Starting phenix.real_space_refine
on Wed Jul 30 16:28:48 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8dou_27623/07_2025/8dou_27623.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8dou_27623/07_2025/8dou_27623.map

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

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

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8dou_27623/07_2025/8dou_27623.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8dou_27623/07_2025/8dou_27623.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8dou_27623/07_2025/8dou_27623.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8dou_27623/07_2025/8dou_27623.cif"
  }
  resolution = 3.54
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.073
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
  Anisotropic ADP refinement not supported. Converting 2287 atoms to isotropic.
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 5
    Type Number    sf(0)   Gaussians
     P       4      5.49       5
     S      32      5.16       5
     C    7090      2.51       5
     N    1676      2.21       5
     O    1864      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 21 residue(s): 0.03s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib"
  Total number of atoms: 10666
  Number of models: 1
  Model: ""
    Number of chains: 6
    Chain: "A"
      Number of atoms: 3175
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 395, 3175
          Classifications: {'peptide': 395}
          Link IDs: {'PTRANS': 12, 'TRANS': 382}
    Chain: "B"
      Number of atoms: 2131
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 255, 2131
          Classifications: {'peptide': 255}
          Link IDs: {'PTRANS': 11, 'TRANS': 243}
    Chain: "C"
      Number of atoms: 3175
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 395, 3175
          Classifications: {'peptide': 395}
          Link IDs: {'PTRANS': 12, 'TRANS': 382}
    Chain: "D"
      Number of atoms: 2131
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 255, 2131
          Classifications: {'peptide': 255}
          Link IDs: {'PTRANS': 11, 'TRANS': 243}
    Chain: "A"
      Number of atoms: 27
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 27
          Unusual residues: {'ADP': 1}
          Classifications: {'undetermined': 1}
    Chain: "C"
      Number of atoms: 27
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 27
          Unusual residues: {'ADP': 1}
          Classifications: {'undetermined': 1}
  Time building chain proxies: 8.59, per 1000 atoms: 0.81
  Number of scatterers: 10666
  At special positions: 0
  Unit cell: (94.08, 101.92, 138.88, 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
     P       4     15.00
     O    1864      8.00
     N    1676      7.00
     C    7090      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 2.83
  Conformation dependent library (CDL) restraints added in 1.4 seconds
  

  2584 Ramachandran restraints generated.
    1292 Oldfield, 0 Emsley, 1292 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2416

