Starting phenix.real_space_refine
on Sun May 11 16:15:05 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8wst_37824/05_2025/8wst_37824.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8wst_37824/05_2025/8wst_37824.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.4
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8wst_37824/05_2025/8wst_37824.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8wst_37824/05_2025/8wst_37824.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8wst_37824/05_2025/8wst_37824.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8wst_37824/05_2025/8wst_37824.cif"
  }
  resolution = 2.4
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.001
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 4
    Type Number    sf(0)   Gaussians
     S      59      5.16       5
     C    5261      2.51       5
     N    1432      2.21       5
     O    1534      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 5 residue(s): 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib"
  Total number of atoms: 8286
  Number of models: 1
  Model: ""
    Number of chains: 6
    Chain: "A"
      Number of atoms: 1876
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 230, 1876
          Classifications: {'peptide': 230}
          Modifications used: {'COO': 1}
          Incomplete info: {'truncation_to_alanine': 1}
          Link IDs: {'PTRANS': 6, 'TRANS': 223}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 8
          Unresolved non-hydrogen angles: 9
          Unresolved non-hydrogen dihedrals: 7
          Planarities with less than four sites: {'ARG:plan': 1}
          Unresolved non-hydrogen planarities: 5
    Chain: "B"
      Number of atoms: 2590
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 337, 2590
          Classifications: {'peptide': 337}
          Link IDs: {'PTRANS': 5, 'TRANS': 331}
          Unresolved non-hydrogen bonds: 1
          Unresolved non-hydrogen angles: 2
          Unresolved non-hydrogen dihedrals: 1
          Unresolved non-hydrogen planarities: 1
    Chain: "G"
      Number of atoms: 438
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 57, 438
          Classifications: {'peptide': 57}
          Link IDs: {'PTRANS': 4, 'TRANS': 52}
    Chain: "L"
      Number of atoms: 129
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 15, 129
          Classifications: {'peptide': 15}
          Link IDs: {'PTRANS': 1, 'TRANS': 13}
    Chain: "N"
      Number of atoms: 973
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 129, 973
          Classifications: {'peptide': 129}
          Incomplete info: {'truncation_to_alanine': 2}
          Link IDs: {'PTRANS': 5, 'TRANS': 123}
          Unresolved non-hydrogen bonds: 10
          Unresolved non-hydrogen angles: 13
          Unresolved non-hydrogen dihedrals: 7
          Unresolved non-hydrogen chiralities: 1
          Planarities with less than four sites: {'ASP:plan': 1}
          Unresolved non-hydrogen planarities: 4
    Chain: "R"
      Number of atoms: 2280
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 287, 2280
          Classifications: {'peptide': 287}
          Incomplete info: {'truncation_to_alanine': 5}
          Link IDs: {'PTRANS': 14, 'TRANS': 272}
          Unresolved non-hydrogen bonds: 25
          Unresolved non-hydrogen angles: 30
          Unresolved non-hydrogen dihedrals: 22
          Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 1, 'ARG:plan': 1, 'PHE:plan': 1}
          Unresolved non-hydrogen planarities: 19
  Time building chain proxies: 5.27, per 1000 atoms: 0.64
  Number of scatterers: 8286
  At special positions: 0
  Unit cell: (83.22, 100.01, 133.59, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     S      59     16.00
     O    1534      8.00
     N    1432      7.00
     C    5261      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=3, symmetry=0
    Simple disulfide: pdb=" SG  CYS N  22 " - pdb=" SG  CYS N  96 " distance=2.03
    Simple disulfide: pdb=" SG  CYS N  99 " - pdb=" SG  CYS N 107 " distance=2.03
    Simple disulfide: pdb=" SG  CYS R 106 " - pdb=" SG  CYS R 184 " distance=1.99

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 1.83
  Conformation dependent library (CDL) restraints added in 1.0 seconds
  

  2082 Ramachandran restraints generated.
    1041 Oldfield, 0 Emsley, 1041 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1986

