Starting phenix.real_space_refine
on Sun May 11 22:29:50 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9mue_48630/05_2025/9mue_48630.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9mue_48630/05_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_48630/05_2025/9mue_48630.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9mue_48630/05_2025/9mue_48630.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9mue_48630/05_2025/9mue_48630.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9mue_48630/05_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): 0.03s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/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: 8.25, per 1000 atoms: 0.98
  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: 2.33
  Conformation dependent library (CDL) restraints added in 1.0 seconds
  

  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: 1.09
  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: 2.33

  Time building geometry restraints manager: 2.70 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:             10.970
  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:          0.300
  Check model and map are aligned:         0.060
  Set scattering table:                    0.140
  Process input model:                     27.370
  Find NCS groups from input model:        0.350
  Set up NCS constraints:                  0.030
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.010
  Load rotamer database and sin/cos tables:2.880
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   42.120
-------------------------------------------------------------------------------
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  : 1.023 
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: 0.2597
  time to fit residues: 51.1576
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  : 1.030 
-------------------------------------------------------------------------------
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 = 0.3095 r_free = 0.3095 target = 0.075441 restraints weight = 18829.706|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 41)----------------|
| r_work = 0.3145 r_free = 0.3145 target = 0.078112 restraints weight = 9484.340|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3176 r_free = 0.3176 target = 0.079809 restraints weight = 6041.296|
|-----------------------------------------------------------------------------|
r_work (final): 0.3183
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8515
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       5.49498 (  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  : 1.025 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   65 TYR cc_start: 0.7830 (t80) cc_final: 0.7630 (t80)
REVERT: A  221 THR cc_start: 0.9310 (m) cc_final: 0.9063 (t)
REVERT: C   55 GLN cc_start: 0.5074 (pp30) cc_final: 0.4656 (pp30)
REVERT: C   99 GLN cc_start: 0.8129 (pm20) cc_final: 0.7778 (pm20)
REVERT: C  132 ARG cc_start: 0.9021 (ttm-80) cc_final: 0.8800 (ttp-110)
REVERT: D   72 TRP cc_start: 0.8747 (OUTLIER) cc_final: 0.7449 (m-90)
REVERT: D   74 GLU cc_start: 0.7118 (pm20) cc_final: 0.6216 (pm20)
REVERT: D  107 ASP cc_start: 0.8536 (p0) cc_final: 0.8286 (p0)
REVERT: D  187 GLU cc_start: 0.8734 (mm-30) cc_final: 0.8454 (mt-10)
  outliers start: 28
  outliers final: 14
  residues processed: 154
  average time/residue: 0.2342
  time to fit residues: 48.6543
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  : 1.020 
-------------------------------------------------------------------------------
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:    5.9990
   chunk 70 optimal weight:    5.9990
   chunk 63 optimal weight:    1.9990
   chunk 22 optimal weight:    2.9990
   chunk 39 optimal weight:    9.9990
   chunk 82 optimal weight:    0.9990
   chunk 23 optimal weight:    4.9990
   chunk 91 optimal weight:    0.8980
   chunk 78 optimal weight:   10.0000
   chunk 49 optimal weight:    9.9990
   chunk 53 optimal weight:    1.9990
   overall best weight:    1.7788

-------------------------------------------------------------------------------
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 = 0.3516 r_free = 0.3516 target = 0.099487 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3071 r_free = 0.3071 target = 0.074305 restraints weight = 19087.909|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3124 r_free = 0.3124 target = 0.076989 restraints weight = 9600.327|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 45)----------------|
| r_work = 0.3157 r_free = 0.3157 target = 0.078740 restraints weight = 6115.172|
|-----------------------------------------------------------------------------|
r_work (final): 0.3163
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8556
moved from start:          0.1667

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039   8678  Z= 0.140
  Angle     :  0.599   8.459  11830  Z= 0.303
  Chirality :  0.044   0.224   1320
  Planarity :  0.005   0.082   1458
  Dihedral  : 11.307 100.535   1278
  Min Nonbonded Distance : 2.548

Molprobity Statistics.
  All-atom Clashscore : 11.73
  Ramachandran Plot:
    Outliers :  0.10 %
    Allowed  :  5.40 %
    Favored  : 94.50 %
  Rotamer:
    Outliers :  4.34 %
    Allowed  : 27.51 %
    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: -0.07 (0.28), residues: 1000
  helix:  0.79 (0.32), residues: 294
  sheet: -0.71 (0.35), residues: 240
  loop : -0.06 (0.29), residues: 466

