Starting phenix.real_space_refine
on Tue Apr 29 07:40:58 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9mue_48630/04_2025/9mue_48630.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9mue_48630/04_2025/9mue_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 {
    real_map_files = "/net/cci-nas-00/data/ceres_data/9mue_48630/04_2025/9mue_48630.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9mue_48630/04_2025/9mue_48630.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9mue_48630/04_2025/9mue_48630.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9mue_48630/04_2025/9mue_48630.cif"
  }
  resolution = 4.0
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.005 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): 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/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: 7.61, per 1000 atoms: 0.90
  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: 2.09
  Conformation dependent library (CDL) restraints added in 905.6 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: 0.95
  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: 2.16

  Time building geometry restraints manager: 2.47 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: 1058
       0.055 -    0.110: 224
       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:             152.930
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.350
  Check model and map are aligned:         0.060
  Set scattering table:                    0.080
  Process input model:                     24.000
  Find NCS groups from input model:        0.330
  Set up NCS constraints:                  0.040
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:2.800
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:  180.600
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8477
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= 0.214
  Angle     :  0.806  16.699  11830  Z= 0.430
  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 : 15.54
  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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.03 (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
 TRP   0.049   0.002   TRP A  70 
 HIS   0.003   0.001   HIS B 128 
 PHE   0.012   0.001   PHE A 112 
 TYR   0.024   0.002   TYR C  56 
 ARG   0.006   0.000   ARG A 148 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.22300 (  282)
  hydrogen bonds       : angle       7.07985 (  756)
  covalent geometry    : bond        0.00477 ( 8678)
  covalent geometry    : angle       0.80647 (11830)

*********************** 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  : 0.925 
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: 0.8178 (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: 0.2408
  time to fit residues: 47.1953
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  : 0.932 
-------------------------------------------------------------------------------
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 82 optimal weight:    0.8980
   chunk 74 optimal weight:    3.9990
   chunk 41 optimal weight:    1.9990
   chunk 25 optimal weight:    0.5980
   chunk 50 optimal weight:   10.0000
   chunk 39 optimal weight:    4.9990
   chunk 76 optimal weight:    1.9990
   chunk 29 optimal weight:    0.9990
   chunk 46 optimal weight:    0.7980
   chunk 57 optimal weight:   20.0000
   chunk 88 optimal weight:    7.9990
   overall best weight:    1.0584

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

Flipped N/Q/H residues before XYZ refinement:
** A   8 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
C  83 GLN
** 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 = 0.3530 r_free = 0.3530 target = 0.100519 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3093 r_free = 0.3093 target = 0.075387 restraints weight = 18829.706|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3144 r_free = 0.3144 target = 0.078071 restraints weight = 9559.157|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 42)----------------|
| r_work = 0.3176 r_free = 0.3176 target = 0.079779 restraints weight = 6087.223|
|-----------------------------------------------------------------------------|
r_work (final): 0.3183
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8514
moved from start:          0.1178

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.074   8678  Z= 0.124
  Angle     :  0.623   6.771  11830  Z= 0.318
  Chirality :  0.045   0.191   1320
  Planarity :  0.005   0.090   1458
  Dihedral  : 11.702  93.912   1283
  Min Nonbonded Distance : 2.506

Molprobity Statistics.
  All-atom Clashscore : 11.49
  Ramachandran Plot:
    Outliers :  0.10 %
    Allowed  :  5.40 %
    Favored  : 94.50 %
  Rotamer:
    Outliers :  3.12 %
    Allowed  : 28.73 %
    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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.02 (0.28), residues: 1000
  helix:  0.76 (0.32), residues: 294
  sheet: -0.63 (0.35), residues: 238
  loop : -0.01 (0.30), residues: 468

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.026   0.001   TRP A  70 
 HIS   0.004   0.001   HIS A   8 
 PHE   0.009   0.001   PHE A   6 
 TYR   0.015   0.001   TYR C 209 
 ARG   0.005   0.000   ARG A 148 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03790 (  282)
  hydrogen bonds       : angle       5.49497 (  756)
  covalent geometry    : bond        0.00296 ( 8678)
  covalent geometry    : angle       0.62322 (11830)