  Finding SS restraints...
    Secondary structure from input PDB file:
      30 helices and 12 sheets defined
      40.9% alpha, 21.1% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.87
  Creating SS restraints...
    Processing helix  chain 'A' and resid 6 through 32
      removed outlier: 3.590A  pdb=" N   ARG A  32 " --> pdb=" O   GLU A  28 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 45 through 55
    Processing helix  chain 'A' and resid 95 through 101
    Processing helix  chain 'A' and resid 117 through 130
    Processing helix  chain 'A' and resid 131 through 135
      removed outlier: 4.135A  pdb=" N   ARG A 135 " --> pdb=" O   ARG A 132 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 145 through 154
    Processing helix  chain 'A' and resid 159 through 164
      removed outlier: 4.118A  pdb=" N   TYR A 163 " --> pdb=" O   LYS A 159 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 183 through 203
    Processing helix  chain 'A' and resid 222 through 243
    Processing helix  chain 'B' and resid 5 through 25
    Processing helix  chain 'B' and resid 29 through 34
    Processing helix  chain 'G' and resid 8 through 23
      removed outlier: 3.505A  pdb=" N   ARG G  13 " --> pdb=" O   ILE G   9 " (cutoff:3.500A)
      removed outlier: 3.780A  pdb=" N   LYS G  14 " --> pdb=" O   ALA G  10 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 29 through 44
      removed outlier: 3.623A  pdb=" N   ALA G  33 " --> pdb=" O   LYS G  29 " (cutoff:3.500A)
    Processing helix  chain 'N' and resid 87 through 91
    Processing helix  chain 'R' and resid 32 through 62
      removed outlier: 3.980A  pdb=" N   LEU R  37 " --> pdb=" O   ASP R  33 " (cutoff:3.500A)
      Proline residue:  R  38  - end of helix
      removed outlier: 4.224A  pdb=" N   ILE R  41 " --> pdb=" O   LEU R  37 " (cutoff:3.500A)
      removed outlier: 3.505A  pdb=" N   GLY R  42 " --> pdb=" O   PRO R  38 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 66 through 85
    Processing helix  chain 'R' and resid 85 through 96
      removed outlier: 3.671A  pdb=" N   LEU R  89 " --> pdb=" O   GLY R  85 " (cutoff:3.500A)
      removed outlier: 4.664A  pdb=" N   GLN R  92 " --> pdb=" O   PHE R  88 " (cutoff:3.500A)
      removed outlier: 4.120A  pdb=" N   TRP R  93 " --> pdb=" O   LEU R  89 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 102 through 137
    Processing helix  chain 'R' and resid 142 through 145
    Processing helix  chain 'R' and resid 146 through 165
      removed outlier: 3.593A  pdb=" N   ALA R 165 " --> pdb=" O   SER R 161 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 165 through 171
      removed outlier: 3.552A  pdb=" N   TRP R 169 " --> pdb=" O   ALA R 165 " (cutoff:3.500A)
      removed outlier: 3.566A  pdb=" N   VAL R 170 " --> pdb=" O   LEU R 166 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 177 through 181
      removed outlier: 4.328A  pdb=" N   VAL R 181 " --> pdb=" O   LYS R 178 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 190 through 206
    Processing helix  chain 'R' and resid 208 through 231
      removed outlier: 3.809A  pdb=" N   LEU R 212 " --> pdb=" O   PHE R 208 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 232 through 235
    Processing helix  chain 'R' and resid 247 through 249
      No H-bonds generated for 'chain 'R' and resid 247 through 249'
    Processing helix  chain 'R' and resid 250 through 276
      Proline residue:  R 266  - end of helix
      removed outlier: 3.561A  pdb=" N   LEU R 272 " --> pdb=" O   HIS R 268 " (cutoff:3.500A)
      removed outlier: 4.043A  pdb=" N   GLN R 276 " --> pdb=" O   LEU R 272 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 281 through 296
      removed outlier: 4.047A  pdb=" N   TYR R 296 " --> pdb=" O   ILE R 292 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 296 through 308
      removed outlier: 3.620A  pdb=" N   SER R 300 " --> pdb=" O   TYR R 296 " (cutoff:3.500A)
      Proline residue:  R 303  - end of helix
    Processing helix  chain 'R' and resid 313 through 317
    Processing sheet with id=AA1, first strand: chain 'A' and resid 70 through 76
      removed outlier: 6.260A  pdb=" N   LEU A  34 " --> pdb=" O   HIS A  82 " (cutoff:3.500A)
      removed outlier: 7.567A  pdb=" N   PHE A  84 " --> pdb=" O   LEU A  34 " (cutoff:3.500A)
      removed outlier: 6.781A  pdb=" N   LEU A  36 " --> pdb=" O   PHE A  84 " (cutoff:3.500A)
      removed outlier: 9.347A  pdb=" N   ALA A 105 " --> pdb=" O   THR A  33 " (cutoff:3.500A)
      removed outlier: 6.928A  pdb=" N   ARG A  35 " --> pdb=" O   ALA A 105 " (cutoff:3.500A)
      removed outlier: 7.967A  pdb=" N   ILE A 107 " --> pdb=" O   ARG A  35 " (cutoff:3.500A)
      removed outlier: 6.397A  pdb=" N   LEU A  37 " --> pdb=" O   ILE A 107 " (cutoff:3.500A)
      removed outlier: 7.708A  pdb=" N   VAL A 109 " --> pdb=" O   LEU A  37 " (cutoff:3.500A)
      removed outlier: 7.257A  pdb=" N   LEU A  39 " --> pdb=" O   VAL A 109 " (cutoff:3.500A)
      removed outlier: 9.056A  pdb=" N   ASP A 111 " --> pdb=" O   LEU A  39 " (cutoff:3.500A)
      removed outlier: 6.212A  pdb=" N   ILE A 106 " --> pdb=" O   ILE A 140 " (cutoff:3.500A)
      removed outlier: 7.281A  pdb=" N   PHE A 142 " --> pdb=" O   ILE A 106 " (cutoff:3.500A)
      removed outlier: 6.360A  pdb=" N   PHE A 108 " --> pdb=" O   PHE A 142 " (cutoff:3.500A)
      removed outlier: 6.709A  pdb=" N   ASN A 144 " --> pdb=" O   PHE A 108 " (cutoff:3.500A)
      removed outlier: 6.033A  pdb=" N   VAL A 110 " --> pdb=" O   ASN A 144 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'B' and resid 46 through 51
      removed outlier: 5.999A  pdb=" N   THR B  47 " --> pdb=" O   ASN B 340 " (cutoff:3.500A)
      removed outlier: 7.126A  pdb=" N   ASN B 340 " --> pdb=" O   THR B  47 " (cutoff:3.500A)
      removed outlier: 3.580A  pdb=" N   ARG B  49 " --> pdb=" O   ILE B 338 " (cutoff:3.500A)
      removed outlier: 3.553A  pdb=" N   CYS B 317 " --> pdb=" O   GLY B 330 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'B' and resid 58 through 63
      removed outlier: 3.759A  pdb=" N   ALA B  60 " --> pdb=" O   ALA B  73 " (cutoff:3.500A)
      removed outlier: 3.739A  pdb=" N   SER B  74 " --> pdb=" O   LYS B  78 " (cutoff:3.500A)
      removed outlier: 4.265A  pdb=" N   LYS B  78 " --> pdb=" O   SER B  74 " (cutoff:3.500A)
      removed outlier: 3.580A  pdb=" N   HIS B  91 " --> pdb=" O   ILE B  81 " (cutoff:3.500A)
      removed outlier: 6.494A  pdb=" N   ASP B  83 " --> pdb=" O   LYS B  89 " (cutoff:3.500A)
      removed outlier: 5.969A  pdb=" N   LYS B  89 " --> pdb=" O   ASP B  83 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'B' and resid 100 through 105
      removed outlier: 6.908A  pdb=" N   GLY B 115 " --> pdb=" O   MET B 101 " (cutoff:3.500A)
      removed outlier: 4.330A  pdb=" N   CYS B 103 " --> pdb=" O   ALA B 113 " (cutoff:3.500A)
      removed outlier: 6.586A  pdb=" N   ALA B 113 " --> pdb=" O   CYS B 103 " (cutoff:3.500A)
      removed outlier: 5.110A  pdb=" N   TYR B 105 " --> pdb=" O   TYR B 111 " (cutoff:3.500A)
      removed outlier: 7.215A  pdb=" N   TYR B 111 " --> pdb=" O   TYR B 105 " (cutoff:3.500A)
      removed outlier: 4.157A  pdb=" N   GLY B 116 " --> pdb=" O   ILE B 120 " (cutoff:3.500A)
      removed outlier: 4.553A  pdb=" N   ILE B 120 " --> pdb=" O   GLY B 116 " (cutoff:3.500A)
      removed outlier: 6.219A  pdb=" N   CYS B 121 " --> pdb=" O   GLU B 138 " (cutoff:3.500A)
      removed outlier: 4.650A  pdb=" N   GLU B 138 " --> pdb=" O   CYS B 121 " (cutoff:3.500A)
      removed outlier: 7.098A  pdb=" N   ILE B 123 " --> pdb=" O   SER B 136 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'B' and resid 146 through 151
      removed outlier: 6.797A  pdb=" N   ASP B 170 " --> pdb=" O   GLN B 176 " (cutoff:3.500A)
      removed outlier: 6.601A  pdb=" N   GLN B 176 " --> pdb=" O   ASP B 170 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'B' and resid 187 through 192
      removed outlier: 3.631A  pdb=" N   GLN B 220 " --> pdb=" O   LEU B 210 " (cutoff:3.500A)
      removed outlier: 6.734A  pdb=" N   ASP B 212 " --> pdb=" O   CYS B 218 " (cutoff:3.500A)
      removed outlier: 6.432A  pdb=" N   CYS B 218 " --> pdb=" O   ASP B 212 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'B' and resid 229 through 234
      removed outlier: 3.951A  pdb=" N   MET B 262 " --> pdb=" O   LEU B 252 " (cutoff:3.500A)
      removed outlier: 7.136A  pdb=" N   ASP B 254 " --> pdb=" O   GLU B 260 " (cutoff:3.500A)
      removed outlier: 6.571A  pdb=" N   GLU B 260 " --> pdb=" O   ASP B 254 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'B' and resid 273 through 278
      removed outlier: 3.895A  pdb=" N   SER B 275 " --> pdb=" O   GLY B 288 " (cutoff:3.500A)
      removed outlier: 3.536A  pdb=" N   ALA B 287 " --> pdb=" O   ASN B 295 " (cutoff:3.500A)
      removed outlier: 3.661A  pdb=" N   ASN B 295 " --> pdb=" O   ALA B 287 " (cutoff:3.500A)
      removed outlier: 3.558A  pdb=" N   GLY B 306 " --> pdb=" O   VAL B 296 " (cutoff:3.500A)
      removed outlier: 6.158A  pdb=" N   ASP B 298 " --> pdb=" O   ARG B 304 " (cutoff:3.500A)
      removed outlier: 6.461A  pdb=" N   ARG B 304 " --> pdb=" O   ASP B 298 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'L' and resid 7 through 9
    Processing sheet with id=AB1, first strand: chain 'N' and resid 3 through 7
      removed outlier: 3.588A  pdb=" N   GLN N   3 " --> pdb=" O   SER N  25 " (cutoff:3.500A)
      removed outlier: 3.580A  pdb=" N   SER N  25 " --> pdb=" O   GLN N   3 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'N' and resid 10 through 12
      removed outlier: 6.162A  pdb=" N   GLY N  10 " --> pdb=" O   THR N 125 " (cutoff:3.500A)
      removed outlier: 3.825A  pdb=" N   SER N  49 " --> pdb=" O   TRP N  36 " (cutoff:3.500A)
      removed outlier: 6.149A  pdb=" N   ARG N  38 " --> pdb=" O   TRP N  47 " (cutoff:3.500A)
      removed outlier: 5.246A  pdb=" N   TRP N  47 " --> pdb=" O   ARG N  38 " (cutoff:3.500A)
      removed outlier: 3.526A  pdb=" N   ASP N  50 " --> pdb=" O   SER N  59 " (cutoff:3.500A)
      removed outlier: 3.902A  pdb=" N   SER N  59 " --> pdb=" O   ASP N  50 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'R' and resid 172 through 175

    408 hydrogen bonds defined for protein.
    1137 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 2.32

  Time building geometry restraints manager: 2.18 seconds

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

  Histogram of bond lengths:
        1.23 -     1.35: 2705
        1.35 -     1.46: 1989
        1.46 -     1.58: 3681
        1.58 -     1.69: 0
        1.69 -     1.81: 82
  Bond restraints: 8457
  Sorted by residual:
  bond pdb=" N   GLU R 182 "
       pdb=" CA  GLU R 182 "
    ideal  model  delta    sigma   weight residual
    1.457  1.494 -0.037 1.29e-02 6.01e+03 8.19e+00
  bond pdb=" N   VAL A  86 "
       pdb=" CA  VAL A  86 "
    ideal  model  delta    sigma   weight residual
    1.459  1.492 -0.033 1.25e-02 6.40e+03 7.07e+00
  bond pdb=" N   GLN A  89 "
       pdb=" CA  GLN A  89 "
    ideal  model  delta    sigma   weight residual
    1.455  1.487 -0.033 1.29e-02 6.01e+03 6.50e+00
  bond pdb=" N   SER R 183 "
       pdb=" CA  SER R 183 "
    ideal  model  delta    sigma   weight residual
    1.455  1.487 -0.032 1.27e-02 6.20e+03 6.27e+00
  bond pdb=" N   VAL R 181 "
       pdb=" CA  VAL R 181 "
    ideal  model  delta    sigma   weight residual
    1.459  1.489 -0.030 1.25e-02 6.40e+03 5.75e+00
  ... (remaining 8452 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.29: 11274
        1.29 -     2.57: 138
        2.57 -     3.86: 46
        3.86 -     5.14: 8
        5.14 -     6.43: 5
  Bond angle restraints: 11471
  Sorted by residual:
  angle pdb=" C   CYS R 184 "
        pdb=" CA  CYS R 184 "
        pdb=" CB  CYS R 184 "
      ideal   model   delta    sigma   weight residual
     110.88  105.02    5.86 1.60e+00 3.91e-01 1.34e+01
  angle pdb=" N   ASP A  85 "
        pdb=" CA  ASP A  85 "
        pdb=" C   ASP A  85 "
      ideal   model   delta    sigma   weight residual
     107.99  101.56    6.43 1.77e+00 3.19e-01 1.32e+01
  angle pdb=" N   CYS R 184 "
        pdb=" CA  CYS R 184 "
        pdb=" C   CYS R 184 "
      ideal   model   delta    sigma   weight residual
     108.63  103.01    5.62 1.60e+00 3.91e-01 1.23e+01
  angle pdb=" N   SER R 183 "
        pdb=" CA  SER R 183 "
        pdb=" C   SER R 183 "
      ideal   model   delta    sigma   weight residual
     109.07  114.41   -5.34 1.52e+00 4.33e-01 1.23e+01
  angle pdb=" C   GLU R 182 "
        pdb=" N   SER R 183 "
        pdb=" CA  SER R 183 "
      ideal   model   delta    sigma   weight residual
     121.75  116.01    5.74 1.73e+00 3.34e-01 1.10e+01
  ... (remaining 11466 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.50: 4890
       17.50 -    35.00: 125
       35.00 -    52.49: 28
       52.49 -    69.99: 5
       69.99 -    87.49: 4
  Dihedral angle restraints: 5052
    sinusoidal: 1979
      harmonic: 3073
  Sorted by residual:
  dihedral pdb=" CB  CYS R 106 "
           pdb=" SG  CYS R 106 "
           pdb=" SG  CYS R 184 "
           pdb=" CB  CYS R 184 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00  153.36  -60.36     1      1.00e+01 1.00e-02 4.85e+01
  dihedral pdb=" C   CYS R 184 "
           pdb=" N   CYS R 184 "
           pdb=" CA  CYS R 184 "
           pdb=" CB  CYS R 184 "
      ideal   model   delta  harmonic     sigma   weight residual
    -122.60 -111.35  -11.25     0      2.50e+00 1.60e-01 2.02e+01
  dihedral pdb=" N   CYS R 184 "
           pdb=" C   CYS R 184 "
           pdb=" CA  CYS R 184 "
           pdb=" CB  CYS R 184 "
      ideal   model   delta  harmonic     sigma   weight residual
     122.80  114.64    8.16     0      2.50e+00 1.60e-01 1.06e+01
  ... (remaining 5049 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.082: 1220
       0.082 -    0.163: 81
       0.163 -    0.245: 2
       0.245 -    0.327: 0
       0.327 -    0.408: 1
  Chirality restraints: 1304
  Sorted by residual:
  chirality pdb=" CA  CYS R 184 "
            pdb=" N   CYS R 184 "
            pdb=" C   CYS R 184 "
            pdb=" CB  CYS R 184 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.92   -0.41 2.00e-01 2.50e+01 4.17e+00
  chirality pdb=" CA  VAL R 181 "
            pdb=" N   VAL R 181 "
            pdb=" C   VAL R 181 "
            pdb=" CB  VAL R 181 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.65   -0.21 2.00e-01 2.50e+01 1.13e+00
  chirality pdb=" CA  VAL A  86 "
            pdb=" N   VAL A  86 "
            pdb=" C   VAL A  86 "
            pdb=" CB  VAL A  86 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.63   -0.18 2.00e-01 2.50e+01 8.46e-01
  ... (remaining 1301 not shown)

