Starting phenix.real_space_refine
on Thu Sep 18 13:34:44 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9u4y_63858/09_2025/9u4y_63858.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9u4y_63858/09_2025/9u4y_63858.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.67
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/9u4y_63858/09_2025/9u4y_63858.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9u4y_63858/09_2025/9u4y_63858.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/9u4y_63858/09_2025/9u4y_63858.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9u4y_63858/09_2025/9u4y_63858.map"
  }
  resolution = 2.67
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=  -0.000 sd=   0.075
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 5
    Type Number    sf(0)   Gaussians
     S      58      5.16       5
     C    5590      2.51       5
     N    1498      2.21       5
     O    1619      1.98       5
     H    8578      0.53       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 5 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 17343
  Number of models: 1
  Model: ""
    Number of chains: 7
    Chain: "B"
      Number of atoms: 5098
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 338, 5098
          Classifications: {'peptide': 338}
          Link IDs: {'PTRANS': 5, 'TRANS': 332}
          Unresolved non-hydrogen bonds: 3
          Unresolved non-hydrogen angles: 3
          Unresolved non-hydrogen dihedrals: 3
    Chain: "G"
      Number of atoms: 840
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 57, 840
          Classifications: {'peptide': 57}
          Link IDs: {'PTRANS': 4, 'TRANS': 52}
          Unresolved non-hydrogen bonds: 17
          Unresolved non-hydrogen angles: 20
          Unresolved non-hydrogen dihedrals: 14
          Planarities with less than four sites: {'GLU:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 1}
          Unresolved non-hydrogen planarities: 10
    Chain: "C"
      Number of atoms: 90
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 10, 90
          Classifications: {'peptide': 10}
          Link IDs: {'PTRANS': 1, 'TRANS': 8}
          Unresolved non-hydrogen bonds: 1
          Unresolved non-hydrogen angles: 2
          Planarities with less than four sites: {'PCA:plan-2': 1}
          Unresolved non-hydrogen planarities: 1
    Chain: "C"
      Number of atoms: 1
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 1
          Unusual residues: {'NH2': 1}
          Classifications: {'undetermined': 1}
    Chain: "A"
      Number of atoms: 3458
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 217, 3458
          Classifications: {'peptide': 217}
          Incomplete info: {'truncation_to_alanine': 2}
          Link IDs: {'PTRANS': 6, 'TRANS': 210}
          Chain breaks: 2
          Unresolved non-hydrogen bonds: 31
          Unresolved non-hydrogen angles: 36
          Unresolved non-hydrogen dihedrals: 26
          Unresolved non-hydrogen chiralities: 1
          Planarities with less than four sites: {'ARG:plan': 2, 'GLU:plan': 2}
          Unresolved non-hydrogen planarities: 18
    Chain: "S"
      Number of atoms: 3507
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 232, 3507
          Classifications: {'peptide': 232}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 10, 'TRANS': 221}
          Chain breaks: 1
    Chain: "R"
      Number of atoms: 4349
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 264, 4349
          Classifications: {'peptide': 264}
          Link IDs: {'PTRANS': 10, 'TRANS': 253}
          Chain breaks: 2
          Unresolved non-hydrogen bonds: 7
          Unresolved non-hydrogen angles: 9
          Unresolved non-hydrogen dihedrals: 5
          Planarities with less than four sites: {'GLN:plan1': 1, 'ASN:plan1': 1}
          Unresolved non-hydrogen planarities: 7
  Time building chain proxies: 2.69, per 1000 atoms: 0.16
  Number of scatterers: 17343
  At special positions: 0
  Unit cell: (97.09, 118.99, 128.48, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S      58     16.00
     O    1619      8.00
     N    1498      7.00
     C    5590      6.00
     H    8578      1.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=2, symmetry=0
    Simple disulfide: pdb=" SG  CYS S 159 " - pdb=" SG  CYS S 229 " distance=2.72
    Simple disulfide: pdb=" SG  CYS R 126 " - pdb=" SG  CYS R 204 " distance=2.03

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=1, symmetry=0
  Number of additional bonds: simple=1, symmetry=0
  Coordination:
  Other bonds:
  Time building additional restraints: 1.34
  Conformation dependent library (CDL) restraints added in 320.9 milliseconds
  
  Enol-peptide restraints added in 476.8 nanoseconds
  

  2190 Ramachandran restraints generated.
    1095 Oldfield, 0 Emsley, 1095 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2100

  Finding SS restraints...
    Secondary structure from input PDB file:
      29 helices and 13 sheets defined
      38.3% alpha, 22.7% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.40
  Creating SS restraints...
    Processing helix  chain 'B' and resid 8 through 31
    Processing helix  chain 'B' and resid 34 through 39
    Processing helix  chain 'G' and resid 7 through 24
    Processing helix  chain 'G' and resid 29 through 44
    Processing helix  chain 'A' and resid 9 through 31
      removed outlier: 4.247A  pdb=" N   ALA A  13 " --> pdb=" O   ASP A   9 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 46 through 50
      removed outlier: 3.786A  pdb=" N   VAL A  50 " --> pdb=" O   SER A  47 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 206 through 211
      removed outlier: 4.265A  pdb=" N   GLN A 211 " --> pdb=" O   ARG A 207 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 212 through 214
      No H-bonds generated for 'chain 'A' and resid 212 through 214'
    Processing helix  chain 'A' and resid 230 through 243
    Processing helix  chain 'A' and resid 244 through 248
      removed outlier: 3.678A  pdb=" N   ARG A 248 " --> pdb=" O   ARG A 245 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 258 through 266
    Processing helix  chain 'A' and resid 296 through 316
    Processing helix  chain 'A' and resid 335 through 356
    Processing helix  chain 'S' and resid 27 through 31
    Processing helix  chain 'S' and resid 52 through 55
      removed outlier: 4.228A  pdb=" N   GLY S  55 " --> pdb=" O   SER S  52 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'S' and resid 52 through 55'
    Processing helix  chain 'S' and resid 86 through 90
    Processing helix  chain 'S' and resid 220 through 224
      removed outlier: 3.638A  pdb=" N   VAL S 224 " --> pdb=" O   ALA S 221 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 51 through 82
      removed outlier: 3.711A  pdb=" N   ALA R  58 " --> pdb=" O   LYS R  54 " (cutoff:3.500A)
      removed outlier: 3.895A  pdb=" N   THR R  79 " --> pdb=" O   LEU R  75 " (cutoff:3.500A)
      removed outlier: 4.024A  pdb=" N   TYR R  80 " --> pdb=" O   TRP R  76 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 86 through 116
      removed outlier: 3.862A  pdb=" N   MET R 107 " --> pdb=" O   THR R 103 " (cutoff:3.500A)
      Proline residue:  R 108  - end of helix
    Processing helix  chain 'R' and resid 122 through 157
    Processing helix  chain 'R' and resid 158 through 162
      removed outlier: 4.378A  pdb=" N   GLY R 162 " --> pdb=" O   LEU R 159 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 163 through 182
    Processing helix  chain 'R' and resid 184 through 190
      removed outlier: 3.984A  pdb=" N   PHE R 188 " --> pdb=" O   ILE R 184 " (cutoff:3.500A)
      removed outlier: 3.512A  pdb=" N   PHE R 190 " --> pdb=" O   GLN R 186 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 212 through 228
      removed outlier: 3.603A  pdb=" N   GLU R 216 " --> pdb=" O   ALA R 212 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 228 through 248
    Processing helix  chain 'R' and resid 269 through 304
      Proline residue:  R 293  - end of helix
    Processing helix  chain 'R' and resid 305 through 310
      removed outlier: 3.882A  pdb=" N   THR R 309 " --> pdb=" O   PRO R 305 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 314 through 322
    Processing helix  chain 'R' and resid 322 through 338
      removed outlier: 4.441A  pdb=" N   LEU R 326 " --> pdb=" O   PHE R 322 " (cutoff:3.500A)
      removed outlier: 3.726A  pdb=" N   ASN R 328 " --> pdb=" O   PHE R 324 " (cutoff:3.500A)
      removed outlier: 4.189A  pdb=" N   THR R 329 " --> pdb=" O   GLY R 325 " (cutoff:3.500A)
      removed outlier: 3.637A  pdb=" N   CYS R 330 " --> pdb=" O   LEU R 326 " (cutoff:3.500A)
      Proline residue:  R 333  - end of helix
    Processing sheet with id=AA1, first strand: chain 'B' and resid 51 through 56
      removed outlier: 5.630A  pdb=" N   THR B  52 " --> pdb=" O   ASN B 345 " (cutoff:3.500A)
      removed outlier: 7.007A  pdb=" N   ASN B 345 " --> pdb=" O   THR B  52 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'B' and resid 63 through 68
      removed outlier: 6.849A  pdb=" N   ALA B  78 " --> pdb=" O   TYR B  64 " (cutoff:3.500A)
      removed outlier: 4.349A  pdb=" N   MET B  66 " --> pdb=" O   VAL B  76 " (cutoff:3.500A)
      removed outlier: 6.741A  pdb=" N   VAL B  76 " --> pdb=" O   MET B  66 " (cutoff:3.500A)
      removed outlier: 5.084A  pdb=" N   TRP B  68 " --> pdb=" O   LEU B  74 " (cutoff:3.500A)
      removed outlier: 7.308A  pdb=" N   LEU B  74 " --> pdb=" O   TRP B  68 " (cutoff:3.500A)
      removed outlier: 3.668A  pdb=" N   LYS B  83 " --> pdb=" O   SER B  79 " (cutoff:3.500A)
      removed outlier: 6.323A  pdb=" N   ASP B  88 " --> pdb=" O   LYS B  94 " (cutoff:3.500A)
      removed outlier: 5.961A  pdb=" N   LYS B  94 " --> pdb=" O   ASP B  88 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'B' and resid 105 through 110
      removed outlier: 6.970A  pdb=" N   GLY B 120 " --> pdb=" O   MET B 106 " (cutoff:3.500A)
      removed outlier: 4.433A  pdb=" N   CYS B 108 " --> pdb=" O   ALA B 118 " (cutoff:3.500A)
      removed outlier: 6.647A  pdb=" N   ALA B 118 " --> pdb=" O   CYS B 108 " (cutoff:3.500A)
      removed outlier: 5.302A  pdb=" N   TYR B 110 " --> pdb=" O   TYR B 116 " (cutoff:3.500A)
      removed outlier: 7.274A  pdb=" N   TYR B 116 " --> pdb=" O   TYR B 110 " (cutoff:3.500A)
      removed outlier: 6.107A  pdb=" N   ASN B 130 " --> pdb=" O   VAL B 140 " (cutoff:3.500A)
      removed outlier: 5.890A  pdb=" N   VAL B 140 " --> pdb=" O   ASN B 130 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'B' and resid 151 through 158
      removed outlier: 3.531A  pdb=" N   CYS B 153 " --> pdb=" O   SER B 165 " (cutoff:3.500A)
      removed outlier: 6.598A  pdb=" N   GLN B 161 " --> pdb=" O   LEU B 157 " (cutoff:3.500A)
      removed outlier: 3.741A  pdb=" N   ILE B 162 " --> pdb=" O   TRP B 174 " (cutoff:3.500A)
      removed outlier: 6.566A  pdb=" N   ASP B 175 " --> pdb=" O   GLN B 181 " (cutoff:3.500A)
      removed outlier: 6.140A  pdb=" N   GLN B 181 " --> pdb=" O   ASP B 175 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'B' and resid 192 through 197
      removed outlier: 6.531A  pdb=" N   ALA B 213 " --> pdb=" O   THR B 226 " (cutoff:3.500A)
      removed outlier: 4.533A  pdb=" N   THR B 226 " --> pdb=" O   ALA B 213 " (cutoff:3.500A)
      removed outlier: 6.700A  pdb=" N   LEU B 215 " --> pdb=" O   ARG B 224 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'B' and resid 234 through 239
      removed outlier: 4.078A  pdb=" N   THR B 254 " --> pdb=" O   SER B 250 " (cutoff:3.500A)
      removed outlier: 6.657A  pdb=" N   CYS B 255 " --> pdb=" O   THR B 268 " (cutoff:3.500A)
      removed outlier: 4.676A  pdb=" N   THR B 268 " --> pdb=" O   CYS B 255 " (cutoff:3.500A)
      removed outlier: 6.679A  pdb=" N   LEU B 257 " --> pdb=" O   LEU B 266 " (cutoff:3.500A)
      removed outlier: 3.540A  pdb=" N   GLN B 264 " --> pdb=" O   ASP B 259 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'B' and resid 278 through 283
      removed outlier: 3.623A  pdb=" N   SER B 280 " --> pdb=" O   GLY B 293 " (cutoff:3.500A)
      removed outlier: 6.220A  pdb=" N   ASP B 303 " --> pdb=" O   ARG B 309 " (cutoff:3.500A)
      removed outlier: 6.437A  pdb=" N   ARG B 309 " --> pdb=" O   ASP B 303 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'A' and resid 183 through 189
      removed outlier: 3.653A  pdb=" N   ALA A 218 " --> pdb=" O   ARG A  35 " (cutoff:3.500A)
      removed outlier: 3.563A  pdb=" N   VAL A 222 " --> pdb=" O   LEU A  39 " (cutoff:3.500A)
      removed outlier: 6.269A  pdb=" N   ILE A 219 " --> pdb=" O   ILE A 253 " (cutoff:3.500A)
      removed outlier: 7.394A  pdb=" N   PHE A 255 " --> pdb=" O   ILE A 219 " (cutoff:3.500A)
      removed outlier: 6.621A  pdb=" N   PHE A 221 " --> pdb=" O   PHE A 255 " (cutoff:3.500A)
      removed outlier: 6.863A  pdb=" N   ASN A 257 " --> pdb=" O   PHE A 221 " (cutoff:3.500A)
      removed outlier: 6.361A  pdb=" N   VAL A 223 " --> pdb=" O   ASN A 257 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'S' and resid 2 through 6
    Processing sheet with id=AB1, first strand: chain 'S' and resid 9 through 11
      removed outlier: 5.938A  pdb=" N   GLY S   9 " --> pdb=" O   THR S 117 " (cutoff:3.500A)
      removed outlier: 6.016A  pdb=" N   ARG S  37 " --> pdb=" O   TRP S  46 " (cutoff:3.500A)
      removed outlier: 5.205A  pdb=" N   TRP S  46 " --> pdb=" O   ARG S  37 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'S' and resid 140 through 142
    Processing sheet with id=AB3, first strand: chain 'S' and resid 146 through 148
      removed outlier: 3.912A  pdb=" N   GLU S 246 " --> pdb=" O   VAL S 147 " (cutoff:3.500A)
      removed outlier: 3.670A  pdb=" N   ILE S 189 " --> pdb=" O   TRP S 176 " (cutoff:3.500A)
      removed outlier: 6.114A  pdb=" N   LEU S 178 " --> pdb=" O   LEU S 187 " (cutoff:3.500A)
      removed outlier: 5.631A  pdb=" N   LEU S 187 " --> pdb=" O   LEU S 178 " (cutoff:3.500A)
    Processing sheet with id=AB4, first strand: chain 'R' and resid 191 through 192

