Starting phenix.real_space_refine
on Wed Mar 12 15:30:16 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/6vx3_21428/03_2025/6vx3_21428_neut.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/6vx3_21428/03_2025/6vx3_21428.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.7
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/6vx3_21428/03_2025/6vx3_21428.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/6vx3_21428/03_2025/6vx3_21428.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/6vx3_21428/03_2025/6vx3_21428_neut.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/6vx3_21428/03_2025/6vx3_21428_neut.cif"
  }
  resolution = 3.7
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.004
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 5
    Type Number    sf(0)   Gaussians
     P       8      5.49       5
     S      24      5.16       5
     C    5336      2.51       5
     N    1188      2.21       5
     O    1224      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 60 residue(s): 0.03s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib"
  Total number of atoms: 7780
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "A"
      Number of atoms: 1841
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 225, 1841
          Classifications: {'peptide': 225}
          Link IDs: {'PTRANS': 7, 'TRANS': 217}
    Chain: "A"
      Number of atoms: 104
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 104
          Unusual residues: {'POV': 2}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
  Restraints were copied for chains:
    C, B, D
  Time building chain proxies: 3.92, per 1000 atoms: 0.50
  Number of scatterers: 7780
  At special positions: 0
  Unit cell: (125.882, 125.882, 65.726, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S      24     16.00
     P       8     15.00
     O    1224      8.00
     N    1188      7.00
     C    5336      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=4, symmetry=0
  Number of additional bonds: simple=4, symmetry=0
  Coordination:
  Other bonds:
  Time building additional restraints: 2.03
  Conformation dependent library (CDL) restraints added in 1.0 seconds
  

  1784 Ramachandran restraints generated.
    892 Oldfield, 0 Emsley, 892 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1728

  Finding SS restraints...
    Secondary structure from input PDB file:
      60 helices and 0 sheets defined
      74.2% alpha, 0.0% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.71
  Creating SS restraints...
    Processing helix  chain 'C' and resid 24 through 43
      removed outlier: 3.554A  pdb=" N   ILE C  42 " --> pdb=" O   LEU C  38 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 45 through 52
    Processing helix  chain 'C' and resid 52 through 76
      removed outlier: 4.310A  pdb=" N   ARG C  58 " --> pdb=" O   TRP C  54 " (cutoff:3.500A)
      removed outlier: 3.938A  pdb=" N   ILE C  59 " --> pdb=" O   LEU C  55 " (cutoff:3.500A)
      removed outlier: 3.630A  pdb=" N   ILE C  69 " --> pdb=" O   TRP C  65 " (cutoff:3.500A)
      removed outlier: 3.590A  pdb=" N   GLU C  70 " --> pdb=" O   ILE C  66 " (cutoff:3.500A)
      removed outlier: 3.872A  pdb=" N   ARG C  74 " --> pdb=" O   GLU C  70 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 90 through 103
    Processing helix  chain 'C' and resid 104 through 106
      No H-bonds generated for 'chain 'C' and resid 104 through 106'
    Processing helix  chain 'C' and resid 110 through 119
      removed outlier: 3.672A  pdb=" N   ILE C 114 " --> pdb=" O   THR C 110 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 120 through 125
    Processing helix  chain 'C' and resid 130 through 140
    Processing helix  chain 'C' and resid 146 through 166
      removed outlier: 3.860A  pdb=" N   PHE C 155 " --> pdb=" O   MET C 151 " (cutoff:3.500A)
      removed outlier: 4.012A  pdb=" N   PHE C 158 " --> pdb=" O   PHE C 154 " (cutoff:3.500A)
      removed outlier: 3.963A  pdb=" N   THR C 163 " --> pdb=" O   ALA C 159 " (cutoff:3.500A)
      removed outlier: 4.122A  pdb=" N   MET C 164 " --> pdb=" O   VAL C 160 " (cutoff:3.500A)
      removed outlier: 3.580A  pdb=" N   LEU C 165 " --> pdb=" O   ILE C 161 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 170 through 175
    Processing helix  chain 'C' and resid 178 through 187
      removed outlier: 4.181A  pdb=" N   LEU C 182 " --> pdb=" O   GLN C 178 " (cutoff:3.500A)
      removed outlier: 3.910A  pdb=" N   THR C 183 " --> pdb=" O   LEU C 179 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 197 through 203
      removed outlier: 4.109A  pdb=" N   ILE C 201 " --> pdb=" O   VAL C 197 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 205 through 207
      No H-bonds generated for 'chain 'C' and resid 205 through 207'
    Processing helix  chain 'C' and resid 208 through 213
      removed outlier: 3.760A  pdb=" N   PHE C 212 " --> pdb=" O   SER C 208 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 221 through 237
      removed outlier: 3.576A  pdb=" N   PHE C 227 " --> pdb=" O   ILE C 223 " (cutoff:3.500A)
      removed outlier: 3.597A  pdb=" N   ASN C 233 " --> pdb=" O   GLY C 229 " (cutoff:3.500A)
      removed outlier: 3.860A  pdb=" N   ASN C 234 " --> pdb=" O   VAL C 230 " (cutoff:3.500A)
      removed outlier: 3.696A  pdb=" N   VAL C 235 " --> pdb=" O   ILE C 231 " (cutoff:3.500A)
      removed outlier: 3.643A  pdb=" N   LYS C 237 " --> pdb=" O   ASN C 233 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 24 through 43
      removed outlier: 3.554A  pdb=" N   ILE A  42 " --> pdb=" O   LEU A  38 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 45 through 52
    Processing helix  chain 'A' and resid 52 through 76
      removed outlier: 4.311A  pdb=" N   ARG A  58 " --> pdb=" O   TRP A  54 " (cutoff:3.500A)
      removed outlier: 3.938A  pdb=" N   ILE A  59 " --> pdb=" O   LEU A  55 " (cutoff:3.500A)
      removed outlier: 3.630A  pdb=" N   ILE A  69 " --> pdb=" O   TRP A  65 " (cutoff:3.500A)
      removed outlier: 3.590A  pdb=" N   GLU A  70 " --> pdb=" O   ILE A  66 " (cutoff:3.500A)
      removed outlier: 3.872A  pdb=" N   ARG A  74 " --> pdb=" O   GLU A  70 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 90 through 103
    Processing helix  chain 'A' and resid 104 through 106
      No H-bonds generated for 'chain 'A' and resid 104 through 106'
    Processing helix  chain 'A' and resid 110 through 119
      removed outlier: 3.672A  pdb=" N   ILE A 114 " --> pdb=" O   THR A 110 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 120 through 125
    Processing helix  chain 'A' and resid 130 through 140
    Processing helix  chain 'A' and resid 146 through 166
      removed outlier: 3.860A  pdb=" N   PHE A 155 " --> pdb=" O   MET A 151 " (cutoff:3.500A)
      removed outlier: 4.012A  pdb=" N   PHE A 158 " --> pdb=" O   PHE A 154 " (cutoff:3.500A)
      removed outlier: 3.964A  pdb=" N   THR A 163 " --> pdb=" O   ALA A 159 " (cutoff:3.500A)
      removed outlier: 4.121A  pdb=" N   MET A 164 " --> pdb=" O   VAL A 160 " (cutoff:3.500A)
      removed outlier: 3.581A  pdb=" N   LEU A 165 " --> pdb=" O   ILE A 161 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 170 through 175
    Processing helix  chain 'A' and resid 178 through 187
      removed outlier: 4.182A  pdb=" N   LEU A 182 " --> pdb=" O   GLN A 178 " (cutoff:3.500A)
      removed outlier: 3.911A  pdb=" N   THR A 183 " --> pdb=" O   LEU A 179 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 197 through 203
      removed outlier: 4.109A  pdb=" N   ILE A 201 " --> pdb=" O   VAL A 197 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 205 through 207
      No H-bonds generated for 'chain 'A' and resid 205 through 207'
    Processing helix  chain 'A' and resid 208 through 213
      removed outlier: 3.760A  pdb=" N   PHE A 212 " --> pdb=" O   SER A 208 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 221 through 237
      removed outlier: 3.576A  pdb=" N   PHE A 227 " --> pdb=" O   ILE A 223 " (cutoff:3.500A)
      removed outlier: 3.596A  pdb=" N   ASN A 233 " --> pdb=" O   GLY A 229 " (cutoff:3.500A)
      removed outlier: 3.861A  pdb=" N   ASN A 234 " --> pdb=" O   VAL A 230 " (cutoff:3.500A)
      removed outlier: 3.696A  pdb=" N   VAL A 235 " --> pdb=" O   ILE A 231 " (cutoff:3.500A)
      removed outlier: 3.643A  pdb=" N   LYS A 237 " --> pdb=" O   ASN A 233 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 24 through 43
      removed outlier: 3.553A  pdb=" N   ILE B  42 " --> pdb=" O   LEU B  38 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 45 through 52
    Processing helix  chain 'B' and resid 52 through 76
      removed outlier: 4.310A  pdb=" N   ARG B  58 " --> pdb=" O   TRP B  54 " (cutoff:3.500A)
      removed outlier: 3.938A  pdb=" N   ILE B  59 " --> pdb=" O   LEU B  55 " (cutoff:3.500A)
      removed outlier: 3.630A  pdb=" N   ILE B  69 " --> pdb=" O   TRP B  65 " (cutoff:3.500A)
      removed outlier: 3.590A  pdb=" N   GLU B  70 " --> pdb=" O   ILE B  66 " (cutoff:3.500A)
      removed outlier: 3.872A  pdb=" N   ARG B  74 " --> pdb=" O   GLU B  70 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 90 through 103
    Processing helix  chain 'B' and resid 104 through 106
      No H-bonds generated for 'chain 'B' and resid 104 through 106'
    Processing helix  chain 'B' and resid 110 through 119
      removed outlier: 3.671A  pdb=" N   ILE B 114 " --> pdb=" O   THR B 110 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 120 through 125
    Processing helix  chain 'B' and resid 130 through 140
    Processing helix  chain 'B' and resid 146 through 166
      removed outlier: 3.861A  pdb=" N   PHE B 155 " --> pdb=" O   MET B 151 " (cutoff:3.500A)
      removed outlier: 4.011A  pdb=" N   PHE B 158 " --> pdb=" O   PHE B 154 " (cutoff:3.500A)
      removed outlier: 3.964A  pdb=" N   THR B 163 " --> pdb=" O   ALA B 159 " (cutoff:3.500A)
      removed outlier: 4.122A  pdb=" N   MET B 164 " --> pdb=" O   VAL B 160 " (cutoff:3.500A)
      removed outlier: 3.580A  pdb=" N   LEU B 165 " --> pdb=" O   ILE B 161 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 170 through 175
    Processing helix  chain 'B' and resid 178 through 187
      removed outlier: 4.182A  pdb=" N   LEU B 182 " --> pdb=" O   GLN B 178 " (cutoff:3.500A)
      removed outlier: 3.910A  pdb=" N   THR B 183 " --> pdb=" O   LEU B 179 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 197 through 203
      removed outlier: 4.109A  pdb=" N   ILE B 201 " --> pdb=" O   VAL B 197 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 205 through 207
      No H-bonds generated for 'chain 'B' and resid 205 through 207'
    Processing helix  chain 'B' and resid 208 through 213
      removed outlier: 3.761A  pdb=" N   PHE B 212 " --> pdb=" O   SER B 208 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 221 through 237
      removed outlier: 3.577A  pdb=" N   PHE B 227 " --> pdb=" O   ILE B 223 " (cutoff:3.500A)
      removed outlier: 3.596A  pdb=" N   ASN B 233 " --> pdb=" O   GLY B 229 " (cutoff:3.500A)
      removed outlier: 3.860A  pdb=" N   ASN B 234 " --> pdb=" O   VAL B 230 " (cutoff:3.500A)
      removed outlier: 3.695A  pdb=" N   VAL B 235 " --> pdb=" O   ILE B 231 " (cutoff:3.500A)
      removed outlier: 3.643A  pdb=" N   LYS B 237 " --> pdb=" O   ASN B 233 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 24 through 43
      removed outlier: 3.553A  pdb=" N   ILE D  42 " --> pdb=" O   LEU D  38 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 45 through 52
    Processing helix  chain 'D' and resid 52 through 76
      removed outlier: 4.310A  pdb=" N   ARG D  58 " --> pdb=" O   TRP D  54 " (cutoff:3.500A)
      removed outlier: 3.938A  pdb=" N   ILE D  59 " --> pdb=" O   LEU D  55 " (cutoff:3.500A)
      removed outlier: 3.630A  pdb=" N   ILE D  69 " --> pdb=" O   TRP D  65 " (cutoff:3.500A)
      removed outlier: 3.590A  pdb=" N   GLU D  70 " --> pdb=" O   ILE D  66 " (cutoff:3.500A)
      removed outlier: 3.872A  pdb=" N   ARG D  74 " --> pdb=" O   GLU D  70 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 90 through 103
    Processing helix  chain 'D' and resid 104 through 106
      No H-bonds generated for 'chain 'D' and resid 104 through 106'
    Processing helix  chain 'D' and resid 110 through 119
      removed outlier: 3.672A  pdb=" N   ILE D 114 " --> pdb=" O   THR D 110 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 120 through 125
    Processing helix  chain 'D' and resid 130 through 140
    Processing helix  chain 'D' and resid 146 through 166
      removed outlier: 3.860A  pdb=" N   PHE D 155 " --> pdb=" O   MET D 151 " (cutoff:3.500A)
      removed outlier: 4.011A  pdb=" N   PHE D 158 " --> pdb=" O   PHE D 154 " (cutoff:3.500A)
      removed outlier: 3.963A  pdb=" N   THR D 163 " --> pdb=" O   ALA D 159 " (cutoff:3.500A)
      removed outlier: 4.122A  pdb=" N   MET D 164 " --> pdb=" O   VAL D 160 " (cutoff:3.500A)
      removed outlier: 3.580A  pdb=" N   LEU D 165 " --> pdb=" O   ILE D 161 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 170 through 175
    Processing helix  chain 'D' and resid 178 through 187
      removed outlier: 4.181A  pdb=" N   LEU D 182 " --> pdb=" O   GLN D 178 " (cutoff:3.500A)
      removed outlier: 3.909A  pdb=" N   THR D 183 " --> pdb=" O   LEU D 179 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 197 through 203
      removed outlier: 4.109A  pdb=" N   ILE D 201 " --> pdb=" O   VAL D 197 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 205 through 207
      No H-bonds generated for 'chain 'D' and resid 205 through 207'
    Processing helix  chain 'D' and resid 208 through 213
      removed outlier: 3.760A  pdb=" N   PHE D 212 " --> pdb=" O   SER D 208 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 221 through 237
      removed outlier: 3.577A  pdb=" N   PHE D 227 " --> pdb=" O   ILE D 223 " (cutoff:3.500A)
      removed outlier: 3.597A  pdb=" N   ASN D 233 " --> pdb=" O   GLY D 229 " (cutoff:3.500A)
      removed outlier: 3.860A  pdb=" N   ASN D 234 " --> pdb=" O   VAL D 230 " (cutoff:3.500A)
      removed outlier: 3.696A  pdb=" N   VAL D 235 " --> pdb=" O   ILE D 231 " (cutoff:3.500A)
      removed outlier: 3.643A  pdb=" N   LYS D 237 " --> pdb=" O   ASN D 233 " (cutoff:3.500A)

