Starting phenix.real_space_refine
on Fri Feb 14 06:42:15 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8g15_29662/02_2025/8g15_29662.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8g15_29662/02_2025/8g15_29662.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.07
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8g15_29662/02_2025/8g15_29662.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8g15_29662/02_2025/8g15_29662.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8g15_29662/02_2025/8g15_29662.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8g15_29662/02_2025/8g15_29662.cif"
  }
  resolution = 2.07
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.001
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 4
    Type Number    sf(0)   Gaussians
     S      48      5.16       5
     C    6352      2.51       5
     N    1744      2.21       5
     O    1912      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 27 residue(s): 0.03s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/chem_data/mon_lib"
  Total number of atoms: 10056
  Number of models: 1
  Model: ""
    Number of chains: 4
    Chain: "A"
      Number of atoms: 2514
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 334, 2514
          Classifications: {'peptide': 334}
          Modifications used: {'COO': 1}
          Incomplete info: {'truncation_to_alanine': 3}
          Link IDs: {'PTRANS': 12, 'TRANS': 321}
          Unresolved non-hydrogen bonds: 13
          Unresolved non-hydrogen angles: 14
          Unresolved non-hydrogen dihedrals: 12
          Unresolved non-hydrogen chiralities: 1
    Chain: "B"
      Number of atoms: 2514
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 334, 2514
          Classifications: {'peptide': 334}
          Modifications used: {'COO': 1}
          Incomplete info: {'truncation_to_alanine': 3}
          Link IDs: {'PTRANS': 12, 'TRANS': 321}
          Unresolved non-hydrogen bonds: 13
          Unresolved non-hydrogen angles: 14
          Unresolved non-hydrogen dihedrals: 12
          Unresolved non-hydrogen chiralities: 1
    Chain: "C"
      Number of atoms: 2514
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 334, 2514
          Classifications: {'peptide': 334}
          Modifications used: {'COO': 1}
          Incomplete info: {'truncation_to_alanine': 3}
          Link IDs: {'PTRANS': 12, 'TRANS': 321}
          Unresolved non-hydrogen bonds: 13
          Unresolved non-hydrogen angles: 14
          Unresolved non-hydrogen dihedrals: 13
          Unresolved non-hydrogen chiralities: 1
    Chain: "D"
      Number of atoms: 2514
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 334, 2514
          Classifications: {'peptide': 334}
          Modifications used: {'COO': 1}
          Incomplete info: {'truncation_to_alanine': 3}
          Link IDs: {'PTRANS': 12, 'TRANS': 321}
          Unresolved non-hydrogen bonds: 13
          Unresolved non-hydrogen angles: 14
          Unresolved non-hydrogen dihedrals: 12
          Unresolved non-hydrogen chiralities: 1
  Time building chain proxies: 5.83, per 1000 atoms: 0.58
  Number of scatterers: 10056
  At special positions: 0
  Unit cell: (99.365, 102.705, 89.345, 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      48     16.00
     O    1912      8.00
     N    1744      7.00
     C    6352      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 2.42
  Conformation dependent library (CDL) restraints added in 1.2 seconds
  

  2656 Ramachandran restraints generated.
    1328 Oldfield, 0 Emsley, 1328 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2408

