Starting phenix.real_space_refine
on Sun Jan 19 01:01:36 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8yx7_39649/01_2025/8yx7_39649.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8yx7_39649/01_2025/8yx7_39649.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.8
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8yx7_39649/01_2025/8yx7_39649.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8yx7_39649/01_2025/8yx7_39649.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8yx7_39649/01_2025/8yx7_39649.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8yx7_39649/01_2025/8yx7_39649.cif"
  }
  resolution = 2.8
  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=   0.024
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      55      5.16       5
     C    8485      2.51       5
     N    2190      2.21       5
     O    2340      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-5571/modules/chem_data/mon_lib"
  Total number of atoms: 13070
  Number of models: 1
  Model: ""
    Number of chains: 3
    Chain: "A"
      Number of atoms: 2572
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 324, 2572
          Classifications: {'peptide': 324}
          Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 306}
          Chain breaks: 1
    Chain: "G"
      Number of atoms: 28
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 28
          Unusual residues: {'NAG': 2}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
          Unresolved non-hydrogen bonds: 2
          Unresolved non-hydrogen angles: 4
          Unresolved non-hydrogen dihedrals: 6
          Unresolved non-hydrogen chiralities: 2
    Chain: "A"
      Number of atoms: 14
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 14
          Unusual residues: {'NAG': 1}
          Classifications: {'undetermined': 1}
          Unresolved non-hydrogen bonds: 1
          Unresolved non-hydrogen angles: 2
          Unresolved non-hydrogen dihedrals: 3
          Unresolved non-hydrogen chiralities: 1
  Restraints were copied for chains:
    C, B, E, D, F, I, H, J
  Residues with excluded nonbonded symmetry interactions: 5
    residue:
      pdb=" C1  NAG F   2 " occ=0.80
      ... (12 atoms not shown)
      pdb=" O7  NAG F   2 " occ=0.80
    residue:
      pdb=" C1  NAG G   2 " occ=0.80
      ... (12 atoms not shown)
      pdb=" O7  NAG G   2 " occ=0.80
    residue:
      pdb=" C1  NAG H   2 " occ=0.80
      ... (12 atoms not shown)
      pdb=" O7  NAG H   2 " occ=0.80
    residue:
      pdb=" C1  NAG I   2 " occ=0.80
      ... (12 atoms not shown)
      pdb=" O7  NAG I   2 " occ=0.80
    residue:
      pdb=" C1  NAG J   2 " occ=0.80
      ... (12 atoms not shown)
      pdb=" O7  NAG J   2 " occ=0.80
  Time building chain proxies: 5.97, per 1000 atoms: 0.46
  Number of scatterers: 13070
  At special positions: 0
  Unit cell: (93, 92.07, 122.76, 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      55     16.00
     O    2340      8.00
     N    2190      7.00
     C    8485      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=2, symmetry=0
    Simple disulfide: pdb=" SG  CYS A 157 " - pdb=" SG  CYS A 171 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 289 " - pdb=" SG  CYS A 394 " distance=2.03

  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
  Links applied
    BETA1-4
      " NAG F   1 " - " NAG F   2 "
      " NAG G   1 " - " NAG G   2 "
      " NAG H   1 " - " NAG H   2 "
      " NAG I   1 " - " NAG I   2 "
      " NAG J   1 " - " NAG J   2 "
    NAG-ASN
      " NAG A 501 " - " ASN A 170 "
      " NAG B 501 " - " ASN B 170 "
      " NAG C 501 " - " ASN C 170 "
      " NAG D 501 " - " ASN D 170 "
      " NAG E 501 " - " ASN E 170 "
      " NAG F   1 " - " ASN A  55 "
      " NAG G   1 " - " ASN B  55 "
      " NAG H   1 " - " ASN C  55 "
      " NAG I   1 " - " ASN D  55 "
      " NAG J   1 " - " ASN E  55 "
  Time building additional restraints: 3.69
  Conformation dependent library (CDL) restraints added in 1.8 seconds
  

  3200 Ramachandran restraints generated.
    1600 Oldfield, 0 Emsley, 1600 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  3140

