Starting phenix.real_space_refine
on Wed Feb 12 15:02:32 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/6vx3_21428/02_2025/6vx3_21428_neut.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/6vx3_21428/02_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_21428/02_2025/6vx3_21428.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/6vx3_21428/02_2025/6vx3_21428.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/6vx3_21428/02_2025/6vx3_21428_neut.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/6vx3_21428/02_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-5592/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: 3.97, per 1000 atoms: 0.51
  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: 2.27
  Conformation dependent library (CDL) restraints added in 1.1 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: 0.80
  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: 1.99

  Time building geometry restraints manager: 2.53 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: 0.06
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:                         0.010
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             1.000
  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:             0.000
  Extract box with map and model:          0.290
  Check model and map are aligned:         0.050
  Set scattering table:                    0.070
  Process input model:                     20.010
  Find NCS groups from input model:        0.160
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:2.710
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   24.320
-------------------------------------------------------------------------------
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  : 0.936 
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: 0.1420
  time to fit residues: 46.0691
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  : 0.778 
-------------------------------------------------------------------------------
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 = 0.111682 restraints weight = 12000.754|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3335 r_free = 0.3335 target = 0.114834 restraints weight = 7014.370|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.3363 r_free = 0.3363 target = 0.116958 restraints weight = 5016.826|
|-----------------------------------------------------------------------------|
r_work (final): 0.3338
-------------------------------------------------------------------------------
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  : 20.430 112.038   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  : 0.806 
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: 0.8659 (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: 0.5900 (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: 0.8327 (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: 0.5711 (m-70)
REVERT: B   57 TYR cc_start: 0.6773 (OUTLIER) cc_final: 0.5541 (t80)
REVERT: B   65 TRP cc_start: 0.5787 (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: 0.6461 (OUTLIER) cc_final: 0.5805 (m-70)
REVERT: D   57 TYR cc_start: 0.6751 (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: 0.8697 (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: 0.1576
  time to fit residues: 44.6195
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  : 0.826 
-------------------------------------------------------------------------------
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   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:    0.9980
   chunk 15 optimal weight:    1.9990
   chunk 37 optimal weight:    1.9990
   chunk 87 optimal weight:    0.7980
   chunk 54 optimal weight:    0.7980
   chunk 46 optimal weight:    0.7980
   chunk 3 optimal weight:    5.9990
   chunk 53 optimal weight:    2.9990
   overall best weight:    1.0782

-------------------------------------------------------------------------------
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 = 0.3735 r_free = 0.3735 target = 0.147535 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3287 r_free = 0.3287 target = 0.111151 restraints weight = 12320.036|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3327 r_free = 0.3327 target = 0.114153 restraints weight = 7211.789|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3353 r_free = 0.3353 target = 0.116157 restraints weight = 5202.549|
|-----------------------------------------------------------------------------|
r_work (final): 0.3314
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7917
moved from start:          0.2488

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.028   7988  Z= 0.240
  Angle     :  0.584   6.658  10804  Z= 0.296
  Chirality :  0.041   0.106   1232
  Planarity :  0.003   0.027   1256
  Dihedral  : 19.406 110.541   1330
  Min Nonbonded Distance : 2.488

Molprobity Statistics.
  All-atom Clashscore : 9.13
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.38 %
    Favored  : 94.62 %
  Rotamer:
    Outliers :  6.16 %
    Allowed  : 22.11 %
    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: -1.06 (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   0.001   HIS D  52 
 PHE   0.015   0.001   PHE D 227 
 TYR   0.009   0.001   TYR C  49 
 ARG   0.006   0.001   ARG D 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
  229 residues out of total 796 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 49
    poor density    : 180
  time to evaluate  : 0.828 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: C   35 PHE cc_start: 0.8814 (t80) cc_final: 0.8441 (t80)
REVERT: C   57 TYR cc_start: 0.6889 (OUTLIER) cc_final: 0.5696 (t80)
REVERT: C   59 ILE cc_start: 0.8681 (tp) cc_final: 0.8470 (tp)
REVERT: C   65 TRP cc_start: 0.6189 (OUTLIER) cc_final: 0.4445 (t60)
REVERT: C  139 MET cc_start: 0.8192 (tpp) cc_final: 0.7806 (tpp)
REVERT: C  191 GLU cc_start: 0.8671 (tm-30) cc_final: 0.8249 (tm-30)
REVERT: A   57 TYR cc_start: 0.6869 (OUTLIER) cc_final: 0.5692 (t80)
REVERT: A   65 TRP cc_start: 0.5996 (OUTLIER) cc_final: 0.4332 (t60)
REVERT: A  138 VAL cc_start: 0.9479 (p) cc_final: 0.9174 (m)
REVERT: A  139 MET cc_start: 0.8298 (tpp) cc_final: 0.7676 (tpp)
REVERT: A  191 GLU cc_start: 0.8661 (tm-30) cc_final: 0.8279 (tm-30)
REVERT: B   57 TYR cc_start: 0.6874 (OUTLIER) cc_final: 0.5638 (t80)
REVERT: B   59 ILE cc_start: 0.8678 (tp) cc_final: 0.8409 (tp)
REVERT: B   63 LEU cc_start: 0.9118 (OUTLIER) cc_final: 0.8781 (mm)
REVERT: B   65 TRP cc_start: 0.6087 (OUTLIER) cc_final: 0.4407 (t60)
REVERT: B  132 ARG cc_start: 0.8231 (mtm-85) cc_final: 0.8028 (mtm-85)
REVERT: B  191 GLU cc_start: 0.8656 (tm-30) cc_final: 0.8062 (tm-30)
REVERT: D   35 PHE cc_start: 0.8811 (t80) cc_final: 0.8366 (t80)
REVERT: D   57 TYR cc_start: 0.6802 (OUTLIER) cc_final: 0.5563 (t80)
REVERT: D   59 ILE cc_start: 0.8721 (tp) cc_final: 0.8504 (tp)
REVERT: D   63 LEU cc_start: 0.9119 (OUTLIER) cc_final: 0.8859 (mm)
REVERT: D   65 TRP cc_start: 0.6052 (OUTLIER) cc_final: 0.4288 (t60)
REVERT: D  191 GLU cc_start: 0.8670 (tm-30) cc_final: 0.8132 (tm-30)
  outliers start: 49
  outliers final: 30
  residues processed: 202
  average time/residue: 0.1846
  time to fit residues: 51.7635
Evaluate side-chains
  208 residues out of total 796 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 40
    poor density    : 168
  time to evaluate  : 0.683 
-------------------------------------------------------------------------------
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:    2.9990
   chunk 27 optimal weight:    0.9980
   chunk 5 optimal weight:    2.9990
   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:    0.9980
   chunk 31 optimal weight:    6.9990
   chunk 22 optimal weight:   20.0000
   chunk 41 optimal weight:    0.3980
   overall best weight:    1.2382