  Finding SS restraints...
    Secondary structure from input PDB file:
      56 helices and 8 sheets defined
      38.0% alpha, 22.8% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 1.33
  Creating SS restraints...
    Processing helix  chain 'A' and resid 12 through 26
    Processing helix  chain 'A' and resid 39 through 49
    Processing helix  chain 'A' and resid 81 through 85
      removed outlier: 3.565A  pdb=" N   ILE A  85 " --> pdb=" O   PRO A  82 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 86 through 91
    Processing helix  chain 'A' and resid 104 through 109
    Processing helix  chain 'A' and resid 110 through 115
      removed outlier: 3.832A  pdb=" N   GLN A 113 " --> pdb=" O   ALA A 110 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 136 through 140
      removed outlier: 3.520A  pdb=" N   TYR A 140 " --> pdb=" O   HIS A 137 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 151 through 169
      Proline residue:  A 159  - end of helix
    Processing helix  chain 'A' and resid 196 through 200
    Processing helix  chain 'A' and resid 216 through 221
    Processing helix  chain 'A' and resid 222 through 225
    Processing helix  chain 'A' and resid 254 through 268
    Processing helix  chain 'A' and resid 282 through 287
      removed outlier: 3.517A  pdb=" N   ASN A 287 " --> pdb=" O   SER A 284 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 317 through 334
      removed outlier: 3.519A  pdb=" N   VAL A 325 " --> pdb=" O   SER A 321 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 12 through 26
    Processing helix  chain 'B' and resid 39 through 49
    Processing helix  chain 'B' and resid 81 through 85
      removed outlier: 3.566A  pdb=" N   ILE B  85 " --> pdb=" O   PRO B  82 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 86 through 91
    Processing helix  chain 'B' and resid 104 through 109
    Processing helix  chain 'B' and resid 110 through 115
      removed outlier: 3.833A  pdb=" N   GLN B 113 " --> pdb=" O   ALA B 110 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 136 through 140
      removed outlier: 3.520A  pdb=" N   TYR B 140 " --> pdb=" O   HIS B 137 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 151 through 169
      Proline residue:  B 159  - end of helix
    Processing helix  chain 'B' and resid 196 through 200
    Processing helix  chain 'B' and resid 216 through 221
    Processing helix  chain 'B' and resid 222 through 225
    Processing helix  chain 'B' and resid 254 through 268
    Processing helix  chain 'B' and resid 282 through 287
      removed outlier: 3.517A  pdb=" N   ASN B 287 " --> pdb=" O   SER B 284 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 317 through 334
      removed outlier: 3.518A  pdb=" N   VAL B 325 " --> pdb=" O   SER B 321 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 12 through 26
    Processing helix  chain 'C' and resid 39 through 49
    Processing helix  chain 'C' and resid 81 through 85
      removed outlier: 3.564A  pdb=" N   ILE C  85 " --> pdb=" O   PRO C  82 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 86 through 91
    Processing helix  chain 'C' and resid 104 through 109
    Processing helix  chain 'C' and resid 110 through 115
      removed outlier: 3.831A  pdb=" N   GLN C 113 " --> pdb=" O   ALA C 110 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 136 through 140
      removed outlier: 3.520A  pdb=" N   TYR C 140 " --> pdb=" O   HIS C 137 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 151 through 169
      Proline residue:  C 159  - end of helix
    Processing helix  chain 'C' and resid 196 through 200
    Processing helix  chain 'C' and resid 216 through 221
    Processing helix  chain 'C' and resid 222 through 225
    Processing helix  chain 'C' and resid 254 through 268
    Processing helix  chain 'C' and resid 282 through 287
      removed outlier: 3.516A  pdb=" N   ASN C 287 " --> pdb=" O   SER C 284 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 317 through 334
      removed outlier: 3.516A  pdb=" N   VAL C 325 " --> pdb=" O   SER C 321 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 12 through 26
    Processing helix  chain 'D' and resid 39 through 49
    Processing helix  chain 'D' and resid 81 through 85
      removed outlier: 3.565A  pdb=" N   ILE D  85 " --> pdb=" O   PRO D  82 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 86 through 91
    Processing helix  chain 'D' and resid 104 through 109
    Processing helix  chain 'D' and resid 110 through 115
      removed outlier: 3.900A  pdb=" N   GLN D 113 " --> pdb=" O   ALA D 110 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 136 through 140
      removed outlier: 3.521A  pdb=" N   TYR D 140 " --> pdb=" O   HIS D 137 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 151 through 169
      Proline residue:  D 159  - end of helix
    Processing helix  chain 'D' and resid 196 through 200
    Processing helix  chain 'D' and resid 216 through 221
    Processing helix  chain 'D' and resid 222 through 225
    Processing helix  chain 'D' and resid 254 through 268
    Processing helix  chain 'D' and resid 282 through 287
      removed outlier: 3.518A  pdb=" N   ASN D 287 " --> pdb=" O   SER D 284 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 317 through 334
      removed outlier: 3.518A  pdb=" N   VAL D 325 " --> pdb=" O   SER D 321 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 60 through 63
      removed outlier: 5.941A  pdb=" N   VAL A  31 " --> pdb=" O   PRO A  73 " (cutoff:3.500A)
      removed outlier: 7.529A  pdb=" N   VAL A   8 " --> pdb=" O   VAL A  31 " (cutoff:3.500A)
      removed outlier: 4.273A  pdb=" N   ILE A  33 " --> pdb=" O   VAL A   8 " (cutoff:3.500A)
      removed outlier: 6.291A  pdb=" N   VAL A  95 " --> pdb=" O   ILE A 120 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 208 through 210
      removed outlier: 3.571A  pdb=" N   THR A 229 " --> pdb=" O   GLY A 173 " (cutoff:3.500A)
      removed outlier: 3.693A  pdb=" N   GLU A 172 " --> pdb=" O   ARG A 248 " (cutoff:3.500A)
      removed outlier: 12.260A  pdb=" N   PHE A 307 " --> pdb=" O   GLY A 300 " (cutoff:3.500A)
      removed outlier: 11.116A  pdb=" N   GLY A 300 " --> pdb=" O   PHE A 307 " (cutoff:3.500A)
      removed outlier: 10.834A  pdb=" N   LYS A 309 " --> pdb=" O   GLY A 298 " (cutoff:3.500A)
      removed outlier: 8.855A  pdb=" N   GLY A 298 " --> pdb=" O   LYS A 309 " (cutoff:3.500A)
      removed outlier: 4.728A  pdb=" N   ILE A 311 " --> pdb=" O   ASP A 296 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'B' and resid 60 through 63
      removed outlier: 5.938A  pdb=" N   VAL B  31 " --> pdb=" O   PRO B  73 " (cutoff:3.500A)
      removed outlier: 6.201A  pdb=" N   VAL B   6 " --> pdb=" O   ILE B  30 " (cutoff:3.500A)
      removed outlier: 3.871A  pdb=" N   ALA B  32 " --> pdb=" O   VAL B   6 " (cutoff:3.500A)
      removed outlier: 6.286A  pdb=" N   VAL B  95 " --> pdb=" O   ILE B 120 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'B' and resid 208 through 210
      removed outlier: 3.531A  pdb=" N   THR B 229 " --> pdb=" O   GLY B 173 " (cutoff:3.500A)
      removed outlier: 3.695A  pdb=" N   GLU B 172 " --> pdb=" O   ARG B 248 " (cutoff:3.500A)
      removed outlier: 12.258A  pdb=" N   PHE B 307 " --> pdb=" O   GLY B 300 " (cutoff:3.500A)
      removed outlier: 11.116A  pdb=" N   GLY B 300 " --> pdb=" O   PHE B 307 " (cutoff:3.500A)
      removed outlier: 10.832A  pdb=" N   LYS B 309 " --> pdb=" O   GLY B 298 " (cutoff:3.500A)
      removed outlier: 8.850A  pdb=" N   GLY B 298 " --> pdb=" O   LYS B 309 " (cutoff:3.500A)
      removed outlier: 4.734A  pdb=" N   ILE B 311 " --> pdb=" O   ASP B 296 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'C' and resid 60 through 63
      removed outlier: 5.939A  pdb=" N   VAL C  31 " --> pdb=" O   PRO C  73 " (cutoff:3.500A)
      removed outlier: 6.201A  pdb=" N   VAL C   6 " --> pdb=" O   ILE C  30 " (cutoff:3.500A)
      removed outlier: 3.872A  pdb=" N   ALA C  32 " --> pdb=" O   VAL C   6 " (cutoff:3.500A)
      removed outlier: 6.277A  pdb=" N   VAL C  95 " --> pdb=" O   ILE C 120 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'C' and resid 208 through 210
      removed outlier: 3.585A  pdb=" N   THR C 229 " --> pdb=" O   GLY C 173 " (cutoff:3.500A)
      removed outlier: 3.694A  pdb=" N   GLU C 172 " --> pdb=" O   ARG C 248 " (cutoff:3.500A)
      removed outlier: 12.256A  pdb=" N   PHE C 307 " --> pdb=" O   GLY C 300 " (cutoff:3.500A)
      removed outlier: 11.113A  pdb=" N   GLY C 300 " --> pdb=" O   PHE C 307 " (cutoff:3.500A)
      removed outlier: 10.832A  pdb=" N   LYS C 309 " --> pdb=" O   GLY C 298 " (cutoff:3.500A)
      removed outlier: 8.853A  pdb=" N   GLY C 298 " --> pdb=" O   LYS C 309 " (cutoff:3.500A)
      removed outlier: 4.726A  pdb=" N   ILE C 311 " --> pdb=" O   ASP C 296 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'D' and resid 60 through 63
      removed outlier: 5.941A  pdb=" N   VAL D  31 " --> pdb=" O   PRO D  73 " (cutoff:3.500A)
      removed outlier: 7.529A  pdb=" N   VAL D   8 " --> pdb=" O   VAL D  31 " (cutoff:3.500A)
      removed outlier: 4.274A  pdb=" N   ILE D  33 " --> pdb=" O   VAL D   8 " (cutoff:3.500A)
      removed outlier: 6.283A  pdb=" N   VAL D  95 " --> pdb=" O   ILE D 120 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'D' and resid 208 through 210
      removed outlier: 3.586A  pdb=" N   THR D 229 " --> pdb=" O   GLY D 173 " (cutoff:3.500A)
      removed outlier: 3.696A  pdb=" N   GLU D 172 " --> pdb=" O   ARG D 248 " (cutoff:3.500A)
      removed outlier: 12.257A  pdb=" N   PHE D 307 " --> pdb=" O   GLY D 300 " (cutoff:3.500A)
      removed outlier: 11.116A  pdb=" N   GLY D 300 " --> pdb=" O   PHE D 307 " (cutoff:3.500A)
      removed outlier: 10.831A  pdb=" N   LYS D 309 " --> pdb=" O   GLY D 298 " (cutoff:3.500A)
      removed outlier: 8.853A  pdb=" N   GLY D 298 " --> pdb=" O   LYS D 309 " (cutoff:3.500A)
      removed outlier: 4.732A  pdb=" N   ILE D 311 " --> pdb=" O   ASP D 296 " (cutoff:3.500A)

    468 hydrogen bonds defined for protein.
    1260 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 3.30

