Starting phenix.real_space_refine
on Wed Feb  4 13:16:54 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7x2f_32966/02_2026/7x2f_32966.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7x2f_32966/02_2026/7x2f_32966.map

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

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

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/7x2f_32966/02_2026/7x2f_32966.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7x2f_32966/02_2026/7x2f_32966.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/7x2f_32966/02_2026/7x2f_32966.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7x2f_32966/02_2026/7x2f_32966.map"
  }
  resolution = 3.0
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=  -0.002 sd=   0.106
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 3031 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
     S      54      5.16       5
     Cl      2      4.86       5
     C    5252      2.51       5
     N    1429      2.21       5
     O    1512      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 4 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 8249
  Number of models: 1
  Model: ""
    Number of chains: 6
    Chain: "F"
      Number of atoms: 2242
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 282, 2242
          Classifications: {'peptide': 282}
          Link IDs: {'PTRANS': 9, 'TRANS': 272}
          Chain breaks: 3
    Chain: "A"
      Number of atoms: 1896
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 228, 1896
          Classifications: {'peptide': 228}
          Modifications used: {'COO': 1}
          Incomplete info: {'truncation_to_alanine': 4}
          Link IDs: {'PTRANS': 6, 'TRANS': 221}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 13
          Unresolved non-hydrogen angles: 16
          Unresolved non-hydrogen dihedrals: 10
          Unresolved non-hydrogen chiralities: 2
          Planarities with less than four sites: {'GLN:plan1': 1}
          Unresolved non-hydrogen planarities: 4
    Chain: "E"
      Number of atoms: 971
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 128, 971
          Classifications: {'peptide': 128}
          Incomplete info: {'truncation_to_alanine': 1}
          Link IDs: {'PTRANS': 5, 'TRANS': 122}
          Unresolved non-hydrogen bonds: 2
          Unresolved non-hydrogen angles: 3
          Unresolved non-hydrogen dihedrals: 1
          Unresolved non-hydrogen chiralities: 1
    Chain: "B"
      Number of atoms: 2609
      Number of conformers: 2
      Conformer: "A"
        Number of residues, atoms: 341, 2599
          Classifications: {'peptide': 341}
          Modifications used: {'COO': 1}
          Incomplete info: {'truncation_to_alanine': 4}
          Link IDs: {'PTRANS': 5, 'TRANS': 335}
          Unresolved non-hydrogen bonds: 18
          Unresolved non-hydrogen angles: 21
          Unresolved non-hydrogen dihedrals: 15
          Planarities with less than four sites: {'GLN:plan1': 1, 'ARG:plan': 1, 'GLU:plan': 1}
          Unresolved non-hydrogen planarities: 13
      Conformer: "B"
        Number of residues, atoms: 341, 2599
          Classifications: {'peptide': 341}
          Modifications used: {'COO': 1}
          Incomplete info: {'truncation_to_alanine': 4}
          Link IDs: {'PTRANS': 5, 'TRANS': 335}
          Unresolved non-hydrogen bonds: 18
          Unresolved non-hydrogen angles: 21
          Unresolved non-hydrogen dihedrals: 15
          Planarities with less than four sites: {'GLN:plan1': 1, 'ARG:plan': 1, 'GLU:plan': 1}
          Unresolved non-hydrogen planarities: 13
          bond proxies already assigned to first conformer: 2633
    Chain: "D"
      Number of atoms: 434
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 57, 434
          Classifications: {'peptide': 57}
          Incomplete info: {'truncation_to_alanine': 2}
          Link IDs: {'PTRANS': 4, 'TRANS': 52}
          Unresolved non-hydrogen bonds: 8
          Unresolved non-hydrogen angles: 8
          Unresolved non-hydrogen dihedrals: 8
    Chain: "F"
      Number of atoms: 97
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 4, 97
          Unusual residues: {'CLR': 2, 'G4C': 1, 'LDP': 1}
          Classifications: {'undetermined': 4}
          Link IDs: {None: 3}
  Time building chain proxies: 2.58, per 1000 atoms: 0.31
  Number of scatterers: 8249
  At special positions: 0
  Unit cell: (78.264, 101.091, 128.266, 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)
     Cl      2     17.00
     S      54     16.00
     O    1512      8.00
     N    1429      7.00
     C    5252      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=3, symmetry=0
    Simple disulfide: pdb=" SG  CYS F  96 " - pdb=" SG  CYS F 186 " distance=2.03
    Simple disulfide: pdb=" SG  CYS E  22 " - pdb=" SG  CYS E  96 " distance=2.03
    Simple disulfide: pdb=" SG  CYS E  99 " - pdb=" SG  CYS E 107 " distance=2.03

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 0.77
  Conformation dependent library (CDL) restraints added in 405.7 milliseconds
  

  2042 Ramachandran restraints generated.
    1021 Oldfield, 0 Emsley, 1021 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1966

