Starting phenix.real_space_refine
on Tue Jul 29 17:45:57 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9b78_44303/07_2025/9b78_44303.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9b78_44303/07_2025/9b78_44303.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.59
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/9b78_44303/07_2025/9b78_44303.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9b78_44303/07_2025/9b78_44303.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9b78_44303/07_2025/9b78_44303.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9b78_44303/07_2025/9b78_44303.cif"
  }
  resolution = 2.59
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.001 sd=   0.055
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      42      5.16       5
     C    7440      2.51       5
     N    2118      2.21       5
     O    2214      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model
  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib"
  Total number of atoms: 11814
  Number of models: 1
  Model: ""
    Number of chains: 6
    Chain: "A"
      Number of atoms: 1969
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 261, 1969
          Classifications: {'peptide': 261}
          Link IDs: {'PTRANS': 10, 'TRANS': 250}
    Chain: "B"
      Number of atoms: 1969
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 261, 1969
          Classifications: {'peptide': 261}
          Link IDs: {'PTRANS': 10, 'TRANS': 250}
    Chain: "C"
      Number of atoms: 1969
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 261, 1969
          Classifications: {'peptide': 261}
          Link IDs: {'PTRANS': 10, 'TRANS': 250}
    Chain: "D"
      Number of atoms: 1969
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 261, 1969
          Classifications: {'peptide': 261}
          Link IDs: {'PTRANS': 10, 'TRANS': 250}
    Chain: "E"
      Number of atoms: 1969
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 261, 1969
          Classifications: {'peptide': 261}
          Link IDs: {'PTRANS': 10, 'TRANS': 250}
    Chain: "F"
      Number of atoms: 1969
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 261, 1969
          Classifications: {'peptide': 261}
          Link IDs: {'PTRANS': 10, 'TRANS': 250}
  Time building chain proxies: 7.20, per 1000 atoms: 0.61
  Number of scatterers: 11814
  At special positions: 0
  Unit cell: (104.902, 108.206, 99.946, 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      42     16.00
     O    2214      8.00
     N    2118      7.00
     C    7440      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 2.53
  Conformation dependent library (CDL) restraints added in 1.7 seconds
  

  3108 Ramachandran restraints generated.
    1554 Oldfield, 0 Emsley, 1554 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2868

  Finding SS restraints...
    Secondary structure from input PDB file:
      60 helices and 12 sheets defined
      46.4% alpha, 20.1% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 1.53
  Creating SS restraints...
    Processing helix  chain 'A' and resid 20 through 24
    Processing helix  chain 'A' and resid 39 through 52
    Processing helix  chain 'A' and resid 53 through 56
      removed outlier: 4.023A  pdb=" N   GLU A  56 " --> pdb=" O   GLU A  53 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 53 through 56'
    Processing helix  chain 'A' and resid 67 through 82
    Processing helix  chain 'A' and resid 109 through 124
      removed outlier: 3.527A  pdb=" N   ILE A 113 " --> pdb=" O   GLY A 109 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 155 through 167
    Processing helix  chain 'A' and resid 185 through 213
    Processing helix  chain 'A' and resid 230 through 235
      removed outlier: 3.525A  pdb=" N   LEU A 234 " --> pdb=" O   THR A 230 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 236 through 238
      No H-bonds generated for 'chain 'A' and resid 236 through 238'
    Processing helix  chain 'A' and resid 247 through 260
    Processing helix  chain 'B' and resid 20 through 24
      removed outlier: 3.704A  pdb=" N   ALA B  24 " --> pdb=" O   LYS B  21 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 39 through 52
    Processing helix  chain 'B' and resid 53 through 58
      removed outlier: 3.800A  pdb=" N   GLU B  56 " --> pdb=" O   GLU B  53 " (cutoff:3.500A)
      removed outlier: 3.847A  pdb=" N   LEU B  58 " --> pdb=" O   SER B  55 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 67 through 82
      removed outlier: 3.735A  pdb=" N   TRP B  82 " --> pdb=" O   LEU B  78 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 109 through 124
    Processing helix  chain 'B' and resid 155 through 167
      removed outlier: 3.619A  pdb=" N   SER B 159 " --> pdb=" O   GLY B 155 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 185 through 213
      removed outlier: 3.752A  pdb=" N   PHE B 198 " --> pdb=" O   ALA B 194 " (cutoff:3.500A)
      removed outlier: 3.502A  pdb=" N   VAL B 213 " --> pdb=" O   ILE B 209 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 230 through 235
      removed outlier: 3.760A  pdb=" N   LEU B 234 " --> pdb=" O   THR B 230 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 236 through 238
      No H-bonds generated for 'chain 'B' and resid 236 through 238'
    Processing helix  chain 'B' and resid 247 through 260
    Processing helix  chain 'C' and resid 20 through 24
      removed outlier: 3.707A  pdb=" N   ALA C  24 " --> pdb=" O   LYS C  21 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 39 through 52
    Processing helix  chain 'C' and resid 53 through 58
      removed outlier: 4.152A  pdb=" N   GLU C  56 " --> pdb=" O   GLU C  53 " (cutoff:3.500A)
      removed outlier: 3.519A  pdb=" N   LEU C  58 " --> pdb=" O   SER C  55 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 67 through 82
    Processing helix  chain 'C' and resid 109 through 124
      removed outlier: 3.528A  pdb=" N   ILE C 113 " --> pdb=" O   GLY C 109 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 155 through 167
    Processing helix  chain 'C' and resid 185 through 212
      removed outlier: 3.614A  pdb=" N   PHE C 198 " --> pdb=" O   ALA C 194 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 230 through 235
      removed outlier: 3.510A  pdb=" N   LEU C 234 " --> pdb=" O   THR C 230 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 236 through 238
      No H-bonds generated for 'chain 'C' and resid 236 through 238'
    Processing helix  chain 'C' and resid 247 through 261
    Processing helix  chain 'D' and resid 20 through 24
    Processing helix  chain 'D' and resid 39 through 52
    Processing helix  chain 'D' and resid 53 through 58
      removed outlier: 3.730A  pdb=" N   GLU D  56 " --> pdb=" O   GLU D  53 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 67 through 82
      removed outlier: 3.904A  pdb=" N   TRP D  82 " --> pdb=" O   LEU D  78 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 109 through 124
    Processing helix  chain 'D' and resid 155 through 167
    Processing helix  chain 'D' and resid 185 through 213
      removed outlier: 3.889A  pdb=" N   PHE D 198 " --> pdb=" O   ALA D 194 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 230 through 235
      removed outlier: 3.932A  pdb=" N   LEU D 234 " --> pdb=" O   THR D 230 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 236 through 238
      No H-bonds generated for 'chain 'D' and resid 236 through 238'
    Processing helix  chain 'D' and resid 247 through 260
    Processing helix  chain 'E' and resid 20 through 24
    Processing helix  chain 'E' and resid 39 through 52
    Processing helix  chain 'E' and resid 53 through 58
      removed outlier: 4.142A  pdb=" N   GLU E  56 " --> pdb=" O   GLU E  53 " (cutoff:3.500A)
      removed outlier: 3.778A  pdb=" N   LEU E  58 " --> pdb=" O   SER E  55 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 67 through 82
    Processing helix  chain 'E' and resid 109 through 124
      removed outlier: 3.565A  pdb=" N   ILE E 113 " --> pdb=" O   GLY E 109 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 155 through 167
    Processing helix  chain 'E' and resid 185 through 213
      removed outlier: 4.034A  pdb=" N   PHE E 198 " --> pdb=" O   ALA E 194 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 230 through 235
      removed outlier: 3.705A  pdb=" N   LEU E 234 " --> pdb=" O   THR E 230 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 236 through 238
      No H-bonds generated for 'chain 'E' and resid 236 through 238'
    Processing helix  chain 'E' and resid 247 through 260
    Processing helix  chain 'F' and resid 20 through 24
    Processing helix  chain 'F' and resid 39 through 52
    Processing helix  chain 'F' and resid 53 through 55
      No H-bonds generated for 'chain 'F' and resid 53 through 55'
    Processing helix  chain 'F' and resid 67 through 82
    Processing helix  chain 'F' and resid 109 through 124
      removed outlier: 3.522A  pdb=" N   ILE F 113 " --> pdb=" O   GLY F 109 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 155 through 167
      removed outlier: 3.523A  pdb=" N   SER F 159 " --> pdb=" O   GLY F 155 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 185 through 213
      removed outlier: 3.862A  pdb=" N   PHE F 198 " --> pdb=" O   ALA F 194 " (cutoff:3.500A)
      removed outlier: 3.509A  pdb=" N   VAL F 213 " --> pdb=" O   ILE F 209 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 230 through 235
      removed outlier: 3.584A  pdb=" N   LEU F 234 " --> pdb=" O   THR F 230 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 236 through 238
      No H-bonds generated for 'chain 'F' and resid 236 through 238'
    Processing helix  chain 'F' and resid 247 through 260
    Processing sheet with id=AA1, first strand: chain 'A' and resid 25 through 33
      removed outlier: 5.340A  pdb=" N   VAL A  26 " --> pdb=" O   SER A  18 " (cutoff:3.500A)
      removed outlier: 6.192A  pdb=" N   SER A  18 " --> pdb=" O   VAL A  26 " (cutoff:3.500A)
      removed outlier: 5.907A  pdb=" N   LEU A   3 " --> pdb=" O   ALA A  62 " (cutoff:3.500A)
      removed outlier: 7.609A  pdb=" N   LEU A  64 " --> pdb=" O   LEU A   3 " (cutoff:3.500A)
      removed outlier: 6.012A  pdb=" N   ILE A   5 " --> pdb=" O   LEU A  64 " (cutoff:3.500A)
      removed outlier: 4.287A  pdb=" N   SER A  65 " --> pdb=" O   ILE A  90 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 147 through 154
      removed outlier: 3.828A  pdb=" N   GLY A 149 " --> pdb=" O   VAL A 140 " (cutoff:3.500A)
      removed outlier: 6.399A  pdb=" N   ILE A 224 " --> pdb=" O   HIS A 243 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'B' and resid 25 through 33
      removed outlier: 5.472A  pdb=" N   VAL B  26 " --> pdb=" O   SER B  18 " (cutoff:3.500A)
      removed outlier: 6.456A  pdb=" N   SER B  18 " --> pdb=" O   VAL B  26 " (cutoff:3.500A)
      removed outlier: 6.150A  pdb=" N   LEU B   3 " --> pdb=" O   ALA B  62 " (cutoff:3.500A)
      removed outlier: 7.986A  pdb=" N   LEU B  64 " --> pdb=" O   LEU B   3 " (cutoff:3.500A)
      removed outlier: 6.260A  pdb=" N   ILE B   5 " --> pdb=" O   LEU B  64 " (cutoff:3.500A)
      removed outlier: 6.593A  pdb=" N   THR B  61 " --> pdb=" O   VAL B  88 " (cutoff:3.500A)
      removed outlier: 8.148A  pdb=" N   ILE B  90 " --> pdb=" O   THR B  61 " (cutoff:3.500A)
      removed outlier: 7.189A  pdb=" N   ALA B  63 " --> pdb=" O   ILE B  90 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'B' and resid 147 through 154
      removed outlier: 3.969A  pdb=" N   GLY B 149 " --> pdb=" O   VAL B 140 " (cutoff:3.500A)
      removed outlier: 6.526A  pdb=" N   ILE B 224 " --> pdb=" O   HIS B 243 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'C' and resid 25 through 33
      removed outlier: 5.495A  pdb=" N   VAL C  26 " --> pdb=" O   SER C  18 " (cutoff:3.500A)
      removed outlier: 6.408A  pdb=" N   SER C  18 " --> pdb=" O   VAL C  26 " (cutoff:3.500A)
      removed outlier: 7.405A  pdb=" N   THR C  61 " --> pdb=" O   VAL C  88 " (cutoff:3.500A)
      removed outlier: 7.831A  pdb=" N   ILE C  90 " --> pdb=" O   THR C  61 " (cutoff:3.500A)
      removed outlier: 7.176A  pdb=" N   ALA C  63 " --> pdb=" O   ILE C  90 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'C' and resid 147 through 154
      removed outlier: 4.090A  pdb=" N   GLY C 149 " --> pdb=" O   VAL C 140 " (cutoff:3.500A)
      removed outlier: 8.121A  pdb=" N   HIS C 243 " --> pdb=" O   VAL C 222 " (cutoff:3.500A)
      removed outlier: 6.585A  pdb=" N   ILE C 224 " --> pdb=" O   HIS C 243 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'D' and resid 25 through 33
      removed outlier: 5.430A  pdb=" N   VAL D  26 " --> pdb=" O   SER D  18 " (cutoff:3.500A)
      removed outlier: 6.389A  pdb=" N   SER D  18 " --> pdb=" O   VAL D  26 " (cutoff:3.500A)
      removed outlier: 6.173A  pdb=" N   LEU D   3 " --> pdb=" O   ALA D  62 " (cutoff:3.500A)
      removed outlier: 7.967A  pdb=" N   LEU D  64 " --> pdb=" O   LEU D   3 " (cutoff:3.500A)
      removed outlier: 6.340A  pdb=" N   ILE D   5 " --> pdb=" O   LEU D  64 " (cutoff:3.500A)
      removed outlier: 4.419A  pdb=" N   SER D  65 " --> pdb=" O   ILE D  90 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'D' and resid 147 through 154
      removed outlier: 4.022A  pdb=" N   GLY D 149 " --> pdb=" O   VAL D 140 " (cutoff:3.500A)
      removed outlier: 6.686A  pdb=" N   ILE D 224 " --> pdb=" O   HIS D 243 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'E' and resid 25 through 33
      removed outlier: 5.445A  pdb=" N   VAL E  26 " --> pdb=" O   SER E  18 " (cutoff:3.500A)
      removed outlier: 6.337A  pdb=" N   SER E  18 " --> pdb=" O   VAL E  26 " (cutoff:3.500A)
      removed outlier: 6.048A  pdb=" N   LEU E   3 " --> pdb=" O   ALA E  62 " (cutoff:3.500A)
      removed outlier: 7.811A  pdb=" N   LEU E  64 " --> pdb=" O   LEU E   3 " (cutoff:3.500A)
      removed outlier: 6.031A  pdb=" N   ILE E   5 " --> pdb=" O   LEU E  64 " (cutoff:3.500A)
      removed outlier: 6.963A  pdb=" N   THR E  61 " --> pdb=" O   VAL E  88 " (cutoff:3.500A)
      removed outlier: 7.582A  pdb=" N   ILE E  90 " --> pdb=" O   THR E  61 " (cutoff:3.500A)
      removed outlier: 6.971A  pdb=" N   ALA E  63 " --> pdb=" O   ILE E  90 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'E' and resid 147 through 154
      removed outlier: 3.729A  pdb=" N   GLY E 149 " --> pdb=" O   VAL E 140 " (cutoff:3.500A)
      removed outlier: 6.390A  pdb=" N   ILE E 224 " --> pdb=" O   HIS E 243 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'F' and resid 25 through 33
      removed outlier: 5.522A  pdb=" N   VAL F  26 " --> pdb=" O   SER F  18 " (cutoff:3.500A)
      removed outlier: 6.454A  pdb=" N   SER F  18 " --> pdb=" O   VAL F  26 " (cutoff:3.500A)
      removed outlier: 5.945A  pdb=" N   LEU F   3 " --> pdb=" O   ALA F  62 " (cutoff:3.500A)
      removed outlier: 7.761A  pdb=" N   LEU F  64 " --> pdb=" O   LEU F   3 " (cutoff:3.500A)
      removed outlier: 6.098A  pdb=" N   ILE F   5 " --> pdb=" O   LEU F  64 " (cutoff:3.500A)
      removed outlier: 7.284A  pdb=" N   THR F  61 " --> pdb=" O   VAL F  88 " (cutoff:3.500A)
      removed outlier: 7.865A  pdb=" N   ILE F  90 " --> pdb=" O   THR F  61 " (cutoff:3.500A)
      removed outlier: 6.854A  pdb=" N   ALA F  63 " --> pdb=" O   ILE F  90 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'F' and resid 147 through 154
      removed outlier: 4.008A  pdb=" N   GLY F 149 " --> pdb=" O   VAL F 140 " (cutoff:3.500A)
      removed outlier: 8.219A  pdb=" N   HIS F 243 " --> pdb=" O   VAL F 222 " (cutoff:3.500A)
      removed outlier: 6.524A  pdb=" N   ILE F 224 " --> pdb=" O   HIS F 243 " (cutoff:3.500A)