-------------------------------------------------------------------------------
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 = 0.3731 r_free = 0.3731 target = 0.146878 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3292 r_free = 0.3292 target = 0.111333 restraints weight = 11985.690|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 41)----------------|
| r_work = 0.3333 r_free = 0.3333 target = 0.114377 restraints weight = 7039.429|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3357 r_free = 0.3357 target = 0.116206 restraints weight = 5092.219|
|-----------------------------------------------------------------------------|
r_work (final): 0.3331
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7929
moved from start:          0.2780

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= 0.257
  Angle     :  0.575   6.381  10804  Z= 0.293
  Chirality :  0.041   0.119   1232
  Planarity :  0.003   0.025   1256
  Dihedral  : 18.551 104.806   1328
  Min Nonbonded Distance : 2.471

Molprobity Statistics.
  All-atom Clashscore : 9.01
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.04 %
    Favored  : 95.96 %
  Rotamer:
    Outliers :  7.04 %
    Allowed  : 24.62 %
    Favored  : 68.34 %
  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: -2.16 (0.28), residues: 892
  helix: -0.84 (0.21), residues: 636
  sheet:  None (None), residues: 0
  loop : -2.71 (0.37), residues: 256

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP A  54 
 HIS   0.002   0.001   HIS C  22 
 PHE   0.016   0.001   PHE D 224 
 TYR   0.015   0.001   TYR C  49 
 ARG   0.007   0.001   ARG D 132 

*********************** 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
  242 residues out of total 796 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 56
    poor density    : 186
  time to evaluate  : 0.892 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: C   35 PHE cc_start: 0.8796 (t80) cc_final: 0.8394 (t80)
REVERT: C   57 TYR cc_start: 0.6965 (OUTLIER) cc_final: 0.5738 (t80)
REVERT: C   59 ILE cc_start: 0.8362 (tp) cc_final: 0.8123 (tp)
REVERT: C  139 MET cc_start: 0.8257 (tpp) cc_final: 0.7887 (tpp)
REVERT: C  191 GLU cc_start: 0.8724 (tm-30) cc_final: 0.8339 (tm-30)
REVERT: A   57 TYR cc_start: 0.7047 (OUTLIER) cc_final: 0.5850 (t80)
REVERT: A   65 TRP cc_start: 0.6747 (OUTLIER) cc_final: 0.4716 (t60)
REVERT: A  139 MET cc_start: 0.8431 (tpp) cc_final: 0.7943 (tpp)
REVERT: A  191 GLU cc_start: 0.8699 (tm-30) cc_final: 0.8273 (tm-30)
REVERT: A  224 PHE cc_start: 0.6077 (t80) cc_final: 0.5549 (t80)
REVERT: B   57 TYR cc_start: 0.6906 (OUTLIER) cc_final: 0.5726 (t80)
REVERT: B   59 ILE cc_start: 0.8343 (tp) cc_final: 0.8011 (tp)
REVERT: B   63 LEU cc_start: 0.9185 (OUTLIER) cc_final: 0.8867 (mm)
REVERT: B   65 TRP cc_start: 0.6648 (OUTLIER) cc_final: 0.4696 (t60)
REVERT: B  139 MET cc_start: 0.8256 (tpp) cc_final: 0.8016 (tpp)
REVERT: B  191 GLU cc_start: 0.8702 (tm-30) cc_final: 0.8044 (tm-30)
REVERT: B  224 PHE cc_start: 0.6293 (t80) cc_final: 0.5676 (t80)
REVERT: D   35 PHE cc_start: 0.8779 (t80) cc_final: 0.8285 (t80)
REVERT: D   57 TYR cc_start: 0.6835 (OUTLIER) cc_final: 0.5590 (t80)
REVERT: D   59 ILE cc_start: 0.8633 (tp) cc_final: 0.8362 (tp)
REVERT: D   63 LEU cc_start: 0.9129 (OUTLIER) cc_final: 0.8860 (mm)
REVERT: D  139 MET cc_start: 0.8257 (tpp) cc_final: 0.7834 (tpp)
REVERT: D  191 GLU cc_start: 0.8727 (tm-30) cc_final: 0.8150 (tm-30)
  outliers start: 56
  outliers final: 40
  residues processed: 211
  average time/residue: 0.1682
  time to fit residues: 49.6045
Evaluate side-chains
  225 residues out of total 796 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 48
    poor density    : 177
  time to evaluate  : 0.807 
-------------------------------------------------------------------------------
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  147 ILE
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  109 VAL
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   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=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 88
   random chunks:
   chunk 24 optimal weight:    2.9990
   chunk 7 optimal weight:    9.9990
   chunk 36 optimal weight:    0.9990
   chunk 12 optimal weight:    4.9990
   chunk 62 optimal weight:    2.9990
   chunk 4 optimal weight:    5.9990
   chunk 9 optimal weight:    8.9990
   chunk 2 optimal weight:    2.9990
   chunk 78 optimal weight:    0.7980
   chunk 74 optimal weight:    1.9990
   chunk 73 optimal weight:    6.9990
   overall best weight:    1.9588