  Time building geometry restraints manager: 2.82 seconds

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

  Histogram of bond lengths:
        1.22 -     1.34: 3109
        1.34 -     1.45: 1446
        1.45 -     1.57: 5617
        1.57 -     1.69: 0
        1.69 -     1.81: 84
  Bond restraints: 10256
  Sorted by residual:
  bond pdb=" C   SER D 312 "
       pdb=" N   TRP D 313 "
    ideal  model  delta    sigma   weight residual
    1.329  1.482 -0.152 1.38e-02 5.25e+03 1.22e+02
  bond pdb=" C   SER B 312 "
       pdb=" N   TRP B 313 "
    ideal  model  delta    sigma   weight residual
    1.329  1.477 -0.148 1.38e-02 5.25e+03 1.15e+02
  bond pdb=" C   SER C 312 "
       pdb=" N   TRP C 313 "
    ideal  model  delta    sigma   weight residual
    1.329  1.475 -0.146 1.38e-02 5.25e+03 1.12e+02
  bond pdb=" N   PRO D 208 "
       pdb=" CD  PRO D 208 "
    ideal  model  delta    sigma   weight residual
    1.473  1.542 -0.069 1.40e-02 5.10e+03 2.42e+01
  bond pdb=" N   VAL D 188 "
       pdb=" CA  VAL D 188 "
    ideal  model  delta    sigma   weight residual
    1.456  1.494 -0.038 1.23e-02 6.61e+03 9.60e+00
  ... (remaining 10251 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     5.66: 13875
        5.66 -    11.32: 10
       11.32 -    16.98: 5
       16.98 -    22.64: 3
       22.64 -    28.30: 3
  Bond angle restraints: 13896
  Sorted by residual:
  angle pdb=" O   SER B 312 "
        pdb=" C   SER B 312 "
        pdb=" N   TRP B 313 "
      ideal   model   delta    sigma   weight residual
     123.24   94.94   28.30 1.23e+00 6.61e-01 5.30e+02
  angle pdb=" O   SER D 312 "
        pdb=" C   SER D 312 "
        pdb=" N   TRP D 313 "
      ideal   model   delta    sigma   weight residual
     123.24   94.94   28.30 1.23e+00 6.61e-01 5.29e+02
  angle pdb=" O   SER C 312 "
        pdb=" C   SER C 312 "
        pdb=" N   TRP C 313 "
      ideal   model   delta    sigma   weight residual
     123.24   95.09   28.15 1.23e+00 6.61e-01 5.24e+02
  angle pdb=" CA  SER D 312 "
        pdb=" C   SER D 312 "
        pdb=" N   TRP D 313 "
      ideal   model   delta    sigma   weight residual
     115.58  134.88  -19.30 1.48e+00 4.57e-01 1.70e+02
  angle pdb=" CA  SER B 312 "
        pdb=" C   SER B 312 "
        pdb=" N   TRP B 313 "
      ideal   model   delta    sigma   weight residual
     115.58  134.81  -19.23 1.48e+00 4.57e-01 1.69e+02
  ... (remaining 13891 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.21: 5348
       17.21 -    34.42: 514
       34.42 -    51.63: 147
       51.63 -    68.84: 53
       68.84 -    86.05: 13
  Dihedral angle restraints: 6075
    sinusoidal: 2299
      harmonic: 3776
  Sorted by residual:
  dihedral pdb=" CA  ASN B 239 "
           pdb=" C   ASN B 239 "
           pdb=" N   VAL B 240 "
           pdb=" CA  VAL B 240 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -161.46  -18.54     0      5.00e+00 4.00e-02 1.37e+01
  dihedral pdb=" CA  ASN D 239 "
           pdb=" C   ASN D 239 "
           pdb=" N   VAL D 240 "
           pdb=" CA  VAL D 240 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -161.48  -18.52     0      5.00e+00 4.00e-02 1.37e+01
  dihedral pdb=" CA  ASN C 239 "
           pdb=" C   ASN C 239 "
           pdb=" N   VAL C 240 "
           pdb=" CA  VAL C 240 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -161.67  -18.33     0      5.00e+00 4.00e-02 1.34e+01
  ... (remaining 6072 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.040: 968
       0.040 -    0.080: 381
       0.080 -    0.120: 172
       0.120 -    0.160: 46
       0.160 -    0.200: 9
  Chirality restraints: 1576
  Sorted by residual:
  chirality pdb=" CA  ILE C 207 "
            pdb=" N   ILE C 207 "
            pdb=" C   ILE C 207 "
            pdb=" CB  ILE C 207 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.23    0.20 2.00e-01 2.50e+01 1.00e+00
  chirality pdb=" CA  ILE D 207 "
            pdb=" N   ILE D 207 "
            pdb=" C   ILE D 207 "
            pdb=" CB  ILE D 207 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.23    0.20 2.00e-01 2.50e+01 1.00e+00
  chirality pdb=" CA  ILE A 207 "
            pdb=" N   ILE A 207 "
            pdb=" C   ILE A 207 "
            pdb=" CB  ILE A 207 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.23    0.20 2.00e-01 2.50e+01 9.97e-01
  ... (remaining 1573 not shown)

  Planarity restraints: 1804
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  SER C 312 "   -0.069 2.00e-02 2.50e+03   1.08e-01 1.16e+02
        pdb=" C   SER C 312 "    0.187 2.00e-02 2.50e+03
        pdb=" O   SER C 312 "   -0.058 2.00e-02 2.50e+03
        pdb=" N   TRP C 313 "   -0.059 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  SER B 312 "    0.068 2.00e-02 2.50e+03   1.06e-01 1.12e+02
        pdb=" C   SER B 312 "   -0.183 2.00e-02 2.50e+03
        pdb=" O   SER B 312 "    0.057 2.00e-02 2.50e+03
        pdb=" N   TRP B 313 "    0.059 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  SER D 312 "   -0.068 2.00e-02 2.50e+03   1.06e-01 1.11e+02
        pdb=" C   SER D 312 "    0.183 2.00e-02 2.50e+03
        pdb=" O   SER D 312 "   -0.056 2.00e-02 2.50e+03
        pdb=" N   TRP D 313 "   -0.058 2.00e-02 2.50e+03
  ... (remaining 1801 not shown)

  Histogram of nonbonded interaction distances:
        2.24 -     2.77: 1932
        2.77 -     3.31: 8802
        3.31 -     3.84: 16550
        3.84 -     4.37: 20098
        4.37 -     4.90: 35079
  Nonbonded interactions: 82461
  Sorted by model distance:
  nonbonded pdb=" O   ASN B 239 "
            pdb=" OD1 ASN B 316 "
     model   vdw
     2.243 3.040
  nonbonded pdb=" O   ASN D 239 "
            pdb=" OD1 ASN D 316 "
     model   vdw
     2.243 3.040
  nonbonded pdb=" O   ASN C 239 "
            pdb=" OD1 ASN C 316 "
     model   vdw
     2.251 3.040
  nonbonded pdb=" O   ASN A 239 "
            pdb=" OD1 ASN A 316 "
     model   vdw
     2.255 3.040
  nonbonded pdb=" NH2 ARG C 118 "
            pdb=" OD1 ASN C 142 "
     model   vdw
     2.257 3.120
  ... (remaining 82456 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: 0.01
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'B'
  selection = chain 'C'
  selection = chain 'D'
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=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:             0.790
  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:          0.390
  Check model and map are aligned:         0.070
  Set scattering table:                    0.090
  Process input model:                     25.280
  Find NCS groups from input model:        0.340
  Set up NCS constraints:                  0.060
  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:12.710
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   39.740
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8876
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      :  0.005   0.152  10256  Z= 0.364
  Angle     :  0.963  28.304  13896  Z= 0.638
  Chirality :  0.054   0.200   1576
  Planarity :  0.009   0.120   1804
  Dihedral  : 16.072  86.054   3667
  Min Nonbonded Distance : 2.243

Molprobity Statistics.
  All-atom Clashscore : 5.30
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.97 %
    Favored  : 95.03 %
  Rotamer:
    Outliers :  1.59 %
    Allowed  : 16.21 %
    Favored  : 82.19 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.62 (0.22), residues: 1328
  helix: -2.29 (0.18), residues: 388
  sheet:  0.29 (0.40), residues: 220
  loop : -0.71 (0.23), residues: 720

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP D  87 
 HIS   0.003   0.001   HIS B  53 
 PHE   0.009   0.001   PHE B 233 
 TYR   0.010   0.002   TYR D  42 
 ARG   0.021   0.001   ARG D  80 

