Starting phenix.real_space_refine
on Sat Aug 23 05:06:47 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8g15_29662/08_2025/8g15_29662.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8g15_29662/08_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_29662/08_2025/8g15_29662.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8g15_29662/08_2025/8g15_29662.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8g15_29662/08_2025/8g15_29662.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8g15_29662/08_2025/8g15_29662.cif"
  }
  resolution = 2.07
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.001
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): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/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: 2.60, per 1000 atoms: 0.26
  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: 1.05
  Conformation dependent library (CDL) restraints added in 412.8 milliseconds
  
  Enol-peptide restraints added in 476.8 nanoseconds
  

  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: 0.31
  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: 1.51

  Time building geometry restraints manager: 1.37 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: 0.02
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:             1.150
  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:          0.110
  Check model and map are aligned:         0.030
  Set scattering table:                    0.020
  Process input model:                     11.590
  Find NCS groups from input model:        0.220
  Set up NCS constraints:                  0.030
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:9.080
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   22.240
-------------------------------------------------------------------------------
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= 0.331
  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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.62 (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
 ARG   0.021   0.001   ARG D  80 
 TYR   0.010   0.002   TYR D  42 
 PHE   0.009   0.001   PHE B 233 
 TRP   0.007   0.001   TRP D  87 
 HIS   0.003   0.001   HIS B  53 

Details of bonding type rmsd
  covalent geometry    : bond        0.00542 (10256)
  covalent geometry    : angle       0.96295 (13896)
  hydrogen bonds       : bond        0.25045 (  468)
  hydrogen bonds       : angle       8.47828 ( 1260)

*********************** 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  : 0.382 
Fit side-chains
  outliers start: 17
  outliers final: 15
  residues processed: 104
  average time/residue: 0.6471
  time to fit residues: 71.2854
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  : 0.273 
-------------------------------------------------------------------------------
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 98 optimal weight:    1.9990
   chunk 107 optimal weight:    0.0970
   chunk 10 optimal weight:    0.9990
   chunk 66 optimal weight:   10.0000
   chunk 130 optimal weight:    3.9990
   chunk 124 optimal weight:    2.9990
   chunk 103 optimal weight:    2.9990
   chunk 77 optimal weight:    2.9990
   chunk 122 optimal weight:    8.9990
   chunk 91 optimal weight:    2.9990
   chunk 55 optimal weight:    1.9990
   overall best weight:    1.6186

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

Flipped N/Q/H residues before XYZ refinement:
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 = 0.3520 r_free = 0.3520 target = 0.093524 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3311 r_free = 0.3311 target = 0.082351 restraints weight = 17056.421|
|-----------------------------------------------------------------------------|
r_work (start): 0.3306 rms_B_bonded: 1.89
r_work: 0.3200 rms_B_bonded: 2.28 restraints_weight: 0.5000
r_work: 0.3099 rms_B_bonded: 3.83 restraints_weight: 0.2500
r_work (final): 0.3099
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8899
moved from start:          0.1326

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041  10256  Z= 0.133
  Angle     :  0.546   5.948  13896  Z= 0.302
  Chirality :  0.047   0.147   1576
  Planarity :  0.005   0.053   1804
  Dihedral  :  5.774  40.630   1431
  Min Nonbonded Distance : 2.567

Molprobity Statistics.
  All-atom Clashscore : 2.10
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.54 %
    Favored  : 96.46 %
  Rotamer:
    Outliers :  3.09 %
    Allowed  : 15.00 %
    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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.39 (0.24), residues: 1328
  helix: -0.06 (0.24), residues: 396
  sheet:  0.27 (0.38), residues: 236
  loop : -0.48 (0.25), residues: 696

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG B  80 
 TYR   0.012   0.001   TYR D 314 
 PHE   0.008   0.001   PHE D 286 
 TRP   0.006   0.001   TRP A 313 
 HIS   0.002   0.000   HIS B  53 

Details of bonding type rmsd
  covalent geometry    : bond        0.00307 (10256)
  covalent geometry    : angle       0.54575 (13896)
  hydrogen bonds       : bond        0.04585 (  468)
  hydrogen bonds       : angle       6.07718 ( 1260)