-------------------------------------------------------------------------------
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 = 0.3693 r_free = 0.3693 target = 0.144072 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3230 r_free = 0.3230 target = 0.106787 restraints weight = 12115.316|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3270 r_free = 0.3270 target = 0.109730 restraints weight = 7333.764|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3298 r_free = 0.3298 target = 0.111750 restraints weight = 5352.834|
|-----------------------------------------------------------------------------|
r_work (final): 0.3259
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7985
moved from start:          0.2839

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.045   7988  Z= 0.367
  Angle     :  0.663   8.402  10804  Z= 0.331
  Chirality :  0.044   0.139   1232
  Planarity :  0.004   0.034   1256
  Dihedral  : 18.283  96.429   1328
  Min Nonbonded Distance : 2.455

Molprobity Statistics.
  All-atom Clashscore : 10.25
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.93 %
    Favored  : 95.07 %
  Rotamer:
    Outliers :  7.66 %
    Allowed  : 26.51 %
    Favored  : 65.83 %
  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: -2.18 (0.27), residues: 892
  helix: -0.88 (0.20), residues: 636
  sheet:  None (None), residues: 0
  loop : -2.63 (0.37), residues: 256

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP A  54 
 HIS   0.002   0.001   HIS D  22 
 PHE   0.019   0.002   PHE B 215 
 TYR   0.009   0.001   TYR C  49 
 ARG   0.010   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
  241 residues out of total 796 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 61
    poor density    : 180
  time to evaluate  : 0.868 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: C   35 PHE cc_start: 0.8796 (t80) cc_final: 0.8314 (t80)
REVERT: C   57 TYR cc_start: 0.7031 (OUTLIER) cc_final: 0.5697 (t80)
REVERT: C   59 ILE cc_start: 0.8421 (tp) cc_final: 0.8196 (tp)
REVERT: C  139 MET cc_start: 0.8300 (tpp) cc_final: 0.7943 (tpp)
REVERT: C  191 GLU cc_start: 0.8772 (tm-30) cc_final: 0.8448 (tm-30)
REVERT: C  224 PHE cc_start: 0.6463 (t80) cc_final: 0.5995 (m-80)
REVERT: C  234 ASN cc_start: 0.8513 (t0) cc_final: 0.8098 (t0)
REVERT: A   57 TYR cc_start: 0.6983 (OUTLIER) cc_final: 0.5734 (t80)
REVERT: A  139 MET cc_start: 0.8463 (tpp) cc_final: 0.7888 (tpp)
REVERT: A  191 GLU cc_start: 0.8762 (tm-30) cc_final: 0.8355 (tm-30)
REVERT: A  234 ASN cc_start: 0.8525 (t0) cc_final: 0.8184 (t0)
REVERT: B   57 TYR cc_start: 0.6813 (OUTLIER) cc_final: 0.5548 (t80)
REVERT: B   59 ILE cc_start: 0.8438 (tp) cc_final: 0.8086 (tp)
REVERT: B   63 LEU cc_start: 0.9133 (OUTLIER) cc_final: 0.8872 (mm)
REVERT: B  191 GLU cc_start: 0.8802 (tm-30) cc_final: 0.8124 (tm-30)
REVERT: B  224 PHE cc_start: 0.6327 (t80) cc_final: 0.5950 (m-80)
REVERT: B  234 ASN cc_start: 0.8515 (t0) cc_final: 0.8214 (t0)
REVERT: D   35 PHE cc_start: 0.8794 (t80) cc_final: 0.8233 (t80)
REVERT: D   57 TYR cc_start: 0.6890 (OUTLIER) cc_final: 0.5646 (t80)
REVERT: D   59 ILE cc_start: 0.8374 (tp) cc_final: 0.8046 (tp)
REVERT: D  139 MET cc_start: 0.8356 (tpp) cc_final: 0.7884 (tpp)
REVERT: D  191 GLU cc_start: 0.8783 (tm-30) cc_final: 0.8209 (tm-30)
REVERT: D  224 PHE cc_start: 0.6164 (t80) cc_final: 0.5573 (t80)
REVERT: D  234 ASN cc_start: 0.8553 (t0) cc_final: 0.8265 (t0)
  outliers start: 61
  outliers final: 38
  residues processed: 210
  average time/residue: 0.1796
  time to fit residues: 52.2429
Evaluate side-chains
  212 residues out of total 796 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 43
    poor density    : 169
  time to evaluate  : 0.804 
-------------------------------------------------------------------------------
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  188 VAL
Chi-restraints excluded: chain C residue  220 THR
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  164 MET
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  235 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   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  188 VAL
Chi-restraints excluded: chain D residue  220 THR
Chi-restraints excluded: chain D residue  235 VAL
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 88
   random chunks:
   chunk 50 optimal weight:    0.3980
   chunk 4 optimal weight:    7.9990
   chunk 60 optimal weight:    0.3980
   chunk 58 optimal weight:    0.9980
   chunk 29 optimal weight:    1.9990
   chunk 62 optimal weight:    0.8980
   chunk 76 optimal weight:    1.9990
   chunk 75 optimal weight:    0.6980
   chunk 86 optimal weight:    0.5980
   chunk 43 optimal weight:    0.7980
   chunk 37 optimal weight:    0.9990
   overall best weight:    0.5780

