Starting phenix.real_space_refine
on Sun May 11 22:30:26 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8z65_39792/05_2025/8z65_39792.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8z65_39792/05_2025/8z65_39792.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.97
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8z65_39792/05_2025/8z65_39792.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8z65_39792/05_2025/8z65_39792.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8z65_39792/05_2025/8z65_39792.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8z65_39792/05_2025/8z65_39792.cif"
  }
  resolution = 2.97
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.001 sd=   0.020
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 4
    Type Number    sf(0)   Gaussians
     S      52      5.16       5
     C    5415      2.51       5
     N    1481      2.21       5
     O    1546      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 34 residue(s): 0.03s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib"
  Total number of atoms: 8494
  Number of models: 1
  Model: ""
    Number of chains: 5
    Chain: "A"
      Number of atoms: 1860
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 238, 1860
          Classifications: {'peptide': 238}
          Incomplete info: {'truncation_to_alanine': 27}
          Link IDs: {'PTRANS': 6, 'TRANS': 231}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 113
          Unresolved non-hydrogen angles: 135
          Unresolved non-hydrogen dihedrals: 94
          Unresolved non-hydrogen chiralities: 1
          Planarities with less than four sites: {'TYR:plan': 1, 'GLU:plan': 7, 'ASN:plan1': 1, 'ARG:plan': 5, 'ASP:plan': 5}
          Unresolved non-hydrogen planarities: 78
    Chain: "B"
      Number of atoms: 2447
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 334, 2447
          Classifications: {'peptide': 334}
          Incomplete info: {'truncation_to_alanine': 30}
          Link IDs: {'PTRANS': 5, 'TRANS': 328}
          Unresolved non-hydrogen bonds: 119
          Unresolved non-hydrogen angles: 146
          Unresolved non-hydrogen dihedrals: 92
          Unresolved non-hydrogen chiralities: 7
          Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 5, 'ARG:plan': 7, 'ASN:plan1': 3, 'ASP:plan': 3}
          Unresolved non-hydrogen planarities: 81
    Chain: "G"
      Number of atoms: 321
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 50, 321
          Classifications: {'peptide': 50}
          Incomplete info: {'truncation_to_alanine': 18}
          Link IDs: {'PTRANS': 4, 'TRANS': 45}
          Unresolved non-hydrogen bonds: 70
          Unresolved non-hydrogen angles: 82
          Unresolved non-hydrogen dihedrals: 58
          Unresolved non-hydrogen chiralities: 2
          Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 5, 'ARG:plan': 2, 'ASN:plan1': 1, 'ASP:plan': 1}
          Unresolved non-hydrogen planarities: 40
    Chain: "S"
      Number of atoms: 1695
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 232, 1695
          Classifications: {'peptide': 232}
          Incomplete info: {'truncation_to_alanine': 25}
          Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 221}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 84
          Unresolved non-hydrogen angles: 101
          Unresolved non-hydrogen dihedrals: 67
          Unresolved non-hydrogen chiralities: 5
          Planarities with less than four sites: {'GLU:plan': 7, 'ARG:plan': 3, 'ASP:plan': 2}
          Unresolved non-hydrogen planarities: 49
    Chain: "R"
      Number of atoms: 2171
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 295, 2171
          Classifications: {'peptide': 295}
          Incomplete info: {'truncation_to_alanine': 58}
          Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 282}
          Chain breaks: 2
          Unresolved non-hydrogen bonds: 223
          Unresolved non-hydrogen angles: 282
          Unresolved non-hydrogen dihedrals: 187
          Unresolved non-hydrogen chiralities: 13
          Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 2, 'ASN:plan1': 3, 'TRP:plan': 1, 'ASP:plan': 8, 'PHE:plan': 5, 'GLU:plan': 6, 'ARG:plan': 7}
          Unresolved non-hydrogen planarities: 149
  Time building chain proxies: 5.63, per 1000 atoms: 0.66
  Number of scatterers: 8494
  At special positions: 0
  Unit cell: (87.74, 121.36, 126.28, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     S      52     16.00
     O    1546      8.00
     N    1481      7.00
     C    5415      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=2, symmetry=0
    Simple disulfide: pdb=" SG  CYS S  22 " - pdb=" SG  CYS S  96 " distance=2.03
    Simple disulfide: pdb=" SG  CYS R  90 " - pdb=" SG  CYS R 168 " distance=2.03

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 2.22
  Conformation dependent library (CDL) restraints added in 1.1 seconds
  

  2262 Ramachandran restraints generated.
    1131 Oldfield, 0 Emsley, 1131 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2152

  Finding SS restraints...
    Secondary structure from input PDB file:
      29 helices and 13 sheets defined
      37.5% alpha, 23.2% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 1.12
  Creating SS restraints...
    Processing helix  chain 'A' and resid 6 through 39
      removed outlier: 3.506A  pdb=" N   ALA A  39 " --> pdb=" O   GLN A  35 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 52 through 64
    Processing helix  chain 'A' and resid 243 through 249
      removed outlier: 3.561A  pdb=" N   ASN A 249 " --> pdb=" O   GLN A 246 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 265 through 278
    Processing helix  chain 'A' and resid 293 through 304
    Processing helix  chain 'A' and resid 312 through 316
      removed outlier: 3.554A  pdb=" N   ALA A 316 " --> pdb=" O   PRO A 313 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 331 through 352
      removed outlier: 3.542A  pdb=" N   THR A 335 " --> pdb=" O   ASP A 331 " (cutoff:3.500A)
      removed outlier: 4.335A  pdb=" N   SER A 352 " --> pdb=" O   ILE A 348 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 370 through 391
    Processing helix  chain 'B' and resid 8 through 25
    Processing helix  chain 'B' and resid 29 through 35
    Processing helix  chain 'G' and resid 14 through 24
    Processing helix  chain 'G' and resid 29 through 44
    Processing helix  chain 'S' and resid 28 through 32
    Processing helix  chain 'S' and resid 62 through 65
    Processing helix  chain 'S' and resid 87 through 91
      removed outlier: 3.891A  pdb=" N   THR S  91 " --> pdb=" O   SER S  88 " (cutoff:3.500A)
    Processing helix  chain 'S' and resid 220 through 224
      removed outlier: 4.091A  pdb=" N   VAL S 224 " --> pdb=" O   ALA S 221 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 18 through 48
      removed outlier: 3.832A  pdb=" N   PHE R  26 " --> pdb=" O   SER R  22 " (cutoff:3.500A)
      Proline residue:  R  33  - end of helix
    Processing helix  chain 'R' and resid 52 through 78
      removed outlier: 3.565A  pdb=" N   ASN R  58 " --> pdb=" O   VAL R  54 " (cutoff:3.500A)
      removed outlier: 4.173A  pdb=" N   TYR R  66 " --> pdb=" O   ALA R  62 " (cutoff:3.500A)
      Proline residue:  R  71  - end of helix
    Processing helix  chain 'R' and resid 86 through 120
      removed outlier: 4.550A  pdb=" N   ILE R 101 " --> pdb=" O   PHE R  97 " (cutoff:3.500A)
      removed outlier: 5.003A  pdb=" N   TYR R 102 " --> pdb=" O   TYR R  98 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 126 through 129
    Processing helix  chain 'R' and resid 130 through 149
    Processing helix  chain 'R' and resid 151 through 155
    Processing helix  chain 'R' and resid 177 through 190
      removed outlier: 3.616A  pdb=" N   PHE R 190 " --> pdb=" O   VAL R 186 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 190 through 210
      removed outlier: 4.299A  pdb=" N   GLY R 210 " --> pdb=" O   ARG R 206 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 215 through 252
      Proline residue:  R 239  - end of helix
      removed outlier: 3.672A  pdb=" N   ILE R 250 " --> pdb=" O   SER R 246 " (cutoff:3.500A)
      removed outlier: 3.719A  pdb=" N   TYR R 251 " --> pdb=" O   ARG R 247 " (cutoff:3.500A)
      removed outlier: 4.116A  pdb=" N   LEU R 252 " --> pdb=" O   SER R 248 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 260 through 263
    Processing helix  chain 'R' and resid 264 through 276
    Processing helix  chain 'R' and resid 277 through 287
      Proline residue:  R 283  - end of helix
    Processing helix  chain 'R' and resid 290 through 304
      removed outlier: 3.647A  pdb=" N   ASN R 303 " --> pdb=" O   LYS R 299 " (cutoff:3.500A)
      removed outlier: 3.763A  pdb=" N   LEU R 304 " --> pdb=" O   ALA R 300 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 217 through 223
      removed outlier: 4.634A  pdb=" N   VAL A 234 " --> pdb=" O   LEU A  45 " (cutoff:3.500A)
      removed outlier: 7.957A  pdb=" N   GLY A  47 " --> pdb=" O   VAL A 234 " (cutoff:3.500A)
      removed outlier: 3.759A  pdb=" N   ALA A 253 " --> pdb=" O   ARG A  42 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'B' and resid 47 through 52
      removed outlier: 4.320A  pdb=" N   PHE B 335 " --> pdb=" O   SER B 331 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'B' and resid 58 through 63
      removed outlier: 3.752A  pdb=" N   ALA B  60 " --> pdb=" O   ALA B  73 " (cutoff:3.500A)
      removed outlier: 3.678A  pdb=" N   LYS B  78 " --> pdb=" O   SER B  74 " (cutoff:3.500A)
      removed outlier: 3.525A  pdb=" N   HIS B  91 " --> pdb=" O   ILE B  81 " (cutoff:3.500A)
      removed outlier: 6.516A  pdb=" N   ASP B  83 " --> pdb=" O   LYS B  89 " (cutoff:3.500A)
      removed outlier: 6.171A  pdb=" N   LYS B  89 " --> pdb=" O   ASP B  83 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'B' and resid 100 through 105
      removed outlier: 6.657A  pdb=" N   GLY B 115 " --> pdb=" O   MET B 101 " (cutoff:3.500A)
      removed outlier: 4.289A  pdb=" N   CYS B 103 " --> pdb=" O   ALA B 113 " (cutoff:3.500A)
      removed outlier: 6.417A  pdb=" N   ALA B 113 " --> pdb=" O   CYS B 103 " (cutoff:3.500A)
      removed outlier: 4.803A  pdb=" N   TYR B 105 " --> pdb=" O   TYR B 111 " (cutoff:3.500A)
      removed outlier: 6.918A  pdb=" N   TYR B 111 " --> pdb=" O   TYR B 105 " (cutoff:3.500A)
      removed outlier: 6.461A  pdb=" N   CYS B 121 " --> pdb=" O   GLU B 138 " (cutoff:3.500A)
      removed outlier: 4.734A  pdb=" N   GLU B 138 " --> pdb=" O   CYS B 121 " (cutoff:3.500A)
      removed outlier: 6.938A  pdb=" N   ILE B 123 " --> pdb=" O   SER B 136 " (cutoff:3.500A)
      removed outlier: 3.654A  pdb=" N   ARG B 134 " --> pdb=" O   ASN B 125 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'B' and resid 146 through 151
      removed outlier: 3.534A  pdb=" N   CYS B 148 " --> pdb=" O   SER B 160 " (cutoff:3.500A)
      removed outlier: 3.539A  pdb=" N   THR B 178 " --> pdb=" O   LEU B 168 " (cutoff:3.500A)
      removed outlier: 6.958A  pdb=" N   ASP B 170 " --> pdb=" O   GLN B 176 " (cutoff:3.500A)
      removed outlier: 6.623A  pdb=" N   GLN B 176 " --> pdb=" O   ASP B 170 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'B' and resid 189 through 192
      removed outlier: 6.906A  pdb=" N   ASP B 212 " --> pdb=" O   CYS B 218 " (cutoff:3.500A)
      removed outlier: 6.513A  pdb=" N   CYS B 218 " --> pdb=" O   ASP B 212 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'B' and resid 229 through 234
      removed outlier: 6.434A  pdb=" N   GLY B 244 " --> pdb=" O   ASN B 230 " (cutoff:3.500A)
      removed outlier: 4.356A  pdb=" N   ILE B 232 " --> pdb=" O   ALA B 242 " (cutoff:3.500A)
      removed outlier: 6.632A  pdb=" N   ALA B 242 " --> pdb=" O   ILE B 232 " (cutoff:3.500A)
      removed outlier: 4.861A  pdb=" N   PHE B 234 " --> pdb=" O   ALA B 240 " (cutoff:3.500A)
      removed outlier: 7.192A  pdb=" N   ALA B 240 " --> pdb=" O   PHE B 234 " (cutoff:3.500A)
      removed outlier: 6.486A  pdb=" N   CYS B 250 " --> pdb=" O   THR B 263 " (cutoff:3.500A)
      removed outlier: 4.603A  pdb=" N   THR B 263 " --> pdb=" O   CYS B 250 " (cutoff:3.500A)
      removed outlier: 6.814A  pdb=" N   LEU B 252 " --> pdb=" O   LEU B 261 " (cutoff:3.500A)
      removed outlier: 3.852A  pdb=" N   GLN B 259 " --> pdb=" O   ASP B 254 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'B' and resid 273 through 278
      removed outlier: 6.259A  pdb=" N   GLY B 288 " --> pdb=" O   THR B 274 " (cutoff:3.500A)
      removed outlier: 4.353A  pdb=" N   VAL B 276 " --> pdb=" O   LEU B 286 " (cutoff:3.500A)
      removed outlier: 6.772A  pdb=" N   LEU B 286 " --> pdb=" O   VAL B 276 " (cutoff:3.500A)
      removed outlier: 4.883A  pdb=" N   PHE B 278 " --> pdb=" O   LEU B 284 " (cutoff:3.500A)
      removed outlier: 7.138A  pdb=" N   LEU B 284 " --> pdb=" O   PHE B 278 " (cutoff:3.500A)
      removed outlier: 6.279A  pdb=" N   ASP B 298 " --> pdb=" O   ARG B 304 " (cutoff:3.500A)
      removed outlier: 6.360A  pdb=" N   ARG B 304 " --> pdb=" O   ASP B 298 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'S' and resid 3 through 7
    Processing sheet with id=AB1, first strand: chain 'S' and resid 58 through 60
      removed outlier: 6.439A  pdb=" N   TRP S  36 " --> pdb=" O   VAL S  48 " (cutoff:3.500A)
      removed outlier: 4.350A  pdb=" N   TYR S  50 " --> pdb=" O   MET S  34 " (cutoff:3.500A)
      removed outlier: 6.582A  pdb=" N   MET S  34 " --> pdb=" O   TYR S  50 " (cutoff:3.500A)
      removed outlier: 4.315A  pdb=" N   PHE S 110 " --> pdb=" O   ARG S  98 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'S' and resid 58 through 60
      removed outlier: 6.439A  pdb=" N   TRP S  36 " --> pdb=" O   VAL S  48 " (cutoff:3.500A)
      removed outlier: 4.350A  pdb=" N   TYR S  50 " --> pdb=" O   MET S  34 " (cutoff:3.500A)
      removed outlier: 6.582A  pdb=" N   MET S  34 " --> pdb=" O   TYR S  50 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'S' and resid 140 through 142
    Processing sheet with id=AB4, first strand: chain 'S' and resid 147 through 148
      removed outlier: 6.152A  pdb=" N   LEU S 178 " --> pdb=" O   LEU S 187 " (cutoff:3.500A)
      removed outlier: 5.431A  pdb=" N   LEU S 187 " --> pdb=" O   LEU S 178 " (cutoff:3.500A)

