Starting phenix.real_space_refine
on Tue Mar  3 21:38:36 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7ypx_34017/03_2026/7ypx_34017.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7ypx_34017/03_2026/7ypx_34017.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.12
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7ypx_34017/03_2026/7ypx_34017.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7ypx_34017/03_2026/7ypx_34017.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7ypx_34017/03_2026/7ypx_34017.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7ypx_34017/03_2026/7ypx_34017.cif"
  }
  resolution = 3.12
  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=   0.001 sd=   0.033
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      12      5.16       5
     C    5481      2.51       5
     N    1572      2.21       5
     O    1743      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 8 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 8808
  Number of models: 1
  Model: ""
    Number of chains: 6
    Chain: "A"
      Number of atoms: 1704
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 250, 1704
          Classifications: {'peptide': 250}
          Link IDs: {'PTRANS': 11, 'TRANS': 238}
    Chain: "B"
      Number of atoms: 1704
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 250, 1704
          Classifications: {'peptide': 250}
          Link IDs: {'PTRANS': 11, 'TRANS': 238}
    Chain: "C"
      Number of atoms: 1704
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 250, 1704
          Classifications: {'peptide': 250}
          Link IDs: {'PTRANS': 11, 'TRANS': 238}
    Chain: "a"
      Number of atoms: 1232
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 162, 1232
          Classifications: {'peptide': 162}
          Modifications used: {'COO': 1}
          Link IDs: {'PCIS': 1, 'PTRANS': 12, 'TRANS': 148}
    Chain: "b"
      Number of atoms: 1232
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 162, 1232
          Classifications: {'peptide': 162}
          Modifications used: {'COO': 1}
          Link IDs: {'PCIS': 1, 'PTRANS': 12, 'TRANS': 148}
    Chain: "c"
      Number of atoms: 1232
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 162, 1232
          Classifications: {'peptide': 162}
          Modifications used: {'COO': 1}
          Link IDs: {'PCIS': 1, 'PTRANS': 12, 'TRANS': 148}
  Time building chain proxies: 1.80, per 1000 atoms: 0.20
  Number of scatterers: 8808
  At special positions: 0
  Unit cell: (92.02, 86.67, 156.22, 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      12     16.00
     O    1743      8.00
     N    1572      7.00
     C    5481      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: 0.65
  Conformation dependent library (CDL) restraints added in 356.2 milliseconds
  

  2448 Ramachandran restraints generated.
    1224 Oldfield, 0 Emsley, 1224 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2052

  Finding SS restraints...
    Secondary structure from input PDB file:
      24 helices and 16 sheets defined
      28.4% alpha, 16.1% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.21
  Creating SS restraints...
    Processing helix  chain 'A' and resid 32 through 54
      removed outlier: 3.576A  pdb=" N   ASP A  36 " --> pdb=" O   ASP A  32 " (cutoff:3.500A)
      removed outlier: 4.076A  pdb=" N   ASN A  37 " --> pdb=" O   VAL A  33 " (cutoff:3.500A)
      removed outlier: 4.051A  pdb=" N   VAL A  50 " --> pdb=" O   GLN A  46 " (cutoff:3.500A)
      removed outlier: 4.139A  pdb=" N   ILE A  51 " --> pdb=" O   VAL A  47 " (cutoff:3.500A)
      removed outlier: 3.724A  pdb=" N   GLU A  52 " --> pdb=" O   ASP A  48 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 64 through 69
    Processing helix  chain 'A' and resid 69 through 75
    Processing helix  chain 'B' and resid 32 through 52
      removed outlier: 3.508A  pdb=" N   ASP B  36 " --> pdb=" O   ASP B  32 " (cutoff:3.500A)
      removed outlier: 4.015A  pdb=" N   ASN B  37 " --> pdb=" O   VAL B  33 " (cutoff:3.500A)
      removed outlier: 3.686A  pdb=" N   ASP B  48 " --> pdb=" O   THR B  44 " (cutoff:3.500A)
      removed outlier: 3.690A  pdb=" N   GLY B  49 " --> pdb=" O   GLY B  45 " (cutoff:3.500A)
      removed outlier: 4.074A  pdb=" N   VAL B  50 " --> pdb=" O   GLN B  46 " (cutoff:3.500A)
      removed outlier: 4.144A  pdb=" N   ILE B  51 " --> pdb=" O   VAL B  47 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 64 through 75
      removed outlier: 5.244A  pdb=" N   GLN B  71 " --> pdb=" O   TYR B  67 " (cutoff:3.500A)
      removed outlier: 6.514A  pdb=" N   SER B  72 " --> pdb=" O   LYS B  68 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 32 through 52
      removed outlier: 3.511A  pdb=" N   ASP C  36 " --> pdb=" O   ASP C  32 " (cutoff:3.500A)
      removed outlier: 4.000A  pdb=" N   ASN C  37 " --> pdb=" O   VAL C  33 " (cutoff:3.500A)
      removed outlier: 3.697A  pdb=" N   ASP C  48 " --> pdb=" O   THR C  44 " (cutoff:3.500A)
      removed outlier: 3.694A  pdb=" N   GLY C  49 " --> pdb=" O   GLY C  45 " (cutoff:3.500A)
      removed outlier: 4.136A  pdb=" N   VAL C  50 " --> pdb=" O   GLN C  46 " (cutoff:3.500A)
      removed outlier: 4.158A  pdb=" N   ILE C  51 " --> pdb=" O   VAL C  47 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 64 through 75
      removed outlier: 5.335A  pdb=" N   GLN C  71 " --> pdb=" O   TYR C  67 " (cutoff:3.500A)
      removed outlier: 6.712A  pdb=" N   SER C  72 " --> pdb=" O   LYS C  68 " (cutoff:3.500A)
    Processing helix  chain 'a' and resid 25 through 31
    Processing helix  chain 'a' and resid 63 through 75
    Processing helix  chain 'a' and resid 76 through 83
      removed outlier: 4.337A  pdb=" N   PHE a  80 " --> pdb=" O   SER a  76 " (cutoff:3.500A)
    Processing helix  chain 'a' and resid 84 through 100
    Processing helix  chain 'a' and resid 107 through 133
    Processing helix  chain 'a' and resid 152 through 162
    Processing helix  chain 'b' and resid 25 through 31
    Processing helix  chain 'b' and resid 63 through 83
      removed outlier: 3.711A  pdb=" N   ARG b  77 " --> pdb=" O   ALA b  73 " (cutoff:3.500A)
      removed outlier: 4.212A  pdb=" N   HIS b  78 " --> pdb=" O   GLU b  74 " (cutoff:3.500A)
      removed outlier: 4.337A  pdb=" N   ILE b  79 " --> pdb=" O   ALA b  75 " (cutoff:3.500A)
      removed outlier: 4.359A  pdb=" N   PHE b  80 " --> pdb=" O   SER b  76 " (cutoff:3.500A)
    Processing helix  chain 'b' and resid 84 through 100
    Processing helix  chain 'b' and resid 107 through 133
    Processing helix  chain 'b' and resid 152 through 162
    Processing helix  chain 'c' and resid 25 through 31
    Processing helix  chain 'c' and resid 63 through 75
    Processing helix  chain 'c' and resid 76 through 83
      removed outlier: 4.384A  pdb=" N   PHE c  80 " --> pdb=" O   SER c  76 " (cutoff:3.500A)
    Processing helix  chain 'c' and resid 84 through 100
    Processing helix  chain 'c' and resid 107 through 133
    Processing helix  chain 'c' and resid 152 through 162
    Processing sheet with id=AA1, first strand: chain 'A' and resid 78 through 83
      removed outlier: 3.964A  pdb=" N   GLN A 273 " --> pdb=" O   TRP A 101 " (cutoff:3.500A)
      removed outlier: 5.266A  pdb=" N   TRP A 101 " --> pdb=" O   GLN A 273 " (cutoff:3.500A)
      removed outlier: 8.271A  pdb=" N   PHE A 275 " --> pdb=" O   LEU A  99 " (cutoff:3.500A)
      removed outlier: 7.999A  pdb=" N   LEU A  99 " --> pdb=" O   PHE A 275 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 78 through 83
      removed outlier: 3.964A  pdb=" N   GLN A 273 " --> pdb=" O   TRP A 101 " (cutoff:3.500A)
      removed outlier: 5.266A  pdb=" N   TRP A 101 " --> pdb=" O   GLN A 273 " (cutoff:3.500A)
      removed outlier: 8.271A  pdb=" N   PHE A 275 " --> pdb=" O   LEU A  99 " (cutoff:3.500A)
      removed outlier: 7.999A  pdb=" N   LEU A  99 " --> pdb=" O   PHE A 275 " (cutoff:3.500A)
      removed outlier: 3.595A  pdb=" N   ILE A 205 " --> pdb=" O   ASP A 131 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 91 through 92
      removed outlier: 3.645A  pdb=" N   GLY A 140 " --> pdb=" O   ILE A  92 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 168 through 170
    Processing sheet with id=AA5, first strand: chain 'B' and resid 78 through 83
      removed outlier: 3.903A  pdb=" N   GLN B 273 " --> pdb=" O   TRP B 101 " (cutoff:3.500A)
      removed outlier: 5.157A  pdb=" N   TRP B 101 " --> pdb=" O   GLN B 273 " (cutoff:3.500A)
      removed outlier: 8.302A  pdb=" N   PHE B 275 " --> pdb=" O   LEU B  99 " (cutoff:3.500A)
      removed outlier: 8.024A  pdb=" N   LEU B  99 " --> pdb=" O   PHE B 275 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'B' and resid 78 through 83
      removed outlier: 3.903A  pdb=" N   GLN B 273 " --> pdb=" O   TRP B 101 " (cutoff:3.500A)
      removed outlier: 5.157A  pdb=" N   TRP B 101 " --> pdb=" O   GLN B 273 " (cutoff:3.500A)
      removed outlier: 8.302A  pdb=" N   PHE B 275 " --> pdb=" O   LEU B  99 " (cutoff:3.500A)
      removed outlier: 8.024A  pdb=" N   LEU B  99 " --> pdb=" O   PHE B 275 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'B' and resid 91 through 92
      removed outlier: 3.617A  pdb=" N   GLY B 140 " --> pdb=" O   ILE B  92 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'B' and resid 168 through 170
    Processing sheet with id=AA9, first strand: chain 'C' and resid 78 through 83
      removed outlier: 3.955A  pdb=" N   GLN C 273 " --> pdb=" O   TRP C 101 " (cutoff:3.500A)
      removed outlier: 5.158A  pdb=" N   TRP C 101 " --> pdb=" O   GLN C 273 " (cutoff:3.500A)
      removed outlier: 8.299A  pdb=" N   PHE C 275 " --> pdb=" O   LEU C  99 " (cutoff:3.500A)
      removed outlier: 8.065A  pdb=" N   LEU C  99 " --> pdb=" O   PHE C 275 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'C' and resid 78 through 83
      removed outlier: 3.955A  pdb=" N   GLN C 273 " --> pdb=" O   TRP C 101 " (cutoff:3.500A)
      removed outlier: 5.158A  pdb=" N   TRP C 101 " --> pdb=" O   GLN C 273 " (cutoff:3.500A)
      removed outlier: 8.299A  pdb=" N   PHE C 275 " --> pdb=" O   LEU C  99 " (cutoff:3.500A)
      removed outlier: 8.065A  pdb=" N   LEU C  99 " --> pdb=" O   PHE C 275 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'C' and resid 91 through 92
      removed outlier: 3.639A  pdb=" N   GLY C 140 " --> pdb=" O   ILE C  92 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'C' and resid 168 through 170
    Processing sheet with id=AB4, first strand: chain 'a' and resid 13 through 21
      removed outlier: 6.970A  pdb=" N   ARG a   8 " --> pdb=" O   VAL a  15 " (cutoff:3.500A)
      removed outlier: 4.690A  pdb=" N   THR a  17 " --> pdb=" O   TYR a   6 " (cutoff:3.500A)
      removed outlier: 6.887A  pdb=" N   TYR a   6 " --> pdb=" O   THR a  17 " (cutoff:3.500A)
      removed outlier: 4.372A  pdb=" N   THR a  19 " --> pdb=" O   LYS a   4 " (cutoff:3.500A)
      removed outlier: 6.322A  pdb=" N   LYS a   4 " --> pdb=" O   THR a  19 " (cutoff:3.500A)
    Processing sheet with id=AB5, first strand: chain 'b' and resid 13 through 21
      removed outlier: 6.937A  pdb=" N   ARG b   8 " --> pdb=" O   VAL b  15 " (cutoff:3.500A)
      removed outlier: 4.670A  pdb=" N   THR b  17 " --> pdb=" O   TYR b   6 " (cutoff:3.500A)
      removed outlier: 6.890A  pdb=" N   TYR b   6 " --> pdb=" O   THR b  17 " (cutoff:3.500A)
      removed outlier: 4.357A  pdb=" N   THR b  19 " --> pdb=" O   LYS b   4 " (cutoff:3.500A)
      removed outlier: 6.395A  pdb=" N   LYS b   4 " --> pdb=" O   THR b  19 " (cutoff:3.500A)
    Processing sheet with id=AB6, first strand: chain 'b' and resid 48 through 50
    Processing sheet with id=AB7, first strand: chain 'c' and resid 13 through 21
      removed outlier: 6.914A  pdb=" N   ARG c   8 " --> pdb=" O   VAL c  15 " (cutoff:3.500A)
      removed outlier: 4.589A  pdb=" N   THR c  17 " --> pdb=" O   TYR c   6 " (cutoff:3.500A)
      removed outlier: 6.804A  pdb=" N   TYR c   6 " --> pdb=" O   THR c  17 " (cutoff:3.500A)
      removed outlier: 4.394A  pdb=" N   THR c  19 " --> pdb=" O   LYS c   4 " (cutoff:3.500A)
      removed outlier: 6.376A  pdb=" N   LYS c   4 " --> pdb=" O   THR c  19 " (cutoff:3.500A)

