Starting phenix.real_space_refine
on Sat Jun  7 05:04:26 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9mue_48630/06_2025/9mue_48630.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9mue_48630/06_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_48630/06_2025/9mue_48630.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9mue_48630/06_2025/9mue_48630.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9mue_48630/06_2025/9mue_48630.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9mue_48630/06_2025/9mue_48630.cif"
  }
  resolution = 4.0
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.005 sd=   0.050
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 5
    Type Number    sf(0)   Gaussians
     P      12      5.49       5
     S      20      5.16       5
     C    5434      2.51       5
     N    1430      2.21       5
     O    1542      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 15 residue(s): 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib"
  Total number of atoms: 8438
  Number of models: 1
  Model: ""
    Number of chains: 8
    Chain: "A"
      Number of atoms: 2022
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 249, 2022
          Classifications: {'peptide': 249}
          Link IDs: {'PTRANS': 12, 'TRANS': 236}
          Chain breaks: 1
    Chain: "a"
      Number of atoms: 88
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 4, 88
          Classifications: {'RNA': 4}
          Modifications used: {'rna2p_pur': 4}
          Link IDs: {'rna2p': 3}
    Chain: "b"
      Number of atoms: 88
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 4, 88
          Classifications: {'RNA': 4}
          Modifications used: {'rna2p_pur': 4}
          Link IDs: {'rna2p': 3}
    Chain: "B"
      Number of atoms: 2073
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 257, 2073
          Classifications: {'peptide': 257}
          Link IDs: {'PTRANS': 13, 'TRANS': 243}
    Chain: "C"
      Number of atoms: 2022
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 249, 2022
          Classifications: {'peptide': 249}
          Link IDs: {'PTRANS': 12, 'TRANS': 236}
          Chain breaks: 1
    Chain: "D"
      Number of atoms: 2073
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 257, 2073
          Classifications: {'peptide': 257}
          Link IDs: {'PTRANS': 13, 'TRANS': 243}
    Chain: "B"
      Number of atoms: 36
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 36
          Unusual residues: {'AR6': 1}
          Classifications: {'undetermined': 1}
    Chain: "D"
      Number of atoms: 36
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 36
          Unusual residues: {'AR6': 1}
          Classifications: {'undetermined': 1}
  Time building chain proxies: 7.77, per 1000 atoms: 0.92
  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: 2.16
  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: 1.05
  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: 2.28

  Time building geometry restraints manager: 2.53 seconds

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

  Histogram of bond lengths:
        1.22 -     1.34: 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:             9.440
  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:          0.320
  Check model and map are aligned:         0.060
  Set scattering table:                    0.090
  Process input model:                     24.470
  Find NCS groups from input model:        0.340
  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:             0.000
  Load rotamer database and sin/cos tables:3.070
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   37.830
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8477
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.205   8678  Z= 0.214
  Angle     :  0.806  16.699  11830  Z= 0.430
  Chirality :  0.048   0.275   1320
  Planarity :  0.007   0.155   1458
  Dihedral  : 18.797 103.628   3268
  Min Nonbonded Distance : 2.101

Molprobity Statistics.
  All-atom Clashscore : 15.54
  Ramachandran Plot:
    Outliers :  0.60 %
    Allowed  :  4.90 %
    Favored  : 94.50 %
  Rotamer:
    Outliers :  1.00 %
    Allowed  : 34.30 %
    Favored  : 64.70 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.03 (0.28), residues: 1000
  helix:  0.74 (0.33), residues: 290
  sheet: -0.51 (0.38), residues: 206
  loop : -0.04 (0.28), residues: 504

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

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

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

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

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

  2000 Ramachandran restraints generated.
    1000 Oldfield, 0 Emsley, 1000 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  151 residues out of total 898 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 142
  time to evaluate  : 0.930 
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: 0.2428
  time to fit residues: 47.9859
Evaluate side-chains
  123 residues out of total 898 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 117
  time to evaluate  : 0.920 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  217 TYR
Chi-restraints excluded: chain B residue   32 ILE
Chi-restraints excluded: chain B residue   46 GLN
Chi-restraints excluded: chain D residue   66 LEU
Chi-restraints excluded: chain D residue   67 LYS
Chi-restraints excluded: chain D residue   72 TRP
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 98
   random chunks:
   chunk 82 optimal weight:    0.8980
   chunk 74 optimal weight:    3.9990
   chunk 41 optimal weight:    1.9990
   chunk 25 optimal weight:    0.5980
   chunk 50 optimal weight:   10.0000
   chunk 39 optimal weight:    4.9990
   chunk 76 optimal weight:    1.9990
   chunk 29 optimal weight:    0.9990
   chunk 46 optimal weight:    0.7980
   chunk 57 optimal weight:   20.0000
   chunk 88 optimal weight:    7.9990
   overall best weight:    1.0584

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

Flipped N/Q/H residues before XYZ refinement:
** A   8 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
C  83 GLN
** C 129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
D  10 ASN
** D 144 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3530 r_free = 0.3530 target = 0.100519 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3093 r_free = 0.3093 target = 0.075387 restraints weight = 18829.706|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3144 r_free = 0.3144 target = 0.078071 restraints weight = 9559.157|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 42)----------------|
| r_work = 0.3176 r_free = 0.3176 target = 0.079779 restraints weight = 6087.223|
|-----------------------------------------------------------------------------|
r_work (final): 0.3183
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8514
moved from start:          0.1178

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

Molprobity Statistics.
  All-atom Clashscore : 11.49
  Ramachandran Plot:
    Outliers :  0.10 %
    Allowed  :  5.40 %
    Favored  : 94.50 %
  Rotamer:
    Outliers :  3.12 %
    Allowed  : 28.73 %
    Favored  : 68.15 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.02 (0.28), residues: 1000
  helix:  0.76 (0.32), residues: 294
  sheet: -0.63 (0.35), residues: 238
  loop : -0.01 (0.30), residues: 468

