Starting phenix.real_space_refine
on Tue Mar  3 20:18:29 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9k3y_62032/03_2026/9k3y_62032_neut.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9k3y_62032/03_2026/9k3y_62032.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.0
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/9k3y_62032/03_2026/9k3y_62032.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9k3y_62032/03_2026/9k3y_62032.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9k3y_62032/03_2026/9k3y_62032_neut.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9k3y_62032/03_2026/9k3y_62032_neut.cif"
  }
  resolution = 3.0
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.003 sd=   0.104
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      49      5.16       5
     C    5438      2.51       5
     N    1365      2.21       5
     O    1485      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 10 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 8337
  Number of models: 1
  Model: ""
    Number of chains: 4
    Chain: "A"
      Number of atoms: 2156
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 281, 2156
          Classifications: {'peptide': 281}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 12, 'TRANS': 268}
          Chain breaks: 1
    Chain: "B"
      Number of atoms: 2267
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 300, 2267
          Classifications: {'peptide': 300}
          Link IDs: {'PTRANS': 15, 'TRANS': 284}
    Chain: "C"
      Number of atoms: 1957
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 246, 1957
          Classifications: {'peptide': 246}
          Link IDs: {'PTRANS': 9, 'TRANS': 236}
    Chain: "D"
      Number of atoms: 1957
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 246, 1957
          Classifications: {'peptide': 246}
          Link IDs: {'PTRANS': 9, 'TRANS': 236}
  Time building chain proxies: 1.77, per 1000 atoms: 0.21
  Number of scatterers: 8337
  At special positions: 0
  Unit cell: (72.76, 108.712, 120.696, 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      49     16.00
     O    1485      8.00
     N    1365      7.00
     C    5438      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 0.78
  Conformation dependent library (CDL) restraints added in 318.3 milliseconds
  

  2128 Ramachandran restraints generated.
    1064 Oldfield, 0 Emsley, 1064 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1990

