cc_final: 0.8209 (mt0)
REVERT: B  195 ASP cc_start: 0.8912 (p0) cc_final: 0.8359 (t0)
REVERT: B  214 LYS cc_start: 0.9204 (tmtt) cc_final: 0.8727 (tppt)
REVERT: B  221 ILE cc_start: 0.8903 (tp) cc_final: 0.8645 (tp)
REVERT: B  232 MET cc_start: 0.8554 (mtp) cc_final: 0.7775 (mtm)
REVERT: B  250 MET cc_start: 0.9430 (tpp) cc_final: 0.9133 (tpp)
REVERT: B  258 ARG cc_start: 0.8763 (mtt180) cc_final: 0.8471 (mtt-85)
REVERT: B  269 PHE cc_start: 0.8215 (m-80) cc_final: 0.7990 (m-10)
REVERT: B  270 LEU cc_start: 0.8493 (mm) cc_final: 0.7819 (mm)
REVERT: B  276 GLU cc_start: 0.8090 (pm20) cc_final: 0.7778 (pm20)
REVERT: B  282 ASN cc_start: 0.8869 (m110) cc_final: 0.8586 (m110)
REVERT: B  293 LYS cc_start: 0.8746 (pptt) cc_final: 0.8490 (pptt)
REVERT: B  305 LEU cc_start: 0.9349 (tp) cc_final: 0.8685 (tp)
REVERT: B  313 TRP cc_start: 0.8001 (t60) cc_final: 0.7053 (t60)
REVERT: B  332 LEU cc_start: 0.8333 (tp) cc_final: 0.8019 (pp)
  outliers start: 0
  outliers final: 0
  residues processed: 119
  average time/residue: 0.1394
  time to fit residues: 19.6910
Evaluate side-chains
  96 residues out of total 278 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 96
  time to evaluate  : 0.301 
-------------------------------------------------------------------------------
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:    4.9990
   chunk 101 optimal weight:    6.9990
   chunk 84 optimal weight:    6.9990
   chunk 28 optimal weight:    3.9990
   chunk 46 optimal weight:    6.9990
   chunk 118 optimal weight:    6.9990
   chunk 2 optimal weight:    8.9990
   chunk 110 optimal weight:    0.0470
   chunk 32 optimal weight:    0.9980
   chunk 115 optimal weight:    0.1980
   chunk 12 optimal weight:    5.9990
   overall best weight:    2.0482
-------------------------------------------------------------------------------
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**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
Update NCS operators
********************
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3382 r_free = 0.3382 target = 0.106163 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3045 r_free = 0.3045 target = 0.085353 restraints weight = 5686.122|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3105 r_free = 0.3105 target = 0.088975 restraints weight = 3589.454|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3147 r_free = 0.3147 target = 0.091586 restraints weight = 2477.809|
|-----------------------------------------------------------------------------|
r_work (final): 0.3140
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7914
moved from start:          0.6183

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.038  10672  Z= 0.240
  Angle     :  0.657   7.633  14464  Z= 0.329
  Chirality :  0.042   0.149   1644
  Planarity :  0.005   0.042   1880
  Dihedral  :  4.594  17.166   1472
  Min Nonbonded Distance : 2.499

Molprobity Statistics.
  All-atom Clashscore : 16.57
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.11 %
    Favored  : 95.89 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.08 %
    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:  0.26 (0.22), residues: 1364
  helix:  1.28 (0.19), residues: 696
  sheet: -1.77 (0.29), residues: 220
  loop : -0.37 (0.30), residues: 448

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.038   0.004   TRP C 295 
 HIS   0.006   0.001   HIS B 219 
 PHE   0.018   0.002   PHE C  79 
 TYR   0.011   0.002   TYR A 213 
 ARG   0.007   0.001   ARG C  42 