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

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

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

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

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

  2000 Ramachandran restraints generated.
    1000 Oldfield, 0 Emsley, 1000 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  161 residues out of total 898 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 133
  time to evaluate  : 1.054 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   65 TYR cc_start: 0.7827 (t80) cc_final: 0.7625 (t80)
REVERT: A  221 THR cc_start: 0.9310 (m) cc_final: 0.9063 (t)
REVERT: C   55 GLN cc_start: 0.5071 (pp30) cc_final: 0.4647 (pp30)
REVERT: C   99 GLN cc_start: 0.8136 (pm20) cc_final: 0.7782 (pm20)
REVERT: C  132 ARG cc_start: 0.9019 (ttm-80) cc_final: 0.8798 (ttp-110)
REVERT: D   72 TRP cc_start: 0.8748 (OUTLIER) cc_final: 0.7453 (m-90)
REVERT: D   74 GLU cc_start: 0.7117 (pm20) cc_final: 0.6218 (pm20)
REVERT: D  107 ASP cc_start: 0.8535 (p0) cc_final: 0.8285 (p0)
REVERT: D  187 GLU cc_start: 0.8731 (mm-30) cc_final: 0.8454 (mt-10)
  outliers start: 28
  outliers final: 14
  residues processed: 154
  average time/residue: 0.3068
  time to fit residues: 64.2619
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  : 1.150 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   32 ILE
Chi-restraints excluded: chain A residue   90 ILE
Chi-restraints excluded: chain A residue  164 VAL
Chi-restraints excluded: chain A residue  217 TYR
Chi-restraints excluded: chain A residue  254 MET
Chi-restraints excluded: chain B residue   32 ILE
Chi-restraints excluded: chain B residue  164 VAL
Chi-restraints excluded: chain B residue  183 ASP
Chi-restraints excluded: chain C residue   30 THR
Chi-restraints excluded: chain C residue  106 THR
Chi-restraints excluded: chain C residue  147 VAL
Chi-restraints excluded: chain D residue   67 LYS
Chi-restraints excluded: chain D residue   72 TRP
Chi-restraints excluded: chain D residue  164 VAL
Chi-restraints excluded: chain D residue  165 VAL
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 98
   random chunks:
   chunk 52 optimal weight:    4.9990
   chunk 70 optimal weight:    5.9990
   chunk 63 optimal weight:    0.8980
   chunk 22 optimal weight:    2.9990
   chunk 39 optimal weight:   10.0000
   chunk 82 optimal weight:    0.9980
   chunk 23 optimal weight:    3.9990
   chunk 91 optimal weight:    4.9990
   chunk 78 optimal weight:   10.0000
   chunk 49 optimal weight:    9.9990
   chunk 53 optimal weight:    3.9990
   overall best weight:    2.5786

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

Flipped N/Q/H residues before XYZ refinement:
** A   8 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 144 ASN
** B  34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 144 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3466 r_free = 0.3466 target = 0.096661 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3013 r_free = 0.3013 target = 0.071385 restraints weight = 19169.659|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 45)----------------|
| r_work = 0.3066 r_free = 0.3066 target = 0.074032 restraints weight = 9698.021|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3097 r_free = 0.3097 target = 0.075682 restraints weight = 6169.985|
|-----------------------------------------------------------------------------|
r_work (final): 0.3101
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8603
moved from start:          0.1823

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.047   8678  Z= 0.180
  Angle     :  0.626   8.119  11830  Z= 0.318
  Chirality :  0.045   0.251   1320
  Planarity :  0.005   0.082   1458
  Dihedral  : 11.381 101.484   1278
  Min Nonbonded Distance : 2.535

Molprobity Statistics.
  All-atom Clashscore : 12.56
  Ramachandran Plot:
    Outliers :  0.10 %
    Allowed  :  6.10 %
    Favored  : 93.80 %
  Rotamer:
    Outliers :  4.68 %
    Allowed  : 27.95 %
    Favored  : 67.37 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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:  0.75 (0.32), residues: 294
  sheet: -0.79 (0.35), residues: 240
  loop : -0.12 (0.29), residues: 466

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.026   0.002   TRP A  70 
 HIS   0.003   0.001   HIS D  22 
 PHE   0.017   0.001   PHE A   5 
 TYR   0.018   0.002   TYR A  56 
 ARG   0.005   0.000   ARG C 148 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03551 (  282)
  hydrogen bonds       : angle       5.04202 (  756)
  covalent geometry    : bond        0.00420 ( 8678)
  covalent geometry    : angle       0.62626 (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
  163 residues out of total 898 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 42
    poor density    : 121
  time to evaluate  : 1.019 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   70 TRP cc_start: 0.7254 (p-90) cc_final: 0.6536 (p-90)
REVERT: A  132 ARG cc_start: 0.8640 (tmt170) cc_final: 0.8266 (mmm160)
REVERT: A  188 ASP cc_start: 0.9002 (p0) cc_final: 0.8549 (p0)
REVERT: A  221 THR cc_start: 0.9348 (OUTLIER) cc_final: 0.9094 (t)
REVERT: B   56 TYR cc_start: 0.7950 (m-10) cc_final: 0.7432 (m-10)
REVERT: B  209 TYR cc_start: 0.8311 (t80) cc_final: 0.8039 (t80)
REVERT: C    6 PHE cc_start: 0.8331 (m-10) cc_final: 0.7980 (m-10)
REVERT: C   55 GLN cc_start: 0.4922 (pp30) cc_final: 0.4552 (pp30)
REVERT: C   56 TYR cc_start: 0.7102 (m-80) cc_final: 0.6839 (m-80)
REVERT: C   99 GLN cc_start: 0.8266 (pm20) cc_final: 0.7803 (pm20)
REVERT: C  145 GLU cc_start: 0.8750 (tp30) cc_final: 0.8371 (tp30)
REVERT: D   72 TRP cc_start: 0.8854 (OUTLIER) cc_final: 0.7720 (m-90)
REVERT: D  130 MET cc_start: 0.9135 (tpp) cc_final: 0.8780 (tpp)
  outliers start: 42
  outliers final: 27
  residues processed: 152
  average time/residue: 0.2598
  time to fit residues: 55.4518
Evaluate side-chains
  145 residues out of total 898 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 116
  time to evaluate  : 1.890 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   90 ILE
Chi-restraints excluded: chain A residue  105 LEU
Chi-restraints excluded: chain A residue  164 VAL
Chi-restraints excluded: chain A residue  165 VAL
Chi-restraints excluded: chain A residue  172 SER
Chi-restraints excluded: chain A residue  206 VAL
Chi-restraints excluded: chain A residue  217 TYR
Chi-restraints excluded: chain A residue  221 THR
Chi-restraints excluded: chain A residue  254 MET
Chi-restraints excluded: chain B residue   12 ASP
Chi-restraints excluded: chain B residue   17 LEU
Chi-restraints excluded: chain B residue   32 ILE
Chi-restraints excluded: chain B residue   61 LEU
Chi-restraints excluded: chain B residue  105 LEU
Chi-restraints excluded: chain B residue  154 MET
Chi-restraints excluded: chain C residue   30 THR
Chi-restraints excluded: chain C residue  106 THR
Chi-restraints excluded: chain C residue  147 VAL
Chi-restraints excluded: chain C residue  206 VAL
Chi-restraints excluded: chain D residue   26 SER
Chi-restraints excluded: chain D residue   30 THR
Chi-restraints excluded: chain D residue   67 LYS
Chi-restraints excluded: chain D residue   72 TRP
Chi-restraints excluded: chain D residue   94 LEU
Chi-restraints excluded: chain D residue  106 THR
Chi-restraints excluded: chain D residue  147 VAL
Chi-restraints excluded: chain D residue  164 VAL
Chi-restraints excluded: chain D residue  165 VAL
Chi-restraints excluded: chain D residue  174 LEU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 98
   random chunks:
   chunk 23 optimal weight:    4.9990
   chunk 49 optimal weight:   10.0000
   chunk 13 optimal weight:    0.4980
   chunk 87 optimal weight:    0.6980
   chunk 62 optimal weight:    2.9990
   chunk 85 optimal weight:    5.9990
   chunk 73 optimal weight:   10.0000
   chunk 54 optimal weight:    9.9990
   chunk 40 optimal weight:    3.9990
   chunk 37 optimal weight:    6.9990
   chunk 83 optimal weight:   10.0000
   overall best weight:    2.6386