    345 hydrogen bonds defined for protein.
    960 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: 1.19

  Time building geometry restraints manager: 0.88 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: 3065
        1.34 -     1.46: 1546
        1.46 -     1.57: 4365
        1.57 -     1.69: 0
        1.69 -     1.80: 24
  Bond restraints: 9000
  Sorted by residual:
  bond pdb=" CB  LYS A  68 "
       pdb=" CG  LYS A  68 "
    ideal  model  delta    sigma   weight residual
    1.520  1.487  0.033 3.00e-02 1.11e+03 1.22e+00
  bond pdb=" CD  LYS A  68 "
       pdb=" CE  LYS A  68 "
    ideal  model  delta    sigma   weight residual
    1.520  1.492  0.028 3.00e-02 1.11e+03 8.58e-01
  bond pdb=" CA  ILE A 170 "
       pdb=" CB  ILE A 170 "
    ideal  model  delta    sigma   weight residual
    1.548  1.538  0.010 1.13e-02 7.83e+03 8.11e-01
  bond pdb=" CB  ILE C 205 "
       pdb=" CG2 ILE C 205 "
    ideal  model  delta    sigma   weight residual
    1.521  1.492  0.029 3.30e-02 9.18e+02 7.82e-01
  bond pdb=" CD  LYS C  68 "
       pdb=" CE  LYS C  68 "
    ideal  model  delta    sigma   weight residual
    1.520  1.494  0.026 3.00e-02 1.11e+03 7.62e-01
  ... (remaining 8995 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.18: 11732
        1.18 -     2.36: 406
        2.36 -     3.54: 117
        3.54 -     4.71: 15
        4.71 -     5.89: 9
  Bond angle restraints: 12279
  Sorted by residual:
  angle pdb=" N   SER A  97 "
        pdb=" CA  SER A  97 "
        pdb=" C   SER A  97 "
      ideal   model   delta    sigma   weight residual
     114.56  110.53    4.03 1.27e+00 6.20e-01 1.01e+01
  angle pdb=" N   GLU c 119 "
        pdb=" CA  GLU c 119 "
        pdb=" CB  GLU c 119 "
      ideal   model   delta    sigma   weight residual
     110.28  115.11   -4.83 1.55e+00 4.16e-01 9.71e+00
  angle pdb=" C   ASN A 186 "
        pdb=" N   ASN A 187 "
        pdb=" CA  ASN A 187 "
      ideal   model   delta    sigma   weight residual
     121.54  127.16   -5.62 1.91e+00 2.74e-01 8.66e+00
  angle pdb=" CA  LYS b  53 "
        pdb=" CB  LYS b  53 "
        pdb=" CG  LYS b  53 "
      ideal   model   delta    sigma   weight residual
     114.10  119.49   -5.39 2.00e+00 2.50e-01 7.27e+00
  angle pdb=" C   VAL A  47 "
        pdb=" N   ASP A  48 "
        pdb=" CA  ASP A  48 "
      ideal   model   delta    sigma   weight residual
     122.06  117.06    5.00 1.86e+00 2.89e-01 7.22e+00
  ... (remaining 12274 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.46: 4857
       17.46 -    34.92: 272
       34.92 -    52.38: 15
       52.38 -    69.84: 1
       69.84 -    87.30: 6
  Dihedral angle restraints: 5151
    sinusoidal: 1851
      harmonic: 3300
  Sorted by residual:
  dihedral pdb=" CA  ILE C 216 "
           pdb=" C   ILE C 216 "
           pdb=" N   VAL C 217 "
           pdb=" CA  VAL C 217 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  163.63   16.37     0      5.00e+00 4.00e-02 1.07e+01
  dihedral pdb=" CA  MET a   1 "
           pdb=" C   MET a   1 "
           pdb=" N   THR a   2 "
           pdb=" CA  THR a   2 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -165.19  -14.81     0      5.00e+00 4.00e-02 8.78e+00
  dihedral pdb=" CA  ILE B 216 "
           pdb=" C   ILE B 216 "
           pdb=" N   VAL B 217 "
           pdb=" CA  VAL B 217 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  165.29   14.71     0      5.00e+00 4.00e-02 8.65e+00
  ... (remaining 5148 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.029: 789
       0.029 -    0.057: 323
       0.057 -    0.086: 147
       0.086 -    0.115: 70
       0.115 -    0.143: 18
  Chirality restraints: 1347
  Sorted by residual:
  chirality pdb=" CA  ASN A 187 "
            pdb=" N   ASN A 187 "
            pdb=" C   ASN A 187 "
            pdb=" CB  ASN A 187 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.37    0.14 2.00e-01 2.50e+01 5.12e-01
  chirality pdb=" CA  VAL B 143 "
            pdb=" N   VAL B 143 "
            pdb=" C   VAL B 143 "
            pdb=" CB  VAL B 143 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.58   -0.14 2.00e-01 2.50e+01 4.93e-01
  chirality pdb=" CA  VAL A 143 "
            pdb=" N   VAL A 143 "
            pdb=" C   VAL A 143 "
            pdb=" CB  VAL A 143 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.58   -0.14 2.00e-01 2.50e+01 4.56e-01
  ... (remaining 1344 not shown)

