Starting phenix.real_space_refine
on Wed Aug  5 03:55:30 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9mue_48630/08_2026/9mue_48630.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9mue_48630/08_2026/9mue_48630.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=4.0
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/9mue_48630/08_2026/9mue_48630.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9mue_48630/08_2026/9mue_48630.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/9mue_48630/08_2026/9mue_48630.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9mue_48630/08_2026/9mue_48630.map"
  }
  resolution = 4.0
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.005 sd=   0.050
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      12      5.49       5
     S      20      5.16       5
     C    5434      2.51       5
     N    1430      2.21       5
     O    1542      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 15 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib"
  Total number of atoms: 8438
  Number of models: 1
  Model: ""
    Number of chains: 8
    Chain: "A"
      Number of atoms: 2022
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 249, 2022
          Classifications: {'peptide': 249}
          Link IDs: {'PTRANS': 12, 'TRANS': 236}
          Chain breaks: 1
    Chain: "a"
      Number of atoms: 88
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 4, 88
          Classifications: {'RNA': 4}
          Modifications used: {'rna2p_pur': 4}
          Link IDs: {'rna2p': 3}
    Chain: "b"
      Number of atoms: 88
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 4, 88
          Classifications: {'RNA': 4}
          Modifications used: {'rna2p_pur': 4}
          Link IDs: {'rna2p': 3}
    Chain: "B"
      Number of atoms: 2073
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 257, 2073
          Classifications: {'peptide': 257}
          Link IDs: {'PTRANS': 13, 'TRANS': 243}
    Chain: "C"
      Number of atoms: 2022
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 249, 2022
          Classifications: {'peptide': 249}
          Link IDs: {'PTRANS': 12, 'TRANS': 236}
          Chain breaks: 1
    Chain: "D"
      Number of atoms: 2073
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 257, 2073
          Classifications: {'peptide': 257}
          Link IDs: {'PTRANS': 13, 'TRANS': 243}
    Chain: "B"
      Number of atoms: 36
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 36
          Unusual residues: {'AR6': 1}
          Classifications: {'undetermined': 1}
    Chain: "D"
      Number of atoms: 36
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 36
          Unusual residues: {'AR6': 1}
          Classifications: {'undetermined': 1}
  Time building chain proxies: 1.90, per 1000 atoms: 0.23
  Number of scatterers: 8438
  At special positions: 0
  Unit cell: (65.912, 130.112, 83.888, 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      20     16.00
     P      12     15.00
     O    1542      8.00
     N    1430      7.00
     C    5434      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 0.53
  Conformation dependent library (CDL) restraints added in 411.3 milliseconds
  

  2000 Ramachandran restraints generated.
    1000 Oldfield, 0 Emsley, 1000 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1932

  Finding SS restraints...
    Secondary structure from input PDB file:
      41 helices and 10 sheets defined
      36.8% alpha, 18.6% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.14
  Creating SS restraints...
    Processing helix  chain 'A' and resid 9 through 11
      No H-bonds generated for 'chain 'A' and resid 9 through 11'
    Processing helix  chain 'A' and resid 12 through 25
    Processing helix  chain 'A' and resid 72 through 83
    Processing helix  chain 'A' and resid 96 through 100
    Processing helix  chain 'A' and resid 106 through 119
    Processing helix  chain 'A' and resid 129 through 142
    Processing helix  chain 'A' and resid 177 through 182
      removed outlier: 4.053A  pdb=" N   HIS A 181 " --> pdb=" O   ASP A 177 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 185 through 190
      removed outlier: 4.090A  pdb=" N   ASP A 188 " --> pdb=" O   LYS A 185 " (cutoff:3.500A)
      removed outlier: 3.689A  pdb=" N   ILE A 190 " --> pdb=" O   GLU A 187 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 213 through 222
    Processing helix  chain 'A' and resid 223 through 225
      No H-bonds generated for 'chain 'A' and resid 223 through 225'
    Processing helix  chain 'B' and resid 9 through 11
      No H-bonds generated for 'chain 'B' and resid 9 through 11'
    Processing helix  chain 'B' and resid 12 through 25
      removed outlier: 3.557A  pdb=" N   GLU B  18 " --> pdb=" O   LYS B  14 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 68 through 83
      removed outlier: 3.666A  pdb=" N   TRP B  72 " --> pdb=" O   SER B  68 " (cutoff:3.500A)
      removed outlier: 4.437A  pdb=" N   GLU B  74 " --> pdb=" O   TRP B  70 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 96 through 100
    Processing helix  chain 'B' and resid 106 through 120
    Processing helix  chain 'B' and resid 129 through 144
      removed outlier: 4.635A  pdb=" N   ASN B 144 " --> pdb=" O   ALA B 140 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 177 through 182
      removed outlier: 4.096A  pdb=" N   HIS B 181 " --> pdb=" O   ASP B 177 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 185 through 190
      removed outlier: 3.570A  pdb=" N   ASP B 188 " --> pdb=" O   LYS B 185 " (cutoff:3.500A)
      removed outlier: 4.138A  pdb=" N   ILE B 190 " --> pdb=" O   GLU B 187 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 213 through 222
    Processing helix  chain 'B' and resid 223 through 225
      No H-bonds generated for 'chain 'B' and resid 223 through 225'
    Processing helix  chain 'C' and resid 12 through 25
    Processing helix  chain 'C' and resid 64 through 67
    Processing helix  chain 'C' and resid 68 through 83
      removed outlier: 5.028A  pdb=" N   GLU C  74 " --> pdb=" O   TRP C  70 " (cutoff:3.500A)
      removed outlier: 3.998A  pdb=" N   LEU C  75 " --> pdb=" O   CYS C  71 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 96 through 100
      removed outlier: 3.774A  pdb=" N   LEU C 100 " --> pdb=" O   ARG C  97 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 106 through 120
    Processing helix  chain 'C' and resid 129 through 142
    Processing helix  chain 'C' and resid 177 through 182
      removed outlier: 3.564A  pdb=" N   TRP C 182 " --> pdb=" O   LEU C 179 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 185 through 190
      removed outlier: 3.903A  pdb=" N   ASP C 188 " --> pdb=" O   LYS C 185 " (cutoff:3.500A)
      removed outlier: 3.894A  pdb=" N   ILE C 190 " --> pdb=" O   GLU C 187 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 213 through 222
    Processing helix  chain 'C' and resid 223 through 225
      No H-bonds generated for 'chain 'C' and resid 223 through 225'
    Processing helix  chain 'D' and resid 9 through 11
      No H-bonds generated for 'chain 'D' and resid 9 through 11'
    Processing helix  chain 'D' and resid 12 through 25
      removed outlier: 3.625A  pdb=" N   GLU D  18 " --> pdb=" O   LYS D  14 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 44 through 48
    Processing helix  chain 'D' and resid 68 through 83
      removed outlier: 3.897A  pdb=" N   TRP D  72 " --> pdb=" O   SER D  68 " (cutoff:3.500A)
      removed outlier: 3.766A  pdb=" N   ASP D  73 " --> pdb=" O   ASP D  69 " (cutoff:3.500A)
      removed outlier: 3.722A  pdb=" N   GLU D  74 " --> pdb=" O   TRP D  70 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 96 through 100
    Processing helix  chain 'D' and resid 106 through 120
    Processing helix  chain 'D' and resid 129 through 143
    Processing helix  chain 'D' and resid 177 through 182
      removed outlier: 3.681A  pdb=" N   TRP D 182 " --> pdb=" O   LEU D 179 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 185 through 190
    Processing helix  chain 'D' and resid 213 through 222
    Processing helix  chain 'D' and resid 223 through 225
      No H-bonds generated for 'chain 'D' and resid 223 through 225'
    Processing sheet with id=AA1, first strand: chain 'A' and resid 29 through 31
      removed outlier: 3.706A  pdb=" N   PHE A   6 " --> pdb=" O   TRP A  31 " (cutoff:3.500A)
      removed outlier: 3.785A  pdb=" N   PHE A   5 " --> pdb=" O   TYR A  56 " (cutoff:3.500A)
      removed outlier: 4.003A  pdb=" N   LYS A  88 " --> pdb=" O   GLN A  55 " (cutoff:3.500A)
      removed outlier: 8.606A  pdb=" N   VAL A 123 " --> pdb=" O   ILE A  89 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 150 through 157
      removed outlier: 4.037A  pdb=" N   GLU A 166 " --> pdb=" O   GLU A 150 " (cutoff:3.500A)
      removed outlier: 4.754A  pdb=" N   ILE A 152 " --> pdb=" O   VAL A 164 " (cutoff:3.500A)
      removed outlier: 6.743A  pdb=" N   VAL A 164 " --> pdb=" O   ILE A 152 " (cutoff:3.500A)
      removed outlier: 4.909A  pdb=" N   MET A 154 " --> pdb=" O   LEU A 162 " (cutoff:3.500A)
      removed outlier: 6.905A  pdb=" N   LEU A 162 " --> pdb=" O   MET A 154 " (cutoff:3.500A)
      removed outlier: 4.682A  pdb=" N   LYS A 156 " --> pdb=" O   THR A 160 " (cutoff:3.500A)
      removed outlier: 5.579A  pdb=" N   THR A 160 " --> pdb=" O   LYS A 156 " (cutoff:3.500A)
      removed outlier: 8.137A  pdb=" N   ALA A 207 " --> pdb=" O   GLU A 161 " (cutoff:3.500A)
      removed outlier: 6.859A  pdb=" N   GLN A 163 " --> pdb=" O   ALA A 207 " (cutoff:3.500A)
      removed outlier: 7.815A  pdb=" N   TYR A 209 " --> pdb=" O   GLN A 163 " (cutoff:3.500A)
      removed outlier: 6.410A  pdb=" N   VAL A 165 " --> pdb=" O   TYR A 209 " (cutoff:3.500A)
      removed outlier: 6.350A  pdb=" N   VAL A 206 " --> pdb=" O   PHE A 231 " (cutoff:3.500A)
      removed outlier: 8.190A  pdb=" N   PHE A 233 " --> pdb=" O   VAL A 206 " (cutoff:3.500A)
      removed outlier: 7.370A  pdb=" N   LEU A 208 " --> pdb=" O   PHE A 233 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'B' and resid 29 through 31
      removed outlier: 4.106A  pdb=" N   PHE B   5 " --> pdb=" O   TYR B  56 " (cutoff:3.500A)
      removed outlier: 5.658A  pdb=" N   PHE B  57 " --> pdb=" O   ILE B  90 " (cutoff:3.500A)
      removed outlier: 6.644A  pdb=" N   ILE B  92 " --> pdb=" O   PHE B  57 " (cutoff:3.500A)
      removed outlier: 6.232A  pdb=" N   ALA B  59 " --> pdb=" O   ILE B  92 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'B' and resid 150 through 157
      removed outlier: 5.272A  pdb=" N   GLU B 166 " --> pdb=" O   PRO B 151 " (cutoff:3.500A)
      removed outlier: 3.556A  pdb=" N   ARG B 153 " --> pdb=" O   VAL B 164 " (cutoff:3.500A)
      removed outlier: 6.247A  pdb=" N   VAL B 206 " --> pdb=" O   PHE B 231 " (cutoff:3.500A)
      removed outlier: 7.843A  pdb=" N   PHE B 233 " --> pdb=" O   VAL B 206 " (cutoff:3.500A)
      removed outlier: 7.103A  pdb=" N   LEU B 208 " --> pdb=" O   PHE B 233 " (cutoff:3.500A)
      removed outlier: 3.542A  pdb=" N   GLU B 239 " --> pdb=" O   ASN B 234 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'C' and resid 29 through 31
      removed outlier: 6.148A  pdb=" N   ALA C   4 " --> pdb=" O   TRP C  31 " (cutoff:3.500A)
      removed outlier: 7.224A  pdb=" N   GLN C   3 " --> pdb=" O   TYR C  56 " (cutoff:3.500A)
      removed outlier: 7.513A  pdb=" N   LEU C  58 " --> pdb=" O   GLN C   3 " (cutoff:3.500A)
      removed outlier: 6.270A  pdb=" N   PHE C   5 " --> pdb=" O   LEU C  58 " (cutoff:3.500A)
      removed outlier: 7.090A  pdb=" N   PHE C  60 " --> pdb=" O   PHE C   5 " (cutoff:3.500A)
      removed outlier: 7.218A  pdb=" N   SER C   7 " --> pdb=" O   PHE C  60 " (cutoff:3.500A)
      removed outlier: 3.930A  pdb=" N   LYS C  88 " --> pdb=" O   GLN C  55 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'C' and resid 150 through 157
      removed outlier: 5.339A  pdb=" N   GLU C 166 " --> pdb=" O   PRO C 151 " (cutoff:3.500A)
      removed outlier: 3.853A  pdb=" N   ARG C 153 " --> pdb=" O   VAL C 164 " (cutoff:3.500A)
      removed outlier: 7.929A  pdb=" N   ALA C 207 " --> pdb=" O   GLU C 161 " (cutoff:3.500A)
      removed outlier: 6.563A  pdb=" N   GLN C 163 " --> pdb=" O   ALA C 207 " (cutoff:3.500A)
      removed outlier: 7.268A  pdb=" N   TYR C 209 " --> pdb=" O   GLN C 163 " (cutoff:3.500A)
      removed outlier: 5.732A  pdb=" N   VAL C 165 " --> pdb=" O   TYR C 209 " (cutoff:3.500A)
      removed outlier: 6.289A  pdb=" N   VAL C 206 " --> pdb=" O   PHE C 231 " (cutoff:3.500A)
      removed outlier: 8.116A  pdb=" N   PHE C 233 " --> pdb=" O   VAL C 206 " (cutoff:3.500A)
      removed outlier: 7.343A  pdb=" N   LEU C 208 " --> pdb=" O   PHE C 233 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'D' and resid 29 through 31
      removed outlier: 6.267A  pdb=" N   ALA D   4 " --> pdb=" O   TRP D  31 " (cutoff:3.500A)
      removed outlier: 7.149A  pdb=" N   GLN D   3 " --> pdb=" O   TYR D  56 " (cutoff:3.500A)
      removed outlier: 7.564A  pdb=" N   LEU D  58 " --> pdb=" O   GLN D   3 " (cutoff:3.500A)
      removed outlier: 6.566A  pdb=" N   PHE D   5 " --> pdb=" O   LEU D  58 " (cutoff:3.500A)
      removed outlier: 7.130A  pdb=" N   PHE D  60 " --> pdb=" O   PHE D   5 " (cutoff:3.500A)
      removed outlier: 7.282A  pdb=" N   SER D   7 " --> pdb=" O   PHE D  60 " (cutoff:3.500A)
      removed outlier: 3.613A  pdb=" N   LYS D  88 " --> pdb=" O   GLN D  55 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'D' and resid 29 through 31
      removed outlier: 6.267A  pdb=" N   ALA D   4 " --> pdb=" O   TRP D  31 " (cutoff:3.500A)
      removed outlier: 7.149A  pdb=" N   GLN D   3 " --> pdb=" O   TYR D  56 " (cutoff:3.500A)
      removed outlier: 7.564A  pdb=" N   LEU D  58 " --> pdb=" O   GLN D   3 " (cutoff:3.500A)
      removed outlier: 6.566A  pdb=" N   PHE D   5 " --> pdb=" O   LEU D  58 " (cutoff:3.500A)
      removed outlier: 7.130A  pdb=" N   PHE D  60 " --> pdb=" O   PHE D   5 " (cutoff:3.500A)
      removed outlier: 7.282A  pdb=" N   SER D   7 " --> pdb=" O   PHE D  60 " (cutoff:3.500A)
      removed outlier: 6.591A  pdb=" N   ILE D  92 " --> pdb=" O   PHE D  57 " (cutoff:3.500A)
      removed outlier: 6.337A  pdb=" N   ALA D  59 " --> pdb=" O   ILE D  92 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'D' and resid 148 through 149
      removed outlier: 3.570A  pdb=" N   LEU D 162 " --> pdb=" O   ILE D 155 " (cutoff:3.500A)
      removed outlier: 3.548A  pdb=" N   ARG D 153 " --> pdb=" O   VAL D 164 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'D' and resid 148 through 149
      removed outlier: 3.853A  pdb=" N   TYR D 209 " --> pdb=" O   VAL D 165 " (cutoff:3.500A)
      removed outlier: 3.759A  pdb=" N   PHE D 167 " --> pdb=" O   TYR D 209 " (cutoff:3.500A)
      removed outlier: 3.503A  pdb=" N   ASN D 234 " --> pdb=" O   GLU D 239 " (cutoff:3.500A)

