Starting phenix.real_space_refine
on Wed Apr 30 10:38:58 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9luc_63394/04_2025/9luc_63394.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9luc_63394/04_2025/9luc_63394.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.5
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/9luc_63394/04_2025/9luc_63394.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9luc_63394/04_2025/9luc_63394.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9luc_63394/04_2025/9luc_63394.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9luc_63394/04_2025/9luc_63394.cif"
  }
  resolution = 3.5
  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=   0.001 sd=   0.031
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: 4
    Type Number    sf(0)   Gaussians
     S      50      5.16       5
     C    6168      2.51       5
     N    1588      2.21       5
     O    1778      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 53 residue(s): 0.03s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/chem_data/mon_lib"
  Total number of atoms: 9584
  Number of models: 1
  Model: ""
    Number of chains: 7
    Chain: "C"
      Number of atoms: 1685
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 220, 1685
          Classifications: {'peptide': 220}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 9, 'TRANS': 210}
    Chain: "B"
      Number of atoms: 1685
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 220, 1685
          Classifications: {'peptide': 220}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 9, 'TRANS': 210}
    Chain: "E"
      Number of atoms: 1866
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 246, 1866
          Classifications: {'peptide': 246}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 9, 'TRANS': 236}
    Chain: "A"
      Number of atoms: 1694
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 221, 1694
          Classifications: {'peptide': 221}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 9, 'TRANS': 211}
    Chain: "D"
      Number of atoms: 1866
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 246, 1866
          Classifications: {'peptide': 246}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 9, 'TRANS': 236}
    Chain: "F"
      Number of atoms: 389
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 47, 389
          Classifications: {'peptide': 47}
          Link IDs: {'TRANS': 46}
    Chain: "G"
      Number of atoms: 399
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 49, 399
          Classifications: {'peptide': 49}
          Link IDs: {'PTRANS': 1, 'TRANS': 47}
  Time building chain proxies: 6.23, per 1000 atoms: 0.65
  Number of scatterers: 9584
  At special positions: 0
  Unit cell: (89.76, 88.88, 110.88, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     S      50     16.00
     O    1778      8.00
     N    1588      7.00
     C    6168      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: 2.51
  Conformation dependent library (CDL) restraints added in 1.2 seconds
  

  2470 Ramachandran restraints generated.
    1235 Oldfield, 0 Emsley, 1235 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2302

  Finding SS restraints...
    Secondary structure from input PDB file:
      70 helices and 0 sheets defined
      91.0% alpha, 0.0% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.88
  Creating SS restraints...
    Processing helix  chain 'C' and resid 33 through 51
    Processing helix  chain 'C' and resid 52 through 57
    Processing helix  chain 'C' and resid 58 through 67
    Processing helix  chain 'C' and resid 73 through 92
      removed outlier: 4.090A  pdb=" N   GLU C  79 " --> pdb=" O   ASN C  75 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 95 through 101
      removed outlier: 4.227A  pdb=" N   LYS C  99 " --> pdb=" O   ALA C  95 " (cutoff:3.500A)
      removed outlier: 3.694A  pdb=" N   LEU C 101 " --> pdb=" O   GLU C  97 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 105 through 117
    Processing helix  chain 'C' and resid 120 through 169
      removed outlier: 3.900A  pdb=" N   ASP C 131 " --> pdb=" O   ILE C 127 " (cutoff:3.500A)
      removed outlier: 4.167A  pdb=" N   LEU C 145 " --> pdb=" O   ASN C 141 " (cutoff:3.500A)
      removed outlier: 4.185A  pdb=" N   PHE C 146 " --> pdb=" O   TYR C 142 " (cutoff:3.500A)
      Proline residue:  C 154  - end of helix
    Processing helix  chain 'C' and resid 170 through 172
      No H-bonds generated for 'chain 'C' and resid 170 through 172'
    Processing helix  chain 'C' and resid 174 through 186
      removed outlier: 3.577A  pdb=" N   LEU C 178 " --> pdb=" O   ASP C 174 " (cutoff:3.500A)
      removed outlier: 4.554A  pdb=" N   GLY C 179 " --> pdb=" O   PRO C 175 " (cutoff:3.500A)
      Proline residue:  C 180  - end of helix
    Processing helix  chain 'C' and resid 186 through 199
      removed outlier: 3.640A  pdb=" N   ALA C 196 " --> pdb=" O   GLY C 192 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 199 through 231
      removed outlier: 3.594A  pdb=" N   GLU C 213 " --> pdb=" O   ALA C 209 " (cutoff:3.500A)
      removed outlier: 3.553A  pdb=" N   GLU C 214 " --> pdb=" O   LYS C 210 " (cutoff:3.500A)
      removed outlier: 4.627A  pdb=" N   VAL C 217 " --> pdb=" O   GLU C 213 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 233 through 242
      removed outlier: 3.505A  pdb=" N   ASN C 242 " --> pdb=" O   ARG C 238 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 243 through 245
      No H-bonds generated for 'chain 'C' and resid 243 through 245'
    Processing helix  chain 'B' and resid 27 through 31
      removed outlier: 3.996A  pdb=" N   PHE B  31 " --> pdb=" O   THR B  28 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 32 through 51
    Processing helix  chain 'B' and resid 52 through 57
      removed outlier: 3.632A  pdb=" N   ILE B  56 " --> pdb=" O   PRO B  52 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 58 through 67
      removed outlier: 3.707A  pdb=" N   GLY B  62 " --> pdb=" O   THR B  58 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 73 through 89
      removed outlier: 3.595A  pdb=" N   ASP B  80 " --> pdb=" O   GLU B  76 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 92 through 95
    Processing helix  chain 'B' and resid 96 through 101
    Processing helix  chain 'B' and resid 105 through 117
      removed outlier: 3.544A  pdb=" N   VAL B 115 " --> pdb=" O   GLY B 111 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 120 through 169
      removed outlier: 3.770A  pdb=" N   LEU B 130 " --> pdb=" O   GLN B 126 " (cutoff:3.500A)
      removed outlier: 3.915A  pdb=" N   ASP B 131 " --> pdb=" O   ILE B 127 " (cutoff:3.500A)
      removed outlier: 3.575A  pdb=" N   TYR B 142 " --> pdb=" O   GLU B 138 " (cutoff:3.500A)
      removed outlier: 4.066A  pdb=" N   LEU B 145 " --> pdb=" O   ASN B 141 " (cutoff:3.500A)
      removed outlier: 3.731A  pdb=" N   PHE B 146 " --> pdb=" O   TYR B 142 " (cutoff:3.500A)
      Proline residue:  B 154  - end of helix
    Processing helix  chain 'B' and resid 170 through 172
      No H-bonds generated for 'chain 'B' and resid 170 through 172'
    Processing helix  chain 'B' and resid 177 through 199
      removed outlier: 3.526A  pdb=" N   VAL B 184 " --> pdb=" O   PRO B 180 " (cutoff:3.500A)
      removed outlier: 4.083A  pdb=" N   THR B 189 " --> pdb=" O   ALA B 185 " (cutoff:3.500A)
      removed outlier: 3.705A  pdb=" N   ALA B 196 " --> pdb=" O   GLY B 192 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 199 through 231
      removed outlier: 3.748A  pdb=" N   GLU B 213 " --> pdb=" O   ALA B 209 " (cutoff:3.500A)
      removed outlier: 3.547A  pdb=" N   GLU B 214 " --> pdb=" O   LYS B 210 " (cutoff:3.500A)
      removed outlier: 3.867A  pdb=" N   LEU B 216 " --> pdb=" O   ALA B 212 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 233 through 242
    Processing helix  chain 'B' and resid 243 through 245
      No H-bonds generated for 'chain 'B' and resid 243 through 245'
    Processing helix  chain 'E' and resid 2 through 23
      removed outlier: 3.534A  pdb=" N   PHE E  20 " --> pdb=" O   ILE E  16 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 26 through 31
      removed outlier: 3.516A  pdb=" N   PHE E  31 " --> pdb=" O   THR E  28 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 32 through 51
    Processing helix  chain 'E' and resid 52 through 57
    Processing helix  chain 'E' and resid 58 through 67
    Processing helix  chain 'E' and resid 73 through 89
      removed outlier: 4.320A  pdb=" N   GLU E  79 " --> pdb=" O   ASN E  75 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 92 through 99
      removed outlier: 4.239A  pdb=" N   LEU E  96 " --> pdb=" O   GLY E  92 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 105 through 117
    Processing helix  chain 'E' and resid 120 through 169
      removed outlier: 3.992A  pdb=" N   GLN E 126 " --> pdb=" O   PRO E 122 " (cutoff:3.500A)
      removed outlier: 4.102A  pdb=" N   LEU E 130 " --> pdb=" O   GLN E 126 " (cutoff:3.500A)
      removed outlier: 3.537A  pdb=" N   LYS E 135 " --> pdb=" O   ASP E 131 " (cutoff:3.500A)
      removed outlier: 4.333A  pdb=" N   LEU E 145 " --> pdb=" O   ASN E 141 " (cutoff:3.500A)
      removed outlier: 4.069A  pdb=" N   PHE E 146 " --> pdb=" O   TYR E 142 " (cutoff:3.500A)
      Proline residue:  E 154  - end of helix
      removed outlier: 4.056A  pdb=" N   MET E 163 " --> pdb=" O   ILE E 159 " (cutoff:3.500A)
      removed outlier: 4.088A  pdb=" N   GLN E 167 " --> pdb=" O   MET E 163 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 170 through 172
      No H-bonds generated for 'chain 'E' and resid 170 through 172'
    Processing helix  chain 'E' and resid 174 through 199
      removed outlier: 4.436A  pdb=" N   GLY E 179 " --> pdb=" O   PRO E 175 " (cutoff:3.500A)
      Proline residue:  E 180  - end of helix
      removed outlier: 3.661A  pdb=" N   ALA E 183 " --> pdb=" O   GLY E 179 " (cutoff:3.500A)
      removed outlier: 4.470A  pdb=" N   VAL E 184 " --> pdb=" O   PRO E 180 " (cutoff:3.500A)
      removed outlier: 4.185A  pdb=" N   ALA E 185 " --> pdb=" O   SER E 181 " (cutoff:3.500A)
      removed outlier: 3.668A  pdb=" N   PHE E 186 " --> pdb=" O   ILE E 182 " (cutoff:3.500A)
      removed outlier: 4.026A  pdb=" N   THR E 189 " --> pdb=" O   ALA E 185 " (cutoff:3.500A)
      removed outlier: 3.716A  pdb=" N   ALA E 196 " --> pdb=" O   GLY E 192 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 199 through 231
      removed outlier: 3.682A  pdb=" N   GLU E 213 " --> pdb=" O   ALA E 209 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 233 through 242
    Processing helix  chain 'E' and resid 243 through 245
      No H-bonds generated for 'chain 'E' and resid 243 through 245'
    Processing helix  chain 'A' and resid 32 through 51
      removed outlier: 3.668A  pdb=" N   ILE A  38 " --> pdb=" O   THR A  34 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 52 through 57
      removed outlier: 3.814A  pdb=" N   ILE A  56 " --> pdb=" O   PRO A  52 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 58 through 67
    Processing helix  chain 'A' and resid 73 through 91
      removed outlier: 4.180A  pdb=" N   GLU A  79 " --> pdb=" O   ASN A  75 " (cutoff:3.500A)
      removed outlier: 3.729A  pdb=" N   MET A  86 " --> pdb=" O   VAL A  82 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 92 through 102
      removed outlier: 3.861A  pdb=" N   GLU A  97 " --> pdb=" O   LEU A  94 " (cutoff:3.500A)
      removed outlier: 3.667A  pdb=" N   GLN A  98 " --> pdb=" O   ALA A  95 " (cutoff:3.500A)
      removed outlier: 3.546A  pdb=" N   LYS A  99 " --> pdb=" O   LEU A  96 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 105 through 116
    Processing helix  chain 'A' and resid 120 through 171
      removed outlier: 3.792A  pdb=" N   ASP A 131 " --> pdb=" O   ILE A 127 " (cutoff:3.500A)
      removed outlier: 4.243A  pdb=" N   LEU A 145 " --> pdb=" O   ASN A 141 " (cutoff:3.500A)
      removed outlier: 3.998A  pdb=" N   PHE A 146 " --> pdb=" O   TYR A 142 " (cutoff:3.500A)
      Proline residue:  A 154  - end of helix
    Processing helix  chain 'A' and resid 177 through 199
      removed outlier: 3.763A  pdb=" N   ILE A 187 " --> pdb=" O   ALA A 183 " (cutoff:3.500A)
      removed outlier: 5.271A  pdb=" N   ALA A 188 " --> pdb=" O   VAL A 184 " (cutoff:3.500A)
      removed outlier: 4.946A  pdb=" N   THR A 189 " --> pdb=" O   ALA A 185 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 199 through 231
      removed outlier: 3.928A  pdb=" N   GLU A 213 " --> pdb=" O   ALA A 209 " (cutoff:3.500A)
      removed outlier: 4.052A  pdb=" N   LEU A 216 " --> pdb=" O   ALA A 212 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 233 through 243
      removed outlier: 3.650A  pdb=" N   THR A 243 " --> pdb=" O   LYS A 239 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 2 through 23
    Processing helix  chain 'D' and resid 26 through 30
    Processing helix  chain 'D' and resid 32 through 51
    Processing helix  chain 'D' and resid 52 through 57
      removed outlier: 3.582A  pdb=" N   ILE D  56 " --> pdb=" O   PRO D  52 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 58 through 67
      removed outlier: 3.505A  pdb=" N   GLY D  62 " --> pdb=" O   THR D  58 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 73 through 92
      removed outlier: 4.101A  pdb=" N   GLU D  79 " --> pdb=" O   ASN D  75 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 95 through 100
      removed outlier: 4.064A  pdb=" N   LYS D  99 " --> pdb=" O   ALA D  95 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 105 through 117
    Processing helix  chain 'D' and resid 120 through 171
      removed outlier: 4.084A  pdb=" N   ASP D 131 " --> pdb=" O   ILE D 127 " (cutoff:3.500A)
      removed outlier: 4.376A  pdb=" N   LEU D 145 " --> pdb=" O   ASN D 141 " (cutoff:3.500A)
      removed outlier: 4.052A  pdb=" N   PHE D 146 " --> pdb=" O   TYR D 142 " (cutoff:3.500A)
      Proline residue:  D 154  - end of helix
    Processing helix  chain 'D' and resid 177 through 186
      removed outlier: 4.620A  pdb=" N   SER D 181 " --> pdb=" O   GLN D 177 " (cutoff:3.500A)
      removed outlier: 3.686A  pdb=" N   ALA D 185 " --> pdb=" O   SER D 181 " (cutoff:3.500A)
      removed outlier: 3.979A  pdb=" N   PHE D 186 " --> pdb=" O   ILE D 182 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 186 through 199
      removed outlier: 3.663A  pdb=" N   ALA D 196 " --> pdb=" O   GLY D 192 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 199 through 231
      removed outlier: 4.092A  pdb=" N   VAL D 217 " --> pdb=" O   GLU D 213 " (cutoff:3.500A)
      removed outlier: 3.522A  pdb=" N   GLN D 229 " --> pdb=" O   VAL D 225 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 233 through 242
      removed outlier: 3.620A  pdb=" N   ASN D 242 " --> pdb=" O   ARG D 238 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 243 through 245
      No H-bonds generated for 'chain 'D' and resid 243 through 245'
    Processing helix  chain 'F' and resid 16 through 39
      removed outlier: 3.971A  pdb=" N   ILE F  20 " --> pdb=" O   ASP F  16 " (cutoff:3.500A)
      removed outlier: 3.789A  pdb=" N   THR F  21 " --> pdb=" O   ARG F  17 " (cutoff:3.500A)
      removed outlier: 4.421A  pdb=" N   ASP F  24 " --> pdb=" O   ILE F  20 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 43 through 58
      removed outlier: 3.573A  pdb=" N   THR F  56 " --> pdb=" O   SER F  52 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 13 through 17
    Processing helix  chain 'G' and resid 18 through 40
      removed outlier: 3.849A  pdb=" N   MET G  39 " --> pdb=" O   MET G  35 " (cutoff:3.500A)
      removed outlier: 3.806A  pdb=" N   SER G  40 " --> pdb=" O   MET G  36 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 43 through 59
      removed outlier: 3.647A  pdb=" N   THR G  56 " --> pdb=" O   SER G  52 " (cutoff:3.500A)
      removed outlier: 4.072A  pdb=" N   THR G  57 " --> pdb=" O   SER G  53 " (cutoff:3.500A)