    356 hydrogen bonds defined for protein.
    1032 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 1.74

  Time building geometry restraints manager: 2.40 seconds

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

  Histogram of bond lengths:
        1.22 -     1.33: 1914
        1.33 -     1.45: 1531
        1.45 -     1.57: 4479
        1.57 -     1.69: 16
        1.69 -     1.80: 48
  Bond restraints: 7988
  Sorted by residual:
  bond pdb=" C31 POV A 301 "
       pdb=" O31 POV A 301 "
    ideal  model  delta    sigma   weight residual
    1.327  1.454 -0.127 2.00e-02 2.50e+03 4.02e+01
  bond pdb=" C31 POV C 301 "
       pdb=" O31 POV C 301 "
    ideal  model  delta    sigma   weight residual
    1.327  1.453 -0.126 2.00e-02 2.50e+03 3.99e+01
  bond pdb=" C31 POV B 301 "
       pdb=" O31 POV B 301 "
    ideal  model  delta    sigma   weight residual
    1.327  1.453 -0.126 2.00e-02 2.50e+03 3.98e+01
  bond pdb=" C31 POV D 301 "
       pdb=" O31 POV D 301 "
    ideal  model  delta    sigma   weight residual
    1.327  1.453 -0.126 2.00e-02 2.50e+03 3.97e+01
  bond pdb=" C31 POV A 302 "
       pdb=" O31 POV A 302 "
    ideal  model  delta    sigma   weight residual
    1.327  1.451 -0.124 2.00e-02 2.50e+03 3.81e+01
  ... (remaining 7983 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.05: 10241
        2.05 -     4.11: 395
        4.11 -     6.16: 104
        6.16 -     8.21: 44
        8.21 -    10.26: 20
  Bond angle restraints: 10804
  Sorted by residual:
  angle pdb=" C   PHE D  67 "
        pdb=" N   THR D  68 "
        pdb=" CA  THR D  68 "
      ideal   model   delta    sigma   weight residual
     120.82  127.73   -6.91 1.50e+00 4.44e-01 2.12e+01
  angle pdb=" C   PHE A  67 "
        pdb=" N   THR A  68 "
        pdb=" CA  THR A  68 "
      ideal   model   delta    sigma   weight residual
     120.82  127.70   -6.88 1.50e+00 4.44e-01 2.10e+01
  angle pdb=" C   PHE C  67 "
        pdb=" N   THR C  68 "
        pdb=" CA  THR C  68 "
      ideal   model   delta    sigma   weight residual
     120.82  127.69   -6.87 1.50e+00 4.44e-01 2.10e+01
  angle pdb=" N   ILE D  59 "
        pdb=" CA  ILE D  59 "
        pdb=" C   ILE D  59 "
      ideal   model   delta    sigma   weight residual
     110.72  115.33   -4.61 1.01e+00 9.80e-01 2.08e+01
  angle pdb=" C   PHE B  67 "
        pdb=" N   THR B  68 "
        pdb=" CA  THR B  68 "
      ideal   model   delta    sigma   weight residual
     120.82  127.66   -6.84 1.50e+00 4.44e-01 2.08e+01
  ... (remaining 10799 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    22.06: 4112
       22.06 -    44.12: 436
       44.12 -    66.18: 84
       66.18 -    88.23: 28
       88.23 -   110.29: 8
  Dihedral angle restraints: 4668
    sinusoidal: 2020
      harmonic: 2648
  Sorted by residual:
  dihedral pdb=" C29 POV C 301 "
           pdb="C210 POV C 301 "
           pdb="C211 POV C 301 "
           pdb="C212 POV C 301 "
      ideal   model   delta sinusoidal    sigma   weight residual
     112.25 -137.46 -110.29     1      3.00e+01 1.11e-03 1.44e+01
  dihedral pdb=" C29 POV A 301 "
           pdb="C210 POV A 301 "
           pdb="C211 POV A 301 "
           pdb="C212 POV A 301 "
      ideal   model   delta sinusoidal    sigma   weight residual
     112.25 -137.46 -110.29     1      3.00e+01 1.11e-03 1.44e+01
  dihedral pdb=" C29 POV D 301 "
           pdb="C210 POV D 301 "
           pdb="C211 POV D 301 "
           pdb="C212 POV D 301 "
      ideal   model   delta sinusoidal    sigma   weight residual
     112.25 -137.47 -110.28     1      3.00e+01 1.11e-03 1.44e+01
  ... (remaining 4665 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.036: 691
       0.036 -    0.072: 381
       0.072 -    0.108: 127
       0.108 -    0.145: 21
       0.145 -    0.181: 12
  Chirality restraints: 1232
  Sorted by residual:
  chirality pdb=" CA  LEU A 177 "
            pdb=" N   LEU A 177 "
            pdb=" C   LEU A 177 "
            pdb=" CB  LEU A 177 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.33    0.18 2.00e-01 2.50e+01 8.17e-01
  chirality pdb=" CA  LEU C 177 "
            pdb=" N   LEU C 177 "
            pdb=" C   LEU C 177 "
            pdb=" CB  LEU C 177 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.33    0.18 2.00e-01 2.50e+01 8.07e-01
  chirality pdb=" CA  LEU B 177 "
            pdb=" N   LEU B 177 "
            pdb=" C   LEU B 177 "
            pdb=" CB  LEU B 177 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.33    0.18 2.00e-01 2.50e+01 7.95e-01
  ... (remaining 1229 not shown)

  Planarity restraints: 1256
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  LEU B  64 "    0.015 2.00e-02 2.50e+03   2.96e-02 8.73e+00
        pdb=" C   LEU B  64 "   -0.051 2.00e-02 2.50e+03
        pdb=" O   LEU B  64 "    0.019 2.00e-02 2.50e+03
        pdb=" N   TRP B  65 "    0.017 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  LEU D  64 "    0.015 2.00e-02 2.50e+03   2.94e-02 8.66e+00
        pdb=" C   LEU D  64 "   -0.051 2.00e-02 2.50e+03
        pdb=" O   LEU D  64 "    0.019 2.00e-02 2.50e+03
        pdb=" N   TRP D  65 "    0.017 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  LEU C  64 "   -0.015 2.00e-02 2.50e+03   2.94e-02 8.64e+00
        pdb=" C   LEU C  64 "    0.051 2.00e-02 2.50e+03
        pdb=" O   LEU C  64 "   -0.019 2.00e-02 2.50e+03
        pdb=" N   TRP C  65 "   -0.017 2.00e-02 2.50e+03
  ... (remaining 1253 not shown)

  Histogram of nonbonded interaction distances:
        1.83 -     2.44: 48
        2.44 -     3.06: 5553
        3.06 -     3.67: 10767
        3.67 -     4.29: 15929
        4.29 -     4.90: 26155
  Nonbonded interactions: 58452
  Sorted by model distance:
  nonbonded pdb=" OD2 ASP D  60 "
            pdb=" NH2 ARG D 116 "
     model   vdw
     1.829 3.120
  nonbonded pdb=" OD2 ASP A  60 "
            pdb=" NH2 ARG A 116 "
     model   vdw
     1.829 3.120
  nonbonded pdb=" OD2 ASP C  60 "
            pdb=" NH2 ARG C 116 "
     model   vdw
     1.829 3.120
  nonbonded pdb=" OD2 ASP B  60 "
            pdb=" NH2 ARG B 116 "
     model   vdw
     1.830 3.120
  nonbonded pdb=" O   GLN D 178 "
            pdb=" O32 POV D 302 "
     model   vdw
     2.014 3.040
  ... (remaining 58447 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: 0.05
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'C'
  selection = chain 'B'
  selection = chain 'D'
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             1.420
  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:          0.290
  Check model and map are aligned:         0.060
  Set scattering table:                    0.090
  Process input model:                     18.820
  Find NCS groups from input model:        0.130
  Set up NCS constraints:                  0.010
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:2.580
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   23.410
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7989
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      :  0.009   0.127   7988  Z= 0.581
  Angle     :  1.110  10.264  10804  Z= 0.573
  Chirality :  0.049   0.181   1232
  Planarity :  0.004   0.030   1256
  Dihedral  : 19.669 110.293   2940
  Min Nonbonded Distance : 1.829

Molprobity Statistics.
  All-atom Clashscore : 25.97
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.40 %
    Favored  : 92.60 %
  Rotamer:
    Outliers :  4.02 %
    Allowed  : 10.55 %
    Favored  : 85.43 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -4.21 (0.24), residues: 892
  helix: -2.22 (0.18), residues: 580
  sheet:  None (None), residues: 0
  loop : -3.72 (0.30), residues: 312

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP C  91 
 HIS   0.003   0.001   HIS D  22 
 PHE   0.023   0.002   PHE D 155 
 TYR   0.008   0.001   TYR C 173 
 ARG   0.001   0.000   ARG B  74 