    284 hydrogen bonds defined for protein.
    756 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: 0.92

  Time building geometry restraints manager: 0.72 seconds

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

  Histogram of bond lengths:
        1.22 -     1.34: 2599
        1.34 -     1.46: 1565
        1.46 -     1.58: 4458
        1.58 -     1.70: 23
        1.70 -     1.82: 33
  Bond restraints: 8678
  Sorted by residual:
  bond pdb=" CG  PRO C  91 "
       pdb=" CD  PRO C  91 "
    ideal  model  delta    sigma   weight residual
    1.503  1.357  0.146 3.40e-02 8.65e+02 1.84e+01
  bond pdb=" CB  PRO C  91 "
       pdb=" CG  PRO C  91 "
    ideal  model  delta    sigma   weight residual
    1.492  1.697 -0.205 5.00e-02 4.00e+02 1.69e+01
  bond pdb=" N   PRO C  91 "
       pdb=" CD  PRO C  91 "
    ideal  model  delta    sigma   weight residual
    1.473  1.513 -0.040 1.40e-02 5.10e+03 8.35e+00
  bond pdb=" N   ILE B  37 "
       pdb=" CA  ILE B  37 "
    ideal  model  delta    sigma   weight residual
    1.461  1.493 -0.032 1.23e-02 6.61e+03 6.87e+00
  bond pdb=" N   ILE B  32 "
       pdb=" CA  ILE B  32 "
    ideal  model  delta    sigma   weight residual
    1.459  1.491 -0.032 1.25e-02 6.40e+03 6.59e+00
  ... (remaining 8673 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     3.34: 11725
        3.34 -     6.68: 84
        6.68 -    10.02: 17
       10.02 -    13.36: 2
       13.36 -    16.70: 2
  Bond angle restraints: 11830
  Sorted by residual:
  angle pdb=" CA  PRO C  91 "
        pdb=" N   PRO C  91 "
        pdb=" CD  PRO C  91 "
      ideal   model   delta    sigma   weight residual
     112.00   95.30   16.70 1.40e+00 5.10e-01 1.42e+02
  angle pdb=" CA  PRO B 127 "
        pdb=" N   PRO B 127 "
        pdb=" CD  PRO B 127 "
      ideal   model   delta    sigma   weight residual
     112.00  101.99   10.01 1.40e+00 5.10e-01 5.11e+01
  angle pdb=" N   PRO C  91 "
        pdb=" CD  PRO C  91 "
        pdb=" CG  PRO C  91 "
      ideal   model   delta    sigma   weight residual
     103.20   93.05   10.15 1.50e+00 4.44e-01 4.58e+01
  angle pdb=" N   PRO C  91 "
        pdb=" CA  PRO C  91 "
        pdb=" CB  PRO C  91 "
      ideal   model   delta    sigma   weight residual
     103.25   98.78    4.47 1.05e+00 9.07e-01 1.81e+01
  angle pdb=" CA  GLN C  83 "
        pdb=" CB  GLN C  83 "
        pdb=" CG  GLN C  83 "
      ideal   model   delta    sigma   weight residual
     114.10  122.31   -8.21 2.00e+00 2.50e-01 1.68e+01
  ... (remaining 11825 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    20.73: 4429
       20.73 -    41.45: 626
       41.45 -    62.18: 113
       62.18 -    82.90: 30
       82.90 -   103.63: 2
  Dihedral angle restraints: 5200
    sinusoidal: 2230
      harmonic: 2970
  Sorted by residual:
  dihedral pdb=" O1A AR6 B 301 "
           pdb=" O3A AR6 B 301 "
           pdb=" PA  AR6 B 301 "
           pdb=" PB  AR6 B 301 "
      ideal   model   delta sinusoidal    sigma   weight residual
     277.49  173.86  103.63     1      3.00e+01 1.11e-03 1.32e+01
  dihedral pdb=" CA  ASP D  69 "
           pdb=" CB  ASP D  69 "
           pdb=" CG  ASP D  69 "
           pdb=" OD1 ASP D  69 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -30.00  -89.96   59.96     1      2.00e+01 2.50e-03 1.20e+01
  dihedral pdb=" CA  TRP C  70 "
           pdb=" C   TRP C  70 "
           pdb=" N   CYS C  71 "
           pdb=" CA  CYS C  71 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  162.93   17.07     0      5.00e+00 4.00e-02 1.17e+01
  ... (remaining 5197 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.055: 1050
       0.055 -    0.110: 232
       0.110 -    0.165: 32
       0.165 -    0.220: 3
       0.220 -    0.275: 3
  Chirality restraints: 1320
  Sorted by residual:
  chirality pdb=" CA  PRO C  91 "
            pdb=" N   PRO C  91 "
            pdb=" C   PRO C  91 "
            pdb=" CB  PRO C  91 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.72    2.44    0.27 2.00e-01 2.50e+01 1.89e+00
  chirality pdb=" C2D AR6 B 301 "
            pdb=" C1D AR6 B 301 "
            pdb=" C3D AR6 B 301 "
            pdb=" O2D AR6 B 301 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.70   -2.43   -0.26 2.00e-01 2.50e+01 1.73e+00
  chirality pdb=" C2D AR6 D 301 "
            pdb=" C1D AR6 D 301 "
            pdb=" C3D AR6 D 301 "
            pdb=" O2D AR6 D 301 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.70   -2.44   -0.25 2.00e-01 2.50e+01 1.59e+00
  ... (remaining 1317 not shown)