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

Flipped N/Q/H residues before XYZ refinement:
A   8 HIS
** B  34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C  83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 144 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3468 r_free = 0.3468 target = 0.096359 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3010 r_free = 0.3010 target = 0.071053 restraints weight = 19012.586|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 41)----------------|
| r_work = 0.3064 r_free = 0.3064 target = 0.073688 restraints weight = 9668.998|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 41)----------------|
| r_work = 0.3096 r_free = 0.3096 target = 0.075354 restraints weight = 6194.869|
|-----------------------------------------------------------------------------|
r_work (final): 0.3098
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8614
moved from start:          0.2157

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.039   8678  Z= 0.178
  Angle     :  0.606   6.799  11830  Z= 0.309
  Chirality :  0.045   0.267   1320
  Planarity :  0.005   0.070   1458
  Dihedral  : 11.119 107.503   1278
  Min Nonbonded Distance : 2.549

Molprobity Statistics.
  All-atom Clashscore : 12.98
  Ramachandran Plot:
    Outliers :  0.10 %
    Allowed  :  5.50 %
    Favored  : 94.40 %
  Rotamer:
    Outliers :  5.01 %
    Allowed  : 27.73 %
    Favored  : 67.26 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.24 (0.27), residues: 1000
  helix:  0.69 (0.32), residues: 294
  sheet: -0.78 (0.36), residues: 240
  loop : -0.21 (0.29), residues: 466

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.001   TRP B  72 
 HIS   0.003   0.001   HIS B  22 
 PHE   0.009   0.001   PHE B 231 
 TYR   0.016   0.002   TYR C 209 
 ARG   0.006   0.000   ARG C 132 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03315 (  282)
  hydrogen bonds       : angle       4.93857 (  756)
  covalent geometry    : bond        0.00419 ( 8678)
  covalent geometry    : angle       0.60633 (11830)

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

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

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

  2000 Ramachandran restraints generated.
    1000 Oldfield, 0 Emsley, 1000 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  159 residues out of total 898 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 45
    poor density    : 114
  time to evaluate  : 1.090 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   70 TRP cc_start: 0.7190 (p-90) cc_final: 0.6392 (p-90)
REVERT: A   79 TYR cc_start: 0.8467 (t80) cc_final: 0.8249 (t80)
REVERT: A  132 ARG cc_start: 0.8632 (tmt170) cc_final: 0.8269 (mmm160)
REVERT: A  188 ASP cc_start: 0.8992 (p0) cc_final: 0.8602 (p0)
REVERT: A  221 THR cc_start: 0.9359 (OUTLIER) cc_final: 0.9149 (t)
REVERT: B   34 GLN cc_start: 0.7643 (tm-30) cc_final: 0.6997 (tm-30)
REVERT: B   56 TYR cc_start: 0.7988 (m-10) cc_final: 0.7527 (m-10)
REVERT: C   55 GLN cc_start: 0.4919 (pp30) cc_final: 0.4616 (pp30)
REVERT: C   77 GLN cc_start: 0.9183 (mt0) cc_final: 0.8864 (mm-40)
REVERT: C   83 GLN cc_start: 0.8783 (mm-40) cc_final: 0.8394 (mm-40)
REVERT: C   99 GLN cc_start: 0.8357 (pm20) cc_final: 0.8136 (pm20)
REVERT: D   72 TRP cc_start: 0.8837 (OUTLIER) cc_final: 0.7437 (m-90)
  outliers start: 45
  outliers final: 25
  residues processed: 148
  average time/residue: 0.2279
  time to fit residues: 45.9845
Evaluate side-chains
  135 residues out of total 898 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 108
  time to evaluate  : 1.122 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   90 ILE
Chi-restraints excluded: chain A residue  164 VAL
Chi-restraints excluded: chain A residue  165 VAL
Chi-restraints excluded: chain A residue  172 SER
Chi-restraints excluded: chain A residue  206 VAL
Chi-restraints excluded: chain A residue  217 TYR
Chi-restraints excluded: chain A residue  221 THR
Chi-restraints excluded: chain A residue  254 MET
Chi-restraints excluded: chain B residue   17 LEU
Chi-restraints excluded: chain B residue   32 ILE
Chi-restraints excluded: chain B residue  106 THR
Chi-restraints excluded: chain B residue  154 MET
Chi-restraints excluded: chain C residue   30 THR
Chi-restraints excluded: chain C residue   32 ILE
Chi-restraints excluded: chain C residue  102 LEU
Chi-restraints excluded: chain C residue  103 ASN
Chi-restraints excluded: chain C residue  106 THR
Chi-restraints excluded: chain C residue  147 VAL
Chi-restraints excluded: chain C residue  206 VAL
Chi-restraints excluded: chain D residue   66 LEU
Chi-restraints excluded: chain D residue   67 LYS
Chi-restraints excluded: chain D residue   72 TRP
Chi-restraints excluded: chain D residue   94 LEU
Chi-restraints excluded: chain D residue  147 VAL
Chi-restraints excluded: chain D residue  164 VAL
Chi-restraints excluded: chain D residue  165 VAL
Chi-restraints excluded: chain D residue  174 LEU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 98
   random chunks:
   chunk 37 optimal weight:    6.9990
   chunk 44 optimal weight:    3.9990
   chunk 49 optimal weight:   10.0000
   chunk 85 optimal weight:    1.9990
   chunk 18 optimal weight:    1.9990
   chunk 2 optimal weight:    3.9990
   chunk 1 optimal weight:    0.9980
   chunk 65 optimal weight:    0.4980
   chunk 43 optimal weight:    4.9990
   chunk 60 optimal weight:    8.9990
   chunk 21 optimal weight:    2.9990
   overall best weight:    1.6986