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

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

  2656 Ramachandran restraints generated.
    1328 Oldfield, 0 Emsley, 1328 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2656 Ramachandran restraints generated.
    1328 Oldfield, 0 Emsley, 1328 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  107 residues out of total 1080 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 90
  time to evaluate  : 1.118 
Fit side-chains
  outliers start: 17
  outliers final: 15
  residues processed: 104
  average time/residue: 1.5486
  time to fit residues: 171.5287
Evaluate side-chains
  97 residues out of total 1080 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 82
  time to evaluate  : 1.160 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  188 VAL
Chi-restraints excluded: chain A residue  195 LEU
Chi-restraints excluded: chain A residue  220 VAL
Chi-restraints excluded: chain A residue  243 VAL
Chi-restraints excluded: chain B residue  188 VAL
Chi-restraints excluded: chain B residue  195 LEU
Chi-restraints excluded: chain B residue  220 VAL
Chi-restraints excluded: chain B residue  243 VAL
Chi-restraints excluded: chain C residue  195 LEU
Chi-restraints excluded: chain C residue  220 VAL
Chi-restraints excluded: chain C residue  243 VAL
Chi-restraints excluded: chain D residue  188 VAL
Chi-restraints excluded: chain D residue  195 LEU
Chi-restraints excluded: chain D residue  220 VAL
Chi-restraints excluded: chain D residue  243 VAL
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 132
   random chunks:
   chunk 111 optimal weight:    0.9980
   chunk 100 optimal weight:    6.9990
   chunk 55 optimal weight:    1.9990
   chunk 34 optimal weight:    6.9990
   chunk 67 optimal weight:    6.9990
   chunk 53 optimal weight:   20.0000
   chunk 103 optimal weight:    1.9990
   chunk 40 optimal weight:    6.9990
   chunk 62 optimal weight:    1.9990
   chunk 77 optimal weight:    4.9990
   chunk 119 optimal weight:    6.9990
   overall best weight:    2.3988

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

Flipped N/Q/H residues before XYZ refinement:
A 149 ASN
B 149 ASN
C 149 ASN
D 149 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3497 r_free = 0.3497 target = 0.092274 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3278 r_free = 0.3278 target = 0.080766 restraints weight = 16965.110|
|-----------------------------------------------------------------------------|
r_work (start): 0.3272 rms_B_bonded: 1.92
r_work: 0.3165 rms_B_bonded: 2.29 restraints_weight: 0.5000
r_work: 0.3063 rms_B_bonded: 3.85 restraints_weight: 0.2500
r_work (final): 0.3063
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8918
moved from start:          0.1294

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.053  10256  Z= 0.264
  Angle     :  0.589   6.925  13896  Z= 0.326
  Chirality :  0.048   0.155   1576
  Planarity :  0.006   0.054   1804
  Dihedral  :  6.106  46.822   1431
  Min Nonbonded Distance : 2.536

Molprobity Statistics.
  All-atom Clashscore : 2.05
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.69 %
    Favored  : 96.31 %
  Rotamer:
    Outliers :  3.00 %
    Allowed  : 14.71 %
    Favored  : 82.29 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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: -0.43 (0.23), residues: 1328
  helix: -0.06 (0.24), residues: 392
  sheet:  0.49 (0.40), residues: 212
  loop : -0.59 (0.24), residues: 724

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP D  87 
 HIS   0.002   0.001   HIS B  53 
 PHE   0.010   0.001   PHE A 286 
 TYR   0.014   0.001   TYR C 314 
 ARG   0.008   0.001   ARG B  80 

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

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

  2656 Ramachandran restraints generated.
    1328 Oldfield, 0 Emsley, 1328 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2656 Ramachandran restraints generated.
    1328 Oldfield, 0 Emsley, 1328 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  110 residues out of total 1080 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 78
  time to evaluate  : 1.119 
Fit side-chains
  outliers start: 32
  outliers final: 23
  residues processed: 101
  average time/residue: 1.5322
  time to fit residues: 164.8623
Evaluate side-chains
  94 residues out of total 1080 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 71
  time to evaluate  : 1.119 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   57 HIS
Chi-restraints excluded: chain A residue   60 VAL
Chi-restraints excluded: chain A residue  188 VAL
Chi-restraints excluded: chain A residue  220 VAL
Chi-restraints excluded: chain A residue  243 VAL
Chi-restraints excluded: chain A residue  318 PHE
Chi-restraints excluded: chain B residue   57 HIS
Chi-restraints excluded: chain B residue   60 VAL
Chi-restraints excluded: chain B residue  188 VAL
Chi-restraints excluded: chain B residue  220 VAL
Chi-restraints excluded: chain B residue  243 VAL
Chi-restraints excluded: chain B residue  318 PHE
Chi-restraints excluded: chain C residue   57 HIS
Chi-restraints excluded: chain C residue   60 VAL
Chi-restraints excluded: chain C residue  220 VAL
Chi-restraints excluded: chain C residue  243 VAL
Chi-restraints excluded: chain C residue  318 PHE
Chi-restraints excluded: chain D residue   57 HIS
Chi-restraints excluded: chain D residue   60 VAL
Chi-restraints excluded: chain D residue  188 VAL
Chi-restraints excluded: chain D residue  220 VAL
Chi-restraints excluded: chain D residue  243 VAL
Chi-restraints excluded: chain D residue  318 PHE
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 132
   random chunks:
   chunk 111 optimal weight:    5.9990
   chunk 81 optimal weight:    4.9990
   chunk 77 optimal weight:    9.9990
   chunk 53 optimal weight:   20.0000
   chunk 3 optimal weight:    4.9990
   chunk 0 optimal weight:    9.9990
   chunk 70 optimal weight:    6.9990
   chunk 88 optimal weight:    1.9990
   chunk 86 optimal weight:    5.9990
   chunk 75 optimal weight:    4.9990
   chunk 58 optimal weight:    2.9990
   overall best weight:    3.9990

-------------------------------------------------------------------------------
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 = 0.3458 r_free = 0.3458 target = 0.090114 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 27)----------------|
| r_work = 0.3233 r_free = 0.3233 target = 0.078513 restraints weight = 17162.438|
|-----------------------------------------------------------------------------|
r_work (start): 0.3226 rms_B_bonded: 1.93
r_work: 0.3117 rms_B_bonded: 2.28 restraints_weight: 0.5000
r_work: 0.3017 rms_B_bonded: 3.80 restraints_weight: 0.2500
r_work (final): 0.3017
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8963
moved from start:          0.1451

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.079  10256  Z= 0.393
  Angle     :  0.650   9.041  13896  Z= 0.358
  Chirality :  0.052   0.151   1576
  Planarity :  0.006   0.055   1804
  Dihedral  :  6.727  59.953   1423
  Min Nonbonded Distance : 2.499

Molprobity Statistics.
  All-atom Clashscore : 2.35
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.61 %
    Favored  : 96.39 %
  Rotamer:
    Outliers :  3.19 %
    Allowed  : 15.56 %
    Favored  : 81.26 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.14 (0.24), residues: 1328
  helix:  0.64 (0.25), residues: 376
  sheet:  0.49 (0.39), residues: 204
  loop : -0.61 (0.24), residues: 748

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.002   TRP D  87 
 HIS   0.003   0.001   HIS B  53 
 PHE   0.013   0.002   PHE D 318 
 TYR   0.015   0.002   TYR D 314 
 ARG   0.006   0.001   ARG D  80 