  Finding SS restraints...
    Secondary structure from input PDB file:
      29 helices and 10 sheets defined
      45.2% alpha, 20.2% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.22
  Creating SS restraints...
    Processing helix  chain 'F' and resid 21 through 51
    Processing helix  chain 'F' and resid 51 through 57
      removed outlier: 4.033A  pdb=" N   ARG F  55 " --> pdb=" O   PHE F  51 " (cutoff:3.500A)
      removed outlier: 4.084A  pdb=" N   LYS F  57 " --> pdb=" O   HIS F  53 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 59 through 77
      removed outlier: 4.081A  pdb=" N   VAL F  63 " --> pdb=" O   THR F  59 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 77 through 88
    Processing helix  chain 'F' and resid 94 through 126
      removed outlier: 4.063A  pdb=" N   ILE F  98 " --> pdb=" O   SER F  94 " (cutoff:3.500A)
      removed outlier: 3.868A  pdb=" N   ALA F 101 " --> pdb=" O   ASN F  97 " (cutoff:3.500A)
      removed outlier: 3.828A  pdb=" N   ASN F 113 " --> pdb=" O   ALA F 109 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 127 through 135
      removed outlier: 3.836A  pdb=" N   GLU F 132 " --> pdb=" O   PRO F 128 " (cutoff:3.500A)
      removed outlier: 3.761A  pdb=" N   ARG F 133 " --> pdb=" O   PHE F 129 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 136 through 161
      removed outlier: 3.554A  pdb=" N   VAL F 152 " --> pdb=" O   TRP F 148 " (cutoff:3.500A)
      removed outlier: 3.981A  pdb=" N   ILE F 157 " --> pdb=" O   LEU F 153 " (cutoff:3.500A)
      Proline residue:  F 158  - end of helix
      removed outlier: 3.586A  pdb=" N   LEU F 161 " --> pdb=" O   ILE F 157 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 191 through 203
      removed outlier: 3.825A  pdb=" N   ILE F 196 " --> pdb=" O   ARG F 192 " (cutoff:3.500A)
      removed outlier: 3.652A  pdb=" N   ILE F 201 " --> pdb=" O   SER F 197 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 203 through 241
      removed outlier: 3.802A  pdb=" N   MET F 210 " --> pdb=" O   PRO F 206 " (cutoff:3.500A)
      removed outlier: 3.640A  pdb=" N   LEU F 231 " --> pdb=" O   ARG F 227 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 265 through 299
      removed outlier: 4.042A  pdb=" N   PHE F 281 " --> pdb=" O   ILE F 277 " (cutoff:3.500A)
      Proline residue:  F 287  - end of helix
      Proline residue:  F 296  - end of helix
    Processing helix  chain 'F' and resid 309 through 332
      removed outlier: 3.892A  pdb=" N   ASN F 323 " --> pdb=" O   PHE F 319 " (cutoff:3.500A)
      removed outlier: 4.629A  pdb=" N   SER F 324 " --> pdb=" O   GLY F 320 " (cutoff:3.500A)
      removed outlier: 3.826A  pdb=" N   SER F 325 " --> pdb=" O   TRP F 321 " (cutoff:3.500A)
      Proline residue:  F 328  - end of helix
    Processing helix  chain 'F' and resid 334 through 346
    Processing helix  chain 'A' and resid 13 through 39
      removed outlier: 3.606A  pdb=" N   GLN A  35 " --> pdb=" O   GLN A  31 " (cutoff:3.500A)
      removed outlier: 3.676A  pdb=" N   VAL A  36 " --> pdb=" O   LYS A  32 " (cutoff:3.500A)
      removed outlier: 3.627A  pdb=" N   ALA A  39 " --> pdb=" O   GLN A  35 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 52 through 60
    Processing helix  chain 'A' and resid 232 through 239
      removed outlier: 3.625A  pdb=" N   GLN A 236 " --> pdb=" O   LYS A 233 " (cutoff:3.500A)
      removed outlier: 4.049A  pdb=" N   ASN A 239 " --> pdb=" O   GLN A 236 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 254 through 278
    Processing helix  chain 'A' and resid 293 through 304
    Processing helix  chain 'A' and resid 307 through 312
      removed outlier: 4.038A  pdb=" N   TYR A 311 " --> pdb=" O   LYS A 307 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 313 through 318
    Processing helix  chain 'A' and resid 331 through 353
      removed outlier: 3.684A  pdb=" N   ILE A 348 " --> pdb=" O   GLU A 344 " (cutoff:3.500A)
      removed outlier: 3.695A  pdb=" N   ALA A 351 " --> pdb=" O   ARG A 347 " (cutoff:3.500A)
      removed outlier: 4.087A  pdb=" N   SER A 352 " --> pdb=" O   ILE A 348 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 370 through 391
    Processing helix  chain 'E' and resid 28 through 32
      removed outlier: 3.670A  pdb=" N   TYR E  32 " --> pdb=" O   PHE E  29 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 87 through 91
      removed outlier: 4.011A  pdb=" N   THR E  91 " --> pdb=" O   PRO E  88 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 2 through 25
      removed outlier: 3.934A  pdb=" N   CYS B  25 " --> pdb=" O   ALA B  21 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 29 through 34
    Processing helix  chain 'B' and resid 35 through 37
      No H-bonds generated for 'chain 'B' and resid 35 through 37'
    Processing helix  chain 'D' and resid 9 through 24
      removed outlier: 3.578A  pdb=" N   GLU D  17 " --> pdb=" O   ARG D  13 " (cutoff:3.500A)
      removed outlier: 3.537A  pdb=" N   ASN D  24 " --> pdb=" O   LYS D  20 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 29 through 44
      removed outlier: 3.563A  pdb=" N   LEU D  37 " --> pdb=" O   ALA D  33 " (cutoff:3.500A)
      removed outlier: 3.547A  pdb=" N   HIS D  44 " --> pdb=" O   TYR D  40 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 45 through 48
    Processing sheet with id=AA1, first strand: chain 'A' and resid 209 through 214
      removed outlier: 8.985A  pdb=" N   ALA A 243 " --> pdb=" O   THR A  40 " (cutoff:3.500A)
      removed outlier: 6.985A  pdb=" N   ARG A  42 " --> pdb=" O   ALA A 243 " (cutoff:3.500A)
      removed outlier: 8.038A  pdb=" N   ILE A 245 " --> pdb=" O   ARG A  42 " (cutoff:3.500A)
      removed outlier: 6.653A  pdb=" N   LEU A  44 " --> pdb=" O   ILE A 245 " (cutoff:3.500A)
      removed outlier: 7.536A  pdb=" N   VAL A 247 " --> pdb=" O   LEU A  44 " (cutoff:3.500A)
      removed outlier: 6.887A  pdb=" N   LEU A  46 " --> pdb=" O   VAL A 247 " (cutoff:3.500A)
      removed outlier: 8.846A  pdb=" N   ASP A 249 " --> pdb=" O   LEU A  46 " (cutoff:3.500A)
      removed outlier: 6.531A  pdb=" N   ILE A 244 " --> pdb=" O   ILE A 288 " (cutoff:3.500A)
      removed outlier: 7.355A  pdb=" N   PHE A 290 " --> pdb=" O   ILE A 244 " (cutoff:3.500A)
      removed outlier: 6.742A  pdb=" N   PHE A 246 " --> pdb=" O   PHE A 290 " (cutoff:3.500A)
      removed outlier: 7.195A  pdb=" N   ASN A 292 " --> pdb=" O   PHE A 246 " (cutoff:3.500A)
      removed outlier: 6.697A  pdb=" N   VAL A 248 " --> pdb=" O   ASN A 292 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'E' and resid 3 through 7
    Processing sheet with id=AA3, first strand: chain 'E' and resid 11 through 12
      removed outlier: 6.097A  pdb=" N   ARG E  38 " --> pdb=" O   TRP E  47 " (cutoff:3.500A)
      removed outlier: 5.308A  pdb=" N   TRP E  47 " --> pdb=" O   ARG E  38 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'B' and resid 47 through 52
      removed outlier: 3.737A  pdb=" N   ARG B  49 " --> pdb=" O   ILE B 338 " (cutoff:3.500A)
      removed outlier: 4.370A  pdb=" N   PHE B 335 " --> pdb=" O   SER B 331 " (cutoff:3.500A)
      removed outlier: 3.541A  pdb=" N   SER B 331 " --> pdb=" O   PHE B 335 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'B' and resid 58 through 63
      removed outlier: 6.771A  pdb=" N   ALA B  73 " --> pdb=" O   TYR B  59 " (cutoff:3.500A)
      removed outlier: 4.152A  pdb=" N   MET B  61 " --> pdb=" O   VAL B  71 " (cutoff:3.500A)
      removed outlier: 6.746A  pdb=" N   VAL B  71 " --> pdb=" O   MET B  61 " (cutoff:3.500A)
      removed outlier: 5.086A  pdb=" N   TRP B  63 " --> pdb=" O   LEU B  69 " (cutoff:3.500A)
      removed outlier: 7.430A  pdb=" N   LEU B  69 " --> pdb=" O   TRP B  63 " (cutoff:3.500A)
      removed outlier: 3.534A  pdb=" N   LYS B  78 " --> pdb=" O   SER B  74 " (cutoff:3.500A)
      removed outlier: 6.116A  pdb=" N   ASP B  83 " --> pdb=" O   LYS B  89 " (cutoff:3.500A)
      removed outlier: 5.933A  pdb=" N   LYS B  89 " --> pdb=" O   ASP B  83 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'B' and resid 100 through 105
      removed outlier: 6.910A  pdb=" N   GLY B 115 " --> pdb=" O   MET B 101 " (cutoff:3.500A)
      removed outlier: 4.318A  pdb=" N   CYS B 103 " --> pdb=" O   ALA B 113 " (cutoff:3.500A)
      removed outlier: 6.430A  pdb=" N   ALA B 113 " --> pdb=" O   CYS B 103 " (cutoff:3.500A)
      removed outlier: 4.923A  pdb=" N   TYR B 105 " --> pdb=" O   TYR B 111 " (cutoff:3.500A)
      removed outlier: 7.079A  pdb=" N   TYR B 111 " --> pdb=" O   TYR B 105 " (cutoff:3.500A)
      removed outlier: 3.676A  pdb=" N   ARG B 137 " --> pdb=" O   ILE B 123 " (cutoff:3.500A)
      removed outlier: 6.192A  pdb=" N   ASN B 125 " --> pdb=" O   VAL B 135 " (cutoff:3.500A)
      removed outlier: 6.908A  pdb=" N   VAL B 135 " --> pdb=" O   ASN B 125 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'B' and resid 146 through 151
      removed outlier: 3.606A  pdb=" N   CYS B 148 " --> pdb=" O   SER B 160 " (cutoff:3.500A)
      removed outlier: 3.963A  pdb=" N   THR B 165 " --> pdb=" O   SER B 161 " (cutoff:3.500A)
      removed outlier: 6.586A  pdb=" N   ASP B 170 " --> pdb=" O   GLN B 176 " (cutoff:3.500A)
      removed outlier: 6.191A  pdb=" N   GLN B 176 " --> pdb=" O   ASP B 170 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'B' and resid 187 through 192
      removed outlier: 6.521A  pdb=" N   ALA B 208 " --> pdb=" O   THR B 221 " (cutoff:3.500A)
      removed outlier: 4.437A  pdb=" N   THR B 221 " --> pdb=" O   ALA B 208 " (cutoff:3.500A)
      removed outlier: 6.573A  pdb=" N   LEU B 210 " --> pdb=" O   ARG B 219 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'B' and resid 229 through 234
      removed outlier: 6.752A  pdb=" N   GLY B 244 " --> pdb=" O   ASN B 230 " (cutoff:3.500A)
      removed outlier: 4.310A  pdb=" N   ILE B 232 " --> pdb=" O   ALA B 242 " (cutoff:3.500A)
      removed outlier: 6.709A  pdb=" N   ALA B 242 " --> pdb=" O   ILE B 232 " (cutoff:3.500A)
      removed outlier: 4.621A  pdb=" N   PHE B 234 " --> pdb=" O   ALA B 240 " (cutoff:3.500A)
      removed outlier: 6.958A  pdb=" N   ALA B 240 " --> pdb=" O   PHE B 234 " (cutoff:3.500A)
      removed outlier: 6.566A  pdb=" N   CYS B 250 " --> pdb=" O   THR B 263 " (cutoff:3.500A)
      removed outlier: 4.534A  pdb=" N   THR B 263 " --> pdb=" O   CYS B 250 " (cutoff:3.500A)
      removed outlier: 6.765A  pdb=" N   LEU B 252 " --> pdb=" O   LEU B 261 " (cutoff:3.500A)
      removed outlier: 3.877A  pdb=" N   GLN B 259 " --> pdb=" O   ASP B 254 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'B' and resid 273 through 278
      removed outlier: 3.606A  pdb=" N   SER B 275 " --> pdb=" O   GLY B 288 " (cutoff:3.500A)
      removed outlier: 6.234A  pdb=" N   CYS B 294 " --> pdb=" O   VAL B 307 " (cutoff:3.500A)
      removed outlier: 4.389A  pdb=" N   VAL B 307 " --> pdb=" O   CYS B 294 " (cutoff:3.500A)
      removed outlier: 6.592A  pdb=" N   VAL B 296 " --> pdb=" O   ALA B 305 " (cutoff:3.500A)

    426 hydrogen bonds defined for protein.
    1221 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 1.39