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

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

  1784 Ramachandran restraints generated.
    892 Oldfield, 0 Emsley, 892 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1784 Ramachandran restraints generated.
    892 Oldfield, 0 Emsley, 892 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  232 residues out of total 796 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 200
  time to evaluate  : 0.822 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: C   48 ILE cc_start: 0.8702 (OUTLIER) cc_final: 0.8310 (mm)
REVERT: C   57 TYR cc_start: 0.6466 (OUTLIER) cc_final: 0.5184 (t80)
REVERT: C  191 GLU cc_start: 0.8749 (tm-30) cc_final: 0.8352 (tm-30)
REVERT: C  224 PHE cc_start: 0.7177 (t80) cc_final: 0.6607 (t80)
REVERT: C  234 ASN cc_start: 0.8423 (t0) cc_final: 0.8048 (t0)
REVERT: A   48 ILE cc_start: 0.8701 (OUTLIER) cc_final: 0.8334 (mm)
REVERT: A   57 TYR cc_start: 0.6508 (OUTLIER) cc_final: 0.5307 (t80)
REVERT: A  191 GLU cc_start: 0.8716 (tm-30) cc_final: 0.8357 (tm-30)
REVERT: A  224 PHE cc_start: 0.7025 (t80) cc_final: 0.6623 (t80)
REVERT: B   48 ILE cc_start: 0.8738 (OUTLIER) cc_final: 0.8348 (mm)
REVERT: B   57 TYR cc_start: 0.6634 (OUTLIER) cc_final: 0.5536 (t80)
REVERT: B   63 LEU cc_start: 0.8927 (OUTLIER) cc_final: 0.8594 (mm)
REVERT: B  191 GLU cc_start: 0.8723 (tm-30) cc_final: 0.8063 (tm-30)
REVERT: D   48 ILE cc_start: 0.8729 (OUTLIER) cc_final: 0.8320 (mm)
REVERT: D   57 TYR cc_start: 0.6457 (OUTLIER) cc_final: 0.5180 (t80)
REVERT: D  191 GLU cc_start: 0.8750 (tm-30) cc_final: 0.8144 (tm-30)
REVERT: D  224 PHE cc_start: 0.7133 (t80) cc_final: 0.6883 (t80)
  outliers start: 32
  outliers final: 14
  residues processed: 220
  average time/residue: 0.1320
  time to fit residues: 43.0227
Evaluate side-chains
  177 residues out of total 796 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 154
  time to evaluate  : 0.819 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue   48 ILE
Chi-restraints excluded: chain C residue   57 TYR
Chi-restraints excluded: chain C residue   63 LEU
Chi-restraints excluded: chain C residue   64 LEU
Chi-restraints excluded: chain C residue   65 TRP
Chi-restraints excluded: chain A residue   48 ILE
Chi-restraints excluded: chain A residue   55 LEU
Chi-restraints excluded: chain A residue   57 TYR
Chi-restraints excluded: chain A residue   63 LEU
Chi-restraints excluded: chain A residue   64 LEU
Chi-restraints excluded: chain A residue   65 TRP
Chi-restraints excluded: chain B residue   48 ILE
Chi-restraints excluded: chain B residue   55 LEU
Chi-restraints excluded: chain B residue   57 TYR
Chi-restraints excluded: chain B residue   63 LEU
Chi-restraints excluded: chain B residue   64 LEU
Chi-restraints excluded: chain B residue   65 TRP
Chi-restraints excluded: chain D residue   48 ILE
Chi-restraints excluded: chain D residue   55 LEU
Chi-restraints excluded: chain D residue   57 TYR
Chi-restraints excluded: chain D residue   63 LEU
Chi-restraints excluded: chain D residue   64 LEU
Chi-restraints excluded: chain D residue   65 TRP
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 88
   random chunks:
   chunk 74 optimal weight:    1.9990
   chunk 66 optimal weight:   20.0000
   chunk 37 optimal weight:    0.0020
   chunk 22 optimal weight:   20.0000
   chunk 44 optimal weight:   20.0000
   chunk 35 optimal weight:    0.7980
   chunk 68 optimal weight:    0.9990
   chunk 26 optimal weight:    5.9990
   chunk 41 optimal weight:    0.8980
   chunk 51 optimal weight:    6.9990
   chunk 79 optimal weight:    1.9990
   overall best weight:    0.9392

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

Flipped N/Q/H residues before XYZ refinement:
C 225 ASN
A  52 HIS
B  52 HIS
B 225 ASN
D  52 HIS
D 225 ASN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3739 r_free = 0.3739 target = 0.147814 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3294 r_free = 0.3294 target = 0.111683 restraints weight = 12000.728|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3335 r_free = 0.3335 target = 0.114833 restraints weight = 7014.243|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 42)----------------|
| r_work = 0.3363 r_free = 0.3363 target = 0.116961 restraints weight = 5017.159|
|-----------------------------------------------------------------------------|
r_work (final): 0.3349
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7909
moved from start:          0.1977

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.036   7988  Z= 0.233
  Angle     :  0.623   8.686  10804  Z= 0.314
  Chirality :  0.042   0.123   1232
  Planarity :  0.003   0.023   1256
  Dihedral  : 20.430 112.039   1358
  Min Nonbonded Distance : 2.451

Molprobity Statistics.
  All-atom Clashscore : 8.14
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.38 %
    Favored  : 94.62 %
  Rotamer:
    Outliers :  4.52 %
    Allowed  : 19.60 %
    Favored  : 75.88 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -3.12 (0.25), residues: 892
  helix: -1.48 (0.19), residues: 636
  sheet:  None (None), residues: 0
  loop : -3.30 (0.34), residues: 256

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP C  54 
 HIS   0.005   0.002   HIS B 101 
 PHE   0.013   0.001   PHE B 224 
 TYR   0.005   0.001   TYR C 173 
 ARG   0.002   0.000   ARG C 116 

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

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

  1784 Ramachandran restraints generated.
    892 Oldfield, 0 Emsley, 892 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1784 Ramachandran restraints generated.
    892 Oldfield, 0 Emsley, 892 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  219 residues out of total 796 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 183
  time to evaluate  : 0.845 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: C   35 PHE cc_start: 0.8852 (t80) cc_final: 0.8511 (t80)
REVERT: C   57 TYR cc_start: 0.6716 (OUTLIER) cc_final: 0.5449 (t80)
REVERT: C   65 TRP cc_start: 0.5850 (OUTLIER) cc_final: 0.4367 (t60)
REVERT: C  139 MET cc_start: 0.8098 (tpp) cc_final: 0.7700 (tpp)
REVERT: C  191 GLU cc_start: 0.8700 (tm-30) cc_final: 0.8357 (tm-30)
REVERT: C  201 ILE cc_start: 0.8908 (OUTLIER) cc_final: 0.8660 (mt)
REVERT: A   35 PHE cc_start: 0.8874 (t80) cc_final: 0.8491 (t80)
REVERT: A   52 HIS cc_start: 0.6583 (OUTLIER) cc_final: 0.5901 (m-70)
REVERT: A   57 TYR cc_start: 0.6826 (OUTLIER) cc_final: 0.5696 (t80)
REVERT: A   63 LEU cc_start: 0.9184 (OUTLIER) cc_final: 0.8774 (mm)
REVERT: A   65 TRP cc_start: 0.5789 (OUTLIER) cc_final: 0.4306 (t60)
REVERT: A  139 MET cc_start: 0.8269 (tpp) cc_final: 0.7766 (tpp)
REVERT: A  191 GLU cc_start: 0.8694 (tm-30) cc_final: 0.8326 (tm-30)
REVERT: A  201 ILE cc_start: 0.8878 (OUTLIER) cc_final: 0.8611 (mt)
REVERT: B   35 PHE cc_start: 0.8762 (t80) cc_final: 0.8376 (t80)
REVERT: B   52 HIS cc_start: 0.6387 (OUTLIER) cc_final: 0.5710 (m-70)
REVERT: B   57 TYR cc_start: 0.6772 (OUTLIER) cc_final: 0.5541 (t80)
REVERT: B   65 TRP cc_start: 0.5786 (OUTLIER) cc_final: 0.4325 (t60)
REVERT: B  191 GLU cc_start: 0.8706 (tm-30) cc_final: 0.8126 (tm-30)
REVERT: B  201 ILE cc_start: 0.8837 (OUTLIER) cc_final: 0.8568 (mt)
REVERT: D   35 PHE cc_start: 0.8831 (t80) cc_final: 0.8435 (t80)
REVERT: D   52 HIS cc_start: 0.6462 (OUTLIER) cc_final: 0.5805 (m-70)
REVERT: D   57 TYR cc_start: 0.6752 (OUTLIER) cc_final: 0.5513 (t80)
REVERT: D   65 TRP cc_start: 0.5770 (OUTLIER) cc_final: 0.4285 (t60)
REVERT: D  191 GLU cc_start: 0.8698 (tm-30) cc_final: 0.8155 (tm-30)
REVERT: D  201 ILE cc_start: 0.8833 (OUTLIER) cc_final: 0.8565 (mt)
REVERT: D  224 PHE cc_start: 0.6859 (t80) cc_final: 0.6653 (t80)
  outliers start: 36
  outliers final: 17
  residues processed: 199
  average time/residue: 0.1624
  time to fit residues: 46.1807
Evaluate side-chains
  187 residues out of total 796 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 154
  time to evaluate  : 0.856 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue   16 MET
Chi-restraints excluded: chain C residue   27 PHE
Chi-restraints excluded: chain C residue   57 TYR
Chi-restraints excluded: chain C residue   65 TRP
Chi-restraints excluded: chain C residue  111 VAL
Chi-restraints excluded: chain C residue  201 ILE
Chi-restraints excluded: chain C residue  230 VAL
Chi-restraints excluded: chain A residue   16 MET
Chi-restraints excluded: chain A residue   27 PHE
Chi-restraints excluded: chain A residue   52 HIS
Chi-restraints excluded: chain A residue   57 TYR
Chi-restraints excluded: chain A residue   63 LEU
Chi-restraints excluded: chain A residue   65 TRP
Chi-restraints excluded: chain A residue  111 VAL
Chi-restraints excluded: chain A residue  201 ILE
Chi-restraints excluded: chain A residue  230 VAL
Chi-restraints excluded: chain B residue   16 MET
Chi-restraints excluded: chain B residue   27 PHE
Chi-restraints excluded: chain B residue   52 HIS
Chi-restraints excluded: chain B residue   57 TYR
Chi-restraints excluded: chain B residue   65 TRP
Chi-restraints excluded: chain B residue  111 VAL
Chi-restraints excluded: chain B residue  201 ILE
Chi-restraints excluded: chain B residue  230 VAL
Chi-restraints excluded: chain D residue   16 MET
Chi-restraints excluded: chain D residue   27 PHE
Chi-restraints excluded: chain D residue   34 LEU
Chi-restraints excluded: chain D residue   52 HIS
Chi-restraints excluded: chain D residue   57 TYR
Chi-restraints excluded: chain D residue   65 TRP
Chi-restraints excluded: chain D residue  111 VAL
Chi-restraints excluded: chain D residue  201 ILE
Chi-restraints excluded: chain D residue  230 VAL
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 88
   random chunks:
   chunk 60 optimal weight:    2.9990
   chunk 72 optimal weight:    1.9990
   chunk 11 optimal weight:    6.9990
   chunk 78 optimal weight:    0.8980
   chunk 15 optimal weight:    1.9990
   chunk 37 optimal weight:    1.9990
   chunk 87 optimal weight:    0.6980
   chunk 54 optimal weight:    0.6980
   chunk 46 optimal weight:    1.9990
   chunk 3 optimal weight:    7.9990
   chunk 53 optimal weight:    3.9990
   overall best weight:    1.2584

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

Flipped N/Q/H residues before XYZ refinement:
C 101 HIS
C 225 ASN
A 101 HIS
A 225 ASN
B 101 HIS
B 225 ASN
D 101 HIS
D 225 ASN

Total number of N/Q/H flips: 8

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3724 r_free = 0.3724 target = 0.146582 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3263 r_free = 0.3263 target = 0.109478 restraints weight = 12301.505|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3302 r_free = 0.3302 target = 0.112426 restraints weight = 7367.484|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.3328 r_free = 0.3328 target = 0.114355 restraints weight = 5410.432|
|-----------------------------------------------------------------------------|
r_work (final): 0.3304
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7943
moved from start:          0.2472

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.031   7988  Z= 0.264
  Angle     :  0.595   6.654  10804  Z= 0.303
  Chirality :  0.042   0.107   1232
  Planarity :  0.003   0.029   1256
  Dihedral  : 19.372 110.475   1330
  Min Nonbonded Distance : 2.488

Molprobity Statistics.
  All-atom Clashscore : 9.32
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.93 %
    Favored  : 95.07 %
  Rotamer:
    Outliers :  6.28 %
    Allowed  : 21.98 %
    Favored  : 71.73 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.49 (0.27), residues: 892
  helix: -1.07 (0.20), residues: 636
  sheet:  None (None), residues: 0
  loop : -2.89 (0.36), residues: 256

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP C  54 
 HIS   0.008   0.002   HIS D  52 
 PHE   0.015   0.001   PHE B 224 
 TYR   0.009   0.001   TYR C  49 
 ARG   0.006   0.001   ARG B 122 