    462 hydrogen bonds defined for protein.
    1299 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 2.72

  Time building geometry restraints manager: 2.58 seconds

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

  Histogram of bond lengths:
        1.17 -     1.30: 1355
        1.30 -     1.43: 2433
        1.43 -     1.56: 4831
        1.56 -     1.69: 0
        1.69 -     1.82: 72
  Bond restraints: 8691
  Sorted by residual:
  bond pdb=" C   GLU A  27 "
       pdb=" O   GLU A  27 "
    ideal  model  delta    sigma   weight residual
    1.237  1.167  0.069 1.17e-02 7.31e+03 3.52e+01
  bond pdb=" CZ  ARG A  15 "
       pdb=" NH2 ARG A  15 "
    ideal  model  delta    sigma   weight residual
    1.330  1.256  0.074 1.30e-02 5.92e+03 3.22e+01
  bond pdb=" CA  ASP A   9 "
       pdb=" CB  ASP A   9 "
    ideal  model  delta    sigma   weight residual
    1.528  1.442  0.087 1.56e-02 4.11e+03 3.08e+01
  bond pdb=" CA  ASP A   9 "
       pdb=" C   ASP A   9 "
    ideal  model  delta    sigma   weight residual
    1.523  1.458  0.066 1.30e-02 5.92e+03 2.54e+01
  bond pdb=" CA  HIS R 269 "
       pdb=" C   HIS R 269 "
    ideal  model  delta    sigma   weight residual
    1.524  1.466  0.058 1.29e-02 6.01e+03 2.01e+01
  ... (remaining 8686 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.39: 11602
        2.39 -     4.78: 215
        4.78 -     7.17: 28
        7.17 -     9.55: 7
        9.55 -    11.94: 3
  Bond angle restraints: 11855
  Sorted by residual:
  angle pdb=" N   ARG R 162 "
        pdb=" CA  ARG R 162 "
        pdb=" C   ARG R 162 "
      ideal   model   delta    sigma   weight residual
     112.54  123.31  -10.77 1.22e+00 6.72e-01 7.79e+01
  angle pdb=" C   HIS R 165 "
        pdb=" CA  HIS R 165 "
        pdb=" CB  HIS R 165 "
      ideal   model   delta    sigma   weight residual
     110.62   99.99   10.63 1.51e+00 4.39e-01 4.96e+01
  angle pdb=" N   ASP R 161 "
        pdb=" CA  ASP R 161 "
        pdb=" C   ASP R 161 "
      ideal   model   delta    sigma   weight residual
     109.24  118.49   -9.25 1.51e+00 4.39e-01 3.76e+01
  angle pdb=" N   TRP R 256 "
        pdb=" CA  TRP R 256 "
        pdb=" C   TRP R 256 "
      ideal   model   delta    sigma   weight residual
     111.07  104.69    6.38 1.07e+00 8.73e-01 3.55e+01
  angle pdb=" N   VAL R 186 "
        pdb=" CA  VAL R 186 "
        pdb=" C   VAL R 186 "
      ideal   model   delta    sigma   weight residual
     110.62  117.01   -6.39 1.14e+00 7.69e-01 3.15e+01
  ... (remaining 11850 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    16.72: 4564
       16.72 -    33.44: 393
       33.44 -    50.16: 75
       50.16 -    66.88: 13
       66.88 -    83.59: 8
  Dihedral angle restraints: 5053
    sinusoidal: 1717
      harmonic: 3336
  Sorted by residual:
  dihedral pdb=" CA  THR B 165 "
           pdb=" C   THR B 165 "
           pdb=" N   CYS B 166 "
           pdb=" CA  CYS B 166 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  152.16   27.84     0      5.00e+00 4.00e-02 3.10e+01
  dihedral pdb=" C   GLN A  29 "
           pdb=" N   GLN A  29 "
           pdb=" CA  GLN A  29 "
           pdb=" CB  GLN A  29 "
      ideal   model   delta  harmonic     sigma   weight residual
    -122.60 -135.48   12.88     0      2.50e+00 1.60e-01 2.65e+01
  dihedral pdb=" C   LYS A  17 "
           pdb=" N   LYS A  17 "
           pdb=" CA  LYS A  17 "
           pdb=" CB  LYS A  17 "
      ideal   model   delta  harmonic     sigma   weight residual
    -122.60 -135.10   12.50     0      2.50e+00 1.60e-01 2.50e+01
  ... (remaining 5050 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.116: 1325
       0.116 -    0.232: 32
       0.232 -    0.348: 5
       0.348 -    0.465: 1
       0.465 -    0.581: 3
  Chirality restraints: 1366
  Sorted by residual:
  chirality pdb=" CA  HIS R 269 "
            pdb=" N   HIS R 269 "
            pdb=" C   HIS R 269 "
            pdb=" CB  HIS R 269 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    1.93    0.58 2.00e-01 2.50e+01 8.43e+00
  chirality pdb=" CA  GLN A  29 "
            pdb=" N   GLN A  29 "
            pdb=" C   GLN A  29 "
            pdb=" CB  GLN A  29 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    1.96    0.55 2.00e-01 2.50e+01 7.51e+00
  chirality pdb=" CA  LYS A  17 "
            pdb=" N   LYS A  17 "
            pdb=" C   LYS A  17 "
            pdb=" CB  LYS A  17 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.03    0.48 2.00e-01 2.50e+01 5.70e+00
  ... (remaining 1363 not shown)