  Finding SS restraints...
    Secondary structure from input PDB file:
      54 helices and 4 sheets defined
      64.9% alpha, 10.5% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.16
  Creating SS restraints...
    Processing helix  chain 'A' and resid 12 through 58
      removed outlier: 3.628A  pdb=" N   ARG A  16 " --> pdb=" O   LEU A  12 " (cutoff:3.500A)
      removed outlier: 3.675A  pdb=" N   ARG A  22 " --> pdb=" O   LYS A  18 " (cutoff:3.500A)
      removed outlier: 3.729A  pdb=" N   ARG A  23 " --> pdb=" O   MET A  19 " (cutoff:3.500A)
      removed outlier: 3.611A  pdb=" N   ARG A  24 " --> pdb=" O   GLN A  20 " (cutoff:3.500A)
      removed outlier: 3.807A  pdb=" N   LEU A  25 " --> pdb=" O   ALA A  21 " (cutoff:3.500A)
      removed outlier: 3.861A  pdb=" N   TRP A  44 " --> pdb=" O   PHE A  40 " (cutoff:3.500A)
      removed outlier: 3.947A  pdb=" N   LEU A  45 " --> pdb=" O   GLY A  41 " (cutoff:3.500A)
      removed outlier: 4.275A  pdb=" N   ASP A  58 " --> pdb=" O   THR A  54 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 79 through 111
      Proline residue:  A  99  - end of helix
    Processing helix  chain 'A' and resid 115 through 129
    Processing helix  chain 'A' and resid 132 through 144
      removed outlier: 4.331A  pdb=" N   VAL A 136 " --> pdb=" O   PRO A 132 " (cutoff:3.500A)
      removed outlier: 3.741A  pdb=" N   GLY A 137 " --> pdb=" O   SER A 133 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 144 through 149
    Processing helix  chain 'A' and resid 152 through 177
      removed outlier: 3.822A  pdb=" N   GLY A 156 " --> pdb=" O   SER A 152 " (cutoff:3.500A)
      Proline residue:  A 166  - end of helix
    Processing helix  chain 'A' and resid 180 through 190
      removed outlier: 3.936A  pdb=" N   ARG A 184 " --> pdb=" O   PRO A 180 " (cutoff:3.500A)
      removed outlier: 3.820A  pdb=" N   LEU A 190 " --> pdb=" O   ALA A 186 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 193 through 201
    Processing helix  chain 'A' and resid 201 through 206
      removed outlier: 3.600A  pdb=" N   SER A 206 " --> pdb=" O   THR A 202 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 206 through 222
      removed outlier: 3.849A  pdb=" N   ILE A 210 " --> pdb=" O   SER A 206 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 226 through 230
      removed outlier: 3.686A  pdb=" N   PHE A 230 " --> pdb=" O   PRO A 227 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 248 through 258
    Processing helix  chain 'A' and resid 261 through 288
      removed outlier: 3.547A  pdb=" N   GLN A 265 " --> pdb=" O   PHE A 261 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 15 through 28
    Processing helix  chain 'B' and resid 28 through 45
    Processing helix  chain 'B' and resid 45 through 53
    Processing helix  chain 'B' and resid 54 through 58
    Processing helix  chain 'B' and resid 71 through 103
      removed outlier: 3.630A  pdb=" N   THR B  81 " --> pdb=" O   GLY B  77 " (cutoff:3.500A)
      removed outlier: 3.592A  pdb=" N   SER B  82 " --> pdb=" O   THR B  78 " (cutoff:3.500A)
      Proline residue:  B  91  - end of helix
    Processing helix  chain 'B' and resid 105 through 107
      No H-bonds generated for 'chain 'B' and resid 105 through 107'
    Processing helix  chain 'B' and resid 108 through 122
      removed outlier: 3.782A  pdb=" N   LEU B 112 " --> pdb=" O   LEU B 108 " (cutoff:3.500A)
      removed outlier: 3.907A  pdb=" N   LEU B 119 " --> pdb=" O   ALA B 115 " (cutoff:3.500A)
      removed outlier: 4.318A  pdb=" N   ALA B 120 " --> pdb=" O   ILE B 116 " (cutoff:3.500A)
      removed outlier: 3.583A  pdb=" N   ALA B 121 " --> pdb=" O   GLU B 117 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 123 through 134
      removed outlier: 3.550A  pdb=" N   TYR B 127 " --> pdb=" O   PRO B 123 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 134 through 143
      removed outlier: 4.135A  pdb=" N   LEU B 138 " --> pdb=" O   ILE B 134 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 143 through 152
      removed outlier: 3.606A  pdb=" N   ASN B 149 " --> pdb=" O   GLU B 145 " (cutoff:3.500A)
      removed outlier: 3.806A  pdb=" N   ILE B 150 " --> pdb=" O   PRO B 146 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 156 through 162
      removed outlier: 4.045A  pdb=" N   SER B 162 " --> pdb=" O   ALA B 159 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 169 through 195
      Proline residue:  B 183  - end of helix
      removed outlier: 3.576A  pdb=" N   VAL B 188 " --> pdb=" O   TYR B 184 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 197 through 206
      removed outlier: 3.732A  pdb=" N   LYS B 201 " --> pdb=" O   PRO B 197 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 210 through 218
    Processing helix  chain 'B' and resid 218 through 223
    Processing helix  chain 'B' and resid 223 through 240
      removed outlier: 3.859A  pdb=" N   GLY B 240 " --> pdb=" O   GLY B 236 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 242 through 250
      removed outlier: 3.631A  pdb=" N   ILE B 248 " --> pdb=" O   ALA B 244 " (cutoff:3.500A)
      removed outlier: 4.616A  pdb=" N   GLY B 250 " --> pdb=" O   THR B 246 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 266 through 275
    Processing helix  chain 'B' and resid 281 through 313
      removed outlier: 3.969A  pdb=" N   ALA B 285 " --> pdb=" O   GLY B 281 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 48 through 56
      removed outlier: 3.539A  pdb=" N   THR C  55 " --> pdb=" O   THR C  51 " (cutoff:3.500A)
      removed outlier: 3.976A  pdb=" N   PHE C  56 " --> pdb=" O   LEU C  52 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 58 through 63
    Processing helix  chain 'C' and resid 85 through 92
      removed outlier: 3.601A  pdb=" N   LYS C  92 " --> pdb=" O   LEU C  88 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 106 through 119
      removed outlier: 4.528A  pdb=" N   GLY C 114 " --> pdb=" O   ASN C 110 " (cutoff:3.500A)
      removed outlier: 4.258A  pdb=" N   VAL C 115 " --> pdb=" O   ILE C 111 " (cutoff:3.500A)
      removed outlier: 3.641A  pdb=" N   LEU C 117 " --> pdb=" O   PHE C 113 " (cutoff:3.500A)
      removed outlier: 4.230A  pdb=" N   PHE C 118 " --> pdb=" O   GLY C 114 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 122 through 137
    Processing helix  chain 'C' and resid 150 through 154
      removed outlier: 3.700A  pdb=" N   LEU C 154 " --> pdb=" O   GLY C 151 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 155 through 170
      removed outlier: 4.130A  pdb=" N   ILE C 170 " --> pdb=" O   ARG C 166 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 187 through 192
      removed outlier: 3.572A  pdb=" N   ILE C 192 " --> pdb=" O   THR C 189 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 194 through 199
      removed outlier: 4.055A  pdb=" N   GLU C 198 " --> pdb=" O   LEU C 195 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 211 through 219
      removed outlier: 3.804A  pdb=" N   ALA C 215 " --> pdb=" O   ASN C 211 " (cutoff:3.500A)
      removed outlier: 3.818A  pdb=" N   ARG C 217 " --> pdb=" O   GLN C 213 " (cutoff:3.500A)
      removed outlier: 3.504A  pdb=" N   SER C 219 " --> pdb=" O   ALA C 215 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 236 through 240
      removed outlier: 3.667A  pdb=" N   PHE C 240 " --> pdb=" O   THR C 236 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'C' and resid 236 through 240'
    Processing helix  chain 'C' and resid 246 through 252
      removed outlier: 3.945A  pdb=" N   ASP C 250 " --> pdb=" O   LYS C 246 " (cutoff:3.500A)
      removed outlier: 4.024A  pdb=" N   ILE C 252 " --> pdb=" O   THR C 248 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 48 through 54
      removed outlier: 3.858A  pdb=" N   LEU D  53 " --> pdb=" O   LYS D  49 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 58 through 63
      removed outlier: 3.615A  pdb=" N   GLU D  61 " --> pdb=" O   LYS D  58 " (cutoff:3.500A)
      removed outlier: 3.690A  pdb=" N   LEU D  62 " --> pdb=" O   MET D  59 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 85 through 91
    Processing helix  chain 'D' and resid 106 through 119
      removed outlier: 3.569A  pdb=" N   ILE D 111 " --> pdb=" O   ILE D 107 " (cutoff:3.500A)
      removed outlier: 5.048A  pdb=" N   GLY D 114 " --> pdb=" O   ASN D 110 " (cutoff:3.500A)
      removed outlier: 3.964A  pdb=" N   VAL D 115 " --> pdb=" O   ILE D 111 " (cutoff:3.500A)
      removed outlier: 3.816A  pdb=" N   PHE D 118 " --> pdb=" O   GLY D 114 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 122 through 137
    Processing helix  chain 'D' and resid 155 through 169
    Processing helix  chain 'D' and resid 185 through 200
      removed outlier: 3.587A  pdb=" N   GLU D 198 " --> pdb=" O   GLU D 194 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 211 through 219
    Processing helix  chain 'D' and resid 236 through 242
      removed outlier: 3.850A  pdb=" N   PHE D 240 " --> pdb=" O   THR D 236 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 246 through 252
      removed outlier: 4.462A  pdb=" N   ASP D 250 " --> pdb=" O   LYS D 246 " (cutoff:3.500A)
      removed outlier: 3.778A  pdb=" N   TYR D 251 " --> pdb=" O   GLN D 247 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'C' and resid 23 through 34
      removed outlier: 6.572A  pdb=" N   ALA C  25 " --> pdb=" O   TYR C  19 " (cutoff:3.500A)
      removed outlier: 7.654A  pdb=" N   TYR C  19 " --> pdb=" O   ALA C  25 " (cutoff:3.500A)
      removed outlier: 6.302A  pdb=" N   LYS C  27 " --> pdb=" O   ASN C  17 " (cutoff:3.500A)
      removed outlier: 5.969A  pdb=" N   ASN C  17 " --> pdb=" O   LYS C  27 " (cutoff:3.500A)
      removed outlier: 5.087A  pdb=" N   ILE C  29 " --> pdb=" O   ASN C  15 " (cutoff:3.500A)
      removed outlier: 4.021A  pdb=" N   ILE C  11 " --> pdb=" O   ILE C  33 " (cutoff:3.500A)
      removed outlier: 5.515A  pdb=" N   VAL C  13 " --> pdb=" O   LEU C  73 " (cutoff:3.500A)
      removed outlier: 7.194A  pdb=" N   LEU C  73 " --> pdb=" O   VAL C  13 " (cutoff:3.500A)
      removed outlier: 5.681A  pdb=" N   ASN C  15 " --> pdb=" O   GLU C  71 " (cutoff:3.500A)
      removed outlier: 5.022A  pdb=" N   GLU C  71 " --> pdb=" O   ASN C  15 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'C' and resid 93 through 96
      removed outlier: 6.472A  pdb=" N   GLY C  94 " --> pdb=" O   LEU C 176 " (cutoff:3.500A)
      removed outlier: 7.995A  pdb=" N   ASP C 178 " --> pdb=" O   GLY C  94 " (cutoff:3.500A)
      removed outlier: 6.982A  pdb=" N   VAL C  96 " --> pdb=" O   ASP C 178 " (cutoff:3.500A)
      removed outlier: 6.456A  pdb=" N   THR C  39 " --> pdb=" O   ILE C 207 " (cutoff:3.500A)
      removed outlier: 6.609A  pdb=" N   VAL C  38 " --> pdb=" O   HIS C 221 " (cutoff:3.500A)
      removed outlier: 8.299A  pdb=" N   ALA C 223 " --> pdb=" O   VAL C  38 " (cutoff:3.500A)
      removed outlier: 6.515A  pdb=" N   ALA C  40 " --> pdb=" O   ALA C 223 " (cutoff:3.500A)
      removed outlier: 7.715A  pdb=" N   MET C 225 " --> pdb=" O   ALA C  40 " (cutoff:3.500A)
      removed outlier: 6.377A  pdb=" N   ILE C  42 " --> pdb=" O   MET C 225 " (cutoff:3.500A)
      removed outlier: 4.207A  pdb=" N   GLU C 232 " --> pdb=" O   PHE C 224 " (cutoff:3.500A)
      removed outlier: 6.405A  pdb=" N   TYR C 226 " --> pdb=" O   LEU C 230 " (cutoff:3.500A)
      removed outlier: 5.118A  pdb=" N   LEU C 230 " --> pdb=" O   TYR C 226 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'D' and resid 23 through 34
      removed outlier: 6.720A  pdb=" N   PHE D  18 " --> pdb=" O   ALA D  25 " (cutoff:3.500A)
      removed outlier: 4.453A  pdb=" N   LYS D  27 " --> pdb=" O   LEU D  16 " (cutoff:3.500A)
      removed outlier: 6.335A  pdb=" N   LEU D  16 " --> pdb=" O   LYS D  27 " (cutoff:3.500A)
      removed outlier: 6.231A  pdb=" N   ILE D  29 " --> pdb=" O   ARG D  14 " (cutoff:3.500A)
      removed outlier: 4.163A  pdb=" N   ARG D  14 " --> pdb=" O   ILE D  29 " (cutoff:3.500A)
      removed outlier: 6.932A  pdb=" N   LEU D  31 " --> pdb=" O   GLN D  12 " (cutoff:3.500A)
      removed outlier: 4.980A  pdb=" N   GLN D  12 " --> pdb=" O   LEU D  31 " (cutoff:3.500A)
      removed outlier: 6.861A  pdb=" N   ILE D  33 " --> pdb=" O   LYS D  10 " (cutoff:3.500A)
      removed outlier: 5.572A  pdb=" N   VAL D  13 " --> pdb=" O   LEU D  73 " (cutoff:3.500A)
      removed outlier: 7.135A  pdb=" N   LEU D  73 " --> pdb=" O   VAL D  13 " (cutoff:3.500A)
      removed outlier: 5.326A  pdb=" N   ASN D  15 " --> pdb=" O   GLU D  71 " (cutoff:3.500A)
      removed outlier: 4.887A  pdb=" N   GLU D  71 " --> pdb=" O   ASN D  15 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'D' and resid 93 through 96
      removed outlier: 6.768A  pdb=" N   VAL D  38 " --> pdb=" O   HIS D 221 " (cutoff:3.500A)
      removed outlier: 8.233A  pdb=" N   ALA D 223 " --> pdb=" O   VAL D  38 " (cutoff:3.500A)
      removed outlier: 6.613A  pdb=" N   ALA D  40 " --> pdb=" O   ALA D 223 " (cutoff:3.500A)
      removed outlier: 7.685A  pdb=" N   MET D 225 " --> pdb=" O   ALA D  40 " (cutoff:3.500A)
      removed outlier: 6.517A  pdb=" N   ILE D  42 " --> pdb=" O   MET D 225 " (cutoff:3.500A)
      removed outlier: 4.006A  pdb=" N   GLU D 232 " --> pdb=" O   PHE D 224 " (cutoff:3.500A)
      removed outlier: 6.893A  pdb=" N   TYR D 226 " --> pdb=" O   LEU D 230 " (cutoff:3.500A)
      removed outlier: 5.654A  pdb=" N   LEU D 230 " --> pdb=" O   TYR D 226 " (cutoff:3.500A)

    454 hydrogen bonds defined for protein.
    1311 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: 1.21