    655 hydrogen bonds defined for protein.
    1890 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 3.88

  Time building geometry restraints manager: 3.08 seconds

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

  Histogram of bond lengths:
        1.23 -     1.34: 4082
        1.34 -     1.46: 2167
        1.46 -     1.58: 5691
        1.58 -     1.69: 0
        1.69 -     1.81: 66
  Bond restraints: 12006
  Sorted by residual:
  bond pdb=" CB  VAL B 114 "
       pdb=" CG1 VAL B 114 "
    ideal  model  delta    sigma   weight residual
    1.521  1.489  0.032 3.30e-02 9.18e+02 9.27e-01
  bond pdb=" CB  VAL F 114 "
       pdb=" CG1 VAL F 114 "
    ideal  model  delta    sigma   weight residual
    1.521  1.489  0.032 3.30e-02 9.18e+02 9.25e-01
  bond pdb=" CB  VAL A 114 "
       pdb=" CG1 VAL A 114 "
    ideal  model  delta    sigma   weight residual
    1.521  1.490  0.031 3.30e-02 9.18e+02 8.55e-01
  bond pdb=" CB  VAL D 114 "
       pdb=" CG1 VAL D 114 "
    ideal  model  delta    sigma   weight residual
    1.521  1.492  0.029 3.30e-02 9.18e+02 7.49e-01
  bond pdb=" C   ALA D 231 "
       pdb=" N   PRO D 232 "
    ideal  model  delta    sigma   weight residual
    1.335  1.345 -0.010 1.19e-02 7.06e+03 6.96e-01
  ... (remaining 12001 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.39: 15977
        1.39 -     2.77: 297
        2.77 -     4.16: 38
        4.16 -     5.55: 21
        5.55 -     6.93: 5
  Bond angle restraints: 16338
  Sorted by residual:
  angle pdb=" C   GLY A 197 "
        pdb=" N   PHE A 198 "
        pdb=" CA  PHE A 198 "
      ideal   model   delta    sigma   weight residual
     120.68  117.02    3.66 1.70e+00 3.46e-01 4.63e+00
  angle pdb=" CA  LEU F 201 "
        pdb=" CB  LEU F 201 "
        pdb=" CG  LEU F 201 "
      ideal   model   delta    sigma   weight residual
     116.30  122.60   -6.30 3.50e+00 8.16e-02 3.24e+00
  angle pdb=" CG1 VAL C  88 "
        pdb=" CB  VAL C  88 "
        pdb=" CG2 VAL C  88 "
      ideal   model   delta    sigma   weight residual
     110.80  106.88    3.92 2.20e+00 2.07e-01 3.17e+00
  angle pdb=" N   ASP E 212 "
        pdb=" CA  ASP E 212 "
        pdb=" C   ASP E 212 "
      ideal   model   delta    sigma   weight residual
     113.16  115.35   -2.19 1.24e+00 6.50e-01 3.11e+00
  angle pdb=" CA  LEU C 201 "
        pdb=" CB  LEU C 201 "
        pdb=" CG  LEU C 201 "
      ideal   model   delta    sigma   weight residual
     116.30  122.40   -6.10 3.50e+00 8.16e-02 3.04e+00
  ... (remaining 16333 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    16.43: 6691
       16.43 -    32.87: 417
       32.87 -    49.30: 79
       49.30 -    65.74: 9
       65.74 -    82.17: 4
  Dihedral angle restraints: 7200
    sinusoidal: 2754
      harmonic: 4446
  Sorted by residual:
  dihedral pdb=" CA  GLN D  80 "
           pdb=" C   GLN D  80 "
           pdb=" N   TYR D  81 "
           pdb=" CA  TYR D  81 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -164.00  -16.00     0      5.00e+00 4.00e-02 1.02e+01
  dihedral pdb=" CA  GLU C  22 "
           pdb=" CB  GLU C  22 "
           pdb=" CG  GLU C  22 "
           pdb=" CD  GLU C  22 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -60.00 -116.82   56.82     3      1.50e+01 4.44e-03 9.42e+00
  dihedral pdb=" CA  LYS B  25 "
           pdb=" CB  LYS B  25 "
           pdb=" CG  LYS B  25 "
           pdb=" CD  LYS B  25 "
      ideal   model   delta sinusoidal    sigma   weight residual
     180.00  124.64   55.36     3      1.50e+01 4.44e-03 9.34e+00
  ... (remaining 7197 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.036: 1265
       0.036 -    0.071: 468
       0.071 -    0.107: 165
       0.107 -    0.143: 75
       0.143 -    0.178: 7
  Chirality restraints: 1980
  Sorted by residual:
  chirality pdb=" CB  VAL F 213 "
            pdb=" CA  VAL F 213 "
            pdb=" CG1 VAL F 213 "
            pdb=" CG2 VAL F 213 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -2.45   -0.18 2.00e-01 2.50e+01 7.93e-01
  chirality pdb=" CB  VAL A 213 "
            pdb=" CA  VAL A 213 "
            pdb=" CG1 VAL A 213 "
            pdb=" CG2 VAL A 213 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -2.45   -0.18 2.00e-01 2.50e+01 7.88e-01
  chirality pdb=" CB  VAL E 213 "
            pdb=" CA  VAL E 213 "
            pdb=" CG1 VAL E 213 "
            pdb=" CG2 VAL E 213 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -2.46   -0.17 2.00e-01 2.50e+01 7.20e-01
  ... (remaining 1977 not shown)

  Planarity restraints: 2118
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ALA A 194 "   -0.017 2.00e-02 2.50e+03   3.33e-02 1.11e+01
        pdb=" C   ALA A 194 "    0.058 2.00e-02 2.50e+03
        pdb=" O   ALA A 194 "   -0.021 2.00e-02 2.50e+03
        pdb=" N   VAL A 195 "   -0.019 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  GLY B 193 "    0.009 2.00e-02 2.50e+03   1.75e-02 3.05e+00
        pdb=" C   GLY B 193 "   -0.030 2.00e-02 2.50e+03
        pdb=" O   GLY B 193 "    0.011 2.00e-02 2.50e+03
        pdb=" N   ALA B 194 "    0.010 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  GLY F 193 "    0.009 2.00e-02 2.50e+03   1.72e-02 2.95e+00
        pdb=" C   GLY F 193 "   -0.030 2.00e-02 2.50e+03
        pdb=" O   GLY F 193 "    0.011 2.00e-02 2.50e+03
        pdb=" N   ALA F 194 "    0.010 2.00e-02 2.50e+03
  ... (remaining 2115 not shown)

