Starting phenix.real_space_refine
on Thu Mar  5 10:49:12 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7mqb_23941/03_2026/7mqb_23941.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7mqb_23941/03_2026/7mqb_23941.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.25
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/7mqb_23941/03_2026/7mqb_23941.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7mqb_23941/03_2026/7mqb_23941.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/7mqb_23941/03_2026/7mqb_23941.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7mqb_23941/03_2026/7mqb_23941.map"
  }
  resolution = 3.25
  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=   0.002 sd=   0.012
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
  Anisotropic ADP refinement not supported. Converting 11544 atoms to isotropic.
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 5
    Type Number    sf(0)   Gaussians
     P      16      5.49       5
     S      48      5.16       5
     C    8064      2.51       5
     N    2328      2.21       5
     O    2304      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 72 residue(s): 0.02s

  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: 12760
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "A"
      Number of atoms: 1548
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 205, 1548
          Classifications: {'peptide': 205}
          Modifications used: {'COO': 1}
          Incomplete info: {'truncation_to_alanine': 26}
          Link IDs: {'PTRANS': 5, 'TRANS': 199}
          Unresolved non-hydrogen bonds: 85
          Unresolved non-hydrogen angles: 105
          Unresolved non-hydrogen dihedrals: 65
          Unresolved non-hydrogen chiralities: 1
          Planarities with less than four sites: {'GLU:plan': 6, 'ASP:plan': 8, 'ASN:plan1': 2, 'ARG:plan': 2, 'GLN:plan1': 1}
          Unresolved non-hydrogen planarities: 68
    Chain: "B"
      Number of atoms: 47
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 47
          Classifications: {'RNA': 2}
          Modifications used: {'p5*END': 1, 'rna3p_pur': 2}
          Link IDs: {'rna3p': 1}
  Restraints were copied for chains:
    C, E, G, I, K, M, O, D, F, H, J, L, N, P
  Time building chain proxies: 1.74, per 1000 atoms: 0.14
  Number of scatterers: 12760
  At special positions: 0
  Unit cell: (105.4, 105.4, 88.04, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S      48     16.00
     P      16     15.00
     O    2304      8.00
     N    2328      7.00
     C    8064      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: 0.82
  Conformation dependent library (CDL) restraints added in 461.8 milliseconds
  

  3248 Ramachandran restraints generated.
    1624 Oldfield, 0 Emsley, 1624 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  3120

