Starting phenix.real_space_refine
on Mon Apr  6 09:50:32 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9qfx_53123/04_2026/9qfx_53123_trim.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9qfx_53123/04_2026/9qfx_53123.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.45
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/9qfx_53123/04_2026/9qfx_53123_trim.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9qfx_53123/04_2026/9qfx_53123_trim.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/9qfx_53123/04_2026/9qfx_53123.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9qfx_53123/04_2026/9qfx_53123.map"
  }
  resolution = 3.45
  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=   0.002 sd=   0.039
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      32      5.16       5
     C    5538      2.51       5
     N    1446      2.21       5
     O    1498      1.98       5
     H    8566      0.53       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 2 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc1-6017/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 17080
  Number of models: 1
  Model: ""
    Number of chains: 6
    Chain: "A"
      Number of atoms: 4441
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 265, 4441
          Classifications: {'peptide': 265}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 12, 'TRANS': 252}
    Chain: "B"
      Number of atoms: 4441
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 265, 4441
          Classifications: {'peptide': 265}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 12, 'TRANS': 252}
    Chain: "C"
      Number of atoms: 4030
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 262, 4030
          Classifications: {'peptide': 262}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 6, 'TRANS': 255}
    Chain: "D"
      Number of atoms: 4030
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 262, 4030
          Classifications: {'peptide': 262}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 6, 'TRANS': 255}
    Chain: "A"
      Number of atoms: 69
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 69
          Unusual residues: {'AV0': 1}
          Classifications: {'undetermined': 1}
    Chain: "B"
      Number of atoms: 69
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 69
          Unusual residues: {'AV0': 1}
          Classifications: {'undetermined': 1}
  Time building chain proxies: 3.20, per 1000 atoms: 0.19
  Number of scatterers: 17080
  At special positions: 0
  Unit cell: (100.1, 79.3, 109.2, 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      32     16.00
     O    1498      8.00
     N    1446      7.00
     C    5538      6.00
     H    8566      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: 1.46
  Conformation dependent library (CDL) restraints added in 603.1 milliseconds
  

  2092 Ramachandran restraints generated.
    1046 Oldfield, 0 Emsley, 1046 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1940