  Time building geometry restraints manager: 0.96 seconds

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

  Histogram of bond lengths:
        1.12 -     1.26: 1326
        1.26 -     1.40: 2139
        1.40 -     1.54: 4786
        1.54 -     1.68: 101
        1.68 -     1.82: 75
  Bond restraints: 8427
  Sorted by residual:
  bond pdb=" C   ARG F 130 "
       pdb=" O   ARG F 130 "
    ideal  model  delta    sigma   weight residual
    1.237  1.121  0.115 1.17e-02 7.31e+03 9.70e+01
  bond pdb=" C05 G4C F 502 "
       pdb=" N04 G4C F 502 "
    ideal  model  delta    sigma   weight residual
    1.355  1.511 -0.156 2.00e-02 2.50e+03 6.08e+01
  bond pdb=" CA  ARG F 130 "
       pdb=" C   ARG F 130 "
    ideal  model  delta    sigma   weight residual
    1.523  1.430  0.093 1.30e-02 5.92e+03 5.13e+01
  bond pdb=" CA  TYR B 145 "
       pdb=" CB  TYR B 145 "
    ideal  model  delta    sigma   weight residual
    1.527  1.431  0.096 1.44e-02 4.82e+03 4.47e+01
  bond pdb=" CA  ARG F 130 "
       pdb=" CB  ARG F 130 "
    ideal  model  delta    sigma   weight residual
    1.528  1.435  0.094 1.56e-02 4.11e+03 3.60e+01
  ... (remaining 8422 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.45: 11177
        2.45 -     4.90: 216
        4.90 -     7.35: 32
        7.35 -     9.79: 7
        9.79 -    12.24: 2
  Bond angle restraints: 11434
  Sorted by residual:
  angle pdb=" C   ARG F 130 "
        pdb=" CA  ARG F 130 "
        pdb=" CB  ARG F 130 "
      ideal   model   delta    sigma   weight residual
     110.79   99.41   11.38 1.66e+00 3.63e-01 4.70e+01
  angle pdb=" N   GLU A 344 "
        pdb=" CA  GLU A 344 "
        pdb=" CB  GLU A 344 "
      ideal   model   delta    sigma   weight residual
     110.28  119.54   -9.26 1.55e+00 4.16e-01 3.57e+01
  angle pdb=" N   ARG A 232 "
        pdb=" CA  ARG A 232 "
        pdb=" C   ARG A 232 "
      ideal   model   delta    sigma   weight residual
     111.04  118.60   -7.56 1.55e+00 4.16e-01 2.38e+01
  angle pdb=" O   GLY B 144 "
        pdb=" C   GLY B 144 "
        pdb=" N   TYR B 145 "
      ideal   model   delta    sigma   weight residual
     123.65  119.24    4.41 9.20e-01 1.18e+00 2.30e+01
  angle pdb=" C   GLY B 144 "
        pdb=" N   TYR B 145 "
        pdb=" CA  TYR B 145 "
      ideal   model   delta    sigma   weight residual
     121.29  113.85    7.44 1.74e+00 3.30e-01 1.83e+01
  ... (remaining 11429 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.93: 4682
       17.93 -    35.85: 373
       35.85 -    53.78: 54
       53.78 -    71.71: 10
       71.71 -    89.64: 4
  Dihedral angle restraints: 5123
    sinusoidal: 2093
      harmonic: 3030
  Sorted by residual:
  dihedral pdb=" C   ARG F 130 "
           pdb=" N   ARG F 130 "
           pdb=" CA  ARG F 130 "
           pdb=" CB  ARG F 130 "
      ideal   model   delta  harmonic     sigma   weight residual
    -122.60 -108.59  -14.01     0      2.50e+00 1.60e-01 3.14e+01
  dihedral pdb=" CA  ASN A 254 "
           pdb=" C   ASN A 254 "
           pdb=" N   ARG A 265 "
           pdb=" CA  ARG A 265 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  155.80   24.20     0      5.00e+00 4.00e-02 2.34e+01
  dihedral pdb=" CB  CYS E  22 "
           pdb=" SG  CYS E  22 "
           pdb=" SG  CYS E  96 "
           pdb=" CB  CYS E  96 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00   55.69   37.31     1      1.00e+01 1.00e-02 1.96e+01
  ... (remaining 5120 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.076: 1142
       0.076 -    0.152: 132
       0.152 -    0.228: 10
       0.228 -    0.303: 2
       0.303 -    0.379: 3
  Chirality restraints: 1289
  Sorted by residual:
  chirality pdb=" CA  TYR B 145 "
            pdb=" N   TYR B 145 "
            pdb=" C   TYR B 145 "
            pdb=" CB  TYR B 145 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.13    0.38 2.00e-01 2.50e+01 3.59e+00
  chirality pdb=" C13 CLR F 501 "
            pdb=" C12 CLR F 501 "
            pdb=" C14 CLR F 501 "
            pdb=" C17 CLR F 501 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.93   -2.57   -0.37 2.00e-01 2.50e+01 3.34e+00
  chirality pdb=" C13 CLR F 503 "
            pdb=" C12 CLR F 503 "
            pdb=" C14 CLR F 503 "
            pdb=" C17 CLR F 503 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.93   -2.58   -0.35 2.00e-01 2.50e+01 3.05e+00
  ... (remaining 1286 not shown)

  Planarity restraints: 1443
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TYR B  59 "   -0.026 2.00e-02 2.50e+03   2.18e-02 9.47e+00
        pdb=" CG  TYR B  59 "    0.054 2.00e-02 2.50e+03
        pdb=" CD1 TYR B  59 "   -0.010 2.00e-02 2.50e+03
        pdb=" CD2 TYR B  59 "   -0.003 2.00e-02 2.50e+03
        pdb=" CE1 TYR B  59 "   -0.004 2.00e-02 2.50e+03
        pdb=" CE2 TYR B  59 "   -0.009 2.00e-02 2.50e+03
        pdb=" CZ  TYR B  59 "   -0.000 2.00e-02 2.50e+03
        pdb=" OH  TYR B  59 "   -0.000 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TYR B 145 "   -0.030 2.00e-02 2.50e+03   2.05e-02 8.40e+00
        pdb=" CG  TYR B 145 "    0.039 2.00e-02 2.50e+03
        pdb=" CD1 TYR B 145 "    0.007 2.00e-02 2.50e+03
        pdb=" CD2 TYR B 145 "   -0.001 2.00e-02 2.50e+03
        pdb=" CE1 TYR B 145 "    0.002 2.00e-02 2.50e+03
        pdb=" CE2 TYR B 145 "    0.010 2.00e-02 2.50e+03
        pdb=" CZ  TYR B 145 "   -0.028 2.00e-02 2.50e+03
        pdb=" OH  TYR B 145 "    0.001 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  LYS A  25 "   -0.013 2.00e-02 2.50e+03   2.51e-02 6.32e+00
        pdb=" C   LYS A  25 "    0.043 2.00e-02 2.50e+03
        pdb=" O   LYS A  25 "   -0.016 2.00e-02 2.50e+03
        pdb=" N   ILE A  26 "   -0.015 2.00e-02 2.50e+03
  ... (remaining 1440 not shown)

  Histogram of nonbonded interaction distances:
        2.16 -     2.71: 324
        2.71 -     3.26: 8343
        3.26 -     3.81: 13470
        3.81 -     4.35: 17006
        4.35 -     4.90: 28942
  Nonbonded interactions: 68085
  Sorted by model distance:
  nonbonded pdb=" OH  TYR A 318 "
            pdb=" OD2 ASP A 343 "
     model   vdw
     2.164 3.040
  nonbonded pdb=" OG  SER F 198 "
            pdb=" O2  LDP F 504 "
     model   vdw
     2.166 3.040
  nonbonded pdb=" NE2 HIS B 225 "
            pdb=" OG1 THR B 243 "
     model   vdw
     2.213 3.120
  nonbonded pdb=" OE1 GLN A  35 "
            pdb=" NH2 ARG A  38 "
     model   vdw
     2.231 3.120
  nonbonded pdb=" O   ARG B  68 "
            pdb=" OG  SER B  84 "
     model   vdw
     2.236 3.040
  ... (remaining 68080 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.00
========== WARNING! ============

  No NCS relation were found !!!

================================

Found NCS groups:
  found none.
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=0.38 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             0.380
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.030
  Construct map_model_manager:             0.020
  Extract box with map and model:          0.120
  Check model and map are aligned:         0.020
  Set scattering table:                    0.030
  Process input model:                     10.090
  Find NCS groups from input model:        0.040
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:9.130
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   19.880
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7045
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      :  0.006   0.156   8430  Z= 0.341
  Angle     :  0.830  12.242  11440  Z= 0.456
  Chirality :  0.053   0.379   1289
  Planarity :  0.005   0.047   1443
  Dihedral  : 12.875  89.636   3148
  Min Nonbonded Distance : 2.164

Molprobity Statistics.
  All-atom Clashscore : 13.34
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.24 %
    Favored  : 96.76 %
  Rotamer:
    Outliers :  0.11 %
    Allowed  :  0.34 %
    Favored  : 99.55 %
  Cbeta Deviations :  0.20 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.87 (0.25), residues: 1021
  helix:  0.04 (0.25), residues: 403
  sheet: -0.60 (0.32), residues: 216
  loop : -1.05 (0.28), residues: 402

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG E  98 
 TYR   0.054   0.002   TYR B  59 
 PHE   0.041   0.002   PHE A 340 
 TRP   0.012   0.001   TRP B 297 
 HIS   0.012   0.002   HIS A 220 

Details of bonding type rmsd
  covalent geometry    : bond        0.00642 ( 8427)
  covalent geometry    : angle       0.82975 (11434)
  SS BOND              : bond        0.00055 (    3)
  SS BOND              : angle       1.19481 (    6)
  hydrogen bonds       : bond        0.14493 (  426)
  hydrogen bonds       : angle       6.67063 ( 1221)

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

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

  2042 Ramachandran restraints generated.
    1021 Oldfield, 0 Emsley, 1021 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2042 Ramachandran restraints generated.
    1021 Oldfield, 0 Emsley, 1021 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  145 residues out of total 887 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 144
  time to evaluate  : 0.322 
Fit side-chains
   revert: symmetry clash
REVERT: A   29 GLN cc_start: 0.8258 (tp-100) cc_final: 0.7826 (tp40)
REVERT: A  315 PHE cc_start: 0.7254 (t80) cc_final: 0.6856 (t80)
REVERT: E   60 TYR cc_start: 0.8383 (m-80) cc_final: 0.8112 (m-80)
REVERT: E   69 THR cc_start: 0.7751 (p) cc_final: 0.7543 (t)
REVERT: B  259 GLN cc_start: 0.8072 (pt0) cc_final: 0.7802 (pt0)
REVERT: D   38 MET cc_start: 0.6412 (mmt) cc_final: 0.5838 (mpp)
  outliers start: 1
  outliers final: 0
  residues processed: 145
  average time/residue: 0.5299
  time to fit residues: 82.1641
Evaluate side-chains
  107 residues out of total 887 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 107
  time to evaluate  : 0.303 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 101
   random chunks:
   chunk 49 optimal weight:    2.9990
   chunk 97 optimal weight:   10.0000
   chunk 53 optimal weight:    5.9990
   chunk 5 optimal weight:    0.7980
   chunk 33 optimal weight:    8.9990
   chunk 65 optimal weight:    4.9990
   chunk 62 optimal weight:   30.0000
   chunk 51 optimal weight:   20.0000
   chunk 100 optimal weight:    7.9990
   chunk 38 optimal weight:    0.8980
   chunk 61 optimal weight:    4.9990
   overall best weight:    2.9386