  Finding SS restraints...
    Secondary structure from input PDB file:
      45 helices and 8 sheets defined
      51.3% alpha, 13.0% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.98
  Creating SS restraints...
    Processing helix  chain 'A' and resid 17 through 27
      removed outlier: 4.214A  pdb=" N   LEU A  21 " --> pdb=" O   PRO A  17 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 59 through 69
    Processing helix  chain 'A' and resid 99 through 112
      removed outlier: 3.757A  pdb=" N   ASN A 103 " --> pdb=" O   SER A  99 " (cutoff:3.500A)
      removed outlier: 4.089A  pdb=" N   TYR A 105 " --> pdb=" O   LEU A 101 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 114 through 130
      removed outlier: 4.770A  pdb=" N   GLU A 123 " --> pdb=" O   ASP A 119 " (cutoff:3.500A)
      removed outlier: 4.924A  pdb=" N   SER A 124 " --> pdb=" O   GLU A 120 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 138 through 142
      removed outlier: 4.071A  pdb=" N   THR A 141 " --> pdb=" O   PRO A 138 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 143 through 158
    Processing helix  chain 'A' and resid 173 through 190
      removed outlier: 3.959A  pdb=" N   LYS A 179 " --> pdb=" O   HIS A 175 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 200 through 204
    Processing helix  chain 'A' and resid 224 through 241
      removed outlier: 4.104A  pdb=" N   ASN A 241 " --> pdb=" O   ALA A 237 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 3 through 18
    Processing helix  chain 'B' and resid 22 through 48
      removed outlier: 5.195A  pdb=" N   TRP B  31 " --> pdb=" O   TRP B  27 " (cutoff:3.500A)
      Proline residue:  B  32  - end of helix
      removed outlier: 3.905A  pdb=" N   ILE B  42 " --> pdb=" O   ILE B  38 " (cutoff:3.500A)
      removed outlier: 3.677A  pdb=" N   SER B  44 " --> pdb=" O   THR B  40 " (cutoff:3.500A)
      removed outlier: 6.449A  pdb=" N   HIS B  45 " --> pdb=" O   LEU B  41 " (cutoff:3.500A)
      removed outlier: 4.861A  pdb=" N   LEU B  46 " --> pdb=" O   ILE B  42 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 49 through 51
      No H-bonds generated for 'chain 'B' and resid 49 through 51'
    Processing helix  chain 'B' and resid 56 through 87
      removed outlier: 3.706A  pdb=" N   TYR B  60 " --> pdb=" O   THR B  56 " (cutoff:3.500A)
      removed outlier: 3.802A  pdb=" N   GLY B  67 " --> pdb=" O   TYR B  63 " (cutoff:3.500A)
      removed outlier: 3.896A  pdb=" N   PHE B  69 " --> pdb=" O   SER B  65 " (cutoff:3.500A)
      Proline residue:  B  70  - end of helix
    Processing helix  chain 'B' and resid 88 through 95
    Processing helix  chain 'B' and resid 101 through 129
      removed outlier: 3.772A  pdb=" N   VAL B 105 " --> pdb=" O   VAL B 101 " (cutoff:3.500A)
      removed outlier: 3.825A  pdb=" N   VAL B 106 " --> pdb=" O   PHE B 102 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 132 through 137
      removed outlier: 4.528A  pdb=" N   LYS B 135 " --> pdb=" O   GLU B 132 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 139 through 163
      removed outlier: 4.012A  pdb=" N   VAL B 163 " --> pdb=" O   GLY B 159 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 167 through 180
    Processing helix  chain 'B' and resid 188 through 192
      removed outlier: 3.603A  pdb=" N   ILE B 191 " --> pdb=" O   THR B 188 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 193 through 201
      removed outlier: 3.617A  pdb=" N   TYR B 201 " --> pdb=" O   LYS B 197 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 205 through 218
    Processing helix  chain 'B' and resid 223 through 256
      Proline residue:  B 235  - end of helix
      removed outlier: 4.586A  pdb=" N   LYS B 250 " --> pdb=" O   LYS B 246 " (cutoff:3.500A)
      removed outlier: 4.944A  pdb=" N   ASP B 251 " --> pdb=" O   LYS B 247 " (cutoff:3.500A)
      removed outlier: 4.182A  pdb=" N   ALA B 256 " --> pdb=" O   ILE B 252 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 18 through 27
    Processing helix  chain 'C' and resid 59 through 69
      removed outlier: 3.507A  pdb=" N   LEU C  63 " --> pdb=" O   GLY C  59 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 100 through 111
      removed outlier: 4.437A  pdb=" N   ILE C 104 " --> pdb=" O   GLY C 100 " (cutoff:3.500A)
      removed outlier: 4.405A  pdb=" N   TYR C 105 " --> pdb=" O   LEU C 101 " (cutoff:3.500A)
      removed outlier: 4.998A  pdb=" N   VAL C 106 " --> pdb=" O   GLU C 102 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 114 through 129
    Processing helix  chain 'C' and resid 138 through 142
      removed outlier: 3.600A  pdb=" N   TYR C 142 " --> pdb=" O   LEU C 139 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 143 through 159
      removed outlier: 4.015A  pdb=" N   GLU C 159 " --> pdb=" O   ALA C 155 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 175 through 191
      removed outlier: 3.984A  pdb=" N   GLN C 189 " --> pdb=" O   LYS C 185 " (cutoff:3.500A)
      removed outlier: 4.160A  pdb=" N   LYS C 190 " --> pdb=" O   GLU C 186 " (cutoff:3.500A)
      removed outlier: 3.515A  pdb=" N   GLY C 191 " --> pdb=" O   HIS C 187 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 201 through 206
      removed outlier: 4.058A  pdb=" N   ILE C 206 " --> pdb=" O   ASN C 202 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 224 through 239
    Processing helix  chain 'C' and resid 315 through 318
    Processing helix  chain 'D' and resid 3 through 18
    Processing helix  chain 'D' and resid 22 through 48
      removed outlier: 4.985A  pdb=" N   TRP D  31 " --> pdb=" O   TRP D  27 " (cutoff:3.500A)
      Proline residue:  D  32  - end of helix
      removed outlier: 3.809A  pdb=" N   ILE D  42 " --> pdb=" O   ILE D  38 " (cutoff:3.500A)
      removed outlier: 3.719A  pdb=" N   SER D  44 " --> pdb=" O   THR D  40 " (cutoff:3.500A)
      removed outlier: 6.305A  pdb=" N   HIS D  45 " --> pdb=" O   LEU D  41 " (cutoff:3.500A)
      removed outlier: 4.826A  pdb=" N   LEU D  46 " --> pdb=" O   ILE D  42 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 49 through 51
      No H-bonds generated for 'chain 'D' and resid 49 through 51'
    Processing helix  chain 'D' and resid 57 through 84
      removed outlier: 3.859A  pdb=" N   GLY D  67 " --> pdb=" O   TYR D  63 " (cutoff:3.500A)
      removed outlier: 3.908A  pdb=" N   PHE D  69 " --> pdb=" O   SER D  65 " (cutoff:3.500A)
      Proline residue:  D  70  - end of helix
      removed outlier: 3.593A  pdb=" N   GLY D  83 " --> pdb=" O   SER D  79 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 89 through 95
      removed outlier: 3.786A  pdb=" N   THR D  93 " --> pdb=" O   LYS D  89 " (cutoff:3.500A)
      removed outlier: 3.988A  pdb=" N   LYS D  94 " --> pdb=" O   PHE D  90 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 101 through 129
      removed outlier: 3.947A  pdb=" N   VAL D 105 " --> pdb=" O   VAL D 101 " (cutoff:3.500A)
      removed outlier: 4.203A  pdb=" N   VAL D 106 " --> pdb=" O   PHE D 102 " (cutoff:3.500A)
      removed outlier: 3.928A  pdb=" N   ILE D 107 " --> pdb=" O   PRO D 103 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 132 through 139
      removed outlier: 4.171A  pdb=" N   LYS D 135 " --> pdb=" O   GLU D 132 " (cutoff:3.500A)
      removed outlier: 4.760A  pdb=" N   TYR D 138 " --> pdb=" O   LYS D 135 " (cutoff:3.500A)
      removed outlier: 3.570A  pdb=" N   LEU D 139 " --> pdb=" O   TYR D 136 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 140 through 163
      removed outlier: 3.505A  pdb=" N   ILE D 154 " --> pdb=" O   TYR D 150 " (cutoff:3.500A)
      removed outlier: 3.749A  pdb=" N   VAL D 163 " --> pdb=" O   GLY D 159 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 168 through 180
    Processing helix  chain 'D' and resid 188 through 192
      removed outlier: 3.541A  pdb=" N   LEU D 192 " --> pdb=" O   LEU D 189 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 193 through 201
      removed outlier: 3.626A  pdb=" N   TYR D 201 " --> pdb=" O   LYS D 197 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 205 through 217
      removed outlier: 3.516A  pdb=" N   VAL D 215 " --> pdb=" O   ILE D 211 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 223 through 256
      Proline residue:  D 235  - end of helix
      removed outlier: 5.733A  pdb=" N   LYS D 250 " --> pdb=" O   LYS D 246 " (cutoff:3.500A)
      removed outlier: 5.172A  pdb=" N   ASP D 251 " --> pdb=" O   LYS D 247 " (cutoff:3.500A)
      removed outlier: 3.915A  pdb=" N   ALA D 256 " --> pdb=" O   ILE D 252 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 32 through 37
      removed outlier: 6.625A  pdb=" N   LYS A   9 " --> pdb=" O   VAL A  36 " (cutoff:3.500A)
      removed outlier: 3.628A  pdb=" N   ILE A   2 " --> pdb=" O   ILE A  44 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 32 through 37
      removed outlier: 6.625A  pdb=" N   LYS A   9 " --> pdb=" O   VAL A  36 " (cutoff:3.500A)
      removed outlier: 3.581A  pdb=" N   PHE A  77 " --> pdb=" O   PHE A   5 " (cutoff:3.500A)
      removed outlier: 4.286A  pdb=" N   VAL A   7 " --> pdb=" O   LYS A  75 " (cutoff:3.500A)
      removed outlier: 6.447A  pdb=" N   LYS A  75 " --> pdb=" O   VAL A   7 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 162 through 166
      removed outlier: 6.397A  pdb=" N   PHE A 163 " --> pdb=" O   ILE A 195 " (cutoff:3.500A)
      removed outlier: 7.721A  pdb=" N   VAL A 197 " --> pdb=" O   PHE A 163 " (cutoff:3.500A)
      removed outlier: 6.065A  pdb=" N   ILE A 165 " --> pdb=" O   VAL A 197 " (cutoff:3.500A)
      removed outlier: 6.408A  pdb=" N   LEU A  50 " --> pdb=" O   PHE A 196 " (cutoff:3.500A)
      removed outlier: 7.130A  pdb=" N   ALA A 211 " --> pdb=" O   GLU A 222 " (cutoff:3.500A)
      removed outlier: 4.542A  pdb=" N   GLU A 222 " --> pdb=" O   ALA A 211 " (cutoff:3.500A)
      removed outlier: 6.911A  pdb=" N   LEU A 213 " --> pdb=" O   ILE A 220 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 263 through 265
      removed outlier: 3.688A  pdb=" N   ILE A 282 " --> pdb=" O   PHE A 332 " (cutoff:3.500A)
      removed outlier: 4.383A  pdb=" N   LEU A 329 " --> pdb=" O   ARG C 392 " (cutoff:3.500A)
      removed outlier: 3.949A  pdb=" N   ARG C 392 " --> pdb=" O   LEU A 329 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'A' and resid 361 through 371
      removed outlier: 8.615A  pdb=" N   ILE A 363 " --> pdb=" O   LEU A 349 " (cutoff:3.500A)
      removed outlier: 8.171A  pdb=" N   LEU A 349 " --> pdb=" O   ILE A 363 " (cutoff:3.500A)
      removed outlier: 7.533A  pdb=" N   ASN A 365 " --> pdb=" O   VAL A 347 " (cutoff:3.500A)
      removed outlier: 8.680A  pdb=" N   VAL A 347 " --> pdb=" O   ASN A 365 " (cutoff:3.500A)
      removed outlier: 3.997A  pdb=" N   CYS A 367 " --> pdb=" O   LEU A 345 " (cutoff:3.500A)
      removed outlier: 3.550A  pdb=" N   PHE A 310 " --> pdb=" O   ILE A 301 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'A' and resid 388 through 394
      removed outlier: 4.050A  pdb=" N   ASN A 390 " --> pdb=" O   THR C 331 " (cutoff:3.500A)
      removed outlier: 3.731A  pdb=" N   THR C 331 " --> pdb=" O   ASN A 390 " (cutoff:3.500A)
      removed outlier: 3.854A  pdb=" N   ARG A 392 " --> pdb=" O   LEU C 329 " (cutoff:3.500A)
      removed outlier: 3.702A  pdb=" N   LEU C 329 " --> pdb=" O   ARG A 392 " (cutoff:3.500A)
      removed outlier: 4.481A  pdb=" N   LYS C 327 " --> pdb=" O   ILE A 394 " (cutoff:3.500A)
      removed outlier: 4.363A  pdb=" N   GLY C 326 " --> pdb=" O   ALA C 288 " (cutoff:3.500A)
      removed outlier: 3.628A  pdb=" N   ALA C 288 " --> pdb=" O   GLY C 326 " (cutoff:3.500A)
      removed outlier: 7.802A  pdb=" N   THR C 279 " --> pdb=" O   SER C 266 " (cutoff:3.500A)
      removed outlier: 5.011A  pdb=" N   SER C 266 " --> pdb=" O   THR C 279 " (cutoff:3.500A)
      removed outlier: 6.544A  pdb=" N   PHE C 281 " --> pdb=" O   LEU C 264 " (cutoff:3.500A)
      removed outlier: 4.387A  pdb=" N   LEU C 264 " --> pdb=" O   PHE C 281 " (cutoff:3.500A)
      removed outlier: 6.497A  pdb=" N   GLU C 283 " --> pdb=" O   VAL C 262 " (cutoff:3.500A)
      removed outlier: 4.261A  pdb=" N   VAL C 262 " --> pdb=" O   GLU C 283 " (cutoff:3.500A)
      removed outlier: 6.564A  pdb=" N   ASP C 285 " --> pdb=" O   LYS C 260 " (cutoff:3.500A)
      removed outlier: 3.606A  pdb=" N   GLY C 269 " --> pdb=" O   SER C 266 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'C' and resid 164 through 165
      removed outlier: 3.726A  pdb=" N   VAL C 197 " --> pdb=" O   ILE C 165 " (cutoff:3.500A)
      removed outlier: 6.154A  pdb=" N   LEU C  50 " --> pdb=" O   PHE C 196 " (cutoff:3.500A)
      removed outlier: 7.408A  pdb=" N   ILE C 212 " --> pdb=" O   VAL C  49 " (cutoff:3.500A)
      removed outlier: 6.006A  pdb=" N   GLY C  51 " --> pdb=" O   ILE C 212 " (cutoff:3.500A)
      removed outlier: 4.554A  pdb=" N   GLU C 221 " --> pdb=" O   LEU C 213 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'C' and resid 308 through 313

    502 hydrogen bonds defined for protein.
    1434 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 2.86