  Histogram of nonbonded interaction distances:
        2.25 -     2.78: 2147
        2.78 -     3.31: 10667
        3.31 -     3.84: 20213
        3.84 -     4.37: 23381
        4.37 -     4.90: 41353
  Nonbonded interactions: 97761
  Sorted by model distance:
  nonbonded pdb=" O   GLY C 155 "
            pdb=" OG  SER C 159 "
     model   vdw
     2.252 3.040
  nonbonded pdb=" OD1 ASP E  41 "
            pdb=" OH  TYR E  81 "
     model   vdw
     2.256 3.040
  nonbonded pdb=" OD1 ASP F  41 "
            pdb=" OH  TYR F  81 "
     model   vdw
     2.272 3.040
  nonbonded pdb=" OD1 ASP A  41 "
            pdb=" OH  TYR A  81 "
     model   vdw
     2.275 3.040
  nonbonded pdb=" O   GLY A 155 "
            pdb=" OG  SER A 159 "
     model   vdw
     2.289 3.040
  ... (remaining 97756 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.03
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'B'
  selection = chain 'C'
  selection = chain 'D'
  selection = chain 'E'
  selection = chain 'F'
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             1.060
  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:          0.420
  Check model and map are aligned:         0.080
  Set scattering table:                    0.100
  Process input model:                     29.540
  Find NCS groups from input model:        0.740
  Set up NCS constraints:                  0.170
  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:12.670
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   44.790
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7737
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      :  0.002   0.032  12006  Z= 0.114
  Angle     :  0.513   6.934  16338  Z= 0.272
  Chirality :  0.046   0.178   1980
  Planarity :  0.005   0.041   2118
  Dihedral  : 11.205  82.170   4332
  Min Nonbonded Distance : 2.252

Molprobity Statistics.
  All-atom Clashscore : 4.07
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.22 %
    Favored  : 98.78 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  7.15 %
    Favored  : 92.85 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.40 (0.20), residues: 1554
  helix:  1.49 (0.21), residues: 582
  sheet:  0.71 (0.30), residues: 294
  loop : -1.03 (0.21), residues: 678

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.002   TRP C  30 
 HIS   0.007   0.001   HIS C  72 
 PHE   0.006   0.001   PHE F 198 
 TYR   0.006   0.001   TYR E 120 
 ARG   0.005   0.001   ARG A  75 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.10652 (  655)
  hydrogen bonds       : angle       5.73282 ( 1890)
  covalent geometry    : bond        0.00243 (12006)
  covalent geometry    : angle       0.51275 (16338)

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

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

  3108 Ramachandran restraints generated.
    1554 Oldfield, 0 Emsley, 1554 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3108 Ramachandran restraints generated.
    1554 Oldfield, 0 Emsley, 1554 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  209 residues out of total 1272 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 209
  time to evaluate  : 1.380 
Fit side-chains
REVERT: A   29 GLN cc_start: 0.8015 (tt0) cc_final: 0.7787 (tm-30)
REVERT: B   35 GLU cc_start: 0.7109 (mm-30) cc_final: 0.6798 (mm-30)
REVERT: B   36 SER cc_start: 0.8595 (m) cc_final: 0.8174 (t)
REVERT: B   57 ARG cc_start: 0.7283 (mtm-85) cc_final: 0.6981 (mtm110)
REVERT: B  106 LYS cc_start: 0.7792 (mppt) cc_final: 0.7558 (mptp)
REVERT: B  107 GLU cc_start: 0.7249 (mm-30) cc_final: 0.6955 (pt0)
REVERT: B  144 LYS cc_start: 0.7081 (mttt) cc_final: 0.6830 (mtpt)
REVERT: C   57 ARG cc_start: 0.7881 (mtm-85) cc_final: 0.7663 (mtt180)
REVERT: C  107 GLU cc_start: 0.7974 (mm-30) cc_final: 0.7282 (pt0)
REVERT: D    1 MET cc_start: 0.7854 (mpp) cc_final: 0.7473 (mtm)
REVERT: D   20 MET cc_start: 0.7318 (mtp) cc_final: 0.6916 (ppp)
REVERT: D   25 LYS cc_start: 0.7862 (ptmt) cc_final: 0.7643 (ptmm)
REVERT: D   96 THR cc_start: 0.7931 (p) cc_final: 0.7618 (p)
REVERT: D  146 GLU cc_start: 0.8367 (mt-10) cc_final: 0.7935 (mt-10)
REVERT: E   25 LYS cc_start: 0.7982 (pptt) cc_final: 0.7465 (pmtt)
REVERT: E  107 GLU cc_start: 0.7494 (mm-30) cc_final: 0.6635 (pt0)
REVERT: F    1 MET cc_start: 0.7886 (mpp) cc_final: 0.7575 (mmm)
REVERT: F  107 GLU cc_start: 0.7215 (mm-30) cc_final: 0.6684 (pt0)
  outliers start: 0
  outliers final: 0
  residues processed: 209
  average time/residue: 1.3129
  time to fit residues: 296.0440
Evaluate side-chains
  141 residues out of total 1272 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 141
  time to evaluate  : 1.220 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 156
   random chunks:
   chunk 131 optimal weight:    8.9990
   chunk 118 optimal weight:    9.9990
   chunk 65 optimal weight:    7.9990
   chunk 40 optimal weight:    7.9990
   chunk 79 optimal weight:    7.9990
   chunk 63 optimal weight:    0.5980
   chunk 122 optimal weight:    9.9990
   chunk 47 optimal weight:    2.9990
   chunk 74 optimal weight:    9.9990
   chunk 91 optimal weight:    6.9990
   chunk 141 optimal weight:    4.9990
   overall best weight:    4.7188

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

Flipped N/Q/H residues before XYZ refinement:
A   9 ASN
B  29 GLN
C  72 HIS
E  87 HIS

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4091 r_free = 0.4091 target = 0.184058 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3738 r_free = 0.3738 target = 0.147981 restraints weight = 12239.701|
|-----------------------------------------------------------------------------|
r_work (start): 0.3712 rms_B_bonded: 1.97
r_work: 0.3584 rms_B_bonded: 2.56 restraints_weight: 0.5000
r_work: 0.3456 rms_B_bonded: 4.17 restraints_weight: 0.2500
r_work (final): 0.3456
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8129
moved from start:          0.1609

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.008   0.064  12006  Z= 0.323
  Angle     :  0.696   8.056  16338  Z= 0.372
  Chirality :  0.053   0.170   1980
  Planarity :  0.006   0.059   2118
  Dihedral  :  4.795  16.969   1686
  Min Nonbonded Distance : 2.496

Molprobity Statistics.
  All-atom Clashscore : 5.58
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.16 %
    Favored  : 98.84 %
  Rotamer:
    Outliers :  3.46 %
    Allowed  : 12.50 %
    Favored  : 84.04 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.00 (0.20), residues: 1554
  helix:  0.97 (0.20), residues: 582
  sheet:  0.57 (0.28), residues: 330
  loop : -1.21 (0.21), residues: 642

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.003   TRP F  30 
 HIS   0.011   0.002   HIS E  87 
 PHE   0.019   0.002   PHE D 198 
 TYR   0.019   0.003   TYR C  81 
 ARG   0.005   0.001   ARG C   8 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05045 (  655)
  hydrogen bonds       : angle       5.53134 ( 1890)
  covalent geometry    : bond        0.00769 (12006)
  covalent geometry    : angle       0.69621 (16338)

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

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

  3108 Ramachandran restraints generated.
    1554 Oldfield, 0 Emsley, 1554 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3108 Ramachandran restraints generated.
    1554 Oldfield, 0 Emsley, 1554 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  187 residues out of total 1272 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 44
    poor density    : 143
  time to evaluate  : 1.326 
Fit side-chains
   revert: symmetry clash
REVERT: A   29 GLN cc_start: 0.8241 (tt0) cc_final: 0.7920 (tm-30)
REVERT: B   36 SER cc_start: 0.8814 (m) cc_final: 0.8507 (t)
REVERT: B  144 LYS cc_start: 0.7641 (mttt) cc_final: 0.7171 (mmpt)
REVERT: C   29 GLN cc_start: 0.8180 (OUTLIER) cc_final: 0.7511 (tt0)
REVERT: C  107 GLU cc_start: 0.8187 (mm-30) cc_final: 0.7424 (pt0)
REVERT: C  146 GLU cc_start: 0.7742 (mp0) cc_final: 0.7332 (mp0)
REVERT: C  237 GLU cc_start: 0.8721 (OUTLIER) cc_final: 0.7913 (mm-30)
REVERT: D    1 MET cc_start: 0.8290 (mpp) cc_final: 0.7794 (mtm)
REVERT: D   20 MET cc_start: 0.7748 (mtp) cc_final: 0.6925 (ppp)
REVERT: D   25 LYS cc_start: 0.8037 (ptmt) cc_final: 0.7726 (ptpt)
REVERT: D   46 THR cc_start: 0.8214 (t) cc_final: 0.7858 (m)
REVERT: D  146 GLU cc_start: 0.8680 (mt-10) cc_final: 0.8342 (mt-10)
REVERT: E  224 ILE cc_start: 0.8280 (OUTLIER) cc_final: 0.8079 (mm)
REVERT: E  235 LEU cc_start: 0.7599 (OUTLIER) cc_final: 0.7341 (mt)
REVERT: F    1 MET cc_start: 0.8150 (mpp) cc_final: 0.7638 (mmm)
REVERT: F   29 GLN cc_start: 0.8281 (OUTLIER) cc_final: 0.8043 (tt0)
REVERT: F   88 VAL cc_start: 0.8579 (p) cc_final: 0.8343 (m)
REVERT: F  107 GLU cc_start: 0.7412 (mm-30) cc_final: 0.6701 (pt0)
  outliers start: 44
  outliers final: 30
  residues processed: 171
  average time/residue: 1.2269
  time to fit residues: 227.8681
Evaluate side-chains
  172 residues out of total 1272 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 137
  time to evaluate  : 1.288 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    6 ASP
Chi-restraints excluded: chain A residue   34 THR
Chi-restraints excluded: chain A residue  235 LEU
Chi-restraints excluded: chain A residue  242 ASP
Chi-restraints excluded: chain B residue   27 VAL
Chi-restraints excluded: chain B residue  108 VAL
Chi-restraints excluded: chain B residue  230 THR
Chi-restraints excluded: chain B residue  235 LEU
Chi-restraints excluded: chain C residue   29 GLN
Chi-restraints excluded: chain C residue   46 THR
Chi-restraints excluded: chain C residue   88 VAL
Chi-restraints excluded: chain C residue  108 VAL
Chi-restraints excluded: chain C residue  134 SER
Chi-restraints excluded: chain C residue  235 LEU
Chi-restraints excluded: chain C residue  237 GLU
Chi-restraints excluded: chain C residue  239 HIS
Chi-restraints excluded: chain D residue   61 THR
Chi-restraints excluded: chain D residue  230 THR
Chi-restraints excluded: chain D residue  235 LEU
Chi-restraints excluded: chain E residue   27 VAL
Chi-restraints excluded: chain E residue   36 SER
Chi-restraints excluded: chain E residue   46 THR
Chi-restraints excluded: chain E residue   61 THR
Chi-restraints excluded: chain E residue   67 VAL
Chi-restraints excluded: chain E residue  102 VAL
Chi-restraints excluded: chain E residue  121 ASP
Chi-restraints excluded: chain E residue  148 LEU
Chi-restraints excluded: chain E residue  156 VAL
Chi-restraints excluded: chain E residue  224 ILE
Chi-restraints excluded: chain E residue  235 LEU
Chi-restraints excluded: chain F residue   29 GLN
Chi-restraints excluded: chain F residue   85 VAL
Chi-restraints excluded: chain F residue  179 ARG
Chi-restraints excluded: chain F residue  222 VAL
Chi-restraints excluded: chain F residue  230 THR
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 156
   random chunks:
   chunk 49 optimal weight:    3.9990
   chunk 14 optimal weight:    0.0970
   chunk 76 optimal weight:    1.9990
   chunk 94 optimal weight:    5.9990
   chunk 51 optimal weight:    0.7980
   chunk 37 optimal weight:    0.7980
   chunk 131 optimal weight:    0.9980
   chunk 115 optimal weight:    0.9980
   chunk 36 optimal weight:    1.9990
   chunk 75 optimal weight:    1.9990
   chunk 119 optimal weight:    0.8980
   overall best weight:    0.7178