  Planarity restraints: 1458
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ASP B 126 "   -0.107 5.00e-02 4.00e+02   1.55e-01 3.82e+01
        pdb=" N   PRO B 127 "    0.267 5.00e-02 4.00e+02
        pdb=" CA  PRO B 127 "   -0.082 5.00e-02 4.00e+02
        pdb=" CD  PRO B 127 "   -0.078 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ASP D 126 "   -0.053 5.00e-02 4.00e+02   8.03e-02 1.03e+01
        pdb=" N   PRO D 127 "    0.139 5.00e-02 4.00e+02
        pdb=" CA  PRO D 127 "   -0.042 5.00e-02 4.00e+02
        pdb=" CD  PRO D 127 "   -0.044 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ILE C  90 "   -0.053 5.00e-02 4.00e+02   7.14e-02 8.15e+00
        pdb=" N   PRO C  91 "    0.123 5.00e-02 4.00e+02
        pdb=" CA  PRO C  91 "   -0.031 5.00e-02 4.00e+02
        pdb=" CD  PRO C  91 "   -0.039 5.00e-02 4.00e+02
  ... (remaining 1455 not shown)

  Histogram of nonbonded interaction distances:
        2.10 -     2.66: 201
        2.66 -     3.22: 8116
        3.22 -     3.78: 13511
        3.78 -     4.34: 17445
        4.34 -     4.90: 27776
  Nonbonded interactions: 67049
  Sorted by model distance:
  nonbonded pdb=" OG1 THR B 237 "
            pdb=" OE1 GLU B 239 "
     model   vdw
     2.101 3.040
  nonbonded pdb=" OH  TYR C  56 "
            pdb=" OE1 GLU C 145 "
     model   vdw
     2.157 3.040
  nonbonded pdb=" OG  SER A  62 "
            pdb=" OE1 GLU A  64 "
     model   vdw
     2.196 3.040
  nonbonded pdb=" O   GLU A 114 "
            pdb=" OG1 THR A 118 "
     model   vdw
     2.196 3.040
  nonbonded pdb=" OG  SER D 245 "
            pdb=" O   LEU D 250 "
     model   vdw
     2.199 3.040
  ... (remaining 67044 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: 0.00
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = (chain 'B' and (resid 2 through 33 or resid 42 through 258))
  selection = chain 'C'
  selection = (chain 'D' and (resid 2 through 33 or resid 42 through 258))
}
ncs_group {
  reference = chain 'a'
  selection = chain 'b'
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             12.040
  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:          0.140
  Check model and map are aligned:         0.030
  Set scattering table:                    0.020
  Process input model:                     7.810
  Find NCS groups from input model:        0.100
  Set up NCS constraints:                  0.010
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.370
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   21.520
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8616
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      :  0.005   0.205   8678  Z= 0.215
  Angle     :  0.810  16.699  11830  Z= 0.438
  Chirality :  0.048   0.275   1320
  Planarity :  0.007   0.155   1458
  Dihedral  : 18.797 103.628   3268
  Min Nonbonded Distance : 2.101

Molprobity Statistics.
  All-atom Clashscore : 15.60
  Ramachandran Plot:
    Outliers :  0.60 %
    Allowed  :  4.90 %
    Favored  : 94.50 %
  Rotamer:
    Outliers :  1.00 %
    Allowed  : 34.30 %
    Favored  : 64.70 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.03 (0.28), residues: 1000
  helix:  0.74 (0.33), residues: 290
  sheet: -0.51 (0.38), residues: 206
  loop : -0.04 (0.28), residues: 504

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG A 148 
 TYR   0.024   0.002   TYR C  56 
 PHE   0.012   0.001   PHE A 112 
 TRP   0.049   0.002   TRP A  70 
 HIS   0.003   0.001   HIS B 128 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00477 /  0.21 ( 8678)
  covalent geometry    : angle       0.81020 /  0.44 (11830)
  hydrogen bonds       : bond        0.22300 / 14.47 (  282)
  hydrogen bonds       : angle       7.07985 /  4.96 (  756)

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

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

  2000 Ramachandran restraints generated.
    1000 Oldfield, 0 Emsley, 1000 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2000 Ramachandran restraints generated.
    1000 Oldfield, 0 Emsley, 1000 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  151 residues out of total 898 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 142
  time to evaluate  : 0.331 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  121 LYS cc_start: 0.8484 (tppt) cc_final: 0.7496 (tppt)
REVERT: A  221 THR cc_start: 0.9298 (m) cc_final: 0.8969 (t)
REVERT: B   46 GLN cc_start: 0.8179 (OUTLIER) cc_final: 0.7930 (mm-40)
REVERT: C  132 ARG cc_start: 0.8966 (ttm-80) cc_final: 0.8739 (ttp-110)
REVERT: D   72 TRP cc_start: 0.8553 (OUTLIER) cc_final: 0.7374 (m-90)
  outliers start: 9
  outliers final: 4
  residues processed: 149
  average time/residue: 0.0919
  time to fit residues: 18.3628
Evaluate side-chains
  123 residues out of total 898 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 117
  time to evaluate  : 0.307 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  217 TYR
Chi-restraints excluded: chain B residue   32 ILE
Chi-restraints excluded: chain B residue   46 GLN
Chi-restraints excluded: chain D residue   66 LEU
Chi-restraints excluded: chain D residue   67 LYS
Chi-restraints excluded: chain D residue   72 TRP
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 98
   random chunks:
   chunk 49 optimal weight:   10.0000
   chunk 97 optimal weight:    0.9980
   chunk 53 optimal weight:    5.9990
   chunk 5 optimal weight:    7.9990
   chunk 33 optimal weight:    7.9990
   chunk 65 optimal weight:    8.9990
   chunk 62 optimal weight:    5.9990
   chunk 51 optimal weight:    2.9990
   chunk 38 optimal weight:    7.9990
   chunk 61 optimal weight:    6.9990
   chunk 45 optimal weight:    1.9990
   overall best weight:    3.5988

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A   3 GLN
** A   8 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** C  83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
D  10 ASN
** D 144 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3444 r_free = 0.3444 target = 0.095612 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3012 r_free = 0.3012 target = 0.071595 restraints weight = 19251.754|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3062 r_free = 0.3062 target = 0.074156 restraints weight = 9620.902|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3093 r_free = 0.3093 target = 0.075799 restraints weight = 6060.241|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.3110 r_free = 0.3110 target = 0.076729 restraints weight = 4477.321|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 41)----------------|
| r_work = 0.3123 r_free = 0.3123 target = 0.077419 restraints weight = 3740.433|
|-----------------------------------------------------------------------------|
r_work (final): 0.3117
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8680
moved from start:          0.1201

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.070   8678  Z= 0.238
  Angle     :  0.701   7.058  11830  Z= 0.360
  Chirality :  0.047   0.226   1320
  Planarity :  0.006   0.080   1458
  Dihedral  : 12.241 100.197   1283
  Min Nonbonded Distance : 2.496

Molprobity Statistics.
  All-atom Clashscore : 13.99
  Ramachandran Plot:
    Outliers :  0.10 %
    Allowed  :  6.10 %
    Favored  : 93.80 %
  Rotamer:
    Outliers :  4.45 %
    Allowed  : 28.62 %
    Favored  : 66.93 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.13 (0.28), residues: 1000
  helix:  0.73 (0.32), residues: 294
  sheet: -0.72 (0.35), residues: 238
  loop : -0.11 (0.30), residues: 468

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A 109 
 TYR   0.022   0.002   TYR B 244 
 PHE   0.015   0.002   PHE B   6 
 TRP   0.026   0.002   TRP A  70 
 HIS   0.004   0.001   HIS B  22 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00553 /  0.24 ( 8678)
  covalent geometry    : angle       0.70095 /  0.36 (11830)
  hydrogen bonds       : bond        0.04213 /  2.81 (  282)
  hydrogen bonds       : angle       5.71145 /  4.04 (  756)