    763 hydrogen bonds defined for protein.
    2250 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: 2.62

  Time building geometry restraints manager: 2.92 seconds

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

  Histogram of bond lengths:
        1.20 -     1.33: 1996
        1.33 -     1.46: 2953
        1.46 -     1.59: 4689
        1.59 -     1.72: 0
        1.72 -     1.85: 100
  Bond restraints: 9738
  Sorted by residual:
  bond pdb=" C   PHE F  58 "
       pdb=" O   PHE F  58 "
    ideal  model  delta    sigma   weight residual
    1.236  1.470 -0.234 1.29e-02 6.01e+03 3.29e+02
  bond pdb=" C   ALA C  46 "
       pdb=" N   VAL C  47 "
    ideal  model  delta    sigma   weight residual
    1.334  1.397 -0.063 1.26e-02 6.30e+03 2.47e+01
  bond pdb=" CA  ALA C  46 "
       pdb=" C   ALA C  46 "
    ideal  model  delta    sigma   weight residual
    1.523  1.580 -0.057 1.30e-02 5.92e+03 1.91e+01
  bond pdb=" C   PHE G  58 "
       pdb=" O   PHE G  58 "
    ideal  model  delta    sigma   weight residual
    1.236  1.284 -0.048 1.32e-02 5.74e+03 1.32e+01
  bond pdb=" CA  ALA A 143 "
       pdb=" CB  ALA A 143 "
    ideal  model  delta    sigma   weight residual
    1.528  1.475  0.053 1.66e-02 3.63e+03 1.02e+01
  ... (remaining 9733 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     5.17: 13144
        5.17 -    10.34: 59
       10.34 -    15.52: 1
       15.52 -    20.69: 1
       20.69 -    25.86: 2
  Bond angle restraints: 13207
  Sorted by residual:
  angle pdb=" CA  PHE G  58 "
        pdb=" C   PHE G  58 "
        pdb=" O   PHE G  58 "
      ideal   model   delta    sigma   weight residual
     119.18   93.79   25.39 1.19e+00 7.06e-01 4.55e+02
  angle pdb=" O   PHE G  58 "
        pdb=" C   PHE G  58 "
        pdb=" N   GLN G  59 "
      ideal   model   delta    sigma   weight residual
     122.41  148.27  -25.86 1.42e+00 4.96e-01 3.32e+02
  angle pdb=" CA  ALA C  46 "
        pdb=" C   ALA C  46 "
        pdb=" N   VAL C  47 "
      ideal   model   delta    sigma   weight residual
     117.30  132.97  -15.67 1.16e+00 7.43e-01 1.83e+02
  angle pdb=" CA  ALA C  46 "
        pdb=" C   ALA C  46 "
        pdb=" O   ALA C  46 "
      ideal   model   delta    sigma   weight residual
     120.55  111.40    9.15 1.06e+00 8.90e-01 7.45e+01
  angle pdb=" O   ALA C  46 "
        pdb=" C   ALA C  46 "
        pdb=" N   VAL C  47 "
      ideal   model   delta    sigma   weight residual
     122.12  114.96    7.16 1.06e+00 8.90e-01 4.56e+01
  ... (remaining 13202 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.57: 5142
       17.57 -    35.15: 466
       35.15 -    52.72: 203
       52.72 -    70.30: 54
       70.30 -    87.87: 21
  Dihedral angle restraints: 5886
    sinusoidal: 2311
      harmonic: 3575
  Sorted by residual:
  dihedral pdb=" CD  ARG A  89 "
           pdb=" NE  ARG A  89 "
           pdb=" CZ  ARG A  89 "
           pdb=" NH1 ARG A  89 "
      ideal   model   delta sinusoidal    sigma   weight residual
       0.00   80.26  -80.26     1      1.00e+01 1.00e-02 7.98e+01
  dihedral pdb=" CD  ARG G  41 "
           pdb=" NE  ARG G  41 "
           pdb=" CZ  ARG G  41 "
           pdb=" NH1 ARG G  41 "
      ideal   model   delta sinusoidal    sigma   weight residual
       0.00   72.87  -72.87     1      1.00e+01 1.00e-02 6.77e+01
  dihedral pdb=" CD  ARG G  17 "
           pdb=" NE  ARG G  17 "
           pdb=" CZ  ARG G  17 "
           pdb=" NH1 ARG G  17 "
      ideal   model   delta sinusoidal    sigma   weight residual
       0.00   70.44  -70.44     1      1.00e+01 1.00e-02 6.39e+01
  ... (remaining 5883 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.086: 1106
       0.086 -    0.171: 414
       0.171 -    0.257: 64
       0.257 -    0.343: 7
       0.343 -    0.428: 2
  Chirality restraints: 1593
  Sorted by residual:
  chirality pdb=" CA  ASP E 133 "
            pdb=" N   ASP E 133 "
            pdb=" C   ASP E 133 "
            pdb=" CB  ASP E 133 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.08    0.43 2.00e-01 2.50e+01 4.59e+00
  chirality pdb=" CA  ALA C  46 "
            pdb=" N   ALA C  46 "
            pdb=" C   ALA C  46 "
            pdb=" CB  ALA C  46 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.48    2.06    0.43 2.00e-01 2.50e+01 4.54e+00
  chirality pdb=" CA  ASN C 197 "
            pdb=" N   ASN C 197 "
            pdb=" C   ASN C 197 "
            pdb=" CB  ASN C 197 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.20    0.31 2.00e-01 2.50e+01 2.46e+00
  ... (remaining 1590 not shown)

  Planarity restraints: 1673
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CD  ARG G  41 "    1.138 9.50e-02 1.11e+02   5.11e-01 1.68e+02
        pdb=" NE  ARG G  41 "   -0.048 2.00e-02 2.50e+03
        pdb=" CZ  ARG G  41 "   -0.071 2.00e-02 2.50e+03
        pdb=" NH1 ARG G  41 "    0.029 2.00e-02 2.50e+03
        pdb=" NH2 ARG G  41 "    0.039 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CD  ARG A  89 "   -1.038 9.50e-02 1.11e+02   4.65e-01 1.35e+02
        pdb=" NE  ARG A  89 "    0.075 2.00e-02 2.50e+03
        pdb=" CZ  ARG A  89 "   -0.026 2.00e-02 2.50e+03
        pdb=" NH1 ARG A  89 "    0.004 2.00e-02 2.50e+03
        pdb=" NH2 ARG A  89 "   -0.007 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CD  ARG G  17 "   -0.960 9.50e-02 1.11e+02   4.31e-01 1.18e+02
        pdb=" NE  ARG G  17 "    0.073 2.00e-02 2.50e+03
        pdb=" CZ  ARG G  17 "   -0.031 2.00e-02 2.50e+03
        pdb=" NH1 ARG G  17 "    0.010 2.00e-02 2.50e+03
        pdb=" NH2 ARG G  17 "   -0.009 2.00e-02 2.50e+03
  ... (remaining 1670 not shown)