  Finding SS restraints...
    Secondary structure from input PDB file:
      56 helices and 4 sheets defined
      70.6% alpha, 9.7% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.45
  Creating SS restraints...
    Processing helix  chain 'A' and resid 32 through 46
      removed outlier: 3.741A  pdb=" N   ALA A  36 " --> pdb=" O   THR A  32 " (cutoff:3.500A)
      removed outlier: 3.842A  pdb=" N   HIS A  46 " --> pdb=" O   GLU A  42 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 47 through 65
    Processing helix  chain 'A' and resid 68 through 91
      removed outlier: 4.260A  pdb=" N   ILE A  72 " --> pdb=" O   GLY A  68 " (cutoff:3.500A)
      removed outlier: 3.925A  pdb=" N   SER A  88 " --> pdb=" O   GLY A  84 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 94 through 118
      Proline residue:  A 100  - end of helix
    Processing helix  chain 'A' and resid 121 through 126
    Processing helix  chain 'A' and resid 126 through 131
      removed outlier: 3.528A  pdb=" N   LYS A 131 " --> pdb=" O   GLU A 127 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 137 through 164
      removed outlier: 3.617A  pdb=" N   VAL A 141 " --> pdb=" O   LEU A 137 " (cutoff:3.500A)
      removed outlier: 4.095A  pdb=" N   ILE A 157 " --> pdb=" O   ALA A 153 " (cutoff:3.500A)
      removed outlier: 5.155A  pdb=" N   ILE A 158 " --> pdb=" O   HIS A 154 " (cutoff:3.500A)
      removed outlier: 3.969A  pdb=" N   PHE A 159 " --> pdb=" O   ASN A 155 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 171 through 175
    Processing helix  chain 'A' and resid 176 through 202
      removed outlier: 3.958A  pdb=" N   THR A 200 " --> pdb=" O   GLY A 196 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 204 through 220
      removed outlier: 3.654A  pdb=" N   LEU A 208 " --> pdb=" O   ASP A 204 " (cutoff:3.500A)
      removed outlier: 3.812A  pdb=" N   GLN A 214 " --> pdb=" O   GLY A 210 " (cutoff:3.500A)
      removed outlier: 4.388A  pdb=" N   PHE A 218 " --> pdb=" O   GLN A 214 " (cutoff:3.500A)
      removed outlier: 3.843A  pdb=" N   MET A 219 " --> pdb=" O   LEU A 215 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 225 through 230
      removed outlier: 3.806A  pdb=" N   MET A 228 " --> pdb=" O   ASN A 225 " (cutoff:3.500A)
      removed outlier: 3.525A  pdb=" N   ASN A 230 " --> pdb=" O   ASN A 227 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 235 through 241
    Processing helix  chain 'A' and resid 243 through 258
      removed outlier: 3.908A  pdb=" N   HIS A 247 " --> pdb=" O   ASN A 243 " (cutoff:3.500A)
      removed outlier: 4.128A  pdb=" N   ILE A 252 " --> pdb=" O   PHE A 248 " (cutoff:3.500A)
      Proline residue:  A 255  - end of helix
    Processing helix  chain 'A' and resid 262 through 288
      removed outlier: 3.950A  pdb=" N   TRP A 266 " --> pdb=" O   GLN A 262 " (cutoff:3.500A)
      removed outlier: 3.538A  pdb=" N   ARG A 288 " --> pdb=" O   MET A 284 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 290 through 295
    Processing helix  chain 'B' and resid 32 through 46
      removed outlier: 3.741A  pdb=" N   ALA B  36 " --> pdb=" O   THR B  32 " (cutoff:3.500A)
      removed outlier: 3.842A  pdb=" N   HIS B  46 " --> pdb=" O   GLU B  42 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 47 through 65
    Processing helix  chain 'B' and resid 68 through 91
      removed outlier: 4.261A  pdb=" N   ILE B  72 " --> pdb=" O   GLY B  68 " (cutoff:3.500A)
      removed outlier: 3.925A  pdb=" N   SER B  88 " --> pdb=" O   GLY B  84 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 94 through 118
      Proline residue:  B 100  - end of helix
    Processing helix  chain 'B' and resid 121 through 126
    Processing helix  chain 'B' and resid 126 through 131
      removed outlier: 3.528A  pdb=" N   LYS B 131 " --> pdb=" O   GLU B 127 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 137 through 164
      removed outlier: 3.617A  pdb=" N   VAL B 141 " --> pdb=" O   LEU B 137 " (cutoff:3.500A)
      removed outlier: 4.094A  pdb=" N   ILE B 157 " --> pdb=" O   ALA B 153 " (cutoff:3.500A)
      removed outlier: 5.155A  pdb=" N   ILE B 158 " --> pdb=" O   HIS B 154 " (cutoff:3.500A)
      removed outlier: 3.969A  pdb=" N   PHE B 159 " --> pdb=" O   ASN B 155 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 171 through 175
    Processing helix  chain 'B' and resid 176 through 202
      removed outlier: 3.958A  pdb=" N   THR B 200 " --> pdb=" O   GLY B 196 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 204 through 220
      removed outlier: 3.654A  pdb=" N   LEU B 208 " --> pdb=" O   ASP B 204 " (cutoff:3.500A)
      removed outlier: 3.813A  pdb=" N   GLN B 214 " --> pdb=" O   GLY B 210 " (cutoff:3.500A)
      removed outlier: 4.388A  pdb=" N   PHE B 218 " --> pdb=" O   GLN B 214 " (cutoff:3.500A)
      removed outlier: 3.843A  pdb=" N   MET B 219 " --> pdb=" O   LEU B 215 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 225 through 230
      removed outlier: 3.806A  pdb=" N   MET B 228 " --> pdb=" O   ASN B 225 " (cutoff:3.500A)
      removed outlier: 3.524A  pdb=" N   ASN B 230 " --> pdb=" O   ASN B 227 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 235 through 241
    Processing helix  chain 'B' and resid 243 through 258
      removed outlier: 3.908A  pdb=" N   HIS B 247 " --> pdb=" O   ASN B 243 " (cutoff:3.500A)
      removed outlier: 4.127A  pdb=" N   ILE B 252 " --> pdb=" O   PHE B 248 " (cutoff:3.500A)
      Proline residue:  B 255  - end of helix
    Processing helix  chain 'B' and resid 262 through 288
      removed outlier: 3.950A  pdb=" N   TRP B 266 " --> pdb=" O   GLN B 262 " (cutoff:3.500A)
      removed outlier: 3.538A  pdb=" N   ARG B 288 " --> pdb=" O   MET B 284 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 290 through 295
    Processing helix  chain 'C' and resid 22 through 31
    Processing helix  chain 'C' and resid 70 through 79
      removed outlier: 3.736A  pdb=" N   LEU C  75 " --> pdb=" O   LYS C  71 " (cutoff:3.500A)
      removed outlier: 3.548A  pdb=" N   ARG C  76 " --> pdb=" O   SER C  72 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 110 through 112
      No H-bonds generated for 'chain 'C' and resid 110 through 112'
    Processing helix  chain 'C' and resid 113 through 122
      removed outlier: 4.095A  pdb=" N   ILE C 117 " --> pdb=" O   GLU C 113 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 125 through 141
      removed outlier: 4.314A  pdb=" N   ALA C 131 " --> pdb=" O   LYS C 127 " (cutoff:3.500A)
      removed outlier: 3.766A  pdb=" N   VAL C 133 " --> pdb=" O   MET C 129 " (cutoff:3.500A)
      removed outlier: 4.617A  pdb=" N   ASP C 134 " --> pdb=" O   GLN C 130 " (cutoff:3.500A)
      removed outlier: 3.652A  pdb=" N   ILE C 136 " --> pdb=" O   LYS C 132 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 142 through 146
      removed outlier: 4.108A  pdb=" N   LEU C 146 " --> pdb=" O   GLY C 143 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 149 through 153
    Processing helix  chain 'C' and resid 154 through 167
    Processing helix  chain 'C' and resid 177 through 183
      removed outlier: 3.610A  pdb=" N   GLY C 181 " --> pdb=" O   GLU C 178 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 184 through 191
      removed outlier: 3.608A  pdb=" N   LYS C 190 " --> pdb=" O   GLU C 186 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 191 through 202
    Processing helix  chain 'C' and resid 211 through 219
    Processing helix  chain 'C' and resid 236 through 263
      removed outlier: 7.576A  pdb=" N   ASP C 246 " --> pdb=" O   ALA C 242 " (cutoff:3.500A)
      removed outlier: 9.174A  pdb=" N   GLU C 247 " --> pdb=" O   TYR C 243 " (cutoff:3.500A)
      removed outlier: 4.070A  pdb=" N   ALA C 248 " --> pdb=" O   GLU C 244 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 22 through 31
    Processing helix  chain 'D' and resid 70 through 79
      removed outlier: 3.736A  pdb=" N   LEU D  75 " --> pdb=" O   LYS D  71 " (cutoff:3.500A)
      removed outlier: 3.549A  pdb=" N   ARG D  76 " --> pdb=" O   SER D  72 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 110 through 112
      No H-bonds generated for 'chain 'D' and resid 110 through 112'
    Processing helix  chain 'D' and resid 113 through 122
      removed outlier: 4.096A  pdb=" N   ILE D 117 " --> pdb=" O   GLU D 113 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 125 through 141
      removed outlier: 4.314A  pdb=" N   ALA D 131 " --> pdb=" O   LYS D 127 " (cutoff:3.500A)
      removed outlier: 3.766A  pdb=" N   VAL D 133 " --> pdb=" O   MET D 129 " (cutoff:3.500A)
      removed outlier: 4.616A  pdb=" N   ASP D 134 " --> pdb=" O   GLN D 130 " (cutoff:3.500A)
      removed outlier: 3.652A  pdb=" N   ILE D 136 " --> pdb=" O   LYS D 132 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 142 through 146
      removed outlier: 4.108A  pdb=" N   LEU D 146 " --> pdb=" O   GLY D 143 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 149 through 153
    Processing helix  chain 'D' and resid 154 through 167
    Processing helix  chain 'D' and resid 177 through 183
      removed outlier: 3.610A  pdb=" N   GLY D 181 " --> pdb=" O   GLU D 178 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 184 through 191
      removed outlier: 3.608A  pdb=" N   LYS D 190 " --> pdb=" O   GLU D 186 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 191 through 202
    Processing helix  chain 'D' and resid 211 through 219
    Processing helix  chain 'D' and resid 236 through 263
      removed outlier: 7.576A  pdb=" N   ASP D 246 " --> pdb=" O   ALA D 242 " (cutoff:3.500A)
      removed outlier: 9.174A  pdb=" N   GLU D 247 " --> pdb=" O   TYR D 243 " (cutoff:3.500A)
      removed outlier: 4.071A  pdb=" N   ALA D 248 " --> pdb=" O   GLU D 244 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'C' and resid 44 through 55
      removed outlier: 6.957A  pdb=" N   ILE C  45 " --> pdb=" O   PRO C  14 " (cutoff:3.500A)
      removed outlier: 6.772A  pdb=" N   ALA C  47 " --> pdb=" O   GLU C  12 " (cutoff:3.500A)
      removed outlier: 7.553A  pdb=" N   GLU C  12 " --> pdb=" O   ALA C  47 " (cutoff:3.500A)
      removed outlier: 6.675A  pdb=" N   ARG C  49 " --> pdb=" O   TRP C  10 " (cutoff:3.500A)
      removed outlier: 6.689A  pdb=" N   TRP C  10 " --> pdb=" O   ARG C  49 " (cutoff:3.500A)
      removed outlier: 5.274A  pdb=" N   ILE C  51 " --> pdb=" O   GLN C   8 " (cutoff:3.500A)
      removed outlier: 3.573A  pdb=" N   GLN C   8 " --> pdb=" O   ILE C  51 " (cutoff:3.500A)
      removed outlier: 4.268A  pdb=" N   ALA C   9 " --> pdb=" O   ARG C  86 " (cutoff:3.500A)
      removed outlier: 6.827A  pdb=" N   ARG C  86 " --> pdb=" O   ALA C   9 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'C' and resid 95 through 97
      removed outlier: 6.588A  pdb=" N   ALA C  96 " --> pdb=" O   LEU C 175 " (cutoff:3.500A)
      removed outlier: 5.995A  pdb=" N   ARG C  60 " --> pdb=" O   THR C 221 " (cutoff:3.500A)
      removed outlier: 7.386A  pdb=" N   MET C 223 " --> pdb=" O   ARG C  60 " (cutoff:3.500A)
      removed outlier: 6.063A  pdb=" N   GLY C  62 " --> pdb=" O   MET C 223 " (cutoff:3.500A)
      removed outlier: 7.150A  pdb=" N   ILE C 225 " --> pdb=" O   GLY C  62 " (cutoff:3.500A)
      removed outlier: 6.057A  pdb=" N   VAL C  64 " --> pdb=" O   ILE C 225 " (cutoff:3.500A)
      removed outlier: 7.577A  pdb=" N   ALA C 222 " --> pdb=" O   SER C 233 " (cutoff:3.500A)
      removed outlier: 5.081A  pdb=" N   SER C 233 " --> pdb=" O   ALA C 222 " (cutoff:3.500A)
      removed outlier: 6.775A  pdb=" N   TRP C 224 " --> pdb=" O   LYS C 231 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'D' and resid 44 through 55
      removed outlier: 6.957A  pdb=" N   ILE D  45 " --> pdb=" O   PRO D  14 " (cutoff:3.500A)
      removed outlier: 6.772A  pdb=" N   ALA D  47 " --> pdb=" O   GLU D  12 " (cutoff:3.500A)
      removed outlier: 7.553A  pdb=" N   GLU D  12 " --> pdb=" O   ALA D  47 " (cutoff:3.500A)
      removed outlier: 6.676A  pdb=" N   ARG D  49 " --> pdb=" O   TRP D  10 " (cutoff:3.500A)
      removed outlier: 6.688A  pdb=" N   TRP D  10 " --> pdb=" O   ARG D  49 " (cutoff:3.500A)
      removed outlier: 5.274A  pdb=" N   ILE D  51 " --> pdb=" O   GLN D   8 " (cutoff:3.500A)
      removed outlier: 3.573A  pdb=" N   GLN D   8 " --> pdb=" O   ILE D  51 " (cutoff:3.500A)
      removed outlier: 4.267A  pdb=" N   ALA D   9 " --> pdb=" O   ARG D  86 " (cutoff:3.500A)
      removed outlier: 6.828A  pdb=" N   ARG D  86 " --> pdb=" O   ALA D   9 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'D' and resid 95 through 97
      removed outlier: 6.587A  pdb=" N   ALA D  96 " --> pdb=" O   LEU D 175 " (cutoff:3.500A)
      removed outlier: 5.996A  pdb=" N   ARG D  60 " --> pdb=" O   THR D 221 " (cutoff:3.500A)
      removed outlier: 7.386A  pdb=" N   MET D 223 " --> pdb=" O   ARG D  60 " (cutoff:3.500A)
      removed outlier: 6.062A  pdb=" N   GLY D  62 " --> pdb=" O   MET D 223 " (cutoff:3.500A)
      removed outlier: 7.150A  pdb=" N   ILE D 225 " --> pdb=" O   GLY D  62 " (cutoff:3.500A)
      removed outlier: 6.057A  pdb=" N   VAL D  64 " --> pdb=" O   ILE D 225 " (cutoff:3.500A)
      removed outlier: 7.577A  pdb=" N   ALA D 222 " --> pdb=" O   SER D 233 " (cutoff:3.500A)
      removed outlier: 5.081A  pdb=" N   SER D 233 " --> pdb=" O   ALA D 222 " (cutoff:3.500A)
      removed outlier: 6.775A  pdb=" N   TRP D 224 " --> pdb=" O   LYS D 231 " (cutoff:3.500A)