  Time building geometry restraints manager: 1.01 seconds

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

  Histogram of bond lengths:
        1.23 -     1.34: 2624
        1.34 -     1.46: 1912
        1.46 -     1.58: 3890
        1.58 -     1.70: 0
        1.70 -     1.82: 88
  Bond restraints: 8514
  Sorted by residual:
  bond pdb=" N   LYS B  14 "
       pdb=" CA  LYS B  14 "
    ideal  model  delta    sigma   weight residual
    1.458  1.492 -0.034 1.90e-02 2.77e+03 3.15e+00
  bond pdb=" N   LEU A  12 "
       pdb=" CA  LEU A  12 "
    ideal  model  delta    sigma   weight residual
    1.458  1.491 -0.033 1.90e-02 2.77e+03 2.93e+00
  bond pdb=" C   GLY B 281 "
       pdb=" O   GLY B 281 "
    ideal  model  delta    sigma   weight residual
    1.236  1.229  0.007 5.30e-03 3.56e+04 1.55e+00
  bond pdb=" C   SER B 280 "
       pdb=" N   GLY B 281 "
    ideal  model  delta    sigma   weight residual
    1.335  1.326  0.009 7.50e-03 1.78e+04 1.32e+00
  bond pdb=" CA  ASN B 251 "
       pdb=" CB  ASN B 251 "
    ideal  model  delta    sigma   weight residual
    1.532  1.544 -0.012 1.48e-02 4.57e+03 6.89e-01
  ... (remaining 8509 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.33: 11149
        1.33 -     2.65: 337
        2.65 -     3.98: 60
        3.98 -     5.30: 9
        5.30 -     6.63: 1
  Bond angle restraints: 11556
  Sorted by residual:
  angle pdb=" N   ILE C 231 "
        pdb=" CA  ILE C 231 "
        pdb=" C   ILE C 231 "
      ideal   model   delta    sigma   weight residual
     113.42  110.16    3.26 1.17e+00 7.31e-01 7.77e+00
  angle pdb=" N   ILE B 249 "
        pdb=" CA  ILE B 249 "
        pdb=" C   ILE B 249 "
      ideal   model   delta    sigma   weight residual
     110.72  113.21   -2.49 1.01e+00 9.80e-01 6.09e+00
  angle pdb=" N   ASN B 251 "
        pdb=" CA  ASN B 251 "
        pdb=" CB  ASN B 251 "
      ideal   model   delta    sigma   weight residual
     111.74  108.54    3.20 1.58e+00 4.01e-01 4.11e+00
  angle pdb=" CA  SER A 206 "
        pdb=" C   SER A 206 "
        pdb=" O   SER A 206 "
      ideal   model   delta    sigma   weight residual
     121.89  119.32    2.57 1.29e+00 6.01e-01 3.97e+00
  angle pdb=" CA  GLU D  61 "
        pdb=" CB  GLU D  61 "
        pdb=" CG  GLU D  61 "
      ideal   model   delta    sigma   weight residual
     114.10  117.99   -3.89 2.00e+00 2.50e-01 3.78e+00
  ... (remaining 11551 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.59: 4560
       17.59 -    35.17: 373
       35.17 -    52.76: 112
       52.76 -    70.34: 20
       70.34 -    87.93: 8
  Dihedral angle restraints: 5073
    sinusoidal: 1986
      harmonic: 3087
  Sorted by residual:
  dihedral pdb=" CA  THR B 101 "
           pdb=" C   THR B 101 "
           pdb=" N   GLU B 102 "
           pdb=" CA  GLU B 102 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -161.99  -18.01     0      5.00e+00 4.00e-02 1.30e+01
  dihedral pdb=" CA  VAL C  96 "
           pdb=" C   VAL C  96 "
           pdb=" N   PHE C  97 "
           pdb=" CA  PHE C  97 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -163.31  -16.69     0      5.00e+00 4.00e-02 1.11e+01
  dihedral pdb=" CA  PHE B 247 "
           pdb=" C   PHE B 247 "
           pdb=" N   ILE B 248 "
           pdb=" CA  ILE B 248 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -163.60  -16.40     0      5.00e+00 4.00e-02 1.08e+01
  ... (remaining 5070 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.039: 1015
       0.039 -    0.077: 262
       0.077 -    0.116: 62
       0.116 -    0.154: 17
       0.154 -    0.193: 1
  Chirality restraints: 1357
  Sorted by residual:
  chirality pdb=" CB  THR A  54 "
            pdb=" CA  THR A  54 "
            pdb=" OG1 THR A  54 "
            pdb=" CG2 THR A  54 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.55    2.36    0.19 2.00e-01 2.50e+01 9.29e-01
  chirality pdb=" CA  ILE B 122 "
            pdb=" N   ILE B 122 "
            pdb=" C   ILE B 122 "
            pdb=" CB  ILE B 122 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.58   -0.14 2.00e-01 2.50e+01 5.16e-01
  chirality pdb=" CA  ILE C  72 "
            pdb=" N   ILE C  72 "
            pdb=" C   ILE C  72 "
            pdb=" CB  ILE C  72 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.58   -0.14 2.00e-01 2.50e+01 5.13e-01
  ... (remaining 1354 not shown)

  Planarity restraints: 1439
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   VAL A 165 "    0.024 5.00e-02 4.00e+02   3.61e-02 2.08e+00
        pdb=" N   PRO A 166 "   -0.062 5.00e-02 4.00e+02
        pdb=" CA  PRO A 166 "    0.018 5.00e-02 4.00e+02
        pdb=" CD  PRO A 166 "    0.020 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   PRO A  70 "   -0.022 5.00e-02 4.00e+02   3.32e-02 1.77e+00
        pdb=" N   PRO A  71 "    0.057 5.00e-02 4.00e+02
        pdb=" CA  PRO A  71 "   -0.017 5.00e-02 4.00e+02
        pdb=" CD  PRO A  71 "   -0.018 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   LEU A 249 "    0.021 5.00e-02 4.00e+02   3.22e-02 1.66e+00
        pdb=" N   PRO A 250 "   -0.056 5.00e-02 4.00e+02
        pdb=" CA  PRO A 250 "    0.016 5.00e-02 4.00e+02
        pdb=" CD  PRO A 250 "    0.018 5.00e-02 4.00e+02
  ... (remaining 1436 not shown)

  Histogram of nonbonded interaction distances:
        2.20 -     2.74: 647
        2.74 -     3.28: 8366
        3.28 -     3.82: 13043
        3.82 -     4.36: 15513
        4.36 -     4.90: 27924
  Nonbonded interactions: 65493
  Sorted by model distance:
  nonbonded pdb=" OE2 GLU B 202 "
            pdb=" OH  TYR D  63 "
     model   vdw
     2.195 3.040
  nonbonded pdb=" O   LYS A 114 "
            pdb=" OG  SER A 115 "
     model   vdw
     2.215 3.040
  nonbonded pdb=" N   GLN D 213 "
            pdb=" OE1 GLN D 213 "
     model   vdw
     2.275 3.120
  nonbonded pdb=" O   ASN C  15 "
            pdb=" ND2 ASN C  15 "
     model   vdw
     2.314 3.120
  nonbonded pdb=" OD1 ASP B 191 "
            pdb=" N   VAL B 192 "
     model   vdw
     2.328 3.120
  ... (remaining 65488 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 'C'
  selection = chain 'D'
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
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:             1.050
  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:          0.080
  Check model and map are aligned:         0.030
  Set scattering table:                    0.030
  Process input model:                     8.470
  Find NCS groups from input model:        0.080
  Set up NCS constraints:                  0.010
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:6.300
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   16.060
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8186
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      :  0.003   0.038   8514  Z= 0.137
  Angle     :  0.563   6.627  11556  Z= 0.326
  Chirality :  0.038   0.193   1357
  Planarity :  0.004   0.040   1439
  Dihedral  : 14.731  87.926   3083
  Min Nonbonded Distance : 2.195

Molprobity Statistics.
  All-atom Clashscore : 2.89
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.91 %
    Favored  : 97.09 %
  Rotamer:
    Outliers :  0.79 %
    Allowed  : 15.17 %
    Favored  : 84.04 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.03 (0.27), residues: 1064
  helix:  1.53 (0.23), residues: 587
  sheet:  1.21 (0.63), residues: 69
  loop : -0.64 (0.32), residues: 408

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG D 191 
 TYR   0.008   0.001   TYR A 188 
 PHE   0.014   0.001   PHE A  40 
 TRP   0.009   0.001   TRP C 132 
 HIS   0.004   0.001   HIS D  24 

Details of bonding type rmsd
  covalent geometry    : bond        0.00286 ( 8514)
  covalent geometry    : angle       0.56263 (11556)
  hydrogen bonds       : bond        0.17471 (  454)
  hydrogen bonds       : angle       5.87040 ( 1311)

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

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

  2128 Ramachandran restraints generated.
    1064 Oldfield, 0 Emsley, 1064 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2128 Ramachandran restraints generated.
    1064 Oldfield, 0 Emsley, 1064 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  137 residues out of total 890 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 130
  time to evaluate  : 0.292 
Fit side-chains
REVERT: A  255 LYS cc_start: 0.7870 (tttt) cc_final: 0.6975 (mmtp)
REVERT: B   61 GLU cc_start: 0.7145 (mm-30) cc_final: 0.6546 (mp0)
REVERT: B  307 PHE cc_start: 0.7417 (t80) cc_final: 0.5785 (m-80)
REVERT: B  308 MET cc_start: 0.8369 (tpp) cc_final: 0.8016 (mmm)
REVERT: C   59 MET cc_start: 0.9003 (OUTLIER) cc_final: 0.8723 (mmt)
REVERT: C   71 GLU cc_start: 0.6965 (pt0) cc_final: 0.6439 (pm20)
REVERT: C  119 GLU cc_start: 0.7777 (OUTLIER) cc_final: 0.7005 (tp30)
REVERT: C  229 GLU cc_start: 0.7134 (tp30) cc_final: 0.6602 (tp30)
REVERT: D  136 LYS cc_start: 0.8204 (tppp) cc_final: 0.7967 (tppp)
REVERT: D  173 GLU cc_start: 0.7658 (mm-30) cc_final: 0.7020 (mt-10)
REVERT: D  200 LYS cc_start: 0.7097 (pttp) cc_final: 0.6790 (pptt)
REVERT: D  229 GLU cc_start: 0.6910 (tt0) cc_final: 0.6563 (tp30)
  outliers start: 7
  outliers final: 4
  residues processed: 134
  average time/residue: 0.6868
  time to fit residues: 96.8128
Evaluate side-chains
  123 residues out of total 890 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 117
  time to evaluate  : 0.303 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   32 THR
Chi-restraints excluded: chain A residue  272 VAL
Chi-restraints excluded: chain B residue   59 THR
Chi-restraints excluded: chain B residue  103 LEU
Chi-restraints excluded: chain C residue   59 MET
Chi-restraints excluded: chain C residue  119 GLU
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 106
   random chunks:
   chunk 49 optimal weight:    0.8980
   chunk 97 optimal weight:    0.7980
   chunk 53 optimal weight:    0.9990
   chunk 5 optimal weight:    0.0170
   chunk 33 optimal weight:    0.6980
   chunk 65 optimal weight:    0.8980
   chunk 62 optimal weight:    0.0170
   chunk 51 optimal weight:    0.8980
   chunk 100 optimal weight:    3.9990
   chunk 38 optimal weight:    2.9990
   chunk 61 optimal weight:    3.9990
   overall best weight:    0.4856