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

Flipped N/Q/H residues before XYZ refinement:
F  53 HIS
** F 323 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B  75 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4064 r_free = 0.4064 target = 0.173109 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3544 r_free = 0.3544 target = 0.122904 restraints weight = 21050.179|
|-----------------------------------------------------------------------------|
r_work (start): 0.3506 rms_B_bonded: 4.14
r_work: 0.3335 rms_B_bonded: 4.46 restraints_weight: 0.5000
r_work (final): 0.3335
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3330
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3330 r_free = 0.3330    target_work(ls_wunit_k1) = 0.107         |
| occupancies: max = 1.00  min = 0.38   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3330 r_free = 0.3330    target_work(ls_wunit_k1) = 0.107         |
| occupancies: max = 1.00  min = 0.27   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3330
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6870
moved from start:          0.1856

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.060   8430  Z= 0.268
  Angle     :  0.680   7.435  11440  Z= 0.364
  Chirality :  0.048   0.161   1289
  Planarity :  0.005   0.048   1443
  Dihedral  :  6.594  83.375   1288
  Min Nonbonded Distance : 2.491

Molprobity Statistics.
  All-atom Clashscore : 8.83
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.75 %
    Favored  : 97.25 %
  Rotamer:
    Outliers :  2.72 %
    Allowed  : 11.92 %
    Favored  : 85.36 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.05 (0.25), residues: 1021
  helix:  1.04 (0.25), residues: 415
  sheet: -0.31 (0.31), residues: 229
  loop : -0.78 (0.30), residues: 377

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG E  98 
 TYR   0.016   0.002   TYR A 339 
 PHE   0.021   0.003   PHE A 212 
 TRP   0.018   0.002   TRP B  82 
 HIS   0.009   0.002   HIS A 220 

Details of bonding type rmsd
  covalent geometry    : bond        0.00636 ( 8427)
  covalent geometry    : angle       0.67987 (11434)
  SS BOND              : bond        0.00130 (    3)
  SS BOND              : angle       1.44530 (    6)
  hydrogen bonds       : bond        0.05233 (  426)
  hydrogen bonds       : angle       4.98280 ( 1221)

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

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

  2042 Ramachandran restraints generated.
    1021 Oldfield, 0 Emsley, 1021 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2042 Ramachandran restraints generated.
    1021 Oldfield, 0 Emsley, 1021 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  133 residues out of total 887 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 109
  time to evaluate  : 0.313 
Fit side-chains
REVERT: F  163 TRP cc_start: 0.7456 (m-10) cc_final: 0.7187 (m-10)
REVERT: F  269 LYS cc_start: 0.7155 (tppt) cc_final: 0.6893 (tttp)
REVERT: A  356 ARG cc_start: 0.8027 (ttp-110) cc_final: 0.7814 (ttp-110)
REVERT: E   60 TYR cc_start: 0.8393 (m-80) cc_final: 0.8165 (m-80)
REVERT: E   83 MET cc_start: 0.6457 (mtm) cc_final: 0.6088 (mtp)
REVERT: B  156 GLN cc_start: 0.6582 (mp10) cc_final: 0.6332 (mp10)
REVERT: B  195 ASP cc_start: 0.6616 (p0) cc_final: 0.6333 (p0)
REVERT: B  217 MET cc_start: 0.7523 (tpp) cc_final: 0.7226 (tpp)
REVERT: B  259 GLN cc_start: 0.6919 (pt0) cc_final: 0.6542 (pt0)
REVERT: B  262 MET cc_start: 0.7098 (ttt) cc_final: 0.6812 (ttt)
REVERT: B  267 ASP cc_start: 0.8201 (m-30) cc_final: 0.7934 (t0)
REVERT: D   38 MET cc_start: 0.5411 (mmt) cc_final: 0.5113 (mpt)
  outliers start: 24
  outliers final: 13
  residues processed: 122
  average time/residue: 0.4593
  time to fit residues: 60.7060
Evaluate side-chains
  104 residues out of total 887 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 91
  time to evaluate  : 0.334 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain F residue   35 LEU
Chi-restraints excluded: chain F residue  165 LYS
Chi-restraints excluded: chain F residue  212 VAL
Chi-restraints excluded: chain A residue  224 VAL
Chi-restraints excluded: chain A residue  254 ASN
Chi-restraints excluded: chain A residue  306 SER
Chi-restraints excluded: chain A residue  308 ILE
Chi-restraints excluded: chain A residue  365 CYS
Chi-restraints excluded: chain E residue  114 THR
Chi-restraints excluded: chain E residue  125 THR
Chi-restraints excluded: chain B residue  184 THR
Chi-restraints excluded: chain B residue  243 THR
Chi-restraints excluded: chain B residue  269 ILE
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 101
   random chunks:
   chunk 93 optimal weight:    0.9990
   chunk 27 optimal weight:    3.9990
   chunk 78 optimal weight:    6.9990
   chunk 6 optimal weight:    0.9990
   chunk 32 optimal weight:    0.7980
   chunk 72 optimal weight:    0.7980
   chunk 66 optimal weight:    7.9990
   chunk 95 optimal weight:    1.9990
   chunk 84 optimal weight:    3.9990
   chunk 61 optimal weight:    1.9990
   chunk 73 optimal weight:    0.6980
   overall best weight:    0.8584

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

Flipped N/Q/H residues before XYZ refinement:
** F 323 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4119 r_free = 0.4119 target = 0.178704 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3619 r_free = 0.3619 target = 0.128603 restraints weight = 23031.150|
|-----------------------------------------------------------------------------|
r_work (start): 0.3577 rms_B_bonded: 4.34
r_work: 0.3401 rms_B_bonded: 4.65 restraints_weight: 0.5000
r_work (final): 0.3401
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3416
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3416 r_free = 0.3416    target_work(ls_wunit_k1) = 0.112         |
| occupancies: max = 1.00  min = 0.27   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3416 r_free = 0.3416    target_work(ls_wunit_k1) = 0.112         |
| occupancies: max = 1.00  min = 0.23   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3416
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6805
moved from start:          0.2048

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.050   8430  Z= 0.127
  Angle     :  0.540   8.500  11440  Z= 0.287
  Chirality :  0.042   0.144   1289
  Planarity :  0.004   0.046   1443
  Dihedral  :  6.122  83.916   1288
  Min Nonbonded Distance : 2.583

Molprobity Statistics.
  All-atom Clashscore : 6.82
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.96 %
    Favored  : 98.04 %
  Rotamer:
    Outliers :  2.50 %
    Allowed  : 14.87 %
    Favored  : 82.63 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 3.45 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.74 (0.26), residues: 1021
  helix:  1.78 (0.26), residues: 409
  sheet: -0.03 (0.32), residues: 221
  loop : -0.52 (0.31), residues: 391

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 317 
 TYR   0.010   0.001   TYR A 339 
 PHE   0.019   0.002   PHE A 340 
 TRP   0.025   0.002   TRP B  82 
 HIS   0.003   0.001   HIS A 357 

Details of bonding type rmsd
  covalent geometry    : bond        0.00291 ( 8427)
  covalent geometry    : angle       0.53895 (11434)
  SS BOND              : bond        0.00555 (    3)
  SS BOND              : angle       1.78453 (    6)
  hydrogen bonds       : bond        0.04096 (  426)
  hydrogen bonds       : angle       4.49874 ( 1221)

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

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

  2042 Ramachandran restraints generated.
    1021 Oldfield, 0 Emsley, 1021 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2042 Ramachandran restraints generated.
    1021 Oldfield, 0 Emsley, 1021 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  143 residues out of total 887 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 121
  time to evaluate  : 0.365 
Fit side-chains
REVERT: F   29 PHE cc_start: 0.6009 (t80) cc_final: 0.5782 (t80)
REVERT: F  163 TRP cc_start: 0.7606 (m-10) cc_final: 0.7361 (m-10)
REVERT: F  269 LYS cc_start: 0.7155 (tppt) cc_final: 0.6899 (tttp)
REVERT: E   60 TYR cc_start: 0.8379 (m-80) cc_final: 0.8167 (m-80)
REVERT: E   83 MET cc_start: 0.6577 (mtm) cc_final: 0.6189 (mtp)
REVERT: B  156 GLN cc_start: 0.6488 (mp10) cc_final: 0.6217 (mp10)
REVERT: B  195 ASP cc_start: 0.6579 (p0) cc_final: 0.6359 (p0)
REVERT: B  217 MET cc_start: 0.7654 (tpp) cc_final: 0.7185 (tpp)
REVERT: B  259 GLN cc_start: 0.6742 (pt0) cc_final: 0.6436 (pt0)
REVERT: D   38 MET cc_start: 0.5371 (mmt) cc_final: 0.5021 (mpt)
  outliers start: 22
  outliers final: 11
  residues processed: 132
  average time/residue: 0.4136
  time to fit residues: 59.4108
Evaluate side-chains
  118 residues out of total 887 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 107
  time to evaluate  : 0.323 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain F residue   35 LEU
Chi-restraints excluded: chain F residue  298 CYS
Chi-restraints excluded: chain A residue   54 SER
Chi-restraints excluded: chain A residue  214 VAL
Chi-restraints excluded: chain A residue  224 VAL
Chi-restraints excluded: chain A residue  365 CYS
Chi-restraints excluded: chain E residue  114 THR
Chi-restraints excluded: chain E residue  125 THR
Chi-restraints excluded: chain B residue  186 ASP
Chi-restraints excluded: chain B residue  269 ILE
Chi-restraints excluded: chain B residue  331 SER
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 101
   random chunks:
   chunk 43 optimal weight:    0.4980
   chunk 80 optimal weight:    8.9990
   chunk 23 optimal weight:    1.9990
   chunk 76 optimal weight:    3.9990
   chunk 6 optimal weight:    7.9990
   chunk 98 optimal weight:    9.9990
   chunk 4 optimal weight:    1.9990
   chunk 57 optimal weight:    3.9990
   chunk 33 optimal weight:    1.9990
   chunk 30 optimal weight:    4.9990
   chunk 15 optimal weight:    3.9990
   overall best weight:    2.0988