    490 hydrogen bonds defined for protein.
    1404 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: 3.52

  Time building geometry restraints manager: 2.11 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: 8562
        1.03 -     1.23: 18
        1.23 -     1.42: 3630
        1.42 -     1.62: 5010
        1.62 -     1.82: 60
  Bond restraints: 17280
  Sorted by residual:
  bond pdb=" C   ASP C 106 "
       pdb=" N   PRO C 107 "
    ideal  model  delta    sigma   weight residual
    1.334  1.378 -0.044 2.34e-02 1.83e+03 3.55e+00
  bond pdb=" C   ASP D 106 "
       pdb=" N   PRO D 107 "
    ideal  model  delta    sigma   weight residual
    1.334  1.378 -0.044 2.34e-02 1.83e+03 3.55e+00
  bond pdb=" CB  ILE C 173 "
       pdb=" CG2 ILE C 173 "
    ideal  model  delta    sigma   weight residual
    1.521  1.565 -0.044 3.30e-02 9.18e+02 1.80e+00
  bond pdb=" CB  ILE D 173 "
       pdb=" CG2 ILE D 173 "
    ideal  model  delta    sigma   weight residual
    1.521  1.565 -0.044 3.30e-02 9.18e+02 1.78e+00
  bond pdb=" CA  PRO D 107 "
       pdb=" C   PRO D 107 "
    ideal  model  delta    sigma   weight residual
    1.520  1.537 -0.017 1.42e-02 4.96e+03 1.51e+00
  ... (remaining 17275 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.41: 29772
        1.41 -     2.82: 1254
        2.82 -     4.22: 139
        4.22 -     5.63: 45
        5.63 -     7.04: 14
  Bond angle restraints: 31224
  Sorted by residual:
  angle pdb=" CA  GLN A 214 "
        pdb=" CB  GLN A 214 "
        pdb=" CG  GLN A 214 "
      ideal   model   delta    sigma   weight residual
     114.10  121.14   -7.04 2.00e+00 2.50e-01 1.24e+01
  angle pdb=" CA  GLN B 214 "
        pdb=" CB  GLN B 214 "
        pdb=" CG  GLN B 214 "
      ideal   model   delta    sigma   weight residual
     114.10  121.08   -6.98 2.00e+00 2.50e-01 1.22e+01
  angle pdb=" CA  GLU D 141 "
        pdb=" CB  GLU D 141 "
        pdb=" CG  GLU D 141 "
      ideal   model   delta    sigma   weight residual
     114.10  120.66   -6.56 2.00e+00 2.50e-01 1.07e+01
  angle pdb=" CA  GLU C 141 "
        pdb=" CB  GLU C 141 "
        pdb=" CG  GLU C 141 "
      ideal   model   delta    sigma   weight residual
     114.10  120.63   -6.53 2.00e+00 2.50e-01 1.07e+01
  angle pdb=" CB  GLN B 214 "
        pdb=" CG  GLN B 214 "
        pdb=" CD  GLN B 214 "
      ideal   model   delta    sigma   weight residual
     112.60  107.36    5.24 1.70e+00 3.46e-01 9.50e+00
  ... (remaining 31219 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    24.80: 7632
       24.80 -    49.60: 450
       49.60 -    74.40: 99
       74.40 -    99.21: 15
       99.21 -   124.01: 2
  Dihedral angle restraints: 8198
    sinusoidal: 4568
      harmonic: 3630
  Sorted by residual:
  dihedral pdb=" CA  GLU A 118 "
           pdb=" C   GLU A 118 "
           pdb=" N   GLY A 119 "
           pdb=" CA  GLY A 119 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  159.21   20.79     0      5.00e+00 4.00e-02 1.73e+01
  dihedral pdb=" CA  GLU B 118 "
           pdb=" C   GLU B 118 "
           pdb=" N   GLY B 119 "
           pdb=" CA  GLY B 119 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  159.23   20.77     0      5.00e+00 4.00e-02 1.73e+01
  dihedral pdb=" CBQ AV0 B 801 "
           pdb=" CBS AV0 B 801 "
           pdb=" CCM AV0 B 801 "
           pdb=" O1  AV0 B 801 "
      ideal   model   delta sinusoidal    sigma   weight residual
      70.26 -165.73 -124.01     1      3.00e+01 1.11e-03 1.66e+01
  ... (remaining 8195 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.084: 1307
       0.084 -    0.168: 67
       0.168 -    0.251: 0
       0.251 -    0.335: 0
       0.335 -    0.419: 2
  Chirality restraints: 1376
  Sorted by residual:
  chirality pdb=" CCS AV0 A 801 "
            pdb=" CCW AV0 A 801 "
            pdb=" OBZ AV0 A 801 "
            pdb=" OCB AV0 A 801 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.24    1.82    0.42 2.00e-01 2.50e+01 4.38e+00
  chirality pdb=" CCS AV0 B 801 "
            pdb=" CCW AV0 B 801 "
            pdb=" OBZ AV0 B 801 "
            pdb=" OCB AV0 B 801 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.24    1.82    0.42 2.00e-01 2.50e+01 4.37e+00
  chirality pdb=" CA  ILE D 173 "
            pdb=" N   ILE D 173 "
            pdb=" C   ILE D 173 "
            pdb=" CB  ILE D 173 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.59   -0.16 2.00e-01 2.50e+01 6.35e-01
  ... (remaining 1373 not shown)

  Planarity restraints: 2472
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CG  GLN B 214 "   -0.022 2.00e-02 2.50e+03   3.65e-02 2.00e+01
        pdb=" CD  GLN B 214 "    0.078 2.00e-02 2.50e+03
        pdb=" OE1 GLN B 214 "   -0.030 2.00e-02 2.50e+03
        pdb=" NE2 GLN B 214 "   -0.024 2.00e-02 2.50e+03
        pdb="HE21 GLN B 214 "   -0.002 2.00e-02 2.50e+03
        pdb="HE22 GLN B 214 "    0.000 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CG  GLN A 214 "    0.022 2.00e-02 2.50e+03   3.64e-02 1.99e+01
        pdb=" CD  GLN A 214 "   -0.077 2.00e-02 2.50e+03
        pdb=" OE1 GLN A 214 "    0.029 2.00e-02 2.50e+03
        pdb=" NE2 GLN A 214 "    0.026 2.00e-02 2.50e+03
        pdb="HE21 GLN A 214 "    0.000 2.00e-02 2.50e+03
        pdb="HE22 GLN A 214 "   -0.000 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  VAL B 191 "   -0.013 2.00e-02 2.50e+03   2.56e-02 6.57e+00
        pdb=" C   VAL B 191 "    0.044 2.00e-02 2.50e+03
        pdb=" O   VAL B 191 "   -0.017 2.00e-02 2.50e+03
        pdb=" N   SER B 192 "   -0.015 2.00e-02 2.50e+03
  ... (remaining 2469 not shown)

  Histogram of nonbonded interaction distances:
        1.80 -     2.36: 5840
        2.36 -     2.92: 39035
        2.92 -     3.48: 44373
        3.48 -     4.04: 59044
        4.04 -     4.60: 89418
  Nonbonded interactions: 237710
  Sorted by model distance:
  nonbonded pdb="HE21 GLN B 214 "
            pdb=" OAL AV0 A 801 "
     model   vdw
     1.801 2.450
  nonbonded pdb=" H   SER C 110 "
            pdb=" HG  SER C 110 "
     model   vdw
     1.898 2.100
  nonbonded pdb=" H   SER D 110 "
            pdb=" HG  SER D 110 "
     model   vdw
     1.899 2.100
  nonbonded pdb=" H   THR B 173 "
            pdb=" HG1 THR B 173 "
     model   vdw
     1.908 2.100
  nonbonded pdb=" H   THR A 173 "
            pdb=" HG1 THR A 173 "
     model   vdw
     1.909 2.100
  ... (remaining 237705 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: 0.02
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'B'
}
ncs_group {
  reference = chain 'C'
  selection = chain 'D'
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.010
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             0.470
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.100
  Extract box with map and model:          0.160
  Check model and map are aligned:         0.050
  Set scattering table:                    0.040
  Process input model:                     16.770
  Find NCS groups from input model:        0.110
  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:1.530
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   19.260
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7290
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      :  0.004   0.044   8714  Z= 0.199
  Angle     :  0.821   7.040  11838  Z= 0.436
  Chirality :  0.044   0.419   1376
  Planarity :  0.007   0.063   1458
  Dihedral  : 16.366 124.008   3338
  Min Nonbonded Distance : 2.530