*********************** 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
  111 residues out of total 1080 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 78
  time to evaluate  : 0.330 
Fit side-chains
  outliers start: 33
  outliers final: 19
  residues processed: 102
  average time/residue: 0.6134
  time to fit residues: 66.5895
Evaluate side-chains
  90 residues out of total 1080 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 71
  time to evaluate  : 0.405 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   57 HIS
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  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  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  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 21 optimal weight:    5.9990
   chunk 131 optimal weight:    2.9990
   chunk 71 optimal weight:   10.0000
   chunk 5 optimal weight:    8.9990
   chunk 34 optimal weight:    5.9990
   chunk 15 optimal weight:    4.9990
   chunk 17 optimal weight:    3.9990
   chunk 85 optimal weight:    2.9990
   chunk 19 optimal weight:    1.9990
   chunk 68 optimal weight:    4.9990
   chunk 37 optimal weight:    0.8980
   overall best weight:    2.5788

-------------------------------------------------------------------------------
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 = 0.3489 r_free = 0.3489 target = 0.091941 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3270 r_free = 0.3270 target = 0.080457 restraints weight = 17059.772|
|-----------------------------------------------------------------------------|
r_work (start): 0.3264 rms_B_bonded: 1.92
r_work: 0.3157 rms_B_bonded: 2.29 restraints_weight: 0.5000
r_work: 0.3055 rms_B_bonded: 3.84 restraints_weight: 0.2500
r_work (final): 0.3055
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8936
moved from start:          0.1401

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.057  10256  Z= 0.174
  Angle     :  0.578   7.081  13896  Z= 0.319
  Chirality :  0.049   0.148   1576
  Planarity :  0.005   0.056   1804
  Dihedral  :  5.819  38.684   1423
  Min Nonbonded Distance : 2.551

Molprobity Statistics.
  All-atom Clashscore : 2.00
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.31 %
    Favored  : 96.69 %
  Rotamer:
    Outliers :  3.37 %
    Allowed  : 15.65 %
    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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.12 (0.24), residues: 1328
  helix:  0.56 (0.25), residues: 396
  sheet:  0.50 (0.39), residues: 204
  loop : -0.57 (0.25), residues: 728

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG D  80 
 TYR   0.014   0.001   TYR C 314 
 PHE   0.010   0.001   PHE B 318 
 TRP   0.006   0.001   TRP D  87 
 HIS   0.002   0.001   HIS D  53 

Details of bonding type rmsd
  covalent geometry    : bond        0.00417 (10256)
  covalent geometry    : angle       0.57790 (13896)
  hydrogen bonds       : bond        0.04992 (  468)
  hydrogen bonds       : angle       5.99740 ( 1260)

*********************** 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
  116 residues out of total 1080 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 80
  time to evaluate  : 0.403 
Fit side-chains
  outliers start: 36
  outliers final: 19
  residues processed: 107
  average time/residue: 0.6201
  time to fit residues: 70.4252
Evaluate side-chains
  90 residues out of total 1080 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 71
  time to evaluate  : 0.243 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   57 HIS
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  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 C residue   57 HIS
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  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=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 132
   random chunks:
   chunk 30 optimal weight:    3.9990
   chunk 104 optimal weight:    9.9990
   chunk 17 optimal weight:    9.9990
   chunk 40 optimal weight:    3.9990
   chunk 42 optimal weight:    4.9990
   chunk 131 optimal weight:    0.9990
   chunk 18 optimal weight:    0.5980
   chunk 63 optimal weight:    3.9990
   chunk 38 optimal weight:    3.9990
   chunk 46 optimal weight:    4.9990
   chunk 75 optimal weight:    6.9990
   overall best weight:    2.7188

-------------------------------------------------------------------------------
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 = 0.3474 r_free = 0.3474 target = 0.091249 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3252 r_free = 0.3252 target = 0.079594 restraints weight = 17150.563|
|-----------------------------------------------------------------------------|
r_work (start): 0.3248 rms_B_bonded: 1.94
r_work: 0.3140 rms_B_bonded: 2.30 restraints_weight: 0.5000
r_work: 0.3039 rms_B_bonded: 3.84 restraints_weight: 0.2500
r_work (final): 0.3039
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8941
moved from start:          0.1526

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.061  10256  Z= 0.178
  Angle     :  0.582   7.810  13896  Z= 0.320
  Chirality :  0.049   0.145   1576
  Planarity :  0.006   0.061   1804
  Dihedral  :  5.898  38.143   1423
  Min Nonbonded Distance : 2.513