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

Flipped N/Q/H residues before XYZ refinement:
B 195 GLN
D  24 HIS
D 211 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3982 r_free = 0.3982 target = 0.181608 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3240 r_free = 0.3240 target = 0.111722 restraints weight = 9185.042|
|-----------------------------------------------------------------------------|
r_work (start): 0.3003 rms_B_bonded: 2.52
r_work: 0.2828 rms_B_bonded: 2.66 restraints_weight: 0.5000
r_work: 0.2687 rms_B_bonded: 4.08 restraints_weight: 0.2500
r_work (final): 0.2687
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8227
moved from start:          0.0919

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.034   8514  Z= 0.123
  Angle     :  0.560   8.374  11556  Z= 0.294
  Chirality :  0.041   0.186   1357
  Planarity :  0.005   0.048   1439
  Dihedral  :  5.134  36.582   1151
  Min Nonbonded Distance : 2.579

Molprobity Statistics.
  All-atom Clashscore : 2.42
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  :  2.26 %
    Favored  : 97.65 %
  Rotamer:
    Outliers :  2.36 %
    Allowed  : 14.27 %
    Favored  : 83.37 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.25 (0.27), residues: 1064
  helix:  1.74 (0.22), residues: 599
  sheet:  1.33 (0.63), residues: 69
  loop : -0.66 (0.32), residues: 396

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG D 191 
 TYR   0.016   0.001   TYR D 226 
 PHE   0.016   0.001   PHE C 224 
 TRP   0.009   0.001   TRP C 132 
 HIS   0.005   0.001   HIS D  24 

Details of bonding type rmsd
  covalent geometry    : bond        0.00245 ( 8514)
  covalent geometry    : angle       0.55950 (11556)
  hydrogen bonds       : bond        0.05226 (  454)
  hydrogen bonds       : angle       4.33403 ( 1311)

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

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

  2128 Ramachandran restraints generated.
    1064 Oldfield, 0 Emsley, 1064 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2128 Ramachandran restraints generated.
    1064 Oldfield, 0 Emsley, 1064 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  150 residues out of total 890 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 129
  time to evaluate  : 0.216 
Fit side-chains
REVERT: A  255 LYS cc_start: 0.8045 (tttt) cc_final: 0.7148 (mmtp)
REVERT: B   23 VAL cc_start: 0.8416 (OUTLIER) cc_final: 0.8038 (m)
REVERT: B   67 ASP cc_start: 0.7603 (OUTLIER) cc_final: 0.7351 (t0)
REVERT: B  150 ILE cc_start: 0.6703 (mt) cc_final: 0.6405 (mp)
REVERT: B  307 PHE cc_start: 0.7506 (t80) cc_final: 0.5888 (m-80)
REVERT: B  308 MET cc_start: 0.8516 (tpp) cc_final: 0.8172 (mmm)
REVERT: C   71 GLU cc_start: 0.7026 (pt0) cc_final: 0.6291 (pm20)
REVERT: C  229 GLU cc_start: 0.7052 (tp30) cc_final: 0.6598 (tp30)
REVERT: D  136 LYS cc_start: 0.8056 (tppp) cc_final: 0.7791 (tppp)
REVERT: D  173 GLU cc_start: 0.7778 (mm-30) cc_final: 0.7068 (mt-10)
REVERT: D  178 ASP cc_start: 0.7526 (t0) cc_final: 0.7150 (t0)
  outliers start: 21
  outliers final: 6
  residues processed: 137
  average time/residue: 0.6000
  time to fit residues: 86.8216
Evaluate side-chains
  126 residues out of total 890 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 118
  time to evaluate  : 0.216 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   32 THR
Chi-restraints excluded: chain A residue  225 THR
Chi-restraints excluded: chain A residue  272 VAL
Chi-restraints excluded: chain B residue   23 VAL
Chi-restraints excluded: chain B residue   67 ASP
Chi-restraints excluded: chain B residue  103 LEU
Chi-restraints excluded: chain D residue  117 LEU
Chi-restraints excluded: chain D residue  148 HIS
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 106
   random chunks:
   chunk 24 optimal weight:    0.7980
   chunk 69 optimal weight:    3.9990
   chunk 62 optimal weight:    5.9990
   chunk 47 optimal weight:    5.9990
   chunk 22 optimal weight:    3.9990
   chunk 50 optimal weight:    1.9990
   chunk 60 optimal weight:   10.0000
   chunk 63 optimal weight:    0.9980
   chunk 26 optimal weight:    2.9990
   chunk 105 optimal weight:   50.0000
   chunk 57 optimal weight:    2.9990
   overall best weight:    1.9586

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3928 r_free = 0.3928 target = 0.176088 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 58)----------------|
| r_work = 0.3139 r_free = 0.3139 target = 0.103465 restraints weight = 9082.545|
|-----------------------------------------------------------------------------|
r_work (start): 0.2928 rms_B_bonded: 2.09
r_work: 0.2796 rms_B_bonded: 2.48 restraints_weight: 0.5000
r_work: 0.2655 rms_B_bonded: 3.82 restraints_weight: 0.2500
r_work (final): 0.2655
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8286
moved from start:          0.1135

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.041   8514  Z= 0.175
  Angle     :  0.582   7.596  11556  Z= 0.309
  Chirality :  0.043   0.198   1357
  Planarity :  0.005   0.056   1439
  Dihedral  :  4.845  39.722   1144
  Min Nonbonded Distance : 2.592

Molprobity Statistics.
  All-atom Clashscore : 2.36
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  :  2.35 %
    Favored  : 97.56 %
  Rotamer:
    Outliers :  3.03 %
    Allowed  : 14.72 %
    Favored  : 82.25 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.14 (0.26), residues: 1064
  helix:  1.66 (0.22), residues: 594
  sheet:  1.18 (0.62), residues: 67
  loop : -0.67 (0.31), residues: 403

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG D 191 
 TYR   0.015   0.002   TYR D 251 
 PHE   0.017   0.001   PHE A  40 
 TRP   0.009   0.001   TRP C 132 
 HIS   0.002   0.001   HIS D  24 

Details of bonding type rmsd
  covalent geometry    : bond        0.00438 ( 8514)
  covalent geometry    : angle       0.58214 (11556)
  hydrogen bonds       : bond        0.06463 (  454)
  hydrogen bonds       : angle       4.26142 ( 1311)

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

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

  2128 Ramachandran restraints generated.
    1064 Oldfield, 0 Emsley, 1064 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2128 Ramachandran restraints generated.
    1064 Oldfield, 0 Emsley, 1064 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  143 residues out of total 890 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 116
  time to evaluate  : 0.314 
Fit side-chains
REVERT: A  255 LYS cc_start: 0.8126 (tttt) cc_final: 0.7197 (mmtp)
REVERT: B   61 GLU cc_start: 0.7250 (mm-30) cc_final: 0.6645 (mp0)
REVERT: B  150 ILE cc_start: 0.6783 (mt) cc_final: 0.6458 (mp)
REVERT: B  307 PHE cc_start: 0.7598 (t80) cc_final: 0.5989 (m-80)
REVERT: B  308 MET cc_start: 0.8554 (tpp) cc_final: 0.8191 (mmm)
REVERT: B  310 MET cc_start: 0.7185 (OUTLIER) cc_final: 0.6851 (ptm)
REVERT: C   59 MET cc_start: 0.8633 (OUTLIER) cc_final: 0.8261 (mmp)
REVERT: C   71 GLU cc_start: 0.7010 (pt0) cc_final: 0.6259 (pm20)
REVERT: C  229 GLU cc_start: 0.6963 (tp30) cc_final: 0.6569 (mm-30)
REVERT: D  173 GLU cc_start: 0.7721 (mm-30) cc_final: 0.7055 (mt-10)
REVERT: D  178 ASP cc_start: 0.7617 (t0) cc_final: 0.7185 (t0)
REVERT: D  200 LYS cc_start: 0.6793 (pttp) cc_final: 0.6516 (pptt)
  outliers start: 27
  outliers final: 16
  residues processed: 129
  average time/residue: 0.6028
  time to fit residues: 82.3310
Evaluate side-chains
  131 residues out of total 890 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 113
  time to evaluate  : 0.298 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   32 THR
Chi-restraints excluded: chain A residue   57 ILE
Chi-restraints excluded: chain A residue   73 ASN
Chi-restraints excluded: chain A residue  225 THR
Chi-restraints excluded: chain A residue  272 VAL
Chi-restraints excluded: chain B residue   23 VAL
Chi-restraints excluded: chain B residue   59 THR
Chi-restraints excluded: chain B residue   66 ASN
Chi-restraints excluded: chain B residue  103 LEU
Chi-restraints excluded: chain B residue  192 VAL
Chi-restraints excluded: chain B residue  194 GLU
Chi-restraints excluded: chain B residue  198 VAL
Chi-restraints excluded: chain B residue  310 MET
Chi-restraints excluded: chain C residue   11 ILE
Chi-restraints excluded: chain C residue   59 MET
Chi-restraints excluded: chain C residue   96 VAL
Chi-restraints excluded: chain D residue  117 LEU
Chi-restraints excluded: chain D residue  148 HIS
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 106
   random chunks:
   chunk 48 optimal weight:    2.9990
   chunk 23 optimal weight:    0.0970
   chunk 2 optimal weight:    0.6980
   chunk 60 optimal weight:    4.9990
   chunk 64 optimal weight:    7.9990
   chunk 73 optimal weight:    0.8980
   chunk 54 optimal weight:    0.0670
   chunk 11 optimal weight:    0.8980
   chunk 57 optimal weight:    0.8980
   chunk 20 optimal weight:    0.9990
   chunk 86 optimal weight:    2.9990
   overall best weight:    0.5316