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

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

  2656 Ramachandran restraints generated.
    1328 Oldfield, 0 Emsley, 1328 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2656 Ramachandran restraints generated.
    1328 Oldfield, 0 Emsley, 1328 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  108 residues out of total 1080 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 74
  time to evaluate  : 1.251 
Fit side-chains
  outliers start: 34
  outliers final: 27
  residues processed: 101
  average time/residue: 1.6467
  time to fit residues: 176.5110
Evaluate side-chains
  96 residues out of total 1080 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 69
  time to evaluate  : 1.123 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   57 HIS
Chi-restraints excluded: chain A residue   60 VAL
Chi-restraints excluded: chain A residue  142 ASN
Chi-restraints excluded: chain A residue  188 VAL
Chi-restraints excluded: chain A residue  220 VAL
Chi-restraints excluded: chain A residue  243 VAL
Chi-restraints excluded: chain A residue  318 PHE
Chi-restraints excluded: chain B residue   57 HIS
Chi-restraints excluded: chain B residue   60 VAL
Chi-restraints excluded: chain B residue  142 ASN
Chi-restraints excluded: chain B residue  188 VAL
Chi-restraints excluded: chain B residue  220 VAL
Chi-restraints excluded: chain B residue  243 VAL
Chi-restraints excluded: chain B residue  318 PHE
Chi-restraints excluded: chain C residue   57 HIS
Chi-restraints excluded: chain C residue   60 VAL
Chi-restraints excluded: chain C residue  142 ASN
Chi-restraints excluded: chain C residue  220 VAL
Chi-restraints excluded: chain C residue  243 VAL
Chi-restraints excluded: chain C residue  318 PHE
Chi-restraints excluded: chain D residue   57 HIS
Chi-restraints excluded: chain D residue   60 VAL
Chi-restraints excluded: chain D residue  142 ASN
Chi-restraints excluded: chain D residue  188 VAL
Chi-restraints excluded: chain D residue  220 VAL
Chi-restraints excluded: chain D residue  243 VAL
Chi-restraints excluded: chain D residue  318 PHE
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 132
   random chunks:
   chunk 59 optimal weight:    4.9990
   chunk 50 optimal weight:   10.0000
   chunk 61 optimal weight:    3.9990
   chunk 48 optimal weight:    2.9990
   chunk 92 optimal weight:    3.9990
   chunk 14 optimal weight:    1.9990
   chunk 74 optimal weight:    3.9990
   chunk 38 optimal weight:    3.9990
   chunk 64 optimal weight:    4.9990
   chunk 37 optimal weight:    2.9990
   chunk 18 optimal weight:    3.9990
   overall best weight:    3.1990

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

Flipped N/Q/H residues before XYZ refinement:
B 149 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3460 r_free = 0.3460 target = 0.090430 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3237 r_free = 0.3237 target = 0.078873 restraints weight = 16987.548|
|-----------------------------------------------------------------------------|
r_work (start): 0.3231 rms_B_bonded: 1.92
r_work: 0.3122 rms_B_bonded: 2.27 restraints_weight: 0.5000
r_work: 0.3021 rms_B_bonded: 3.79 restraints_weight: 0.2500
r_work (final): 0.3021
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8953
moved from start:          0.1547

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.067  10256  Z= 0.322
  Angle     :  0.615   9.115  13896  Z= 0.336
  Chirality :  0.050   0.145   1576
  Planarity :  0.006   0.054   1804
  Dihedral  :  6.723  59.312   1423
  Min Nonbonded Distance : 2.500

Molprobity Statistics.
  All-atom Clashscore : 1.85
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.46 %
    Favored  : 96.54 %
  Rotamer:
    Outliers :  4.03 %
    Allowed  : 14.53 %
    Favored  : 81.44 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.02 (0.24), residues: 1328
  helix:  0.84 (0.26), residues: 376
  sheet:  0.44 (0.39), residues: 204
  loop : -0.56 (0.25), residues: 748

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP B  87 
 HIS   0.002   0.001   HIS A  53 
 PHE   0.012   0.002   PHE C 318 
 TYR   0.013   0.001   TYR C 314 
 ARG   0.008   0.001   ARG B  80 

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

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

  2656 Ramachandran restraints generated.
    1328 Oldfield, 0 Emsley, 1328 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2656 Ramachandran restraints generated.
    1328 Oldfield, 0 Emsley, 1328 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  115 residues out of total 1080 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 43
    poor density    : 72
  time to evaluate  : 1.176 
Fit side-chains
REVERT: B  203 LEU cc_start: 0.9054 (OUTLIER) cc_final: 0.8840 (tp)
  outliers start: 43
  outliers final: 23
  residues processed: 105
  average time/residue: 1.4498
  time to fit residues: 162.8610
Evaluate side-chains
  95 residues out of total 1080 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 71
  time to evaluate  : 1.131 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   57 HIS
Chi-restraints excluded: chain A residue   60 VAL
Chi-restraints excluded: chain A residue  142 ASN
Chi-restraints excluded: chain A residue  188 VAL
Chi-restraints excluded: chain A residue  220 VAL
Chi-restraints excluded: chain A residue  243 VAL
Chi-restraints excluded: chain B residue   57 HIS
Chi-restraints excluded: chain B residue   60 VAL
Chi-restraints excluded: chain B residue  142 ASN
Chi-restraints excluded: chain B residue  188 VAL
Chi-restraints excluded: chain B residue  203 LEU
Chi-restraints excluded: chain B residue  220 VAL
Chi-restraints excluded: chain B residue  243 VAL
Chi-restraints excluded: chain C residue   57 HIS
Chi-restraints excluded: chain C residue   60 VAL
Chi-restraints excluded: chain C residue  142 ASN
Chi-restraints excluded: chain C residue  220 VAL
Chi-restraints excluded: chain C residue  243 VAL
Chi-restraints excluded: chain D residue   57 HIS
Chi-restraints excluded: chain D residue   60 VAL
Chi-restraints excluded: chain D residue  142 ASN
Chi-restraints excluded: chain D residue  188 VAL
Chi-restraints excluded: chain D residue  220 VAL
Chi-restraints excluded: chain D residue  243 VAL
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 132
   random chunks:
   chunk 1 optimal weight:    5.9990
   chunk 72 optimal weight:    5.9990
   chunk 96 optimal weight:    0.8980
   chunk 89 optimal weight:    6.9990
   chunk 88 optimal weight:    0.8980
   chunk 62 optimal weight:    9.9990
   chunk 9 optimal weight:    2.9990
   chunk 17 optimal weight:    2.9990
   chunk 53 optimal weight:   20.0000
   chunk 31 optimal weight:    6.9990
   chunk 23 optimal weight:    8.9990
   overall best weight:    2.7586

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

Flipped N/Q/H residues before XYZ refinement:
A 149 ASN
D 149 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3467 r_free = 0.3467 target = 0.090887 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3244 r_free = 0.3244 target = 0.079263 restraints weight = 16980.017|
|-----------------------------------------------------------------------------|
r_work (start): 0.3237 rms_B_bonded: 1.95
r_work: 0.3128 rms_B_bonded: 2.29 restraints_weight: 0.5000
r_work: 0.3027 rms_B_bonded: 3.82 restraints_weight: 0.2500
r_work (final): 0.3027
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8948
moved from start:          0.1570

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.062  10256  Z= 0.283
  Angle     :  0.594   8.722  13896  Z= 0.325
  Chirality :  0.049   0.144   1576
  Planarity :  0.005   0.053   1804
  Dihedral  :  6.052  49.672   1423
  Min Nonbonded Distance : 2.499

Molprobity Statistics.
  All-atom Clashscore : 1.45
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.61 %
    Favored  : 96.39 %
  Rotamer:
    Outliers :  3.00 %
    Allowed  : 15.28 %
    Favored  : 81.72 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.08 (0.24), residues: 1328
  helix:  1.03 (0.26), residues: 376
  sheet:  0.44 (0.38), residues: 204
  loop : -0.53 (0.25), residues: 748

