Starting phenix.real_space_refine
on Sat Oct 11 18:16:14 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8wm8_37645/10_2025/8wm8_37645.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8wm8_37645/10_2025/8wm8_37645.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.54
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8wm8_37645/10_2025/8wm8_37645.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8wm8_37645/10_2025/8wm8_37645.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8wm8_37645/10_2025/8wm8_37645.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8wm8_37645/10_2025/8wm8_37645.cif"
  }
  resolution = 3.54
  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=   0.001 sd=   0.073
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 5
    Type Number    sf(0)   Gaussians
     S      25      5.16       5
     C    5396      2.51       5
     N    1374      2.21       5
     O    1459      1.98       5
     H    8522      0.53       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 23 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5842/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 16776
  Number of models: 1
  Model: ""
    Number of chains: 5
    Chain: "D"
      Number of atoms: 4116
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 259, 4116
          Classifications: {'peptide': 259}
          Link IDs: {'PTRANS': 17, 'TRANS': 241}
    Chain: "B"
      Number of atoms: 4198
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 265, 4198
          Classifications: {'peptide': 265}
          Link IDs: {'PTRANS': 17, 'TRANS': 247}
    Chain: "A"
      Number of atoms: 4170
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 263, 4170
          Classifications: {'peptide': 263}
          Link IDs: {'PTRANS': 17, 'TRANS': 245}
    Chain: "C"
      Number of atoms: 4288
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 268, 4288
          Classifications: {'peptide': 268}
          Link IDs: {'PTRANS': 11, 'TRANS': 256}
    Chain: "A"
      Number of atoms: 4
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 4
          Unusual residues: {'NO3': 1}
          Classifications: {'undetermined': 1}
  Time building chain proxies: 3.33, per 1000 atoms: 0.20
  Number of scatterers: 16776
  At special positions: 0
  Unit cell: (81.32, 118.77, 95.23, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S      25     16.00
     O    1459      8.00
     N    1374      7.00
     C    5396      6.00
     H    8522      1.00
    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: 1.48
  Conformation dependent library (CDL) restraints added in 398.5 milliseconds
  
  Enol-peptide restraints added in 476.8 nanoseconds
  

  2094 Ramachandran restraints generated.
    1047 Oldfield, 0 Emsley, 1047 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1948

