Starting phenix.real_space_refine
on Wed Mar  4 03:39:54 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7k9l_22754/03_2026/7k9l_22754.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7k9l_22754/03_2026/7k9l_22754.map

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

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

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/7k9l_22754/03_2026/7k9l_22754.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7k9l_22754/03_2026/7k9l_22754.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/7k9l_22754/03_2026/7k9l_22754.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7k9l_22754/03_2026/7k9l_22754.map"
  }
  resolution = 4.9
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.004
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 4
    Type Number    sf(0)   Gaussians
     S      44      5.16       5
     C    6588      2.51       5
     N    1860      2.21       5
     O    1980      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

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

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 10472
  Number of models: 1
  Model: ""
    Number of chains: 1
    Chain: "B"
      Number of atoms: 2618
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 343, 2618
          Classifications: {'peptide': 343}
          Link IDs: {'PCIS': 1, 'PTRANS': 17, 'TRANS': 324}
  Restraints were copied for chains:
    A, C, D
  Time building chain proxies: 2.07, per 1000 atoms: 0.20
  Number of scatterers: 10472
  At special positions: 0
  Unit cell: (97.37, 80.99, 106.47, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     S      44     16.00
     O    1980      8.00
     N    1860      7.00
     C    6588      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 0.75
  Conformation dependent library (CDL) restraints added in 474.9 milliseconds
  

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

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

    564 hydrogen bonds defined for protein.
    1632 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 1.81

  Time building geometry restraints manager: 1.09 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: 0.02
Found NCS groups:
ncs_group {
  reference = chain 'B'
  selection = chain 'A'
  selection = chain 'C'
  selection = chain 'D'
}

Set up NCS constraints
  Number of NCS constrained groups: 1
  pdb_interpretation.ncs_group {
  reference = chain 'B'
  selection = chain 'A'
  selection = chain 'C'
  selection = chain 'D'
}
Set refine NCS operators
  NCS operators will be refined.
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             2.480
  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:          0.180
  Check model and map are aligned:         0.030
  Set scattering table:                    0.030
  Process input model:                     10.150
  Find NCS groups from input model:        0.060
  Set up NCS constraints:                  0.010
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.270
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   14.220
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7921
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.007   0.065  10672  Z= 0.348
  Angle     :  1.189  17.902  14464  Z= 0.639
  Chirality :  0.066   0.398   1644
  Planarity :  0.008   0.048   1880
  Dihedral  : 15.276  86.709   3984
  Min Nonbonded Distance : 2.254

Molprobity Statistics.
  All-atom Clashscore : 9.21
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.52 %
    Favored  : 96.48 %
  Rotamer:
    Outliers :  3.96 %
    Allowed  : 10.79 %
    Favored  : 85.25 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.56 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.98 (0.19), residues: 1364
  helix: -0.95 (0.16), residues: 652
  sheet: -2.05 (0.33), residues: 196
  loop : -1.22 (0.24), residues: 516

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

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

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

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

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

  2728 Ramachandran restraints generated.
    1364 Oldfield, 0 Emsley, 1364 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Update NCS operators
********************
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  163 residues out of total 278 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 152
  time to evaluate  : 0.109 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: B    7 LEU cc_start: 0.9205 (mt) cc_final: 0.8958 (mt)
REVERT: B   11 GLN cc_start: 0.9279 (mt0) cc_final: 0.9078 (mt0)
REVERT: B   12 LYS cc_start: 0.8899 (mttt) cc_final: 0.8450 (mmtp)
REVERT: B   61 LEU cc_start: 0.9116 (mt) cc_final: 0.8858 (mt)
REVERT: B   81 GLU cc_start: 0.9142 (OUTLIER) cc_final: 0.8747 (tm-30)
REVERT: B  104 VAL cc_start: 0.8517 (t) cc_final: 0.8260 (t)
REVERT: B  122 THR cc_start: 0.7989 (t) cc_final: 0.7603 (t)
REVERT: B  144 PHE cc_start: 0.8330 (p90) cc_final: 0.7925 (p90)
REVERT: B  149 CYS cc_start: 0.8554 (p) cc_final: 0.7978 (t)
REVERT: B  152 LYS cc_start: 0.8379 (pttp) cc_final: 0.8027 (pttp)
REVERT: B  178 GLN cc_start: 0.8979 (mt0) cc_final: 0.8572 (mt0)
REVERT: B  191 LEU cc_start: 0.8986 (OUTLIER) cc_final: 0.8774 (tp)
REVERT: B  199 LYS cc_start: 0.9345 (mtmm) cc_final: 0.8875 (mmmt)
REVERT: B  241 GLN cc_start: 0.8287 (mp10) cc_final: 0.8083 (mp10)
REVERT: B  247 GLU cc_start: 0.9312 (mt-10) cc_final: 0.8765 (mt-10)
REVERT: B  248 ILE cc_start: 0.9122 (mt) cc_final: 0.8826 (tt)
REVERT: B  254 THR cc_start: 0.8856 (p) cc_final: 0.8626 (t)
REVERT: B  276 GLU cc_start: 0.8821 (OUTLIER) cc_final: 0.8302 (mt-10)
REVERT: B  284 ASN cc_start: 0.8222 (t0) cc_final: 0.7351 (t0)
REVERT: B  305 LEU cc_start: 0.9474 (tp) cc_final: 0.9082 (tp)
REVERT: B  313 TRP cc_start: 0.7668 (t60) cc_final: 0.6634 (t60)
  outliers start: 11
  outliers final: 3
  residues processed: 157
  average time/residue: 0.0654
  time to fit residues: 11.8926
Evaluate side-chains
  118 residues out of total 278 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 112
  time to evaluate  : 0.066 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 136
   random chunks:
   chunk 98 optimal weight:    3.9990
   chunk 107 optimal weight:    2.9990
   chunk 10 optimal weight:    6.9990
   chunk 66 optimal weight:    8.9990
   chunk 130 optimal weight:    0.0980
   chunk 124 optimal weight:    0.9990
   chunk 103 optimal weight:    6.9990
   chunk 77 optimal weight:    3.9990
   chunk 122 optimal weight:    2.9990
   chunk 91 optimal weight:    0.0060
   chunk 55 optimal weight:    3.9990
   overall best weight:    1.4202
-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