-------------------------------------------------------------------------------
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
D 225 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3766 r_free = 0.3766 target = 0.149803 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3322 r_free = 0.3322 target = 0.113602 restraints weight = 11761.939|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 45)----------------|
| r_work = 0.3365 r_free = 0.3365 target = 0.116772 restraints weight = 6998.499|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3393 r_free = 0.3393 target = 0.118846 restraints weight = 5039.893|
|-----------------------------------------------------------------------------|
r_work (final): 0.3379
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7865
moved from start:          0.3329

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.021   7988  Z= 0.164
  Angle     :  0.570   8.167  10804  Z= 0.284
  Chirality :  0.040   0.148   1232
  Planarity :  0.003   0.032   1256
  Dihedral  : 16.943  88.940   1320
  Min Nonbonded Distance : 2.441

Molprobity Statistics.
  All-atom Clashscore : 8.01
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.48 %
    Favored  : 96.52 %
  Rotamer:
    Outliers :  5.78 %
    Allowed  : 28.89 %
    Favored  : 65.33 %
  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: -1.85 (0.28), residues: 892
  helix: -0.57 (0.21), residues: 636
  sheet:  None (None), residues: 0
  loop : -2.71 (0.36), residues: 256

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP A 193 
 HIS   0.001   0.000   HIS C  22 
 PHE   0.022   0.001   PHE B 215 
 TYR   0.007   0.001   TYR C  49 
 ARG   0.008   0.001   ARG D 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
  236 residues out of total 796 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 46
    poor density    : 190
  time to evaluate  : 0.821 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: C   35 PHE cc_start: 0.8731 (t80) cc_final: 0.8384 (t80)
REVERT: C   57 TYR cc_start: 0.7015 (OUTLIER) cc_final: 0.5818 (t80)
REVERT: C   59 ILE cc_start: 0.8352 (tp) cc_final: 0.8131 (tp)
REVERT: C  139 MET cc_start: 0.8269 (tpp) cc_final: 0.7964 (tpp)
REVERT: C  191 GLU cc_start: 0.8643 (tm-30) cc_final: 0.8317 (tm-30)
REVERT: C  224 PHE cc_start: 0.6289 (t80) cc_final: 0.5533 (t80)
REVERT: A   57 TYR cc_start: 0.7015 (OUTLIER) cc_final: 0.5800 (t80)
REVERT: A  139 MET cc_start: 0.8389 (tpp) cc_final: 0.7885 (tpp)
REVERT: A  191 GLU cc_start: 0.8597 (tm-30) cc_final: 0.8252 (tm-30)
REVERT: A  230 VAL cc_start: 0.9146 (OUTLIER) cc_final: 0.8757 (p)
REVERT: B   57 TYR cc_start: 0.6928 (OUTLIER) cc_final: 0.5681 (t80)
REVERT: B   63 LEU cc_start: 0.9141 (OUTLIER) cc_final: 0.8871 (mm)
REVERT: B  138 VAL cc_start: 0.9507 (p) cc_final: 0.9238 (m)
REVERT: B  139 MET cc_start: 0.8243 (tpp) cc_final: 0.7864 (tpp)
REVERT: B  191 GLU cc_start: 0.8601 (tm-30) cc_final: 0.7924 (tm-30)
REVERT: B  224 PHE cc_start: 0.6273 (t80) cc_final: 0.5983 (m-80)
REVERT: D   35 PHE cc_start: 0.8701 (t80) cc_final: 0.8380 (t80)
REVERT: D   57 TYR cc_start: 0.7033 (OUTLIER) cc_final: 0.5782 (t80)
REVERT: D  139 MET cc_start: 0.8308 (tpp) cc_final: 0.7931 (tpp)
REVERT: D  191 GLU cc_start: 0.8646 (tm-30) cc_final: 0.8116 (tm-30)
REVERT: D  224 PHE cc_start: 0.6054 (t80) cc_final: 0.5800 (m-80)
  outliers start: 46
  outliers final: 25
  residues processed: 206
  average time/residue: 0.1476
  time to fit residues: 44.0071
Evaluate side-chains
  197 residues out of total 796 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 166
  time to evaluate  : 0.857 
-------------------------------------------------------------------------------
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  111 VAL
Chi-restraints excluded: chain C residue  147 ILE
Chi-restraints excluded: chain C residue  164 MET
Chi-restraints excluded: chain C residue  188 VAL
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  111 VAL
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   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  111 VAL
Chi-restraints excluded: chain B residue  168 HIS
Chi-restraints excluded: chain B residue  188 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   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  188 VAL
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 88
   random chunks:
   chunk 1 optimal weight:    0.9990
   chunk 76 optimal weight:    0.9980
   chunk 4 optimal weight:    1.9990
   chunk 20 optimal weight:    1.9990
   chunk 0 optimal weight:   10.0000
   chunk 25 optimal weight:    0.8980
   chunk 52 optimal weight:    0.6980
   chunk 34 optimal weight:    0.7980
   chunk 15 optimal weight:    0.7980
   chunk 22 optimal weight:   10.0000
   chunk 16 optimal weight:    0.6980
   overall best weight:    0.7780