Molprobity Statistics.
  All-atom Clashscore : 2.00
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.54 %
    Favored  : 96.46 %
  Rotamer:
    Outliers :  2.91 %
    Allowed  : 15.75 %
    Favored  : 81.35 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.05 (0.24), residues: 1328
  helix:  0.92 (0.26), residues: 376
  sheet:  0.47 (0.39), residues: 204
  loop : -0.52 (0.25), residues: 748

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG D  80 
 TYR   0.013   0.001   TYR D 314 
 PHE   0.009   0.001   PHE A 286 
 TRP   0.006   0.001   TRP C  87 
 HIS   0.002   0.001   HIS C  53 

Details of bonding type rmsd
  covalent geometry    : bond        0.00428 (10256)
  covalent geometry    : angle       0.58180 (13896)
  hydrogen bonds       : bond        0.04892 (  468)
  hydrogen bonds       : angle       5.97056 ( 1260)

*********************** 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
  105 residues out of total 1080 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 74
  time to evaluate  : 0.342 
Fit side-chains
  outliers start: 31
  outliers final: 29
  residues processed: 97
  average time/residue: 0.6146
  time to fit residues: 63.4604
Evaluate side-chains
  99 residues out of total 1080 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 70
  time to evaluate  : 0.250 
-------------------------------------------------------------------------------
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  105 MET
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  105 MET
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=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 132
   random chunks:
   chunk 106 optimal weight:    3.9990
   chunk 105 optimal weight:    1.9990
   chunk 44 optimal weight:    3.9990
   chunk 119 optimal weight:    4.9990
   chunk 34 optimal weight:    0.7980
   chunk 9 optimal weight:    6.9990
   chunk 123 optimal weight:    3.9990
   chunk 0 optimal weight:    3.9990
   chunk 83 optimal weight:    2.9990
   chunk 16 optimal weight:    1.9990
   chunk 86 optimal weight:    8.9990
   overall best weight:    2.3588

-------------------------------------------------------------------------------
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 = 0.3483 r_free = 0.3483 target = 0.091840 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.3261 r_free = 0.3261 target = 0.080162 restraints weight = 17198.984|
|-----------------------------------------------------------------------------|
r_work (start): 0.3256 rms_B_bonded: 1.97
r_work: 0.3147 rms_B_bonded: 2.32 restraints_weight: 0.5000
r_work: 0.3046 rms_B_bonded: 3.87 restraints_weight: 0.2500
r_work (final): 0.3046
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8928
moved from start:          0.1553

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.055  10256  Z= 0.161
  Angle     :  0.569   7.910  13896  Z= 0.312
  Chirality :  0.048   0.142   1576
  Planarity :  0.005   0.056   1804
  Dihedral  :  5.720  34.365   1423
  Min Nonbonded Distance : 2.527

Molprobity Statistics.
  All-atom Clashscore : 2.00
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.54 %
    Favored  : 96.46 %
  Rotamer:
    Outliers :  3.75 %
    Allowed  : 15.18 %
    Favored  : 81.07 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.13 (0.24), residues: 1328
  helix:  1.12 (0.26), residues: 376
  sheet:  0.40 (0.38), residues: 204
  loop : -0.51 (0.25), residues: 748

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG B  80 
 TYR   0.012   0.001   TYR B 314 
 PHE   0.008   0.001   PHE A 286 
 TRP   0.006   0.001   TRP C  87 
 HIS   0.002   0.001   HIS A  53 

Details of bonding type rmsd
  covalent geometry    : bond        0.00384 (10256)
  covalent geometry    : angle       0.56872 (13896)
  hydrogen bonds       : bond        0.04566 (  468)
  hydrogen bonds       : angle       5.87626 ( 1260)

*********************** 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
  118 residues out of total 1080 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 40
    poor density    : 78
  time to evaluate  : 0.349 
Fit side-chains
  outliers start: 40
  outliers final: 35
  residues processed: 113
  average time/residue: 0.5817
  time to fit residues: 70.2143
Evaluate side-chains
  105 residues out of total 1080 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 70
  time to evaluate  : 0.385 
-------------------------------------------------------------------------------
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  192 SER
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  188 VAL
Chi-restraints excluded: chain B residue  192 SER
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 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  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  188 VAL
Chi-restraints excluded: chain D residue  192 SER
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 87 optimal weight:    3.9990
   chunk 127 optimal weight:    1.9990
   chunk 11 optimal weight:    3.9990
   chunk 29 optimal weight:    9.9990
   chunk 14 optimal weight:    1.9990
   chunk 31 optimal weight:    3.9990
   chunk 109 optimal weight:    0.0980
   chunk 82 optimal weight:    0.5980
   chunk 124 optimal weight:    0.6980
   chunk 126 optimal weight:    8.9990
   chunk 78 optimal weight:    4.9990
   overall best weight:    1.0784