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

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

  1784 Ramachandran restraints generated.
    892 Oldfield, 0 Emsley, 892 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1784 Ramachandran restraints generated.
    892 Oldfield, 0 Emsley, 892 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  231 residues out of total 796 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 50
    poor density    : 181
  time to evaluate  : 0.749 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: C   35 PHE cc_start: 0.8850 (t80) cc_final: 0.8436 (t80)
REVERT: C   57 TYR cc_start: 0.6891 (OUTLIER) cc_final: 0.5700 (t80)
REVERT: C   59 ILE cc_start: 0.8677 (tp) cc_final: 0.8476 (tp)
REVERT: C   65 TRP cc_start: 0.6294 (OUTLIER) cc_final: 0.4430 (t60)
REVERT: C  139 MET cc_start: 0.8206 (tpp) cc_final: 0.7818 (tpp)
REVERT: C  191 GLU cc_start: 0.8688 (tm-30) cc_final: 0.8349 (tm-30)
REVERT: A   57 TYR cc_start: 0.6878 (OUTLIER) cc_final: 0.5698 (t80)
REVERT: A   65 TRP cc_start: 0.6122 (OUTLIER) cc_final: 0.4476 (t60)
REVERT: A  139 MET cc_start: 0.8320 (tpp) cc_final: 0.7783 (tpp)
REVERT: A  191 GLU cc_start: 0.8666 (tm-30) cc_final: 0.8281 (tm-30)
REVERT: B   57 TYR cc_start: 0.6877 (OUTLIER) cc_final: 0.5645 (t80)
REVERT: B   59 ILE cc_start: 0.8677 (tp) cc_final: 0.8417 (tp)
REVERT: B   63 LEU cc_start: 0.9119 (OUTLIER) cc_final: 0.8818 (mm)
REVERT: B   65 TRP cc_start: 0.6124 (OUTLIER) cc_final: 0.4394 (t60)
REVERT: B  191 GLU cc_start: 0.8674 (tm-30) cc_final: 0.8082 (tm-30)
REVERT: D   35 PHE cc_start: 0.8818 (t80) cc_final: 0.8353 (t80)
REVERT: D   57 TYR cc_start: 0.6803 (OUTLIER) cc_final: 0.5560 (t80)
REVERT: D   59 ILE cc_start: 0.8699 (tp) cc_final: 0.8486 (tp)
REVERT: D   63 LEU cc_start: 0.9123 (OUTLIER) cc_final: 0.8857 (mm)
REVERT: D   65 TRP cc_start: 0.6270 (OUTLIER) cc_final: 0.4389 (t60)
REVERT: D  191 GLU cc_start: 0.8687 (tm-30) cc_final: 0.8145 (tm-30)
  outliers start: 50
  outliers final: 30
  residues processed: 203
  average time/residue: 0.1707
  time to fit residues: 47.5918
Evaluate side-chains
  214 residues out of total 796 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 40
    poor density    : 174
  time to evaluate  : 0.759 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue   16 MET
Chi-restraints excluded: chain C residue   27 PHE
Chi-restraints excluded: chain C residue   34 LEU
Chi-restraints excluded: chain C residue   51 ASP
Chi-restraints excluded: chain C residue   57 TYR
Chi-restraints excluded: chain C residue   65 TRP
Chi-restraints excluded: chain C residue  109 VAL
Chi-restraints excluded: chain C residue  111 VAL
Chi-restraints excluded: chain C residue  188 VAL
Chi-restraints excluded: chain C residue  230 VAL
Chi-restraints excluded: chain A residue   16 MET
Chi-restraints excluded: chain A residue   27 PHE
Chi-restraints excluded: chain A residue   34 LEU
Chi-restraints excluded: chain A residue   57 TYR
Chi-restraints excluded: chain A residue   65 TRP
Chi-restraints excluded: chain A residue  109 VAL
Chi-restraints excluded: chain A residue  111 VAL
Chi-restraints excluded: chain A residue  188 VAL
Chi-restraints excluded: chain A residue  230 VAL
Chi-restraints excluded: chain B residue   16 MET
Chi-restraints excluded: chain B residue   27 PHE
Chi-restraints excluded: chain B residue   34 LEU
Chi-restraints excluded: chain B residue   57 TYR
Chi-restraints excluded: chain B residue   63 LEU
Chi-restraints excluded: chain B residue   65 TRP
Chi-restraints excluded: chain B residue  109 VAL
Chi-restraints excluded: chain B residue  111 VAL
Chi-restraints excluded: chain B residue  164 MET
Chi-restraints excluded: chain B residue  188 VAL
Chi-restraints excluded: chain B residue  230 VAL
Chi-restraints excluded: chain D residue   16 MET
Chi-restraints excluded: chain D residue   27 PHE
Chi-restraints excluded: chain D residue   34 LEU
Chi-restraints excluded: chain D residue   57 TYR
Chi-restraints excluded: chain D residue   63 LEU
Chi-restraints excluded: chain D residue   65 TRP
Chi-restraints excluded: chain D residue  111 VAL
Chi-restraints excluded: chain D residue  147 ILE
Chi-restraints excluded: chain D residue  188 VAL
Chi-restraints excluded: chain D residue  230 VAL
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 88
   random chunks:
   chunk 50 optimal weight:    5.9990
   chunk 27 optimal weight:    0.9990
   chunk 5 optimal weight:    1.9990
   chunk 84 optimal weight:    2.9990
   chunk 75 optimal weight:    4.9990
   chunk 58 optimal weight:    0.7980
   chunk 44 optimal weight:   10.0000
   chunk 67 optimal weight:    0.8980
   chunk 31 optimal weight:    4.9990
   chunk 22 optimal weight:   10.0000
   chunk 41 optimal weight:    0.1980
   overall best weight:    0.9784

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

Flipped N/Q/H residues before XYZ refinement:
C 225 ASN
A 225 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3745 r_free = 0.3745 target = 0.147963 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3313 r_free = 0.3313 target = 0.112799 restraints weight = 11950.352|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3354 r_free = 0.3354 target = 0.115868 restraints weight = 6969.297|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 41)----------------|
| r_work = 0.3381 r_free = 0.3381 target = 0.117863 restraints weight = 5006.487|
|-----------------------------------------------------------------------------|
r_work (final): 0.3354
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7900
moved from start:          0.2802

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.026   7988  Z= 0.217
  Angle     :  0.572   7.011  10804  Z= 0.288
  Chirality :  0.041   0.127   1232
  Planarity :  0.003   0.025   1256
  Dihedral  : 18.584 105.876   1328
  Min Nonbonded Distance : 2.476

Molprobity Statistics.
  All-atom Clashscore : 8.26
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.04 %
    Favored  : 95.96 %
  Rotamer:
    Outliers :  6.41 %
    Allowed  : 24.75 %
    Favored  : 68.84 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.14 (0.28), residues: 892
  helix: -0.80 (0.21), residues: 636
  sheet:  None (None), residues: 0
  loop : -2.77 (0.36), residues: 256

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP C  54 
 HIS   0.002   0.001   HIS A  22 
 PHE   0.014   0.001   PHE D 224 
 TYR   0.015   0.001   TYR C  49 
 ARG   0.007   0.001   ARG B 122 

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

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

  1784 Ramachandran restraints generated.
    892 Oldfield, 0 Emsley, 892 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1784 Ramachandran restraints generated.
    892 Oldfield, 0 Emsley, 892 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  229 residues out of total 796 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 51
    poor density    : 178
  time to evaluate  : 0.836 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: C   35 PHE cc_start: 0.8761 (t80) cc_final: 0.8374 (t80)
REVERT: C   57 TYR cc_start: 0.6930 (OUTLIER) cc_final: 0.5746 (t80)
REVERT: C   59 ILE cc_start: 0.8374 (tp) cc_final: 0.8128 (tp)
REVERT: C   65 TRP cc_start: 0.6623 (OUTLIER) cc_final: 0.4656 (t60)
REVERT: C  138 VAL cc_start: 0.9477 (p) cc_final: 0.9184 (m)
REVERT: C  139 MET cc_start: 0.8232 (tpp) cc_final: 0.7752 (tpp)
REVERT: C  191 GLU cc_start: 0.8687 (tm-30) cc_final: 0.8332 (tm-30)
REVERT: C  224 PHE cc_start: 0.6371 (t80) cc_final: 0.5687 (t80)
REVERT: A   57 TYR cc_start: 0.7015 (OUTLIER) cc_final: 0.5816 (t80)
REVERT: A   65 TRP cc_start: 0.6544 (OUTLIER) cc_final: 0.4602 (t60)
REVERT: A  138 VAL cc_start: 0.9480 (p) cc_final: 0.9207 (m)
REVERT: A  139 MET cc_start: 0.8393 (tpp) cc_final: 0.7785 (tpp)
REVERT: A  191 GLU cc_start: 0.8677 (tm-30) cc_final: 0.8282 (tm-30)
REVERT: A  224 PHE cc_start: 0.6062 (t80) cc_final: 0.5586 (t80)
REVERT: B   35 PHE cc_start: 0.8745 (t80) cc_final: 0.8520 (t80)
REVERT: B   57 TYR cc_start: 0.6867 (OUTLIER) cc_final: 0.5693 (t80)
REVERT: B   59 ILE cc_start: 0.8629 (tp) cc_final: 0.8319 (tp)
REVERT: B   63 LEU cc_start: 0.9172 (OUTLIER) cc_final: 0.8791 (mm)
REVERT: B   65 TRP cc_start: 0.6503 (OUTLIER) cc_final: 0.4576 (t60)
REVERT: B  139 MET cc_start: 0.8209 (tpp) cc_final: 0.7977 (tpp)
REVERT: B  191 GLU cc_start: 0.8671 (tm-30) cc_final: 0.7954 (tm-30)
REVERT: B  224 PHE cc_start: 0.6280 (t80) cc_final: 0.5639 (t80)
REVERT: D   35 PHE cc_start: 0.8749 (t80) cc_final: 0.8302 (t80)
REVERT: D   57 TYR cc_start: 0.6847 (OUTLIER) cc_final: 0.5636 (t80)
REVERT: D   59 ILE cc_start: 0.8646 (tp) cc_final: 0.8379 (tp)
REVERT: D   63 LEU cc_start: 0.9138 (OUTLIER) cc_final: 0.8845 (mm)
REVERT: D   65 TRP cc_start: 0.6583 (OUTLIER) cc_final: 0.4639 (t60)
REVERT: D  139 MET cc_start: 0.8279 (tpp) cc_final: 0.7837 (tpp)
REVERT: D  191 GLU cc_start: 0.8694 (tm-30) cc_final: 0.8127 (tm-30)
  outliers start: 51
  outliers final: 35
  residues processed: 200
  average time/residue: 0.1732
  time to fit residues: 48.2432
Evaluate side-chains
  216 residues out of total 796 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 45
    poor density    : 171
  time to evaluate  : 0.826 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue   16 MET
Chi-restraints excluded: chain C residue   27 PHE
Chi-restraints excluded: chain C residue   34 LEU
Chi-restraints excluded: chain C residue   57 TYR
Chi-restraints excluded: chain C residue   65 TRP
Chi-restraints excluded: chain C residue  109 VAL
Chi-restraints excluded: chain C residue  111 VAL
Chi-restraints excluded: chain C residue  168 HIS
Chi-restraints excluded: chain C residue  188 VAL
Chi-restraints excluded: chain C residue  220 THR
Chi-restraints excluded: chain C residue  230 VAL
Chi-restraints excluded: chain A residue   16 MET
Chi-restraints excluded: chain A residue   27 PHE
Chi-restraints excluded: chain A residue   34 LEU
Chi-restraints excluded: chain A residue   57 TYR
Chi-restraints excluded: chain A residue   65 TRP
Chi-restraints excluded: chain A residue  109 VAL
Chi-restraints excluded: chain A residue  111 VAL
Chi-restraints excluded: chain A residue  188 VAL
Chi-restraints excluded: chain A residue  220 THR
Chi-restraints excluded: chain A residue  230 VAL
Chi-restraints excluded: chain B residue   16 MET
Chi-restraints excluded: chain B residue   27 PHE
Chi-restraints excluded: chain B residue   34 LEU
Chi-restraints excluded: chain B residue   57 TYR
Chi-restraints excluded: chain B residue   63 LEU
Chi-restraints excluded: chain B residue   65 TRP
Chi-restraints excluded: chain B residue  111 VAL
Chi-restraints excluded: chain B residue  147 ILE
Chi-restraints excluded: chain B residue  188 VAL
Chi-restraints excluded: chain B residue  220 THR
Chi-restraints excluded: chain B residue  230 VAL
Chi-restraints excluded: chain D residue   16 MET
Chi-restraints excluded: chain D residue   27 PHE
Chi-restraints excluded: chain D residue   34 LEU
Chi-restraints excluded: chain D residue   57 TYR
Chi-restraints excluded: chain D residue   63 LEU
Chi-restraints excluded: chain D residue   65 TRP
Chi-restraints excluded: chain D residue  109 VAL
Chi-restraints excluded: chain D residue  111 VAL
Chi-restraints excluded: chain D residue  147 ILE
Chi-restraints excluded: chain D residue  168 HIS
Chi-restraints excluded: chain D residue  188 VAL
Chi-restraints excluded: chain D residue  220 THR
Chi-restraints excluded: chain D residue  230 VAL
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 88
   random chunks:
   chunk 24 optimal weight:    2.9990
   chunk 7 optimal weight:    0.0050
   chunk 36 optimal weight:    0.9990
   chunk 12 optimal weight:    1.9990
   chunk 62 optimal weight:    0.6980
   chunk 4 optimal weight:    6.9990
   chunk 9 optimal weight:    8.9990
   chunk 2 optimal weight:    2.9990
   chunk 78 optimal weight:    3.9990
   chunk 74 optimal weight:    0.9980
   chunk 73 optimal weight:    6.9990
   overall best weight:    0.9398