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

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

  2000 Ramachandran restraints generated.
    1000 Oldfield, 0 Emsley, 1000 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2000 Ramachandran restraints generated.
    1000 Oldfield, 0 Emsley, 1000 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  170 residues out of total 898 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 40
    poor density    : 130
  time to evaluate  : 0.316 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  221 THR cc_start: 0.9337 (OUTLIER) cc_final: 0.9008 (t)
REVERT: B   56 TYR cc_start: 0.7883 (m-10) cc_final: 0.7597 (m-10)
REVERT: B  105 LEU cc_start: 0.9007 (OUTLIER) cc_final: 0.8793 (mt)
REVERT: C   83 GLN cc_start: 0.8672 (mm-40) cc_final: 0.8211 (mm-40)
REVERT: C   99 GLN cc_start: 0.8306 (pm20) cc_final: 0.8102 (pm20)
REVERT: D   72 TRP cc_start: 0.8888 (OUTLIER) cc_final: 0.7543 (m-90)
REVERT: D   74 GLU cc_start: 0.7270 (pm20) cc_final: 0.6175 (pm20)
REVERT: D  188 ASP cc_start: 0.8652 (m-30) cc_final: 0.8011 (t0)
  outliers start: 40
  outliers final: 21
  residues processed: 158
  average time/residue: 0.0861
  time to fit residues: 18.7757
Evaluate side-chains
  136 residues out of total 898 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 112
  time to evaluate  : 0.211 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   47 ILE
Chi-restraints excluded: chain A residue   93 LEU
Chi-restraints excluded: chain A residue  164 VAL
Chi-restraints excluded: chain A residue  165 VAL
Chi-restraints excluded: chain A residue  172 SER
Chi-restraints excluded: chain A residue  217 TYR
Chi-restraints excluded: chain A residue  221 THR
Chi-restraints excluded: chain A residue  254 MET
Chi-restraints excluded: chain B residue   17 LEU
Chi-restraints excluded: chain B residue   32 ILE
Chi-restraints excluded: chain B residue   61 LEU
Chi-restraints excluded: chain B residue  105 LEU
Chi-restraints excluded: chain B residue  119 ARG
Chi-restraints excluded: chain B residue  164 VAL
Chi-restraints excluded: chain B residue  183 ASP
Chi-restraints excluded: chain C residue   30 THR
Chi-restraints excluded: chain C residue  106 THR
Chi-restraints excluded: chain C residue  206 VAL
Chi-restraints excluded: chain D residue   67 LYS
Chi-restraints excluded: chain D residue   72 TRP
Chi-restraints excluded: chain D residue   94 LEU
Chi-restraints excluded: chain D residue  106 THR
Chi-restraints excluded: chain D residue  164 VAL
Chi-restraints excluded: chain D residue  165 VAL
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 98
   random chunks:
   chunk 6 optimal weight:    0.8980
   chunk 38 optimal weight:    0.9980
   chunk 75 optimal weight:    0.4980
   chunk 33 optimal weight:    0.9990
   chunk 76 optimal weight:    2.9990
   chunk 93 optimal weight:    5.9990
   chunk 28 optimal weight:    2.9990
   chunk 83 optimal weight:    3.9990
   chunk 66 optimal weight:    0.0370
   chunk 41 optimal weight:    0.9980
   chunk 70 optimal weight:    0.9990
   overall best weight:    0.6858

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A   8 HIS
A 144 ASN
C  83 GLN
** C 129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 144 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3513 r_free = 0.3513 target = 0.099623 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3071 r_free = 0.3071 target = 0.074326 restraints weight = 18855.166|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 43)----------------|
| r_work = 0.3123 r_free = 0.3123 target = 0.076981 restraints weight = 9517.427|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.3154 r_free = 0.3154 target = 0.078692 restraints weight = 6092.641|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 32)----------------|
| r_work = 0.3171 r_free = 0.3171 target = 0.079680 restraints weight = 4563.500|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 43)----------------|
| r_work = 0.3183 r_free = 0.3183 target = 0.080342 restraints weight = 3849.109|
|-----------------------------------------------------------------------------|
r_work (final): 0.3185
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8630
moved from start:          0.1380

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.044   8678  Z= 0.123
  Angle     :  0.628   8.260  11830  Z= 0.319
  Chirality :  0.045   0.204   1320
  Planarity :  0.005   0.090   1458
  Dihedral  : 11.630  97.626   1278
  Min Nonbonded Distance : 2.520

Molprobity Statistics.
  All-atom Clashscore : 11.79
  Ramachandran Plot:
    Outliers :  0.10 %
    Allowed  :  5.80 %
    Favored  : 94.10 %
  Rotamer:
    Outliers :  3.90 %
    Allowed  : 28.06 %
    Favored  : 68.04 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.08 (0.28), residues: 1000
  helix:  0.71 (0.32), residues: 294
  sheet: -0.64 (0.36), residues: 238
  loop : -0.05 (0.30), residues: 468

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.000   ARG D  24 
 TYR   0.016   0.001   TYR C 209 
 PHE   0.012   0.001   PHE A   5 
 TRP   0.024   0.001   TRP A  70 
 HIS   0.003   0.001   HIS D   8 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00279 /  0.12 ( 8678)
  covalent geometry    : angle       0.62842 /  0.32 (11830)
  hydrogen bonds       : bond        0.03753 /  2.51 (  282)
  hydrogen bonds       : angle       5.33679 /  3.76 (  756)

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

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

  2000 Ramachandran restraints generated.
    1000 Oldfield, 0 Emsley, 1000 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2000 Ramachandran restraints generated.
    1000 Oldfield, 0 Emsley, 1000 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  170 residues out of total 898 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 135
  time to evaluate  : 0.316 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  188 ASP cc_start: 0.8975 (p0) cc_final: 0.8394 (p0)
REVERT: A  221 THR cc_start: 0.9316 (m) cc_final: 0.9106 (t)
REVERT: B   56 TYR cc_start: 0.7755 (m-10) cc_final: 0.7299 (m-10)
REVERT: C   55 GLN cc_start: 0.4748 (pp30) cc_final: 0.4254 (pp30)
REVERT: C   83 GLN cc_start: 0.8701 (mm110) cc_final: 0.8295 (mm-40)
REVERT: C   99 GLN cc_start: 0.8136 (pm20) cc_final: 0.7899 (pm20)
REVERT: D   72 TRP cc_start: 0.8798 (OUTLIER) cc_final: 0.7539 (m-90)
REVERT: D   74 GLU cc_start: 0.6806 (pm20) cc_final: 0.6520 (pm20)
REVERT: D  187 GLU cc_start: 0.8740 (mm-30) cc_final: 0.8478 (mt-10)
REVERT: D  188 ASP cc_start: 0.8542 (m-30) cc_final: 0.8019 (t0)
  outliers start: 35
  outliers final: 21
  residues processed: 161
  average time/residue: 0.0789
  time to fit residues: 17.6271
Evaluate side-chains
  142 residues out of total 898 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 120
  time to evaluate  : 0.251 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   32 ILE
Chi-restraints excluded: chain A residue   90 ILE
Chi-restraints excluded: chain A residue  123 VAL
Chi-restraints excluded: chain A residue  164 VAL
Chi-restraints excluded: chain A residue  206 VAL
Chi-restraints excluded: chain A residue  217 TYR
Chi-restraints excluded: chain B residue   12 ASP
Chi-restraints excluded: chain B residue   17 LEU
Chi-restraints excluded: chain B residue   32 ILE
Chi-restraints excluded: chain B residue  106 THR
Chi-restraints excluded: chain B residue  154 MET
Chi-restraints excluded: chain B residue  183 ASP
Chi-restraints excluded: chain C residue   30 THR
Chi-restraints excluded: chain C residue  106 THR
Chi-restraints excluded: chain C residue  147 VAL
Chi-restraints excluded: chain C residue  193 SER
Chi-restraints excluded: chain D residue   67 LYS
Chi-restraints excluded: chain D residue   72 TRP
Chi-restraints excluded: chain D residue  147 VAL
Chi-restraints excluded: chain D residue  164 VAL
Chi-restraints excluded: chain D residue  165 VAL
Chi-restraints excluded: chain D residue  174 LEU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 98
   random chunks:
   chunk 68 optimal weight:    0.0870
   chunk 56 optimal weight:    8.9990
   chunk 95 optimal weight:    0.0370
   chunk 92 optimal weight:    0.5980
   chunk 18 optimal weight:    7.9990
   chunk 67 optimal weight:   10.0000
   chunk 91 optimal weight:    0.9990
   chunk 47 optimal weight:    0.9980
   chunk 97 optimal weight:    0.0770
   chunk 64 optimal weight:    2.9990
   chunk 40 optimal weight:    9.9990
   overall best weight:    0.3594

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** B  34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 144 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3558 r_free = 0.3558 target = 0.101801 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3121 r_free = 0.3121 target = 0.076575 restraints weight = 19135.332|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 44)----------------|
| r_work = 0.3176 r_free = 0.3176 target = 0.079386 restraints weight = 9458.420|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 50)----------------|
| r_work = 0.3208 r_free = 0.3208 target = 0.081168 restraints weight = 5922.579|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 33)----------------|
| r_work = 0.3225 r_free = 0.3225 target = 0.082169 restraints weight = 4378.020|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 25)----------------|
| r_work = 0.3232 r_free = 0.3232 target = 0.082545 restraints weight = 3667.770|
|-----------------------------------------------------------------------------|
r_work (final): 0.3237
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8607
moved from start:          0.1623

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.043   8678  Z= 0.110
  Angle     :  0.602   8.236  11830  Z= 0.305
  Chirality :  0.045   0.208   1320
  Planarity :  0.005   0.073   1458
  Dihedral  : 11.374  97.170   1278
  Min Nonbonded Distance : 2.548

Molprobity Statistics.
  All-atom Clashscore : 11.85
  Ramachandran Plot:
    Outliers :  0.10 %
    Allowed  :  5.80 %
    Favored  : 94.10 %
  Rotamer:
    Outliers :  3.79 %
    Allowed  : 28.17 %
    Favored  : 68.04 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.08 (0.28), residues: 1000
  helix:  0.73 (0.32), residues: 294
  sheet: -0.67 (0.36), residues: 238
  loop : -0.06 (0.29), residues: 468

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG C 148 
 TYR   0.017   0.001   TYR C 209 
 PHE   0.009   0.001   PHE B   6 
 TRP   0.016   0.001   TRP A  70 
 HIS   0.003   0.000   HIS D   8 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00248 /  0.11 ( 8678)
  covalent geometry    : angle       0.60208 /  0.30 (11830)
  hydrogen bonds       : bond        0.03298 /  2.19 (  282)
  hydrogen bonds       : angle       5.11221 /  3.59 (  756)