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

Flipped N/Q/H residues before XYZ refinement:
B  29 GLN
E  87 HIS
E 191 GLN
F 185 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4148 r_free = 0.4148 target = 0.189971 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3806 r_free = 0.3806 target = 0.154293 restraints weight = 12269.152|
|-----------------------------------------------------------------------------|
r_work (start): 0.3780 rms_B_bonded: 2.01
r_work: 0.3659 rms_B_bonded: 2.59 restraints_weight: 0.5000
r_work: 0.3531 rms_B_bonded: 4.25 restraints_weight: 0.2500
r_work (final): 0.3531
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8034
moved from start:          0.1485

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.028  12006  Z= 0.107
  Angle     :  0.473   6.131  16338  Z= 0.253
  Chirality :  0.044   0.147   1980
  Planarity :  0.004   0.040   2118
  Dihedral  :  4.059  16.618   1686
  Min Nonbonded Distance : 2.552

Molprobity Statistics.
  All-atom Clashscore : 5.04
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.84 %
    Favored  : 99.16 %
  Rotamer:
    Outliers :  2.75 %
    Allowed  : 14.86 %
    Favored  : 82.39 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.90 (0.20), residues: 1554
  helix:  1.94 (0.21), residues: 582
  sheet:  0.97 (0.29), residues: 300
  loop : -0.79 (0.22), residues: 672

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP C  30 
 HIS   0.011   0.001   HIS E  72 
 PHE   0.008   0.001   PHE B 132 
 TYR   0.010   0.001   TYR E 120 
 ARG   0.006   0.000   ARG A  57 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03427 (  655)
  hydrogen bonds       : angle       4.91134 ( 1890)
  covalent geometry    : bond        0.00233 (12006)
  covalent geometry    : angle       0.47331 (16338)

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

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

  3108 Ramachandran restraints generated.
    1554 Oldfield, 0 Emsley, 1554 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3108 Ramachandran restraints generated.
    1554 Oldfield, 0 Emsley, 1554 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  178 residues out of total 1272 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 143
  time to evaluate  : 1.193 
Fit side-chains
REVERT: A   29 GLN cc_start: 0.8188 (tt0) cc_final: 0.7913 (tm-30)
REVERT: A  260 ASN cc_start: 0.7448 (m-40) cc_final: 0.6925 (t0)
REVERT: B   36 SER cc_start: 0.8722 (m) cc_final: 0.8409 (t)
REVERT: B  144 LYS cc_start: 0.7647 (mttt) cc_final: 0.7139 (mmpt)
REVERT: B  212 ASP cc_start: 0.7905 (m-30) cc_final: 0.7697 (m-30)
REVERT: C   29 GLN cc_start: 0.8151 (OUTLIER) cc_final: 0.7517 (tt0)
REVERT: C  107 GLU cc_start: 0.8028 (mm-30) cc_final: 0.7331 (pt0)
REVERT: D    1 MET cc_start: 0.8281 (mpp) cc_final: 0.7948 (mtm)
REVERT: D   20 MET cc_start: 0.7704 (mtp) cc_final: 0.6747 (ppp)
REVERT: D   25 LYS cc_start: 0.7989 (ptmt) cc_final: 0.7627 (ptmm)
REVERT: D   46 THR cc_start: 0.8032 (t) cc_final: 0.7774 (m)
REVERT: D   96 THR cc_start: 0.8236 (p) cc_final: 0.7967 (p)
REVERT: D  146 GLU cc_start: 0.8647 (mt-10) cc_final: 0.8442 (mt-10)
REVERT: E  235 LEU cc_start: 0.7480 (OUTLIER) cc_final: 0.7243 (mt)
REVERT: F    1 MET cc_start: 0.8102 (mpp) cc_final: 0.7654 (mmm)
REVERT: F   20 MET cc_start: 0.6665 (pmm) cc_final: 0.5756 (ppp)
REVERT: F  107 GLU cc_start: 0.7318 (mm-30) cc_final: 0.6704 (pt0)
  outliers start: 35
  outliers final: 18
  residues processed: 165
  average time/residue: 1.3064
  time to fit residues: 235.4002
Evaluate side-chains
  154 residues out of total 1272 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 134
  time to evaluate  : 1.293 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   56 GLU
Chi-restraints excluded: chain A residue   88 VAL
Chi-restraints excluded: chain A residue  102 VAL
Chi-restraints excluded: chain A residue  242 ASP
Chi-restraints excluded: chain B residue  230 THR
Chi-restraints excluded: chain B residue  235 LEU
Chi-restraints excluded: chain C residue   29 GLN
Chi-restraints excluded: chain C residue   88 VAL
Chi-restraints excluded: chain C residue  108 VAL
Chi-restraints excluded: chain C residue  140 VAL
Chi-restraints excluded: chain C residue  239 HIS
Chi-restraints excluded: chain D residue   61 THR
Chi-restraints excluded: chain D residue  230 THR
Chi-restraints excluded: chain E residue   67 VAL
Chi-restraints excluded: chain E residue   88 VAL
Chi-restraints excluded: chain E residue  235 LEU
Chi-restraints excluded: chain F residue   74 VAL
Chi-restraints excluded: chain F residue  102 VAL
Chi-restraints excluded: chain F residue  141 VAL
Chi-restraints excluded: chain F residue  230 THR
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 156
   random chunks:
   chunk 62 optimal weight:   10.0000
   chunk 106 optimal weight:    0.9980
   chunk 129 optimal weight:    3.9990
   chunk 45 optimal weight:   10.0000
   chunk 103 optimal weight:    6.9990
   chunk 139 optimal weight:    2.9990
   chunk 7 optimal weight:    4.9990
   chunk 8 optimal weight:    3.9990
   chunk 58 optimal weight:    6.9990
   chunk 111 optimal weight:    4.9990
   chunk 59 optimal weight:    0.9980
   overall best weight:    2.5986

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

Flipped N/Q/H residues before XYZ refinement:
** A   9 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
E  87 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4105 r_free = 0.4105 target = 0.185818 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3752 r_free = 0.3752 target = 0.149978 restraints weight = 12253.956|
|-----------------------------------------------------------------------------|
r_work (start): 0.3743 rms_B_bonded: 2.06
r_work: 0.3621 rms_B_bonded: 2.50 restraints_weight: 0.5000
r_work: 0.3492 rms_B_bonded: 4.09 restraints_weight: 0.2500
r_work (final): 0.3492
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8092
moved from start:          0.1713

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.051  12006  Z= 0.197
  Angle     :  0.554   7.086  16338  Z= 0.297
  Chirality :  0.047   0.147   1980
  Planarity :  0.005   0.043   2118
  Dihedral  :  4.349  16.869   1686
  Min Nonbonded Distance : 2.529

Molprobity Statistics.
  All-atom Clashscore : 5.08
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.29 %
    Favored  : 98.71 %
  Rotamer:
    Outliers :  3.69 %
    Allowed  : 14.78 %
    Favored  : 81.53 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.70 (0.20), residues: 1554
  helix:  1.72 (0.21), residues: 582
  sheet:  0.78 (0.29), residues: 312
  loop : -0.82 (0.22), residues: 660

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.002   TRP C  30 
 HIS   0.014   0.001   HIS E  72 
 PHE   0.014   0.002   PHE D 198 
 TYR   0.014   0.002   TYR E 120 
 ARG   0.006   0.000   ARG A  57 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04110 (  655)
  hydrogen bonds       : angle       5.12761 ( 1890)
  covalent geometry    : bond        0.00464 (12006)
  covalent geometry    : angle       0.55367 (16338)

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

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

  3108 Ramachandran restraints generated.
    1554 Oldfield, 0 Emsley, 1554 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3108 Ramachandran restraints generated.
    1554 Oldfield, 0 Emsley, 1554 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  179 residues out of total 1272 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 47
    poor density    : 132
  time to evaluate  : 2.785 
Fit side-chains
REVERT: A   29 GLN cc_start: 0.8229 (tt0) cc_final: 0.7951 (tm-30)
REVERT: B   29 GLN cc_start: 0.8308 (OUTLIER) cc_final: 0.7799 (tm-30)
REVERT: B   36 SER cc_start: 0.8775 (m) cc_final: 0.8471 (t)
REVERT: B  144 LYS cc_start: 0.7655 (mttt) cc_final: 0.7182 (mmpt)
REVERT: B  166 ARG cc_start: 0.6330 (OUTLIER) cc_final: 0.5896 (mtp85)
REVERT: C   29 GLN cc_start: 0.8119 (OUTLIER) cc_final: 0.7469 (tt0)
REVERT: C   57 ARG cc_start: 0.8154 (OUTLIER) cc_final: 0.7747 (mtt180)
REVERT: C  107 GLU cc_start: 0.8127 (mm-30) cc_final: 0.7425 (pt0)
REVERT: D    1 MET cc_start: 0.8254 (mpp) cc_final: 0.7770 (mtm)
REVERT: D   20 MET cc_start: 0.7712 (mtp) cc_final: 0.6777 (ppp)
REVERT: D   25 LYS cc_start: 0.8005 (ptmt) cc_final: 0.7690 (ptpt)
REVERT: D   46 THR cc_start: 0.8128 (t) cc_final: 0.7818 (m)
REVERT: E   72 HIS cc_start: 0.5804 (OUTLIER) cc_final: 0.5075 (p-80)
REVERT: E  235 LEU cc_start: 0.7536 (OUTLIER) cc_final: 0.7286 (mt)
REVERT: F    1 MET cc_start: 0.8123 (mpp) cc_final: 0.7629 (mmp)
REVERT: F  107 GLU cc_start: 0.7352 (mm-30) cc_final: 0.6705 (pt0)
  outliers start: 47
  outliers final: 31
  residues processed: 164
  average time/residue: 2.6424
  time to fit residues: 474.0927
Evaluate side-chains
  166 residues out of total 1272 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 37
    poor density    : 129
  time to evaluate  : 4.580 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   56 GLU
Chi-restraints excluded: chain A residue   85 VAL
Chi-restraints excluded: chain A residue  102 VAL
Chi-restraints excluded: chain A residue  242 ASP
Chi-restraints excluded: chain B residue   27 VAL
Chi-restraints excluded: chain B residue   29 GLN
Chi-restraints excluded: chain B residue  108 VAL
Chi-restraints excluded: chain B residue  166 ARG
Chi-restraints excluded: chain B residue  230 THR
Chi-restraints excluded: chain B residue  235 LEU
Chi-restraints excluded: chain C residue   29 GLN
Chi-restraints excluded: chain C residue   57 ARG
Chi-restraints excluded: chain C residue   88 VAL
Chi-restraints excluded: chain C residue  108 VAL
Chi-restraints excluded: chain C residue  235 LEU
Chi-restraints excluded: chain C residue  239 HIS
Chi-restraints excluded: chain D residue   61 THR
Chi-restraints excluded: chain D residue  173 VAL
Chi-restraints excluded: chain D residue  230 THR
Chi-restraints excluded: chain D residue  235 LEU
Chi-restraints excluded: chain E residue   27 VAL
Chi-restraints excluded: chain E residue   36 SER
Chi-restraints excluded: chain E residue   46 THR
Chi-restraints excluded: chain E residue   61 THR
Chi-restraints excluded: chain E residue   67 VAL
Chi-restraints excluded: chain E residue   72 HIS
Chi-restraints excluded: chain E residue   88 VAL
Chi-restraints excluded: chain E residue  148 LEU
Chi-restraints excluded: chain E residue  235 LEU
Chi-restraints excluded: chain F residue   46 THR
Chi-restraints excluded: chain F residue   74 VAL
Chi-restraints excluded: chain F residue   85 VAL
Chi-restraints excluded: chain F residue  102 VAL
Chi-restraints excluded: chain F residue  141 VAL
Chi-restraints excluded: chain F residue  173 VAL
Chi-restraints excluded: chain F residue  214 SER
Chi-restraints excluded: chain F residue  230 THR
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 156
   random chunks:
   chunk 141 optimal weight:    0.9990
   chunk 89 optimal weight:    0.9980
   chunk 116 optimal weight:   10.0000
   chunk 61 optimal weight:    0.0040
   chunk 53 optimal weight:    2.9990
   chunk 15 optimal weight:    6.9990
   chunk 148 optimal weight:    9.9990
   chunk 84 optimal weight:    4.9990
   chunk 150 optimal weight:    4.9990
   chunk 29 optimal weight:    2.9990
   chunk 2 optimal weight:    6.9990
   overall best weight:    1.5998