    447 hydrogen bonds defined for protein.
    1263 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 3.47

  Time building geometry restraints manager: 1.77 seconds

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

  Histogram of bond lengths:
        0.82 -     1.02: 8543
        1.02 -     1.22: 37
        1.22 -     1.41: 3724
        1.41 -     1.61: 5145
        1.61 -     1.81: 84
  Bond restraints: 17533
  Sorted by residual:
  bond pdb=" N   PCA C   1 "
       pdb=" H   PCA C   1 "
    ideal  model  delta    sigma   weight residual
    0.860  1.010 -0.150 2.00e-02 2.50e+03 5.60e+01
  bond pdb=" CA  LEU C   7 "
       pdb=" C   LEU C   7 "
    ideal  model  delta    sigma   weight residual
    1.522  1.440  0.082 1.31e-02 5.83e+03 3.91e+01
  bond pdb=" CA  PCA C   1 "
       pdb=" HA  PCA C   1 "
    ideal  model  delta    sigma   weight residual
    0.970  1.093 -0.123 2.00e-02 2.50e+03 3.76e+01
  bond pdb=" CG  PCA C   1 "
       pdb=" HG2 PCA C   1 "
    ideal  model  delta    sigma   weight residual
    0.970  1.092 -0.122 2.00e-02 2.50e+03 3.74e+01
  bond pdb=" CG  PCA C   1 "
       pdb=" HG3 PCA C   1 "
    ideal  model  delta    sigma   weight residual
    0.970  1.090 -0.120 2.00e-02 2.50e+03 3.63e+01
  ... (remaining 17528 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     6.67: 31503
        6.67 -    13.35: 11
       13.35 -    20.02: 1
       20.02 -    26.69: 0
       26.69 -    33.37: 3
  Bond angle restraints: 31518
  Sorted by residual:
  angle pdb=" N   SER A 271 "
        pdb=" CA  SER A 271 "
        pdb=" HA  SER A 271 "
      ideal   model   delta    sigma   weight residual
     110.00   76.63   33.37 3.00e+00 1.11e-01 1.24e+02
  angle pdb=" N   GLU A 205 "
        pdb=" CA  GLU A 205 "
        pdb=" C   GLU A 205 "
      ideal   model   delta    sigma   weight residual
     111.71   99.13   12.58 1.15e+00 7.56e-01 1.20e+02
  angle pdb=" C   SER A 271 "
        pdb=" CA  SER A 271 "
        pdb=" HA  SER A 271 "
      ideal   model   delta    sigma   weight residual
     109.00   77.73   31.27 3.00e+00 1.11e-01 1.09e+02
  angle pdb=" N   LEU C   7 "
        pdb=" CA  LEU C   7 "
        pdb=" C   LEU C   7 "
      ideal   model   delta    sigma   weight residual
     113.30   99.80   13.50 1.34e+00 5.57e-01 1.01e+02
  angle pdb=" CB  SER A 271 "
        pdb=" CA  SER A 271 "
        pdb=" HA  SER A 271 "
      ideal   model   delta    sigma   weight residual
     109.00   79.41   29.59 3.00e+00 1.11e-01 9.73e+01
  ... (remaining 31513 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    35.97: 8057
       35.97 -    71.94: 226
       71.94 -   107.91: 8
      107.91 -   143.88: 0
      143.88 -   179.86: 1
  Dihedral angle restraints: 8292
    sinusoidal: 4407
      harmonic: 3885
  Sorted by residual:
  dihedral pdb=" N   SER A 271 "
           pdb=" C   SER A 271 "
           pdb=" CA  SER A 271 "
           pdb=" CB  SER A 271 "
      ideal   model   delta  harmonic     sigma   weight residual
     122.80  139.18  -16.38     0      2.50e+00 1.60e-01 4.30e+01
  dihedral pdb=" C   SER A 271 "
           pdb=" N   SER A 271 "
           pdb=" CA  SER A 271 "
           pdb=" CB  SER A 271 "
      ideal   model   delta  harmonic     sigma   weight residual
    -122.60 -138.95   16.35     0      2.50e+00 1.60e-01 4.28e+01
  dihedral pdb=" N   PCA C   1 "
           pdb=" CA  PCA C   1 "
           pdb=" CB  PCA C   1 "
           pdb=" HB3 PCA C   1 "
      ideal   model   delta sinusoidal    sigma   weight residual
     273.91   94.05  179.86     1      3.00e+01 1.11e-03 2.13e+01
  ... (remaining 8289 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.129: 1363
       0.129 -    0.258: 12
       0.258 -    0.386: 0
       0.386 -    0.515: 0
       0.515 -    0.644: 1
  Chirality restraints: 1376
  Sorted by residual:
  chirality pdb=" CA  SER A 271 "
            pdb=" N   SER A 271 "
            pdb=" C   SER A 271 "
            pdb=" CB  SER A 271 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    1.87    0.64 2.00e-01 2.50e+01 1.04e+01
  chirality pdb=" CA  TYR S 190 "
            pdb=" N   TYR S 190 "
            pdb=" C   TYR S 190 "
            pdb=" CB  TYR S 190 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.35    0.16 2.00e-01 2.50e+01 6.27e-01
  chirality pdb=" CA  ILE S 189 "
            pdb=" N   ILE S 189 "
            pdb=" C   ILE S 189 "
            pdb=" CB  ILE S 189 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.59   -0.15 2.00e-01 2.50e+01 5.96e-01
  ... (remaining 1373 not shown)

  Planarity restraints: 2594
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CG  GLN A 202 "   -0.079 2.00e-02 2.50e+03   8.34e-02 1.04e+02
        pdb=" CD  GLN A 202 "    0.007 2.00e-02 2.50e+03
        pdb=" OE1 GLN A 202 "    0.073 2.00e-02 2.50e+03
        pdb=" NE2 GLN A 202 "    0.003 2.00e-02 2.50e+03
        pdb="HE21 GLN A 202 "    0.121 2.00e-02 2.50e+03
        pdb="HE22 GLN A 202 "   -0.124 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  VAL R 193 "   -0.023 2.00e-02 2.50e+03   4.67e-02 2.18e+01
        pdb=" C   VAL R 193 "    0.081 2.00e-02 2.50e+03
        pdb=" O   VAL R 193 "   -0.031 2.00e-02 2.50e+03
        pdb=" N   SER R 194 "   -0.026 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  TRP R 119 "   -0.021 2.00e-02 2.50e+03   4.09e-02 1.67e+01
        pdb=" C   TRP R 119 "    0.071 2.00e-02 2.50e+03
        pdb=" O   TRP R 119 "   -0.027 2.00e-02 2.50e+03
        pdb=" N   TYR R 120 "   -0.023 2.00e-02 2.50e+03
  ... (remaining 2591 not shown)

  Histogram of nonbonded interaction distances:
        1.80 -     2.36: 6191
        2.36 -     2.92: 39701
        2.92 -     3.48: 45400
        3.48 -     4.04: 62690
        4.04 -     4.60: 92242
  Nonbonded interactions: 246224
  Sorted by model distance:
  nonbonded pdb=" HA  VAL A 266 "
            pdb=" HB2 SER A 271 "
     model   vdw
     1.795 2.440
  nonbonded pdb=" HD1 HIS S  34 "
            pdb=" HE1 TRP S  46 "
     model   vdw
     1.858 2.100
  nonbonded pdb=" HG1 THR B 326 "
            pdb=" H   MET B 330 "
     model   vdw
     1.861 2.100
  nonbonded pdb=" HG1 THR B 133 "
            pdb=" H   ASN B 137 "
     model   vdw
     1.864 2.100
  nonbonded pdb=" HB2 GLN B 264 "
            pdb="HE21 GLN B 264 "
     model   vdw
     1.867 2.270
  ... (remaining 246219 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:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             2.430
  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:             0.060
  Extract box with map and model:          0.240
  Check model and map are aligned:         0.050
  Set scattering table:                    0.040
  Process input model:                     15.090
  Find NCS groups from input model:        0.070
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.010
  Load rotamer database and sin/cos tables:9.080
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   27.090
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7842
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      :  0.009   0.687   8958  Z= 0.450
  Angle     :  0.709  13.499  12148  Z= 0.417
  Chirality :  0.045   0.644   1376
  Planarity :  0.005   0.056   1533
  Dihedral  : 15.132  82.392   3196
  Min Nonbonded Distance : 2.279

Molprobity Statistics.
  All-atom Clashscore : 7.47
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.29 %
    Favored  : 96.71 %
  Rotamer:
    Outliers :  1.16 %
    Allowed  : 19.37 %
    Favored  : 79.47 %
  Cbeta Deviations :  0.10 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.28 (0.26), residues: 1095
  helix:  1.21 (0.28), residues: 369
  sheet:  0.02 (0.29), residues: 292
  loop : -0.47 (0.30), residues: 434

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.000   ARG A  31 
 TYR   0.031   0.002   TYR S 235 
 PHE   0.012   0.001   PHE B 246 
 TRP   0.018   0.002   TRP B  87 
 HIS   0.004   0.001   HIS B  59 