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

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

  2000 Ramachandran restraints generated.
    1000 Oldfield, 0 Emsley, 1000 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2000 Ramachandran restraints generated.
    1000 Oldfield, 0 Emsley, 1000 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  165 residues out of total 898 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 131
  time to evaluate  : 0.300 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   70 TRP cc_start: 0.7260 (p-90) cc_final: 0.6388 (p-90)
REVERT: A   73 ASP cc_start: 0.8794 (m-30) cc_final: 0.8365 (p0)
REVERT: A  132 ARG cc_start: 0.8611 (tmt170) cc_final: 0.8240 (mmm160)
REVERT: A  188 ASP cc_start: 0.8935 (p0) cc_final: 0.8415 (p0)
REVERT: C   87 VAL cc_start: 0.8006 (OUTLIER) cc_final: 0.7640 (p)
REVERT: C   99 GLN cc_start: 0.8144 (pm20) cc_final: 0.7917 (pm20)
REVERT: D   69 ASP cc_start: 0.8991 (t70) cc_final: 0.8771 (t0)
REVERT: D   72 TRP cc_start: 0.8746 (OUTLIER) cc_final: 0.7569 (m-90)
REVERT: D   73 ASP cc_start: 0.8880 (m-30) cc_final: 0.8598 (m-30)
REVERT: D  188 ASP cc_start: 0.8544 (m-30) cc_final: 0.8020 (t0)
  outliers start: 34
  outliers final: 21
  residues processed: 154
  average time/residue: 0.0843
  time to fit residues: 17.6422
Evaluate side-chains
  146 residues out of total 898 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 123
  time to evaluate  : 0.197 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   32 ILE
Chi-restraints excluded: chain A residue   90 ILE
Chi-restraints excluded: chain A residue  123 VAL
Chi-restraints excluded: chain A residue  165 VAL
Chi-restraints excluded: chain A residue  206 VAL
Chi-restraints excluded: chain A residue  217 TYR
Chi-restraints excluded: chain B residue   12 ASP
Chi-restraints excluded: chain B residue   32 ILE
Chi-restraints excluded: chain B residue   61 LEU
Chi-restraints excluded: chain B residue  106 THR
Chi-restraints excluded: chain B residue  154 MET
Chi-restraints excluded: chain B residue  183 ASP
Chi-restraints excluded: chain C residue   30 THR
Chi-restraints excluded: chain C residue   87 VAL
Chi-restraints excluded: chain C residue  106 THR
Chi-restraints excluded: chain C residue  147 VAL
Chi-restraints excluded: chain C residue  254 MET
Chi-restraints excluded: chain D residue   67 LYS
Chi-restraints excluded: chain D residue   72 TRP
Chi-restraints excluded: chain D residue   94 LEU
Chi-restraints excluded: chain D residue  164 VAL
Chi-restraints excluded: chain D residue  165 VAL
Chi-restraints excluded: chain D residue  174 LEU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 98
   random chunks:
   chunk 52 optimal weight:    0.0870
   chunk 55 optimal weight:    0.9990
   chunk 49 optimal weight:   10.0000
   chunk 35 optimal weight:   10.0000
   chunk 50 optimal weight:    2.9990
   chunk 59 optimal weight:    7.9990
   chunk 64 optimal weight:    2.9990
   chunk 85 optimal weight:    6.9990
   chunk 62 optimal weight:    2.9990
   chunk 93 optimal weight:    3.9990
   chunk 77 optimal weight:    5.9990
   overall best weight:    2.0166

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** C  83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D   8 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 144 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3525 r_free = 0.3525 target = 0.099774 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3074 r_free = 0.3074 target = 0.074292 restraints weight = 19129.642|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3128 r_free = 0.3128 target = 0.077007 restraints weight = 9742.268|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 46)----------------|
| r_work = 0.3160 r_free = 0.3160 target = 0.078725 restraints weight = 6227.628|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.3177 r_free = 0.3177 target = 0.079665 restraints weight = 4666.290|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 42)----------------|
| r_work = 0.3190 r_free = 0.3190 target = 0.080368 restraints weight = 3954.425|
|-----------------------------------------------------------------------------|
r_work (final): 0.3190
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8646
moved from start:          0.1838

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.039   8678  Z= 0.152
  Angle     :  0.615   8.727  11830  Z= 0.309
  Chirality :  0.045   0.217   1320
  Planarity :  0.005   0.091   1458
  Dihedral  : 11.310  98.760   1278
  Min Nonbonded Distance : 2.543

Molprobity Statistics.
  All-atom Clashscore : 13.40
  Ramachandran Plot:
    Outliers :  0.10 %
    Allowed  :  6.20 %
    Favored  : 93.70 %
  Rotamer:
    Outliers :  4.45 %
    Allowed  : 27.39 %
    Favored  : 68.15 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.10 (0.28), residues: 1000
  helix:  0.74 (0.33), residues: 294
  sheet: -0.72 (0.36), residues: 240
  loop : -0.05 (0.29), residues: 466

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A 110 
 TYR   0.018   0.001   TYR C 209 
 PHE   0.012   0.001   PHE C   5 
 TRP   0.012   0.001   TRP A  70 
 HIS   0.003   0.001   HIS B  22 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00358 /  0.15 ( 8678)
  covalent geometry    : angle       0.61458 /  0.31 (11830)
  hydrogen bonds       : bond        0.03246 /  2.15 (  282)
  hydrogen bonds       : angle       5.06298 /  3.56 (  756)

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

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

  2000 Ramachandran restraints generated.
    1000 Oldfield, 0 Emsley, 1000 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2000 Ramachandran restraints generated.
    1000 Oldfield, 0 Emsley, 1000 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  160 residues out of total 898 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 40
    poor density    : 120
  time to evaluate  : 0.287 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   70 TRP cc_start: 0.7230 (p-90) cc_final: 0.6418 (p-90)
REVERT: A  132 ARG cc_start: 0.8612 (tmt170) cc_final: 0.8250 (mmm160)
REVERT: A  188 ASP cc_start: 0.8965 (p0) cc_final: 0.8511 (p0)
REVERT: B   56 TYR cc_start: 0.7926 (m-10) cc_final: 0.7467 (m-10)
REVERT: B  105 LEU cc_start: 0.8955 (OUTLIER) cc_final: 0.8709 (mt)
REVERT: B  209 TYR cc_start: 0.8569 (t80) cc_final: 0.8271 (t80)
REVERT: C   79 TYR cc_start: 0.8019 (t80) cc_final: 0.7595 (t80)
REVERT: C   83 GLN cc_start: 0.8735 (mm-40) cc_final: 0.8354 (mm-40)
REVERT: C   99 GLN cc_start: 0.8231 (pm20) cc_final: 0.7975 (pm20)
REVERT: C  145 GLU cc_start: 0.8708 (tp30) cc_final: 0.8474 (tp30)
REVERT: D   69 ASP cc_start: 0.8938 (t70) cc_final: 0.8704 (t0)
REVERT: D   72 TRP cc_start: 0.8815 (OUTLIER) cc_final: 0.7604 (m-90)
REVERT: D   73 ASP cc_start: 0.8872 (m-30) cc_final: 0.8591 (m-30)
REVERT: D  188 ASP cc_start: 0.8555 (m-30) cc_final: 0.8045 (t0)
  outliers start: 40
  outliers final: 31
  residues processed: 151
  average time/residue: 0.0928
  time to fit residues: 19.1323
Evaluate side-chains
  148 residues out of total 898 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 115
  time to evaluate  : 0.319 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   32 ILE
Chi-restraints excluded: chain A residue   90 ILE
Chi-restraints excluded: chain A residue  123 VAL
Chi-restraints excluded: chain A residue  165 VAL
Chi-restraints excluded: chain A residue  172 SER
Chi-restraints excluded: chain A residue  193 SER
Chi-restraints excluded: chain A residue  206 VAL
Chi-restraints excluded: chain A residue  217 TYR
Chi-restraints excluded: chain A residue  254 MET
Chi-restraints excluded: chain B residue   12 ASP
Chi-restraints excluded: chain B residue   17 LEU
Chi-restraints excluded: chain B residue   32 ILE
Chi-restraints excluded: chain B residue   61 LEU
Chi-restraints excluded: chain B residue  105 LEU
Chi-restraints excluded: chain B residue  106 THR
Chi-restraints excluded: chain B residue  154 MET
Chi-restraints excluded: chain B residue  183 ASP
Chi-restraints excluded: chain B residue  217 TYR
Chi-restraints excluded: chain C residue   30 THR
Chi-restraints excluded: chain C residue   32 ILE
Chi-restraints excluded: chain C residue  102 LEU
Chi-restraints excluded: chain C residue  103 ASN
Chi-restraints excluded: chain C residue  106 THR
Chi-restraints excluded: chain C residue  147 VAL
Chi-restraints excluded: chain C residue  193 SER
Chi-restraints excluded: chain C residue  206 VAL
Chi-restraints excluded: chain C residue  254 MET
Chi-restraints excluded: chain D residue   67 LYS
Chi-restraints excluded: chain D residue   72 TRP
Chi-restraints excluded: chain D residue   94 LEU
Chi-restraints excluded: chain D residue  105 LEU
Chi-restraints excluded: chain D residue  164 VAL
Chi-restraints excluded: chain D residue  165 VAL
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 98
   random chunks:
   chunk 36 optimal weight:    5.9990
   chunk 85 optimal weight:    5.9990
   chunk 95 optimal weight:    0.0070
   chunk 44 optimal weight:    0.9990
   chunk 78 optimal weight:    7.9990
   chunk 14 optimal weight:    0.0670
   chunk 35 optimal weight:    0.8980
   chunk 23 optimal weight:    6.9990
   chunk 16 optimal weight:    0.1980
   chunk 82 optimal weight:    1.9990
   chunk 12 optimal weight:    0.7980
   overall best weight:    0.3936

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A  55 GLN
C  83 GLN
** C 129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 144 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3561 r_free = 0.3561 target = 0.101842 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3114 r_free = 0.3114 target = 0.076339 restraints weight = 18914.764|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3166 r_free = 0.3166 target = 0.079078 restraints weight = 9502.708|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3200 r_free = 0.3200 target = 0.080881 restraints weight = 6058.405|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 22)----------------|
| r_work = 0.3217 r_free = 0.3217 target = 0.081854 restraints weight = 4518.277|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 44)----------------|
| r_work = 0.3230 r_free = 0.3230 target = 0.082555 restraints weight = 3811.867|
|-----------------------------------------------------------------------------|
r_work (final): 0.3238
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8603
moved from start:          0.1971