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

Flipped N/Q/H residues before XYZ refinement:
A  46 GLN
** A  55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B  34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C   8 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
C  83 GLN
** C 129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 144 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3486 r_free = 0.3486 target = 0.097688 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3040 r_free = 0.3040 target = 0.072395 restraints weight = 18849.319|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3093 r_free = 0.3093 target = 0.075057 restraints weight = 9549.321|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 43)----------------|
| r_work = 0.3126 r_free = 0.3126 target = 0.076751 restraints weight = 6093.775|
|-----------------------------------------------------------------------------|
r_work (final): 0.3126
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8584
moved from start:          0.2325

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= 0.134
  Angle     :  0.589  10.909  11830  Z= 0.298
  Chirality :  0.044   0.252   1320
  Planarity :  0.005   0.066   1458
  Dihedral  : 11.067 107.720   1278
  Min Nonbonded Distance : 2.534

Molprobity Statistics.
  All-atom Clashscore : 12.32
  Ramachandran Plot:
    Outliers :  0.10 %
    Allowed  :  6.10 %
    Favored  : 93.80 %
  Rotamer:
    Outliers :  4.45 %
    Allowed  : 29.29 %
    Favored  : 66.26 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.17 (0.28), residues: 1000
  helix:  0.73 (0.32), residues: 294
  sheet: -0.71 (0.36), residues: 240
  loop : -0.18 (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 128 
 PHE   0.008   0.001   PHE B 231 
 TYR   0.016   0.001   TYR C 209 
 ARG   0.005   0.000   ARG C 132 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03101 (  282)
  hydrogen bonds       : angle       4.78324 (  756)
  covalent geometry    : bond        0.00316 ( 8678)
  covalent geometry    : angle       0.58937 (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
  161 residues out of total 898 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 40
    poor density    : 121
  time to evaluate  : 0.907 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   31 TRP cc_start: 0.8437 (m-10) cc_final: 0.8203 (m-10)
REVERT: A  132 ARG cc_start: 0.8641 (tmt170) cc_final: 0.8287 (mmm160)
REVERT: A  188 ASP cc_start: 0.8946 (p0) cc_final: 0.8600 (p0)
REVERT: A  221 THR cc_start: 0.9373 (OUTLIER) cc_final: 0.9163 (t)
REVERT: B  154 MET cc_start: 0.8185 (OUTLIER) cc_final: 0.7865 (tpp)
REVERT: C   55 GLN cc_start: 0.4836 (pp30) cc_final: 0.4633 (pp30)
REVERT: C   77 GLN cc_start: 0.9191 (mt0) cc_final: 0.8864 (mm-40)
REVERT: C   99 GLN cc_start: 0.8397 (pm20) cc_final: 0.8184 (pm20)
REVERT: D   72 TRP cc_start: 0.8821 (OUTLIER) cc_final: 0.7229 (m-90)
  outliers start: 40
  outliers final: 28
  residues processed: 153
  average time/residue: 0.2211
  time to fit residues: 45.4160
Evaluate side-chains
  135 residues out of total 898 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 104
  time to evaluate  : 0.929 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   32 ILE
Chi-restraints excluded: chain A residue   47 ILE
Chi-restraints excluded: chain A residue   90 ILE
Chi-restraints excluded: chain A residue  165 VAL
Chi-restraints excluded: chain A residue  172 SER
Chi-restraints excluded: chain A residue  206 VAL
Chi-restraints excluded: chain A residue  217 TYR
Chi-restraints excluded: chain A residue  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 B residue  164 VAL
Chi-restraints excluded: chain C residue   30 THR
Chi-restraints excluded: chain C residue   32 ILE
Chi-restraints excluded: chain C residue  102 LEU
Chi-restraints excluded: chain C residue  103 ASN
Chi-restraints excluded: chain C residue  106 THR
Chi-restraints excluded: chain C residue  147 VAL
Chi-restraints excluded: chain C residue  206 VAL
Chi-restraints excluded: chain D residue   67 LYS
Chi-restraints excluded: chain D residue   72 TRP
Chi-restraints excluded: chain D residue   94 LEU
Chi-restraints excluded: chain D residue  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=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 98
   random chunks:
   chunk 34 optimal weight:    0.0040
   chunk 60 optimal weight:    0.9990
   chunk 39 optimal weight:    0.5980
   chunk 84 optimal weight:    8.9990
   chunk 49 optimal weight:   10.0000
   chunk 30 optimal weight:    6.9990
   chunk 96 optimal weight:    4.9990
   chunk 86 optimal weight:    2.9990
   chunk 87 optimal weight:    0.7980
   chunk 79 optimal weight:    0.0370
   chunk 15 optimal weight:   10.0000
   overall best weight:    0.4872

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

Flipped N/Q/H residues before XYZ refinement:
C  83 GLN
D 144 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3533 r_free = 0.3533 target = 0.100300 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3092 r_free = 0.3092 target = 0.074935 restraints weight = 18662.577|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 41)----------------|
| r_work = 0.3147 r_free = 0.3147 target = 0.077687 restraints weight = 9514.267|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3179 r_free = 0.3179 target = 0.079440 restraints weight = 6069.829|
|-----------------------------------------------------------------------------|
r_work (final): 0.3181
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8528
moved from start:          0.2496