Molprobity Statistics.
  All-atom Clashscore : 2.84
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.02 %
    Favored  : 95.98 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  : 13.45 %
    Favored  : 86.55 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.18 (0.24), residues: 1046
  helix: -1.38 (0.19), residues: 624
  sheet: -0.24 (0.68), residues: 66
  loop : -1.49 (0.31), residues: 356

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.012   0.001   ARG B  63 
 TYR   0.025   0.002   TYR B 287 
 PHE   0.011   0.001   PHE B 152 
 TRP   0.018   0.001   TRP A 190 
 HIS   0.005   0.001   HIS B 140 

Details of bonding type rmsd
  covalent geometry    : bond        0.00440 ( 8714)
  covalent geometry    : angle       0.82143 (11838)
  hydrogen bonds       : bond        0.16166 (  490)
  hydrogen bonds       : angle       7.87068 ( 1404)

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

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

  2092 Ramachandran restraints generated.
    1046 Oldfield, 0 Emsley, 1046 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2092 Ramachandran restraints generated.
    1046 Oldfield, 0 Emsley, 1046 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  121 residues out of total 892 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 121
  time to evaluate  : 0.418 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   45 GLU cc_start: 0.7183 (tp30) cc_final: 0.6913 (tp30)
REVERT: A   63 ARG cc_start: 0.7961 (ttm110) cc_final: 0.7670 (mtp85)
REVERT: A  121 ASP cc_start: 0.8063 (t0) cc_final: 0.7635 (t0)
REVERT: B   45 GLU cc_start: 0.7193 (tp30) cc_final: 0.6926 (tp30)
REVERT: B   63 ARG cc_start: 0.7965 (ttm110) cc_final: 0.7673 (mtp85)
REVERT: B  121 ASP cc_start: 0.8058 (t0) cc_final: 0.7629 (t0)
REVERT: C  105 MET cc_start: 0.5374 (tpp) cc_final: 0.4264 (tpp)
REVERT: C  129 MET cc_start: 0.7937 (tpp) cc_final: 0.7225 (tpp)
REVERT: D  105 MET cc_start: 0.5348 (tpp) cc_final: 0.4244 (tpp)
REVERT: D  129 MET cc_start: 0.7948 (tpp) cc_final: 0.7230 (tpp)
  outliers start: 0
  outliers final: 0
  residues processed: 121
  average time/residue: 0.2041
  time to fit residues: 34.6773
Evaluate side-chains
  88 residues out of total 892 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 88
  time to evaluate  : 0.434 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 104
   random chunks:
   chunk 49 optimal weight:    3.9990
   chunk 97 optimal weight:    4.9990
   chunk 53 optimal weight:    3.9990
   chunk 5 optimal weight:    2.9990
   chunk 33 optimal weight:    0.9990
   chunk 65 optimal weight:    0.5980
   chunk 62 optimal weight:    2.9990
   chunk 51 optimal weight:    0.9990
   chunk 100 optimal weight:    3.9990
   chunk 38 optimal weight:    0.6980
   chunk 61 optimal weight:    1.9990
   overall best weight:    1.0586

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

Flipped N/Q/H residues before XYZ refinement:
A  52 GLN
A 126 ASN
B  52 GLN
B  89 GLN
B 126 ASN
C 114 ASN
C 130 GLN
D 114 ASN
D 130 GLN

Total number of N/Q/H flips: 9

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4324 r_free = 0.4324 target = 0.206412 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.3919 r_free = 0.3919 target = 0.167964 restraints weight = 30353.764|
|-----------------------------------------------------------------------------|
r_work (start): 0.3948 rms_B_bonded: 2.25
r_work: 0.3789 rms_B_bonded: 2.83 restraints_weight: 0.5000
r_work: 0.3642 rms_B_bonded: 4.79 restraints_weight: 0.2500
r_work (final): 0.3642
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7648
moved from start:          0.1295

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.027   8714  Z= 0.150
  Angle     :  0.573   6.480  11838  Z= 0.302
  Chirality :  0.040   0.332   1376
  Planarity :  0.005   0.056   1458
  Dihedral  : 10.945 131.361   1400
  Min Nonbonded Distance : 2.418

Molprobity Statistics.
  All-atom Clashscore : 5.16
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.29 %
    Favored  : 97.71 %
  Rotamer:
    Outliers :  1.23 %
    Allowed  : 15.13 %
    Favored  : 83.63 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.10 (0.25), residues: 1046
  helix: -0.42 (0.20), residues: 636
  sheet:  0.04 (0.69), residues: 68
  loop : -1.23 (0.31), residues: 342

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG B  63 
 TYR   0.018   0.002   TYR A 287 
 PHE   0.010   0.001   PHE B 195 
 TRP   0.011   0.001   TRP B  50 
 HIS   0.003   0.001   HIS A  98 

Details of bonding type rmsd
  covalent geometry    : bond        0.00340 ( 8714)
  covalent geometry    : angle       0.57298 (11838)
  hydrogen bonds       : bond        0.04732 (  490)
  hydrogen bonds       : angle       4.92577 ( 1404)

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

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

  2092 Ramachandran restraints generated.
    1046 Oldfield, 0 Emsley, 1046 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2092 Ramachandran restraints generated.
    1046 Oldfield, 0 Emsley, 1046 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  104 residues out of total 892 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 93
  time to evaluate  : 0.454 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   63 ARG cc_start: 0.8270 (ttm110) cc_final: 0.7771 (mtp85)
REVERT: A  121 ASP cc_start: 0.8252 (t0) cc_final: 0.7838 (t0)
REVERT: B   63 ARG cc_start: 0.8284 (ttm110) cc_final: 0.7780 (mtp85)
REVERT: B   89 GLN cc_start: 0.8387 (tt0) cc_final: 0.8182 (tt0)
REVERT: B  121 ASP cc_start: 0.8254 (t0) cc_final: 0.7837 (t0)
REVERT: C  105 MET cc_start: 0.6056 (tpp) cc_final: 0.5273 (tpp)
REVERT: D  105 MET cc_start: 0.6075 (tpp) cc_final: 0.5301 (tpp)
  outliers start: 11
  outliers final: 7
  residues processed: 102
  average time/residue: 0.2254
  time to fit residues: 31.7217
Evaluate side-chains
  96 residues out of total 892 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 89
  time to evaluate  : 0.442 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   32 THR
Chi-restraints excluded: chain B residue   32 THR
Chi-restraints excluded: chain B residue  214 GLN
Chi-restraints excluded: chain C residue   59 ASP
Chi-restraints excluded: chain C residue   88 SER
Chi-restraints excluded: chain D residue   59 ASP
Chi-restraints excluded: chain D residue   88 SER
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 104
   random chunks:
   chunk 78 optimal weight:    3.9990
   chunk 51 optimal weight:    0.9980
   chunk 12 optimal weight:    1.9990
   chunk 89 optimal weight:    1.9990
   chunk 69 optimal weight:    0.9990
   chunk 4 optimal weight:    1.9990
   chunk 77 optimal weight:    3.9990
   chunk 102 optimal weight:    9.9990
   chunk 9 optimal weight:    1.9990
   chunk 13 optimal weight:    0.2980
   chunk 36 optimal weight:    1.9990
   overall best weight:    1.2586

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

Flipped N/Q/H residues before XYZ refinement:
A  56 GLN
B  56 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4122 r_free = 0.4122 target = 0.185457 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3693 r_free = 0.3693 target = 0.145563 restraints weight = 31190.669|
|-----------------------------------------------------------------------------|
r_work (start): 0.3712 rms_B_bonded: 2.27
r_work: 0.3591 rms_B_bonded: 2.62 restraints_weight: 0.5000
r_work: 0.3449 rms_B_bonded: 4.44 restraints_weight: 0.2500
r_work (final): 0.3449
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7727
moved from start:          0.1873

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.030   8714  Z= 0.162
  Angle     :  0.556   5.811  11838  Z= 0.292
  Chirality :  0.039   0.310   1376
  Planarity :  0.004   0.043   1458
  Dihedral  : 10.864 135.640   1400
  Min Nonbonded Distance : 2.447