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.043   8678  Z= 0.106
  Angle     :  0.601   9.174  11830  Z= 0.301
  Chirality :  0.044   0.207   1320
  Planarity :  0.005   0.073   1458
  Dihedral  : 11.281 100.807   1278
  Min Nonbonded Distance : 2.558

Molprobity Statistics.
  All-atom Clashscore : 11.91
  Ramachandran Plot:
    Outliers :  0.10 %
    Allowed  :  5.90 %
    Favored  : 94.00 %
  Rotamer:
    Outliers :  4.01 %
    Allowed  : 29.29 %
    Favored  : 66.70 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.05 (0.28), residues: 1000
  helix:  0.78 (0.32), residues: 294
  sheet: -0.64 (0.36), residues: 238
  loop : -0.08 (0.29), residues: 468

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG A 148 
 TYR   0.017   0.001   TYR A  65 
 PHE   0.006   0.001   PHE D 231 
 TRP   0.012   0.001   TRP B  72 
 HIS   0.004   0.000   HIS D   8 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00245 /  0.11 ( 8678)
  covalent geometry    : angle       0.60075 /  0.30 (11830)
  hydrogen bonds       : bond        0.03099 /  2.03 (  282)
  hydrogen bonds       : angle       4.94580 /  3.47 (  756)

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

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

  2000 Ramachandran restraints generated.
    1000 Oldfield, 0 Emsley, 1000 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2000 Ramachandran restraints generated.
    1000 Oldfield, 0 Emsley, 1000 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  166 residues out of total 898 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 130
  time to evaluate  : 0.238 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   70 TRP cc_start: 0.7289 (p-90) cc_final: 0.6422 (p-90)
REVERT: A   73 ASP cc_start: 0.8709 (m-30) cc_final: 0.8171 (p0)
REVERT: A  105 LEU cc_start: 0.7297 (mp) cc_final: 0.6518 (mm)
REVERT: A  132 ARG cc_start: 0.8605 (tmt170) cc_final: 0.8260 (mmm160)
REVERT: A  188 ASP cc_start: 0.8910 (p0) cc_final: 0.8469 (p0)
REVERT: B  209 TYR cc_start: 0.8530 (t80) cc_final: 0.8063 (t80)
REVERT: C   79 TYR cc_start: 0.7959 (t80) cc_final: 0.7642 (t80)
REVERT: C   83 GLN cc_start: 0.8701 (mm110) cc_final: 0.8478 (mm-40)
REVERT: C   99 GLN cc_start: 0.8231 (pm20) cc_final: 0.7978 (pm20)
REVERT: C  145 GLU cc_start: 0.8656 (tp30) cc_final: 0.8455 (tp30)
REVERT: D   72 TRP cc_start: 0.8752 (OUTLIER) cc_final: 0.7482 (m-90)
REVERT: D  177 ASP cc_start: 0.8691 (p0) cc_final: 0.8458 (p0)
REVERT: D  188 ASP cc_start: 0.8520 (m-30) cc_final: 0.8036 (t0)
  outliers start: 36
  outliers final: 27
  residues processed: 153
  average time/residue: 0.0855
  time to fit residues: 17.8546
Evaluate side-chains
  149 residues out of total 898 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 121
  time to evaluate  : 0.316 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   32 ILE
Chi-restraints excluded: chain A residue   55 GLN
Chi-restraints excluded: chain A residue   90 ILE
Chi-restraints excluded: chain A residue  123 VAL
Chi-restraints excluded: chain A residue  165 VAL
Chi-restraints excluded: chain A residue  206 VAL
Chi-restraints excluded: chain A residue  217 TYR
Chi-restraints excluded: chain B residue   12 ASP
Chi-restraints excluded: chain B residue   17 LEU
Chi-restraints excluded: chain B residue   32 ILE
Chi-restraints excluded: chain B residue  106 THR
Chi-restraints excluded: chain B residue  154 MET
Chi-restraints excluded: chain B residue  217 TYR
Chi-restraints excluded: chain C residue   30 THR
Chi-restraints excluded: chain C residue   32 ILE
Chi-restraints excluded: chain C residue  102 LEU
Chi-restraints excluded: chain C residue  103 ASN
Chi-restraints excluded: chain C residue  106 THR
Chi-restraints excluded: chain C residue  147 VAL
Chi-restraints excluded: chain C residue  193 SER
Chi-restraints excluded: chain C residue  254 MET
Chi-restraints excluded: chain D residue   67 LYS
Chi-restraints excluded: chain D residue   72 TRP
Chi-restraints excluded: chain D residue   94 LEU
Chi-restraints excluded: chain D residue  105 LEU
Chi-restraints excluded: chain D residue  164 VAL
Chi-restraints excluded: chain D residue  165 VAL
Chi-restraints excluded: chain D residue  174 LEU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 98
   random chunks:
   chunk 20 optimal weight:    0.9990
   chunk 68 optimal weight:    0.9990
   chunk 23 optimal weight:    5.9990
   chunk 77 optimal weight:    0.9990
   chunk 89 optimal weight:    3.9990
   chunk 19 optimal weight:    4.9990
   chunk 79 optimal weight:    4.9990
   chunk 66 optimal weight:    7.9990
   chunk 57 optimal weight:    7.9990
   chunk 88 optimal weight:    0.7980
   chunk 12 optimal weight:    0.6980
   overall best weight:    0.8986

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A  55 GLN
C 129 ASN
** D 144 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3561 r_free = 0.3561 target = 0.101829 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3107 r_free = 0.3107 target = 0.076091 restraints weight = 19124.540|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 45)----------------|
| r_work = 0.3162 r_free = 0.3162 target = 0.078895 restraints weight = 9644.212|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3194 r_free = 0.3194 target = 0.080633 restraints weight = 6144.137|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 37)----------------|
| r_work = 0.3212 r_free = 0.3212 target = 0.081650 restraints weight = 4602.330|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 31)----------------|
| r_work = 0.3225 r_free = 0.3225 target = 0.082359 restraints weight = 3874.098|
|-----------------------------------------------------------------------------|
r_work (final): 0.3229
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8610
moved from start:          0.2015

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.043   8678  Z= 0.111
  Angle     :  0.599   8.973  11830  Z= 0.299
  Chirality :  0.044   0.197   1320
  Planarity :  0.005   0.097   1458
  Dihedral  : 11.190 101.901   1278
  Min Nonbonded Distance : 2.519

Molprobity Statistics.
  All-atom Clashscore : 12.15
  Ramachandran Plot:
    Outliers :  0.10 %
    Allowed  :  6.20 %
    Favored  : 93.70 %
  Rotamer:
    Outliers :  4.01 %
    Allowed  : 29.29 %
    Favored  : 66.70 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.04 (0.28), residues: 1000
  helix:  0.77 (0.32), residues: 294
  sheet: -0.69 (0.36), residues: 240
  loop : -0.02 (0.29), residues: 466

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.011   0.000   ARG A 110 
 TYR   0.022   0.001   TYR C 217 
 PHE   0.008   0.001   PHE B   6 
 TRP   0.014   0.001   TRP B  70 
 HIS   0.003   0.000   HIS D   8 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00262 /  0.11 ( 8678)
  covalent geometry    : angle       0.59884 /  0.30 (11830)
  hydrogen bonds       : bond        0.03012 /  1.98 (  282)
  hydrogen bonds       : angle       4.88866 /  3.43 (  756)

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

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

  2000 Ramachandran restraints generated.
    1000 Oldfield, 0 Emsley, 1000 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2000 Ramachandran restraints generated.
    1000 Oldfield, 0 Emsley, 1000 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  163 residues out of total 898 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 127
  time to evaluate  : 0.314 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  132 ARG cc_start: 0.8616 (tmt170) cc_final: 0.8265 (mmm160)
REVERT: A  188 ASP cc_start: 0.8922 (p0) cc_final: 0.8516 (p0)
REVERT: C   99 GLN cc_start: 0.8252 (pm20) cc_final: 0.7994 (pm20)
REVERT: C  145 GLU cc_start: 0.8752 (tp30) cc_final: 0.8519 (tp30)
REVERT: D   72 TRP cc_start: 0.8768 (OUTLIER) cc_final: 0.7509 (m-90)
REVERT: D  177 ASP cc_start: 0.8726 (p0) cc_final: 0.8469 (p0)
REVERT: D  188 ASP cc_start: 0.8530 (m-30) cc_final: 0.8046 (t0)
  outliers start: 36
  outliers final: 30
  residues processed: 153
  average time/residue: 0.0894
  time to fit residues: 18.6915
Evaluate side-chains
  153 residues out of total 898 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 122
  time to evaluate  : 0.308 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   32 ILE
Chi-restraints excluded: chain A residue   55 GLN
Chi-restraints excluded: chain A residue   90 ILE
Chi-restraints excluded: chain A residue  165 VAL
Chi-restraints excluded: chain A residue  172 SER
Chi-restraints excluded: chain A residue  206 VAL
Chi-restraints excluded: chain A residue  217 TYR
Chi-restraints excluded: chain B residue   12 ASP
Chi-restraints excluded: chain B residue   17 LEU
Chi-restraints excluded: chain B residue   32 ILE
Chi-restraints excluded: chain B residue   44 ILE
Chi-restraints excluded: chain B residue   61 LEU
Chi-restraints excluded: chain B residue  106 THR
Chi-restraints excluded: chain B residue  154 MET
Chi-restraints excluded: chain B residue  217 TYR
Chi-restraints excluded: chain C residue   30 THR
Chi-restraints excluded: chain C residue   32 ILE
Chi-restraints excluded: chain C residue  102 LEU
Chi-restraints excluded: chain C residue  103 ASN
Chi-restraints excluded: chain C residue  106 THR
Chi-restraints excluded: chain C residue  147 VAL
Chi-restraints excluded: chain C residue  193 SER
Chi-restraints excluded: chain C residue  206 VAL
Chi-restraints excluded: chain C residue  254 MET
Chi-restraints excluded: chain D residue   67 LYS
Chi-restraints excluded: chain D residue   72 TRP
Chi-restraints excluded: chain D residue   94 LEU
Chi-restraints excluded: chain D residue  105 LEU
Chi-restraints excluded: chain D residue  164 VAL
Chi-restraints excluded: chain D residue  165 VAL
Chi-restraints excluded: chain D residue  174 LEU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 98
   random chunks:
   chunk 4 optimal weight:    5.9990
   chunk 92 optimal weight:    3.9990
   chunk 75 optimal weight:   10.0000
   chunk 77 optimal weight:    0.8980
   chunk 17 optimal weight:    8.9990
   chunk 6 optimal weight:    3.9990
   chunk 51 optimal weight:    9.9990
   chunk 8 optimal weight:    6.9990
   chunk 83 optimal weight:    5.9990
   chunk 59 optimal weight:    6.9990
   chunk 19 optimal weight:    5.9990
   overall best weight:    4.1788