  Histogram of nonbonded interaction distances:
        2.24 -     2.77: 1402
        2.77 -     3.30: 10488
        3.30 -     3.84: 15450
        3.84 -     4.37: 18281
        4.37 -     4.90: 30050
  Nonbonded interactions: 75671
  Sorted by model distance:
  nonbonded pdb=" OD1 ASN D 197 "
            pdb=" NH2 ARG F  17 "
     model   vdw
     2.239 3.120
  nonbonded pdb=" OD1 ASP A 174 "
            pdb=" N   SER A 176 "
     model   vdw
     2.382 3.120
  nonbonded pdb=" NZ  LYS B 206 "
            pdb=" O   ILE A  49 "
     model   vdw
     2.430 3.120
  nonbonded pdb=" O   SER B 176 "
            pdb=" OG  SER F  53 "
     model   vdw
     2.431 3.040
  nonbonded pdb=" O   LEU D 172 "
            pdb=" C   THR D 173 "
     model   vdw
     2.439 3.270
  ... (remaining 75666 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' and resid 27 through 246)
  selection = chain 'B'
  selection = chain 'C'
  selection = (chain 'D' and resid 27 through 246)
  selection = (chain 'E' and resid 27 through 246)
}
ncs_group {
  reference = chain 'F'
  selection = (chain 'G' and resid 14 through 60)
}

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=0.00 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:             1.370
  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:          0.390
  Check model and map are aligned:         0.070
  Set scattering table:                    0.100
  Process input model:                     24.270
  Find NCS groups from input model:        0.400
  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:2.910
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   29.550
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8568
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      :  0.010   0.234   9738  Z= 0.634
  Angle     :  1.490  25.860  13207  Z= 0.988
  Chirality :  0.086   0.428   1593
  Planarity :  0.032   0.511   1673
  Dihedral  : 17.826  87.872   3584
  Min Nonbonded Distance : 2.239

Molprobity Statistics.
  All-atom Clashscore : 8.46
  Ramachandran Plot:
    Outliers :  0.08 %
    Allowed  :  2.59 %
    Favored  : 97.33 %
  Rotamer:
    Outliers : 11.92 %
    Allowed  :  6.78 %
    Favored  : 81.30 %
  Cbeta Deviations :  0.17 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.36 (0.22), residues: 1235
  helix: -0.89 (0.14), residues: 1026
  sheet:  None (None), residues: 0
  loop :  0.17 (0.50), residues: 209

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.034   0.009   TRP C  77 
 HIS   0.020   0.005   HIS A 103 
 PHE   0.045   0.009   PHE A 146 
 TYR   0.068   0.012   TYR B  51 
 ARG   0.063   0.008   ARG A 238 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.22476 (  763)
  hydrogen bonds       : angle       8.42119 ( 2250)
  covalent geometry    : bond        0.00972 ( 9738)
  covalent geometry    : angle       1.48964 (13207)

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

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

  2470 Ramachandran restraints generated.
    1235 Oldfield, 0 Emsley, 1235 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2470 Ramachandran restraints generated.
    1235 Oldfield, 0 Emsley, 1235 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  439 residues out of total 1032 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 123
    poor density    : 316
  time to evaluate  : 1.070 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: C   79 GLU cc_start: 0.9026 (mm-30) cc_final: 0.8736 (mm-30)
REVERT: C  156 MET cc_start: 0.9027 (mmt) cc_final: 0.8783 (mmt)
REVERT: C  177 GLN cc_start: 0.7521 (OUTLIER) cc_final: 0.7266 (tp40)
REVERT: C  213 GLU cc_start: 0.9031 (mt-10) cc_final: 0.8394 (tm-30)
REVERT: B   89 ARG cc_start: 0.8405 (mmm160) cc_final: 0.7714 (mtm-85)
REVERT: B  117 ASP cc_start: 0.8540 (m-30) cc_final: 0.8264 (m-30)
REVERT: B  156 MET cc_start: 0.9049 (mmp) cc_final: 0.8745 (mmp)
REVERT: B  239 LYS cc_start: 0.9341 (tppt) cc_final: 0.8966 (ttpt)
REVERT: E   32 GLN cc_start: 0.8543 (tt0) cc_final: 0.8212 (tp40)
REVERT: E   64 LYS cc_start: 0.8181 (tptt) cc_final: 0.7841 (mttm)
REVERT: E  110 GLU cc_start: 0.8734 (OUTLIER) cc_final: 0.8502 (tt0)
REVERT: E  156 MET cc_start: 0.8860 (OUTLIER) cc_final: 0.8591 (mmm)
REVERT: A   68 LYS cc_start: 0.8713 (OUTLIER) cc_final: 0.8254 (pttp)
REVERT: A   83 GLU cc_start: 0.8931 (OUTLIER) cc_final: 0.8629 (tm-30)
REVERT: A   97 GLU cc_start: 0.8813 (OUTLIER) cc_final: 0.8602 (pp20)
REVERT: A  110 GLU cc_start: 0.9055 (OUTLIER) cc_final: 0.8695 (mp0)
REVERT: A  119 THR cc_start: 0.8523 (p) cc_final: 0.8222 (p)
REVERT: A  233 ASN cc_start: 0.7352 (OUTLIER) cc_final: 0.6865 (p0)
REVERT: D   27 ILE cc_start: 0.8378 (mp) cc_final: 0.7987 (mt)
REVERT: D   89 ARG cc_start: 0.7458 (ttm-80) cc_final: 0.7201 (ttm-80)
REVERT: D  177 GLN cc_start: 0.7480 (OUTLIER) cc_final: 0.6918 (tm-30)
REVERT: D  205 SER cc_start: 0.9140 (t) cc_final: 0.8746 (p)
REVERT: D  213 GLU cc_start: 0.9507 (OUTLIER) cc_final: 0.9050 (mt-10)
REVERT: F   49 GLU cc_start: 0.8399 (OUTLIER) cc_final: 0.8133 (tp30)
REVERT: G   17 ARG cc_start: 0.8735 (OUTLIER) cc_final: 0.8467 (ptp-170)
REVERT: G   49 GLU cc_start: 0.7568 (OUTLIER) cc_final: 0.6587 (mt-10)
  outliers start: 123
  outliers final: 48
  residues processed: 397
  average time/residue: 0.2419
  time to fit residues: 126.7249
Evaluate side-chains
  273 residues out of total 1032 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 61
    poor density    : 212
  time to evaluate  : 1.217 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue  168 VAL
Chi-restraints excluded: chain C residue  169 LEU
Chi-restraints excluded: chain C residue  173 THR
Chi-restraints excluded: chain C residue  176 SER
Chi-restraints excluded: chain C residue  177 GLN
Chi-restraints excluded: chain C residue  182 ILE
Chi-restraints excluded: chain B residue  168 VAL
Chi-restraints excluded: chain B residue  178 LEU
Chi-restraints excluded: chain B residue  182 ILE
Chi-restraints excluded: chain B residue  195 SER
Chi-restraints excluded: chain E residue  110 GLU
Chi-restraints excluded: chain E residue  156 MET
Chi-restraints excluded: chain E residue  168 VAL
Chi-restraints excluded: chain E residue  169 LEU
Chi-restraints excluded: chain E residue  216 LEU
Chi-restraints excluded: chain A residue   30 LEU
Chi-restraints excluded: chain A residue   32 GLN
Chi-restraints excluded: chain A residue   34 THR
Chi-restraints excluded: chain A residue   68 LYS
Chi-restraints excluded: chain A residue   77 TRP
Chi-restraints excluded: chain A residue   83 GLU
Chi-restraints excluded: chain A residue   97 GLU
Chi-restraints excluded: chain A residue   99 LYS
Chi-restraints excluded: chain A residue  106 ILE
Chi-restraints excluded: chain A residue  110 GLU
Chi-restraints excluded: chain A residue  169 LEU
Chi-restraints excluded: chain A residue  174 ASP
Chi-restraints excluded: chain A residue  178 LEU
Chi-restraints excluded: chain A residue  181 SER
Chi-restraints excluded: chain A residue  184 VAL
Chi-restraints excluded: chain A residue  195 SER
Chi-restraints excluded: chain A residue  198 LEU
Chi-restraints excluded: chain A residue  233 ASN
Chi-restraints excluded: chain A residue  237 VAL
Chi-restraints excluded: chain D residue  166 ILE
Chi-restraints excluded: chain D residue  168 VAL
Chi-restraints excluded: chain D residue  177 GLN
Chi-restraints excluded: chain D residue  182 ILE
Chi-restraints excluded: chain D residue  184 VAL
Chi-restraints excluded: chain D residue  213 GLU
Chi-restraints excluded: chain F residue   19 MET
Chi-restraints excluded: chain F residue   20 ILE
Chi-restraints excluded: chain F residue   30 LEU
Chi-restraints excluded: chain F residue   39 MET
Chi-restraints excluded: chain F residue   41 ARG
Chi-restraints excluded: chain F residue   43 ASP
Chi-restraints excluded: chain F residue   45 SER
Chi-restraints excluded: chain F residue   49 GLU
Chi-restraints excluded: chain F residue   58 PHE
Chi-restraints excluded: chain G residue   13 SER
Chi-restraints excluded: chain G residue   17 ARG
Chi-restraints excluded: chain G residue   28 LEU
Chi-restraints excluded: chain G residue   29 LEU
Chi-restraints excluded: chain G residue   30 LEU
Chi-restraints excluded: chain G residue   31 ILE
Chi-restraints excluded: chain G residue   34 VAL
Chi-restraints excluded: chain G residue   39 MET
Chi-restraints excluded: chain G residue   40 SER
Chi-restraints excluded: chain G residue   43 ASP
Chi-restraints excluded: chain G residue   49 GLU
Chi-restraints excluded: chain G residue   50 VAL
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 122
   random chunks:
   chunk 103 optimal weight:    2.9990
   chunk 92 optimal weight:    3.9990
   chunk 51 optimal weight:    0.9980
   chunk 31 optimal weight:    2.9990
   chunk 62 optimal weight:    0.9990
   chunk 49 optimal weight:    0.7980
   chunk 95 optimal weight:    0.9990
   chunk 37 optimal weight:    2.9990
   chunk 58 optimal weight:    0.8980
   chunk 71 optimal weight:    3.9990
   chunk 110 optimal weight:    0.0060
   overall best weight:    0.7398

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

Flipped N/Q/H residues before XYZ refinement:
C  98 GLN
B 113 GLN
E 171 HIS
E 197 ASN
A  75 ASN
A 177 GLN
A 197 ASN
D  32 GLN
** D 171 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
D 177 GLN

Total number of N/Q/H flips: 9

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3543 r_free = 0.3543 target = 0.123430 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3177 r_free = 0.3177 target = 0.095975 restraints weight = 14046.191|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3234 r_free = 0.3234 target = 0.100038 restraints weight = 6503.883|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 44)----------------|
| r_work = 0.3269 r_free = 0.3269 target = 0.102684 restraints weight = 4107.347|
|-----------------------------------------------------------------------------|
r_work (final): 0.3253
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8012
moved from start:          0.3512

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   9738  Z= 0.158
  Angle     :  0.615   7.639  13207  Z= 0.324
  Chirality :  0.041   0.146   1593
  Planarity :  0.005   0.052   1673
  Dihedral  : 11.215  75.459   1453
  Min Nonbonded Distance : 2.560

Molprobity Statistics.
  All-atom Clashscore : 6.05
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.78 %
    Favored  : 98.22 %
  Rotamer:
    Outliers :  6.20 %
    Allowed  : 14.53 %
    Favored  : 79.26 %
  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:  1.65 (0.24), residues: 1235
  helix:  1.39 (0.16), residues: 1062
  sheet:  None (None), residues: 0
  loop : -0.43 (0.50), residues: 173

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.001   TRP G  18 
 HIS   0.027   0.001   HIS D 171 
 PHE   0.014   0.001   PHE D  31 
 TYR   0.014   0.002   TYR C 191 
 ARG   0.008   0.001   ARG G  41 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05513 (  763)
  hydrogen bonds       : angle       4.50604 ( 2250)
  covalent geometry    : bond        0.00304 ( 9738)
  covalent geometry    : angle       0.61548 (13207)