  Planarity restraints: 1513
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TYR B  59 "    0.022 2.00e-02 2.50e+03   1.67e-02 5.57e+00
        pdb=" CG  TYR B  59 "   -0.040 2.00e-02 2.50e+03
        pdb=" CD1 TYR B  59 "    0.009 2.00e-02 2.50e+03
        pdb=" CD2 TYR B  59 "    0.001 2.00e-02 2.50e+03
        pdb=" CE1 TYR B  59 "   -0.001 2.00e-02 2.50e+03
        pdb=" CE2 TYR B  59 "    0.006 2.00e-02 2.50e+03
        pdb=" CZ  TYR B  59 "   -0.003 2.00e-02 2.50e+03
        pdb=" OH  TYR B  59 "    0.005 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ASP S  74 "    0.032 5.00e-02 4.00e+02   4.86e-02 3.78e+00
        pdb=" N   PRO S  75 "   -0.084 5.00e-02 4.00e+02
        pdb=" CA  PRO S  75 "    0.025 5.00e-02 4.00e+02
        pdb=" CD  PRO S  75 "    0.027 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  PHE R 260 "   -0.011 2.00e-02 2.50e+03   1.40e-02 3.44e+00
        pdb=" CG  PHE R 260 "    0.032 2.00e-02 2.50e+03
        pdb=" CD1 PHE R 260 "   -0.012 2.00e-02 2.50e+03
        pdb=" CD2 PHE R 260 "   -0.008 2.00e-02 2.50e+03
        pdb=" CE1 PHE R 260 "    0.001 2.00e-02 2.50e+03
        pdb=" CE2 PHE R 260 "   -0.002 2.00e-02 2.50e+03
        pdb=" CZ  PHE R 260 "   -0.000 2.00e-02 2.50e+03
  ... (remaining 1510 not shown)

  Histogram of nonbonded interaction distances:
        2.02 -     2.60: 75
        2.60 -     3.17: 7267
        3.17 -     3.75: 13156
        3.75 -     4.32: 18392
        4.32 -     4.90: 30999
  Nonbonded interactions: 69889
  Sorted by model distance:
  nonbonded pdb=" OG  SER R 112 "
            pdb=" OG  SER R 200 "
     model   vdw
     2.023 3.040
  nonbonded pdb=" O   ILE B  58 "
            pdb=" OG  SER B 316 "
     model   vdw
     2.063 3.040
  nonbonded pdb=" NZ  LYS A 243 "
            pdb=" OD2 ASP B 228 "
     model   vdw
     2.159 3.120
  nonbonded pdb=" OG  SER B 281 "
            pdb=" OD2 ASP G  48 "
     model   vdw
     2.189 3.040
  nonbonded pdb=" OG1 THR B  86 "
            pdb=" OD1 ASN B  88 "
     model   vdw
     2.202 3.040
  ... (remaining 69884 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:             2.180
  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:             0.010
  Extract box with map and model:          0.360
  Check model and map are aligned:         0.070
  Set scattering table:                    0.080
  Process input model:                     23.490
  Find NCS groups from input model:        0.110
  Set up NCS constraints:                  0.040
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:13.080
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   39.420
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7392
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      :  0.008   0.087   8693  Z= 0.429
  Angle     :  0.818  11.942  11859  Z= 0.482
  Chirality :  0.060   0.581   1366
  Planarity :  0.005   0.049   1513
  Dihedral  : 13.564  83.594   2895
  Min Nonbonded Distance : 2.023

Molprobity Statistics.
  All-atom Clashscore : 9.65
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.22 %
    Favored  : 94.78 %
  Rotamer:
    Outliers :  0.24 %
    Allowed  :  0.73 %
    Favored  : 99.03 %
  Cbeta Deviations :  0.37 %
  Peptide Plane:
    Cis-proline     : 5.41 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.38 (0.25), residues: 1131
  helix:  0.69 (0.27), residues: 381
  sheet: -0.07 (0.30), residues: 289
  loop : -1.11 (0.29), residues: 461

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.002   TRP A 244 
 HIS   0.018   0.002   HIS A 357 
 PHE   0.032   0.002   PHE R 260 
 TYR   0.040   0.003   TYR B  59 
 ARG   0.011   0.001   ARG S 180 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.18118 (  449)
  hydrogen bonds       : angle       7.34065 ( 1299)
  SS BOND              : bond        0.00084 (    2)
  SS BOND              : angle       1.35901 (    4)
  covalent geometry    : bond        0.00800 ( 8691)
  covalent geometry    : angle       0.81764 (11855)

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

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

  2262 Ramachandran restraints generated.
    1131 Oldfield, 0 Emsley, 1131 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2262 Ramachandran restraints generated.
    1131 Oldfield, 0 Emsley, 1131 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  231 residues out of total 983 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 229
  time to evaluate  : 0.835 
Fit side-chains
   revert: symmetry clash
REVERT: A  221 LYS cc_start: 0.7680 (mppt) cc_final: 0.7444 (mppt)
REVERT: A  258 VAL cc_start: 0.8657 (p) cc_final: 0.8311 (t)
REVERT: A  347 ARG cc_start: 0.7860 (ttm-80) cc_final: 0.7653 (ttm-80)
REVERT: B  258 ASP cc_start: 0.6702 (t70) cc_final: 0.6419 (t0)
REVERT: S  116 THR cc_start: 0.8119 (t) cc_final: 0.7831 (p)
REVERT: R  104 SER cc_start: 0.7867 (m) cc_final: 0.7663 (m)
REVERT: R  141 VAL cc_start: 0.8343 (p) cc_final: 0.8008 (t)
REVERT: R  174 MET cc_start: 0.7142 (tpp) cc_final: 0.6686 (mmm)
REVERT: R  190 PHE cc_start: 0.7758 (t80) cc_final: 0.7494 (t80)
  outliers start: 2
  outliers final: 2
  residues processed: 230
  average time/residue: 0.9086
  time to fit residues: 225.6076
Evaluate side-chains
  207 residues out of total 983 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 205
  time to evaluate  : 0.895 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    9 ASP
Chi-restraints excluded: chain R residue  105 ILE
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 113
   random chunks:
   chunk 95 optimal weight:    0.9990
   chunk 85 optimal weight:    0.9980
   chunk 47 optimal weight:    0.7980
   chunk 29 optimal weight:    0.5980
   chunk 57 optimal weight:    0.9980
   chunk 45 optimal weight:    0.7980
   chunk 88 optimal weight:    0.9990
   chunk 34 optimal weight:    0.5980
   chunk 53 optimal weight:    0.1980
   chunk 65 optimal weight:    0.4980
   chunk 102 optimal weight:    0.6980
   overall best weight:    0.5180

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

Flipped N/Q/H residues before XYZ refinement:
A  35 GLN
B  88 ASN
B 230 ASN
S  39 GLN
S  82 GLN
R  58 ASN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3574 r_free = 0.3574 target = 0.122016 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3334 r_free = 0.3334 target = 0.105663 restraints weight = 12699.877|
|-----------------------------------------------------------------------------|
r_work (start): 0.3328 rms_B_bonded: 1.81
r_work: 0.3226 rms_B_bonded: 2.22 restraints_weight: 0.5000
r_work: 0.3094 rms_B_bonded: 3.89 restraints_weight: 0.2500
r_work (final): 0.3094
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7750
moved from start:          0.1579

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.038   8693  Z= 0.168
  Angle     :  0.615  11.380  11859  Z= 0.325
  Chirality :  0.044   0.137   1366
  Planarity :  0.005   0.046   1513
  Dihedral  :  4.817  38.160   1241
  Min Nonbonded Distance : 2.500

Molprobity Statistics.
  All-atom Clashscore : 7.63
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.27 %
    Favored  : 96.73 %
  Rotamer:
    Outliers :  2.91 %
    Allowed  : 10.91 %
    Favored  : 86.18 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.41 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.20 (0.25), residues: 1131
  helix:  1.46 (0.27), residues: 377
  sheet:  0.09 (0.31), residues: 277
  loop : -0.89 (0.29), residues: 477

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.019   0.002   TRP B 339 
 HIS   0.009   0.001   HIS A 357 
 PHE   0.016   0.002   PHE A 222 
 TYR   0.025   0.002   TYR B  59 
 ARG   0.005   0.000   ARG R 202 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04705 (  449)
  hydrogen bonds       : angle       5.15906 ( 1299)
  SS BOND              : bond        0.00175 (    2)
  SS BOND              : angle       0.99597 (    4)
  covalent geometry    : bond        0.00383 ( 8691)
  covalent geometry    : angle       0.61501 (11855)

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

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

  2262 Ramachandran restraints generated.
    1131 Oldfield, 0 Emsley, 1131 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2262 Ramachandran restraints generated.
    1131 Oldfield, 0 Emsley, 1131 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  233 residues out of total 983 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 209
  time to evaluate  : 1.033 
Fit side-chains
   revert: symmetry clash
REVERT: A   36 VAL cc_start: 0.8458 (t) cc_final: 0.8120 (t)
REVERT: A   56 ILE cc_start: 0.7755 (mt) cc_final: 0.7450 (tp)
REVERT: A  221 LYS cc_start: 0.8199 (mppt) cc_final: 0.7779 (mppt)
REVERT: A  299 GLU cc_start: 0.7325 (mt-10) cc_final: 0.7116 (mt-10)
REVERT: A  347 ARG cc_start: 0.8263 (ttm-80) cc_final: 0.8061 (ttp-110)
REVERT: A  368 ASP cc_start: 0.6978 (m-30) cc_final: 0.6584 (m-30)
REVERT: B  136 SER cc_start: 0.8416 (t) cc_final: 0.8181 (m)
REVERT: B  170 ASP cc_start: 0.7946 (t0) cc_final: 0.7661 (t70)
REVERT: B  225 HIS cc_start: 0.8091 (OUTLIER) cc_final: 0.7807 (m-70)
REVERT: B  230 ASN cc_start: 0.8404 (m110) cc_final: 0.8197 (m-40)
REVERT: B  258 ASP cc_start: 0.7330 (t70) cc_final: 0.6793 (t0)
REVERT: B  304 ARG cc_start: 0.8050 (mmm-85) cc_final: 0.7724 (mmm-85)
REVERT: B  323 ASP cc_start: 0.7819 (OUTLIER) cc_final: 0.7584 (p0)
REVERT: B  329 THR cc_start: 0.8343 (OUTLIER) cc_final: 0.8139 (m)
REVERT: S  116 THR cc_start: 0.8236 (t) cc_final: 0.7959 (p)
REVERT: R   95 PHE cc_start: 0.7204 (t80) cc_final: 0.6787 (t80)
REVERT: R  174 MET cc_start: 0.7039 (tpp) cc_final: 0.6760 (mmm)
REVERT: R  190 PHE cc_start: 0.8238 (t80) cc_final: 0.8037 (t80)
REVERT: R  280 VAL cc_start: 0.8534 (OUTLIER) cc_final: 0.8265 (m)
  outliers start: 24
  outliers final: 11
  residues processed: 217
  average time/residue: 0.8880
  time to fit residues: 208.6846
Evaluate side-chains
  219 residues out of total 983 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 204
  time to evaluate  : 0.945 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   51 SER
Chi-restraints excluded: chain A residue  234 VAL
Chi-restraints excluded: chain A residue  252 THR
Chi-restraints excluded: chain B residue  225 HIS
Chi-restraints excluded: chain B residue  228 ASP
Chi-restraints excluded: chain B residue  317 CYS
Chi-restraints excluded: chain B residue  323 ASP
Chi-restraints excluded: chain B residue  329 THR
Chi-restraints excluded: chain B residue  331 SER
Chi-restraints excluded: chain S residue    7 SER
Chi-restraints excluded: chain S residue  158 SER
Chi-restraints excluded: chain R residue   78 LEU
Chi-restraints excluded: chain R residue  105 ILE
Chi-restraints excluded: chain R residue  276 SER
Chi-restraints excluded: chain R residue  280 VAL
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 113
   random chunks:
   chunk 87 optimal weight:    0.9980
   chunk 8 optimal weight:    0.8980
   chunk 101 optimal weight:    0.9980
   chunk 82 optimal weight:    2.9990
   chunk 84 optimal weight:    4.9990
   chunk 21 optimal weight:    1.9990
   chunk 14 optimal weight:    1.9990
   chunk 73 optimal weight:    0.7980
   chunk 109 optimal weight:    0.0020
   chunk 54 optimal weight:    0.8980
   chunk 106 optimal weight:    0.1980
   overall best weight:    0.5588