  Planarity restraints: 1662
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ALA b  52 "    0.006 2.00e-02 2.50e+03   1.14e-02 1.30e+00
        pdb=" C   ALA b  52 "   -0.020 2.00e-02 2.50e+03
        pdb=" O   ALA b  52 "    0.008 2.00e-02 2.50e+03
        pdb=" N   LYS b  53 "    0.007 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   GLN B 260 "    0.017 5.00e-02 4.00e+02   2.54e-02 1.04e+00
        pdb=" N   PRO B 261 "   -0.044 5.00e-02 4.00e+02
        pdb=" CA  PRO B 261 "    0.013 5.00e-02 4.00e+02
        pdb=" CD  PRO B 261 "    0.014 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  HIS b 132 "   -0.008 2.00e-02 2.50e+03   8.24e-03 1.02e+00
        pdb=" CG  HIS b 132 "    0.018 2.00e-02 2.50e+03
        pdb=" ND1 HIS b 132 "   -0.002 2.00e-02 2.50e+03
        pdb=" CD2 HIS b 132 "   -0.005 2.00e-02 2.50e+03
        pdb=" CE1 HIS b 132 "   -0.003 2.00e-02 2.50e+03
        pdb=" NE2 HIS b 132 "    0.000 2.00e-02 2.50e+03
  ... (remaining 1659 not shown)

  Histogram of nonbonded interaction distances:
        2.09 -     2.65: 161
        2.65 -     3.21: 9150
        3.21 -     3.78: 14695
        3.78 -     4.34: 19188
        4.34 -     4.90: 30696
  Nonbonded interactions: 73890
  Sorted by model distance:
  nonbonded pdb=" NZ  LYS b  49 "
            pdb=" O   GLY b  51 "
     model   vdw
     2.092 3.120
  nonbonded pdb=" OG  SER B 119 "
            pdb=" O   ASN B 185 "
     model   vdw
     2.154 3.040
  nonbonded pdb=" OG  SER A 119 "
            pdb=" O   ASN A 185 "
     model   vdw
     2.162 3.040
  nonbonded pdb=" OG  SER C 119 "
            pdb=" O   ASN C 185 "
     model   vdw
     2.221 3.040
  nonbonded pdb=" NH1 ARG A 231 "
            pdb=" O   GLY A 252 "
     model   vdw
     2.228 3.120
  ... (remaining 73885 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.00
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'B'
  selection = chain 'C'
}
ncs_group {
  reference = chain 'a'
  selection = chain 'b'
  selection = chain 'c'
}

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:             1.180
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.100
  Check model and map are aligned:         0.030
  Set scattering table:                    0.020
  Process input model:                     8.110
  Find NCS groups from input model:        0.100
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.350
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   10.910
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8363
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      :  0.004   0.033   9000  Z= 0.185
  Angle     :  0.567   5.893  12279  Z= 0.302
  Chirality :  0.043   0.143   1347
  Planarity :  0.004   0.034   1662
  Dihedral  : 10.613  87.301   3099
  Min Nonbonded Distance : 2.092

Molprobity Statistics.
  All-atom Clashscore : 12.71
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.68 %
    Favored  : 96.32 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.23 %
    Favored  : 99.77 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.17 %
    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 are not related in a simple way.
  whole: -0.23 (0.23), residues: 1224
  helix:  0.64 (0.27), residues: 348
  sheet: -0.31 (0.27), residues: 276
  loop : -0.45 (0.26), residues: 600

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG b  48 
 TYR   0.013   0.001   TYR A 207 
 PHE   0.006   0.001   PHE b  54 
 TRP   0.007   0.001   TRP A 259 
 HIS   0.009   0.002   HIS b 132 

Details of bonding type rmsd
  covalent geometry    : bond        0.00386 ( 9000)
  covalent geometry    : angle       0.56747 (12279)
  hydrogen bonds       : bond        0.13308 (  321)
  hydrogen bonds       : angle       6.53891 (  960)

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

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

  2448 Ramachandran restraints generated.
    1224 Oldfield, 0 Emsley, 1224 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2448 Ramachandran restraints generated.
    1224 Oldfield, 0 Emsley, 1224 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  95 residues out of total 867 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 95
  time to evaluate  : 0.351 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   48 ASP cc_start: 0.9311 (p0) cc_final: 0.9027 (p0)
REVERT: A   59 ASP cc_start: 0.9161 (t0) cc_final: 0.8747 (t0)
REVERT: A  131 ASP cc_start: 0.8716 (p0) cc_final: 0.8323 (p0)
REVERT: B   52 GLU cc_start: 0.9226 (pm20) cc_final: 0.9021 (pm20)
REVERT: B   59 ASP cc_start: 0.9256 (t0) cc_final: 0.8743 (t0)
REVERT: B   62 ASP cc_start: 0.9163 (t70) cc_final: 0.8953 (t0)
REVERT: B  160 TYR cc_start: 0.8901 (m-80) cc_final: 0.8538 (m-80)
REVERT: B  204 GLU cc_start: 0.8702 (mp0) cc_final: 0.8437 (mp0)
REVERT: C   40 MET cc_start: 0.9143 (ptp) cc_final: 0.8727 (ptp)
REVERT: C   59 ASP cc_start: 0.9207 (t0) cc_final: 0.8693 (t0)
REVERT: C   62 ASP cc_start: 0.9237 (t70) cc_final: 0.9020 (t0)
REVERT: c  111 ARG cc_start: 0.9608 (mpp80) cc_final: 0.9276 (ptp90)
  outliers start: 0
  outliers final: 0
  residues processed: 95
  average time/residue: 0.1553
  time to fit residues: 18.2015
Evaluate side-chains
  72 residues out of total 867 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 72
  time to evaluate  : 0.340 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 123
   random chunks:
   chunk 108 optimal weight:    0.0270
   chunk 49 optimal weight:    0.9990
   chunk 97 optimal weight:    5.9990
   chunk 113 optimal weight:   30.0000
   chunk 53 optimal weight:    0.6980
   chunk 5 optimal weight:    0.9980
   chunk 33 optimal weight:   10.0000
   chunk 65 optimal weight:    0.0970
   chunk 62 optimal weight:    9.9990
   chunk 51 optimal weight:    0.8980
   chunk 117 optimal weight:    6.9990
   overall best weight:    0.5436

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

Flipped N/Q/H residues before XYZ refinement:
A 227 GLN
A 230 GLN
B 113 ASN
C  46 GLN
C 113 ASN
C 227 GLN
C 230 GLN
** b 132 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
c  78 HIS