  Planarity restraints: 1460
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  CYS R 184 "   -0.007 2.00e-02 2.50e+03   1.33e-02 1.76e+00
        pdb=" C   CYS R 184 "    0.023 2.00e-02 2.50e+03
        pdb=" O   CYS R 184 "   -0.008 2.00e-02 2.50e+03
        pdb=" N   ALA R 185 "   -0.008 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  GLY R 180 "   -0.006 2.00e-02 2.50e+03   1.22e-02 1.48e+00
        pdb=" C   GLY R 180 "    0.021 2.00e-02 2.50e+03
        pdb=" O   GLY R 180 "   -0.008 2.00e-02 2.50e+03
        pdb=" N   VAL R 181 "   -0.007 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ILE R 203 "    0.006 2.00e-02 2.50e+03   1.10e-02 1.22e+00
        pdb=" C   ILE R 203 "   -0.019 2.00e-02 2.50e+03
        pdb=" O   ILE R 203 "    0.007 2.00e-02 2.50e+03
        pdb=" N   THR R 204 "    0.006 2.00e-02 2.50e+03
  ... (remaining 1457 not shown)

  Histogram of nonbonded interaction distances:
        2.16 -     2.71: 225
        2.71 -     3.25: 8403
        3.25 -     3.80: 13293
        3.80 -     4.35: 17161
        4.35 -     4.90: 29572
  Nonbonded interactions: 68654
  Sorted by model distance:
  nonbonded pdb=" OD1 ASP N  50 "
            pdb=" OG  SER N  59 "
     model   vdw
     2.158 3.040
  nonbonded pdb=" OD1 ASP B 247 "
            pdb=" OH  TYR N  32 "
     model   vdw
     2.199 3.040
  nonbonded pdb=" O   LEU R 164 "
            pdb=" OH  TYR R 200 "
     model   vdw
     2.244 3.040
  nonbonded pdb=" O   PHE N  29 "
            pdb=" NH2 ARG N  72 "
     model   vdw
     2.264 3.120
  nonbonded pdb=" NH1 ARG B 283 "
            pdb=" OD1 ASP B 298 "
     model   vdw
     2.269 3.120
  ... (remaining 68649 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=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.010
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             6.590
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.000
  Extract box with map and model:          1.220
  Check model and map are aligned:         0.000
  Set scattering table:                    0.000
  Process input model:                     20.220
  Find NCS groups from input model:        0.080
  Set up NCS constraints:                  0.040
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:11.480
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   39.640
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7274
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.038   8460  Z= 0.128
  Angle     :  0.450   6.429  11477  Z= 0.260
  Chirality :  0.041   0.408   1304
  Planarity :  0.002   0.028   1460
  Dihedral  :  8.866  87.491   3057
  Min Nonbonded Distance : 2.158

Molprobity Statistics.
  All-atom Clashscore : 4.97
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.07 %
    Favored  : 96.93 %
  Rotamer:
    Outliers :  0.22 %
    Allowed  :  3.77 %
    Favored  : 96.01 %
  Cbeta Deviations :  0.10 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.41 (0.28), residues: 1041
  helix:  3.55 (0.27), residues: 383
  sheet:  1.45 (0.36), residues: 217
  loop : -0.12 (0.31), residues: 441

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP A  96 
 HIS   0.004   0.001   HIS A 209 
 PHE   0.006   0.001   PHE A 228 
 TYR   0.008   0.001   TYR R 148 
 ARG   0.002   0.000   ARG B 214 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.16969 (  408)
  hydrogen bonds       : angle       6.21704 ( 1137)
  SS BOND              : bond        0.02177 (    3)
  SS BOND              : angle       1.41833 (    6)
  covalent geometry    : bond        0.00211 ( 8457)
  covalent geometry    : angle       0.44919 (11471)

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

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

  2082 Ramachandran restraints generated.
    1041 Oldfield, 0 Emsley, 1041 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2082 Ramachandran restraints generated.
    1041 Oldfield, 0 Emsley, 1041 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  198 residues out of total 912 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 196
  time to evaluate  : 0.877 
Fit side-chains
REVERT: A   21 LYS cc_start: 0.7531 (ttpp) cc_final: 0.7306 (ttmm)
REVERT: A  221 THR cc_start: 0.7341 (p) cc_final: 0.7068 (p)
REVERT: B  325 MET cc_start: 0.8336 (mmt) cc_final: 0.8102 (mmt)
REVERT: N    5 GLN cc_start: 0.5573 (mm-40) cc_final: 0.5205 (mm110)
REVERT: N   49 SER cc_start: 0.7623 (p) cc_final: 0.7056 (t)
REVERT: R   98 GLU cc_start: 0.6329 (tt0) cc_final: 0.6076 (tt0)
REVERT: R  140 ARG cc_start: 0.5925 (tpp80) cc_final: 0.5404 (tpt90)
REVERT: R  247 MET cc_start: 0.5781 (mmm) cc_final: 0.5440 (mmt)
  outliers start: 2
  outliers final: 0
  residues processed: 198
  average time/residue: 1.2804
  time to fit residues: 268.1913
Evaluate side-chains
  112 residues out of total 912 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 112
  time to evaluate  : 0.841 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 86 optimal weight:    4.9990
   chunk 77 optimal weight:    0.0370
   chunk 42 optimal weight:    0.8980
   chunk 26 optimal weight:    0.0170
   chunk 52 optimal weight:    0.6980
   chunk 41 optimal weight:    0.6980
   chunk 79 optimal weight:    0.8980
   chunk 30 optimal weight:    1.9990
   chunk 48 optimal weight:    1.9990
   chunk 59 optimal weight:    3.9990
   chunk 92 optimal weight:    0.8980
   overall best weight:    0.4696

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

Flipped N/Q/H residues before XYZ refinement:
A  89 GLN
B  75 GLN
B 220 GLN
B 237 ASN
B 268 ASN
B 340 ASN
R 230 GLN
R 268 HIS

Total number of N/Q/H flips: 8

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4310 r_free = 0.4310 target = 0.199146 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3943 r_free = 0.3943 target = 0.162252 restraints weight = 8308.230|
|-----------------------------------------------------------------------------|
r_work (start): 0.3941 rms_B_bonded: 1.95
r_work: 0.3675 rms_B_bonded: 2.63 restraints_weight: 0.5000
r_work: 0.3544 rms_B_bonded: 4.23 restraints_weight: 0.2500
r_work (final): 0.3544
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7663
moved from start:          0.2092

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.032   8460  Z= 0.116
  Angle     :  0.530   7.218  11477  Z= 0.275
  Chirality :  0.042   0.143   1304
  Planarity :  0.004   0.044   1460
  Dihedral  :  3.785  18.752   1152
  Min Nonbonded Distance : 2.529

Molprobity Statistics.
  All-atom Clashscore : 3.58
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.17 %
    Favored  : 96.83 %
  Rotamer:
    Outliers :  3.10 %
    Allowed  : 10.86 %
    Favored  : 86.03 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.07 (0.27), residues: 1041
  helix:  3.12 (0.27), residues: 387
  sheet:  1.28 (0.34), residues: 226
  loop : -0.25 (0.31), residues: 428

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.001   TRP B 169 
 HIS   0.006   0.001   HIS A 209 
 PHE   0.010   0.001   PHE B 199 
 TYR   0.012   0.001   TYR R 148 
 ARG   0.007   0.001   ARG B 137 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04034 (  408)
  hydrogen bonds       : angle       4.73816 ( 1137)
  SS BOND              : bond        0.00425 (    3)
  SS BOND              : angle       0.68994 (    6)
  covalent geometry    : bond        0.00247 ( 8457)
  covalent geometry    : angle       0.52993 (11471)