  Finding SS restraints...
    Secondary structure from input PDB file:
      56 helices and 8 sheets defined
      45.4% alpha, 13.7% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.29
  Creating SS restraints...
    Processing helix  chain 'A' and resid 62 through 71
    Processing helix  chain 'A' and resid 80 through 93
      removed outlier: 3.886A  pdb=" N   ASP A  84 " --> pdb=" O   PHE A  80 " (cutoff:3.500A)
      removed outlier: 3.618A  pdb=" N   ALA A  86 " --> pdb=" O   ARG A  82 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 102 through 110
    Processing helix  chain 'A' and resid 117 through 127
    Processing helix  chain 'A' and resid 145 through 155
    Processing helix  chain 'A' and resid 158 through 173
    Processing helix  chain 'A' and resid 175 through 196
      Proline residue:  A 187  - end of helix
    Processing helix  chain 'C' and resid 62 through 71
    Processing helix  chain 'C' and resid 80 through 93
      removed outlier: 3.886A  pdb=" N   ASP C  84 " --> pdb=" O   PHE C  80 " (cutoff:3.500A)
      removed outlier: 3.619A  pdb=" N   ALA C  86 " --> pdb=" O   ARG C  82 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 102 through 110
    Processing helix  chain 'C' and resid 117 through 127
    Processing helix  chain 'C' and resid 145 through 155
    Processing helix  chain 'C' and resid 158 through 173
    Processing helix  chain 'C' and resid 175 through 196
      Proline residue:  C 187  - end of helix
    Processing helix  chain 'E' and resid 62 through 71
    Processing helix  chain 'E' and resid 80 through 93
      removed outlier: 3.887A  pdb=" N   ASP E  84 " --> pdb=" O   PHE E  80 " (cutoff:3.500A)
      removed outlier: 3.618A  pdb=" N   ALA E  86 " --> pdb=" O   ARG E  82 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 102 through 110
    Processing helix  chain 'E' and resid 117 through 127
    Processing helix  chain 'E' and resid 145 through 155
    Processing helix  chain 'E' and resid 158 through 173
    Processing helix  chain 'E' and resid 175 through 196
      Proline residue:  E 187  - end of helix
    Processing helix  chain 'G' and resid 62 through 71
    Processing helix  chain 'G' and resid 80 through 93
      removed outlier: 3.886A  pdb=" N   ASP G  84 " --> pdb=" O   PHE G  80 " (cutoff:3.500A)
      removed outlier: 3.618A  pdb=" N   ALA G  86 " --> pdb=" O   ARG G  82 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 102 through 110
    Processing helix  chain 'G' and resid 117 through 127
    Processing helix  chain 'G' and resid 145 through 155
    Processing helix  chain 'G' and resid 158 through 173
    Processing helix  chain 'G' and resid 175 through 196
      Proline residue:  G 187  - end of helix
    Processing helix  chain 'I' and resid 62 through 71
    Processing helix  chain 'I' and resid 80 through 93
      removed outlier: 3.886A  pdb=" N   ASP I  84 " --> pdb=" O   PHE I  80 " (cutoff:3.500A)
      removed outlier: 3.619A  pdb=" N   ALA I  86 " --> pdb=" O   ARG I  82 " (cutoff:3.500A)
    Processing helix  chain 'I' and resid 102 through 110
    Processing helix  chain 'I' and resid 117 through 127
    Processing helix  chain 'I' and resid 145 through 155
    Processing helix  chain 'I' and resid 158 through 173
    Processing helix  chain 'I' and resid 175 through 196
      Proline residue:  I 187  - end of helix
    Processing helix  chain 'K' and resid 62 through 71
    Processing helix  chain 'K' and resid 80 through 93
      removed outlier: 3.886A  pdb=" N   ASP K  84 " --> pdb=" O   PHE K  80 " (cutoff:3.500A)
      removed outlier: 3.618A  pdb=" N   ALA K  86 " --> pdb=" O   ARG K  82 " (cutoff:3.500A)
    Processing helix  chain 'K' and resid 102 through 110
    Processing helix  chain 'K' and resid 117 through 127
    Processing helix  chain 'K' and resid 145 through 155
    Processing helix  chain 'K' and resid 158 through 173
    Processing helix  chain 'K' and resid 175 through 196
      Proline residue:  K 187  - end of helix
    Processing helix  chain 'M' and resid 62 through 71
    Processing helix  chain 'M' and resid 80 through 93
      removed outlier: 3.886A  pdb=" N   ASP M  84 " --> pdb=" O   PHE M  80 " (cutoff:3.500A)
      removed outlier: 3.619A  pdb=" N   ALA M  86 " --> pdb=" O   ARG M  82 " (cutoff:3.500A)
    Processing helix  chain 'M' and resid 102 through 110
    Processing helix  chain 'M' and resid 117 through 127
    Processing helix  chain 'M' and resid 145 through 155
    Processing helix  chain 'M' and resid 158 through 173
    Processing helix  chain 'M' and resid 175 through 196
      Proline residue:  M 187  - end of helix
    Processing helix  chain 'O' and resid 62 through 71
    Processing helix  chain 'O' and resid 80 through 93
      removed outlier: 3.886A  pdb=" N   ASP O  84 " --> pdb=" O   PHE O  80 " (cutoff:3.500A)
      removed outlier: 3.618A  pdb=" N   ALA O  86 " --> pdb=" O   ARG O  82 " (cutoff:3.500A)
    Processing helix  chain 'O' and resid 102 through 110
    Processing helix  chain 'O' and resid 117 through 127
    Processing helix  chain 'O' and resid 145 through 155
    Processing helix  chain 'O' and resid 158 through 173
    Processing helix  chain 'O' and resid 175 through 196
      Proline residue:  O 187  - end of helix
    Processing sheet with id=AA1, first strand: chain 'A' and resid 3 through 8
      removed outlier: 6.483A  pdb=" N   GLU A   3 " --> pdb=" O   ALA A  50 " (cutoff:3.500A)
      removed outlier: 7.637A  pdb=" N   VAL A  52 " --> pdb=" O   GLU A   3 " (cutoff:3.500A)
      removed outlier: 6.331A  pdb=" N   ARG A   5 " --> pdb=" O   VAL A  52 " (cutoff:3.500A)
      removed outlier: 7.534A  pdb=" N   GLN A  54 " --> pdb=" O   ARG A   5 " (cutoff:3.500A)
      removed outlier: 6.824A  pdb=" N   HIS A   7 " --> pdb=" O   GLN A  54 " (cutoff:3.500A)
      removed outlier: 6.681A  pdb=" N   GLU A  27 " --> pdb=" O   CYS A  39 " (cutoff:3.500A)
      removed outlier: 4.846A  pdb=" N   VAL A  41 " --> pdb=" O   ASP A  25 " (cutoff:3.500A)
      removed outlier: 6.804A  pdb=" N   ASP A  25 " --> pdb=" O   VAL A  41 " (cutoff:3.500A)
      removed outlier: 4.342A  pdb=" N   LEU A  43 " --> pdb=" O   ALA A  23 " (cutoff:3.500A)
      removed outlier: 6.678A  pdb=" N   ALA A  23 " --> pdb=" O   LEU A  43 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'C' and resid 3 through 8
      removed outlier: 6.483A  pdb=" N   GLU C   3 " --> pdb=" O   ALA C  50 " (cutoff:3.500A)
      removed outlier: 7.636A  pdb=" N   VAL C  52 " --> pdb=" O   GLU C   3 " (cutoff:3.500A)
      removed outlier: 6.331A  pdb=" N   ARG C   5 " --> pdb=" O   VAL C  52 " (cutoff:3.500A)
      removed outlier: 7.533A  pdb=" N   GLN C  54 " --> pdb=" O   ARG C   5 " (cutoff:3.500A)
      removed outlier: 6.824A  pdb=" N   HIS C   7 " --> pdb=" O   GLN C  54 " (cutoff:3.500A)
      removed outlier: 6.681A  pdb=" N   GLU C  27 " --> pdb=" O   CYS C  39 " (cutoff:3.500A)
      removed outlier: 4.846A  pdb=" N   VAL C  41 " --> pdb=" O   ASP C  25 " (cutoff:3.500A)
      removed outlier: 6.804A  pdb=" N   ASP C  25 " --> pdb=" O   VAL C  41 " (cutoff:3.500A)
      removed outlier: 4.342A  pdb=" N   LEU C  43 " --> pdb=" O   ALA C  23 " (cutoff:3.500A)
      removed outlier: 6.678A  pdb=" N   ALA C  23 " --> pdb=" O   LEU C  43 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'E' and resid 3 through 8
      removed outlier: 6.483A  pdb=" N   GLU E   3 " --> pdb=" O   ALA E  50 " (cutoff:3.500A)
      removed outlier: 7.637A  pdb=" N   VAL E  52 " --> pdb=" O   GLU E   3 " (cutoff:3.500A)
      removed outlier: 6.331A  pdb=" N   ARG E   5 " --> pdb=" O   VAL E  52 " (cutoff:3.500A)
      removed outlier: 7.534A  pdb=" N   GLN E  54 " --> pdb=" O   ARG E   5 " (cutoff:3.500A)
      removed outlier: 6.824A  pdb=" N   HIS E   7 " --> pdb=" O   GLN E  54 " (cutoff:3.500A)
      removed outlier: 6.680A  pdb=" N   GLU E  27 " --> pdb=" O   CYS E  39 " (cutoff:3.500A)
      removed outlier: 4.847A  pdb=" N   VAL E  41 " --> pdb=" O   ASP E  25 " (cutoff:3.500A)
      removed outlier: 6.805A  pdb=" N   ASP E  25 " --> pdb=" O   VAL E  41 " (cutoff:3.500A)
      removed outlier: 4.342A  pdb=" N   LEU E  43 " --> pdb=" O   ALA E  23 " (cutoff:3.500A)
      removed outlier: 6.678A  pdb=" N   ALA E  23 " --> pdb=" O   LEU E  43 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'G' and resid 3 through 8
      removed outlier: 6.483A  pdb=" N   GLU G   3 " --> pdb=" O   ALA G  50 " (cutoff:3.500A)
      removed outlier: 7.637A  pdb=" N   VAL G  52 " --> pdb=" O   GLU G   3 " (cutoff:3.500A)
      removed outlier: 6.331A  pdb=" N   ARG G   5 " --> pdb=" O   VAL G  52 " (cutoff:3.500A)
      removed outlier: 7.533A  pdb=" N   GLN G  54 " --> pdb=" O   ARG G   5 " (cutoff:3.500A)
      removed outlier: 6.825A  pdb=" N   HIS G   7 " --> pdb=" O   GLN G  54 " (cutoff:3.500A)
      removed outlier: 6.681A  pdb=" N   GLU G  27 " --> pdb=" O   CYS G  39 " (cutoff:3.500A)
      removed outlier: 4.846A  pdb=" N   VAL G  41 " --> pdb=" O   ASP G  25 " (cutoff:3.500A)
      removed outlier: 6.804A  pdb=" N   ASP G  25 " --> pdb=" O   VAL G  41 " (cutoff:3.500A)
      removed outlier: 4.343A  pdb=" N   LEU G  43 " --> pdb=" O   ALA G  23 " (cutoff:3.500A)
      removed outlier: 6.678A  pdb=" N   ALA G  23 " --> pdb=" O   LEU G  43 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'I' and resid 3 through 8
      removed outlier: 6.484A  pdb=" N   GLU I   3 " --> pdb=" O   ALA I  50 " (cutoff:3.500A)
      removed outlier: 7.637A  pdb=" N   VAL I  52 " --> pdb=" O   GLU I   3 " (cutoff:3.500A)
      removed outlier: 6.331A  pdb=" N   ARG I   5 " --> pdb=" O   VAL I  52 " (cutoff:3.500A)
      removed outlier: 7.534A  pdb=" N   GLN I  54 " --> pdb=" O   ARG I   5 " (cutoff:3.500A)
      removed outlier: 6.825A  pdb=" N   HIS I   7 " --> pdb=" O   GLN I  54 " (cutoff:3.500A)
      removed outlier: 6.681A  pdb=" N   GLU I  27 " --> pdb=" O   CYS I  39 " (cutoff:3.500A)
      removed outlier: 4.847A  pdb=" N   VAL I  41 " --> pdb=" O   ASP I  25 " (cutoff:3.500A)
      removed outlier: 6.803A  pdb=" N   ASP I  25 " --> pdb=" O   VAL I  41 " (cutoff:3.500A)
      removed outlier: 4.342A  pdb=" N   LEU I  43 " --> pdb=" O   ALA I  23 " (cutoff:3.500A)
      removed outlier: 6.678A  pdb=" N   ALA I  23 " --> pdb=" O   LEU I  43 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'K' and resid 3 through 8
      removed outlier: 6.483A  pdb=" N   GLU K   3 " --> pdb=" O   ALA K  50 " (cutoff:3.500A)
      removed outlier: 7.637A  pdb=" N   VAL K  52 " --> pdb=" O   GLU K   3 " (cutoff:3.500A)
      removed outlier: 6.331A  pdb=" N   ARG K   5 " --> pdb=" O   VAL K  52 " (cutoff:3.500A)
      removed outlier: 7.534A  pdb=" N   GLN K  54 " --> pdb=" O   ARG K   5 " (cutoff:3.500A)
      removed outlier: 6.824A  pdb=" N   HIS K   7 " --> pdb=" O   GLN K  54 " (cutoff:3.500A)
      removed outlier: 6.680A  pdb=" N   GLU K  27 " --> pdb=" O   CYS K  39 " (cutoff:3.500A)
      removed outlier: 4.847A  pdb=" N   VAL K  41 " --> pdb=" O   ASP K  25 " (cutoff:3.500A)
      removed outlier: 6.804A  pdb=" N   ASP K  25 " --> pdb=" O   VAL K  41 " (cutoff:3.500A)
      removed outlier: 4.343A  pdb=" N   LEU K  43 " --> pdb=" O   ALA K  23 " (cutoff:3.500A)
      removed outlier: 6.678A  pdb=" N   ALA K  23 " --> pdb=" O   LEU K  43 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'M' and resid 3 through 8
      removed outlier: 6.483A  pdb=" N   GLU M   3 " --> pdb=" O   ALA M  50 " (cutoff:3.500A)
      removed outlier: 7.637A  pdb=" N   VAL M  52 " --> pdb=" O   GLU M   3 " (cutoff:3.500A)
      removed outlier: 6.331A  pdb=" N   ARG M   5 " --> pdb=" O   VAL M  52 " (cutoff:3.500A)
      removed outlier: 7.534A  pdb=" N   GLN M  54 " --> pdb=" O   ARG M   5 " (cutoff:3.500A)
      removed outlier: 6.825A  pdb=" N   HIS M   7 " --> pdb=" O   GLN M  54 " (cutoff:3.500A)
      removed outlier: 6.681A  pdb=" N   GLU M  27 " --> pdb=" O   CYS M  39 " (cutoff:3.500A)
      removed outlier: 4.846A  pdb=" N   VAL M  41 " --> pdb=" O   ASP M  25 " (cutoff:3.500A)
      removed outlier: 6.805A  pdb=" N   ASP M  25 " --> pdb=" O   VAL M  41 " (cutoff:3.500A)
      removed outlier: 4.342A  pdb=" N   LEU M  43 " --> pdb=" O   ALA M  23 " (cutoff:3.500A)
      removed outlier: 6.678A  pdb=" N   ALA M  23 " --> pdb=" O   LEU M  43 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'O' and resid 3 through 8
      removed outlier: 6.483A  pdb=" N   GLU O   3 " --> pdb=" O   ALA O  50 " (cutoff:3.500A)
      removed outlier: 7.637A  pdb=" N   VAL O  52 " --> pdb=" O   GLU O   3 " (cutoff:3.500A)
      removed outlier: 6.332A  pdb=" N   ARG O   5 " --> pdb=" O   VAL O  52 " (cutoff:3.500A)
      removed outlier: 7.534A  pdb=" N   GLN O  54 " --> pdb=" O   ARG O   5 " (cutoff:3.500A)
      removed outlier: 6.824A  pdb=" N   HIS O   7 " --> pdb=" O   GLN O  54 " (cutoff:3.500A)
      removed outlier: 6.680A  pdb=" N   GLU O  27 " --> pdb=" O   CYS O  39 " (cutoff:3.500A)
      removed outlier: 4.846A  pdb=" N   VAL O  41 " --> pdb=" O   ASP O  25 " (cutoff:3.500A)
      removed outlier: 6.804A  pdb=" N   ASP O  25 " --> pdb=" O   VAL O  41 " (cutoff:3.500A)
      removed outlier: 4.343A  pdb=" N   LEU O  43 " --> pdb=" O   ALA O  23 " (cutoff:3.500A)
      removed outlier: 6.677A  pdb=" N   ALA O  23 " --> pdb=" O   LEU O  43 " (cutoff:3.500A)