-------------------------------------------------------------------------------
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
D 225 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3758 r_free = 0.3758 target = 0.149357 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3303 r_free = 0.3303 target = 0.112332 restraints weight = 11920.611|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3343 r_free = 0.3343 target = 0.115379 restraints weight = 7235.853|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3373 r_free = 0.3373 target = 0.117549 restraints weight = 5267.462|
|-----------------------------------------------------------------------------|
r_work (final): 0.3361
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7891
moved from start:          0.3463

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= 0.190
  Angle     :  0.575   7.622  10804  Z= 0.283
  Chirality :  0.041   0.144   1232
  Planarity :  0.004   0.037   1256
  Dihedral  : 16.495  89.938   1320
  Min Nonbonded Distance : 2.425

Molprobity Statistics.
  All-atom Clashscore : 8.32
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.92 %
    Favored  : 96.08 %
  Rotamer:
    Outliers :  7.29 %
    Allowed  : 28.14 %
    Favored  : 64.57 %
  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: -1.61 (0.28), residues: 892
  helix: -0.35 (0.21), residues: 616
  sheet:  None (None), residues: 0
  loop : -2.58 (0.34), residues: 276

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   0.021   0.001   PHE C 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
  237 residues out of total 796 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 58
    poor density    : 179
  time to evaluate  : 0.802 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: C   19 ILE cc_start: 0.4119 (OUTLIER) cc_final: 0.3369 (mm)
REVERT: C   35 PHE cc_start: 0.8727 (t80) cc_final: 0.8379 (t80)
REVERT: C   57 TYR cc_start: 0.7049 (OUTLIER) cc_final: 0.5889 (t80)
REVERT: C   59 ILE cc_start: 0.8339 (tp) cc_final: 0.8065 (tp)
REVERT: C  139 MET cc_start: 0.8208 (tpp) cc_final: 0.7936 (tpp)
REVERT: C  191 GLU cc_start: 0.8636 (tm-30) cc_final: 0.8421 (tm-30)
REVERT: C  224 PHE cc_start: 0.6348 (t80) cc_final: 0.5611 (t80)
REVERT: A   19 ILE cc_start: 0.4343 (OUTLIER) cc_final: 0.3635 (mm)
REVERT: A   57 TYR cc_start: 0.7070 (OUTLIER) cc_final: 0.5814 (t80)
REVERT: A  139 MET cc_start: 0.8398 (tpp) cc_final: 0.7884 (tpp)
REVERT: A  191 GLU cc_start: 0.8637 (tm-30) cc_final: 0.8300 (tm-30)
REVERT: A  230 VAL cc_start: 0.9170 (OUTLIER) cc_final: 0.8775 (p)
REVERT: B   19 ILE cc_start: 0.4213 (OUTLIER) cc_final: 0.3463 (mm)
REVERT: B   35 PHE cc_start: 0.8763 (t80) cc_final: 0.8467 (t80)
REVERT: B   57 TYR cc_start: 0.7052 (OUTLIER) cc_final: 0.5769 (t80)
REVERT: B   63 LEU cc_start: 0.9151 (OUTLIER) cc_final: 0.8906 (mm)
REVERT: B  139 MET cc_start: 0.8241 (tpp) cc_final: 0.7926 (tpp)
REVERT: B  191 GLU cc_start: 0.8560 (tm-30) cc_final: 0.7932 (tm-30)
REVERT: B  224 PHE cc_start: 0.6315 (t80) cc_final: 0.6060 (m-80)
REVERT: D   19 ILE cc_start: 0.4153 (OUTLIER) cc_final: 0.3406 (mm)
REVERT: D   35 PHE cc_start: 0.8694 (t80) cc_final: 0.8337 (t80)
REVERT: D   57 TYR cc_start: 0.7123 (OUTLIER) cc_final: 0.5846 (t80)
REVERT: D  139 MET cc_start: 0.8321 (tpp) cc_final: 0.7740 (tpp)
REVERT: D  191 GLU cc_start: 0.8578 (tm-30) cc_final: 0.8123 (tm-30)
REVERT: D  224 PHE cc_start: 0.6065 (t80) cc_final: 0.5801 (m-80)
  outliers start: 58
  outliers final: 34
  residues processed: 209
  average time/residue: 0.1399
  time to fit residues: 43.2646
Evaluate side-chains
  211 residues out of total 796 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 44
    poor density    : 167
  time to evaluate  : 0.863 
-------------------------------------------------------------------------------
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   61 LEU
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  187 VAL
Chi-restraints excluded: chain C residue  188 VAL
Chi-restraints excluded: chain C residue  220 THR
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  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   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  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  187 VAL
Chi-restraints excluded: chain B residue  188 VAL
Chi-restraints excluded: chain B residue  220 THR
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  220 THR
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 88
   random chunks:
   chunk 76 optimal weight:    0.5980
   chunk 81 optimal weight:    1.9990
   chunk 80 optimal weight:    0.8980
   chunk 51 optimal weight:    5.9990
   chunk 71 optimal weight:    0.8980
   chunk 20 optimal weight:    0.0570
   chunk 6 optimal weight:    6.9990
   chunk 23 optimal weight:    0.4980
   chunk 74 optimal weight:    0.9990
   chunk 41 optimal weight:    0.9990
   chunk 5 optimal weight:    1.9990
   overall best weight:    0.5898

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

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

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3775 r_free = 0.3775 target = 0.151172 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3319 r_free = 0.3319 target = 0.113772 restraints weight = 11923.533|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.3362 r_free = 0.3362 target = 0.116965 restraints weight = 7170.835|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3389 r_free = 0.3389 target = 0.119022 restraints weight = 5224.021|
|-----------------------------------------------------------------------------|
r_work (final): 0.3373
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7868
moved from start:          0.3673