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3978 r_free = 0.3978 target = 0.181210 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 63)----------------|
| r_work = 0.3214 r_free = 0.3214 target = 0.109216 restraints weight = 9288.167|
|-----------------------------------------------------------------------------|
r_work (start): 0.2982 rms_B_bonded: 2.15
r_work: 0.2859 rms_B_bonded: 2.48 restraints_weight: 0.5000
r_work: 0.2718 rms_B_bonded: 3.86 restraints_weight: 0.2500
r_work (final): 0.2718
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8168
moved from start:          0.1420

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.035   8514  Z= 0.107
  Angle     :  0.501   6.020  11556  Z= 0.264
  Chirality :  0.040   0.176   1357
  Planarity :  0.004   0.056   1439
  Dihedral  :  4.540  36.646   1144
  Min Nonbonded Distance : 2.599

Molprobity Statistics.
  All-atom Clashscore : 2.48
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  :  1.79 %
    Favored  : 98.12 %
  Rotamer:
    Outliers :  2.13 %
    Allowed  : 15.62 %
    Favored  : 82.25 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.37 (0.27), residues: 1064
  helix:  1.88 (0.22), residues: 596
  sheet:  1.01 (0.60), residues: 74
  loop : -0.62 (0.32), residues: 394

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG D 191 
 TYR   0.015   0.001   TYR D 226 
 PHE   0.013   0.001   PHE A  40 
 TRP   0.007   0.001   TRP B  46 
 HIS   0.001   0.000   HIS D  24 

Details of bonding type rmsd
  covalent geometry    : bond        0.00220 ( 8514)
  covalent geometry    : angle       0.50110 (11556)
  hydrogen bonds       : bond        0.04455 (  454)
  hydrogen bonds       : angle       3.97769 ( 1311)

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

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

  2128 Ramachandran restraints generated.
    1064 Oldfield, 0 Emsley, 1064 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2128 Ramachandran restraints generated.
    1064 Oldfield, 0 Emsley, 1064 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  133 residues out of total 890 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 114
  time to evaluate  : 0.302 
Fit side-chains
REVERT: A   17 ARG cc_start: 0.6035 (ttp-110) cc_final: 0.5769 (mtp-110)
REVERT: A  255 LYS cc_start: 0.7975 (tttt) cc_final: 0.7038 (mmtp)
REVERT: B   23 VAL cc_start: 0.8220 (OUTLIER) cc_final: 0.7894 (m)
REVERT: B  102 GLU cc_start: 0.7518 (tp30) cc_final: 0.7061 (mp0)
REVERT: B  150 ILE cc_start: 0.6720 (mt) cc_final: 0.6413 (mp)
REVERT: B  307 PHE cc_start: 0.7407 (t80) cc_final: 0.5781 (m-80)
REVERT: B  308 MET cc_start: 0.8442 (tpp) cc_final: 0.8093 (mmm)
REVERT: C   59 MET cc_start: 0.8583 (OUTLIER) cc_final: 0.8196 (mmp)
REVERT: C   71 GLU cc_start: 0.6960 (pt0) cc_final: 0.6264 (pm20)
REVERT: C  217 ARG cc_start: 0.6825 (OUTLIER) cc_final: 0.6476 (mtt90)
REVERT: C  229 GLU cc_start: 0.7025 (tp30) cc_final: 0.6752 (tp30)
REVERT: D   31 LEU cc_start: 0.7661 (OUTLIER) cc_final: 0.7447 (pt)
REVERT: D   75 ASP cc_start: 0.7289 (t0) cc_final: 0.7026 (t0)
REVERT: D   80 LEU cc_start: 0.7927 (OUTLIER) cc_final: 0.7669 (mm)
REVERT: D  178 ASP cc_start: 0.7439 (t0) cc_final: 0.7032 (t0)
  outliers start: 19
  outliers final: 7
  residues processed: 127
  average time/residue: 0.5896
  time to fit residues: 79.2120
Evaluate side-chains
  122 residues out of total 890 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 110
  time to evaluate  : 0.200 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  211 MET
Chi-restraints excluded: chain A residue  225 THR
Chi-restraints excluded: chain A residue  272 VAL
Chi-restraints excluded: chain B residue   23 VAL
Chi-restraints excluded: chain B residue  103 LEU
Chi-restraints excluded: chain C residue   59 MET
Chi-restraints excluded: chain C residue  217 ARG
Chi-restraints excluded: chain D residue   31 LEU
Chi-restraints excluded: chain D residue   80 LEU
Chi-restraints excluded: chain D residue  117 LEU
Chi-restraints excluded: chain D residue  148 HIS
Chi-restraints excluded: chain D residue  248 THR
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 106
   random chunks:
   chunk 67 optimal weight:    1.9990
   chunk 66 optimal weight:    0.9990
   chunk 18 optimal weight:    0.7980
   chunk 48 optimal weight:    3.9990
   chunk 53 optimal weight:    2.9990
   chunk 65 optimal weight:    8.9990
   chunk 40 optimal weight:    0.9980
   chunk 57 optimal weight:    5.9990
   chunk 37 optimal weight:    1.9990
   chunk 64 optimal weight:   10.0000
   chunk 82 optimal weight:    6.9990
   overall best weight:    1.3586

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3946 r_free = 0.3946 target = 0.177750 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 65)----------------|
| r_work = 0.3165 r_free = 0.3165 target = 0.105376 restraints weight = 9166.025|
|-----------------------------------------------------------------------------|
r_work (start): 0.2956 rms_B_bonded: 2.10
r_work: 0.2825 rms_B_bonded: 2.49 restraints_weight: 0.5000
r_work: 0.2684 rms_B_bonded: 3.85 restraints_weight: 0.2500
r_work (final): 0.2684
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8254
moved from start:          0.1457

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   8514  Z= 0.140
  Angle     :  0.531   6.526  11556  Z= 0.279
  Chirality :  0.042   0.176   1357
  Planarity :  0.004   0.059   1439
  Dihedral  :  4.511  38.818   1143
  Min Nonbonded Distance : 2.609

Molprobity Statistics.
  All-atom Clashscore : 2.83
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  :  2.35 %
    Favored  : 97.56 %
  Rotamer:
    Outliers :  2.92 %
    Allowed  : 15.28 %
    Favored  : 81.80 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.30 (0.27), residues: 1064
  helix:  1.81 (0.22), residues: 597
  sheet:  0.94 (0.60), residues: 74
  loop : -0.61 (0.32), residues: 393

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG D 191 
 TYR   0.013   0.001   TYR A 188 
 PHE   0.016   0.001   PHE A  40 
 TRP   0.009   0.001   TRP C 132 
 HIS   0.002   0.000   HIS A 150 

Details of bonding type rmsd
  covalent geometry    : bond        0.00335 ( 8514)
  covalent geometry    : angle       0.53121 (11556)
  hydrogen bonds       : bond        0.05529 (  454)
  hydrogen bonds       : angle       3.99331 ( 1311)

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

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

  2128 Ramachandran restraints generated.
    1064 Oldfield, 0 Emsley, 1064 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2128 Ramachandran restraints generated.
    1064 Oldfield, 0 Emsley, 1064 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  137 residues out of total 890 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 111
  time to evaluate  : 0.320 
Fit side-chains
REVERT: A   17 ARG cc_start: 0.6081 (ttp-110) cc_final: 0.5810 (mtp-110)
REVERT: A  255 LYS cc_start: 0.8050 (tttt) cc_final: 0.7102 (mmtp)
REVERT: B   23 VAL cc_start: 0.8341 (OUTLIER) cc_final: 0.8006 (m)
REVERT: B   61 GLU cc_start: 0.7213 (mm-30) cc_final: 0.6623 (mp0)
REVERT: B   81 THR cc_start: 0.8908 (m) cc_final: 0.8699 (m)
REVERT: B  102 GLU cc_start: 0.7447 (tp30) cc_final: 0.7006 (mp0)
REVERT: B  150 ILE cc_start: 0.6865 (mt) cc_final: 0.6547 (mp)
REVERT: B  307 PHE cc_start: 0.7503 (t80) cc_final: 0.5895 (m-80)
REVERT: B  308 MET cc_start: 0.8517 (tpp) cc_final: 0.8155 (mmm)
REVERT: B  310 MET cc_start: 0.7036 (OUTLIER) cc_final: 0.6822 (ptm)
REVERT: C   59 MET cc_start: 0.8601 (OUTLIER) cc_final: 0.8297 (mmp)
REVERT: C   71 GLU cc_start: 0.6996 (pt0) cc_final: 0.6265 (pm20)
REVERT: C  119 GLU cc_start: 0.7741 (OUTLIER) cc_final: 0.7004 (tp30)
REVERT: C  229 GLU cc_start: 0.7159 (tp30) cc_final: 0.6909 (tp30)
REVERT: D   75 ASP cc_start: 0.7319 (t0) cc_final: 0.6999 (t0)
REVERT: D   80 LEU cc_start: 0.7956 (OUTLIER) cc_final: 0.7668 (mm)
REVERT: D  178 ASP cc_start: 0.7568 (t0) cc_final: 0.7233 (t0)
  outliers start: 26
  outliers final: 11
  residues processed: 129
  average time/residue: 0.5877
  time to fit residues: 80.3418
Evaluate side-chains
  124 residues out of total 890 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 108
  time to evaluate  : 0.299 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   73 ASN
Chi-restraints excluded: chain A residue  211 MET
Chi-restraints excluded: chain A residue  225 THR
Chi-restraints excluded: chain A residue  272 VAL
Chi-restraints excluded: chain B residue   23 VAL
Chi-restraints excluded: chain B residue   59 THR
Chi-restraints excluded: chain B residue   66 ASN
Chi-restraints excluded: chain B residue  103 LEU
Chi-restraints excluded: chain B residue  310 MET
Chi-restraints excluded: chain C residue   59 MET
Chi-restraints excluded: chain C residue  119 GLU
Chi-restraints excluded: chain D residue   32 ASP
Chi-restraints excluded: chain D residue   80 LEU
Chi-restraints excluded: chain D residue  117 LEU
Chi-restraints excluded: chain D residue  148 HIS
Chi-restraints excluded: chain D residue  248 THR
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 106
   random chunks:
   chunk 27 optimal weight:    1.9990
   chunk 6 optimal weight:    5.9990
   chunk 59 optimal weight:    2.9990
   chunk 98 optimal weight:    3.9990
   chunk 91 optimal weight:    0.8980
   chunk 103 optimal weight:   20.0000
   chunk 8 optimal weight:    0.5980
   chunk 105 optimal weight:    9.9990
   chunk 99 optimal weight:    3.9990
   chunk 33 optimal weight:    6.9990
   chunk 52 optimal weight:    5.9990
   overall best weight:    2.0986