  Finding SS restraints...
    Secondary structure from input PDB file:
      52 helices and 4 sheets defined
      56.6% alpha, 5.0% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.38
  Creating SS restraints...
    Processing helix  chain 'D' and resid 62 through 71
    Processing helix  chain 'D' and resid 83 through 86
    Processing helix  chain 'D' and resid 100 through 104
      removed outlier: 3.852A  pdb=" N   CYS D 103 " --> pdb=" O   GLN D 100 " (cutoff:3.500A)
      removed outlier: 4.607A  pdb=" N   LEU D 104 " --> pdb=" O   ASN D 101 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'D' and resid 100 through 104'
    Processing helix  chain 'D' and resid 109 through 119
      removed outlier: 4.008A  pdb=" N   ALA D 117 " --> pdb=" O   ASN D 113 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 126 through 140
      removed outlier: 3.710A  pdb=" N   ALA D 132 " --> pdb=" O   ALA D 128 " (cutoff:3.500A)
      removed outlier: 4.184A  pdb=" N   ARG D 135 " --> pdb=" O   ARG D 131 " (cutoff:3.500A)
      removed outlier: 3.536A  pdb=" N   MET D 140 " --> pdb=" O   GLU D 136 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 155 through 170
      removed outlier: 3.663A  pdb=" N   GLN D 160 " --> pdb=" O   GLY D 156 " (cutoff:3.500A)
      removed outlier: 4.413A  pdb=" N   ARG D 161 " --> pdb=" O   GLY D 157 " (cutoff:3.500A)
      removed outlier: 4.041A  pdb=" N   VAL D 162 " --> pdb=" O   MET D 158 " (cutoff:3.500A)
      removed outlier: 4.058A  pdb=" N   ILE D 170 " --> pdb=" O   ARG D 166 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 185 through 204
      removed outlier: 3.548A  pdb=" N   GLU D 191 " --> pdb=" O   ILE D 187 " (cutoff:3.500A)
      removed outlier: 3.817A  pdb=" N   GLN D 193 " --> pdb=" O   LYS D 189 " (cutoff:3.500A)
      removed outlier: 4.081A  pdb=" N   GLU D 194 " --> pdb=" O   GLU D 190 " (cutoff:3.500A)
      removed outlier: 3.501A  pdb=" N   GLU D 195 " --> pdb=" O   GLU D 191 " (cutoff:3.500A)
      removed outlier: 3.999A  pdb=" N   GLN D 198 " --> pdb=" O   GLU D 194 " (cutoff:3.500A)
      removed outlier: 4.349A  pdb=" N   ILE D 199 " --> pdb=" O   GLU D 195 " (cutoff:3.500A)
      removed outlier: 3.531A  pdb=" N   HIS D 203 " --> pdb=" O   ILE D 199 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 216 through 221
    Processing helix  chain 'D' and resid 256 through 271
      removed outlier: 3.769A  pdb=" N   ASP D 260 " --> pdb=" O   PRO D 256 " (cutoff:3.500A)
      removed outlier: 3.509A  pdb=" N   ASN D 271 " --> pdb=" O   ASP D 267 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 15 through 23
      removed outlier: 3.643A  pdb=" N   ASN B  19 " --> pdb=" O   GLN B  15 " (cutoff:3.500A)
      removed outlier: 3.922A  pdb=" N   PHE B  21 " --> pdb=" O   ALA B  17 " (cutoff:3.500A)
      removed outlier: 4.119A  pdb=" N   TRP B  23 " --> pdb=" O   ASN B  19 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 26 through 44
      removed outlier: 3.553A  pdb=" N   LEU B  30 " --> pdb=" O   VAL B  26 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 55 through 60
    Processing helix  chain 'B' and resid 61 through 67
      removed outlier: 3.686A  pdb=" N   PHE B  65 " --> pdb=" O   THR B  61 " (cutoff:3.500A)
      removed outlier: 3.539A  pdb=" N   ILE B  66 " --> pdb=" O   TRP B  62 " (cutoff:3.500A)
      removed outlier: 3.797A  pdb=" N   ILE B  67 " --> pdb=" O   ASP B  63 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 61 through 67'
    Processing helix  chain 'B' and resid 80 through 94
      removed outlier: 3.832A  pdb=" N   SER B  87 " --> pdb=" O   GLN B  83 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 95 through 111
      removed outlier: 3.823A  pdb=" N   ILE B 103 " --> pdb=" O   ALA B  99 " (cutoff:3.500A)
      removed outlier: 3.565A  pdb=" N   ILE B 104 " --> pdb=" O   ILE B 100 " (cutoff:3.500A)
      removed outlier: 4.012A  pdb=" N   LEU B 105 " --> pdb=" O   ALA B 101 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 112 through 129
      removed outlier: 4.034A  pdb=" N   ALA B 118 " --> pdb=" O   LEU B 114 " (cutoff:3.500A)
      Proline residue:  B 121  - end of helix
      removed outlier: 4.340A  pdb=" N   VAL B 125 " --> pdb=" O   PRO B 121 " (cutoff:3.500A)
      removed outlier: 4.169A  pdb=" N   LEU B 126 " --> pdb=" O   ILE B 122 " (cutoff:3.500A)
      removed outlier: 3.986A  pdb=" N   THR B 128 " --> pdb=" O   GLN B 124 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 130 through 133
    Processing helix  chain 'B' and resid 134 through 142
    Processing helix  chain 'B' and resid 145 through 155
      removed outlier: 3.664A  pdb=" N   ILE B 150 " --> pdb=" O   ASN B 146 " (cutoff:3.500A)
      removed outlier: 4.893A  pdb=" N   PHE B 151 " --> pdb=" O   PRO B 147 " (cutoff:3.500A)
      removed outlier: 3.677A  pdb=" N   ILE B 153 " --> pdb=" O   ALA B 149 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 158 through 171
      removed outlier: 3.871A  pdb=" N   ASN B 164 " --> pdb=" O   PRO B 160 " (cutoff:3.500A)
      removed outlier: 3.537A  pdb=" N   THR B 166 " --> pdb=" O   LEU B 162 " (cutoff:3.500A)
      removed outlier: 4.496A  pdb=" N   VAL B 167 " --> pdb=" O   LEU B 163 " (cutoff:3.500A)
      removed outlier: 3.826A  pdb=" N   GLY B 168 " --> pdb=" O   ASN B 164 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 173 through 183
      removed outlier: 3.620A  pdb=" N   ILE B 177 " --> pdb=" O   PRO B 173 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 187 through 195
    Processing helix  chain 'B' and resid 195 through 208
      Proline residue:  B 201  - end of helix
    Processing helix  chain 'B' and resid 208 through 219
      removed outlier: 3.804A  pdb=" N   GLY B 212 " --> pdb=" O   ARG B 208 " (cutoff:3.500A)
      removed outlier: 3.750A  pdb=" N   LEU B 213 " --> pdb=" O   ILE B 209 " (cutoff:3.500A)
      removed outlier: 3.905A  pdb=" N   SER B 214 " --> pdb=" O   GLY B 210 " (cutoff:3.500A)
      removed outlier: 3.622A  pdb=" N   ALA B 217 " --> pdb=" O   LEU B 213 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 235 through 240
      removed outlier: 3.610A  pdb=" N   ASN B 239 " --> pdb=" O   TRP B 235 " (cutoff:3.500A)
      removed outlier: 4.090A  pdb=" N   THR B 240 " --> pdb=" O   ASP B 236 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 235 through 240'
    Processing helix  chain 'B' and resid 244 through 275
      removed outlier: 3.950A  pdb=" N   GLU B 248 " --> pdb=" O   THR B 244 " (cutoff:3.500A)
      removed outlier: 4.031A  pdb=" N   ILE B 249 " --> pdb=" O   ASN B 245 " (cutoff:3.500A)
      removed outlier: 4.007A  pdb=" N   ILE B 250 " --> pdb=" O   LEU B 246 " (cutoff:3.500A)
      removed outlier: 3.725A  pdb=" N   LEU B 253 " --> pdb=" O   ILE B 249 " (cutoff:3.500A)
      removed outlier: 3.632A  pdb=" N   VAL B 267 " --> pdb=" O   LEU B 263 " (cutoff:3.500A)
      removed outlier: 4.108A  pdb=" N   GLY B 268 " --> pdb=" O   ASP B 264 " (cutoff:3.500A)
      removed outlier: 3.647A  pdb=" N   LYS B 273 " --> pdb=" O   PHE B 269 " (cutoff:3.500A)
      removed outlier: 3.700A  pdb=" N   VAL B 274 " --> pdb=" O   VAL B 270 " (cutoff:3.500A)
      removed outlier: 3.651A  pdb=" N   VAL B 275 " --> pdb=" O   ALA B 271 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 21 through 25
    Processing helix  chain 'A' and resid 26 through 44
    Processing helix  chain 'A' and resid 53 through 60
    Processing helix  chain 'A' and resid 83 through 88
    Processing helix  chain 'A' and resid 89 through 94
    Processing helix  chain 'A' and resid 96 through 109
      removed outlier: 3.530A  pdb=" N   GLY A 102 " --> pdb=" O   ALA A  98 " (cutoff:3.500A)
      removed outlier: 3.914A  pdb=" N   ILE A 104 " --> pdb=" O   ILE A 100 " (cutoff:3.500A)
      removed outlier: 4.356A  pdb=" N   LEU A 105 " --> pdb=" O   ALA A 101 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 130 through 133
    Processing helix  chain 'A' and resid 134 through 143
    Processing helix  chain 'A' and resid 144 through 157
    Processing helix  chain 'A' and resid 158 through 171
      removed outlier: 4.024A  pdb=" N   ASN A 164 " --> pdb=" O   PRO A 160 " (cutoff:3.500A)
      removed outlier: 3.873A  pdb=" N   VAL A 167 " --> pdb=" O   LEU A 163 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 173 through 182
      removed outlier: 3.549A  pdb=" N   ILE A 177 " --> pdb=" O   PRO A 173 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 187 through 192
    Processing helix  chain 'A' and resid 199 through 214
      removed outlier: 3.569A  pdb=" N   THR A 205 " --> pdb=" O   PRO A 201 " (cutoff:3.500A)
      removed outlier: 4.120A  pdb=" N   ILE A 209 " --> pdb=" O   THR A 205 " (cutoff:3.500A)
      removed outlier: 4.658A  pdb=" N   GLY A 212 " --> pdb=" O   ARG A 208 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 214 through 221
    Processing helix  chain 'A' and resid 221 through 226
      removed outlier: 3.736A  pdb=" N   VAL A 225 " --> pdb=" O   ALA A 221 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 246 through 256
      removed outlier: 3.562A  pdb=" N   LEU A 251 " --> pdb=" O   SER A 247 " (cutoff:3.500A)
      removed outlier: 3.870A  pdb=" N   ALA A 252 " --> pdb=" O   GLU A 248 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 263 through 275
      removed outlier: 3.697A  pdb=" N   VAL A 267 " --> pdb=" O   LEU A 263 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 48 through 57
      removed outlier: 3.534A  pdb=" N   ILE C  55 " --> pdb=" O   LEU C  51 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 67 through 71
    Processing helix  chain 'C' and resid 94 through 105
      removed outlier: 3.507A  pdb=" N   VAL C  99 " --> pdb=" O   VAL C  95 " (cutoff:3.500A)
      removed outlier: 3.626A  pdb=" N   ALA C 100 " --> pdb=" O   ARG C  96 " (cutoff:3.500A)
      removed outlier: 3.804A  pdb=" N   ALA C 102 " --> pdb=" O   ASN C  98 " (cutoff:3.500A)
      removed outlier: 3.959A  pdb=" N   GLU C 105 " --> pdb=" O   LEU C 101 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 111 through 123
      removed outlier: 3.745A  pdb=" N   ALA C 117 " --> pdb=" O   GLY C 113 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 142 through 155
      removed outlier: 3.805A  pdb=" N   ARG C 146 " --> pdb=" O   GLY C 142 " (cutoff:3.500A)
      removed outlier: 3.668A  pdb=" N   VAL C 147 " --> pdb=" O   MET C 143 " (cutoff:3.500A)
      removed outlier: 4.033A  pdb=" N   ALA C 148 " --> pdb=" O   LYS C 144 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 172 through 186
      removed outlier: 3.825A  pdb=" N   GLU C 179 " --> pdb=" O   GLY C 175 " (cutoff:3.500A)
      removed outlier: 4.252A  pdb=" N   GLN C 180 " --> pdb=" O   SER C 176 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 198 through 203
      removed outlier: 3.837A  pdb=" N   ALA C 202 " --> pdb=" O   ASP C 198 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 233 through 238
      removed outlier: 3.831A  pdb=" N   VAL C 238 " --> pdb=" O   ARG C 234 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 240 through 269
      removed outlier: 4.187A  pdb=" N   TYR C 244 " --> pdb=" O   HIS C 240 " (cutoff:3.500A)
      removed outlier: 3.816A  pdb=" N   ASN C 245 " --> pdb=" O   PRO C 241 " (cutoff:3.500A)
      removed outlier: 3.533A  pdb=" N   GLU C 249 " --> pdb=" O   ASN C 245 " (cutoff:3.500A)
      removed outlier: 3.598A  pdb=" N   ALA C 268 " --> pdb=" O   GLN C 264 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'D' and resid 37 through 47
      removed outlier: 6.433A  pdb=" N   LYS D  28 " --> pdb=" O   VAL D  39 " (cutoff:3.500A)
      removed outlier: 4.877A  pdb=" N   ASP D  41 " --> pdb=" O   VAL D  26 " (cutoff:3.500A)
      removed outlier: 6.615A  pdb=" N   VAL D  26 " --> pdb=" O   ASP D  41 " (cutoff:3.500A)
      removed outlier: 6.811A  pdb=" N   ILE D  43 " --> pdb=" O   GLU D  24 " (cutoff:3.500A)
      removed outlier: 4.359A  pdb=" N   GLU D  24 " --> pdb=" O   ILE D  43 " (cutoff:3.500A)
      removed outlier: 6.988A  pdb=" N   LEU D  45 " --> pdb=" O   VAL D  22 " (cutoff:3.500A)
      removed outlier: 4.996A  pdb=" N   VAL D  22 " --> pdb=" O   LEU D  45 " (cutoff:3.500A)
      removed outlier: 4.688A  pdb=" N   GLU D  24 " --> pdb=" O   VAL D  80 " (cutoff:3.500A)
      removed outlier: 4.653A  pdb=" N   VAL D  80 " --> pdb=" O   GLU D  24 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'D' and resid 97 through 98
      removed outlier: 3.518A  pdb=" N   LEU D 208 " --> pdb=" O   LEU D 175 " (cutoff:3.500A)
      removed outlier: 8.093A  pdb=" N   VAL D 225 " --> pdb=" O   PHE D  52 " (cutoff:3.500A)
      removed outlier: 6.365A  pdb=" N   CYS D  54 " --> pdb=" O   VAL D 225 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'C' and resid 23 through 25
      removed outlier: 6.529A  pdb=" N   ARG C  12 " --> pdb=" O   ALA C  24 " (cutoff:3.500A)
      removed outlier: 5.868A  pdb=" N   HIS C   9 " --> pdb=" O   GLY C  65 " (cutoff:3.500A)
      removed outlier: 4.357A  pdb=" N   GLY C  65 " --> pdb=" O   HIS C   9 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'C' and resid 161 through 162
      removed outlier: 7.129A  pdb=" N   LEU C 162 " --> pdb=" O   VAL C 195 " (cutoff:3.500A)
      removed outlier: 5.673A  pdb=" N   SER C  39 " --> pdb=" O   VAL C 210 " (cutoff:3.500A)