*********************** 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
  161 residues out of total 898 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 133
  time to evaluate  : 1.286 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   65 TYR cc_start: 0.7827 (t80) cc_final: 0.7626 (t80)
REVERT: A  221 THR cc_start: 0.9310 (m) cc_final: 0.9063 (t)
REVERT: C   55 GLN cc_start: 0.5071 (pp30) cc_final: 0.4647 (pp30)
REVERT: C   99 GLN cc_start: 0.8136 (pm20) cc_final: 0.7782 (pm20)
REVERT: C  132 ARG cc_start: 0.9019 (ttm-80) cc_final: 0.8798 (ttp-110)
REVERT: D   72 TRP cc_start: 0.8748 (OUTLIER) cc_final: 0.7452 (m-90)
REVERT: D   74 GLU cc_start: 0.7117 (pm20) cc_final: 0.6219 (pm20)
REVERT: D  107 ASP cc_start: 0.8535 (p0) cc_final: 0.8285 (p0)
REVERT: D  187 GLU cc_start: 0.8731 (mm-30) cc_final: 0.8453 (mt-10)
  outliers start: 28
  outliers final: 14
  residues processed: 154
  average time/residue: 0.2629
  time to fit residues: 54.4806
Evaluate side-chains
  133 residues out of total 898 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 118
  time to evaluate  : 1.206 
-------------------------------------------------------------------------------
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  164 VAL
Chi-restraints excluded: chain A residue  217 TYR
Chi-restraints excluded: chain A residue  254 MET
Chi-restraints excluded: chain B residue   32 ILE
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  147 VAL
Chi-restraints excluded: chain D residue   67 LYS
Chi-restraints excluded: chain D residue   72 TRP
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 52 optimal weight:    4.9990
   chunk 70 optimal weight:    5.9990
   chunk 63 optimal weight:    0.8980
   chunk 22 optimal weight:    2.9990
   chunk 39 optimal weight:   10.0000
   chunk 82 optimal weight:    0.9980
   chunk 23 optimal weight:    3.9990
   chunk 91 optimal weight:    4.9990
   chunk 78 optimal weight:   10.0000
   chunk 49 optimal weight:    9.9990
   chunk 53 optimal weight:    3.9990
   overall best weight:    2.5786

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

Flipped N/Q/H residues before XYZ refinement:
** A   8 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 144 ASN
** 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: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3467 r_free = 0.3467 target = 0.096717 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3017 r_free = 0.3017 target = 0.071559 restraints weight = 19123.178|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.3069 r_free = 0.3069 target = 0.074200 restraints weight = 9652.983|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3100 r_free = 0.3100 target = 0.075824 restraints weight = 6143.651|
|-----------------------------------------------------------------------------|
r_work (final): 0.3103
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8601
moved from start:          0.1807

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.045   8678  Z= 0.181
  Angle     :  0.628   8.129  11830  Z= 0.318
  Chirality :  0.045   0.250   1320
  Planarity :  0.005   0.083   1458
  Dihedral  : 11.364 102.364   1278
  Min Nonbonded Distance : 2.536

Molprobity Statistics.
  All-atom Clashscore : 12.62
  Ramachandran Plot:
    Outliers :  0.10 %
    Allowed  :  5.80 %
    Favored  : 94.10 %
  Rotamer:
    Outliers :  4.68 %
    Allowed  : 27.84 %
    Favored  : 67.48 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.15 (0.28), residues: 1000
  helix:  0.76 (0.32), residues: 294
  sheet: -0.78 (0.35), residues: 240
  loop : -0.11 (0.29), residues: 466

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.026   0.002   TRP A  70 
 HIS   0.003   0.001   HIS B  22 
 PHE   0.018   0.001   PHE A   5 
 TYR   0.016   0.002   TYR A  56 
 ARG   0.005   0.000   ARG A 148 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03525 (  282)
  hydrogen bonds       : angle       5.04289 (  756)
  covalent geometry    : bond        0.00425 ( 8678)
  covalent geometry    : angle       0.62778 (11830)

*********************** 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
  162 residues out of total 898 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 42
    poor density    : 120
  time to evaluate  : 1.657 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   70 TRP cc_start: 0.7262 (p-90) cc_final: 0.6553 (p-90)
REVERT: A  132 ARG cc_start: 0.8643 (tmt170) cc_final: 0.8267 (mmm160)
REVERT: A  188 ASP cc_start: 0.9003 (p0) cc_final: 0.8543 (p0)
REVERT: A  221 THR cc_start: 0.9348 (OUTLIER) cc_final: 0.9096 (t)
REVERT: B   56 TYR cc_start: 0.7946 (m-10) cc_final: 0.7428 (m-10)
REVERT: B   70 TRP cc_start: 0.7979 (m-10) cc_final: 0.7778 (m-10)
REVERT: B  209 TYR cc_start: 0.8310 (t80) cc_final: 0.8044 (t80)
REVERT: C    6 PHE cc_start: 0.8323 (m-10) cc_final: 0.7971 (m-10)
REVERT: C   55 GLN cc_start: 0.4959 (pp30) cc_final: 0.4593 (pp30)
REVERT: C   56 TYR cc_start: 0.7116 (m-80) cc_final: 0.6817 (m-80)
REVERT: C   99 GLN cc_start: 0.8264 (pm20) cc_final: 0.7803 (pm20)
REVERT: C  145 GLU cc_start: 0.8761 (tp30) cc_final: 0.8347 (tp30)
REVERT: D   72 TRP cc_start: 0.8856 (OUTLIER) cc_final: 0.7629 (m-90)
REVERT: D  130 MET cc_start: 0.9139 (tpp) cc_final: 0.8773 (tpp)
  outliers start: 42
  outliers final: 27
  residues processed: 151
  average time/residue: 0.2851
  time to fit residues: 59.5985
Evaluate side-chains
  145 residues out of total 898 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 116
  time to evaluate  : 1.214 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   90 ILE
Chi-restraints excluded: chain A residue  105 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  206 VAL
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   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  154 MET
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  206 VAL
Chi-restraints excluded: chain D residue   26 SER
Chi-restraints excluded: chain D residue   30 THR
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  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 23 optimal weight:    4.9990
   chunk 49 optimal weight:   10.0000
   chunk 13 optimal weight:    0.3980
   chunk 87 optimal weight:    2.9990
   chunk 62 optimal weight:    0.9990
   chunk 85 optimal weight:    6.9990
   chunk 73 optimal weight:   10.0000
   chunk 54 optimal weight:    9.9990
   chunk 40 optimal weight:    3.9990
   chunk 37 optimal weight:    4.9990
   chunk 83 optimal weight:    3.9990
   overall best weight:    2.4788