-------------------------------------------------------------------------------
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 = 0.3529 r_free = 0.3529 target = 0.094516 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3318 r_free = 0.3318 target = 0.083073 restraints weight = 17319.320|
|-----------------------------------------------------------------------------|
r_work (start): 0.3311 rms_B_bonded: 1.96
r_work: 0.3205 rms_B_bonded: 2.33 restraints_weight: 0.5000
r_work: 0.3106 rms_B_bonded: 3.90 restraints_weight: 0.2500
r_work (final): 0.3106
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8891
moved from start:          0.1710

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.032  10256  Z= 0.104
  Angle     :  0.506   6.360  13896  Z= 0.276
  Chirality :  0.046   0.135   1576
  Planarity :  0.005   0.059   1804
  Dihedral  :  5.012  30.694   1423
  Min Nonbonded Distance : 2.565

Molprobity Statistics.
  All-atom Clashscore : 2.35
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.39 %
    Favored  : 96.61 %
  Rotamer:
    Outliers :  2.25 %
    Allowed  : 16.68 %
    Favored  : 81.07 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.30 (0.25), residues: 1328
  helix:  1.21 (0.27), residues: 396
  sheet:  0.39 (0.38), residues: 212
  loop : -0.38 (0.26), residues: 720

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.001   ARG C  80 
 TYR   0.009   0.001   TYR A 314 
 PHE   0.006   0.001   PHE B 286 
 TRP   0.005   0.001   TRP C 313 
 HIS   0.002   0.000   HIS D 179 

Details of bonding type rmsd
  covalent geometry    : bond        0.00236 (10256)
  covalent geometry    : angle       0.50604 (13896)
  hydrogen bonds       : bond        0.03471 (  468)
  hydrogen bonds       : angle       5.58362 ( 1260)

*********************** 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
  102 residues out of total 1080 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 78
  time to evaluate  : 0.401 
Fit side-chains
  outliers start: 24
  outliers final: 19
  residues processed: 97
  average time/residue: 0.6295
  time to fit residues: 64.9877
Evaluate side-chains
  93 residues out of total 1080 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 74
  time to evaluate  : 0.378 
-------------------------------------------------------------------------------
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  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  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  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  318 PHE
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 132
   random chunks:
   chunk 129 optimal weight:    7.9990
   chunk 36 optimal weight:    6.9990
   chunk 12 optimal weight:    0.0870
   chunk 107 optimal weight:    9.9990
   chunk 74 optimal weight:    9.9990
   chunk 28 optimal weight:    6.9990
   chunk 55 optimal weight:    2.9990
   chunk 34 optimal weight:    3.9990
   chunk 73 optimal weight:    1.9990
   chunk 27 optimal weight:    4.9990
   chunk 49 optimal weight:    1.9990
   overall best weight:    2.2166

-------------------------------------------------------------------------------
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 = 0.3489 r_free = 0.3489 target = 0.091901 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3272 r_free = 0.3272 target = 0.080491 restraints weight = 17235.537|
|-----------------------------------------------------------------------------|
r_work (start): 0.3269 rms_B_bonded: 1.93
r_work: 0.3162 rms_B_bonded: 2.29 restraints_weight: 0.5000
r_work: 0.3062 rms_B_bonded: 3.83 restraints_weight: 0.2500
r_work (final): 0.3062
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8920
moved from start:          0.1561

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.051  10256  Z= 0.151
  Angle     :  0.549   7.520  13896  Z= 0.302
  Chirality :  0.048   0.145   1576
  Planarity :  0.006   0.063   1804
  Dihedral  :  5.121  34.951   1415
  Min Nonbonded Distance : 2.537

Molprobity Statistics.
  All-atom Clashscore : 1.75
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.01 %
    Favored  : 96.99 %
  Rotamer:
    Outliers :  2.72 %
    Allowed  : 16.49 %
    Favored  : 80.79 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.18 (0.24), residues: 1328
  helix:  1.16 (0.26), residues: 392
  sheet:  0.40 (0.38), residues: 204
  loop : -0.50 (0.25), residues: 732