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

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

  2082 Ramachandran restraints generated.
    1041 Oldfield, 0 Emsley, 1041 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2082 Ramachandran restraints generated.
    1041 Oldfield, 0 Emsley, 1041 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  148 residues out of total 912 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 120
  time to evaluate  : 0.938 
Fit side-chains
REVERT: A   28 GLU cc_start: 0.6491 (OUTLIER) cc_final: 0.5626 (mt-10)
REVERT: A  132 ARG cc_start: 0.7302 (ptm160) cc_final: 0.6678 (tpt90)
REVERT: A  221 THR cc_start: 0.7421 (p) cc_final: 0.7130 (p)
REVERT: B   59 TYR cc_start: 0.7986 (OUTLIER) cc_final: 0.7244 (m-80)
REVERT: B  217 MET cc_start: 0.7881 (ppp) cc_final: 0.7639 (pmt)
REVERT: N   49 SER cc_start: 0.7595 (p) cc_final: 0.6981 (t)
REVERT: R  140 ARG cc_start: 0.6292 (tpp80) cc_final: 0.5566 (tpt90)
REVERT: R  228 TYR cc_start: 0.7398 (t80) cc_final: 0.7172 (t80)
REVERT: R  247 MET cc_start: 0.5911 (mmm) cc_final: 0.5638 (mmt)
  outliers start: 28
  outliers final: 8
  residues processed: 136
  average time/residue: 1.1339
  time to fit residues: 164.9177
Evaluate side-chains
  116 residues out of total 912 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 106
  time to evaluate  : 0.857 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   28 GLU
Chi-restraints excluded: chain A residue   33 THR
Chi-restraints excluded: chain B residue   59 TYR
Chi-restraints excluded: chain B residue  161 SER
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  268 ASN
Chi-restraints excluded: chain R residue   86 MET
Chi-restraints excluded: chain R residue  148 TYR
Chi-restraints excluded: chain R residue  161 SER
Chi-restraints excluded: chain R residue  263 SER
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 62 optimal weight:    6.9990
   chunk 98 optimal weight:    0.9990
   chunk 93 optimal weight:    0.6980
   chunk 100 optimal weight:    0.8980
   chunk 95 optimal weight:    0.6980
   chunk 22 optimal weight:    0.9990
   chunk 97 optimal weight:    1.9990
   chunk 7 optimal weight:    4.9990
   chunk 28 optimal weight:    0.8980
   chunk 80 optimal weight:    6.9990
   chunk 101 optimal weight:    0.9980
   overall best weight:    0.8380

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

Flipped N/Q/H residues before XYZ refinement:
B  88 ASN
B 237 ASN
B 268 ASN
R 230 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4263 r_free = 0.4263 target = 0.194306 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3861 r_free = 0.3861 target = 0.155399 restraints weight = 8409.882|
|-----------------------------------------------------------------------------|
r_work (start): 0.3861 rms_B_bonded: 1.99
r_work: 0.3612 rms_B_bonded: 2.51 restraints_weight: 0.5000
r_work: 0.3481 rms_B_bonded: 3.98 restraints_weight: 0.2500
r_work (final): 0.3481
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7743
moved from start:          0.2690

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041   8460  Z= 0.133
  Angle     :  0.549   9.763  11477  Z= 0.285
  Chirality :  0.043   0.137   1304
  Planarity :  0.004   0.036   1460
  Dihedral  :  4.130  19.547   1152
  Min Nonbonded Distance : 2.500

Molprobity Statistics.
  All-atom Clashscore : 4.97
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.55 %
    Favored  : 96.45 %
  Rotamer:
    Outliers :  3.66 %
    Allowed  : 10.98 %
    Favored  : 85.37 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.71 (0.27), residues: 1041
  helix:  2.75 (0.26), residues: 393
  sheet:  1.05 (0.32), residues: 231
  loop : -0.40 (0.31), residues: 417

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.002   TRP B  82 
 HIS   0.006   0.001   HIS A 209 
 PHE   0.012   0.001   PHE B 151 
 TYR   0.011   0.001   TYR A 191 
 ARG   0.005   0.001   ARG B  19 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04193 (  408)
  hydrogen bonds       : angle       4.62288 ( 1137)
  SS BOND              : bond        0.00232 (    3)
  SS BOND              : angle       0.59787 (    6)
  covalent geometry    : bond        0.00297 ( 8457)
  covalent geometry    : angle       0.54916 (11471)

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

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

  2082 Ramachandran restraints generated.
    1041 Oldfield, 0 Emsley, 1041 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2082 Ramachandran restraints generated.
    1041 Oldfield, 0 Emsley, 1041 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  145 residues out of total 912 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 112
  time to evaluate  : 0.819 
Fit side-chains
REVERT: A   28 GLU cc_start: 0.6484 (OUTLIER) cc_final: 0.5603 (mt-10)
REVERT: A  132 ARG cc_start: 0.7388 (ptm160) cc_final: 0.6689 (tpt170)
REVERT: A  221 THR cc_start: 0.7465 (p) cc_final: 0.7155 (p)
REVERT: B   59 TYR cc_start: 0.8181 (OUTLIER) cc_final: 0.7428 (m-80)
REVERT: B  217 MET cc_start: 0.8156 (OUTLIER) cc_final: 0.7751 (pmt)
REVERT: R  140 ARG cc_start: 0.6342 (tpp80) cc_final: 0.5588 (tpt90)
REVERT: R  228 TYR cc_start: 0.7447 (t80) cc_final: 0.7195 (t80)
REVERT: R  232 LYS cc_start: 0.5744 (OUTLIER) cc_final: 0.5327 (mmtm)
REVERT: R  247 MET cc_start: 0.6067 (mmm) cc_final: 0.5794 (mmt)
  outliers start: 33
  outliers final: 13
  residues processed: 130
  average time/residue: 1.2743
  time to fit residues: 176.0846
Evaluate side-chains
  112 residues out of total 912 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 95
  time to evaluate  : 0.931 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   28 GLU
Chi-restraints excluded: chain A residue   33 THR
Chi-restraints excluded: chain A residue  112 SER
Chi-restraints excluded: chain A residue  136 THR
Chi-restraints excluded: chain A residue  199 ASP
Chi-restraints excluded: chain B residue   43 ILE
Chi-restraints excluded: chain B residue   59 TYR
Chi-restraints excluded: chain B residue  161 SER
Chi-restraints excluded: chain B residue  217 MET
Chi-restraints excluded: chain B residue  263 THR
Chi-restraints excluded: chain B residue  327 VAL
Chi-restraints excluded: chain R residue   86 MET
Chi-restraints excluded: chain R residue  148 TYR
Chi-restraints excluded: chain R residue  161 SER
Chi-restraints excluded: chain R residue  181 VAL
Chi-restraints excluded: chain R residue  232 LYS
Chi-restraints excluded: chain R residue  263 SER
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 59 optimal weight:    4.9990
   chunk 44 optimal weight:    0.9990
   chunk 57 optimal weight:    2.9990
   chunk 96 optimal weight:    2.9990
   chunk 43 optimal weight:    1.9990
   chunk 76 optimal weight:    0.7980
   chunk 70 optimal weight:    2.9990
   chunk 18 optimal weight:    4.9990
   chunk 53 optimal weight:    0.9990
   chunk 2 optimal weight:    0.0870
   chunk 64 optimal weight:    4.9990
   overall best weight:    0.9764

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

Flipped N/Q/H residues before XYZ refinement:
B 237 ASN
R  52 ASN
R 230 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4239 r_free = 0.4239 target = 0.191907 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3862 r_free = 0.3862 target = 0.155008 restraints weight = 8299.180|
|-----------------------------------------------------------------------------|
r_work (start): 0.3857 rms_B_bonded: 2.01
r_work: 0.3573 rms_B_bonded: 2.58 restraints_weight: 0.5000
r_work: 0.3444 rms_B_bonded: 4.07 restraints_weight: 0.2500
r_work (final): 0.3444
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7788
moved from start:          0.3236

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.046   8460  Z= 0.143
  Angle     :  0.543   6.979  11477  Z= 0.287
  Chirality :  0.043   0.138   1304
  Planarity :  0.004   0.039   1460
  Dihedral  :  4.359  19.984   1152
  Min Nonbonded Distance : 2.495

Molprobity Statistics.
  All-atom Clashscore : 5.03
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.84 %
    Favored  : 96.16 %
  Rotamer:
    Outliers :  3.99 %
    Allowed  : 12.08 %
    Favored  : 83.92 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.33 (0.26), residues: 1041
  helix:  2.52 (0.26), residues: 395
  sheet:  0.82 (0.32), residues: 218
  loop : -0.68 (0.30), residues: 428

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.002   TRP B  82 
 HIS   0.005   0.001   HIS A 209 
 PHE   0.013   0.002   PHE B 199 
 TYR   0.015   0.002   TYR A 191 
 ARG   0.005   0.000   ARG B  19 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04163 (  408)
  hydrogen bonds       : angle       4.65640 ( 1137)
  SS BOND              : bond        0.00135 (    3)
  SS BOND              : angle       0.65707 (    6)
  covalent geometry    : bond        0.00317 ( 8457)
  covalent geometry    : angle       0.54253 (11471)