Total number of N/Q/H flips: 8

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3497 r_free = 0.3497 target = 0.056044 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.2864 r_free = 0.2864 target = 0.036315 restraints weight = 41220.461|
|-----------------------------------------------------------------------------|
r_work (start): 0.2757 rms_B_bonded: 4.39
r_work: 0.2602 rms_B_bonded: 4.62 restraints_weight: 0.5000
r_work (final): 0.2602
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8532
moved from start:          0.1094

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.027   9000  Z= 0.118
  Angle     :  0.576   9.253  12279  Z= 0.297
  Chirality :  0.043   0.143   1347
  Planarity :  0.004   0.048   1662
  Dihedral  :  4.043  24.825   1299
  Min Nonbonded Distance : 2.552

Molprobity Statistics.
  All-atom Clashscore : 8.66
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.00 %
    Favored  : 96.00 %
  Rotamer:
    Outliers :  0.12 %
    Allowed  :  6.69 %
    Favored  : 93.19 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.17 %
    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 are not related in a simple way.
  whole: -0.18 (0.24), residues: 1224
  helix:  0.25 (0.27), residues: 375
  sheet: -0.20 (0.29), residues: 237
  loop : -0.18 (0.26), residues: 612

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG b  48 
 TYR   0.008   0.001   TYR B 207 
 PHE   0.008   0.001   PHE A 133 
 TRP   0.014   0.001   TRP c 148 
 HIS   0.012   0.001   HIS b 132 

Details of bonding type rmsd
  covalent geometry    : bond        0.00246 ( 9000)
  covalent geometry    : angle       0.57609 (12279)
  hydrogen bonds       : bond        0.03900 (  321)
  hydrogen bonds       : angle       5.15437 (  960)

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

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

  2448 Ramachandran restraints generated.
    1224 Oldfield, 0 Emsley, 1224 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2448 Ramachandran restraints generated.
    1224 Oldfield, 0 Emsley, 1224 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  94 residues out of total 867 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 93
  time to evaluate  : 0.197 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   59 ASP cc_start: 0.9095 (t0) cc_final: 0.8590 (t0)
REVERT: A   62 ASP cc_start: 0.9202 (t0) cc_final: 0.8903 (t0)
REVERT: B   48 ASP cc_start: 0.9362 (p0) cc_final: 0.9115 (p0)
REVERT: B   52 GLU cc_start: 0.9184 (pm20) cc_final: 0.8982 (pm20)
REVERT: B   59 ASP cc_start: 0.9172 (t0) cc_final: 0.8607 (t0)
REVERT: B  160 TYR cc_start: 0.8918 (m-80) cc_final: 0.8451 (m-80)
REVERT: B  204 GLU cc_start: 0.8792 (mp0) cc_final: 0.8558 (mp0)
REVERT: C   40 MET cc_start: 0.9346 (ptp) cc_final: 0.8987 (ptp)
REVERT: C   59 ASP cc_start: 0.9132 (t0) cc_final: 0.8556 (t0)
REVERT: a   25 ASN cc_start: 0.9190 (t0) cc_final: 0.8796 (t0)
REVERT: a  111 ARG cc_start: 0.9541 (mtm-85) cc_final: 0.9262 (ptp-110)
REVERT: a  158 MET cc_start: 0.9502 (ptt) cc_final: 0.9254 (ptt)
REVERT: c  111 ARG cc_start: 0.9621 (mpp80) cc_final: 0.9353 (ptp90)
  outliers start: 1
  outliers final: 0
  residues processed: 93
  average time/residue: 0.1416
  time to fit residues: 16.3159
Evaluate side-chains
  70 residues out of total 867 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 70
  time to evaluate  : 0.318 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 123
   random chunks:
   chunk 32 optimal weight:    4.9990
   chunk 106 optimal weight:    1.9990
   chunk 120 optimal weight:    0.0170
   chunk 76 optimal weight:    0.8980
   chunk 75 optimal weight:    4.9990
   chunk 14 optimal weight:    8.9990
   chunk 81 optimal weight:    9.9990
   chunk 22 optimal weight:    6.9990
   chunk 36 optimal weight:    5.9990
   chunk 21 optimal weight:    2.9990
   chunk 84 optimal weight:    0.7980
   overall best weight:    1.3422

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

Flipped N/Q/H residues before XYZ refinement:
B 230 GLN
** b 132 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3485 r_free = 0.3485 target = 0.055504 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.2850 r_free = 0.2850 target = 0.035844 restraints weight = 41163.849|
|-----------------------------------------------------------------------------|
r_work (start): 0.2765 rms_B_bonded: 4.33
r_work: 0.2611 rms_B_bonded: 4.55 restraints_weight: 0.5000
r_work (final): 0.2611
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8549
moved from start:          0.1282

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   9000  Z= 0.146
  Angle     :  0.564   8.369  12279  Z= 0.290
  Chirality :  0.042   0.145   1347
  Planarity :  0.003   0.029   1662
  Dihedral  :  3.993  23.914   1299
  Min Nonbonded Distance : 2.549

Molprobity Statistics.
  All-atom Clashscore : 9.24
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.43 %
    Favored  : 96.57 %
  Rotamer:
    Outliers :  0.12 %
    Allowed  : 10.61 %
    Favored  : 89.27 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.17 %
    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 are not related in a simple way.
  whole: -0.24 (0.23), residues: 1224
  helix:  0.23 (0.27), residues: 375
  sheet: -0.40 (0.28), residues: 258
  loop : -0.13 (0.26), residues: 591

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG b  48 
 TYR   0.008   0.001   TYR B 207 
 PHE   0.009   0.001   PHE a 162 
 TRP   0.015   0.001   TRP b 148 
 HIS   0.005   0.001   HIS a  78 

Details of bonding type rmsd
  covalent geometry    : bond        0.00314 ( 9000)
  covalent geometry    : angle       0.56450 (12279)
  hydrogen bonds       : bond        0.03451 (  321)
  hydrogen bonds       : angle       4.87406 (  960)

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

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

  2448 Ramachandran restraints generated.
    1224 Oldfield, 0 Emsley, 1224 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2448 Ramachandran restraints generated.
    1224 Oldfield, 0 Emsley, 1224 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  83 residues out of total 867 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 82
  time to evaluate  : 0.288 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   59 ASP cc_start: 0.9090 (t0) cc_final: 0.8534 (t0)
REVERT: A   62 ASP cc_start: 0.9191 (t70) cc_final: 0.8991 (t70)
REVERT: B   48 ASP cc_start: 0.9389 (p0) cc_final: 0.9125 (p0)
REVERT: B   59 ASP cc_start: 0.9192 (t0) cc_final: 0.8609 (t0)
REVERT: B  238 ASN cc_start: 0.9137 (m110) cc_final: 0.8886 (p0)
REVERT: C   40 MET cc_start: 0.9365 (ptp) cc_final: 0.9029 (ptp)
REVERT: C   46 GLN cc_start: 0.9673 (mm-40) cc_final: 0.9307 (mm-40)
REVERT: C   59 ASP cc_start: 0.9124 (t0) cc_final: 0.8526 (t0)
REVERT: C  214 GLU cc_start: 0.8441 (pp20) cc_final: 0.7788 (pp20)
REVERT: a  158 MET cc_start: 0.9470 (ptt) cc_final: 0.9259 (ptt)
REVERT: c  111 ARG cc_start: 0.9631 (mpp80) cc_final: 0.9384 (ptp90)
  outliers start: 1
  outliers final: 1
  residues processed: 83
  average time/residue: 0.1293
  time to fit residues: 13.7482
Evaluate side-chains
  69 residues out of total 867 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 68
  time to evaluate  : 0.300 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  254 ASP
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 123
   random chunks:
   chunk 74 optimal weight:    1.9990
   chunk 94 optimal weight:    6.9990
   chunk 67 optimal weight:    4.9990
   chunk 3 optimal weight:    0.8980
   chunk 82 optimal weight:    2.9990
   chunk 97 optimal weight:    7.9990
   chunk 51 optimal weight:    1.9990
   chunk 48 optimal weight:    1.9990
   chunk 112 optimal weight:    0.9990
   chunk 18 optimal weight:   10.0000
   chunk 80 optimal weight:    2.9990
   overall best weight:    1.5788