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

Flipped N/Q/H residues before XYZ refinement:
** F 323 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 220 HIS
B  75 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4066 r_free = 0.4066 target = 0.173527 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3608 r_free = 0.3608 target = 0.126698 restraints weight = 27299.966|
|-----------------------------------------------------------------------------|
r_work (start): 0.3564 rms_B_bonded: 4.53
r_work: 0.3336 rms_B_bonded: 4.69 restraints_weight: 0.5000
r_work (final): 0.3336
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3328
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3328 r_free = 0.3328    target_work(ls_wunit_k1) = 0.106         |
| occupancies: max = 1.00  min = 0.23   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3328 r_free = 0.3328    target_work(ls_wunit_k1) = 0.106         |
| occupancies: max = 1.00  min = 0.20   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3328
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7011
moved from start:          0.2414

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.046   8430  Z= 0.200
  Angle     :  0.597   8.080  11440  Z= 0.316
  Chirality :  0.044   0.156   1289
  Planarity :  0.004   0.045   1443
  Dihedral  :  6.145  81.312   1288
  Min Nonbonded Distance : 2.567

Molprobity Statistics.
  All-atom Clashscore : 6.64
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.46 %
    Favored  : 97.54 %
  Rotamer:
    Outliers :  3.29 %
    Allowed  : 16.23 %
    Favored  : 80.48 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 3.45 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.73 (0.26), residues: 1021
  helix:  1.86 (0.26), residues: 409
  sheet: -0.07 (0.32), residues: 220
  loop : -0.60 (0.31), residues: 392

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 317 
 TYR   0.012   0.001   TYR B 111 
 PHE   0.028   0.002   PHE A 315 
 TRP   0.023   0.002   TRP B  82 
 HIS   0.004   0.001   HIS A 357 

Details of bonding type rmsd
  covalent geometry    : bond        0.00476 ( 8427)
  covalent geometry    : angle       0.59621 (11434)
  SS BOND              : bond        0.00344 (    3)
  SS BOND              : angle       1.78518 (    6)
  hydrogen bonds       : bond        0.04449 (  426)
  hydrogen bonds       : angle       4.54015 ( 1221)

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

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

  2042 Ramachandran restraints generated.
    1021 Oldfield, 0 Emsley, 1021 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2042 Ramachandran restraints generated.
    1021 Oldfield, 0 Emsley, 1021 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  143 residues out of total 887 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 114
  time to evaluate  : 0.248 
Fit side-chains
REVERT: F  163 TRP cc_start: 0.7690 (m-10) cc_final: 0.7452 (m-10)
REVERT: F  269 LYS cc_start: 0.7363 (tppt) cc_final: 0.7077 (tttp)
REVERT: F  333 PHE cc_start: 0.8179 (OUTLIER) cc_final: 0.7603 (m-10)
REVERT: A   29 GLN cc_start: 0.8129 (tp-100) cc_final: 0.7699 (tm-30)
REVERT: A   31 GLN cc_start: 0.7650 (tp-100) cc_final: 0.7372 (tp40)
REVERT: A  213 GLN cc_start: 0.8392 (OUTLIER) cc_final: 0.8171 (tt0)
REVERT: A  370 GLU cc_start: 0.7454 (mp0) cc_final: 0.7183 (mp0)
REVERT: E   83 MET cc_start: 0.6840 (mtm) cc_final: 0.6527 (mtp)
REVERT: B   59 TYR cc_start: 0.8561 (OUTLIER) cc_final: 0.8092 (m-80)
REVERT: B  156 GLN cc_start: 0.6560 (mp10) cc_final: 0.6304 (mp10)
REVERT: B  184 THR cc_start: 0.8810 (p) cc_final: 0.8585 (t)
REVERT: B  217 MET cc_start: 0.7817 (tpp) cc_final: 0.7166 (tpp)
REVERT: B  259 GLN cc_start: 0.6900 (pt0) cc_final: 0.6614 (pt0)
REVERT: D   38 MET cc_start: 0.5561 (mmt) cc_final: 0.5227 (mpt)
  outliers start: 29
  outliers final: 18
  residues processed: 132
  average time/residue: 0.4610
  time to fit residues: 65.5962
Evaluate side-chains
  122 residues out of total 887 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 101
  time to evaluate  : 0.187 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain F residue   35 LEU
Chi-restraints excluded: chain F residue   48 VAL
Chi-restraints excluded: chain F residue  155 SER
Chi-restraints excluded: chain F residue  207 VAL
Chi-restraints excluded: chain F residue  212 VAL
Chi-restraints excluded: chain F residue  298 CYS
Chi-restraints excluded: chain F residue  333 PHE
Chi-restraints excluded: chain A residue   54 SER
Chi-restraints excluded: chain A residue  213 GLN
Chi-restraints excluded: chain A residue  214 VAL
Chi-restraints excluded: chain A residue  224 VAL
Chi-restraints excluded: chain A residue  306 SER
Chi-restraints excluded: chain A residue  308 ILE
Chi-restraints excluded: chain A residue  365 CYS
Chi-restraints excluded: chain E residue   91 THR
Chi-restraints excluded: chain E residue  125 THR
Chi-restraints excluded: chain B residue   59 TYR
Chi-restraints excluded: chain B residue  158 VAL
Chi-restraints excluded: chain B residue  186 ASP
Chi-restraints excluded: chain B residue  269 ILE
Chi-restraints excluded: chain B residue  331 SER
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 101
   random chunks:
   chunk 78 optimal weight:    4.9990
   chunk 49 optimal weight:    0.7980
   chunk 39 optimal weight:    1.9990
   chunk 32 optimal weight:    0.2980
   chunk 3 optimal weight:    5.9990
   chunk 30 optimal weight:    0.9980
   chunk 46 optimal weight:    4.9990
   chunk 42 optimal weight:    1.9990
   chunk 11 optimal weight:    0.8980
   chunk 50 optimal weight:    8.9990
   chunk 90 optimal weight:    2.9990
   overall best weight:    0.9982

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

Flipped N/Q/H residues before XYZ refinement:
** F 323 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 294 GLN
E  35 ASN
B  75 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4101 r_free = 0.4101 target = 0.177101 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3612 r_free = 0.3612 target = 0.128233 restraints weight = 17908.136|
|-----------------------------------------------------------------------------|
r_work (start): 0.3584 rms_B_bonded: 3.81
r_work: 0.3423 rms_B_bonded: 4.23 restraints_weight: 0.5000
r_work (final): 0.3423
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3410
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3410 r_free = 0.3410    target_work(ls_wunit_k1) = 0.112         |
| occupancies: max = 1.00  min = 0.20   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3410 r_free = 0.3410    target_work(ls_wunit_k1) = 0.112         |
| occupancies: max = 1.00  min = 0.26   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3410
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6804
moved from start:          0.2545

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038   8430  Z= 0.129
  Angle     :  0.527   6.308  11440  Z= 0.280
  Chirality :  0.042   0.141   1289
  Planarity :  0.003   0.044   1443
  Dihedral  :  5.840  79.957   1288
  Min Nonbonded Distance : 2.554

Molprobity Statistics.
  All-atom Clashscore : 6.27
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.06 %
    Favored  : 97.94 %
  Rotamer:
    Outliers :  3.18 %
    Allowed  : 17.37 %
    Favored  : 79.46 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 3.45 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.86 (0.26), residues: 1021
  helix:  2.00 (0.26), residues: 409
  sheet: -0.13 (0.32), residues: 221
  loop : -0.48 (0.31), residues: 391

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A 317 
 TYR   0.020   0.001   TYR E  60 
 PHE   0.034   0.002   PHE A 315 
 TRP   0.026   0.001   TRP B  82 
 HIS   0.003   0.001   HIS A 357 

Details of bonding type rmsd
  covalent geometry    : bond        0.00297 ( 8427)
  covalent geometry    : angle       0.52674 (11434)
  SS BOND              : bond        0.00328 (    3)
  SS BOND              : angle       1.18620 (    6)
  hydrogen bonds       : bond        0.03915 (  426)
  hydrogen bonds       : angle       4.33659 ( 1221)

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

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

  2042 Ramachandran restraints generated.
    1021 Oldfield, 0 Emsley, 1021 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2042 Ramachandran restraints generated.
    1021 Oldfield, 0 Emsley, 1021 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  136 residues out of total 887 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 108
  time to evaluate  : 0.230 
Fit side-chains
   revert: symmetry clash
REVERT: F  163 TRP cc_start: 0.7638 (m-10) cc_final: 0.7386 (m-10)
REVERT: F  269 LYS cc_start: 0.7165 (tppt) cc_final: 0.6932 (tttp)
REVERT: F  333 PHE cc_start: 0.8063 (OUTLIER) cc_final: 0.7413 (m-10)
REVERT: A   31 GLN cc_start: 0.7543 (tp-100) cc_final: 0.7235 (tp40)
REVERT: A  213 GLN cc_start: 0.8372 (OUTLIER) cc_final: 0.8158 (tt0)
REVERT: A  370 GLU cc_start: 0.7428 (mp0) cc_final: 0.7037 (mp0)
REVERT: B   59 TYR cc_start: 0.8436 (OUTLIER) cc_final: 0.7750 (m-80)
REVERT: B  259 GLN cc_start: 0.6813 (pt0) cc_final: 0.6530 (pt0)
REVERT: D   38 MET cc_start: 0.5660 (mmt) cc_final: 0.5164 (mpt)
  outliers start: 28
  outliers final: 18
  residues processed: 124
  average time/residue: 0.4035
  time to fit residues: 53.8649
Evaluate side-chains
  120 residues out of total 887 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 99
  time to evaluate  : 0.248 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain F residue   35 LEU
Chi-restraints excluded: chain F residue   48 VAL
Chi-restraints excluded: chain F residue  119 VAL
Chi-restraints excluded: chain F residue  155 SER
Chi-restraints excluded: chain F residue  207 VAL
Chi-restraints excluded: chain F residue  298 CYS
Chi-restraints excluded: chain F residue  333 PHE
Chi-restraints excluded: chain A residue   54 SER
Chi-restraints excluded: chain A residue  213 GLN
Chi-restraints excluded: chain A residue  214 VAL
Chi-restraints excluded: chain A residue  224 VAL
Chi-restraints excluded: chain A residue  306 SER
Chi-restraints excluded: chain A residue  365 CYS
Chi-restraints excluded: chain E residue   46 GLU
Chi-restraints excluded: chain E residue   91 THR
Chi-restraints excluded: chain E residue  125 THR
Chi-restraints excluded: chain B residue   59 TYR
Chi-restraints excluded: chain B residue  186 ASP
Chi-restraints excluded: chain B residue  217 MET
Chi-restraints excluded: chain B residue  269 ILE
Chi-restraints excluded: chain B residue  331 SER
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 101
   random chunks:
   chunk 9 optimal weight:    0.9990
   chunk 66 optimal weight:    4.9990
   chunk 81 optimal weight:    4.9990
   chunk 25 optimal weight:    0.6980
   chunk 86 optimal weight:    3.9990
   chunk 87 optimal weight:    1.9990
   chunk 32 optimal weight:    0.5980
   chunk 69 optimal weight:    2.9990
   chunk 56 optimal weight:    8.9990
   chunk 21 optimal weight:    0.8980
   chunk 6 optimal weight:    1.9990
   overall best weight:    1.0384