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

Flipped N/Q/H residues before XYZ refinement:
D 211 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3934 r_free = 0.3934 target = 0.175728 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3218 r_free = 0.3218 target = 0.109403 restraints weight = 9188.728|
|-----------------------------------------------------------------------------|
r_work (start): 0.2956 rms_B_bonded: 2.60
r_work: 0.2735 rms_B_bonded: 2.65 restraints_weight: 0.5000
r_work: 0.2594 rms_B_bonded: 4.06 restraints_weight: 0.2500
r_work (final): 0.2594
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8293
moved from start:          0.1524

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.043   8514  Z= 0.182
  Angle     :  0.574   6.919  11556  Z= 0.301
  Chirality :  0.044   0.207   1357
  Planarity :  0.005   0.061   1439
  Dihedral  :  4.663  38.923   1143
  Min Nonbonded Distance : 2.610

Molprobity Statistics.
  All-atom Clashscore : 2.89
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  :  2.54 %
    Favored  : 97.37 %
  Rotamer:
    Outliers :  3.60 %
    Allowed  : 14.83 %
    Favored  : 81.57 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.07 (0.26), residues: 1064
  helix:  1.63 (0.22), residues: 594
  sheet:  0.70 (0.61), residues: 72
  loop : -0.69 (0.31), residues: 398

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG D 191 
 TYR   0.013   0.001   TYR A 188 
 PHE   0.016   0.001   PHE A  40 
 TRP   0.008   0.001   TRP C 132 
 HIS   0.002   0.001   HIS A 150 

Details of bonding type rmsd
  covalent geometry    : bond        0.00461 ( 8514)
  covalent geometry    : angle       0.57440 (11556)
  hydrogen bonds       : bond        0.06420 (  454)
  hydrogen bonds       : angle       4.09314 ( 1311)

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

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

  2128 Ramachandran restraints generated.
    1064 Oldfield, 0 Emsley, 1064 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2128 Ramachandran restraints generated.
    1064 Oldfield, 0 Emsley, 1064 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  145 residues out of total 890 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 113
  time to evaluate  : 0.307 
Fit side-chains
REVERT: A   17 ARG cc_start: 0.6068 (ttp-110) cc_final: 0.5774 (mtp-110)
REVERT: A  255 LYS cc_start: 0.8164 (tttt) cc_final: 0.7216 (mmtp)
REVERT: B   23 VAL cc_start: 0.8456 (OUTLIER) cc_final: 0.8084 (m)
REVERT: B   61 GLU cc_start: 0.7169 (mm-30) cc_final: 0.6555 (mp0)
REVERT: B  150 ILE cc_start: 0.6935 (mt) cc_final: 0.6607 (mp)
REVERT: B  307 PHE cc_start: 0.7637 (t80) cc_final: 0.6065 (m-80)
REVERT: B  308 MET cc_start: 0.8531 (tpp) cc_final: 0.8178 (mmm)
REVERT: B  310 MET cc_start: 0.7264 (OUTLIER) cc_final: 0.6883 (ptm)
REVERT: C   59 MET cc_start: 0.8581 (OUTLIER) cc_final: 0.8293 (mmp)
REVERT: C   71 GLU cc_start: 0.7106 (pt0) cc_final: 0.6466 (pm20)
REVERT: C  119 GLU cc_start: 0.7763 (OUTLIER) cc_final: 0.7025 (tp30)
REVERT: C  229 GLU cc_start: 0.7163 (tp30) cc_final: 0.6899 (tp30)
REVERT: D   75 ASP cc_start: 0.7384 (t0) cc_final: 0.7078 (t0)
REVERT: D   80 LEU cc_start: 0.7906 (OUTLIER) cc_final: 0.7693 (mm)
REVERT: D  245 LYS cc_start: 0.6127 (mmtt) cc_final: 0.5899 (mmmm)
  outliers start: 32
  outliers final: 18
  residues processed: 132
  average time/residue: 0.5945
  time to fit residues: 82.9244
Evaluate side-chains
  130 residues out of total 890 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 107
  time to evaluate  : 0.235 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   32 THR
Chi-restraints excluded: chain A residue   73 ASN
Chi-restraints excluded: chain A residue   86 SER
Chi-restraints excluded: chain A residue   95 VAL
Chi-restraints excluded: chain A residue  184 ARG
Chi-restraints excluded: chain A residue  211 MET
Chi-restraints excluded: chain A residue  225 THR
Chi-restraints excluded: chain A residue  272 VAL
Chi-restraints excluded: chain B residue   23 VAL
Chi-restraints excluded: chain B residue   59 THR
Chi-restraints excluded: chain B residue  103 LEU
Chi-restraints excluded: chain B residue  198 VAL
Chi-restraints excluded: chain B residue  310 MET
Chi-restraints excluded: chain C residue   11 ILE
Chi-restraints excluded: chain C residue   59 MET
Chi-restraints excluded: chain C residue   96 VAL
Chi-restraints excluded: chain C residue  119 GLU
Chi-restraints excluded: chain D residue   32 ASP
Chi-restraints excluded: chain D residue   52 LEU
Chi-restraints excluded: chain D residue   80 LEU
Chi-restraints excluded: chain D residue  117 LEU
Chi-restraints excluded: chain D residue  148 HIS
Chi-restraints excluded: chain D residue  248 THR
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 106
   random chunks:
   chunk 91 optimal weight:    1.9990
   chunk 77 optimal weight:    2.9990
   chunk 41 optimal weight:    0.9980
   chunk 40 optimal weight:    0.9980
   chunk 82 optimal weight:    0.0170
   chunk 44 optimal weight:    0.7980
   chunk 75 optimal weight:    0.0170
   chunk 88 optimal weight:    7.9990
   chunk 35 optimal weight:    0.0980
   chunk 99 optimal weight:    6.9990
   chunk 59 optimal weight:    2.9990
   overall best weight:    0.3856

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3979 r_free = 0.3979 target = 0.180376 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3227 r_free = 0.3227 target = 0.109866 restraints weight = 9234.023|
|-----------------------------------------------------------------------------|
r_work (start): 0.2988 rms_B_bonded: 2.13
r_work: 0.2865 rms_B_bonded: 2.47 restraints_weight: 0.5000
r_work: 0.2725 rms_B_bonded: 3.83 restraints_weight: 0.2500
r_work (final): 0.2725
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8093
moved from start:          0.1735

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.034   8514  Z= 0.104
  Angle     :  0.502   9.795  11556  Z= 0.260
  Chirality :  0.039   0.145   1357
  Planarity :  0.004   0.060   1439
  Dihedral  :  4.387  36.008   1143
  Min Nonbonded Distance : 2.633

Molprobity Statistics.
  All-atom Clashscore : 2.72
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  :  1.79 %
    Favored  : 98.12 %
  Rotamer:
    Outliers :  2.47 %
    Allowed  : 16.52 %
    Favored  : 81.01 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.38 (0.27), residues: 1064
  helix:  1.95 (0.22), residues: 596
  sheet:  0.78 (0.62), residues: 74
  loop : -0.68 (0.31), residues: 394

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG D 191 
 TYR   0.011   0.001   TYR D 226 
 PHE   0.012   0.001   PHE A  40 
 TRP   0.007   0.001   TRP B  46 
 HIS   0.001   0.000   HIS C 221 

Details of bonding type rmsd
  covalent geometry    : bond        0.00210 ( 8514)
  covalent geometry    : angle       0.50175 (11556)
  hydrogen bonds       : bond        0.04210 (  454)
  hydrogen bonds       : angle       3.86087 ( 1311)