    318 hydrogen bonds defined for protein.
    927 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: 3.48

  Time building geometry restraints manager: 2.06 seconds

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

  Histogram of bond lengths:
        0.84 -     1.03: 8514
        1.03 -     1.23: 9
        1.23 -     1.42: 3400
        1.42 -     1.62: 4997
        1.62 -     1.81: 42
  Bond restraints: 16962
  Sorted by residual:
  bond pdb=" N   NO3 A 301 "
       pdb=" O3  NO3 A 301 "
    ideal  model  delta    sigma   weight residual
    1.237  1.264 -0.027 2.00e-02 2.50e+03 1.84e+00
  bond pdb=" N   NO3 A 301 "
       pdb=" O2  NO3 A 301 "
    ideal  model  delta    sigma   weight residual
    1.237  1.264 -0.027 2.00e-02 2.50e+03 1.80e+00
  bond pdb=" N   NO3 A 301 "
       pdb=" O1  NO3 A 301 "
    ideal  model  delta    sigma   weight residual
    1.237  1.263 -0.026 2.00e-02 2.50e+03 1.73e+00
  bond pdb=" C   ILE B 209 "
       pdb=" O   ILE B 209 "
    ideal  model  delta    sigma   weight residual
    1.241  1.228  0.013 1.19e-02 7.06e+03 1.28e+00
  bond pdb=" C   GLY D  35 "
       pdb=" N   PRO D  36 "
    ideal  model  delta    sigma   weight residual
    1.333  1.343 -0.010 1.01e-02 9.80e+03 9.72e-01
  ... (remaining 16957 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.19: 29168
        1.19 -     2.38: 1571
        2.38 -     3.56: 100
        3.56 -     4.75: 33
        4.75 -     5.94: 6
  Bond angle restraints: 30878
  Sorted by residual:
  angle pdb=" N   SER A  96 "
        pdb=" CA  SER A  96 "
        pdb=" C   SER A  96 "
      ideal   model   delta    sigma   weight residual
     113.41  107.47    5.94 1.22e+00 6.72e-01 2.37e+01
  angle pdb=" N   ASN A 117 "
        pdb=" CA  ASN A 117 "
        pdb=" C   ASN A 117 "
      ideal   model   delta    sigma   weight residual
     114.62  109.17    5.45 1.14e+00 7.69e-01 2.28e+01
  angle pdb=" N   VAL C 106 "
        pdb=" CA  VAL C 106 "
        pdb=" C   VAL C 106 "
      ideal   model   delta    sigma   weight residual
     111.62  108.23    3.39 7.90e-01 1.60e+00 1.84e+01
  angle pdb=" N   ASP D 178 "
        pdb=" CA  ASP D 178 "
        pdb=" C   ASP D 178 "
      ideal   model   delta    sigma   weight residual
     110.41  106.28    4.13 1.23e+00 6.61e-01 1.13e+01
  angle pdb=" CA  ASN A 117 "
        pdb=" C   ASN A 117 "
        pdb=" N   ALA A 118 "
      ideal   model   delta    sigma   weight residual
     119.71  116.30    3.41 1.17e+00 7.31e-01 8.47e+00
  ... (remaining 30873 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.96: 7061
       17.96 -    35.92: 570
       35.92 -    53.88: 221
       53.88 -    71.84: 37
       71.84 -    89.80: 16
  Dihedral angle restraints: 7905
    sinusoidal: 4361
      harmonic: 3544
  Sorted by residual:
  dihedral pdb=" CA  TRP A 235 "
           pdb=" C   TRP A 235 "
           pdb=" N   ASP A 236 "
           pdb=" CA  ASP A 236 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  155.45   24.55     0      5.00e+00 4.00e-02 2.41e+01
  dihedral pdb=" CA  SER A 157 "
           pdb=" C   SER A 157 "
           pdb=" N   ILE A 158 "
           pdb=" CA  ILE A 158 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  157.86   22.14     0      5.00e+00 4.00e-02 1.96e+01
  dihedral pdb=" CA  TRP A  23 "
           pdb=" C   TRP A  23 "
           pdb=" N   LYS A  24 "
           pdb=" CA  LYS A  24 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  160.16   19.84     0      5.00e+00 4.00e-02 1.58e+01
  ... (remaining 7902 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.030: 851
       0.030 -    0.059: 303
       0.059 -    0.089: 118
       0.089 -    0.118: 62
       0.118 -    0.148: 13
  Chirality restraints: 1347
  Sorted by residual:
  chirality pdb=" CA  ILE B 172 "
            pdb=" N   ILE B 172 "
            pdb=" C   ILE B 172 "
            pdb=" CB  ILE B 172 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.58   -0.15 2.00e-01 2.50e+01 5.46e-01
  chirality pdb=" CA  ILE A 172 "
            pdb=" N   ILE A 172 "
            pdb=" C   ILE A 172 "
            pdb=" CB  ILE A 172 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.58   -0.14 2.00e-01 2.50e+01 5.24e-01
  chirality pdb=" CA  ILE D 241 "
            pdb=" N   ILE D 241 "
            pdb=" C   ILE D 241 "
            pdb=" CB  ILE D 241 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.57   -0.14 2.00e-01 2.50e+01 4.62e-01
  ... (remaining 1344 not shown)

  Planarity restraints: 2447
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ASN A 112 "    0.030 5.00e-02 4.00e+02   4.61e-02 3.40e+00
        pdb=" N   PRO A 113 "   -0.080 5.00e-02 4.00e+02
        pdb=" CA  PRO A 113 "    0.024 5.00e-02 4.00e+02
        pdb=" CD  PRO A 113 "    0.026 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ASN B 146 "    0.030 5.00e-02 4.00e+02   4.49e-02 3.23e+00
        pdb=" N   PRO B 147 "   -0.078 5.00e-02 4.00e+02
        pdb=" CA  PRO B 147 "    0.023 5.00e-02 4.00e+02
        pdb=" CD  PRO B 147 "    0.025 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ARG D 245 "    0.026 5.00e-02 4.00e+02   3.90e-02 2.44e+00
        pdb=" N   PRO D 246 "   -0.068 5.00e-02 4.00e+02
        pdb=" CA  PRO D 246 "    0.020 5.00e-02 4.00e+02
        pdb=" CD  PRO D 246 "    0.022 5.00e-02 4.00e+02
  ... (remaining 2444 not shown)