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

Flipped N/Q/H residues before XYZ refinement:
A   9 ASN
A 185 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4121 r_free = 0.4121 target = 0.187333 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3771 r_free = 0.3771 target = 0.151701 restraints weight = 12159.788|
|-----------------------------------------------------------------------------|
r_work (start): 0.3762 rms_B_bonded: 2.06
r_work: 0.3640 rms_B_bonded: 2.49 restraints_weight: 0.5000
r_work: 0.3511 rms_B_bonded: 4.11 restraints_weight: 0.2500
r_work (final): 0.3511
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8066
moved from start:          0.1711

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038  12006  Z= 0.142
  Angle     :  0.499   7.513  16338  Z= 0.267
  Chirality :  0.045   0.144   1980
  Planarity :  0.004   0.043   2118
  Dihedral  :  4.169  16.804   1686
  Min Nonbonded Distance : 2.545

Molprobity Statistics.
  All-atom Clashscore : 5.16
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.22 %
    Favored  : 98.78 %
  Rotamer:
    Outliers :  3.77 %
    Allowed  : 16.27 %
    Favored  : 79.95 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.89 (0.21), residues: 1554
  helix:  1.92 (0.21), residues: 582
  sheet:  0.83 (0.29), residues: 312
  loop : -0.74 (0.22), residues: 660

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP C  30 
 HIS   0.014   0.001   HIS E  72 
 PHE   0.011   0.001   PHE A 198 
 TYR   0.012   0.002   TYR E 120 
 ARG   0.006   0.000   ARG A  57 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03682 (  655)
  hydrogen bonds       : angle       4.95886 ( 1890)
  covalent geometry    : bond        0.00328 (12006)
  covalent geometry    : angle       0.49940 (16338)

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

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

  3108 Ramachandran restraints generated.
    1554 Oldfield, 0 Emsley, 1554 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3108 Ramachandran restraints generated.
    1554 Oldfield, 0 Emsley, 1554 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  181 residues out of total 1272 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 48
    poor density    : 133
  time to evaluate  : 1.296 
Fit side-chains
REVERT: A   29 GLN cc_start: 0.8192 (tt0) cc_final: 0.7926 (tm-30)
REVERT: A  260 ASN cc_start: 0.7559 (m-40) cc_final: 0.6933 (t0)
REVERT: B   29 GLN cc_start: 0.8316 (OUTLIER) cc_final: 0.7818 (tm-30)
REVERT: B   36 SER cc_start: 0.8741 (m) cc_final: 0.8429 (t)
REVERT: B  144 LYS cc_start: 0.7608 (mttt) cc_final: 0.7124 (mmpt)
REVERT: C   29 GLN cc_start: 0.8157 (OUTLIER) cc_final: 0.7531 (tt0)
REVERT: C   57 ARG cc_start: 0.8141 (OUTLIER) cc_final: 0.7727 (mtt180)
REVERT: C  107 GLU cc_start: 0.8129 (mm-30) cc_final: 0.7403 (pt0)
REVERT: D    1 MET cc_start: 0.8283 (mpp) cc_final: 0.7803 (mtm)
REVERT: D   20 MET cc_start: 0.7735 (mtp) cc_final: 0.6773 (ppp)
REVERT: D   25 LYS cc_start: 0.7992 (ptmt) cc_final: 0.7623 (ptmm)
REVERT: D   46 THR cc_start: 0.8102 (t) cc_final: 0.7809 (m)
REVERT: E   72 HIS cc_start: 0.5743 (OUTLIER) cc_final: 0.5021 (p-80)
REVERT: E  235 LEU cc_start: 0.7511 (OUTLIER) cc_final: 0.7261 (mt)
REVERT: F    1 MET cc_start: 0.8109 (mpp) cc_final: 0.7623 (mmp)
REVERT: F   20 MET cc_start: 0.6698 (pmm) cc_final: 0.5713 (ppp)
REVERT: F   88 VAL cc_start: 0.8483 (OUTLIER) cc_final: 0.8259 (m)
REVERT: F  107 GLU cc_start: 0.7330 (mm-30) cc_final: 0.6710 (pt0)
  outliers start: 48
  outliers final: 33
  residues processed: 167
  average time/residue: 1.2449
  time to fit residues: 225.7265
Evaluate side-chains
  164 residues out of total 1272 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 39
    poor density    : 125
  time to evaluate  : 1.387 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    6 ASP
Chi-restraints excluded: chain A residue   56 GLU
Chi-restraints excluded: chain A residue   85 VAL
Chi-restraints excluded: chain A residue   88 VAL
Chi-restraints excluded: chain A residue  102 VAL
Chi-restraints excluded: chain A residue  108 VAL
Chi-restraints excluded: chain A residue  235 LEU
Chi-restraints excluded: chain A residue  242 ASP
Chi-restraints excluded: chain B residue   27 VAL
Chi-restraints excluded: chain B residue   29 GLN
Chi-restraints excluded: chain B residue  108 VAL
Chi-restraints excluded: chain B residue  134 SER
Chi-restraints excluded: chain B residue  230 THR
Chi-restraints excluded: chain B residue  235 LEU
Chi-restraints excluded: chain C residue   29 GLN
Chi-restraints excluded: chain C residue   57 ARG
Chi-restraints excluded: chain C residue   88 VAL
Chi-restraints excluded: chain C residue  108 VAL
Chi-restraints excluded: chain C residue  134 SER
Chi-restraints excluded: chain C residue  235 LEU
Chi-restraints excluded: chain C residue  239 HIS
Chi-restraints excluded: chain D residue   61 THR
Chi-restraints excluded: chain D residue  173 VAL
Chi-restraints excluded: chain D residue  230 THR
Chi-restraints excluded: chain E residue   27 VAL
Chi-restraints excluded: chain E residue   36 SER
Chi-restraints excluded: chain E residue   67 VAL
Chi-restraints excluded: chain E residue   72 HIS
Chi-restraints excluded: chain E residue   88 VAL
Chi-restraints excluded: chain E residue  148 LEU
Chi-restraints excluded: chain E residue  156 VAL
Chi-restraints excluded: chain E residue  235 LEU
Chi-restraints excluded: chain F residue   74 VAL
Chi-restraints excluded: chain F residue   88 VAL
Chi-restraints excluded: chain F residue  102 VAL
Chi-restraints excluded: chain F residue  141 VAL
Chi-restraints excluded: chain F residue  173 VAL
Chi-restraints excluded: chain F residue  214 SER
Chi-restraints excluded: chain F residue  230 THR
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 156
   random chunks:
   chunk 3 optimal weight:    3.9990
   chunk 145 optimal weight:    1.9990
   chunk 80 optimal weight:    0.9980
   chunk 116 optimal weight:    9.9990
   chunk 151 optimal weight:    3.9990
   chunk 40 optimal weight:    0.7980
   chunk 105 optimal weight:    7.9990
   chunk 138 optimal weight:    1.9990
   chunk 52 optimal weight:    7.9990
   chunk 100 optimal weight:   10.0000
   chunk 88 optimal weight:    0.9990
   overall best weight:    1.3586

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

Flipped N/Q/H residues before XYZ refinement:
A 185 ASN
E   9 ASN
E  87 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4133 r_free = 0.4133 target = 0.188400 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3786 r_free = 0.3786 target = 0.152358 restraints weight = 12312.964|
|-----------------------------------------------------------------------------|
r_work (start): 0.3752 rms_B_bonded: 2.08
r_work: 0.3627 rms_B_bonded: 2.63 restraints_weight: 0.5000
r_work: 0.3498 rms_B_bonded: 4.31 restraints_weight: 0.2500
r_work (final): 0.3498
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8065
moved from start:          0.1740

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031  12006  Z= 0.129
  Angle     :  0.481   5.701  16338  Z= 0.257
  Chirality :  0.045   0.143   1980
  Planarity :  0.004   0.043   2118
  Dihedral  :  4.020  16.613   1686
  Min Nonbonded Distance : 2.549

Molprobity Statistics.
  All-atom Clashscore : 5.08
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.16 %
    Favored  : 98.84 %
  Rotamer:
    Outliers :  3.85 %
    Allowed  : 16.51 %
    Favored  : 79.64 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.06 (0.21), residues: 1554
  helix:  2.08 (0.21), residues: 582
  sheet:  0.88 (0.29), residues: 312
  loop : -0.63 (0.23), residues: 660

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP C  30 
 HIS   0.014   0.001   HIS E  72 
 PHE   0.011   0.001   PHE A 198 
 TYR   0.010   0.001   TYR E 120 
 ARG   0.007   0.000   ARG A  57 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03520 (  655)
  hydrogen bonds       : angle       4.87038 ( 1890)
  covalent geometry    : bond        0.00295 (12006)
  covalent geometry    : angle       0.48059 (16338)