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.025   0.001   TRP A  70 
 HIS   0.003   0.001   HIS A   8 
 PHE   0.014   0.001   PHE A   5 
 TYR   0.016   0.001   TYR A  56 
 ARG   0.005   0.000   ARG C 148 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03339 (  282)
  hydrogen bonds       : angle       5.01541 (  756)
  covalent geometry    : bond        0.00330 ( 8678)
  covalent geometry    : angle       0.59935 (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
  165 residues out of total 898 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 39
    poor density    : 126
  time to evaluate  : 0.950 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   70 TRP cc_start: 0.7288 (p-90) cc_final: 0.6525 (p-90)
REVERT: A  132 ARG cc_start: 0.8646 (tmt170) cc_final: 0.8281 (mmm160)
REVERT: A  188 ASP cc_start: 0.8953 (p0) cc_final: 0.8469 (p0)
REVERT: A  221 THR cc_start: 0.9328 (OUTLIER) cc_final: 0.9089 (t)
REVERT: B   56 TYR cc_start: 0.7927 (m-10) cc_final: 0.7442 (m-10)
REVERT: B   70 TRP cc_start: 0.7898 (m-10) cc_final: 0.7356 (m-10)
REVERT: B  101 ASP cc_start: 0.7966 (t0) cc_final: 0.7631 (t0)
REVERT: B  209 TYR cc_start: 0.8228 (t80) cc_final: 0.7964 (t80)
REVERT: C   55 GLN cc_start: 0.4893 (pp30) cc_final: 0.4566 (pp30)
REVERT: C   56 TYR cc_start: 0.7013 (m-80) cc_final: 0.6579 (m-80)
REVERT: C   77 GLN cc_start: 0.9156 (mt0) cc_final: 0.8846 (mm-40)
REVERT: C   79 TYR cc_start: 0.7987 (t80) cc_final: 0.7723 (t80)
REVERT: C   83 GLN cc_start: 0.8803 (mm110) cc_final: 0.8595 (mm-40)
REVERT: C   99 GLN cc_start: 0.8263 (pm20) cc_final: 0.7789 (pm20)
REVERT: C  145 GLU cc_start: 0.8695 (tp30) cc_final: 0.8320 (tp30)
REVERT: D   72 TRP cc_start: 0.8814 (OUTLIER) cc_final: 0.7674 (m-90)
  outliers start: 39
  outliers final: 24
  residues processed: 154
  average time/residue: 0.2187
  time to fit residues: 45.5645
Evaluate side-chains
  147 residues out of total 898 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 121
  time to evaluate  : 0.963 
-------------------------------------------------------------------------------
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  123 VAL
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   61 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   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=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 98
   random chunks:
   chunk 23 optimal weight:    6.9990
   chunk 49 optimal weight:   10.0000
   chunk 13 optimal weight:    2.9990
   chunk 87 optimal weight:    5.9990
   chunk 62 optimal weight:    8.9990
   chunk 85 optimal weight:    3.9990
   chunk 73 optimal weight:   10.0000
   chunk 54 optimal weight:    2.9990
   chunk 40 optimal weight:    2.9990
   chunk 37 optimal weight:    7.9990
   chunk 83 optimal weight:    0.0970
   overall best weight:    2.6186

-------------------------------------------------------------------------------
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 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 = 0.3474 r_free = 0.3474 target = 0.096784 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3022 r_free = 0.3022 target = 0.071571 restraints weight = 19106.145|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3074 r_free = 0.3074 target = 0.074235 restraints weight = 9711.863|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3106 r_free = 0.3106 target = 0.075882 restraints weight = 6179.184|
|-----------------------------------------------------------------------------|
r_work (final): 0.3110
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8603
moved from start:          0.2099

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= 0.179
  Angle     :  0.602   6.765  11830  Z= 0.307
  Chirality :  0.045   0.263   1320
  Planarity :  0.005   0.070   1458
  Dihedral  : 11.117 109.236   1278
  Min Nonbonded Distance : 2.566

Molprobity Statistics.
  All-atom Clashscore : 12.38
  Ramachandran Plot:
    Outliers :  0.10 %
    Allowed  :  5.70 %
    Favored  : 94.20 %
  Rotamer:
    Outliers :  5.12 %
    Allowed  : 27.39 %
    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: -0.16 (0.28), residues: 1000
  helix:  0.78 (0.32), residues: 294
  sheet: -0.76 (0.35), residues: 240
  loop : -0.16 (0.29), residues: 466