  Histogram of nonbonded interaction distances:
        1.57 -     2.18: 795
        2.18 -     2.78: 34458
        2.78 -     3.39: 46449
        3.39 -     3.99: 59381
        3.99 -     4.60: 92618
  Nonbonded interactions: 233701
  Sorted by model distance:
  nonbonded pdb=" O   PRO A 160 "
            pdb="HD21 ASN A 164 "
     model   vdw
     1.572 2.450
  nonbonded pdb=" OD1 ASP D 267 "
            pdb="HD21 ASN D 271 "
     model   vdw
     1.592 2.450
  nonbonded pdb=" O   PHE D 219 "
            pdb="HH11 ARG D 247 "
     model   vdw
     1.614 2.450
  nonbonded pdb=" OD1 ASN D 263 "
            pdb=" HH  TYR C 244 "
     model   vdw
     1.650 2.450
  nonbonded pdb=" OD1 ASP C   8 "
            pdb=" HD1 HIS C   9 "
     model   vdw
     1.675 2.450
  ... (remaining 233696 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.00
Found NCS groups:
ncs_group {
  reference = (chain 'A' and resid 15 through 277)
  selection = (chain 'B' and ((resid 15 and (name N or name CA or name C or name O or name CB  \ 
or name CG or name CD or name OE1 or name NE2 or name HA or name HB2 or name HB3 \ 
 or name HG2 or name HG3 or name HE21 or name HE22)) or resid 16 through 277))
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             1.120
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.010
  Construct map_model_manager:             0.110
  Extract box with map and model:          0.230
  Check model and map are aligned:         0.050
  Set scattering table:                    0.040
  Process input model:                     16.280
  Find NCS groups from input model:        0.150
  Set up NCS constraints:                  0.020
  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:1.230
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   19.240
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7547
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      :  0.002   0.044   8440  Z= 0.114
  Angle     :  0.581   5.941  11494  Z= 0.328
  Chirality :  0.040   0.148   1347
  Planarity :  0.004   0.046   1458
  Dihedral  : 14.853  89.805   3077
  Min Nonbonded Distance : 1.963

Molprobity Statistics.
  All-atom Clashscore : 8.64
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.26 %
    Favored  : 92.74 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.22 %
    Favored  : 99.78 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -2.51 (0.26), residues: 1047
  helix: -1.14 (0.24), residues: 517
  sheet: -2.40 (0.66), residues: 66
  loop : -2.07 (0.28), residues: 464

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 127 
 TYR   0.011   0.001   TYR D 102 
 PHE   0.015   0.001   PHE D  20 
 TRP   0.010   0.001   TRP A 159 
 HIS   0.002   0.001   HIS C 240 

Details of bonding type rmsd
  covalent geometry    : bond        0.00238 ( 8440)
  covalent geometry    : angle       0.58135 (11494)
  hydrogen bonds       : bond        0.28261 (  318)
  hydrogen bonds       : angle       9.87400 (  927)

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

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

  2094 Ramachandran restraints generated.
    1047 Oldfield, 0 Emsley, 1047 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2094 Ramachandran restraints generated.
    1047 Oldfield, 0 Emsley, 1047 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  181 residues out of total 897 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 181
  time to evaluate  : 0.458 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  236 ASP cc_start: 0.7786 (t0) cc_final: 0.7582 (t0)
  outliers start: 0
  outliers final: 0
  residues processed: 181
  average time/residue: 0.1707
  time to fit residues: 45.4912
Evaluate side-chains
  150 residues out of total 897 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 150
  time to evaluate  : 0.522 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 103
   random chunks:
   chunk 49 optimal weight:    1.9990
   chunk 97 optimal weight:    2.9990
   chunk 53 optimal weight:    1.9990
   chunk 5 optimal weight:    3.9990
   chunk 33 optimal weight:    2.9990
   chunk 65 optimal weight:    0.9980
   chunk 62 optimal weight:    0.6980
   chunk 51 optimal weight:    0.6980
   chunk 100 optimal weight:    3.9990
   chunk 38 optimal weight:    0.6980
   chunk 61 optimal weight:    0.9980
   overall best weight:    0.8180

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

Flipped N/Q/H residues before XYZ refinement:
B 164 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3791 r_free = 0.3791 target = 0.150071 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3395 r_free = 0.3395 target = 0.116989 restraints weight = 34576.969|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 43)----------------|
| r_work = 0.3474 r_free = 0.3474 target = 0.123118 restraints weight = 15320.280|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 51)----------------|
| r_work = 0.3521 r_free = 0.3521 target = 0.126935 restraints weight = 9283.915|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 37)----------------|
| r_work = 0.3548 r_free = 0.3548 target = 0.129179 restraints weight = 6760.053|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 33)----------------|
| r_work = 0.3565 r_free = 0.3565 target = 0.130541 restraints weight = 5537.484|
|-----------------------------------------------------------------------------|
r_work (final): 0.3557
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7270
moved from start:          0.1160

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   8440  Z= 0.151
  Angle     :  0.638   6.371  11494  Z= 0.335
  Chirality :  0.043   0.142   1347
  Planarity :  0.005   0.053   1458
  Dihedral  :  5.127  25.330   1122
  Min Nonbonded Distance : 2.355

Molprobity Statistics.
  All-atom Clashscore : 7.87
  Ramachandran Plot:
    Outliers :  0.10 %
    Allowed  :  6.69 %
    Favored  : 93.22 %
  Rotamer:
    Outliers :  0.56 %
    Allowed  :  8.25 %
    Favored  : 91.19 %
  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 aren not related in a simple way.
  whole: -2.59 (0.25), residues: 1047
  helix: -1.07 (0.22), residues: 528
  sheet: -2.64 (0.63), residues: 65
  loop : -2.29 (0.28), residues: 454

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG C 129 
 TYR   0.019   0.001   TYR A 116 
 PHE   0.010   0.001   PHE A 151 
 TRP   0.013   0.001   TRP A 159 
 HIS   0.007   0.001   HIS C 197 

Details of bonding type rmsd
  covalent geometry    : bond        0.00339 ( 8440)
  covalent geometry    : angle       0.63843 (11494)
  hydrogen bonds       : bond        0.05825 (  318)
  hydrogen bonds       : angle       6.41059 (  927)

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

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

  2094 Ramachandran restraints generated.
    1047 Oldfield, 0 Emsley, 1047 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2094 Ramachandran restraints generated.
    1047 Oldfield, 0 Emsley, 1047 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  168 residues out of total 897 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 163
  time to evaluate  : 0.465 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  236 ASP cc_start: 0.8034 (t0) cc_final: 0.7734 (t0)
REVERT: C   75 GLU cc_start: 0.7630 (mm-30) cc_final: 0.7391 (mp0)
  outliers start: 5
  outliers final: 3
  residues processed: 165
  average time/residue: 0.1585
  time to fit residues: 39.5013
Evaluate side-chains
  155 residues out of total 897 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 152
  time to evaluate  : 0.500 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain D residue  181 PHE
Chi-restraints excluded: chain C residue   94 THR
Chi-restraints excluded: chain C residue  203 LEU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 103
   random chunks:
   chunk 88 optimal weight:    2.9990
   chunk 33 optimal weight:    1.9990
   chunk 57 optimal weight:    4.9990
   chunk 95 optimal weight:    0.6980
   chunk 13 optimal weight:    1.9990
   chunk 9 optimal weight:    0.9980
   chunk 59 optimal weight:    0.0470
   chunk 45 optimal weight:    0.9990
   chunk 37 optimal weight:    0.9980
   chunk 17 optimal weight:    3.9990
   chunk 38 optimal weight:    0.0970
   overall best weight:    0.5676

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

Flipped N/Q/H residues before XYZ refinement:

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3782 r_free = 0.3782 target = 0.149556 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3393 r_free = 0.3393 target = 0.116825 restraints weight = 34756.497|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 41)----------------|
| r_work = 0.3466 r_free = 0.3466 target = 0.122613 restraints weight = 15852.412|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 43)----------------|
| r_work = 0.3511 r_free = 0.3511 target = 0.126282 restraints weight = 9811.162|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 42)----------------|
| r_work = 0.3538 r_free = 0.3538 target = 0.128506 restraints weight = 7251.317|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 40)----------------|
| r_work = 0.3555 r_free = 0.3555 target = 0.129899 restraints weight = 5974.637|
|-----------------------------------------------------------------------------|
r_work (final): 0.3568
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7275
moved from start:          0.1452