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.042   8678  Z= 0.103
  Angle     :  0.588   8.875  11830  Z= 0.295
  Chirality :  0.044   0.216   1320
  Planarity :  0.005   0.068   1458
  Dihedral  : 11.012 107.896   1278
  Min Nonbonded Distance : 2.536

Molprobity Statistics.
  All-atom Clashscore : 11.19
  Ramachandran Plot:
    Outliers :  0.10 %
    Allowed  :  5.70 %
    Favored  : 94.20 %
  Rotamer:
    Outliers :  3.56 %
    Allowed  : 31.18 %
    Favored  : 65.26 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.05 (0.28), residues: 1000
  helix:  0.95 (0.32), residues: 286
  sheet: -0.61 (0.36), residues: 240
  loop : -0.19 (0.29), residues: 474

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.019   0.001   TRP B  72 
 HIS   0.003   0.000   HIS D   8 
 PHE   0.006   0.001   PHE B   6 
 TYR   0.020   0.001   TYR C  56 
 ARG   0.006   0.000   ARG C 132 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02854 (  282)
  hydrogen bonds       : angle       4.68974 (  756)
  covalent geometry    : bond        0.00240 ( 8678)
  covalent geometry    : angle       0.58760 (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
  166 residues out of total 898 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 134
  time to evaluate  : 1.031 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   73 ASP cc_start: 0.8873 (m-30) cc_final: 0.8273 (p0)
REVERT: A  132 ARG cc_start: 0.8642 (tmt170) cc_final: 0.8297 (mmm160)
REVERT: A  188 ASP cc_start: 0.8907 (p0) cc_final: 0.8597 (p0)
REVERT: B   56 TYR cc_start: 0.7715 (m-10) cc_final: 0.7505 (m-10)
REVERT: B  154 MET cc_start: 0.8159 (OUTLIER) cc_final: 0.7821 (tpp)
REVERT: C   11 LYS cc_start: 0.8588 (mmtm) cc_final: 0.8280 (mmtm)
REVERT: C   55 GLN cc_start: 0.4777 (pp30) cc_final: 0.4542 (pp30)
REVERT: C   77 GLN cc_start: 0.9193 (mt0) cc_final: 0.8877 (mm-40)
REVERT: C   83 GLN cc_start: 0.8671 (mm110) cc_final: 0.8285 (mm-40)
REVERT: C   87 VAL cc_start: 0.8034 (OUTLIER) cc_final: 0.7731 (p)
REVERT: C   99 GLN cc_start: 0.8413 (pm20) cc_final: 0.8191 (pm20)
REVERT: C  145 GLU cc_start: 0.8863 (tp30) cc_final: 0.8278 (tp30)
REVERT: D   72 TRP cc_start: 0.8836 (OUTLIER) cc_final: 0.7541 (m-90)
  outliers start: 32
  outliers final: 21
  residues processed: 154
  average time/residue: 0.2172
  time to fit residues: 45.6239
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  : 0.997 
-------------------------------------------------------------------------------
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  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 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   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   94 LEU
Chi-restraints excluded: chain D residue  164 VAL
Chi-restraints excluded: chain D residue  165 VAL
Chi-restraints excluded: chain D residue  174 LEU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 98
   random chunks:
   chunk 1 optimal weight:    6.9990
   chunk 48 optimal weight:    0.6980
   chunk 71 optimal weight:    5.9990
   chunk 80 optimal weight:    0.7980
   chunk 45 optimal weight:    0.8980
   chunk 61 optimal weight:    9.9990
   chunk 35 optimal weight:   10.0000
   chunk 16 optimal weight:    3.9990
   chunk 25 optimal weight:    7.9990
   chunk 27 optimal weight:    4.9990
   chunk 32 optimal weight:    9.9990
   overall best weight:    2.2784

-------------------------------------------------------------------------------
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**
C 163 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3482 r_free = 0.3482 target = 0.097062 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3029 r_free = 0.3029 target = 0.071889 restraints weight = 19173.419|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 52)----------------|
| r_work = 0.3084 r_free = 0.3084 target = 0.074580 restraints weight = 9745.951|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3116 r_free = 0.3116 target = 0.076239 restraints weight = 6224.857|
|-----------------------------------------------------------------------------|
r_work (final): 0.3118
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8593
moved from start:          0.2670

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.039   8678  Z= 0.165
  Angle     :  0.605   7.988  11830  Z= 0.309
  Chirality :  0.045   0.236   1320
  Planarity :  0.005   0.069   1458
  Dihedral  : 10.984 111.010   1278
  Min Nonbonded Distance : 2.484

Molprobity Statistics.
  All-atom Clashscore : 12.98
  Ramachandran Plot:
    Outliers :  0.10 %
    Allowed  :  6.60 %
    Favored  : 93.30 %
  Rotamer:
    Outliers :  3.67 %
    Allowed  : 32.18 %
    Favored  : 64.14 %
  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: -0.06 (0.28), residues: 1000
  helix:  0.96 (0.33), residues: 286
  sheet: -0.64 (0.36), residues: 242
  loop : -0.19 (0.29), residues: 472