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.001   TRP A  70 
 HIS   0.003   0.001   HIS B  22 
 PHE   0.010   0.001   PHE B 231 
 TYR   0.016   0.002   TYR C 209 
 ARG   0.005   0.000   ARG A 110 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03296 (  282)
  hydrogen bonds       : angle       4.87689 (  756)
  covalent geometry    : bond        0.00419 ( 8678)
  covalent geometry    : angle       0.60214 (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
  168 residues out of total 898 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 46
    poor density    : 122
  time to evaluate  : 0.932 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   70 TRP cc_start: 0.7179 (p-90) cc_final: 0.6384 (p-90)
REVERT: A  132 ARG cc_start: 0.8621 (tmt170) cc_final: 0.8251 (mmm160)
REVERT: A  188 ASP cc_start: 0.8975 (p0) cc_final: 0.8572 (p0)
REVERT: A  221 THR cc_start: 0.9354 (OUTLIER) cc_final: 0.9148 (t)
REVERT: B   56 TYR cc_start: 0.7985 (m-10) cc_final: 0.7528 (m-10)
REVERT: C    6 PHE cc_start: 0.8374 (m-10) cc_final: 0.7988 (m-10)
REVERT: C   55 GLN cc_start: 0.4842 (pp30) cc_final: 0.4589 (pp30)
REVERT: C   77 GLN cc_start: 0.9206 (mt0) cc_final: 0.8860 (mm-40)
REVERT: C  145 GLU cc_start: 0.8889 (tp30) cc_final: 0.8413 (tp30)
REVERT: D   72 TRP cc_start: 0.8856 (OUTLIER) cc_final: 0.7534 (m-90)
REVERT: D  187 GLU cc_start: 0.8732 (mm-30) cc_final: 0.8474 (mt-10)
  outliers start: 46
  outliers final: 28
  residues processed: 156
  average time/residue: 0.2106
  time to fit residues: 44.6998
Evaluate side-chains
  142 residues out of total 898 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 112
  time to evaluate  : 0.941 
-------------------------------------------------------------------------------
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   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   89 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  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=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 98
   random chunks:
   chunk 37 optimal weight:    6.9990
   chunk 44 optimal weight:    3.9990
   chunk 49 optimal weight:   10.0000
   chunk 85 optimal weight:    4.9990
   chunk 18 optimal weight:    0.8980
   chunk 2 optimal weight:    5.9990
   chunk 1 optimal weight:    0.9980
   chunk 65 optimal weight:    0.6980
   chunk 43 optimal weight:    2.9990
   chunk 60 optimal weight:    5.9990
   chunk 21 optimal weight:    2.9990
   overall best weight:    1.7184

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

Flipped N/Q/H residues before XYZ refinement:
** 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: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3496 r_free = 0.3496 target = 0.098132 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3046 r_free = 0.3046 target = 0.072787 restraints weight = 18932.720|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.3099 r_free = 0.3099 target = 0.075466 restraints weight = 9585.055|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3131 r_free = 0.3131 target = 0.077149 restraints weight = 6140.356|
|-----------------------------------------------------------------------------|
r_work (final): 0.3132
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8582
moved from start:          0.2246

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039   8678  Z= 0.135
  Angle     :  0.591  10.984  11830  Z= 0.297
  Chirality :  0.044   0.246   1320
  Planarity :  0.005   0.066   1458
  Dihedral  : 11.042 107.487   1278
  Min Nonbonded Distance : 2.569

Molprobity Statistics.
  All-atom Clashscore : 12.03
  Ramachandran Plot:
    Outliers :  0.10 %
    Allowed  :  6.00 %
    Favored  : 93.90 %
  Rotamer:
    Outliers :  3.90 %
    Allowed  : 29.51 %
    Favored  : 66.59 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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: -0.14 (0.28), residues: 1000
  helix:  0.74 (0.32), residues: 294
  sheet: -0.70 (0.36), residues: 240
  loop : -0.14 (0.29), residues: 466

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.001   TRP B  72 
 HIS   0.002   0.001   HIS B  22 
 PHE   0.007   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        0.03120 (  282)
  hydrogen bonds       : angle       4.79833 (  756)
  covalent geometry    : bond        0.00319 ( 8678)
  covalent geometry    : angle       0.59063 (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
  156 residues out of total 898 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 121
  time to evaluate  : 0.963 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   73 ASP cc_start: 0.8944 (m-30) cc_final: 0.8355 (p0)
REVERT: A  132 ARG cc_start: 0.8637 (tmt170) cc_final: 0.8284 (mmm160)
REVERT: A  188 ASP cc_start: 0.8956 (p0) cc_final: 0.8607 (p0)
REVERT: A  221 THR cc_start: 0.9352 (OUTLIER) cc_final: 0.9133 (t)
REVERT: B  154 MET cc_start: 0.8130 (OUTLIER) cc_final: 0.7797 (tpp)
REVERT: C   55 GLN cc_start: 0.4829 (pp30) cc_final: 0.4506 (pp30)
REVERT: C   77 GLN cc_start: 0.9201 (mt0) cc_final: 0.8872 (mm-40)
REVERT: C   79 TYR cc_start: 0.8004 (t80) cc_final: 0.7664 (t80)
REVERT: C   83 GLN cc_start: 0.8760 (mm110) cc_final: 0.8354 (mm-40)
REVERT: C   99 GLN cc_start: 0.8325 (pm20) cc_final: 0.8123 (pm20)
REVERT: D   72 TRP cc_start: 0.8814 (OUTLIER) cc_final: 0.7341 (m-90)
  outliers start: 35
  outliers final: 22
  residues processed: 148
  average time/residue: 0.2359
  time to fit residues: 46.5425
Evaluate side-chains
  134 residues out of total 898 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 109
  time to evaluate  : 1.013 
-------------------------------------------------------------------------------
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  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  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  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=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 98
   random chunks:
   chunk 34 optimal weight:    1.9990
   chunk 60 optimal weight:    3.9990
   chunk 39 optimal weight:    0.7980
   chunk 84 optimal weight:    8.9990
   chunk 49 optimal weight:   10.0000
   chunk 30 optimal weight:    5.9990
   chunk 96 optimal weight:    5.9990
   chunk 86 optimal weight:    3.9990
   chunk 87 optimal weight:    5.9990
   chunk 79 optimal weight:    5.9990
   chunk 15 optimal weight:    7.9990
   overall best weight:    3.3588