Flipped N/Q/H residues before XYZ refinement:
D 119 ASN
D 156 HIS
D 168 ASN
D 245 HIS
D 284 ASN
D 324 GLN
D 334 ASN
D 339 GLN

Total number of N/Q/H flips: 8

-------------------------------------------------------------------------------
Update NCS operators
********************
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3230 r_free = 0.3230 target = 0.099424 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.2909 r_free = 0.2909 target = 0.078905 restraints weight = 5863.351|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.2958 r_free = 0.2958 target = 0.082000 restraints weight = 3648.068|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.2998 r_free = 0.2998 target = 0.084498 restraints weight = 2551.311|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 34)----------------|
| r_work = 0.3026 r_free = 0.3026 target = 0.086364 restraints weight = 1867.219|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.3047 r_free = 0.3047 target = 0.087716 restraints weight = 1441.862|
|-----------------------------------------------------------------------------|
r_work (final): 0.3040
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7899
moved from start:          0.3298

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032  10672  Z= 0.158
  Angle     :  0.670   7.572  14464  Z= 0.342
  Chirality :  0.044   0.136   1644
  Planarity :  0.005   0.047   1880
  Dihedral  :  5.109  17.408   1472
  Min Nonbonded Distance : 2.419

Molprobity Statistics.
  All-atom Clashscore : 12.72
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.64 %
    Favored  : 97.36 %
  Rotamer:
    Outliers :  0.72 %
    Allowed  :  3.96 %
    Favored  : 95.32 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.56 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.06 (0.22), residues: 1364
  helix:  0.92 (0.19), residues: 664
  sheet: -1.56 (0.35), residues: 200
  loop : -0.54 (0.27), residues: 500

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

Details of bonding type rmsd
  covalent geometry    : bond        0.00348 (10672)
  covalent geometry    : angle       0.67028 (14464)
  hydrogen bonds       : bond        0.04189 (  564)
  hydrogen bonds       : angle       4.80873 ( 1632)

*********************** 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
  124 residues out of total 278 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 122
  time to evaluate  : 0.082 
Fit side-chains
REVERT: D    7 LEU cc_start: 0.8939 (mt) cc_final: 0.8636 (mt)
REVERT: D   11 GLN cc_start: 0.9548 (mt0) cc_final: 0.9334 (mt0)
REVERT: D   12 LYS cc_start: 0.9110 (mttt) cc_final: 0.8700 (mmtp)
REVERT: D   58 TYR cc_start: 0.8282 (t80) cc_final: 0.7906 (t80)
REVERT: D   61 LEU cc_start: 0.8816 (OUTLIER) cc_final: 0.8550 (mp)
REVERT: D   79 PHE cc_start: 0.8030 (t80) cc_final: 0.7811 (t80)
REVERT: D   80 HIS cc_start: 0.8504 (t70) cc_final: 0.8291 (t70)
REVERT: D  178 GLN cc_start: 0.8993 (mt0) cc_final: 0.8783 (mt0)
REVERT: D  195 ASP cc_start: 0.8838 (p0) cc_final: 0.8205 (t0)
REVERT: D  229 LYS cc_start: 0.8279 (tttm) cc_final: 0.7628 (tptp)
REVERT: D  247 GLU cc_start: 0.9186 (mt-10) cc_final: 0.8699 (mt-10)
REVERT: D  248 ILE cc_start: 0.9452 (mt) cc_final: 0.9179 (tt)
REVERT: D  254 THR cc_start: 0.8711 (p) cc_final: 0.8483 (t)
REVERT: D  270 LEU cc_start: 0.8626 (mm) cc_final: 0.8329 (mm)
REVERT: D  276 GLU cc_start: 0.8804 (mt-10) cc_final: 0.8596 (pm20)
REVERT: D  283 LEU cc_start: 0.9281 (tp) cc_final: 0.9081 (tp)
REVERT: D  284 ASN cc_start: 0.8193 (t0) cc_final: 0.7879 (m110)
REVERT: D  303 ARG cc_start: 0.8342 (ttp-110) cc_final: 0.7868 (mtp180)
REVERT: D  329 LYS cc_start: 0.8876 (mttp) cc_final: 0.8370 (mttm)
REVERT: D  332 LEU cc_start: 0.8537 (tp) cc_final: 0.8300 (tp)
REVERT: D  339 GLN cc_start: 0.8530 (tt0) cc_final: 0.7748 (pp30)
  outliers start: 2
  outliers final: 0
  residues processed: 123
  average time/residue: 0.0540
  time to fit residues: 7.8553
Evaluate side-chains
  96 residues out of total 278 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 95
  time to evaluate  : 0.089 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 136
   random chunks:
   chunk 86 optimal weight:    7.9990
   chunk 131 optimal weight:    0.0060
   chunk 3 optimal weight:    8.9990
   chunk 41 optimal weight:    9.9990
   chunk 126 optimal weight:    0.8980
   chunk 5 optimal weight:    3.9990
   chunk 66 optimal weight:    6.9990
   chunk 84 optimal weight:    4.9990
   chunk 35 optimal weight:    5.9990
   chunk 88 optimal weight:    0.5980
   chunk 25 optimal weight:    5.9990
   overall best weight:    2.1000
-------------------------------------------------------------------------------
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
B 287 ASN
B 324 GLN
B 334 ASN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
Update NCS operators
********************
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3265 r_free = 0.3265 target = 0.100187 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.2931 r_free = 0.2931 target = 0.079284 restraints weight = 5808.003|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.2984 r_free = 0.2984 target = 0.082527 restraints weight = 3661.462|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3025 r_free = 0.3025 target = 0.085015 restraints weight = 2566.279|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.3056 r_free = 0.3056 target = 0.086891 restraints weight = 1898.863|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 31)----------------|
| r_work = 0.3079 r_free = 0.3079 target = 0.088336 restraints weight = 1479.618|
|-----------------------------------------------------------------------------|
r_work (final): 0.3068
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7954
moved from start:          0.4138

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.037  10672  Z= 0.159
  Angle     :  0.631   8.728  14464  Z= 0.314
  Chirality :  0.042   0.125   1644
  Planarity :  0.005   0.051   1880
  Dihedral  :  4.766  17.207   1472
  Min Nonbonded Distance : 2.485