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

Flipped N/Q/H residues before XYZ refinement:
** F 323 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B  75 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4104 r_free = 0.4104 target = 0.177332 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3602 r_free = 0.3602 target = 0.126864 restraints weight = 23728.001|
|-----------------------------------------------------------------------------|
r_work (start): 0.3571 rms_B_bonded: 4.43
r_work: 0.3396 rms_B_bonded: 4.69 restraints_weight: 0.5000
r_work (final): 0.3396
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3401
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3401 r_free = 0.3401    target_work(ls_wunit_k1) = 0.111         |
| occupancies: max = 1.00  min = 0.26   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3401 r_free = 0.3401    target_work(ls_wunit_k1) = 0.111         |
| occupancies: max = 1.00  min = 0.19   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3401
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6819
moved from start:          0.2669

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   8430  Z= 0.130
  Angle     :  0.536   9.664  11440  Z= 0.280
  Chirality :  0.042   0.144   1289
  Planarity :  0.003   0.044   1443
  Dihedral  :  5.682  77.922   1288
  Min Nonbonded Distance : 2.553

Molprobity Statistics.
  All-atom Clashscore : 6.27
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.46 %
    Favored  : 97.54 %
  Rotamer:
    Outliers :  3.18 %
    Allowed  : 18.84 %
    Favored  : 77.98 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 3.45 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.93 (0.26), residues: 1021
  helix:  2.08 (0.25), residues: 411
  sheet: -0.21 (0.32), residues: 223
  loop : -0.41 (0.32), residues: 387

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 356 
 TYR   0.012   0.001   TYR B 111 
 PHE   0.016   0.001   PHE A 212 
 TRP   0.023   0.001   TRP B  82 
 HIS   0.003   0.001   HIS A 357 

Details of bonding type rmsd
  covalent geometry    : bond        0.00302 ( 8427)
  covalent geometry    : angle       0.53551 (11434)
  SS BOND              : bond        0.00332 (    3)
  SS BOND              : angle       1.17674 (    6)
  hydrogen bonds       : bond        0.03856 (  426)
  hydrogen bonds       : angle       4.25277 ( 1221)

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

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

  2042 Ramachandran restraints generated.
    1021 Oldfield, 0 Emsley, 1021 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2042 Ramachandran restraints generated.
    1021 Oldfield, 0 Emsley, 1021 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  141 residues out of total 887 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 113
  time to evaluate  : 0.314 
Fit side-chains
   revert: symmetry clash
REVERT: F  163 TRP cc_start: 0.7759 (m-10) cc_final: 0.7508 (m-10)
REVERT: F  223 LYS cc_start: 0.8461 (ttpt) cc_final: 0.8205 (ttpt)
REVERT: F  269 LYS cc_start: 0.7172 (tppt) cc_final: 0.6916 (tttp)
REVERT: F  333 PHE cc_start: 0.8030 (OUTLIER) cc_final: 0.7357 (m-10)
REVERT: A   29 GLN cc_start: 0.8037 (tp-100) cc_final: 0.7596 (tp40)
REVERT: A   31 GLN cc_start: 0.7541 (tp-100) cc_final: 0.7186 (tp40)
REVERT: A  356 ARG cc_start: 0.7945 (ttp-110) cc_final: 0.7660 (ttp-110)
REVERT: A  370 GLU cc_start: 0.7439 (mp0) cc_final: 0.7177 (mp0)
REVERT: B  259 GLN cc_start: 0.6726 (pt0) cc_final: 0.6458 (pt0)
REVERT: D   38 MET cc_start: 0.5573 (mmt) cc_final: 0.5091 (mpt)
  outliers start: 28
  outliers final: 19
  residues processed: 127
  average time/residue: 0.4390
  time to fit residues: 60.3530
Evaluate side-chains
  128 residues out of total 887 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 108
  time to evaluate  : 0.296 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain F residue   35 LEU
Chi-restraints excluded: chain F residue   48 VAL
Chi-restraints excluded: chain F residue  119 VAL
Chi-restraints excluded: chain F residue  120 ASP
Chi-restraints excluded: chain F residue  207 VAL
Chi-restraints excluded: chain F residue  212 VAL
Chi-restraints excluded: chain F residue  298 CYS
Chi-restraints excluded: chain F residue  333 PHE
Chi-restraints excluded: chain A residue   54 SER
Chi-restraints excluded: chain A residue  214 VAL
Chi-restraints excluded: chain A residue  306 SER
Chi-restraints excluded: chain A residue  365 CYS
Chi-restraints excluded: chain E residue   91 THR
Chi-restraints excluded: chain E residue  125 THR
Chi-restraints excluded: chain B residue   76 ASP
Chi-restraints excluded: chain B residue  186 ASP
Chi-restraints excluded: chain B residue  217 MET
Chi-restraints excluded: chain B residue  269 ILE
Chi-restraints excluded: chain B residue  325 MET
Chi-restraints excluded: chain B residue  331 SER
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 101
   random chunks:
   chunk 87 optimal weight:    8.9990
   chunk 23 optimal weight:    1.9990
   chunk 53 optimal weight:    6.9990
   chunk 67 optimal weight:    2.9990
   chunk 3 optimal weight:    5.9990
   chunk 26 optimal weight:    1.9990
   chunk 94 optimal weight:    1.9990
   chunk 5 optimal weight:    1.9990
   chunk 72 optimal weight:    4.9990
   chunk 82 optimal weight:   10.0000
   chunk 70 optimal weight:    0.9980
   overall best weight:    1.7988

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

Flipped N/Q/H residues before XYZ refinement:
** F 323 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 220 HIS
A 294 GLN
B  75 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4075 r_free = 0.4075 target = 0.174438 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3562 r_free = 0.3562 target = 0.123778 restraints weight = 24146.186|
|-----------------------------------------------------------------------------|
r_work (start): 0.3533 rms_B_bonded: 4.45
r_work: 0.3358 rms_B_bonded: 4.67 restraints_weight: 0.5000
r_work (final): 0.3358
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3359
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3359 r_free = 0.3359    target_work(ls_wunit_k1) = 0.108         |
| occupancies: max = 1.00  min = 0.19   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3359 r_free = 0.3359    target_work(ls_wunit_k1) = 0.108         |
| occupancies: max = 1.00  min = 0.14   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3359
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6853
moved from start:          0.2794

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.039   8430  Z= 0.175
  Angle     :  0.563   5.981  11440  Z= 0.298
  Chirality :  0.043   0.148   1289
  Planarity :  0.004   0.043   1443
  Dihedral  :  5.798  76.222   1288
  Min Nonbonded Distance : 2.563

Molprobity Statistics.
  All-atom Clashscore : 6.52
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.75 %
    Favored  : 97.25 %
  Rotamer:
    Outliers :  3.75 %
    Allowed  : 18.73 %
    Favored  : 77.53 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 3.45 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.86 (0.26), residues: 1021
  helix:  2.03 (0.26), residues: 409
  sheet: -0.22 (0.32), residues: 223
  loop : -0.46 (0.32), residues: 389

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 356 
 TYR   0.013   0.001   TYR B 111 
 PHE   0.036   0.002   PHE A 315 
 TRP   0.021   0.001   TRP B  82 
 HIS   0.006   0.001   HIS F  53 

Details of bonding type rmsd
  covalent geometry    : bond        0.00415 ( 8427)
  covalent geometry    : angle       0.56223 (11434)
  SS BOND              : bond        0.00374 (    3)
  SS BOND              : angle       1.28889 (    6)
  hydrogen bonds       : bond        0.04156 (  426)
  hydrogen bonds       : angle       4.32452 ( 1221)