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

Flipped N/Q/H residues before XYZ refinement:
A   8 HIS
** B  34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C  83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 144 ASN ** 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 = 0.3473 r_free = 0.3473 target = 0.096708 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3015 r_free = 0.3015 target = 0.071337 restraints weight = 19024.826|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3067 r_free = 0.3067 target = 0.073970 restraints weight = 9712.316|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 45)----------------|
| r_work = 0.3099 r_free = 0.3099 target = 0.075629 restraints weight = 6244.846|
|-----------------------------------------------------------------------------|
r_work (final): 0.3102
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8608
moved from start:          0.2106

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.038   8678  Z= 0.170
  Angle     :  0.600   6.816  11830  Z= 0.305
  Chirality :  0.045   0.257   1320
  Planarity :  0.005   0.070   1458
  Dihedral  : 11.108 106.804   1278
  Min Nonbonded Distance : 2.565

Molprobity Statistics.
  All-atom Clashscore : 12.62
  Ramachandran Plot:
    Outliers :  0.10 %
    Allowed  :  5.60 %
    Favored  : 94.30 %
  Rotamer:
    Outliers :  4.79 %
    Allowed  : 27.95 %
    Favored  : 67.26 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.22 (0.28), residues: 1000
  helix:  0.71 (0.32), residues: 294
  sheet: -0.78 (0.36), residues: 240
  loop : -0.19 (0.29), residues: 466

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.001   TRP B  72 
 HIS   0.003   0.001   HIS B  22 
 PHE   0.008   0.001   PHE B 231 
 TYR   0.016   0.002   TYR C 209 
 ARG   0.006   0.000   ARG C 132 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03287 (  282)
  hydrogen bonds       : angle       4.92108 (  756)
  covalent geometry    : bond        0.00401 ( 8678)
  covalent geometry    : angle       0.60036 (11830)

*********************** 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
  159 residues out of total 898 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 43
    poor density    : 116
  time to evaluate  : 1.010 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   70 TRP cc_start: 0.7185 (p-90) cc_final: 0.6383 (p-90)
REVERT: A  132 ARG cc_start: 0.8629 (tmt170) cc_final: 0.8266 (mmm160)
REVERT: A  188 ASP cc_start: 0.8984 (p0) cc_final: 0.8592 (p0)
REVERT: A  221 THR cc_start: 0.9355 (OUTLIER) cc_final: 0.9148 (t)
REVERT: B   56 TYR cc_start: 0.7956 (m-10) cc_final: 0.7488 (m-10)
REVERT: C   55 GLN cc_start: 0.4901 (pp30) cc_final: 0.4600 (pp30)
REVERT: C   77 GLN cc_start: 0.9178 (mt0) cc_final: 0.8863 (mm-40)
REVERT: C   83 GLN cc_start: 0.8787 (mm-40) cc_final: 0.8550 (mm-40)
REVERT: C   99 GLN cc_start: 0.8353 (pm20) cc_final: 0.8135 (pm20)
REVERT: D   72 TRP cc_start: 0.8836 (OUTLIER) cc_final: 0.7437 (m-90)
REVERT: D  130 MET cc_start: 0.9134 (tpp) cc_final: 0.8890 (tpp)
  outliers start: 43
  outliers final: 25
  residues processed: 148
  average time/residue: 0.2210
  time to fit residues: 44.2781
Evaluate side-chains
  138 residues out of total 898 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 111
  time to evaluate  : 1.024 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   90 ILE
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  206 VAL
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  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  206 VAL
Chi-restraints excluded: chain D residue   66 LEU
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  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=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 98
   random chunks:
   chunk 37 optimal weight:    6.9990
   chunk 44 optimal weight:    2.9990
   chunk 49 optimal weight:   10.0000
   chunk 85 optimal weight:    3.9990
   chunk 18 optimal weight:    0.9980
   chunk 2 optimal weight:    4.9990
   chunk 1 optimal weight:    0.7980
   chunk 65 optimal weight:    0.5980
   chunk 43 optimal weight:    3.9990
   chunk 60 optimal weight:    2.9990
   chunk 21 optimal weight:    0.0980
   overall best weight:    1.0982