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

Flipped N/Q/H residues before XYZ refinement:
C 225 ASN
D 225 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3744 r_free = 0.3744 target = 0.148029 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3289 r_free = 0.3289 target = 0.111392 restraints weight = 12015.936|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3333 r_free = 0.3333 target = 0.114542 restraints weight = 7046.461|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3360 r_free = 0.3360 target = 0.116577 restraints weight = 5111.588|
|-----------------------------------------------------------------------------|
r_work (final): 0.3348
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7905
moved from start:          0.3010

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.025   7988  Z= 0.210
  Angle     :  0.565   8.675  10804  Z= 0.282
  Chirality :  0.040   0.119   1232
  Planarity :  0.003   0.032   1256
  Dihedral  : 17.714  94.766   1328
  Min Nonbonded Distance : 2.458

Molprobity Statistics.
  All-atom Clashscore : 7.70
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.92 %
    Favored  : 96.08 %
  Rotamer:
    Outliers :  6.28 %
    Allowed  : 25.88 %
    Favored  : 67.84 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.88 (0.28), residues: 892
  helix: -0.63 (0.21), residues: 636
  sheet:  None (None), residues: 0
  loop : -2.62 (0.37), residues: 256

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP C  54 
 HIS   0.001   0.000   HIS D  22 
 PHE   0.012   0.001   PHE D 224 
 TYR   0.009   0.001   TYR C  49 
 ARG   0.012   0.001   ARG D  74 

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

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

  1784 Ramachandran restraints generated.
    892 Oldfield, 0 Emsley, 892 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1784 Ramachandran restraints generated.
    892 Oldfield, 0 Emsley, 892 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  233 residues out of total 796 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 50
    poor density    : 183
  time to evaluate  : 1.108 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: C   35 PHE cc_start: 0.8768 (t80) cc_final: 0.8408 (t80)
REVERT: C   57 TYR cc_start: 0.6961 (OUTLIER) cc_final: 0.5719 (t80)
REVERT: C   59 ILE cc_start: 0.8341 (tp) cc_final: 0.8091 (tp)
REVERT: C  139 MET cc_start: 0.8280 (tpp) cc_final: 0.7977 (tpp)
REVERT: C  191 GLU cc_start: 0.8675 (tm-30) cc_final: 0.8289 (tm-30)
REVERT: C  224 PHE cc_start: 0.6380 (t80) cc_final: 0.5740 (t80)
REVERT: A   57 TYR cc_start: 0.6940 (OUTLIER) cc_final: 0.5740 (t80)
REVERT: A  139 MET cc_start: 0.8427 (tpp) cc_final: 0.7965 (tpp)
REVERT: A  191 GLU cc_start: 0.8669 (tm-30) cc_final: 0.8276 (tm-30)
REVERT: A  224 PHE cc_start: 0.6099 (t80) cc_final: 0.5608 (t80)
REVERT: B   35 PHE cc_start: 0.8744 (t80) cc_final: 0.8525 (t80)
REVERT: B   57 TYR cc_start: 0.6795 (OUTLIER) cc_final: 0.5629 (t80)
REVERT: B   59 ILE cc_start: 0.8316 (tp) cc_final: 0.7892 (tp)
REVERT: B   63 LEU cc_start: 0.9146 (OUTLIER) cc_final: 0.8786 (mm)
REVERT: B  138 VAL cc_start: 0.9523 (p) cc_final: 0.9221 (m)
REVERT: B  139 MET cc_start: 0.8277 (tpp) cc_final: 0.7893 (tpp)
REVERT: B  191 GLU cc_start: 0.8522 (tm-30) cc_final: 0.8030 (tm-30)
REVERT: B  224 PHE cc_start: 0.6218 (t80) cc_final: 0.5652 (t80)
REVERT: D   35 PHE cc_start: 0.8723 (t80) cc_final: 0.8308 (t80)
REVERT: D   57 TYR cc_start: 0.6758 (OUTLIER) cc_final: 0.5565 (t80)
REVERT: D   59 ILE cc_start: 0.8341 (tp) cc_final: 0.7998 (tp)
REVERT: D   63 LEU cc_start: 0.9112 (OUTLIER) cc_final: 0.8845 (mm)
REVERT: D  138 VAL cc_start: 0.9513 (p) cc_final: 0.9202 (m)
REVERT: D  139 MET cc_start: 0.8295 (tpp) cc_final: 0.7797 (tpp)
REVERT: D  191 GLU cc_start: 0.8700 (tm-30) cc_final: 0.8082 (tm-30)
REVERT: D  224 PHE cc_start: 0.6086 (t80) cc_final: 0.5605 (t80)
  outliers start: 50
  outliers final: 40
  residues processed: 203
  average time/residue: 0.2255
  time to fit residues: 62.2062
Evaluate side-chains
  216 residues out of total 796 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 46
    poor density    : 170
  time to evaluate  : 1.530 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue   16 MET
Chi-restraints excluded: chain C residue   27 PHE
Chi-restraints excluded: chain C residue   34 LEU
Chi-restraints excluded: chain C residue   57 TYR
Chi-restraints excluded: chain C residue  109 VAL
Chi-restraints excluded: chain C residue  111 VAL
Chi-restraints excluded: chain C residue  147 ILE
Chi-restraints excluded: chain C residue  168 HIS
Chi-restraints excluded: chain C residue  178 GLN
Chi-restraints excluded: chain C residue  188 VAL
Chi-restraints excluded: chain C residue  220 THR
Chi-restraints excluded: chain C residue  230 VAL
Chi-restraints excluded: chain A residue   16 MET
Chi-restraints excluded: chain A residue   27 PHE
Chi-restraints excluded: chain A residue   34 LEU
Chi-restraints excluded: chain A residue   57 TYR
Chi-restraints excluded: chain A residue  109 VAL
Chi-restraints excluded: chain A residue  111 VAL
Chi-restraints excluded: chain A residue  168 HIS
Chi-restraints excluded: chain A residue  188 VAL
Chi-restraints excluded: chain A residue  220 THR
Chi-restraints excluded: chain A residue  230 VAL
Chi-restraints excluded: chain B residue   16 MET
Chi-restraints excluded: chain B residue   27 PHE
Chi-restraints excluded: chain B residue   34 LEU
Chi-restraints excluded: chain B residue   57 TYR
Chi-restraints excluded: chain B residue   63 LEU
Chi-restraints excluded: chain B residue  109 VAL
Chi-restraints excluded: chain B residue  111 VAL
Chi-restraints excluded: chain B residue  147 ILE
Chi-restraints excluded: chain B residue  168 HIS
Chi-restraints excluded: chain B residue  188 VAL
Chi-restraints excluded: chain B residue  220 THR
Chi-restraints excluded: chain B residue  230 VAL
Chi-restraints excluded: chain D residue   16 MET
Chi-restraints excluded: chain D residue   27 PHE
Chi-restraints excluded: chain D residue   34 LEU
Chi-restraints excluded: chain D residue   57 TYR
Chi-restraints excluded: chain D residue   63 LEU
Chi-restraints excluded: chain D residue  109 VAL
Chi-restraints excluded: chain D residue  111 VAL
Chi-restraints excluded: chain D residue  147 ILE
Chi-restraints excluded: chain D residue  168 HIS
Chi-restraints excluded: chain D residue  188 VAL
Chi-restraints excluded: chain D residue  220 THR
Chi-restraints excluded: chain D residue  230 VAL
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 88
   random chunks:
   chunk 50 optimal weight:    0.9980
   chunk 4 optimal weight:    5.9990
   chunk 60 optimal weight:    0.8980
   chunk 58 optimal weight:    0.8980
   chunk 29 optimal weight:    5.9990
   chunk 62 optimal weight:    3.9990
   chunk 76 optimal weight:    0.8980
   chunk 75 optimal weight:    6.9990
   chunk 86 optimal weight:    0.7980
   chunk 43 optimal weight:    0.5980
   chunk 37 optimal weight:    1.9990
   overall best weight:    0.8180

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

Flipped N/Q/H residues before XYZ refinement:
C 225 ASN
A 225 ASN
B 225 ASN
D 225 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3759 r_free = 0.3759 target = 0.149093 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3307 r_free = 0.3307 target = 0.112569 restraints weight = 11877.250|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3349 r_free = 0.3349 target = 0.115710 restraints weight = 7027.343|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3375 r_free = 0.3375 target = 0.117651 restraints weight = 5085.786|
|-----------------------------------------------------------------------------|
r_work (final): 0.3360
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7886
moved from start:          0.3218

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.024   7988  Z= 0.192
  Angle     :  0.557   7.538  10804  Z= 0.276
  Chirality :  0.040   0.144   1232
  Planarity :  0.003   0.030   1256
  Dihedral  : 16.815  89.499   1320
  Min Nonbonded Distance : 2.447

Molprobity Statistics.
  All-atom Clashscore : 7.89
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.48 %
    Favored  : 96.52 %
  Rotamer:
    Outliers :  7.41 %
    Allowed  : 25.75 %
    Favored  : 66.83 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.76 (0.28), residues: 892
  helix: -0.51 (0.21), residues: 632
  sheet:  None (None), residues: 0
  loop : -2.63 (0.36), residues: 260

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP B  54 
 HIS   0.001   0.000   HIS D  22 
 PHE   0.017   0.001   PHE B 215 
 TYR   0.008   0.001   TYR C  49 
 ARG   0.008   0.001   ARG B 122 