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

Flipped N/Q/H residues before XYZ refinement:
** b 132 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3481 r_free = 0.3481 target = 0.055153 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.2848 r_free = 0.2848 target = 0.035652 restraints weight = 41782.185|
|-----------------------------------------------------------------------------|
r_work (start): 0.2761 rms_B_bonded: 4.35
r_work: 0.2606 rms_B_bonded: 4.56 restraints_weight: 0.5000
r_work (final): 0.2606
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8545
moved from start:          0.1415

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   9000  Z= 0.158
  Angle     :  0.553   6.985  12279  Z= 0.284
  Chirality :  0.042   0.144   1347
  Planarity :  0.003   0.030   1662
  Dihedral  :  3.978  21.809   1299
  Min Nonbonded Distance : 2.548

Molprobity Statistics.
  All-atom Clashscore : 9.12
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.00 %
    Favored  : 96.00 %
  Rotamer:
    Outliers :  0.69 %
    Allowed  : 11.53 %
    Favored  : 87.77 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.17 %
    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 are not related in a simple way.
  whole: -0.22 (0.23), residues: 1224
  helix:  0.34 (0.27), residues: 375
  sheet: -0.44 (0.28), residues: 258
  loop : -0.17 (0.26), residues: 591

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG a  62 
 TYR   0.009   0.001   TYR C 207 
 PHE   0.008   0.001   PHE a 162 
 TRP   0.009   0.001   TRP a 148 
 HIS   0.005   0.001   HIS a  78 

Details of bonding type rmsd
  covalent geometry    : bond        0.00341 ( 9000)
  covalent geometry    : angle       0.55311 (12279)
  hydrogen bonds       : bond        0.03183 (  321)
  hydrogen bonds       : angle       4.75913 (  960)

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

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

  2448 Ramachandran restraints generated.
    1224 Oldfield, 0 Emsley, 1224 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2448 Ramachandran restraints generated.
    1224 Oldfield, 0 Emsley, 1224 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  87 residues out of total 867 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 81
  time to evaluate  : 0.338 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   59 ASP cc_start: 0.9063 (t0) cc_final: 0.8502 (t0)
REVERT: B   46 GLN cc_start: 0.9442 (mm110) cc_final: 0.9048 (mm-40)
REVERT: B   59 ASP cc_start: 0.9221 (t0) cc_final: 0.8648 (t0)
REVERT: B  160 TYR cc_start: 0.8679 (m-10) cc_final: 0.8211 (m-80)
REVERT: B  238 ASN cc_start: 0.9161 (m110) cc_final: 0.8912 (p0)
REVERT: C   40 MET cc_start: 0.9362 (ptp) cc_final: 0.9022 (ptp)
REVERT: C   46 GLN cc_start: 0.9689 (mm-40) cc_final: 0.9294 (mm-40)
REVERT: C   59 ASP cc_start: 0.9121 (t0) cc_final: 0.8497 (t0)
REVERT: C   62 ASP cc_start: 0.9133 (t0) cc_final: 0.8923 (t0)
REVERT: C  214 GLU cc_start: 0.8467 (pp20) cc_final: 0.7801 (pp20)
REVERT: a   53 LYS cc_start: 0.9540 (tppp) cc_final: 0.9220 (tptt)
REVERT: c  111 ARG cc_start: 0.9632 (mpp80) cc_final: 0.9400 (ptp90)
  outliers start: 6
  outliers final: 1
  residues processed: 85
  average time/residue: 0.1446
  time to fit residues: 15.5623
Evaluate side-chains
  69 residues out of total 867 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 68
  time to evaluate  : 0.335 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain a residue  119 GLU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 123
   random chunks:
   chunk 38 optimal weight:   10.0000
   chunk 108 optimal weight:    6.9990
   chunk 63 optimal weight:   10.0000
   chunk 117 optimal weight:    0.0060
   chunk 46 optimal weight:    6.9990
   chunk 71 optimal weight:    6.9990
   chunk 109 optimal weight:    3.9990
   chunk 106 optimal weight:    2.9990
   chunk 13 optimal weight:    8.9990
   chunk 60 optimal weight:    3.9990
   chunk 73 optimal weight:    1.9990
   overall best weight:    2.6004

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

Flipped N/Q/H residues before XYZ refinement:
** A  46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 113 ASN
A 260 GLN
** B 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 260 GLN
** b 132 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3452 r_free = 0.3452 target = 0.054092 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.2802 r_free = 0.2802 target = 0.034381 restraints weight = 42034.061|
|-----------------------------------------------------------------------------|
r_work (start): 0.2718 rms_B_bonded: 4.33
r_work: 0.2565 rms_B_bonded: 4.52 restraints_weight: 0.5000
r_work (final): 0.2565
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8548
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      :  0.005   0.041   9000  Z= 0.237
  Angle     :  0.604   8.184  12279  Z= 0.311
  Chirality :  0.043   0.166   1347
  Planarity :  0.003   0.027   1662
  Dihedral  :  4.164  20.006   1299
  Min Nonbonded Distance : 2.495

Molprobity Statistics.
  All-atom Clashscore : 11.67
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.00 %
    Favored  : 96.00 %
  Rotamer:
    Outliers :  1.96 %
    Allowed  : 11.42 %
    Favored  : 86.62 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.17 %
    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 are not related in a simple way.
  whole: -0.36 (0.24), residues: 1224
  helix:  0.23 (0.27), residues: 375
  sheet: -0.47 (0.27), residues: 279
  loop : -0.27 (0.27), residues: 570

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG b  62 
 TYR   0.009   0.001   TYR A 207 
 PHE   0.006   0.001   PHE a 162 
 TRP   0.008   0.001   TRP C 101 
 HIS   0.006   0.001   HIS b  78 

Details of bonding type rmsd
  covalent geometry    : bond        0.00506 ( 9000)
  covalent geometry    : angle       0.60402 (12279)
  hydrogen bonds       : bond        0.03348 (  321)
  hydrogen bonds       : angle       4.85189 (  960)

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

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

  2448 Ramachandran restraints generated.
    1224 Oldfield, 0 Emsley, 1224 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2448 Ramachandran restraints generated.
    1224 Oldfield, 0 Emsley, 1224 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  96 residues out of total 867 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 79
  time to evaluate  : 0.316 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   59 ASP cc_start: 0.9049 (t0) cc_final: 0.8483 (t0)
REVERT: A   62 ASP cc_start: 0.9254 (t70) cc_final: 0.8953 (t0)
REVERT: B   46 GLN cc_start: 0.9454 (mm110) cc_final: 0.9175 (mm-40)
REVERT: B   59 ASP cc_start: 0.9218 (t0) cc_final: 0.8662 (t0)
REVERT: B  238 ASN cc_start: 0.9158 (m110) cc_final: 0.8914 (p0)
REVERT: C   40 MET cc_start: 0.9366 (ptp) cc_final: 0.9040 (ptp)
REVERT: C   46 GLN cc_start: 0.9727 (mm-40) cc_final: 0.9283 (mm-40)
REVERT: C   59 ASP cc_start: 0.9111 (t0) cc_final: 0.8494 (t0)
REVERT: C   62 ASP cc_start: 0.9150 (t0) cc_final: 0.8922 (t0)
REVERT: C  214 GLU cc_start: 0.8555 (pp20) cc_final: 0.7884 (pp20)
REVERT: a   62 ARG cc_start: 0.8441 (tpp-160) cc_final: 0.8240 (tpm170)
REVERT: c   62 ARG cc_start: 0.8886 (mmm-85) cc_final: 0.8482 (tpt90)
REVERT: c  111 ARG cc_start: 0.9611 (mpp80) cc_final: 0.9331 (ptp90)
  outliers start: 17
  outliers final: 5
  residues processed: 90
  average time/residue: 0.1346
  time to fit residues: 15.1923
Evaluate side-chains
  73 residues out of total 867 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 68
  time to evaluate  : 0.245 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  254 ASP
Chi-restraints excluded: chain B residue  204 GLU
Chi-restraints excluded: chain C residue  204 GLU
Chi-restraints excluded: chain C residue  217 VAL
Chi-restraints excluded: chain a residue  141 THR
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 123
   random chunks:
   chunk 1 optimal weight:    6.9990
   chunk 56 optimal weight:    7.9990
   chunk 24 optimal weight:    0.9990
   chunk 30 optimal weight:    0.9980
   chunk 107 optimal weight:    0.9980
   chunk 13 optimal weight:    8.9990
   chunk 119 optimal weight:    3.9990
   chunk 87 optimal weight:    0.9990
   chunk 78 optimal weight:    0.0070
   chunk 108 optimal weight:    0.9990
   chunk 94 optimal weight:    0.9990
   overall best weight:    0.8002