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

Flipped N/Q/H residues before XYZ refinement:
A  46 GLN
** A  55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B  34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
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 = 0.3505 r_free = 0.3505 target = 0.098852 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3065 r_free = 0.3065 target = 0.073573 restraints weight = 18772.124|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3116 r_free = 0.3116 target = 0.076232 restraints weight = 9423.281|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 42)----------------|
| r_work = 0.3149 r_free = 0.3149 target = 0.077987 restraints weight = 6018.923|
|-----------------------------------------------------------------------------|
r_work (final): 0.3151
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8557
moved from start:          0.2228

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040   8678  Z= 0.112
  Angle     :  0.578  10.098  11830  Z= 0.292
  Chirality :  0.044   0.230   1320
  Planarity :  0.005   0.066   1458
  Dihedral  : 11.028 105.942   1278
  Min Nonbonded Distance : 2.549

Molprobity Statistics.
  All-atom Clashscore : 12.15
  Ramachandran Plot:
    Outliers :  0.10 %
    Allowed  :  5.90 %
    Favored  : 94.00 %
  Rotamer:
    Outliers :  4.34 %
    Allowed  : 29.29 %
    Favored  : 66.37 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.11 (0.28), residues: 1000
  helix:  0.77 (0.32), residues: 294
  sheet: -0.71 (0.36), residues: 240
  loop : -0.12 (0.29), residues: 466

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.001   TRP B  72 
 HIS   0.002   0.000   HIS D   8 
 PHE   0.006   0.001   PHE B   6 
 TYR   0.016   0.001   TYR C 209 
 ARG   0.006   0.000   ARG C 132 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02988 (  282)
  hydrogen bonds       : angle       4.76653 (  756)
  covalent geometry    : bond        0.00265 ( 8678)
  covalent geometry    : angle       0.57847 (11830)

*********************** 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
  165 residues out of total 898 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 39
    poor density    : 126
  time to evaluate  : 1.034 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  132 ARG cc_start: 0.8646 (tmt170) cc_final: 0.8295 (mmm160)
REVERT: A  188 ASP cc_start: 0.8935 (p0) cc_final: 0.8573 (p0)
REVERT: A  221 THR cc_start: 0.9362 (m) cc_final: 0.9155 (t)
REVERT: B  154 MET cc_start: 0.8144 (OUTLIER) cc_final: 0.7817 (tpp)
REVERT: C   77 GLN cc_start: 0.9188 (mt0) cc_final: 0.8862 (mm-40)
REVERT: C   99 GLN cc_start: 0.8359 (pm20) cc_final: 0.8136 (pm20)
REVERT: D   72 TRP cc_start: 0.8787 (OUTLIER) cc_final: 0.7344 (m-90)
  outliers start: 39
  outliers final: 25
  residues processed: 155
  average time/residue: 0.2305
  time to fit residues: 47.7888
Evaluate side-chains
  147 residues out of total 898 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 120
  time to evaluate  : 0.935 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   32 ILE
Chi-restraints excluded: chain A residue   47 ILE
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   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 B residue  164 VAL
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  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  164 VAL
Chi-restraints excluded: chain D residue  165 VAL
Chi-restraints excluded: chain D residue  174 LEU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 98
   random chunks:
   chunk 34 optimal weight:    0.3980
   chunk 60 optimal weight:    4.9990
   chunk 39 optimal weight:    0.8980
   chunk 84 optimal weight:    8.9990
   chunk 49 optimal weight:   10.0000
   chunk 30 optimal weight:   10.0000
   chunk 96 optimal weight:    5.9990
   chunk 86 optimal weight:    2.9990
   chunk 87 optimal weight:   10.0000
   chunk 79 optimal weight:    0.2980
   chunk 15 optimal weight:    5.9990
   overall best weight:    1.9184

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

Flipped N/Q/H residues before XYZ refinement:
** C  83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
D 144 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3487 r_free = 0.3487 target = 0.097572 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.3038 r_free = 0.3038 target = 0.072279 restraints weight = 18848.532|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 46)----------------|
| r_work = 0.3091 r_free = 0.3091 target = 0.074934 restraints weight = 9610.951|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 44)----------------|
| r_work = 0.3123 r_free = 0.3123 target = 0.076633 restraints weight = 6177.478|
|-----------------------------------------------------------------------------|
r_work (final): 0.3128
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8583
moved from start:          0.2474

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040   8678  Z= 0.145
  Angle     :  0.597   8.309  11830  Z= 0.302
  Chirality :  0.044   0.238   1320
  Planarity :  0.005   0.069   1458
  Dihedral  : 10.983 109.285   1278
  Min Nonbonded Distance : 2.538

Molprobity Statistics.
  All-atom Clashscore : 12.86
  Ramachandran Plot:
    Outliers :  0.10 %
    Allowed  :  6.20 %
    Favored  : 93.70 %
  Rotamer:
    Outliers :  4.01 %
    Allowed  : 30.62 %
    Favored  : 65.37 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.03 (0.28), residues: 1000
  helix:  1.00 (0.32), residues: 286
  sheet: -0.67 (0.36), residues: 240
  loop : -0.16 (0.29), residues: 474