Details of bonding type rmsd
  covalent geometry    : bond        0.00433 ( 8955)
  covalent geometry    : angle       0.69826 (12144)
  SS BOND              : bond        0.48572 (    2)
  SS BOND              : angle       6.69196 (    4)
  hydrogen bonds       : bond        0.11324 (  447)
  hydrogen bonds       : angle       6.02690 ( 1263)
  Misc. bond           : bond        0.11594 (    1)

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

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

  2190 Ramachandran restraints generated.
    1095 Oldfield, 0 Emsley, 1095 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2190 Ramachandran restraints generated.
    1095 Oldfield, 0 Emsley, 1095 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue MET  222 is missing expected H atoms. Skipping.
Residue LYS   20 is missing expected H atoms. Skipping.
Residue MET   21 is missing expected H atoms. Skipping.
Residue LYS  345 is missing expected H atoms. Skipping.
Evaluate side-chains
  253 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 242
  time to evaluate  : 0.463 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   49 GLN cc_start: 0.8517 (mm-40) cc_final: 0.8189 (mp10)
REVERT: B   51 ARG cc_start: 0.8478 (mtp180) cc_final: 0.8083 (mtm180)
REVERT: B  134 ARG cc_start: 0.7625 (ttt90) cc_final: 0.7380 (ttt90)
REVERT: B  224 ARG cc_start: 0.8180 (mmt90) cc_final: 0.7805 (mmt90)
REVERT: G   31 SER cc_start: 0.7618 (m) cc_final: 0.7382 (p)
REVERT: A   17 LYS cc_start: 0.8347 (mmtm) cc_final: 0.7920 (mtmt)
REVERT: A   32 ARG cc_start: 0.8013 (ptp-110) cc_final: 0.7754 (mtm-85)
REVERT: A  211 GLN cc_start: 0.8736 (pt0) cc_final: 0.8365 (mt0)
REVERT: A  233 GLU cc_start: 0.7814 (mp0) cc_final: 0.7604 (mp0)
REVERT: A  248 ARG cc_start: 0.7997 (mtm180) cc_final: 0.7775 (ptp-110)
REVERT: A  291 PRO cc_start: 0.7298 (Cg_endo) cc_final: 0.7075 (Cg_exo)
REVERT: A  307 ARG cc_start: 0.8365 (ttm-80) cc_final: 0.7960 (ttm-80)
REVERT: S   12 GLN cc_start: 0.7451 (mp10) cc_final: 0.7113 (mp10)
REVERT: S   75 LYS cc_start: 0.8036 (pttt) cc_final: 0.7807 (pttm)
REVERT: S  116 LEU cc_start: 0.8092 (tt) cc_final: 0.7839 (tt)
REVERT: R  124 LEU cc_start: 0.6433 (tm) cc_final: 0.6140 (pt)
REVERT: R  130 MET cc_start: 0.7008 (mmm) cc_final: 0.6757 (mmp)
REVERT: R  177 PHE cc_start: 0.7239 (t80) cc_final: 0.7009 (t80)
REVERT: R  244 MET cc_start: 0.6397 (ptp) cc_final: 0.6083 (mmt)
REVERT: R  326 LEU cc_start: 0.8275 (mp) cc_final: 0.8000 (mt)
REVERT: R  328 ASN cc_start: 0.7616 (t0) cc_final: 0.7309 (t0)
  outliers start: 11
  outliers final: 2
  residues processed: 248
  average time/residue: 1.0168
  time to fit residues: 268.9140
Evaluate side-chains
  169 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 167
  time to evaluate  : 0.448 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue  107 MET
Chi-restraints excluded: chain R residue  113 TRP
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 109
   random chunks:
   chunk 108 optimal weight:    0.7980
   chunk 49 optimal weight:    0.9980
   chunk 97 optimal weight:    7.9990
   chunk 53 optimal weight:    5.9990
   chunk 5 optimal weight:    2.9990
   chunk 33 optimal weight:   10.0000
   chunk 65 optimal weight:    0.7980
   chunk 62 optimal weight:    2.9990
   chunk 51 optimal weight:    4.9990
   chunk 100 optimal weight:    0.6980
   chunk 106 optimal weight:    9.9990
   overall best weight:    1.2582

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

Flipped N/Q/H residues before XYZ refinement:
** B  59 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 264 GLN
A 232 GLN
A 259 GLN
S 171 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4085 r_free = 0.4085 target = 0.171406 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.3605 r_free = 0.3605 target = 0.126275 restraints weight = 30684.976|
|-----------------------------------------------------------------------------|
r_work (start): 0.3589 rms_B_bonded: 2.27
r_work: 0.3501 rms_B_bonded: 2.42 restraints_weight: 0.5000
r_work: 0.3397 rms_B_bonded: 3.95 restraints_weight: 0.2500
r_work (final): 0.3397
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8031
moved from start:          0.2059

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.034   8958  Z= 0.156
  Angle     :  0.560  10.766  12148  Z= 0.301
  Chirality :  0.043   0.461   1376
  Planarity :  0.005   0.061   1533
  Dihedral  :  5.461  51.300   1219
  Min Nonbonded Distance : 2.338

Molprobity Statistics.
  All-atom Clashscore : 5.34
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.74 %
    Favored  : 97.26 %
  Rotamer:
    Outliers :  2.86 %
    Allowed  : 21.27 %
    Favored  : 75.87 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.73 (0.26), residues: 1095
  helix:  1.76 (0.27), residues: 372
  sheet:  0.21 (0.30), residues: 288
  loop : -0.35 (0.30), residues: 435

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG B 139 
 TYR   0.027   0.002   TYR S 235 
 PHE   0.011   0.001   PHE R 101 
 TRP   0.015   0.001   TRP B  87 
 HIS   0.004   0.001   HIS A 322 

Details of bonding type rmsd
  covalent geometry    : bond        0.00354 ( 8955)
  covalent geometry    : angle       0.55965 (12144)
  SS BOND              : bond        0.01155 (    2)
  SS BOND              : angle       1.42431 (    4)
  hydrogen bonds       : bond        0.04714 (  447)
  hydrogen bonds       : angle       4.95400 ( 1263)
  Misc. bond           : bond        0.00060 (    1)

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

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

  2190 Ramachandran restraints generated.
    1095 Oldfield, 0 Emsley, 1095 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2190 Ramachandran restraints generated.
    1095 Oldfield, 0 Emsley, 1095 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue MET  222 is missing expected H atoms. Skipping.
Residue LYS   20 is missing expected H atoms. Skipping.
Residue MET   21 is missing expected H atoms. Skipping.
Residue LYS  345 is missing expected H atoms. Skipping.
Evaluate side-chains
  195 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 168
  time to evaluate  : 0.463 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   49 GLN cc_start: 0.8502 (mm-40) cc_final: 0.8090 (mp10)
REVERT: B   51 ARG cc_start: 0.8427 (mtp180) cc_final: 0.8044 (mpt180)
REVERT: B  134 ARG cc_start: 0.7733 (ttt90) cc_final: 0.7475 (ttt90)
REVERT: B  139 ARG cc_start: 0.7702 (mtm110) cc_final: 0.7284 (mtm180)
REVERT: B  263 ASP cc_start: 0.8210 (t0) cc_final: 0.7689 (t70)
REVERT: G   31 SER cc_start: 0.7385 (m) cc_final: 0.7140 (p)
REVERT: G   58 GLU cc_start: 0.8401 (OUTLIER) cc_final: 0.7728 (mp0)
REVERT: C    8 ARG cc_start: 0.6756 (mmm-85) cc_final: 0.5994 (mtm180)
REVERT: A   17 LYS cc_start: 0.8256 (mmtm) cc_final: 0.7886 (mtmt)
REVERT: A   32 ARG cc_start: 0.7962 (ptp-110) cc_final: 0.7628 (mtm-85)
REVERT: A  211 GLN cc_start: 0.8717 (pt0) cc_final: 0.8277 (mt0)
REVERT: A  231 LEU cc_start: 0.8594 (OUTLIER) cc_final: 0.8283 (tt)
REVERT: A  233 GLU cc_start: 0.7571 (mp0) cc_final: 0.7127 (mp0)
REVERT: A  248 ARG cc_start: 0.7733 (mtm180) cc_final: 0.7298 (ptp-110)
REVERT: A  291 PRO cc_start: 0.7157 (Cg_endo) cc_final: 0.6861 (Cg_exo)
REVERT: A  307 ARG cc_start: 0.8147 (ttm-80) cc_final: 0.7669 (ttm-80)
REVERT: S   12 GLN cc_start: 0.7487 (mp10) cc_final: 0.7157 (mp10)
REVERT: R  124 LEU cc_start: 0.6397 (tm) cc_final: 0.6097 (pt)
REVERT: R  178 LEU cc_start: 0.7946 (OUTLIER) cc_final: 0.7627 (tt)
REVERT: R  182 LEU cc_start: 0.7694 (mt) cc_final: 0.7465 (mt)
REVERT: R  244 MET cc_start: 0.5667 (ptp) cc_final: 0.5369 (mmt)
REVERT: R  326 LEU cc_start: 0.8186 (mp) cc_final: 0.7973 (mt)
REVERT: R  332 ASP cc_start: 0.6720 (OUTLIER) cc_final: 0.6510 (m-30)
  outliers start: 27
  outliers final: 8
  residues processed: 185
  average time/residue: 1.0673
  time to fit residues: 210.5856
Evaluate side-chains
  166 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 154
  time to evaluate  : 0.419 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   87 TRP
Chi-restraints excluded: chain B residue  251 ASP
Chi-restraints excluded: chain G residue   58 GLU
Chi-restraints excluded: chain A residue   47 SER
Chi-restraints excluded: chain A residue  231 LEU
Chi-restraints excluded: chain S residue  168 SER
Chi-restraints excluded: chain R residue  107 MET
Chi-restraints excluded: chain R residue  113 TRP
Chi-restraints excluded: chain R residue  178 LEU
Chi-restraints excluded: chain R residue  226 CYS
Chi-restraints excluded: chain R residue  275 ARG
Chi-restraints excluded: chain R residue  332 ASP
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 109
   random chunks:
   chunk 47 optimal weight:    1.9990
   chunk 44 optimal weight:    1.9990
   chunk 102 optimal weight:    5.9990
   chunk 106 optimal weight:    0.0170
   chunk 71 optimal weight:    4.9990
   chunk 31 optimal weight:    1.9990
   chunk 6 optimal weight:    0.9980
   chunk 97 optimal weight:    0.9990
   chunk 53 optimal weight:    2.9990
   chunk 107 optimal weight:    0.9980
   chunk 88 optimal weight:    0.8980
   overall best weight:    0.7820

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

Flipped N/Q/H residues before XYZ refinement:
B  37 GLN
** B  59 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 225 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4110 r_free = 0.4110 target = 0.173436 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3640 r_free = 0.3640 target = 0.128474 restraints weight = 30738.731|
|-----------------------------------------------------------------------------|
r_work (start): 0.3626 rms_B_bonded: 2.27
r_work: 0.3548 rms_B_bonded: 2.37 restraints_weight: 0.5000
r_work: 0.3448 rms_B_bonded: 3.90 restraints_weight: 0.2500
r_work (final): 0.3448
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8044
moved from start:          0.2409

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.026   8958  Z= 0.120
  Angle     :  0.519  10.623  12148  Z= 0.277
  Chirality :  0.042   0.458   1376
  Planarity :  0.004   0.038   1533
  Dihedral  :  5.295  57.446   1219
  Min Nonbonded Distance : 2.283

Molprobity Statistics.
  All-atom Clashscore : 4.88
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.37 %
    Favored  : 97.63 %
  Rotamer:
    Outliers :  2.22 %
    Allowed  : 20.74 %
    Favored  : 77.04 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.01 (0.26), residues: 1095
  helix:  2.14 (0.28), residues: 370
  sheet:  0.19 (0.29), residues: 298
  loop : -0.19 (0.31), residues: 427

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG B 139 
 TYR   0.023   0.001   TYR S 235 
 PHE   0.013   0.001   PHE R 322 
 TRP   0.015   0.001   TRP B  87 
 HIS   0.006   0.001   HIS R 319 