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.001   TRP B  72 
 HIS   0.003   0.001   HIS B  22 
 PHE   0.018   0.001   PHE A 112 
 TYR   0.016   0.002   TYR C  56 
 ARG   0.003   0.000   ARG A 110 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03164 (  282)
  hydrogen bonds       : angle       4.70028 (  756)
  covalent geometry    : bond        0.00392 ( 8678)
  covalent geometry    : angle       0.60549 (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
  148 residues out of total 898 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 115
  time to evaluate  : 0.919 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   73 ASP cc_start: 0.8902 (m-30) cc_final: 0.8301 (p0)
REVERT: A  110 ARG cc_start: 0.7756 (mtt90) cc_final: 0.7540 (mmt90)
REVERT: A  132 ARG cc_start: 0.8629 (tmt170) cc_final: 0.8285 (mmm160)
REVERT: A  188 ASP cc_start: 0.8957 (p0) cc_final: 0.8644 (p0)
REVERT: C   55 GLN cc_start: 0.4924 (pp30) cc_final: 0.4540 (pp30)
REVERT: C   77 GLN cc_start: 0.9225 (mt0) cc_final: 0.8903 (mm-40)
REVERT: C   99 GLN cc_start: 0.8417 (pm20) cc_final: 0.8191 (pm20)
REVERT: D   72 TRP cc_start: 0.8836 (OUTLIER) cc_final: 0.7341 (m-90)
REVERT: D   73 ASP cc_start: 0.8771 (m-30) cc_final: 0.8515 (m-30)
REVERT: D  188 ASP cc_start: 0.8694 (m-30) cc_final: 0.8265 (t0)
  outliers start: 33
  outliers final: 26
  residues processed: 142
  average time/residue: 0.2138
  time to fit residues: 41.1776
Evaluate side-chains
  138 residues out of total 898 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 111
  time to evaluate  : 0.907 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   47 ILE
Chi-restraints excluded: chain A residue   90 ILE
Chi-restraints excluded: chain A residue  165 VAL
Chi-restraints excluded: chain A residue  172 SER
Chi-restraints excluded: chain A residue  206 VAL
Chi-restraints excluded: chain A residue  217 TYR
Chi-restraints excluded: chain A residue  254 MET
Chi-restraints excluded: chain B residue   12 ASP
Chi-restraints excluded: chain B residue   17 LEU
Chi-restraints excluded: chain B residue   32 ILE
Chi-restraints excluded: chain B residue   61 LEU
Chi-restraints excluded: chain B residue  106 THR
Chi-restraints excluded: chain B residue  154 MET
Chi-restraints excluded: chain C residue   30 THR
Chi-restraints excluded: chain C residue   32 ILE
Chi-restraints excluded: chain C residue  102 LEU
Chi-restraints excluded: chain C residue  103 ASN
Chi-restraints excluded: chain C residue  106 THR
Chi-restraints excluded: chain C residue  147 VAL
Chi-restraints excluded: chain C residue  193 SER
Chi-restraints excluded: chain C residue  206 VAL
Chi-restraints excluded: chain D residue   67 LYS
Chi-restraints excluded: chain D residue   72 TRP
Chi-restraints excluded: chain D residue   94 LEU
Chi-restraints excluded: chain D residue  164 VAL
Chi-restraints excluded: chain D residue  165 VAL
Chi-restraints excluded: chain D residue  174 LEU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 98
   random chunks:
   chunk 42 optimal weight:    0.7980
   chunk 10 optimal weight:    8.9990
   chunk 24 optimal weight:   10.0000
   chunk 21 optimal weight:    0.9980
   chunk 61 optimal weight:   10.0000
   chunk 37 optimal weight:    8.9990
   chunk 12 optimal weight:   10.0000
   chunk 28 optimal weight:    0.0060
   chunk 41 optimal weight:    4.9990
   chunk 19 optimal weight:    0.9990
   chunk 30 optimal weight:    7.9990
   overall best weight:    1.5600

-------------------------------------------------------------------------------
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 = 0.3498 r_free = 0.3498 target = 0.098020 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3061 r_free = 0.3061 target = 0.073292 restraints weight = 18869.239|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3114 r_free = 0.3114 target = 0.076009 restraints weight = 9418.674|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 41)----------------|
| r_work = 0.3147 r_free = 0.3147 target = 0.077736 restraints weight = 5921.312|
|-----------------------------------------------------------------------------|
r_work (final): 0.3145
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8561
moved from start:          0.2776

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= 0.130
  Angle     :  0.601  10.040  11830  Z= 0.302
  Chirality :  0.044   0.226   1320
  Planarity :  0.005   0.071   1458
  Dihedral  : 10.962 111.555   1278
  Min Nonbonded Distance : 2.511

Molprobity Statistics.
  All-atom Clashscore : 12.09
  Ramachandran Plot:
    Outliers :  0.10 %
    Allowed  :  6.00 %
    Favored  : 93.90 %
  Rotamer:
    Outliers :  3.67 %
    Allowed  : 32.07 %
    Favored  : 64.25 %
  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:  0.97 (0.33), residues: 286
  sheet: -0.67 (0.35), residues: 242
  loop : -0.19 (0.29), residues: 472

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.025   0.001   TRP B  72 
 HIS   0.002   0.000   HIS D  22 
 PHE   0.014   0.001   PHE A 112 
 TYR   0.016   0.001   TYR C 209 
 ARG   0.007   0.000   ARG C 132 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02976 (  282)
  hydrogen bonds       : angle       4.67761 (  756)
  covalent geometry    : bond        0.00311 ( 8678)
  covalent geometry    : angle       0.60070 (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
  150 residues out of total 898 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 117
  time to evaluate  : 0.968 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  110 ARG cc_start: 0.7757 (mtt90) cc_final: 0.7525 (mmt90)
REVERT: A  132 ARG cc_start: 0.8618 (tmt170) cc_final: 0.8272 (mmm160)
REVERT: B   56 TYR cc_start: 0.7707 (m-10) cc_final: 0.7329 (m-10)
REVERT: C   55 GLN cc_start: 0.4793 (pp30) cc_final: 0.4578 (pp30)
REVERT: C   77 GLN cc_start: 0.9216 (mt0) cc_final: 0.8891 (mm-40)
REVERT: C   79 TYR cc_start: 0.8002 (t80) cc_final: 0.7670 (t80)
REVERT: C   83 GLN cc_start: 0.8694 (mm-40) cc_final: 0.8334 (mm-40)
REVERT: C   87 VAL cc_start: 0.8167 (OUTLIER) cc_final: 0.7821 (p)
REVERT: C   99 GLN cc_start: 0.8457 (pm20) cc_final: 0.8042 (pm20)
REVERT: D   72 TRP cc_start: 0.8834 (OUTLIER) cc_final: 0.7179 (m-90)
REVERT: D   73 ASP cc_start: 0.8669 (m-30) cc_final: 0.8374 (m-30)
REVERT: D  101 ASP cc_start: 0.8289 (t0) cc_final: 0.7993 (t0)
REVERT: D  177 ASP cc_start: 0.8879 (p0) cc_final: 0.8598 (p0)
REVERT: D  188 ASP cc_start: 0.8700 (m-30) cc_final: 0.8246 (t0)
  outliers start: 33
  outliers final: 24
  residues processed: 143
  average time/residue: 0.2414
  time to fit residues: 46.0379
Evaluate side-chains
  138 residues out of total 898 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 112
  time to evaluate  : 0.923 
-------------------------------------------------------------------------------
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  176 VAL
Chi-restraints excluded: chain A residue  206 VAL
Chi-restraints excluded: chain A residue  217 TYR
Chi-restraints excluded: chain A residue  254 MET
Chi-restraints excluded: chain B residue   17 LEU
Chi-restraints excluded: chain B residue   32 ILE
Chi-restraints excluded: chain B residue   61 LEU
Chi-restraints excluded: chain B residue  106 THR
Chi-restraints excluded: chain B residue  154 MET
Chi-restraints excluded: chain C residue   30 THR
Chi-restraints excluded: chain C residue   32 ILE
Chi-restraints excluded: chain C residue   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  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:    6.9990
   chunk 96 optimal weight:    0.4980
   chunk 30 optimal weight:   10.0000
   chunk 92 optimal weight:   10.0000
   chunk 21 optimal weight:    0.7980
   chunk 67 optimal weight:    5.9990
   chunk 84 optimal weight:   10.0000
   chunk 29 optimal weight:    2.9990
   chunk 80 optimal weight:    0.9980
   chunk 51 optimal weight:    2.9990
   chunk 53 optimal weight:    7.9990
   overall best weight:    1.6584