    560 hydrogen bonds defined for protein.
    1680 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: 1.24

  Time building geometry restraints manager: 1.18 seconds

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

  Histogram of bond lengths:
        1.23 -     1.34: 4216
        1.34 -     1.46: 2302
        1.46 -     1.57: 6418
        1.57 -     1.69: 24
        1.69 -     1.81: 64
  Bond restraints: 13024
  Sorted by residual:
  bond pdb=" CG  LYS C 103 "
       pdb=" CD  LYS C 103 "
    ideal  model  delta    sigma   weight residual
    1.520  1.486  0.034 3.00e-02 1.11e+03 1.28e+00
  bond pdb=" CG  LYS E 103 "
       pdb=" CD  LYS E 103 "
    ideal  model  delta    sigma   weight residual
    1.520  1.486  0.034 3.00e-02 1.11e+03 1.26e+00
  bond pdb=" CG  LYS O 103 "
       pdb=" CD  LYS O 103 "
    ideal  model  delta    sigma   weight residual
    1.520  1.486  0.034 3.00e-02 1.11e+03 1.26e+00
  bond pdb=" CG  LYS I 103 "
       pdb=" CD  LYS I 103 "
    ideal  model  delta    sigma   weight residual
    1.520  1.486  0.034 3.00e-02 1.11e+03 1.26e+00
  bond pdb=" CG  LYS A 103 "
       pdb=" CD  LYS A 103 "
    ideal  model  delta    sigma   weight residual
    1.520  1.487  0.033 3.00e-02 1.11e+03 1.24e+00
  ... (remaining 13019 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     0.95: 15225
        0.95 -     1.90: 2092
        1.90 -     2.85: 354
        2.85 -     3.80: 71
        3.80 -     4.75: 34
  Bond angle restraints: 17776
  Sorted by residual:
  angle pdb=" C   SER E  61 "
        pdb=" N   ALA E  62 "
        pdb=" CA  ALA E  62 "
      ideal   model   delta    sigma   weight residual
     122.28  125.74   -3.46 8.80e-01 1.29e+00 1.55e+01
  angle pdb=" C   SER C  61 "
        pdb=" N   ALA C  62 "
        pdb=" CA  ALA C  62 "
      ideal   model   delta    sigma   weight residual
     122.28  125.74   -3.46 8.80e-01 1.29e+00 1.55e+01
  angle pdb=" C   SER A  61 "
        pdb=" N   ALA A  62 "
        pdb=" CA  ALA A  62 "
      ideal   model   delta    sigma   weight residual
     122.28  125.74   -3.46 8.80e-01 1.29e+00 1.54e+01
  angle pdb=" C   SER G  61 "
        pdb=" N   ALA G  62 "
        pdb=" CA  ALA G  62 "
      ideal   model   delta    sigma   weight residual
     122.28  125.73   -3.45 8.80e-01 1.29e+00 1.54e+01
  angle pdb=" C   SER I  61 "
        pdb=" N   ALA I  62 "
        pdb=" CA  ALA I  62 "
      ideal   model   delta    sigma   weight residual
     122.28  125.72   -3.44 8.80e-01 1.29e+00 1.53e+01
  ... (remaining 17771 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.25: 7169
       17.25 -    34.50: 459
       34.50 -    51.75: 116
       51.75 -    69.00: 48
       69.00 -    86.25: 16
  Dihedral angle restraints: 7808
    sinusoidal: 3024
      harmonic: 4784
  Sorted by residual:
  dihedral pdb=" CA  PHE M  78 "
           pdb=" C   PHE M  78 "
           pdb=" N   HIS M  79 "
           pdb=" CA  HIS M  79 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  158.03   21.97     0      5.00e+00 4.00e-02 1.93e+01
  dihedral pdb=" CA  PHE K  78 "
           pdb=" C   PHE K  78 "
           pdb=" N   HIS K  79 "
           pdb=" CA  HIS K  79 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  158.04   21.96     0      5.00e+00 4.00e-02 1.93e+01
  dihedral pdb=" CA  PHE A  78 "
           pdb=" C   PHE A  78 "
           pdb=" N   HIS A  79 "
           pdb=" CA  HIS A  79 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  158.04   21.96     0      5.00e+00 4.00e-02 1.93e+01
  ... (remaining 7805 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.030: 978
       0.030 -    0.061: 617
       0.061 -    0.091: 339
       0.091 -    0.121: 157
       0.121 -    0.152: 37
  Chirality restraints: 2128
  Sorted by residual:
  chirality pdb=" CA  VAL E  40 "
            pdb=" N   VAL E  40 "
            pdb=" C   VAL E  40 "
            pdb=" CB  VAL E  40 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.59   -0.15 2.00e-01 2.50e+01 5.75e-01
  chirality pdb=" CA  VAL I  40 "
            pdb=" N   VAL I  40 "
            pdb=" C   VAL I  40 "
            pdb=" CB  VAL I  40 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.59   -0.15 2.00e-01 2.50e+01 5.60e-01
  chirality pdb=" CA  VAL O  40 "
            pdb=" N   VAL O  40 "
            pdb=" C   VAL O  40 "
            pdb=" CB  VAL O  40 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.59   -0.15 2.00e-01 2.50e+01 5.60e-01
  ... (remaining 2125 not shown)