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

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

  2082 Ramachandran restraints generated.
    1041 Oldfield, 0 Emsley, 1041 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2082 Ramachandran restraints generated.
    1041 Oldfield, 0 Emsley, 1041 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  145 residues out of total 912 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 109
  time to evaluate  : 0.943 
Fit side-chains
REVERT: A   28 GLU cc_start: 0.6379 (OUTLIER) cc_final: 0.5516 (mt-10)
REVERT: A  132 ARG cc_start: 0.7321 (ptm160) cc_final: 0.6632 (tpt170)
REVERT: B   59 TYR cc_start: 0.8219 (OUTLIER) cc_final: 0.7448 (m-80)
REVERT: B  217 MET cc_start: 0.8207 (OUTLIER) cc_final: 0.7859 (pmt)
REVERT: B  260 GLU cc_start: 0.7918 (tt0) cc_final: 0.7709 (tt0)
REVERT: B  304 ARG cc_start: 0.8213 (OUTLIER) cc_final: 0.7853 (mtm180)
REVERT: R  140 ARG cc_start: 0.6411 (tpp80) cc_final: 0.5655 (tpt90)
REVERT: R  228 TYR cc_start: 0.7532 (t80) cc_final: 0.7268 (t80)
REVERT: R  232 LYS cc_start: 0.5775 (OUTLIER) cc_final: 0.5399 (mmtm)
REVERT: R  282 LEU cc_start: 0.6636 (OUTLIER) cc_final: 0.6221 (tp)
  outliers start: 36
  outliers final: 16
  residues processed: 130
  average time/residue: 1.1695
  time to fit residues: 161.9766
Evaluate side-chains
  121 residues out of total 912 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 99
  time to evaluate  : 0.829 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   15 ARG
Chi-restraints excluded: chain A residue   23 LEU
Chi-restraints excluded: chain A residue   28 GLU
Chi-restraints excluded: chain A residue   33 THR
Chi-restraints excluded: chain A residue  112 SER
Chi-restraints excluded: chain A residue  136 THR
Chi-restraints excluded: chain A residue  171 THR
Chi-restraints excluded: chain A residue  199 ASP
Chi-restraints excluded: chain B residue   43 ILE
Chi-restraints excluded: chain B residue   59 TYR
Chi-restraints excluded: chain B residue  161 SER
Chi-restraints excluded: chain B residue  217 MET
Chi-restraints excluded: chain B residue  263 THR
Chi-restraints excluded: chain B residue  294 CYS
Chi-restraints excluded: chain B residue  304 ARG
Chi-restraints excluded: chain B residue  327 VAL
Chi-restraints excluded: chain R residue  148 TYR
Chi-restraints excluded: chain R residue  161 SER
Chi-restraints excluded: chain R residue  181 VAL
Chi-restraints excluded: chain R residue  232 LYS
Chi-restraints excluded: chain R residue  263 SER
Chi-restraints excluded: chain R residue  282 LEU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 45 optimal weight:    3.9990
   chunk 84 optimal weight:    2.9990
   chunk 19 optimal weight:    0.1980
   chunk 22 optimal weight:    0.9990
   chunk 41 optimal weight:    0.7980
   chunk 35 optimal weight:    0.7980
   chunk 28 optimal weight:    2.9990
   chunk 72 optimal weight:    0.9980
   chunk 62 optimal weight:    9.9990
   chunk 76 optimal weight:    0.7980
   chunk 10 optimal weight:    5.9990
   overall best weight:    0.7180

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

Flipped N/Q/H residues before XYZ refinement:
B 175 GLN
B 237 ASN
R 230 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4242 r_free = 0.4242 target = 0.192320 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3839 r_free = 0.3839 target = 0.153412 restraints weight = 8277.464|
|-----------------------------------------------------------------------------|
r_work (start): 0.3841 rms_B_bonded: 2.06
r_work: 0.3572 rms_B_bonded: 2.68 restraints_weight: 0.5000
r_work: 0.3442 rms_B_bonded: 4.24 restraints_weight: 0.2500
r_work (final): 0.3442
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7787
moved from start:          0.3414

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   8460  Z= 0.118
  Angle     :  0.513   9.869  11477  Z= 0.268
  Chirality :  0.042   0.138   1304
  Planarity :  0.004   0.038   1460
  Dihedral  :  4.232  19.832   1152
  Min Nonbonded Distance : 2.525

Molprobity Statistics.
  All-atom Clashscore : 4.73
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.55 %
    Favored  : 96.45 %
  Rotamer:
    Outliers :  3.77 %
    Allowed  : 12.97 %
    Favored  : 83.26 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.43 (0.26), residues: 1041
  helix:  2.75 (0.26), residues: 388
  sheet:  0.83 (0.32), residues: 218
  loop : -0.69 (0.30), residues: 435

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.002   TRP B  82 
 HIS   0.005   0.001   HIS A 209 
 PHE   0.016   0.001   PHE B 199 
 TYR   0.012   0.001   TYR A 191 
 ARG   0.003   0.000   ARG B  19 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03808 (  408)
  hydrogen bonds       : angle       4.45398 ( 1137)
  SS BOND              : bond        0.00134 (    3)
  SS BOND              : angle       0.59646 (    6)
  covalent geometry    : bond        0.00260 ( 8457)
  covalent geometry    : angle       0.51281 (11471)

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

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

  2082 Ramachandran restraints generated.
    1041 Oldfield, 0 Emsley, 1041 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2082 Ramachandran restraints generated.
    1041 Oldfield, 0 Emsley, 1041 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  141 residues out of total 912 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 107
  time to evaluate  : 0.913 
Fit side-chains
REVERT: A   21 LYS cc_start: 0.8070 (ttpp) cc_final: 0.7596 (ttmm)
REVERT: A   28 GLU cc_start: 0.6388 (OUTLIER) cc_final: 0.5566 (mt-10)
REVERT: A  132 ARG cc_start: 0.7345 (OUTLIER) cc_final: 0.6620 (tpt170)
REVERT: B   23 LYS cc_start: 0.7280 (tptm) cc_final: 0.7064 (ttpp)
REVERT: B   59 TYR cc_start: 0.8197 (OUTLIER) cc_final: 0.7407 (m-80)
REVERT: B  101 MET cc_start: 0.8666 (ptm) cc_final: 0.8464 (ptm)
REVERT: B  217 MET cc_start: 0.8180 (OUTLIER) cc_final: 0.7822 (pmt)
REVERT: B  230 ASN cc_start: 0.8021 (OUTLIER) cc_final: 0.7757 (m110)
REVERT: G   47 GLU cc_start: 0.7850 (OUTLIER) cc_final: 0.7488 (pt0)
REVERT: R  140 ARG cc_start: 0.6414 (tpp80) cc_final: 0.5702 (tpt90)
REVERT: R  195 LEU cc_start: 0.6721 (OUTLIER) cc_final: 0.6353 (tm)
REVERT: R  228 TYR cc_start: 0.7501 (t80) cc_final: 0.7232 (t80)
REVERT: R  232 LYS cc_start: 0.5858 (OUTLIER) cc_final: 0.5477 (mmtm)
REVERT: R  282 LEU cc_start: 0.6660 (OUTLIER) cc_final: 0.6223 (tp)
  outliers start: 34
  outliers final: 18
  residues processed: 127
  average time/residue: 1.2193
  time to fit residues: 164.7313
Evaluate side-chains
  125 residues out of total 912 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 98
  time to evaluate  : 0.825 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   15 ARG
Chi-restraints excluded: chain A residue   23 LEU
Chi-restraints excluded: chain A residue   28 GLU
Chi-restraints excluded: chain A residue   33 THR
Chi-restraints excluded: chain A residue  112 SER
Chi-restraints excluded: chain A residue  132 ARG
Chi-restraints excluded: chain A residue  136 THR
Chi-restraints excluded: chain A residue  195 LYS
Chi-restraints excluded: chain A residue  199 ASP
Chi-restraints excluded: chain A residue  232 LYS
Chi-restraints excluded: chain B residue   43 ILE
Chi-restraints excluded: chain B residue   59 TYR
Chi-restraints excluded: chain B residue  161 SER
Chi-restraints excluded: chain B residue  217 MET
Chi-restraints excluded: chain B residue  230 ASN
Chi-restraints excluded: chain B residue  263 THR
Chi-restraints excluded: chain B residue  294 CYS
Chi-restraints excluded: chain B residue  327 VAL
Chi-restraints excluded: chain G residue   42 GLU
Chi-restraints excluded: chain G residue   47 GLU
Chi-restraints excluded: chain R residue  148 TYR
Chi-restraints excluded: chain R residue  161 SER
Chi-restraints excluded: chain R residue  181 VAL
Chi-restraints excluded: chain R residue  195 LEU
Chi-restraints excluded: chain R residue  232 LYS
Chi-restraints excluded: chain R residue  263 SER
Chi-restraints excluded: chain R residue  282 LEU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 101 optimal weight:    5.9990
   chunk 3 optimal weight:    0.9990
   chunk 22 optimal weight:    0.7980
   chunk 60 optimal weight:    3.9990
   chunk 85 optimal weight:    0.7980
   chunk 40 optimal weight:    0.1980
   chunk 38 optimal weight:    2.9990
   chunk 42 optimal weight:    0.8980
   chunk 4 optimal weight:    0.9980
   chunk 20 optimal weight:    0.0870
   chunk 93 optimal weight:    3.9990
   overall best weight:    0.5558

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

Flipped N/Q/H residues before XYZ refinement:
B 237 ASN
R 230 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4245 r_free = 0.4245 target = 0.192680 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3847 r_free = 0.3847 target = 0.154180 restraints weight = 8319.564|
|-----------------------------------------------------------------------------|
r_work (start): 0.3849 rms_B_bonded: 2.04
r_work: 0.3584 rms_B_bonded: 2.67 restraints_weight: 0.5000
r_work: 0.3454 rms_B_bonded: 4.23 restraints_weight: 0.2500
r_work (final): 0.3454
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7774
moved from start:          0.3502

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.039   8460  Z= 0.108
  Angle     :  0.496   8.541  11477  Z= 0.260
  Chirality :  0.041   0.136   1304
  Planarity :  0.004   0.039   1460
  Dihedral  :  4.133  19.477   1152
  Min Nonbonded Distance : 2.521

Molprobity Statistics.
  All-atom Clashscore : 4.79
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.46 %
    Favored  : 96.54 %
  Rotamer:
    Outliers :  3.44 %
    Allowed  : 14.19 %
    Favored  : 82.37 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.48 (0.26), residues: 1041
  helix:  2.80 (0.26), residues: 393
  sheet:  0.82 (0.32), residues: 218
  loop : -0.71 (0.30), residues: 430

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP B  82 
 HIS   0.005   0.001   HIS A 209 
 PHE   0.014   0.001   PHE B 199 
 TYR   0.011   0.001   TYR A 191 
 ARG   0.003   0.000   ARG B  19 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03623 (  408)
  hydrogen bonds       : angle       4.35268 ( 1137)
  SS BOND              : bond        0.00121 (    3)
  SS BOND              : angle       0.58705 (    6)
  covalent geometry    : bond        0.00235 ( 8457)
  covalent geometry    : angle       0.49591 (11471)