Molprobity Statistics.
  All-atom Clashscore : 13.63
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.52 %
    Favored  : 96.48 %
  Rotamer:
    Outliers :  0.72 %
    Allowed  :  5.76 %
    Favored  : 93.53 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.56 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.45 (0.22), residues: 1364
  helix:  1.27 (0.19), residues: 700
  sheet: -1.45 (0.34), residues: 200
  loop : -0.21 (0.28), residues: 464

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A  42 
 TYR   0.014   0.002   TYR D 203 
 PHE   0.010   0.002   PHE C 144 
 TRP   0.018   0.002   TRP C 295 
 HIS   0.005   0.001   HIS D 219 

Details of bonding type rmsd
  covalent geometry    : bond        0.00360 (10672)
  covalent geometry    : angle       0.63078 (14464)
  hydrogen bonds       : bond        0.03704 (  564)
  hydrogen bonds       : angle       4.60612 ( 1632)

*********************** 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
  135 residues out of total 278 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 133
  time to evaluate  : 0.099 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   11 GLN cc_start: 0.9593 (mt0) cc_final: 0.9255 (mt0)
REVERT: B   12 LYS cc_start: 0.9243 (mttt) cc_final: 0.8698 (mmtp)
REVERT: B   30 LEU cc_start: 0.8469 (tp) cc_final: 0.8246 (tp)
REVERT: B   58 TYR cc_start: 0.8352 (t80) cc_final: 0.7882 (t80)
REVERT: B  144 PHE cc_start: 0.8688 (p90) cc_final: 0.8476 (p90)
REVERT: B  247 GLU cc_start: 0.9168 (mt-10) cc_final: 0.8694 (mt-10)
REVERT: B  248 ILE cc_start: 0.9422 (mt) cc_final: 0.9155 (tt)
REVERT: B  254 THR cc_start: 0.8751 (p) cc_final: 0.8505 (t)
REVERT: B  282 ASN cc_start: 0.9023 (m-40) cc_final: 0.8758 (m-40)
REVERT: B  284 ASN cc_start: 0.8072 (t0) cc_final: 0.7529 (m-40)
REVERT: B  313 TRP cc_start: 0.8279 (t60) cc_final: 0.7579 (t60)
REVERT: B  329 LYS cc_start: 0.8808 (mttp) cc_final: 0.8411 (mttm)
REVERT: B  332 LEU cc_start: 0.8469 (tp) cc_final: 0.8153 (tp)
  outliers start: 2
  outliers final: 1
  residues processed: 133
  average time/residue: 0.0500
  time to fit residues: 8.0260
Evaluate side-chains
  95 residues out of total 278 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 94
  time to evaluate  : 0.090 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 136
   random chunks:
   chunk 77 optimal weight:    6.9990
   chunk 7 optimal weight:    7.9990
   chunk 81 optimal weight:    0.6980
   chunk 29 optimal weight:    3.9990
   chunk 33 optimal weight:    7.9990
   chunk 135 optimal weight:    7.9990
   chunk 46 optimal weight:    0.3980
   chunk 106 optimal weight:    1.9990
   chunk 65 optimal weight:    0.0470
   chunk 3 optimal weight:    8.9990
   chunk 93 optimal weight:    4.9990
   overall best weight:    1.4282
-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

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

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Update NCS operators
********************
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3310 r_free = 0.3310 target = 0.102273 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.2990 r_free = 0.2990 target = 0.082089 restraints weight = 5612.038|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 24)----------------|
| r_work = 0.3048 r_free = 0.3048 target = 0.085517 restraints weight = 3539.275|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3090 r_free = 0.3090 target = 0.088039 restraints weight = 2436.984|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 37)----------------|
| r_work = 0.3121 r_free = 0.3121 target = 0.089951 restraints weight = 1780.740|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 38)----------------|
| r_work = 0.3143 r_free = 0.3143 target = 0.091357 restraints weight = 1375.040|
|-----------------------------------------------------------------------------|
r_work (final): 0.3131
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7945
moved from start:          0.4669

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036  10672  Z= 0.126
  Angle     :  0.609   7.835  14464  Z= 0.299
  Chirality :  0.043   0.154   1644
  Planarity :  0.004   0.055   1880
  Dihedral  :  4.543  16.736   1472
  Min Nonbonded Distance : 2.572

Molprobity Statistics.
  All-atom Clashscore : 13.20
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.23 %
    Favored  : 96.77 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.16 %
    Favored  : 97.84 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.56 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.55 (0.23), residues: 1364
  helix:  1.37 (0.20), residues: 696
  sheet: -1.36 (0.34), residues: 200
  loop : -0.22 (0.29), residues: 468

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A  42 
 TYR   0.011   0.002   TYR C 203 
 PHE   0.011   0.002   PHE C  93 
 TRP   0.023   0.002   TRP D 295 
 HIS   0.003   0.001   HIS D 219 

Details of bonding type rmsd
  covalent geometry    : bond        0.00294 (10672)
  covalent geometry    : angle       0.60918 (14464)
  hydrogen bonds       : bond        0.03378 (  564)
  hydrogen bonds       : angle       4.31920 ( 1632)