  Planarity restraints: 2200
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  PHE K  83 "    0.008 2.00e-02 2.50e+03   1.53e-02 2.34e+00
        pdb=" C   PHE K  83 "   -0.026 2.00e-02 2.50e+03
        pdb=" O   PHE K  83 "    0.010 2.00e-02 2.50e+03
        pdb=" N   ASP K  84 "    0.009 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  PHE O  83 "   -0.008 2.00e-02 2.50e+03   1.53e-02 2.33e+00
        pdb=" C   PHE O  83 "    0.026 2.00e-02 2.50e+03
        pdb=" O   PHE O  83 "   -0.010 2.00e-02 2.50e+03
        pdb=" N   ASP O  84 "   -0.009 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  PHE C  83 "    0.008 2.00e-02 2.50e+03   1.53e-02 2.33e+00
        pdb=" C   PHE C  83 "   -0.026 2.00e-02 2.50e+03
        pdb=" O   PHE C  83 "    0.010 2.00e-02 2.50e+03
        pdb=" N   ASP C  84 "    0.009 2.00e-02 2.50e+03
  ... (remaining 2197 not shown)

  Histogram of nonbonded interaction distances:
        2.30 -     2.82: 3579
        2.82 -     3.34: 11494
        3.34 -     3.86: 21299
        3.86 -     4.38: 25619
        4.38 -     4.90: 43455
  Nonbonded interactions: 105446
  Sorted by model distance:
  nonbonded pdb=" NE2 HIS K  79 "
            pdb=" OP1   G L 603 "
     model   vdw
     2.302 3.120
  nonbonded pdb=" NE2 HIS A  79 "
            pdb=" OP1   G B 603 "
     model   vdw
     2.341 3.120
  nonbonded pdb=" OH  TYR M  17 "
            pdb=" OD2 ASP M  51 "
     model   vdw
     2.341 3.040
  nonbonded pdb=" OH  TYR O  17 "
            pdb=" OD2 ASP O  51 "
     model   vdw
     2.341 3.040
  nonbonded pdb=" OH  TYR C  17 "
            pdb=" OD2 ASP C  51 "
     model   vdw
     2.341 3.040
  ... (remaining 105441 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: 0.04
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'C'
  selection = chain 'E'
  selection = chain 'G'
  selection = chain 'I'
  selection = chain 'K'
  selection = chain 'M'
  selection = chain 'O'
}
ncs_group {
  reference = chain 'B'
  selection = chain 'D'
  selection = chain 'F'
  selection = chain 'H'
  selection = chain 'J'
  selection = chain 'L'
  selection = chain 'N'
  selection = chain 'P'
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             0.080
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.050
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.170
  Check model and map are aligned:         0.040
  Set scattering table:                    0.050
  Process input model:                     9.830
  Find NCS groups from input model:        0.120
  Set up NCS constraints:                  0.010
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.010
  Load rotamer database and sin/cos tables:1.370
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   11.740
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8293
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      :  0.007   0.034  13024  Z= 0.288
  Angle     :  0.721   4.752  17776  Z= 0.456
  Chirality :  0.052   0.152   2128
  Planarity :  0.004   0.021   2200
  Dihedral  : 14.343  86.249   4688
  Min Nonbonded Distance : 2.302

Molprobity Statistics.
  All-atom Clashscore : 2.32
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.49 %
    Favored  : 99.51 %
  Rotamer:
    Outliers :  0.66 %
    Allowed  :  1.32 %
    Favored  : 98.03 %
  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 are not related in a simple way.
  whole:  1.28 (0.20), residues: 1624
  helix:  0.73 (0.19), residues: 704
  sheet:  0.72 (0.23), residues: 248
  loop :  1.33 (0.26), residues: 672

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.001   ARG M  37 
 TYR   0.006   0.002   TYR M  17 
 PHE   0.018   0.002   PHE E  78 
 TRP   0.021   0.003   TRP G 197 
 HIS   0.004   0.001   HIS G  79 

Details of bonding type rmsd
  covalent geometry    : bond        0.00652 (13024)
  covalent geometry    : angle       0.72147 (17776)
  hydrogen bonds       : bond        0.11665 (  560)
  hydrogen bonds       : angle       7.70024 ( 1680)

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

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

  3248 Ramachandran restraints generated.
    1624 Oldfield, 0 Emsley, 1624 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3248 Ramachandran restraints generated.
    1624 Oldfield, 0 Emsley, 1624 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  249 residues out of total 1424 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 241
  time to evaluate  : 0.337 
Fit side-chains
REVERT: A   51 ASP cc_start: 0.7823 (m-30) cc_final: 0.7491 (m-30)
REVERT: A  119 LYS cc_start: 0.8624 (tttm) cc_final: 0.8314 (tttp)
REVERT: C  119 LYS cc_start: 0.8704 (tttm) cc_final: 0.8405 (tttp)
REVERT: I   51 ASP cc_start: 0.7900 (m-30) cc_final: 0.7616 (m-30)
REVERT: K   51 ASP cc_start: 0.7863 (m-30) cc_final: 0.7541 (m-30)
REVERT: K  119 LYS cc_start: 0.8611 (tttm) cc_final: 0.8295 (tttp)
REVERT: K  138 ASP cc_start: 0.8546 (t0) cc_final: 0.8340 (t0)
REVERT: O  119 LYS cc_start: 0.8787 (tttm) cc_final: 0.8481 (tttt)
  outliers start: 8
  outliers final: 0
  residues processed: 241
  average time/residue: 0.1059
  time to fit residues: 37.1281
Evaluate side-chains
  193 residues out of total 1424 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 193
  time to evaluate  : 0.508 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 160
   random chunks:
   chunk 98 optimal weight:    4.9990
   chunk 107 optimal weight:    6.9990
   chunk 10 optimal weight:    0.9990
   chunk 66 optimal weight:    2.9990
   chunk 130 optimal weight:    2.9990
   chunk 124 optimal weight:    6.9990
   chunk 103 optimal weight:    1.9990
   chunk 77 optimal weight:    0.9990
   chunk 122 optimal weight:    0.9990
   chunk 91 optimal weight:    7.9990
   chunk 149 optimal weight:    0.9990
   overall best weight:    1.1990