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A  55 GLN
** C  83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D   8 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
D 144 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3476 r_free = 0.3476 target = 0.096820 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3033 r_free = 0.3033 target = 0.072193 restraints weight = 18980.477|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3086 r_free = 0.3086 target = 0.074857 restraints weight = 9498.642|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 47)----------------|
| r_work = 0.3117 r_free = 0.3117 target = 0.076494 restraints weight = 5990.494|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.3133 r_free = 0.3133 target = 0.077416 restraints weight = 4479.352|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 42)----------------|
| r_work = 0.3147 r_free = 0.3147 target = 0.078102 restraints weight = 3777.738|
|-----------------------------------------------------------------------------|
r_work (final): 0.3153
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8695
moved from start:          0.2231

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.055   8678  Z= 0.259
  Angle     :  0.679   7.570  11830  Z= 0.344
  Chirality :  0.046   0.240   1320
  Planarity :  0.005   0.072   1458
  Dihedral  : 11.086 105.846   1278
  Min Nonbonded Distance : 2.497

Molprobity Statistics.
  All-atom Clashscore : 14.05
  Ramachandran Plot:
    Outliers :  0.10 %
    Allowed  :  6.30 %
    Favored  : 93.60 %
  Rotamer:
    Outliers :  4.34 %
    Allowed  : 28.29 %
    Favored  : 67.37 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.21 (0.28), residues: 1000
  helix:  0.66 (0.32), residues: 294
  sheet: -0.78 (0.36), residues: 240
  loop : -0.14 (0.29), residues: 466

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG C 132 
 TYR   0.020   0.002   TYR C 217 
 PHE   0.013   0.002   PHE B 231 
 TRP   0.017   0.002   TRP B  72 
 HIS   0.005   0.001   HIS B  22 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00601 /  0.26 ( 8678)
  covalent geometry    : angle       0.67899 /  0.34 (11830)
  hydrogen bonds       : bond        0.03299 /  2.17 (  282)
  hydrogen bonds       : angle       5.04533 /  3.55 (  756)

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

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

  2000 Ramachandran restraints generated.
    1000 Oldfield, 0 Emsley, 1000 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2000 Ramachandran restraints generated.
    1000 Oldfield, 0 Emsley, 1000 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  156 residues out of total 898 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 39
    poor density    : 117
  time to evaluate  : 0.320 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   73 ASP cc_start: 0.8781 (m-30) cc_final: 0.8147 (p0)
REVERT: A  132 ARG cc_start: 0.8602 (tmt170) cc_final: 0.8237 (mmm160)
REVERT: A  188 ASP cc_start: 0.8984 (p0) cc_final: 0.8588 (p0)
REVERT: C   83 GLN cc_start: 0.8728 (mm-40) cc_final: 0.8170 (mm-40)
REVERT: C   99 GLN cc_start: 0.8333 (pm20) cc_final: 0.8051 (pm20)
REVERT: C  145 GLU cc_start: 0.8840 (tp30) cc_final: 0.8618 (tp30)
REVERT: D   69 ASP cc_start: 0.8874 (t70) cc_final: 0.8654 (t0)
REVERT: D   72 TRP cc_start: 0.8879 (OUTLIER) cc_final: 0.7425 (m-90)
REVERT: D   73 ASP cc_start: 0.8881 (m-30) cc_final: 0.8578 (m-30)
REVERT: D  101 ASP cc_start: 0.8167 (t0) cc_final: 0.7961 (t0)
REVERT: D  188 ASP cc_start: 0.8586 (m-30) cc_final: 0.8126 (t0)
  outliers start: 39
  outliers final: 29
  residues processed: 147
  average time/residue: 0.0880
  time to fit residues: 17.6166
Evaluate side-chains
  140 residues out of total 898 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 110
  time to evaluate  : 0.205 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   55 GLN
Chi-restraints excluded: chain A residue   90 ILE
Chi-restraints excluded: chain A residue  123 VAL
Chi-restraints excluded: chain A residue  165 VAL
Chi-restraints excluded: chain A residue  172 SER
Chi-restraints excluded: chain A residue  193 SER
Chi-restraints excluded: chain A residue  206 VAL
Chi-restraints excluded: chain A residue  217 TYR
Chi-restraints excluded: chain A residue  254 MET
Chi-restraints excluded: chain B residue   12 ASP
Chi-restraints excluded: chain B residue   17 LEU
Chi-restraints excluded: chain B residue   32 ILE
Chi-restraints excluded: chain B residue   61 LEU
Chi-restraints excluded: chain B residue  106 THR
Chi-restraints excluded: chain B residue  154 MET
Chi-restraints excluded: chain C residue   30 THR
Chi-restraints excluded: chain C residue   32 ILE
Chi-restraints excluded: chain C residue  102 LEU
Chi-restraints excluded: chain C residue  103 ASN
Chi-restraints excluded: chain C residue  106 THR
Chi-restraints excluded: chain C residue  147 VAL
Chi-restraints excluded: chain C residue  193 SER
Chi-restraints excluded: chain C residue  206 VAL
Chi-restraints excluded: chain C residue  254 MET
Chi-restraints excluded: chain D residue   67 LYS
Chi-restraints excluded: chain D residue   72 TRP
Chi-restraints excluded: chain D residue   94 LEU
Chi-restraints excluded: chain D residue  164 VAL
Chi-restraints excluded: chain D residue  165 VAL
Chi-restraints excluded: chain D residue  174 LEU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 98
   random chunks:
   chunk 7 optimal weight:    7.9990
   chunk 2 optimal weight:    3.9990
   chunk 77 optimal weight:    0.9980
   chunk 21 optimal weight:    0.0470
   chunk 29 optimal weight:    3.9990
   chunk 85 optimal weight:    3.9990
   chunk 59 optimal weight:    2.9990
   chunk 3 optimal weight:    2.9990
   chunk 13 optimal weight:    5.9990
   chunk 54 optimal weight:    6.9990
   chunk 34 optimal weight:    2.9990
   overall best weight:    2.0084

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** C   8 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** C  83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D   8 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3507 r_free = 0.3507 target = 0.098656 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3058 r_free = 0.3058 target = 0.073525 restraints weight = 19053.537|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3110 r_free = 0.3110 target = 0.076201 restraints weight = 9677.872|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 43)----------------|
| r_work = 0.3142 r_free = 0.3142 target = 0.077866 restraints weight = 6174.299|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 32)----------------|
| r_work = 0.3159 r_free = 0.3159 target = 0.078855 restraints weight = 4644.052|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 40)----------------|
| r_work = 0.3172 r_free = 0.3172 target = 0.079527 restraints weight = 3902.822|
|-----------------------------------------------------------------------------|
r_work (final): 0.3176
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8670
moved from start:          0.2287

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.044   8678  Z= 0.156
  Angle     :  0.655   9.468  11830  Z= 0.327
  Chirality :  0.046   0.245   1320
  Planarity :  0.005   0.071   1458
  Dihedral  : 11.090 107.712   1278
  Min Nonbonded Distance : 2.507

Molprobity Statistics.
  All-atom Clashscore : 13.10
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.30 %
    Favored  : 93.70 %
  Rotamer:
    Outliers :  3.79 %
    Allowed  : 29.62 %
    Favored  : 66.59 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.15 (0.28), residues: 1000
  helix:  0.81 (0.32), residues: 286
  sheet: -0.77 (0.36), residues: 240
  loop : -0.15 (0.29), residues: 474

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.000   ARG A 148 
 TYR   0.017   0.002   TYR C 209 
 PHE   0.010   0.001   PHE A   5 
 TRP   0.016   0.001   TRP B  72 
 HIS   0.002   0.001   HIS B  22 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00375 /  0.16 ( 8678)
  covalent geometry    : angle       0.65517 /  0.33 (11830)
  hydrogen bonds       : bond        0.03164 /  2.07 (  282)
  hydrogen bonds       : angle       4.99050 /  3.50 (  756)