*********************** 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
  132 residues out of total 278 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 132
  time to evaluate  : 0.104 
Fit side-chains
   revert: symmetry clash
REVERT: B   11 GLN cc_start: 0.9600 (mt0) cc_final: 0.9287 (mt0)
REVERT: B   12 LYS cc_start: 0.9205 (mttt) cc_final: 0.8706 (mmtp)
REVERT: B   58 TYR cc_start: 0.8220 (t80) cc_final: 0.7893 (t80)
REVERT: B   61 LEU cc_start: 0.8842 (mt) cc_final: 0.8577 (mt)
REVERT: B  138 LYS cc_start: 0.8388 (tptt) cc_final: 0.7756 (ttmt)
REVERT: B  140 ASP cc_start: 0.8777 (m-30) cc_final: 0.8518 (m-30)
REVERT: B  195 ASP cc_start: 0.8692 (p0) cc_final: 0.8266 (t0)
REVERT: B  245 HIS cc_start: 0.8603 (p-80) cc_final: 0.8398 (p90)
REVERT: B  254 THR cc_start: 0.8630 (p) cc_final: 0.8378 (t)
REVERT: B  276 GLU cc_start: 0.8110 (pm20) cc_final: 0.7635 (pm20)
REVERT: B  282 ASN cc_start: 0.9000 (m-40) cc_final: 0.8757 (m-40)
REVERT: B  284 ASN cc_start: 0.8078 (t0) cc_final: 0.7553 (t0)
REVERT: B  305 LEU cc_start: 0.9367 (tp) cc_final: 0.8699 (tp)
REVERT: B  306 GLN cc_start: 0.7617 (pp30) cc_final: 0.7222 (pp30)
REVERT: B  313 TRP cc_start: 0.8284 (t60) cc_final: 0.7250 (t60)
REVERT: B  326 GLU cc_start: 0.8953 (mm-30) cc_final: 0.8307 (mm-30)
REVERT: B  329 LYS cc_start: 0.8987 (mttp) cc_final: 0.8522 (mttm)
REVERT: B  332 LEU cc_start: 0.8443 (tp) cc_final: 0.8091 (tp)
REVERT: B  336 LEU cc_start: 0.9043 (mt) cc_final: 0.8841 (mt)
  outliers start: 0
  outliers final: 0
  residues processed: 132
  average time/residue: 0.0508
  time to fit residues: 8.0565
Evaluate side-chains
  94 residues out of total 278 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 94
  time to evaluate  : 0.091 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 136
   random chunks:
   chunk 104 optimal weight:    0.9990
   chunk 32 optimal weight:    5.9990
   chunk 33 optimal weight:    7.9990
   chunk 99 optimal weight:    0.0010
   chunk 94 optimal weight:    4.9990
   chunk 135 optimal weight:    7.9990
   chunk 50 optimal weight:    4.9990
   chunk 52 optimal weight:    0.0370
   chunk 91 optimal weight:    0.0270
   chunk 57 optimal weight:    1.9990
   chunk 127 optimal weight:    6.9990
   overall best weight:    0.6126
-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

Flipped N/Q/H residues before XYZ refinement:
B  44 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 = 0.3337 r_free = 0.3337 target = 0.104574 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3023 r_free = 0.3023 target = 0.083891 restraints weight = 5515.607|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3081 r_free = 0.3081 target = 0.087460 restraints weight = 3519.887|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.3125 r_free = 0.3125 target = 0.090261 restraints weight = 2433.787|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.3156 r_free = 0.3156 target = 0.092279 restraints weight = 1775.397|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 19)----------------|
| r_work = 0.3177 r_free = 0.3177 target = 0.093658 restraints weight = 1363.236|
|-----------------------------------------------------------------------------|
r_work (final): 0.3169
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7845
moved from start:          0.4980

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.053  10672  Z= 0.112
  Angle     :  0.610   6.433  14464  Z= 0.297
  Chirality :  0.042   0.128   1644
  Planarity :  0.005   0.058   1880
  Dihedral  :  4.320  16.795   1472
  Min Nonbonded Distance : 2.511

Molprobity Statistics.
  All-atom Clashscore : 10.78
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.64 %
    Favored  : 97.36 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.88 %
    Favored  : 97.12 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.56 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.67 (0.23), residues: 1364
  helix:  1.53 (0.19), residues: 696
  sheet: -1.35 (0.31), residues: 220
  loop : -0.16 (0.30), residues: 448

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG C  42 
 TYR   0.012   0.001   TYR B 203 
 PHE   0.014   0.002   PHE A  79 
 TRP   0.025   0.002   TRP B 295 
 HIS   0.005   0.001   HIS B 219 

Details of bonding type rmsd
  covalent geometry    : bond        0.00274 (10672)
  covalent geometry    : angle       0.61034 (14464)
  hydrogen bonds       : bond        0.03090 (  564)
  hydrogen bonds       : angle       4.16126 ( 1632)

*********************** 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
  131 residues out of total 278 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 131
  time to evaluate  : 0.096 
Fit side-chains
   revert: symmetry clash
REVERT: B   11 GLN cc_start: 0.9581 (mt0) cc_final: 0.9316 (mt0)
REVERT: B   12 LYS cc_start: 0.9108 (mttt) cc_final: 0.8646 (mmtp)
REVERT: B   30 LEU cc_start: 0.8206 (tt) cc_final: 0.7873 (tp)
REVERT: B   61 LEU cc_start: 0.8758 (mt) cc_final: 0.8350 (mt)
REVERT: B  130 LEU cc_start: 0.9004 (mt) cc_final: 0.8800 (mt)
REVERT: B  138 LYS cc_start: 0.8376 (tptt) cc_final: 0.7788 (ttmt)
REVERT: B  144 PHE cc_start: 0.8687 (p90) cc_final: 0.8477 (p90)
REVERT: B  178 GLN cc_start: 0.8873 (mt0) cc_final: 0.8622 (mt0)
REVERT: B  195 ASP cc_start: 0.8789 (p0) cc_final: 0.8305 (t0)
REVERT: B  254 THR cc_start: 0.8675 (p) cc_final: 0.8376 (t)
REVERT: B  269 PHE cc_start: 0.8371 (m-80) cc_final: 0.8065 (m-80)
REVERT: B  276 GLU cc_start: 0.8097 (pm20) cc_final: 0.7695 (pm20)
REVERT: B  282 ASN cc_start: 0.9039 (m-40) cc_final: 0.8805 (m-40)
REVERT: B  284 ASN cc_start: 0.8201 (t0) cc_final: 0.7704 (t0)
REVERT: B  313 TRP cc_start: 0.8175 (t60) cc_final: 0.7256 (t60)
REVERT: B  329 LYS cc_start: 0.8890 (mttp) cc_final: 0.8642 (mttm)
REVERT: B  332 LEU cc_start: 0.8478 (tp) cc_final: 0.8221 (tp)
  outliers start: 0
  outliers final: 0
  residues processed: 131
  average time/residue: 0.0488
  time to fit residues: 7.7585
Evaluate side-chains
  95 residues out of total 278 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 95
  time to evaluate  : 0.057 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 136
   random chunks:
   chunk 22 optimal weight:    4.9990
   chunk 89 optimal weight:    4.9990
   chunk 2 optimal weight:    3.9990
   chunk 123 optimal weight:    4.9990
   chunk 75 optimal weight:    8.9990
   chunk 99 optimal weight:    0.0370
   chunk 113 optimal weight:    7.9990
   chunk 126 optimal weight:    0.9990
   chunk 91 optimal weight:    0.4980
   chunk 122 optimal weight:    0.8980
   chunk 129 optimal weight:    3.9990
   overall best weight:    1.2862
-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