  Finding SS restraints...
    Secondary structure from input PDB file:
      40 helices and 15 sheets defined
      39.2% alpha, 33.3% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 1.57
  Creating SS restraints...
    Processing helix  chain 'A' and resid 94 through 97
    Processing helix  chain 'A' and resid 113 through 115
      No H-bonds generated for 'chain 'A' and resid 113 through 115'
    Processing helix  chain 'A' and resid 160 through 164
      removed outlier: 4.224A  pdb=" N   HIS A 163 " --> pdb=" O   GLU A 160 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 231 through 252
      removed outlier: 4.692A  pdb=" N   VAL A 239 " --> pdb=" O   ILE A 235 " (cutoff:3.500A)
      Proline residue:  A 240  - end of helix
    Processing helix  chain 'A' and resid 258 through 283
      removed outlier: 4.400A  pdb=" N   ILE A 262 " --> pdb=" O   ALA A 258 " (cutoff:3.500A)
      removed outlier: 3.989A  pdb=" N   GLY A 263 " --> pdb=" O   ILE A 259 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 291 through 320
      removed outlier: 3.859A  pdb=" N   TYR A 295 " --> pdb=" O   PRO A 291 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 361 through 391
    Processing helix  chain 'A' and resid 399 through 404
    Processing helix  chain 'B' and resid 94 through 97
    Processing helix  chain 'B' and resid 113 through 115
      No H-bonds generated for 'chain 'B' and resid 113 through 115'
    Processing helix  chain 'B' and resid 160 through 164
      removed outlier: 4.224A  pdb=" N   HIS B 163 " --> pdb=" O   GLU B 160 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 231 through 252
      removed outlier: 4.692A  pdb=" N   VAL B 239 " --> pdb=" O   ILE B 235 " (cutoff:3.500A)
      Proline residue:  B 240  - end of helix
    Processing helix  chain 'B' and resid 258 through 283
      removed outlier: 4.400A  pdb=" N   ILE B 262 " --> pdb=" O   ALA B 258 " (cutoff:3.500A)
      removed outlier: 3.989A  pdb=" N   GLY B 263 " --> pdb=" O   ILE B 259 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 291 through 320
      removed outlier: 3.859A  pdb=" N   TYR B 295 " --> pdb=" O   PRO B 291 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 361 through 391
    Processing helix  chain 'B' and resid 399 through 404
    Processing helix  chain 'C' and resid 94 through 97
    Processing helix  chain 'C' and resid 113 through 115
      No H-bonds generated for 'chain 'C' and resid 113 through 115'
    Processing helix  chain 'C' and resid 160 through 164
      removed outlier: 4.224A  pdb=" N   HIS C 163 " --> pdb=" O   GLU C 160 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 231 through 252
      removed outlier: 4.693A  pdb=" N   VAL C 239 " --> pdb=" O   ILE C 235 " (cutoff:3.500A)
      Proline residue:  C 240  - end of helix
    Processing helix  chain 'C' and resid 258 through 283
      removed outlier: 4.400A  pdb=" N   ILE C 262 " --> pdb=" O   ALA C 258 " (cutoff:3.500A)
      removed outlier: 3.989A  pdb=" N   GLY C 263 " --> pdb=" O   ILE C 259 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 291 through 320
      removed outlier: 3.858A  pdb=" N   TYR C 295 " --> pdb=" O   PRO C 291 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 361 through 391
    Processing helix  chain 'C' and resid 399 through 404
    Processing helix  chain 'D' and resid 94 through 97
    Processing helix  chain 'D' and resid 113 through 115
      No H-bonds generated for 'chain 'D' and resid 113 through 115'
    Processing helix  chain 'D' and resid 160 through 164
      removed outlier: 4.224A  pdb=" N   HIS D 163 " --> pdb=" O   GLU D 160 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 231 through 252
      removed outlier: 4.692A  pdb=" N   VAL D 239 " --> pdb=" O   ILE D 235 " (cutoff:3.500A)
      Proline residue:  D 240  - end of helix
    Processing helix  chain 'D' and resid 258 through 283
      removed outlier: 4.400A  pdb=" N   ILE D 262 " --> pdb=" O   ALA D 258 " (cutoff:3.500A)
      removed outlier: 3.989A  pdb=" N   GLY D 263 " --> pdb=" O   ILE D 259 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 291 through 320
      removed outlier: 3.859A  pdb=" N   TYR D 295 " --> pdb=" O   PRO D 291 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 361 through 391
    Processing helix  chain 'D' and resid 399 through 404
    Processing helix  chain 'E' and resid 94 through 97
    Processing helix  chain 'E' and resid 113 through 115
      No H-bonds generated for 'chain 'E' and resid 113 through 115'
    Processing helix  chain 'E' and resid 160 through 164
      removed outlier: 4.224A  pdb=" N   HIS E 163 " --> pdb=" O   GLU E 160 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 231 through 252
      removed outlier: 4.692A  pdb=" N   VAL E 239 " --> pdb=" O   ILE E 235 " (cutoff:3.500A)
      Proline residue:  E 240  - end of helix
    Processing helix  chain 'E' and resid 258 through 283
      removed outlier: 4.400A  pdb=" N   ILE E 262 " --> pdb=" O   ALA E 258 " (cutoff:3.500A)
      removed outlier: 3.989A  pdb=" N   GLY E 263 " --> pdb=" O   ILE E 259 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 291 through 320
      removed outlier: 3.859A  pdb=" N   TYR E 295 " --> pdb=" O   PRO E 291 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 361 through 391
    Processing helix  chain 'E' and resid 399 through 404
    Processing sheet with id=AA1, first strand: chain 'A' and resid 107 through 111
      removed outlier: 5.773A  pdb=" N   GLN A 136 " --> pdb=" O   ASN A 148 " (cutoff:3.500A)
      removed outlier: 4.999A  pdb=" N   ASN A 148 " --> pdb=" O   GLN A 136 " (cutoff:3.500A)
      removed outlier: 4.440A  pdb=" N   HIS A 144 " --> pdb=" O   ASP A 140 " (cutoff:3.500A)
      removed outlier: 7.217A  pdb=" N   ALA A 150 " --> pdb=" O   TRP A 130 " (cutoff:3.500A)
      removed outlier: 4.785A  pdb=" N   TRP A 130 " --> pdb=" O   ALA A 150 " (cutoff:3.500A)
      removed outlier: 6.589A  pdb=" N   ALA A 152 " --> pdb=" O   VAL A 128 " (cutoff:3.500A)
      removed outlier: 4.542A  pdb=" N   VAL A 128 " --> pdb=" O   ALA A 152 " (cutoff:3.500A)
      removed outlier: 6.651A  pdb=" N   GLU A 154 " --> pdb=" O   LEU A 126 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 107 through 111
      removed outlier: 5.773A  pdb=" N   GLN A 136 " --> pdb=" O   ASN A 148 " (cutoff:3.500A)
      removed outlier: 4.999A  pdb=" N   ASN A 148 " --> pdb=" O   GLN A 136 " (cutoff:3.500A)
      removed outlier: 4.440A  pdb=" N   HIS A 144 " --> pdb=" O   ASP A 140 " (cutoff:3.500A)
      removed outlier: 3.837A  pdb=" N   ASN A  73 " --> pdb=" O   SER A  82 " (cutoff:3.500A)
      removed outlier: 7.366A  pdb=" N   MET A  84 " --> pdb=" O   VAL A  71 " (cutoff:3.500A)
      removed outlier: 5.890A  pdb=" N   VAL A  71 " --> pdb=" O   MET A  84 " (cutoff:3.500A)
      removed outlier: 8.601A  pdb=" N   LEU A  86 " --> pdb=" O   SER A  69 " (cutoff:3.500A)
      removed outlier: 7.122A  pdb=" N   SER A  69 " --> pdb=" O   LEU A  86 " (cutoff:3.500A)
      removed outlier: 7.855A  pdb=" N   ARG A  88 " --> pdb=" O   PHE A  67 " (cutoff:3.500A)
      removed outlier: 7.893A  pdb=" N   PHE A  67 " --> pdb=" O   ARG A  88 " (cutoff:3.500A)
      removed outlier: 7.859A  pdb=" N   SER A  90 " --> pdb=" O   ARG A  65 " (cutoff:3.500A)
      removed outlier: 7.797A  pdb=" N   ARG A  65 " --> pdb=" O   SER A  90 " (cutoff:3.500A)
      removed outlier: 8.760A  pdb=" N   LEU A  92 " --> pdb=" O   ASP A  63 " (cutoff:3.500A)
      removed outlier: 9.665A  pdb=" N   ASP A  63 " --> pdb=" O   LEU A  92 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 120 through 122
      removed outlier: 4.072A  pdb=" N   ASP A 206 " --> pdb=" O   ARG A 225 " (cutoff:3.500A)
      removed outlier: 7.102A  pdb=" N   LYS A 227 " --> pdb=" O   VAL A 204 " (cutoff:3.500A)
      removed outlier: 5.500A  pdb=" N   VAL A 204 " --> pdb=" O   LYS A 227 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'B' and resid 107 through 111
      removed outlier: 5.773A  pdb=" N   GLN B 136 " --> pdb=" O   ASN B 148 " (cutoff:3.500A)
      removed outlier: 4.998A  pdb=" N   ASN B 148 " --> pdb=" O   GLN B 136 " (cutoff:3.500A)
      removed outlier: 4.439A  pdb=" N   HIS B 144 " --> pdb=" O   ASP B 140 " (cutoff:3.500A)
      removed outlier: 7.217A  pdb=" N   ALA B 150 " --> pdb=" O   TRP B 130 " (cutoff:3.500A)
      removed outlier: 4.786A  pdb=" N   TRP B 130 " --> pdb=" O   ALA B 150 " (cutoff:3.500A)
      removed outlier: 6.589A  pdb=" N   ALA B 152 " --> pdb=" O   VAL B 128 " (cutoff:3.500A)
      removed outlier: 4.543A  pdb=" N   VAL B 128 " --> pdb=" O   ALA B 152 " (cutoff:3.500A)
      removed outlier: 6.652A  pdb=" N   GLU B 154 " --> pdb=" O   LEU B 126 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'B' and resid 107 through 111
      removed outlier: 5.773A  pdb=" N   GLN B 136 " --> pdb=" O   ASN B 148 " (cutoff:3.500A)
      removed outlier: 4.998A  pdb=" N   ASN B 148 " --> pdb=" O   GLN B 136 " (cutoff:3.500A)
      removed outlier: 4.439A  pdb=" N   HIS B 144 " --> pdb=" O   ASP B 140 " (cutoff:3.500A)
      removed outlier: 3.838A  pdb=" N   ASN B  73 " --> pdb=" O   SER B  82 " (cutoff:3.500A)
      removed outlier: 7.366A  pdb=" N   MET B  84 " --> pdb=" O   VAL B  71 " (cutoff:3.500A)
      removed outlier: 5.890A  pdb=" N   VAL B  71 " --> pdb=" O   MET B  84 " (cutoff:3.500A)
      removed outlier: 8.601A  pdb=" N   LEU B  86 " --> pdb=" O   SER B  69 " (cutoff:3.500A)
      removed outlier: 7.123A  pdb=" N   SER B  69 " --> pdb=" O   LEU B  86 " (cutoff:3.500A)
      removed outlier: 7.855A  pdb=" N   ARG B  88 " --> pdb=" O   PHE B  67 " (cutoff:3.500A)
      removed outlier: 7.893A  pdb=" N   PHE B  67 " --> pdb=" O   ARG B  88 " (cutoff:3.500A)
      removed outlier: 7.859A  pdb=" N   SER B  90 " --> pdb=" O   ARG B  65 " (cutoff:3.500A)
      removed outlier: 7.797A  pdb=" N   ARG B  65 " --> pdb=" O   SER B  90 " (cutoff:3.500A)
      removed outlier: 8.759A  pdb=" N   LEU B  92 " --> pdb=" O   ASP B  63 " (cutoff:3.500A)
      removed outlier: 9.665A  pdb=" N   ASP B  63 " --> pdb=" O   LEU B  92 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'B' and resid 120 through 122
      removed outlier: 4.073A  pdb=" N   ASP B 206 " --> pdb=" O   ARG B 225 " (cutoff:3.500A)
      removed outlier: 7.102A  pdb=" N   LYS B 227 " --> pdb=" O   VAL B 204 " (cutoff:3.500A)
      removed outlier: 5.500A  pdb=" N   VAL B 204 " --> pdb=" O   LYS B 227 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'C' and resid 107 through 111
      removed outlier: 5.772A  pdb=" N   GLN C 136 " --> pdb=" O   ASN C 148 " (cutoff:3.500A)
      removed outlier: 4.999A  pdb=" N   ASN C 148 " --> pdb=" O   GLN C 136 " (cutoff:3.500A)
      removed outlier: 4.440A  pdb=" N   HIS C 144 " --> pdb=" O   ASP C 140 " (cutoff:3.500A)
      removed outlier: 7.217A  pdb=" N   ALA C 150 " --> pdb=" O   TRP C 130 " (cutoff:3.500A)
      removed outlier: 4.786A  pdb=" N   TRP C 130 " --> pdb=" O   ALA C 150 " (cutoff:3.500A)
      removed outlier: 6.588A  pdb=" N   ALA C 152 " --> pdb=" O   VAL C 128 " (cutoff:3.500A)
      removed outlier: 4.543A  pdb=" N   VAL C 128 " --> pdb=" O   ALA C 152 " (cutoff:3.500A)
      removed outlier: 6.652A  pdb=" N   GLU C 154 " --> pdb=" O   LEU C 126 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'C' and resid 107 through 111
      removed outlier: 5.772A  pdb=" N   GLN C 136 " --> pdb=" O   ASN C 148 " (cutoff:3.500A)
      removed outlier: 4.999A  pdb=" N   ASN C 148 " --> pdb=" O   GLN C 136 " (cutoff:3.500A)
      removed outlier: 4.440A  pdb=" N   HIS C 144 " --> pdb=" O   ASP C 140 " (cutoff:3.500A)
      removed outlier: 3.837A  pdb=" N   ASN C  73 " --> pdb=" O   SER C  82 " (cutoff:3.500A)
      removed outlier: 7.366A  pdb=" N   MET C  84 " --> pdb=" O   VAL C  71 " (cutoff:3.500A)
      removed outlier: 5.890A  pdb=" N   VAL C  71 " --> pdb=" O   MET C  84 " (cutoff:3.500A)
      removed outlier: 8.601A  pdb=" N   LEU C  86 " --> pdb=" O   SER C  69 " (cutoff:3.500A)
      removed outlier: 7.122A  pdb=" N   SER C  69 " --> pdb=" O   LEU C  86 " (cutoff:3.500A)
      removed outlier: 7.854A  pdb=" N   ARG C  88 " --> pdb=" O   PHE C  67 " (cutoff:3.500A)
      removed outlier: 7.893A  pdb=" N   PHE C  67 " --> pdb=" O   ARG C  88 " (cutoff:3.500A)
      removed outlier: 7.859A  pdb=" N   SER C  90 " --> pdb=" O   ARG C  65 " (cutoff:3.500A)
      removed outlier: 7.796A  pdb=" N   ARG C  65 " --> pdb=" O   SER C  90 " (cutoff:3.500A)
      removed outlier: 8.760A  pdb=" N   LEU C  92 " --> pdb=" O   ASP C  63 " (cutoff:3.500A)
      removed outlier: 9.665A  pdb=" N   ASP C  63 " --> pdb=" O   LEU C  92 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'C' and resid 120 through 122
      removed outlier: 4.072A  pdb=" N   ASP C 206 " --> pdb=" O   ARG C 225 " (cutoff:3.500A)
      removed outlier: 7.103A  pdb=" N   LYS C 227 " --> pdb=" O   VAL C 204 " (cutoff:3.500A)
      removed outlier: 5.500A  pdb=" N   VAL C 204 " --> pdb=" O   LYS C 227 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'D' and resid 107 through 111
      removed outlier: 5.773A  pdb=" N   GLN D 136 " --> pdb=" O   ASN D 148 " (cutoff:3.500A)
      removed outlier: 4.999A  pdb=" N   ASN D 148 " --> pdb=" O   GLN D 136 " (cutoff:3.500A)
      removed outlier: 4.439A  pdb=" N   HIS D 144 " --> pdb=" O   ASP D 140 " (cutoff:3.500A)
      removed outlier: 7.217A  pdb=" N   ALA D 150 " --> pdb=" O   TRP D 130 " (cutoff:3.500A)
      removed outlier: 4.786A  pdb=" N   TRP D 130 " --> pdb=" O   ALA D 150 " (cutoff:3.500A)
      removed outlier: 6.589A  pdb=" N   ALA D 152 " --> pdb=" O   VAL D 128 " (cutoff:3.500A)
      removed outlier: 4.543A  pdb=" N   VAL D 128 " --> pdb=" O   ALA D 152 " (cutoff:3.500A)
      removed outlier: 6.652A  pdb=" N   GLU D 154 " --> pdb=" O   LEU D 126 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'D' and resid 107 through 111
      removed outlier: 5.773A  pdb=" N   GLN D 136 " --> pdb=" O   ASN D 148 " (cutoff:3.500A)
      removed outlier: 4.999A  pdb=" N   ASN D 148 " --> pdb=" O   GLN D 136 " (cutoff:3.500A)
      removed outlier: 4.439A  pdb=" N   HIS D 144 " --> pdb=" O   ASP D 140 " (cutoff:3.500A)
      removed outlier: 3.837A  pdb=" N   ASN D  73 " --> pdb=" O   SER D  82 " (cutoff:3.500A)
      removed outlier: 7.366A  pdb=" N   MET D  84 " --> pdb=" O   VAL D  71 " (cutoff:3.500A)
      removed outlier: 5.890A  pdb=" N   VAL D  71 " --> pdb=" O   MET D  84 " (cutoff:3.500A)
      removed outlier: 8.601A  pdb=" N   LEU D  86 " --> pdb=" O   SER D  69 " (cutoff:3.500A)
      removed outlier: 7.123A  pdb=" N   SER D  69 " --> pdb=" O   LEU D  86 " (cutoff:3.500A)
      removed outlier: 7.855A  pdb=" N   ARG D  88 " --> pdb=" O   PHE D  67 " (cutoff:3.500A)
      removed outlier: 7.893A  pdb=" N   PHE D  67 " --> pdb=" O   ARG D  88 " (cutoff:3.500A)
      removed outlier: 7.859A  pdb=" N   SER D  90 " --> pdb=" O   ARG D  65 " (cutoff:3.500A)
      removed outlier: 7.796A  pdb=" N   ARG D  65 " --> pdb=" O   SER D  90 " (cutoff:3.500A)
      removed outlier: 8.760A  pdb=" N   LEU D  92 " --> pdb=" O   ASP D  63 " (cutoff:3.500A)
      removed outlier: 9.664A  pdb=" N   ASP D  63 " --> pdb=" O   LEU D  92 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'D' and resid 120 through 122
      removed outlier: 4.073A  pdb=" N   ASP D 206 " --> pdb=" O   ARG D 225 " (cutoff:3.500A)
      removed outlier: 7.102A  pdb=" N   LYS D 227 " --> pdb=" O   VAL D 204 " (cutoff:3.500A)
      removed outlier: 5.500A  pdb=" N   VAL D 204 " --> pdb=" O   LYS D 227 " (cutoff:3.500A)
    Processing sheet with id=AB4, first strand: chain 'E' and resid 107 through 111
      removed outlier: 5.772A  pdb=" N   GLN E 136 " --> pdb=" O   ASN E 148 " (cutoff:3.500A)
      removed outlier: 4.998A  pdb=" N   ASN E 148 " --> pdb=" O   GLN E 136 " (cutoff:3.500A)
      removed outlier: 4.439A  pdb=" N   HIS E 144 " --> pdb=" O   ASP E 140 " (cutoff:3.500A)
      removed outlier: 7.217A  pdb=" N   ALA E 150 " --> pdb=" O   TRP E 130 " (cutoff:3.500A)
      removed outlier: 4.785A  pdb=" N   TRP E 130 " --> pdb=" O   ALA E 150 " (cutoff:3.500A)
      removed outlier: 6.588A  pdb=" N   ALA E 152 " --> pdb=" O   VAL E 128 " (cutoff:3.500A)
      removed outlier: 4.543A  pdb=" N   VAL E 128 " --> pdb=" O   ALA E 152 " (cutoff:3.500A)
      removed outlier: 6.652A  pdb=" N   GLU E 154 " --> pdb=" O   LEU E 126 " (cutoff:3.500A)
    Processing sheet with id=AB5, first strand: chain 'E' and resid 107 through 111
      removed outlier: 5.772A  pdb=" N   GLN E 136 " --> pdb=" O   ASN E 148 " (cutoff:3.500A)
      removed outlier: 4.998A  pdb=" N   ASN E 148 " --> pdb=" O   GLN E 136 " (cutoff:3.500A)
      removed outlier: 4.439A  pdb=" N   HIS E 144 " --> pdb=" O   ASP E 140 " (cutoff:3.500A)
      removed outlier: 3.838A  pdb=" N   ASN E  73 " --> pdb=" O   SER E  82 " (cutoff:3.500A)
      removed outlier: 7.366A  pdb=" N   MET E  84 " --> pdb=" O   VAL E  71 " (cutoff:3.500A)
      removed outlier: 5.890A  pdb=" N   VAL E  71 " --> pdb=" O   MET E  84 " (cutoff:3.500A)
      removed outlier: 8.601A  pdb=" N   LEU E  86 " --> pdb=" O   SER E  69 " (cutoff:3.500A)
      removed outlier: 7.123A  pdb=" N   SER E  69 " --> pdb=" O   LEU E  86 " (cutoff:3.500A)
      removed outlier: 7.855A  pdb=" N   ARG E  88 " --> pdb=" O   PHE E  67 " (cutoff:3.500A)
      removed outlier: 7.893A  pdb=" N   PHE E  67 " --> pdb=" O   ARG E  88 " (cutoff:3.500A)
      removed outlier: 7.859A  pdb=" N   SER E  90 " --> pdb=" O   ARG E  65 " (cutoff:3.500A)
      removed outlier: 7.797A  pdb=" N   ARG E  65 " --> pdb=" O   SER E  90 " (cutoff:3.500A)
      removed outlier: 8.760A  pdb=" N   LEU E  92 " --> pdb=" O   ASP E  63 " (cutoff:3.500A)
      removed outlier: 9.665A  pdb=" N   ASP E  63 " --> pdb=" O   LEU E  92 " (cutoff:3.500A)
    Processing sheet with id=AB6, first strand: chain 'E' and resid 120 through 122
      removed outlier: 4.073A  pdb=" N   ASP E 206 " --> pdb=" O   ARG E 225 " (cutoff:3.500A)
      removed outlier: 7.102A  pdb=" N   LYS E 227 " --> pdb=" O   VAL E 204 " (cutoff:3.500A)
      removed outlier: 5.500A  pdb=" N   VAL E 204 " --> pdb=" O   LYS E 227 " (cutoff:3.500A)

    715 hydrogen bonds defined for protein.
    2100 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: 4.36