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

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

  2042 Ramachandran restraints generated.
    1021 Oldfield, 0 Emsley, 1021 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2042 Ramachandran restraints generated.
    1021 Oldfield, 0 Emsley, 1021 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  138 residues out of total 887 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 105
  time to evaluate  : 0.340 
Fit side-chains
   revert: symmetry clash
REVERT: F  163 TRP cc_start: 0.7706 (m-10) cc_final: 0.7481 (m-10)
REVERT: F  269 LYS cc_start: 0.7184 (tppt) cc_final: 0.6944 (tttm)
REVERT: F  333 PHE cc_start: 0.8042 (OUTLIER) cc_final: 0.7308 (m-10)
REVERT: A   31 GLN cc_start: 0.7575 (tp-100) cc_final: 0.7256 (tp40)
REVERT: A  356 ARG cc_start: 0.8050 (ttp-110) cc_final: 0.7813 (ttp-110)
REVERT: A  368 ASP cc_start: 0.7287 (t70) cc_final: 0.6969 (t70)
REVERT: A  370 GLU cc_start: 0.7474 (mp0) cc_final: 0.6972 (mp0)
REVERT: E  105 ARG cc_start: 0.6736 (OUTLIER) cc_final: 0.6519 (mtp180)
REVERT: B   82 TRP cc_start: 0.8120 (OUTLIER) cc_final: 0.6923 (m-10)
REVERT: B  259 GLN cc_start: 0.6731 (pt0) cc_final: 0.6473 (pt0)
REVERT: D   38 MET cc_start: 0.5515 (mmt) cc_final: 0.5024 (mpt)
  outliers start: 33
  outliers final: 19
  residues processed: 128
  average time/residue: 0.4407
  time to fit residues: 61.0874
Evaluate side-chains
  121 residues out of total 887 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 99
  time to evaluate  : 0.369 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain F residue   35 LEU
Chi-restraints excluded: chain F residue   48 VAL
Chi-restraints excluded: chain F residue  119 VAL
Chi-restraints excluded: chain F residue  120 ASP
Chi-restraints excluded: chain F residue  155 SER
Chi-restraints excluded: chain F residue  207 VAL
Chi-restraints excluded: chain F residue  212 VAL
Chi-restraints excluded: chain F residue  298 CYS
Chi-restraints excluded: chain F residue  333 PHE
Chi-restraints excluded: chain A residue   54 SER
Chi-restraints excluded: chain A residue  214 VAL
Chi-restraints excluded: chain A residue  306 SER
Chi-restraints excluded: chain A residue  365 CYS
Chi-restraints excluded: chain A residue  393 LEU
Chi-restraints excluded: chain E residue   91 THR
Chi-restraints excluded: chain E residue  105 ARG
Chi-restraints excluded: chain E residue  125 THR
Chi-restraints excluded: chain B residue   76 ASP
Chi-restraints excluded: chain B residue   82 TRP
Chi-restraints excluded: chain B residue  186 ASP
Chi-restraints excluded: chain B residue  217 MET
Chi-restraints excluded: chain B residue  269 ILE
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 101
   random chunks:
   chunk 87 optimal weight:    1.9990
   chunk 11 optimal weight:    2.9990
   chunk 56 optimal weight:    0.7980
   chunk 32 optimal weight:    0.7980
   chunk 3 optimal weight:    4.9990
   chunk 4 optimal weight:    0.6980
   chunk 94 optimal weight:    3.9990
   chunk 81 optimal weight:    5.9990
   chunk 20 optimal weight:   10.0000
   chunk 89 optimal weight:    0.8980
   chunk 6 optimal weight:    3.9990
   overall best weight:    1.0382

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

Flipped N/Q/H residues before XYZ refinement:
** F 323 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B  75 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4099 r_free = 0.4099 target = 0.176965 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3584 r_free = 0.3584 target = 0.125465 restraints weight = 29643.301|
|-----------------------------------------------------------------------------|
r_work (start): 0.3560 rms_B_bonded: 4.89
r_work (final): 0.3560
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3556
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3556 r_free = 0.3556    target_work(ls_wunit_k1) = 0.123         |
| occupancies: max = 1.00  min = 0.14   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3556 r_free = 0.3556    target_work(ls_wunit_k1) = 0.123         |
| occupancies: max = 1.00  min = 0.28   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3556
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6704
moved from start:          0.2841

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   8430  Z= 0.129
  Angle     :  0.542   9.550  11440  Z= 0.282
  Chirality :  0.042   0.142   1289
  Planarity :  0.003   0.042   1443
  Dihedral  :  5.633  74.635   1288
  Min Nonbonded Distance : 2.516

Molprobity Statistics.
  All-atom Clashscore : 6.58
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.36 %
    Favored  : 97.64 %
  Rotamer:
    Outliers :  2.84 %
    Allowed  : 19.86 %
    Favored  : 77.30 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 3.45 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.96 (0.26), residues: 1021
  helix:  2.15 (0.26), residues: 408
  sheet: -0.21 (0.32), residues: 223
  loop : -0.41 (0.32), residues: 390

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG A 317 
 TYR   0.014   0.001   TYR B 111 
 PHE   0.016   0.001   PHE A 212 
 TRP   0.025   0.001   TRP B  82 
 HIS   0.006   0.001   HIS F  53 

Details of bonding type rmsd
  covalent geometry    : bond        0.00298 ( 8427)
  covalent geometry    : angle       0.54158 (11434)
  SS BOND              : bond        0.00354 (    3)
  SS BOND              : angle       1.03103 (    6)
  hydrogen bonds       : bond        0.03828 (  426)
  hydrogen bonds       : angle       4.21166 ( 1221)

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

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

  2042 Ramachandran restraints generated.
    1021 Oldfield, 0 Emsley, 1021 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2042 Ramachandran restraints generated.
    1021 Oldfield, 0 Emsley, 1021 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  130 residues out of total 887 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 105
  time to evaluate  : 0.319 
Fit side-chains
   revert: symmetry clash
REVERT: F  163 TRP cc_start: 0.7471 (m-10) cc_final: 0.7246 (m-10)
REVERT: F  223 LYS cc_start: 0.8385 (ttpt) cc_final: 0.8138 (ttpt)
REVERT: F  269 LYS cc_start: 0.6966 (tppt) cc_final: 0.6688 (tttm)
REVERT: F  333 PHE cc_start: 0.8035 (OUTLIER) cc_final: 0.7378 (m-10)
REVERT: A  356 ARG cc_start: 0.7520 (ttp-110) cc_final: 0.7251 (ttp-110)
REVERT: B  259 GLN cc_start: 0.6741 (pt0) cc_final: 0.6444 (pt0)
REVERT: D   38 MET cc_start: 0.5524 (mmt) cc_final: 0.5012 (mpt)
  outliers start: 25
  outliers final: 19
  residues processed: 122
  average time/residue: 0.4235
  time to fit residues: 56.0249
Evaluate side-chains
  123 residues out of total 887 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 103
  time to evaluate  : 0.298 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain F residue   35 LEU
Chi-restraints excluded: chain F residue   39 LEU
Chi-restraints excluded: chain F residue   48 VAL
Chi-restraints excluded: chain F residue  119 VAL
Chi-restraints excluded: chain F residue  120 ASP
Chi-restraints excluded: chain F residue  155 SER
Chi-restraints excluded: chain F residue  207 VAL
Chi-restraints excluded: chain F residue  298 CYS
Chi-restraints excluded: chain F residue  333 PHE
Chi-restraints excluded: chain A residue   54 SER
Chi-restraints excluded: chain A residue  214 VAL
Chi-restraints excluded: chain A residue  306 SER
Chi-restraints excluded: chain A residue  365 CYS
Chi-restraints excluded: chain A residue  393 LEU
Chi-restraints excluded: chain E residue   83 MET
Chi-restraints excluded: chain E residue   91 THR
Chi-restraints excluded: chain E residue  125 THR
Chi-restraints excluded: chain B residue  217 MET
Chi-restraints excluded: chain B residue  269 ILE
Chi-restraints excluded: chain B residue  325 MET
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 101
   random chunks:
   chunk 20 optimal weight:    5.9990
   chunk 44 optimal weight:    0.9980
   chunk 39 optimal weight:    0.8980
   chunk 97 optimal weight:    7.9990
   chunk 33 optimal weight:    2.9990
   chunk 43 optimal weight:    3.9990
   chunk 34 optimal weight:    0.8980
   chunk 82 optimal weight:    6.9990
   chunk 70 optimal weight:    3.9990
   chunk 37 optimal weight:    0.5980
   chunk 51 optimal weight:    4.9990
   overall best weight:    1.2782

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

Flipped N/Q/H residues before XYZ refinement:
** F 323 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 220 HIS
B  75 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4093 r_free = 0.4093 target = 0.176306 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3586 r_free = 0.3586 target = 0.125704 restraints weight = 24033.745|
|-----------------------------------------------------------------------------|
r_work (start): 0.3561 rms_B_bonded: 4.44
r_work: 0.3384 rms_B_bonded: 4.72 restraints_weight: 0.5000
r_work (final): 0.3384
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3386
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3386 r_free = 0.3386    target_work(ls_wunit_k1) = 0.110         |
| occupancies: max = 1.00  min = 0.28   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3386 r_free = 0.3386    target_work(ls_wunit_k1) = 0.110         |
| occupancies: max = 1.00  min = 0.20   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3386
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6829
moved from start:          0.2906

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   8430  Z= 0.143
  Angle     :  0.548   7.606  11440  Z= 0.289
  Chirality :  0.042   0.144   1289
  Planarity :  0.003   0.042   1443
  Dihedral  :  5.589  73.029   1288
  Min Nonbonded Distance : 2.527

Molprobity Statistics.
  All-atom Clashscore : 6.70
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.55 %
    Favored  : 97.45 %
  Rotamer:
    Outliers :  2.50 %
    Allowed  : 20.43 %
    Favored  : 77.07 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 3.45 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.96 (0.26), residues: 1021
  helix:  2.15 (0.26), residues: 407
  sheet: -0.19 (0.32), residues: 223
  loop : -0.42 (0.32), residues: 391

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG A 317 
 TYR   0.014   0.001   TYR B 111 
 PHE   0.036   0.002   PHE A 315 
 TRP   0.016   0.001   TRP B  82 
 HIS   0.007   0.001   HIS F  53 

Details of bonding type rmsd
  covalent geometry    : bond        0.00338 ( 8427)
  covalent geometry    : angle       0.54758 (11434)
  SS BOND              : bond        0.00345 (    3)
  SS BOND              : angle       1.11455 (    6)
  hydrogen bonds       : bond        0.03908 (  426)
  hydrogen bonds       : angle       4.23093 ( 1221)