  Time building geometry restraints manager: 3.03 seconds

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

  Histogram of bond lengths:
        1.17 -     1.30: 1656
        1.30 -     1.43: 2980
        1.43 -     1.56: 6254
        1.56 -     1.69: 6
        1.69 -     1.82: 52
  Bond restraints: 10948
  Sorted by residual:
  bond pdb=" C   HIS B 212 "
       pdb=" O   HIS B 212 "
    ideal  model  delta    sigma   weight residual
    1.237  1.168  0.068 1.16e-02 7.43e+03 3.46e+01
  bond pdb=" C4  ADP C 501 "
       pdb=" C5  ADP C 501 "
    ideal  model  delta    sigma   weight residual
    1.490  1.380  0.110 2.00e-02 2.50e+03 3.04e+01
  bond pdb=" N   ILE D 211 "
       pdb=" CA  ILE D 211 "
    ideal  model  delta    sigma   weight residual
    1.459  1.531 -0.071 1.33e-02 5.65e+03 2.88e+01
  bond pdb=" C5  ADP C 501 "
       pdb=" C6  ADP C 501 "
    ideal  model  delta    sigma   weight residual
    1.490  1.405  0.085 2.00e-02 2.50e+03 1.81e+01
  bond pdb=" N   LEU D 139 "
       pdb=" CA  LEU D 139 "
    ideal  model  delta    sigma   weight residual
    1.457  1.502 -0.045 1.16e-02 7.43e+03 1.50e+01
  ... (remaining 10943 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.83: 14512
        1.83 -     3.65: 214
        3.65 -     5.48: 61
        5.48 -     7.31: 20
        7.31 -     9.13: 11
  Bond angle restraints: 14818
  Sorted by residual:
  angle pdb=" N   THR B 128 "
        pdb=" CA  THR B 128 "
        pdb=" C   THR B 128 "
      ideal   model   delta    sigma   weight residual
     111.07  117.99   -6.92 1.07e+00 8.73e-01 4.18e+01
  angle pdb=" O   PHE B 126 "
        pdb=" C   PHE B 126 "
        pdb=" N   ILE B 127 "
      ideal   model   delta    sigma   weight residual
     122.12  116.24    5.88 1.06e+00 8.90e-01 3.08e+01
  angle pdb=" C   TYR B 114 "
        pdb=" CA  TYR B 114 "
        pdb=" CB  TYR B 114 "
      ideal   model   delta    sigma   weight residual
     110.96  119.46   -8.50 1.54e+00 4.22e-01 3.05e+01
  angle pdb=" CA  TYR B 114 "
        pdb=" C   TYR B 114 "
        pdb=" O   TYR B 114 "
      ideal   model   delta    sigma   weight residual
     121.00  115.24    5.76 1.05e+00 9.07e-01 3.01e+01
  angle pdb=" C   PHE B 126 "
        pdb=" N   ILE B 127 "
        pdb=" CA  ILE B 127 "
      ideal   model   delta    sigma   weight residual
     120.72  114.17    6.55 1.22e+00 6.72e-01 2.88e+01
  ... (remaining 14813 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    27.15: 6079
       27.15 -    54.30: 298
       54.30 -    81.44: 13
       81.44 -   108.59: 1
      108.59 -   135.74: 5
  Dihedral angle restraints: 6396
    sinusoidal: 2616
      harmonic: 3780
  Sorted by residual:
  dihedral pdb=" O2A ADP C 501 "
           pdb=" O3A ADP C 501 "
           pdb=" PA  ADP C 501 "
           pdb=" PB  ADP C 501 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -60.00   75.74 -135.74     1      2.00e+01 2.50e-03 4.12e+01
  dihedral pdb=" O2A ADP A 501 "
           pdb=" O3A ADP A 501 "
           pdb=" PA  ADP A 501 "
           pdb=" PB  ADP A 501 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -60.00   68.82 -128.82     1      2.00e+01 2.50e-03 3.90e+01
  dihedral pdb=" O1B ADP A 501 "
           pdb=" O3A ADP A 501 "
           pdb=" PB  ADP A 501 "
           pdb=" PA  ADP A 501 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -60.00   65.56 -125.56     1      2.00e+01 2.50e-03 3.80e+01
  ... (remaining 6393 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.058: 1411
       0.058 -    0.116: 220
       0.116 -    0.174: 19
       0.174 -    0.233: 2
       0.233 -    0.291: 2
  Chirality restraints: 1654
  Sorted by residual:
  chirality pdb=" CB  ILE D 211 "
            pdb=" CA  ILE D 211 "
            pdb=" CG1 ILE D 211 "
            pdb=" CG2 ILE D 211 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.35    0.29 2.00e-01 2.50e+01 2.11e+00
  chirality pdb=" CA  THR B 128 "
            pdb=" N   THR B 128 "
            pdb=" C   THR B 128 "
            pdb=" CB  THR B 128 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.53    2.24    0.28 2.00e-01 2.50e+01 2.00e+00
  chirality pdb=" CA  TYR B 114 "
            pdb=" N   TYR B 114 "
            pdb=" C   TYR B 114 "
            pdb=" CB  TYR B 114 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.32    0.19 2.00e-01 2.50e+01 9.30e-01
  ... (remaining 1651 not shown)

  Planarity restraints: 1816
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  LEU D 139 "   -0.018 2.00e-02 2.50e+03   3.76e-02 1.41e+01
        pdb=" C   LEU D 139 "    0.065 2.00e-02 2.50e+03
        pdb=" O   LEU D 139 "   -0.024 2.00e-02 2.50e+03
        pdb=" N   PHE D 140 "   -0.023 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TYR B 114 "    0.026 2.00e-02 2.50e+03   1.61e-02 5.21e+00
        pdb=" CG  TYR B 114 "   -0.036 2.00e-02 2.50e+03
        pdb=" CD1 TYR B 114 "    0.004 2.00e-02 2.50e+03
        pdb=" CD2 TYR B 114 "   -0.002 2.00e-02 2.50e+03
        pdb=" CE1 TYR B 114 "   -0.003 2.00e-02 2.50e+03
        pdb=" CE2 TYR B 114 "    0.002 2.00e-02 2.50e+03
        pdb=" CZ  TYR B 114 "   -0.000 2.00e-02 2.50e+03
        pdb=" OH  TYR B 114 "    0.009 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  PHE B  92 "   -0.013 2.00e-02 2.50e+03   1.61e-02 4.51e+00
        pdb=" CG  PHE B  92 "    0.037 2.00e-02 2.50e+03
        pdb=" CD1 PHE B  92 "   -0.010 2.00e-02 2.50e+03
        pdb=" CD2 PHE B  92 "   -0.012 2.00e-02 2.50e+03
        pdb=" CE1 PHE B  92 "   -0.002 2.00e-02 2.50e+03
        pdb=" CE2 PHE B  92 "   -0.000 2.00e-02 2.50e+03
        pdb=" CZ  PHE B  92 "    0.000 2.00e-02 2.50e+03
  ... (remaining 1813 not shown)

  Histogram of nonbonded interaction distances:
        2.23 -     2.77: 1828
        2.77 -     3.30: 9797
        3.30 -     3.83: 16897
        3.83 -     4.37: 18279
        4.37 -     4.90: 33388
  Nonbonded interactions: 80189
  Sorted by model distance:
  nonbonded pdb=" OG  SER A 114 "
            pdb=" OE1 GLU A 117 "
     model   vdw
     2.233 3.040
  nonbonded pdb=" O   PHE A 134 "
            pdb=" OH  TYR A 142 "
     model   vdw
     2.249 3.040
  nonbonded pdb=" OD1 ASP C 294 "
            pdb=" OH  TYR C 315 "
     model   vdw
     2.264 3.040
  nonbonded pdb=" O   PHE C 134 "
            pdb=" OH  TYR C 142 "
     model   vdw
     2.267 3.040
  nonbonded pdb=" O   ILE C 154 "
            pdb=" OG1 THR C 158 "
     model   vdw
     2.270 3.040
  ... (remaining 80184 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: 0.03
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'C'
}
ncs_group {
  reference = chain 'B'
  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=0.15 max=1.00 mean=0.99
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             210.090
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.070
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.480
  Check model and map are aligned:         0.080
  Set scattering table:                    0.100
  Process input model:                     28.350
  Find NCS groups from input model:        0.330
  Set up NCS constraints:                  0.040
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:3.000
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:  242.550
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7409
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.110  10948  Z= 0.183
  Angle     :  0.632   9.135  14818  Z= 0.343
  Chirality :  0.042   0.291   1654
  Planarity :  0.003   0.038   1816
  Dihedral  : 14.699 135.740   3980
  Min Nonbonded Distance : 2.233

Molprobity Statistics.
  All-atom Clashscore : 7.01
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.72 %
    Favored  : 95.28 %
  Rotamer:
    Outliers :  0.34 %
    Allowed  :  0.43 %
    Favored  : 99.22 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.61 (0.24), residues: 1292
  helix:  1.82 (0.23), residues: 595
  sheet:  1.26 (0.43), residues: 170
  loop : -1.64 (0.25), residues: 527

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP D 181 
 HIS   0.005   0.000   HIS B 212 
 PHE   0.037   0.001   PHE B  92 
 TYR   0.036   0.001   TYR B 114 
 ARG   0.003   0.000   ARG C 116 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.16040 (  497)
  hydrogen bonds       : angle       6.05912 ( 1434)
  covalent geometry    : bond        0.00302 (10948)
  covalent geometry    : angle       0.63213 (14818)

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

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

  2584 Ramachandran restraints generated.
    1292 Oldfield, 0 Emsley, 1292 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2584 Ramachandran restraints generated.
    1292 Oldfield, 0 Emsley, 1292 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  171 residues out of total 1160 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 167
  time to evaluate  : 1.367 
Fit side-chains
REVERT: A  343 TYR cc_start: 0.7548 (m-80) cc_final: 0.6931 (m-80)
REVERT: B  129 LEU cc_start: 0.7428 (OUTLIER) cc_final: 0.7077 (mt)
  outliers start: 4
  outliers final: 0
  residues processed: 170
  average time/residue: 0.2186
  time to fit residues: 55.9576
Evaluate side-chains
  133 residues out of total 1160 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 132
  time to evaluate  : 1.196 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  129 LEU
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 128
   random chunks:
   chunk 108 optimal weight:    0.0970
   chunk 97 optimal weight:    4.9990
   chunk 53 optimal weight:    1.9990
   chunk 33 optimal weight:    5.9990
   chunk 65 optimal weight:    2.9990
   chunk 51 optimal weight:    2.9990
   chunk 100 optimal weight:    3.9990
   chunk 38 optimal weight:    5.9990
   chunk 61 optimal weight:    2.9990
   chunk 74 optimal weight:    8.9990
   chunk 116 optimal weight:    1.9990
   overall best weight:    2.0186