Flipped N/Q/H residues before XYZ refinement:
** B  60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 306 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 324 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 = 0.3345 r_free = 0.3345 target = 0.105004 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3038 r_free = 0.3038 target = 0.084898 restraints weight = 5496.689|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3091 r_free = 0.3091 target = 0.088150 restraints weight = 3513.524|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3134 r_free = 0.3134 target = 0.090845 restraints weight = 2487.777|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 35)----------------|
| r_work = 0.3165 r_free = 0.3165 target = 0.092837 restraints weight = 1829.568|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 22)----------------|
| r_work = 0.3187 r_free = 0.3187 target = 0.094268 restraints weight = 1400.951|
|-----------------------------------------------------------------------------|
r_work (final): 0.3181
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7886
moved from start:          0.5392

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.044  10672  Z= 0.123
  Angle     :  0.603   7.126  14464  Z= 0.295
  Chirality :  0.041   0.121   1644
  Planarity :  0.005   0.061   1880
  Dihedral  :  4.330  16.861   1472
  Min Nonbonded Distance : 2.645

Molprobity Statistics.
  All-atom Clashscore : 13.96
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.81 %
    Favored  : 96.19 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.16 %
    Favored  : 97.84 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.56 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.52 (0.22), residues: 1364
  helix:  1.36 (0.19), residues: 700
  sheet: -1.26 (0.31), residues: 224
  loop : -0.25 (0.29), residues: 440

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG A 303 
 TYR   0.010   0.001   TYR A 203 
 PHE   0.022   0.002   PHE D  79 
 TRP   0.026   0.003   TRP B 295 
 HIS   0.006   0.001   HIS B 219 

Details of bonding type rmsd
  covalent geometry    : bond        0.00293 (10672)
  covalent geometry    : angle       0.60350 (14464)
  hydrogen bonds       : bond        0.03251 (  564)
  hydrogen bonds       : angle       4.23389 ( 1632)

*********************** 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
  127 residues out of total 278 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 127
  time to evaluate  : 0.091 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   11 GLN cc_start: 0.9596 (mt0) cc_final: 0.9291 (mt0)
REVERT: B   12 LYS cc_start: 0.9197 (mttt) cc_final: 0.8728 (mmtp)
REVERT: B   14 GLU cc_start: 0.8916 (mm-30) cc_final: 0.8706 (mm-30)
REVERT: B   30 LEU cc_start: 0.8230 (tt) cc_final: 0.7703 (tp)
REVERT: B   61 LEU cc_start: 0.8774 (mt) cc_final: 0.8373 (mt)
REVERT: B  128 ASP cc_start: 0.8364 (t0) cc_final: 0.8123 (t70)
REVERT: B  138 LYS cc_start: 0.8428 (tptt) cc_final: 0.7855 (ttmt)
REVERT: B  140 ASP cc_start: 0.8874 (m-30) cc_final: 0.8619 (m-30)
REVERT: B  178 GLN cc_start: 0.8705 (mt0) cc_final: 0.8485 (mt0)
REVERT: B  195 ASP cc_start: 0.8818 (p0) cc_final: 0.8313 (t0)
REVERT: B  229 LYS cc_start: 0.7974 (tttm) cc_final: 0.7203 (tptt)
REVERT: B  232 MET cc_start: 0.8906 (mtt) cc_final: 0.8351 (mtp)
REVERT: B  269 PHE cc_start: 0.8368 (m-80) cc_final: 0.8079 (m-80)
REVERT: B  276 GLU cc_start: 0.8179 (pm20) cc_final: 0.7777 (pm20)
REVERT: B  305 LEU cc_start: 0.9340 (tp) cc_final: 0.8729 (tp)
REVERT: B  313 TRP cc_start: 0.8363 (t60) cc_final: 0.7309 (t60)
REVERT: B  329 LYS cc_start: 0.8666 (mttp) cc_final: 0.8388 (mttm)
REVERT: B  332 LEU cc_start: 0.8391 (tp) cc_final: 0.8129 (tp)
  outliers start: 0
  outliers final: 0
  residues processed: 127
  average time/residue: 0.0508
  time to fit residues: 7.7685
Evaluate side-chains
  90 residues out of total 278 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 90
  time to evaluate  : 0.093 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 136
   random chunks:
   chunk 49 optimal weight:    6.9990
   chunk 7 optimal weight:    7.9990
   chunk 53 optimal weight:    6.9990
   chunk 69 optimal weight:    0.7980
   chunk 37 optimal weight:   20.0000
   chunk 26 optimal weight:    0.2980
   chunk 38 optimal weight:    6.9990
   chunk 90 optimal weight:    0.2980
   chunk 30 optimal weight:    0.8980
   chunk 2 optimal weight:    5.9990
   chunk 20 optimal weight:    0.9980
   overall best weight:    0.6580
-------------------------------------------------------------------------------
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
B 219 HIS
B 284 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
Update NCS operators
********************
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3387 r_free = 0.3387 target = 0.108093 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3065 r_free = 0.3065 target = 0.087116 restraints weight = 5355.973|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3123 r_free = 0.3123 target = 0.090839 restraints weight = 3430.413|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3168 r_free = 0.3168 target = 0.093683 restraints weight = 2370.134|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.3202 r_free = 0.3202 target = 0.095806 restraints weight = 1728.964|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 22)----------------|
| r_work = 0.3228 r_free = 0.3228 target = 0.097406 restraints weight = 1316.722|
|-----------------------------------------------------------------------------|
r_work (final): 0.3214
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7781
moved from start:          0.5652