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

Flipped N/Q/H residues before XYZ refinement:
A 260 GLN
C 260 GLN
** b 132 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3488 r_free = 0.3488 target = 0.055447 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.2851 r_free = 0.2851 target = 0.035777 restraints weight = 41242.242|
|-----------------------------------------------------------------------------|
r_work (start): 0.2766 rms_B_bonded: 4.36
r_work: 0.2615 rms_B_bonded: 4.56 restraints_weight: 0.5000
r_work (final): 0.2615
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8538
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      :  0.003   0.044   9000  Z= 0.118
  Angle     :  0.585   7.570  12279  Z= 0.295
  Chirality :  0.043   0.143   1347
  Planarity :  0.003   0.030   1662
  Dihedral  :  3.977  23.031   1299
  Min Nonbonded Distance : 2.538

Molprobity Statistics.
  All-atom Clashscore : 9.07
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.59 %
    Favored  : 96.41 %
  Rotamer:
    Outliers :  0.92 %
    Allowed  : 12.69 %
    Favored  : 86.39 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.17 %
    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 are not related in a simple way.
  whole: -0.32 (0.23), residues: 1224
  helix:  0.17 (0.27), residues: 375
  sheet: -0.24 (0.28), residues: 255
  loop : -0.32 (0.26), residues: 594

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG b 111 
 TYR   0.007   0.001   TYR B 207 
 PHE   0.007   0.001   PHE A 133 
 TRP   0.010   0.001   TRP a 148 
 HIS   0.002   0.001   HIS b  78 

Details of bonding type rmsd
  covalent geometry    : bond        0.00252 ( 9000)
  covalent geometry    : angle       0.58523 (12279)
  hydrogen bonds       : bond        0.03085 (  321)
  hydrogen bonds       : angle       4.84475 (  960)

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

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

  2448 Ramachandran restraints generated.
    1224 Oldfield, 0 Emsley, 1224 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2448 Ramachandran restraints generated.
    1224 Oldfield, 0 Emsley, 1224 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  85 residues out of total 867 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 77
  time to evaluate  : 0.236 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   59 ASP cc_start: 0.9077 (t0) cc_final: 0.8536 (t0)
REVERT: A   62 ASP cc_start: 0.9255 (t70) cc_final: 0.9007 (t0)
REVERT: B   59 ASP cc_start: 0.9230 (t0) cc_final: 0.8659 (t0)
REVERT: B  214 GLU cc_start: 0.8001 (pp20) cc_final: 0.7774 (pp20)
REVERT: B  238 ASN cc_start: 0.9062 (m110) cc_final: 0.8843 (p0)
REVERT: C   40 MET cc_start: 0.9377 (ptp) cc_final: 0.9068 (ptp)
REVERT: C   46 GLN cc_start: 0.9701 (mm-40) cc_final: 0.9265 (mm-40)
REVERT: C   59 ASP cc_start: 0.9200 (t0) cc_final: 0.8632 (t0)
REVERT: C  214 GLU cc_start: 0.8466 (pp20) cc_final: 0.7846 (pp20)
REVERT: a   62 ARG cc_start: 0.8709 (tpp-160) cc_final: 0.8481 (tpp-160)
REVERT: a  158 MET cc_start: 0.9498 (mtm) cc_final: 0.9292 (mmm)
REVERT: b   62 ARG cc_start: 0.8535 (tpt90) cc_final: 0.8105 (tpm170)
REVERT: c   62 ARG cc_start: 0.8900 (mmm-85) cc_final: 0.8416 (tpt90)
REVERT: c  111 ARG cc_start: 0.9624 (mpp80) cc_final: 0.9352 (ptp90)
  outliers start: 8
  outliers final: 5
  residues processed: 82
  average time/residue: 0.1345
  time to fit residues: 14.1532
Evaluate side-chains
  77 residues out of total 867 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 72
  time to evaluate  : 0.340 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  254 ASP
Chi-restraints excluded: chain B residue  204 GLU
Chi-restraints excluded: chain C residue  174 THR
Chi-restraints excluded: chain C residue  204 GLU
Chi-restraints excluded: chain a residue  119 GLU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 123
   random chunks:
   chunk 27 optimal weight:    4.9990
   chunk 79 optimal weight:    2.9990
   chunk 9 optimal weight:   10.0000
   chunk 52 optimal weight:    6.9990
   chunk 59 optimal weight:    8.9990
   chunk 65 optimal weight:    0.0010
   chunk 68 optimal weight:    0.9990
   chunk 53 optimal weight:    1.9990
   chunk 101 optimal weight:    4.9990
   chunk 46 optimal weight:    0.0980
   chunk 73 optimal weight:    0.6980
   overall best weight:    0.7590

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

Flipped N/Q/H residues before XYZ refinement:
** b 132 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3492 r_free = 0.3492 target = 0.055511 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.2858 r_free = 0.2858 target = 0.035774 restraints weight = 41381.469|
|-----------------------------------------------------------------------------|
r_work (start): 0.2770 rms_B_bonded: 4.36
r_work: 0.2621 rms_B_bonded: 4.58 restraints_weight: 0.5000
r_work (final): 0.2621
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8534
moved from start:          0.1795

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.035   9000  Z= 0.112
  Angle     :  0.575   8.043  12279  Z= 0.290
  Chirality :  0.042   0.142   1347
  Planarity :  0.003   0.030   1662
  Dihedral  :  3.875  23.685   1299
  Min Nonbonded Distance : 2.469

Molprobity Statistics.
  All-atom Clashscore : 8.43
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.27 %
    Favored  : 96.73 %
  Rotamer:
    Outliers :  1.50 %
    Allowed  : 12.34 %
    Favored  : 86.16 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.17 %
    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 are not related in a simple way.
  whole: -0.26 (0.23), residues: 1224
  helix:  0.20 (0.27), residues: 375
  sheet: -0.31 (0.29), residues: 237
  loop : -0.20 (0.26), residues: 612

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG b  77 
 TYR   0.006   0.001   TYR B 207 
 PHE   0.007   0.001   PHE A 133 
 TRP   0.007   0.001   TRP C 101 
 HIS   0.002   0.001   HIS a  78 

Details of bonding type rmsd
  covalent geometry    : bond        0.00241 ( 9000)
  covalent geometry    : angle       0.57494 (12279)
  hydrogen bonds       : bond        0.03026 (  321)
  hydrogen bonds       : angle       4.80877 (  960)

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

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

  2448 Ramachandran restraints generated.
    1224 Oldfield, 0 Emsley, 1224 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2448 Ramachandran restraints generated.
    1224 Oldfield, 0 Emsley, 1224 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  90 residues out of total 867 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 77
  time to evaluate  : 0.315 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   59 ASP cc_start: 0.9081 (t0) cc_final: 0.8519 (t0)
REVERT: A   62 ASP cc_start: 0.9280 (t70) cc_final: 0.9038 (t0)
REVERT: B   59 ASP cc_start: 0.9244 (t0) cc_final: 0.8672 (t0)
REVERT: B  160 TYR cc_start: 0.8624 (m-10) cc_final: 0.8341 (m-80)
REVERT: B  214 GLU cc_start: 0.8129 (pp20) cc_final: 0.7515 (pp20)
REVERT: B  238 ASN cc_start: 0.9067 (m110) cc_final: 0.8808 (p0)
REVERT: C   40 MET cc_start: 0.9377 (ptp) cc_final: 0.9057 (ptp)
REVERT: C   46 GLN cc_start: 0.9707 (mm-40) cc_final: 0.9273 (mm-40)
REVERT: C   59 ASP cc_start: 0.9223 (t0) cc_final: 0.8656 (t0)
REVERT: C  160 TYR cc_start: 0.8477 (m-10) cc_final: 0.8060 (m-80)
REVERT: C  214 GLU cc_start: 0.8476 (pp20) cc_final: 0.7821 (pp20)
REVERT: a   62 ARG cc_start: 0.8862 (tpp-160) cc_final: 0.8616 (tpp-160)
REVERT: b   62 ARG cc_start: 0.8555 (tpt90) cc_final: 0.8111 (tpm170)
REVERT: c  111 ARG cc_start: 0.9633 (mpp80) cc_final: 0.9359 (ptp90)
  outliers start: 13
  outliers final: 5
  residues processed: 87
  average time/residue: 0.1225
  time to fit residues: 13.9977
Evaluate side-chains
  78 residues out of total 867 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 73
  time to evaluate  : 0.306 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  254 ASP
Chi-restraints excluded: chain B residue  239 ASN
Chi-restraints excluded: chain C residue  174 THR
Chi-restraints excluded: chain C residue  217 VAL
Chi-restraints excluded: chain a residue  119 GLU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 123
   random chunks:
   chunk 107 optimal weight:    0.6980
   chunk 48 optimal weight:    0.9990
   chunk 7 optimal weight:    6.9990
   chunk 87 optimal weight:    0.9990
   chunk 94 optimal weight:    6.9990
   chunk 64 optimal weight:    3.9990
   chunk 59 optimal weight:    7.9990
   chunk 61 optimal weight:    1.9990
   chunk 20 optimal weight:    0.8980
   chunk 110 optimal weight:    0.9980
   chunk 97 optimal weight:    0.9990
   overall best weight:    0.9184