*********************** 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: 0
    poor density    : 115
  time to evaluate  : 0.318 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   12 LYS cc_start: 0.9134 (mttt) cc_final: 0.8674 (mtpp)
REVERT: B   14 GLU cc_start: 0.9006 (mm-30) cc_final: 0.8667 (mm-30)
REVERT: B   30 LEU cc_start: 0.7912 (tt) cc_final: 0.7540 (mt)
REVERT: B   61 LEU cc_start: 0.8960 (mt) cc_final: 0.8661 (mt)
REVERT: B  128 ASP cc_start: 0.8434 (t0) cc_final: 0.8132 (t70)
REVERT: B  130 LEU cc_start: 0.8903 (mt) cc_final: 0.8674 (mt)
REVERT: B  140 ASP cc_start: 0.8801 (m-30) cc_final: 0.8573 (m-30)
REVERT: B  195 ASP cc_start: 0.8922 (p0) cc_final: 0.8321 (t0)
REVERT: B  232 MET cc_start: 0.8642 (mtp) cc_final: 0.8013 (mtm)
REVERT: B  250 MET cc_start: 0.9379 (tpp) cc_final: 0.9049 (tpp)
REVERT: B  269 PHE cc_start: 0.8310 (m-80) cc_final: 0.8012 (m-10)
REVERT: B  276 GLU cc_start: 0.8115 (pm20) cc_final: 0.7800 (pm20)
REVERT: B  283 LEU cc_start: 0.9177 (tp) cc_final: 0.8963 (tp)
REVERT: B  293 LYS cc_start: 0.8694 (pptt) cc_final: 0.8398 (pptt)
REVERT: B  303 ARG cc_start: 0.8244 (tpp80) cc_final: 0.7660 (mmm160)
REVERT: B  313 TRP cc_start: 0.8156 (t60) cc_final: 0.7538 (t60)
  outliers start: 0
  outliers final: 0
  residues processed: 115
  average time/residue: 0.1304
  time to fit residues: 18.0532
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  : 0.323 
-------------------------------------------------------------------------------
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:    2.9990
   chunk 73 optimal weight:    6.9990
   chunk 106 optimal weight:    0.9990
   chunk 132 optimal weight:    4.9990
   chunk 25 optimal weight:    2.9990
   chunk 12 optimal weight:    0.0670
   chunk 74 optimal weight:    7.9990
   chunk 41 optimal weight:    9.9990
   chunk 24 optimal weight:    0.9990
   chunk 14 optimal weight:    2.9990
   chunk 98 optimal weight:    3.9990
   overall best weight:    1.6126
-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

Flipped N/Q/H residues before XYZ refinement:
B 219 HIS
B 334 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
Update NCS operators
********************
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3383 r_free = 0.3383 target = 0.107390 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3032 r_free = 0.3032 target = 0.084817 restraints weight = 5519.137|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3093 r_free = 0.3093 target = 0.088467 restraints weight = 3643.753|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3135 r_free = 0.3135 target = 0.091082 restraints weight = 2580.979|
|-----------------------------------------------------------------------------|
r_work (final): 0.3128
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7874
moved from start:          0.6319

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= 0.231
  Angle     :  0.678   8.351  14464  Z= 0.335
  Chirality :  0.042   0.137   1644
  Planarity :  0.005   0.042   1880
  Dihedral  :  4.618  17.449   1472
  Min Nonbonded Distance : 2.517

Molprobity Statistics.
  All-atom Clashscore : 16.52
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.40 %
    Favored  : 95.60 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.00 %
    Favored  : 100.00 %
  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:  0.13 (0.23), residues: 1364
  helix:  1.26 (0.20), residues: 688
  sheet: -1.95 (0.30), residues: 212
  loop : -0.54 (0.29), residues: 464

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.034   0.003   TRP A 295 
 HIS   0.010   0.001   HIS B 219 
 PHE   0.028   0.003   PHE D  79 
 TYR   0.011   0.002   TYR C 137 
 ARG   0.008   0.000   ARG C  42 