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040  10672  Z= 0.109
  Angle     :  0.618   7.365  14464  Z= 0.296
  Chirality :  0.041   0.116   1644
  Planarity :  0.005   0.062   1880
  Dihedral  :  4.192  16.912   1472
  Min Nonbonded Distance : 2.466

Molprobity Statistics.
  All-atom Clashscore : 13.25
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.23 %
    Favored  : 96.77 %
  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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.55 (0.22), residues: 1364
  helix:  1.36 (0.19), residues: 696
  sheet: -1.34 (0.30), residues: 224
  loop : -0.12 (0.30), residues: 444

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG A 303 
 TYR   0.021   0.002   TYR D  58 
 PHE   0.017   0.002   PHE C  79 
 TRP   0.030   0.003   TRP B 295 
 HIS   0.005   0.001   HIS B 219 

Details of bonding type rmsd
  covalent geometry    : bond        0.00258 (10672)
  covalent geometry    : angle       0.61779 (14464)
  hydrogen bonds       : bond        0.03084 (  564)
  hydrogen bonds       : angle       4.07820 ( 1632)

*********************** 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
  129 residues out of total 278 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 128
  time to evaluate  : 0.063 
Fit side-chains
   revert: symmetry clash
REVERT: B   11 GLN cc_start: 0.9584 (mt0) cc_final: 0.9316 (mt0)
REVERT: B   12 LYS cc_start: 0.9118 (mttt) cc_final: 0.8680 (mmtp)
REVERT: B   14 GLU cc_start: 0.8912 (mm-30) cc_final: 0.8704 (mm-30)
REVERT: B   30 LEU cc_start: 0.7902 (tt) cc_final: 0.7626 (tp)
REVERT: B   79 PHE cc_start: 0.8183 (t80) cc_final: 0.7797 (t80)
REVERT: B  128 ASP cc_start: 0.8389 (t0) cc_final: 0.7689 (m-30)
REVERT: B  130 LEU cc_start: 0.8986 (mt) cc_final: 0.8765 (mt)
REVERT: B  138 LYS cc_start: 0.8381 (tptt) cc_final: 0.7805 (ttmt)
REVERT: B  140 ASP cc_start: 0.8821 (m-30) cc_final: 0.8544 (m-30)
REVERT: B  178 GLN cc_start: 0.8765 (mt0) cc_final: 0.8520 (mt0)
REVERT: B  195 ASP cc_start: 0.8822 (p0) cc_final: 0.8281 (t0)
REVERT: B  221 ILE cc_start: 0.9273 (tp) cc_final: 0.9061 (tp)
REVERT: B  229 LYS cc_start: 0.7825 (tttm) cc_final: 0.7234 (tptt)
REVERT: B  232 MET cc_start: 0.8725 (mtt) cc_final: 0.8183 (mtp)
REVERT: B  269 PHE cc_start: 0.8308 (m-80) cc_final: 0.8031 (m-80)
REVERT: B  276 GLU cc_start: 0.8202 (pm20) cc_final: 0.7717 (pm20)
REVERT: B  306 GLN cc_start: 0.8043 (pp30) cc_final: 0.7642 (pp30)
REVERT: B  313 TRP cc_start: 0.8185 (t60) cc_final: 0.7203 (t60)
REVERT: B  329 LYS cc_start: 0.8655 (mttp) cc_final: 0.8326 (mttm)
REVERT: B  332 LEU cc_start: 0.8406 (tp) cc_final: 0.8055 (pp)
  outliers start: 1
  outliers final: 1
  residues processed: 128
  average time/residue: 0.0511
  time to fit residues: 7.8534
Evaluate side-chains
  95 residues out of total 278 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 94
  time to evaluate  : 0.097 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 136
   random chunks:
   chunk 53 optimal weight:    6.9990
   chunk 33 optimal weight:    6.9990
   chunk 59 optimal weight:    6.9990
   chunk 15 optimal weight:   10.0000
   chunk 56 optimal weight:    2.9990
   chunk 97 optimal weight:    3.9990
   chunk 14 optimal weight:    4.9990
   chunk 67 optimal weight:    6.9990
   chunk 114 optimal weight:    5.9990
   chunk 123 optimal weight:    4.9990
   chunk 80 optimal weight:    6.9990
   overall best weight:    4.5990
-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

Flipped N/Q/H residues before XYZ refinement:
** B  60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 282 ASN
B 284 ASN
** B 306 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 324 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
Update NCS operators
********************
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3227 r_free = 0.3227 target = 0.096988 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.2900 r_free = 0.2900 target = 0.076952 restraints weight = 5925.184|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.2951 r_free = 0.2951 target = 0.080042 restraints weight = 3884.694|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.2993 r_free = 0.2993 target = 0.082517 restraints weight = 2748.733|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3024 r_free = 0.3024 target = 0.084316 restraints weight = 2042.466|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.3048 r_free = 0.3048 target = 0.085769 restraints weight = 1595.358|
|-----------------------------------------------------------------------------|
r_work (final): 0.3033
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8079
moved from start:          0.5782

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.062  10672  Z= 0.269
  Angle     :  0.797   7.635  14464  Z= 0.401
  Chirality :  0.045   0.137   1644
  Planarity :  0.006   0.068   1880
  Dihedral  :  5.086  18.060   1472
  Min Nonbonded Distance : 2.546

Molprobity Statistics.
  All-atom Clashscore : 22.22
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.16 %
    Favored  : 93.84 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.16 %
    Favored  : 97.84 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.56 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.53 (0.22), residues: 1364
  helix:  0.50 (0.19), residues: 700
  sheet: -1.43 (0.32), residues: 224
  loop : -0.94 (0.28), residues: 440

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG A 303 
 TYR   0.021   0.003   TYR A 213 
 PHE   0.012   0.003   PHE B  79 
 TRP   0.043   0.005   TRP C 295 
 HIS   0.009   0.003   HIS A 219 

Details of bonding type rmsd
  covalent geometry    : bond        0.00564 (10672)
  covalent geometry    : angle       0.79666 (14464)
  hydrogen bonds       : bond        0.04482 (  564)
  hydrogen bonds       : angle       4.89917 ( 1632)