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.001   TRP B  72 
 HIS   0.003   0.001   HIS B  22 
 PHE   0.009   0.001   PHE B 231 
 TYR   0.021   0.002   TYR D  56 
 ARG   0.006   0.000   ARG C 132 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03066 (  282)
  hydrogen bonds       : angle       4.72838 (  756)
  covalent geometry    : bond        0.00346 ( 8678)
  covalent geometry    : angle       0.59658 (11830)

*********************** 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
  156 residues out of total 898 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 120
  time to evaluate  : 0.990 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   73 ASP cc_start: 0.8800 (m-30) cc_final: 0.8159 (p0)
REVERT: A  132 ARG cc_start: 0.8626 (tmt170) cc_final: 0.8280 (mmm160)
REVERT: A  188 ASP cc_start: 0.8929 (p0) cc_final: 0.8597 (p0)
REVERT: A  221 THR cc_start: 0.9356 (m) cc_final: 0.9135 (t)
REVERT: B  154 MET cc_start: 0.8181 (OUTLIER) cc_final: 0.7866 (tpp)
REVERT: C   77 GLN cc_start: 0.9223 (mt0) cc_final: 0.8902 (mm-40)
REVERT: C   83 GLN cc_start: 0.8721 (mm-40) cc_final: 0.8334 (mm-40)
REVERT: C   99 GLN cc_start: 0.8418 (pm20) cc_final: 0.8179 (pm20)
REVERT: C  145 GLU cc_start: 0.8905 (tp30) cc_final: 0.8287 (tp30)
REVERT: D   72 TRP cc_start: 0.8774 (OUTLIER) cc_final: 0.7187 (m-90)
  outliers start: 36
  outliers final: 26
  residues processed: 147
  average time/residue: 0.2264
  time to fit residues: 44.8307
Evaluate side-chains
  144 residues out of total 898 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 116
  time to evaluate  : 0.978 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   47 ILE
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  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  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=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 98
   random chunks:
   chunk 1 optimal weight:    7.9990
   chunk 48 optimal weight:    0.0020
   chunk 71 optimal weight:    5.9990
   chunk 80 optimal weight:    0.6980
   chunk 45 optimal weight:    3.9990
   chunk 61 optimal weight:   10.0000
   chunk 35 optimal weight:    5.9990
   chunk 16 optimal weight:    7.9990
   chunk 25 optimal weight:    0.7980
   chunk 27 optimal weight:    0.8980
   chunk 32 optimal weight:    2.9990
   overall best weight:    1.0790

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

Flipped N/Q/H residues before XYZ refinement:
A  46 GLN
** A  55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C  83 GLN
** C 129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 163 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3534 r_free = 0.3534 target = 0.100218 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3093 r_free = 0.3093 target = 0.074988 restraints weight = 19003.652|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3147 r_free = 0.3147 target = 0.077758 restraints weight = 9575.107|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 60)----------------|
| r_work = 0.3179 r_free = 0.3179 target = 0.079497 restraints weight = 6083.439|
|-----------------------------------------------------------------------------|
r_work (final): 0.3172
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8543
moved from start:          0.2644

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041   8678  Z= 0.113
  Angle     :  0.584   9.077  11830  Z= 0.295
  Chirality :  0.044   0.223   1320
  Planarity :  0.005   0.071   1458
  Dihedral  : 10.970 109.339   1278
  Min Nonbonded Distance : 2.532

Molprobity Statistics.
  All-atom Clashscore : 11.73
  Ramachandran Plot:
    Outliers :  0.10 %
    Allowed  :  6.20 %
    Favored  : 93.70 %
  Rotamer:
    Outliers :  4.01 %
    Allowed  : 31.07 %
    Favored  : 64.92 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.02 (0.28), residues: 1000
  helix:  1.01 (0.32), residues: 286
  sheet: -0.68 (0.36), residues: 240
  loop : -0.14 (0.29), residues: 474

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP B  70 
 HIS   0.003   0.000   HIS D   8 
 PHE   0.006   0.001   PHE B   6 
 TYR   0.025   0.002   TYR A  56 
 ARG   0.006   0.000   ARG C 132 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02926 (  282)
  hydrogen bonds       : angle       4.67750 (  756)
  covalent geometry    : bond        0.00270 ( 8678)
  covalent geometry    : angle       0.58374 (11830)