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

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

  2470 Ramachandran restraints generated.
    1235 Oldfield, 0 Emsley, 1235 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2470 Ramachandran restraints generated.
    1235 Oldfield, 0 Emsley, 1235 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  299 residues out of total 1032 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 64
    poor density    : 235
  time to evaluate  : 1.111 
Fit side-chains
   revert: symmetry clash
REVERT: C   50 SER cc_start: 0.9418 (t) cc_final: 0.8681 (p)
REVERT: C  124 VAL cc_start: 0.7804 (OUTLIER) cc_final: 0.7571 (p)
REVERT: C  177 GLN cc_start: 0.7838 (OUTLIER) cc_final: 0.7442 (mm-40)
REVERT: B   76 GLU cc_start: 0.7389 (mp0) cc_final: 0.6980 (mp0)
REVERT: B   77 TRP cc_start: 0.8901 (m-10) cc_final: 0.8139 (m-90)
REVERT: B   89 ARG cc_start: 0.7641 (mmm160) cc_final: 0.7327 (ttp80)
REVERT: B  140 ASP cc_start: 0.8330 (t70) cc_final: 0.7846 (t0)
REVERT: B  144 LYS cc_start: 0.8383 (mtpp) cc_final: 0.8130 (ttmm)
REVERT: B  156 MET cc_start: 0.8959 (mmp) cc_final: 0.8671 (mmp)
REVERT: B  239 LYS cc_start: 0.9111 (tppt) cc_final: 0.8331 (ttpt)
REVERT: E   64 LYS cc_start: 0.7786 (tptt) cc_final: 0.7452 (mttm)
REVERT: E   71 ARG cc_start: 0.6900 (mmm160) cc_final: 0.6546 (mtt180)
REVERT: E  126 GLN cc_start: 0.8551 (tm-30) cc_final: 0.8231 (tm-30)
REVERT: E  167 GLN cc_start: 0.8283 (mm-40) cc_final: 0.8021 (tp-100)
REVERT: A   83 GLU cc_start: 0.8555 (OUTLIER) cc_final: 0.8293 (tm-30)
REVERT: A  205 SER cc_start: 0.8403 (t) cc_final: 0.8053 (p)
REVERT: A  206 LYS cc_start: 0.8510 (ttpt) cc_final: 0.8197 (tttt)
REVERT: A  218 MET cc_start: 0.8636 (mtt) cc_final: 0.8417 (mtp)
REVERT: A  233 ASN cc_start: 0.5679 (OUTLIER) cc_final: 0.5067 (p0)
REVERT: D   10 ILE cc_start: 0.7973 (mm) cc_final: 0.7749 (mt)
REVERT: D  174 ASP cc_start: 0.7547 (m-30) cc_final: 0.7227 (m-30)
REVERT: D  213 GLU cc_start: 0.8397 (OUTLIER) cc_final: 0.7947 (mt-10)
REVERT: F   19 MET cc_start: 0.7880 (ptp) cc_final: 0.7658 (ptt)
REVERT: G   49 GLU cc_start: 0.7675 (OUTLIER) cc_final: 0.6319 (mt-10)
  outliers start: 64
  outliers final: 23
  residues processed: 276
  average time/residue: 0.2348
  time to fit residues: 87.8831
Evaluate side-chains
  232 residues out of total 1032 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 203
  time to evaluate  : 0.977 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue   56 ILE
Chi-restraints excluded: chain C residue  124 VAL
Chi-restraints excluded: chain C residue  177 GLN
Chi-restraints excluded: chain B residue   27 ILE
Chi-restraints excluded: chain B residue   73 GLU
Chi-restraints excluded: chain B residue  158 ILE
Chi-restraints excluded: chain B residue  178 LEU
Chi-restraints excluded: chain B residue  195 SER
Chi-restraints excluded: chain B residue  203 ILE
Chi-restraints excluded: chain E residue  169 LEU
Chi-restraints excluded: chain E residue  195 SER
Chi-restraints excluded: chain E residue  233 ASN
Chi-restraints excluded: chain A residue   30 LEU
Chi-restraints excluded: chain A residue   77 TRP
Chi-restraints excluded: chain A residue   83 GLU
Chi-restraints excluded: chain A residue   93 VAL
Chi-restraints excluded: chain A residue  106 ILE
Chi-restraints excluded: chain A residue  169 LEU
Chi-restraints excluded: chain A residue  195 SER
Chi-restraints excluded: chain A residue  233 ASN
Chi-restraints excluded: chain A residue  237 VAL
Chi-restraints excluded: chain D residue  147 GLU
Chi-restraints excluded: chain D residue  181 SER
Chi-restraints excluded: chain D residue  184 VAL
Chi-restraints excluded: chain D residue  213 GLU
Chi-restraints excluded: chain D residue  235 LEU
Chi-restraints excluded: chain G residue   31 ILE
Chi-restraints excluded: chain G residue   34 VAL
Chi-restraints excluded: chain G residue   49 GLU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 122
   random chunks:
   chunk 75 optimal weight:    9.9990
   chunk 76 optimal weight:    1.9990
   chunk 71 optimal weight:    4.9990
   chunk 22 optimal weight:   10.0000
   chunk 51 optimal weight:    2.9990
   chunk 58 optimal weight:    2.9990
   chunk 80 optimal weight:    0.9990
   chunk 60 optimal weight:    0.9990
   chunk 11 optimal weight:    0.6980
   chunk 3 optimal weight:    0.8980
   chunk 70 optimal weight:    0.7980
   overall best weight:    0.8784

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

Flipped N/Q/H residues before XYZ refinement:
B 121 GLN
B 229 GLN
E 171 HIS
A  75 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3529 r_free = 0.3529 target = 0.121874 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3171 r_free = 0.3171 target = 0.094949 restraints weight = 13925.539|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 42)----------------|
| r_work = 0.3225 r_free = 0.3225 target = 0.098873 restraints weight = 6431.775|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3259 r_free = 0.3259 target = 0.101395 restraints weight = 4055.088|
|-----------------------------------------------------------------------------|
r_work (final): 0.3264
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8041
moved from start:          0.4270

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   9738  Z= 0.129
  Angle     :  0.543   8.579  13207  Z= 0.279
  Chirality :  0.038   0.140   1593
  Planarity :  0.004   0.046   1673
  Dihedral  :  7.199  64.289   1360
  Min Nonbonded Distance : 2.579

Molprobity Statistics.
  All-atom Clashscore : 5.44
  Ramachandran Plot:
    Outliers :  0.08 %
    Allowed  :  1.46 %
    Favored  : 98.46 %
  Rotamer:
    Outliers :  3.68 %
    Allowed  : 19.67 %
    Favored  : 76.65 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.51 (0.25), residues: 1235
  helix:  2.01 (0.16), residues: 1049
  sheet:  None (None), residues: 0
  loop : -0.26 (0.47), residues: 186

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP E  77 
 HIS   0.002   0.001   HIS B  54 
 PHE   0.011   0.001   PHE G  33 
 TYR   0.012   0.001   TYR F  47 
 ARG   0.006   0.001   ARG F  41 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04712 (  763)
  hydrogen bonds       : angle       4.09189 ( 2250)
  covalent geometry    : bond        0.00265 ( 9738)
  covalent geometry    : angle       0.54281 (13207)

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

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

  2470 Ramachandran restraints generated.
    1235 Oldfield, 0 Emsley, 1235 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2470 Ramachandran restraints generated.
    1235 Oldfield, 0 Emsley, 1235 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  249 residues out of total 1032 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 38
    poor density    : 211
  time to evaluate  : 1.087 
Fit side-chains
   revert: symmetry clash
REVERT: C  117 ASP cc_start: 0.7719 (OUTLIER) cc_final: 0.7244 (m-30)
REVERT: C  177 GLN cc_start: 0.7827 (OUTLIER) cc_final: 0.7391 (mm-40)
REVERT: B   73 GLU cc_start: 0.7539 (OUTLIER) cc_final: 0.6637 (pm20)
REVERT: B   77 TRP cc_start: 0.8805 (m-10) cc_final: 0.8138 (m-90)
REVERT: B   86 MET cc_start: 0.8314 (mmm) cc_final: 0.7401 (mtm)
REVERT: B  239 LYS cc_start: 0.9068 (tppt) cc_final: 0.8350 (ttpt)
REVERT: E   64 LYS cc_start: 0.7761 (tptt) cc_final: 0.7394 (mttm)
REVERT: E  113 GLN cc_start: 0.8195 (mt0) cc_final: 0.7958 (mt0)
REVERT: E  156 MET cc_start: 0.9131 (mpp) cc_final: 0.8732 (mmm)
REVERT: E  219 GLU cc_start: 0.8440 (mm-30) cc_final: 0.8106 (mt-10)
REVERT: A   70 ASN cc_start: 0.8065 (p0) cc_final: 0.7248 (t0)
REVERT: A  205 SER cc_start: 0.8349 (t) cc_final: 0.8106 (p)
REVERT: A  206 LYS cc_start: 0.8496 (ttpt) cc_final: 0.8269 (tttt)
REVERT: A  218 MET cc_start: 0.8665 (mtt) cc_final: 0.8451 (mtm)
REVERT: A  220 MET cc_start: 0.8595 (ttp) cc_final: 0.8293 (tmm)
REVERT: A  233 ASN cc_start: 0.5690 (OUTLIER) cc_final: 0.5142 (p0)
REVERT: D   10 ILE cc_start: 0.8040 (mm) cc_final: 0.7806 (mt)
REVERT: D  174 ASP cc_start: 0.7558 (m-30) cc_final: 0.7232 (m-30)
REVERT: D  213 GLU cc_start: 0.8307 (OUTLIER) cc_final: 0.7872 (mt-10)
REVERT: F   19 MET cc_start: 0.7864 (ptp) cc_final: 0.7570 (ptt)
REVERT: F   41 ARG cc_start: 0.7697 (ttp-110) cc_final: 0.7483 (mtm-85)
  outliers start: 38
  outliers final: 22
  residues processed: 240
  average time/residue: 0.2307
  time to fit residues: 75.0928
Evaluate side-chains
  220 residues out of total 1032 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 193
  time to evaluate  : 0.974 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue   27 ILE
Chi-restraints excluded: chain C residue   86 MET
Chi-restraints excluded: chain C residue  117 ASP
Chi-restraints excluded: chain C residue  177 GLN
Chi-restraints excluded: chain C residue  195 SER
Chi-restraints excluded: chain B residue   27 ILE
Chi-restraints excluded: chain B residue   73 GLU
Chi-restraints excluded: chain B residue  158 ILE
Chi-restraints excluded: chain B residue  195 SER
Chi-restraints excluded: chain B residue  203 ILE
Chi-restraints excluded: chain B residue  211 SER
Chi-restraints excluded: chain B residue  236 LEU
Chi-restraints excluded: chain E residue  133 ASP
Chi-restraints excluded: chain E residue  169 LEU
Chi-restraints excluded: chain E residue  195 SER
Chi-restraints excluded: chain A residue   77 TRP
Chi-restraints excluded: chain A residue  106 ILE
Chi-restraints excluded: chain A residue  169 LEU
Chi-restraints excluded: chain A residue  184 VAL
Chi-restraints excluded: chain A residue  233 ASN
Chi-restraints excluded: chain D residue  147 GLU
Chi-restraints excluded: chain D residue  181 SER
Chi-restraints excluded: chain D residue  213 GLU
Chi-restraints excluded: chain D residue  226 LEU
Chi-restraints excluded: chain D residue  235 LEU
Chi-restraints excluded: chain G residue   20 ILE
Chi-restraints excluded: chain G residue   31 ILE
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 122
   random chunks:
   chunk 69 optimal weight:    2.9990
   chunk 73 optimal weight:    0.9990
   chunk 95 optimal weight:    0.9980
   chunk 102 optimal weight:    0.9990
   chunk 32 optimal weight:    8.9990
   chunk 86 optimal weight:    4.9990
   chunk 56 optimal weight:    0.5980
   chunk 109 optimal weight:    2.9990
   chunk 6 optimal weight:    3.9990
   chunk 0 optimal weight:   10.0000
   chunk 57 optimal weight:    0.9980
   overall best weight:    0.9184