Details of bonding type rmsd
  covalent geometry    : bond        0.00264 ( 8955)
  covalent geometry    : angle       0.51860 (12144)
  SS BOND              : bond        0.00523 (    2)
  SS BOND              : angle       1.11106 (    4)
  hydrogen bonds       : bond        0.04186 (  447)
  hydrogen bonds       : angle       4.72546 ( 1263)
  Misc. bond           : bond        0.00029 (    1)

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

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

  2190 Ramachandran restraints generated.
    1095 Oldfield, 0 Emsley, 1095 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2190 Ramachandran restraints generated.
    1095 Oldfield, 0 Emsley, 1095 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue MET  222 is missing expected H atoms. Skipping.
Residue LYS   20 is missing expected H atoms. Skipping.
Residue MET   21 is missing expected H atoms. Skipping.
Residue LYS  345 is missing expected H atoms. Skipping.
Evaluate side-chains
  180 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 159
  time to evaluate  : 0.406 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   49 GLN cc_start: 0.8483 (mm-40) cc_final: 0.8146 (mm110)
REVERT: B   51 ARG cc_start: 0.8411 (mtp180) cc_final: 0.8038 (mpt180)
REVERT: B  134 ARG cc_start: 0.7707 (ttt90) cc_final: 0.7437 (ttt90)
REVERT: B  139 ARG cc_start: 0.7738 (mtm110) cc_final: 0.7325 (mtm180)
REVERT: B  177 GLU cc_start: 0.8118 (tp30) cc_final: 0.7909 (tp30)
REVERT: B  263 ASP cc_start: 0.8182 (t0) cc_final: 0.7555 (t70)
REVERT: G   31 SER cc_start: 0.7502 (m) cc_final: 0.7211 (p)
REVERT: G   58 GLU cc_start: 0.8364 (OUTLIER) cc_final: 0.7706 (mp0)
REVERT: A   17 LYS cc_start: 0.8258 (mmtm) cc_final: 0.7921 (mtmt)
REVERT: A   32 ARG cc_start: 0.7945 (ptp-110) cc_final: 0.7617 (mtm-85)
REVERT: A  211 GLN cc_start: 0.8686 (pt0) cc_final: 0.8285 (mt0)
REVERT: A  231 LEU cc_start: 0.8651 (OUTLIER) cc_final: 0.8319 (tt)
REVERT: A  233 GLU cc_start: 0.7526 (mp0) cc_final: 0.7127 (mp0)
REVERT: A  248 ARG cc_start: 0.7733 (mtm180) cc_final: 0.7367 (ptp-110)
REVERT: A  291 PRO cc_start: 0.7083 (Cg_endo) cc_final: 0.6816 (Cg_exo)
REVERT: A  307 ARG cc_start: 0.8092 (ttm-80) cc_final: 0.7508 (ttm-80)
REVERT: S   12 GLN cc_start: 0.7509 (mp10) cc_final: 0.7183 (mp10)
REVERT: S  243 THR cc_start: 0.8487 (m) cc_final: 0.8173 (p)
REVERT: R  124 LEU cc_start: 0.6377 (tm) cc_final: 0.6032 (pt)
REVERT: R  130 MET cc_start: 0.6543 (mmm) cc_final: 0.6231 (mmm)
REVERT: R  178 LEU cc_start: 0.8047 (OUTLIER) cc_final: 0.7709 (tt)
REVERT: R  182 LEU cc_start: 0.7684 (mt) cc_final: 0.7470 (mt)
REVERT: R  244 MET cc_start: 0.5858 (ptp) cc_final: 0.5475 (mmt)
REVERT: R  274 MET cc_start: 0.7314 (mmm) cc_final: 0.7088 (tmt)
REVERT: R  319 HIS cc_start: 0.7514 (m-70) cc_final: 0.7019 (m90)
REVERT: R  326 LEU cc_start: 0.8108 (mp) cc_final: 0.7903 (mt)
REVERT: R  332 ASP cc_start: 0.6804 (OUTLIER) cc_final: 0.6552 (m-30)
  outliers start: 21
  outliers final: 9
  residues processed: 170
  average time/residue: 1.0201
  time to fit residues: 185.5984
Evaluate side-chains
  166 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 153
  time to evaluate  : 0.441 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   87 TRP
Chi-restraints excluded: chain B residue  251 ASP
Chi-restraints excluded: chain G residue   58 GLU
Chi-restraints excluded: chain A residue   28 GLU
Chi-restraints excluded: chain A residue   47 SER
Chi-restraints excluded: chain A residue   48 THR
Chi-restraints excluded: chain A residue  231 LEU
Chi-restraints excluded: chain S residue  238 THR
Chi-restraints excluded: chain R residue  113 TRP
Chi-restraints excluded: chain R residue  178 LEU
Chi-restraints excluded: chain R residue  226 CYS
Chi-restraints excluded: chain R residue  275 ARG
Chi-restraints excluded: chain R residue  332 ASP
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 109
   random chunks:
   chunk 43 optimal weight:    2.9990
   chunk 19 optimal weight:    0.7980
   chunk 85 optimal weight:   10.0000
   chunk 101 optimal weight:    0.9990
   chunk 54 optimal weight:    4.9990
   chunk 71 optimal weight:    3.9990
   chunk 68 optimal weight:    0.7980
   chunk 63 optimal weight:    1.9990
   chunk 78 optimal weight:    2.9990
   chunk 2 optimal weight:    8.9990
   chunk 102 optimal weight:    2.9990
   overall best weight:    1.5186

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

Flipped N/Q/H residues before XYZ refinement:
** B  59 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4081 r_free = 0.4081 target = 0.170640 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3595 r_free = 0.3595 target = 0.125046 restraints weight = 30750.351|
|-----------------------------------------------------------------------------|
r_work (start): 0.3605 rms_B_bonded: 2.26
r_work: 0.3522 rms_B_bonded: 2.35 restraints_weight: 0.5000
r_work: 0.3420 rms_B_bonded: 3.84 restraints_weight: 0.2500
r_work (final): 0.3420
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8001
moved from start:          0.2743

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.033   8958  Z= 0.162
  Angle     :  0.538  10.727  12148  Z= 0.288
  Chirality :  0.043   0.461   1376
  Planarity :  0.004   0.040   1533
  Dihedral  :  4.967  46.548   1216
  Min Nonbonded Distance : 2.336

Molprobity Statistics.
  All-atom Clashscore : 4.65
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.83 %
    Favored  : 97.17 %
  Rotamer:
    Outliers :  3.60 %
    Allowed  : 19.15 %
    Favored  : 77.25 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.06 (0.26), residues: 1095
  helix:  2.17 (0.27), residues: 374
  sheet:  0.22 (0.29), residues: 298
  loop : -0.19 (0.31), residues: 423

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B  54 
 TYR   0.033   0.002   TYR S 235 
 PHE   0.011   0.001   PHE S 109 
 TRP   0.015   0.001   TRP B  87 
 HIS   0.004   0.001   HIS R  87 

Details of bonding type rmsd
  covalent geometry    : bond        0.00367 ( 8955)
  covalent geometry    : angle       0.53734 (12144)
  SS BOND              : bond        0.00528 (    2)
  SS BOND              : angle       1.07498 (    4)
  hydrogen bonds       : bond        0.04198 (  447)
  hydrogen bonds       : angle       4.69059 ( 1263)
  Misc. bond           : bond        0.00095 (    1)

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

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

  2190 Ramachandran restraints generated.
    1095 Oldfield, 0 Emsley, 1095 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2190 Ramachandran restraints generated.
    1095 Oldfield, 0 Emsley, 1095 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue MET  222 is missing expected H atoms. Skipping.
Residue LYS   20 is missing expected H atoms. Skipping.
Residue MET   21 is missing expected H atoms. Skipping.
Residue LYS  345 is missing expected H atoms. Skipping.
Evaluate side-chains
  194 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 160
  time to evaluate  : 0.394 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   49 GLN cc_start: 0.8461 (mm-40) cc_final: 0.8208 (mm110)
REVERT: B   51 ARG cc_start: 0.8393 (mtp180) cc_final: 0.7891 (mpt180)
REVERT: B   93 ASN cc_start: 0.8380 (p0) cc_final: 0.8070 (p0)
REVERT: B  134 ARG cc_start: 0.7689 (ttt90) cc_final: 0.7401 (ttp80)
REVERT: B  139 ARG cc_start: 0.7664 (mtm110) cc_final: 0.7219 (mtm-85)
REVERT: B  263 ASP cc_start: 0.8311 (t0) cc_final: 0.7677 (t70)
REVERT: G   31 SER cc_start: 0.7452 (m) cc_final: 0.7171 (p)
REVERT: G   58 GLU cc_start: 0.8320 (OUTLIER) cc_final: 0.7628 (mp0)
REVERT: A    9 ASP cc_start: 0.5843 (OUTLIER) cc_final: 0.4313 (t0)
REVERT: A   17 LYS cc_start: 0.8168 (mmtm) cc_final: 0.7782 (mtmt)
REVERT: A  211 GLN cc_start: 0.8752 (pt0) cc_final: 0.8363 (mt0)
REVERT: A  231 LEU cc_start: 0.8640 (OUTLIER) cc_final: 0.8318 (tt)
REVERT: A  233 GLU cc_start: 0.7493 (mp0) cc_final: 0.7014 (mp0)
REVERT: A  248 ARG cc_start: 0.7657 (mtm180) cc_final: 0.7238 (ptp-110)
REVERT: A  291 PRO cc_start: 0.7057 (Cg_endo) cc_final: 0.6674 (Cg_exo)
REVERT: A  307 ARG cc_start: 0.8059 (ttm-80) cc_final: 0.7473 (ttm-80)
REVERT: S   10 LEU cc_start: 0.8543 (mp) cc_final: 0.8155 (mp)
REVERT: S   12 GLN cc_start: 0.7547 (mp10) cc_final: 0.7217 (mp10)
REVERT: S  235 TYR cc_start: 0.6800 (OUTLIER) cc_final: 0.6337 (t80)
REVERT: S  243 THR cc_start: 0.8413 (m) cc_final: 0.8066 (p)
REVERT: S  246 GLU cc_start: 0.6923 (pt0) cc_final: 0.6722 (pt0)
REVERT: R  124 LEU cc_start: 0.6413 (tm) cc_final: 0.6035 (pt)
REVERT: R  178 LEU cc_start: 0.8039 (OUTLIER) cc_final: 0.7664 (tt)
REVERT: R  182 LEU cc_start: 0.7615 (mt) cc_final: 0.7382 (mt)
REVERT: R  244 MET cc_start: 0.5748 (ptp) cc_final: 0.5315 (mmt)
REVERT: R  319 HIS cc_start: 0.7439 (m-70) cc_final: 0.6843 (m90)
REVERT: R  332 ASP cc_start: 0.6763 (OUTLIER) cc_final: 0.6496 (m-30)
  outliers start: 34
  outliers final: 14
  residues processed: 182
  average time/residue: 1.0426
  time to fit residues: 203.1063
Evaluate side-chains
  174 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 154
  time to evaluate  : 0.437 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   87 TRP
Chi-restraints excluded: chain B residue  251 ASP
Chi-restraints excluded: chain G residue   58 GLU
Chi-restraints excluded: chain A residue    9 ASP
Chi-restraints excluded: chain A residue   47 SER
Chi-restraints excluded: chain A residue   48 THR
Chi-restraints excluded: chain A residue  182 ILE
Chi-restraints excluded: chain A residue  231 LEU
Chi-restraints excluded: chain S residue   50 ILE
Chi-restraints excluded: chain S residue   88 GLU
Chi-restraints excluded: chain S residue  168 SER
Chi-restraints excluded: chain S residue  235 TYR
Chi-restraints excluded: chain S residue  238 THR
Chi-restraints excluded: chain R residue  113 TRP
Chi-restraints excluded: chain R residue  178 LEU
Chi-restraints excluded: chain R residue  226 CYS
Chi-restraints excluded: chain R residue  240 THR
Chi-restraints excluded: chain R residue  275 ARG
Chi-restraints excluded: chain R residue  288 ILE
Chi-restraints excluded: chain R residue  332 ASP
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 109
   random chunks:
   chunk 65 optimal weight:    0.3980
   chunk 13 optimal weight:    2.9990
   chunk 71 optimal weight:    5.9990
   chunk 40 optimal weight:    0.6980
   chunk 72 optimal weight:    3.9990
   chunk 37 optimal weight:    1.9990
   chunk 9 optimal weight:    1.9990
   chunk 89 optimal weight:    3.9990
   chunk 20 optimal weight:    2.9990
   chunk 94 optimal weight:    7.9990
   chunk 30 optimal weight:    4.9990
   overall best weight:    1.6186