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

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

  2128 Ramachandran restraints generated.
    1064 Oldfield, 0 Emsley, 1064 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2128 Ramachandran restraints generated.
    1064 Oldfield, 0 Emsley, 1064 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  140 residues out of total 890 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 118
  time to evaluate  : 0.323 
Fit side-chains
REVERT: A   17 ARG cc_start: 0.5955 (ttp-110) cc_final: 0.5733 (mtp-110)
REVERT: A  255 LYS cc_start: 0.7884 (tttt) cc_final: 0.6923 (mmtp)
REVERT: B   23 VAL cc_start: 0.8084 (OUTLIER) cc_final: 0.7815 (m)
REVERT: B   61 GLU cc_start: 0.7081 (mm-30) cc_final: 0.6477 (mp0)
REVERT: B  150 ILE cc_start: 0.6883 (mt) cc_final: 0.6597 (mp)
REVERT: B  307 PHE cc_start: 0.7339 (t80) cc_final: 0.5692 (m-80)
REVERT: B  308 MET cc_start: 0.8334 (tpp) cc_final: 0.7983 (mmm)
REVERT: C   59 MET cc_start: 0.8526 (OUTLIER) cc_final: 0.8213 (mmp)
REVERT: C   71 GLU cc_start: 0.7002 (pt0) cc_final: 0.6280 (pm20)
REVERT: C  229 GLU cc_start: 0.7245 (tp30) cc_final: 0.7022 (mm-30)
REVERT: D   80 LEU cc_start: 0.7847 (OUTLIER) cc_final: 0.7570 (mm)
REVERT: D  178 ASP cc_start: 0.7267 (t0) cc_final: 0.6934 (t0)
REVERT: D  245 LYS cc_start: 0.5979 (mmtt) cc_final: 0.5767 (mmmm)
  outliers start: 22
  outliers final: 10
  residues processed: 133
  average time/residue: 0.5781
  time to fit residues: 81.4780
Evaluate side-chains
  127 residues out of total 890 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 114
  time to evaluate  : 0.369 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  211 MET
Chi-restraints excluded: chain A residue  225 THR
Chi-restraints excluded: chain A residue  272 VAL
Chi-restraints excluded: chain B residue   23 VAL
Chi-restraints excluded: chain B residue  103 LEU
Chi-restraints excluded: chain C residue   59 MET
Chi-restraints excluded: chain C residue   88 LEU
Chi-restraints excluded: chain D residue   52 LEU
Chi-restraints excluded: chain D residue   80 LEU
Chi-restraints excluded: chain D residue  117 LEU
Chi-restraints excluded: chain D residue  148 HIS
Chi-restraints excluded: chain D residue  236 THR
Chi-restraints excluded: chain D residue  248 THR
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 106
   random chunks:
   chunk 97 optimal weight:    0.9990
   chunk 35 optimal weight:    0.9990
   chunk 104 optimal weight:   20.0000
   chunk 91 optimal weight:    0.7980
   chunk 87 optimal weight:    3.9990
   chunk 21 optimal weight:    2.9990
   chunk 63 optimal weight:    3.9990
   chunk 64 optimal weight:   10.0000
   chunk 93 optimal weight:    1.9990
   chunk 7 optimal weight:    1.9990
   chunk 27 optimal weight:    0.5980
   overall best weight:    1.0786

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

Flipped N/Q/H residues before XYZ refinement:
A 236 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3957 r_free = 0.3957 target = 0.177803 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3197 r_free = 0.3197 target = 0.107392 restraints weight = 9105.282|
|-----------------------------------------------------------------------------|
r_work (start): 0.2967 rms_B_bonded: 2.08
r_work: 0.2837 rms_B_bonded: 2.47 restraints_weight: 0.5000
r_work: 0.2696 rms_B_bonded: 3.81 restraints_weight: 0.2500
r_work (final): 0.2696
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8222
moved from start:          0.1782

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   8514  Z= 0.125
  Angle     :  0.526  10.983  11556  Z= 0.273
  Chirality :  0.041   0.164   1357
  Planarity :  0.004   0.056   1439
  Dihedral  :  4.397  39.042   1143
  Min Nonbonded Distance : 2.624

Molprobity Statistics.
  All-atom Clashscore : 3.13
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  :  2.54 %
    Favored  : 97.37 %
  Rotamer:
    Outliers :  2.36 %
    Allowed  : 17.08 %
    Favored  : 80.56 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.37 (0.27), residues: 1064
  helix:  1.94 (0.22), residues: 597
  sheet:  0.80 (0.62), residues: 74
  loop : -0.69 (0.31), residues: 393

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG D 217 
 TYR   0.012   0.001   TYR A 188 
 PHE   0.016   0.001   PHE A  40 
 TRP   0.007   0.001   TRP D 140 
 HIS   0.001   0.000   HIS A 150 

Details of bonding type rmsd
  covalent geometry    : bond        0.00292 ( 8514)
  covalent geometry    : angle       0.52649 (11556)
  hydrogen bonds       : bond        0.04995 (  454)
  hydrogen bonds       : angle       3.87421 ( 1311)

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

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

  2128 Ramachandran restraints generated.
    1064 Oldfield, 0 Emsley, 1064 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2128 Ramachandran restraints generated.
    1064 Oldfield, 0 Emsley, 1064 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  133 residues out of total 890 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 112
  time to evaluate  : 0.232 
Fit side-chains
REVERT: A   17 ARG cc_start: 0.6044 (ttp-110) cc_final: 0.5787 (mtp-110)
REVERT: A  255 LYS cc_start: 0.8014 (tttt) cc_final: 0.7080 (mmtp)
REVERT: B   23 VAL cc_start: 0.8288 (OUTLIER) cc_final: 0.7990 (m)
REVERT: B  150 ILE cc_start: 0.6984 (mt) cc_final: 0.6692 (mp)
REVERT: B  307 PHE cc_start: 0.7476 (t80) cc_final: 0.5842 (m-80)
REVERT: B  308 MET cc_start: 0.8490 (tpp) cc_final: 0.8128 (mmm)
REVERT: C   59 MET cc_start: 0.8595 (OUTLIER) cc_final: 0.8294 (mmp)
REVERT: C   71 GLU cc_start: 0.7120 (pt0) cc_final: 0.6384 (pm20)
REVERT: C  119 GLU cc_start: 0.7776 (OUTLIER) cc_final: 0.7003 (tp30)
REVERT: C  229 GLU cc_start: 0.7249 (tp30) cc_final: 0.7046 (mm-30)
REVERT: D   80 LEU cc_start: 0.7879 (OUTLIER) cc_final: 0.7647 (mm)
REVERT: D  178 ASP cc_start: 0.7517 (t0) cc_final: 0.7160 (t0)
REVERT: D  187 ILE cc_start: 0.6882 (OUTLIER) cc_final: 0.6606 (tp)
REVERT: D  245 LYS cc_start: 0.6017 (mmtt) cc_final: 0.5811 (mmmm)
  outliers start: 21
  outliers final: 11
  residues processed: 127
  average time/residue: 0.5519
  time to fit residues: 74.4507
Evaluate side-chains
  129 residues out of total 890 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 113
  time to evaluate  : 0.302 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   32 THR
Chi-restraints excluded: chain A residue   86 SER
Chi-restraints excluded: chain A residue  211 MET
Chi-restraints excluded: chain A residue  225 THR
Chi-restraints excluded: chain A residue  272 VAL
Chi-restraints excluded: chain B residue   23 VAL
Chi-restraints excluded: chain B residue  103 LEU
Chi-restraints excluded: chain B residue  198 VAL
Chi-restraints excluded: chain C residue   59 MET
Chi-restraints excluded: chain C residue  119 GLU
Chi-restraints excluded: chain D residue   80 LEU
Chi-restraints excluded: chain D residue  117 LEU
Chi-restraints excluded: chain D residue  148 HIS
Chi-restraints excluded: chain D residue  187 ILE
Chi-restraints excluded: chain D residue  236 THR
Chi-restraints excluded: chain D residue  248 THR
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 106
   random chunks:
   chunk 15 optimal weight:    0.9990
   chunk 45 optimal weight:    0.5980
   chunk 28 optimal weight:    0.9990
   chunk 39 optimal weight:    0.0970
   chunk 1 optimal weight:    0.9990
   chunk 30 optimal weight:    0.9990
   chunk 53 optimal weight:    1.9990
   chunk 72 optimal weight:    3.9990
   chunk 75 optimal weight:    0.1980
   chunk 55 optimal weight:    0.7980
   chunk 64 optimal weight:    7.9990
   overall best weight:    0.5380

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3988 r_free = 0.3988 target = 0.181027 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.3250 r_free = 0.3250 target = 0.111293 restraints weight = 9174.213|
|-----------------------------------------------------------------------------|
r_work (start): 0.2998 rms_B_bonded: 2.07
r_work: 0.2873 rms_B_bonded: 2.44 restraints_weight: 0.5000
r_work: 0.2733 rms_B_bonded: 3.78 restraints_weight: 0.2500
r_work (final): 0.2733
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8105
moved from start:          0.1910

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.034   8514  Z= 0.104
  Angle     :  0.512  11.840  11556  Z= 0.261
  Chirality :  0.040   0.162   1357
  Planarity :  0.004   0.052   1439
  Dihedral  :  4.286  38.458   1143
  Min Nonbonded Distance : 2.633

Molprobity Statistics.
  All-atom Clashscore : 2.89
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  :  1.88 %
    Favored  : 98.03 %
  Rotamer:
    Outliers :  1.69 %
    Allowed  : 17.87 %
    Favored  : 80.45 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.50 (0.27), residues: 1064
  helix:  2.09 (0.22), residues: 596
  sheet:  0.82 (0.62), residues: 74
  loop : -0.70 (0.31), residues: 394

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG D 191 
 TYR   0.011   0.001   TYR D 226 
 PHE   0.014   0.001   PHE A  40 
 TRP   0.008   0.001   TRP D 140 
 HIS   0.001   0.000   HIS C 221 

Details of bonding type rmsd
  covalent geometry    : bond        0.00223 ( 8514)
  covalent geometry    : angle       0.51240 (11556)
  hydrogen bonds       : bond        0.04213 (  454)
  hydrogen bonds       : angle       3.80345 ( 1311)