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   8440  Z= 0.120
  Angle     :  0.585   6.116  11494  Z= 0.304
  Chirality :  0.041   0.150   1347
  Planarity :  0.005   0.056   1458
  Dihedral  :  5.058  24.708   1122
  Min Nonbonded Distance : 2.354

Molprobity Statistics.
  All-atom Clashscore : 7.39
  Ramachandran Plot:
    Outliers :  0.10 %
    Allowed  :  6.69 %
    Favored  : 93.22 %
  Rotamer:
    Outliers :  0.56 %
    Allowed  : 10.70 %
    Favored  : 88.74 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -2.48 (0.25), residues: 1047
  helix: -0.99 (0.23), residues: 534
  sheet: -2.52 (0.64), residues: 60
  loop : -2.26 (0.28), residues: 453

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG D 166 
 TYR   0.013   0.001   TYR D 102 
 PHE   0.011   0.001   PHE A  95 
 TRP   0.010   0.001   TRP A 159 
 HIS   0.004   0.001   HIS C 197 

Details of bonding type rmsd
  covalent geometry    : bond        0.00273 ( 8440)
  covalent geometry    : angle       0.58488 (11494)
  hydrogen bonds       : bond        0.04686 (  318)
  hydrogen bonds       : angle       5.79653 (  927)

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

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

  2094 Ramachandran restraints generated.
    1047 Oldfield, 0 Emsley, 1047 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2094 Ramachandran restraints generated.
    1047 Oldfield, 0 Emsley, 1047 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  166 residues out of total 897 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 161
  time to evaluate  : 0.439 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: D  115 TYR cc_start: 0.8128 (t80) cc_final: 0.7925 (t80)
REVERT: A  144 GLN cc_start: 0.6657 (mp-120) cc_final: 0.6415 (mp10)
REVERT: A  236 ASP cc_start: 0.8008 (t0) cc_final: 0.7727 (t0)
REVERT: C   75 GLU cc_start: 0.7577 (mm-30) cc_final: 0.7357 (mp0)
  outliers start: 5
  outliers final: 5
  residues processed: 161
  average time/residue: 0.1567
  time to fit residues: 38.2469
Evaluate side-chains
  156 residues out of total 897 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 151
  time to evaluate  : 0.458 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain D residue  181 PHE
Chi-restraints excluded: chain A residue   44 CYS
Chi-restraints excluded: chain A residue  171 GLN
Chi-restraints excluded: chain C residue   94 THR
Chi-restraints excluded: chain C residue  203 LEU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 103
   random chunks:
   chunk 37 optimal weight:    1.9990
   chunk 77 optimal weight:    4.9990
   chunk 50 optimal weight:    1.9990
   chunk 84 optimal weight:    0.9980
   chunk 4 optimal weight:    3.9990
   chunk 26 optimal weight:    0.0670
   chunk 102 optimal weight:    3.9990
   chunk 19 optimal weight:    0.9990
   chunk 28 optimal weight:    0.0670
   chunk 94 optimal weight:    0.7980
   chunk 10 optimal weight:    2.9990
   overall best weight:    0.5858

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

Flipped N/Q/H residues before XYZ refinement:
D  19 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3789 r_free = 0.3789 target = 0.150340 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3402 r_free = 0.3402 target = 0.117701 restraints weight = 34768.982|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 42)----------------|
| r_work = 0.3477 r_free = 0.3477 target = 0.123552 restraints weight = 15852.015|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 41)----------------|
| r_work = 0.3522 r_free = 0.3522 target = 0.127209 restraints weight = 9804.209|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 41)----------------|
| r_work = 0.3549 r_free = 0.3549 target = 0.129458 restraints weight = 7249.636|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.3563 r_free = 0.3563 target = 0.130661 restraints weight = 5960.057|
|-----------------------------------------------------------------------------|
r_work (final): 0.3582
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7278
moved from start:          0.1705

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   8440  Z= 0.116
  Angle     :  0.570   6.069  11494  Z= 0.294
  Chirality :  0.041   0.145   1347
  Planarity :  0.005   0.058   1458
  Dihedral  :  5.021  24.645   1122
  Min Nonbonded Distance : 2.375

Molprobity Statistics.
  All-atom Clashscore : 7.39
  Ramachandran Plot:
    Outliers :  0.10 %
    Allowed  :  6.40 %
    Favored  : 93.51 %
  Rotamer:
    Outliers :  0.89 %
    Allowed  : 12.82 %
    Favored  : 86.29 %
  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 aren not related in a simple way.
  whole: -2.39 (0.26), residues: 1047
  helix: -0.89 (0.23), residues: 536
  sheet: -2.49 (0.60), residues: 70
  loop : -2.24 (0.29), residues: 441

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG C 129 
 TYR   0.016   0.001   TYR A 116 
 PHE   0.011   0.001   PHE A  95 
 TRP   0.009   0.001   TRP A 159 
 HIS   0.003   0.001   HIS C  43 

Details of bonding type rmsd
  covalent geometry    : bond        0.00268 ( 8440)
  covalent geometry    : angle       0.56950 (11494)
  hydrogen bonds       : bond        0.03868 (  318)
  hydrogen bonds       : angle       5.42011 (  927)

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

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

  2094 Ramachandran restraints generated.
    1047 Oldfield, 0 Emsley, 1047 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2094 Ramachandran restraints generated.
    1047 Oldfield, 0 Emsley, 1047 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  171 residues out of total 897 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 163
  time to evaluate  : 0.468 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  144 GLN cc_start: 0.6673 (mp-120) cc_final: 0.6409 (mp10)
REVERT: A  156 THR cc_start: 0.8686 (t) cc_final: 0.8465 (t)
REVERT: A  236 ASP cc_start: 0.8014 (t0) cc_final: 0.7738 (t0)
REVERT: C   75 GLU cc_start: 0.7549 (mm-30) cc_final: 0.7344 (mp0)
  outliers start: 8
  outliers final: 7
  residues processed: 165
  average time/residue: 0.1616
  time to fit residues: 40.2856
Evaluate side-chains
  158 residues out of total 897 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 151
  time to evaluate  : 0.488 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain D residue  181 PHE
Chi-restraints excluded: chain B residue   23 TRP
Chi-restraints excluded: chain A residue   44 CYS
Chi-restraints excluded: chain C residue   67 THR
Chi-restraints excluded: chain C residue   94 THR
Chi-restraints excluded: chain C residue  103 VAL
Chi-restraints excluded: chain C residue  203 LEU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 103
   random chunks:
   chunk 18 optimal weight:    2.9990
   chunk 6 optimal weight:    2.9990
   chunk 83 optimal weight:    1.9990
   chunk 53 optimal weight:    2.9990
   chunk 85 optimal weight:    2.9990
   chunk 88 optimal weight:    0.8980
   chunk 37 optimal weight:    0.9980
   chunk 14 optimal weight:    1.9990
   chunk 27 optimal weight:    1.9990
   chunk 76 optimal weight:    0.6980
   chunk 17 optimal weight:    2.9990
   overall best weight:    1.3184

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

Flipped N/Q/H residues before XYZ refinement:
D  19 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3750 r_free = 0.3750 target = 0.146984 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3355 r_free = 0.3355 target = 0.113963 restraints weight = 35033.898|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 44)----------------|
| r_work = 0.3427 r_free = 0.3427 target = 0.119630 restraints weight = 16251.442|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 42)----------------|
| r_work = 0.3472 r_free = 0.3472 target = 0.123204 restraints weight = 10139.308|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 41)----------------|
| r_work = 0.3499 r_free = 0.3499 target = 0.125355 restraints weight = 7554.209|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 32)----------------|
| r_work = 0.3514 r_free = 0.3514 target = 0.126647 restraints weight = 6280.422|
|-----------------------------------------------------------------------------|
r_work (final): 0.3537
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7323
moved from start:          0.1814

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.041   8440  Z= 0.169
  Angle     :  0.594   6.564  11494  Z= 0.309
  Chirality :  0.042   0.145   1347
  Planarity :  0.005   0.057   1458
  Dihedral  :  5.129  24.844   1122
  Min Nonbonded Distance : 2.378