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

Flipped N/Q/H residues before XYZ refinement:
B  37 GLN
** B  59 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
S   2 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4078 r_free = 0.4078 target = 0.170399 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3592 r_free = 0.3592 target = 0.124805 restraints weight = 30429.152|
|-----------------------------------------------------------------------------|
r_work (start): 0.3581 rms_B_bonded: 2.24
r_work: 0.3500 rms_B_bonded: 2.34 restraints_weight: 0.5000
r_work: 0.3402 rms_B_bonded: 3.82 restraints_weight: 0.2500
r_work (final): 0.3402
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8098
moved from start:          0.3078

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.037   8958  Z= 0.168
  Angle     :  0.544  10.808  12148  Z= 0.289
  Chirality :  0.043   0.460   1376
  Planarity :  0.004   0.037   1533
  Dihedral  :  4.991  47.063   1216
  Min Nonbonded Distance : 2.321

Molprobity Statistics.
  All-atom Clashscore : 5.00
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.74 %
    Favored  : 97.26 %
  Rotamer:
    Outliers :  3.49 %
    Allowed  : 19.58 %
    Favored  : 76.93 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.97 (0.26), residues: 1095
  helix:  2.06 (0.27), residues: 380
  sheet:  0.21 (0.29), residues: 298
  loop : -0.28 (0.31), residues: 417

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B  54 
 TYR   0.032   0.002   TYR S 235 
 PHE   0.010   0.001   PHE S 109 
 TRP   0.015   0.001   TRP B  87 
 HIS   0.004   0.001   HIS R  87 

Details of bonding type rmsd
  covalent geometry    : bond        0.00384 ( 8955)
  covalent geometry    : angle       0.54350 (12144)
  SS BOND              : bond        0.00492 (    2)
  SS BOND              : angle       1.01446 (    4)
  hydrogen bonds       : bond        0.04158 (  447)
  hydrogen bonds       : angle       4.69770 ( 1263)
  Misc. bond           : bond        0.00072 (    1)

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

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

  2190 Ramachandran restraints generated.
    1095 Oldfield, 0 Emsley, 1095 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2190 Ramachandran restraints generated.
    1095 Oldfield, 0 Emsley, 1095 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue MET  222 is missing expected H atoms. Skipping.
Residue LYS   20 is missing expected H atoms. Skipping.
Residue MET   21 is missing expected H atoms. Skipping.
Residue LYS  345 is missing expected H atoms. Skipping.
Evaluate side-chains
  183 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 150
  time to evaluate  : 0.475 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   49 GLN cc_start: 0.8423 (mm-40) cc_final: 0.8165 (mm110)
REVERT: B   51 ARG cc_start: 0.8386 (mtp180) cc_final: 0.8006 (mpt180)
REVERT: B   93 ASN cc_start: 0.8468 (p0) cc_final: 0.8116 (p0)
REVERT: B  123 ASP cc_start: 0.8780 (OUTLIER) cc_final: 0.8569 (p0)
REVERT: B  134 ARG cc_start: 0.7786 (ttt90) cc_final: 0.7510 (ttp80)
REVERT: B  139 ARG cc_start: 0.7724 (mtm110) cc_final: 0.7375 (mtm180)
REVERT: B  231 GLU cc_start: 0.8330 (OUTLIER) cc_final: 0.8075 (mt-10)
REVERT: B  263 ASP cc_start: 0.8370 (t0) cc_final: 0.7744 (t70)
REVERT: G   31 SER cc_start: 0.7490 (m) cc_final: 0.7210 (p)
REVERT: G   58 GLU cc_start: 0.8316 (OUTLIER) cc_final: 0.7648 (mp0)
REVERT: A   17 LYS cc_start: 0.8259 (mmtm) cc_final: 0.7850 (mtmt)
REVERT: A  211 GLN cc_start: 0.8743 (pt0) cc_final: 0.8400 (mt0)
REVERT: A  231 LEU cc_start: 0.8697 (OUTLIER) cc_final: 0.8354 (tt)
REVERT: A  233 GLU cc_start: 0.7565 (mp0) cc_final: 0.7094 (mp0)
REVERT: A  248 ARG cc_start: 0.7775 (mtm180) cc_final: 0.7349 (ptp-110)
REVERT: A  291 PRO cc_start: 0.6982 (Cg_endo) cc_final: 0.6635 (Cg_exo)
REVERT: A  307 ARG cc_start: 0.8150 (ttm-80) cc_final: 0.7551 (ttm-80)
REVERT: S   10 LEU cc_start: 0.8565 (mp) cc_final: 0.8202 (mp)
REVERT: S   12 GLN cc_start: 0.7557 (mp10) cc_final: 0.7193 (mp10)
REVERT: S  235 TYR cc_start: 0.6752 (OUTLIER) cc_final: 0.6265 (t80)
REVERT: S  243 THR cc_start: 0.8454 (m) cc_final: 0.8122 (p)
REVERT: R  118 GLN cc_start: 0.4190 (tp40) cc_final: 0.3114 (mm-40)
REVERT: R  124 LEU cc_start: 0.6457 (tm) cc_final: 0.6058 (pt)
REVERT: R  130 MET cc_start: 0.6187 (mmm) cc_final: 0.5858 (mmp)
REVERT: R  178 LEU cc_start: 0.8158 (OUTLIER) cc_final: 0.7756 (tt)
REVERT: R  182 LEU cc_start: 0.7664 (mt) cc_final: 0.7444 (mt)
REVERT: R  244 MET cc_start: 0.5892 (ptp) cc_final: 0.5463 (mmt)
REVERT: R  299 ILE cc_start: 0.7958 (mt) cc_final: 0.7733 (mp)
REVERT: R  303 PHE cc_start: 0.6610 (m-10) cc_final: 0.6001 (m-80)
REVERT: R  319 HIS cc_start: 0.7470 (m-70) cc_final: 0.6812 (m90)
REVERT: R  332 ASP cc_start: 0.6806 (OUTLIER) cc_final: 0.6598 (m-30)
  outliers start: 33
  outliers final: 16
  residues processed: 167
  average time/residue: 1.1170
  time to fit residues: 198.9654
Evaluate side-chains
  173 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 150
  time to evaluate  : 0.382 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   87 TRP
Chi-restraints excluded: chain B residue  123 ASP
Chi-restraints excluded: chain B residue  231 GLU
Chi-restraints excluded: chain B residue  251 ASP
Chi-restraints excluded: chain G residue   58 GLU
Chi-restraints excluded: chain A residue   28 GLU
Chi-restraints excluded: chain A residue   47 SER
Chi-restraints excluded: chain A residue   48 THR
Chi-restraints excluded: chain A residue  182 ILE
Chi-restraints excluded: chain A residue  231 LEU
Chi-restraints excluded: chain S residue    2 GLN
Chi-restraints excluded: chain S residue   50 ILE
Chi-restraints excluded: chain S residue   88 GLU
Chi-restraints excluded: chain S residue  114 THR
Chi-restraints excluded: chain S residue  168 SER
Chi-restraints excluded: chain S residue  235 TYR
Chi-restraints excluded: chain S residue  238 THR
Chi-restraints excluded: chain R residue  107 MET
Chi-restraints excluded: chain R residue  113 TRP
Chi-restraints excluded: chain R residue  178 LEU
Chi-restraints excluded: chain R residue  226 CYS
Chi-restraints excluded: chain R residue  275 ARG
Chi-restraints excluded: chain R residue  332 ASP
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 109
   random chunks:
   chunk 10 optimal weight:    1.9990
   chunk 20 optimal weight:    2.9990
   chunk 99 optimal weight:    4.9990
   chunk 73 optimal weight:    0.9980
   chunk 30 optimal weight:    4.9990
   chunk 13 optimal weight:    0.0370
   chunk 65 optimal weight:    0.7980
   chunk 12 optimal weight:    1.9990
   chunk 60 optimal weight:    4.9990
   chunk 7 optimal weight:    0.9990
   chunk 108 optimal weight:    7.9990
   overall best weight:    0.9662

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

Flipped N/Q/H residues before XYZ refinement:
** B  59 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4089 r_free = 0.4089 target = 0.171454 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.3607 r_free = 0.3607 target = 0.126081 restraints weight = 30481.378|
|-----------------------------------------------------------------------------|
r_work (start): 0.3589 rms_B_bonded: 2.24
r_work: 0.3505 rms_B_bonded: 2.37 restraints_weight: 0.5000
r_work: 0.3404 rms_B_bonded: 3.86 restraints_weight: 0.2500
r_work (final): 0.3404
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8085
moved from start:          0.3172

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039   8958  Z= 0.128
  Angle     :  0.522  10.747  12148  Z= 0.277
  Chirality :  0.042   0.458   1376
  Planarity :  0.004   0.038   1533
  Dihedral  :  4.869  47.343   1216
  Min Nonbonded Distance : 2.336

Molprobity Statistics.
  All-atom Clashscore : 5.17
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.65 %
    Favored  : 97.35 %
  Rotamer:
    Outliers :  3.17 %
    Allowed  : 20.63 %
    Favored  : 76.19 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.05 (0.26), residues: 1095
  helix:  2.15 (0.27), residues: 380
  sheet:  0.24 (0.29), residues: 299
  loop : -0.23 (0.31), residues: 416

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B  54 
 TYR   0.028   0.001   TYR S 235 
 PHE   0.011   0.001   PHE S 109 
 TRP   0.015   0.001   TRP B  87 
 HIS   0.003   0.001   HIS R  87 

Details of bonding type rmsd
  covalent geometry    : bond        0.00288 ( 8955)
  covalent geometry    : angle       0.52210 (12144)
  SS BOND              : bond        0.00447 (    2)
  SS BOND              : angle       0.88464 (    4)
  hydrogen bonds       : bond        0.03978 (  447)
  hydrogen bonds       : angle       4.63951 ( 1263)
  Misc. bond           : bond        0.00041 (    1)