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

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

  2042 Ramachandran restraints generated.
    1021 Oldfield, 0 Emsley, 1021 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2042 Ramachandran restraints generated.
    1021 Oldfield, 0 Emsley, 1021 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  130 residues out of total 887 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 108
  time to evaluate  : 0.357 
Fit side-chains
   revert: symmetry clash
REVERT: F  163 TRP cc_start: 0.7713 (m-10) cc_final: 0.6857 (m100)
REVERT: F  223 LYS cc_start: 0.8494 (ttpt) cc_final: 0.8249 (ttpt)
REVERT: F  269 LYS cc_start: 0.7148 (tppt) cc_final: 0.6924 (tttm)
REVERT: F  333 PHE cc_start: 0.8023 (OUTLIER) cc_final: 0.7253 (m-10)
REVERT: A   29 GLN cc_start: 0.8026 (tp-100) cc_final: 0.7617 (tm-30)
REVERT: A  305 LYS cc_start: 0.8589 (mmmt) cc_final: 0.8278 (pmtt)
REVERT: A  356 ARG cc_start: 0.8069 (ttp-110) cc_final: 0.7831 (ttp-110)
REVERT: A  370 GLU cc_start: 0.7426 (mp0) cc_final: 0.7175 (mp0)
REVERT: B  259 GLN cc_start: 0.6718 (pt0) cc_final: 0.6462 (pt0)
REVERT: D   38 MET cc_start: 0.5560 (mmt) cc_final: 0.5096 (mpt)
  outliers start: 22
  outliers final: 19
  residues processed: 124
  average time/residue: 0.4803
  time to fit residues: 64.3134
Evaluate side-chains
  128 residues out of total 887 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 108
  time to evaluate  : 0.323 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain F residue   35 LEU
Chi-restraints excluded: chain F residue   39 LEU
Chi-restraints excluded: chain F residue   48 VAL
Chi-restraints excluded: chain F residue  119 VAL
Chi-restraints excluded: chain F residue  120 ASP
Chi-restraints excluded: chain F residue  155 SER
Chi-restraints excluded: chain F residue  207 VAL
Chi-restraints excluded: chain F residue  298 CYS
Chi-restraints excluded: chain F residue  333 PHE
Chi-restraints excluded: chain A residue   54 SER
Chi-restraints excluded: chain A residue  214 VAL
Chi-restraints excluded: chain A residue  306 SER
Chi-restraints excluded: chain A residue  365 CYS
Chi-restraints excluded: chain A residue  393 LEU
Chi-restraints excluded: chain E residue   83 MET
Chi-restraints excluded: chain E residue   91 THR
Chi-restraints excluded: chain E residue  125 THR
Chi-restraints excluded: chain B residue  186 ASP
Chi-restraints excluded: chain B residue  217 MET
Chi-restraints excluded: chain B residue  269 ILE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 101
   random chunks:
   chunk 30 optimal weight:    4.9990
   chunk 1 optimal weight:    1.9990
   chunk 28 optimal weight:    0.4980
   chunk 69 optimal weight:    4.9990
   chunk 92 optimal weight:    5.9990
   chunk 39 optimal weight:    1.9990
   chunk 90 optimal weight:    4.9990
   chunk 83 optimal weight:    1.9990
   chunk 59 optimal weight:    4.9990
   chunk 63 optimal weight:    0.0970
   chunk 86 optimal weight:    0.7980
   overall best weight:    1.0782

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

Flipped N/Q/H residues before XYZ refinement:
** F 323 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B  75 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4102 r_free = 0.4102 target = 0.177281 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3598 r_free = 0.3598 target = 0.126815 restraints weight = 24484.053|
|-----------------------------------------------------------------------------|
r_work (start): 0.3571 rms_B_bonded: 4.49
r_work: 0.3393 rms_B_bonded: 4.74 restraints_weight: 0.5000
r_work (final): 0.3393
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3381
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3381 r_free = 0.3381    target_work(ls_wunit_k1) = 0.110         |
| occupancies: max = 1.00  min = 0.20   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3381 r_free = 0.3381    target_work(ls_wunit_k1) = 0.110         |
| occupancies: max = 1.00  min = 0.14   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3381
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6819
moved from start:          0.2955

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   8430  Z= 0.133
  Angle     :  0.552  10.353  11440  Z= 0.287
  Chirality :  0.042   0.145   1289
  Planarity :  0.003   0.043   1443
  Dihedral  :  5.514  71.539   1288
  Min Nonbonded Distance : 2.532

Molprobity Statistics.
  All-atom Clashscore : 6.82
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.65 %
    Favored  : 97.35 %
  Rotamer:
    Outliers :  2.50 %
    Allowed  : 20.89 %
    Favored  : 76.62 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 3.45 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.00 (0.26), residues: 1021
  helix:  2.22 (0.26), residues: 407
  sheet: -0.22 (0.32), residues: 223
  loop : -0.41 (0.32), residues: 391

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG A 317 
 TYR   0.014   0.001   TYR B 111 
 PHE   0.016   0.001   PHE A 212 
 TRP   0.018   0.001   TRP B  82 
 HIS   0.007   0.001   HIS F  53 

Details of bonding type rmsd
  covalent geometry    : bond        0.00311 ( 8427)
  covalent geometry    : angle       0.55172 (11434)
  SS BOND              : bond        0.00371 (    3)
  SS BOND              : angle       1.02874 (    6)
  hydrogen bonds       : bond        0.03776 (  426)
  hydrogen bonds       : angle       4.18744 ( 1221)

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

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

  2042 Ramachandran restraints generated.
    1021 Oldfield, 0 Emsley, 1021 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2042 Ramachandran restraints generated.
    1021 Oldfield, 0 Emsley, 1021 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  135 residues out of total 887 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 113
  time to evaluate  : 0.332 
Fit side-chains
   revert: symmetry clash
REVERT: F  163 TRP cc_start: 0.7722 (m-10) cc_final: 0.6865 (m100)
REVERT: F  223 LYS cc_start: 0.8478 (ttpt) cc_final: 0.8245 (ttpt)
REVERT: F  269 LYS cc_start: 0.7127 (tppt) cc_final: 0.6905 (tttm)
REVERT: F  333 PHE cc_start: 0.8027 (OUTLIER) cc_final: 0.7249 (m-10)
REVERT: A   29 GLN cc_start: 0.8038 (tp-100) cc_final: 0.7632 (tm-30)
REVERT: A  356 ARG cc_start: 0.8063 (ttp-110) cc_final: 0.7823 (ttp-110)
REVERT: A  368 ASP cc_start: 0.7335 (t70) cc_final: 0.7093 (t70)
REVERT: A  370 GLU cc_start: 0.7502 (mp0) cc_final: 0.7154 (mp0)
REVERT: B  259 GLN cc_start: 0.6697 (pt0) cc_final: 0.6439 (pt0)
REVERT: D   38 MET cc_start: 0.5559 (mmt) cc_final: 0.5095 (mpt)
  outliers start: 22
  outliers final: 17
  residues processed: 129
  average time/residue: 0.4883
  time to fit residues: 67.7532
Evaluate side-chains
  120 residues out of total 887 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 102
  time to evaluate  : 0.312 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain F residue   35 LEU
Chi-restraints excluded: chain F residue   39 LEU
Chi-restraints excluded: chain F residue   48 VAL
Chi-restraints excluded: chain F residue  119 VAL
Chi-restraints excluded: chain F residue  120 ASP
Chi-restraints excluded: chain F residue  155 SER
Chi-restraints excluded: chain F residue  207 VAL
Chi-restraints excluded: chain F residue  298 CYS
Chi-restraints excluded: chain F residue  333 PHE
Chi-restraints excluded: chain A residue   54 SER
Chi-restraints excluded: chain A residue  214 VAL
Chi-restraints excluded: chain A residue  306 SER
Chi-restraints excluded: chain A residue  365 CYS
Chi-restraints excluded: chain A residue  393 LEU
Chi-restraints excluded: chain E residue   91 THR
Chi-restraints excluded: chain E residue  125 THR
Chi-restraints excluded: chain B residue  217 MET
Chi-restraints excluded: chain B residue  269 ILE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 101
   random chunks:
   chunk 14 optimal weight:    6.9990
   chunk 23 optimal weight:    0.9990
   chunk 12 optimal weight:    0.8980
   chunk 45 optimal weight:    3.9990
   chunk 6 optimal weight:    4.9990
   chunk 22 optimal weight:    0.6980
   chunk 28 optimal weight:    0.0270
   chunk 49 optimal weight:    0.9980
   chunk 48 optimal weight:    1.9990
   chunk 9 optimal weight:    0.7980
   chunk 79 optimal weight:    0.8980
   overall best weight:    0.6638

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

Flipped N/Q/H residues before XYZ refinement:
** F 323 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A  31 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4123 r_free = 0.4123 target = 0.179613 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3634 r_free = 0.3634 target = 0.129798 restraints weight = 21283.703|
|-----------------------------------------------------------------------------|
r_work (start): 0.3613 rms_B_bonded: 4.22
r_work: 0.3442 rms_B_bonded: 4.58 restraints_weight: 0.5000
r_work (final): 0.3442
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3445
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3445 r_free = 0.3445    target_work(ls_wunit_k1) = 0.114         |
| occupancies: max = 1.00  min = 0.14   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3445 r_free = 0.3445    target_work(ls_wunit_k1) = 0.114         |
| occupancies: max = 1.00  min = 0.14   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3445
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6785
moved from start:          0.3026

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   8430  Z= 0.114
  Angle     :  0.526   8.059  11440  Z= 0.277
  Chirality :  0.041   0.144   1289
  Planarity :  0.003   0.042   1443
  Dihedral  :  5.318  69.354   1288
  Min Nonbonded Distance : 2.536

Molprobity Statistics.
  All-atom Clashscore : 6.39
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.36 %
    Favored  : 97.64 %
  Rotamer:
    Outliers :  1.93 %
    Allowed  : 21.34 %
    Favored  : 76.73 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 3.45 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.10 (0.26), residues: 1021
  helix:  2.33 (0.26), residues: 400
  sheet: -0.10 (0.32), residues: 217
  loop : -0.39 (0.31), residues: 404

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG A 317 
 TYR   0.014   0.001   TYR B 111 
 PHE   0.033   0.001   PHE A 315 
 TRP   0.018   0.001   TRP B  82 
 HIS   0.007   0.001   HIS F  53 

Details of bonding type rmsd
  covalent geometry    : bond        0.00261 ( 8427)
  covalent geometry    : angle       0.52590 (11434)
  SS BOND              : bond        0.00341 (    3)
  SS BOND              : angle       0.88055 (    6)
  hydrogen bonds       : bond        0.03579 (  426)
  hydrogen bonds       : angle       4.10891 ( 1221)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2977.74 seconds
wall clock time: 51 minutes 30.73 seconds (3090.73 seconds total)