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

Flipped N/Q/H residues before XYZ refinement:
C   8 HIS
** C 129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 163 GLN
** D   8 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
D 144 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3405 r_free = 0.3405 target = 0.093458 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.2940 r_free = 0.2940 target = 0.068012 restraints weight = 18935.008|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 41)----------------|
| r_work = 0.2991 r_free = 0.2991 target = 0.070587 restraints weight = 9776.770|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 42)----------------|
| r_work = 0.3023 r_free = 0.3023 target = 0.072230 restraints weight = 6296.362|
|-----------------------------------------------------------------------------|
r_work (final): 0.3026
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8640
moved from start:          0.2643

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.046   8678  Z= 0.221
  Angle     :  0.649   8.607  11830  Z= 0.329
  Chirality :  0.046   0.279   1320
  Planarity :  0.005   0.068   1458
  Dihedral  : 11.090 110.991   1278
  Min Nonbonded Distance : 2.513

Molprobity Statistics.
  All-atom Clashscore : 13.93
  Ramachandran Plot:
    Outliers :  0.10 %
    Allowed  :  7.00 %
    Favored  : 92.90 %
  Rotamer:
    Outliers :  4.57 %
    Allowed  : 29.96 %
    Favored  : 65.48 %
  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: -0.26 (0.28), residues: 1000
  helix:  0.69 (0.32), residues: 294
  sheet: -0.69 (0.35), residues: 240
  loop : -0.30 (0.29), residues: 466

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.002   TRP B  72 
 HIS   0.004   0.001   HIS B  22 
 PHE   0.011   0.001   PHE D 231 
 TYR   0.018   0.002   TYR B 244 
 ARG   0.005   0.000   ARG C 132 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03381 (  282)
  hydrogen bonds       : angle       4.84207 (  756)
  covalent geometry    : bond        0.00519 ( 8678)
  covalent geometry    : angle       0.64949 (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
  152 residues out of total 898 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 41
    poor density    : 111
  time to evaluate  : 0.937 
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: 0.8953 (m-30) cc_final: 0.8368 (p0)
REVERT: A  132 ARG cc_start: 0.8660 (tmt170) cc_final: 0.8298 (mmm160)
REVERT: A  188 ASP cc_start: 0.9001 (p0) cc_final: 0.8525 (p0)
REVERT: A  221 THR cc_start: 0.9362 (OUTLIER) cc_final: 0.9112 (t)
REVERT: C   55 GLN cc_start: 0.4840 (pp30) cc_final: 0.4534 (pp30)
REVERT: C   77 GLN cc_start: 0.9251 (mt0) cc_final: 0.8876 (mm-40)
REVERT: C   99 GLN cc_start: 0.8395 (pm20) cc_final: 0.8171 (pm20)
REVERT: D   72 TRP cc_start: 0.8871 (OUTLIER) cc_final: 0.7092 (m-90)
REVERT: D  187 GLU cc_start: 0.8787 (mm-30) cc_final: 0.8539 (mt-10)
  outliers start: 41
  outliers final: 31
  residues processed: 141
  average time/residue: 0.2184
  time to fit residues: 41.5037
Evaluate side-chains
  140 residues out of total 898 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 107
  time to evaluate  : 0.941 
-------------------------------------------------------------------------------
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  193 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  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  106 THR
Chi-restraints excluded: chain D residue  141 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=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 98
   random chunks:
   chunk 1 optimal weight:    2.9990
   chunk 48 optimal weight:    0.5980
   chunk 71 optimal weight:    3.9990
   chunk 80 optimal weight:    3.9990
   chunk 45 optimal weight:    3.9990
   chunk 61 optimal weight:    9.9990
   chunk 35 optimal weight:    7.9990
   chunk 16 optimal weight:    3.9990
   chunk 25 optimal weight:    3.9990
   chunk 27 optimal weight:    0.6980
   chunk 32 optimal weight:    0.7980
   overall best weight:    1.8184