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP C 313 
 HIS   0.002   0.001   HIS C  53 
 PHE   0.009   0.001   PHE B 286 
 TYR   0.012   0.001   TYR C 314 
 ARG   0.009   0.001   ARG B  80 

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

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

  2656 Ramachandran restraints generated.
    1328 Oldfield, 0 Emsley, 1328 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2656 Ramachandran restraints generated.
    1328 Oldfield, 0 Emsley, 1328 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  108 residues out of total 1080 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 76
  time to evaluate  : 1.180 
Fit side-chains
REVERT: B  203 LEU cc_start: 0.9038 (OUTLIER) cc_final: 0.8824 (tp)
  outliers start: 32
  outliers final: 28
  residues processed: 102
  average time/residue: 1.4870
  time to fit residues: 162.0487
Evaluate side-chains
  101 residues out of total 1080 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 72
  time to evaluate  : 1.128 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   57 HIS
Chi-restraints excluded: chain A residue   60 VAL
Chi-restraints excluded: chain A residue  142 ASN
Chi-restraints excluded: chain A residue  195 LEU
Chi-restraints excluded: chain A residue  220 VAL
Chi-restraints excluded: chain A residue  243 VAL
Chi-restraints excluded: chain A residue  318 PHE
Chi-restraints excluded: chain B residue   57 HIS
Chi-restraints excluded: chain B residue   60 VAL
Chi-restraints excluded: chain B residue  142 ASN
Chi-restraints excluded: chain B residue  195 LEU
Chi-restraints excluded: chain B residue  203 LEU
Chi-restraints excluded: chain B residue  220 VAL
Chi-restraints excluded: chain B residue  243 VAL
Chi-restraints excluded: chain B residue  318 PHE
Chi-restraints excluded: chain C residue   57 HIS
Chi-restraints excluded: chain C residue   60 VAL
Chi-restraints excluded: chain C residue  142 ASN
Chi-restraints excluded: chain C residue  195 LEU
Chi-restraints excluded: chain C residue  220 VAL
Chi-restraints excluded: chain C residue  243 VAL
Chi-restraints excluded: chain C residue  318 PHE
Chi-restraints excluded: chain D residue   57 HIS
Chi-restraints excluded: chain D residue   60 VAL
Chi-restraints excluded: chain D residue  142 ASN
Chi-restraints excluded: chain D residue  195 LEU
Chi-restraints excluded: chain D residue  220 VAL
Chi-restraints excluded: chain D residue  243 VAL
Chi-restraints excluded: chain D residue  318 PHE
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 132
   random chunks:
   chunk 100 optimal weight:    0.7980
   chunk 58 optimal weight:    4.9990
   chunk 28 optimal weight:    5.9990
   chunk 31 optimal weight:    5.9990
   chunk 38 optimal weight:    0.9990
   chunk 17 optimal weight:    2.9990
   chunk 78 optimal weight:    4.9990
   chunk 41 optimal weight:    3.9990
   chunk 128 optimal weight:    3.9990
   chunk 65 optimal weight:    6.9990
   chunk 68 optimal weight:    0.5980
   overall best weight:    1.8786

-------------------------------------------------------------------------------
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 = 0.3487 r_free = 0.3487 target = 0.092031 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3270 r_free = 0.3270 target = 0.080567 restraints weight = 17011.342|
|-----------------------------------------------------------------------------|
r_work (start): 0.3264 rms_B_bonded: 1.93
r_work: 0.3157 rms_B_bonded: 2.27 restraints_weight: 0.5000
r_work: 0.3057 rms_B_bonded: 3.80 restraints_weight: 0.2500
r_work (final): 0.3057
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8923
moved from start:          0.1608

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.046  10256  Z= 0.215
  Angle     :  0.563   7.933  13896  Z= 0.306
  Chirality :  0.048   0.140   1576
  Planarity :  0.006   0.062   1804
  Dihedral  :  5.818  47.711   1420
  Min Nonbonded Distance : 2.528

Molprobity Statistics.
  All-atom Clashscore : 1.55
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.61 %
    Favored  : 96.39 %
  Rotamer:
    Outliers :  3.00 %
    Allowed  : 15.09 %
    Favored  : 81.91 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.17 (0.24), residues: 1328
  helix:  1.20 (0.27), residues: 376
  sheet:  0.46 (0.38), residues: 204
  loop : -0.53 (0.25), residues: 748

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP C 313 
 HIS   0.002   0.001   HIS D 179 
 PHE   0.007   0.001   PHE D 286 
 TYR   0.010   0.001   TYR D 314 
 ARG   0.015   0.001   ARG D  80 

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

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

  2656 Ramachandran restraints generated.
    1328 Oldfield, 0 Emsley, 1328 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2656 Ramachandran restraints generated.
    1328 Oldfield, 0 Emsley, 1328 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  108 residues out of total 1080 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 76
  time to evaluate  : 1.134 
Fit side-chains
REVERT: B  203 LEU cc_start: 0.9031 (OUTLIER) cc_final: 0.8815 (tp)
  outliers start: 32
  outliers final: 27
  residues processed: 103
  average time/residue: 1.3474
  time to fit residues: 148.7167
Evaluate side-chains
  104 residues out of total 1080 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 76
  time to evaluate  : 1.051 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   57 HIS
Chi-restraints excluded: chain A residue   60 VAL
Chi-restraints excluded: chain A residue  142 ASN
Chi-restraints excluded: chain A residue  192 SER
Chi-restraints excluded: chain A residue  220 VAL
Chi-restraints excluded: chain A residue  243 VAL
Chi-restraints excluded: chain A residue  318 PHE
Chi-restraints excluded: chain B residue   57 HIS
Chi-restraints excluded: chain B residue   60 VAL
Chi-restraints excluded: chain B residue  142 ASN
Chi-restraints excluded: chain B residue  192 SER
Chi-restraints excluded: chain B residue  203 LEU
Chi-restraints excluded: chain B residue  220 VAL
Chi-restraints excluded: chain B residue  243 VAL
Chi-restraints excluded: chain B residue  318 PHE
Chi-restraints excluded: chain C residue   57 HIS
Chi-restraints excluded: chain C residue   60 VAL
Chi-restraints excluded: chain C residue  142 ASN
Chi-restraints excluded: chain C residue  192 SER
Chi-restraints excluded: chain C residue  220 VAL
Chi-restraints excluded: chain C residue  243 VAL
Chi-restraints excluded: chain C residue  318 PHE
Chi-restraints excluded: chain D residue   57 HIS
Chi-restraints excluded: chain D residue   60 VAL
Chi-restraints excluded: chain D residue  142 ASN
Chi-restraints excluded: chain D residue  220 VAL
Chi-restraints excluded: chain D residue  243 VAL
Chi-restraints excluded: chain D residue  318 PHE
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 132
   random chunks:
   chunk 28 optimal weight:    0.7980
   chunk 108 optimal weight:    1.9990
   chunk 50 optimal weight:    2.9990
   chunk 10 optimal weight:    2.9990
   chunk 124 optimal weight:    0.5980
   chunk 36 optimal weight:    0.0370
   chunk 22 optimal weight:    5.9990
   chunk 123 optimal weight:    5.9990
   chunk 91 optimal weight:    0.6980
   chunk 58 optimal weight:    0.0170
   chunk 51 optimal weight:    0.3980
   overall best weight:    0.3496

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

Flipped N/Q/H residues before XYZ refinement:
C 149 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3581 r_free = 0.3581 target = 0.097779 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3379 r_free = 0.3379 target = 0.086551 restraints weight = 17252.168|
|-----------------------------------------------------------------------------|
r_work (start): 0.3376 rms_B_bonded: 1.94
r_work: 0.3274 rms_B_bonded: 2.32 restraints_weight: 0.5000
r_work: 0.3176 rms_B_bonded: 3.90 restraints_weight: 0.2500
r_work (final): 0.3176
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8833
moved from start:          0.1977