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

Flipped N/Q/H residues before XYZ refinement:
C 177 GLN
** E 103 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
E 171 HIS
A  75 ASN
** A 103 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3560 r_free = 0.3560 target = 0.121981 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3189 r_free = 0.3189 target = 0.094588 restraints weight = 14359.670|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 42)----------------|
| r_work = 0.3242 r_free = 0.3242 target = 0.098353 restraints weight = 6853.121|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 47)----------------|
| r_work = 0.3276 r_free = 0.3276 target = 0.100796 restraints weight = 4426.812|
|-----------------------------------------------------------------------------|
r_work (final): 0.3275
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8076
moved from start:          0.4581

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.027   9738  Z= 0.125
  Angle     :  0.537   8.627  13207  Z= 0.272
  Chirality :  0.037   0.134   1593
  Planarity :  0.004   0.047   1673
  Dihedral  :  5.840  63.655   1346
  Min Nonbonded Distance : 2.570

Molprobity Statistics.
  All-atom Clashscore : 5.13
  Ramachandran Plot:
    Outliers :  0.08 %
    Allowed  :  1.70 %
    Favored  : 98.22 %
  Rotamer:
    Outliers :  3.00 %
    Allowed  : 21.22 %
    Favored  : 75.78 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.80 (0.25), residues: 1235
  helix:  2.23 (0.16), residues: 1047
  sheet:  None (None), residues: 0
  loop : -0.33 (0.46), residues: 188

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP E  77 
 HIS   0.007   0.001   HIS A 103 
 PHE   0.011   0.001   PHE G  33 
 TYR   0.013   0.001   TYR G  47 
 ARG   0.004   0.000   ARG B  90 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04370 (  763)
  hydrogen bonds       : angle       3.89471 ( 2250)
  covalent geometry    : bond        0.00263 ( 9738)
  covalent geometry    : angle       0.53675 (13207)

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

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

  2470 Ramachandran restraints generated.
    1235 Oldfield, 0 Emsley, 1235 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2470 Ramachandran restraints generated.
    1235 Oldfield, 0 Emsley, 1235 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  238 residues out of total 1032 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 207
  time to evaluate  : 1.087 
Fit side-chains
   revert: symmetry clash
REVERT: C   64 LYS cc_start: 0.8200 (ttmm) cc_final: 0.7785 (ttmt)
REVERT: C  117 ASP cc_start: 0.7692 (OUTLIER) cc_final: 0.7184 (m-30)
REVERT: B   68 LYS cc_start: 0.8917 (ttmt) cc_final: 0.8590 (ttmm)
REVERT: B   73 GLU cc_start: 0.7420 (OUTLIER) cc_final: 0.6561 (pm20)
REVERT: B   77 TRP cc_start: 0.8778 (m-10) cc_final: 0.8243 (m-90)
REVERT: E   64 LYS cc_start: 0.7765 (tptt) cc_final: 0.7409 (mttm)
REVERT: E  113 GLN cc_start: 0.8139 (mt0) cc_final: 0.7885 (mt0)
REVERT: E  128 MET cc_start: 0.8838 (mmm) cc_final: 0.8533 (mtp)
REVERT: E  156 MET cc_start: 0.9142 (mpp) cc_final: 0.8702 (mmm)
REVERT: E  219 GLU cc_start: 0.8373 (mm-30) cc_final: 0.8059 (mt-10)
REVERT: A   70 ASN cc_start: 0.7987 (p0) cc_final: 0.7206 (t0)
REVERT: A   98 GLN cc_start: 0.7800 (pp30) cc_final: 0.7547 (tp-100)
REVERT: A  205 SER cc_start: 0.8450 (t) cc_final: 0.8183 (p)
REVERT: A  206 LYS cc_start: 0.8553 (ttpt) cc_final: 0.8347 (tttt)
REVERT: A  218 MET cc_start: 0.8694 (mtt) cc_final: 0.8448 (mtm)
REVERT: A  220 MET cc_start: 0.8755 (ttp) cc_final: 0.8520 (tmm)
REVERT: A  233 ASN cc_start: 0.5565 (OUTLIER) cc_final: 0.5048 (p0)
REVERT: D   10 ILE cc_start: 0.8080 (mm) cc_final: 0.7863 (mt)
REVERT: D  174 ASP cc_start: 0.7536 (m-30) cc_final: 0.7265 (m-30)
REVERT: D  213 GLU cc_start: 0.8202 (OUTLIER) cc_final: 0.7786 (mt-10)
REVERT: F   19 MET cc_start: 0.7817 (ptp) cc_final: 0.7488 (ptt)
  outliers start: 31
  outliers final: 19
  residues processed: 227
  average time/residue: 0.2230
  time to fit residues: 69.1706
Evaluate side-chains
  215 residues out of total 1032 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 192
  time to evaluate  : 1.010 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue   56 ILE
Chi-restraints excluded: chain C residue  117 ASP
Chi-restraints excluded: chain C residue  195 SER
Chi-restraints excluded: chain B residue   27 ILE
Chi-restraints excluded: chain B residue   73 GLU
Chi-restraints excluded: chain B residue  120 ASP
Chi-restraints excluded: chain B residue  158 ILE
Chi-restraints excluded: chain B residue  203 ILE
Chi-restraints excluded: chain B residue  236 LEU
Chi-restraints excluded: chain E residue  169 LEU
Chi-restraints excluded: chain E residue  195 SER
Chi-restraints excluded: chain A residue   77 TRP
Chi-restraints excluded: chain A residue  106 ILE
Chi-restraints excluded: chain A residue  169 LEU
Chi-restraints excluded: chain A residue  184 VAL
Chi-restraints excluded: chain A residue  198 LEU
Chi-restraints excluded: chain A residue  233 ASN
Chi-restraints excluded: chain D residue  213 GLU
Chi-restraints excluded: chain D residue  226 LEU
Chi-restraints excluded: chain D residue  235 LEU
Chi-restraints excluded: chain F residue   54 LEU
Chi-restraints excluded: chain G residue   20 ILE
Chi-restraints excluded: chain G residue   31 ILE
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 122
   random chunks:
   chunk 119 optimal weight:    1.9990
   chunk 23 optimal weight:    0.9980
   chunk 90 optimal weight:    3.9990
   chunk 52 optimal weight:    3.9990
   chunk 10 optimal weight:    1.9990
   chunk 11 optimal weight:    0.8980
   chunk 110 optimal weight:    2.9990
   chunk 0 optimal weight:    8.9990
   chunk 40 optimal weight:    0.6980
   chunk 48 optimal weight:    2.9990
   chunk 61 optimal weight:    9.9990
   overall best weight:    1.3184

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

Flipped N/Q/H residues before XYZ refinement:
** E 103 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
E 171 HIS
A  75 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3537 r_free = 0.3537 target = 0.120163 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 28)----------------|
| r_work = 0.3158 r_free = 0.3158 target = 0.092504 restraints weight = 14456.404|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 41)----------------|
| r_work = 0.3209 r_free = 0.3209 target = 0.096152 restraints weight = 7012.266|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3242 r_free = 0.3242 target = 0.098530 restraints weight = 4574.219|
|-----------------------------------------------------------------------------|
r_work (final): 0.3243
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8118
moved from start:          0.4719

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   9738  Z= 0.136
  Angle     :  0.547   7.376  13207  Z= 0.277
  Chirality :  0.038   0.138   1593
  Planarity :  0.004   0.046   1673
  Dihedral  :  5.578  65.020   1342
  Min Nonbonded Distance : 2.544

Molprobity Statistics.
  All-atom Clashscore : 5.33
  Ramachandran Plot:
    Outliers :  0.08 %
    Allowed  :  1.78 %
    Favored  : 98.14 %
  Rotamer:
    Outliers :  3.10 %
    Allowed  : 22.29 %
    Favored  : 74.61 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.91 (0.25), residues: 1235
  helix:  2.33 (0.16), residues: 1048
  sheet:  None (None), residues: 0
  loop : -0.47 (0.46), residues: 187

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP E  77 
 HIS   0.009   0.001   HIS A 103 
 PHE   0.007   0.001   PHE G  33 
 TYR   0.009   0.001   TYR A  51 
 ARG   0.004   0.000   ARG A  57 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04485 (  763)
  hydrogen bonds       : angle       3.88248 ( 2250)
  covalent geometry    : bond        0.00311 ( 9738)
  covalent geometry    : angle       0.54739 (13207)

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

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

  2470 Ramachandran restraints generated.
    1235 Oldfield, 0 Emsley, 1235 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2470 Ramachandran restraints generated.
    1235 Oldfield, 0 Emsley, 1235 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  229 residues out of total 1032 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 197
  time to evaluate  : 1.166 
Fit side-chains
   revert: symmetry clash
REVERT: C   64 LYS cc_start: 0.8157 (ttmm) cc_final: 0.7748 (ttmt)
REVERT: C  117 ASP cc_start: 0.7683 (m-30) cc_final: 0.7217 (m-30)
REVERT: C  177 GLN cc_start: 0.7864 (tt0) cc_final: 0.7407 (mm-40)
REVERT: B   68 LYS cc_start: 0.8913 (ttmt) cc_final: 0.8617 (ttmm)
REVERT: B   73 GLU cc_start: 0.7437 (OUTLIER) cc_final: 0.6714 (pm20)
REVERT: B   77 TRP cc_start: 0.8757 (m-10) cc_final: 0.8179 (m-90)
REVERT: B   86 MET cc_start: 0.8377 (mmm) cc_final: 0.7399 (mtm)
REVERT: B  239 LYS cc_start: 0.9295 (tppt) cc_final: 0.8228 (ttpt)
REVERT: E   64 LYS cc_start: 0.7791 (tptt) cc_final: 0.7404 (mttm)
REVERT: E  219 GLU cc_start: 0.8426 (mm-30) cc_final: 0.8106 (mt-10)
REVERT: A   67 PHE cc_start: 0.8515 (m-80) cc_final: 0.8261 (m-10)
REVERT: A  206 LYS cc_start: 0.8612 (ttpt) cc_final: 0.8388 (tttt)
REVERT: A  220 MET cc_start: 0.8781 (ttp) cc_final: 0.8569 (tmm)
REVERT: A  233 ASN cc_start: 0.5716 (OUTLIER) cc_final: 0.5111 (p0)
REVERT: D  167 GLN cc_start: 0.7826 (tp40) cc_final: 0.7476 (tt0)
REVERT: D  174 ASP cc_start: 0.7510 (m-30) cc_final: 0.7224 (m-30)
REVERT: D  213 GLU cc_start: 0.8221 (OUTLIER) cc_final: 0.7737 (mt-10)
REVERT: F   19 MET cc_start: 0.7814 (ptp) cc_final: 0.7457 (ptt)
  outliers start: 32
  outliers final: 23
  residues processed: 219
  average time/residue: 0.2341
  time to fit residues: 69.9865
Evaluate side-chains
  215 residues out of total 1032 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 189
  time to evaluate  : 1.010 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue   56 ILE
Chi-restraints excluded: chain C residue   74 VAL
Chi-restraints excluded: chain C residue   86 MET
Chi-restraints excluded: chain C residue  173 THR
Chi-restraints excluded: chain C residue  195 SER
Chi-restraints excluded: chain B residue   27 ILE
Chi-restraints excluded: chain B residue   73 GLU
Chi-restraints excluded: chain B residue  120 ASP
Chi-restraints excluded: chain B residue  158 ILE
Chi-restraints excluded: chain B residue  203 ILE
Chi-restraints excluded: chain B residue  211 SER
Chi-restraints excluded: chain B residue  236 LEU
Chi-restraints excluded: chain E residue  133 ASP
Chi-restraints excluded: chain E residue  169 LEU
Chi-restraints excluded: chain E residue  195 SER
Chi-restraints excluded: chain A residue   77 TRP
Chi-restraints excluded: chain A residue  106 ILE
Chi-restraints excluded: chain A residue  184 VAL
Chi-restraints excluded: chain A residue  195 SER
Chi-restraints excluded: chain A residue  233 ASN
Chi-restraints excluded: chain D residue  213 GLU
Chi-restraints excluded: chain D residue  226 LEU
Chi-restraints excluded: chain D residue  235 LEU
Chi-restraints excluded: chain G residue   20 ILE
Chi-restraints excluded: chain G residue   31 ILE
Chi-restraints excluded: chain G residue   60 SER
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 122
   random chunks:
   chunk 110 optimal weight:    0.7980
   chunk 7 optimal weight:    2.9990
   chunk 38 optimal weight:    4.9990
   chunk 2 optimal weight:    0.9980
   chunk 32 optimal weight:    2.9990
   chunk 16 optimal weight:    2.9990
   chunk 15 optimal weight:    1.9990
   chunk 34 optimal weight:    0.9990
   chunk 78 optimal weight:    7.9990
   chunk 68 optimal weight:    1.9990
   chunk 76 optimal weight:    1.9990
   overall best weight:    1.3586