Molprobity Statistics.
  All-atom Clashscore : 6.20
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.44 %
    Favored  : 96.56 %
  Rotamer:
    Outliers :  1.12 %
    Allowed  : 16.03 %
    Favored  : 82.85 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.61 (0.25), residues: 1046
  helix:  0.02 (0.20), residues: 644
  sheet:  0.57 (0.62), residues: 80
  loop : -1.32 (0.32), residues: 322

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG C 241 
 TYR   0.014   0.002   TYR A  87 
 PHE   0.008   0.001   PHE B 195 
 TRP   0.011   0.001   TRP B 190 
 HIS   0.004   0.001   HIS A 264 

Details of bonding type rmsd
  covalent geometry    : bond        0.00378 ( 8714)
  covalent geometry    : angle       0.55616 (11838)
  hydrogen bonds       : bond        0.04263 (  490)
  hydrogen bonds       : angle       4.53996 ( 1404)

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

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

  2092 Ramachandran restraints generated.
    1046 Oldfield, 0 Emsley, 1046 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2092 Ramachandran restraints generated.
    1046 Oldfield, 0 Emsley, 1046 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  105 residues out of total 892 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 95
  time to evaluate  : 0.435 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   34 LYS cc_start: 0.8009 (tptm) cc_final: 0.7625 (mmtt)
REVERT: A   63 ARG cc_start: 0.8136 (ttm110) cc_final: 0.7616 (ttm110)
REVERT: A  121 ASP cc_start: 0.8335 (t0) cc_final: 0.7868 (t0)
REVERT: B   45 GLU cc_start: 0.7993 (tp30) cc_final: 0.7768 (tp30)
REVERT: B   63 ARG cc_start: 0.8138 (ttm110) cc_final: 0.7608 (ttm110)
REVERT: B  121 ASP cc_start: 0.8345 (t0) cc_final: 0.7881 (t0)
REVERT: C  105 MET cc_start: 0.6069 (tpp) cc_final: 0.5560 (tpp)
REVERT: C  223 MET cc_start: 0.8889 (mtm) cc_final: 0.8678 (mtm)
REVERT: D  105 MET cc_start: 0.6032 (tpp) cc_final: 0.5538 (tpp)
REVERT: D  223 MET cc_start: 0.8916 (mtm) cc_final: 0.8705 (mtm)
  outliers start: 10
  outliers final: 6
  residues processed: 101
  average time/residue: 0.2313
  time to fit residues: 31.8516
Evaluate side-chains
  93 residues out of total 892 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 87
  time to evaluate  : 0.455 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   32 THR
Chi-restraints excluded: chain A residue   39 ASP
Chi-restraints excluded: chain B residue   32 THR
Chi-restraints excluded: chain B residue   39 ASP
Chi-restraints excluded: chain C residue  125 THR
Chi-restraints excluded: chain D residue  125 THR
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 104
   random chunks:
   chunk 32 optimal weight:    0.6980
   chunk 63 optimal weight:    2.9990
   chunk 2 optimal weight:    0.9990
   chunk 25 optimal weight:    1.9990
   chunk 4 optimal weight:    2.9990
   chunk 74 optimal weight:    1.9990
   chunk 86 optimal weight:    0.9980
   chunk 37 optimal weight:    0.9980
   chunk 79 optimal weight:    2.9990
   chunk 24 optimal weight:    0.9980
   chunk 72 optimal weight:    2.9990
   overall best weight:    0.9382

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

Flipped N/Q/H residues before XYZ refinement:
A  56 GLN
B  56 GLN
C 114 ASN
D 114 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4131 r_free = 0.4131 target = 0.186108 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3707 r_free = 0.3707 target = 0.146388 restraints weight = 31028.050|
|-----------------------------------------------------------------------------|
r_work (start): 0.3726 rms_B_bonded: 2.25
r_work: 0.3581 rms_B_bonded: 2.78 restraints_weight: 0.5000
r_work: 0.3435 rms_B_bonded: 4.68 restraints_weight: 0.2500
r_work (final): 0.3435
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7707
moved from start:          0.2105

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.026   8714  Z= 0.130
  Angle     :  0.510   4.517  11838  Z= 0.269
  Chirality :  0.038   0.251   1376
  Planarity :  0.004   0.046   1458
  Dihedral  : 10.636 137.351   1400
  Min Nonbonded Distance : 2.456

Molprobity Statistics.
  All-atom Clashscore : 6.61
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.29 %
    Favored  : 97.71 %
  Rotamer:
    Outliers :  1.79 %
    Allowed  : 16.03 %
    Favored  : 82.17 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.32 (0.26), residues: 1046
  helix:  0.28 (0.21), residues: 644
  sheet:  0.68 (0.63), residues: 80
  loop : -1.29 (0.32), residues: 322

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG C 241 
 TYR   0.012   0.001   TYR A 287 
 PHE   0.007   0.001   PHE A 195 
 TRP   0.011   0.001   TRP B 190 
 HIS   0.003   0.001   HIS B 264 

Details of bonding type rmsd
  covalent geometry    : bond        0.00296 ( 8714)
  covalent geometry    : angle       0.51019 (11838)
  hydrogen bonds       : bond        0.03896 (  490)
  hydrogen bonds       : angle       4.31024 ( 1404)

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

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

  2092 Ramachandran restraints generated.
    1046 Oldfield, 0 Emsley, 1046 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2092 Ramachandran restraints generated.
    1046 Oldfield, 0 Emsley, 1046 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  109 residues out of total 892 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 93
  time to evaluate  : 0.445 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   34 LYS cc_start: 0.7958 (tptm) cc_final: 0.7570 (mmtt)
REVERT: A   63 ARG cc_start: 0.8159 (ttm110) cc_final: 0.7685 (ttm110)
REVERT: A  121 ASP cc_start: 0.8334 (t0) cc_final: 0.7830 (t0)
REVERT: B   34 LYS cc_start: 0.7954 (tptm) cc_final: 0.7570 (mmtt)
REVERT: B   63 ARG cc_start: 0.8120 (ttm110) cc_final: 0.7640 (ttm110)
REVERT: B  121 ASP cc_start: 0.8346 (t0) cc_final: 0.7905 (t0)
REVERT: C  105 MET cc_start: 0.6086 (tpp) cc_final: 0.5633 (tpp)
REVERT: C  114 ASN cc_start: 0.8330 (OUTLIER) cc_final: 0.8079 (m110)
REVERT: C  116 ILE cc_start: 0.8084 (OUTLIER) cc_final: 0.7825 (mt)
REVERT: D  105 MET cc_start: 0.6028 (tpp) cc_final: 0.5569 (tpp)
REVERT: D  114 ASN cc_start: 0.8338 (OUTLIER) cc_final: 0.8079 (m110)
REVERT: D  116 ILE cc_start: 0.8103 (OUTLIER) cc_final: 0.7815 (mt)
  outliers start: 16
  outliers final: 6
  residues processed: 107
  average time/residue: 0.2335
  time to fit residues: 34.1816
Evaluate side-chains
  102 residues out of total 892 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 92
  time to evaluate  : 0.409 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   32 THR
Chi-restraints excluded: chain B residue   32 THR
Chi-restraints excluded: chain C residue   59 ASP
Chi-restraints excluded: chain C residue  106 ASP
Chi-restraints excluded: chain C residue  114 ASN
Chi-restraints excluded: chain C residue  116 ILE
Chi-restraints excluded: chain D residue   59 ASP
Chi-restraints excluded: chain D residue  106 ASP
Chi-restraints excluded: chain D residue  114 ASN
Chi-restraints excluded: chain D residue  116 ILE
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 104
   random chunks:
   chunk 95 optimal weight:    1.9990
   chunk 56 optimal weight:    0.9980
   chunk 14 optimal weight:    0.7980
   chunk 2 optimal weight:    1.9990
   chunk 49 optimal weight:    1.9990
   chunk 98 optimal weight:    0.7980
   chunk 37 optimal weight:    0.9990
   chunk 97 optimal weight:    0.8980
   chunk 101 optimal weight:    2.9990
   chunk 90 optimal weight:    2.9990
   chunk 6 optimal weight:    0.7980
   overall best weight:    0.8580

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4132 r_free = 0.4132 target = 0.186222 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3705 r_free = 0.3705 target = 0.146300 restraints weight = 30997.059|
|-----------------------------------------------------------------------------|
r_work (start): 0.3723 rms_B_bonded: 2.26
r_work: 0.3583 rms_B_bonded: 2.76 restraints_weight: 0.5000
r_work: 0.3436 rms_B_bonded: 4.68 restraints_weight: 0.2500
r_work (final): 0.3436
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7703
moved from start:          0.2205

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.027   8714  Z= 0.125
  Angle     :  0.505   4.424  11838  Z= 0.267
  Chirality :  0.038   0.234   1376
  Planarity :  0.004   0.045   1458
  Dihedral  : 10.623 138.176   1400
  Min Nonbonded Distance : 2.462