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

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

  3108 Ramachandran restraints generated.
    1554 Oldfield, 0 Emsley, 1554 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3108 Ramachandran restraints generated.
    1554 Oldfield, 0 Emsley, 1554 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  176 residues out of total 1272 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 49
    poor density    : 127
  time to evaluate  : 1.199 
Fit side-chains
REVERT: A   29 GLN cc_start: 0.8208 (tt0) cc_final: 0.7927 (tm-30)
REVERT: A  260 ASN cc_start: 0.7521 (m-40) cc_final: 0.6976 (t0)
REVERT: B   29 GLN cc_start: 0.8323 (OUTLIER) cc_final: 0.7813 (tm-30)
REVERT: B   36 SER cc_start: 0.8747 (m) cc_final: 0.8423 (t)
REVERT: B  144 LYS cc_start: 0.7595 (mttt) cc_final: 0.7107 (mmpt)
REVERT: B  166 ARG cc_start: 0.6291 (OUTLIER) cc_final: 0.5878 (mtp85)
REVERT: C   29 GLN cc_start: 0.8157 (OUTLIER) cc_final: 0.7498 (tt0)
REVERT: C   57 ARG cc_start: 0.8128 (OUTLIER) cc_final: 0.7702 (mtt180)
REVERT: C  107 GLU cc_start: 0.8142 (mm-30) cc_final: 0.7415 (pt0)
REVERT: D    1 MET cc_start: 0.8303 (mpp) cc_final: 0.7840 (mtm)
REVERT: D   20 MET cc_start: 0.7717 (mtp) cc_final: 0.6755 (ppp)
REVERT: D   25 LYS cc_start: 0.7992 (ptmt) cc_final: 0.7603 (ptmm)
REVERT: D   46 THR cc_start: 0.8071 (t) cc_final: 0.7776 (m)
REVERT: E  235 LEU cc_start: 0.7463 (OUTLIER) cc_final: 0.7215 (mt)
REVERT: F    1 MET cc_start: 0.8065 (mpp) cc_final: 0.7563 (mmp)
REVERT: F   20 MET cc_start: 0.6631 (pmm) cc_final: 0.5749 (ppp)
REVERT: F   88 VAL cc_start: 0.8494 (p) cc_final: 0.8281 (m)
REVERT: F   95 ARG cc_start: 0.6487 (mmm160) cc_final: 0.5664 (mtm-85)
REVERT: F  107 GLU cc_start: 0.7359 (mm-30) cc_final: 0.6747 (pt0)
  outliers start: 49
  outliers final: 36
  residues processed: 163
  average time/residue: 1.1524
  time to fit residues: 204.3996
Evaluate side-chains
  165 residues out of total 1272 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 41
    poor density    : 124
  time to evaluate  : 1.187 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    6 ASP
Chi-restraints excluded: chain A residue   56 GLU
Chi-restraints excluded: chain A residue   85 VAL
Chi-restraints excluded: chain A residue   88 VAL
Chi-restraints excluded: chain A residue  102 VAL
Chi-restraints excluded: chain A residue  108 VAL
Chi-restraints excluded: chain A residue  185 ASN
Chi-restraints excluded: chain A residue  224 ILE
Chi-restraints excluded: chain A residue  235 LEU
Chi-restraints excluded: chain A residue  242 ASP
Chi-restraints excluded: chain B residue   27 VAL
Chi-restraints excluded: chain B residue   29 GLN
Chi-restraints excluded: chain B residue  108 VAL
Chi-restraints excluded: chain B residue  166 ARG
Chi-restraints excluded: chain B residue  230 THR
Chi-restraints excluded: chain B residue  235 LEU
Chi-restraints excluded: chain C residue   29 GLN
Chi-restraints excluded: chain C residue   57 ARG
Chi-restraints excluded: chain C residue   88 VAL
Chi-restraints excluded: chain C residue  108 VAL
Chi-restraints excluded: chain C residue  134 SER
Chi-restraints excluded: chain C residue  235 LEU
Chi-restraints excluded: chain C residue  239 HIS
Chi-restraints excluded: chain D residue   61 THR
Chi-restraints excluded: chain D residue  114 VAL
Chi-restraints excluded: chain D residue  134 SER
Chi-restraints excluded: chain D residue  230 THR
Chi-restraints excluded: chain E residue   36 SER
Chi-restraints excluded: chain E residue   61 THR
Chi-restraints excluded: chain E residue   67 VAL
Chi-restraints excluded: chain E residue   88 VAL
Chi-restraints excluded: chain E residue  148 LEU
Chi-restraints excluded: chain E residue  156 VAL
Chi-restraints excluded: chain E residue  235 LEU
Chi-restraints excluded: chain F residue   74 VAL
Chi-restraints excluded: chain F residue   85 VAL
Chi-restraints excluded: chain F residue  102 VAL
Chi-restraints excluded: chain F residue  141 VAL
Chi-restraints excluded: chain F residue  213 VAL
Chi-restraints excluded: chain F residue  214 SER
Chi-restraints excluded: chain F residue  230 THR
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 156
   random chunks:
   chunk 110 optimal weight:    0.9980
   chunk 33 optimal weight:    0.9980
   chunk 139 optimal weight:   10.0000
   chunk 126 optimal weight:    9.9990
   chunk 0 optimal weight:   10.0000
   chunk 39 optimal weight:    0.0980
   chunk 19 optimal weight:    7.9990
   chunk 52 optimal weight:    7.9990
   chunk 117 optimal weight:    5.9990
   chunk 20 optimal weight:    5.9990
   chunk 7 optimal weight:    1.9990
   overall best weight:    2.0184

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

Flipped N/Q/H residues before XYZ refinement:
A 185 ASN
E   9 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4125 r_free = 0.4125 target = 0.187549 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3778 r_free = 0.3778 target = 0.152036 restraints weight = 12348.746|
|-----------------------------------------------------------------------------|
r_work (start): 0.3757 rms_B_bonded: 2.06
r_work: 0.3636 rms_B_bonded: 2.49 restraints_weight: 0.5000
r_work: 0.3507 rms_B_bonded: 4.10 restraints_weight: 0.2500
r_work (final): 0.3507
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8075
moved from start:          0.1792

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.036  12006  Z= 0.163
  Angle     :  0.513   6.370  16338  Z= 0.274
  Chirality :  0.046   0.144   1980
  Planarity :  0.004   0.044   2118
  Dihedral  :  4.133  16.711   1686
  Min Nonbonded Distance : 2.537

Molprobity Statistics.
  All-atom Clashscore : 4.91
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.22 %
    Favored  : 98.78 %
  Rotamer:
    Outliers :  4.48 %
    Allowed  : 16.67 %
    Favored  : 78.85 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.95 (0.21), residues: 1554
  helix:  1.93 (0.21), residues: 582
  sheet:  0.84 (0.29), residues: 312
  loop : -0.66 (0.22), residues: 660

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP C  30 
 HIS   0.015   0.001   HIS E  72 
 PHE   0.013   0.002   PHE F 196 
 TYR   0.012   0.002   TYR E 120 
 ARG   0.006   0.000   ARG A  57 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03765 (  655)
  hydrogen bonds       : angle       4.95244 ( 1890)
  covalent geometry    : bond        0.00380 (12006)
  covalent geometry    : angle       0.51280 (16338)

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

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

  3108 Ramachandran restraints generated.
    1554 Oldfield, 0 Emsley, 1554 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3108 Ramachandran restraints generated.
    1554 Oldfield, 0 Emsley, 1554 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  182 residues out of total 1272 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 57
    poor density    : 125
  time to evaluate  : 1.293 
Fit side-chains
REVERT: A   29 GLN cc_start: 0.8179 (tt0) cc_final: 0.7911 (tm-30)
REVERT: A  260 ASN cc_start: 0.7553 (m-40) cc_final: 0.6979 (t0)
REVERT: B   36 SER cc_start: 0.8746 (m) cc_final: 0.8430 (t)
REVERT: B  144 LYS cc_start: 0.7636 (mttt) cc_final: 0.7165 (mmpt)
REVERT: B  166 ARG cc_start: 0.6307 (OUTLIER) cc_final: 0.5895 (mtp85)
REVERT: C   29 GLN cc_start: 0.8104 (OUTLIER) cc_final: 0.7463 (tt0)
REVERT: C   57 ARG cc_start: 0.8139 (OUTLIER) cc_final: 0.7722 (mtt180)
REVERT: C  107 GLU cc_start: 0.8109 (mm-30) cc_final: 0.7395 (pt0)
REVERT: D    1 MET cc_start: 0.8341 (mpp) cc_final: 0.7900 (mtm)
REVERT: D   20 MET cc_start: 0.7723 (mtp) cc_final: 0.6782 (ppp)
REVERT: D   25 LYS cc_start: 0.8044 (ptmt) cc_final: 0.7656 (ptmm)
REVERT: D   46 THR cc_start: 0.8083 (t) cc_final: 0.7791 (m)
REVERT: E   72 HIS cc_start: 0.5782 (OUTLIER) cc_final: 0.5240 (p-80)
REVERT: E  235 LEU cc_start: 0.7503 (OUTLIER) cc_final: 0.7256 (mt)
REVERT: F    1 MET cc_start: 0.8102 (mpp) cc_final: 0.7599 (mmp)
REVERT: F   29 GLN cc_start: 0.8242 (OUTLIER) cc_final: 0.8028 (tt0)
REVERT: F   88 VAL cc_start: 0.8490 (OUTLIER) cc_final: 0.8269 (m)
REVERT: F  107 GLU cc_start: 0.7360 (mm-30) cc_final: 0.6752 (pt0)
  outliers start: 57
  outliers final: 40
  residues processed: 168
  average time/residue: 1.1509
  time to fit residues: 210.8002
Evaluate side-chains
  172 residues out of total 1272 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 47
    poor density    : 125
  time to evaluate  : 1.163 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    6 ASP
Chi-restraints excluded: chain A residue   32 ILE
Chi-restraints excluded: chain A residue   34 THR
Chi-restraints excluded: chain A residue   56 GLU
Chi-restraints excluded: chain A residue   85 VAL
Chi-restraints excluded: chain A residue   88 VAL
Chi-restraints excluded: chain A residue  102 VAL
Chi-restraints excluded: chain A residue  108 VAL
Chi-restraints excluded: chain A residue  235 LEU
Chi-restraints excluded: chain A residue  242 ASP
Chi-restraints excluded: chain B residue   27 VAL
Chi-restraints excluded: chain B residue  108 VAL
Chi-restraints excluded: chain B residue  134 SER
Chi-restraints excluded: chain B residue  166 ARG
Chi-restraints excluded: chain B residue  230 THR
Chi-restraints excluded: chain B residue  235 LEU
Chi-restraints excluded: chain C residue   29 GLN
Chi-restraints excluded: chain C residue   57 ARG
Chi-restraints excluded: chain C residue   88 VAL
Chi-restraints excluded: chain C residue  108 VAL
Chi-restraints excluded: chain C residue  134 SER
Chi-restraints excluded: chain C residue  235 LEU
Chi-restraints excluded: chain C residue  239 HIS
Chi-restraints excluded: chain D residue   61 THR
Chi-restraints excluded: chain D residue  114 VAL
Chi-restraints excluded: chain D residue  173 VAL
Chi-restraints excluded: chain D residue  230 THR
Chi-restraints excluded: chain D residue  235 LEU
Chi-restraints excluded: chain E residue   27 VAL
Chi-restraints excluded: chain E residue   61 THR
Chi-restraints excluded: chain E residue   67 VAL
Chi-restraints excluded: chain E residue   72 HIS
Chi-restraints excluded: chain E residue   88 VAL
Chi-restraints excluded: chain E residue  148 LEU
Chi-restraints excluded: chain E residue  156 VAL
Chi-restraints excluded: chain E residue  235 LEU
Chi-restraints excluded: chain F residue   29 GLN
Chi-restraints excluded: chain F residue   46 THR
Chi-restraints excluded: chain F residue   74 VAL
Chi-restraints excluded: chain F residue   85 VAL
Chi-restraints excluded: chain F residue   88 VAL
Chi-restraints excluded: chain F residue  102 VAL
Chi-restraints excluded: chain F residue  141 VAL
Chi-restraints excluded: chain F residue  173 VAL
Chi-restraints excluded: chain F residue  213 VAL
Chi-restraints excluded: chain F residue  214 SER
Chi-restraints excluded: chain F residue  230 THR
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 156
   random chunks:
   chunk 119 optimal weight:    9.9990
   chunk 80 optimal weight:    1.9990
   chunk 54 optimal weight:    4.9990
   chunk 101 optimal weight:    2.9990
   chunk 52 optimal weight:    7.9990
   chunk 100 optimal weight:   10.0000
   chunk 17 optimal weight:    0.8980
   chunk 88 optimal weight:    1.9990
   chunk 38 optimal weight:    7.9990
   chunk 75 optimal weight:    0.2980
   chunk 53 optimal weight:    1.9990
   overall best weight:    1.4386

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

Flipped N/Q/H residues before XYZ refinement:
E   9 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4127 r_free = 0.4127 target = 0.187839 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3777 r_free = 0.3777 target = 0.152165 restraints weight = 12329.892|
|-----------------------------------------------------------------------------|
r_work (start): 0.3768 rms_B_bonded: 2.05
r_work: 0.3649 rms_B_bonded: 2.49 restraints_weight: 0.5000
r_work: 0.3521 rms_B_bonded: 4.09 restraints_weight: 0.2500
r_work (final): 0.3521
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8056
moved from start:          0.1803