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

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

  2082 Ramachandran restraints generated.
    1041 Oldfield, 0 Emsley, 1041 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2082 Ramachandran restraints generated.
    1041 Oldfield, 0 Emsley, 1041 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  132 residues out of total 912 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 101
  time to evaluate  : 0.993 
Fit side-chains
REVERT: A   18 MET cc_start: 0.7622 (mtt) cc_final: 0.7231 (tmm)
REVERT: A   28 GLU cc_start: 0.6358 (OUTLIER) cc_final: 0.5547 (mt-10)
REVERT: A  132 ARG cc_start: 0.7365 (OUTLIER) cc_final: 0.6666 (tpt170)
REVERT: B   23 LYS cc_start: 0.7265 (tptm) cc_final: 0.7047 (ttpp)
REVERT: B   59 TYR cc_start: 0.8171 (OUTLIER) cc_final: 0.7387 (m-80)
REVERT: B  135 VAL cc_start: 0.6756 (t) cc_final: 0.6476 (p)
REVERT: B  217 MET cc_start: 0.8174 (OUTLIER) cc_final: 0.7971 (pp-130)
REVERT: L    8 MET cc_start: 0.7594 (mpp) cc_final: 0.7260 (mtm)
REVERT: R  140 ARG cc_start: 0.6437 (tpp80) cc_final: 0.5712 (tpt90)
REVERT: R  152 ARG cc_start: 0.7023 (mpt180) cc_final: 0.6821 (mpt180)
REVERT: R  195 LEU cc_start: 0.6687 (OUTLIER) cc_final: 0.6335 (tm)
REVERT: R  228 TYR cc_start: 0.7498 (t80) cc_final: 0.7277 (t80)
REVERT: R  232 LYS cc_start: 0.5870 (OUTLIER) cc_final: 0.5487 (mmtm)
REVERT: R  282 LEU cc_start: 0.6610 (OUTLIER) cc_final: 0.6168 (OUTLIER)
  outliers start: 31
  outliers final: 18
  residues processed: 121
  average time/residue: 1.1873
  time to fit residues: 153.2848
Evaluate side-chains
  122 residues out of total 912 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 98
  time to evaluate  : 0.895 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   15 ARG
Chi-restraints excluded: chain A residue   23 LEU
Chi-restraints excluded: chain A residue   28 GLU
Chi-restraints excluded: chain A residue   33 THR
Chi-restraints excluded: chain A residue  132 ARG
Chi-restraints excluded: chain A residue  136 THR
Chi-restraints excluded: chain A residue  171 THR
Chi-restraints excluded: chain A residue  195 LYS
Chi-restraints excluded: chain A residue  199 ASP
Chi-restraints excluded: chain A residue  232 LYS
Chi-restraints excluded: chain B residue   43 ILE
Chi-restraints excluded: chain B residue   59 TYR
Chi-restraints excluded: chain B residue  161 SER
Chi-restraints excluded: chain B residue  172 GLU
Chi-restraints excluded: chain B residue  217 MET
Chi-restraints excluded: chain B residue  294 CYS
Chi-restraints excluded: chain B residue  327 VAL
Chi-restraints excluded: chain G residue   42 GLU
Chi-restraints excluded: chain R residue  161 SER
Chi-restraints excluded: chain R residue  181 VAL
Chi-restraints excluded: chain R residue  195 LEU
Chi-restraints excluded: chain R residue  232 LYS
Chi-restraints excluded: chain R residue  263 SER
Chi-restraints excluded: chain R residue  282 LEU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 99 optimal weight:    7.9990
   chunk 78 optimal weight:    0.9990
   chunk 23 optimal weight:    2.9990
   chunk 36 optimal weight:    1.9990
   chunk 97 optimal weight:    0.9980
   chunk 0 optimal weight:    9.9990
   chunk 42 optimal weight:    3.9990
   chunk 12 optimal weight:    1.9990
   chunk 76 optimal weight:    0.7980
   chunk 31 optimal weight:    0.0270
   chunk 86 optimal weight:    4.9990
   overall best weight:    0.9642

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

Flipped N/Q/H residues before XYZ refinement:
B 237 ASN
R 230 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4225 r_free = 0.4225 target = 0.190610 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3833 r_free = 0.3833 target = 0.152975 restraints weight = 8280.879|
|-----------------------------------------------------------------------------|
r_work (start): 0.3835 rms_B_bonded: 2.04
r_work: 0.3567 rms_B_bonded: 2.48 restraints_weight: 0.5000
r_work: 0.3434 rms_B_bonded: 3.96 restraints_weight: 0.2500
r_work (final): 0.3434
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7786
moved from start:          0.3710

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.045   8460  Z= 0.139
  Angle     :  0.540   8.541  11477  Z= 0.284
  Chirality :  0.042   0.143   1304
  Planarity :  0.004   0.040   1460
  Dihedral  :  4.411  20.676   1152
  Min Nonbonded Distance : 2.504

Molprobity Statistics.
  All-atom Clashscore : 5.16
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.84 %
    Favored  : 96.16 %
  Rotamer:
    Outliers :  4.32 %
    Allowed  : 13.41 %
    Favored  : 82.26 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.23 (0.26), residues: 1041
  helix:  2.50 (0.25), residues: 399
  sheet:  0.75 (0.32), residues: 218
  loop : -0.83 (0.30), residues: 424

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.002   TRP B  82 
 HIS   0.005   0.001   HIS A 209 
 PHE   0.015   0.001   PHE B 199 
 TYR   0.015   0.001   TYR A 191 
 ARG   0.003   0.000   ARG A 188 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04046 (  408)
  hydrogen bonds       : angle       4.50457 ( 1137)
  SS BOND              : bond        0.00085 (    3)
  SS BOND              : angle       0.59673 (    6)
  covalent geometry    : bond        0.00311 ( 8457)
  covalent geometry    : angle       0.54037 (11471)

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

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

  2082 Ramachandran restraints generated.
    1041 Oldfield, 0 Emsley, 1041 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2082 Ramachandran restraints generated.
    1041 Oldfield, 0 Emsley, 1041 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  143 residues out of total 912 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 39
    poor density    : 104
  time to evaluate  : 0.836 
Fit side-chains
REVERT: A   18 MET cc_start: 0.7588 (mtt) cc_final: 0.7210 (tmm)
REVERT: A   21 LYS cc_start: 0.8048 (ttpp) cc_final: 0.7567 (ttmm)
REVERT: A   28 GLU cc_start: 0.6354 (OUTLIER) cc_final: 0.5560 (mt-10)
REVERT: A  132 ARG cc_start: 0.7323 (OUTLIER) cc_final: 0.6621 (tpt170)
REVERT: B   23 LYS cc_start: 0.7262 (tptm) cc_final: 0.7044 (ttpp)
REVERT: B  135 VAL cc_start: 0.6867 (t) cc_final: 0.6544 (p)
REVERT: B  217 MET cc_start: 0.8170 (OUTLIER) cc_final: 0.7950 (pp-130)
REVERT: G   47 GLU cc_start: 0.7834 (OUTLIER) cc_final: 0.7460 (pt0)
REVERT: L    8 MET cc_start: 0.7636 (mpp) cc_final: 0.7320 (mtm)
REVERT: R  140 ARG cc_start: 0.6425 (tpp80) cc_final: 0.5700 (tpt90)
REVERT: R  195 LEU cc_start: 0.6699 (OUTLIER) cc_final: 0.6293 (tm)
REVERT: R  228 TYR cc_start: 0.7505 (t80) cc_final: 0.7279 (t80)
REVERT: R  232 LYS cc_start: 0.5768 (OUTLIER) cc_final: 0.5396 (mmtm)
REVERT: R  282 LEU cc_start: 0.6593 (OUTLIER) cc_final: 0.6151 (tp)
  outliers start: 39
  outliers final: 18
  residues processed: 128
  average time/residue: 1.2117
  time to fit residues: 164.8201
Evaluate side-chains
  122 residues out of total 912 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 97
  time to evaluate  : 0.921 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   15 ARG
Chi-restraints excluded: chain A residue   23 LEU
Chi-restraints excluded: chain A residue   28 GLU
Chi-restraints excluded: chain A residue   33 THR
Chi-restraints excluded: chain A residue  112 SER
Chi-restraints excluded: chain A residue  132 ARG
Chi-restraints excluded: chain A residue  136 THR
Chi-restraints excluded: chain A residue  171 THR
Chi-restraints excluded: chain A residue  195 LYS
Chi-restraints excluded: chain A residue  199 ASP
Chi-restraints excluded: chain A residue  232 LYS
Chi-restraints excluded: chain B residue  161 SER
Chi-restraints excluded: chain B residue  172 GLU
Chi-restraints excluded: chain B residue  217 MET
Chi-restraints excluded: chain B residue  294 CYS
Chi-restraints excluded: chain B residue  327 VAL
Chi-restraints excluded: chain G residue   42 GLU
Chi-restraints excluded: chain G residue   47 GLU
Chi-restraints excluded: chain R residue  106 CYS
Chi-restraints excluded: chain R residue  161 SER
Chi-restraints excluded: chain R residue  181 VAL
Chi-restraints excluded: chain R residue  195 LEU
Chi-restraints excluded: chain R residue  232 LYS
Chi-restraints excluded: chain R residue  263 SER
Chi-restraints excluded: chain R residue  282 LEU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 72 optimal weight:   10.0000
   chunk 87 optimal weight:    0.7980
   chunk 83 optimal weight:    2.9990
   chunk 70 optimal weight:    3.9990
   chunk 24 optimal weight:    1.9990
   chunk 6 optimal weight:    1.9990
   chunk 80 optimal weight:    4.9990
   chunk 79 optimal weight:    0.9980
   chunk 60 optimal weight:    0.0570
   chunk 65 optimal weight:    1.9990
   chunk 18 optimal weight:    4.9990
   overall best weight:    1.1702

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

Flipped N/Q/H residues before XYZ refinement:
B 230 ASN
R 230 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4210 r_free = 0.4210 target = 0.189204 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.3758 r_free = 0.3758 target = 0.145543 restraints weight = 8403.383|
|-----------------------------------------------------------------------------|
r_work (start): 0.3733 rms_B_bonded: 1.84
r_work: 0.3581 rms_B_bonded: 2.22 restraints_weight: 0.5000
r_work: 0.3448 rms_B_bonded: 3.56 restraints_weight: 0.2500
r_work (final): 0.3448
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7790
moved from start:          0.3918