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

Flipped N/Q/H residues before XYZ refinement:
B 125 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3573 r_free = 0.3573 target = 0.121638 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3330 r_free = 0.3330 target = 0.105149 restraints weight = 12863.671|
|-----------------------------------------------------------------------------|
r_work (start): 0.3323 rms_B_bonded: 1.83
r_work: 0.3217 rms_B_bonded: 2.25 restraints_weight: 0.5000
r_work: 0.3081 rms_B_bonded: 3.95 restraints_weight: 0.2500
r_work (final): 0.3081
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7769
moved from start:          0.1987

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.031   8693  Z= 0.165
  Angle     :  0.582   9.471  11859  Z= 0.306
  Chirality :  0.043   0.137   1366
  Planarity :  0.004   0.050   1513
  Dihedral  :  4.614  40.624   1239
  Min Nonbonded Distance : 2.555

Molprobity Statistics.
  All-atom Clashscore : 7.02
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.71 %
    Favored  : 96.29 %
  Rotamer:
    Outliers :  4.00 %
    Allowed  : 15.27 %
    Favored  : 80.73 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.41 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.37 (0.25), residues: 1131
  helix:  1.72 (0.27), residues: 374
  sheet:  0.01 (0.31), residues: 274
  loop : -0.75 (0.28), residues: 483

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.002   TRP B 339 
 HIS   0.010   0.001   HIS A 357 
 PHE   0.016   0.002   PHE A 222 
 TYR   0.018   0.002   TYR B  59 
 ARG   0.006   0.000   ARG R 124 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04447 (  449)
  hydrogen bonds       : angle       4.79029 ( 1299)
  SS BOND              : bond        0.00230 (    2)
  SS BOND              : angle       0.92033 (    4)
  covalent geometry    : bond        0.00378 ( 8691)
  covalent geometry    : angle       0.58157 (11855)

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

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

  2262 Ramachandran restraints generated.
    1131 Oldfield, 0 Emsley, 1131 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2262 Ramachandran restraints generated.
    1131 Oldfield, 0 Emsley, 1131 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  239 residues out of total 983 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 206
  time to evaluate  : 1.096 
Fit side-chains
   revert: symmetry clash
REVERT: A   36 VAL cc_start: 0.8468 (t) cc_final: 0.8122 (t)
REVERT: A   56 ILE cc_start: 0.7698 (mt) cc_final: 0.7389 (tp)
REVERT: A  219 GLU cc_start: 0.7236 (OUTLIER) cc_final: 0.6958 (tp30)
REVERT: A  221 LYS cc_start: 0.8157 (mppt) cc_final: 0.7739 (mppt)
REVERT: A  299 GLU cc_start: 0.7402 (mt-10) cc_final: 0.7181 (mt-10)
REVERT: A  347 ARG cc_start: 0.8289 (ttm-80) cc_final: 0.8076 (ttp-110)
REVERT: A  368 ASP cc_start: 0.7001 (m-30) cc_final: 0.6600 (m-30)
REVERT: A  380 ARG cc_start: 0.8429 (OUTLIER) cc_final: 0.7274 (ttp80)
REVERT: B  158 VAL cc_start: 0.8499 (t) cc_final: 0.8266 (p)
REVERT: B  170 ASP cc_start: 0.7952 (t0) cc_final: 0.7659 (t70)
REVERT: B  228 ASP cc_start: 0.8173 (OUTLIER) cc_final: 0.7956 (OUTLIER)
REVERT: B  258 ASP cc_start: 0.7348 (t70) cc_final: 0.6834 (t0)
REVERT: B  304 ARG cc_start: 0.8087 (mmm-85) cc_final: 0.7761 (mmm-85)
REVERT: B  323 ASP cc_start: 0.7835 (OUTLIER) cc_final: 0.7613 (p0)
REVERT: S    7 SER cc_start: 0.8361 (OUTLIER) cc_final: 0.8021 (m)
REVERT: S  116 THR cc_start: 0.8225 (t) cc_final: 0.7971 (p)
REVERT: S  227 TYR cc_start: 0.8278 (m-80) cc_final: 0.7956 (m-80)
REVERT: R  174 MET cc_start: 0.7201 (tpp) cc_final: 0.6939 (mmm)
  outliers start: 33
  outliers final: 16
  residues processed: 220
  average time/residue: 0.8675
  time to fit residues: 207.5206
Evaluate side-chains
  226 residues out of total 983 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 206
  time to evaluate  : 0.866 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   18 MET
Chi-restraints excluded: chain A residue  219 GLU
Chi-restraints excluded: chain A residue  234 VAL
Chi-restraints excluded: chain A residue  252 THR
Chi-restraints excluded: chain A residue  275 SER
Chi-restraints excluded: chain A residue  289 LEU
Chi-restraints excluded: chain A residue  380 ARG
Chi-restraints excluded: chain B residue  101 MET
Chi-restraints excluded: chain B residue  228 ASP
Chi-restraints excluded: chain B residue  317 CYS
Chi-restraints excluded: chain B residue  323 ASP
Chi-restraints excluded: chain B residue  331 SER
Chi-restraints excluded: chain S residue    7 SER
Chi-restraints excluded: chain S residue   48 VAL
Chi-restraints excluded: chain S residue   91 THR
Chi-restraints excluded: chain R residue   39 LEU
Chi-restraints excluded: chain R residue  105 ILE
Chi-restraints excluded: chain R residue  112 SER
Chi-restraints excluded: chain R residue  146 LEU
Chi-restraints excluded: chain R residue  178 VAL
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 113
   random chunks:
   chunk 84 optimal weight:    5.9990
   chunk 112 optimal weight:    0.6980
   chunk 7 optimal weight:    2.9990
   chunk 108 optimal weight:    0.3980
   chunk 107 optimal weight:    0.9990
   chunk 69 optimal weight:    0.8980
   chunk 3 optimal weight:    0.9980
   chunk 9 optimal weight:    0.6980
   chunk 45 optimal weight:    0.7980
   chunk 59 optimal weight:    2.9990
   chunk 101 optimal weight:    1.9990
   overall best weight:    0.6980

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

Flipped N/Q/H residues before XYZ refinement:
B 125 ASN
B 156 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3561 r_free = 0.3561 target = 0.121265 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3319 r_free = 0.3319 target = 0.104849 restraints weight = 12758.101|
|-----------------------------------------------------------------------------|
r_work (start): 0.3311 rms_B_bonded: 1.84
r_work: 0.3204 rms_B_bonded: 2.25 restraints_weight: 0.5000
r_work: 0.3067 rms_B_bonded: 3.95 restraints_weight: 0.2500
r_work (final): 0.3067
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7780
moved from start:          0.2236

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.037   8693  Z= 0.188
  Angle     :  0.594  11.382  11859  Z= 0.311
  Chirality :  0.044   0.142   1366
  Planarity :  0.005   0.052   1513
  Dihedral  :  4.696  45.699   1239
  Min Nonbonded Distance : 2.572

Molprobity Statistics.
  All-atom Clashscore : 7.09
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.07 %
    Favored  : 95.93 %
  Rotamer:
    Outliers :  3.88 %
    Allowed  : 16.73 %
    Favored  : 79.39 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.41 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.32 (0.25), residues: 1131
  helix:  1.66 (0.27), residues: 379
  sheet: -0.07 (0.30), residues: 279
  loop : -0.76 (0.29), residues: 473

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.002   TRP B 339 
 HIS   0.011   0.001   HIS A 357 
 PHE   0.019   0.002   PHE R  93 
 TYR   0.016   0.002   TYR B  59 
 ARG   0.009   0.000   ARG R 124 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04471 (  449)
  hydrogen bonds       : angle       4.74490 ( 1299)
  SS BOND              : bond        0.00237 (    2)
  SS BOND              : angle       0.96142 (    4)
  covalent geometry    : bond        0.00437 ( 8691)
  covalent geometry    : angle       0.59423 (11855)