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

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

  2190 Ramachandran restraints generated.
    1095 Oldfield, 0 Emsley, 1095 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2190 Ramachandran restraints generated.
    1095 Oldfield, 0 Emsley, 1095 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue MET  222 is missing expected H atoms. Skipping.
Residue LYS   20 is missing expected H atoms. Skipping.
Residue MET   21 is missing expected H atoms. Skipping.
Residue LYS  345 is missing expected H atoms. Skipping.
Evaluate side-chains
  191 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 161
  time to evaluate  : 0.363 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   49 GLN cc_start: 0.8475 (mm-40) cc_final: 0.8223 (mm110)
REVERT: B   51 ARG cc_start: 0.8410 (mtp180) cc_final: 0.7969 (mpt180)
REVERT: B   93 ASN cc_start: 0.8384 (p0) cc_final: 0.8063 (p0)
REVERT: B  134 ARG cc_start: 0.7781 (ttt90) cc_final: 0.7499 (ttp80)
REVERT: B  139 ARG cc_start: 0.7716 (mtm110) cc_final: 0.7370 (mtm180)
REVERT: B  263 ASP cc_start: 0.8339 (t0) cc_final: 0.7756 (t70)
REVERT: G   31 SER cc_start: 0.7467 (m) cc_final: 0.7192 (p)
REVERT: G   58 GLU cc_start: 0.8320 (OUTLIER) cc_final: 0.7653 (mp0)
REVERT: A   17 LYS cc_start: 0.8257 (mmtm) cc_final: 0.7839 (mtmt)
REVERT: A  211 GLN cc_start: 0.8736 (pt0) cc_final: 0.8372 (mt0)
REVERT: A  231 LEU cc_start: 0.8649 (OUTLIER) cc_final: 0.8303 (tt)
REVERT: A  233 GLU cc_start: 0.7531 (mp0) cc_final: 0.7056 (mp0)
REVERT: A  291 PRO cc_start: 0.6947 (Cg_endo) cc_final: 0.6609 (Cg_exo)
REVERT: A  307 ARG cc_start: 0.8120 (ttm-80) cc_final: 0.7519 (ttm-80)
REVERT: S   10 LEU cc_start: 0.8552 (mp) cc_final: 0.8139 (mp)
REVERT: S   12 GLN cc_start: 0.7553 (mp10) cc_final: 0.7197 (mp10)
REVERT: S  158 SER cc_start: 0.8821 (m) cc_final: 0.8615 (p)
REVERT: S  235 TYR cc_start: 0.6561 (OUTLIER) cc_final: 0.6051 (t80)
REVERT: S  243 THR cc_start: 0.8412 (m) cc_final: 0.8090 (p)
REVERT: R  104 LEU cc_start: 0.6468 (mt) cc_final: 0.6247 (mm)
REVERT: R  118 GLN cc_start: 0.4166 (tp40) cc_final: 0.3034 (mm-40)
REVERT: R  124 LEU cc_start: 0.6438 (tm) cc_final: 0.6021 (pt)
REVERT: R  130 MET cc_start: 0.6297 (mmm) cc_final: 0.6051 (mmp)
REVERT: R  178 LEU cc_start: 0.8126 (OUTLIER) cc_final: 0.7727 (tt)
REVERT: R  182 LEU cc_start: 0.7641 (mt) cc_final: 0.7439 (mt)
REVERT: R  244 MET cc_start: 0.5859 (ptp) cc_final: 0.5429 (mmt)
REVERT: R  299 ILE cc_start: 0.7989 (mt) cc_final: 0.7771 (mp)
REVERT: R  303 PHE cc_start: 0.6657 (m-10) cc_final: 0.6064 (m-80)
REVERT: R  319 HIS cc_start: 0.7452 (m-70) cc_final: 0.6767 (m90)
REVERT: R  332 ASP cc_start: 0.6780 (OUTLIER) cc_final: 0.6547 (m-30)
  outliers start: 30
  outliers final: 18
  residues processed: 178
  average time/residue: 1.0853
  time to fit residues: 206.0789
Evaluate side-chains
  178 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 155
  time to evaluate  : 0.418 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   87 TRP
Chi-restraints excluded: chain B residue  239 PHE
Chi-restraints excluded: chain B residue  251 ASP
Chi-restraints excluded: chain G residue   58 GLU
Chi-restraints excluded: chain A residue   28 GLU
Chi-restraints excluded: chain A residue   47 SER
Chi-restraints excluded: chain A residue   48 THR
Chi-restraints excluded: chain A residue  182 ILE
Chi-restraints excluded: chain A residue  231 LEU
Chi-restraints excluded: chain S residue   50 ILE
Chi-restraints excluded: chain S residue   88 GLU
Chi-restraints excluded: chain S residue  114 THR
Chi-restraints excluded: chain S residue  168 SER
Chi-restraints excluded: chain S residue  235 TYR
Chi-restraints excluded: chain S residue  238 THR
Chi-restraints excluded: chain R residue  107 MET
Chi-restraints excluded: chain R residue  113 TRP
Chi-restraints excluded: chain R residue  171 MET
Chi-restraints excluded: chain R residue  178 LEU
Chi-restraints excluded: chain R residue  226 CYS
Chi-restraints excluded: chain R residue  240 THR
Chi-restraints excluded: chain R residue  275 ARG
Chi-restraints excluded: chain R residue  332 ASP
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 109
   random chunks:
   chunk 0 optimal weight:   20.0000
   chunk 86 optimal weight:    8.9990
   chunk 50 optimal weight:    1.9990
   chunk 5 optimal weight:    1.9990
   chunk 28 optimal weight:    2.9990
   chunk 54 optimal weight:    2.9990
   chunk 12 optimal weight:    2.9990
   chunk 102 optimal weight:    0.9980
   chunk 78 optimal weight:    2.9990
   chunk 44 optimal weight:    3.9990
   chunk 46 optimal weight:    0.7980
   overall best weight:    1.7586

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

Flipped N/Q/H residues before XYZ refinement:
** B  59 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4068 r_free = 0.4068 target = 0.169398 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3574 r_free = 0.3574 target = 0.123379 restraints weight = 30632.040|
|-----------------------------------------------------------------------------|
r_work (start): 0.3562 rms_B_bonded: 2.27
r_work: 0.3478 rms_B_bonded: 2.38 restraints_weight: 0.5000
r_work: 0.3376 rms_B_bonded: 3.88 restraints_weight: 0.2500
r_work (final): 0.3376
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8112
moved from start:          0.3349

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.037   8958  Z= 0.178
  Angle     :  0.547  10.886  12148  Z= 0.291
  Chirality :  0.043   0.461   1376
  Planarity :  0.004   0.039   1533
  Dihedral  :  4.970  47.203   1216
  Min Nonbonded Distance : 2.310

Molprobity Statistics.
  All-atom Clashscore : 5.57
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.83 %
    Favored  : 97.17 %
  Rotamer:
    Outliers :  3.17 %
    Allowed  : 21.38 %
    Favored  : 75.45 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.00 (0.26), residues: 1095
  helix:  2.11 (0.27), residues: 382
  sheet:  0.20 (0.29), residues: 299
  loop : -0.27 (0.31), residues: 414

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B 202 
 TYR   0.032   0.002   TYR S 235 
 PHE   0.013   0.001   PHE S 109 
 TRP   0.015   0.001   TRP B  87 
 HIS   0.003   0.001   HIS A 322 

Details of bonding type rmsd
  covalent geometry    : bond        0.00410 ( 8955)
  covalent geometry    : angle       0.54705 (12144)
  SS BOND              : bond        0.00499 (    2)
  SS BOND              : angle       0.97706 (    4)
  hydrogen bonds       : bond        0.04168 (  447)
  hydrogen bonds       : angle       4.70843 ( 1263)
  Misc. bond           : bond        0.00065 (    1)

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

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

  2190 Ramachandran restraints generated.
    1095 Oldfield, 0 Emsley, 1095 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2190 Ramachandran restraints generated.
    1095 Oldfield, 0 Emsley, 1095 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue MET  222 is missing expected H atoms. Skipping.
Residue LYS   20 is missing expected H atoms. Skipping.
Residue MET   21 is missing expected H atoms. Skipping.
Residue LYS  345 is missing expected H atoms. Skipping.
Evaluate side-chains
  186 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 156
  time to evaluate  : 0.390 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   49 GLN cc_start: 0.8474 (mm-40) cc_final: 0.8251 (mm110)
REVERT: B   51 ARG cc_start: 0.8416 (mtp180) cc_final: 0.7960 (mpt180)
REVERT: B   93 ASN cc_start: 0.8538 (p0) cc_final: 0.8205 (p0)
REVERT: B  123 ASP cc_start: 0.8798 (OUTLIER) cc_final: 0.8592 (p0)
REVERT: B  134 ARG cc_start: 0.7804 (ttt90) cc_final: 0.7514 (ttp80)
REVERT: B  139 ARG cc_start: 0.7764 (mtm110) cc_final: 0.7418 (mtm180)
REVERT: B  263 ASP cc_start: 0.8396 (t0) cc_final: 0.7780 (t70)
REVERT: G   31 SER cc_start: 0.7388 (m) cc_final: 0.7110 (p)
REVERT: G   58 GLU cc_start: 0.8296 (OUTLIER) cc_final: 0.7644 (mp0)
REVERT: A    9 ASP cc_start: 0.6165 (OUTLIER) cc_final: 0.4423 (t0)
REVERT: A   17 LYS cc_start: 0.8249 (mmtm) cc_final: 0.7828 (mtmt)
REVERT: A  188 GLN cc_start: 0.8286 (OUTLIER) cc_final: 0.8031 (tt0)
REVERT: A  211 GLN cc_start: 0.8809 (pt0) cc_final: 0.8441 (mt0)
REVERT: A  231 LEU cc_start: 0.8651 (OUTLIER) cc_final: 0.8323 (tt)
REVERT: A  233 GLU cc_start: 0.7573 (mp0) cc_final: 0.7057 (mp0)
REVERT: A  291 PRO cc_start: 0.6934 (Cg_endo) cc_final: 0.6555 (Cg_exo)
REVERT: A  307 ARG cc_start: 0.8148 (ttm-80) cc_final: 0.7558 (ttm-80)
REVERT: S   10 LEU cc_start: 0.8528 (mp) cc_final: 0.8211 (mp)
REVERT: S   12 GLN cc_start: 0.7554 (mp10) cc_final: 0.7200 (mp10)
REVERT: S  189 ILE cc_start: 0.8627 (OUTLIER) cc_final: 0.8423 (mp)
REVERT: S  235 TYR cc_start: 0.6735 (OUTLIER) cc_final: 0.6129 (t80)
REVERT: R  118 GLN cc_start: 0.4135 (tp40) cc_final: 0.3062 (mm-40)
REVERT: R  124 LEU cc_start: 0.6418 (tm) cc_final: 0.5997 (pt)
REVERT: R  130 MET cc_start: 0.6337 (mmm) cc_final: 0.6068 (mmp)
REVERT: R  178 LEU cc_start: 0.8122 (OUTLIER) cc_final: 0.7728 (tt)
REVERT: R  240 THR cc_start: 0.7268 (OUTLIER) cc_final: 0.6774 (m)
REVERT: R  244 MET cc_start: 0.5889 (ptp) cc_final: 0.5459 (mmt)
REVERT: R  299 ILE cc_start: 0.7994 (mt) cc_final: 0.7787 (mp)
REVERT: R  303 PHE cc_start: 0.6704 (m-10) cc_final: 0.6072 (m-80)
REVERT: R  319 HIS cc_start: 0.7419 (m-70) cc_final: 0.6749 (m90)
  outliers start: 30
  outliers final: 14
  residues processed: 172
  average time/residue: 1.1405
  time to fit residues: 208.8759
Evaluate side-chains
  173 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 150
  time to evaluate  : 0.430 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   87 TRP
Chi-restraints excluded: chain B residue  123 ASP
Chi-restraints excluded: chain B residue  251 ASP
Chi-restraints excluded: chain G residue   58 GLU
Chi-restraints excluded: chain A residue    9 ASP
Chi-restraints excluded: chain A residue   47 SER
Chi-restraints excluded: chain A residue   48 THR
Chi-restraints excluded: chain A residue  182 ILE
Chi-restraints excluded: chain A residue  188 GLN
Chi-restraints excluded: chain A residue  231 LEU
Chi-restraints excluded: chain S residue   50 ILE
Chi-restraints excluded: chain S residue   88 GLU
Chi-restraints excluded: chain S residue  114 THR
Chi-restraints excluded: chain S residue  168 SER
Chi-restraints excluded: chain S residue  189 ILE
Chi-restraints excluded: chain S residue  235 TYR
Chi-restraints excluded: chain S residue  238 THR
Chi-restraints excluded: chain R residue  107 MET
Chi-restraints excluded: chain R residue  113 TRP
Chi-restraints excluded: chain R residue  178 LEU
Chi-restraints excluded: chain R residue  226 CYS
Chi-restraints excluded: chain R residue  240 THR
Chi-restraints excluded: chain R residue  275 ARG
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 109
   random chunks:
   chunk 91 optimal weight:    2.9990
   chunk 68 optimal weight:    2.9990
   chunk 54 optimal weight:    2.9990
   chunk 45 optimal weight:    3.9990
   chunk 97 optimal weight:    5.9990
   chunk 55 optimal weight:    2.9990
   chunk 64 optimal weight:    2.9990
   chunk 46 optimal weight:    3.9990
   chunk 47 optimal weight:    0.5980
   chunk 39 optimal weight:    0.9990
   chunk 58 optimal weight:    3.9990
   overall best weight:    2.1188