Molprobity Statistics.
  All-atom Clashscore : 8.17
  Ramachandran Plot:
    Outliers :  0.10 %
    Allowed  :  7.93 %
    Favored  : 91.98 %
  Rotamer:
    Outliers :  1.00 %
    Allowed  : 14.60 %
    Favored  : 84.39 %
  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 aren not related in a simple way.
  whole: -2.45 (0.25), residues: 1047
  helix: -0.90 (0.22), residues: 539
  sheet: -2.63 (0.59), residues: 70
  loop : -2.30 (0.29), residues: 438

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG C 234 
 TYR   0.014   0.001   TYR B 176 
 PHE   0.020   0.001   PHE A 154 
 TRP   0.011   0.001   TRP A 159 
 HIS   0.002   0.001   HIS C  43 

Details of bonding type rmsd
  covalent geometry    : bond        0.00393 ( 8440)
  covalent geometry    : angle       0.59428 (11494)
  hydrogen bonds       : bond        0.03769 (  318)
  hydrogen bonds       : angle       5.33138 (  927)

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

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

  2094 Ramachandran restraints generated.
    1047 Oldfield, 0 Emsley, 1047 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2094 Ramachandran restraints generated.
    1047 Oldfield, 0 Emsley, 1047 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  162 residues out of total 897 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 153
  time to evaluate  : 0.457 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  144 GLN cc_start: 0.6790 (mp-120) cc_final: 0.6521 (mp10)
REVERT: A  236 ASP cc_start: 0.8120 (t0) cc_final: 0.7829 (t0)
REVERT: C   75 GLU cc_start: 0.7652 (mm-30) cc_final: 0.7436 (mp0)
  outliers start: 9
  outliers final: 8
  residues processed: 156
  average time/residue: 0.1557
  time to fit residues: 36.7176
Evaluate side-chains
  156 residues out of total 897 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 148
  time to evaluate  : 0.448 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain D residue  181 PHE
Chi-restraints excluded: chain B residue   23 TRP
Chi-restraints excluded: chain A residue   44 CYS
Chi-restraints excluded: chain A residue  132 LEU
Chi-restraints excluded: chain C residue   67 THR
Chi-restraints excluded: chain C residue   94 THR
Chi-restraints excluded: chain C residue  103 VAL
Chi-restraints excluded: chain C residue  203 LEU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 103
   random chunks:
   chunk 85 optimal weight:    2.9990
   chunk 88 optimal weight:    1.9990
   chunk 41 optimal weight:    2.9990
   chunk 56 optimal weight:    0.4980
   chunk 90 optimal weight:    0.8980
   chunk 60 optimal weight:    0.7980
   chunk 48 optimal weight:    0.8980
   chunk 8 optimal weight:    0.6980
   chunk 89 optimal weight:    2.9990
   chunk 21 optimal weight:    2.9990
   chunk 93 optimal weight:    0.9990
   overall best weight:    0.7580

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

Flipped N/Q/H residues before XYZ refinement:

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3772 r_free = 0.3772 target = 0.149025 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3385 r_free = 0.3385 target = 0.116229 restraints weight = 34421.611|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.3458 r_free = 0.3458 target = 0.121921 restraints weight = 15847.205|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 41)----------------|
| r_work = 0.3503 r_free = 0.3503 target = 0.125516 restraints weight = 9883.176|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 40)----------------|
| r_work = 0.3530 r_free = 0.3530 target = 0.127709 restraints weight = 7333.889|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.3545 r_free = 0.3545 target = 0.129048 restraints weight = 6064.453|
|-----------------------------------------------------------------------------|
r_work (final): 0.3553
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7321
moved from start:          0.1922

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   8440  Z= 0.123
  Angle     :  0.576   6.177  11494  Z= 0.296
  Chirality :  0.041   0.151   1347
  Planarity :  0.005   0.057   1458
  Dihedral  :  5.086  25.455   1122
  Min Nonbonded Distance : 2.390

Molprobity Statistics.
  All-atom Clashscore : 8.35
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.97 %
    Favored  : 93.03 %
  Rotamer:
    Outliers :  0.89 %
    Allowed  : 15.72 %
    Favored  : 83.39 %
  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 aren not related in a simple way.
  whole: -2.35 (0.26), residues: 1047
  helix: -0.81 (0.23), residues: 534
  sheet: -2.62 (0.59), residues: 70
  loop : -2.25 (0.29), residues: 443

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG C 234 
 TYR   0.011   0.001   TYR B 238 
 PHE   0.019   0.001   PHE A 154 
 TRP   0.011   0.001   TRP A 159 
 HIS   0.002   0.001   HIS C  43 

Details of bonding type rmsd
  covalent geometry    : bond        0.00292 ( 8440)
  covalent geometry    : angle       0.57619 (11494)
  hydrogen bonds       : bond        0.03463 (  318)
  hydrogen bonds       : angle       5.13616 (  927)

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

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

  2094 Ramachandran restraints generated.
    1047 Oldfield, 0 Emsley, 1047 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2094 Ramachandran restraints generated.
    1047 Oldfield, 0 Emsley, 1047 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  160 residues out of total 897 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 152
  time to evaluate  : 0.462 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  144 GLN cc_start: 0.6712 (mp-120) cc_final: 0.6439 (mp10)
REVERT: A  236 ASP cc_start: 0.8054 (t0) cc_final: 0.7768 (t0)
REVERT: C   75 GLU cc_start: 0.7616 (mm-30) cc_final: 0.7409 (mp0)
  outliers start: 8
  outliers final: 8
  residues processed: 154
  average time/residue: 0.1587
  time to fit residues: 36.7511
Evaluate side-chains
  156 residues out of total 897 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 148
  time to evaluate  : 0.447 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain D residue  181 PHE
Chi-restraints excluded: chain B residue   23 TRP
Chi-restraints excluded: chain A residue   44 CYS
Chi-restraints excluded: chain A residue  132 LEU
Chi-restraints excluded: chain C residue   67 THR
Chi-restraints excluded: chain C residue   94 THR
Chi-restraints excluded: chain C residue  103 VAL
Chi-restraints excluded: chain C residue  203 LEU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 103
   random chunks:
   chunk 5 optimal weight:    2.9990
   chunk 56 optimal weight:    0.1980
   chunk 0 optimal weight:    3.9990
   chunk 18 optimal weight:    3.9990
   chunk 96 optimal weight:    2.9990
   chunk 31 optimal weight:    3.9990
   chunk 62 optimal weight:    0.7980
   chunk 84 optimal weight:    0.6980
   chunk 89 optimal weight:    5.9990
   chunk 97 optimal weight:    3.9990
   chunk 91 optimal weight:    0.5980
   overall best weight:    1.0582

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

Flipped N/Q/H residues before XYZ refinement:

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3764 r_free = 0.3764 target = 0.148255 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3368 r_free = 0.3368 target = 0.115006 restraints weight = 34607.815|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3442 r_free = 0.3442 target = 0.120747 restraints weight = 16080.903|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 41)----------------|
| r_work = 0.3488 r_free = 0.3488 target = 0.124379 restraints weight = 10074.305|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 33)----------------|
| r_work = 0.3515 r_free = 0.3515 target = 0.126633 restraints weight = 7504.422|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 47)----------------|
| r_work = 0.3534 r_free = 0.3534 target = 0.128045 restraints weight = 6184.095|
|-----------------------------------------------------------------------------|
r_work (final): 0.3552
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7320
moved from start:          0.1999

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   8440  Z= 0.146
  Angle     :  0.587   6.566  11494  Z= 0.303
  Chirality :  0.042   0.146   1347
  Planarity :  0.005   0.058   1458
  Dihedral  :  5.117  25.315   1122
  Min Nonbonded Distance : 2.384

Molprobity Statistics.
  All-atom Clashscore : 8.17
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.21 %
    Favored  : 91.79 %
  Rotamer:
    Outliers :  1.00 %
    Allowed  : 16.16 %
    Favored  : 82.83 %
  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 aren not related in a simple way.
  whole: -2.33 (0.26), residues: 1047
  helix: -0.83 (0.23), residues: 540
  sheet: -2.68 (0.59), residues: 70
  loop : -2.19 (0.29), residues: 437

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG C 234 
 TYR   0.012   0.001   TYR B 176 
 PHE   0.019   0.001   PHE A 154 
 TRP   0.011   0.001   TRP A 159 
 HIS   0.002   0.001   HIS C 122 