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

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

  2262 Ramachandran restraints generated.
    1131 Oldfield, 0 Emsley, 1131 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2262 Ramachandran restraints generated.
    1131 Oldfield, 0 Emsley, 1131 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  240 residues out of total 983 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 208
  time to evaluate  : 0.901 
Fit side-chains
   revert: symmetry clash
REVERT: A   56 ILE cc_start: 0.7747 (mt) cc_final: 0.7493 (tp)
REVERT: A  221 LYS cc_start: 0.8134 (mppt) cc_final: 0.7708 (mppt)
REVERT: A  299 GLU cc_start: 0.7384 (mt-10) cc_final: 0.7166 (mt-10)
REVERT: A  347 ARG cc_start: 0.8285 (ttm-80) cc_final: 0.7953 (ttp-110)
REVERT: A  368 ASP cc_start: 0.7008 (m-30) cc_final: 0.6594 (m-30)
REVERT: A  380 ARG cc_start: 0.8435 (OUTLIER) cc_final: 0.7309 (ttp80)
REVERT: B  155 ASN cc_start: 0.8072 (t0) cc_final: 0.7787 (t0)
REVERT: B  158 VAL cc_start: 0.8479 (t) cc_final: 0.8215 (p)
REVERT: B  190 LEU cc_start: 0.8370 (tp) cc_final: 0.8136 (tt)
REVERT: B  228 ASP cc_start: 0.8236 (OUTLIER) cc_final: 0.7993 (p0)
REVERT: B  258 ASP cc_start: 0.7421 (t70) cc_final: 0.6903 (OUTLIER)
REVERT: B  323 ASP cc_start: 0.7891 (OUTLIER) cc_final: 0.7661 (p0)
REVERT: S    7 SER cc_start: 0.8216 (OUTLIER) cc_final: 0.7884 (m)
REVERT: R  174 MET cc_start: 0.7290 (tpp) cc_final: 0.6548 (tpp)
  outliers start: 32
  outliers final: 22
  residues processed: 221
  average time/residue: 0.8828
  time to fit residues: 211.4992
Evaluate side-chains
  227 residues out of total 983 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 202
  time to evaluate  : 0.811 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   18 MET
Chi-restraints excluded: chain A residue  225 ASP
Chi-restraints excluded: chain A residue  234 VAL
Chi-restraints excluded: chain A residue  252 THR
Chi-restraints excluded: chain A residue  275 SER
Chi-restraints excluded: chain A residue  289 LEU
Chi-restraints excluded: chain A residue  380 ARG
Chi-restraints excluded: chain B residue  101 MET
Chi-restraints excluded: chain B residue  157 ILE
Chi-restraints excluded: chain B residue  228 ASP
Chi-restraints excluded: chain B residue  317 CYS
Chi-restraints excluded: chain B residue  323 ASP
Chi-restraints excluded: chain B residue  331 SER
Chi-restraints excluded: chain S residue    7 SER
Chi-restraints excluded: chain S residue   48 VAL
Chi-restraints excluded: chain S residue   91 THR
Chi-restraints excluded: chain S residue  226 VAL
Chi-restraints excluded: chain S residue  233 LEU
Chi-restraints excluded: chain R residue   39 LEU
Chi-restraints excluded: chain R residue  105 ILE
Chi-restraints excluded: chain R residue  112 SER
Chi-restraints excluded: chain R residue  146 LEU
Chi-restraints excluded: chain R residue  178 VAL
Chi-restraints excluded: chain R residue  212 VAL
Chi-restraints excluded: chain R residue  276 SER
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 113
   random chunks:
   chunk 16 optimal weight:    0.7980
   chunk 9 optimal weight:    1.9990
   chunk 12 optimal weight:    0.6980
   chunk 94 optimal weight:    0.5980
   chunk 105 optimal weight:    0.5980
   chunk 81 optimal weight:    0.6980
   chunk 54 optimal weight:    0.8980
   chunk 20 optimal weight:    0.6980
   chunk 38 optimal weight:    0.9980
   chunk 15 optimal weight:    0.6980
   chunk 31 optimal weight:    0.9990
   overall best weight:    0.6580

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

Flipped N/Q/H residues before XYZ refinement:
B 156 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3561 r_free = 0.3561 target = 0.120669 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3320 r_free = 0.3320 target = 0.104328 restraints weight = 12725.852|
|-----------------------------------------------------------------------------|
r_work (start): 0.3315 rms_B_bonded: 1.83
r_work: 0.3209 rms_B_bonded: 2.24 restraints_weight: 0.5000
r_work: 0.3072 rms_B_bonded: 3.93 restraints_weight: 0.2500
r_work (final): 0.3072
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7780
moved from start:          0.2427

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.033   8693  Z= 0.178
  Angle     :  0.581   9.982  11859  Z= 0.304
  Chirality :  0.043   0.136   1366
  Planarity :  0.004   0.051   1513
  Dihedral  :  4.675  49.613   1239
  Min Nonbonded Distance : 2.500

Molprobity Statistics.
  All-atom Clashscore : 7.21
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.07 %
    Favored  : 95.93 %
  Rotamer:
    Outliers :  4.61 %
    Allowed  : 17.94 %
    Favored  : 77.45 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.41 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.37 (0.25), residues: 1131
  helix:  1.72 (0.27), residues: 379
  sheet: -0.02 (0.30), residues: 284
  loop : -0.76 (0.29), residues: 468

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.002   TRP B  63 
 HIS   0.010   0.001   HIS A 357 
 PHE   0.016   0.002   PHE R  93 
 TYR   0.021   0.002   TYR B  59 
 ARG   0.009   0.000   ARG R 124 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04306 (  449)
  hydrogen bonds       : angle       4.66954 ( 1299)
  SS BOND              : bond        0.00225 (    2)
  SS BOND              : angle       0.88243 (    4)
  covalent geometry    : bond        0.00413 ( 8691)
  covalent geometry    : angle       0.58126 (11855)

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

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

  2262 Ramachandran restraints generated.
    1131 Oldfield, 0 Emsley, 1131 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2262 Ramachandran restraints generated.
    1131 Oldfield, 0 Emsley, 1131 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  253 residues out of total 983 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 38
    poor density    : 215
  time to evaluate  : 0.920 
Fit side-chains
   revert: symmetry clash
REVERT: A   36 VAL cc_start: 0.8483 (t) cc_final: 0.8163 (t)
REVERT: A   56 ILE cc_start: 0.7726 (mt) cc_final: 0.7468 (tp)
REVERT: A  299 GLU cc_start: 0.7389 (mt-10) cc_final: 0.7171 (mt-10)
REVERT: A  347 ARG cc_start: 0.8290 (ttm-80) cc_final: 0.7959 (ttp-110)
REVERT: A  368 ASP cc_start: 0.6984 (m-30) cc_final: 0.6590 (m-30)
REVERT: A  380 ARG cc_start: 0.8440 (OUTLIER) cc_final: 0.7310 (ttp80)
REVERT: B  155 ASN cc_start: 0.8057 (t0) cc_final: 0.7655 (t0)
REVERT: B  158 VAL cc_start: 0.8481 (t) cc_final: 0.8232 (p)
REVERT: B  175 GLN cc_start: 0.7743 (mm110) cc_final: 0.7526 (mm110)
REVERT: B  228 ASP cc_start: 0.8183 (OUTLIER) cc_final: 0.7947 (p0)
REVERT: B  258 ASP cc_start: 0.7443 (t70) cc_final: 0.6929 (t0)
REVERT: B  304 ARG cc_start: 0.8104 (mmm-85) cc_final: 0.7748 (mmm-85)
REVERT: B  323 ASP cc_start: 0.7887 (OUTLIER) cc_final: 0.7679 (p0)
REVERT: S    7 SER cc_start: 0.8339 (OUTLIER) cc_final: 0.8084 (m)
REVERT: R  242 VAL cc_start: 0.8280 (t) cc_final: 0.8007 (p)
  outliers start: 38
  outliers final: 23
  residues processed: 232
  average time/residue: 0.8746
  time to fit residues: 219.9881
Evaluate side-chains
  237 residues out of total 983 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 210
  time to evaluate  : 0.940 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   18 MET
Chi-restraints excluded: chain A residue  225 ASP
Chi-restraints excluded: chain A residue  234 VAL
Chi-restraints excluded: chain A residue  252 THR
Chi-restraints excluded: chain A residue  275 SER
Chi-restraints excluded: chain A residue  289 LEU
Chi-restraints excluded: chain A residue  296 LEU
Chi-restraints excluded: chain A residue  380 ARG
Chi-restraints excluded: chain B residue  101 MET
Chi-restraints excluded: chain B residue  157 ILE
Chi-restraints excluded: chain B residue  228 ASP
Chi-restraints excluded: chain B residue  317 CYS
Chi-restraints excluded: chain B residue  323 ASP
Chi-restraints excluded: chain B residue  331 SER
Chi-restraints excluded: chain S residue    7 SER
Chi-restraints excluded: chain S residue   48 VAL
Chi-restraints excluded: chain S residue   91 THR
Chi-restraints excluded: chain S residue  158 SER
Chi-restraints excluded: chain S residue  226 VAL
Chi-restraints excluded: chain R residue   39 LEU
Chi-restraints excluded: chain R residue  105 ILE
Chi-restraints excluded: chain R residue  112 SER
Chi-restraints excluded: chain R residue  146 LEU
Chi-restraints excluded: chain R residue  178 VAL
Chi-restraints excluded: chain R residue  183 LEU
Chi-restraints excluded: chain R residue  212 VAL
Chi-restraints excluded: chain R residue  276 SER
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 113
   random chunks:
   chunk 68 optimal weight:    0.0670
   chunk 108 optimal weight:    0.0000
   chunk 47 optimal weight:    2.9990
   chunk 12 optimal weight:    0.6980
   chunk 28 optimal weight:    0.9980
   chunk 10 optimal weight:    1.9990
   chunk 41 optimal weight:    1.9990
   chunk 62 optimal weight:    0.6980
   chunk 95 optimal weight:    0.0270
   chunk 35 optimal weight:    2.9990
   chunk 19 optimal weight:    0.9990
   overall best weight:    0.2980

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

Flipped N/Q/H residues before XYZ refinement:
B 156 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3594 r_free = 0.3594 target = 0.123973 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3359 r_free = 0.3359 target = 0.107926 restraints weight = 12725.491|
|-----------------------------------------------------------------------------|
r_work (start): 0.3351 rms_B_bonded: 1.77
r_work: 0.3251 rms_B_bonded: 2.17 restraints_weight: 0.5000
r_work: 0.3121 rms_B_bonded: 3.82 restraints_weight: 0.2500
r_work (final): 0.3121
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7737
moved from start:          0.2693

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   8693  Z= 0.116
  Angle     :  0.535   8.584  11859  Z= 0.280
  Chirality :  0.041   0.134   1366
  Planarity :  0.004   0.050   1513
  Dihedral  :  4.431  50.867   1239
  Min Nonbonded Distance : 2.564

Molprobity Statistics.
  All-atom Clashscore : 7.27
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.80 %
    Favored  : 96.20 %
  Rotamer:
    Outliers :  3.64 %
    Allowed  : 20.24 %
    Favored  : 76.12 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.41 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.58 (0.26), residues: 1131
  helix:  1.94 (0.27), residues: 384
  sheet:  0.04 (0.31), residues: 281
  loop : -0.69 (0.30), residues: 466