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

Flipped N/Q/H residues before XYZ refinement:
A 357 GLN
B  55 ASN
B 218 ASN
C 361 HIS
C 368 ASN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4039 r_free = 0.4039 target = 0.173782 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3688 r_free = 0.3688 target = 0.141520 restraints weight = 14072.243|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3673 r_free = 0.3673 target = 0.140533 restraints weight = 17680.262|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3691 r_free = 0.3691 target = 0.142363 restraints weight = 16246.074|
|-----------------------------------------------------------------------------|
r_work (final): 0.3489
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3505
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3505 r_free = 0.3505    target_work(ls_wunit_k1) = 0.128         |
| occupancies: max = 1.00  min = 0.15   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3437 r_free = 0.3437    target_work(ls_wunit_k1) = 0.123         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        9 |
|-----------------------------------------------------------------------------|
r_final: 0.3437
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7780
moved from start:          0.2676

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.072  10948  Z= 0.249
  Angle     :  0.708   8.443  14818  Z= 0.360
  Chirality :  0.047   0.170   1654
  Planarity :  0.004   0.034   1816
  Dihedral  :  8.236 155.539   1424
  Min Nonbonded Distance : 2.468

Molprobity Statistics.
  All-atom Clashscore : 7.53
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.27 %
    Favored  : 93.73 %
  Rotamer:
    Outliers :  1.55 %
    Allowed  : 12.76 %
    Favored  : 85.69 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.10 (0.24), residues: 1292
  helix:  1.17 (0.22), residues: 599
  sheet:  0.37 (0.41), residues: 189
  loop : -1.79 (0.26), residues: 504

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.002   TRP B  71 
 HIS   0.005   0.002   HIS D 223 
 PHE   0.028   0.002   PHE C 369 
 TYR   0.027   0.002   TYR B 243 
 ARG   0.006   0.001   ARG B  17 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.06674 (  497)
  hydrogen bonds       : angle       5.04321 ( 1434)
  covalent geometry    : bond        0.00610 (10948)
  covalent geometry    : angle       0.70802 (14818)

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

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

  2584 Ramachandran restraints generated.
    1292 Oldfield, 0 Emsley, 1292 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2584 Ramachandran restraints generated.
    1292 Oldfield, 0 Emsley, 1292 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  167 residues out of total 1160 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 149
  time to evaluate  : 1.471 
Fit side-chains
REVERT: A  117 GLU cc_start: 0.7725 (mp0) cc_final: 0.7442 (mp0)
REVERT: A  318 GLU cc_start: 0.7261 (mp0) cc_final: 0.6866 (mp0)
REVERT: B   16 ASN cc_start: 0.8803 (p0) cc_final: 0.8445 (p0)
REVERT: B  205 MET cc_start: 0.6428 (OUTLIER) cc_final: 0.5980 (ttm)
REVERT: B  220 LEU cc_start: 0.8247 (OUTLIER) cc_final: 0.7955 (mm)
REVERT: D  156 MET cc_start: 0.8244 (tmm) cc_final: 0.8013 (tpp)
  outliers start: 18
  outliers final: 12
  residues processed: 160
  average time/residue: 0.2587
  time to fit residues: 59.8751
Evaluate side-chains
  135 residues out of total 1160 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 121
  time to evaluate  : 1.257 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   42 LEU
Chi-restraints excluded: chain A residue  262 VAL
Chi-restraints excluded: chain A residue  344 THR
Chi-restraints excluded: chain A residue  367 CYS
Chi-restraints excluded: chain A residue  387 THR
Chi-restraints excluded: chain B residue  196 VAL
Chi-restraints excluded: chain B residue  205 MET
Chi-restraints excluded: chain B residue  211 ILE
Chi-restraints excluded: chain B residue  220 LEU
Chi-restraints excluded: chain C residue   85 VAL
Chi-restraints excluded: chain D residue    3 LEU
Chi-restraints excluded: chain D residue  121 VAL
Chi-restraints excluded: chain D residue  122 THR
Chi-restraints excluded: chain D residue  174 VAL
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 128
   random chunks:
   chunk 32 optimal weight:    6.9990
   chunk 62 optimal weight:    1.9990
   chunk 2 optimal weight:    1.9990
   chunk 65 optimal weight:    0.9990
   chunk 14 optimal weight:   10.0000
   chunk 79 optimal weight:    6.9990
   chunk 75 optimal weight:    1.9990
   chunk 20 optimal weight:    0.7980
   chunk 30 optimal weight:    0.8980
   chunk 8 optimal weight:    4.9990
   chunk 123 optimal weight:    0.5980
   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 103 ASN
A 357 GLN
B 218 ASN
C  31 HIS
C 157 HIS
C 187 HIS

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4002 r_free = 0.4002 target = 0.171390 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3643 r_free = 0.3643 target = 0.138662 restraints weight = 13985.167|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3636 r_free = 0.3636 target = 0.138428 restraints weight = 16495.773|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3654 r_free = 0.3654 target = 0.140292 restraints weight = 15830.886|
|-----------------------------------------------------------------------------|
r_work (final): 0.3466
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3466
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3466 r_free = 0.3466    target_work(ls_wunit_k1) = 0.126         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        9 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3462 r_free = 0.3462    target_work(ls_wunit_k1) = 0.126         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       24 |
|-----------------------------------------------------------------------------|
r_final: 0.3462
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7730
moved from start:          0.2864

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.050  10948  Z= 0.150
  Angle     :  0.599   7.564  14818  Z= 0.300
  Chirality :  0.042   0.139   1654
  Planarity :  0.004   0.035   1816
  Dihedral  :  7.928 170.754   1422
  Min Nonbonded Distance : 2.489

Molprobity Statistics.
  All-atom Clashscore : 6.56
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.19 %
    Favored  : 94.81 %
  Rotamer:
    Outliers :  2.33 %
    Allowed  : 15.78 %
    Favored  : 81.90 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.12 (0.24), residues: 1292
  helix:  1.49 (0.22), residues: 588
  sheet:  0.72 (0.43), residues: 177
  loop : -1.86 (0.25), residues: 527

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.002   TRP D 181 
 HIS   0.011   0.001   HIS C 187 
 PHE   0.016   0.001   PHE B 152 
 TYR   0.021   0.001   TYR B 243 
 ARG   0.007   0.000   ARG B  17 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05088 (  497)
  hydrogen bonds       : angle       4.68273 ( 1434)
  covalent geometry    : bond        0.00355 (10948)
  covalent geometry    : angle       0.59887 (14818)

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

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

  2584 Ramachandran restraints generated.
    1292 Oldfield, 0 Emsley, 1292 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2584 Ramachandran restraints generated.
    1292 Oldfield, 0 Emsley, 1292 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  160 residues out of total 1160 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 133
  time to evaluate  : 1.171 
Fit side-chains
REVERT: A    5 PHE cc_start: 0.6992 (t80) cc_final: 0.6766 (t80)
REVERT: A  318 GLU cc_start: 0.7275 (mp0) cc_final: 0.6912 (mp0)
REVERT: B   16 ASN cc_start: 0.8714 (p0) cc_final: 0.8284 (p0)
REVERT: B  220 LEU cc_start: 0.8187 (OUTLIER) cc_final: 0.7910 (mm)
REVERT: C  125 ILE cc_start: 0.8474 (OUTLIER) cc_final: 0.8250 (mt)
  outliers start: 27
  outliers final: 11
  residues processed: 148
  average time/residue: 0.2001
  time to fit residues: 43.4947
Evaluate side-chains
  138 residues out of total 1160 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 125
  time to evaluate  : 1.154 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   42 LEU
Chi-restraints excluded: chain A residue  262 VAL
Chi-restraints excluded: chain B residue  122 THR
Chi-restraints excluded: chain B residue  131 PHE
Chi-restraints excluded: chain B residue  205 MET
Chi-restraints excluded: chain B residue  220 LEU
Chi-restraints excluded: chain C residue   53 VAL
Chi-restraints excluded: chain C residue  125 ILE
Chi-restraints excluded: chain C residue  128 PHE
Chi-restraints excluded: chain C residue  295 VAL
Chi-restraints excluded: chain D residue    3 LEU
Chi-restraints excluded: chain D residue   68 ILE
Chi-restraints excluded: chain D residue  122 THR
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 128
   random chunks:
   chunk 46 optimal weight:    0.9990
   chunk 58 optimal weight:    0.9980
   chunk 13 optimal weight:    9.9990
   chunk 22 optimal weight:    2.9990
   chunk 107 optimal weight:    0.9980
   chunk 36 optimal weight:    4.9990
   chunk 84 optimal weight:    2.9990
   chunk 51 optimal weight:    0.0980
   chunk 35 optimal weight:    0.9990
   chunk 74 optimal weight:    7.9990
   chunk 61 optimal weight:    1.9990
   overall best weight:    0.8184

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

Flipped N/Q/H residues before XYZ refinement:
A 357 GLN
B  16 ASN
B 218 ASN
C 157 HIS

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4241 r_free = 0.4241 target = 0.187405 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3895 r_free = 0.3895 target = 0.153325 restraints weight = 14732.951|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3900 r_free = 0.3900 target = 0.155670 restraints weight = 12462.675|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3910 r_free = 0.3910 target = 0.156873 restraints weight = 9010.746|
|-----------------------------------------------------------------------------|
r_work (final): 0.3905
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3898
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3898 r_free = 0.3898    target_work(ls_wunit_k1) = 0.155         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       24 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3896 r_free = 0.3896    target_work(ls_wunit_k1) = 0.155         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       33 |
|-----------------------------------------------------------------------------|
r_final: 0.3896
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7854
moved from start:          0.2980