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

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

  1784 Ramachandran restraints generated.
    892 Oldfield, 0 Emsley, 892 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1784 Ramachandran restraints generated.
    892 Oldfield, 0 Emsley, 892 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  240 residues out of total 796 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 59
    poor density    : 181
  time to evaluate  : 0.872 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: C   35 PHE cc_start: 0.8756 (t80) cc_final: 0.8399 (t80)
REVERT: C   57 TYR cc_start: 0.7030 (OUTLIER) cc_final: 0.5816 (t80)
REVERT: C   59 ILE cc_start: 0.8309 (tp) cc_final: 0.8082 (tp)
REVERT: C  139 MET cc_start: 0.8229 (tpp) cc_final: 0.7932 (tpp)
REVERT: C  191 GLU cc_start: 0.8682 (tm-30) cc_final: 0.8320 (tm-30)
REVERT: C  224 PHE cc_start: 0.6255 (t80) cc_final: 0.5687 (t80)
REVERT: A   57 TYR cc_start: 0.7132 (OUTLIER) cc_final: 0.5873 (t80)
REVERT: A  138 VAL cc_start: 0.9475 (p) cc_final: 0.9212 (m)
REVERT: A  139 MET cc_start: 0.8410 (tpp) cc_final: 0.7818 (tpp)
REVERT: A  191 GLU cc_start: 0.8653 (tm-30) cc_final: 0.8265 (tm-30)
REVERT: A  224 PHE cc_start: 0.6057 (t80) cc_final: 0.5496 (t80)
REVERT: A  230 VAL cc_start: 0.9199 (OUTLIER) cc_final: 0.8864 (p)
REVERT: B   57 TYR cc_start: 0.7016 (OUTLIER) cc_final: 0.5786 (t80)
REVERT: B   63 LEU cc_start: 0.9149 (OUTLIER) cc_final: 0.8883 (mm)
REVERT: B  138 VAL cc_start: 0.9520 (p) cc_final: 0.9216 (m)
REVERT: B  139 MET cc_start: 0.8352 (tpp) cc_final: 0.7941 (tpp)
REVERT: B  191 GLU cc_start: 0.8512 (tm-30) cc_final: 0.8039 (tm-30)
REVERT: B  224 PHE cc_start: 0.6169 (t80) cc_final: 0.5576 (t80)
REVERT: B  230 VAL cc_start: 0.9203 (OUTLIER) cc_final: 0.8874 (p)
REVERT: D   35 PHE cc_start: 0.8704 (t80) cc_final: 0.8301 (t80)
REVERT: D   57 TYR cc_start: 0.7055 (OUTLIER) cc_final: 0.5817 (t80)
REVERT: D   59 ILE cc_start: 0.8310 (tp) cc_final: 0.7956 (tp)
REVERT: D   63 LEU cc_start: 0.9154 (OUTLIER) cc_final: 0.8898 (mm)
REVERT: D  139 MET cc_start: 0.8331 (tpp) cc_final: 0.7939 (tpp)
REVERT: D  191 GLU cc_start: 0.8684 (tm-30) cc_final: 0.8182 (tm-30)
REVERT: D  224 PHE cc_start: 0.6049 (t80) cc_final: 0.5529 (t80)
REVERT: D  230 VAL cc_start: 0.9171 (OUTLIER) cc_final: 0.8745 (p)
  outliers start: 59
  outliers final: 41
  residues processed: 201
  average time/residue: 0.1727
  time to fit residues: 48.9925
Evaluate side-chains
  215 residues out of total 796 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 50
    poor density    : 165
  time to evaluate  : 0.860 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue   16 MET
Chi-restraints excluded: chain C residue   27 PHE
Chi-restraints excluded: chain C residue   34 LEU
Chi-restraints excluded: chain C residue   57 TYR
Chi-restraints excluded: chain C residue   68 THR
Chi-restraints excluded: chain C residue  111 VAL
Chi-restraints excluded: chain C residue  147 ILE
Chi-restraints excluded: chain C residue  168 HIS
Chi-restraints excluded: chain C residue  178 GLN
Chi-restraints excluded: chain C residue  188 VAL
Chi-restraints excluded: chain C residue  220 THR
Chi-restraints excluded: chain C residue  230 VAL
Chi-restraints excluded: chain A residue   16 MET
Chi-restraints excluded: chain A residue   27 PHE
Chi-restraints excluded: chain A residue   34 LEU
Chi-restraints excluded: chain A residue   57 TYR
Chi-restraints excluded: chain A residue   61 LEU
Chi-restraints excluded: chain A residue   68 THR
Chi-restraints excluded: chain A residue  111 VAL
Chi-restraints excluded: chain A residue  164 MET
Chi-restraints excluded: chain A residue  168 HIS
Chi-restraints excluded: chain A residue  188 VAL
Chi-restraints excluded: chain A residue  220 THR
Chi-restraints excluded: chain A residue  230 VAL
Chi-restraints excluded: chain B residue   16 MET
Chi-restraints excluded: chain B residue   27 PHE
Chi-restraints excluded: chain B residue   34 LEU
Chi-restraints excluded: chain B residue   57 TYR
Chi-restraints excluded: chain B residue   63 LEU
Chi-restraints excluded: chain B residue  109 VAL
Chi-restraints excluded: chain B residue  111 VAL
Chi-restraints excluded: chain B residue  147 ILE
Chi-restraints excluded: chain B residue  164 MET
Chi-restraints excluded: chain B residue  168 HIS
Chi-restraints excluded: chain B residue  188 VAL
Chi-restraints excluded: chain B residue  220 THR
Chi-restraints excluded: chain B residue  230 VAL
Chi-restraints excluded: chain D residue   16 MET
Chi-restraints excluded: chain D residue   27 PHE
Chi-restraints excluded: chain D residue   34 LEU
Chi-restraints excluded: chain D residue   57 TYR
Chi-restraints excluded: chain D residue   63 LEU
Chi-restraints excluded: chain D residue   68 THR
Chi-restraints excluded: chain D residue  109 VAL
Chi-restraints excluded: chain D residue  111 VAL
Chi-restraints excluded: chain D residue  147 ILE
Chi-restraints excluded: chain D residue  168 HIS
Chi-restraints excluded: chain D residue  188 VAL
Chi-restraints excluded: chain D residue  220 THR
Chi-restraints excluded: chain D residue  230 VAL
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 88
   random chunks:
   chunk 1 optimal weight:    0.8980
   chunk 76 optimal weight:    0.5980
   chunk 4 optimal weight:    2.9990
   chunk 20 optimal weight:    1.9990
   chunk 0 optimal weight:   10.0000
   chunk 25 optimal weight:    4.9990
   chunk 52 optimal weight:    0.8980
   chunk 34 optimal weight:    0.0970
   chunk 15 optimal weight:    0.8980
   chunk 22 optimal weight:   10.0000
   chunk 16 optimal weight:    0.5980
   overall best weight:    0.6178

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

Flipped N/Q/H residues before XYZ refinement:
C 225 ASN
A 225 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3773 r_free = 0.3773 target = 0.150314 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3321 r_free = 0.3321 target = 0.113868 restraints weight = 11922.626|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 25)----------------|
| r_work = 0.3364 r_free = 0.3364 target = 0.117081 restraints weight = 6990.524|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 43)----------------|
| r_work = 0.3393 r_free = 0.3393 target = 0.119205 restraints weight = 5018.746|
|-----------------------------------------------------------------------------|
r_work (final): 0.3385
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7854
moved from start:          0.3457

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.026   7988  Z= 0.164
  Angle     :  0.533   7.691  10804  Z= 0.264
  Chirality :  0.039   0.132   1232
  Planarity :  0.003   0.034   1256
  Dihedral  : 16.071  89.625   1320
  Min Nonbonded Distance : 2.429

Molprobity Statistics.
  All-atom Clashscore : 8.08
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.70 %
    Favored  : 96.30 %
  Rotamer:
    Outliers :  8.92 %
    Allowed  : 25.00 %
    Favored  : 66.08 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.63 (0.28), residues: 892
  helix: -0.39 (0.21), residues: 632
  sheet:  None (None), residues: 0
  loop : -2.63 (0.36), residues: 260

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP C  54 
 HIS   0.001   0.000   HIS A  22 
 PHE   0.021   0.001   PHE B 215 
 TYR   0.007   0.001   TYR C  49 
 ARG   0.008   0.001   ARG B 122 

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

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

  1784 Ramachandran restraints generated.
    892 Oldfield, 0 Emsley, 892 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1784 Ramachandran restraints generated.
    892 Oldfield, 0 Emsley, 892 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  251 residues out of total 796 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 71
    poor density    : 180
  time to evaluate  : 0.749 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: C   19 ILE cc_start: 0.4218 (OUTLIER) cc_final: 0.3492 (mm)
REVERT: C   35 PHE cc_start: 0.8820 (t80) cc_final: 0.8509 (t80)
REVERT: C   57 TYR cc_start: 0.7027 (OUTLIER) cc_final: 0.5861 (t80)
REVERT: C  139 MET cc_start: 0.8229 (tpp) cc_final: 0.7935 (tpp)
REVERT: C  191 GLU cc_start: 0.8655 (tm-30) cc_final: 0.8330 (tm-30)
REVERT: C  224 PHE cc_start: 0.6216 (t80) cc_final: 0.5648 (t80)
REVERT: C  230 VAL cc_start: 0.9156 (OUTLIER) cc_final: 0.8789 (p)
REVERT: A   19 ILE cc_start: 0.4255 (OUTLIER) cc_final: 0.3565 (mm)
REVERT: A   57 TYR cc_start: 0.7075 (OUTLIER) cc_final: 0.5878 (t80)
REVERT: A  139 MET cc_start: 0.8385 (tpp) cc_final: 0.7975 (tpp)
REVERT: A  187 VAL cc_start: 0.9222 (OUTLIER) cc_final: 0.8918 (p)
REVERT: A  191 GLU cc_start: 0.8558 (tm-30) cc_final: 0.8299 (tm-30)
REVERT: A  224 PHE cc_start: 0.6022 (t80) cc_final: 0.5489 (t80)
REVERT: A  230 VAL cc_start: 0.9183 (OUTLIER) cc_final: 0.8828 (p)
REVERT: B   19 ILE cc_start: 0.4193 (OUTLIER) cc_final: 0.3446 (mm)
REVERT: B   57 TYR cc_start: 0.7038 (OUTLIER) cc_final: 0.5775 (t80)
REVERT: B   63 LEU cc_start: 0.9121 (OUTLIER) cc_final: 0.8893 (mm)
REVERT: B  139 MET cc_start: 0.8354 (tpp) cc_final: 0.7998 (tpp)
REVERT: B  191 GLU cc_start: 0.8679 (tm-30) cc_final: 0.8114 (tm-30)
REVERT: B  224 PHE cc_start: 0.6108 (t80) cc_final: 0.5516 (t80)
REVERT: B  230 VAL cc_start: 0.9185 (OUTLIER) cc_final: 0.8793 (p)
REVERT: D   19 ILE cc_start: 0.4096 (OUTLIER) cc_final: 0.3335 (mm)
REVERT: D   35 PHE cc_start: 0.8685 (t80) cc_final: 0.8354 (t80)
REVERT: D   57 TYR cc_start: 0.7008 (OUTLIER) cc_final: 0.5771 (t80)
REVERT: D  139 MET cc_start: 0.8343 (tpp) cc_final: 0.7963 (tpp)
REVERT: D  191 GLU cc_start: 0.8506 (tm-30) cc_final: 0.8161 (tm-30)
REVERT: D  224 PHE cc_start: 0.6012 (t80) cc_final: 0.5523 (t80)
REVERT: D  230 VAL cc_start: 0.9140 (OUTLIER) cc_final: 0.8657 (p)
  outliers start: 71
  outliers final: 37
  residues processed: 212
  average time/residue: 0.1398
  time to fit residues: 43.4602
Evaluate side-chains
  217 residues out of total 796 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 51
    poor density    : 166
  time to evaluate  : 0.776 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue   16 MET
Chi-restraints excluded: chain C residue   19 ILE
Chi-restraints excluded: chain C residue   27 PHE
Chi-restraints excluded: chain C residue   34 LEU
Chi-restraints excluded: chain C residue   57 TYR
Chi-restraints excluded: chain C residue   68 THR
Chi-restraints excluded: chain C residue  109 VAL
Chi-restraints excluded: chain C residue  111 VAL
Chi-restraints excluded: chain C residue  147 ILE
Chi-restraints excluded: chain C residue  168 HIS
Chi-restraints excluded: chain C residue  178 GLN
Chi-restraints excluded: chain C residue  188 VAL
Chi-restraints excluded: chain C residue  230 VAL
Chi-restraints excluded: chain A residue   19 ILE
Chi-restraints excluded: chain A residue   27 PHE
Chi-restraints excluded: chain A residue   34 LEU
Chi-restraints excluded: chain A residue   57 TYR
Chi-restraints excluded: chain A residue   61 LEU
Chi-restraints excluded: chain A residue   68 THR
Chi-restraints excluded: chain A residue  109 VAL
Chi-restraints excluded: chain A residue  111 VAL
Chi-restraints excluded: chain A residue  164 MET
Chi-restraints excluded: chain A residue  168 HIS
Chi-restraints excluded: chain A residue  187 VAL
Chi-restraints excluded: chain A residue  188 VAL
Chi-restraints excluded: chain A residue  230 VAL
Chi-restraints excluded: chain B residue   19 ILE
Chi-restraints excluded: chain B residue   27 PHE
Chi-restraints excluded: chain B residue   57 TYR
Chi-restraints excluded: chain B residue   63 LEU
Chi-restraints excluded: chain B residue   68 THR
Chi-restraints excluded: chain B residue  109 VAL
Chi-restraints excluded: chain B residue  111 VAL
Chi-restraints excluded: chain B residue  147 ILE
Chi-restraints excluded: chain B residue  164 MET
Chi-restraints excluded: chain B residue  168 HIS
Chi-restraints excluded: chain B residue  188 VAL
Chi-restraints excluded: chain B residue  220 THR
Chi-restraints excluded: chain B residue  230 VAL
Chi-restraints excluded: chain D residue   16 MET
Chi-restraints excluded: chain D residue   19 ILE
Chi-restraints excluded: chain D residue   27 PHE
Chi-restraints excluded: chain D residue   34 LEU
Chi-restraints excluded: chain D residue   57 TYR
Chi-restraints excluded: chain D residue   68 THR
Chi-restraints excluded: chain D residue  109 VAL
Chi-restraints excluded: chain D residue  111 VAL
Chi-restraints excluded: chain D residue  147 ILE
Chi-restraints excluded: chain D residue  168 HIS
Chi-restraints excluded: chain D residue  188 VAL
Chi-restraints excluded: chain D residue  230 VAL
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 88
   random chunks:
   chunk 76 optimal weight:    3.9990
   chunk 81 optimal weight:    1.9990
   chunk 80 optimal weight:    0.7980
   chunk 51 optimal weight:    5.9990
   chunk 71 optimal weight:    1.9990
   chunk 20 optimal weight:    0.9990
   chunk 6 optimal weight:    8.9990
   chunk 23 optimal weight:    0.5980
   chunk 74 optimal weight:    1.9990
   chunk 41 optimal weight:    0.0770
   chunk 5 optimal weight:    0.9980
   overall best weight:    0.6940

-------------------------------------------------------------------------------
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 = 0.3773 r_free = 0.3773 target = 0.150493 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3331 r_free = 0.3331 target = 0.114550 restraints weight = 11824.003|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3374 r_free = 0.3374 target = 0.117793 restraints weight = 6913.941|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3400 r_free = 0.3400 target = 0.119815 restraints weight = 4947.561|
|-----------------------------------------------------------------------------|
r_work (final): 0.3380
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7862
moved from start:          0.3581

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.022   7988  Z= 0.175
  Angle     :  0.553   7.803  10804  Z= 0.270
  Chirality :  0.041   0.212   1232
  Planarity :  0.004   0.039   1256
  Dihedral  : 15.855  89.244   1320
  Min Nonbonded Distance : 2.421