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.001   ARG B  80 
 TYR   0.012   0.001   TYR B 314 
 PHE   0.008   0.001   PHE A 286 
 TRP   0.006   0.001   TRP D  87 
 HIS   0.002   0.001   HIS B  53 

Details of bonding type rmsd
  covalent geometry    : bond        0.00359 (10256)
  covalent geometry    : angle       0.54885 (13896)
  hydrogen bonds       : bond        0.04361 (  468)
  hydrogen bonds       : angle       5.74200 ( 1260)

*********************** 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
  107 residues out of total 1080 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 78
  time to evaluate  : 0.246 
Fit side-chains
REVERT: A  264 GLN cc_start: 0.8486 (mt0) cc_final: 0.8270 (tm-30)
REVERT: B  264 GLN cc_start: 0.8480 (mt0) cc_final: 0.8271 (tm-30)
REVERT: C  264 GLN cc_start: 0.8468 (mt0) cc_final: 0.8255 (tm-30)
REVERT: D  264 GLN cc_start: 0.8484 (mt0) cc_final: 0.8274 (tm-30)
  outliers start: 29
  outliers final: 20
  residues processed: 99
  average time/residue: 0.6548
  time to fit residues: 68.8970
Evaluate side-chains
  94 residues out of total 1080 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 74
  time to evaluate  : 0.367 
-------------------------------------------------------------------------------
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  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  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  318 PHE
Chi-restraints excluded: chain D residue   57 HIS
Chi-restraints excluded: chain D residue   60 VAL
Chi-restraints excluded: chain D residue  105 MET
Chi-restraints excluded: chain D residue  142 ASN
Chi-restraints excluded: chain D residue  188 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 50 optimal weight:    9.9990
   chunk 61 optimal weight:    5.9990
   chunk 95 optimal weight:    0.9990
   chunk 16 optimal weight:    3.9990
   chunk 115 optimal weight:    2.9990
   chunk 22 optimal weight:    5.9990
   chunk 112 optimal weight:    0.0670
   chunk 131 optimal weight:    2.9990
   chunk 60 optimal weight:    5.9990
   chunk 100 optimal weight:    0.7980
   chunk 46 optimal weight:    0.5980
   overall best weight:    1.0922

-------------------------------------------------------------------------------
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 = 0.3529 r_free = 0.3529 target = 0.094367 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3320 r_free = 0.3320 target = 0.083024 restraints weight = 17085.008|
|-----------------------------------------------------------------------------|
r_work (start): 0.3314 rms_B_bonded: 1.94
r_work: 0.3209 rms_B_bonded: 2.31 restraints_weight: 0.5000
r_work: 0.3109 rms_B_bonded: 3.88 restraints_weight: 0.2500
r_work (final): 0.3109
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8889
moved from start:          0.1703

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.029  10256  Z= 0.101
  Angle     :  0.494   6.398  13896  Z= 0.269
  Chirality :  0.046   0.135   1576
  Planarity :  0.005   0.062   1804
  Dihedral  :  4.819  31.216   1415
  Min Nonbonded Distance : 2.572

Molprobity Statistics.
  All-atom Clashscore : 2.05
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.39 %
    Favored  : 96.61 %
  Rotamer:
    Outliers :  2.06 %
    Allowed  : 16.87 %
    Favored  : 81.07 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.31 (0.25), residues: 1328
  helix:  1.25 (0.27), residues: 396
  sheet:  0.45 (0.38), residues: 212
  loop : -0.42 (0.26), residues: 720

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.011   0.001   ARG B  80 
 TYR   0.009   0.001   TYR D 314 
 PHE   0.006   0.001   PHE B 286 
 TRP   0.005   0.001   TRP C 313 
 HIS   0.002   0.000   HIS A 179 

Details of bonding type rmsd
  covalent geometry    : bond        0.00225 (10256)
  covalent geometry    : angle       0.49380 (13896)
  hydrogen bonds       : bond        0.03457 (  468)
  hydrogen bonds       : angle       5.52543 ( 1260)