  Time building geometry restraints manager: 4.15 seconds

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

  Histogram of bond lengths:
        1.18 -     1.31: 2020
        1.31 -     1.43: 3605
        1.43 -     1.56: 7685
        1.56 -     1.68: 0
        1.68 -     1.81: 75
  Bond restraints: 13385
  Sorted by residual:
  bond pdb=" C7  NAG I   2 "
       pdb=" N2  NAG I   2 "
    ideal  model  delta    sigma   weight residual
    1.346  1.463 -0.117 2.00e-02 2.50e+03 3.40e+01
  bond pdb=" C7  NAG G   2 "
       pdb=" N2  NAG G   2 "
    ideal  model  delta    sigma   weight residual
    1.346  1.463 -0.117 2.00e-02 2.50e+03 3.40e+01
  bond pdb=" C7  NAG H   2 "
       pdb=" N2  NAG H   2 "
    ideal  model  delta    sigma   weight residual
    1.346  1.463 -0.117 2.00e-02 2.50e+03 3.40e+01
  bond pdb=" C7  NAG F   2 "
       pdb=" N2  NAG F   2 "
    ideal  model  delta    sigma   weight residual
    1.346  1.462 -0.116 2.00e-02 2.50e+03 3.39e+01
  bond pdb=" C7  NAG J   2 "
       pdb=" N2  NAG J   2 "
    ideal  model  delta    sigma   weight residual
    1.346  1.462 -0.116 2.00e-02 2.50e+03 3.39e+01
  ... (remaining 13380 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.19: 17651
        1.19 -     2.37: 391
        2.37 -     3.56: 178
        3.56 -     4.74: 38
        4.74 -     5.93: 47
  Bond angle restraints: 18305
  Sorted by residual:
  angle pdb=" N   LEU B 237 "
        pdb=" CA  LEU B 237 "
        pdb=" C   LEU B 237 "
      ideal   model   delta    sigma   weight residual
     113.18  115.61   -2.43 1.33e+00 5.65e-01 3.35e+00
  angle pdb=" N   LEU D 237 "
        pdb=" CA  LEU D 237 "
        pdb=" C   LEU D 237 "
      ideal   model   delta    sigma   weight residual
     113.18  115.61   -2.43 1.33e+00 5.65e-01 3.34e+00
  angle pdb=" N   LEU C 237 "
        pdb=" CA  LEU C 237 "
        pdb=" C   LEU C 237 "
      ideal   model   delta    sigma   weight residual
     113.18  115.60   -2.42 1.33e+00 5.65e-01 3.31e+00
  angle pdb=" N   LEU E 237 "
        pdb=" CA  LEU E 237 "
        pdb=" C   LEU E 237 "
      ideal   model   delta    sigma   weight residual
     113.18  115.58   -2.40 1.33e+00 5.65e-01 3.25e+00
  angle pdb=" N   LEU A 237 "
        pdb=" CA  LEU A 237 "
        pdb=" C   LEU A 237 "
      ideal   model   delta    sigma   weight residual
     113.18  115.57   -2.39 1.33e+00 5.65e-01 3.24e+00
  ... (remaining 18300 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    11.22: 7026
       11.22 -    22.45: 795
       22.45 -    33.67: 258
       33.67 -    44.90: 57
       44.90 -    56.12: 20
  Dihedral angle restraints: 8156
    sinusoidal: 3361
      harmonic: 4795
  Sorted by residual:
  dihedral pdb=" CB  CYS A 289 "
           pdb=" SG  CYS A 289 "
           pdb=" SG  CYS A 394 "
           pdb=" CB  CYS A 394 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -86.00 -117.09   31.09     1      1.00e+01 1.00e-02 1.38e+01
  dihedral pdb=" CA  VAL A  71 "
           pdb=" C   VAL A  71 "
           pdb=" N   PHE A  72 "
           pdb=" CA  PHE A  72 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -164.59  -15.41     0      5.00e+00 4.00e-02 9.49e+00
  dihedral pdb=" CA  VAL C  71 "
           pdb=" C   VAL C  71 "
           pdb=" N   PHE C  72 "
           pdb=" CA  PHE C  72 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -164.60  -15.40     0      5.00e+00 4.00e-02 9.49e+00
  ... (remaining 8153 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.030: 1432
       0.030 -    0.059: 544
       0.059 -    0.088: 124
       0.088 -    0.118: 76
       0.118 -    0.147: 59
  Chirality restraints: 2235
  Sorted by residual:
  chirality pdb=" C5  NAG B 501 "
            pdb=" C4  NAG B 501 "
            pdb=" C6  NAG B 501 "
            pdb=" O5  NAG B 501 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.41   -2.56    0.15 2.00e-01 2.50e+01 5.44e-01
  chirality pdb=" C5  NAG E 501 "
            pdb=" C4  NAG E 501 "
            pdb=" C6  NAG E 501 "
            pdb=" O5  NAG E 501 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.41   -2.56    0.15 2.00e-01 2.50e+01 5.29e-01
  chirality pdb=" CA  TRP E 362 "
            pdb=" N   TRP E 362 "
            pdb=" C   TRP E 362 "
            pdb=" CB  TRP E 362 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.37    0.14 2.00e-01 2.50e+01 5.19e-01
  ... (remaining 2232 not shown)

  Planarity restraints: 2260
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ILE B 234 "    0.005 2.00e-02 2.50e+03   1.08e-02 1.17e+00
        pdb=" C   ILE B 234 "   -0.019 2.00e-02 2.50e+03
        pdb=" O   ILE B 234 "    0.007 2.00e-02 2.50e+03
        pdb=" N   ILE B 235 "    0.006 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ILE C 234 "    0.005 2.00e-02 2.50e+03   1.08e-02 1.16e+00
        pdb=" C   ILE C 234 "   -0.019 2.00e-02 2.50e+03
        pdb=" O   ILE C 234 "    0.007 2.00e-02 2.50e+03
        pdb=" N   ILE C 235 "    0.006 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ILE D 234 "    0.005 2.00e-02 2.50e+03   1.07e-02 1.15e+00
        pdb=" C   ILE D 234 "   -0.019 2.00e-02 2.50e+03
        pdb=" O   ILE D 234 "    0.007 2.00e-02 2.50e+03
        pdb=" N   ILE D 235 "    0.006 2.00e-02 2.50e+03
  ... (remaining 2257 not shown)

  Histogram of nonbonded interaction distances:
        2.03 -     2.60: 58
        2.60 -     3.18: 10619
        3.18 -     3.75: 20083
        3.75 -     4.33: 28687
        4.33 -     4.90: 47415
  Nonbonded interactions: 106862
  Sorted by model distance:
  nonbonded pdb=" SG  CYS C 157 "
            pdb=" SG  CYS C 171 "
     model   vdw
     2.030 3.760
  nonbonded pdb=" SG  CYS E 157 "
            pdb=" SG  CYS E 171 "
     model   vdw
     2.030 3.760
  nonbonded pdb=" SG  CYS B 157 "
            pdb=" SG  CYS B 171 "
     model   vdw
     2.030 3.760
  nonbonded pdb=" SG  CYS C 289 "
            pdb=" SG  CYS C 394 "
     model   vdw
     2.030 3.760
  nonbonded pdb=" SG  CYS E 289 "
            pdb=" SG  CYS E 394 "
     model   vdw
     2.031 3.760
  ... (remaining 106857 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: 0.14
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'C'
  selection = chain 'B'
  selection = chain 'E'
  selection = chain 'D'
}
ncs_group {
  reference = chain 'G'
  selection = chain 'F'
  selection = chain 'I'
  selection = chain 'H'
  selection = chain 'J'
}

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=0.80 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:                         0.010
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             1.470
  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:          0.530
  Check model and map are aligned:         0.090
  Set scattering table:                    0.110
  Process input model:                     30.150
  Find NCS groups from input model:        0.350
  Set up NCS constraints:                  0.040
  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:             0.010
  Load rotamer database and sin/cos tables:12.330
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   45.100
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8031
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.007   0.117  13385  Z= 0.439
  Angle     :  0.579   5.926  18305  Z= 0.263
  Chirality :  0.041   0.147   2235
  Planarity :  0.003   0.024   2250
  Dihedral  : 10.872  56.122   5010
  Min Nonbonded Distance : 2.030

Molprobity Statistics.
  All-atom Clashscore : 7.55
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.94 %
    Favored  : 99.06 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.00 %
    Favored  : 100.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.88 %
    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:  2.69 (0.21), residues: 1600
  helix:  3.39 (0.20), residues: 545
  sheet:  1.80 (0.24), residues: 405
  loop :  0.38 (0.26), residues: 650

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP A 116 
 HIS   0.001   0.000   HIS A 276 
 PHE   0.016   0.001   PHE A  72 
 TYR   0.013   0.001   TYR E 264 
 ARG   0.002   0.000   ARG A 138 

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

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

  3200 Ramachandran restraints generated.
    1600 Oldfield, 0 Emsley, 1600 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3200 Ramachandran restraints generated.
    1600 Oldfield, 0 Emsley, 1600 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  428 residues out of total 1430 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 428
  time to evaluate  : 1.515 
Fit side-chains
REVERT: A   75 ASP cc_start: 0.8373 (t0) cc_final: 0.7986 (t0)
REVERT: A  124 GLU cc_start: 0.8208 (mp0) cc_final: 0.7921 (pm20)
REVERT: A  221 GLN cc_start: 0.8634 (pt0) cc_final: 0.8187 (pt0)
REVERT: A  259 ILE cc_start: 0.9352 (pt) cc_final: 0.9139 (pt)
REVERT: A  391 TRP cc_start: 0.8159 (m-90) cc_final: 0.7825 (m-90)
REVERT: B  124 GLU cc_start: 0.8189 (mp0) cc_final: 0.7985 (mp0)
REVERT: B  259 ILE cc_start: 0.9409 (pt) cc_final: 0.9192 (pt)
REVERT: B  391 TRP cc_start: 0.8253 (m-90) cc_final: 0.7967 (m-90)
REVERT: C  124 GLU cc_start: 0.8134 (mp0) cc_final: 0.7791 (pm20)
REVERT: C  210 GLN cc_start: 0.8137 (pt0) cc_final: 0.7922 (pt0)
REVERT: C  221 GLN cc_start: 0.8665 (pt0) cc_final: 0.8148 (pt0)
REVERT: C  364 GLU cc_start: 0.7627 (mt-10) cc_final: 0.7405 (mt-10)
REVERT: D  124 GLU cc_start: 0.8114 (mp0) cc_final: 0.7801 (pm20)
REVERT: D  364 GLU cc_start: 0.7805 (mt-10) cc_final: 0.7501 (mt-10)
REVERT: D  391 TRP cc_start: 0.8195 (m-90) cc_final: 0.7946 (m-90)
REVERT: E  221 GLN cc_start: 0.8614 (pt0) cc_final: 0.8293 (pt0)
REVERT: E  391 TRP cc_start: 0.8111 (m-90) cc_final: 0.7818 (m-10)
  outliers start: 0
  outliers final: 1
  residues processed: 428
  average time/residue: 1.1831
  time to fit residues: 554.9373
Evaluate side-chains
  290 residues out of total 1430 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 289
  time to evaluate  : 1.638 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue  259 ILE
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 160
   random chunks:
   chunk 135 optimal weight:    4.9990
   chunk 121 optimal weight:    4.9990
   chunk 67 optimal weight:    2.9990
   chunk 41 optimal weight:    6.9990
   chunk 81 optimal weight:    0.7980
   chunk 64 optimal weight:    0.6980
   chunk 125 optimal weight:    3.9990
   chunk 48 optimal weight:    5.9990
   chunk 76 optimal weight:    0.8980
   chunk 93 optimal weight:    4.9990
   chunk 145 optimal weight:    0.0470
   overall best weight:    1.0880

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

Flipped N/Q/H residues before XYZ refinement:
A 188 GLN
A 382 GLN
B 188 GLN
C 156 ASN
C 382 GLN
D 188 GLN
E 188 GLN
E 382 GLN

Total number of N/Q/H flips: 8

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3260 r_free = 0.3260 target = 0.098233 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3018 r_free = 0.3018 target = 0.081934 restraints weight = 20743.486|
|-----------------------------------------------------------------------------|
r_work (start): 0.3013 rms_B_bonded: 3.02
r_work: 0.2852 rms_B_bonded: 3.49 restraints_weight: 0.5000
r_work (final): 0.2852
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2852
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2852 r_free = 0.2852    target_work(ls_wunit_k1) = 0.072         |
| occupancies: max = 1.00  min = 0.80   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2852 r_free = 0.2852    target_work(ls_wunit_k1) = 0.072         |
| occupancies: max = 1.00  min = 0.82   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2852
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7684
moved from start:          0.1861

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.031  13385  Z= 0.233
  Angle     :  0.571   6.632  18305  Z= 0.280
  Chirality :  0.041   0.143   2235
  Planarity :  0.004   0.049   2250
  Dihedral  :  4.358  29.543   2062
  Min Nonbonded Distance : 2.581

Molprobity Statistics.
  All-atom Clashscore : 8.08
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.75 %
    Favored  : 98.25 %
  Rotamer:
    Outliers :  3.29 %
    Allowed  : 11.26 %
    Favored  : 85.45 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.88 %
    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:  2.48 (0.21), residues: 1600
  helix:  3.65 (0.20), residues: 515
  sheet:  1.47 (0.24), residues: 405
  loop :  0.18 (0.24), residues: 680

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP A 112 
 HIS   0.002   0.000   HIS B 276 
 PHE   0.020   0.002   PHE E  72 
 TYR   0.014   0.002   TYR D 176 
 ARG   0.006   0.001   ARG B 257 