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.049   8460  Z= 0.153
  Angle     :  0.558   8.458  11477  Z= 0.296
  Chirality :  0.043   0.148   1304
  Planarity :  0.004   0.041   1460
  Dihedral  :  4.575  21.529   1152
  Min Nonbonded Distance : 2.509

Molprobity Statistics.
  All-atom Clashscore : 5.40
  Ramachandran Plot:
    Outliers :  0.10 %
    Allowed  :  3.84 %
    Favored  : 96.06 %
  Rotamer:
    Outliers :  3.99 %
    Allowed  : 14.30 %
    Favored  : 81.71 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.09 (0.26), residues: 1041
  helix:  2.33 (0.25), residues: 399
  sheet:  0.64 (0.33), residues: 220
  loop : -0.83 (0.30), residues: 422

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.002   TRP R 169 
 HIS   0.006   0.001   HIS A 209 
 PHE   0.016   0.002   PHE B 199 
 TYR   0.026   0.002   TYR R 148 
 ARG   0.003   0.000   ARG A 208 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04238 (  408)
  hydrogen bonds       : angle       4.61333 ( 1137)
  SS BOND              : bond        0.00112 (    3)
  SS BOND              : angle       0.69670 (    6)
  covalent geometry    : bond        0.00348 ( 8457)
  covalent geometry    : angle       0.55766 (11471)

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

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

  2082 Ramachandran restraints generated.
    1041 Oldfield, 0 Emsley, 1041 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2082 Ramachandran restraints generated.
    1041 Oldfield, 0 Emsley, 1041 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  135 residues out of total 912 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 99
  time to evaluate  : 0.880 
Fit side-chains
REVERT: A   18 MET cc_start: 0.7517 (OUTLIER) cc_final: 0.7236 (tmm)
REVERT: A   21 LYS cc_start: 0.8056 (ttpp) cc_final: 0.7555 (ttmm)
REVERT: A   28 GLU cc_start: 0.6361 (OUTLIER) cc_final: 0.5549 (mt-10)
REVERT: A  132 ARG cc_start: 0.7292 (OUTLIER) cc_final: 0.6646 (tpt170)
REVERT: A  208 ARG cc_start: 0.5717 (tpt90) cc_final: 0.5487 (tpt90)
REVERT: B   23 LYS cc_start: 0.7266 (tptm) cc_final: 0.7052 (ttpp)
REVERT: B  135 VAL cc_start: 0.6874 (t) cc_final: 0.6573 (p)
REVERT: B  217 MET cc_start: 0.8192 (OUTLIER) cc_final: 0.7876 (pmt)
REVERT: B  304 ARG cc_start: 0.8150 (OUTLIER) cc_final: 0.7842 (mtm180)
REVERT: G   47 GLU cc_start: 0.7814 (OUTLIER) cc_final: 0.7440 (pt0)
REVERT: L    8 MET cc_start: 0.7630 (mpp) cc_final: 0.7397 (mtm)
REVERT: N   79 LEU cc_start: 0.4515 (tp) cc_final: 0.4294 (tp)
REVERT: R  140 ARG cc_start: 0.6374 (tpp80) cc_final: 0.5691 (tpt90)
REVERT: R  195 LEU cc_start: 0.6683 (OUTLIER) cc_final: 0.6274 (tm)
REVERT: R  212 LEU cc_start: 0.7963 (OUTLIER) cc_final: 0.7690 (mp)
REVERT: R  228 TYR cc_start: 0.7521 (t80) cc_final: 0.7256 (t80)
REVERT: R  232 LYS cc_start: 0.5844 (OUTLIER) cc_final: 0.5491 (mmtm)
REVERT: R  282 LEU cc_start: 0.6588 (OUTLIER) cc_final: 0.6172 (tp)
  outliers start: 36
  outliers final: 19
  residues processed: 124
  average time/residue: 1.2374
  time to fit residues: 163.7775
Evaluate side-chains
  124 residues out of total 912 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 95
  time to evaluate  : 0.866 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   15 ARG
Chi-restraints excluded: chain A residue   18 MET
Chi-restraints excluded: chain A residue   23 LEU
Chi-restraints excluded: chain A residue   28 GLU
Chi-restraints excluded: chain A residue   33 THR
Chi-restraints excluded: chain A residue  112 SER
Chi-restraints excluded: chain A residue  132 ARG
Chi-restraints excluded: chain A residue  136 THR
Chi-restraints excluded: chain A residue  171 THR
Chi-restraints excluded: chain A residue  195 LYS
Chi-restraints excluded: chain A residue  199 ASP
Chi-restraints excluded: chain A residue  232 LYS
Chi-restraints excluded: chain B residue   43 ILE
Chi-restraints excluded: chain B residue  161 SER
Chi-restraints excluded: chain B residue  172 GLU
Chi-restraints excluded: chain B residue  217 MET
Chi-restraints excluded: chain B residue  294 CYS
Chi-restraints excluded: chain B residue  304 ARG
Chi-restraints excluded: chain B residue  327 VAL
Chi-restraints excluded: chain G residue   42 GLU
Chi-restraints excluded: chain G residue   47 GLU
Chi-restraints excluded: chain R residue  106 CYS
Chi-restraints excluded: chain R residue  161 SER
Chi-restraints excluded: chain R residue  181 VAL
Chi-restraints excluded: chain R residue  195 LEU
Chi-restraints excluded: chain R residue  212 LEU
Chi-restraints excluded: chain R residue  232 LYS
Chi-restraints excluded: chain R residue  263 SER
Chi-restraints excluded: chain R residue  282 LEU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 55 optimal weight:    3.9990
   chunk 72 optimal weight:    0.0070
   chunk 74 optimal weight:    8.9990
   chunk 30 optimal weight:    1.9990
   chunk 86 optimal weight:    0.9980
   chunk 7 optimal weight:    0.8980
   chunk 10 optimal weight:    1.9990
   chunk 36 optimal weight:    0.7980
   chunk 33 optimal weight:    0.9990
   chunk 53 optimal weight:    2.9990
   chunk 73 optimal weight:    0.2980
   overall best weight:    0.5998

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

Flipped N/Q/H residues before XYZ refinement:
B 230 ASN
R 230 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4228 r_free = 0.4228 target = 0.191071 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3849 r_free = 0.3849 target = 0.154101 restraints weight = 8391.183|
|-----------------------------------------------------------------------------|
r_work (start): 0.3849 rms_B_bonded: 1.95
r_work: 0.3570 rms_B_bonded: 2.57 restraints_weight: 0.5000
r_work: 0.3442 rms_B_bonded: 4.07 restraints_weight: 0.2500
r_work (final): 0.3442
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7786
moved from start:          0.3858

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.038   8460  Z= 0.110
  Angle     :  0.505   8.225  11477  Z= 0.266
  Chirality :  0.041   0.143   1304
  Planarity :  0.004   0.039   1460
  Dihedral  :  4.270  19.161   1152
  Min Nonbonded Distance : 2.531

Molprobity Statistics.
  All-atom Clashscore : 5.03
  Ramachandran Plot:
    Outliers :  0.10 %
    Allowed  :  3.55 %
    Favored  : 96.35 %
  Rotamer:
    Outliers :  3.10 %
    Allowed  : 15.08 %
    Favored  : 81.82 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.35 (0.26), residues: 1041
  helix:  2.67 (0.25), residues: 393
  sheet:  0.74 (0.32), residues: 218
  loop : -0.74 (0.30), residues: 430

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.001   TRP B  82 
 HIS   0.005   0.001   HIS A 209 
 PHE   0.015   0.001   PHE B 199 
 TYR   0.025   0.001   TYR R 148 
 ARG   0.003   0.000   ARG B  19 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03686 (  408)
  hydrogen bonds       : angle       4.39685 ( 1137)
  SS BOND              : bond        0.00137 (    3)
  SS BOND              : angle       0.62567 (    6)
  covalent geometry    : bond        0.00240 ( 8457)
  covalent geometry    : angle       0.50501 (11471)

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

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

  2082 Ramachandran restraints generated.
    1041 Oldfield, 0 Emsley, 1041 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2082 Ramachandran restraints generated.
    1041 Oldfield, 0 Emsley, 1041 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  128 residues out of total 912 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 100
  time to evaluate  : 0.846 
Fit side-chains
REVERT: A   18 MET cc_start: 0.7583 (mtt) cc_final: 0.7245 (tmt)
REVERT: A   28 GLU cc_start: 0.6377 (OUTLIER) cc_final: 0.5629 (mt-10)
REVERT: A  132 ARG cc_start: 0.7336 (OUTLIER) cc_final: 0.6663 (tpt170)
REVERT: A  208 ARG cc_start: 0.5765 (tpt90) cc_final: 0.5505 (tpt90)
REVERT: B   23 LYS cc_start: 0.7258 (tptm) cc_final: 0.7048 (ttpp)
REVERT: B  135 VAL cc_start: 0.6924 (t) cc_final: 0.6621 (p)
REVERT: B  217 MET cc_start: 0.8211 (OUTLIER) cc_final: 0.7995 (pp-130)
REVERT: G   47 GLU cc_start: 0.7808 (OUTLIER) cc_final: 0.7465 (pt0)
REVERT: L    8 MET cc_start: 0.7593 (mpp) cc_final: 0.7388 (mtm)
REVERT: R  140 ARG cc_start: 0.6386 (tpp80) cc_final: 0.5727 (tpt90)
REVERT: R  228 TYR cc_start: 0.7548 (t80) cc_final: 0.7183 (t80)
REVERT: R  232 LYS cc_start: 0.5855 (OUTLIER) cc_final: 0.5482 (mmtm)
REVERT: R  282 LEU cc_start: 0.6630 (OUTLIER) cc_final: 0.6322 (tt)
  outliers start: 28
  outliers final: 18
  residues processed: 120
  average time/residue: 1.2096
  time to fit residues: 154.4076
Evaluate side-chains
  122 residues out of total 912 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 98
  time to evaluate  : 0.882 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   15 ARG
Chi-restraints excluded: chain A residue   23 LEU
Chi-restraints excluded: chain A residue   28 GLU
Chi-restraints excluded: chain A residue   33 THR
Chi-restraints excluded: chain A residue  132 ARG
Chi-restraints excluded: chain A residue  136 THR
Chi-restraints excluded: chain A residue  171 THR
Chi-restraints excluded: chain A residue  195 LYS
Chi-restraints excluded: chain A residue  199 ASP
Chi-restraints excluded: chain A residue  232 LYS
Chi-restraints excluded: chain B residue  161 SER
Chi-restraints excluded: chain B residue  172 GLU
Chi-restraints excluded: chain B residue  217 MET
Chi-restraints excluded: chain B residue  262 MET
Chi-restraints excluded: chain B residue  294 CYS
Chi-restraints excluded: chain B residue  327 VAL
Chi-restraints excluded: chain G residue   47 GLU
Chi-restraints excluded: chain R residue  106 CYS
Chi-restraints excluded: chain R residue  161 SER
Chi-restraints excluded: chain R residue  181 VAL
Chi-restraints excluded: chain R residue  225 TRP
Chi-restraints excluded: chain R residue  232 LYS
Chi-restraints excluded: chain R residue  263 SER
Chi-restraints excluded: chain R residue  282 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 57 optimal weight:    5.9990
   chunk 48 optimal weight:    0.9980
   chunk 77 optimal weight:    0.3980
   chunk 62 optimal weight:   10.0000
   chunk 70 optimal weight:    7.9990
   chunk 43 optimal weight:    4.9990
   chunk 20 optimal weight:    1.9990
   chunk 99 optimal weight:    4.9990
   chunk 37 optimal weight:    3.9990
   chunk 11 optimal weight:    0.8980
   chunk 10 optimal weight:    0.9990
   overall best weight:    1.0584