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042  10948  Z= 0.131
  Angle     :  0.576   7.559  14818  Z= 0.287
  Chirality :  0.041   0.142   1654
  Planarity :  0.003   0.029   1816
  Dihedral  :  7.845 178.971   1422
  Min Nonbonded Distance : 2.488

Molprobity Statistics.
  All-atom Clashscore : 6.29
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.34 %
    Favored  : 94.66 %
  Rotamer:
    Outliers :  2.33 %
    Allowed  : 17.16 %
    Favored  : 80.52 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.20 (0.24), residues: 1292
  helix:  1.57 (0.22), residues: 592
  sheet:  0.62 (0.43), residues: 181
  loop : -1.83 (0.25), residues: 519

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP D 181 
 HIS   0.002   0.001   HIS C 350 
 PHE   0.015   0.001   PHE B  92 
 TYR   0.018   0.001   TYR B 243 
 ARG   0.004   0.000   ARG B  17 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04690 (  497)
  hydrogen bonds       : angle       4.49564 ( 1434)
  covalent geometry    : bond        0.00301 (10948)
  covalent geometry    : angle       0.57570 (14818)

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

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

  2584 Ramachandran restraints generated.
    1292 Oldfield, 0 Emsley, 1292 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2584 Ramachandran restraints generated.
    1292 Oldfield, 0 Emsley, 1292 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  158 residues out of total 1160 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 131
  time to evaluate  : 1.168 
Fit side-chains
REVERT: A  102 GLU cc_start: 0.7811 (tp30) cc_final: 0.7409 (tp30)
REVERT: A  122 LEU cc_start: 0.7211 (OUTLIER) cc_final: 0.6930 (mp)
REVERT: A  318 GLU cc_start: 0.7074 (mp0) cc_final: 0.6856 (mp0)
REVERT: B   16 ASN cc_start: 0.8579 (OUTLIER) cc_final: 0.8235 (p0)
REVERT: B  205 MET cc_start: 0.6155 (OUTLIER) cc_final: 0.5748 (ttm)
REVERT: B  220 LEU cc_start: 0.7992 (OUTLIER) cc_final: 0.7740 (mm)
REVERT: C  125 ILE cc_start: 0.8359 (OUTLIER) cc_final: 0.8116 (mt)
  outliers start: 27
  outliers final: 12
  residues processed: 145
  average time/residue: 0.1965
  time to fit residues: 42.3139
Evaluate side-chains
  140 residues out of total 1160 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 123
  time to evaluate  : 1.217 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   42 LEU
Chi-restraints excluded: chain A residue  122 LEU
Chi-restraints excluded: chain A residue  166 ASP
Chi-restraints excluded: chain A residue  262 VAL
Chi-restraints excluded: chain B residue   16 ASN
Chi-restraints excluded: chain B residue   90 PHE
Chi-restraints excluded: chain B residue  205 MET
Chi-restraints excluded: chain B residue  220 LEU
Chi-restraints excluded: chain B residue  239 PHE
Chi-restraints excluded: chain C residue   53 VAL
Chi-restraints excluded: chain C residue  125 ILE
Chi-restraints excluded: chain C residue  295 VAL
Chi-restraints excluded: chain C residue  383 CYS
Chi-restraints excluded: chain D residue    3 LEU
Chi-restraints excluded: chain D residue   68 ILE
Chi-restraints excluded: chain D residue  118 ILE
Chi-restraints excluded: chain D residue  122 THR
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 128
   random chunks:
   chunk 95 optimal weight:    5.9990
   chunk 81 optimal weight:    0.9990
   chunk 113 optimal weight:    1.9990
   chunk 66 optimal weight:    1.9990
   chunk 77 optimal weight:   10.0000
   chunk 115 optimal weight:    3.9990
   chunk 58 optimal weight:    0.7980
   chunk 4 optimal weight:    0.7980
   chunk 112 optimal weight:    0.2980
   chunk 110 optimal weight:    1.9990
   chunk 50 optimal weight:    0.6980
   overall best weight:    0.7182

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

Flipped N/Q/H residues before XYZ refinement:
** A 357 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 218 ASN
C 157 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4239 r_free = 0.4239 target = 0.187348 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3895 r_free = 0.3895 target = 0.153391 restraints weight = 14787.262|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3896 r_free = 0.3896 target = 0.155399 restraints weight = 12624.355|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3904 r_free = 0.3904 target = 0.156479 restraints weight = 9552.140|
|-----------------------------------------------------------------------------|
r_work (final): 0.3900
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3902
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3902 r_free = 0.3902    target_work(ls_wunit_k1) = 0.155         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       33 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3902 r_free = 0.3902    target_work(ls_wunit_k1) = 0.155         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       34 |
|-----------------------------------------------------------------------------|
r_final: 0.3902
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7854
moved from start:          0.3099

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040  10948  Z= 0.124
  Angle     :  0.576   9.046  14818  Z= 0.285
  Chirality :  0.041   0.152   1654
  Planarity :  0.003   0.044   1816
  Dihedral  :  7.641 172.524   1422
  Min Nonbonded Distance : 2.476

Molprobity Statistics.
  All-atom Clashscore : 6.01
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.57 %
    Favored  : 94.43 %
  Rotamer:
    Outliers :  3.02 %
    Allowed  : 17.93 %
    Favored  : 79.05 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.25 (0.24), residues: 1292
  helix:  1.59 (0.23), residues: 596
  sheet:  0.59 (0.43), residues: 176
  loop : -1.76 (0.25), residues: 520

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP D 181 
 HIS   0.002   0.001   HIS C 361 
 PHE   0.016   0.001   PHE B  92 
 TYR   0.022   0.001   TYR B 243 
 ARG   0.003   0.000   ARG B  17 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04497 (  497)
  hydrogen bonds       : angle       4.42298 ( 1434)
  covalent geometry    : bond        0.00283 (10948)
  covalent geometry    : angle       0.57574 (14818)

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

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

  2584 Ramachandran restraints generated.
    1292 Oldfield, 0 Emsley, 1292 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2584 Ramachandran restraints generated.
    1292 Oldfield, 0 Emsley, 1292 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  163 residues out of total 1160 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 128
  time to evaluate  : 1.184 
Fit side-chains
REVERT: A  318 GLU cc_start: 0.7145 (mp0) cc_final: 0.6922 (mp0)
REVERT: B   16 ASN cc_start: 0.8562 (OUTLIER) cc_final: 0.8209 (p0)
REVERT: B  205 MET cc_start: 0.6212 (OUTLIER) cc_final: 0.5731 (ttm)
REVERT: B  220 LEU cc_start: 0.8000 (OUTLIER) cc_final: 0.7764 (mm)
REVERT: C  125 ILE cc_start: 0.8392 (OUTLIER) cc_final: 0.8148 (mt)
  outliers start: 35
  outliers final: 21
  residues processed: 148
  average time/residue: 0.1929
  time to fit residues: 42.6654
Evaluate side-chains
  149 residues out of total 1160 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 124
  time to evaluate  : 1.277 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   42 LEU
Chi-restraints excluded: chain A residue   78 VAL
Chi-restraints excluded: chain A residue  166 ASP
Chi-restraints excluded: chain A residue  197 VAL
Chi-restraints excluded: chain A residue  207 LEU
Chi-restraints excluded: chain B residue   16 ASN
Chi-restraints excluded: chain B residue   90 PHE
Chi-restraints excluded: chain B residue  205 MET
Chi-restraints excluded: chain B residue  217 VAL
Chi-restraints excluded: chain B residue  220 LEU
Chi-restraints excluded: chain B residue  239 PHE
Chi-restraints excluded: chain C residue   53 VAL
Chi-restraints excluded: chain C residue   78 VAL
Chi-restraints excluded: chain C residue  125 ILE
Chi-restraints excluded: chain C residue  295 VAL
Chi-restraints excluded: chain C residue  317 MET
Chi-restraints excluded: chain C residue  321 VAL
Chi-restraints excluded: chain C residue  363 ILE
Chi-restraints excluded: chain C residue  383 CYS
Chi-restraints excluded: chain D residue    3 LEU
Chi-restraints excluded: chain D residue   56 THR
Chi-restraints excluded: chain D residue   68 ILE
Chi-restraints excluded: chain D residue  122 THR
Chi-restraints excluded: chain D residue  142 VAL
Chi-restraints excluded: chain D residue  190 ASP
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 128
   random chunks:
   chunk 18 optimal weight:    3.9990
   chunk 85 optimal weight:    0.0770
   chunk 122 optimal weight:    0.6980
   chunk 55 optimal weight:    2.9990
   chunk 109 optimal weight:    2.9990
   chunk 15 optimal weight:    3.9990
   chunk 43 optimal weight:    2.9990
   chunk 7 optimal weight:    0.0570
   chunk 73 optimal weight:    9.9990
   chunk 118 optimal weight:    2.9990
   chunk 100 optimal weight:    3.9990
   overall best weight:    1.3660

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

Flipped N/Q/H residues before XYZ refinement:
A 178 GLN
** A 357 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 361 HIS
** B  12 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 218 ASN
C 157 HIS
D  55 ASN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4193 r_free = 0.4193 target = 0.181565 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3843 r_free = 0.3843 target = 0.148708 restraints weight = 14487.401|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3830 r_free = 0.3830 target = 0.148639 restraints weight = 12856.267|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3842 r_free = 0.3842 target = 0.150066 restraints weight = 12319.907|
|-----------------------------------------------------------------------------|
r_work (final): 0.3843
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3843
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3843 r_free = 0.3843    target_work(ls_wunit_k1) = 0.150         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       34 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3841 r_free = 0.3841    target_work(ls_wunit_k1) = 0.150         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       33 |
|-----------------------------------------------------------------------------|
r_final: 0.3841
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7905
moved from start:          0.3484