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

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

  3200 Ramachandran restraints generated.
    1600 Oldfield, 0 Emsley, 1600 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3200 Ramachandran restraints generated.
    1600 Oldfield, 0 Emsley, 1600 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  353 residues out of total 1430 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 47
    poor density    : 306
  time to evaluate  : 1.462 
Fit side-chains
REVERT: A   75 ASP cc_start: 0.7839 (t0) cc_final: 0.7497 (t0)
REVERT: A  201 GLU cc_start: 0.8544 (mt-10) cc_final: 0.7937 (mp0)
REVERT: A  210 GLN cc_start: 0.7970 (pt0) cc_final: 0.7696 (pt0)
REVERT: A  221 GLN cc_start: 0.8462 (pt0) cc_final: 0.7824 (pt0)
REVERT: A  260 GLU cc_start: 0.8775 (pt0) cc_final: 0.8404 (pm20)
REVERT: A  391 TRP cc_start: 0.8064 (m-90) cc_final: 0.7856 (m-90)
REVERT: A  402 GLU cc_start: 0.8209 (OUTLIER) cc_final: 0.8009 (mt-10)
REVERT: B   48 GLU cc_start: 0.7841 (tp30) cc_final: 0.7547 (tp30)
REVERT: B  124 GLU cc_start: 0.8467 (mp0) cc_final: 0.8154 (mp0)
REVERT: B  154 GLU cc_start: 0.8748 (tt0) cc_final: 0.8547 (tt0)
REVERT: B  201 GLU cc_start: 0.8496 (mt-10) cc_final: 0.8033 (mp0)
REVERT: B  391 TRP cc_start: 0.8136 (m-90) cc_final: 0.7812 (m-90)
REVERT: C  124 GLU cc_start: 0.8402 (mp0) cc_final: 0.8183 (mp0)
REVERT: C  141 GLN cc_start: 0.8905 (pt0) cc_final: 0.8124 (pm20)
REVERT: C  154 GLU cc_start: 0.8788 (tt0) cc_final: 0.8476 (tt0)
REVERT: C  176 TYR cc_start: 0.8316 (m-80) cc_final: 0.7912 (m-80)
REVERT: C  188 GLN cc_start: 0.8142 (tt0) cc_final: 0.7490 (tt0)
REVERT: C  201 GLU cc_start: 0.8590 (mt-10) cc_final: 0.8074 (mp0)
REVERT: C  221 GLN cc_start: 0.8486 (pt0) cc_final: 0.7781 (pt0)
REVERT: D   75 ASP cc_start: 0.7683 (t0) cc_final: 0.7479 (t0)
REVERT: D   78 ARG cc_start: 0.8574 (OUTLIER) cc_final: 0.8234 (mtp85)
REVERT: D  113 GLU cc_start: 0.8515 (mp0) cc_final: 0.8213 (mp0)
REVERT: D  188 GLN cc_start: 0.8051 (tt0) cc_final: 0.7725 (tt0)
REVERT: D  364 GLU cc_start: 0.7839 (mt-10) cc_final: 0.7440 (mt-10)
REVERT: D  372 LEU cc_start: 0.8092 (OUTLIER) cc_final: 0.7869 (tt)
REVERT: D  391 TRP cc_start: 0.8193 (m-90) cc_final: 0.7898 (m-90)
REVERT: E  113 GLU cc_start: 0.8526 (mp0) cc_final: 0.8276 (mp0)
REVERT: E  124 GLU cc_start: 0.8387 (mp0) cc_final: 0.8047 (mp0)
REVERT: E  221 GLN cc_start: 0.8518 (pt0) cc_final: 0.8064 (pt0)
REVERT: E  257 ARG cc_start: 0.8932 (ptp90) cc_final: 0.8281 (ptp-110)
REVERT: E  391 TRP cc_start: 0.8137 (m-90) cc_final: 0.7801 (m-10)
  outliers start: 47
  outliers final: 19
  residues processed: 337
  average time/residue: 1.1812
  time to fit residues: 435.8881
Evaluate side-chains
  281 residues out of total 1430 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 259
  time to evaluate  : 1.607 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  198 VAL
Chi-restraints excluded: chain A residue  275 LEU
Chi-restraints excluded: chain A residue  373 VAL
Chi-restraints excluded: chain A residue  402 GLU
Chi-restraints excluded: chain B residue  245 LEU
Chi-restraints excluded: chain B residue  372 LEU
Chi-restraints excluded: chain B residue  373 VAL
Chi-restraints excluded: chain C residue  198 VAL
Chi-restraints excluded: chain C residue  259 ILE
Chi-restraints excluded: chain C residue  275 LEU
Chi-restraints excluded: chain C residue  373 VAL
Chi-restraints excluded: chain D residue   78 ARG
Chi-restraints excluded: chain D residue  191 VAL
Chi-restraints excluded: chain D residue  275 LEU
Chi-restraints excluded: chain D residue  372 LEU
Chi-restraints excluded: chain D residue  373 VAL
Chi-restraints excluded: chain E residue  198 VAL
Chi-restraints excluded: chain E residue  210 GLN
Chi-restraints excluded: chain E residue  293 LEU
Chi-restraints excluded: chain E residue  299 ILE
Chi-restraints excluded: chain E residue  372 LEU
Chi-restraints excluded: chain E residue  373 VAL
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 160
   random chunks:
   chunk 107 optimal weight:    0.9980
   chunk 88 optimal weight:    0.0570
   chunk 65 optimal weight:    3.9990
   chunk 98 optimal weight:    3.9990
   chunk 63 optimal weight:   10.0000
   chunk 114 optimal weight:    0.5980
   chunk 42 optimal weight:    5.9990
   chunk 53 optimal weight:    2.9990
   chunk 105 optimal weight:    3.9990
   chunk 92 optimal weight:    3.9990
   chunk 102 optimal weight:    2.9990
   overall best weight:    1.5302

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

Flipped N/Q/H residues before XYZ refinement:
E 382 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3207 r_free = 0.3207 target = 0.095017 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.2964 r_free = 0.2964 target = 0.078908 restraints weight = 21078.373|
|-----------------------------------------------------------------------------|
r_work (start): 0.2981 rms_B_bonded: 3.01
r_work: 0.2820 rms_B_bonded: 3.43 restraints_weight: 0.5000
r_work (final): 0.2820
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2805
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2805 r_free = 0.2805    target_work(ls_wunit_k1) = 0.070         |
| occupancies: max = 1.00  min = 0.82   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2805 r_free = 0.2805    target_work(ls_wunit_k1) = 0.070         |
| occupancies: max = 1.00  min = 0.84   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2805
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7711
moved from start:          0.2121

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.035  13385  Z= 0.283
  Angle     :  0.572   8.645  18305  Z= 0.278
  Chirality :  0.041   0.150   2235
  Planarity :  0.004   0.025   2250
  Dihedral  :  4.175  29.642   2062
  Min Nonbonded Distance : 2.601

Molprobity Statistics.
  All-atom Clashscore : 7.43
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.62 %
    Favored  : 98.38 %
  Rotamer:
    Outliers :  3.92 %
    Allowed  : 13.08 %
    Favored  : 83.01 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.88 %
    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:  2.20 (0.21), residues: 1600
  helix:  3.48 (0.20), residues: 515
  sheet:  1.16 (0.24), residues: 420
  loop :  0.03 (0.24), residues: 665

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.001   TRP C 112 
 HIS   0.002   0.000   HIS D 276 
 PHE   0.020   0.002   PHE E  72 
 TYR   0.018   0.002   TYR A 176 
 ARG   0.006   0.000   ARG E  78 

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

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

  3200 Ramachandran restraints generated.
    1600 Oldfield, 0 Emsley, 1600 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3200 Ramachandran restraints generated.
    1600 Oldfield, 0 Emsley, 1600 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  330 residues out of total 1430 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 56
    poor density    : 274
  time to evaluate  : 1.509 
Fit side-chains
REVERT: A   75 ASP cc_start: 0.7832 (t0) cc_final: 0.7470 (t0)
REVERT: A  201 GLU cc_start: 0.8587 (mt-10) cc_final: 0.7953 (mp0)
REVERT: A  391 TRP cc_start: 0.8047 (m-90) cc_final: 0.7842 (m-90)
REVERT: B   48 GLU cc_start: 0.7839 (tp30) cc_final: 0.7558 (tp30)
REVERT: B   75 ASP cc_start: 0.7670 (t0) cc_final: 0.7274 (t0)
REVERT: B  112 TRP cc_start: 0.8107 (OUTLIER) cc_final: 0.7331 (t-100)
REVERT: B  124 GLU cc_start: 0.8448 (mp0) cc_final: 0.8052 (mp0)
REVERT: B  154 GLU cc_start: 0.8812 (tt0) cc_final: 0.8528 (tt0)
REVERT: B  201 GLU cc_start: 0.8540 (mt-10) cc_final: 0.8048 (mp0)
REVERT: B  260 GLU cc_start: 0.8623 (pm20) cc_final: 0.8374 (pm20)
REVERT: B  391 TRP cc_start: 0.8163 (m-90) cc_final: 0.7841 (m-90)
REVERT: C  112 TRP cc_start: 0.8067 (OUTLIER) cc_final: 0.7319 (t-100)
REVERT: C  129 ASP cc_start: 0.8441 (t0) cc_final: 0.8090 (t0)
REVERT: C  132 ASP cc_start: 0.8067 (p0) cc_final: 0.7656 (t0)
REVERT: C  176 TYR cc_start: 0.8409 (m-80) cc_final: 0.7955 (m-80)
REVERT: C  188 GLN cc_start: 0.8125 (tt0) cc_final: 0.7563 (tt0)
REVERT: C  201 GLU cc_start: 0.8622 (mt-10) cc_final: 0.8056 (mp0)
REVERT: C  221 GLN cc_start: 0.8550 (pt0) cc_final: 0.8169 (pt0)
REVERT: D   63 ASP cc_start: 0.8428 (t70) cc_final: 0.8102 (t0)
REVERT: D   78 ARG cc_start: 0.8540 (OUTLIER) cc_final: 0.8259 (mtp85)
REVERT: D  113 GLU cc_start: 0.8536 (mp0) cc_final: 0.8325 (mp0)
REVERT: D  364 GLU cc_start: 0.7843 (mt-10) cc_final: 0.7448 (mt-10)
REVERT: D  372 LEU cc_start: 0.8095 (OUTLIER) cc_final: 0.7870 (tt)
REVERT: D  391 TRP cc_start: 0.8223 (m-90) cc_final: 0.7919 (m-10)
REVERT: E   81 MET cc_start: 0.8624 (ttp) cc_final: 0.8406 (ptm)
REVERT: E  132 ASP cc_start: 0.8039 (OUTLIER) cc_final: 0.7658 (t0)
REVERT: E  221 GLN cc_start: 0.8554 (pt0) cc_final: 0.8184 (pt0)
REVERT: E  257 ARG cc_start: 0.8926 (ptp90) cc_final: 0.8293 (ptp-110)
REVERT: E  260 GLU cc_start: 0.8885 (pm20) cc_final: 0.8289 (pm20)
REVERT: E  382 GLN cc_start: 0.8368 (mm110) cc_final: 0.8104 (mm-40)
REVERT: E  391 TRP cc_start: 0.8137 (m-90) cc_final: 0.7837 (m-10)
  outliers start: 56
  outliers final: 22
  residues processed: 311
  average time/residue: 1.1387
  time to fit residues: 390.1902
Evaluate side-chains
  288 residues out of total 1430 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 261
  time to evaluate  : 1.434 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  198 VAL
Chi-restraints excluded: chain A residue  275 LEU
Chi-restraints excluded: chain A residue  373 VAL
Chi-restraints excluded: chain B residue  112 TRP
Chi-restraints excluded: chain B residue  245 LEU
Chi-restraints excluded: chain B residue  275 LEU
Chi-restraints excluded: chain B residue  364 GLU
Chi-restraints excluded: chain B residue  372 LEU
Chi-restraints excluded: chain B residue  373 VAL
Chi-restraints excluded: chain C residue  112 TRP
Chi-restraints excluded: chain C residue  172 SER
Chi-restraints excluded: chain C residue  179 SER
Chi-restraints excluded: chain C residue  198 VAL
Chi-restraints excluded: chain C residue  259 ILE
Chi-restraints excluded: chain C residue  275 LEU
Chi-restraints excluded: chain C residue  372 LEU
Chi-restraints excluded: chain C residue  373 VAL
Chi-restraints excluded: chain D residue   78 ARG
Chi-restraints excluded: chain D residue  146 LYS
Chi-restraints excluded: chain D residue  372 LEU
Chi-restraints excluded: chain D residue  373 VAL
Chi-restraints excluded: chain E residue  132 ASP
Chi-restraints excluded: chain E residue  198 VAL
Chi-restraints excluded: chain E residue  210 GLN
Chi-restraints excluded: chain E residue  275 LEU
Chi-restraints excluded: chain E residue  372 LEU
Chi-restraints excluded: chain E residue  373 VAL
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 160
   random chunks:
   chunk 88 optimal weight:    3.9990
   chunk 83 optimal weight:    0.9980
   chunk 135 optimal weight:    4.9990
   chunk 5 optimal weight:    0.4980
   chunk 138 optimal weight:    3.9990
   chunk 15 optimal weight:    4.9990
   chunk 106 optimal weight:    3.9990
   chunk 113 optimal weight:    3.9990
   chunk 46 optimal weight:    1.9990
   chunk 148 optimal weight:    2.9990
   chunk 98 optimal weight:    1.9990
   overall best weight:    1.6986

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

Flipped N/Q/H residues before XYZ refinement:
A 276 HIS
B 276 HIS
C 276 HIS
D 276 HIS

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3190 r_free = 0.3190 target = 0.093793 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.2946 r_free = 0.2946 target = 0.077842 restraints weight = 20924.186|
|-----------------------------------------------------------------------------|
r_work (start): 0.2902 rms_B_bonded: 2.98
r_work: 0.2740 rms_B_bonded: 3.41 restraints_weight: 0.5000
r_work (final): 0.2740
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2777
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2777 r_free = 0.2777    target_work(ls_wunit_k1) = 0.068         |
| occupancies: max = 1.00  min = 0.84   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2777 r_free = 0.2777    target_work(ls_wunit_k1) = 0.068         |
| occupancies: max = 1.00  min = 0.85   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2777
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7711
moved from start:          0.2450

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.037  13385  Z= 0.305
  Angle     :  0.567   6.598  18305  Z= 0.278
  Chirality :  0.041   0.149   2235
  Planarity :  0.004   0.029   2250
  Dihedral  :  4.105  30.488   2062
  Min Nonbonded Distance : 2.599

Molprobity Statistics.
  All-atom Clashscore : 7.92
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.88 %
    Favored  : 98.12 %
  Rotamer:
    Outliers :  3.78 %
    Allowed  : 14.62 %
    Favored  : 81.61 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.88 %
    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:  2.08 (0.21), residues: 1600
  helix:  3.36 (0.20), residues: 515
  sheet:  0.94 (0.24), residues: 420
  loop :  0.10 (0.25), residues: 665

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.021   0.001   TRP B 112 
 HIS   0.003   0.000   HIS D 276 
 PHE   0.021   0.002   PHE E  72 
 TYR   0.011   0.002   TYR A 272 
 ARG   0.006   0.000   ARG B  78 