-------------------------------------------------------------------------------
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 = 0.3502 r_free = 0.3502 target = 0.098187 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3046 r_free = 0.3046 target = 0.072771 restraints weight = 19120.060|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3100 r_free = 0.3100 target = 0.075489 restraints weight = 9668.882|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 55)----------------|
| r_work = 0.3134 r_free = 0.3134 target = 0.077219 restraints weight = 6183.242|
|-----------------------------------------------------------------------------|
r_work (final): 0.3136
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8575
moved from start:          0.2897

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= 0.136
  Angle     :  0.610  10.170  11830  Z= 0.307
  Chirality :  0.044   0.228   1320
  Planarity :  0.005   0.072   1458
  Dihedral  : 10.964 112.179   1278
  Min Nonbonded Distance : 2.504

Molprobity Statistics.
  All-atom Clashscore : 12.62
  Ramachandran Plot:
    Outliers :  0.10 %
    Allowed  :  6.50 %
    Favored  : 93.40 %
  Rotamer:
    Outliers :  3.34 %
    Allowed  : 32.29 %
    Favored  : 64.37 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.02 (0.28), residues: 1000
  helix:  1.03 (0.33), residues: 286
  sheet: -0.62 (0.36), residues: 242
  loop : -0.20 (0.29), residues: 472

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.022   0.001   TRP B  72 
 HIS   0.002   0.001   HIS B  22 
 PHE   0.014   0.001   PHE A 112 
 TYR   0.018   0.001   TYR C  56 
 ARG   0.008   0.000   ARG C 132 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02999 (  282)
  hydrogen bonds       : angle       4.62507 (  756)
  covalent geometry    : bond        0.00326 ( 8678)
  covalent geometry    : angle       0.60971 (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
  155 residues out of total 898 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 125
  time to evaluate  : 1.411 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   73 ASP cc_start: 0.8869 (m-30) cc_final: 0.8271 (p0)
REVERT: A  110 ARG cc_start: 0.7765 (mtt90) cc_final: 0.7513 (mmt90)
REVERT: A  132 ARG cc_start: 0.8626 (tmt170) cc_final: 0.8280 (mmm160)
REVERT: C   55 GLN cc_start: 0.4878 (pp30) cc_final: 0.4628 (pp30)
REVERT: C   77 GLN cc_start: 0.9241 (mt0) cc_final: 0.8914 (mm-40)
REVERT: C   79 TYR cc_start: 0.7963 (t80) cc_final: 0.7725 (t80)
REVERT: C   83 GLN cc_start: 0.8640 (mm-40) cc_final: 0.8311 (mm-40)
REVERT: C   87 VAL cc_start: 0.8205 (OUTLIER) cc_final: 0.7920 (p)
REVERT: C   99 GLN cc_start: 0.8423 (pm20) cc_final: 0.7990 (pm20)
REVERT: C  145 GLU cc_start: 0.8818 (tp30) cc_final: 0.8557 (tp30)
REVERT: D   72 TRP cc_start: 0.8864 (OUTLIER) cc_final: 0.7332 (m-90)
REVERT: D   73 ASP cc_start: 0.8658 (m-30) cc_final: 0.8355 (m-30)
REVERT: D  119 ARG cc_start: 0.9030 (mtm110) cc_final: 0.8822 (mtm110)
REVERT: D  188 ASP cc_start: 0.8682 (m-30) cc_final: 0.8243 (t0)
  outliers start: 30
  outliers final: 26
  residues processed: 149
  average time/residue: 0.2448
  time to fit residues: 48.9295
Evaluate side-chains
  146 residues out of total 898 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 118
  time to evaluate  : 0.939 
-------------------------------------------------------------------------------
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  176 VAL
Chi-restraints excluded: chain A residue  206 VAL
Chi-restraints excluded: chain A residue  217 TYR
Chi-restraints excluded: chain A residue  254 MET
Chi-restraints excluded: chain B residue   12 ASP
Chi-restraints excluded: chain B residue   17 LEU
Chi-restraints excluded: chain B residue   32 ILE
Chi-restraints excluded: chain B residue   61 LEU
Chi-restraints excluded: chain B residue  106 THR
Chi-restraints excluded: chain B residue  154 MET
Chi-restraints excluded: chain C residue   30 THR
Chi-restraints excluded: chain C residue   32 ILE
Chi-restraints excluded: chain C residue   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  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=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 98
   random chunks:
   chunk 23 optimal weight:    2.9990
   chunk 45 optimal weight:    2.9990
   chunk 90 optimal weight:    0.7980
   chunk 92 optimal weight:   10.0000
   chunk 69 optimal weight:    0.9990
   chunk 87 optimal weight:    7.9990
   chunk 11 optimal weight:    1.9990
   chunk 0 optimal weight:   20.0000
   chunk 76 optimal weight:    0.0470
   chunk 56 optimal weight:    9.9990
   chunk 5 optimal weight:    2.9990
   overall best weight:    1.3684

-------------------------------------------------------------------------------
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 = 0.3511 r_free = 0.3511 target = 0.098830 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3064 r_free = 0.3064 target = 0.073657 restraints weight = 19061.152|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 47)----------------|
| r_work = 0.3119 r_free = 0.3119 target = 0.076390 restraints weight = 9618.233|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 41)----------------|
| r_work = 0.3152 r_free = 0.3152 target = 0.078105 restraints weight = 6126.336|
|-----------------------------------------------------------------------------|
r_work (final): 0.3151
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8561
moved from start:          0.2975