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.057  10948  Z= 0.179
  Angle     :  0.621   7.933  14818  Z= 0.313
  Chirality :  0.043   0.170   1654
  Planarity :  0.004   0.029   1816
  Dihedral  :  7.635 165.186   1422
  Min Nonbonded Distance : 2.453

Molprobity Statistics.
  All-atom Clashscore : 6.57
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.19 %
    Favored  : 93.81 %
  Rotamer:
    Outliers :  3.36 %
    Allowed  : 18.62 %
    Favored  : 78.02 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.08 (0.24), residues: 1292
  helix:  1.37 (0.22), residues: 599
  sheet: -0.02 (0.41), residues: 196
  loop : -1.90 (0.26), residues: 497

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.002   TRP D 181 
 HIS   0.003   0.001   HIS D 212 
 PHE   0.018   0.002   PHE B  85 
 TYR   0.025   0.001   TYR B 243 
 ARG   0.003   0.000   ARG B  17 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05518 (  497)
  hydrogen bonds       : angle       4.57590 ( 1434)
  covalent geometry    : bond        0.00435 (10948)
  covalent geometry    : angle       0.62147 (14818)

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

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

  2584 Ramachandran restraints generated.
    1292 Oldfield, 0 Emsley, 1292 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2584 Ramachandran restraints generated.
    1292 Oldfield, 0 Emsley, 1292 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  177 residues out of total 1160 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 39
    poor density    : 138
  time to evaluate  : 1.431 
Fit side-chains
   revert: symmetry clash
REVERT: A  318 GLU cc_start: 0.7183 (mp0) cc_final: 0.6970 (mp0)
REVERT: B   16 ASN cc_start: 0.8514 (OUTLIER) cc_final: 0.8179 (p0)
REVERT: B  205 MET cc_start: 0.6329 (OUTLIER) cc_final: 0.5925 (ttm)
REVERT: B  220 LEU cc_start: 0.8025 (OUTLIER) cc_final: 0.7807 (mm)
REVERT: C  125 ILE cc_start: 0.8378 (OUTLIER) cc_final: 0.8134 (mt)
  outliers start: 39
  outliers final: 27
  residues processed: 158
  average time/residue: 0.2583
  time to fit residues: 60.7974
Evaluate side-chains
  157 residues out of total 1160 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 126
  time to evaluate  : 1.539 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   42 LEU
Chi-restraints excluded: chain A residue   78 VAL
Chi-restraints excluded: chain A residue  116 ARG
Chi-restraints excluded: chain A residue  166 ASP
Chi-restraints excluded: chain A residue  197 VAL
Chi-restraints excluded: chain A residue  207 LEU
Chi-restraints excluded: chain A residue  262 VAL
Chi-restraints excluded: chain B residue   16 ASN
Chi-restraints excluded: chain B residue   64 LEU
Chi-restraints excluded: chain B residue   84 ILE
Chi-restraints excluded: chain B residue   90 PHE
Chi-restraints excluded: chain B residue  131 PHE
Chi-restraints excluded: chain B residue  205 MET
Chi-restraints excluded: chain B residue  217 VAL
Chi-restraints excluded: chain B residue  220 LEU
Chi-restraints excluded: chain C residue   53 VAL
Chi-restraints excluded: chain C residue   78 VAL
Chi-restraints excluded: chain C residue  125 ILE
Chi-restraints excluded: chain C residue  128 PHE
Chi-restraints excluded: chain C residue  295 VAL
Chi-restraints excluded: chain C residue  317 MET
Chi-restraints excluded: chain C residue  321 VAL
Chi-restraints excluded: chain C residue  383 CYS
Chi-restraints excluded: chain D residue    3 LEU
Chi-restraints excluded: chain D residue   56 THR
Chi-restraints excluded: chain D residue   68 ILE
Chi-restraints excluded: chain D residue  118 ILE
Chi-restraints excluded: chain D residue  121 VAL
Chi-restraints excluded: chain D residue  122 THR
Chi-restraints excluded: chain D residue  142 VAL
Chi-restraints excluded: chain D residue  190 ASP
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 128
   random chunks:
   chunk 22 optimal weight:    2.9990
   chunk 15 optimal weight:    3.9990
   chunk 64 optimal weight:    5.9990
   chunk 89 optimal weight:    4.9990
   chunk 71 optimal weight:    4.9990
   chunk 95 optimal weight:    4.9990
   chunk 119 optimal weight:    3.9990
   chunk 80 optimal weight:    5.9990
   chunk 9 optimal weight:   10.0000
   chunk 37 optimal weight:    5.9990
   chunk 49 optimal weight:    1.9990
   overall best weight:    3.5990

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

Flipped N/Q/H residues before XYZ refinement:
A 103 ASN
** A 357 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B  12 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B  55 ASN
C 157 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4099 r_free = 0.4099 target = 0.172726 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3740 r_free = 0.3740 target = 0.140529 restraints weight = 14864.229|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 24)----------------|
| r_work = 0.3727 r_free = 0.3727 target = 0.140706 restraints weight = 14131.895|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3735 r_free = 0.3735 target = 0.141682 restraints weight = 15669.603|
|-----------------------------------------------------------------------------|
r_work (final): 0.3739
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3739
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3739 r_free = 0.3739    target_work(ls_wunit_k1) = 0.141         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       33 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3738 r_free = 0.3738    target_work(ls_wunit_k1) = 0.141         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       33 |
|-----------------------------------------------------------------------------|
r_final: 0.3738
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8031
moved from start:          0.4349

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.010   0.106  10948  Z= 0.401
  Angle     :  0.847  10.681  14818  Z= 0.433
  Chirality :  0.051   0.161   1654
  Planarity :  0.005   0.050   1816
  Dihedral  :  8.311 165.245   1422
  Min Nonbonded Distance : 2.391

Molprobity Statistics.
  All-atom Clashscore : 8.52
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.59 %
    Favored  : 92.41 %
  Rotamer:
    Outliers :  4.91 %
    Allowed  : 18.45 %
    Favored  : 76.64 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.06 (0.23), residues: 1292
  helix:  0.57 (0.21), residues: 605
  sheet: -0.58 (0.41), residues: 186
  loop : -2.38 (0.24), residues: 501

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.022   0.003   TRP A   8 
 HIS   0.008   0.002   HIS D 212 
 PHE   0.046   0.003   PHE B  85 
 TYR   0.031   0.003   TYR B 243 
 ARG   0.004   0.001   ARG A 302 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.08060 (  497)
  hydrogen bonds       : angle       5.23267 ( 1434)
  covalent geometry    : bond        0.01004 (10948)
  covalent geometry    : angle       0.84732 (14818)

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

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

  2584 Ramachandran restraints generated.
    1292 Oldfield, 0 Emsley, 1292 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2584 Ramachandran restraints generated.
    1292 Oldfield, 0 Emsley, 1292 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  195 residues out of total 1160 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 57
    poor density    : 138
  time to evaluate  : 1.914 
Fit side-chains
   revert: symmetry clash
REVERT: A    5 PHE cc_start: 0.7288 (t80) cc_final: 0.7079 (t80)
REVERT: A  318 GLU cc_start: 0.7179 (mp0) cc_final: 0.6868 (mp0)
REVERT: B  172 ILE cc_start: 0.9107 (OUTLIER) cc_final: 0.8892 (tp)
REVERT: B  220 LEU cc_start: 0.8265 (OUTLIER) cc_final: 0.7915 (mm)
REVERT: B  254 ASP cc_start: 0.7977 (m-30) cc_final: 0.7687 (m-30)
REVERT: C  249 GLN cc_start: 0.7103 (tm-30) cc_final: 0.6376 (tm-30)
REVERT: D  136 TYR cc_start: 0.7975 (m-80) cc_final: 0.7647 (m-80)
REVERT: D  254 ASP cc_start: 0.7321 (m-30) cc_final: 0.6934 (m-30)
  outliers start: 57
  outliers final: 38
  residues processed: 174
  average time/residue: 0.3131
  time to fit residues: 80.6522
Evaluate side-chains
  164 residues out of total 1160 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 40
    poor density    : 124
  time to evaluate  : 1.829 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   42 LEU
Chi-restraints excluded: chain A residue   78 VAL
Chi-restraints excluded: chain A residue  116 ARG
Chi-restraints excluded: chain A residue  166 ASP
Chi-restraints excluded: chain A residue  197 VAL
Chi-restraints excluded: chain A residue  207 LEU
Chi-restraints excluded: chain A residue  235 LEU
Chi-restraints excluded: chain A residue  250 ASN
Chi-restraints excluded: chain A residue  262 VAL
Chi-restraints excluded: chain A residue  367 CYS
Chi-restraints excluded: chain B residue   16 ASN
Chi-restraints excluded: chain B residue   84 ILE
Chi-restraints excluded: chain B residue   90 PHE
Chi-restraints excluded: chain B residue  122 THR
Chi-restraints excluded: chain B residue  131 PHE
Chi-restraints excluded: chain B residue  172 ILE
Chi-restraints excluded: chain B residue  205 MET
Chi-restraints excluded: chain B residue  217 VAL
Chi-restraints excluded: chain B residue  220 LEU
Chi-restraints excluded: chain C residue   53 VAL
Chi-restraints excluded: chain C residue   78 VAL
Chi-restraints excluded: chain C residue   85 VAL
Chi-restraints excluded: chain C residue   92 THR
Chi-restraints excluded: chain C residue  125 ILE
Chi-restraints excluded: chain C residue  295 VAL
Chi-restraints excluded: chain C residue  317 MET
Chi-restraints excluded: chain C residue  363 ILE
Chi-restraints excluded: chain C residue  383 CYS
Chi-restraints excluded: chain D residue    3 LEU
Chi-restraints excluded: chain D residue   38 ILE
Chi-restraints excluded: chain D residue   68 ILE
Chi-restraints excluded: chain D residue   86 THR
Chi-restraints excluded: chain D residue  101 VAL
Chi-restraints excluded: chain D residue  118 ILE
Chi-restraints excluded: chain D residue  121 VAL
Chi-restraints excluded: chain D residue  122 THR
Chi-restraints excluded: chain D residue  142 VAL
Chi-restraints excluded: chain D residue  171 ILE
Chi-restraints excluded: chain D residue  186 VAL
Chi-restraints excluded: chain D residue  190 ASP
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 128
   random chunks:
   chunk 56 optimal weight:    0.5980
   chunk 106 optimal weight:    0.5980
   chunk 50 optimal weight:    0.5980
   chunk 61 optimal weight:    0.9980
   chunk 77 optimal weight:    1.9990
   chunk 9 optimal weight:    0.4980
   chunk 43 optimal weight:    0.5980
   chunk 42 optimal weight:    1.9990
   chunk 11 optimal weight:    2.9990
   chunk 121 optimal weight:    0.7980
   chunk 117 optimal weight:    0.8980
   overall best weight:    0.5780