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

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

  3200 Ramachandran restraints generated.
    1600 Oldfield, 0 Emsley, 1600 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3200 Ramachandran restraints generated.
    1600 Oldfield, 0 Emsley, 1600 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  310 residues out of total 1430 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 54
    poor density    : 256
  time to evaluate  : 1.449 
Fit side-chains
REVERT: A   75 ASP cc_start: 0.7865 (t0) cc_final: 0.7493 (t0)
REVERT: A  112 TRP cc_start: 0.8269 (OUTLIER) cc_final: 0.7583 (t-100)
REVERT: A  124 GLU cc_start: 0.8375 (mp0) cc_final: 0.8056 (mp0)
REVERT: A  154 GLU cc_start: 0.8718 (tt0) cc_final: 0.8496 (tt0)
REVERT: A  184 GLU cc_start: 0.8349 (pt0) cc_final: 0.8135 (pt0)
REVERT: A  201 GLU cc_start: 0.8585 (mt-10) cc_final: 0.7977 (mp0)
REVERT: A  214 GLN cc_start: 0.8145 (mm-40) cc_final: 0.7813 (pt0)
REVERT: A  260 GLU cc_start: 0.8779 (pm20) cc_final: 0.8217 (pm20)
REVERT: A  391 TRP cc_start: 0.8053 (m-90) cc_final: 0.7841 (m-90)
REVERT: B   48 GLU cc_start: 0.7925 (tp30) cc_final: 0.7670 (tp30)
REVERT: B   75 ASP cc_start: 0.7701 (t0) cc_final: 0.7274 (t0)
REVERT: B  124 GLU cc_start: 0.8453 (mp0) cc_final: 0.7993 (mp0)
REVERT: B  132 ASP cc_start: 0.7347 (t0) cc_final: 0.7115 (p0)
REVERT: B  146 LYS cc_start: 0.8266 (mtmm) cc_final: 0.7966 (mtpp)
REVERT: B  154 GLU cc_start: 0.8817 (tt0) cc_final: 0.8567 (tt0)
REVERT: B  201 GLU cc_start: 0.8574 (mt-10) cc_final: 0.8049 (mp0)
REVERT: B  214 GLN cc_start: 0.8260 (mm-40) cc_final: 0.8024 (pt0)
REVERT: B  260 GLU cc_start: 0.8666 (pm20) cc_final: 0.8362 (pm20)
REVERT: B  391 TRP cc_start: 0.8176 (m-90) cc_final: 0.7905 (m-90)
REVERT: C  112 TRP cc_start: 0.8218 (OUTLIER) cc_final: 0.7459 (t-100)
REVERT: C  129 ASP cc_start: 0.8522 (t0) cc_final: 0.8108 (t0)
REVERT: C  146 LYS cc_start: 0.8103 (OUTLIER) cc_final: 0.7684 (mtpp)
REVERT: C  188 GLN cc_start: 0.8127 (tt0) cc_final: 0.7565 (tt0)
REVERT: C  201 GLU cc_start: 0.8639 (mt-10) cc_final: 0.8055 (mp0)
REVERT: D   63 ASP cc_start: 0.8455 (t70) cc_final: 0.8141 (t0)
REVERT: D   78 ARG cc_start: 0.8586 (OUTLIER) cc_final: 0.8135 (mtm-85)
REVERT: D  112 TRP cc_start: 0.8244 (OUTLIER) cc_final: 0.7509 (t-100)
REVERT: D  160 GLU cc_start: 0.8466 (mt-10) cc_final: 0.8109 (mt-10)
REVERT: D  364 GLU cc_start: 0.7836 (mt-10) cc_final: 0.7450 (mt-10)
REVERT: D  372 LEU cc_start: 0.8079 (OUTLIER) cc_final: 0.7850 (tt)
REVERT: D  391 TRP cc_start: 0.8226 (m-90) cc_final: 0.7949 (m-90)
REVERT: E  112 TRP cc_start: 0.8095 (OUTLIER) cc_final: 0.7058 (t-100)
REVERT: E  132 ASP cc_start: 0.8056 (OUTLIER) cc_final: 0.7639 (t0)
REVERT: E  221 GLN cc_start: 0.8512 (pt0) cc_final: 0.8159 (pt0)
REVERT: E  257 ARG cc_start: 0.8941 (ptp90) cc_final: 0.8286 (ptp-110)
REVERT: E  260 GLU cc_start: 0.8885 (pm20) cc_final: 0.8397 (pm20)
REVERT: E  391 TRP cc_start: 0.8191 (m-90) cc_final: 0.7927 (m-10)
  outliers start: 54
  outliers final: 23
  residues processed: 283
  average time/residue: 1.3100
  time to fit residues: 409.2516
Evaluate side-chains
  268 residues out of total 1430 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 237
  time to evaluate  : 1.587 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   84 MET
Chi-restraints excluded: chain A residue  112 TRP
Chi-restraints excluded: chain A residue  123 LEU
Chi-restraints excluded: chain A residue  210 GLN
Chi-restraints excluded: chain A residue  275 LEU
Chi-restraints excluded: chain A residue  373 VAL
Chi-restraints excluded: chain B residue  245 LEU
Chi-restraints excluded: chain B residue  275 LEU
Chi-restraints excluded: chain B residue  372 LEU
Chi-restraints excluded: chain B residue  373 VAL
Chi-restraints excluded: chain C residue  112 TRP
Chi-restraints excluded: chain C residue  146 LYS
Chi-restraints excluded: chain C residue  172 SER
Chi-restraints excluded: chain C residue  198 VAL
Chi-restraints excluded: chain C residue  259 ILE
Chi-restraints excluded: chain C residue  275 LEU
Chi-restraints excluded: chain C residue  372 LEU
Chi-restraints excluded: chain C residue  373 VAL
Chi-restraints excluded: chain D residue   78 ARG
Chi-restraints excluded: chain D residue  112 TRP
Chi-restraints excluded: chain D residue  299 ILE
Chi-restraints excluded: chain D residue  372 LEU
Chi-restraints excluded: chain D residue  373 VAL
Chi-restraints excluded: chain E residue  112 TRP
Chi-restraints excluded: chain E residue  132 ASP
Chi-restraints excluded: chain E residue  198 VAL
Chi-restraints excluded: chain E residue  210 GLN
Chi-restraints excluded: chain E residue  237 LEU
Chi-restraints excluded: chain E residue  275 LEU
Chi-restraints excluded: chain E residue  372 LEU
Chi-restraints excluded: chain E residue  373 VAL
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 160
   random chunks:
   chunk 124 optimal weight:    4.9990
   chunk 0 optimal weight:    5.9990
   chunk 98 optimal weight:    0.9990
   chunk 151 optimal weight:    8.9990
   chunk 114 optimal weight:    3.9990
   chunk 122 optimal weight:    3.9990
   chunk 34 optimal weight:    0.9990
   chunk 111 optimal weight:    0.8980
   chunk 35 optimal weight:    2.9990
   chunk 102 optimal weight:    0.0970
   chunk 127 optimal weight:    1.9990
   overall best weight:    0.9984

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

Flipped N/Q/H residues before XYZ refinement:
E 382 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3195 r_free = 0.3195 target = 0.094349 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 26)----------------|
| r_work = 0.2952 r_free = 0.2952 target = 0.078375 restraints weight = 21147.769|
|-----------------------------------------------------------------------------|
r_work (start): 0.2923 rms_B_bonded: 3.01
r_work: 0.2762 rms_B_bonded: 3.44 restraints_weight: 0.5000
r_work (final): 0.2762
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2790
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2790 r_free = 0.2790    target_work(ls_wunit_k1) = 0.069         |
| occupancies: max = 1.00  min = 0.85   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2790 r_free = 0.2790    target_work(ls_wunit_k1) = 0.069         |
| occupancies: max = 1.00  min = 0.85   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2790
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7661
moved from start:          0.2573

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032  13385  Z= 0.212
  Angle     :  0.540   7.066  18305  Z= 0.263
  Chirality :  0.040   0.146   2235
  Planarity :  0.004   0.031   2250
  Dihedral  :  3.980  30.498   2062
  Min Nonbonded Distance : 2.591

Molprobity Statistics.
  All-atom Clashscore : 8.11
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.19 %
    Favored  : 97.81 %
  Rotamer:
    Outliers :  3.36 %
    Allowed  : 14.48 %
    Favored  : 82.17 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.88 %
    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:  2.05 (0.21), residues: 1600
  helix:  3.38 (0.20), residues: 515
  sheet:  0.84 (0.24), residues: 420
  loop :  0.11 (0.25), residues: 665

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.021   0.001   TRP B 112 
 HIS   0.002   0.000   HIS E 276 
 PHE   0.019   0.002   PHE D  72 
 TYR   0.014   0.002   TYR B 176 
 ARG   0.006   0.000   ARG C  78 

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

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

  3200 Ramachandran restraints generated.
    1600 Oldfield, 0 Emsley, 1600 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3200 Ramachandran restraints generated.
    1600 Oldfield, 0 Emsley, 1600 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  307 residues out of total 1430 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 48
    poor density    : 259
  time to evaluate  : 1.457 
Fit side-chains
REVERT: A   75 ASP cc_start: 0.7763 (t0) cc_final: 0.7414 (t0)
REVERT: A  124 GLU cc_start: 0.8335 (mp0) cc_final: 0.7900 (mp0)
REVERT: A  154 GLU cc_start: 0.8670 (tt0) cc_final: 0.8464 (tt0)
REVERT: A  184 GLU cc_start: 0.8317 (pt0) cc_final: 0.8110 (pt0)
REVERT: A  201 GLU cc_start: 0.8581 (mt-10) cc_final: 0.7971 (mp0)
REVERT: A  214 GLN cc_start: 0.8202 (mm-40) cc_final: 0.7854 (pt0)
REVERT: A  260 GLU cc_start: 0.8776 (pm20) cc_final: 0.8282 (pm20)
REVERT: A  391 TRP cc_start: 0.8031 (m-90) cc_final: 0.7783 (m-90)
REVERT: B   48 GLU cc_start: 0.7921 (tp30) cc_final: 0.7570 (tp30)
REVERT: B   75 ASP cc_start: 0.7574 (t0) cc_final: 0.7288 (t0)
REVERT: B  124 GLU cc_start: 0.8425 (mp0) cc_final: 0.7940 (mp0)
REVERT: B  132 ASP cc_start: 0.7483 (t0) cc_final: 0.7031 (p0)
REVERT: B  146 LYS cc_start: 0.8256 (mtmm) cc_final: 0.7962 (mtpp)
REVERT: B  154 GLU cc_start: 0.8733 (tt0) cc_final: 0.8509 (tt0)
REVERT: B  201 GLU cc_start: 0.8538 (mt-10) cc_final: 0.8040 (mp0)
REVERT: B  214 GLN cc_start: 0.8255 (mm-40) cc_final: 0.8023 (pt0)
REVERT: B  260 GLU cc_start: 0.8653 (pm20) cc_final: 0.8317 (pm20)
REVERT: B  364 GLU cc_start: 0.7636 (mp0) cc_final: 0.6729 (mp0)
REVERT: B  391 TRP cc_start: 0.8148 (m-90) cc_final: 0.7910 (m-90)
REVERT: C  112 TRP cc_start: 0.8112 (OUTLIER) cc_final: 0.7336 (t-100)
REVERT: C  129 ASP cc_start: 0.8503 (t0) cc_final: 0.8065 (t0)
REVERT: C  188 GLN cc_start: 0.8054 (tt0) cc_final: 0.7471 (tt0)
REVERT: C  201 GLU cc_start: 0.8624 (mt-10) cc_final: 0.8043 (mp0)
REVERT: D   63 ASP cc_start: 0.8378 (t70) cc_final: 0.8076 (t0)
REVERT: D   75 ASP cc_start: 0.7623 (t0) cc_final: 0.7411 (t0)
REVERT: D  113 GLU cc_start: 0.8772 (mp0) cc_final: 0.8259 (mp0)
REVERT: D  129 ASP cc_start: 0.8288 (t0) cc_final: 0.7940 (t0)
REVERT: D  364 GLU cc_start: 0.7850 (mt-10) cc_final: 0.7459 (mt-10)
REVERT: D  372 LEU cc_start: 0.8035 (OUTLIER) cc_final: 0.7821 (tt)
REVERT: D  391 TRP cc_start: 0.8170 (m-90) cc_final: 0.7889 (m-90)
REVERT: E   81 MET cc_start: 0.8638 (ttp) cc_final: 0.8388 (ptt)
REVERT: E  221 GLN cc_start: 0.8424 (pt0) cc_final: 0.8067 (pt0)
REVERT: E  260 GLU cc_start: 0.8895 (pm20) cc_final: 0.8430 (pm20)
REVERT: E  391 TRP cc_start: 0.8122 (m-90) cc_final: 0.7867 (m-10)
  outliers start: 48
  outliers final: 19
  residues processed: 287
  average time/residue: 1.1945
  time to fit residues: 375.2687
Evaluate side-chains
  278 residues out of total 1430 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 257
  time to evaluate  : 1.473 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   84 MET
Chi-restraints excluded: chain A residue  235 ILE
Chi-restraints excluded: chain A residue  275 LEU
Chi-restraints excluded: chain B residue  245 LEU
Chi-restraints excluded: chain B residue  275 LEU
Chi-restraints excluded: chain B residue  372 LEU
Chi-restraints excluded: chain C residue  112 TRP
Chi-restraints excluded: chain C residue  172 SER
Chi-restraints excluded: chain C residue  198 VAL
Chi-restraints excluded: chain C residue  275 LEU
Chi-restraints excluded: chain C residue  306 LEU
Chi-restraints excluded: chain C residue  372 LEU
Chi-restraints excluded: chain C residue  373 VAL
Chi-restraints excluded: chain D residue  146 LYS
Chi-restraints excluded: chain D residue  198 VAL
Chi-restraints excluded: chain D residue  237 LEU
Chi-restraints excluded: chain D residue  275 LEU
Chi-restraints excluded: chain D residue  299 ILE
Chi-restraints excluded: chain D residue  372 LEU
Chi-restraints excluded: chain E residue  198 VAL
Chi-restraints excluded: chain E residue  372 LEU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 160
   random chunks:
   chunk 107 optimal weight:    2.9990
   chunk 72 optimal weight:    1.9990
   chunk 125 optimal weight:    4.9990
   chunk 39 optimal weight:    2.9990
   chunk 151 optimal weight:    0.9980
   chunk 101 optimal weight:    7.9990
   chunk 89 optimal weight:    4.9990
   chunk 124 optimal weight:    4.9990
   chunk 20 optimal weight:    3.9990
   chunk 155 optimal weight:    0.8980
   chunk 75 optimal weight:    0.7980
   overall best weight:    1.5384

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3178 r_free = 0.3178 target = 0.093362 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.2932 r_free = 0.2932 target = 0.077188 restraints weight = 21284.494|
|-----------------------------------------------------------------------------|
r_work (start): 0.2928 rms_B_bonded: 3.03
r_work: 0.2767 rms_B_bonded: 3.44 restraints_weight: 0.5000
r_work (final): 0.2767
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2748
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2748 r_free = 0.2748    target_work(ls_wunit_k1) = 0.067         |
| occupancies: max = 1.00  min = 0.85   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2747 r_free = 0.2747    target_work(ls_wunit_k1) = 0.067         |
| occupancies: max = 1.00  min = 0.88   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2747
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7698
moved from start:          0.2670

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.040  13385  Z= 0.285
  Angle     :  0.564   8.632  18305  Z= 0.273
  Chirality :  0.040   0.150   2235
  Planarity :  0.004   0.047   2250
  Dihedral  :  3.933  16.331   2060
  Min Nonbonded Distance : 2.613

Molprobity Statistics.
  All-atom Clashscore : 8.04
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.19 %
    Favored  : 97.81 %
  Rotamer:
    Outliers :  3.71 %
    Allowed  : 14.76 %
    Favored  : 81.54 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.88 %
    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:  1.99 (0.21), residues: 1600
  helix:  3.03 (0.20), residues: 545
  sheet:  0.78 (0.24), residues: 420
  loop :  0.23 (0.26), residues: 635

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.024   0.001   TRP B 112 
 HIS   0.002   0.000   HIS E 276 
 PHE   0.021   0.002   PHE C  72 
 TYR   0.016   0.002   TYR A 272 
 ARG   0.011   0.000   ARG D 257 