*********************** 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
  164 residues out of total 898 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 128
  time to evaluate  : 0.962 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   73 ASP cc_start: 0.8790 (m-30) cc_final: 0.8159 (p0)
REVERT: A  132 ARG cc_start: 0.8649 (tmt170) cc_final: 0.8300 (mmm160)
REVERT: A  188 ASP cc_start: 0.8888 (p0) cc_final: 0.8607 (p0)
REVERT: A  221 THR cc_start: 0.9365 (m) cc_final: 0.9161 (t)
REVERT: B  154 MET cc_start: 0.8159 (OUTLIER) cc_final: 0.7839 (tpp)
REVERT: C   77 GLN cc_start: 0.9231 (mt0) cc_final: 0.8925 (mm-40)
REVERT: C   99 GLN cc_start: 0.8422 (pm20) cc_final: 0.8181 (pm20)
REVERT: C  145 GLU cc_start: 0.8727 (tp30) cc_final: 0.8433 (tp30)
REVERT: D   72 TRP cc_start: 0.8692 (OUTLIER) cc_final: 0.7028 (m-90)
  outliers start: 36
  outliers final: 27
  residues processed: 152
  average time/residue: 0.2552
  time to fit residues: 52.6767
Evaluate side-chains
  148 residues out of total 898 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 119
  time to evaluate  : 1.129 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   90 ILE
Chi-restraints excluded: chain A residue   99 GLN
Chi-restraints excluded: chain A residue  165 VAL
Chi-restraints excluded: chain A residue  172 SER
Chi-restraints excluded: chain A residue  176 VAL
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  206 VAL
Chi-restraints excluded: chain D residue   32 ILE
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=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 98
   random chunks:
   chunk 42 optimal weight:    0.8980
   chunk 10 optimal weight:    0.0470
   chunk 24 optimal weight:    9.9990
   chunk 21 optimal weight:    0.9980
   chunk 61 optimal weight:    9.9990
   chunk 37 optimal weight:    7.9990
   chunk 12 optimal weight:    9.9990
   chunk 28 optimal weight:    4.9990
   chunk 41 optimal weight:    7.9990
   chunk 19 optimal weight:    3.9990
   chunk 30 optimal weight:    9.9990
   overall best weight:    2.1882

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

Flipped N/Q/H residues before XYZ refinement:
** C  83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 129 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 = 0.3492 r_free = 0.3492 target = 0.097570 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3060 r_free = 0.3060 target = 0.073085 restraints weight = 18936.919|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 45)----------------|
| r_work = 0.3113 r_free = 0.3113 target = 0.075764 restraints weight = 9447.015|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 45)----------------|
| r_work = 0.3145 r_free = 0.3145 target = 0.077478 restraints weight = 5973.798|
|-----------------------------------------------------------------------------|
r_work (final): 0.3149
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8581
moved from start:          0.2787

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.040   8678  Z= 0.157
  Angle     :  0.602   8.621  11830  Z= 0.306
  Chirality :  0.044   0.238   1320
  Planarity :  0.005   0.073   1458
  Dihedral  : 10.937 111.743   1278
  Min Nonbonded Distance : 2.527

Molprobity Statistics.
  All-atom Clashscore : 12.74
  Ramachandran Plot:
    Outliers :  0.10 %
    Allowed  :  6.40 %
    Favored  : 93.50 %
  Rotamer:
    Outliers :  3.90 %
    Allowed  : 30.73 %
    Favored  : 65.37 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.01 (0.28), residues: 1000
  helix:  1.11 (0.33), residues: 286
  sheet: -0.65 (0.36), residues: 240
  loop : -0.20 (0.29), residues: 474

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.023   0.001   TRP B  72 
 HIS   0.003   0.001   HIS B  22 
 PHE   0.009   0.001   PHE B 231 
 TYR   0.020   0.002   TYR A  56 
 ARG   0.007   0.000   ARG C 132 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03114 (  282)
  hydrogen bonds       : angle       4.69799 (  756)
  covalent geometry    : bond        0.00373 ( 8678)
  covalent geometry    : angle       0.60239 (11830)

*********************** 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
  149 residues out of total 898 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 114
  time to evaluate  : 0.930 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   73 ASP cc_start: 0.8789 (m-30) cc_final: 0.8154 (p0)
REVERT: A  132 ARG cc_start: 0.8617 (tmt170) cc_final: 0.8274 (mmm160)
REVERT: A  143 GLN cc_start: 0.8096 (pm20) cc_final: 0.7862 (pm20)
REVERT: A  221 THR cc_start: 0.9362 (m) cc_final: 0.9131 (t)
REVERT: C   11 LYS cc_start: 0.8555 (mmtm) cc_final: 0.8210 (mmtm)
REVERT: C   77 GLN cc_start: 0.9227 (mt0) cc_final: 0.8912 (mm-40)
REVERT: C   99 GLN cc_start: 0.8473 (pm20) cc_final: 0.8040 (pm20)
REVERT: C  145 GLU cc_start: 0.8837 (tp30) cc_final: 0.8582 (tp30)
  outliers start: 35
  outliers final: 27
  residues processed: 142
  average time/residue: 0.2243
  time to fit residues: 42.6900
Evaluate side-chains
  136 residues out of total 898 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 109
  time to evaluate  : 0.907 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   47 ILE
Chi-restraints excluded: chain A residue   90 ILE
Chi-restraints excluded: chain A residue   99 GLN
Chi-restraints excluded: chain A residue  165 VAL
Chi-restraints excluded: chain A residue  172 SER
Chi-restraints excluded: chain A residue  176 VAL
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  206 VAL
Chi-restraints excluded: chain D residue   67 LYS
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=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 98
   random chunks:
   chunk 65 optimal weight:    0.0170
   chunk 96 optimal weight:    4.9990
   chunk 30 optimal weight:   10.0000
   chunk 92 optimal weight:    6.9990
   chunk 21 optimal weight:    0.8980
   chunk 67 optimal weight:    5.9990
   chunk 84 optimal weight:    8.9990
   chunk 29 optimal weight:    2.9990
   chunk 80 optimal weight:    0.7980
   chunk 51 optimal weight:    0.9990
   chunk 53 optimal weight:    0.8980
   overall best weight:    0.7220