Molprobity Statistics.
  All-atom Clashscore : 6.84
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.96 %
    Favored  : 97.04 %
  Rotamer:
    Outliers :  1.35 %
    Allowed  : 17.38 %
    Favored  : 81.28 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.17 (0.26), residues: 1046
  helix:  0.39 (0.20), residues: 644
  sheet:  0.73 (0.64), residues: 80
  loop : -1.20 (0.33), residues: 322

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG B  63 
 TYR   0.009   0.001   TYR A  87 
 PHE   0.007   0.001   PHE B 195 
 TRP   0.011   0.001   TRP B 190 
 HIS   0.003   0.001   HIS B 264 

Details of bonding type rmsd
  covalent geometry    : bond        0.00286 ( 8714)
  covalent geometry    : angle       0.50487 (11838)
  hydrogen bonds       : bond        0.03819 (  490)
  hydrogen bonds       : angle       4.26074 ( 1404)

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

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

  2092 Ramachandran restraints generated.
    1046 Oldfield, 0 Emsley, 1046 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2092 Ramachandran restraints generated.
    1046 Oldfield, 0 Emsley, 1046 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  108 residues out of total 892 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 96
  time to evaluate  : 0.469 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   63 ARG cc_start: 0.8177 (ttm110) cc_final: 0.7685 (ttm110)
REVERT: A  121 ASP cc_start: 0.8344 (t0) cc_final: 0.7901 (t0)
REVERT: B   63 ARG cc_start: 0.8112 (ttm110) cc_final: 0.7624 (ttm110)
REVERT: B  121 ASP cc_start: 0.8347 (t0) cc_final: 0.7911 (t0)
REVERT: C  105 MET cc_start: 0.5646 (tpp) cc_final: 0.5389 (tpp)
REVERT: C  116 ILE cc_start: 0.8075 (OUTLIER) cc_final: 0.7776 (mt)
REVERT: D  105 MET cc_start: 0.5601 (tpp) cc_final: 0.5342 (tpp)
REVERT: D  116 ILE cc_start: 0.8085 (OUTLIER) cc_final: 0.7777 (mt)
  outliers start: 12
  outliers final: 8
  residues processed: 106
  average time/residue: 0.2391
  time to fit residues: 34.7294
Evaluate side-chains
  97 residues out of total 892 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 87
  time to evaluate  : 0.454 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   32 THR
Chi-restraints excluded: chain A residue   39 ASP
Chi-restraints excluded: chain A residue  130 ILE
Chi-restraints excluded: chain B residue   32 THR
Chi-restraints excluded: chain B residue   39 ASP
Chi-restraints excluded: chain B residue  130 ILE
Chi-restraints excluded: chain C residue   59 ASP
Chi-restraints excluded: chain C residue  116 ILE
Chi-restraints excluded: chain D residue   59 ASP
Chi-restraints excluded: chain D residue  116 ILE
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 104
   random chunks:
   chunk 11 optimal weight:    1.9990
   chunk 100 optimal weight:    4.9990
   chunk 31 optimal weight:    1.9990
   chunk 0 optimal weight:    3.9990
   chunk 92 optimal weight:    4.9990
   chunk 2 optimal weight:    0.9980
   chunk 93 optimal weight:    0.6980
   chunk 77 optimal weight:    2.9990
   chunk 24 optimal weight:    1.9990
   chunk 22 optimal weight:    0.5980
   chunk 48 optimal weight:    0.9990
   overall best weight:    1.0584

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

Flipped N/Q/H residues before XYZ refinement:
A 148 GLN
B 148 GLN
C 114 ASN
D 114 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4120 r_free = 0.4120 target = 0.185391 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3687 r_free = 0.3687 target = 0.144989 restraints weight = 30951.469|
|-----------------------------------------------------------------------------|
r_work (start): 0.3706 rms_B_bonded: 2.25
r_work: 0.3565 rms_B_bonded: 2.77 restraints_weight: 0.5000
r_work: 0.3415 rms_B_bonded: 4.70 restraints_weight: 0.2500
r_work (final): 0.3415
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7731
moved from start:          0.2423

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   8714  Z= 0.141
  Angle     :  0.517   4.439  11838  Z= 0.274
  Chirality :  0.038   0.235   1376
  Planarity :  0.004   0.045   1458
  Dihedral  : 10.558 139.160   1400
  Min Nonbonded Distance : 2.441

Molprobity Statistics.
  All-atom Clashscore : 7.19
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.96 %
    Favored  : 97.04 %
  Rotamer:
    Outliers :  2.02 %
    Allowed  : 17.71 %
    Favored  : 80.27 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.10 (0.26), residues: 1046
  helix:  0.43 (0.20), residues: 646
  sheet:  0.80 (0.63), residues: 80
  loop : -1.14 (0.33), residues: 320

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG D 241 
 TYR   0.009   0.001   TYR B 287 
 PHE   0.007   0.001   PHE A 195 
 TRP   0.011   0.001   TRP B 190 
 HIS   0.004   0.001   HIS B 264 

Details of bonding type rmsd
  covalent geometry    : bond        0.00329 ( 8714)
  covalent geometry    : angle       0.51684 (11838)
  hydrogen bonds       : bond        0.03873 (  490)
  hydrogen bonds       : angle       4.24761 ( 1404)

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

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

  2092 Ramachandran restraints generated.
    1046 Oldfield, 0 Emsley, 1046 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2092 Ramachandran restraints generated.
    1046 Oldfield, 0 Emsley, 1046 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  116 residues out of total 892 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 98
  time to evaluate  : 0.431 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   63 ARG cc_start: 0.8120 (ttm110) cc_final: 0.7599 (ttm110)
REVERT: A  121 ASP cc_start: 0.8309 (t0) cc_final: 0.7839 (t0)
REVERT: B   83 MET cc_start: 0.8161 (ttm) cc_final: 0.7765 (ttm)
REVERT: B  121 ASP cc_start: 0.8335 (t0) cc_final: 0.7862 (t0)
  outliers start: 18
  outliers final: 13
  residues processed: 114
  average time/residue: 0.2201
  time to fit residues: 34.5661
Evaluate side-chains
  105 residues out of total 892 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 92
  time to evaluate  : 0.399 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   32 THR
Chi-restraints excluded: chain A residue   39 ASP
Chi-restraints excluded: chain A residue  130 ILE
Chi-restraints excluded: chain A residue  191 VAL
Chi-restraints excluded: chain B residue   32 THR
Chi-restraints excluded: chain B residue   39 ASP
Chi-restraints excluded: chain B residue  130 ILE
Chi-restraints excluded: chain B residue  190 TRP
Chi-restraints excluded: chain B residue  191 VAL
Chi-restraints excluded: chain C residue  114 ASN
Chi-restraints excluded: chain C residue  125 THR
Chi-restraints excluded: chain D residue  114 ASN
Chi-restraints excluded: chain D residue  125 THR
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 104
   random chunks:
   chunk 16 optimal weight:    1.9990
   chunk 8 optimal weight:    0.7980
   chunk 66 optimal weight:    3.9990
   chunk 3 optimal weight:    1.9990
   chunk 53 optimal weight:    0.6980
   chunk 45 optimal weight:    0.4980
   chunk 100 optimal weight:    4.9990
   chunk 32 optimal weight:    0.5980
   chunk 97 optimal weight:    0.7980
   chunk 35 optimal weight:    2.9990
   chunk 2 optimal weight:    1.9990
   overall best weight:    0.6780

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

Flipped N/Q/H residues before XYZ refinement:
** B 264 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 = 0.4132 r_free = 0.4132 target = 0.186170 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3700 r_free = 0.3700 target = 0.145828 restraints weight = 30913.322|
|-----------------------------------------------------------------------------|
r_work (start): 0.3718 rms_B_bonded: 2.26
r_work: 0.3572 rms_B_bonded: 2.80 restraints_weight: 0.5000
r_work: 0.3428 rms_B_bonded: 4.72 restraints_weight: 0.2500
r_work (final): 0.3428
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7705
moved from start:          0.2490

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.025   8714  Z= 0.113
  Angle     :  0.494   4.435  11838  Z= 0.262
  Chirality :  0.038   0.210   1376
  Planarity :  0.004   0.045   1458
  Dihedral  : 10.445 140.112   1400
  Min Nonbonded Distance : 2.458

Molprobity Statistics.
  All-atom Clashscore : 7.36
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.68 %
    Favored  : 97.32 %
  Rotamer:
    Outliers :  1.35 %
    Allowed  : 18.27 %
    Favored  : 80.38 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.06 (0.26), residues: 1046
  helix:  0.56 (0.21), residues: 646
  sheet:  0.86 (0.64), residues: 80
  loop : -1.11 (0.33), residues: 320