*********************** 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
  104 residues out of total 278 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 104
  time to evaluate  : 0.096 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   11 GLN cc_start: 0.9621 (mt0) cc_final: 0.9264 (mt0)
REVERT: B   12 LYS cc_start: 0.9207 (mttt) cc_final: 0.8875 (mmmm)
REVERT: B   14 GLU cc_start: 0.8895 (mm-30) cc_final: 0.8694 (mm-30)
REVERT: B   61 LEU cc_start: 0.8704 (mt) cc_final: 0.8462 (mt)
REVERT: B  128 ASP cc_start: 0.8675 (t0) cc_final: 0.7930 (p0)
REVERT: B  178 GLN cc_start: 0.8749 (mt0) cc_final: 0.8548 (mt0)
REVERT: B  195 ASP cc_start: 0.8849 (p0) cc_final: 0.8114 (t0)
REVERT: B  276 GLU cc_start: 0.8203 (pm20) cc_final: 0.7976 (pm20)
REVERT: B  329 LYS cc_start: 0.8700 (mttp) cc_final: 0.8334 (mttm)
  outliers start: 0
  outliers final: 0
  residues processed: 104
  average time/residue: 0.0531
  time to fit residues: 6.6217
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  : 0.135 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 136
   random chunks:
   chunk 35 optimal weight:    4.9990
   chunk 71 optimal weight:    7.9990
   chunk 2 optimal weight:    0.0970
   chunk 122 optimal weight:    0.6980
   chunk 78 optimal weight:    0.1980
   chunk 24 optimal weight:    0.9990
   chunk 26 optimal weight:    5.9990
   chunk 77 optimal weight:    5.9990
   chunk 23 optimal weight:    1.9990
   chunk 49 optimal weight:    3.9990
   chunk 66 optimal weight:    4.9990
   overall best weight:    0.7982
-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

Flipped N/Q/H residues before XYZ refinement:
B  44 GLN
B 219 HIS
B 324 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
Update NCS operators
********************
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3337 r_free = 0.3337 target = 0.104154 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3002 r_free = 0.3002 target = 0.082882 restraints weight = 5493.644|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3060 r_free = 0.3060 target = 0.086339 restraints weight = 3585.766|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3103 r_free = 0.3103 target = 0.089014 restraints weight = 2536.610|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3136 r_free = 0.3136 target = 0.091079 restraints weight = 1893.729|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.3160 r_free = 0.3160 target = 0.092591 restraints weight = 1473.434|
|-----------------------------------------------------------------------------|
r_work (final): 0.3149
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7947
moved from start:          0.5978

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= 0.135
  Angle     :  0.661   7.153  14464  Z= 0.322
  Chirality :  0.043   0.118   1644
  Planarity :  0.005   0.066   1880
  Dihedral  :  4.534  16.993   1472
  Min Nonbonded Distance : 2.392

Molprobity Statistics.
  All-atom Clashscore : 14.81
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.64 %
    Favored  : 97.36 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.36 %
    Favored  : 99.64 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.56 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.01 (0.22), residues: 1364
  helix:  0.87 (0.19), residues: 696
  sheet: -1.48 (0.31), residues: 224
  loop : -0.39 (0.29), residues: 444

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG D  42 
 TYR   0.012   0.002   TYR D 213 
 PHE   0.030   0.003   PHE D 299 
 TRP   0.046   0.004   TRP A 295 
 HIS   0.008   0.001   HIS B 219 

Details of bonding type rmsd
  covalent geometry    : bond        0.00327 (10672)
  covalent geometry    : angle       0.66134 (14464)
  hydrogen bonds       : bond        0.03600 (  564)
  hydrogen bonds       : angle       4.37782 ( 1632)

*********************** 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
  118 residues out of total 278 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 118
  time to evaluate  : 0.088 
Fit side-chains
   revert: symmetry clash
REVERT: B    7 LEU cc_start: 0.8735 (mt) cc_final: 0.8534 (mt)
REVERT: B   11 GLN cc_start: 0.9609 (mt0) cc_final: 0.9294 (mt0)
REVERT: B   12 LYS cc_start: 0.9198 (mttt) cc_final: 0.8734 (mmmm)
REVERT: B   14 GLU cc_start: 0.8860 (mm-30) cc_final: 0.8657 (mm-30)
REVERT: B  128 ASP cc_start: 0.8512 (t0) cc_final: 0.7820 (m-30)
REVERT: B  130 LEU cc_start: 0.9097 (mt) cc_final: 0.8869 (mt)
REVERT: B  195 ASP cc_start: 0.8758 (p0) cc_final: 0.8258 (t0)
REVERT: B  220 HIS cc_start: 0.9303 (m90) cc_final: 0.8907 (m90)
REVERT: B  269 PHE cc_start: 0.8442 (m-80) cc_final: 0.8195 (m-10)
REVERT: B  276 GLU cc_start: 0.8208 (pm20) cc_final: 0.7839 (pm20)
REVERT: B  282 ASN cc_start: 0.8874 (m110) cc_final: 0.8654 (m110)
REVERT: B  284 ASN cc_start: 0.8427 (t0) cc_final: 0.8069 (t0)
REVERT: B  313 TRP cc_start: 0.7979 (t60) cc_final: 0.7241 (t60)
REVERT: B  329 LYS cc_start: 0.8639 (mttp) cc_final: 0.8281 (mttm)
REVERT: B  332 LEU cc_start: 0.8348 (tp) cc_final: 0.8031 (pp)
  outliers start: 0
  outliers final: 0
  residues processed: 118
  average time/residue: 0.0410
  time to fit residues: 5.9292
Evaluate side-chains
  90 residues out of total 278 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 90
  time to evaluate  : 0.092 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 136
   random chunks:
   chunk 5 optimal weight:    1.9990
   chunk 18 optimal weight:    0.0980
   chunk 93 optimal weight:    4.9990
   chunk 14 optimal weight:    0.0040
   chunk 126 optimal weight:    0.9990
   chunk 96 optimal weight:    0.4980
   chunk 16 optimal weight:    1.9990
   chunk 25 optimal weight:    5.9990
   chunk 86 optimal weight:    0.0010
   chunk 135 optimal weight:    6.9990
   chunk 0 optimal weight:    7.9990
   overall best weight:    0.3200
-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