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

Flipped N/Q/H residues before XYZ refinement:
** C  83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 129 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 = 0.3556 r_free = 0.3556 target = 0.101254 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3109 r_free = 0.3109 target = 0.075859 restraints weight = 19045.699|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 43)----------------|
| r_work = 0.3164 r_free = 0.3164 target = 0.078659 restraints weight = 9666.179|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3197 r_free = 0.3197 target = 0.080391 restraints weight = 6171.027|
|-----------------------------------------------------------------------------|
r_work (final): 0.3198
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8530
moved from start:          0.2883

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.042   8678  Z= 0.106
  Angle     :  0.609  10.367  11830  Z= 0.305
  Chirality :  0.044   0.212   1320
  Planarity :  0.005   0.073   1458
  Dihedral  : 10.839 110.677   1276
  Min Nonbonded Distance : 2.551

Molprobity Statistics.
  All-atom Clashscore : 11.13
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.00 %
    Favored  : 94.00 %
  Rotamer:
    Outliers :  2.90 %
    Allowed  : 31.74 %
    Favored  : 65.37 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.02 (0.28), residues: 1000
  helix:  1.11 (0.33), residues: 286
  sheet: -0.76 (0.35), residues: 236
  loop : -0.10 (0.29), residues: 478

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.022   0.001   TRP B  72 
 HIS   0.002   0.000   HIS D   8 
 PHE   0.006   0.001   PHE B   6 
 TYR   0.021   0.001   TYR A  56 
 ARG   0.002   0.000   ARG C 148 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02997 (  282)
  hydrogen bonds       : angle       4.66495 (  756)
  covalent geometry    : bond        0.00250 ( 8678)
  covalent geometry    : angle       0.60933 (11830)

*********************** 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
  159 residues out of total 898 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 133
  time to evaluate  : 1.024 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A    3 GLN cc_start: 0.9101 (mp10) cc_final: 0.8459 (mp10)
REVERT: A   73 ASP cc_start: 0.8837 (m-30) cc_final: 0.8209 (p0)
REVERT: A  132 ARG cc_start: 0.8624 (tmt170) cc_final: 0.8297 (mmm160)
REVERT: A  188 ASP cc_start: 0.8837 (p0) cc_final: 0.8559 (p0)
REVERT: A  221 THR cc_start: 0.9369 (m) cc_final: 0.9144 (t)
REVERT: C   77 GLN cc_start: 0.9254 (mt0) cc_final: 0.8929 (mm-40)
REVERT: C   99 GLN cc_start: 0.8417 (pm20) cc_final: 0.7979 (pm20)
REVERT: D   67 LYS cc_start: 0.9030 (OUTLIER) cc_final: 0.8635 (mtmm)
REVERT: D  188 ASP cc_start: 0.8724 (m-30) cc_final: 0.8325 (t0)
  outliers start: 26
  outliers final: 23
  residues processed: 149
  average time/residue: 0.2615
  time to fit residues: 52.8506
Evaluate side-chains
  147 residues out of total 898 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 123
  time to evaluate  : 1.073 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   90 ILE
Chi-restraints excluded: chain A residue   99 GLN
Chi-restraints excluded: chain A residue  165 VAL
Chi-restraints excluded: chain A residue  172 SER
Chi-restraints excluded: chain A residue  176 VAL
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   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  206 VAL
Chi-restraints excluded: chain D residue   67 LYS
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 23 optimal weight:    2.9990
   chunk 45 optimal weight:    4.9990
   chunk 90 optimal weight:    4.9990
   chunk 92 optimal weight:    8.9990
   chunk 69 optimal weight:    2.9990
   chunk 87 optimal weight:    7.9990
   chunk 11 optimal weight:    0.3980
   chunk 0 optimal weight:   10.0000
   chunk 76 optimal weight:    7.9990
   chunk 56 optimal weight:    7.9990
   chunk 5 optimal weight:    0.8980
   overall best weight:    2.4586

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

Flipped N/Q/H residues before XYZ refinement:
** B  34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C   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**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3492 r_free = 0.3492 target = 0.097375 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3056 r_free = 0.3056 target = 0.072954 restraints weight = 18898.509|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3108 r_free = 0.3108 target = 0.075575 restraints weight = 9541.989|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 49)----------------|
| r_work = 0.3141 r_free = 0.3141 target = 0.077294 restraints weight = 6051.803|
|-----------------------------------------------------------------------------|
r_work (final): 0.3144
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8589
moved from start:          0.3001