Molprobity Statistics.
  All-atom Clashscore : 8.32
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.03 %
    Favored  : 96.97 %
  Rotamer:
    Outliers :  7.79 %
    Allowed  : 26.63 %
    Favored  : 65.58 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.70 (0.28), residues: 892
  helix: -0.43 (0.21), residues: 640
  sheet:  None (None), residues: 0
  loop : -2.78 (0.35), residues: 252

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP B  54 
 HIS   0.001   0.000   HIS D  22 
 PHE   0.022   0.001   PHE B  35 
 TYR   0.006   0.001   TYR C  49 
 ARG   0.009   0.001   ARG B 122 

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

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

  1784 Ramachandran restraints generated.
    892 Oldfield, 0 Emsley, 892 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1784 Ramachandran restraints generated.
    892 Oldfield, 0 Emsley, 892 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  239 residues out of total 796 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 62
    poor density    : 177
  time to evaluate  : 0.763 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: C   19 ILE cc_start: 0.4197 (OUTLIER) cc_final: 0.3472 (mm)
REVERT: C   35 PHE cc_start: 0.8798 (t80) cc_final: 0.8480 (t80)
REVERT: C   57 TYR cc_start: 0.7051 (OUTLIER) cc_final: 0.5827 (t80)
REVERT: C  139 MET cc_start: 0.8236 (tpp) cc_final: 0.7956 (tpp)
REVERT: C  191 GLU cc_start: 0.8606 (tm-30) cc_final: 0.8331 (tm-30)
REVERT: C  224 PHE cc_start: 0.6220 (t80) cc_final: 0.5659 (t80)
REVERT: C  230 VAL cc_start: 0.9169 (OUTLIER) cc_final: 0.8788 (p)
REVERT: A   19 ILE cc_start: 0.4289 (OUTLIER) cc_final: 0.3596 (mm)
REVERT: A   57 TYR cc_start: 0.7144 (OUTLIER) cc_final: 0.5940 (t80)
REVERT: A  139 MET cc_start: 0.8381 (tpp) cc_final: 0.8006 (tpp)
REVERT: A  187 VAL cc_start: 0.9227 (OUTLIER) cc_final: 0.8876 (p)
REVERT: A  191 GLU cc_start: 0.8596 (tm-30) cc_final: 0.8253 (tm-30)
REVERT: A  224 PHE cc_start: 0.6050 (t80) cc_final: 0.5502 (t80)
REVERT: A  230 VAL cc_start: 0.9197 (OUTLIER) cc_final: 0.8824 (p)
REVERT: B   19 ILE cc_start: 0.4191 (OUTLIER) cc_final: 0.3437 (mm)
REVERT: B   57 TYR cc_start: 0.7054 (OUTLIER) cc_final: 0.5805 (t80)
REVERT: B  139 MET cc_start: 0.8375 (tpp) cc_final: 0.8015 (tpp)
REVERT: B  191 GLU cc_start: 0.8597 (tm-30) cc_final: 0.8032 (tm-30)
REVERT: B  224 PHE cc_start: 0.6118 (t80) cc_final: 0.5500 (t80)
REVERT: B  230 VAL cc_start: 0.9196 (OUTLIER) cc_final: 0.8796 (p)
REVERT: D   19 ILE cc_start: 0.4133 (OUTLIER) cc_final: 0.3372 (mm)
REVERT: D   35 PHE cc_start: 0.8672 (t80) cc_final: 0.8328 (t80)
REVERT: D   57 TYR cc_start: 0.7048 (OUTLIER) cc_final: 0.5791 (t80)
REVERT: D  139 MET cc_start: 0.8351 (tpp) cc_final: 0.7975 (tpp)
REVERT: D  191 GLU cc_start: 0.8537 (tm-30) cc_final: 0.8111 (tm-30)
REVERT: D  224 PHE cc_start: 0.6008 (t80) cc_final: 0.5528 (t80)
REVERT: D  230 VAL cc_start: 0.9147 (OUTLIER) cc_final: 0.8657 (p)
  outliers start: 62
  outliers final: 38
  residues processed: 204
  average time/residue: 0.1590
  time to fit residues: 46.0826
Evaluate side-chains
  221 residues out of total 796 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 51
    poor density    : 170
  time to evaluate  : 0.789 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue   16 MET
Chi-restraints excluded: chain C residue   19 ILE
Chi-restraints excluded: chain C residue   27 PHE
Chi-restraints excluded: chain C residue   34 LEU
Chi-restraints excluded: chain C residue   57 TYR
Chi-restraints excluded: chain C residue   68 THR
Chi-restraints excluded: chain C residue  109 VAL
Chi-restraints excluded: chain C residue  111 VAL
Chi-restraints excluded: chain C residue  168 HIS
Chi-restraints excluded: chain C residue  178 GLN
Chi-restraints excluded: chain C residue  188 VAL
Chi-restraints excluded: chain C residue  220 THR
Chi-restraints excluded: chain C residue  230 VAL
Chi-restraints excluded: chain A residue   19 ILE
Chi-restraints excluded: chain A residue   27 PHE
Chi-restraints excluded: chain A residue   34 LEU
Chi-restraints excluded: chain A residue   57 TYR
Chi-restraints excluded: chain A residue   61 LEU
Chi-restraints excluded: chain A residue   68 THR
Chi-restraints excluded: chain A residue  109 VAL
Chi-restraints excluded: chain A residue  111 VAL
Chi-restraints excluded: chain A residue  147 ILE
Chi-restraints excluded: chain A residue  164 MET
Chi-restraints excluded: chain A residue  168 HIS
Chi-restraints excluded: chain A residue  187 VAL
Chi-restraints excluded: chain A residue  188 VAL
Chi-restraints excluded: chain A residue  230 VAL
Chi-restraints excluded: chain B residue   19 ILE
Chi-restraints excluded: chain B residue   27 PHE
Chi-restraints excluded: chain B residue   34 LEU
Chi-restraints excluded: chain B residue   57 TYR
Chi-restraints excluded: chain B residue  109 VAL
Chi-restraints excluded: chain B residue  111 VAL
Chi-restraints excluded: chain B residue  147 ILE
Chi-restraints excluded: chain B residue  168 HIS
Chi-restraints excluded: chain B residue  188 VAL
Chi-restraints excluded: chain B residue  220 THR
Chi-restraints excluded: chain B residue  230 VAL
Chi-restraints excluded: chain D residue   16 MET
Chi-restraints excluded: chain D residue   19 ILE
Chi-restraints excluded: chain D residue   27 PHE
Chi-restraints excluded: chain D residue   34 LEU
Chi-restraints excluded: chain D residue   57 TYR
Chi-restraints excluded: chain D residue   68 THR
Chi-restraints excluded: chain D residue  109 VAL
Chi-restraints excluded: chain D residue  111 VAL
Chi-restraints excluded: chain D residue  147 ILE
Chi-restraints excluded: chain D residue  168 HIS
Chi-restraints excluded: chain D residue  187 VAL
Chi-restraints excluded: chain D residue  188 VAL
Chi-restraints excluded: chain D residue  230 VAL
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 88
   random chunks:
   chunk 4 optimal weight:    0.9980
   chunk 53 optimal weight:    8.9990
   chunk 20 optimal weight:    0.0070
   chunk 2 optimal weight:    1.9990
   chunk 45 optimal weight:    0.6980
   chunk 52 optimal weight:    4.9990
   chunk 74 optimal weight:    1.9990
   chunk 21 optimal weight:    0.5980
   chunk 9 optimal weight:    0.0870
   chunk 48 optimal weight:    3.9990
   chunk 37 optimal weight:    0.8980
   overall best weight:    0.4576

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

Flipped N/Q/H residues before XYZ refinement:
C 101 HIS
A 101 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3789 r_free = 0.3789 target = 0.152208 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3341 r_free = 0.3341 target = 0.115445 restraints weight = 11948.369|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3384 r_free = 0.3384 target = 0.118726 restraints weight = 7053.301|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 23)----------------|
| r_work = 0.3413 r_free = 0.3413 target = 0.120882 restraints weight = 5087.654|
|-----------------------------------------------------------------------------|
r_work (final): 0.3400
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7842
moved from start:          0.3760

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.023   7988  Z= 0.152
  Angle     :  0.577   9.685  10804  Z= 0.278
  Chirality :  0.042   0.221   1232
  Planarity :  0.004   0.038   1256
  Dihedral  : 15.535  89.527   1320
  Min Nonbonded Distance : 2.411

Molprobity Statistics.
  All-atom Clashscore : 7.70
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.48 %
    Favored  : 96.52 %
  Rotamer:
    Outliers :  7.66 %
    Allowed  : 28.14 %
    Favored  : 64.20 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.75 (0.27), residues: 892
  helix: -0.40 (0.21), residues: 644
  sheet:  None (None), residues: 0
  loop : -3.01 (0.33), residues: 248

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP A  54 
 HIS   0.001   0.000   HIS B 101 
 PHE   0.018   0.001   PHE D 215 
 TYR   0.006   0.001   TYR D 156 
 ARG   0.009   0.001   ARG B 122 

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

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

  1784 Ramachandran restraints generated.
    892 Oldfield, 0 Emsley, 892 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1784 Ramachandran restraints generated.
    892 Oldfield, 0 Emsley, 892 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  250 residues out of total 796 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 61
    poor density    : 189
  time to evaluate  : 1.507 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: C   19 ILE cc_start: 0.4175 (OUTLIER) cc_final: 0.3463 (mm)
REVERT: C   35 PHE cc_start: 0.8750 (t80) cc_final: 0.8474 (t80)
REVERT: C   57 TYR cc_start: 0.7002 (OUTLIER) cc_final: 0.5802 (t80)
REVERT: C  139 MET cc_start: 0.8225 (tpp) cc_final: 0.7943 (tpp)
REVERT: C  191 GLU cc_start: 0.8549 (tm-30) cc_final: 0.8262 (tm-30)
REVERT: C  224 PHE cc_start: 0.6176 (t80) cc_final: 0.5651 (t80)
REVERT: C  230 VAL cc_start: 0.9144 (OUTLIER) cc_final: 0.8735 (p)
REVERT: A   19 ILE cc_start: 0.4271 (OUTLIER) cc_final: 0.3579 (mm)
REVERT: A   57 TYR cc_start: 0.7057 (OUTLIER) cc_final: 0.5886 (t80)
REVERT: A  139 MET cc_start: 0.8357 (tpp) cc_final: 0.7992 (tpp)
REVERT: A  187 VAL cc_start: 0.9214 (OUTLIER) cc_final: 0.8859 (p)
REVERT: A  191 GLU cc_start: 0.8529 (tm-30) cc_final: 0.8201 (tm-30)
REVERT: A  224 PHE cc_start: 0.6010 (t80) cc_final: 0.5497 (t80)
REVERT: A  230 VAL cc_start: 0.9169 (OUTLIER) cc_final: 0.8789 (p)
REVERT: B   19 ILE cc_start: 0.4184 (OUTLIER) cc_final: 0.3440 (mm)
REVERT: B   57 TYR cc_start: 0.7047 (OUTLIER) cc_final: 0.5778 (t80)
REVERT: B  139 MET cc_start: 0.8336 (tpp) cc_final: 0.7995 (tpp)
REVERT: B  191 GLU cc_start: 0.8546 (tm-30) cc_final: 0.7982 (tm-30)
REVERT: B  224 PHE cc_start: 0.6005 (t80) cc_final: 0.5428 (t80)
REVERT: B  230 VAL cc_start: 0.9169 (OUTLIER) cc_final: 0.8742 (p)
REVERT: D   19 ILE cc_start: 0.4117 (OUTLIER) cc_final: 0.3379 (mm)
REVERT: D   35 PHE cc_start: 0.8620 (t80) cc_final: 0.8337 (t80)
REVERT: D   57 TYR cc_start: 0.7075 (OUTLIER) cc_final: 0.5826 (t80)
REVERT: D  139 MET cc_start: 0.8355 (tpp) cc_final: 0.8006 (tpp)
REVERT: D  191 GLU cc_start: 0.8490 (tm-30) cc_final: 0.8091 (tm-30)
REVERT: D  224 PHE cc_start: 0.6122 (t80) cc_final: 0.5632 (t80)
REVERT: D  230 VAL cc_start: 0.9096 (OUTLIER) cc_final: 0.8577 (p)
  outliers start: 61
  outliers final: 37
  residues processed: 215
  average time/residue: 0.1540
  time to fit residues: 48.7740
Evaluate side-chains
  224 residues out of total 796 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 50
    poor density    : 174
  time to evaluate  : 0.814 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue   16 MET
Chi-restraints excluded: chain C residue   19 ILE
Chi-restraints excluded: chain C residue   27 PHE
Chi-restraints excluded: chain C residue   57 TYR
Chi-restraints excluded: chain C residue   68 THR
Chi-restraints excluded: chain C residue  109 VAL
Chi-restraints excluded: chain C residue  111 VAL
Chi-restraints excluded: chain C residue  147 ILE
Chi-restraints excluded: chain C residue  168 HIS
Chi-restraints excluded: chain C residue  178 GLN
Chi-restraints excluded: chain C residue  188 VAL
Chi-restraints excluded: chain C residue  220 THR
Chi-restraints excluded: chain C residue  230 VAL
Chi-restraints excluded: chain A residue   19 ILE
Chi-restraints excluded: chain A residue   27 PHE
Chi-restraints excluded: chain A residue   34 LEU
Chi-restraints excluded: chain A residue   57 TYR
Chi-restraints excluded: chain A residue   61 LEU
Chi-restraints excluded: chain A residue   68 THR
Chi-restraints excluded: chain A residue  109 VAL
Chi-restraints excluded: chain A residue  111 VAL
Chi-restraints excluded: chain A residue  147 ILE
Chi-restraints excluded: chain A residue  187 VAL
Chi-restraints excluded: chain A residue  188 VAL
Chi-restraints excluded: chain A residue  220 THR
Chi-restraints excluded: chain A residue  230 VAL
Chi-restraints excluded: chain B residue   19 ILE
Chi-restraints excluded: chain B residue   27 PHE
Chi-restraints excluded: chain B residue   34 LEU
Chi-restraints excluded: chain B residue   57 TYR
Chi-restraints excluded: chain B residue   68 THR
Chi-restraints excluded: chain B residue  109 VAL
Chi-restraints excluded: chain B residue  111 VAL
Chi-restraints excluded: chain B residue  147 ILE
Chi-restraints excluded: chain B residue  168 HIS
Chi-restraints excluded: chain B residue  188 VAL
Chi-restraints excluded: chain B residue  220 THR
Chi-restraints excluded: chain B residue  230 VAL
Chi-restraints excluded: chain D residue   19 ILE
Chi-restraints excluded: chain D residue   27 PHE
Chi-restraints excluded: chain D residue   34 LEU
Chi-restraints excluded: chain D residue   57 TYR
Chi-restraints excluded: chain D residue   68 THR
Chi-restraints excluded: chain D residue  109 VAL
Chi-restraints excluded: chain D residue  111 VAL
Chi-restraints excluded: chain D residue  168 HIS
Chi-restraints excluded: chain D residue  187 VAL
Chi-restraints excluded: chain D residue  188 VAL
Chi-restraints excluded: chain D residue  220 THR
Chi-restraints excluded: chain D residue  230 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 88
   random chunks:
   chunk 40 optimal weight:    0.7980
   chunk 33 optimal weight:    2.9990
   chunk 79 optimal weight:    0.5980
   chunk 28 optimal weight:    3.9990
   chunk 74 optimal weight:    0.7980
   chunk 4 optimal weight:    0.8980
   chunk 72 optimal weight:    1.9990
   chunk 25 optimal weight:    1.9990
   chunk 7 optimal weight:    0.9980
   chunk 12 optimal weight:    3.9990
   chunk 24 optimal weight:    3.9990
   overall best weight:    0.8180