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031  12006  Z= 0.132
  Angle     :  0.490   8.250  16338  Z= 0.261
  Chirality :  0.045   0.143   1980
  Planarity :  0.004   0.043   2118
  Dihedral  :  4.016  16.559   1686
  Min Nonbonded Distance : 2.547

Molprobity Statistics.
  All-atom Clashscore : 4.87
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.22 %
    Favored  : 98.78 %
  Rotamer:
    Outliers :  3.77 %
    Allowed  : 17.85 %
    Favored  : 78.38 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.08 (0.21), residues: 1554
  helix:  2.07 (0.21), residues: 582
  sheet:  0.86 (0.29), residues: 312
  loop : -0.59 (0.23), residues: 660

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP C  30 
 HIS   0.015   0.001   HIS E  72 
 PHE   0.012   0.001   PHE F 196 
 TYR   0.011   0.001   TYR E 120 
 ARG   0.007   0.000   ARG A  57 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03539 (  655)
  hydrogen bonds       : angle       4.85451 ( 1890)
  covalent geometry    : bond        0.00304 (12006)
  covalent geometry    : angle       0.48955 (16338)

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

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

  3108 Ramachandran restraints generated.
    1554 Oldfield, 0 Emsley, 1554 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3108 Ramachandran restraints generated.
    1554 Oldfield, 0 Emsley, 1554 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  175 residues out of total 1272 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 48
    poor density    : 127
  time to evaluate  : 1.204 
Fit side-chains
REVERT: A   29 GLN cc_start: 0.8198 (tt0) cc_final: 0.7912 (tm-30)
REVERT: A  260 ASN cc_start: 0.7568 (m-40) cc_final: 0.7016 (t0)
REVERT: B   36 SER cc_start: 0.8731 (m) cc_final: 0.8411 (t)
REVERT: B  144 LYS cc_start: 0.7591 (mttt) cc_final: 0.7107 (mmpt)
REVERT: B  166 ARG cc_start: 0.6296 (OUTLIER) cc_final: 0.5895 (mtp85)
REVERT: B  212 ASP cc_start: 0.7808 (m-30) cc_final: 0.7596 (m-30)
REVERT: C   29 GLN cc_start: 0.8130 (OUTLIER) cc_final: 0.7503 (tt0)
REVERT: C   42 GLU cc_start: 0.8095 (mt-10) cc_final: 0.7839 (mt-10)
REVERT: C   57 ARG cc_start: 0.8114 (OUTLIER) cc_final: 0.7692 (mtt180)
REVERT: C  107 GLU cc_start: 0.8106 (mm-30) cc_final: 0.7411 (pt0)
REVERT: D    1 MET cc_start: 0.8316 (mpp) cc_final: 0.7866 (mtm)
REVERT: D   20 MET cc_start: 0.7717 (mtp) cc_final: 0.6766 (ppp)
REVERT: D   25 LYS cc_start: 0.7995 (ptmt) cc_final: 0.7605 (ptmm)
REVERT: D   46 THR cc_start: 0.8058 (t) cc_final: 0.7782 (m)
REVERT: E   72 HIS cc_start: 0.5782 (OUTLIER) cc_final: 0.5250 (p-80)
REVERT: E  235 LEU cc_start: 0.7488 (OUTLIER) cc_final: 0.7245 (mt)
REVERT: F    1 MET cc_start: 0.8087 (mpp) cc_final: 0.7586 (mmp)
REVERT: F   20 MET cc_start: 0.6504 (pmm) cc_final: 0.5556 (ppp)
REVERT: F   29 GLN cc_start: 0.8225 (OUTLIER) cc_final: 0.8005 (tt0)
REVERT: F   88 VAL cc_start: 0.8524 (OUTLIER) cc_final: 0.8302 (m)
REVERT: F  107 GLU cc_start: 0.7332 (mm-30) cc_final: 0.6746 (pt0)
  outliers start: 48
  outliers final: 40
  residues processed: 163
  average time/residue: 1.1300
  time to fit residues: 201.3042
Evaluate side-chains
  174 residues out of total 1272 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 47
    poor density    : 127
  time to evaluate  : 1.216 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    6 ASP
Chi-restraints excluded: chain A residue   32 ILE
Chi-restraints excluded: chain A residue   34 THR
Chi-restraints excluded: chain A residue   56 GLU
Chi-restraints excluded: chain A residue   85 VAL
Chi-restraints excluded: chain A residue   88 VAL
Chi-restraints excluded: chain A residue  102 VAL
Chi-restraints excluded: chain A residue  108 VAL
Chi-restraints excluded: chain A residue  235 LEU
Chi-restraints excluded: chain A residue  242 ASP
Chi-restraints excluded: chain B residue   27 VAL
Chi-restraints excluded: chain B residue  108 VAL
Chi-restraints excluded: chain B residue  134 SER
Chi-restraints excluded: chain B residue  166 ARG
Chi-restraints excluded: chain B residue  230 THR
Chi-restraints excluded: chain B residue  235 LEU
Chi-restraints excluded: chain C residue   29 GLN
Chi-restraints excluded: chain C residue   57 ARG
Chi-restraints excluded: chain C residue   88 VAL
Chi-restraints excluded: chain C residue  108 VAL
Chi-restraints excluded: chain C residue  134 SER
Chi-restraints excluded: chain C residue  235 LEU
Chi-restraints excluded: chain C residue  239 HIS
Chi-restraints excluded: chain D residue   61 THR
Chi-restraints excluded: chain D residue  114 VAL
Chi-restraints excluded: chain D residue  134 SER
Chi-restraints excluded: chain D residue  173 VAL
Chi-restraints excluded: chain D residue  230 THR
Chi-restraints excluded: chain D residue  235 LEU
Chi-restraints excluded: chain E residue   27 VAL
Chi-restraints excluded: chain E residue   61 THR
Chi-restraints excluded: chain E residue   67 VAL
Chi-restraints excluded: chain E residue   72 HIS
Chi-restraints excluded: chain E residue   88 VAL
Chi-restraints excluded: chain E residue  148 LEU
Chi-restraints excluded: chain E residue  156 VAL
Chi-restraints excluded: chain E residue  235 LEU
Chi-restraints excluded: chain F residue   29 GLN
Chi-restraints excluded: chain F residue   74 VAL
Chi-restraints excluded: chain F residue   85 VAL
Chi-restraints excluded: chain F residue   88 VAL
Chi-restraints excluded: chain F residue  102 VAL
Chi-restraints excluded: chain F residue  141 VAL
Chi-restraints excluded: chain F residue  173 VAL
Chi-restraints excluded: chain F residue  213 VAL
Chi-restraints excluded: chain F residue  214 SER
Chi-restraints excluded: chain F residue  230 THR
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 156
   random chunks:
   chunk 3 optimal weight:    4.9990
   chunk 59 optimal weight:    8.9990
   chunk 135 optimal weight:    3.9990
   chunk 45 optimal weight:    8.9990
   chunk 145 optimal weight:    6.9990
   chunk 27 optimal weight:    3.9990
   chunk 0 optimal weight:    8.9990
   chunk 40 optimal weight:    5.9990
   chunk 127 optimal weight:    7.9990
   chunk 84 optimal weight:    3.9990
   chunk 107 optimal weight:    0.8980
   overall best weight:    3.5788

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

Flipped N/Q/H residues before XYZ refinement:
E   9 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4090 r_free = 0.4090 target = 0.184142 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3731 r_free = 0.3731 target = 0.148193 restraints weight = 12262.655|
|-----------------------------------------------------------------------------|
r_work (start): 0.3722 rms_B_bonded: 2.09
r_work: 0.3600 rms_B_bonded: 2.47 restraints_weight: 0.5000
r_work: 0.3472 rms_B_bonded: 4.05 restraints_weight: 0.2500
r_work (final): 0.3472
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8114
moved from start:          0.2001

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.051  12006  Z= 0.253
  Angle     :  0.609   7.420  16338  Z= 0.326
  Chirality :  0.050   0.156   1980
  Planarity :  0.005   0.048   2118
  Dihedral  :  4.534  16.991   1686
  Min Nonbonded Distance : 2.513

Molprobity Statistics.
  All-atom Clashscore : 5.41
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.29 %
    Favored  : 98.71 %
  Rotamer:
    Outliers :  4.09 %
    Allowed  : 17.45 %
    Favored  : 78.46 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.56 (0.20), residues: 1554
  helix:  1.48 (0.20), residues: 582
  sheet:  0.72 (0.29), residues: 312
  loop : -0.79 (0.22), residues: 660

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.002   TRP C  30 
 HIS   0.016   0.001   HIS E  72 
 PHE   0.016   0.002   PHE F 196 
 TYR   0.018   0.002   TYR C  81 
 ARG   0.006   0.001   ARG A  57 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04454 (  655)
  hydrogen bonds       : angle       5.23910 ( 1890)
  covalent geometry    : bond        0.00603 (12006)
  covalent geometry    : angle       0.60859 (16338)

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

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

  3108 Ramachandran restraints generated.
    1554 Oldfield, 0 Emsley, 1554 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3108 Ramachandran restraints generated.
    1554 Oldfield, 0 Emsley, 1554 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  184 residues out of total 1272 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 52
    poor density    : 132
  time to evaluate  : 1.213 
Fit side-chains
REVERT: A   29 GLN cc_start: 0.8264 (tt0) cc_final: 0.7981 (tm-30)
REVERT: B   36 SER cc_start: 0.8784 (m) cc_final: 0.8486 (t)
REVERT: B   57 ARG cc_start: 0.7717 (mtm-85) cc_final: 0.7505 (mtm-85)
REVERT: B  144 LYS cc_start: 0.7639 (mttt) cc_final: 0.7172 (mmpt)
REVERT: B  166 ARG cc_start: 0.6301 (OUTLIER) cc_final: 0.5891 (mtp85)
REVERT: C   29 GLN cc_start: 0.8136 (OUTLIER) cc_final: 0.7481 (tt0)
REVERT: C   57 ARG cc_start: 0.8135 (OUTLIER) cc_final: 0.7736 (mtt180)
REVERT: C  107 GLU cc_start: 0.8114 (mm-30) cc_final: 0.7392 (pt0)
REVERT: D    1 MET cc_start: 0.8310 (mpp) cc_final: 0.7943 (mtm)
REVERT: D   20 MET cc_start: 0.7754 (mtp) cc_final: 0.6750 (ppp)
REVERT: D   25 LYS cc_start: 0.8066 (ptmt) cc_final: 0.7776 (ptpt)
REVERT: D   46 THR cc_start: 0.8164 (t) cc_final: 0.7824 (m)
REVERT: E   72 HIS cc_start: 0.5834 (OUTLIER) cc_final: 0.5076 (p-80)
REVERT: E  235 LEU cc_start: 0.7558 (OUTLIER) cc_final: 0.7315 (mt)
REVERT: F    1 MET cc_start: 0.8093 (mpp) cc_final: 0.7573 (mmp)
REVERT: F   20 MET cc_start: 0.6569 (pmm) cc_final: 0.5540 (ppp)
REVERT: F   29 GLN cc_start: 0.8257 (OUTLIER) cc_final: 0.8049 (tt0)
REVERT: F  107 GLU cc_start: 0.7432 (mm-30) cc_final: 0.6765 (pt0)
  outliers start: 52
  outliers final: 39
  residues processed: 172
  average time/residue: 1.1551
  time to fit residues: 216.7409
Evaluate side-chains
  175 residues out of total 1272 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 45
    poor density    : 130
  time to evaluate  : 1.223 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    6 ASP
Chi-restraints excluded: chain A residue   32 ILE
Chi-restraints excluded: chain A residue   34 THR
Chi-restraints excluded: chain A residue   56 GLU
Chi-restraints excluded: chain A residue   85 VAL
Chi-restraints excluded: chain A residue  102 VAL
Chi-restraints excluded: chain A residue  108 VAL
Chi-restraints excluded: chain A residue  224 ILE
Chi-restraints excluded: chain A residue  235 LEU
Chi-restraints excluded: chain B residue   27 VAL
Chi-restraints excluded: chain B residue  108 VAL
Chi-restraints excluded: chain B residue  134 SER
Chi-restraints excluded: chain B residue  166 ARG
Chi-restraints excluded: chain B residue  230 THR
Chi-restraints excluded: chain B residue  235 LEU
Chi-restraints excluded: chain C residue   29 GLN
Chi-restraints excluded: chain C residue   57 ARG
Chi-restraints excluded: chain C residue   88 VAL
Chi-restraints excluded: chain C residue  108 VAL
Chi-restraints excluded: chain C residue  134 SER
Chi-restraints excluded: chain C residue  235 LEU
Chi-restraints excluded: chain C residue  239 HIS
Chi-restraints excluded: chain D residue   61 THR
Chi-restraints excluded: chain D residue  114 VAL
Chi-restraints excluded: chain D residue  173 VAL
Chi-restraints excluded: chain D residue  230 THR
Chi-restraints excluded: chain D residue  235 LEU
Chi-restraints excluded: chain E residue   27 VAL
Chi-restraints excluded: chain E residue   46 THR
Chi-restraints excluded: chain E residue   61 THR
Chi-restraints excluded: chain E residue   67 VAL
Chi-restraints excluded: chain E residue   72 HIS
Chi-restraints excluded: chain E residue   88 VAL
Chi-restraints excluded: chain E residue  148 LEU
Chi-restraints excluded: chain E residue  156 VAL
Chi-restraints excluded: chain E residue  235 LEU
Chi-restraints excluded: chain F residue   29 GLN
Chi-restraints excluded: chain F residue   46 THR
Chi-restraints excluded: chain F residue   74 VAL
Chi-restraints excluded: chain F residue   85 VAL
Chi-restraints excluded: chain F residue  102 VAL
Chi-restraints excluded: chain F residue  141 VAL
Chi-restraints excluded: chain F residue  173 VAL
Chi-restraints excluded: chain F residue  214 SER
Chi-restraints excluded: chain F residue  230 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 156
   random chunks:
   chunk 81 optimal weight:    4.9990
   chunk 117 optimal weight:    7.9990
   chunk 66 optimal weight:    6.9990
   chunk 31 optimal weight:    0.7980
   chunk 33 optimal weight:    0.9990
   chunk 129 optimal weight:    0.8980
   chunk 51 optimal weight:    0.9980
   chunk 42 optimal weight:    9.9990
   chunk 71 optimal weight:    1.9990
   chunk 36 optimal weight:    6.9990
   chunk 54 optimal weight:    3.9990
   overall best weight:    1.1384