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

Flipped N/Q/H residues before XYZ refinement:
** B  59 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
R 328 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4059 r_free = 0.4059 target = 0.168569 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3565 r_free = 0.3565 target = 0.122613 restraints weight = 30891.320|
|-----------------------------------------------------------------------------|
r_work (start): 0.3552 rms_B_bonded: 2.25
r_work: 0.3468 rms_B_bonded: 2.37 restraints_weight: 0.5000
r_work: 0.3365 rms_B_bonded: 3.86 restraints_weight: 0.2500
r_work (final): 0.3365
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8129
moved from start:          0.3490

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.043   8958  Z= 0.205
  Angle     :  0.572  10.948  12148  Z= 0.304
  Chirality :  0.044   0.462   1376
  Planarity :  0.004   0.038   1533
  Dihedral  :  5.064  47.791   1216
  Min Nonbonded Distance : 2.315

Molprobity Statistics.
  All-atom Clashscore : 5.75
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.11 %
    Favored  : 96.89 %
  Rotamer:
    Outliers :  3.17 %
    Allowed  : 22.33 %
    Favored  : 74.50 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.94 (0.26), residues: 1095
  helix:  2.10 (0.27), residues: 381
  sheet:  0.16 (0.29), residues: 300
  loop : -0.35 (0.30), residues: 414

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B  54 
 TYR   0.035   0.002   TYR S 235 
 PHE   0.014   0.002   PHE S 109 
 TRP   0.015   0.001   TRP B  87 
 HIS   0.004   0.001   HIS A 322 

Details of bonding type rmsd
  covalent geometry    : bond        0.00471 ( 8955)
  covalent geometry    : angle       0.57188 (12144)
  SS BOND              : bond        0.00535 (    2)
  SS BOND              : angle       1.10292 (    4)
  hydrogen bonds       : bond        0.04298 (  447)
  hydrogen bonds       : angle       4.78177 ( 1263)
  Misc. bond           : bond        0.00086 (    1)

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

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

  2190 Ramachandran restraints generated.
    1095 Oldfield, 0 Emsley, 1095 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2190 Ramachandran restraints generated.
    1095 Oldfield, 0 Emsley, 1095 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue MET  222 is missing expected H atoms. Skipping.
Residue LYS   20 is missing expected H atoms. Skipping.
Residue MET   21 is missing expected H atoms. Skipping.
Residue LYS  345 is missing expected H atoms. Skipping.
Evaluate side-chains
  176 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 146
  time to evaluate  : 0.453 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   49 GLN cc_start: 0.8464 (mm-40) cc_final: 0.8224 (mm110)
REVERT: B   51 ARG cc_start: 0.8396 (mtp180) cc_final: 0.7944 (mpt180)
REVERT: B  123 ASP cc_start: 0.8812 (OUTLIER) cc_final: 0.8609 (p0)
REVERT: B  134 ARG cc_start: 0.7821 (ttt90) cc_final: 0.7539 (ttp80)
REVERT: B  231 GLU cc_start: 0.8377 (OUTLIER) cc_final: 0.8132 (mt-10)
REVERT: B  263 ASP cc_start: 0.8434 (t0) cc_final: 0.7799 (t70)
REVERT: G   31 SER cc_start: 0.7389 (m) cc_final: 0.7114 (p)
REVERT: G   58 GLU cc_start: 0.8282 (OUTLIER) cc_final: 0.7624 (mp0)
REVERT: A    9 ASP cc_start: 0.6194 (OUTLIER) cc_final: 0.5129 (m-30)
REVERT: A   17 LYS cc_start: 0.8262 (mmtm) cc_final: 0.7892 (mtmt)
REVERT: A  188 GLN cc_start: 0.8285 (OUTLIER) cc_final: 0.8029 (tt0)
REVERT: A  211 GLN cc_start: 0.8822 (pt0) cc_final: 0.8444 (mt0)
REVERT: A  231 LEU cc_start: 0.8621 (OUTLIER) cc_final: 0.8292 (tt)
REVERT: A  233 GLU cc_start: 0.7558 (mp0) cc_final: 0.7012 (mp0)
REVERT: A  291 PRO cc_start: 0.6863 (Cg_endo) cc_final: 0.6461 (Cg_exo)
REVERT: A  307 ARG cc_start: 0.8183 (ttm-80) cc_final: 0.7591 (ttm-80)
REVERT: S   10 LEU cc_start: 0.8525 (mp) cc_final: 0.8214 (mp)
REVERT: S   12 GLN cc_start: 0.7539 (mp10) cc_final: 0.7190 (mp10)
REVERT: S  189 ILE cc_start: 0.8689 (OUTLIER) cc_final: 0.8474 (mt)
REVERT: S  235 TYR cc_start: 0.6829 (OUTLIER) cc_final: 0.6136 (t80)
REVERT: S  244 LYS cc_start: 0.7762 (ttpt) cc_final: 0.7482 (ttpt)
REVERT: R  118 GLN cc_start: 0.4180 (tp40) cc_final: 0.3083 (mm-40)
REVERT: R  124 LEU cc_start: 0.6440 (tm) cc_final: 0.6002 (pt)
REVERT: R  130 MET cc_start: 0.6450 (mmm) cc_final: 0.6180 (mmp)
REVERT: R  178 LEU cc_start: 0.8142 (OUTLIER) cc_final: 0.7840 (tt)
REVERT: R  240 THR cc_start: 0.7296 (OUTLIER) cc_final: 0.6861 (m)
REVERT: R  244 MET cc_start: 0.5907 (ptp) cc_final: 0.5474 (mmt)
REVERT: R  299 ILE cc_start: 0.8011 (mt) cc_final: 0.7798 (mp)
REVERT: R  303 PHE cc_start: 0.6734 (m-10) cc_final: 0.6137 (m-80)
REVERT: R  319 HIS cc_start: 0.7445 (m-70) cc_final: 0.6738 (m90)
  outliers start: 30
  outliers final: 12
  residues processed: 162
  average time/residue: 1.2215
  time to fit residues: 210.3120
Evaluate side-chains
  164 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 142
  time to evaluate  : 0.366 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   87 TRP
Chi-restraints excluded: chain B residue  123 ASP
Chi-restraints excluded: chain B residue  231 GLU
Chi-restraints excluded: chain B residue  251 ASP
Chi-restraints excluded: chain G residue   58 GLU
Chi-restraints excluded: chain A residue    9 ASP
Chi-restraints excluded: chain A residue   47 SER
Chi-restraints excluded: chain A residue  182 ILE
Chi-restraints excluded: chain A residue  188 GLN
Chi-restraints excluded: chain A residue  231 LEU
Chi-restraints excluded: chain S residue   50 ILE
Chi-restraints excluded: chain S residue   88 GLU
Chi-restraints excluded: chain S residue  114 THR
Chi-restraints excluded: chain S residue  168 SER
Chi-restraints excluded: chain S residue  189 ILE
Chi-restraints excluded: chain S residue  235 TYR
Chi-restraints excluded: chain S residue  238 THR
Chi-restraints excluded: chain R residue  107 MET
Chi-restraints excluded: chain R residue  113 TRP
Chi-restraints excluded: chain R residue  178 LEU
Chi-restraints excluded: chain R residue  240 THR
Chi-restraints excluded: chain R residue  275 ARG
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 109
   random chunks:
   chunk 9 optimal weight:    1.9990
   chunk 23 optimal weight:    1.9990
   chunk 13 optimal weight:    3.9990
   chunk 70 optimal weight:    1.9990
   chunk 34 optimal weight:    8.9990
   chunk 15 optimal weight:    0.5980
   chunk 17 optimal weight:    1.9990
   chunk 42 optimal weight:    2.9990
   chunk 74 optimal weight:    5.9990
   chunk 48 optimal weight:    4.9990
   chunk 1 optimal weight:    1.9990
   overall best weight:    1.7188

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

Flipped N/Q/H residues before XYZ refinement:
** B  59 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4062 r_free = 0.4062 target = 0.168910 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 54)----------------|
| r_work = 0.3571 r_free = 0.3571 target = 0.123026 restraints weight = 30864.027|
|-----------------------------------------------------------------------------|
r_work (start): 0.3557 rms_B_bonded: 2.24
r_work: 0.3473 rms_B_bonded: 2.36 restraints_weight: 0.5000
r_work: 0.3370 rms_B_bonded: 3.86 restraints_weight: 0.2500
r_work (final): 0.3370
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8118
moved from start:          0.3570

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.039   8958  Z= 0.176
  Angle     :  0.552  10.909  12148  Z= 0.294
  Chirality :  0.043   0.460   1376
  Planarity :  0.004   0.066   1533
  Dihedral  :  5.035  48.364   1216
  Min Nonbonded Distance : 2.264

Molprobity Statistics.
  All-atom Clashscore : 6.15
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.74 %
    Favored  : 97.26 %
  Rotamer:
    Outliers :  3.39 %
    Allowed  : 22.33 %
    Favored  : 74.29 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.96 (0.26), residues: 1095
  helix:  2.14 (0.27), residues: 381
  sheet:  0.20 (0.29), residues: 299
  loop : -0.37 (0.30), residues: 415

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.000   ARG B 139 
 TYR   0.033   0.002   TYR S 235 
 PHE   0.017   0.001   PHE R  66 
 TRP   0.015   0.001   TRP B  87 
 HIS   0.003   0.001   HIS R 319 

Details of bonding type rmsd
  covalent geometry    : bond        0.00403 ( 8955)
  covalent geometry    : angle       0.55136 (12144)
  SS BOND              : bond        0.00525 (    2)
  SS BOND              : angle       1.03620 (    4)
  hydrogen bonds       : bond        0.04184 (  447)
  hydrogen bonds       : angle       4.74842 ( 1263)
  Misc. bond           : bond        0.00064 (    1)