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.035  10256  Z= 0.121
  Angle     :  0.490   6.152  13896  Z= 0.263
  Chirality :  0.044   0.126   1576
  Planarity :  0.005   0.064   1804
  Dihedral  :  4.898  39.576   1420
  Min Nonbonded Distance : 2.583

Molprobity Statistics.
  All-atom Clashscore : 2.70
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.01 %
    Favored  : 96.99 %
  Rotamer:
    Outliers :  1.78 %
    Allowed  : 16.59 %
    Favored  : 81.63 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.34 (0.25), residues: 1328
  helix:  1.24 (0.27), residues: 396
  sheet:  0.51 (0.39), residues: 212
  loop : -0.40 (0.26), residues: 720

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.004   0.001   TRP C 313 
 HIS   0.002   0.000   HIS B 179 
 PHE   0.005   0.001   PHE B 286 
 TYR   0.008   0.001   TYR C 140 
 ARG   0.016   0.001   ARG B  80 

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

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

  2656 Ramachandran restraints generated.
    1328 Oldfield, 0 Emsley, 1328 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2656 Ramachandran restraints generated.
    1328 Oldfield, 0 Emsley, 1328 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  94 residues out of total 1080 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 75
  time to evaluate  : 1.144 
Fit side-chains
REVERT: D  113 GLN cc_start: 0.8512 (pm20) cc_final: 0.8286 (pm20)
  outliers start: 19
  outliers final: 12
  residues processed: 89
  average time/residue: 1.5220
  time to fit residues: 144.6005
Evaluate side-chains
  84 residues out of total 1080 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 72
  time to evaluate  : 1.187 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   57 HIS
Chi-restraints excluded: chain A residue  220 VAL
Chi-restraints excluded: chain A residue  318 PHE
Chi-restraints excluded: chain B residue   57 HIS
Chi-restraints excluded: chain B residue  220 VAL
Chi-restraints excluded: chain B residue  318 PHE
Chi-restraints excluded: chain C residue   57 HIS
Chi-restraints excluded: chain C residue  220 VAL
Chi-restraints excluded: chain C residue  318 PHE
Chi-restraints excluded: chain D residue   57 HIS
Chi-restraints excluded: chain D residue  220 VAL
Chi-restraints excluded: chain D residue  318 PHE
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 132
   random chunks:
   chunk 108 optimal weight:    2.9990
   chunk 94 optimal weight:    7.9990
   chunk 55 optimal weight:    0.9980
   chunk 18 optimal weight:    3.9990
   chunk 51 optimal weight:    3.9990
   chunk 12 optimal weight:    2.9990
   chunk 31 optimal weight:    6.9990
   chunk 48 optimal weight:    0.7980
   chunk 107 optimal weight:    4.9990
   chunk 127 optimal weight:    7.9990
   chunk 126 optimal weight:   20.0000
   overall best weight:    2.3586

-------------------------------------------------------------------------------
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 = 0.3486 r_free = 0.3486 target = 0.091719 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3273 r_free = 0.3273 target = 0.080369 restraints weight = 17236.304|
|-----------------------------------------------------------------------------|
r_work (start): 0.3266 rms_B_bonded: 1.92
r_work: 0.3158 rms_B_bonded: 2.28 restraints_weight: 0.5000
r_work: 0.3058 rms_B_bonded: 3.81 restraints_weight: 0.2500
r_work (final): 0.3058
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8926
moved from start:          0.1586

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.053  10256  Z= 0.251
  Angle     :  0.564   7.221  13896  Z= 0.310
  Chirality :  0.048   0.146   1576
  Planarity :  0.006   0.071   1804
  Dihedral  :  5.435  44.552   1416
  Min Nonbonded Distance : 2.528

Molprobity Statistics.
  All-atom Clashscore : 1.45
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.01 %
    Favored  : 96.99 %
  Rotamer:
    Outliers :  1.50 %
    Allowed  : 17.06 %
    Favored  : 81.44 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.21 (0.24), residues: 1328
  helix:  1.34 (0.27), residues: 376
  sheet:  0.46 (0.38), residues: 204
  loop : -0.56 (0.25), residues: 748

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP C  87 
 HIS   0.002   0.001   HIS A  53 
 PHE   0.008   0.001   PHE B 286 
 TYR   0.011   0.001   TYR D 314 
 ARG   0.017   0.001   ARG D  80 

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

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

  2656 Ramachandran restraints generated.
    1328 Oldfield, 0 Emsley, 1328 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2656 Ramachandran restraints generated.
    1328 Oldfield, 0 Emsley, 1328 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  86 residues out of total 1080 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 70
  time to evaluate  : 1.164 
Fit side-chains
REVERT: A  264 GLN cc_start: 0.8481 (mt0) cc_final: 0.8265 (tm-30)
REVERT: B  113 GLN cc_start: 0.8498 (pm20) cc_final: 0.8259 (pm20)
REVERT: C  113 GLN cc_start: 0.8504 (pm20) cc_final: 0.8263 (pm20)
REVERT: C  264 GLN cc_start: 0.8462 (mt0) cc_final: 0.8258 (tm-30)
REVERT: D  264 GLN cc_start: 0.8484 (mt0) cc_final: 0.8270 (tm-30)
  outliers start: 16
  outliers final: 12
  residues processed: 78
  average time/residue: 1.6141
  time to fit residues: 134.1868
Evaluate side-chains
  82 residues out of total 1080 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 70
  time to evaluate  : 1.239 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   57 HIS
Chi-restraints excluded: chain A residue  220 VAL
Chi-restraints excluded: chain A residue  318 PHE
Chi-restraints excluded: chain B residue   57 HIS
Chi-restraints excluded: chain B residue  220 VAL
Chi-restraints excluded: chain B residue  318 PHE
Chi-restraints excluded: chain C residue   57 HIS
Chi-restraints excluded: chain C residue  220 VAL
Chi-restraints excluded: chain C residue  318 PHE
Chi-restraints excluded: chain D residue   57 HIS
Chi-restraints excluded: chain D residue  220 VAL
Chi-restraints excluded: chain D residue  318 PHE
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 132
   random chunks:
   chunk 59 optimal weight:    4.9990
   chunk 123 optimal weight:    1.9990
   chunk 47 optimal weight:    3.9990
   chunk 56 optimal weight:    9.9990
   chunk 3 optimal weight:    3.9990
   chunk 44 optimal weight:    4.9990
   chunk 84 optimal weight:    8.9990
   chunk 115 optimal weight:    1.9990
   chunk 79 optimal weight:    0.9980
   chunk 1 optimal weight:    5.9990
   chunk 78 optimal weight:    0.0000
   overall best weight:    1.7990

-------------------------------------------------------------------------------
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 = 0.3498 r_free = 0.3498 target = 0.092468 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3287 r_free = 0.3287 target = 0.081110 restraints weight = 17148.745|
|-----------------------------------------------------------------------------|
r_work (start): 0.3280 rms_B_bonded: 1.93
r_work: 0.3172 rms_B_bonded: 2.29 restraints_weight: 0.5000
r_work: 0.3072 rms_B_bonded: 3.83 restraints_weight: 0.2500
r_work (final): 0.3072
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8914
moved from start:          0.1633

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.045  10256  Z= 0.206
  Angle     :  0.552   7.062  13896  Z= 0.301
  Chirality :  0.047   0.149   1576
  Planarity :  0.006   0.077   1804
  Dihedral  :  5.424  44.244   1416
  Min Nonbonded Distance : 2.548