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG B  63 
 TYR   0.009   0.001   TYR B 287 
 PHE   0.006   0.001   PHE A 195 
 TRP   0.011   0.001   TRP B 190 
 HIS   0.003   0.001   HIS B 264 

Details of bonding type rmsd
  covalent geometry    : bond        0.00254 ( 8714)
  covalent geometry    : angle       0.49366 (11838)
  hydrogen bonds       : bond        0.03721 (  490)
  hydrogen bonds       : angle       4.25744 ( 1404)

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

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

  2092 Ramachandran restraints generated.
    1046 Oldfield, 0 Emsley, 1046 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2092 Ramachandran restraints generated.
    1046 Oldfield, 0 Emsley, 1046 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  103 residues out of total 892 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 91
  time to evaluate  : 0.456 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   63 ARG cc_start: 0.8122 (ttm110) cc_final: 0.7604 (ttm110)
REVERT: A  121 ASP cc_start: 0.8287 (t0) cc_final: 0.7847 (t0)
REVERT: B  121 ASP cc_start: 0.8305 (t0) cc_final: 0.7861 (t0)
REVERT: C  105 MET cc_start: 0.5649 (tpp) cc_final: 0.5306 (tpp)
REVERT: D  105 MET cc_start: 0.5604 (tpp) cc_final: 0.5256 (tpp)
  outliers start: 12
  outliers final: 9
  residues processed: 103
  average time/residue: 0.2311
  time to fit residues: 32.5995
Evaluate side-chains
  99 residues out of total 892 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 90
  time to evaluate  : 0.480 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   32 THR
Chi-restraints excluded: chain A residue   39 ASP
Chi-restraints excluded: chain A residue  130 ILE
Chi-restraints excluded: chain A residue  191 VAL
Chi-restraints excluded: chain A residue  206 SER
Chi-restraints excluded: chain B residue   32 THR
Chi-restraints excluded: chain B residue   39 ASP
Chi-restraints excluded: chain B residue  130 ILE
Chi-restraints excluded: chain B residue  206 SER
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 104
   random chunks:
   chunk 70 optimal weight:    0.9980
   chunk 9 optimal weight:    2.9990
   chunk 49 optimal weight:    1.9990
   chunk 32 optimal weight:    0.1980
   chunk 97 optimal weight:    0.7980
   chunk 93 optimal weight:    0.9980
   chunk 62 optimal weight:    0.5980
   chunk 14 optimal weight:    1.9990
   chunk 33 optimal weight:    0.9990
   chunk 52 optimal weight:    3.9990
   chunk 24 optimal weight:    0.5980
   overall best weight:    0.6380

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

Flipped N/Q/H residues before XYZ refinement:
A  60 GLN
** A 264 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B  60 GLN
** B 264 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4137 r_free = 0.4137 target = 0.186664 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 55)----------------|
| r_work = 0.3708 r_free = 0.3708 target = 0.146372 restraints weight = 30953.034|
|-----------------------------------------------------------------------------|
r_work (start): 0.3727 rms_B_bonded: 2.27
r_work: 0.3582 rms_B_bonded: 2.80 restraints_weight: 0.5000
r_work: 0.3439 rms_B_bonded: 4.70 restraints_weight: 0.2500
r_work (final): 0.3439
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7694
moved from start:          0.2551

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.029   8714  Z= 0.110
  Angle     :  0.490   4.782  11838  Z= 0.259
  Chirality :  0.038   0.186   1376
  Planarity :  0.004   0.046   1458
  Dihedral  : 10.235 140.356   1400
  Min Nonbonded Distance : 2.464

Molprobity Statistics.
  All-atom Clashscore : 7.25
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.96 %
    Favored  : 97.04 %
  Rotamer:
    Outliers :  2.02 %
    Allowed  : 17.38 %
    Favored  : 80.61 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.15 (0.26), residues: 1046
  helix:  0.64 (0.21), residues: 646
  sheet:  0.90 (0.64), residues: 80
  loop : -1.10 (0.33), residues: 320

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG B  63 
 TYR   0.009   0.001   TYR B 287 
 PHE   0.006   0.001   PHE A 195 
 TRP   0.010   0.001   TRP A 190 
 HIS   0.003   0.001   HIS B 264 

Details of bonding type rmsd
  covalent geometry    : bond        0.00249 ( 8714)
  covalent geometry    : angle       0.48962 (11838)
  hydrogen bonds       : bond        0.03639 (  490)
  hydrogen bonds       : angle       4.12907 ( 1404)

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

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

  2092 Ramachandran restraints generated.
    1046 Oldfield, 0 Emsley, 1046 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2092 Ramachandran restraints generated.
    1046 Oldfield, 0 Emsley, 1046 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  110 residues out of total 892 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 92
  time to evaluate  : 0.452 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   60 GLN cc_start: 0.6367 (OUTLIER) cc_final: 0.6035 (mm-40)
REVERT: A   63 ARG cc_start: 0.8104 (ttm110) cc_final: 0.7640 (ttm110)
REVERT: A  121 ASP cc_start: 0.8270 (t0) cc_final: 0.7828 (t0)
REVERT: B   60 GLN cc_start: 0.6344 (OUTLIER) cc_final: 0.6087 (mm-40)
REVERT: B   63 ARG cc_start: 0.8223 (ttm110) cc_final: 0.7836 (ttm110)
REVERT: B  121 ASP cc_start: 0.8291 (t0) cc_final: 0.7849 (t0)
REVERT: C  105 MET cc_start: 0.5822 (tpp) cc_final: 0.5510 (tpp)
REVERT: C  129 MET cc_start: 0.8206 (tpp) cc_final: 0.7606 (tpp)
REVERT: D  105 MET cc_start: 0.5759 (tpp) cc_final: 0.5443 (tpp)
REVERT: D  129 MET cc_start: 0.8228 (tpp) cc_final: 0.7630 (tpp)
  outliers start: 18
  outliers final: 11
  residues processed: 108
  average time/residue: 0.2491
  time to fit residues: 36.2933
Evaluate side-chains
  102 residues out of total 892 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 89
  time to evaluate  : 0.567 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   32 THR
Chi-restraints excluded: chain A residue   39 ASP
Chi-restraints excluded: chain A residue   60 GLN
Chi-restraints excluded: chain A residue  130 ILE
Chi-restraints excluded: chain A residue  206 SER
Chi-restraints excluded: chain B residue   32 THR
Chi-restraints excluded: chain B residue   39 ASP
Chi-restraints excluded: chain B residue   60 GLN
Chi-restraints excluded: chain B residue  130 ILE
Chi-restraints excluded: chain B residue  191 VAL
Chi-restraints excluded: chain B residue  206 SER
Chi-restraints excluded: chain C residue  125 THR
Chi-restraints excluded: chain D residue  125 THR
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 104
   random chunks:
   chunk 77 optimal weight:    7.9990
   chunk 79 optimal weight:    5.9990
   chunk 48 optimal weight:    1.9990
   chunk 92 optimal weight:    3.9990
   chunk 59 optimal weight:    1.9990
   chunk 56 optimal weight:    2.9990
   chunk 39 optimal weight:    1.9990
   chunk 53 optimal weight:    0.9980
   chunk 87 optimal weight:    0.5980
   chunk 81 optimal weight:   10.0000
   chunk 78 optimal weight:    3.9990
   overall best weight:    1.5186

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

Flipped N/Q/H residues before XYZ refinement:
A  60 GLN
B  60 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4107 r_free = 0.4107 target = 0.183575 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3668 r_free = 0.3668 target = 0.142874 restraints weight = 31023.222|
|-----------------------------------------------------------------------------|
r_work (start): 0.3689 rms_B_bonded: 2.27
r_work: 0.3540 rms_B_bonded: 2.81 restraints_weight: 0.5000
r_work: 0.3397 rms_B_bonded: 4.74 restraints_weight: 0.2500
r_work (final): 0.3397
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7761
moved from start:          0.2696

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.048   8714  Z= 0.186
  Angle     :  0.552   4.518  11838  Z= 0.293
  Chirality :  0.039   0.242   1376
  Planarity :  0.004   0.046   1458
  Dihedral  : 10.253 139.531   1400
  Min Nonbonded Distance : 2.331

Molprobity Statistics.
  All-atom Clashscore : 8.17
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.06 %
    Favored  : 96.94 %
  Rotamer:
    Outliers :  2.13 %
    Allowed  : 16.70 %
    Favored  : 81.17 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.01 (0.26), residues: 1046
  helix:  0.51 (0.20), residues: 646
  sheet:  0.97 (0.63), residues: 80
  loop : -1.18 (0.33), residues: 320