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

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

  3200 Ramachandran restraints generated.
    1600 Oldfield, 0 Emsley, 1600 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3200 Ramachandran restraints generated.
    1600 Oldfield, 0 Emsley, 1600 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  309 residues out of total 1430 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 53
    poor density    : 256
  time to evaluate  : 1.482 
Fit side-chains
REVERT: A   81 MET cc_start: 0.8745 (ttp) cc_final: 0.8443 (ptm)
REVERT: A  112 TRP cc_start: 0.8049 (OUTLIER) cc_final: 0.7596 (t-100)
REVERT: A  124 GLU cc_start: 0.8358 (mp0) cc_final: 0.7983 (mp0)
REVERT: A  154 GLU cc_start: 0.8669 (tt0) cc_final: 0.8455 (tt0)
REVERT: A  184 GLU cc_start: 0.8340 (pt0) cc_final: 0.8138 (pt0)
REVERT: A  201 GLU cc_start: 0.8588 (mt-10) cc_final: 0.7963 (mp0)
REVERT: A  214 GLN cc_start: 0.8213 (mm-40) cc_final: 0.7856 (pt0)
REVERT: A  260 GLU cc_start: 0.8777 (pm20) cc_final: 0.8232 (pm20)
REVERT: A  364 GLU cc_start: 0.8083 (mt-10) cc_final: 0.7669 (mt-10)
REVERT: A  391 TRP cc_start: 0.8062 (m-90) cc_final: 0.7820 (m-90)
REVERT: B   48 GLU cc_start: 0.7988 (tp30) cc_final: 0.7744 (tp30)
REVERT: B  112 TRP cc_start: 0.7897 (OUTLIER) cc_final: 0.6943 (t-100)
REVERT: B  124 GLU cc_start: 0.8437 (mp0) cc_final: 0.7989 (mp0)
REVERT: B  132 ASP cc_start: 0.7321 (t0) cc_final: 0.6801 (p0)
REVERT: B  146 LYS cc_start: 0.8282 (mtmm) cc_final: 0.7989 (mtpp)
REVERT: B  154 GLU cc_start: 0.8797 (tt0) cc_final: 0.8559 (tt0)
REVERT: B  201 GLU cc_start: 0.8561 (mt-10) cc_final: 0.8020 (mp0)
REVERT: B  214 GLN cc_start: 0.8291 (mm-40) cc_final: 0.8015 (pt0)
REVERT: B  260 GLU cc_start: 0.8684 (pm20) cc_final: 0.8319 (pm20)
REVERT: B  364 GLU cc_start: 0.7603 (mt-10) cc_final: 0.6670 (mp0)
REVERT: B  391 TRP cc_start: 0.8214 (m-90) cc_final: 0.7965 (m-90)
REVERT: C  112 TRP cc_start: 0.8233 (OUTLIER) cc_final: 0.7830 (t-100)
REVERT: C  129 ASP cc_start: 0.8530 (t0) cc_final: 0.8057 (t0)
REVERT: C  132 ASP cc_start: 0.7871 (OUTLIER) cc_final: 0.7571 (t0)
REVERT: C  146 LYS cc_start: 0.8132 (OUTLIER) cc_final: 0.7699 (mtpp)
REVERT: C  188 GLN cc_start: 0.8069 (tt0) cc_final: 0.7485 (tt0)
REVERT: C  201 GLU cc_start: 0.8647 (mt-10) cc_final: 0.8053 (mp0)
REVERT: D   63 ASP cc_start: 0.8401 (t70) cc_final: 0.8110 (t0)
REVERT: D   75 ASP cc_start: 0.7683 (t0) cc_final: 0.7475 (t0)
REVERT: D  113 GLU cc_start: 0.8737 (mp0) cc_final: 0.8336 (mp0)
REVERT: D  129 ASP cc_start: 0.8380 (t0) cc_final: 0.8032 (t0)
REVERT: D  132 ASP cc_start: 0.7929 (p0) cc_final: 0.7544 (t0)
REVERT: D  160 GLU cc_start: 0.8453 (mt-10) cc_final: 0.8083 (mt-10)
REVERT: D  364 GLU cc_start: 0.7852 (mt-10) cc_final: 0.7482 (mt-10)
REVERT: D  372 LEU cc_start: 0.8045 (OUTLIER) cc_final: 0.7826 (tt)
REVERT: D  391 TRP cc_start: 0.8184 (m-90) cc_final: 0.7951 (m-90)
REVERT: E   81 MET cc_start: 0.8642 (ttp) cc_final: 0.8387 (ptt)
REVERT: E  112 TRP cc_start: 0.8164 (OUTLIER) cc_final: 0.6967 (t-100)
REVERT: E  132 ASP cc_start: 0.7945 (OUTLIER) cc_final: 0.7588 (t0)
REVERT: E  221 GLN cc_start: 0.8487 (pt0) cc_final: 0.8175 (pt0)
REVERT: E  257 ARG cc_start: 0.8902 (ptp90) cc_final: 0.8279 (ptp-110)
REVERT: E  260 GLU cc_start: 0.8929 (pm20) cc_final: 0.8479 (pm20)
REVERT: E  285 SER cc_start: 0.8762 (t) cc_final: 0.8369 (t)
REVERT: E  391 TRP cc_start: 0.8176 (m-90) cc_final: 0.7957 (m-10)
  outliers start: 53
  outliers final: 25
  residues processed: 288
  average time/residue: 1.2289
  time to fit residues: 386.9104
Evaluate side-chains
  265 residues out of total 1430 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 232
  time to evaluate  : 1.514 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  112 TRP
Chi-restraints excluded: chain A residue  123 LEU
Chi-restraints excluded: chain A residue  210 GLN
Chi-restraints excluded: chain A residue  275 LEU
Chi-restraints excluded: chain A residue  373 VAL
Chi-restraints excluded: chain B residue  112 TRP
Chi-restraints excluded: chain B residue  245 LEU
Chi-restraints excluded: chain B residue  275 LEU
Chi-restraints excluded: chain B residue  372 LEU
Chi-restraints excluded: chain B residue  373 VAL
Chi-restraints excluded: chain C residue  112 TRP
Chi-restraints excluded: chain C residue  132 ASP
Chi-restraints excluded: chain C residue  146 LYS
Chi-restraints excluded: chain C residue  172 SER
Chi-restraints excluded: chain C residue  198 VAL
Chi-restraints excluded: chain C residue  210 GLN
Chi-restraints excluded: chain C residue  275 LEU
Chi-restraints excluded: chain C residue  306 LEU
Chi-restraints excluded: chain C residue  372 LEU
Chi-restraints excluded: chain C residue  373 VAL
Chi-restraints excluded: chain D residue  146 LYS
Chi-restraints excluded: chain D residue  153 THR
Chi-restraints excluded: chain D residue  198 VAL
Chi-restraints excluded: chain D residue  237 LEU
Chi-restraints excluded: chain D residue  275 LEU
Chi-restraints excluded: chain D residue  372 LEU
Chi-restraints excluded: chain D residue  373 VAL
Chi-restraints excluded: chain E residue  112 TRP
Chi-restraints excluded: chain E residue  132 ASP
Chi-restraints excluded: chain E residue  198 VAL
Chi-restraints excluded: chain E residue  275 LEU
Chi-restraints excluded: chain E residue  372 LEU
Chi-restraints excluded: chain E residue  373 VAL
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 160
   random chunks:
   chunk 95 optimal weight:    0.1980
   chunk 28 optimal weight:    4.9990
   chunk 122 optimal weight:    2.9990
   chunk 136 optimal weight:    2.9990
   chunk 157 optimal weight:    4.9990
   chunk 135 optimal weight:    1.9990
   chunk 3 optimal weight:    2.9990
   chunk 71 optimal weight:    2.9990
   chunk 100 optimal weight:    2.9990
   chunk 105 optimal weight:    0.7980
   chunk 108 optimal weight:    0.9990
   overall best weight:    1.3986

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

Flipped N/Q/H residues before XYZ refinement:
E 276 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3210 r_free = 0.3210 target = 0.094700 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.2960 r_free = 0.2960 target = 0.078472 restraints weight = 20870.103|
|-----------------------------------------------------------------------------|
r_work (start): 0.2905 rms_B_bonded: 3.03
r_work: 0.2742 rms_B_bonded: 3.43 restraints_weight: 0.5000
r_work (final): 0.2742
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2780
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2780 r_free = 0.2780    target_work(ls_wunit_k1) = 0.069         |
| occupancies: max = 1.00  min = 0.88   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2780 r_free = 0.2780    target_work(ls_wunit_k1) = 0.069         |
| occupancies: max = 1.00  min = 0.86   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2780
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7703
moved from start:          0.2774

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.036  13385  Z= 0.264
  Angle     :  0.560   9.134  18305  Z= 0.271
  Chirality :  0.040   0.148   2235
  Planarity :  0.004   0.048   2250
  Dihedral  :  3.916  15.367   2060
  Min Nonbonded Distance : 2.594

Molprobity Statistics.
  All-atom Clashscore : 8.30
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.38 %
    Favored  : 97.62 %
  Rotamer:
    Outliers :  3.22 %
    Allowed  : 15.94 %
    Favored  : 80.84 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.88 %
    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:  1.96 (0.21), residues: 1600
  helix:  3.00 (0.20), residues: 545
  sheet:  0.78 (0.24), residues: 420
  loop :  0.20 (0.26), residues: 635

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.022   0.001   TRP B 112 
 HIS   0.002   0.000   HIS E 276 
 PHE   0.033   0.002   PHE D 385 
 TYR   0.016   0.002   TYR A 272 
 ARG   0.012   0.000   ARG D 257 

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

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

  3200 Ramachandran restraints generated.
    1600 Oldfield, 0 Emsley, 1600 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3200 Ramachandran restraints generated.
    1600 Oldfield, 0 Emsley, 1600 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  292 residues out of total 1430 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 46
    poor density    : 246
  time to evaluate  : 1.613 
Fit side-chains
REVERT: A   75 ASP cc_start: 0.7826 (t0) cc_final: 0.7447 (t0)
REVERT: A   81 MET cc_start: 0.8750 (ttp) cc_final: 0.8528 (ptm)
REVERT: A  124 GLU cc_start: 0.8357 (mp0) cc_final: 0.7958 (mp0)
REVERT: A  154 GLU cc_start: 0.8728 (tt0) cc_final: 0.8512 (tt0)
REVERT: A  184 GLU cc_start: 0.8371 (pt0) cc_final: 0.8158 (pt0)
REVERT: A  201 GLU cc_start: 0.8594 (mt-10) cc_final: 0.7971 (mp0)
REVERT: A  214 GLN cc_start: 0.8216 (mm-40) cc_final: 0.7899 (pt0)
REVERT: A  260 GLU cc_start: 0.8793 (pm20) cc_final: 0.8283 (pm20)
REVERT: A  364 GLU cc_start: 0.8081 (mt-10) cc_final: 0.7608 (mt-10)
REVERT: A  391 TRP cc_start: 0.8078 (m-90) cc_final: 0.7838 (m-90)
REVERT: B   48 GLU cc_start: 0.8007 (tp30) cc_final: 0.7759 (tp30)
REVERT: B  124 GLU cc_start: 0.8430 (mp0) cc_final: 0.7946 (mp0)
REVERT: B  132 ASP cc_start: 0.7323 (t0) cc_final: 0.7020 (t0)
REVERT: B  146 LYS cc_start: 0.8291 (mtmm) cc_final: 0.8003 (mtpp)
REVERT: B  154 GLU cc_start: 0.8820 (tt0) cc_final: 0.8565 (tt0)
REVERT: B  201 GLU cc_start: 0.8530 (mt-10) cc_final: 0.7992 (mp0)
REVERT: B  214 GLN cc_start: 0.8319 (mm-40) cc_final: 0.8051 (pt0)
REVERT: B  260 GLU cc_start: 0.8738 (pm20) cc_final: 0.8370 (pm20)
REVERT: B  272 TYR cc_start: 0.8605 (t80) cc_final: 0.8339 (t80)
REVERT: B  364 GLU cc_start: 0.7612 (mt-10) cc_final: 0.6665 (mp0)
REVERT: B  391 TRP cc_start: 0.8191 (m-90) cc_final: 0.7937 (m-90)
REVERT: C  112 TRP cc_start: 0.8242 (OUTLIER) cc_final: 0.7930 (t-100)
REVERT: C  132 ASP cc_start: 0.7814 (OUTLIER) cc_final: 0.7507 (t0)
REVERT: C  188 GLN cc_start: 0.8077 (tt0) cc_final: 0.7475 (tt0)
REVERT: C  201 GLU cc_start: 0.8636 (mt-10) cc_final: 0.8032 (mp0)
REVERT: C  260 GLU cc_start: 0.8924 (pm20) cc_final: 0.8552 (pm20)
REVERT: D  113 GLU cc_start: 0.8730 (mp0) cc_final: 0.8115 (mp0)
REVERT: D  364 GLU cc_start: 0.7932 (mt-10) cc_final: 0.7561 (mt-10)
REVERT: D  372 LEU cc_start: 0.8044 (OUTLIER) cc_final: 0.7825 (tt)
REVERT: D  391 TRP cc_start: 0.8183 (m-90) cc_final: 0.7951 (m-90)
REVERT: E  112 TRP cc_start: 0.8170 (OUTLIER) cc_final: 0.7011 (t-100)
REVERT: E  132 ASP cc_start: 0.7931 (OUTLIER) cc_final: 0.7630 (t0)
REVERT: E  221 GLN cc_start: 0.8498 (pt0) cc_final: 0.8186 (pt0)
REVERT: E  257 ARG cc_start: 0.8897 (ptp90) cc_final: 0.8274 (ptp-110)
REVERT: E  260 GLU cc_start: 0.8925 (pm20) cc_final: 0.8497 (pm20)
REVERT: E  285 SER cc_start: 0.8767 (t) cc_final: 0.8396 (t)
REVERT: E  391 TRP cc_start: 0.8145 (m-90) cc_final: 0.7922 (m-10)
  outliers start: 46
  outliers final: 24
  residues processed: 272
  average time/residue: 1.2543
  time to fit residues: 371.9652
Evaluate side-chains
  278 residues out of total 1430 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 249
  time to evaluate  : 1.440 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  123 LEU
Chi-restraints excluded: chain A residue  210 GLN
Chi-restraints excluded: chain A residue  275 LEU
Chi-restraints excluded: chain A residue  372 LEU
Chi-restraints excluded: chain A residue  373 VAL
Chi-restraints excluded: chain A residue  394 CYS
Chi-restraints excluded: chain B residue  245 LEU
Chi-restraints excluded: chain B residue  275 LEU
Chi-restraints excluded: chain B residue  372 LEU
Chi-restraints excluded: chain B residue  373 VAL
Chi-restraints excluded: chain C residue  112 TRP
Chi-restraints excluded: chain C residue  132 ASP
Chi-restraints excluded: chain C residue  172 SER
Chi-restraints excluded: chain C residue  198 VAL
Chi-restraints excluded: chain C residue  210 GLN
Chi-restraints excluded: chain C residue  275 LEU
Chi-restraints excluded: chain C residue  306 LEU
Chi-restraints excluded: chain C residue  372 LEU
Chi-restraints excluded: chain C residue  373 VAL
Chi-restraints excluded: chain D residue  153 THR
Chi-restraints excluded: chain D residue  299 ILE
Chi-restraints excluded: chain D residue  372 LEU
Chi-restraints excluded: chain D residue  373 VAL
Chi-restraints excluded: chain E residue  112 TRP
Chi-restraints excluded: chain E residue  132 ASP
Chi-restraints excluded: chain E residue  198 VAL
Chi-restraints excluded: chain E residue  275 LEU
Chi-restraints excluded: chain E residue  372 LEU
Chi-restraints excluded: chain E residue  373 VAL
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 160
   random chunks:
   chunk 32 optimal weight:    5.9990
   chunk 10 optimal weight:    0.8980
   chunk 153 optimal weight:    1.9990
   chunk 89 optimal weight:    0.7980
   chunk 101 optimal weight:    0.9990
   chunk 27 optimal weight:    3.9990
   chunk 28 optimal weight:    4.9990
   chunk 8 optimal weight:    0.7980
   chunk 116 optimal weight:    3.9990
   chunk 50 optimal weight:    1.9990
   chunk 71 optimal weight:    0.7980
   overall best weight:    0.8582