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

Flipped N/Q/H residues before XYZ refinement:
** E 103 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
E 171 HIS
A  75 ASN
D 242 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3533 r_free = 0.3533 target = 0.119898 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3158 r_free = 0.3158 target = 0.092466 restraints weight = 14421.369|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3209 r_free = 0.3209 target = 0.096055 restraints weight = 6968.961|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3241 r_free = 0.3241 target = 0.098445 restraints weight = 4535.302|
|-----------------------------------------------------------------------------|
r_work (final): 0.3242
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8121
moved from start:          0.4848

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   9738  Z= 0.135
  Angle     :  0.539   7.274  13207  Z= 0.274
  Chirality :  0.038   0.143   1593
  Planarity :  0.004   0.048   1673
  Dihedral  :  5.347  65.079   1340
  Min Nonbonded Distance : 2.526

Molprobity Statistics.
  All-atom Clashscore : 4.98
  Ramachandran Plot:
    Outliers :  0.08 %
    Allowed  :  1.78 %
    Favored  : 98.14 %
  Rotamer:
    Outliers :  3.88 %
    Allowed  : 22.97 %
    Favored  : 73.16 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.98 (0.25), residues: 1235
  helix:  2.38 (0.16), residues: 1051
  sheet:  None (None), residues: 0
  loop : -0.54 (0.46), residues: 184

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP D  77 
 HIS   0.008   0.001   HIS A 103 
 PHE   0.007   0.001   PHE G  33 
 TYR   0.009   0.001   TYR A  51 
 ARG   0.004   0.000   ARG B  90 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04463 (  763)
  hydrogen bonds       : angle       3.86230 ( 2250)
  covalent geometry    : bond        0.00310 ( 9738)
  covalent geometry    : angle       0.53949 (13207)

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

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

  2470 Ramachandran restraints generated.
    1235 Oldfield, 0 Emsley, 1235 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2470 Ramachandran restraints generated.
    1235 Oldfield, 0 Emsley, 1235 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  230 residues out of total 1032 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 40
    poor density    : 190
  time to evaluate  : 0.983 
Fit side-chains
REVERT: C   64 LYS cc_start: 0.8170 (ttmm) cc_final: 0.7747 (ttmt)
REVERT: C  117 ASP cc_start: 0.7693 (OUTLIER) cc_final: 0.7217 (m-30)
REVERT: B   68 LYS cc_start: 0.8891 (ttmt) cc_final: 0.8550 (ttmm)
REVERT: B   73 GLU cc_start: 0.7396 (OUTLIER) cc_final: 0.6659 (pm20)
REVERT: B   77 TRP cc_start: 0.8749 (m-10) cc_final: 0.8107 (m-90)
REVERT: B  239 LYS cc_start: 0.9316 (tppt) cc_final: 0.8378 (ttpt)
REVERT: E   64 LYS cc_start: 0.7788 (tptt) cc_final: 0.7401 (mttm)
REVERT: E  219 GLU cc_start: 0.8449 (mm-30) cc_final: 0.8130 (mt-10)
REVERT: A   67 PHE cc_start: 0.8470 (m-80) cc_final: 0.8207 (m-10)
REVERT: A  206 LYS cc_start: 0.8604 (ttpt) cc_final: 0.8400 (tttt)
REVERT: A  218 MET cc_start: 0.8734 (mtt) cc_final: 0.8456 (mtm)
REVERT: A  233 ASN cc_start: 0.5703 (OUTLIER) cc_final: 0.5065 (p0)
REVERT: D  174 ASP cc_start: 0.7520 (m-30) cc_final: 0.7219 (m-30)
REVERT: D  213 GLU cc_start: 0.8175 (OUTLIER) cc_final: 0.7615 (mt-10)
REVERT: F   19 MET cc_start: 0.7799 (ptp) cc_final: 0.7427 (ptt)
REVERT: F   39 MET cc_start: 0.8355 (tpp) cc_final: 0.8109 (mmp)
REVERT: F   41 ARG cc_start: 0.6837 (ptp-110) cc_final: 0.6325 (ptp90)
  outliers start: 40
  outliers final: 24
  residues processed: 222
  average time/residue: 0.2312
  time to fit residues: 69.4515
Evaluate side-chains
  215 residues out of total 1032 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 187
  time to evaluate  : 1.142 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue   56 ILE
Chi-restraints excluded: chain C residue   74 VAL
Chi-restraints excluded: chain C residue   86 MET
Chi-restraints excluded: chain C residue  117 ASP
Chi-restraints excluded: chain C residue  119 THR
Chi-restraints excluded: chain C residue  173 THR
Chi-restraints excluded: chain C residue  195 SER
Chi-restraints excluded: chain B residue   27 ILE
Chi-restraints excluded: chain B residue   73 GLU
Chi-restraints excluded: chain B residue  120 ASP
Chi-restraints excluded: chain B residue  158 ILE
Chi-restraints excluded: chain B residue  203 ILE
Chi-restraints excluded: chain B residue  211 SER
Chi-restraints excluded: chain B residue  236 LEU
Chi-restraints excluded: chain E residue  169 LEU
Chi-restraints excluded: chain E residue  195 SER
Chi-restraints excluded: chain A residue   77 TRP
Chi-restraints excluded: chain A residue  106 ILE
Chi-restraints excluded: chain A residue  184 VAL
Chi-restraints excluded: chain A residue  195 SER
Chi-restraints excluded: chain A residue  233 ASN
Chi-restraints excluded: chain D residue  184 VAL
Chi-restraints excluded: chain D residue  213 GLU
Chi-restraints excluded: chain D residue  226 LEU
Chi-restraints excluded: chain D residue  235 LEU
Chi-restraints excluded: chain D residue  246 THR
Chi-restraints excluded: chain G residue   20 ILE
Chi-restraints excluded: chain G residue   31 ILE
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 122
   random chunks:
   chunk 98 optimal weight:    1.9990
   chunk 120 optimal weight:    6.9990
   chunk 51 optimal weight:    0.9990
   chunk 80 optimal weight:    1.9990
   chunk 11 optimal weight:    0.9990
   chunk 37 optimal weight:    0.7980
   chunk 18 optimal weight:    0.7980
   chunk 63 optimal weight:    0.8980
   chunk 79 optimal weight:    0.9990
   chunk 5 optimal weight:    1.9990
   chunk 68 optimal weight:    7.9990
   overall best weight:    0.8984

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

Flipped N/Q/H residues before XYZ refinement:
** E 103 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
E 171 HIS
A  75 ASN
D 242 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3558 r_free = 0.3558 target = 0.122056 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3187 r_free = 0.3187 target = 0.094500 restraints weight = 14390.135|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3237 r_free = 0.3237 target = 0.098177 restraints weight = 6902.279|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.3270 r_free = 0.3270 target = 0.100592 restraints weight = 4478.863|
|-----------------------------------------------------------------------------|
r_work (final): 0.3271
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8086
moved from start:          0.5049

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   9738  Z= 0.119
  Angle     :  0.523   7.196  13207  Z= 0.264
  Chirality :  0.037   0.146   1593
  Planarity :  0.004   0.049   1673
  Dihedral  :  5.195  61.755   1340
  Min Nonbonded Distance : 2.525

Molprobity Statistics.
  All-atom Clashscore : 4.72
  Ramachandran Plot:
    Outliers :  0.08 %
    Allowed  :  1.70 %
    Favored  : 98.22 %
  Rotamer:
    Outliers :  3.00 %
    Allowed  : 23.26 %
    Favored  : 73.74 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  3.12 (0.25), residues: 1235
  helix:  2.50 (0.16), residues: 1047
  sheet:  None (None), residues: 0
  loop : -0.54 (0.45), residues: 188

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP D  22 
 HIS   0.007   0.001   HIS A 103 
 PHE   0.007   0.001   PHE G  33 
 TYR   0.007   0.001   TYR A  51 
 ARG   0.005   0.000   ARG B  90 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04132 (  763)
  hydrogen bonds       : angle       3.76730 ( 2250)
  covalent geometry    : bond        0.00258 ( 9738)
  covalent geometry    : angle       0.52344 (13207)

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

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

  2470 Ramachandran restraints generated.
    1235 Oldfield, 0 Emsley, 1235 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2470 Ramachandran restraints generated.
    1235 Oldfield, 0 Emsley, 1235 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  229 residues out of total 1032 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 198
  time to evaluate  : 1.958 
Fit side-chains
REVERT: C   64 LYS cc_start: 0.8096 (ttmm) cc_final: 0.7674 (ttmt)
REVERT: C   80 ASP cc_start: 0.7568 (m-30) cc_final: 0.7227 (m-30)
REVERT: C  117 ASP cc_start: 0.7644 (m-30) cc_final: 0.7182 (m-30)
REVERT: B   68 LYS cc_start: 0.8864 (ttmt) cc_final: 0.8494 (ttmm)
REVERT: B   73 GLU cc_start: 0.7322 (OUTLIER) cc_final: 0.6662 (pm20)
REVERT: B   77 TRP cc_start: 0.8718 (m-10) cc_final: 0.8052 (m-90)
REVERT: B   86 MET cc_start: 0.8537 (tpp) cc_final: 0.7579 (mtm)
REVERT: B  191 TYR cc_start: 0.8723 (m-10) cc_final: 0.8484 (m-10)
REVERT: B  239 LYS cc_start: 0.9294 (tppt) cc_final: 0.8382 (ttpt)
REVERT: E   64 LYS cc_start: 0.7779 (tptt) cc_final: 0.7387 (mttm)
REVERT: E  151 SER cc_start: 0.8927 (m) cc_final: 0.8715 (t)
REVERT: E  219 GLU cc_start: 0.8379 (mm-30) cc_final: 0.8084 (mt-10)
REVERT: A   67 PHE cc_start: 0.8411 (m-80) cc_final: 0.8182 (m-10)
REVERT: A  233 ASN cc_start: 0.5649 (OUTLIER) cc_final: 0.4996 (p0)
REVERT: D  167 GLN cc_start: 0.8131 (tp40) cc_final: 0.7848 (tp40)
REVERT: D  174 ASP cc_start: 0.7533 (m-30) cc_final: 0.7237 (m-30)
REVERT: D  213 GLU cc_start: 0.8099 (OUTLIER) cc_final: 0.7550 (mt-10)
REVERT: F   19 MET cc_start: 0.7741 (ptp) cc_final: 0.7354 (ptt)
REVERT: F   39 MET cc_start: 0.8328 (tpp) cc_final: 0.7407 (mmm)
REVERT: F   41 ARG cc_start: 0.6852 (ptp-110) cc_final: 0.6362 (ptp90)
  outliers start: 31
  outliers final: 22
  residues processed: 223
  average time/residue: 0.2487
  time to fit residues: 75.3097
Evaluate side-chains
  214 residues out of total 1032 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 189
  time to evaluate  : 0.956 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue   56 ILE
Chi-restraints excluded: chain C residue   74 VAL
Chi-restraints excluded: chain C residue   86 MET
Chi-restraints excluded: chain C residue  173 THR
Chi-restraints excluded: chain C residue  195 SER
Chi-restraints excluded: chain B residue   27 ILE
Chi-restraints excluded: chain B residue   73 GLU
Chi-restraints excluded: chain B residue  120 ASP
Chi-restraints excluded: chain B residue  158 ILE
Chi-restraints excluded: chain B residue  203 ILE
Chi-restraints excluded: chain B residue  211 SER
Chi-restraints excluded: chain B residue  236 LEU
Chi-restraints excluded: chain E residue  169 LEU
Chi-restraints excluded: chain E residue  195 SER
Chi-restraints excluded: chain A residue   30 LEU
Chi-restraints excluded: chain A residue   77 TRP
Chi-restraints excluded: chain A residue  106 ILE
Chi-restraints excluded: chain A residue  184 VAL
Chi-restraints excluded: chain A residue  233 ASN
Chi-restraints excluded: chain D residue  213 GLU
Chi-restraints excluded: chain D residue  226 LEU
Chi-restraints excluded: chain D residue  235 LEU
Chi-restraints excluded: chain D residue  246 THR
Chi-restraints excluded: chain G residue   20 ILE
Chi-restraints excluded: chain G residue   31 ILE
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 122
   random chunks:
   chunk 43 optimal weight:    4.9990
   chunk 19 optimal weight:    0.8980
   chunk 72 optimal weight:    4.9990
   chunk 97 optimal weight:    4.9990
   chunk 10 optimal weight:    0.7980
   chunk 99 optimal weight:    9.9990
   chunk 51 optimal weight:    0.3980
   chunk 106 optimal weight:    4.9990
   chunk 111 optimal weight:    0.6980
   chunk 1 optimal weight:    2.9990
   chunk 112 optimal weight:    0.9990
   overall best weight:    0.7582