Details of bonding type rmsd
  covalent geometry    : bond        0.00345 ( 8440)
  covalent geometry    : angle       0.58683 (11494)
  hydrogen bonds       : bond        0.03366 (  318)
  hydrogen bonds       : angle       5.09022 (  927)

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

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

  2094 Ramachandran restraints generated.
    1047 Oldfield, 0 Emsley, 1047 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2094 Ramachandran restraints generated.
    1047 Oldfield, 0 Emsley, 1047 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  159 residues out of total 897 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 150
  time to evaluate  : 0.372 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  144 GLN cc_start: 0.6767 (mp-120) cc_final: 0.6500 (mp10)
REVERT: A  236 ASP cc_start: 0.8089 (t0) cc_final: 0.7822 (t0)
REVERT: C   75 GLU cc_start: 0.7650 (mm-30) cc_final: 0.7440 (mp0)
  outliers start: 9
  outliers final: 9
  residues processed: 153
  average time/residue: 0.1556
  time to fit residues: 35.5117
Evaluate side-chains
  157 residues out of total 897 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 148
  time to evaluate  : 0.343 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain D residue  181 PHE
Chi-restraints excluded: chain A residue   42 LEU
Chi-restraints excluded: chain A residue   44 CYS
Chi-restraints excluded: chain A residue  132 LEU
Chi-restraints excluded: chain A residue  139 LEU
Chi-restraints excluded: chain C residue   67 THR
Chi-restraints excluded: chain C residue   94 THR
Chi-restraints excluded: chain C residue  103 VAL
Chi-restraints excluded: chain C residue  203 LEU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 103
   random chunks:
   chunk 63 optimal weight:    0.9990
   chunk 72 optimal weight:    1.9990
   chunk 19 optimal weight:    2.9990
   chunk 27 optimal weight:    1.9990
   chunk 53 optimal weight:    0.9990
   chunk 52 optimal weight:    0.6980
   chunk 84 optimal weight:    1.9990
   chunk 70 optimal weight:    0.9980
   chunk 102 optimal weight:    4.9990
   chunk 36 optimal weight:    0.8980
   chunk 85 optimal weight:    1.9990
   overall best weight:    0.9184

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

Flipped N/Q/H residues before XYZ refinement:

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3769 r_free = 0.3769 target = 0.148693 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3373 r_free = 0.3373 target = 0.115363 restraints weight = 34680.907|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 43)----------------|
| r_work = 0.3448 r_free = 0.3448 target = 0.121170 restraints weight = 16057.543|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 45)----------------|
| r_work = 0.3494 r_free = 0.3494 target = 0.124799 restraints weight = 10018.096|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 47)----------------|
| r_work = 0.3521 r_free = 0.3521 target = 0.127017 restraints weight = 7467.301|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 37)----------------|
| r_work = 0.3537 r_free = 0.3537 target = 0.128362 restraints weight = 6181.164|
|-----------------------------------------------------------------------------|
r_work (final): 0.3544
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7341
moved from start:          0.2090

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   8440  Z= 0.132
  Angle     :  0.579   6.646  11494  Z= 0.298
  Chirality :  0.042   0.150   1347
  Planarity :  0.005   0.057   1458
  Dihedral  :  5.097  25.802   1122
  Min Nonbonded Distance : 2.389

Molprobity Statistics.
  All-atom Clashscore : 7.93
  Ramachandran Plot:
    Outliers :  0.10 %
    Allowed  :  7.26 %
    Favored  : 92.65 %
  Rotamer:
    Outliers :  1.11 %
    Allowed  : 15.83 %
    Favored  : 83.05 %
  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 aren not related in a simple way.
  whole: -2.24 (0.26), residues: 1047
  helix: -0.74 (0.23), residues: 540
  sheet: -2.62 (0.60), residues: 70
  loop : -2.17 (0.29), residues: 437

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG C 234 
 TYR   0.011   0.001   TYR B 176 
 PHE   0.019   0.001   PHE A 154 
 TRP   0.011   0.001   TRP A 159 
 HIS   0.002   0.001   HIS D 275 

Details of bonding type rmsd
  covalent geometry    : bond        0.00315 ( 8440)
  covalent geometry    : angle       0.57913 (11494)
  hydrogen bonds       : bond        0.03234 (  318)
  hydrogen bonds       : angle       5.00435 (  927)

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

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

  2094 Ramachandran restraints generated.
    1047 Oldfield, 0 Emsley, 1047 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2094 Ramachandran restraints generated.
    1047 Oldfield, 0 Emsley, 1047 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  160 residues out of total 897 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 150
  time to evaluate  : 0.466 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  144 GLN cc_start: 0.6738 (mp-120) cc_final: 0.6470 (mp10)
REVERT: A  236 ASP cc_start: 0.8037 (t0) cc_final: 0.7774 (t0)
REVERT: C   75 GLU cc_start: 0.7635 (mm-30) cc_final: 0.7432 (mp0)
  outliers start: 10
  outliers final: 10
  residues processed: 154
  average time/residue: 0.1544
  time to fit residues: 36.2725
Evaluate side-chains
  158 residues out of total 897 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 148
  time to evaluate  : 0.470 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain D residue  181 PHE
Chi-restraints excluded: chain A residue   42 LEU
Chi-restraints excluded: chain A residue   44 CYS
Chi-restraints excluded: chain A residue  132 LEU
Chi-restraints excluded: chain A residue  139 LEU
Chi-restraints excluded: chain A residue  158 ILE
Chi-restraints excluded: chain C residue   67 THR
Chi-restraints excluded: chain C residue   94 THR
Chi-restraints excluded: chain C residue  103 VAL
Chi-restraints excluded: chain C residue  203 LEU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 103
   random chunks:
   chunk 22 optimal weight:    2.9990
   chunk 19 optimal weight:    3.9990
   chunk 64 optimal weight:    0.9980
   chunk 47 optimal weight:    0.8980
   chunk 70 optimal weight:    0.9990
   chunk 10 optimal weight:    1.9990
   chunk 20 optimal weight:    0.5980
   chunk 42 optimal weight:    1.9990
   chunk 31 optimal weight:    3.9990
   chunk 0 optimal weight:    5.9990
   chunk 58 optimal weight:    0.7980
   overall best weight:    0.8582

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

Flipped N/Q/H residues before XYZ refinement:

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3761 r_free = 0.3761 target = 0.147953 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3367 r_free = 0.3367 target = 0.114755 restraints weight = 34594.384|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 45)----------------|
| r_work = 0.3442 r_free = 0.3442 target = 0.120495 restraints weight = 15993.089|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 51)----------------|
| r_work = 0.3487 r_free = 0.3487 target = 0.124088 restraints weight = 9975.025|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 42)----------------|
| r_work = 0.3513 r_free = 0.3513 target = 0.126274 restraints weight = 7427.484|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 32)----------------|
| r_work = 0.3528 r_free = 0.3528 target = 0.127534 restraints weight = 6161.866|
|-----------------------------------------------------------------------------|
r_work (final): 0.3553
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7308
moved from start:          0.2125

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   8440  Z= 0.131
  Angle     :  0.586   7.004  11494  Z= 0.301
  Chirality :  0.042   0.148   1347
  Planarity :  0.005   0.058   1458
  Dihedral  :  5.088  25.412   1122
  Min Nonbonded Distance : 2.370

Molprobity Statistics.
  All-atom Clashscore : 8.17
  Ramachandran Plot:
    Outliers :  0.10 %
    Allowed  :  8.21 %
    Favored  : 91.69 %
  Rotamer:
    Outliers :  1.11 %
    Allowed  : 15.94 %
    Favored  : 82.94 %
  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 aren not related in a simple way.
  whole: -2.16 (0.26), residues: 1047
  helix: -0.66 (0.23), residues: 540
  sheet: -2.60 (0.60), residues: 70
  loop : -2.15 (0.29), residues: 437

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG C 234 
 TYR   0.016   0.001   TYR D 102 
 PHE   0.018   0.001   PHE A 154 
 TRP   0.011   0.001   TRP A 159 
 HIS   0.002   0.001   HIS D 275 

Details of bonding type rmsd
  covalent geometry    : bond        0.00312 ( 8440)
  covalent geometry    : angle       0.58558 (11494)
  hydrogen bonds       : bond        0.03139 (  318)
  hydrogen bonds       : angle       4.95236 (  927)