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

Flipped N/Q/H residues before XYZ refinement:
** b 132 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3493 r_free = 0.3493 target = 0.055566 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.2850 r_free = 0.2850 target = 0.035787 restraints weight = 41558.784|
|-----------------------------------------------------------------------------|
r_work (start): 0.2742 rms_B_bonded: 4.39
r_work: 0.2589 rms_B_bonded: 4.60 restraints_weight: 0.5000
r_work (final): 0.2589
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8517
moved from start:          0.1894

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   9000  Z= 0.120
  Angle     :  0.595   7.920  12279  Z= 0.300
  Chirality :  0.042   0.141   1347
  Planarity :  0.003   0.030   1662
  Dihedral  :  3.816  24.379   1299
  Min Nonbonded Distance : 2.511

Molprobity Statistics.
  All-atom Clashscore : 8.55
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.10 %
    Favored  : 96.90 %
  Rotamer:
    Outliers :  1.38 %
    Allowed  : 13.49 %
    Favored  : 85.12 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.17 %
    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 are not related in a simple way.
  whole: -0.30 (0.23), residues: 1224
  helix:  0.09 (0.27), residues: 375
  sheet: -0.16 (0.29), residues: 228
  loop : -0.26 (0.25), residues: 621

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG b  77 
 TYR   0.005   0.001   TYR A 207 
 PHE   0.004   0.001   PHE B 130 
 TRP   0.007   0.001   TRP C 101 
 HIS   0.003   0.001   HIS a  78 

Details of bonding type rmsd
  covalent geometry    : bond        0.00256 ( 9000)
  covalent geometry    : angle       0.59508 (12279)
  hydrogen bonds       : bond        0.03094 (  321)
  hydrogen bonds       : angle       4.84049 (  960)

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

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

  2448 Ramachandran restraints generated.
    1224 Oldfield, 0 Emsley, 1224 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2448 Ramachandran restraints generated.
    1224 Oldfield, 0 Emsley, 1224 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  86 residues out of total 867 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 74
  time to evaluate  : 0.241 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   59 ASP cc_start: 0.9071 (t0) cc_final: 0.8505 (t0)
REVERT: A   62 ASP cc_start: 0.9280 (t70) cc_final: 0.8992 (t0)
REVERT: B   59 ASP cc_start: 0.9248 (t0) cc_final: 0.8677 (t0)
REVERT: B  160 TYR cc_start: 0.8575 (m-10) cc_final: 0.8254 (m-80)
REVERT: B  214 GLU cc_start: 0.8214 (pp20) cc_final: 0.7662 (pp20)
REVERT: B  238 ASN cc_start: 0.9082 (m110) cc_final: 0.8816 (p0)
REVERT: C   40 MET cc_start: 0.9395 (ptp) cc_final: 0.9074 (ptp)
REVERT: C   46 GLN cc_start: 0.9701 (mm-40) cc_final: 0.9281 (mm-40)
REVERT: C   59 ASP cc_start: 0.9214 (t0) cc_final: 0.8641 (t0)
REVERT: C  160 TYR cc_start: 0.8483 (m-10) cc_final: 0.8049 (m-80)
REVERT: C  214 GLU cc_start: 0.8454 (pp20) cc_final: 0.7767 (pp20)
REVERT: a   62 ARG cc_start: 0.8936 (tpp-160) cc_final: 0.8667 (tpp-160)
REVERT: b   62 ARG cc_start: 0.8650 (tpt90) cc_final: 0.8178 (tpm170)
REVERT: c  111 ARG cc_start: 0.9634 (mpp80) cc_final: 0.9418 (ptp-110)
  outliers start: 12
  outliers final: 7
  residues processed: 82
  average time/residue: 0.1218
  time to fit residues: 13.0142
Evaluate side-chains
  78 residues out of total 867 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 71
  time to evaluate  : 0.257 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  254 ASP
Chi-restraints excluded: chain B residue  204 GLU
Chi-restraints excluded: chain B residue  239 ASN
Chi-restraints excluded: chain C residue  174 THR
Chi-restraints excluded: chain C residue  204 GLU
Chi-restraints excluded: chain C residue  217 VAL
Chi-restraints excluded: chain a residue  119 GLU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 123
   random chunks:
   chunk 66 optimal weight:    6.9990
   chunk 65 optimal weight:    3.9990
   chunk 21 optimal weight:    0.2980
   chunk 33 optimal weight:   20.0000
   chunk 84 optimal weight:    0.9990
   chunk 82 optimal weight:    0.7980
   chunk 90 optimal weight:    0.2980
   chunk 83 optimal weight:    7.9990
   chunk 48 optimal weight:    1.9990
   chunk 8 optimal weight:    8.9990
   chunk 40 optimal weight:    8.9990
   overall best weight:    0.8784

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

Flipped N/Q/H residues before XYZ refinement:
** b 132 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3496 r_free = 0.3496 target = 0.055711 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.2850 r_free = 0.2850 target = 0.035836 restraints weight = 41296.389|
|-----------------------------------------------------------------------------|
r_work (start): 0.2765 rms_B_bonded: 4.39
r_work: 0.2616 rms_B_bonded: 4.58 restraints_weight: 0.5000
r_work (final): 0.2616
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8537
moved from start:          0.1958

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038   9000  Z= 0.121
  Angle     :  0.627  10.119  12279  Z= 0.318
  Chirality :  0.043   0.209   1347
  Planarity :  0.003   0.030   1662
  Dihedral  :  3.808  24.791   1299
  Min Nonbonded Distance : 2.446

Molprobity Statistics.
  All-atom Clashscore : 8.95
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.78 %
    Favored  : 97.22 %
  Rotamer:
    Outliers :  1.61 %
    Allowed  : 13.73 %
    Favored  : 84.66 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.17 %
    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 are not related in a simple way.
  whole: -0.29 (0.23), residues: 1224
  helix:  0.06 (0.27), residues: 375
  sheet: -0.14 (0.29), residues: 228
  loop : -0.23 (0.26), residues: 621

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG b  77 
 TYR   0.005   0.001   TYR A 207 
 PHE   0.004   0.001   PHE B 130 
 TRP   0.007   0.001   TRP C 101 
 HIS   0.003   0.001   HIS a  78 

Details of bonding type rmsd
  covalent geometry    : bond        0.00261 ( 9000)
  covalent geometry    : angle       0.62694 (12279)
  hydrogen bonds       : bond        0.03053 (  321)
  hydrogen bonds       : angle       4.98217 (  960)