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

Flipped N/Q/H residues before XYZ refinement:
D 382 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3200 r_free = 0.3200 target = 0.094573 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.2958 r_free = 0.2958 target = 0.078530 restraints weight = 21141.009|
|-----------------------------------------------------------------------------|
r_work (start): 0.2929 rms_B_bonded: 3.00
r_work: 0.2766 rms_B_bonded: 3.44 restraints_weight: 0.5000
r_work (final): 0.2766
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2804
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2804 r_free = 0.2804    target_work(ls_wunit_k1) = 0.070         |
| occupancies: max = 1.00  min = 0.86   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2804 r_free = 0.2804    target_work(ls_wunit_k1) = 0.070         |
| occupancies: max = 1.00  min = 0.85   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2804
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7703
moved from start:          0.2797

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032  13385  Z= 0.197
  Angle     :  0.545   9.928  18305  Z= 0.261
  Chirality :  0.040   0.146   2235
  Planarity :  0.003   0.048   2250
  Dihedral  :  3.892  16.293   2060
  Min Nonbonded Distance : 2.596

Molprobity Statistics.
  All-atom Clashscore : 8.19
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.19 %
    Favored  : 97.81 %
  Rotamer:
    Outliers :  2.17 %
    Allowed  : 17.13 %
    Favored  : 80.70 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.88 %
    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:  1.99 (0.21), residues: 1600
  helix:  3.09 (0.20), residues: 545
  sheet:  0.73 (0.23), residues: 440
  loop :  0.19 (0.27), residues: 615

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.022   0.001   TRP B 112 
 HIS   0.001   0.000   HIS D 163 
 PHE   0.025   0.001   PHE D 385 
 TYR   0.022   0.002   TYR B 176 
 ARG   0.010   0.000   ARG D 257 

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

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

  3200 Ramachandran restraints generated.
    1600 Oldfield, 0 Emsley, 1600 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3200 Ramachandran restraints generated.
    1600 Oldfield, 0 Emsley, 1600 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  299 residues out of total 1430 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 268
  time to evaluate  : 1.615 
Fit side-chains
REVERT: A   75 ASP cc_start: 0.7814 (t0) cc_final: 0.7433 (t0)
REVERT: A   81 MET cc_start: 0.8733 (ttp) cc_final: 0.8514 (ptm)
REVERT: A  124 GLU cc_start: 0.8384 (mp0) cc_final: 0.7833 (mp0)
REVERT: A  184 GLU cc_start: 0.8368 (pt0) cc_final: 0.8159 (pt0)
REVERT: A  201 GLU cc_start: 0.8595 (mt-10) cc_final: 0.7977 (mp0)
REVERT: A  214 GLN cc_start: 0.8204 (mm-40) cc_final: 0.7941 (pt0)
REVERT: A  260 GLU cc_start: 0.8810 (pm20) cc_final: 0.8333 (pm20)
REVERT: A  364 GLU cc_start: 0.8058 (mt-10) cc_final: 0.7587 (mt-10)
REVERT: A  391 TRP cc_start: 0.8053 (m-90) cc_final: 0.7813 (m-90)
REVERT: B   48 GLU cc_start: 0.8010 (tp30) cc_final: 0.7750 (tp30)
REVERT: B  124 GLU cc_start: 0.8431 (mp0) cc_final: 0.7986 (mp0)
REVERT: B  132 ASP cc_start: 0.7331 (t0) cc_final: 0.7006 (t0)
REVERT: B  146 LYS cc_start: 0.8287 (mtmm) cc_final: 0.8006 (mtpp)
REVERT: B  154 GLU cc_start: 0.8817 (tt0) cc_final: 0.8589 (tt0)
REVERT: B  201 GLU cc_start: 0.8553 (mt-10) cc_final: 0.8022 (mp0)
REVERT: B  214 GLN cc_start: 0.8316 (mm-40) cc_final: 0.8048 (pt0)
REVERT: B  260 GLU cc_start: 0.8771 (pm20) cc_final: 0.8403 (pm20)
REVERT: B  272 TYR cc_start: 0.8544 (t80) cc_final: 0.8293 (t80)
REVERT: B  364 GLU cc_start: 0.7534 (mt-10) cc_final: 0.6555 (mp0)
REVERT: B  391 TRP cc_start: 0.8188 (m-90) cc_final: 0.7943 (m-90)
REVERT: C  112 TRP cc_start: 0.8157 (OUTLIER) cc_final: 0.7841 (t-100)
REVERT: C  129 ASP cc_start: 0.8600 (t0) cc_final: 0.8072 (t0)
REVERT: C  132 ASP cc_start: 0.7792 (p0) cc_final: 0.7466 (t0)
REVERT: C  154 GLU cc_start: 0.8707 (tt0) cc_final: 0.8342 (tt0)
REVERT: C  188 GLN cc_start: 0.8103 (tt0) cc_final: 0.7484 (tt0)
REVERT: C  201 GLU cc_start: 0.8679 (mt-10) cc_final: 0.8036 (mp0)
REVERT: C  260 GLU cc_start: 0.8922 (pm20) cc_final: 0.8649 (pm20)
REVERT: C  364 GLU cc_start: 0.8042 (mt-10) cc_final: 0.7638 (mt-10)
REVERT: D  113 GLU cc_start: 0.8747 (mp0) cc_final: 0.8213 (mp0)
REVERT: D  364 GLU cc_start: 0.7926 (mt-10) cc_final: 0.7550 (mt-10)
REVERT: D  372 LEU cc_start: 0.8039 (OUTLIER) cc_final: 0.7692 (tp)
REVERT: D  391 TRP cc_start: 0.8192 (m-90) cc_final: 0.7957 (m-90)
REVERT: D  402 GLU cc_start: 0.8343 (mt-10) cc_final: 0.8091 (mm-30)
REVERT: E   81 MET cc_start: 0.8678 (ttp) cc_final: 0.8397 (ptt)
REVERT: E  112 TRP cc_start: 0.8075 (OUTLIER) cc_final: 0.6859 (t-100)
REVERT: E  132 ASP cc_start: 0.7883 (OUTLIER) cc_final: 0.7610 (t0)
REVERT: E  221 GLN cc_start: 0.8505 (pt0) cc_final: 0.8158 (pt0)
REVERT: E  257 ARG cc_start: 0.8906 (ptp90) cc_final: 0.8268 (ptp-110)
REVERT: E  260 GLU cc_start: 0.8939 (pm20) cc_final: 0.8551 (pm20)
REVERT: E  285 SER cc_start: 0.8712 (t) cc_final: 0.8347 (t)
  outliers start: 31
  outliers final: 14
  residues processed: 286
  average time/residue: 1.2865
  time to fit residues: 400.2945
Evaluate side-chains
  261 residues out of total 1430 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 243
  time to evaluate  : 1.547 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  123 LEU
Chi-restraints excluded: chain A residue  275 LEU
Chi-restraints excluded: chain A residue  394 CYS
Chi-restraints excluded: chain B residue  245 LEU
Chi-restraints excluded: chain B residue  372 LEU
Chi-restraints excluded: chain C residue  112 TRP
Chi-restraints excluded: chain C residue  172 SER
Chi-restraints excluded: chain C residue  210 GLN
Chi-restraints excluded: chain C residue  275 LEU
Chi-restraints excluded: chain C residue  306 LEU
Chi-restraints excluded: chain C residue  372 LEU
Chi-restraints excluded: chain D residue  153 THR
Chi-restraints excluded: chain D residue  299 ILE
Chi-restraints excluded: chain D residue  372 LEU
Chi-restraints excluded: chain E residue  112 TRP
Chi-restraints excluded: chain E residue  132 ASP
Chi-restraints excluded: chain E residue  372 LEU
Chi-restraints excluded: chain E residue  373 VAL
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 160
   random chunks:
   chunk 92 optimal weight:    4.9990
   chunk 23 optimal weight:    0.9990
   chunk 128 optimal weight:    5.9990
   chunk 81 optimal weight:    4.9990
   chunk 25 optimal weight:    0.9980
   chunk 43 optimal weight:    0.9990
   chunk 106 optimal weight:    4.9990
   chunk 112 optimal weight:    2.9990
   chunk 75 optimal weight:    0.7980
   chunk 137 optimal weight:    6.9990
   chunk 13 optimal weight:    3.9990
   overall best weight:    1.3586

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3201 r_free = 0.3201 target = 0.094259 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 22)----------------|
| r_work = 0.2960 r_free = 0.2960 target = 0.078375 restraints weight = 20970.186|
|-----------------------------------------------------------------------------|
r_work (start): 0.2943 rms_B_bonded: 3.00
r_work: 0.2784 rms_B_bonded: 3.41 restraints_weight: 0.5000
r_work (final): 0.2784
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2791
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2791 r_free = 0.2791    target_work(ls_wunit_k1) = 0.069         |
| occupancies: max = 1.00  min = 0.85   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2791 r_free = 0.2791    target_work(ls_wunit_k1) = 0.069         |
| occupancies: max = 1.00  min = 0.85   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2791
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7693
moved from start:          0.2832

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.057  13385  Z= 0.258
  Angle     :  0.579  10.472  18305  Z= 0.277
  Chirality :  0.040   0.159   2235
  Planarity :  0.003   0.043   2250
  Dihedral  :  3.893  14.419   2060
  Min Nonbonded Distance : 2.492

Molprobity Statistics.
  All-atom Clashscore : 8.27
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.25 %
    Favored  : 97.75 %
  Rotamer:
    Outliers :  2.94 %
    Allowed  : 16.99 %
    Favored  : 80.07 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.88 %
    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:  1.96 (0.21), residues: 1600
  helix:  3.07 (0.20), residues: 545
  sheet:  0.71 (0.24), residues: 440
  loop :  0.18 (0.27), residues: 615

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.023   0.001   TRP B 112 
 HIS   0.002   0.000   HIS A 276 
 PHE   0.026   0.002   PHE D 385 
 TYR   0.030   0.002   TYR C 176 
 ARG   0.010   0.000   ARG D 257 