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

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

  2000 Ramachandran restraints generated.
    1000 Oldfield, 0 Emsley, 1000 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2000 Ramachandran restraints generated.
    1000 Oldfield, 0 Emsley, 1000 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  151 residues out of total 898 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 117
  time to evaluate  : 0.309 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   73 ASP cc_start: 0.8769 (m-30) cc_final: 0.8130 (p0)
REVERT: A  132 ARG cc_start: 0.8606 (tmt170) cc_final: 0.8237 (mmm160)
REVERT: A  188 ASP cc_start: 0.8947 (p0) cc_final: 0.8554 (p0)
REVERT: C   83 GLN cc_start: 0.8706 (mm-40) cc_final: 0.8195 (mm-40)
REVERT: C   99 GLN cc_start: 0.8325 (pm20) cc_final: 0.8058 (pm20)
REVERT: D   69 ASP cc_start: 0.8853 (t70) cc_final: 0.8638 (t0)
REVERT: D   72 TRP cc_start: 0.8930 (OUTLIER) cc_final: 0.7698 (m-90)
REVERT: D   73 ASP cc_start: 0.8826 (m-30) cc_final: 0.8526 (m-30)
REVERT: D  101 ASP cc_start: 0.8215 (t0) cc_final: 0.8005 (t0)
REVERT: D  154 MET cc_start: 0.8721 (mtp) cc_final: 0.8457 (ttm)
REVERT: D  188 ASP cc_start: 0.8555 (m-30) cc_final: 0.8111 (t0)
  outliers start: 34
  outliers final: 26
  residues processed: 142
  average time/residue: 0.0779
  time to fit residues: 15.0927
Evaluate side-chains
  140 residues out of total 898 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 113
  time to evaluate  : 0.194 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   90 ILE
Chi-restraints excluded: chain A residue  165 VAL
Chi-restraints excluded: chain A residue  172 SER
Chi-restraints excluded: chain A residue  206 VAL
Chi-restraints excluded: chain A residue  217 TYR
Chi-restraints excluded: chain A residue  254 MET
Chi-restraints excluded: chain B residue   12 ASP
Chi-restraints excluded: chain B residue   17 LEU
Chi-restraints excluded: chain B residue   32 ILE
Chi-restraints excluded: chain B residue   61 LEU
Chi-restraints excluded: chain B residue  106 THR
Chi-restraints excluded: chain B residue  154 MET
Chi-restraints excluded: chain C residue   30 THR
Chi-restraints excluded: chain C residue   32 ILE
Chi-restraints excluded: chain C residue  102 LEU
Chi-restraints excluded: chain C residue  103 ASN
Chi-restraints excluded: chain C residue  106 THR
Chi-restraints excluded: chain C residue  147 VAL
Chi-restraints excluded: chain C residue  193 SER
Chi-restraints excluded: chain C residue  206 VAL
Chi-restraints excluded: chain C residue  254 MET
Chi-restraints excluded: chain D residue   67 LYS
Chi-restraints excluded: chain D residue   72 TRP
Chi-restraints excluded: chain D residue   94 LEU
Chi-restraints excluded: chain D residue  164 VAL
Chi-restraints excluded: chain D residue  165 VAL
Chi-restraints excluded: chain D residue  174 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 98
   random chunks:
   chunk 29 optimal weight:    4.9990
   chunk 9 optimal weight:    8.9990
   chunk 50 optimal weight:    9.9990
   chunk 0 optimal weight:   10.0000
   chunk 56 optimal weight:    0.5980
   chunk 17 optimal weight:    0.9990
   chunk 73 optimal weight:   10.0000
   chunk 1 optimal weight:    2.9990
   chunk 4 optimal weight:    6.9990
   chunk 87 optimal weight:    4.9990
   chunk 92 optimal weight:    0.1980
   overall best weight:    1.9586

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** C  83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D   8 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3509 r_free = 0.3509 target = 0.098821 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3054 r_free = 0.3054 target = 0.073426 restraints weight = 19004.117|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3108 r_free = 0.3108 target = 0.076086 restraints weight = 9738.150|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3140 r_free = 0.3140 target = 0.077782 restraints weight = 6283.509|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.3156 r_free = 0.3156 target = 0.078696 restraints weight = 4738.779|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3166 r_free = 0.3166 target = 0.079247 restraints weight = 4032.674|
|-----------------------------------------------------------------------------|
r_work (final): 0.3172
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8679
moved from start:          0.2365

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.042   8678  Z= 0.155
  Angle     :  0.669  10.400  11830  Z= 0.336
  Chirality :  0.045   0.251   1320
  Planarity :  0.005   0.073   1458
  Dihedral  : 11.094 108.014   1278
  Min Nonbonded Distance : 2.517

Molprobity Statistics.
  All-atom Clashscore : 13.28
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.10 %
    Favored  : 93.90 %
  Rotamer:
    Outliers :  3.56 %
    Allowed  : 30.29 %
    Favored  : 66.15 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.18 (0.28), residues: 1000
  helix:  0.77 (0.32), residues: 286
  sheet: -0.77 (0.36), residues: 240
  loop : -0.16 (0.29), residues: 474

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.001   ARG A 110 
 TYR   0.018   0.002   TYR C 217 
 PHE   0.008   0.001   PHE B 231 
 TRP   0.016   0.002   TRP B  72 
 HIS   0.002   0.001   HIS C  22 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00371 /  0.16 ( 8678)
  covalent geometry    : angle       0.66905 /  0.34 (11830)
  hydrogen bonds       : bond        0.03200 /  2.08 (  282)
  hydrogen bonds       : angle       5.03509 /  3.54 (  756)

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

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

  2000 Ramachandran restraints generated.
    1000 Oldfield, 0 Emsley, 1000 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2000 Ramachandran restraints generated.
    1000 Oldfield, 0 Emsley, 1000 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  146 residues out of total 898 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 114
  time to evaluate  : 0.314 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   31 TRP cc_start: 0.8464 (m-10) cc_final: 0.8053 (m-10)
REVERT: A   73 ASP cc_start: 0.8803 (m-30) cc_final: 0.8150 (p0)
REVERT: A  132 ARG cc_start: 0.8620 (tmt170) cc_final: 0.8249 (mmm160)
REVERT: A  188 ASP cc_start: 0.8945 (p0) cc_final: 0.8551 (p0)
REVERT: B   56 TYR cc_start: 0.7834 (m-10) cc_final: 0.7416 (m-10)
REVERT: C   83 GLN cc_start: 0.8760 (mm-40) cc_final: 0.8248 (mm-40)
REVERT: C   99 GLN cc_start: 0.8297 (pm20) cc_final: 0.8036 (pm20)
REVERT: D   72 TRP cc_start: 0.8907 (OUTLIER) cc_final: 0.7579 (m-90)
REVERT: D  154 MET cc_start: 0.8690 (mtp) cc_final: 0.8440 (ttm)
REVERT: D  177 ASP cc_start: 0.8762 (p0) cc_final: 0.8497 (p0)
REVERT: D  188 ASP cc_start: 0.8554 (m-30) cc_final: 0.8113 (t0)
  outliers start: 32
  outliers final: 28
  residues processed: 140
  average time/residue: 0.0836
  time to fit residues: 16.0403
Evaluate side-chains
  143 residues out of total 898 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 114
  time to evaluate  : 0.231 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   90 ILE
Chi-restraints excluded: chain A residue  165 VAL
Chi-restraints excluded: chain A residue  172 SER
Chi-restraints excluded: chain A residue  193 SER
Chi-restraints excluded: chain A residue  206 VAL
Chi-restraints excluded: chain A residue  217 TYR
Chi-restraints excluded: chain A residue  254 MET
Chi-restraints excluded: chain B residue   12 ASP
Chi-restraints excluded: chain B residue   17 LEU
Chi-restraints excluded: chain B residue   32 ILE
Chi-restraints excluded: chain B residue   61 LEU
Chi-restraints excluded: chain B residue  106 THR
Chi-restraints excluded: chain B residue  154 MET
Chi-restraints excluded: chain C residue   30 THR
Chi-restraints excluded: chain C residue   32 ILE
Chi-restraints excluded: chain C residue  102 LEU
Chi-restraints excluded: chain C residue  103 ASN
Chi-restraints excluded: chain C residue  106 THR
Chi-restraints excluded: chain C residue  147 VAL
Chi-restraints excluded: chain C residue  193 SER
Chi-restraints excluded: chain C residue  206 VAL
Chi-restraints excluded: chain C residue  254 MET
Chi-restraints excluded: chain D residue   67 LYS
Chi-restraints excluded: chain D residue   72 TRP
Chi-restraints excluded: chain D residue   94 LEU
Chi-restraints excluded: chain D residue  106 THR
Chi-restraints excluded: chain D residue  164 VAL
Chi-restraints excluded: chain D residue  165 VAL
Chi-restraints excluded: chain D residue  174 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 98
   random chunks:
   chunk 93 optimal weight:    3.9990
   chunk 32 optimal weight:    8.9990
   chunk 28 optimal weight:    0.0970
   chunk 63 optimal weight:    0.0050
   chunk 2 optimal weight:    3.9990
   chunk 56 optimal weight:    7.9990
   chunk 11 optimal weight:   20.0000
   chunk 39 optimal weight:    3.9990
   chunk 37 optimal weight:    9.9990
   chunk 13 optimal weight:    9.9990
   chunk 46 optimal weight:    1.9990
   overall best weight:    2.0198

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** C  83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 163 GLN
** D   8 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3507 r_free = 0.3507 target = 0.098647 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3060 r_free = 0.3060 target = 0.073589 restraints weight = 19076.704|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 43)----------------|
| r_work = 0.3113 r_free = 0.3113 target = 0.076277 restraints weight = 9586.277|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3146 r_free = 0.3146 target = 0.077972 restraints weight = 6094.787|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 20)----------------|
| r_work = 0.3161 r_free = 0.3161 target = 0.078864 restraints weight = 4548.673|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 39)----------------|
| r_work = 0.3176 r_free = 0.3176 target = 0.079647 restraints weight = 3870.954|
|-----------------------------------------------------------------------------|
r_work (final): 0.3177
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8671
moved from start:          0.2442

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.043   8678  Z= 0.157
  Angle     :  0.663   9.567  11830  Z= 0.334
  Chirality :  0.046   0.260   1320
  Planarity :  0.005   0.073   1458
  Dihedral  : 11.105 108.159   1278
  Min Nonbonded Distance : 2.522

Molprobity Statistics.
  All-atom Clashscore : 13.10
  Ramachandran Plot:
    Outliers :  0.10 %
    Allowed  :  6.30 %
    Favored  : 93.60 %
  Rotamer:
    Outliers :  3.45 %
    Allowed  : 30.51 %
    Favored  : 66.04 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.19 (0.28), residues: 1000
  helix:  0.72 (0.32), residues: 286
  sheet: -0.73 (0.36), residues: 240
  loop : -0.17 (0.29), residues: 474

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.001   ARG A 110 
 TYR   0.017   0.002   TYR C 209 
 PHE   0.009   0.001   PHE B 231 
 TRP   0.028   0.002   TRP C  72 
 HIS   0.002   0.001   HIS B  22 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00374 /  0.16 ( 8678)
  covalent geometry    : angle       0.66321 /  0.33 (11830)
  hydrogen bonds       : bond        0.03215 /  2.10 (  282)
  hydrogen bonds       : angle       5.07437 /  3.56 (  756)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1330.92 seconds
wall clock time: 23 minutes 45.58 seconds (1425.58 seconds total)