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

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

  2448 Ramachandran restraints generated.
    1224 Oldfield, 0 Emsley, 1224 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2448 Ramachandran restraints generated.
    1224 Oldfield, 0 Emsley, 1224 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  87 residues out of total 867 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 73
  time to evaluate  : 0.290 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   59 ASP cc_start: 0.9080 (t0) cc_final: 0.8552 (t0)
REVERT: A   62 ASP cc_start: 0.9301 (t70) cc_final: 0.9019 (t0)
REVERT: B   40 MET cc_start: 0.9515 (ptp) cc_final: 0.9184 (pmm)
REVERT: B   59 ASP cc_start: 0.9253 (t0) cc_final: 0.8683 (t0)
REVERT: B  160 TYR cc_start: 0.8503 (m-10) cc_final: 0.8158 (m-80)
REVERT: B  214 GLU cc_start: 0.8276 (pp20) cc_final: 0.7741 (pp20)
REVERT: B  238 ASN cc_start: 0.9056 (m110) cc_final: 0.8827 (p0)
REVERT: C   40 MET cc_start: 0.9391 (ptp) cc_final: 0.9039 (ptp)
REVERT: C   59 ASP cc_start: 0.9219 (t0) cc_final: 0.8642 (t0)
REVERT: C  160 TYR cc_start: 0.8556 (m-10) cc_final: 0.8126 (m-80)
REVERT: C  214 GLU cc_start: 0.8463 (pp20) cc_final: 0.7835 (pp20)
REVERT: a   62 ARG cc_start: 0.8975 (tpp-160) cc_final: 0.8705 (tpp-160)
REVERT: a   77 ARG cc_start: 0.7188 (pmt-80) cc_final: 0.6947 (pmt-80)
REVERT: b   62 ARG cc_start: 0.8670 (tpt90) cc_final: 0.8194 (tpm170)
REVERT: c  111 ARG cc_start: 0.9632 (mpp80) cc_final: 0.9401 (ptp-110)
  outliers start: 14
  outliers final: 9
  residues processed: 83
  average time/residue: 0.1217
  time to fit residues: 13.3027
Evaluate side-chains
  81 residues out of total 867 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 72
  time to evaluate  : 0.326 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  217 VAL
Chi-restraints excluded: chain A residue  254 ASP
Chi-restraints excluded: chain B residue  174 THR
Chi-restraints excluded: chain B residue  204 GLU
Chi-restraints excluded: chain B residue  239 ASN
Chi-restraints excluded: chain C residue  174 THR
Chi-restraints excluded: chain C residue  204 GLU
Chi-restraints excluded: chain C residue  217 VAL
Chi-restraints excluded: chain a residue  119 GLU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 123
   random chunks:
   chunk 41 optimal weight:    1.9990
   chunk 16 optimal weight:    9.9990
   chunk 8 optimal weight:    6.9990
   chunk 27 optimal weight:    5.9990
   chunk 74 optimal weight:    2.9990
   chunk 71 optimal weight:    2.9990
   chunk 28 optimal weight:    0.9990
   chunk 120 optimal weight:    0.0170
   chunk 3 optimal weight:    0.7980
   chunk 18 optimal weight:    4.9990
   chunk 102 optimal weight:    4.9990
   overall best weight:    1.3624

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

Flipped N/Q/H residues before XYZ refinement:
** b 132 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3483 r_free = 0.3483 target = 0.055240 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.2836 r_free = 0.2836 target = 0.035419 restraints weight = 41185.611|
|-----------------------------------------------------------------------------|
r_work (start): 0.2745 rms_B_bonded: 4.37
r_work: 0.2596 rms_B_bonded: 4.55 restraints_weight: 0.5000
r_work (final): 0.2596
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8534
moved from start:          0.1990

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   9000  Z= 0.148
  Angle     :  0.634   9.404  12279  Z= 0.324
  Chirality :  0.043   0.160   1347
  Planarity :  0.003   0.030   1662
  Dihedral  :  3.845  24.832   1299
  Min Nonbonded Distance : 2.467

Molprobity Statistics.
  All-atom Clashscore : 10.51
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.94 %
    Favored  : 97.06 %
  Rotamer:
    Outliers :  1.38 %
    Allowed  : 13.49 %
    Favored  : 85.12 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.17 %
    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 are not related in a simple way.
  whole: -0.32 (0.24), residues: 1224
  helix: -0.01 (0.27), residues: 375
  sheet: -0.18 (0.30), residues: 228
  loop : -0.21 (0.26), residues: 621

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG b  77 
 TYR   0.006   0.001   TYR A 160 
 PHE   0.005   0.001   PHE a  24 
 TRP   0.007   0.001   TRP C 101 
 HIS   0.003   0.001   HIS a  78 

Details of bonding type rmsd
  covalent geometry    : bond        0.00320 ( 9000)
  covalent geometry    : angle       0.63433 (12279)
  hydrogen bonds       : bond        0.03151 (  321)
  hydrogen bonds       : angle       5.07085 (  960)

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

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

  2448 Ramachandran restraints generated.
    1224 Oldfield, 0 Emsley, 1224 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2448 Ramachandran restraints generated.
    1224 Oldfield, 0 Emsley, 1224 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  85 residues out of total 867 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 73
  time to evaluate  : 0.308 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   40 MET cc_start: 0.9712 (ptp) cc_final: 0.9497 (pmm)
REVERT: A   59 ASP cc_start: 0.9070 (t0) cc_final: 0.8524 (t0)
REVERT: A  254 ASP cc_start: 0.3639 (OUTLIER) cc_final: 0.3050 (t70)
REVERT: B   59 ASP cc_start: 0.9258 (t0) cc_final: 0.8693 (t0)
REVERT: B  160 TYR cc_start: 0.8543 (m-10) cc_final: 0.8188 (m-80)
REVERT: B  214 GLU cc_start: 0.8363 (pp20) cc_final: 0.7812 (pp20)
REVERT: B  238 ASN cc_start: 0.9089 (m110) cc_final: 0.8833 (p0)
REVERT: C   40 MET cc_start: 0.9390 (ptp) cc_final: 0.9060 (ptp)
REVERT: C   46 GLN cc_start: 0.9691 (mm-40) cc_final: 0.9262 (mm-40)
REVERT: C   59 ASP cc_start: 0.9215 (t0) cc_final: 0.8641 (t0)
REVERT: C  160 TYR cc_start: 0.8589 (m-10) cc_final: 0.8145 (m-80)
REVERT: C  214 GLU cc_start: 0.8491 (pp20) cc_final: 0.7847 (pp20)
REVERT: a   62 ARG cc_start: 0.8984 (tpp-160) cc_final: 0.8697 (tpp-160)
REVERT: b   62 ARG cc_start: 0.8670 (tpt90) cc_final: 0.8210 (tpm170)
REVERT: c  111 ARG cc_start: 0.9632 (mpp80) cc_final: 0.9406 (ptp-110)
  outliers start: 12
  outliers final: 8
  residues processed: 82
  average time/residue: 0.1243
  time to fit residues: 13.1777
Evaluate side-chains
  81 residues out of total 867 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 72
  time to evaluate  : 0.323 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  217 VAL
Chi-restraints excluded: chain A residue  254 ASP
Chi-restraints excluded: chain B residue  174 THR
Chi-restraints excluded: chain B residue  204 GLU
Chi-restraints excluded: chain B residue  239 ASN
Chi-restraints excluded: chain C residue  174 THR
Chi-restraints excluded: chain C residue  217 VAL
Chi-restraints excluded: chain a residue  119 GLU
Chi-restraints excluded: chain a residue  158 MET
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 123
   random chunks:
   chunk 78 optimal weight:    0.6980
   chunk 34 optimal weight:    4.9990
   chunk 102 optimal weight:    3.9990
   chunk 121 optimal weight:    3.9990
   chunk 84 optimal weight:    5.9990
   chunk 60 optimal weight:    0.7980
   chunk 54 optimal weight:    0.9990
   chunk 55 optimal weight:    0.8980
   chunk 11 optimal weight:    0.9980
   chunk 90 optimal weight:    0.0050
   chunk 23 optimal weight:    2.9990
   overall best weight:    0.6794

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

Flipped N/Q/H residues before XYZ refinement:
** b 132 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3501 r_free = 0.3501 target = 0.055903 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.2861 r_free = 0.2861 target = 0.036131 restraints weight = 40935.064|
|-----------------------------------------------------------------------------|
r_work (start): 0.2771 rms_B_bonded: 4.37
r_work: 0.2622 rms_B_bonded: 4.56 restraints_weight: 0.5000
r_work (final): 0.2622
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8540
moved from start:          0.2080

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.036   9000  Z= 0.112
  Angle     :  0.622   9.435  12279  Z= 0.316
  Chirality :  0.043   0.160   1347
  Planarity :  0.003   0.031   1662
  Dihedral  :  3.761  25.506   1299
  Min Nonbonded Distance : 2.485

Molprobity Statistics.
  All-atom Clashscore : 9.12
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.37 %
    Favored  : 97.63 %
  Rotamer:
    Outliers :  1.27 %
    Allowed  : 13.73 %
    Favored  : 85.01 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.17 %
    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 are not related in a simple way.
  whole: -0.32 (0.24), residues: 1224
  helix: -0.01 (0.27), residues: 375
  sheet: -0.49 (0.28), residues: 264
  loop : -0.02 (0.27), residues: 585

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG b  77 
 TYR   0.006   0.001   TYR A 160 
 PHE   0.004   0.001   PHE B 130 
 TRP   0.008   0.001   TRP a 148 
 HIS   0.003   0.001   HIS a  78 

Details of bonding type rmsd
  covalent geometry    : bond        0.00243 ( 9000)
  covalent geometry    : angle       0.62184 (12279)
  hydrogen bonds       : bond        0.03072 (  321)
  hydrogen bonds       : angle       5.01786 (  960)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2402.45 seconds
wall clock time: 41 minutes 43.78 seconds (2503.78 seconds total)