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

Flipped N/Q/H residues before XYZ refinement:
** C 129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D   8 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3482 r_free = 0.3482 target = 0.097057 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3024 r_free = 0.3024 target = 0.071530 restraints weight = 19167.297|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3079 r_free = 0.3079 target = 0.074238 restraints weight = 9798.076|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.3112 r_free = 0.3112 target = 0.075961 restraints weight = 6266.236|
|-----------------------------------------------------------------------------|
r_work (final): 0.3115
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8600
moved from start:          0.2707

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= 0.142
  Angle     :  0.604   8.963  11830  Z= 0.304
  Chirality :  0.045   0.251   1320
  Planarity :  0.005   0.069   1458
  Dihedral  : 11.064 110.023   1278
  Min Nonbonded Distance : 2.523

Molprobity Statistics.
  All-atom Clashscore : 12.86
  Ramachandran Plot:
    Outliers :  0.10 %
    Allowed  :  6.30 %
    Favored  : 93.60 %
  Rotamer:
    Outliers :  4.23 %
    Allowed  : 30.40 %
    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: -0.18 (0.28), residues: 1000
  helix:  0.85 (0.32), residues: 286
  sheet: -0.70 (0.35), residues: 242
  loop : -0.27 (0.29), residues: 472

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP B  70 
 HIS   0.002   0.001   HIS B  22 
 PHE   0.008   0.001   PHE B 231 
 TYR   0.017   0.001   TYR C  56 
 ARG   0.006   0.000   ARG C 132 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03072 (  282)
  hydrogen bonds       : angle       4.72223 (  756)
  covalent geometry    : bond        0.00340 ( 8678)
  covalent geometry    : angle       0.60393 (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
  152 residues out of total 898 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 38
    poor density    : 114
  time to evaluate  : 1.067 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   73 ASP cc_start: 0.8880 (m-30) cc_final: 0.8319 (p0)
REVERT: A  132 ARG cc_start: 0.8657 (tmt170) cc_final: 0.8300 (mmm160)
REVERT: A  188 ASP cc_start: 0.8943 (p0) cc_final: 0.8630 (p0)
REVERT: A  221 THR cc_start: 0.9361 (m) cc_final: 0.9127 (t)
REVERT: B   72 TRP cc_start: 0.8355 (OUTLIER) cc_final: 0.8124 (t60)
REVERT: B  154 MET cc_start: 0.8188 (OUTLIER) cc_final: 0.7882 (tpp)
REVERT: C   55 GLN cc_start: 0.4884 (pp30) cc_final: 0.4670 (pp30)
REVERT: C   77 GLN cc_start: 0.9292 (mt0) cc_final: 0.8878 (mm-40)
REVERT: C   87 VAL cc_start: 0.8255 (OUTLIER) cc_final: 0.7916 (p)
REVERT: C   99 GLN cc_start: 0.8402 (pm20) cc_final: 0.8150 (pm20)
REVERT: D   72 TRP cc_start: 0.8910 (OUTLIER) cc_final: 0.7719 (m-90)
REVERT: D  187 GLU cc_start: 0.8744 (mm-30) cc_final: 0.8511 (mt-10)
  outliers start: 38
  outliers final: 26
  residues processed: 142
  average time/residue: 0.2327
  time to fit residues: 44.5314
Evaluate side-chains
  139 residues out of total 898 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 109
  time to evaluate  : 1.013 
-------------------------------------------------------------------------------
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   72 TRP
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   87 VAL
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  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=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 98
   random chunks:
   chunk 42 optimal weight:    2.9990
   chunk 10 optimal weight:    2.9990
   chunk 24 optimal weight:    9.9990
   chunk 21 optimal weight:    0.0770
   chunk 61 optimal weight:    9.9990
   chunk 37 optimal weight:    8.9990
   chunk 12 optimal weight:    9.9990
   chunk 28 optimal weight:    0.1980
   chunk 41 optimal weight:    4.9990
   chunk 19 optimal weight:    3.9990
   chunk 30 optimal weight:   10.0000
   overall best weight:    2.0544

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

Flipped N/Q/H residues before XYZ refinement:
** C 129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D   8 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3482 r_free = 0.3482 target = 0.096931 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3021 r_free = 0.3021 target = 0.071448 restraints weight = 19149.027|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3076 r_free = 0.3076 target = 0.074131 restraints weight = 9740.359|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3107 r_free = 0.3107 target = 0.075761 restraints weight = 6256.884|
|-----------------------------------------------------------------------------|
r_work (final): 0.3107
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8608
moved from start:          0.2846