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= 0.165
  Angle     :  0.569   7.907  10804  Z= 0.279
  Chirality :  0.040   0.175   1232
  Planarity :  0.004   0.037   1256
  Dihedral  : 16.085  89.763   1320
  Min Nonbonded Distance : 2.423

Molprobity Statistics.
  All-atom Clashscore : 8.01
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.70 %
    Favored  : 96.30 %
  Rotamer:
    Outliers :  7.04 %
    Allowed  : 28.39 %
    Favored  : 64.57 %
  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: -1.67 (0.27), residues: 892
  helix: -0.37 (0.21), residues: 632
  sheet:  None (None), residues: 0
  loop : -2.80 (0.33), residues: 260

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP A  54 
 HIS   0.001   0.000   HIS D  22 
 PHE   0.018   0.001   PHE C 215 
 TYR   0.005   0.001   TYR C  49 
 ARG   0.009   0.001   ARG D 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
  235 residues out of total 796 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 56
    poor density    : 179
  time to evaluate  : 0.959 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: C   19 ILE cc_start: 0.4206 (OUTLIER) cc_final: 0.3491 (mm)
REVERT: C   35 PHE cc_start: 0.8715 (t80) cc_final: 0.8428 (t80)
REVERT: C   57 TYR cc_start: 0.7072 (OUTLIER) cc_final: 0.5853 (t80)
REVERT: C  139 MET cc_start: 0.8239 (tpp) cc_final: 0.7959 (tpp)
REVERT: C  224 PHE cc_start: 0.6326 (t80) cc_final: 0.5568 (t80)
REVERT: A   19 ILE cc_start: 0.4302 (OUTLIER) cc_final: 0.3598 (mm)
REVERT: A   35 PHE cc_start: 0.8838 (t80) cc_final: 0.8536 (t80)
REVERT: A   57 TYR cc_start: 0.7094 (OUTLIER) cc_final: 0.5876 (t80)
REVERT: A  139 MET cc_start: 0.8376 (tpp) cc_final: 0.7967 (tpp)
REVERT: A  191 GLU cc_start: 0.8607 (tm-30) cc_final: 0.8216 (tm-30)
REVERT: A  230 VAL cc_start: 0.9167 (OUTLIER) cc_final: 0.8744 (p)
REVERT: B   19 ILE cc_start: 0.4189 (OUTLIER) cc_final: 0.3442 (mm)
REVERT: B   57 TYR cc_start: 0.6999 (OUTLIER) cc_final: 0.5751 (t80)
REVERT: B  139 MET cc_start: 0.8261 (tpp) cc_final: 0.7937 (tpp)
REVERT: B  191 GLU cc_start: 0.8534 (tm-30) cc_final: 0.7939 (tm-30)
REVERT: B  224 PHE cc_start: 0.6276 (t80) cc_final: 0.6042 (m-80)
REVERT: D   19 ILE cc_start: 0.4132 (OUTLIER) cc_final: 0.3383 (mm)
REVERT: D   35 PHE cc_start: 0.8678 (t80) cc_final: 0.8326 (t80)
REVERT: D   57 TYR cc_start: 0.7114 (OUTLIER) cc_final: 0.5841 (t80)
REVERT: D  139 MET cc_start: 0.8334 (tpp) cc_final: 0.7765 (tpp)
REVERT: D  191 GLU cc_start: 0.8551 (tm-30) cc_final: 0.8110 (tm-30)
REVERT: D  224 PHE cc_start: 0.6042 (t80) cc_final: 0.5799 (m-80)
  outliers start: 56
  outliers final: 32
  residues processed: 211
  average time/residue: 0.1424
  time to fit residues: 44.4017
Evaluate side-chains
  209 residues out of total 796 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 41
    poor density    : 168
  time to evaluate  : 0.871 
-------------------------------------------------------------------------------
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   57 TYR
Chi-restraints excluded: chain C residue   61 LEU
Chi-restraints excluded: chain C residue  109 VAL
Chi-restraints excluded: chain C residue  111 VAL
Chi-restraints excluded: chain C residue  164 MET
Chi-restraints excluded: chain C residue  187 VAL
Chi-restraints excluded: chain C residue  188 VAL
Chi-restraints excluded: chain C residue  220 THR
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  109 VAL
Chi-restraints excluded: chain A residue  111 VAL
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  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  187 VAL
Chi-restraints excluded: chain B residue  188 VAL
Chi-restraints excluded: chain B residue  220 THR
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  187 VAL
Chi-restraints excluded: chain D residue  188 VAL
Chi-restraints excluded: chain D residue  220 THR
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 88
   random chunks:
   chunk 4 optimal weight:    0.8980
   chunk 53 optimal weight:    6.9990
   chunk 20 optimal weight:    0.7980
   chunk 2 optimal weight:    3.9990
   chunk 45 optimal weight:    0.4980
   chunk 52 optimal weight:    5.9990
   chunk 74 optimal weight:    5.9990
   chunk 21 optimal weight:    0.9980
   chunk 9 optimal weight:    6.9990
   chunk 48 optimal weight:    4.9990
   chunk 37 optimal weight:    2.9990
   overall best weight:    1.2382

-------------------------------------------------------------------------------
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 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 = 0.3740 r_free = 0.3740 target = 0.148445 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3277 r_free = 0.3277 target = 0.110636 restraints weight = 12019.734|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3319 r_free = 0.3319 target = 0.113718 restraints weight = 7320.191|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3347 r_free = 0.3347 target = 0.115779 restraints weight = 5381.136|
|-----------------------------------------------------------------------------|
r_work (final): 0.3319
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7924
moved from start:          0.3574