-------------------------------------------------------------------------------
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 = 0.3768 r_free = 0.3768 target = 0.150592 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3321 r_free = 0.3321 target = 0.113652 restraints weight = 11827.206|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3362 r_free = 0.3362 target = 0.116819 restraints weight = 7068.497|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3391 r_free = 0.3391 target = 0.118939 restraints weight = 5091.701|
|-----------------------------------------------------------------------------|
r_work (final): 0.3376
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7875
moved from start:          0.3787

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   7988  Z= 0.200
  Angle     :  0.628  11.869  10804  Z= 0.298
  Chirality :  0.045   0.337   1232
  Planarity :  0.004   0.038   1256
  Dihedral  : 15.519  89.595   1320
  Min Nonbonded Distance : 2.405

Molprobity Statistics.
  All-atom Clashscore : 7.83
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.91 %
    Favored  : 97.09 %
  Rotamer:
    Outliers :  6.41 %
    Allowed  : 29.27 %
    Favored  : 64.32 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.76 (0.28), residues: 892
  helix: -0.44 (0.21), residues: 644
  sheet:  None (None), residues: 0
  loop : -2.93 (0.35), residues: 248

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.022   0.001   TRP B 193 
 HIS   0.001   0.001   HIS C  52 
 PHE   0.029   0.001   PHE D 215 
 TYR   0.005   0.001   TYR C  49 
 ARG   0.009   0.001   ARG D 122 

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

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

  1784 Ramachandran restraints generated.
    892 Oldfield, 0 Emsley, 892 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1784 Ramachandran restraints generated.
    892 Oldfield, 0 Emsley, 892 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  219 residues out of total 796 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 51
    poor density    : 168
  time to evaluate  : 0.859 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: C   19 ILE cc_start: 0.4190 (OUTLIER) cc_final: 0.3472 (mm)
REVERT: C   35 PHE cc_start: 0.8701 (t80) cc_final: 0.8304 (t80)
REVERT: C   57 TYR cc_start: 0.6965 (OUTLIER) cc_final: 0.5783 (t80)
REVERT: C  139 MET cc_start: 0.8250 (tpp) cc_final: 0.8008 (tpp)
REVERT: C  191 GLU cc_start: 0.8537 (tm-30) cc_final: 0.8242 (tm-30)
REVERT: C  224 PHE cc_start: 0.6259 (t80) cc_final: 0.5707 (t80)
REVERT: C  230 VAL cc_start: 0.9187 (OUTLIER) cc_final: 0.8770 (p)
REVERT: A   19 ILE cc_start: 0.4272 (OUTLIER) cc_final: 0.3578 (mm)
REVERT: A   57 TYR cc_start: 0.7010 (OUTLIER) cc_final: 0.5818 (t80)
REVERT: A  139 MET cc_start: 0.8355 (tpp) cc_final: 0.7982 (tpp)
REVERT: A  187 VAL cc_start: 0.9244 (OUTLIER) cc_final: 0.8955 (p)
REVERT: A  191 GLU cc_start: 0.8514 (tm-30) cc_final: 0.8124 (tm-30)
REVERT: A  224 PHE cc_start: 0.6073 (t80) cc_final: 0.5531 (t80)
REVERT: A  230 VAL cc_start: 0.9198 (OUTLIER) cc_final: 0.8826 (p)
REVERT: B   19 ILE cc_start: 0.4198 (OUTLIER) cc_final: 0.3449 (mm)
REVERT: B   57 TYR cc_start: 0.7083 (OUTLIER) cc_final: 0.5820 (t80)
REVERT: B  139 MET cc_start: 0.8377 (tpp) cc_final: 0.8014 (tpp)
REVERT: B  191 GLU cc_start: 0.8620 (tm-30) cc_final: 0.7896 (tm-30)
REVERT: B  224 PHE cc_start: 0.6067 (t80) cc_final: 0.5468 (t80)
REVERT: B  230 VAL cc_start: 0.9203 (OUTLIER) cc_final: 0.8784 (p)
REVERT: D   19 ILE cc_start: 0.4137 (OUTLIER) cc_final: 0.3379 (mm)
REVERT: D   35 PHE cc_start: 0.8669 (t80) cc_final: 0.8342 (t80)
REVERT: D   57 TYR cc_start: 0.7065 (OUTLIER) cc_final: 0.5782 (t80)
REVERT: D  191 GLU cc_start: 0.8537 (tm-30) cc_final: 0.8290 (tm-30)
REVERT: D  224 PHE cc_start: 0.6195 (t80) cc_final: 0.5684 (t80)
REVERT: D  230 VAL cc_start: 0.9167 (OUTLIER) cc_final: 0.8664 (p)
  outliers start: 51
  outliers final: 33
  residues processed: 192
  average time/residue: 0.1327
  time to fit residues: 38.5378
Evaluate side-chains
  213 residues out of total 796 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 46
    poor density    : 167
  time to evaluate  : 0.857 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue   19 ILE
Chi-restraints excluded: chain C residue   27 PHE
Chi-restraints excluded: chain C residue   34 LEU
Chi-restraints excluded: chain C residue   57 TYR
Chi-restraints excluded: chain C residue  109 VAL
Chi-restraints excluded: chain C residue  111 VAL
Chi-restraints excluded: chain C residue  147 ILE
Chi-restraints excluded: chain C residue  168 HIS
Chi-restraints excluded: chain C residue  178 GLN
Chi-restraints excluded: chain C residue  188 VAL
Chi-restraints excluded: chain C residue  220 THR
Chi-restraints excluded: chain C residue  230 VAL
Chi-restraints excluded: chain A residue   19 ILE
Chi-restraints excluded: chain A residue   27 PHE
Chi-restraints excluded: chain A residue   57 TYR
Chi-restraints excluded: chain A residue   61 LEU
Chi-restraints excluded: chain A residue   68 THR
Chi-restraints excluded: chain A residue  109 VAL
Chi-restraints excluded: chain A residue  111 VAL
Chi-restraints excluded: chain A residue  147 ILE
Chi-restraints excluded: chain A residue  187 VAL
Chi-restraints excluded: chain A residue  188 VAL
Chi-restraints excluded: chain A residue  220 THR
Chi-restraints excluded: chain A residue  230 VAL
Chi-restraints excluded: chain B residue   19 ILE
Chi-restraints excluded: chain B residue   27 PHE
Chi-restraints excluded: chain B residue   34 LEU
Chi-restraints excluded: chain B residue   57 TYR
Chi-restraints excluded: chain B residue   68 THR
Chi-restraints excluded: chain B residue  109 VAL
Chi-restraints excluded: chain B residue  111 VAL
Chi-restraints excluded: chain B residue  168 HIS
Chi-restraints excluded: chain B residue  188 VAL
Chi-restraints excluded: chain B residue  220 THR
Chi-restraints excluded: chain B residue  230 VAL
Chi-restraints excluded: chain D residue   19 ILE
Chi-restraints excluded: chain D residue   27 PHE
Chi-restraints excluded: chain D residue   34 LEU
Chi-restraints excluded: chain D residue   57 TYR
Chi-restraints excluded: chain D residue  109 VAL
Chi-restraints excluded: chain D residue  111 VAL
Chi-restraints excluded: chain D residue  168 HIS
Chi-restraints excluded: chain D residue  187 VAL
Chi-restraints excluded: chain D residue  188 VAL
Chi-restraints excluded: chain D residue  220 THR
Chi-restraints excluded: chain D residue  230 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 88
   random chunks:
   chunk 25 optimal weight:    3.9990
   chunk 7 optimal weight:    0.6980
   chunk 86 optimal weight:    0.6980
   chunk 10 optimal weight:    0.0980
   chunk 55 optimal weight:    3.9990
   chunk 87 optimal weight:    0.6980
   chunk 67 optimal weight:    1.9990
   chunk 72 optimal weight:    9.9990
   chunk 36 optimal weight:    0.6980
   chunk 61 optimal weight:    0.8980
   chunk 32 optimal weight:    0.7980
   overall best weight:    0.5780

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

Flipped N/Q/H residues before XYZ refinement:
B 101 HIS
D 101 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3787 r_free = 0.3787 target = 0.152359 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3342 r_free = 0.3342 target = 0.115449 restraints weight = 11721.814|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3384 r_free = 0.3384 target = 0.118616 restraints weight = 6995.450|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3413 r_free = 0.3413 target = 0.120765 restraints weight = 5086.569|
|-----------------------------------------------------------------------------|
r_work (final): 0.3400
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7852
moved from start:          0.3926

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   7988  Z= 0.169
  Angle     :  0.618  11.420  10804  Z= 0.291
  Chirality :  0.044   0.300   1232
  Planarity :  0.004   0.038   1256
  Dihedral  : 15.259  89.865   1320
  Min Nonbonded Distance : 2.398

Molprobity Statistics.
  All-atom Clashscore : 7.76
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.59 %
    Favored  : 96.41 %
  Rotamer:
    Outliers :  5.65 %
    Allowed  : 29.65 %
    Favored  : 64.70 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.65 (0.28), residues: 892
  helix: -0.40 (0.21), residues: 648
  sheet:  None (None), residues: 0
  loop : -2.82 (0.35), residues: 244

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.022   0.001   TRP B 193 
 HIS   0.001   0.000   HIS D  52 
 PHE   0.023   0.001   PHE D 215 
 TYR   0.006   0.001   TYR C  49 
 ARG   0.009   0.001   ARG D 122 
Origin is already at (0, 0, 0), no shifts will be applied

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Job complete
usr+sys time: 2534.63 seconds
wall clock time: 45 minutes 36.11 seconds (2736.11 seconds total)