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.041   8678  Z= 0.153
  Angle     :  0.606   7.956  11830  Z= 0.306
  Chirality :  0.045   0.257   1320
  Planarity :  0.005   0.072   1458
  Dihedral  : 11.025 110.824   1278
  Min Nonbonded Distance : 2.513

Molprobity Statistics.
  All-atom Clashscore : 13.04
  Ramachandran Plot:
    Outliers :  0.10 %
    Allowed  :  7.10 %
    Favored  : 92.80 %
  Rotamer:
    Outliers :  3.79 %
    Allowed  : 30.85 %
    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: -0.14 (0.27), residues: 1000
  helix:  0.87 (0.32), residues: 286
  sheet: -0.63 (0.36), residues: 238
  loop : -0.27 (0.29), residues: 476

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP B  72 
 HIS   0.003   0.001   HIS B  22 
 PHE   0.008   0.001   PHE B 231 
 TYR   0.021   0.002   TYR A  56 
 ARG   0.006   0.000   ARG C 132 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03091 (  282)
  hydrogen bonds       : angle       4.69620 (  756)
  covalent geometry    : bond        0.00363 ( 8678)
  covalent geometry    : angle       0.60557 (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
  147 residues out of total 898 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 113
  time to evaluate  : 0.934 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   56 TYR cc_start: 0.6696 (m-10) cc_final: 0.6320 (m-10)
REVERT: A   70 TRP cc_start: 0.7104 (p-90) cc_final: 0.6354 (p-90)
REVERT: A   73 ASP cc_start: 0.8930 (m-30) cc_final: 0.8325 (p0)
REVERT: A  110 ARG cc_start: 0.7761 (mtt90) cc_final: 0.7450 (mmt90)
REVERT: A  132 ARG cc_start: 0.8653 (tmt170) cc_final: 0.8324 (mmm160)
REVERT: A  141 LEU cc_start: 0.6842 (tp) cc_final: 0.6081 (tp)
REVERT: A  188 ASP cc_start: 0.8942 (p0) cc_final: 0.8512 (p0)
REVERT: A  221 THR cc_start: 0.9368 (OUTLIER) cc_final: 0.9126 (t)
REVERT: B   56 TYR cc_start: 0.7863 (m-10) cc_final: 0.7448 (m-10)
REVERT: B   72 TRP cc_start: 0.8430 (OUTLIER) cc_final: 0.8136 (t60)
REVERT: B  154 MET cc_start: 0.8203 (OUTLIER) cc_final: 0.7907 (tpp)
REVERT: C   77 GLN cc_start: 0.9284 (mt0) cc_final: 0.8864 (mm-40)
REVERT: C   87 VAL cc_start: 0.8287 (OUTLIER) cc_final: 0.7974 (p)
REVERT: C   99 GLN cc_start: 0.8368 (pm20) cc_final: 0.8105 (pm20)
REVERT: D   72 TRP cc_start: 0.8876 (OUTLIER) cc_final: 0.7461 (m-90)
REVERT: D  187 GLU cc_start: 0.8763 (mm-30) cc_final: 0.8527 (mt-10)
REVERT: D  188 ASP cc_start: 0.8653 (m-30) cc_final: 0.8178 (t0)
  outliers start: 34
  outliers final: 25
  residues processed: 137
  average time/residue: 0.2239
  time to fit residues: 41.5609
Evaluate side-chains
  143 residues out of total 898 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 113
  time to evaluate  : 0.930 
-------------------------------------------------------------------------------
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  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   72 TRP
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   87 VAL
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  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=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 98
   random chunks:
   chunk 65 optimal weight:    0.2980
   chunk 96 optimal weight:    5.9990
   chunk 30 optimal weight:    8.9990
   chunk 92 optimal weight:    0.0770
   chunk 21 optimal weight:    0.0770
   chunk 67 optimal weight:    8.9990
   chunk 84 optimal weight:    6.9990
   chunk 29 optimal weight:    2.9990
   chunk 80 optimal weight:    1.9990
   chunk 51 optimal weight:    0.9980
   chunk 53 optimal weight:    0.9980
   overall best weight:    0.4896

-------------------------------------------------------------------------------
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 = 0.101268 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 55)----------------|
| r_work = 0.3112 r_free = 0.3112 target = 0.076039 restraints weight = 18857.342|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3166 r_free = 0.3166 target = 0.078822 restraints weight = 9548.072|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 50)----------------|
| r_work = 0.3200 r_free = 0.3200 target = 0.080602 restraints weight = 6082.209|
|-----------------------------------------------------------------------------|
r_work (final): 0.3208
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8526
moved from start:          0.2893

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.041   8678  Z= 0.105
  Angle     :  0.598   8.692  11830  Z= 0.301
  Chirality :  0.044   0.223   1320
  Planarity :  0.005   0.074   1458
  Dihedral  : 10.949 109.293   1278
  Min Nonbonded Distance : 2.502