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

Flipped N/Q/H residues before XYZ refinement:
A  16 ASN
A  59 GLN
C  16 ASN
C  59 GLN
E   8 GLN
E  16 ASN
E  59 GLN
G   8 GLN
G  16 ASN
G  59 GLN
I  16 ASN
I  59 GLN
K  16 ASN
M  16 ASN
M  59 GLN
O   8 GLN
O  16 ASN
O  59 GLN

Total number of N/Q/H flips: 18

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3123 r_free = 0.3123 target = 0.103451 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.2848 r_free = 0.2848 target = 0.084737 restraints weight = 16347.933|
|-----------------------------------------------------------------------------|
r_work (start): 0.2919 rms_B_bonded: 1.70
r_work: 0.2807 rms_B_bonded: 2.27 restraints_weight: 0.5000
r_work: 0.2651 rms_B_bonded: 3.87 restraints_weight: 0.2500
r_work (final): 0.2651
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8541
moved from start:          0.1567

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.016  13024  Z= 0.098
  Angle     :  0.435   4.709  17776  Z= 0.238
  Chirality :  0.045   0.124   2128
  Planarity :  0.003   0.024   2200
  Dihedral  :  9.974  63.737   2040
  Min Nonbonded Distance : 2.506

Molprobity Statistics.
  All-atom Clashscore : 2.36
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.49 %
    Favored  : 99.51 %
  Rotamer:
    Outliers :  1.40 %
    Allowed  :  6.41 %
    Favored  : 92.19 %
  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 are not related in a simple way.
  whole:  2.11 (0.21), residues: 1624
  helix:  2.07 (0.20), residues: 704
  sheet:  1.08 (0.24), residues: 248
  loop :  0.97 (0.26), residues: 672

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG M 169 
 TYR   0.006   0.001   TYR E 158 
 PHE   0.011   0.001   PHE G  78 
 TRP   0.004   0.001   TRP I 197 
 HIS   0.002   0.001   HIS K  79 

Details of bonding type rmsd
  covalent geometry    : bond        0.00208 (13024)
  covalent geometry    : angle       0.43525 (17776)
  hydrogen bonds       : bond        0.03369 (  560)
  hydrogen bonds       : angle       5.90160 ( 1680)

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

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

  3248 Ramachandran restraints generated.
    1624 Oldfield, 0 Emsley, 1624 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3248 Ramachandran restraints generated.
    1624 Oldfield, 0 Emsley, 1624 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  229 residues out of total 1424 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 212
  time to evaluate  : 0.498 
Fit side-chains
REVERT: A   17 TYR cc_start: 0.8982 (m-80) cc_final: 0.8758 (m-80)
REVERT: A   51 ASP cc_start: 0.8602 (m-30) cc_final: 0.8221 (m-30)
REVERT: A  119 LYS cc_start: 0.8800 (tttm) cc_final: 0.8495 (tttp)
REVERT: C   16 ASN cc_start: 0.8629 (OUTLIER) cc_final: 0.8423 (t0)
REVERT: C   17 TYR cc_start: 0.9000 (m-80) cc_final: 0.8719 (m-80)
REVERT: C  115 ARG cc_start: 0.8827 (mtm180) cc_final: 0.8566 (mtm180)
REVERT: C  119 LYS cc_start: 0.8875 (tttm) cc_final: 0.8576 (tttp)
REVERT: E   51 ASP cc_start: 0.8729 (m-30) cc_final: 0.8352 (m-30)
REVERT: E  115 ARG cc_start: 0.8909 (mtm180) cc_final: 0.8607 (mtm180)
REVERT: G   51 ASP cc_start: 0.8721 (m-30) cc_final: 0.8334 (m-30)
REVERT: I   16 ASN cc_start: 0.8600 (OUTLIER) cc_final: 0.8387 (t0)
REVERT: I   17 TYR cc_start: 0.8981 (m-80) cc_final: 0.8731 (m-80)
REVERT: I   51 ASP cc_start: 0.8613 (m-30) cc_final: 0.8275 (m-30)
REVERT: K   17 TYR cc_start: 0.8967 (m-80) cc_final: 0.8744 (m-80)
REVERT: K   51 ASP cc_start: 0.8554 (m-30) cc_final: 0.8193 (m-30)
REVERT: K  119 LYS cc_start: 0.8817 (tttm) cc_final: 0.8501 (tttp)
REVERT: M  119 LYS cc_start: 0.8709 (tttm) cc_final: 0.8461 (tttp)
REVERT: O   51 ASP cc_start: 0.8662 (m-30) cc_final: 0.8338 (m-30)
REVERT: O  115 ARG cc_start: 0.8838 (mtm180) cc_final: 0.8582 (mtm180)
REVERT: O  119 LYS cc_start: 0.8926 (tttm) cc_final: 0.8638 (tttp)
  outliers start: 17
  outliers final: 9
  residues processed: 220
  average time/residue: 0.1195
  time to fit residues: 38.2270
Evaluate side-chains
  211 residues out of total 1424 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 200
  time to evaluate  : 0.469 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  154 SER
Chi-restraints excluded: chain C residue   16 ASN
Chi-restraints excluded: chain C residue  154 SER
Chi-restraints excluded: chain E residue  131 SER
Chi-restraints excluded: chain E residue  154 SER
Chi-restraints excluded: chain G residue  154 SER
Chi-restraints excluded: chain I residue   16 ASN
Chi-restraints excluded: chain I residue  154 SER
Chi-restraints excluded: chain K residue  154 SER
Chi-restraints excluded: chain M residue  154 SER
Chi-restraints excluded: chain O residue  154 SER
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 160
   random chunks:
   chunk 147 optimal weight:   10.0000
   chunk 88 optimal weight:    7.9990
   chunk 46 optimal weight:   10.0000
   chunk 98 optimal weight:    3.9990
   chunk 0 optimal weight:   10.0000
   chunk 145 optimal weight:    9.9990
   chunk 38 optimal weight:    0.6980
   chunk 24 optimal weight:    6.9990
   chunk 11 optimal weight:    9.9990
   chunk 120 optimal weight:   10.0000
   chunk 5 optimal weight:    4.9990
   overall best weight:    4.9388

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

Flipped N/Q/H residues before XYZ refinement:
A  16 ASN
C  16 ASN
E  16 ASN
G  16 ASN
I  16 ASN
K  16 ASN
M  16 ASN
O  16 ASN

Total number of N/Q/H flips: 8

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3033 r_free = 0.3033 target = 0.097769 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.2759 r_free = 0.2759 target = 0.079410 restraints weight = 16911.433|
|-----------------------------------------------------------------------------|
r_work (start): 0.2849 rms_B_bonded: 1.66
r_work: 0.2734 rms_B_bonded: 2.20 restraints_weight: 0.5000
r_work: 0.2586 rms_B_bonded: 3.72 restraints_weight: 0.2500
r_work (final): 0.2586
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8641
moved from start:          0.1961

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.007   0.033  13024  Z= 0.280
  Angle     :  0.539   4.657  17776  Z= 0.290
  Chirality :  0.049   0.139   2128
  Planarity :  0.004   0.031   2200
  Dihedral  : 10.122  63.884   2040
  Min Nonbonded Distance : 2.480