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

Flipped N/Q/H residues before XYZ refinement:
** E 103 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
E 171 HIS
D 242 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3567 r_free = 0.3567 target = 0.122765 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3196 r_free = 0.3196 target = 0.095210 restraints weight = 14574.742|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.3248 r_free = 0.3248 target = 0.099010 restraints weight = 6939.100|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3281 r_free = 0.3281 target = 0.101448 restraints weight = 4469.595|
|-----------------------------------------------------------------------------|
r_work (final): 0.3281
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8073
moved from start:          0.5181

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.036   9738  Z= 0.115
  Angle     :  0.526   7.410  13207  Z= 0.264
  Chirality :  0.037   0.142   1593
  Planarity :  0.004   0.050   1673
  Dihedral  :  5.046  60.306   1340
  Min Nonbonded Distance : 2.512

Molprobity Statistics.
  All-atom Clashscore : 4.67
  Ramachandran Plot:
    Outliers :  0.08 %
    Allowed  :  1.62 %
    Favored  : 98.30 %
  Rotamer:
    Outliers :  3.49 %
    Allowed  : 22.87 %
    Favored  : 73.64 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  3.21 (0.25), residues: 1235
  helix:  2.56 (0.16), residues: 1051
  sheet:  None (None), residues: 0
  loop : -0.60 (0.45), residues: 184

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.004   0.001   TRP D  22 
 HIS   0.004   0.001   HIS A 103 
 PHE   0.007   0.001   PHE G  33 
 TYR   0.008   0.001   TYR A 142 
 ARG   0.005   0.000   ARG B  90 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03990 (  763)
  hydrogen bonds       : angle       3.69303 ( 2250)
  covalent geometry    : bond        0.00244 ( 9738)
  covalent geometry    : angle       0.52587 (13207)

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

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

  2470 Ramachandran restraints generated.
    1235 Oldfield, 0 Emsley, 1235 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2470 Ramachandran restraints generated.
    1235 Oldfield, 0 Emsley, 1235 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  232 residues out of total 1032 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 196
  time to evaluate  : 1.018 
Fit side-chains
REVERT: C   64 LYS cc_start: 0.8073 (ttmm) cc_final: 0.7646 (ttmt)
REVERT: C  117 ASP cc_start: 0.7631 (OUTLIER) cc_final: 0.7136 (m-30)
REVERT: B   68 LYS cc_start: 0.8841 (ttmt) cc_final: 0.8490 (ttmm)
REVERT: B   73 GLU cc_start: 0.7192 (OUTLIER) cc_final: 0.6596 (pm20)
REVERT: B   77 TRP cc_start: 0.8698 (m-10) cc_final: 0.8100 (m-90)
REVERT: B   86 MET cc_start: 0.8525 (tpp) cc_final: 0.7490 (mtm)
REVERT: B  191 TYR cc_start: 0.8716 (m-10) cc_final: 0.8501 (m-10)
REVERT: B  239 LYS cc_start: 0.9290 (tppt) cc_final: 0.8392 (ttpt)
REVERT: E   51 TYR cc_start: 0.8434 (m-80) cc_final: 0.7815 (m-80)
REVERT: E   64 LYS cc_start: 0.7780 (tptt) cc_final: 0.7381 (mttm)
REVERT: E  219 GLU cc_start: 0.8408 (mm-30) cc_final: 0.8104 (mt-10)
REVERT: D   80 ASP cc_start: 0.8481 (t0) cc_final: 0.8108 (t70)
REVERT: D   83 GLU cc_start: 0.8429 (tm-30) cc_final: 0.8101 (tm-30)
REVERT: D   84 MET cc_start: 0.8872 (mtp) cc_final: 0.8657 (mtp)
REVERT: D  167 GLN cc_start: 0.8125 (tp40) cc_final: 0.7854 (tp40)
REVERT: D  174 ASP cc_start: 0.7533 (m-30) cc_final: 0.7235 (m-30)
REVERT: D  213 GLU cc_start: 0.8089 (OUTLIER) cc_final: 0.7571 (mt-10)
REVERT: F   19 MET cc_start: 0.7738 (ptp) cc_final: 0.7346 (ptt)
REVERT: F   41 ARG cc_start: 0.6806 (ptp-110) cc_final: 0.6370 (ptp90)
  outliers start: 36
  outliers final: 28
  residues processed: 220
  average time/residue: 0.2670
  time to fit residues: 80.1481
Evaluate side-chains
  219 residues out of total 1032 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 188
  time to evaluate  : 1.840 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue   56 ILE
Chi-restraints excluded: chain C residue   74 VAL
Chi-restraints excluded: chain C residue   86 MET
Chi-restraints excluded: chain C residue  117 ASP
Chi-restraints excluded: chain C residue  173 THR
Chi-restraints excluded: chain C residue  195 SER
Chi-restraints excluded: chain B residue   27 ILE
Chi-restraints excluded: chain B residue   73 GLU
Chi-restraints excluded: chain B residue  120 ASP
Chi-restraints excluded: chain B residue  158 ILE
Chi-restraints excluded: chain B residue  203 ILE
Chi-restraints excluded: chain B residue  211 SER
Chi-restraints excluded: chain B residue  236 LEU
Chi-restraints excluded: chain E residue  125 ARG
Chi-restraints excluded: chain E residue  133 ASP
Chi-restraints excluded: chain E residue  169 LEU
Chi-restraints excluded: chain E residue  195 SER
Chi-restraints excluded: chain A residue   30 LEU
Chi-restraints excluded: chain A residue   77 TRP
Chi-restraints excluded: chain A residue  106 ILE
Chi-restraints excluded: chain A residue  119 THR
Chi-restraints excluded: chain A residue  184 VAL
Chi-restraints excluded: chain A residue  195 SER
Chi-restraints excluded: chain A residue  233 ASN
Chi-restraints excluded: chain D residue  184 VAL
Chi-restraints excluded: chain D residue  213 GLU
Chi-restraints excluded: chain D residue  226 LEU
Chi-restraints excluded: chain D residue  235 LEU
Chi-restraints excluded: chain G residue   20 ILE
Chi-restraints excluded: chain G residue   31 ILE
Chi-restraints excluded: chain G residue   60 SER
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 122
   random chunks:
   chunk 78 optimal weight:    6.9990
   chunk 9 optimal weight:    6.9990
   chunk 95 optimal weight:    0.7980
   chunk 90 optimal weight:    2.9990
   chunk 110 optimal weight:    0.9980
   chunk 102 optimal weight:    0.9980
   chunk 33 optimal weight:    1.9990
   chunk 40 optimal weight:    0.9980
   chunk 60 optimal weight:    4.9990
   chunk 75 optimal weight:    0.4980
   chunk 67 optimal weight:    7.9990
   overall best weight:    0.8580

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

Flipped N/Q/H residues before XYZ refinement:
E 171 HIS
** A 233 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 = 0.3570 r_free = 0.3570 target = 0.122814 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3199 r_free = 0.3199 target = 0.095389 restraints weight = 14301.138|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 45)----------------|
| r_work = 0.3249 r_free = 0.3249 target = 0.099078 restraints weight = 6864.822|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 48)----------------|
| r_work = 0.3282 r_free = 0.3282 target = 0.101486 restraints weight = 4453.884|
|-----------------------------------------------------------------------------|
r_work (final): 0.3275
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8089
moved from start:          0.5247

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   9738  Z= 0.121
  Angle     :  0.550   9.174  13207  Z= 0.276
  Chirality :  0.038   0.143   1593
  Planarity :  0.004   0.051   1673
  Dihedral  :  4.987  59.222   1340
  Min Nonbonded Distance : 2.492

Molprobity Statistics.
  All-atom Clashscore : 5.08
  Ramachandran Plot:
    Outliers :  0.08 %
    Allowed  :  1.70 %
    Favored  : 98.22 %
  Rotamer:
    Outliers :  3.29 %
    Allowed  : 23.06 %
    Favored  : 73.64 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  3.16 (0.25), residues: 1235
  helix:  2.53 (0.16), residues: 1048
  sheet:  None (None), residues: 0
  loop : -0.58 (0.45), residues: 187

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.001   TRP E  77 
 HIS   0.006   0.001   HIS A 103 
 PHE   0.009   0.001   PHE A  67 
 TYR   0.009   0.001   TYR G  22 
 ARG   0.006   0.000   ARG B  90 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04027 (  763)
  hydrogen bonds       : angle       3.74351 ( 2250)
  covalent geometry    : bond        0.00262 ( 9738)
  covalent geometry    : angle       0.55048 (13207)