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.030   7988  Z= 0.255
  Angle     :  0.633   9.329  10804  Z= 0.307
  Chirality :  0.044   0.194   1232
  Planarity :  0.004   0.038   1256
  Dihedral  : 16.141  89.127   1320
  Min Nonbonded Distance : 2.411

Molprobity Statistics.
  All-atom Clashscore : 8.45
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.48 %
    Favored  : 96.52 %
  Rotamer:
    Outliers :  7.16 %
    Allowed  : 28.77 %
    Favored  : 64.07 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.67 (0.27), residues: 892
  helix: -0.41 (0.21), residues: 632
  sheet:  None (None), residues: 0
  loop : -2.69 (0.35), residues: 260

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP A  65 
 HIS   0.002   0.000   HIS A 101 
 PHE   0.020   0.001   PHE D 215 
 TYR   0.006   0.001   TYR C  49 
 ARG   0.009   0.001   ARG D 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
  238 residues out of total 796 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 57
    poor density    : 181
  time to evaluate  : 0.822 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: C   19 ILE cc_start: 0.4126 (OUTLIER) cc_final: 0.3379 (mm)
REVERT: C   35 PHE cc_start: 0.8739 (t80) cc_final: 0.8403 (t80)
REVERT: C   57 TYR cc_start: 0.7093 (OUTLIER) cc_final: 0.5869 (t80)
REVERT: C  139 MET cc_start: 0.8248 (tpp) cc_final: 0.7986 (tpp)
REVERT: C  224 PHE cc_start: 0.6312 (t80) cc_final: 0.5644 (t80)
REVERT: A   19 ILE cc_start: 0.4385 (OUTLIER) cc_final: 0.3962 (mt)
REVERT: A   57 TYR cc_start: 0.7170 (OUTLIER) cc_final: 0.5933 (t80)
REVERT: A  139 MET cc_start: 0.8385 (tpp) cc_final: 0.8009 (tpp)
REVERT: A  191 GLU cc_start: 0.8616 (tm-30) cc_final: 0.8297 (tm-30)
REVERT: B   19 ILE cc_start: 0.4226 (OUTLIER) cc_final: 0.3476 (mm)
REVERT: B   35 PHE cc_start: 0.8733 (t80) cc_final: 0.8462 (t80)
REVERT: B   57 TYR cc_start: 0.7076 (OUTLIER) cc_final: 0.5785 (t80)
REVERT: B  139 MET cc_start: 0.8301 (tpp) cc_final: 0.7940 (tpp)
REVERT: B  191 GLU cc_start: 0.8612 (tm-30) cc_final: 0.7964 (tm-30)
REVERT: B  224 PHE cc_start: 0.6341 (t80) cc_final: 0.5667 (t80)
REVERT: D   19 ILE cc_start: 0.4177 (OUTLIER) cc_final: 0.3418 (mm)
REVERT: D   35 PHE cc_start: 0.8710 (t80) cc_final: 0.8321 (t80)
REVERT: D   57 TYR cc_start: 0.7108 (OUTLIER) cc_final: 0.5838 (t80)
REVERT: D  139 MET cc_start: 0.8367 (tpp) cc_final: 0.7761 (tpp)
REVERT: D  191 GLU cc_start: 0.8632 (tm-30) cc_final: 0.8247 (tm-30)
REVERT: D  224 PHE cc_start: 0.6092 (t80) cc_final: 0.5678 (t80)
  outliers start: 57
  outliers final: 35
  residues processed: 211
  average time/residue: 0.1522
  time to fit residues: 46.4183
Evaluate side-chains
  218 residues out of total 796 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 43
    poor density    : 175
  time to evaluate  : 0.863 
-------------------------------------------------------------------------------
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   68 THR
Chi-restraints excluded: chain C residue  101 HIS
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  164 MET
Chi-restraints excluded: chain C residue  168 HIS
Chi-restraints excluded: chain C residue  187 VAL
Chi-restraints excluded: chain C residue  188 VAL
Chi-restraints excluded: chain C residue  220 THR
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  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   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 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  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
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:    0.7980
   chunk 79 optimal weight:    0.9990
   chunk 28 optimal weight:    7.9990
   chunk 74 optimal weight:    2.9990
   chunk 4 optimal weight:    1.9990
   chunk 72 optimal weight:    9.9990
   chunk 25 optimal weight:    0.6980
   chunk 7 optimal weight:    0.5980
   chunk 12 optimal weight:    1.9990
   chunk 24 optimal weight:    0.9980
   overall best weight:    0.7780

-------------------------------------------------------------------------------
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 225 ASN
B 101 HIS
D 101 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 = 0.3757 r_free = 0.3757 target = 0.149763 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3306 r_free = 0.3306 target = 0.112551 restraints weight = 11698.395|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3347 r_free = 0.3347 target = 0.115669 restraints weight = 7104.519|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3376 r_free = 0.3376 target = 0.117749 restraints weight = 5189.487|
|-----------------------------------------------------------------------------|
r_work (final): 0.3366
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7891
moved from start:          0.3706

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028   7988  Z= 0.199
  Angle     :  0.631   9.149  10804  Z= 0.303
  Chirality :  0.044   0.246   1232
  Planarity :  0.004   0.039   1256
  Dihedral  : 15.861  89.771   1320
  Min Nonbonded Distance : 2.406