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.002   TRP B 339 
 HIS   0.006   0.001   HIS A 357 
 PHE   0.014   0.001   PHE R 237 
 TYR   0.012   0.001   TYR A  37 
 ARG   0.009   0.000   ARG R 124 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03673 (  449)
  hydrogen bonds       : angle       4.45877 ( 1299)
  SS BOND              : bond        0.00321 (    2)
  SS BOND              : angle       0.94522 (    4)
  covalent geometry    : bond        0.00259 ( 8691)
  covalent geometry    : angle       0.53494 (11855)

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

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

  2262 Ramachandran restraints generated.
    1131 Oldfield, 0 Emsley, 1131 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2262 Ramachandran restraints generated.
    1131 Oldfield, 0 Emsley, 1131 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  241 residues out of total 983 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 211
  time to evaluate  : 1.169 
Fit side-chains
   revert: symmetry clash
REVERT: A   36 VAL cc_start: 0.8408 (t) cc_final: 0.8061 (t)
REVERT: A   53 LYS cc_start: 0.8033 (pttt) cc_final: 0.7796 (pttt)
REVERT: A   56 ILE cc_start: 0.7726 (mt) cc_final: 0.7517 (tp)
REVERT: A  258 VAL cc_start: 0.8705 (p) cc_final: 0.8461 (t)
REVERT: A  299 GLU cc_start: 0.7358 (mt-10) cc_final: 0.7138 (mt-10)
REVERT: A  347 ARG cc_start: 0.8254 (ttm-80) cc_final: 0.7998 (ttp-110)
REVERT: A  368 ASP cc_start: 0.6967 (m-30) cc_final: 0.6573 (m-30)
REVERT: A  391 TYR cc_start: 0.8509 (m-80) cc_final: 0.8239 (m-80)
REVERT: B  155 ASN cc_start: 0.7975 (t0) cc_final: 0.7671 (t0)
REVERT: B  170 ASP cc_start: 0.7882 (t0) cc_final: 0.7585 (t70)
REVERT: B  175 GLN cc_start: 0.7699 (mm110) cc_final: 0.7469 (mm110)
REVERT: B  228 ASP cc_start: 0.8148 (OUTLIER) cc_final: 0.7946 (p0)
REVERT: B  258 ASP cc_start: 0.7400 (t70) cc_final: 0.6963 (t0)
REVERT: B  340 ASN cc_start: 0.7331 (t0) cc_final: 0.6995 (t0)
REVERT: S    7 SER cc_start: 0.8301 (p) cc_final: 0.8057 (m)
REVERT: R  174 MET cc_start: 0.6916 (mmm) cc_final: 0.6564 (mmm)
REVERT: R  186 VAL cc_start: 0.8059 (OUTLIER) cc_final: 0.7783 (t)
REVERT: R  242 VAL cc_start: 0.8275 (t) cc_final: 0.8017 (p)
REVERT: R  271 SER cc_start: 0.7540 (p) cc_final: 0.7324 (m)
  outliers start: 30
  outliers final: 17
  residues processed: 224
  average time/residue: 0.8751
  time to fit residues: 212.6958
Evaluate side-chains
  222 residues out of total 983 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 203
  time to evaluate  : 0.819 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   18 MET
Chi-restraints excluded: chain A residue  234 VAL
Chi-restraints excluded: chain A residue  249 ASN
Chi-restraints excluded: chain A residue  289 LEU
Chi-restraints excluded: chain B residue  101 MET
Chi-restraints excluded: chain B residue  157 ILE
Chi-restraints excluded: chain B residue  228 ASP
Chi-restraints excluded: chain B residue  317 CYS
Chi-restraints excluded: chain B residue  331 SER
Chi-restraints excluded: chain S residue   48 VAL
Chi-restraints excluded: chain S residue   91 THR
Chi-restraints excluded: chain S residue  149 VAL
Chi-restraints excluded: chain S residue  158 SER
Chi-restraints excluded: chain S residue  226 VAL
Chi-restraints excluded: chain R residue   39 LEU
Chi-restraints excluded: chain R residue  105 ILE
Chi-restraints excluded: chain R residue  112 SER
Chi-restraints excluded: chain R residue  183 LEU
Chi-restraints excluded: chain R residue  186 VAL
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 113
   random chunks:
   chunk 80 optimal weight:    3.9990
   chunk 40 optimal weight:    2.9990
   chunk 6 optimal weight:    0.0370
   chunk 10 optimal weight:    1.9990
   chunk 36 optimal weight:    0.0970
   chunk 31 optimal weight:    0.9980
   chunk 38 optimal weight:    0.9980
   chunk 109 optimal weight:    0.8980
   chunk 58 optimal weight:    0.7980
   chunk 45 optimal weight:    0.6980
   chunk 5 optimal weight:    2.9990
   overall best weight:    0.5056

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

Flipped N/Q/H residues before XYZ refinement:
B 125 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3575 r_free = 0.3575 target = 0.121855 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3333 r_free = 0.3333 target = 0.105440 restraints weight = 12854.486|
|-----------------------------------------------------------------------------|
r_work (start): 0.3328 rms_B_bonded: 1.85
r_work: 0.3222 rms_B_bonded: 2.26 restraints_weight: 0.5000
r_work: 0.3085 rms_B_bonded: 3.97 restraints_weight: 0.2500
r_work (final): 0.3085
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7760
moved from start:          0.2708

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   8693  Z= 0.149
  Angle     :  0.567  12.984  11859  Z= 0.293
  Chirality :  0.043   0.155   1366
  Planarity :  0.004   0.045   1513
  Dihedral  :  4.491  50.857   1239
  Min Nonbonded Distance : 2.560

Molprobity Statistics.
  All-atom Clashscore : 7.70
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.71 %
    Favored  : 96.29 %
  Rotamer:
    Outliers :  3.64 %
    Allowed  : 21.21 %
    Favored  : 75.15 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.41 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.59 (0.26), residues: 1131
  helix:  1.93 (0.27), residues: 384
  sheet:  0.04 (0.30), residues: 289
  loop : -0.66 (0.30), residues: 458

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.030   0.002   TRP R 142 
 HIS   0.008   0.001   HIS A 357 
 PHE   0.014   0.002   PHE A 222 
 TYR   0.016   0.002   TYR A  37 
 ARG   0.009   0.000   ARG R 124 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03955 (  449)
  hydrogen bonds       : angle       4.54769 ( 1299)
  SS BOND              : bond        0.00236 (    2)
  SS BOND              : angle       0.77947 (    4)
  covalent geometry    : bond        0.00346 ( 8691)
  covalent geometry    : angle       0.56708 (11855)

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

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

  2262 Ramachandran restraints generated.
    1131 Oldfield, 0 Emsley, 1131 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2262 Ramachandran restraints generated.
    1131 Oldfield, 0 Emsley, 1131 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  238 residues out of total 983 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 208
  time to evaluate  : 0.916 
Fit side-chains
   revert: symmetry clash
REVERT: A   36 VAL cc_start: 0.8455 (t) cc_final: 0.8124 (t)
REVERT: A   53 LYS cc_start: 0.8029 (pttt) cc_final: 0.7815 (pttt)
REVERT: A   56 ILE cc_start: 0.7681 (mt) cc_final: 0.7442 (tp)
REVERT: A  258 VAL cc_start: 0.8705 (p) cc_final: 0.8473 (t)
REVERT: A  299 GLU cc_start: 0.7392 (mt-10) cc_final: 0.7180 (mt-10)
REVERT: A  347 ARG cc_start: 0.8214 (ttm-80) cc_final: 0.7998 (ttp-110)
REVERT: A  368 ASP cc_start: 0.7000 (m-30) cc_final: 0.6538 (m-30)
REVERT: B  155 ASN cc_start: 0.7997 (t0) cc_final: 0.7529 (t0)
REVERT: B  157 ILE cc_start: 0.8383 (OUTLIER) cc_final: 0.8145 (tp)
REVERT: B  175 GLN cc_start: 0.7727 (mm110) cc_final: 0.7462 (mm110)
REVERT: B  190 LEU cc_start: 0.8346 (tp) cc_final: 0.8116 (tt)
REVERT: B  228 ASP cc_start: 0.8193 (OUTLIER) cc_final: 0.7976 (p0)
REVERT: B  258 ASP cc_start: 0.7427 (t70) cc_final: 0.6915 (t0)
REVERT: B  340 ASN cc_start: 0.7456 (t0) cc_final: 0.7080 (t0)
REVERT: S    7 SER cc_start: 0.8406 (p) cc_final: 0.8177 (m)
REVERT: R  174 MET cc_start: 0.6951 (mmm) cc_final: 0.6521 (mmm)
REVERT: R  186 VAL cc_start: 0.8008 (OUTLIER) cc_final: 0.7727 (t)
REVERT: R  242 VAL cc_start: 0.8322 (t) cc_final: 0.8049 (p)
REVERT: R  271 SER cc_start: 0.7681 (p) cc_final: 0.7471 (m)
  outliers start: 30
  outliers final: 20
  residues processed: 219
  average time/residue: 0.8885
  time to fit residues: 210.6866
Evaluate side-chains
  227 residues out of total 983 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 204
  time to evaluate  : 0.934 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   18 MET
Chi-restraints excluded: chain A residue  234 VAL
Chi-restraints excluded: chain A residue  249 ASN
Chi-restraints excluded: chain A residue  252 THR
Chi-restraints excluded: chain A residue  266 LEU
Chi-restraints excluded: chain A residue  275 SER
Chi-restraints excluded: chain A residue  289 LEU
Chi-restraints excluded: chain A residue  296 LEU
Chi-restraints excluded: chain B residue  101 MET
Chi-restraints excluded: chain B residue  157 ILE
Chi-restraints excluded: chain B residue  228 ASP
Chi-restraints excluded: chain B residue  317 CYS
Chi-restraints excluded: chain B residue  331 SER
Chi-restraints excluded: chain S residue   48 VAL
Chi-restraints excluded: chain S residue   91 THR
Chi-restraints excluded: chain S residue  149 VAL
Chi-restraints excluded: chain S residue  158 SER
Chi-restraints excluded: chain S residue  226 VAL
Chi-restraints excluded: chain R residue   39 LEU
Chi-restraints excluded: chain R residue  105 ILE
Chi-restraints excluded: chain R residue  183 LEU
Chi-restraints excluded: chain R residue  186 VAL
Chi-restraints excluded: chain R residue  276 SER
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 113
   random chunks:
   chunk 46 optimal weight:    2.9990
   chunk 56 optimal weight:    0.8980
   chunk 37 optimal weight:    0.5980
   chunk 49 optimal weight:    3.9990
   chunk 73 optimal weight:    3.9990
   chunk 42 optimal weight:    0.5980
   chunk 84 optimal weight:    0.6980
   chunk 69 optimal weight:    0.8980
   chunk 102 optimal weight:    0.9990
   chunk 109 optimal weight:    0.8980
   chunk 101 optimal weight:    0.8980
   overall best weight:    0.7380