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.046   8678  Z= 0.178
  Angle     :  0.655   8.882  11830  Z= 0.333
  Chirality :  0.045   0.239   1320
  Planarity :  0.005   0.074   1458
  Dihedral  : 10.843 112.607   1276
  Min Nonbonded Distance : 2.519

Molprobity Statistics.
  All-atom Clashscore : 12.38
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.70 %
    Favored  : 93.30 %
  Rotamer:
    Outliers :  3.12 %
    Allowed  : 32.52 %
    Favored  : 64.37 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.05 (0.28), residues: 1000
  helix:  1.16 (0.32), residues: 286
  sheet: -0.61 (0.36), residues: 240
  loop : -0.19 (0.29), residues: 474

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.023   0.001   TRP B  72 
 HIS   0.004   0.001   HIS C   8 
 PHE   0.009   0.001   PHE B 231 
 TYR   0.016   0.002   TYR C  56 
 ARG   0.008   0.000   ARG C 132 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03191 (  282)
  hydrogen bonds       : angle       4.72132 (  756)
  covalent geometry    : bond        0.00424 ( 8678)
  covalent geometry    : angle       0.65472 (11830)

********************** 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
  144 residues out of total 898 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 116
  time to evaluate  : 1.062 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   73 ASP cc_start: 0.8822 (m-30) cc_final: 0.8216 (p0)
REVERT: A  132 ARG cc_start: 0.8604 (tmt170) cc_final: 0.8277 (mmm160)
REVERT: A  188 ASP cc_start: 0.8904 (p0) cc_final: 0.8526 (p0)
REVERT: A  221 THR cc_start: 0.9355 (m) cc_final: 0.9108 (t)
REVERT: C    6 PHE cc_start: 0.8369 (m-10) cc_final: 0.8130 (m-10)
REVERT: C   77 GLN cc_start: 0.9216 (mt0) cc_final: 0.8895 (mm-40)
REVERT: C   83 GLN cc_start: 0.8682 (mm-40) cc_final: 0.8367 (mm-40)
REVERT: C   99 GLN cc_start: 0.8450 (pm20) cc_final: 0.7999 (pm20)
REVERT: D  188 ASP cc_start: 0.8698 (m-30) cc_final: 0.8323 (t0)
  outliers start: 28
  outliers final: 25
  residues processed: 138
  average time/residue: 0.2375
  time to fit residues: 43.8320
Evaluate side-chains
  137 residues out of total 898 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 112
  time to evaluate  : 1.047 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   90 ILE
Chi-restraints excluded: chain A residue   99 GLN
Chi-restraints excluded: chain A residue  165 VAL
Chi-restraints excluded: chain A residue  172 SER
Chi-restraints excluded: chain A residue  176 VAL
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   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  206 VAL
Chi-restraints excluded: chain D residue   67 LYS
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 22 optimal weight:    5.9990
   chunk 79 optimal weight:    0.3980
   chunk 25 optimal weight:    6.9990
   chunk 97 optimal weight:   10.0000
   chunk 35 optimal weight:    9.9990
   chunk 48 optimal weight:    0.9980
   chunk 44 optimal weight:    2.9990
   chunk 72 optimal weight:    0.7980
   chunk 13 optimal weight:    8.9990
   chunk 36 optimal weight:    4.9990
   chunk 82 optimal weight:    0.9990
   overall best weight:    1.2384

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

Flipped N/Q/H residues before XYZ refinement:
** B  34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C  83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 129 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 = 0.3522 r_free = 0.3522 target = 0.099258 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3093 r_free = 0.3093 target = 0.074919 restraints weight = 18938.433|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3147 r_free = 0.3147 target = 0.077608 restraints weight = 9402.547|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.3180 r_free = 0.3180 target = 0.079358 restraints weight = 5918.562|
|-----------------------------------------------------------------------------|
r_work (final): 0.3184
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8548
moved from start:          0.3056

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041   8678  Z= 0.126
  Angle     :  0.637   9.133  11830  Z= 0.322
  Chirality :  0.045   0.225   1320
  Planarity :  0.005   0.074   1458
  Dihedral  : 10.863 112.076   1276
  Min Nonbonded Distance : 2.528

Molprobity Statistics.
  All-atom Clashscore : 11.37
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.20 %
    Favored  : 93.80 %
  Rotamer:
    Outliers :  2.78 %
    Allowed  : 33.30 %
    Favored  : 63.92 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.01 (0.28), residues: 1000
  helix:  1.10 (0.32), residues: 286
  sheet: -0.80 (0.35), residues: 252
  loop : -0.10 (0.29), residues: 462

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.021   0.001   TRP B  72 
 HIS   0.002   0.000   HIS D   8 
 PHE   0.008   0.001   PHE D 231 
 TYR   0.017   0.002   TYR C  56 
 ARG   0.005   0.000   ARG A 148 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02979 (  282)
  hydrogen bonds       : angle       4.68140 (  756)
  covalent geometry    : bond        0.00304 ( 8678)
  covalent geometry    : angle       0.63700 (11830)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3518.28 seconds
wall clock time: 64 minutes 5.75 seconds (3845.75 seconds total)