Molprobity Statistics.
  All-atom Clashscore : 1.45
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.46 %
    Favored  : 96.54 %
  Rotamer:
    Outliers :  1.12 %
    Allowed  : 17.24 %
    Favored  : 81.63 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.15 (0.24), residues: 1328
  helix:  1.25 (0.27), residues: 380
  sheet:  0.47 (0.39), residues: 204
  loop : -0.59 (0.25), residues: 744

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP C 313 
 HIS   0.002   0.001   HIS B  53 
 PHE   0.008   0.001   PHE D 233 
 TYR   0.010   0.001   TYR D 314 
 ARG   0.019   0.001   ARG D  80 

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

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

  2656 Ramachandran restraints generated.
    1328 Oldfield, 0 Emsley, 1328 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2656 Ramachandran restraints generated.
    1328 Oldfield, 0 Emsley, 1328 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  83 residues out of total 1080 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 71
  time to evaluate  : 1.147 
Fit side-chains
REVERT: A  264 GLN cc_start: 0.8449 (mt0) cc_final: 0.8235 (tm-30)
REVERT: C  113 GLN cc_start: 0.8468 (pm20) cc_final: 0.8268 (pm20)
REVERT: D  113 GLN cc_start: 0.8477 (pm20) cc_final: 0.8263 (pm20)
  outliers start: 12
  outliers final: 12
  residues processed: 79
  average time/residue: 1.6725
  time to fit residues: 140.8921
Evaluate side-chains
  80 residues out of total 1080 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 68
  time to evaluate  : 1.079 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   57 HIS
Chi-restraints excluded: chain A residue  220 VAL
Chi-restraints excluded: chain A residue  318 PHE
Chi-restraints excluded: chain B residue   57 HIS
Chi-restraints excluded: chain B residue  220 VAL
Chi-restraints excluded: chain B residue  318 PHE
Chi-restraints excluded: chain C residue   57 HIS
Chi-restraints excluded: chain C residue  220 VAL
Chi-restraints excluded: chain C residue  318 PHE
Chi-restraints excluded: chain D residue   57 HIS
Chi-restraints excluded: chain D residue  220 VAL
Chi-restraints excluded: chain D residue  318 PHE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 132
   random chunks:
   chunk 14 optimal weight:    3.9990
   chunk 10 optimal weight:    0.3980
   chunk 116 optimal weight:    0.9980
   chunk 100 optimal weight:    0.8980
   chunk 3 optimal weight:    3.9990
   chunk 118 optimal weight:    0.6980
   chunk 79 optimal weight:    0.8980
   chunk 60 optimal weight:    4.9990
   chunk 123 optimal weight:    8.9990
   chunk 65 optimal weight:    2.9990
   chunk 114 optimal weight:    0.8980
   overall best weight:    0.7580

-------------------------------------------------------------------------------
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 = 0.3540 r_free = 0.3540 target = 0.095104 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3336 r_free = 0.3336 target = 0.083762 restraints weight = 17114.014|
|-----------------------------------------------------------------------------|
r_work (start): 0.3329 rms_B_bonded: 1.95
r_work: 0.3225 rms_B_bonded: 2.32 restraints_weight: 0.5000
r_work: 0.3126 rms_B_bonded: 3.88 restraints_weight: 0.2500
r_work (final): 0.3126
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8868
moved from start:          0.1831

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.042  10256  Z= 0.139
  Angle     :  0.511   6.996  13896  Z= 0.277
  Chirality :  0.045   0.130   1576
  Planarity :  0.006   0.080   1804
  Dihedral  :  5.001  39.737   1416
  Min Nonbonded Distance : 2.549

Molprobity Statistics.
  All-atom Clashscore : 2.15
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.46 %
    Favored  : 96.54 %
  Rotamer:
    Outliers :  1.22 %
    Allowed  : 17.81 %
    Favored  : 80.97 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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:  0.26 (0.25), residues: 1328
  helix:  1.19 (0.27), residues: 396
  sheet:  0.50 (0.39), residues: 212
  loop : -0.47 (0.26), residues: 720

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP C 313 
 HIS   0.001   0.000   HIS B 179 
 PHE   0.006   0.001   PHE A 233 
 TYR   0.007   0.001   TYR C 140 
 ARG   0.019   0.001   ARG D  80 

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

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

  2656 Ramachandran restraints generated.
    1328 Oldfield, 0 Emsley, 1328 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2656 Ramachandran restraints generated.
    1328 Oldfield, 0 Emsley, 1328 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  81 residues out of total 1080 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 68
  time to evaluate  : 1.179 
Fit side-chains
  outliers start: 13
  outliers final: 12
  residues processed: 77
  average time/residue: 1.5576
  time to fit residues: 128.1082
Evaluate side-chains
  78 residues out of total 1080 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 66
  time to evaluate  : 1.134 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   57 HIS
Chi-restraints excluded: chain A residue  220 VAL
Chi-restraints excluded: chain A residue  318 PHE
Chi-restraints excluded: chain B residue   57 HIS
Chi-restraints excluded: chain B residue  220 VAL
Chi-restraints excluded: chain B residue  318 PHE
Chi-restraints excluded: chain C residue   57 HIS
Chi-restraints excluded: chain C residue  220 VAL
Chi-restraints excluded: chain C residue  318 PHE
Chi-restraints excluded: chain D residue   57 HIS
Chi-restraints excluded: chain D residue  220 VAL
Chi-restraints excluded: chain D residue  318 PHE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 132
   random chunks:
   chunk 94 optimal weight:    0.4980
   chunk 34 optimal weight:    4.9990
   chunk 90 optimal weight:    9.9990
   chunk 74 optimal weight:    9.9990
   chunk 85 optimal weight:    0.2980
   chunk 52 optimal weight:    4.9990
   chunk 28 optimal weight:    4.9990
   chunk 47 optimal weight:    0.2980
   chunk 59 optimal weight:    6.9990
   chunk 84 optimal weight:    0.5980
   chunk 25 optimal weight:    0.1980
   overall best weight:    0.3780

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

Flipped N/Q/H residues before XYZ refinement:
C 264 GLN
D 264 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3592 r_free = 0.3592 target = 0.098356 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3392 r_free = 0.3392 target = 0.087159 restraints weight = 17033.837|
|-----------------------------------------------------------------------------|
r_work (start): 0.3385 rms_B_bonded: 1.94
r_work: 0.3284 rms_B_bonded: 2.30 restraints_weight: 0.5000
r_work: 0.3186 rms_B_bonded: 3.89 restraints_weight: 0.2500
r_work (final): 0.3186
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8828
moved from start:          0.2081

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.040  10256  Z= 0.120
  Angle     :  0.492   7.280  13896  Z= 0.266
  Chirality :  0.044   0.126   1576
  Planarity :  0.006   0.081   1804
  Dihedral  :  4.435  25.810   1416
  Min Nonbonded Distance : 2.536

Molprobity Statistics.
  All-atom Clashscore : 2.60
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.54 %
    Favored  : 96.46 %
  Rotamer:
    Outliers :  0.75 %
    Allowed  : 17.81 %
    Favored  : 81.44 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.36 (0.25), residues: 1328
  helix:  1.31 (0.27), residues: 396
  sheet:  0.58 (0.39), residues: 212
  loop : -0.45 (0.26), residues: 720

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP B 313 
 HIS   0.001   0.000   HIS C 179 
 PHE   0.005   0.001   PHE A 233 
 TYR   0.008   0.001   TYR D 140 
 ARG   0.019   0.001   ARG B  80 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 7478.46 seconds
wall clock time: 132 minutes 54.04 seconds (7974.04 seconds total)