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

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

  2128 Ramachandran restraints generated.
    1064 Oldfield, 0 Emsley, 1064 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2128 Ramachandran restraints generated.
    1064 Oldfield, 0 Emsley, 1064 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  129 residues out of total 890 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 114
  time to evaluate  : 0.297 
Fit side-chains
REVERT: A   17 ARG cc_start: 0.5973 (ttp-110) cc_final: 0.5741 (mtp-110)
REVERT: A  236 GLN cc_start: 0.8040 (tp40) cc_final: 0.7818 (mm110)
REVERT: A  255 LYS cc_start: 0.7868 (tttt) cc_final: 0.6905 (mmtp)
REVERT: B   23 VAL cc_start: 0.8100 (OUTLIER) cc_final: 0.7831 (m)
REVERT: B  150 ILE cc_start: 0.6893 (mt) cc_final: 0.6604 (mp)
REVERT: B  307 PHE cc_start: 0.7336 (t80) cc_final: 0.5672 (m-80)
REVERT: B  308 MET cc_start: 0.8364 (tpp) cc_final: 0.8003 (mmm)
REVERT: C   59 MET cc_start: 0.8533 (OUTLIER) cc_final: 0.8212 (mmp)
REVERT: C   71 GLU cc_start: 0.7055 (pt0) cc_final: 0.6440 (pm20)
REVERT: C  119 GLU cc_start: 0.7710 (OUTLIER) cc_final: 0.6938 (tp30)
REVERT: D   80 LEU cc_start: 0.7816 (OUTLIER) cc_final: 0.7540 (mm)
REVERT: D  178 ASP cc_start: 0.7300 (t0) cc_final: 0.6997 (t0)
REVERT: D  245 LYS cc_start: 0.6031 (mmtt) cc_final: 0.5814 (mmmm)
  outliers start: 15
  outliers final: 9
  residues processed: 125
  average time/residue: 0.6011
  time to fit residues: 79.6505
Evaluate side-chains
  119 residues out of total 890 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 106
  time to evaluate  : 0.304 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   32 THR
Chi-restraints excluded: chain A residue  225 THR
Chi-restraints excluded: chain A residue  272 VAL
Chi-restraints excluded: chain B residue   23 VAL
Chi-restraints excluded: chain B residue  103 LEU
Chi-restraints excluded: chain B residue  198 VAL
Chi-restraints excluded: chain C residue   59 MET
Chi-restraints excluded: chain C residue  119 GLU
Chi-restraints excluded: chain D residue   80 LEU
Chi-restraints excluded: chain D residue  117 LEU
Chi-restraints excluded: chain D residue  148 HIS
Chi-restraints excluded: chain D residue  236 THR
Chi-restraints excluded: chain D residue  248 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 106
   random chunks:
   chunk 61 optimal weight:   20.0000
   chunk 91 optimal weight:    0.7980
   chunk 101 optimal weight:   10.0000
   chunk 21 optimal weight:    2.9990
   chunk 100 optimal weight:    4.9990
   chunk 32 optimal weight:    0.8980
   chunk 81 optimal weight:    7.9990
   chunk 79 optimal weight:   30.0000
   chunk 90 optimal weight:    4.9990
   chunk 66 optimal weight:    4.9990
   chunk 76 optimal weight:    0.8980
   overall best weight:    2.1184

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

Flipped N/Q/H residues before XYZ refinement:
** C  24 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3940 r_free = 0.3940 target = 0.176287 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 64)----------------|
| r_work = 0.3170 r_free = 0.3170 target = 0.105192 restraints weight = 9225.050|
|-----------------------------------------------------------------------------|
r_work (start): 0.2903 rms_B_bonded: 2.06
r_work: 0.2771 rms_B_bonded: 2.43 restraints_weight: 0.5000
r_work: 0.2631 rms_B_bonded: 3.74 restraints_weight: 0.2500
r_work (final): 0.2631
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8212
moved from start:          0.1818

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.043   8514  Z= 0.185
  Angle     :  0.597  11.807  11556  Z= 0.309
  Chirality :  0.044   0.207   1357
  Planarity :  0.005   0.054   1439
  Dihedral  :  4.547  41.539   1143
  Min Nonbonded Distance : 2.541

Molprobity Statistics.
  All-atom Clashscore : 3.48
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  :  2.63 %
    Favored  : 97.27 %
  Rotamer:
    Outliers :  2.25 %
    Allowed  : 17.75 %
    Favored  : 80.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.19 (0.27), residues: 1064
  helix:  1.79 (0.22), residues: 595
  sheet:  0.30 (0.59), residues: 79
  loop : -0.67 (0.32), residues: 390

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG D 217 
 TYR   0.013   0.001   TYR A 188 
 PHE   0.016   0.001   PHE A  40 
 TRP   0.009   0.001   TRP D 140 
 HIS   0.002   0.001   HIS C  24 

Details of bonding type rmsd
  covalent geometry    : bond        0.00468 ( 8514)
  covalent geometry    : angle       0.59678 (11556)
  hydrogen bonds       : bond        0.06212 (  454)
  hydrogen bonds       : angle       4.01661 ( 1311)

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

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

  2128 Ramachandran restraints generated.
    1064 Oldfield, 0 Emsley, 1064 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2128 Ramachandran restraints generated.
    1064 Oldfield, 0 Emsley, 1064 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  125 residues out of total 890 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 105
  time to evaluate  : 0.213 
Fit side-chains
REVERT: A   17 ARG cc_start: 0.6044 (ttp-110) cc_final: 0.5771 (mtp-110)
REVERT: A  255 LYS cc_start: 0.8043 (tttt) cc_final: 0.7085 (mmtp)
REVERT: B   23 VAL cc_start: 0.8336 (OUTLIER) cc_final: 0.8000 (m)
REVERT: B   83 PHE cc_start: 0.8331 (t80) cc_final: 0.8104 (t80)
REVERT: B  150 ILE cc_start: 0.6854 (mt) cc_final: 0.6560 (mp)
REVERT: B  307 PHE cc_start: 0.7511 (t80) cc_final: 0.5877 (m-80)
REVERT: B  308 MET cc_start: 0.8455 (tpp) cc_final: 0.8102 (mmm)
REVERT: C   59 MET cc_start: 0.8542 (OUTLIER) cc_final: 0.8262 (mmp)
REVERT: C   71 GLU cc_start: 0.7169 (pt0) cc_final: 0.6283 (pm20)
REVERT: C  119 GLU cc_start: 0.7751 (OUTLIER) cc_final: 0.6993 (tp30)
REVERT: D  178 ASP cc_start: 0.7516 (t0) cc_final: 0.7173 (t0)
  outliers start: 20
  outliers final: 12
  residues processed: 120
  average time/residue: 0.5688
  time to fit residues: 72.3353
Evaluate side-chains
  119 residues out of total 890 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 104
  time to evaluate  : 0.302 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   32 THR
Chi-restraints excluded: chain A residue   86 SER
Chi-restraints excluded: chain A residue  211 MET
Chi-restraints excluded: chain A residue  225 THR
Chi-restraints excluded: chain A residue  272 VAL
Chi-restraints excluded: chain B residue   23 VAL
Chi-restraints excluded: chain B residue  103 LEU
Chi-restraints excluded: chain B residue  192 VAL
Chi-restraints excluded: chain B residue  198 VAL
Chi-restraints excluded: chain C residue   59 MET
Chi-restraints excluded: chain C residue  119 GLU
Chi-restraints excluded: chain D residue  117 LEU
Chi-restraints excluded: chain D residue  148 HIS
Chi-restraints excluded: chain D residue  236 THR
Chi-restraints excluded: chain D residue  248 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 106
   random chunks:
   chunk 51 optimal weight:    0.0070
   chunk 63 optimal weight:    4.9990
   chunk 5 optimal weight:   10.0000
   chunk 56 optimal weight:    0.9990
   chunk 28 optimal weight:    0.9980
   chunk 78 optimal weight:   10.0000
   chunk 40 optimal weight:    1.9990
   chunk 41 optimal weight:    0.9990
   chunk 37 optimal weight:    0.0570
   chunk 21 optimal weight:    0.0000
   chunk 22 optimal weight:    0.9980
   overall best weight:    0.4120

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

Flipped N/Q/H residues before XYZ refinement:
A 236 GLN
D  28 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3987 r_free = 0.3987 target = 0.181006 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3247 r_free = 0.3247 target = 0.111016 restraints weight = 9179.727|
|-----------------------------------------------------------------------------|
r_work (start): 0.3020 rms_B_bonded: 2.07
r_work: 0.2896 rms_B_bonded: 2.45 restraints_weight: 0.5000
r_work: 0.2756 rms_B_bonded: 3.79 restraints_weight: 0.2500
r_work (final): 0.2756
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8142
moved from start:          0.1994

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.035   8514  Z= 0.107
  Angle     :  0.532  12.078  11556  Z= 0.271
  Chirality :  0.040   0.162   1357
  Planarity :  0.004   0.051   1439
  Dihedral  :  4.338  39.168   1143
  Min Nonbonded Distance : 2.611

Molprobity Statistics.
  All-atom Clashscore : 3.13
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  :  1.79 %
    Favored  : 98.12 %
  Rotamer:
    Outliers :  1.91 %
    Allowed  : 18.09 %
    Favored  : 80.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.38 (0.27), residues: 1064
  helix:  2.00 (0.22), residues: 597
  sheet:  0.38 (0.59), residues: 79
  loop : -0.69 (0.32), residues: 388

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG D 217 
 TYR   0.012   0.001   TYR D 226 
 PHE   0.016   0.001   PHE C 224 
 TRP   0.009   0.001   TRP D 140 
 HIS   0.001   0.000   HIS C  24 

Details of bonding type rmsd
  covalent geometry    : bond        0.00224 ( 8514)
  covalent geometry    : angle       0.53249 (11556)
  hydrogen bonds       : bond        0.04245 (  454)
  hydrogen bonds       : angle       3.84024 ( 1311)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3395.85 seconds
wall clock time: 58 minutes 13.38 seconds (3493.38 seconds total)