*********************** 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
  92 residues out of total 1080 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 70
  time to evaluate  : 0.346 
Fit side-chains
  outliers start: 22
  outliers final: 19
  residues processed: 88
  average time/residue: 0.5848
  time to fit residues: 55.3339
Evaluate side-chains
  89 residues out of total 1080 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 70
  time to evaluate  : 0.319 
-------------------------------------------------------------------------------
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  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  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  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  318 PHE
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 132
   random chunks:
   chunk 61 optimal weight:    4.9990
   chunk 103 optimal weight:    7.9990
   chunk 79 optimal weight:    0.8980
   chunk 107 optimal weight:    4.9990
   chunk 130 optimal weight:    5.9990
   chunk 111 optimal weight:    2.9990
   chunk 122 optimal weight:    1.9990
   chunk 50 optimal weight:   10.0000
   chunk 64 optimal weight:   10.0000
   chunk 5 optimal weight:    8.9990
   chunk 18 optimal weight:    6.9990
   overall best weight:    3.1788

-------------------------------------------------------------------------------
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 = 0.3472 r_free = 0.3472 target = 0.091027 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3251 r_free = 0.3251 target = 0.079482 restraints weight = 17121.537|
|-----------------------------------------------------------------------------|
r_work (start): 0.3252 rms_B_bonded: 1.94
r_work: 0.3142 rms_B_bonded: 2.30 restraints_weight: 0.5000
r_work: 0.3039 rms_B_bonded: 3.84 restraints_weight: 0.2500
r_work (final): 0.3039
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8940
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      :  0.005   0.068  10256  Z= 0.202
  Angle     :  0.631   8.156  13896  Z= 0.346
  Chirality :  0.050   0.144   1576
  Planarity :  0.006   0.065   1804
  Dihedral  :  5.334  39.638   1415
  Min Nonbonded Distance : 2.487

Molprobity Statistics.
  All-atom Clashscore : 1.90
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.31 %
    Favored  : 96.69 %
  Rotamer:
    Outliers :  1.97 %
    Allowed  : 17.43 %
    Favored  : 80.60 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.09 (0.24), residues: 1328
  helix:  1.26 (0.27), residues: 376
  sheet:  0.39 (0.38), residues: 204
  loop : -0.66 (0.24), residues: 748

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.001   ARG B  80 
 TYR   0.015   0.002   TYR D 314 
 PHE   0.009   0.002   PHE A 286 
 TRP   0.006   0.001   TRP D  87 
 HIS   0.003   0.001   HIS D  53 

Details of bonding type rmsd
  covalent geometry    : bond        0.00490 (10256)
  covalent geometry    : angle       0.63135 (13896)
  hydrogen bonds       : bond        0.04916 (  468)
  hydrogen bonds       : angle       5.86694 ( 1260)

*********************** 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
  91 residues out of total 1080 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 70
  time to evaluate  : 0.431 
Fit side-chains
  outliers start: 21
  outliers final: 19
  residues processed: 86
  average time/residue: 0.6919
  time to fit residues: 63.2786
Evaluate side-chains
  88 residues out of total 1080 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 69
  time to evaluate  : 0.381 
-------------------------------------------------------------------------------
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  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  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  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  318 PHE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 132
   random chunks:
   chunk 66 optimal weight:   10.0000
   chunk 12 optimal weight:    0.8980
   chunk 20 optimal weight:   10.0000
   chunk 29 optimal weight:    9.9990
   chunk 25 optimal weight:    1.9990
   chunk 93 optimal weight:    8.9990
   chunk 86 optimal weight:    8.9990
   chunk 108 optimal weight:    2.9990
   chunk 100 optimal weight:    5.9990
   chunk 119 optimal weight:    0.7980
   chunk 104 optimal weight:    5.9990
   overall best weight:    2.5386

-------------------------------------------------------------------------------
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 = 0.3485 r_free = 0.3485 target = 0.091642 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3266 r_free = 0.3266 target = 0.080186 restraints weight = 17117.721|
|-----------------------------------------------------------------------------|
r_work (start): 0.3260 rms_B_bonded: 1.93
r_work: 0.3152 rms_B_bonded: 2.29 restraints_weight: 0.5000
r_work: 0.3051 rms_B_bonded: 3.82 restraints_weight: 0.2500
r_work (final): 0.3051
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8926
moved from start:          0.1603

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.059  10256  Z= 0.169
  Angle     :  0.590   8.340  13896  Z= 0.321
  Chirality :  0.049   0.144   1576
  Planarity :  0.006   0.067   1804
  Dihedral  :  5.297  39.144   1415
  Min Nonbonded Distance : 2.516