Molprobity Statistics.
  All-atom Clashscore : 11.85
  Ramachandran Plot:
    Outliers :  0.10 %
    Allowed  :  5.80 %
    Favored  : 94.10 %
  Rotamer:
    Outliers :  2.90 %
    Allowed  : 32.18 %
    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: -0.12 (0.28), residues: 1000
  helix:  0.91 (0.33), residues: 284
  sheet: -0.77 (0.35), residues: 236
  loop : -0.19 (0.29), residues: 480

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP A  70 
 HIS   0.003   0.000   HIS D   8 
 PHE   0.007   0.001   PHE C  57 
 TYR   0.013   0.001   TYR A  56 
 ARG   0.004   0.000   ARG A 110 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02884 (  282)
  hydrogen bonds       : angle       4.63273 (  756)
  covalent geometry    : bond        0.00244 ( 8678)
  covalent geometry    : angle       0.59849 (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
  168 residues out of total 898 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 142
  time to evaluate  : 1.065 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   56 TYR cc_start: 0.6672 (m-10) cc_final: 0.6331 (m-10)
REVERT: A   70 TRP cc_start: 0.7007 (p-90) cc_final: 0.6255 (p-90)
REVERT: A   73 ASP cc_start: 0.8790 (m-30) cc_final: 0.8237 (p0)
REVERT: A  143 GLN cc_start: 0.7995 (pm20) cc_final: 0.7771 (pm20)
REVERT: A  188 ASP cc_start: 0.8863 (p0) cc_final: 0.8556 (p0)
REVERT: A  221 THR cc_start: 0.9374 (m) cc_final: 0.9155 (t)
REVERT: B   72 TRP cc_start: 0.8326 (OUTLIER) cc_final: 0.8117 (t60)
REVERT: B  154 MET cc_start: 0.8137 (OUTLIER) cc_final: 0.7811 (tpp)
REVERT: C   77 GLN cc_start: 0.9240 (mt0) cc_final: 0.8849 (mm-40)
REVERT: C   99 GLN cc_start: 0.8375 (pm20) cc_final: 0.8101 (pm20)
REVERT: D   72 TRP cc_start: 0.8831 (OUTLIER) cc_final: 0.7390 (m-90)
REVERT: D   73 ASP cc_start: 0.8648 (m-30) cc_final: 0.8380 (m-30)
REVERT: D  188 ASP cc_start: 0.8618 (m-30) cc_final: 0.8136 (t0)
  outliers start: 26
  outliers final: 21
  residues processed: 157
  average time/residue: 0.2395
  time to fit residues: 51.2157
Evaluate side-chains
  145 residues out of total 898 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 121
  time to evaluate  : 0.926 
-------------------------------------------------------------------------------
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   61 LEU
Chi-restraints excluded: chain B residue   72 TRP
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 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
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:    4.9990
   chunk 45 optimal weight:    0.7980
   chunk 90 optimal weight:    4.9990
   chunk 92 optimal weight:    0.9990
   chunk 69 optimal weight:    0.8980
   chunk 87 optimal weight:    4.9990
   chunk 11 optimal weight:    5.9990
   chunk 0 optimal weight:   20.0000
   chunk 76 optimal weight:    0.7980
   chunk 56 optimal weight:    6.9990
   chunk 5 optimal weight:   20.0000
   overall best weight:    1.6984

-------------------------------------------------------------------------------
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  82 HIS
** 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: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3519 r_free = 0.3519 target = 0.099202 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3075 r_free = 0.3075 target = 0.074084 restraints weight = 19085.573|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3129 r_free = 0.3129 target = 0.076822 restraints weight = 9661.635|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 43)----------------|
| r_work = 0.3162 r_free = 0.3162 target = 0.078546 restraints weight = 6154.694|
|-----------------------------------------------------------------------------|
r_work (final): 0.3161
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8572
moved from start:          0.3057

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042   8678  Z= 0.142
  Angle     :  0.628   9.415  11830  Z= 0.318
  Chirality :  0.045   0.239   1320
  Planarity :  0.005   0.073   1458
  Dihedral  : 10.873 110.308   1276
  Min Nonbonded Distance : 2.464

Molprobity Statistics.
  All-atom Clashscore : 12.74
  Ramachandran Plot:
    Outliers :  0.10 %
    Allowed  :  6.40 %
    Favored  : 93.50 %
  Rotamer:
    Outliers :  2.90 %
    Allowed  : 33.07 %
    Favored  : 64.03 %
  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: -0.09 (0.28), residues: 1000
  helix:  0.95 (0.33), residues: 284
  sheet: -0.66 (0.35), residues: 242
  loop : -0.22 (0.29), residues: 474