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

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

  2470 Ramachandran restraints generated.
    1235 Oldfield, 0 Emsley, 1235 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2470 Ramachandran restraints generated.
    1235 Oldfield, 0 Emsley, 1235 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  223 residues out of total 1032 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 189
  time to evaluate  : 1.045 
Fit side-chains
REVERT: C   64 LYS cc_start: 0.8108 (ttmm) cc_final: 0.7685 (ttmt)
REVERT: C  117 ASP cc_start: 0.7657 (m-30) cc_final: 0.7175 (m-30)
REVERT: B   68 LYS cc_start: 0.8825 (ttmt) cc_final: 0.8486 (ttmm)
REVERT: B   73 GLU cc_start: 0.7206 (OUTLIER) cc_final: 0.6606 (pm20)
REVERT: B   77 TRP cc_start: 0.8686 (m-10) cc_final: 0.8077 (m-90)
REVERT: B   86 MET cc_start: 0.8531 (tpp) cc_final: 0.8202 (mmm)
REVERT: B  239 LYS cc_start: 0.9285 (tppt) cc_final: 0.8423 (ttpt)
REVERT: E   51 TYR cc_start: 0.8441 (m-80) cc_final: 0.7848 (m-80)
REVERT: E   64 LYS cc_start: 0.7793 (tptt) cc_final: 0.7402 (mttm)
REVERT: E  219 GLU cc_start: 0.8400 (mm-30) cc_final: 0.8116 (mt-10)
REVERT: A   30 LEU cc_start: 0.6910 (OUTLIER) cc_final: 0.6616 (tp)
REVERT: A   75 ASN cc_start: 0.8314 (m110) cc_final: 0.7642 (t0)
REVERT: A  197 ASN cc_start: 0.8902 (m-40) cc_final: 0.8654 (m-40)
REVERT: D   57 ARG cc_start: 0.8718 (mtp85) cc_final: 0.8375 (mtt90)
REVERT: D   80 ASP cc_start: 0.8408 (t0) cc_final: 0.8046 (t70)
REVERT: D   83 GLU cc_start: 0.8416 (tm-30) cc_final: 0.8086 (tm-30)
REVERT: D  167 GLN cc_start: 0.8173 (tp40) cc_final: 0.7922 (tp40)
REVERT: D  174 ASP cc_start: 0.7472 (m-30) cc_final: 0.7187 (m-30)
REVERT: D  191 TYR cc_start: 0.8469 (m-10) cc_final: 0.8239 (m-10)
REVERT: D  213 GLU cc_start: 0.8081 (OUTLIER) cc_final: 0.7650 (mt-10)
REVERT: F   19 MET cc_start: 0.7740 (ptp) cc_final: 0.7346 (ptt)
REVERT: F   41 ARG cc_start: 0.6901 (ptp-110) cc_final: 0.6472 (ptp90)
  outliers start: 34
  outliers final: 27
  residues processed: 214
  average time/residue: 0.2454
  time to fit residues: 70.9524
Evaluate side-chains
  217 residues out of total 1032 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 187
  time to evaluate  : 1.254 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue   56 ILE
Chi-restraints excluded: chain C residue   74 VAL
Chi-restraints excluded: chain C residue   86 MET
Chi-restraints excluded: chain C residue  173 THR
Chi-restraints excluded: chain C residue  195 SER
Chi-restraints excluded: chain B residue   27 ILE
Chi-restraints excluded: chain B residue   73 GLU
Chi-restraints excluded: chain B residue  120 ASP
Chi-restraints excluded: chain B residue  158 ILE
Chi-restraints excluded: chain B residue  203 ILE
Chi-restraints excluded: chain B residue  211 SER
Chi-restraints excluded: chain B residue  236 LEU
Chi-restraints excluded: chain E residue  113 GLN
Chi-restraints excluded: chain E residue  125 ARG
Chi-restraints excluded: chain E residue  133 ASP
Chi-restraints excluded: chain E residue  169 LEU
Chi-restraints excluded: chain E residue  195 SER
Chi-restraints excluded: chain A residue   30 LEU
Chi-restraints excluded: chain A residue   77 TRP
Chi-restraints excluded: chain A residue  119 THR
Chi-restraints excluded: chain A residue  184 VAL
Chi-restraints excluded: chain A residue  195 SER
Chi-restraints excluded: chain A residue  233 ASN
Chi-restraints excluded: chain D residue  213 GLU
Chi-restraints excluded: chain D residue  226 LEU
Chi-restraints excluded: chain D residue  235 LEU
Chi-restraints excluded: chain D residue  246 THR
Chi-restraints excluded: chain G residue   20 ILE
Chi-restraints excluded: chain G residue   31 ILE
Chi-restraints excluded: chain G residue   60 SER
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 122
   random chunks:
   chunk 25 optimal weight:    0.0980
   chunk 43 optimal weight:    3.9990
   chunk 22 optimal weight:   10.0000
   chunk 18 optimal weight:    2.9990
   chunk 12 optimal weight:    0.9980
   chunk 32 optimal weight:    2.9990
   chunk 16 optimal weight:    0.7980
   chunk 109 optimal weight:    1.9990
   chunk 5 optimal weight:    0.9990
   chunk 44 optimal weight:    5.9990
   chunk 35 optimal weight:    0.9990
   overall best weight:    0.7784

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

Flipped N/Q/H residues before XYZ refinement:
E 171 HIS
A 233 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3626 r_free = 0.3626 target = 0.125218 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3271 r_free = 0.3271 target = 0.098046 restraints weight = 14600.854|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.3320 r_free = 0.3320 target = 0.101734 restraints weight = 7076.720|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3351 r_free = 0.3351 target = 0.104125 restraints weight = 4616.852|
|-----------------------------------------------------------------------------|
r_work (final): 0.3345
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8107
moved from start:          0.5359

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.049   9738  Z= 0.119
  Angle     :  0.552   8.837  13207  Z= 0.277
  Chirality :  0.038   0.144   1593
  Planarity :  0.004   0.053   1673
  Dihedral  :  4.682  56.397   1338
  Min Nonbonded Distance : 2.507

Molprobity Statistics.
  All-atom Clashscore : 5.03
  Ramachandran Plot:
    Outliers :  0.08 %
    Allowed  :  1.54 %
    Favored  : 98.38 %
  Rotamer:
    Outliers :  2.81 %
    Allowed  : 23.74 %
    Favored  : 73.45 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  3.20 (0.25), residues: 1235
  helix:  2.54 (0.16), residues: 1050
  sheet:  None (None), residues: 0
  loop : -0.45 (0.45), residues: 185

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP E  77 
 HIS   0.005   0.001   HIS A 103 
 PHE   0.007   0.001   PHE G  33 
 TYR   0.010   0.001   TYR A 191 
 ARG   0.006   0.000   ARG B  90 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03948 (  763)
  hydrogen bonds       : angle       3.71510 ( 2250)
  covalent geometry    : bond        0.00258 ( 9738)
  covalent geometry    : angle       0.55168 (13207)

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

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

  2470 Ramachandran restraints generated.
    1235 Oldfield, 0 Emsley, 1235 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2470 Ramachandran restraints generated.
    1235 Oldfield, 0 Emsley, 1235 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  222 residues out of total 1032 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 193
  time to evaluate  : 1.200 
Fit side-chains
REVERT: C   64 LYS cc_start: 0.8132 (ttmm) cc_final: 0.7711 (ttmt)
REVERT: C  117 ASP cc_start: 0.7648 (m-30) cc_final: 0.7158 (m-30)
REVERT: B   68 LYS cc_start: 0.8827 (ttmt) cc_final: 0.8507 (ttmm)
REVERT: B   73 GLU cc_start: 0.7163 (OUTLIER) cc_final: 0.6613 (pm20)
REVERT: B   77 TRP cc_start: 0.8669 (m-10) cc_final: 0.8095 (m-90)
REVERT: B   86 MET cc_start: 0.8474 (tpp) cc_final: 0.8140 (mmm)
REVERT: B  239 LYS cc_start: 0.9273 (tppt) cc_final: 0.8444 (ttpt)
REVERT: E   51 TYR cc_start: 0.8414 (m-80) cc_final: 0.7825 (m-80)
REVERT: E   64 LYS cc_start: 0.7845 (tptt) cc_final: 0.7468 (mttm)
REVERT: E  219 GLU cc_start: 0.8399 (mm-30) cc_final: 0.8133 (mt-10)
REVERT: A   75 ASN cc_start: 0.8294 (m110) cc_final: 0.7739 (t0)
REVERT: A  197 ASN cc_start: 0.8863 (m-40) cc_final: 0.8595 (m-40)
REVERT: D   57 ARG cc_start: 0.8720 (mtp85) cc_final: 0.8387 (mtt90)
REVERT: D   80 ASP cc_start: 0.8431 (t0) cc_final: 0.7760 (t0)
REVERT: D   83 GLU cc_start: 0.8355 (tm-30) cc_final: 0.7981 (tm-30)
REVERT: D  174 ASP cc_start: 0.7386 (m-30) cc_final: 0.7103 (m-30)
REVERT: D  191 TYR cc_start: 0.8499 (m-10) cc_final: 0.8291 (m-10)
REVERT: D  213 GLU cc_start: 0.8025 (OUTLIER) cc_final: 0.7720 (mt-10)
REVERT: F   19 MET cc_start: 0.7687 (ptp) cc_final: 0.7311 (ptt)
REVERT: F   41 ARG cc_start: 0.6928 (ptp-110) cc_final: 0.6525 (ptp90)
  outliers start: 29
  outliers final: 26
  residues processed: 215
  average time/residue: 0.2592
  time to fit residues: 75.9988
Evaluate side-chains
  214 residues out of total 1032 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 186
  time to evaluate  : 1.548 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue   56 ILE
Chi-restraints excluded: chain C residue   74 VAL
Chi-restraints excluded: chain C residue   86 MET
Chi-restraints excluded: chain C residue  173 THR
Chi-restraints excluded: chain C residue  195 SER
Chi-restraints excluded: chain B residue   27 ILE
Chi-restraints excluded: chain B residue   73 GLU
Chi-restraints excluded: chain B residue  120 ASP
Chi-restraints excluded: chain B residue  158 ILE
Chi-restraints excluded: chain B residue  203 ILE
Chi-restraints excluded: chain B residue  211 SER
Chi-restraints excluded: chain B residue  236 LEU
Chi-restraints excluded: chain E residue  125 ARG
Chi-restraints excluded: chain E residue  133 ASP
Chi-restraints excluded: chain E residue  169 LEU
Chi-restraints excluded: chain E residue  195 SER
Chi-restraints excluded: chain A residue   77 TRP
Chi-restraints excluded: chain A residue  119 THR
Chi-restraints excluded: chain A residue  184 VAL
Chi-restraints excluded: chain A residue  195 SER
Chi-restraints excluded: chain A residue  233 ASN
Chi-restraints excluded: chain D residue  213 GLU
Chi-restraints excluded: chain D residue  226 LEU
Chi-restraints excluded: chain D residue  235 LEU
Chi-restraints excluded: chain D residue  246 THR
Chi-restraints excluded: chain G residue   20 ILE
Chi-restraints excluded: chain G residue   31 ILE
Chi-restraints excluded: chain G residue   60 SER
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 122
   random chunks:
   chunk 96 optimal weight:    2.9990
   chunk 46 optimal weight:    1.9990
   chunk 2 optimal weight:    0.9990
   chunk 10 optimal weight:    0.9980
   chunk 116 optimal weight:    2.9990
   chunk 79 optimal weight:    2.9990
   chunk 1 optimal weight:    2.9990
   chunk 102 optimal weight:    3.9990
   chunk 26 optimal weight:    0.0040
   chunk 90 optimal weight:    0.9990
   chunk 107 optimal weight:    9.9990
   overall best weight:    0.9998

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

Flipped N/Q/H residues before XYZ refinement:
E 171 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3617 r_free = 0.3617 target = 0.124415 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3255 r_free = 0.3255 target = 0.097020 restraints weight = 14478.639|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3306 r_free = 0.3306 target = 0.100701 restraints weight = 7063.923|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.3337 r_free = 0.3337 target = 0.103091 restraints weight = 4615.093|
|-----------------------------------------------------------------------------|
r_work (final): 0.3334
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8117
moved from start:          0.5351

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.047   9738  Z= 0.125
  Angle     :  0.564   9.453  13207  Z= 0.283
  Chirality :  0.038   0.140   1593
  Planarity :  0.004   0.052   1673
  Dihedral  :  4.663  56.079   1338
  Min Nonbonded Distance : 2.514

Molprobity Statistics.
  All-atom Clashscore : 5.33
  Ramachandran Plot:
    Outliers :  0.08 %
    Allowed  :  1.62 %
    Favored  : 98.30 %
  Rotamer:
    Outliers :  3.00 %
    Allowed  : 23.93 %
    Favored  : 73.06 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  3.17 (0.24), residues: 1235
  helix:  2.51 (0.16), residues: 1050
  sheet:  None (None), residues: 0
  loop : -0.47 (0.45), residues: 185

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.001   TRP E  77 
 HIS   0.005   0.001   HIS A 103 
 PHE   0.008   0.001   PHE C  67 
 TYR   0.013   0.001   TYR A 191 
 ARG   0.006   0.000   ARG B  90 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04071 (  763)
  hydrogen bonds       : angle       3.76827 ( 2250)
  covalent geometry    : bond        0.00281 ( 9738)
  covalent geometry    : angle       0.56368 (13207)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3245.11 seconds
wall clock time: 58 minutes 28.28 seconds (3508.28 seconds total)