Molprobity Statistics.
  All-atom Clashscore : 1.90
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.54 %
    Favored  : 96.46 %
  Rotamer:
    Outliers :  2.16 %
    Allowed  : 17.53 %
    Favored  : 80.32 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.12 (0.24), residues: 1328
  helix:  1.32 (0.27), residues: 376
  sheet:  0.40 (0.38), residues: 204
  loop : -0.65 (0.24), residues: 748

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.011   0.001   ARG B  80 
 TYR   0.013   0.001   TYR D 314 
 PHE   0.008   0.001   PHE A 286 
 TRP   0.006   0.001   TRP A  87 
 HIS   0.002   0.001   HIS C  53 

Details of bonding type rmsd
  covalent geometry    : bond        0.00405 (10256)
  covalent geometry    : angle       0.58981 (13896)
  hydrogen bonds       : bond        0.04567 (  468)
  hydrogen bonds       : angle       5.78963 ( 1260)

********************** 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
  89 residues out of total 1080 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 66
  time to evaluate  : 0.376 
Fit side-chains
REVERT: A  264 GLN cc_start: 0.8505 (mt0) cc_final: 0.8252 (tm-30)
REVERT: B  264 GLN cc_start: 0.8493 (mt0) cc_final: 0.8252 (tm-30)
REVERT: C  264 GLN cc_start: 0.8487 (mt0) cc_final: 0.8236 (tm-30)
REVERT: D  264 GLN cc_start: 0.8502 (mt0) cc_final: 0.8255 (tm-30)
  outliers start: 23
  outliers final: 19
  residues processed: 85
  average time/residue: 0.5670
  time to fit residues: 52.0328
Evaluate side-chains
  85 residues out of total 1080 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 66
  time to evaluate  : 0.385 
-------------------------------------------------------------------------------
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  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  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  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  318 PHE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 132
   random chunks:
   chunk 61 optimal weight:    3.9990
   chunk 34 optimal weight:    4.9990
   chunk 77 optimal weight:    8.9990
   chunk 48 optimal weight:    0.7980
   chunk 37 optimal weight:    1.9990
   chunk 69 optimal weight:    1.9990
   chunk 91 optimal weight:    4.9990
   chunk 119 optimal weight:    3.9990
   chunk 23 optimal weight:    2.9990
   chunk 53 optimal weight:    0.6980
   chunk 104 optimal weight:    0.4980
   overall best weight:    1.1984

-------------------------------------------------------------------------------
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 = 0.3521 r_free = 0.3521 target = 0.093976 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3312 r_free = 0.3312 target = 0.082695 restraints weight = 17177.051|
|-----------------------------------------------------------------------------|
r_work (start): 0.3311 rms_B_bonded: 1.92
r_work: 0.3206 rms_B_bonded: 2.29 restraints_weight: 0.5000
r_work: 0.3106 rms_B_bonded: 3.84 restraints_weight: 0.2500
r_work (final): 0.3106
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8895
moved from start:          0.1718

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.031  10256  Z= 0.108
  Angle     :  0.525   9.876  13896  Z= 0.283
  Chirality :  0.046   0.136   1576
  Planarity :  0.005   0.063   1804
  Dihedral  :  4.865  30.339   1415
  Min Nonbonded Distance : 2.559

Molprobity Statistics.
  All-atom Clashscore : 2.05
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.84 %
    Favored  : 96.16 %
  Rotamer:
    Outliers :  1.78 %
    Allowed  : 17.90 %
    Favored  : 80.32 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.22 (0.25), residues: 1328
  helix:  1.25 (0.27), residues: 396
  sheet:  0.42 (0.39), residues: 212
  loop : -0.54 (0.25), residues: 720

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.011   0.001   ARG A  80 
 TYR   0.008   0.001   TYR A 314 
 PHE   0.006   0.001   PHE B 286 
 TRP   0.005   0.001   TRP A 313 
 HIS   0.002   0.000   HIS A 179 

Details of bonding type rmsd
  covalent geometry    : bond        0.00246 (10256)
  covalent geometry    : angle       0.52521 (13896)
  hydrogen bonds       : bond        0.03553 (  468)
  hydrogen bonds       : angle       5.54712 ( 1260)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3375.50 seconds
wall clock time: 58 minutes 16.50 seconds (3496.50 seconds total)