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

Flipped N/Q/H residues before XYZ refinement:
** A   9 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 185 ASN
D 260 ASN
E   9 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4124 r_free = 0.4124 target = 0.187740 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3773 r_free = 0.3773 target = 0.151819 restraints weight = 12193.498|
|-----------------------------------------------------------------------------|
r_work (start): 0.3757 rms_B_bonded: 2.07
r_work: 0.3641 rms_B_bonded: 2.48 restraints_weight: 0.5000
r_work: 0.3514 rms_B_bonded: 4.07 restraints_weight: 0.2500
r_work (final): 0.3514
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8053
moved from start:          0.1863

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031  12006  Z= 0.122
  Angle     :  0.489   7.285  16338  Z= 0.261
  Chirality :  0.045   0.151   1980
  Planarity :  0.004   0.043   2118
  Dihedral  :  4.080  16.643   1686
  Min Nonbonded Distance : 2.549

Molprobity Statistics.
  All-atom Clashscore : 5.08
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.03 %
    Favored  : 98.97 %
  Rotamer:
    Outliers :  3.30 %
    Allowed  : 18.63 %
    Favored  : 78.07 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.98 (0.21), residues: 1554
  helix:  1.96 (0.21), residues: 582
  sheet:  0.81 (0.29), residues: 312
  loop : -0.62 (0.22), residues: 660

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP C  30 
 HIS   0.015   0.001   HIS E  72 
 PHE   0.013   0.001   PHE F 196 
 TYR   0.011   0.001   TYR E 120 
 ARG   0.007   0.000   ARG A  57 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03516 (  655)
  hydrogen bonds       : angle       4.88813 ( 1890)
  covalent geometry    : bond        0.00275 (12006)
  covalent geometry    : angle       0.48934 (16338)

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

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

  3108 Ramachandran restraints generated.
    1554 Oldfield, 0 Emsley, 1554 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3108 Ramachandran restraints generated.
    1554 Oldfield, 0 Emsley, 1554 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  174 residues out of total 1272 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 42
    poor density    : 132
  time to evaluate  : 1.201 
Fit side-chains
REVERT: A   29 GLN cc_start: 0.8214 (tt0) cc_final: 0.7917 (tm-30)
REVERT: A  260 ASN cc_start: 0.7621 (m-40) cc_final: 0.6962 (t0)
REVERT: B   36 SER cc_start: 0.8725 (m) cc_final: 0.8403 (t)
REVERT: B  144 LYS cc_start: 0.7607 (mttt) cc_final: 0.7121 (mmpt)
REVERT: B  166 ARG cc_start: 0.6251 (OUTLIER) cc_final: 0.5484 (ttp-110)
REVERT: B  212 ASP cc_start: 0.7793 (m-30) cc_final: 0.7571 (m-30)
REVERT: C   29 GLN cc_start: 0.8137 (OUTLIER) cc_final: 0.7484 (tt0)
REVERT: C   57 ARG cc_start: 0.8112 (OUTLIER) cc_final: 0.7703 (mtt180)
REVERT: C  107 GLU cc_start: 0.8054 (mm-30) cc_final: 0.7362 (pt0)
REVERT: D    1 MET cc_start: 0.8329 (mpp) cc_final: 0.7855 (mtm)
REVERT: D   20 MET cc_start: 0.7724 (mtp) cc_final: 0.6765 (ppp)
REVERT: D   25 LYS cc_start: 0.8029 (ptmt) cc_final: 0.7598 (ptmm)
REVERT: D   46 THR cc_start: 0.8076 (t) cc_final: 0.7782 (m)
REVERT: E  235 LEU cc_start: 0.7461 (OUTLIER) cc_final: 0.7220 (mt)
REVERT: F    1 MET cc_start: 0.8084 (mpp) cc_final: 0.7574 (mmp)
REVERT: F   20 MET cc_start: 0.6565 (pmm) cc_final: 0.5577 (ppp)
REVERT: F   29 GLN cc_start: 0.8232 (OUTLIER) cc_final: 0.8008 (tt0)
REVERT: F   88 VAL cc_start: 0.8464 (p) cc_final: 0.8257 (m)
REVERT: F  107 GLU cc_start: 0.7339 (mm-30) cc_final: 0.6706 (pt0)
  outliers start: 42
  outliers final: 34
  residues processed: 161
  average time/residue: 1.1743
  time to fit residues: 206.6036
Evaluate side-chains
  168 residues out of total 1272 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 39
    poor density    : 129
  time to evaluate  : 1.197 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    6 ASP
Chi-restraints excluded: chain A residue   56 GLU
Chi-restraints excluded: chain A residue   85 VAL
Chi-restraints excluded: chain A residue  102 VAL
Chi-restraints excluded: chain A residue  108 VAL
Chi-restraints excluded: chain A residue  235 LEU
Chi-restraints excluded: chain B residue   27 VAL
Chi-restraints excluded: chain B residue  108 VAL
Chi-restraints excluded: chain B residue  134 SER
Chi-restraints excluded: chain B residue  166 ARG
Chi-restraints excluded: chain B residue  230 THR
Chi-restraints excluded: chain B residue  235 LEU
Chi-restraints excluded: chain C residue   29 GLN
Chi-restraints excluded: chain C residue   57 ARG
Chi-restraints excluded: chain C residue   88 VAL
Chi-restraints excluded: chain C residue  108 VAL
Chi-restraints excluded: chain C residue  134 SER
Chi-restraints excluded: chain C residue  235 LEU
Chi-restraints excluded: chain C residue  239 HIS
Chi-restraints excluded: chain D residue   61 THR
Chi-restraints excluded: chain D residue  114 VAL
Chi-restraints excluded: chain D residue  173 VAL
Chi-restraints excluded: chain D residue  230 THR
Chi-restraints excluded: chain D residue  235 LEU
Chi-restraints excluded: chain E residue   27 VAL
Chi-restraints excluded: chain E residue   61 THR
Chi-restraints excluded: chain E residue   67 VAL
Chi-restraints excluded: chain E residue   88 VAL
Chi-restraints excluded: chain E residue  148 LEU
Chi-restraints excluded: chain E residue  156 VAL
Chi-restraints excluded: chain E residue  235 LEU
Chi-restraints excluded: chain F residue   29 GLN
Chi-restraints excluded: chain F residue   74 VAL
Chi-restraints excluded: chain F residue   85 VAL
Chi-restraints excluded: chain F residue  102 VAL
Chi-restraints excluded: chain F residue  141 VAL
Chi-restraints excluded: chain F residue  173 VAL
Chi-restraints excluded: chain F residue  214 SER
Chi-restraints excluded: chain F residue  230 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 156
   random chunks:
   chunk 67 optimal weight:    0.0270
   chunk 145 optimal weight:    3.9990
   chunk 123 optimal weight:    5.9990
   chunk 3 optimal weight:    2.9990
   chunk 84 optimal weight:    3.9990
   chunk 22 optimal weight:   10.0000
   chunk 78 optimal weight:    4.9990
   chunk 92 optimal weight:    0.0170
   chunk 24 optimal weight:    5.9990
   chunk 136 optimal weight:    5.9990
   chunk 104 optimal weight:   10.0000
   overall best weight:    2.2082

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

Flipped N/Q/H residues before XYZ refinement:
A   9 ASN
A 185 ASN
E   9 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4110 r_free = 0.4110 target = 0.186207 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3752 r_free = 0.3752 target = 0.150271 restraints weight = 12213.649|
|-----------------------------------------------------------------------------|
r_work (start): 0.3737 rms_B_bonded: 2.09
r_work: 0.3615 rms_B_bonded: 2.50 restraints_weight: 0.5000
r_work: 0.3488 rms_B_bonded: 4.09 restraints_weight: 0.2500
r_work (final): 0.3488
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8083
moved from start:          0.1932

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.037  12006  Z= 0.175
  Angle     :  0.536   7.684  16338  Z= 0.286
  Chirality :  0.046   0.152   1980
  Planarity :  0.004   0.045   2118
  Dihedral  :  4.244  16.824   1686
  Min Nonbonded Distance : 2.533

Molprobity Statistics.
  All-atom Clashscore : 5.08
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.42 %
    Favored  : 98.58 %
  Rotamer:
    Outliers :  3.46 %
    Allowed  : 18.40 %
    Favored  : 78.14 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.88 (0.20), residues: 1554
  helix:  1.85 (0.21), residues: 582
  sheet:  0.78 (0.28), residues: 312
  loop : -0.65 (0.22), residues: 660

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP C  30 
 HIS   0.016   0.001   HIS E  72 
 PHE   0.013   0.002   PHE C 198 
 TYR   0.014   0.002   TYR E 120 
 ARG   0.007   0.000   ARG A  57 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03903 (  655)
  hydrogen bonds       : angle       5.00844 ( 1890)
  covalent geometry    : bond        0.00411 (12006)
  covalent geometry    : angle       0.53578 (16338)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 9954.25 seconds
wall clock time: 175 minutes 21.08 seconds (10521.08 seconds total)