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

Flipped N/Q/H residues before XYZ refinement:
A 103 ASN
A 175 HIS
A 268 HIS
A 357 GLN
B  16 ASN
B 218 ASN
C 361 HIS
D 177 GLN

Total number of N/Q/H flips: 8

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4198 r_free = 0.4198 target = 0.182311 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3853 r_free = 0.3853 target = 0.149793 restraints weight = 14518.217|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3859 r_free = 0.3859 target = 0.151730 restraints weight = 12796.690|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3868 r_free = 0.3868 target = 0.152592 restraints weight = 10222.798|
|-----------------------------------------------------------------------------|
r_work (final): 0.3870
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3870
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3870 r_free = 0.3870    target_work(ls_wunit_k1) = 0.152         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       33 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3870 r_free = 0.3870    target_work(ls_wunit_k1) = 0.152         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       38 |
|-----------------------------------------------------------------------------|
r_final: 0.3870
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7870
moved from start:          0.3963

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037  10948  Z= 0.130
  Angle     :  0.632   8.200  14818  Z= 0.318
  Chirality :  0.042   0.179   1654
  Planarity :  0.004   0.038   1816
  Dihedral  :  7.627 165.562   1422
  Min Nonbonded Distance : 2.442

Molprobity Statistics.
  All-atom Clashscore : 6.61
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.88 %
    Favored  : 95.12 %
  Rotamer:
    Outliers :  3.36 %
    Allowed  : 20.26 %
    Favored  : 76.38 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.47 (0.24), residues: 1292
  helix:  1.20 (0.22), residues: 594
  sheet: -0.46 (0.41), residues: 193
  loop : -2.14 (0.25), residues: 505

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP B  31 
 HIS   0.005   0.001   HIS A 268 
 PHE   0.033   0.001   PHE B 152 
 TYR   0.023   0.001   TYR B 243 
 ARG   0.004   0.000   ARG A 116 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04886 (  497)
  hydrogen bonds       : angle       4.57723 ( 1434)
  covalent geometry    : bond        0.00289 (10948)
  covalent geometry    : angle       0.63204 (14818)

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

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

  2584 Ramachandran restraints generated.
    1292 Oldfield, 0 Emsley, 1292 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2584 Ramachandran restraints generated.
    1292 Oldfield, 0 Emsley, 1292 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  172 residues out of total 1160 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 39
    poor density    : 133
  time to evaluate  : 2.388 
Fit side-chains
REVERT: A  102 GLU cc_start: 0.7814 (tp30) cc_final: 0.7489 (tp30)
REVERT: A  318 GLU cc_start: 0.7136 (mp0) cc_final: 0.6880 (mp0)
REVERT: B  220 LEU cc_start: 0.7949 (OUTLIER) cc_final: 0.7729 (mm)
REVERT: C  125 ILE cc_start: 0.8389 (OUTLIER) cc_final: 0.8184 (mt)
REVERT: D  136 TYR cc_start: 0.7694 (m-80) cc_final: 0.7473 (m-80)
  outliers start: 39
  outliers final: 25
  residues processed: 155
  average time/residue: 0.4479
  time to fit residues: 103.0194
Evaluate side-chains
  155 residues out of total 1160 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 128
  time to evaluate  : 1.879 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   42 LEU
Chi-restraints excluded: chain A residue   78 VAL
Chi-restraints excluded: chain A residue  166 ASP
Chi-restraints excluded: chain A residue  197 VAL
Chi-restraints excluded: chain A residue  207 LEU
Chi-restraints excluded: chain A residue  262 VAL
Chi-restraints excluded: chain B residue   16 ASN
Chi-restraints excluded: chain B residue   84 ILE
Chi-restraints excluded: chain B residue   90 PHE
Chi-restraints excluded: chain B residue  118 ILE
Chi-restraints excluded: chain B residue  205 MET
Chi-restraints excluded: chain B residue  217 VAL
Chi-restraints excluded: chain B residue  220 LEU
Chi-restraints excluded: chain B residue  239 PHE
Chi-restraints excluded: chain C residue   53 VAL
Chi-restraints excluded: chain C residue   78 VAL
Chi-restraints excluded: chain C residue   92 THR
Chi-restraints excluded: chain C residue  125 ILE
Chi-restraints excluded: chain C residue  363 ILE
Chi-restraints excluded: chain D residue   68 ILE
Chi-restraints excluded: chain D residue  118 ILE
Chi-restraints excluded: chain D residue  121 VAL
Chi-restraints excluded: chain D residue  134 ILE
Chi-restraints excluded: chain D residue  142 VAL
Chi-restraints excluded: chain D residue  168 ILE
Chi-restraints excluded: chain D residue  171 ILE
Chi-restraints excluded: chain D residue  190 ASP
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 128
   random chunks:
   chunk 32 optimal weight:    1.9990
   chunk 113 optimal weight:    0.5980
   chunk 82 optimal weight:    3.9990
   chunk 59 optimal weight:    0.9980
   chunk 92 optimal weight:    4.9990
   chunk 65 optimal weight:    0.4980
   chunk 49 optimal weight:    0.5980
   chunk 119 optimal weight:    1.9990
   chunk 60 optimal weight:    0.9990
   chunk 8 optimal weight:    4.9990
   chunk 53 optimal weight:    0.6980
   overall best weight:    0.6780

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

Flipped N/Q/H residues before XYZ refinement:
A 250 ASN
A 357 GLN
B  16 ASN
B 213 HIS
B 218 ASN
D 177 GLN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4204 r_free = 0.4204 target = 0.183404 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3849 r_free = 0.3849 target = 0.149771 restraints weight = 14994.076|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3856 r_free = 0.3856 target = 0.151820 restraints weight = 12639.588|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3861 r_free = 0.3861 target = 0.152474 restraints weight = 10813.438|
|-----------------------------------------------------------------------------|
r_work (final): 0.3855
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3855
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3855 r_free = 0.3855    target_work(ls_wunit_k1) = 0.151         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       38 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3855 r_free = 0.3855    target_work(ls_wunit_k1) = 0.151         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       37 |
|-----------------------------------------------------------------------------|
r_final: 0.3855
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7894
moved from start:          0.3926

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040  10948  Z= 0.131
  Angle     :  0.626   9.859  14818  Z= 0.313
  Chirality :  0.042   0.176   1654
  Planarity :  0.004   0.036   1816
  Dihedral  :  7.489 167.828   1422
  Min Nonbonded Distance : 2.451

Molprobity Statistics.
  All-atom Clashscore : 6.52
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.96 %
    Favored  : 94.04 %
  Rotamer:
    Outliers :  2.84 %
    Allowed  : 20.60 %
    Favored  : 76.55 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.38 (0.24), residues: 1292
  helix:  1.29 (0.23), residues: 594
  sheet: -0.47 (0.41), residues: 191
  loop : -2.10 (0.25), residues: 507

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP D 181 
 HIS   0.004   0.001   HIS C 361 
 PHE   0.024   0.001   PHE B 152 
 TYR   0.024   0.001   TYR B 243 
 ARG   0.004   0.000   ARG C 392 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04729 (  497)
  hydrogen bonds       : angle       4.49933 ( 1434)
  covalent geometry    : bond        0.00300 (10948)
  covalent geometry    : angle       0.62580 (14818)