********************** 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
  117 residues out of total 278 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 117
  time to evaluate  : 0.277 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B    7 LEU cc_start: 0.8725 (mt) cc_final: 0.8210 (mt)
REVERT: B   12 LYS cc_start: 0.9096 (mttt) cc_final: 0.8624 (mtpp)
REVERT: B   14 GLU cc_start: 0.9026 (mm-30) cc_final: 0.8695 (mm-30)
REVERT: B   30 LEU cc_start: 0.7835 (tt) cc_final: 0.7518 (mt)
REVERT: B   61 LEU cc_start: 0.8937 (mt) cc_final: 0.8541 (mt)
REVERT: B   81 GLU cc_start: 0.8789 (tm-30) cc_final: 0.8533 (tm-30)
REVERT: B  128 ASP cc_start: 0.8444 (t0) cc_final: 0.8132 (t70)
REVERT: B  130 LEU cc_start: 0.8839 (mt) cc_final: 0.8619 (mt)
REVERT: B  140 ASP cc_start: 0.8737 (m-30) cc_final: 0.8511 (m-30)
REVERT: B  165 GLU cc_start: 0.8435 (tt0) cc_final: 0.8065 (tt0)
REVERT: B  195 ASP cc_start: 0.8951 (p0) cc_final: 0.8312 (t0)
REVERT: B  221 ILE cc_start: 0.9009 (tp) cc_final: 0.8717 (tp)
REVERT: B  250 MET cc_start: 0.9410 (tpp) cc_final: 0.9091 (tpp)
REVERT: B  276 GLU cc_start: 0.8068 (pm20) cc_final: 0.7847 (pm20)
REVERT: B  282 ASN cc_start: 0.8691 (m110) cc_final: 0.8429 (m110)
REVERT: B  303 ARG cc_start: 0.8245 (tpp80) cc_final: 0.7704 (mmm160)
REVERT: B  313 TRP cc_start: 0.8014 (t60) cc_final: 0.7109 (t60)
REVERT: B  332 LEU cc_start: 0.8479 (tp) cc_final: 0.8264 (tp)
  outliers start: 0
  outliers final: 0
  residues processed: 117
  average time/residue: 0.1277
  time to fit residues: 17.9997
Evaluate side-chains
  89 residues out of total 278 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 89
  time to evaluate  : 0.288 
-------------------------------------------------------------------------------
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:    3.9990
   chunk 135 optimal weight:    5.9990
   chunk 125 optimal weight:    0.0870
   chunk 95 optimal weight:    0.8980
   chunk 66 optimal weight:    6.9990
   chunk 114 optimal weight:    3.9990
   chunk 119 optimal weight:    0.6980
   chunk 80 optimal weight:    4.9990
   chunk 68 optimal weight:    7.9990
   chunk 5 optimal weight:    0.9980
   chunk 91 optimal weight:    2.9990
   overall best weight:    1.1360
-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

Flipped N/Q/H residues before XYZ refinement:
B  54 ASN
** B  60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 178 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 = 0.3421 r_free = 0.3421 target = 0.111228 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3098 r_free = 0.3098 target = 0.089442 restraints weight = 5546.815|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3160 r_free = 0.3160 target = 0.093250 restraints weight = 3568.768|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3206 r_free = 0.3206 target = 0.096071 restraints weight = 2479.142|
|-----------------------------------------------------------------------------|
r_work (final): 0.3179
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7883
moved from start:          0.6550

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.043  10672  Z= 0.221
  Angle     :  0.665   8.530  14464  Z= 0.329
  Chirality :  0.042   0.131   1644
  Planarity :  0.005   0.042   1880
  Dihedral  :  4.626  17.370   1472
  Min Nonbonded Distance : 2.526

Molprobity Statistics.
  All-atom Clashscore : 16.66
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.11 %
    Favored  : 95.89 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.00 %
    Favored  : 100.00 %
  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: -0.01 (0.22), residues: 1364
  helix:  1.24 (0.19), residues: 692
  sheet: -2.06 (0.28), residues: 220
  loop : -0.72 (0.29), residues: 452

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.043   0.004   TRP C 295 
 HIS   0.006   0.001   HIS B 219 
 PHE   0.011   0.003   PHE C 144 
 TYR   0.012   0.002   TYR B 137 
 ARG   0.007   0.000   ARG C  42 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1924.52 seconds
wall clock time: 36 minutes 7.81 seconds (2167.81 seconds total)