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

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

  3200 Ramachandran restraints generated.
    1600 Oldfield, 0 Emsley, 1600 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3200 Ramachandran restraints generated.
    1600 Oldfield, 0 Emsley, 1600 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  291 residues out of total 1430 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 42
    poor density    : 249
  time to evaluate  : 1.603 
Fit side-chains
REVERT: A   75 ASP cc_start: 0.7791 (t0) cc_final: 0.7422 (t0)
REVERT: A  112 TRP cc_start: 0.7986 (OUTLIER) cc_final: 0.7745 (t-100)
REVERT: A  124 GLU cc_start: 0.8390 (mp0) cc_final: 0.7818 (mp0)
REVERT: A  154 GLU cc_start: 0.8675 (tt0) cc_final: 0.8177 (tt0)
REVERT: A  184 GLU cc_start: 0.8377 (pt0) cc_final: 0.8177 (pt0)
REVERT: A  201 GLU cc_start: 0.8591 (mt-10) cc_final: 0.7969 (mp0)
REVERT: A  214 GLN cc_start: 0.8167 (mm-40) cc_final: 0.7934 (pt0)
REVERT: A  260 GLU cc_start: 0.8786 (pm20) cc_final: 0.8302 (pm20)
REVERT: A  364 GLU cc_start: 0.8067 (mt-10) cc_final: 0.7626 (mt-10)
REVERT: A  391 TRP cc_start: 0.8044 (m-90) cc_final: 0.7818 (m-90)
REVERT: B   48 GLU cc_start: 0.8028 (tp30) cc_final: 0.7762 (tp30)
REVERT: B  124 GLU cc_start: 0.8401 (mp0) cc_final: 0.7920 (mp0)
REVERT: B  132 ASP cc_start: 0.7433 (t0) cc_final: 0.7111 (t0)
REVERT: B  146 LYS cc_start: 0.8267 (mtmm) cc_final: 0.7985 (mtpp)
REVERT: B  154 GLU cc_start: 0.8791 (tt0) cc_final: 0.8531 (tt0)
REVERT: B  201 GLU cc_start: 0.8553 (mt-10) cc_final: 0.8000 (mp0)
REVERT: B  214 GLN cc_start: 0.8304 (mm-40) cc_final: 0.8032 (pt0)
REVERT: B  260 GLU cc_start: 0.8782 (pm20) cc_final: 0.8415 (pm20)
REVERT: B  272 TYR cc_start: 0.8562 (t80) cc_final: 0.8285 (t80)
REVERT: B  364 GLU cc_start: 0.7486 (OUTLIER) cc_final: 0.6518 (mp0)
REVERT: B  391 TRP cc_start: 0.8215 (m-90) cc_final: 0.7962 (m-90)
REVERT: C   75 ASP cc_start: 0.7533 (t0) cc_final: 0.6941 (t0)
REVERT: C  112 TRP cc_start: 0.8084 (OUTLIER) cc_final: 0.7420 (t-100)
REVERT: C  124 GLU cc_start: 0.8238 (mp0) cc_final: 0.7977 (mp0)
REVERT: C  132 ASP cc_start: 0.7811 (OUTLIER) cc_final: 0.7455 (t0)
REVERT: C  146 LYS cc_start: 0.8135 (OUTLIER) cc_final: 0.7683 (mtpp)
REVERT: C  154 GLU cc_start: 0.8663 (tt0) cc_final: 0.8300 (tt0)
REVERT: C  188 GLN cc_start: 0.8049 (tt0) cc_final: 0.7435 (tt0)
REVERT: C  201 GLU cc_start: 0.8667 (mt-10) cc_final: 0.8035 (mp0)
REVERT: C  260 GLU cc_start: 0.8931 (pm20) cc_final: 0.8599 (pm20)
REVERT: C  364 GLU cc_start: 0.8060 (mt-10) cc_final: 0.7688 (mt-10)
REVERT: D  113 GLU cc_start: 0.8740 (mp0) cc_final: 0.8431 (mp0)
REVERT: D  364 GLU cc_start: 0.7938 (mt-10) cc_final: 0.7559 (mt-10)
REVERT: D  372 LEU cc_start: 0.8030 (OUTLIER) cc_final: 0.7818 (tt)
REVERT: D  402 GLU cc_start: 0.8339 (mt-10) cc_final: 0.8087 (mm-30)
REVERT: E   81 MET cc_start: 0.8634 (ttp) cc_final: 0.8378 (ptt)
REVERT: E  112 TRP cc_start: 0.8163 (OUTLIER) cc_final: 0.6962 (t-100)
REVERT: E  132 ASP cc_start: 0.7897 (OUTLIER) cc_final: 0.7591 (t0)
REVERT: E  221 GLN cc_start: 0.8521 (pt0) cc_final: 0.8138 (pt0)
REVERT: E  257 ARG cc_start: 0.8896 (ptp90) cc_final: 0.8246 (ptp-110)
REVERT: E  260 GLU cc_start: 0.8928 (pm20) cc_final: 0.8530 (pm20)
REVERT: E  285 SER cc_start: 0.8710 (t) cc_final: 0.8366 (t)
  outliers start: 42
  outliers final: 21
  residues processed: 269
  average time/residue: 1.3519
  time to fit residues: 395.0844
Evaluate side-chains
  276 residues out of total 1430 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 247
  time to evaluate  : 1.651 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  112 TRP
Chi-restraints excluded: chain A residue  123 LEU
Chi-restraints excluded: chain A residue  275 LEU
Chi-restraints excluded: chain A residue  372 LEU
Chi-restraints excluded: chain A residue  373 VAL
Chi-restraints excluded: chain A residue  394 CYS
Chi-restraints excluded: chain B residue  245 LEU
Chi-restraints excluded: chain B residue  364 GLU
Chi-restraints excluded: chain B residue  372 LEU
Chi-restraints excluded: chain C residue  112 TRP
Chi-restraints excluded: chain C residue  132 ASP
Chi-restraints excluded: chain C residue  146 LYS
Chi-restraints excluded: chain C residue  172 SER
Chi-restraints excluded: chain C residue  179 SER
Chi-restraints excluded: chain C residue  210 GLN
Chi-restraints excluded: chain C residue  275 LEU
Chi-restraints excluded: chain C residue  306 LEU
Chi-restraints excluded: chain C residue  372 LEU
Chi-restraints excluded: chain C residue  373 VAL
Chi-restraints excluded: chain D residue  123 LEU
Chi-restraints excluded: chain D residue  153 THR
Chi-restraints excluded: chain D residue  172 SER
Chi-restraints excluded: chain D residue  299 ILE
Chi-restraints excluded: chain D residue  372 LEU
Chi-restraints excluded: chain D residue  373 VAL
Chi-restraints excluded: chain E residue  112 TRP
Chi-restraints excluded: chain E residue  132 ASP
Chi-restraints excluded: chain E residue  372 LEU
Chi-restraints excluded: chain E residue  373 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 160
   random chunks:
   chunk 49 optimal weight:    3.9990
   chunk 23 optimal weight:    0.9980
   chunk 85 optimal weight:    2.9990
   chunk 1 optimal weight:    5.9990
   chunk 127 optimal weight:    0.0980
   chunk 73 optimal weight:    5.9990
   chunk 106 optimal weight:    4.9990
   chunk 136 optimal weight:    3.9990
   chunk 81 optimal weight:    0.9990
   chunk 22 optimal weight:    0.6980
   chunk 8 optimal weight:    3.9990
   overall best weight:    1.1584

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

Flipped N/Q/H residues before XYZ refinement:
D 382 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3192 r_free = 0.3192 target = 0.094007 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.2949 r_free = 0.2949 target = 0.078013 restraints weight = 20908.525|
|-----------------------------------------------------------------------------|
r_work (start): 0.2946 rms_B_bonded: 3.00
r_work: 0.2788 rms_B_bonded: 3.41 restraints_weight: 0.5000
r_work (final): 0.2788
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2797
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2797 r_free = 0.2797    target_work(ls_wunit_k1) = 0.069         |
| occupancies: max = 1.00  min = 0.85   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2797 r_free = 0.2797    target_work(ls_wunit_k1) = 0.069         |
| occupancies: max = 1.00  min = 0.85   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2797
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7687
moved from start:          0.2862

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.034  13385  Z= 0.234
  Angle     :  0.583  10.938  18305  Z= 0.277
  Chirality :  0.040   0.145   2235
  Planarity :  0.004   0.041   2250
  Dihedral  :  3.887  14.349   2060
  Min Nonbonded Distance : 2.492

Molprobity Statistics.
  All-atom Clashscore : 8.04
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.31 %
    Favored  : 97.69 %
  Rotamer:
    Outliers :  2.17 %
    Allowed  : 18.11 %
    Favored  : 79.72 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.88 %
    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:  1.95 (0.21), residues: 1600
  helix:  3.09 (0.20), residues: 545
  sheet:  0.73 (0.24), residues: 420
  loop :  0.12 (0.26), residues: 635

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.023   0.001   TRP B 112 
 HIS   0.001   0.000   HIS A 276 
 PHE   0.024   0.002   PHE D 385 
 TYR   0.034   0.002   TYR E 176 
 ARG   0.010   0.000   ARG D 257 

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

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

  3200 Ramachandran restraints generated.
    1600 Oldfield, 0 Emsley, 1600 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3200 Ramachandran restraints generated.
    1600 Oldfield, 0 Emsley, 1600 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  282 residues out of total 1430 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 251
  time to evaluate  : 1.456 
Fit side-chains
REVERT: A   75 ASP cc_start: 0.7784 (t0) cc_final: 0.7415 (t0)
REVERT: A   81 MET cc_start: 0.8736 (ttp) cc_final: 0.8387 (ptt)
REVERT: A  124 GLU cc_start: 0.8387 (mp0) cc_final: 0.7816 (mp0)
REVERT: A  184 GLU cc_start: 0.8377 (pt0) cc_final: 0.8167 (pt0)
REVERT: A  201 GLU cc_start: 0.8592 (mt-10) cc_final: 0.7964 (mp0)
REVERT: A  260 GLU cc_start: 0.8792 (pm20) cc_final: 0.8309 (pm20)
REVERT: A  364 GLU cc_start: 0.8057 (mt-10) cc_final: 0.7612 (mt-10)
REVERT: A  391 TRP cc_start: 0.8020 (m-90) cc_final: 0.7792 (m-90)
REVERT: B   48 GLU cc_start: 0.8041 (tp30) cc_final: 0.7768 (tp30)
REVERT: B  124 GLU cc_start: 0.8388 (mp0) cc_final: 0.7905 (mp0)
REVERT: B  146 LYS cc_start: 0.8267 (mtmm) cc_final: 0.7985 (mtpp)
REVERT: B  154 GLU cc_start: 0.8797 (tt0) cc_final: 0.8540 (tt0)
REVERT: B  201 GLU cc_start: 0.8550 (mt-10) cc_final: 0.8000 (mp0)
REVERT: B  214 GLN cc_start: 0.8300 (mm-40) cc_final: 0.8031 (pt0)
REVERT: B  260 GLU cc_start: 0.8778 (pm20) cc_final: 0.8409 (pm20)
REVERT: B  272 TYR cc_start: 0.8577 (t80) cc_final: 0.8289 (t80)
REVERT: B  364 GLU cc_start: 0.7478 (mt-10) cc_final: 0.6506 (mp0)
REVERT: B  391 TRP cc_start: 0.8187 (m-90) cc_final: 0.7927 (m-90)
REVERT: C   75 ASP cc_start: 0.7547 (t0) cc_final: 0.7150 (t0)
REVERT: C  123 LEU cc_start: 0.8731 (mt) cc_final: 0.8453 (mt)
REVERT: C  124 GLU cc_start: 0.8338 (mp0) cc_final: 0.8044 (mp0)
REVERT: C  132 ASP cc_start: 0.7765 (OUTLIER) cc_final: 0.7430 (t0)
REVERT: C  154 GLU cc_start: 0.8683 (tt0) cc_final: 0.8297 (tt0)
REVERT: C  188 GLN cc_start: 0.8052 (tt0) cc_final: 0.7440 (tt0)
REVERT: C  201 GLU cc_start: 0.8670 (mt-10) cc_final: 0.8035 (mp0)
REVERT: C  260 GLU cc_start: 0.8932 (pm20) cc_final: 0.8634 (pm20)
REVERT: C  364 GLU cc_start: 0.8069 (mt-10) cc_final: 0.7670 (mt-10)
REVERT: D   81 MET cc_start: 0.8276 (ttp) cc_final: 0.8052 (ttm)
REVERT: D  112 TRP cc_start: 0.8033 (t-100) cc_final: 0.7788 (t-100)
REVERT: D  113 GLU cc_start: 0.8711 (mp0) cc_final: 0.8111 (mp0)
REVERT: D  364 GLU cc_start: 0.7934 (mt-10) cc_final: 0.7550 (mt-10)
REVERT: D  372 LEU cc_start: 0.8021 (OUTLIER) cc_final: 0.7667 (tp)
REVERT: D  402 GLU cc_start: 0.8304 (mt-10) cc_final: 0.8065 (mm-30)
REVERT: E   81 MET cc_start: 0.8627 (ttp) cc_final: 0.8378 (ptt)
REVERT: E  112 TRP cc_start: 0.8141 (OUTLIER) cc_final: 0.6946 (t-100)
REVERT: E  132 ASP cc_start: 0.7855 (OUTLIER) cc_final: 0.7583 (t0)
REVERT: E  221 GLN cc_start: 0.8503 (pt0) cc_final: 0.8162 (pt0)
REVERT: E  257 ARG cc_start: 0.8887 (ptp90) cc_final: 0.8243 (ptp-110)
REVERT: E  260 GLU cc_start: 0.8921 (pm20) cc_final: 0.8518 (pm20)
REVERT: E  285 SER cc_start: 0.8687 (t) cc_final: 0.8348 (t)
  outliers start: 31
  outliers final: 18
  residues processed: 266
  average time/residue: 1.3797
  time to fit residues: 398.5641
Evaluate side-chains
  270 residues out of total 1430 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 248
  time to evaluate  : 1.673 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  123 LEU
Chi-restraints excluded: chain A residue  275 LEU
Chi-restraints excluded: chain A residue  373 VAL
Chi-restraints excluded: chain A residue  394 CYS
Chi-restraints excluded: chain B residue  245 LEU
Chi-restraints excluded: chain B residue  372 LEU
Chi-restraints excluded: chain C residue  132 ASP
Chi-restraints excluded: chain C residue  172 SER
Chi-restraints excluded: chain C residue  210 GLN
Chi-restraints excluded: chain C residue  275 LEU
Chi-restraints excluded: chain C residue  306 LEU
Chi-restraints excluded: chain C residue  372 LEU
Chi-restraints excluded: chain C residue  373 VAL
Chi-restraints excluded: chain D residue  123 LEU
Chi-restraints excluded: chain D residue  153 THR
Chi-restraints excluded: chain D residue  299 ILE
Chi-restraints excluded: chain D residue  372 LEU
Chi-restraints excluded: chain D residue  373 VAL
Chi-restraints excluded: chain E residue  112 TRP
Chi-restraints excluded: chain E residue  132 ASP
Chi-restraints excluded: chain E residue  372 LEU
Chi-restraints excluded: chain E residue  373 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 160
   random chunks:
   chunk 74 optimal weight:    1.9990
   chunk 1 optimal weight:    2.9990
   chunk 88 optimal weight:    0.0670
   chunk 126 optimal weight:    3.9990
   chunk 111 optimal weight:    0.8980
   chunk 10 optimal weight:    3.9990
   chunk 56 optimal weight:    2.9990
   chunk 154 optimal weight:    1.9990
   chunk 36 optimal weight:    0.7980
   chunk 83 optimal weight:    0.9980
   chunk 127 optimal weight:    0.0040
   overall best weight:    0.5530

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3231 r_free = 0.3231 target = 0.096289 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.2991 r_free = 0.2991 target = 0.080338 restraints weight = 20776.476|
|-----------------------------------------------------------------------------|
r_work (start): 0.2977 rms_B_bonded: 3.02
r_work: 0.2819 rms_B_bonded: 3.43 restraints_weight: 0.5000
r_work (final): 0.2819
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2831
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2831 r_free = 0.2831    target_work(ls_wunit_k1) = 0.071         |
| occupancies: max = 1.00  min = 0.85   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2831 r_free = 0.2831    target_work(ls_wunit_k1) = 0.071         |
| occupancies: max = 1.00  min = 0.85   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2831
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7665
moved from start:          0.2880

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035  13385  Z= 0.167
  Angle     :  0.563  10.471  18305  Z= 0.266
  Chirality :  0.039   0.147   2235
  Planarity :  0.003   0.038   2250
  Dihedral  :  3.782  14.958   2060
  Min Nonbonded Distance : 2.513

Molprobity Statistics.
  All-atom Clashscore : 7.77
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.88 %
    Favored  : 98.12 %
  Rotamer:
    Outliers :  1.12 %
    Allowed  : 19.58 %
    Favored  : 79.30 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.88 %
    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:  2.02 (0.21), residues: 1600
  helix:  3.27 (0.20), residues: 540
  sheet:  0.75 (0.24), residues: 420
  loop :  0.09 (0.26), residues: 640

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.023   0.001   TRP C 112 
 HIS   0.001   0.000   HIS A 276 
 PHE   0.020   0.001   PHE A 385 
 TYR   0.030   0.002   TYR E 176 
 ARG   0.010   0.000   ARG D 257 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 8390.04 seconds
wall clock time: 149 minutes 32.37 seconds (8972.37 seconds total)