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

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

  2190 Ramachandran restraints generated.
    1095 Oldfield, 0 Emsley, 1095 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2190 Ramachandran restraints generated.
    1095 Oldfield, 0 Emsley, 1095 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue MET  222 is missing expected H atoms. Skipping.
Residue LYS   20 is missing expected H atoms. Skipping.
Residue MET   21 is missing expected H atoms. Skipping.
Residue LYS  345 is missing expected H atoms. Skipping.
Evaluate side-chains
  181 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 149
  time to evaluate  : 0.391 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   49 GLN cc_start: 0.8464 (mm-40) cc_final: 0.8231 (mm110)
REVERT: B   51 ARG cc_start: 0.8408 (mtp180) cc_final: 0.7948 (mpt180)
REVERT: B  134 ARG cc_start: 0.7818 (ttt90) cc_final: 0.7532 (ttp80)
REVERT: B  139 ARG cc_start: 0.7814 (mtm110) cc_final: 0.7394 (mtm180)
REVERT: B  231 GLU cc_start: 0.8367 (OUTLIER) cc_final: 0.8123 (mt-10)
REVERT: B  263 ASP cc_start: 0.8413 (t0) cc_final: 0.7791 (t70)
REVERT: G   31 SER cc_start: 0.7384 (m) cc_final: 0.7086 (p)
REVERT: G   58 GLU cc_start: 0.8255 (OUTLIER) cc_final: 0.7598 (mp0)
REVERT: A    9 ASP cc_start: 0.6204 (OUTLIER) cc_final: 0.5116 (m-30)
REVERT: A   17 LYS cc_start: 0.8245 (mmtm) cc_final: 0.7874 (mtmt)
REVERT: A  188 GLN cc_start: 0.8290 (OUTLIER) cc_final: 0.8032 (tt0)
REVERT: A  231 LEU cc_start: 0.8609 (OUTLIER) cc_final: 0.8270 (tt)
REVERT: A  233 GLU cc_start: 0.7546 (mp0) cc_final: 0.7000 (mp0)
REVERT: A  291 PRO cc_start: 0.6795 (Cg_endo) cc_final: 0.6386 (Cg_exo)
REVERT: A  307 ARG cc_start: 0.8174 (ttm-80) cc_final: 0.7505 (ttm-80)
REVERT: S   10 LEU cc_start: 0.8532 (mp) cc_final: 0.8233 (mp)
REVERT: S   12 GLN cc_start: 0.7532 (mp10) cc_final: 0.7190 (mp10)
REVERT: S  189 ILE cc_start: 0.8650 (OUTLIER) cc_final: 0.8422 (mp)
REVERT: S  235 TYR cc_start: 0.6732 (OUTLIER) cc_final: 0.6016 (t80)
REVERT: S  244 LYS cc_start: 0.7779 (ttpt) cc_final: 0.7469 (ttpt)
REVERT: R  118 GLN cc_start: 0.4239 (tp40) cc_final: 0.3177 (mm-40)
REVERT: R  124 LEU cc_start: 0.6459 (tm) cc_final: 0.6011 (pt)
REVERT: R  130 MET cc_start: 0.6435 (mmm) cc_final: 0.6150 (mmp)
REVERT: R  240 THR cc_start: 0.7298 (OUTLIER) cc_final: 0.6876 (m)
REVERT: R  244 MET cc_start: 0.5916 (ptp) cc_final: 0.5478 (mmt)
REVERT: R  303 PHE cc_start: 0.6695 (m-10) cc_final: 0.6092 (m-80)
REVERT: R  319 HIS cc_start: 0.7414 (m-70) cc_final: 0.6715 (m90)
  outliers start: 32
  outliers final: 16
  residues processed: 166
  average time/residue: 1.2151
  time to fit residues: 214.4442
Evaluate side-chains
  169 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 145
  time to evaluate  : 0.485 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   87 TRP
Chi-restraints excluded: chain B residue  231 GLU
Chi-restraints excluded: chain B residue  251 ASP
Chi-restraints excluded: chain G residue   58 GLU
Chi-restraints excluded: chain A residue    9 ASP
Chi-restraints excluded: chain A residue   28 GLU
Chi-restraints excluded: chain A residue   47 SER
Chi-restraints excluded: chain A residue   48 THR
Chi-restraints excluded: chain A residue  182 ILE
Chi-restraints excluded: chain A residue  188 GLN
Chi-restraints excluded: chain A residue  231 LEU
Chi-restraints excluded: chain S residue   22 SER
Chi-restraints excluded: chain S residue   50 ILE
Chi-restraints excluded: chain S residue   88 GLU
Chi-restraints excluded: chain S residue  114 THR
Chi-restraints excluded: chain S residue  168 SER
Chi-restraints excluded: chain S residue  189 ILE
Chi-restraints excluded: chain S residue  235 TYR
Chi-restraints excluded: chain S residue  238 THR
Chi-restraints excluded: chain R residue  107 MET
Chi-restraints excluded: chain R residue  113 TRP
Chi-restraints excluded: chain R residue  236 VAL
Chi-restraints excluded: chain R residue  240 THR
Chi-restraints excluded: chain R residue  275 ARG
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 109
   random chunks:
   chunk 87 optimal weight:    4.9990
   chunk 93 optimal weight:    0.7980
   chunk 39 optimal weight:    1.9990
   chunk 48 optimal weight:    0.9990
   chunk 0 optimal weight:   20.0000
   chunk 59 optimal weight:    0.6980
   chunk 28 optimal weight:    2.9990
   chunk 49 optimal weight:    0.0270
   chunk 35 optimal weight:    5.9990
   chunk 51 optimal weight:    2.9990
   chunk 3 optimal weight:    0.9980
   overall best weight:    0.7040

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

Flipped N/Q/H residues before XYZ refinement:
** B  59 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4087 r_free = 0.4087 target = 0.171200 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.3605 r_free = 0.3605 target = 0.125855 restraints weight = 30482.649|
|-----------------------------------------------------------------------------|
r_work (start): 0.3590 rms_B_bonded: 2.24
r_work: 0.3508 rms_B_bonded: 2.36 restraints_weight: 0.5000
r_work: 0.3405 rms_B_bonded: 3.85 restraints_weight: 0.2500
r_work (final): 0.3405
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8078
moved from start:          0.3606

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028   8958  Z= 0.114
  Angle     :  0.522  10.696  12148  Z= 0.276
  Chirality :  0.042   0.456   1376
  Planarity :  0.004   0.054   1533
  Dihedral  :  4.808  48.976   1216
  Min Nonbonded Distance : 2.250

Molprobity Statistics.
  All-atom Clashscore : 5.63
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.83 %
    Favored  : 97.17 %
  Rotamer:
    Outliers :  2.33 %
    Allowed  : 23.70 %
    Favored  : 73.97 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.10 (0.26), residues: 1095
  helix:  2.26 (0.27), residues: 380
  sheet:  0.26 (0.29), residues: 299
  loop : -0.29 (0.31), residues: 416

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.000   ARG B 139 
 TYR   0.026   0.001   TYR S 235 
 PHE   0.021   0.001   PHE R  66 
 TRP   0.016   0.001   TRP B  87 
 HIS   0.003   0.001   HIS R 319 

Details of bonding type rmsd
  covalent geometry    : bond        0.00251 ( 8955)
  covalent geometry    : angle       0.52225 (12144)
  SS BOND              : bond        0.00407 (    2)
  SS BOND              : angle       0.78986 (    4)
  hydrogen bonds       : bond        0.03809 (  447)
  hydrogen bonds       : angle       4.63693 ( 1263)
  Misc. bond           : bond        0.00027 (    1)

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

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

  2190 Ramachandran restraints generated.
    1095 Oldfield, 0 Emsley, 1095 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2190 Ramachandran restraints generated.
    1095 Oldfield, 0 Emsley, 1095 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue MET  222 is missing expected H atoms. Skipping.
Residue LYS   20 is missing expected H atoms. Skipping.
Residue MET   21 is missing expected H atoms. Skipping.
Residue LYS  345 is missing expected H atoms. Skipping.
Evaluate side-chains
  167 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 145
  time to evaluate  : 0.315 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   49 GLN cc_start: 0.8460 (mm-40) cc_final: 0.8232 (mm110)
REVERT: B   51 ARG cc_start: 0.8382 (mtp180) cc_final: 0.7958 (mpt180)
REVERT: B   93 ASN cc_start: 0.8325 (p0) cc_final: 0.8005 (p0)
REVERT: B  134 ARG cc_start: 0.7782 (ttt90) cc_final: 0.7495 (ttp80)
REVERT: B  139 ARG cc_start: 0.7808 (mtm110) cc_final: 0.7377 (mtm180)
REVERT: B  263 ASP cc_start: 0.8311 (t0) cc_final: 0.7742 (t70)
REVERT: G   31 SER cc_start: 0.7398 (m) cc_final: 0.7117 (p)
REVERT: G   58 GLU cc_start: 0.8230 (OUTLIER) cc_final: 0.7599 (mp0)
REVERT: A    9 ASP cc_start: 0.6140 (OUTLIER) cc_final: 0.4387 (t70)
REVERT: A   17 LYS cc_start: 0.8240 (mmtm) cc_final: 0.7826 (mtmt)
REVERT: A  231 LEU cc_start: 0.8595 (OUTLIER) cc_final: 0.8278 (tt)
REVERT: A  233 GLU cc_start: 0.7530 (mp0) cc_final: 0.7024 (mp0)
REVERT: A  291 PRO cc_start: 0.6788 (Cg_endo) cc_final: 0.6390 (Cg_exo)
REVERT: A  307 ARG cc_start: 0.8082 (ttm-80) cc_final: 0.7489 (ttm-80)
REVERT: S   10 LEU cc_start: 0.8523 (mp) cc_final: 0.8239 (mp)
REVERT: S   12 GLN cc_start: 0.7575 (mp10) cc_final: 0.7180 (mp10)
REVERT: S  235 TYR cc_start: 0.6330 (OUTLIER) cc_final: 0.5516 (t80)
REVERT: S  243 THR cc_start: 0.8344 (m) cc_final: 0.8047 (p)
REVERT: S  244 LYS cc_start: 0.7785 (ttpt) cc_final: 0.7529 (ttpt)
REVERT: R  118 GLN cc_start: 0.4212 (tp40) cc_final: 0.3140 (mm-40)
REVERT: R  124 LEU cc_start: 0.6398 (tm) cc_final: 0.5997 (pt)
REVERT: R  130 MET cc_start: 0.6396 (mmm) cc_final: 0.6103 (mmp)
REVERT: R  240 THR cc_start: 0.7304 (OUTLIER) cc_final: 0.6851 (m)
REVERT: R  244 MET cc_start: 0.5963 (ptp) cc_final: 0.5525 (mmt)
REVERT: R  303 PHE cc_start: 0.6619 (m-10) cc_final: 0.5982 (m-80)
REVERT: R  319 HIS cc_start: 0.7375 (m-70) cc_final: 0.6684 (m90)
  outliers start: 22
  outliers final: 12
  residues processed: 158
  average time/residue: 1.2293
  time to fit residues: 206.3104
Evaluate side-chains
  162 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 145
  time to evaluate  : 0.487 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   87 TRP
Chi-restraints excluded: chain B residue  251 ASP
Chi-restraints excluded: chain G residue   58 GLU
Chi-restraints excluded: chain A residue    9 ASP
Chi-restraints excluded: chain A residue   48 THR
Chi-restraints excluded: chain A residue  231 LEU
Chi-restraints excluded: chain S residue   22 SER
Chi-restraints excluded: chain S residue   50 ILE
Chi-restraints excluded: chain S residue   88 GLU
Chi-restraints excluded: chain S residue  114 THR
Chi-restraints excluded: chain S residue  168 SER
Chi-restraints excluded: chain S residue  235 TYR
Chi-restraints excluded: chain S residue  238 THR
Chi-restraints excluded: chain R residue  107 MET
Chi-restraints excluded: chain R residue  113 TRP
Chi-restraints excluded: chain R residue  240 THR
Chi-restraints excluded: chain R residue  275 ARG
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 109
   random chunks:
   chunk 13 optimal weight:    2.9990
   chunk 50 optimal weight:    1.9990
   chunk 102 optimal weight:    2.9990
   chunk 86 optimal weight:    4.9990
   chunk 96 optimal weight:    0.0050
   chunk 38 optimal weight:    9.9990
   chunk 81 optimal weight:    4.9990
   chunk 10 optimal weight:    2.9990
   chunk 23 optimal weight:    0.9990
   chunk 22 optimal weight:    0.6980
   chunk 14 optimal weight:    0.5980
   overall best weight:    0.8598

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

Flipped N/Q/H residues before XYZ refinement:
** B  59 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4089 r_free = 0.4089 target = 0.171293 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 55)----------------|
| r_work = 0.3609 r_free = 0.3609 target = 0.126121 restraints weight = 30813.048|
|-----------------------------------------------------------------------------|
r_work (start): 0.3590 rms_B_bonded: 2.23
r_work: 0.3507 rms_B_bonded: 2.37 restraints_weight: 0.5000
r_work: 0.3404 rms_B_bonded: 3.87 restraints_weight: 0.2500
r_work (final): 0.3404
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8084
moved from start:          0.3656

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.026   8958  Z= 0.122
  Angle     :  0.523  10.698  12148  Z= 0.277
  Chirality :  0.042   0.457   1376
  Planarity :  0.004   0.054   1533
  Dihedral  :  4.756  48.610   1216
  Min Nonbonded Distance : 2.233

Molprobity Statistics.
  All-atom Clashscore : 5.86
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.83 %
    Favored  : 97.17 %
  Rotamer:
    Outliers :  1.90 %
    Allowed  : 23.70 %
    Favored  : 74.39 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.16 (0.26), residues: 1095
  helix:  2.34 (0.27), residues: 380
  sheet:  0.30 (0.29), residues: 298
  loop : -0.29 (0.31), residues: 417

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.000   ARG B 139 
 TYR   0.026   0.001   TYR S 235 
 PHE   0.016   0.001   PHE R  66 
 TRP   0.016   0.001   TRP B  87 
 HIS   0.003   0.001   HIS R 319 

Details of bonding type rmsd
  covalent geometry    : bond        0.00272 ( 8955)
  covalent geometry    : angle       0.52330 (12144)
  SS BOND              : bond        0.00417 (    2)
  SS BOND              : angle       0.79134 (    4)
  hydrogen bonds       : bond        0.03773 (  447)
  hydrogen bonds       : angle       4.59047 ( 1263)
  Misc. bond           : bond        0.00033 (    1)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 7201.42 seconds
wall clock time: 122 minutes 19.64 seconds (7339.64 seconds total)