Molprobity Statistics.
  All-atom Clashscore : 2.24
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.49 %
    Favored  : 99.51 %
  Rotamer:
    Outliers :  2.14 %
    Allowed  :  7.15 %
    Favored  : 90.71 %
  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 are not related in a simple way.
  whole:  1.52 (0.21), residues: 1624
  helix:  1.64 (0.20), residues: 704
  sheet:  0.99 (0.26), residues: 240
  loop :  0.48 (0.25), residues: 680

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.001   ARG K  35 
 TYR   0.015   0.002   TYR I  17 
 PHE   0.015   0.002   PHE G  78 
 TRP   0.007   0.002   TRP C 197 
 HIS   0.005   0.002   HIS E  79 

Details of bonding type rmsd
  covalent geometry    : bond        0.00672 (13024)
  covalent geometry    : angle       0.53925 (17776)
  hydrogen bonds       : bond        0.04590 (  560)
  hydrogen bonds       : angle       6.14073 ( 1680)

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

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

  3248 Ramachandran restraints generated.
    1624 Oldfield, 0 Emsley, 1624 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3248 Ramachandran restraints generated.
    1624 Oldfield, 0 Emsley, 1624 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  221 residues out of total 1424 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 195
  time to evaluate  : 0.506 
Fit side-chains
REVERT: A   25 ASP cc_start: 0.8299 (t70) cc_final: 0.8095 (t0)
REVERT: A   51 ASP cc_start: 0.8677 (m-30) cc_final: 0.8453 (m-30)
REVERT: A  119 LYS cc_start: 0.9036 (tttm) cc_final: 0.8773 (tttt)
REVERT: C   16 ASN cc_start: 0.8590 (OUTLIER) cc_final: 0.8275 (t0)
REVERT: C   25 ASP cc_start: 0.8271 (t70) cc_final: 0.8061 (t0)
REVERT: C  119 LYS cc_start: 0.9035 (tttm) cc_final: 0.8756 (tttt)
REVERT: E   51 ASP cc_start: 0.8695 (m-30) cc_final: 0.8494 (m-30)
REVERT: G   51 ASP cc_start: 0.8638 (m-30) cc_final: 0.8375 (m-30)
REVERT: I   16 ASN cc_start: 0.8574 (OUTLIER) cc_final: 0.8217 (t0)
REVERT: I   17 TYR cc_start: 0.9129 (m-80) cc_final: 0.8893 (m-80)
REVERT: I   25 ASP cc_start: 0.8228 (t70) cc_final: 0.8013 (t0)
REVERT: I   51 ASP cc_start: 0.8711 (m-30) cc_final: 0.8432 (m-30)
REVERT: K   17 TYR cc_start: 0.9093 (m-80) cc_final: 0.8874 (m-80)
REVERT: K   25 ASP cc_start: 0.8260 (t70) cc_final: 0.8045 (t0)
REVERT: K   51 ASP cc_start: 0.8662 (m-30) cc_final: 0.8419 (m-30)
REVERT: K  119 LYS cc_start: 0.9060 (tttm) cc_final: 0.8784 (tttt)
REVERT: K  164 ASP cc_start: 0.7756 (m-30) cc_final: 0.7316 (m-30)
REVERT: M   25 ASP cc_start: 0.8249 (t70) cc_final: 0.8034 (t0)
REVERT: O   25 ASP cc_start: 0.8282 (t70) cc_final: 0.8070 (t0)
REVERT: O   51 ASP cc_start: 0.8720 (m-30) cc_final: 0.8455 (m-30)
REVERT: O  115 ARG cc_start: 0.9010 (mtm180) cc_final: 0.8809 (mtm180)
REVERT: O  119 LYS cc_start: 0.9039 (tttm) cc_final: 0.8770 (tttt)
  outliers start: 26
  outliers final: 16
  residues processed: 206
  average time/residue: 0.1073
  time to fit residues: 33.2509
Evaluate side-chains
  206 residues out of total 1424 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 188
  time to evaluate  : 0.379 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  131 SER
Chi-restraints excluded: chain A residue  154 SER
Chi-restraints excluded: chain C residue   16 ASN
Chi-restraints excluded: chain C residue  131 SER
Chi-restraints excluded: chain C residue  154 SER
Chi-restraints excluded: chain E residue  131 SER
Chi-restraints excluded: chain E residue  154 SER
Chi-restraints excluded: chain G residue  131 SER
Chi-restraints excluded: chain G residue  154 SER
Chi-restraints excluded: chain I residue   16 ASN
Chi-restraints excluded: chain I residue  131 SER
Chi-restraints excluded: chain I residue  154 SER
Chi-restraints excluded: chain K residue  131 SER
Chi-restraints excluded: chain K residue  154 SER
Chi-restraints excluded: chain M residue  131 SER
Chi-restraints excluded: chain M residue  154 SER
Chi-restraints excluded: chain O residue  131 SER
Chi-restraints excluded: chain O residue  154 SER
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 160
   random chunks:
   chunk 70 optimal weight:    1.9990
   chunk 26 optimal weight:    0.9990
   chunk 81 optimal weight:    6.9990
   chunk 153 optimal weight:    0.9990
   chunk 86 optimal weight:    4.9990
   chunk 130 optimal weight:    3.9990
   chunk 8 optimal weight:    0.9990
   chunk 59 optimal weight:    6.9990
   chunk 74 optimal weight:    1.9990
   chunk 107 optimal weight:    6.9990
   chunk 110 optimal weight:    3.9990
   overall best weight:    1.3990

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

Flipped N/Q/H residues before XYZ refinement:
A  16 ASN
E  16 ASN
G  16 ASN
K  16 ASN
M  16 ASN
O  16 ASN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3095 r_free = 0.3095 target = 0.101768 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.2817 r_free = 0.2817 target = 0.082990 restraints weight = 16514.457|
|-----------------------------------------------------------------------------|
r_work (start): 0.2869 rms_B_bonded: 1.71
r_work: 0.2755 rms_B_bonded: 2.25 restraints_weight: 0.5000
r_work: 0.2605 rms_B_bonded: 3.80 restraints_weight: 0.2500
r_work (final): 0.2605
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8581
moved from start:          0.2124

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.017  13024  Z= 0.103
  Angle     :  0.401   4.476  17776  Z= 0.220
  Chirality :  0.044   0.122   2128
  Planarity :  0.003   0.026   2200
  Dihedral  :  9.859  63.760   2040
  Min Nonbonded Distance : 2.473

Molprobity Statistics.
  All-atom Clashscore : 2.04
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.00 %
    Favored  : 100.00 %
  Rotamer:
    Outliers :  1.15 %
    Allowed  :  9.29 %
    Favored  : 89.56 %
  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 are not related in a simple way.
  whole:  1.66 (0.21), residues: 1624
  helix:  1.82 (0.20), residues: 704
  sheet:  1.37 (0.28), residues: 240
  loop :  0.32 (0.25), residues: 680

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG M   5 
 TYR   0.009   0.001   TYR C  17 
 PHE   0.009   0.001   PHE K  78 
 TRP   0.001   0.000   TRP O 197 
 HIS   0.002   0.000   HIS O  79 

Details of bonding type rmsd
  covalent geometry    : bond        0.00232 (13024)
  covalent geometry    : angle       0.40100 (17776)
  hydrogen bonds       : bond        0.03189 (  560)
  hydrogen bonds       : angle       5.48943 ( 1680)