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

Flipped N/Q/H residues before XYZ refinement:
R 230 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4213 r_free = 0.4213 target = 0.189570 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 53)----------------|
| r_work = 0.3774 r_free = 0.3774 target = 0.146698 restraints weight = 8297.851|
|-----------------------------------------------------------------------------|
r_work (start): 0.3744 rms_B_bonded: 1.72
r_work: 0.3586 rms_B_bonded: 2.22 restraints_weight: 0.5000
r_work: 0.3453 rms_B_bonded: 3.55 restraints_weight: 0.2500
r_work (final): 0.3453
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7782
moved from start:          0.3983

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.045   8460  Z= 0.142
  Angle     :  0.545   8.228  11477  Z= 0.288
  Chirality :  0.043   0.150   1304
  Planarity :  0.004   0.040   1460
  Dihedral  :  4.494  20.454   1152
  Min Nonbonded Distance : 2.518

Molprobity Statistics.
  All-atom Clashscore : 5.09
  Ramachandran Plot:
    Outliers :  0.10 %
    Allowed  :  3.94 %
    Favored  : 95.97 %
  Rotamer:
    Outliers :  3.33 %
    Allowed  : 14.97 %
    Favored  : 81.71 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.15 (0.26), residues: 1041
  helix:  2.40 (0.25), residues: 399
  sheet:  0.70 (0.33), residues: 218
  loop : -0.84 (0.30), residues: 424

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.002   TRP B  82 
 HIS   0.005   0.001   HIS A 209 
 PHE   0.015   0.001   PHE B 199 
 TYR   0.024   0.002   TYR R 148 
 ARG   0.003   0.000   ARG A 208 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04076 (  408)
  hydrogen bonds       : angle       4.51442 ( 1137)
  SS BOND              : bond        0.00126 (    3)
  SS BOND              : angle       0.70604 (    6)
  covalent geometry    : bond        0.00323 ( 8457)
  covalent geometry    : angle       0.54491 (11471)

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

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

  2082 Ramachandran restraints generated.
    1041 Oldfield, 0 Emsley, 1041 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2082 Ramachandran restraints generated.
    1041 Oldfield, 0 Emsley, 1041 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  126 residues out of total 912 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 96
  time to evaluate  : 0.861 
Fit side-chains
REVERT: A   18 MET cc_start: 0.7504 (mtt) cc_final: 0.7191 (tmm)
REVERT: A   21 LYS cc_start: 0.8102 (ttpp) cc_final: 0.7576 (ttmm)
REVERT: A   28 GLU cc_start: 0.6359 (OUTLIER) cc_final: 0.5580 (mt-10)
REVERT: A  132 ARG cc_start: 0.7286 (OUTLIER) cc_final: 0.6655 (tpt170)
REVERT: A  208 ARG cc_start: 0.5754 (tpt90) cc_final: 0.5490 (tpt90)
REVERT: B   23 LYS cc_start: 0.7252 (tptm) cc_final: 0.7050 (ttpp)
REVERT: B   59 TYR cc_start: 0.8140 (OUTLIER) cc_final: 0.7356 (m-80)
REVERT: B  135 VAL cc_start: 0.6963 (t) cc_final: 0.6662 (p)
REVERT: B  217 MET cc_start: 0.8206 (OUTLIER) cc_final: 0.7983 (pp-130)
REVERT: G   47 GLU cc_start: 0.7806 (OUTLIER) cc_final: 0.7460 (pt0)
REVERT: R  140 ARG cc_start: 0.6415 (tpp80) cc_final: 0.5725 (tpt90)
REVERT: R  195 LEU cc_start: 0.6707 (OUTLIER) cc_final: 0.6317 (tm)
REVERT: R  228 TYR cc_start: 0.7558 (t80) cc_final: 0.7251 (t80)
REVERT: R  232 LYS cc_start: 0.5879 (OUTLIER) cc_final: 0.5516 (mmtm)
REVERT: R  282 LEU cc_start: 0.6658 (OUTLIER) cc_final: 0.6318 (tt)
  outliers start: 30
  outliers final: 19
  residues processed: 118
  average time/residue: 1.2462
  time to fit residues: 156.0162
Evaluate side-chains
  122 residues out of total 912 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 95
  time to evaluate  : 0.992 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   15 ARG
Chi-restraints excluded: chain A residue   23 LEU
Chi-restraints excluded: chain A residue   28 GLU
Chi-restraints excluded: chain A residue   33 THR
Chi-restraints excluded: chain A residue  112 SER
Chi-restraints excluded: chain A residue  132 ARG
Chi-restraints excluded: chain A residue  136 THR
Chi-restraints excluded: chain A residue  171 THR
Chi-restraints excluded: chain A residue  195 LYS
Chi-restraints excluded: chain A residue  199 ASP
Chi-restraints excluded: chain B residue   43 ILE
Chi-restraints excluded: chain B residue   59 TYR
Chi-restraints excluded: chain B residue  161 SER
Chi-restraints excluded: chain B residue  172 GLU
Chi-restraints excluded: chain B residue  217 MET
Chi-restraints excluded: chain B residue  262 MET
Chi-restraints excluded: chain B residue  294 CYS
Chi-restraints excluded: chain B residue  327 VAL
Chi-restraints excluded: chain G residue   47 GLU
Chi-restraints excluded: chain R residue  106 CYS
Chi-restraints excluded: chain R residue  161 SER
Chi-restraints excluded: chain R residue  181 VAL
Chi-restraints excluded: chain R residue  195 LEU
Chi-restraints excluded: chain R residue  225 TRP
Chi-restraints excluded: chain R residue  232 LYS
Chi-restraints excluded: chain R residue  263 SER
Chi-restraints excluded: chain R residue  282 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 52 optimal weight:    0.6980
   chunk 20 optimal weight:    1.9990
   chunk 65 optimal weight:    0.9990
   chunk 80 optimal weight:    3.9990
   chunk 97 optimal weight:    0.0980
   chunk 11 optimal weight:    0.6980
   chunk 59 optimal weight:    3.9990
   chunk 57 optimal weight:    9.9990
   chunk 43 optimal weight:    2.9990
   chunk 90 optimal weight:    3.9990
   chunk 35 optimal weight:    0.0970
   overall best weight:    0.5180

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

Flipped N/Q/H residues before XYZ refinement:
R 230 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4232 r_free = 0.4232 target = 0.191506 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.3802 r_free = 0.3802 target = 0.149040 restraints weight = 8450.310|
|-----------------------------------------------------------------------------|
r_work (start): 0.3772 rms_B_bonded: 1.69
r_work: 0.3616 rms_B_bonded: 2.24 restraints_weight: 0.5000
r_work: 0.3487 rms_B_bonded: 3.57 restraints_weight: 0.2500
r_work (final): 0.3487
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7747
moved from start:          0.3919

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.034   8460  Z= 0.106
  Angle     :  0.503   8.196  11477  Z= 0.264
  Chirality :  0.041   0.143   1304
  Planarity :  0.004   0.039   1460
  Dihedral  :  4.221  18.860   1152
  Min Nonbonded Distance : 2.540

Molprobity Statistics.
  All-atom Clashscore : 5.09
  Ramachandran Plot:
    Outliers :  0.10 %
    Allowed  :  3.94 %
    Favored  : 95.97 %
  Rotamer:
    Outliers :  2.88 %
    Allowed  : 15.63 %
    Favored  : 81.49 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.41 (0.26), residues: 1041
  helix:  2.71 (0.25), residues: 393
  sheet:  0.77 (0.33), residues: 223
  loop : -0.71 (0.31), residues: 425

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.001   TRP B  82 
 HIS   0.005   0.001   HIS A 209 
 PHE   0.015   0.001   PHE B 199 
 TYR   0.024   0.001   TYR R 148 
 ARG   0.004   0.000   ARG B  19 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03584 (  408)
  hydrogen bonds       : angle       4.33565 ( 1137)
  SS BOND              : bond        0.00149 (    3)
  SS BOND              : angle       0.64606 (    6)
  covalent geometry    : bond        0.00227 ( 8457)
  covalent geometry    : angle       0.50327 (11471)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 8102.33 seconds
wall clock time: 139 minutes 45.84 seconds (8385.84 seconds total)