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.043   8678  Z= 0.127
  Angle     :  0.632  10.455  11830  Z= 0.316
  Chirality :  0.045   0.222   1320
  Planarity :  0.005   0.073   1458
  Dihedral  : 10.943 112.399   1278
  Min Nonbonded Distance : 2.479

Molprobity Statistics.
  All-atom Clashscore : 12.03
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.30 %
    Favored  : 93.70 %
  Rotamer:
    Outliers :  3.23 %
    Allowed  : 33.30 %
    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: -0.03 (0.28), residues: 1000
  helix:  0.98 (0.33), residues: 286
  sheet: -0.65 (0.36), residues: 242
  loop : -0.16 (0.29), residues: 472

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.025   0.001   TRP B  72 
 HIS   0.002   0.000   HIS D   8 
 PHE   0.015   0.001   PHE A 112 
 TYR   0.019   0.001   TYR C  56 
 ARG   0.003   0.000   ARG C 132 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02981 (  282)
  hydrogen bonds       : angle       4.65073 (  756)
  covalent geometry    : bond        0.00306 ( 8678)
  covalent geometry    : angle       0.63219 (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
  154 residues out of total 898 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 125
  time to evaluate  : 1.630 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   73 ASP cc_start: 0.8846 (m-30) cc_final: 0.8254 (p0)
REVERT: A  110 ARG cc_start: 0.7760 (mtt90) cc_final: 0.7503 (mmt90)
REVERT: A  132 ARG cc_start: 0.8613 (tmt170) cc_final: 0.8270 (mmm160)
REVERT: B   56 TYR cc_start: 0.7695 (m-10) cc_final: 0.7279 (m-10)
REVERT: C   55 GLN cc_start: 0.4883 (pp30) cc_final: 0.4631 (pp30)
REVERT: C   77 GLN cc_start: 0.9243 (mt0) cc_final: 0.8920 (mm-40)
REVERT: C   79 TYR cc_start: 0.7993 (t80) cc_final: 0.7772 (t80)
REVERT: C   83 GLN cc_start: 0.8611 (mm-40) cc_final: 0.8229 (mm-40)
REVERT: C   87 VAL cc_start: 0.8131 (OUTLIER) cc_final: 0.7819 (p)
REVERT: C   99 GLN cc_start: 0.8371 (pm20) cc_final: 0.7954 (pm20)
REVERT: C  145 GLU cc_start: 0.8828 (tp30) cc_final: 0.8592 (tp30)
REVERT: D   73 ASP cc_start: 0.8655 (m-30) cc_final: 0.8369 (m-30)
REVERT: D  101 ASP cc_start: 0.8263 (t0) cc_final: 0.8018 (t0)
REVERT: D  119 ARG cc_start: 0.9034 (mtm110) cc_final: 0.8810 (mtm110)
REVERT: D  177 ASP cc_start: 0.8833 (p0) cc_final: 0.8537 (p0)
REVERT: D  188 ASP cc_start: 0.8679 (m-30) cc_final: 0.8229 (t0)
  outliers start: 29
  outliers final: 25
  residues processed: 146
  average time/residue: 0.3522
  time to fit residues: 69.2279
Evaluate side-chains
  145 residues out of total 898 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 119
  time to evaluate  : 1.153 
-------------------------------------------------------------------------------
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  176 VAL
Chi-restraints excluded: chain A residue  206 VAL
Chi-restraints excluded: chain A residue  217 TYR
Chi-restraints excluded: chain A residue  254 MET
Chi-restraints excluded: chain B residue   17 LEU
Chi-restraints excluded: chain B residue   32 ILE
Chi-restraints excluded: chain B residue   61 LEU
Chi-restraints excluded: chain B residue  106 THR
Chi-restraints excluded: chain B residue  154 MET
Chi-restraints excluded: chain C residue   30 THR
Chi-restraints excluded: chain C residue   32 ILE
Chi-restraints excluded: chain C residue   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  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=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 98
   random chunks:
   chunk 22 optimal weight:    0.6980
   chunk 79 optimal weight:    0.0020
   chunk 25 optimal weight:    7.9990
   chunk 97 optimal weight:    9.9990
   chunk 35 optimal weight:    2.9990
   chunk 48 optimal weight:    4.9990
   chunk 44 optimal weight:    2.9990
   chunk 72 optimal weight:    0.2980
   chunk 13 optimal weight:    7.9990
   chunk 36 optimal weight:    3.9990
   chunk 82 optimal weight:    2.9990
   overall best weight:    1.3992

-------------------------------------------------------------------------------
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 = 0.3512 r_free = 0.3512 target = 0.098832 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3061 r_free = 0.3061 target = 0.073478 restraints weight = 19210.523|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3116 r_free = 0.3116 target = 0.076227 restraints weight = 9663.415|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3147 r_free = 0.3147 target = 0.077904 restraints weight = 6137.581|
|-----------------------------------------------------------------------------|
r_work (final): 0.3150
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8564
moved from start:          0.3081

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= 0.126
  Angle     :  0.624  10.042  11830  Z= 0.311
  Chirality :  0.044   0.222   1320
  Planarity :  0.005   0.072   1458
  Dihedral  : 10.851 112.513   1276
  Min Nonbonded Distance : 2.508

Molprobity Statistics.
  All-atom Clashscore : 12.03
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.50 %
    Favored  : 93.50 %
  Rotamer:
    Outliers :  3.23 %
    Allowed  : 33.30 %
    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: -0.00 (0.28), residues: 1000
  helix:  1.00 (0.33), residues: 286
  sheet: -0.66 (0.36), residues: 242
  loop : -0.12 (0.29), residues: 472

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.023   0.001   TRP B  72 
 HIS   0.002   0.000   HIS B  22 
 PHE   0.014   0.001   PHE A 112 
 TYR   0.019   0.001   TYR C  56 
 ARG   0.004   0.000   ARG C 132 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02946 (  282)
  hydrogen bonds       : angle       4.59265 (  756)
  covalent geometry    : bond        0.00304 ( 8678)
  covalent geometry    : angle       0.62434 (11830)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3914.89 seconds
wall clock time: 71 minutes 42.14 seconds (4302.14 seconds total)