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

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

  3248 Ramachandran restraints generated.
    1624 Oldfield, 0 Emsley, 1624 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3248 Ramachandran restraints generated.
    1624 Oldfield, 0 Emsley, 1624 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  219 residues out of total 1424 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 205
  time to evaluate  : 0.519 
Fit side-chains
   revert: symmetry clash
REVERT: A   51 ASP cc_start: 0.8553 (m-30) cc_final: 0.8270 (m-30)
REVERT: A  119 LYS cc_start: 0.8967 (tttm) cc_final: 0.8702 (tttt)
REVERT: C   16 ASN cc_start: 0.8542 (t0) cc_final: 0.8149 (t0)
REVERT: C  119 LYS cc_start: 0.8966 (tttm) cc_final: 0.8694 (tttt)
REVERT: E   51 ASP cc_start: 0.8669 (m-30) cc_final: 0.8462 (m-30)
REVERT: G   51 ASP cc_start: 0.8602 (m-30) cc_final: 0.8224 (m-30)
REVERT: I   16 ASN cc_start: 0.8507 (t0) cc_final: 0.7959 (t0)
REVERT: K   51 ASP cc_start: 0.8570 (m-30) cc_final: 0.8365 (m-30)
REVERT: M   17 TYR cc_start: 0.9080 (m-80) cc_final: 0.8731 (m-80)
REVERT: O   17 TYR cc_start: 0.9192 (m-80) cc_final: 0.8844 (m-80)
REVERT: O   51 ASP cc_start: 0.8685 (m-30) cc_final: 0.8466 (m-30)
REVERT: O  119 LYS cc_start: 0.8972 (tttm) cc_final: 0.8709 (tttt)
  outliers start: 14
  outliers final: 8
  residues processed: 213
  average time/residue: 0.1073
  time to fit residues: 34.2544
Evaluate side-chains
  200 residues out of total 1424 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 192
  time to evaluate  : 0.491 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  154 SER
Chi-restraints excluded: chain C residue  154 SER
Chi-restraints excluded: chain E residue  154 SER
Chi-restraints excluded: chain G residue  154 SER
Chi-restraints excluded: chain I residue  154 SER
Chi-restraints excluded: chain K residue  154 SER
Chi-restraints excluded: chain M residue  154 SER
Chi-restraints excluded: chain O residue  154 SER
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 160
   random chunks:
   chunk 17 optimal weight:    9.9990
   chunk 37 optimal weight:   10.0000
   chunk 11 optimal weight:    8.9990
   chunk 22 optimal weight:   10.0000
   chunk 114 optimal weight:    9.9990
   chunk 32 optimal weight:   10.0000
   chunk 136 optimal weight:    3.9990
   chunk 130 optimal weight:    7.9990
   chunk 42 optimal weight:    9.9990
   chunk 156 optimal weight:    8.9990
   chunk 157 optimal weight:    4.9990
   overall best weight:    6.9990

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

Flipped N/Q/H residues before XYZ refinement:
A  16 ASN
E  16 ASN
G  16 ASN
K  16 ASN
M  16 ASN
O  16 ASN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3017 r_free = 0.3017 target = 0.096618 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.2726 r_free = 0.2726 target = 0.077314 restraints weight = 17130.527|
|-----------------------------------------------------------------------------|
r_work (start): 0.2798 rms_B_bonded: 1.81
r_work: 0.2679 rms_B_bonded: 2.35 restraints_weight: 0.5000
r_work: 0.2530 rms_B_bonded: 3.94 restraints_weight: 0.2500
r_work (final): 0.2530
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8621
moved from start:          0.2262

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.009   0.042  13024  Z= 0.385
  Angle     :  0.582   4.629  17776  Z= 0.310
  Chirality :  0.052   0.144   2128
  Planarity :  0.004   0.035   2200
  Dihedral  : 10.226  63.942   2040
  Min Nonbonded Distance : 2.446

Molprobity Statistics.
  All-atom Clashscore : 2.24
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.48 %
    Favored  : 98.52 %
  Rotamer:
    Outliers :  1.73 %
    Allowed  : 10.44 %
    Favored  : 87.83 %
  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 are not related in a simple way.
  whole:  0.88 (0.20), residues: 1624
  helix:  1.28 (0.19), residues: 704
  sheet:  0.84 (0.28), residues: 240
  loop : -0.16 (0.24), residues: 680

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG C 169 
 TYR   0.008   0.002   TYR C  17 
 PHE   0.013   0.003   PHE M  78 
 TRP   0.005   0.002   TRP G 197 
 HIS   0.006   0.002   HIS A 116 

Details of bonding type rmsd
  covalent geometry    : bond        0.00928 (13024)
  covalent geometry    : angle       0.58179 (17776)
  hydrogen bonds       : bond        0.05033 (  560)
  hydrogen bonds       : angle       6.11900 ( 1680)

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

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

  3248 Ramachandran restraints generated.
    1624 Oldfield, 0 Emsley, 1624 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3248 Ramachandran restraints generated.
    1624 Oldfield, 0 Emsley, 1624 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  203 residues out of total 1424 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 182
  time to evaluate  : 0.443 
Fit side-chains
REVERT: A   25 ASP cc_start: 0.8457 (t70) cc_final: 0.8248 (t0)
REVERT: C   16 ASN cc_start: 0.8774 (t0) cc_final: 0.8466 (t0)
REVERT: C   25 ASP cc_start: 0.8447 (t70) cc_final: 0.8222 (t0)
REVERT: E   25 ASP cc_start: 0.8459 (t70) cc_final: 0.8243 (t0)
REVERT: E   51 ASP cc_start: 0.8857 (m-30) cc_final: 0.8456 (m-30)
REVERT: G   25 ASP cc_start: 0.8477 (t70) cc_final: 0.8259 (t0)
REVERT: I   16 ASN cc_start: 0.8760 (t0) cc_final: 0.8428 (t0)
REVERT: I   25 ASP cc_start: 0.8459 (t70) cc_final: 0.8241 (t0)
REVERT: I   51 ASP cc_start: 0.8962 (m-30) cc_final: 0.8508 (m-30)
REVERT: K   25 ASP cc_start: 0.8466 (t70) cc_final: 0.8255 (t0)
REVERT: M   25 ASP cc_start: 0.8464 (t70) cc_final: 0.8241 (t0)
REVERT: O   25 ASP cc_start: 0.8441 (t70) cc_final: 0.8232 (t0)
  outliers start: 21
  outliers final: 14
  residues processed: 195
  average time/residue: 0.1042
  time to fit residues: 30.3618
Evaluate side-chains
  190 residues out of total 1424 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 176
  time to evaluate  : 0.483 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  131 SER
Chi-restraints excluded: chain A residue  154 SER
Chi-restraints excluded: chain C residue  131 SER
Chi-restraints excluded: chain C residue  154 SER
Chi-restraints excluded: chain E residue  131 SER
Chi-restraints excluded: chain E residue  154 SER
Chi-restraints excluded: chain G residue  131 SER
Chi-restraints excluded: chain G residue  154 SER
Chi-restraints excluded: chain I residue  131 SER
Chi-restraints excluded: chain I residue  154 SER
Chi-restraints excluded: chain K residue  154 SER
Chi-restraints excluded: chain M residue  131 SER
Chi-restraints excluded: chain M residue  154 SER
Chi-restraints excluded: chain O residue  154 SER
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 160
   random chunks:
   chunk 58 optimal weight:    0.7980
   chunk 106 optimal weight:    5.9990
   chunk 6 optimal weight:    6.9990
   chunk 138 optimal weight:    0.7980
   chunk 118 optimal weight:    0.6980
   chunk 91 optimal weight:    6.9990
   chunk 78 optimal weight:    0.9990
   chunk 70 optimal weight:    0.8980
   chunk 140 optimal weight:   10.0000
   chunk 124 optimal weight:    7.9990
   chunk 85 optimal weight:    6.9990
   overall best weight:    0.8382