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3562 r_free = 0.3562 target = 0.120671 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3317 r_free = 0.3317 target = 0.104186 restraints weight = 12856.105|
|-----------------------------------------------------------------------------|
r_work (start): 0.3313 rms_B_bonded: 1.86
r_work: 0.3207 rms_B_bonded: 2.25 restraints_weight: 0.5000
r_work: 0.3070 rms_B_bonded: 3.95 restraints_weight: 0.2500
r_work (final): 0.3070
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7781
moved from start:          0.2679

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.040   8693  Z= 0.194
  Angle     :  0.599  11.990  11859  Z= 0.311
  Chirality :  0.044   0.167   1366
  Planarity :  0.004   0.045   1513
  Dihedral  :  4.681  51.135   1239
  Min Nonbonded Distance : 2.540

Molprobity Statistics.
  All-atom Clashscore : 7.94
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.07 %
    Favored  : 95.93 %
  Rotamer:
    Outliers :  4.12 %
    Allowed  : 21.33 %
    Favored  : 74.55 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.41 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.48 (0.25), residues: 1131
  helix:  1.83 (0.26), residues: 381
  sheet:  0.00 (0.30), residues: 289
  loop : -0.71 (0.30), residues: 461

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.029   0.002   TRP R 142 
 HIS   0.010   0.001   HIS A 357 
 PHE   0.015   0.002   PHE B 151 
 TYR   0.017   0.002   TYR A  37 
 ARG   0.009   0.001   ARG R 124 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04340 (  449)
  hydrogen bonds       : angle       4.68933 ( 1299)
  SS BOND              : bond        0.00220 (    2)
  SS BOND              : angle       0.90970 (    4)
  covalent geometry    : bond        0.00453 ( 8691)
  covalent geometry    : angle       0.59924 (11855)

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

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

  2262 Ramachandran restraints generated.
    1131 Oldfield, 0 Emsley, 1131 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2262 Ramachandran restraints generated.
    1131 Oldfield, 0 Emsley, 1131 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  239 residues out of total 983 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 205
  time to evaluate  : 0.832 
Fit side-chains
   revert: symmetry clash
REVERT: A   53 LYS cc_start: 0.8077 (pttt) cc_final: 0.7868 (pttt)
REVERT: A   56 ILE cc_start: 0.7726 (mt) cc_final: 0.7473 (tp)
REVERT: A  221 LYS cc_start: 0.8094 (mppt) cc_final: 0.7871 (mppt)
REVERT: A  258 VAL cc_start: 0.8715 (p) cc_final: 0.8483 (t)
REVERT: A  299 GLU cc_start: 0.7407 (mt-10) cc_final: 0.7187 (mt-10)
REVERT: A  347 ARG cc_start: 0.8269 (ttm-80) cc_final: 0.7940 (ttp-110)
REVERT: A  368 ASP cc_start: 0.6999 (m-30) cc_final: 0.6527 (m-30)
REVERT: A  380 ARG cc_start: 0.8496 (OUTLIER) cc_final: 0.7405 (ttp80)
REVERT: B  155 ASN cc_start: 0.8028 (t0) cc_final: 0.7561 (t0)
REVERT: B  157 ILE cc_start: 0.8385 (OUTLIER) cc_final: 0.8163 (tp)
REVERT: B  170 ASP cc_start: 0.7996 (t70) cc_final: 0.7549 (t70)
REVERT: B  175 GLN cc_start: 0.7751 (mm110) cc_final: 0.7489 (mm110)
REVERT: B  228 ASP cc_start: 0.8204 (OUTLIER) cc_final: 0.7944 (p0)
REVERT: B  258 ASP cc_start: 0.7451 (t70) cc_final: 0.6938 (t0)
REVERT: B  262 MET cc_start: 0.6213 (tpt) cc_final: 0.6013 (tpt)
REVERT: B  340 ASN cc_start: 0.7428 (t0) cc_final: 0.7050 (t0)
REVERT: S    7 SER cc_start: 0.8390 (p) cc_final: 0.8171 (m)
REVERT: R   61 ILE cc_start: 0.8254 (mm) cc_final: 0.7978 (mp)
REVERT: R  174 MET cc_start: 0.7065 (mmm) cc_final: 0.6748 (mmm)
REVERT: R  186 VAL cc_start: 0.8023 (OUTLIER) cc_final: 0.7733 (t)
REVERT: R  242 VAL cc_start: 0.8296 (t) cc_final: 0.8026 (p)
  outliers start: 34
  outliers final: 23
  residues processed: 222
  average time/residue: 0.8346
  time to fit residues: 201.8975
Evaluate side-chains
  231 residues out of total 983 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 204
  time to evaluate  : 0.806 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   18 MET
Chi-restraints excluded: chain A residue  234 VAL
Chi-restraints excluded: chain A residue  249 ASN
Chi-restraints excluded: chain A residue  252 THR
Chi-restraints excluded: chain A residue  266 LEU
Chi-restraints excluded: chain A residue  275 SER
Chi-restraints excluded: chain A residue  289 LEU
Chi-restraints excluded: chain A residue  296 LEU
Chi-restraints excluded: chain A residue  380 ARG
Chi-restraints excluded: chain B residue  101 MET
Chi-restraints excluded: chain B residue  112 VAL
Chi-restraints excluded: chain B residue  157 ILE
Chi-restraints excluded: chain B residue  228 ASP
Chi-restraints excluded: chain B residue  317 CYS
Chi-restraints excluded: chain B residue  331 SER
Chi-restraints excluded: chain S residue    6 GLU
Chi-restraints excluded: chain S residue   48 VAL
Chi-restraints excluded: chain S residue   91 THR
Chi-restraints excluded: chain S residue  149 VAL
Chi-restraints excluded: chain S residue  158 SER
Chi-restraints excluded: chain S residue  226 VAL
Chi-restraints excluded: chain R residue   39 LEU
Chi-restraints excluded: chain R residue  105 ILE
Chi-restraints excluded: chain R residue  146 LEU
Chi-restraints excluded: chain R residue  183 LEU
Chi-restraints excluded: chain R residue  186 VAL
Chi-restraints excluded: chain R residue  276 SER
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 113
   random chunks:
   chunk 40 optimal weight:    2.9990
   chunk 95 optimal weight:    0.4980
   chunk 20 optimal weight:    0.7980
   chunk 6 optimal weight:    1.9990
   chunk 109 optimal weight:    1.9990
   chunk 46 optimal weight:    1.9990
   chunk 5 optimal weight:    4.9990
   chunk 35 optimal weight:    0.9980
   chunk 103 optimal weight:    0.8980
   chunk 83 optimal weight:    1.9990
   chunk 107 optimal weight:    0.5980
   overall best weight:    0.7580

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

Flipped N/Q/H residues before XYZ refinement:
B 156 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3562 r_free = 0.3562 target = 0.121052 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3316 r_free = 0.3316 target = 0.104589 restraints weight = 12866.602|
|-----------------------------------------------------------------------------|
r_work (start): 0.3309 rms_B_bonded: 1.86
r_work: 0.3202 rms_B_bonded: 2.26 restraints_weight: 0.5000
r_work: 0.3064 rms_B_bonded: 3.96 restraints_weight: 0.2500
r_work (final): 0.3064
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7785
moved from start:          0.2773

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.041   8693  Z= 0.198
  Angle     :  0.608  11.585  11859  Z= 0.315
  Chirality :  0.044   0.161   1366
  Planarity :  0.004   0.046   1513
  Dihedral  :  4.731  51.694   1239
  Min Nonbonded Distance : 2.542

Molprobity Statistics.
  All-atom Clashscore : 7.88
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.98 %
    Favored  : 96.02 %
  Rotamer:
    Outliers :  3.64 %
    Allowed  : 22.18 %
    Favored  : 74.18 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.41 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.41 (0.25), residues: 1131
  helix:  1.77 (0.26), residues: 381
  sheet:  0.01 (0.30), residues: 289
  loop : -0.79 (0.30), residues: 461

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.039   0.002   TRP R 142 
 HIS   0.010   0.001   HIS A 357 
 PHE   0.017   0.002   PHE R 237 
 TYR   0.018   0.002   TYR B  59 
 ARG   0.009   0.001   ARG R 124 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04387 (  449)
  hydrogen bonds       : angle       4.72039 ( 1299)
  SS BOND              : bond        0.00275 (    2)
  SS BOND              : angle       0.85443 (    4)
  covalent geometry    : bond        0.00461 ( 8691)
  covalent geometry    : angle       0.60767 (11855)