Molprobity Statistics.
  All-atom Clashscore : 8.76
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.36 %
    Favored  : 96.64 %
  Rotamer:
    Outliers :  6.16 %
    Allowed  : 29.52 %
    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: -1.63 (0.27), residues: 892
  helix: -0.35 (0.21), residues: 632
  sheet:  None (None), residues: 0
  loop : -2.75 (0.34), residues: 260

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP A  54 
 HIS   0.001   0.000   HIS C 101 
 PHE   0.017   0.001   PHE D 215 
 TYR   0.006   0.001   TYR C  49 
 ARG   0.009   0.001   ARG B 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
  222 residues out of total 796 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 49
    poor density    : 173
  time to evaluate  : 0.823 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: C   19 ILE cc_start: 0.4172 (OUTLIER) cc_final: 0.3467 (mm)
REVERT: C   35 PHE cc_start: 0.8696 (t80) cc_final: 0.8400 (t80)
REVERT: C   57 TYR cc_start: 0.7112 (OUTLIER) cc_final: 0.5897 (t80)
REVERT: C  139 MET cc_start: 0.8227 (tpp) cc_final: 0.7973 (tpp)
REVERT: C  224 PHE cc_start: 0.6294 (t80) cc_final: 0.5641 (t80)
REVERT: A   19 ILE cc_start: 0.4361 (OUTLIER) cc_final: 0.3665 (mm)
REVERT: A   35 PHE cc_start: 0.8845 (t80) cc_final: 0.8517 (t80)
REVERT: A   57 TYR cc_start: 0.7102 (OUTLIER) cc_final: 0.5883 (t80)
REVERT: A  139 MET cc_start: 0.8355 (tpp) cc_final: 0.7984 (tpp)
REVERT: A  191 GLU cc_start: 0.8571 (tm-30) cc_final: 0.8281 (tm-30)
REVERT: B   19 ILE cc_start: 0.4158 (OUTLIER) cc_final: 0.3419 (mm)
REVERT: B   35 PHE cc_start: 0.8703 (t80) cc_final: 0.8429 (t80)
REVERT: B   57 TYR cc_start: 0.7096 (OUTLIER) cc_final: 0.5809 (t80)
REVERT: B  139 MET cc_start: 0.8279 (tpp) cc_final: 0.7906 (tpp)
REVERT: B  191 GLU cc_start: 0.8561 (tm-30) cc_final: 0.8025 (tm-30)
REVERT: B  224 PHE cc_start: 0.6301 (t80) cc_final: 0.5659 (t80)
REVERT: D   19 ILE cc_start: 0.4128 (OUTLIER) cc_final: 0.3374 (mm)
REVERT: D   35 PHE cc_start: 0.8666 (t80) cc_final: 0.8338 (t80)
REVERT: D   57 TYR cc_start: 0.7051 (OUTLIER) cc_final: 0.5818 (t80)
REVERT: D  139 MET cc_start: 0.8366 (tpp) cc_final: 0.7828 (tpp)
REVERT: D  191 GLU cc_start: 0.8587 (tm-30) cc_final: 0.8191 (tm-30)
REVERT: D  224 PHE cc_start: 0.6061 (t80) cc_final: 0.5646 (t80)
  outliers start: 49
  outliers final: 38
  residues processed: 197
  average time/residue: 0.1389
  time to fit residues: 40.8196
Evaluate side-chains
  217 residues out of total 796 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 46
    poor density    : 171
  time to evaluate  : 0.865 
-------------------------------------------------------------------------------
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  101 HIS
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  164 MET
Chi-restraints excluded: chain C residue  168 HIS
Chi-restraints excluded: chain C residue  187 VAL
Chi-restraints excluded: chain C residue  188 VAL
Chi-restraints excluded: chain C residue  220 THR
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  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   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  101 HIS
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 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  101 HIS
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  220 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 88
   random chunks:
   chunk 25 optimal weight:    1.9990
   chunk 7 optimal weight:    0.0980
   chunk 86 optimal weight:    0.9990
   chunk 10 optimal weight:    0.8980
   chunk 55 optimal weight:    0.2980
   chunk 87 optimal weight:    1.9990
   chunk 67 optimal weight:    0.7980
   chunk 72 optimal weight:   10.0000
   chunk 36 optimal weight:    0.6980
   chunk 61 optimal weight:    1.9990
   chunk 32 optimal weight:    0.8980
   overall best weight:    0.5580

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

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

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3776 r_free = 0.3776 target = 0.151458 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.3324 r_free = 0.3324 target = 0.114144 restraints weight = 11622.241|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3365 r_free = 0.3365 target = 0.117227 restraints weight = 7129.044|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 43)----------------|
| r_work = 0.3394 r_free = 0.3394 target = 0.119362 restraints weight = 5214.534|
|-----------------------------------------------------------------------------|
r_work (final): 0.3385
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7875
moved from start:          0.3817

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028   7988  Z= 0.174
  Angle     :  0.620   9.026  10804  Z= 0.296
  Chirality :  0.043   0.209   1232
  Planarity :  0.004   0.039   1256
  Dihedral  : 15.552  89.774   1320
  Min Nonbonded Distance : 2.402

Molprobity Statistics.
  All-atom Clashscore : 8.39
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.81 %
    Favored  : 96.19 %
  Rotamer:
    Outliers :  5.90 %
    Allowed  : 29.90 %
    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: -1.54 (0.27), residues: 892
  helix: -0.29 (0.21), residues: 636
  sheet:  None (None), residues: 0
  loop : -2.73 (0.34), residues: 256

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP C  54 
 HIS   0.002   0.001   HIS D 101 
 PHE   0.015   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

===============================================================================
Job complete
usr+sys time: 2506.92 seconds
wall clock time: 45 minutes 34.64 seconds (2734.64 seconds total)