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG B  63 
 TYR   0.010   0.001   TYR A 101 
 PHE   0.007   0.001   PHE A 195 
 TRP   0.010   0.001   TRP A  50 
 HIS   0.004   0.001   HIS B 264 

Details of bonding type rmsd
  covalent geometry    : bond        0.00438 ( 8714)
  covalent geometry    : angle       0.55182 (11838)
  hydrogen bonds       : bond        0.03891 (  490)
  hydrogen bonds       : angle       4.23413 ( 1404)

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

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

  2092 Ramachandran restraints generated.
    1046 Oldfield, 0 Emsley, 1046 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2092 Ramachandran restraints generated.
    1046 Oldfield, 0 Emsley, 1046 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  114 residues out of total 892 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 95
  time to evaluate  : 0.535 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  121 ASP cc_start: 0.8339 (t0) cc_final: 0.7872 (t0)
REVERT: B   63 ARG cc_start: 0.8308 (ttm110) cc_final: 0.8023 (ttm110)
REVERT: B  121 ASP cc_start: 0.8361 (t0) cc_final: 0.7894 (t0)
  outliers start: 19
  outliers final: 15
  residues processed: 112
  average time/residue: 0.2332
  time to fit residues: 35.9729
Evaluate side-chains
  107 residues out of total 892 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 92
  time to evaluate  : 0.446 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   32 THR
Chi-restraints excluded: chain A residue   39 ASP
Chi-restraints excluded: chain A residue   60 GLN
Chi-restraints excluded: chain A residue  130 ILE
Chi-restraints excluded: chain A residue  191 VAL
Chi-restraints excluded: chain A residue  206 SER
Chi-restraints excluded: chain B residue   32 THR
Chi-restraints excluded: chain B residue   39 ASP
Chi-restraints excluded: chain B residue   60 GLN
Chi-restraints excluded: chain B residue  130 ILE
Chi-restraints excluded: chain B residue  191 VAL
Chi-restraints excluded: chain B residue  206 SER
Chi-restraints excluded: chain B residue  214 GLN
Chi-restraints excluded: chain C residue  125 THR
Chi-restraints excluded: chain D residue  125 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 104
   random chunks:
   chunk 90 optimal weight:    3.9990
   chunk 17 optimal weight:    3.9990
   chunk 81 optimal weight:    5.9990
   chunk 57 optimal weight:    3.9990
   chunk 1 optimal weight:    0.9980
   chunk 6 optimal weight:    0.4980
   chunk 61 optimal weight:    0.8980
   chunk 75 optimal weight:    0.9990
   chunk 16 optimal weight:    0.5980
   chunk 40 optimal weight:    0.7980
   chunk 43 optimal weight:    3.9990
   overall best weight:    0.7580

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

Flipped N/Q/H residues before XYZ refinement:
A  60 GLN
B  60 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4122 r_free = 0.4122 target = 0.185299 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3688 r_free = 0.3688 target = 0.145090 restraints weight = 30560.221|
|-----------------------------------------------------------------------------|
r_work (start): 0.3711 rms_B_bonded: 2.23
r_work: 0.3565 rms_B_bonded: 2.79 restraints_weight: 0.5000
r_work: 0.3427 rms_B_bonded: 4.66 restraints_weight: 0.2500
r_work (final): 0.3427
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7724
moved from start:          0.2721

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.025   8714  Z= 0.120
  Angle     :  0.508   4.450  11838  Z= 0.268
  Chirality :  0.038   0.208   1376
  Planarity :  0.004   0.045   1458
  Dihedral  : 10.214 141.028   1400
  Min Nonbonded Distance : 2.377

Molprobity Statistics.
  All-atom Clashscore : 7.77
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.06 %
    Favored  : 96.94 %
  Rotamer:
    Outliers :  1.79 %
    Allowed  : 17.26 %
    Favored  : 80.94 %
  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 are not related in a simple way.
  whole:  0.12 (0.26), residues: 1046
  helix:  0.61 (0.20), residues: 646
  sheet:  1.03 (0.64), residues: 80
  loop : -1.14 (0.33), residues: 320

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.000   ARG A  63 
 TYR   0.010   0.001   TYR A  62 
 PHE   0.006   0.001   PHE B 195 
 TRP   0.011   0.001   TRP B  50 
 HIS   0.003   0.001   HIS B 264 

Details of bonding type rmsd
  covalent geometry    : bond        0.00274 ( 8714)
  covalent geometry    : angle       0.50771 (11838)
  hydrogen bonds       : bond        0.03725 (  490)
  hydrogen bonds       : angle       4.14777 ( 1404)

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

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

  2092 Ramachandran restraints generated.
    1046 Oldfield, 0 Emsley, 1046 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2092 Ramachandran restraints generated.
    1046 Oldfield, 0 Emsley, 1046 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  107 residues out of total 892 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 91
  time to evaluate  : 0.440 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   63 ARG cc_start: 0.8225 (ttm110) cc_final: 0.7918 (ttm110)
REVERT: A  121 ASP cc_start: 0.8291 (t0) cc_final: 0.7839 (t0)
REVERT: B   45 GLU cc_start: 0.8176 (tp30) cc_final: 0.7887 (tp30)
REVERT: B   63 ARG cc_start: 0.8228 (ttm110) cc_final: 0.7910 (ttm110)
REVERT: B  121 ASP cc_start: 0.8306 (t0) cc_final: 0.7853 (t0)
  outliers start: 16
  outliers final: 14
  residues processed: 105
  average time/residue: 0.2359
  time to fit residues: 33.7512
Evaluate side-chains
  105 residues out of total 892 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 91
  time to evaluate  : 0.454 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   32 THR
Chi-restraints excluded: chain A residue   39 ASP
Chi-restraints excluded: chain A residue  130 ILE
Chi-restraints excluded: chain A residue  191 VAL
Chi-restraints excluded: chain A residue  206 SER
Chi-restraints excluded: chain B residue   32 THR
Chi-restraints excluded: chain B residue   39 ASP
Chi-restraints excluded: chain B residue  130 ILE
Chi-restraints excluded: chain B residue  191 VAL
Chi-restraints excluded: chain B residue  204 ASP
Chi-restraints excluded: chain B residue  206 SER
Chi-restraints excluded: chain B residue  214 GLN
Chi-restraints excluded: chain C residue  125 THR
Chi-restraints excluded: chain D residue  125 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 104
   random chunks:
   chunk 40 optimal weight:    0.5980
   chunk 55 optimal weight:    0.0970
   chunk 25 optimal weight:    0.8980
   chunk 74 optimal weight:    0.9980
   chunk 30 optimal weight:    2.9990
   chunk 8 optimal weight:    0.6980
   chunk 28 optimal weight:    1.9990
   chunk 37 optimal weight:    0.9990
   chunk 57 optimal weight:    0.8980
   chunk 82 optimal weight:    0.4980
   chunk 102 optimal weight:    7.9990
   overall best weight:    0.5578

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

Flipped N/Q/H residues before XYZ refinement:
** A 264 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 264 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 = 0.4139 r_free = 0.4139 target = 0.186841 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 55)----------------|
| r_work = 0.3708 r_free = 0.3708 target = 0.146677 restraints weight = 30810.250|
|-----------------------------------------------------------------------------|
r_work (start): 0.3727 rms_B_bonded: 2.26
r_work: 0.3586 rms_B_bonded: 2.77 restraints_weight: 0.5000
r_work: 0.3444 rms_B_bonded: 4.68 restraints_weight: 0.2500
r_work (final): 0.3444
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7693
moved from start:          0.2750

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.025   8714  Z= 0.104
  Angle     :  0.484   4.437  11838  Z= 0.255
  Chirality :  0.038   0.171   1376
  Planarity :  0.004   0.046   1458
  Dihedral  : 10.093 140.914   1400
  Min Nonbonded Distance : 2.448

Molprobity Statistics.
  All-atom Clashscore : 7.59
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.87 %
    Favored  : 97.13 %
  Rotamer:
    Outliers :  1.79 %
    Allowed  : 17.60 %
    Favored  : 80.61 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.26 (0.26), residues: 1046
  helix:  0.75 (0.21), residues: 646
  sheet:  1.02 (0.63), residues: 80
  loop : -1.12 (0.33), residues: 320

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG A  63 
 TYR   0.009   0.001   TYR B 287 
 PHE   0.006   0.001   PHE A 195 
 TRP   0.011   0.001   TRP A 190 
 HIS   0.003   0.001   HIS B 264 

Details of bonding type rmsd
  covalent geometry    : bond        0.00234 ( 8714)
  covalent geometry    : angle       0.48366 (11838)
  hydrogen bonds       : bond        0.03566 (  490)
  hydrogen bonds       : angle       4.02888 ( 1404)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 4659.22 seconds
wall clock time: 79 minutes 33.69 seconds (4773.69 seconds total)