Flipped N/Q/H residues before XYZ refinement:
** B  60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 284 ASN
** B 306 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 324 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
Update NCS operators
********************
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3399 r_free = 0.3399 target = 0.109403 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3050 r_free = 0.3050 target = 0.087080 restraints weight = 5407.554|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3108 r_free = 0.3108 target = 0.090661 restraints weight = 3578.709|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3153 r_free = 0.3153 target = 0.093496 restraints weight = 2552.575|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 39)----------------|
| r_work = 0.3190 r_free = 0.3190 target = 0.095694 restraints weight = 1915.979|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 24)----------------|
| r_work = 0.3213 r_free = 0.3213 target = 0.097125 restraints weight = 1503.054|
|-----------------------------------------------------------------------------|
r_work (final): 0.3204
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7883
moved from start:          0.6254

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= 0.123
  Angle     :  0.649   7.223  14464  Z= 0.321
  Chirality :  0.044   0.134   1644
  Planarity :  0.005   0.068   1880
  Dihedral  :  4.364  17.236   1472
  Min Nonbonded Distance : 2.585

Molprobity Statistics.
  All-atom Clashscore : 14.86
  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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.05 (0.22), residues: 1364
  helix:  1.03 (0.19), residues: 700
  sheet: -1.28 (0.33), residues: 176
  loop : -0.79 (0.27), residues: 488

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 303 
 TYR   0.009   0.001   TYR D 137 
 PHE   0.015   0.002   PHE D 299 
 TRP   0.045   0.004   TRP C 295 
 HIS   0.006   0.001   HIS A 219 

Details of bonding type rmsd
  covalent geometry    : bond        0.00285 (10672)
  covalent geometry    : angle       0.64943 (14464)
  hydrogen bonds       : bond        0.03368 (  564)
  hydrogen bonds       : angle       4.15996 ( 1632)

********************** 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
  122 residues out of total 278 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 122
  time to evaluate  : 0.091 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   11 GLN cc_start: 0.9572 (mt0) cc_final: 0.9283 (mt0)
REVERT: B   12 LYS cc_start: 0.9122 (mttt) cc_final: 0.8660 (mmmm)
REVERT: B  115 LEU cc_start: 0.8072 (mm) cc_final: 0.7774 (mp)
REVERT: B  128 ASP cc_start: 0.8462 (t0) cc_final: 0.7744 (m-30)
REVERT: B  130 LEU cc_start: 0.9053 (mt) cc_final: 0.8826 (mt)
REVERT: B  166 ASN cc_start: 0.8948 (t0) cc_final: 0.8184 (t0)
REVERT: B  195 ASP cc_start: 0.8700 (p0) cc_final: 0.8305 (t0)
REVERT: B  214 LYS cc_start: 0.9284 (tmtt) cc_final: 0.8745 (tppt)
REVERT: B  220 HIS cc_start: 0.9197 (m90) cc_final: 0.8949 (m90)
REVERT: B  237 HIS cc_start: 0.8185 (t70) cc_final: 0.7803 (t70)
REVERT: B  269 PHE cc_start: 0.8283 (m-80) cc_final: 0.7869 (m-80)
REVERT: B  276 GLU cc_start: 0.8247 (pm20) cc_final: 0.7810 (pm20)
REVERT: B  313 TRP cc_start: 0.7962 (t60) cc_final: 0.7276 (t60)
REVERT: B  332 LEU cc_start: 0.8359 (tp) cc_final: 0.8058 (pp)
  outliers start: 0
  outliers final: 0
  residues processed: 122
  average time/residue: 0.0522
  time to fit residues: 7.7137
Evaluate side-chains
  88 residues out of total 278 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 88
  time to evaluate  : 0.099 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 136
   random chunks:
   chunk 5 optimal weight:    0.7980
   chunk 75 optimal weight:    6.9990
   chunk 42 optimal weight:    2.9990
   chunk 124 optimal weight:    0.0870
   chunk 41 optimal weight:    4.9990
   chunk 89 optimal weight:    4.9990
   chunk 77 optimal weight:    6.9990
   chunk 122 optimal weight:    0.9980
   chunk 3 optimal weight:   20.0000
   chunk 22 optimal weight:    0.0870
   chunk 29 optimal weight:    2.9990
   overall best weight:    0.9938
-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

Flipped N/Q/H residues before XYZ refinement:
** B 166 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 219 HIS
** B 306 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Update NCS operators
********************
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3364 r_free = 0.3364 target = 0.106806 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3032 r_free = 0.3032 target = 0.085519 restraints weight = 5392.226|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3087 r_free = 0.3087 target = 0.088910 restraints weight = 3495.243|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3130 r_free = 0.3130 target = 0.091632 restraints weight = 2462.196|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 26)----------------|
| r_work = 0.3159 r_free = 0.3159 target = 0.093471 restraints weight = 1828.849|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.3187 r_free = 0.3187 target = 0.095118 restraints weight = 1434.583|
|-----------------------------------------------------------------------------|
r_work (final): 0.3175
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7902
moved from start:          0.6283

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035  10672  Z= 0.122
  Angle     :  0.637   7.216  14464  Z= 0.313
  Chirality :  0.043   0.139   1644
  Planarity :  0.005   0.070   1880
  Dihedral  :  4.328  14.464   1472
  Min Nonbonded Distance : 2.572

Molprobity Statistics.
  All-atom Clashscore : 15.14
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.52 %
    Favored  : 96.48 %
  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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.11 (0.22), residues: 1364
  helix:  1.06 (0.20), residues: 708
  sheet: -1.24 (0.32), residues: 176
  loop : -0.78 (0.28), residues: 480

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG D  42 
 TYR   0.008   0.001   TYR D 137 
 PHE   0.015   0.002   PHE D 299 
 TRP   0.039   0.004   TRP C 295 
 HIS   0.009   0.001   HIS B 219 

Details of bonding type rmsd
  covalent geometry    : bond        0.00289 (10672)
  covalent geometry    : angle       0.63680 (14464)
  hydrogen bonds       : bond        0.03411 (  564)
  hydrogen bonds       : angle       4.19951 ( 1632)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 936.30 seconds
wall clock time: 17 minutes 21.34 seconds (1041.34 seconds total)