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

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

  2262 Ramachandran restraints generated.
    1131 Oldfield, 0 Emsley, 1131 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2262 Ramachandran restraints generated.
    1131 Oldfield, 0 Emsley, 1131 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  234 residues out of total 983 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 204
  time to evaluate  : 0.946 
Fit side-chains
   revert: symmetry clash
REVERT: A   53 LYS cc_start: 0.8072 (pttt) cc_final: 0.7871 (pttt)
REVERT: A   56 ILE cc_start: 0.7723 (mt) cc_final: 0.7465 (tp)
REVERT: A  221 LYS cc_start: 0.8104 (mppt) cc_final: 0.7874 (mppt)
REVERT: A  258 VAL cc_start: 0.8673 (p) cc_final: 0.8443 (t)
REVERT: A  299 GLU cc_start: 0.7495 (mt-10) cc_final: 0.7244 (mt-10)
REVERT: A  347 ARG cc_start: 0.8271 (ttm-80) cc_final: 0.7941 (ttp-110)
REVERT: A  368 ASP cc_start: 0.7017 (m-30) cc_final: 0.6595 (m-30)
REVERT: A  380 ARG cc_start: 0.8492 (OUTLIER) cc_final: 0.7417 (ttp80)
REVERT: B  155 ASN cc_start: 0.8027 (t0) cc_final: 0.7576 (t0)
REVERT: B  157 ILE cc_start: 0.8386 (OUTLIER) cc_final: 0.8163 (tp)
REVERT: B  170 ASP cc_start: 0.7990 (t70) cc_final: 0.7550 (t70)
REVERT: B  175 GLN cc_start: 0.7756 (mm110) cc_final: 0.7477 (mm110)
REVERT: B  228 ASP cc_start: 0.8229 (OUTLIER) cc_final: 0.7980 (p0)
REVERT: B  258 ASP cc_start: 0.7417 (t70) cc_final: 0.6912 (t0)
REVERT: S    7 SER cc_start: 0.8402 (p) cc_final: 0.8185 (m)
REVERT: R  186 VAL cc_start: 0.8007 (OUTLIER) cc_final: 0.7725 (t)
  outliers start: 30
  outliers final: 23
  residues processed: 217
  average time/residue: 0.9303
  time to fit residues: 218.7318
Evaluate side-chains
  232 residues out of total 983 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 205
  time to evaluate  : 0.801 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   18 MET
Chi-restraints excluded: chain A residue  234 VAL
Chi-restraints excluded: chain A residue  249 ASN
Chi-restraints excluded: chain A residue  252 THR
Chi-restraints excluded: chain A residue  266 LEU
Chi-restraints excluded: chain A residue  275 SER
Chi-restraints excluded: chain A residue  289 LEU
Chi-restraints excluded: chain A residue  296 LEU
Chi-restraints excluded: chain A residue  380 ARG
Chi-restraints excluded: chain B residue  101 MET
Chi-restraints excluded: chain B residue  112 VAL
Chi-restraints excluded: chain B residue  157 ILE
Chi-restraints excluded: chain B residue  228 ASP
Chi-restraints excluded: chain B residue  317 CYS
Chi-restraints excluded: chain B residue  331 SER
Chi-restraints excluded: chain S residue    6 GLU
Chi-restraints excluded: chain S residue   48 VAL
Chi-restraints excluded: chain S residue   91 THR
Chi-restraints excluded: chain S residue  149 VAL
Chi-restraints excluded: chain S residue  226 VAL
Chi-restraints excluded: chain S residue  233 LEU
Chi-restraints excluded: chain R residue   39 LEU
Chi-restraints excluded: chain R residue  105 ILE
Chi-restraints excluded: chain R residue  146 LEU
Chi-restraints excluded: chain R residue  183 LEU
Chi-restraints excluded: chain R residue  186 VAL
Chi-restraints excluded: chain R residue  276 SER
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 113
   random chunks:
   chunk 101 optimal weight:    0.9990
   chunk 110 optimal weight:    0.9980
   chunk 27 optimal weight:    1.9990
   chunk 24 optimal weight:    0.0470
   chunk 109 optimal weight:    0.6980
   chunk 107 optimal weight:    1.9990
   chunk 60 optimal weight:    0.0980
   chunk 18 optimal weight:    0.9980
   chunk 8 optimal weight:    0.3980
   chunk 65 optimal weight:    0.5980
   chunk 16 optimal weight:    2.9990
   overall best weight:    0.3678

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

Flipped N/Q/H residues before XYZ refinement:
B  35 ASN
B 156 GLN
B 230 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3590 r_free = 0.3590 target = 0.123979 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3349 r_free = 0.3349 target = 0.107567 restraints weight = 12797.203|
|-----------------------------------------------------------------------------|
r_work (start): 0.3337 rms_B_bonded: 1.87
r_work: 0.3232 rms_B_bonded: 2.28 restraints_weight: 0.5000
r_work: 0.3096 rms_B_bonded: 4.01 restraints_weight: 0.2500
r_work (final): 0.3096
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7750
moved from start:          0.2937

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   8693  Z= 0.128
  Angle     :  0.561  10.974  11859  Z= 0.292
  Chirality :  0.042   0.145   1366
  Planarity :  0.004   0.047   1513
  Dihedral  :  4.511  49.437   1239
  Min Nonbonded Distance : 2.569

Molprobity Statistics.
  All-atom Clashscore : 7.33
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.71 %
    Favored  : 96.29 %
  Rotamer:
    Outliers :  2.91 %
    Allowed  : 23.03 %
    Favored  : 74.06 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.41 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.62 (0.26), residues: 1131
  helix:  1.95 (0.26), residues: 385
  sheet:  0.11 (0.30), residues: 290
  loop : -0.68 (0.31), residues: 456

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.039   0.002   TRP R 142 
 HIS   0.006   0.001   HIS A 357 
 PHE   0.018   0.001   PHE R 237 
 TYR   0.016   0.001   TYR A 391 
 ARG   0.009   0.001   ARG R 124 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03802 (  449)
  hydrogen bonds       : angle       4.56978 ( 1299)
  SS BOND              : bond        0.00270 (    2)
  SS BOND              : angle       0.60538 (    4)
  covalent geometry    : bond        0.00292 ( 8691)
  covalent geometry    : angle       0.56137 (11855)

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

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

  2262 Ramachandran restraints generated.
    1131 Oldfield, 0 Emsley, 1131 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2262 Ramachandran restraints generated.
    1131 Oldfield, 0 Emsley, 1131 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  224 residues out of total 983 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 200
  time to evaluate  : 0.864 
Fit side-chains
   revert: symmetry clash
REVERT: A   36 VAL cc_start: 0.8409 (t) cc_final: 0.8064 (t)
REVERT: A   53 LYS cc_start: 0.8018 (pttt) cc_final: 0.7788 (pttt)
REVERT: A   56 ILE cc_start: 0.7674 (mt) cc_final: 0.7444 (tp)
REVERT: A  258 VAL cc_start: 0.8713 (p) cc_final: 0.8470 (t)
REVERT: A  299 GLU cc_start: 0.7440 (mt-10) cc_final: 0.7204 (mt-10)
REVERT: A  347 ARG cc_start: 0.8239 (ttm-80) cc_final: 0.7902 (ttp-110)
REVERT: A  368 ASP cc_start: 0.7004 (m-30) cc_final: 0.6623 (m-30)
REVERT: B  110 ASN cc_start: 0.8412 (m110) cc_final: 0.8026 (m-40)
REVERT: B  155 ASN cc_start: 0.7967 (t0) cc_final: 0.7469 (t0)
REVERT: B  170 ASP cc_start: 0.7915 (t70) cc_final: 0.7606 (t0)
REVERT: B  175 GLN cc_start: 0.7731 (mm110) cc_final: 0.7469 (mm110)
REVERT: B  190 LEU cc_start: 0.8322 (tp) cc_final: 0.8100 (tt)
REVERT: B  228 ASP cc_start: 0.8186 (OUTLIER) cc_final: 0.7964 (p0)
REVERT: B  258 ASP cc_start: 0.7397 (t70) cc_final: 0.6912 (t0)
REVERT: B  340 ASN cc_start: 0.7374 (t0) cc_final: 0.6979 (t0)
REVERT: S    7 SER cc_start: 0.8377 (p) cc_final: 0.8141 (m)
REVERT: S  116 THR cc_start: 0.8260 (t) cc_final: 0.8016 (p)
REVERT: R  142 TRP cc_start: 0.8303 (m100) cc_final: 0.8047 (m100)
REVERT: R  186 VAL cc_start: 0.7979 (OUTLIER) cc_final: 0.7703 (t)
REVERT: R  271 SER cc_start: 0.7640 (p) cc_final: 0.7432 (m)
  outliers start: 24
  outliers final: 16
  residues processed: 213
  average time/residue: 0.9114
  time to fit residues: 209.8283
Evaluate side-chains
  215 residues out of total 983 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 197
  time to evaluate  : 0.834 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   18 MET
Chi-restraints excluded: chain A residue  234 VAL
Chi-restraints excluded: chain A residue  249 ASN
Chi-restraints excluded: chain A residue  252 THR
Chi-restraints excluded: chain A residue  289 LEU
Chi-restraints excluded: chain B residue   47 THR
Chi-restraints excluded: chain B residue  101 MET
Chi-restraints excluded: chain B residue  112 VAL
Chi-restraints excluded: chain B residue  228 ASP
Chi-restraints excluded: chain B residue  317 CYS
Chi-restraints excluded: chain B residue  331 SER
Chi-restraints excluded: chain S residue   48 VAL
Chi-restraints excluded: chain S residue   91 THR
Chi-restraints excluded: chain S residue  149 VAL
Chi-restraints excluded: chain R residue   39 LEU
Chi-restraints excluded: chain R residue  105 ILE
Chi-restraints excluded: chain R residue  183 LEU
Chi-restraints excluded: chain R residue  186 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 113
   random chunks:
   chunk 19 optimal weight:    1.9990
   chunk 86 optimal weight:    0.0040
   chunk 72 optimal weight:    1.9990
   chunk 35 optimal weight:    0.0980
   chunk 97 optimal weight:    0.8980
   chunk 79 optimal weight:    0.8980
   chunk 40 optimal weight:    2.9990
   chunk 64 optimal weight:    0.5980
   chunk 11 optimal weight:    1.9990
   chunk 46 optimal weight:    0.9980
   chunk 84 optimal weight:    0.5980
   overall best weight:    0.4392

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3586 r_free = 0.3586 target = 0.123763 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3344 r_free = 0.3344 target = 0.107316 restraints weight = 12928.402|
|-----------------------------------------------------------------------------|
r_work (start): 0.3337 rms_B_bonded: 1.88
r_work: 0.3231 rms_B_bonded: 2.29 restraints_weight: 0.5000
r_work: 0.3094 rms_B_bonded: 4.02 restraints_weight: 0.2500
r_work (final): 0.3094
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7754
moved from start:          0.2977

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041   8693  Z= 0.141
  Angle     :  0.571  10.963  11859  Z= 0.296
  Chirality :  0.043   0.144   1366
  Planarity :  0.004   0.048   1513
  Dihedral  :  4.536  51.250   1239
  Min Nonbonded Distance : 2.567

Molprobity Statistics.
  All-atom Clashscore : 8.00
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.98 %
    Favored  : 96.02 %
  Rotamer:
    Outliers :  2.91 %
    Allowed  : 22.67 %
    Favored  : 74.42 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.41 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.62 (0.26), residues: 1131
  helix:  1.94 (0.26), residues: 385
  sheet:  0.13 (0.30), residues: 290
  loop : -0.68 (0.30), residues: 456

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.035   0.002   TRP R 142 
 HIS   0.007   0.001   HIS A 357 
 PHE   0.020   0.002   PHE R 237 
 TYR   0.014   0.001   TYR A  37 
 ARG   0.009   0.001   ARG R 124 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03924 (  449)
  hydrogen bonds       : angle       4.57011 ( 1299)
  SS BOND              : bond        0.00240 (    2)
  SS BOND              : angle       0.70966 (    4)
  covalent geometry    : bond        0.00326 ( 8691)
  covalent geometry    : angle       0.57129 (11855)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 6420.39 seconds
wall clock time: 111 minutes 9.93 seconds (6669.93 seconds total)