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

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

  2094 Ramachandran restraints generated.
    1047 Oldfield, 0 Emsley, 1047 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2094 Ramachandran restraints generated.
    1047 Oldfield, 0 Emsley, 1047 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  161 residues out of total 897 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 151
  time to evaluate  : 0.618 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  144 GLN cc_start: 0.6734 (mp-120) cc_final: 0.6473 (mp10)
REVERT: A  236 ASP cc_start: 0.8082 (t0) cc_final: 0.7824 (t0)
REVERT: C   75 GLU cc_start: 0.7636 (mm-30) cc_final: 0.7434 (mp0)
  outliers start: 10
  outliers final: 10
  residues processed: 155
  average time/residue: 0.1510
  time to fit residues: 35.3831
Evaluate side-chains
  158 residues out of total 897 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 148
  time to evaluate  : 0.435 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain D residue  181 PHE
Chi-restraints excluded: chain A residue   42 LEU
Chi-restraints excluded: chain A residue   44 CYS
Chi-restraints excluded: chain A residue  132 LEU
Chi-restraints excluded: chain A residue  139 LEU
Chi-restraints excluded: chain A residue  158 ILE
Chi-restraints excluded: chain C residue   67 THR
Chi-restraints excluded: chain C residue   94 THR
Chi-restraints excluded: chain C residue  103 VAL
Chi-restraints excluded: chain C residue  203 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 103
   random chunks:
   chunk 68 optimal weight:    2.9990
   chunk 46 optimal weight:    2.9990
   chunk 71 optimal weight:    1.9990
   chunk 31 optimal weight:    2.9990
   chunk 48 optimal weight:    0.9980
   chunk 22 optimal weight:    2.9990
   chunk 9 optimal weight:    1.9990
   chunk 6 optimal weight:    2.9990
   chunk 94 optimal weight:    2.9990
   chunk 27 optimal weight:    0.9990
   chunk 73 optimal weight:    0.7980
   overall best weight:    1.3586

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

Flipped N/Q/H residues before XYZ refinement:
** C 197 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 = 0.3747 r_free = 0.3747 target = 0.146691 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3345 r_free = 0.3345 target = 0.113249 restraints weight = 34828.705|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 46)----------------|
| r_work = 0.3420 r_free = 0.3420 target = 0.118953 restraints weight = 16324.855|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.3465 r_free = 0.3465 target = 0.122498 restraints weight = 10244.509|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 32)----------------|
| r_work = 0.3492 r_free = 0.3492 target = 0.124679 restraints weight = 7666.988|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 34)----------------|
| r_work = 0.3510 r_free = 0.3510 target = 0.126085 restraints weight = 6379.569|
|-----------------------------------------------------------------------------|
r_work (final): 0.3505
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7365
moved from start:          0.2194

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.046   8440  Z= 0.173
  Angle     :  0.606   7.210  11494  Z= 0.313
  Chirality :  0.042   0.146   1347
  Planarity :  0.005   0.057   1458
  Dihedral  :  5.180  26.160   1122
  Min Nonbonded Distance : 2.345

Molprobity Statistics.
  All-atom Clashscore : 8.11
  Ramachandran Plot:
    Outliers :  0.10 %
    Allowed  :  7.74 %
    Favored  : 92.17 %
  Rotamer:
    Outliers :  1.11 %
    Allowed  : 16.50 %
    Favored  : 82.39 %
  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 aren not related in a simple way.
  whole: -2.25 (0.26), residues: 1047
  helix: -0.73 (0.23), residues: 548
  sheet: -2.71 (0.59), residues: 71
  loop : -2.20 (0.29), residues: 428

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG C 234 
 TYR   0.015   0.001   TYR B 176 
 PHE   0.018   0.001   PHE A  95 
 TRP   0.011   0.001   TRP A 159 
 HIS   0.004   0.001   HIS C 197 

Details of bonding type rmsd
  covalent geometry    : bond        0.00408 ( 8440)
  covalent geometry    : angle       0.60628 (11494)
  hydrogen bonds       : bond        0.03250 (  318)
  hydrogen bonds       : angle       5.02503 (  927)

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

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

  2094 Ramachandran restraints generated.
    1047 Oldfield, 0 Emsley, 1047 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2094 Ramachandran restraints generated.
    1047 Oldfield, 0 Emsley, 1047 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  161 residues out of total 897 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 151
  time to evaluate  : 0.448 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: D   20 PHE cc_start: 0.7591 (t80) cc_final: 0.7348 (t80)
REVERT: A  144 GLN cc_start: 0.6884 (mp-120) cc_final: 0.6629 (mp10)
REVERT: A  236 ASP cc_start: 0.8158 (t0) cc_final: 0.7734 (t0)
REVERT: C   75 GLU cc_start: 0.7659 (mm-30) cc_final: 0.7453 (mp0)
  outliers start: 10
  outliers final: 10
  residues processed: 155
  average time/residue: 0.1476
  time to fit residues: 34.9478
Evaluate side-chains
  158 residues out of total 897 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 148
  time to evaluate  : 0.392 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain D residue  181 PHE
Chi-restraints excluded: chain A residue   42 LEU
Chi-restraints excluded: chain A residue   44 CYS
Chi-restraints excluded: chain A residue  132 LEU
Chi-restraints excluded: chain A residue  139 LEU
Chi-restraints excluded: chain A residue  158 ILE
Chi-restraints excluded: chain C residue   67 THR
Chi-restraints excluded: chain C residue   94 THR
Chi-restraints excluded: chain C residue  103 VAL
Chi-restraints excluded: chain C residue  203 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 103
   random chunks:
   chunk 96 optimal weight:    1.9990
   chunk 70 optimal weight:    0.9980
   chunk 52 optimal weight:    1.9990
   chunk 7 optimal weight:    0.5980
   chunk 18 optimal weight:    2.9990
   chunk 56 optimal weight:    0.9980
   chunk 68 optimal weight:    2.9990
   chunk 77 optimal weight:    0.7980
   chunk 102 optimal weight:    4.9990
   chunk 50 optimal weight:    1.9990
   chunk 87 optimal weight:    0.0040
   overall best weight:    0.6792

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

Flipped N/Q/H residues before XYZ refinement:
D  19 ASN
** C 197 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3763 r_free = 0.3763 target = 0.148013 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3369 r_free = 0.3369 target = 0.114926 restraints weight = 34624.453|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.3443 r_free = 0.3443 target = 0.120632 restraints weight = 15970.828|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.3488 r_free = 0.3488 target = 0.124166 restraints weight = 9925.575|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 40)----------------|
| r_work = 0.3516 r_free = 0.3516 target = 0.126410 restraints weight = 7429.939|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.3530 r_free = 0.3530 target = 0.127653 restraints weight = 6140.409|
|-----------------------------------------------------------------------------|
r_work (final): 0.3556
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7305
moved from start:          0.2232

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038   8440  Z= 0.119
  Angle     :  0.588   7.188  11494  Z= 0.302
  Chirality :  0.042   0.151   1347
  Planarity :  0.005   0.058   1458
  Dihedral  :  5.097  25.862   1122
  Min Nonbonded Distance : 2.354

Molprobity Statistics.
  All-atom Clashscore : 8.46
  Ramachandran Plot:
    Outliers :  0.10 %
    Allowed  :  7.16 %
    Favored  : 92.74 %
  Rotamer:
    Outliers :  1.23 %
    Allowed  : 16.95 %
    Favored  : 81.83 %
  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 aren not related in a simple way.
  whole: -2.09 (0.26), residues: 1047
  helix: -0.61 (0.23), residues: 548
  sheet: -2.64 (0.59), residues: 71
  loop : -2.11 (0.30), residues: 428

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG C 234 
 TYR   0.014   0.001   TYR D 102 
 PHE   0.019   0.001   PHE A 154 
 TRP   0.013   0.001   TRP A 159 
 HIS   0.007   0.001   HIS D 137 

Details of bonding type rmsd
  covalent geometry    : bond        0.00286 ( 8440)
  covalent geometry    : angle       0.58837 (11494)
  hydrogen bonds       : bond        0.03110 (  318)
  hydrogen bonds       : angle       4.89796 (  927)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2897.99 seconds
wall clock time: 50 minutes 0.02 seconds (3000.02 seconds total)