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP A  31 
 HIS   0.002   0.001   HIS C   8 
 PHE   0.021   0.001   PHE A 112 
 TYR   0.016   0.002   TYR C 209 
 ARG   0.007   0.000   ARG C 132 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02992 (  282)
  hydrogen bonds       : angle       4.63396 (  756)
  covalent geometry    : bond        0.00343 ( 8678)
  covalent geometry    : angle       0.62811 (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
  152 residues out of total 898 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 126
  time to evaluate  : 1.003 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   56 TYR cc_start: 0.6757 (m-10) cc_final: 0.6248 (m-10)
REVERT: A   73 ASP cc_start: 0.8865 (m-30) cc_final: 0.8250 (p0)
REVERT: A  141 LEU cc_start: 0.6882 (tp) cc_final: 0.6003 (tp)
REVERT: A  188 ASP cc_start: 0.8900 (p0) cc_final: 0.8577 (p0)
REVERT: A  221 THR cc_start: 0.9354 (m) cc_final: 0.9112 (t)
REVERT: B   72 TRP cc_start: 0.8424 (OUTLIER) cc_final: 0.8143 (t60)
REVERT: C   46 GLN cc_start: 0.8567 (pm20) cc_final: 0.8345 (pm20)
REVERT: C   77 GLN cc_start: 0.9268 (mt0) cc_final: 0.8877 (mm-40)
REVERT: C   99 GLN cc_start: 0.8363 (pm20) cc_final: 0.8091 (pm20)
REVERT: D   72 TRP cc_start: 0.8859 (OUTLIER) cc_final: 0.7424 (m-90)
REVERT: D   73 ASP cc_start: 0.8650 (m-30) cc_final: 0.8373 (m-30)
REVERT: D   79 TYR cc_start: 0.9035 (t80) cc_final: 0.8457 (t80)
REVERT: D  101 ASP cc_start: 0.8273 (t0) cc_final: 0.8056 (t0)
REVERT: D  119 ARG cc_start: 0.9037 (mtm110) cc_final: 0.8795 (mtm110)
REVERT: D  177 ASP cc_start: 0.8859 (p0) cc_final: 0.8570 (p0)
REVERT: D  188 ASP cc_start: 0.8578 (m-30) cc_final: 0.8147 (t0)
  outliers start: 26
  outliers final: 23
  residues processed: 144
  average time/residue: 0.2263
  time to fit residues: 43.9850
Evaluate side-chains
  147 residues out of total 898 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 122
  time to evaluate  : 0.915 
-------------------------------------------------------------------------------
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   61 LEU
Chi-restraints excluded: chain B residue   72 TRP
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  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:    2.9990
   chunk 79 optimal weight:    0.0980
   chunk 25 optimal weight:    0.8980
   chunk 97 optimal weight:    0.8980
   chunk 35 optimal weight:   10.0000
   chunk 48 optimal weight:    4.9990
   chunk 44 optimal weight:    2.9990
   chunk 72 optimal weight:    6.9990
   chunk 13 optimal weight:    2.9990
   chunk 36 optimal weight:    7.9990
   chunk 82 optimal weight:    0.9980
   overall best weight:    1.1782

-------------------------------------------------------------------------------
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 = 0.3535 r_free = 0.3535 target = 0.100034 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3095 r_free = 0.3095 target = 0.075154 restraints weight = 19278.112|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3149 r_free = 0.3149 target = 0.077911 restraints weight = 9616.929|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3182 r_free = 0.3182 target = 0.079667 restraints weight = 6065.709|
|-----------------------------------------------------------------------------|
r_work (final): 0.3181
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8549
moved from start:          0.3112

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042   8678  Z= 0.123
  Angle     :  0.628   9.022  11830  Z= 0.318
  Chirality :  0.044   0.232   1320
  Planarity :  0.005   0.074   1458
  Dihedral  : 10.864 110.590   1276
  Min Nonbonded Distance : 2.522

Molprobity Statistics.
  All-atom Clashscore : 12.15
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.00 %
    Favored  : 94.00 %
  Rotamer:
    Outliers :  2.67 %
    Allowed  : 33.85 %
    Favored  : 63.47 %
  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: -0.09 (0.28), residues: 1000
  helix:  0.93 (0.33), residues: 284
  sheet: -0.75 (0.35), residues: 250
  loop : -0.14 (0.29), residues: 466

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP B  72 
 HIS   0.002   0.000   HIS D   8 
 PHE   0.019   0.001   PHE A 112 
 TYR   0.011   0.001   TYR A  56 
 ARG   0.004   0.000   ARG A 110 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02890 (  282)
  hydrogen bonds       : angle       4.61208 (  756)
  covalent geometry    : bond        0.00295 ( 8678)
  covalent geometry    : angle       0.62802 (11830)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2853.57 seconds
wall clock time: 51 minutes 21.20 seconds (3081.20 seconds total)