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

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

  2584 Ramachandran restraints generated.
    1292 Oldfield, 0 Emsley, 1292 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2584 Ramachandran restraints generated.
    1292 Oldfield, 0 Emsley, 1292 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  163 residues out of total 1160 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 130
  time to evaluate  : 1.037 
Fit side-chains
REVERT: A  102 GLU cc_start: 0.7888 (tp30) cc_final: 0.7528 (tp30)
REVERT: A  318 GLU cc_start: 0.7156 (mp0) cc_final: 0.6927 (mp0)
REVERT: B  205 MET cc_start: 0.6240 (OUTLIER) cc_final: 0.5819 (ttm)
REVERT: B  220 LEU cc_start: 0.7970 (OUTLIER) cc_final: 0.7762 (mm)
REVERT: C  125 ILE cc_start: 0.8457 (OUTLIER) cc_final: 0.8246 (mt)
REVERT: D  136 TYR cc_start: 0.7641 (m-80) cc_final: 0.7436 (m-80)
  outliers start: 33
  outliers final: 26
  residues processed: 149
  average time/residue: 0.2413
  time to fit residues: 52.6614
Evaluate side-chains
  153 residues out of total 1160 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 124
  time to evaluate  : 1.128 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   42 LEU
Chi-restraints excluded: chain A residue   78 VAL
Chi-restraints excluded: chain A residue  104 ILE
Chi-restraints excluded: chain A residue  166 ASP
Chi-restraints excluded: chain A residue  197 VAL
Chi-restraints excluded: chain A residue  207 LEU
Chi-restraints excluded: chain A residue  262 VAL
Chi-restraints excluded: chain B residue   16 ASN
Chi-restraints excluded: chain B residue   84 ILE
Chi-restraints excluded: chain B residue   90 PHE
Chi-restraints excluded: chain B residue  205 MET
Chi-restraints excluded: chain B residue  217 VAL
Chi-restraints excluded: chain B residue  220 LEU
Chi-restraints excluded: chain B residue  239 PHE
Chi-restraints excluded: chain C residue   53 VAL
Chi-restraints excluded: chain C residue   78 VAL
Chi-restraints excluded: chain C residue   92 THR
Chi-restraints excluded: chain C residue  125 ILE
Chi-restraints excluded: chain C residue  363 ILE
Chi-restraints excluded: chain C residue  383 CYS
Chi-restraints excluded: chain D residue   68 ILE
Chi-restraints excluded: chain D residue  118 ILE
Chi-restraints excluded: chain D residue  121 VAL
Chi-restraints excluded: chain D residue  134 ILE
Chi-restraints excluded: chain D residue  142 VAL
Chi-restraints excluded: chain D residue  168 ILE
Chi-restraints excluded: chain D residue  171 ILE
Chi-restraints excluded: chain D residue  186 VAL
Chi-restraints excluded: chain D residue  190 ASP
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 128
   random chunks:
   chunk 102 optimal weight:    2.9990
   chunk 117 optimal weight:    0.8980
   chunk 53 optimal weight:    2.9990
   chunk 24 optimal weight:    8.9990
   chunk 25 optimal weight:    0.1980
   chunk 39 optimal weight:    4.9990
   chunk 76 optimal weight:    4.9990
   chunk 48 optimal weight:    0.3980
   chunk 126 optimal weight:    2.9990
   chunk 18 optimal weight:    0.8980
   chunk 49 optimal weight:    0.7980
   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 357 GLN
B  16 ASN
B 218 ASN
D 177 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4214 r_free = 0.4214 target = 0.184008 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3873 r_free = 0.3873 target = 0.151668 restraints weight = 14523.574|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3874 r_free = 0.3874 target = 0.153080 restraints weight = 12838.849|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3881 r_free = 0.3881 target = 0.154113 restraints weight = 11867.810|
|-----------------------------------------------------------------------------|
r_work (final): 0.3883
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3883
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3883 r_free = 0.3883    target_work(ls_wunit_k1) = 0.154         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       37 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3883 r_free = 0.3883    target_work(ls_wunit_k1) = 0.154         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       38 |
|-----------------------------------------------------------------------------|
r_final: 0.3883
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7848
moved from start:          0.3854

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042  10948  Z= 0.129
  Angle     :  0.637   8.180  14818  Z= 0.315
  Chirality :  0.042   0.173   1654
  Planarity :  0.004   0.034   1816
  Dihedral  :  7.471 171.960   1422
  Min Nonbonded Distance : 2.431

Molprobity Statistics.
  All-atom Clashscore : 6.43
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.57 %
    Favored  : 94.43 %
  Rotamer:
    Outliers :  2.93 %
    Allowed  : 20.86 %
    Favored  : 76.21 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.29 (0.24), residues: 1292
  helix:  1.33 (0.23), residues: 598
  sheet: -0.38 (0.41), residues: 193
  loop : -2.05 (0.25), residues: 501

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP B  71 
 HIS   0.004   0.001   HIS C 361 
 PHE   0.018   0.001   PHE B  92 
 TYR   0.023   0.001   TYR B 243 
 ARG   0.009   0.001   ARG A 116 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04544 (  497)
  hydrogen bonds       : angle       4.44982 ( 1434)
  covalent geometry    : bond        0.00294 (10948)
  covalent geometry    : angle       0.63681 (14818)

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

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

  2584 Ramachandran restraints generated.
    1292 Oldfield, 0 Emsley, 1292 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2584 Ramachandran restraints generated.
    1292 Oldfield, 0 Emsley, 1292 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  162 residues out of total 1160 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 128
  time to evaluate  : 1.291 
Fit side-chains
REVERT: A  146 MET cc_start: 0.7228 (mpp) cc_final: 0.6896 (mtm)
REVERT: A  318 GLU cc_start: 0.7128 (mp0) cc_final: 0.6915 (mp0)
REVERT: B  205 MET cc_start: 0.6234 (OUTLIER) cc_final: 0.5822 (ttm)
REVERT: B  220 LEU cc_start: 0.7989 (OUTLIER) cc_final: 0.7782 (mm)
REVERT: C  125 ILE cc_start: 0.8381 (OUTLIER) cc_final: 0.8168 (mt)
  outliers start: 34
  outliers final: 25
  residues processed: 147
  average time/residue: 0.1933
  time to fit residues: 42.4775
Evaluate side-chains
  150 residues out of total 1160 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 122
  time to evaluate  : 1.156 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   42 LEU
Chi-restraints excluded: chain A residue  166 ASP
Chi-restraints excluded: chain A residue  197 VAL
Chi-restraints excluded: chain A residue  207 LEU
Chi-restraints excluded: chain A residue  262 VAL
Chi-restraints excluded: chain B residue   84 ILE
Chi-restraints excluded: chain B residue   90 PHE
Chi-restraints excluded: chain B residue  118 ILE
Chi-restraints excluded: chain B residue  205 MET
Chi-restraints excluded: chain B residue  217 VAL
Chi-restraints excluded: chain B residue  220 LEU
Chi-restraints excluded: chain B residue  239 PHE
Chi-restraints excluded: chain C residue   53 VAL
Chi-restraints excluded: chain C residue   78 VAL
Chi-restraints excluded: chain C residue   92 THR
Chi-restraints excluded: chain C residue  125 ILE
Chi-restraints excluded: chain C residue  295 VAL
Chi-restraints excluded: chain C residue  363 ILE
Chi-restraints excluded: chain C residue  383 CYS
Chi-restraints excluded: chain D residue   68 ILE
Chi-restraints excluded: chain D residue  118 ILE
Chi-restraints excluded: chain D residue  121 VAL
Chi-restraints excluded: chain D residue  134 ILE
Chi-restraints excluded: chain D residue  142 VAL
Chi-restraints excluded: chain D residue  168 ILE
Chi-restraints excluded: chain D residue  171 ILE
Chi-restraints excluded: chain D residue  186 VAL
Chi-restraints excluded: chain D residue  190 ASP
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 128
   random chunks:
   chunk 49 optimal weight:    2.9990
   chunk 126 optimal weight:    1.9990
   chunk 70 optimal weight:    0.7980
   chunk 12 optimal weight:    0.9990
   chunk 48 optimal weight:    0.0050
   chunk 55 optimal weight:    2.9990
   chunk 91 optimal weight:    6.9990
   chunk 115 optimal weight:    4.9990
   chunk 15 optimal weight:    1.9990
   chunk 65 optimal weight:    0.6980
   chunk 95 optimal weight:    0.6980
   overall best weight:    0.6396

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

Flipped N/Q/H residues before XYZ refinement:
A 357 GLN
B 218 ASN
D 177 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4221 r_free = 0.4221 target = 0.184588 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3877 r_free = 0.3877 target = 0.151890 restraints weight = 14456.739|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3874 r_free = 0.3874 target = 0.152749 restraints weight = 13297.166|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3882 r_free = 0.3882 target = 0.153662 restraints weight = 11772.957|
|-----------------------------------------------------------------------------|
r_work (final): 0.3880
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3880
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3880 r_free = 0.3880    target_work(ls_wunit_k1) = 0.153         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       38 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3879 r_free = 0.3879    target_work(ls_wunit_k1) = 0.153         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       39 |
|-----------------------------------------------------------------------------|
r_final: 0.3879
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7860
moved from start:          0.3828

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042  10948  Z= 0.128
  Angle     :  0.649  10.970  14818  Z= 0.317
  Chirality :  0.043   0.338   1654
  Planarity :  0.004   0.037   1816
  Dihedral  :  7.487 177.557   1422
  Min Nonbonded Distance : 2.436

Molprobity Statistics.
  All-atom Clashscore : 6.62
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.80 %
    Favored  : 94.20 %
  Rotamer:
    Outliers :  3.02 %
    Allowed  : 21.03 %
    Favored  : 75.95 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.29 (0.24), residues: 1292
  helix:  1.34 (0.22), residues: 598
  sheet: -0.35 (0.41), residues: 193
  loop : -2.08 (0.25), residues: 501

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP B  31 
 HIS   0.004   0.001   HIS C 361 
 PHE   0.017   0.001   PHE B  92 
 TYR   0.024   0.001   TYR B 243 
 ARG   0.010   0.001   ARG B  17 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04450 (  497)
  hydrogen bonds       : angle       4.42399 ( 1434)
  covalent geometry    : bond        0.00292 (10948)
  covalent geometry    : angle       0.64869 (14818)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 4195.51 seconds
wall clock time: 77 minutes 54.84 seconds (4674.84 seconds total)