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

Flipped N/Q/H residues before XYZ refinement:
A  16 ASN
E  16 ASN
G  16 ASN
K  16 ASN
K  59 GLN
M  16 ASN
O  16 ASN

Total number of N/Q/H flips: 7

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3108 r_free = 0.3108 target = 0.102892 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.2820 r_free = 0.2820 target = 0.083317 restraints weight = 16470.443|
|-----------------------------------------------------------------------------|
r_work (start): 0.2896 rms_B_bonded: 1.84
r_work: 0.2777 rms_B_bonded: 2.40 restraints_weight: 0.5000
r_work: 0.2626 rms_B_bonded: 4.03 restraints_weight: 0.2500
r_work (final): 0.2626
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8540
moved from start:          0.2366

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.018  13024  Z= 0.084
  Angle     :  0.388   4.422  17776  Z= 0.214
  Chirality :  0.043   0.118   2128
  Planarity :  0.003   0.027   2200
  Dihedral  :  9.781  63.784   2040
  Min Nonbonded Distance : 2.447

Molprobity Statistics.
  All-atom Clashscore : 2.20
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.68 %
    Favored  : 99.32 %
  Rotamer:
    Outliers :  0.74 %
    Allowed  : 12.09 %
    Favored  : 87.17 %
  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 are not related in a simple way.
  whole:  1.29 (0.21), residues: 1624
  helix:  1.65 (0.20), residues: 704
  sheet:  1.31 (0.29), residues: 248
  loop : -0.12 (0.25), residues: 672

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A   5 
 TYR   0.004   0.001   TYR O 158 
 PHE   0.008   0.001   PHE A  78 
 TRP   0.002   0.000   TRP I 139 
 HIS   0.002   0.001   HIS A  79 

Details of bonding type rmsd
  covalent geometry    : bond        0.00182 (13024)
  covalent geometry    : angle       0.38827 (17776)
  hydrogen bonds       : bond        0.02877 (  560)
  hydrogen bonds       : angle       5.28191 ( 1680)

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

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

  3248 Ramachandran restraints generated.
    1624 Oldfield, 0 Emsley, 1624 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3248 Ramachandran restraints generated.
    1624 Oldfield, 0 Emsley, 1624 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  217 residues out of total 1424 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 208
  time to evaluate  : 0.469 
Fit side-chains
REVERT: A  119 LYS cc_start: 0.8859 (tttm) cc_final: 0.8613 (tttt)
REVERT: C   16 ASN cc_start: 0.8725 (t0) cc_final: 0.8434 (t0)
REVERT: C   17 TYR cc_start: 0.8952 (m-80) cc_final: 0.8703 (m-80)
REVERT: E   25 ASP cc_start: 0.8155 (t70) cc_final: 0.7889 (t0)
REVERT: E   51 ASP cc_start: 0.8620 (m-30) cc_final: 0.8302 (m-30)
REVERT: G   17 TYR cc_start: 0.9112 (m-80) cc_final: 0.8849 (m-80)
REVERT: G   25 ASP cc_start: 0.8173 (t70) cc_final: 0.7905 (t0)
REVERT: I   16 ASN cc_start: 0.8723 (t0) cc_final: 0.8440 (t0)
REVERT: I   17 TYR cc_start: 0.8896 (m-80) cc_final: 0.8674 (m-80)
REVERT: I   51 ASP cc_start: 0.8811 (m-30) cc_final: 0.8438 (m-30)
REVERT: K  119 LYS cc_start: 0.8883 (tttm) cc_final: 0.8644 (tttt)
REVERT: M   17 TYR cc_start: 0.9086 (m-80) cc_final: 0.8829 (m-80)
REVERT: O   17 TYR cc_start: 0.9064 (m-80) cc_final: 0.8833 (m-80)
  outliers start: 9
  outliers final: 3
  residues processed: 208
  average time/residue: 0.1075
  time to fit residues: 33.2799
Evaluate side-chains
  196 residues out of total 1424 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 193
  time to evaluate  : 0.457 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  131 SER
Chi-restraints excluded: chain C residue  131 SER
Chi-restraints excluded: chain O residue  131 SER
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 160
   random chunks:
   chunk 82 optimal weight:    4.9990
   chunk 125 optimal weight:    4.9990
   chunk 72 optimal weight:   10.0000
   chunk 84 optimal weight:    4.9990
   chunk 86 optimal weight:    0.9990
   chunk 22 optimal weight:   10.0000
   chunk 42 optimal weight:   10.0000
   chunk 133 optimal weight:    0.4980
   chunk 102 optimal weight:   10.0000
   chunk 128 optimal weight:    8.9990
   chunk 12 optimal weight:    9.9990
   overall best weight:    3.2988

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

Flipped N/Q/H residues before XYZ refinement:
A  16 ASN
E  16 ASN
G  16 ASN
K  16 ASN
M  16 ASN
O  16 ASN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3060 r_free = 0.3060 target = 0.099624 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.2782 r_free = 0.2782 target = 0.080749 restraints weight = 16707.851|
|-----------------------------------------------------------------------------|
r_work (start): 0.2874 rms_B_bonded: 1.68
r_work: 0.2761 rms_B_bonded: 2.23 restraints_weight: 0.5000
r_work: 0.2616 rms_B_bonded: 3.76 restraints_weight: 0.2500
r_work (final): 0.2616
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8614
moved from start:          0.2327

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.024  13024  Z= 0.196
  Angle     :  0.449   4.519  17776  Z= 0.242
  Chirality :  0.046   0.129   2128
  Planarity :  0.003   0.030   2200
  Dihedral  :  9.924  63.839   2040
  Min Nonbonded Distance : 2.429

Molprobity Statistics.
  All-atom Clashscore : 1.80
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.09 %
    Favored  : 97.91 %
  Rotamer:
    Outliers :  1.81 %
    Allowed  : 11.51 %
    Favored  : 86.68 %
  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 are not related in a simple way.
  whole:  1.15 (0.21), residues: 1624
  helix:  1.54 (0.20), residues: 704
  sheet:  1.27 (0.29), residues: 240
  loop : -0.19 (0.24), residues: 680

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A  67 
 TYR   0.006   0.001   TYR C  17 
 PHE   0.012   0.002   PHE G  78 
 TRP   0.002   0.001   TRP K 197 
 HIS   0.003   0.001   HIS C  79 

Details of bonding type rmsd
  covalent geometry    : bond        0.00468 (13024)
  covalent geometry    : angle       0.44947 (17776)
  hydrogen bonds       : bond        0.03799 (  560)
  hydrogen bonds       : angle       5.57422 ( 1680)

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

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

  3248 Ramachandran restraints generated.
    1624 Oldfield, 0 Emsley, 1624 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3248 Ramachandran restraints generated.
    1624 Oldfield, 0 Emsley, 1624 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  227 residues out of total 1424 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 205
  time to evaluate  : 0.500 
Fit side-chains
REVERT: A   25 ASP cc_start: 0.8331 (t70) cc_final: 0.8065 (t0)
REVERT: A  119 LYS cc_start: 0.8936 (tttm) cc_final: 0.8683 (tttt)
REVERT: C   16 ASN cc_start: 0.8782 (t0) cc_final: 0.8498 (t0)
REVERT: C   25 ASP cc_start: 0.8329 (t70) cc_final: 0.8072 (t0)
REVERT: C  115 ARG cc_start: 0.9029 (mtm180) cc_final: 0.8819 (mtm180)
REVERT: E   17 TYR cc_start: 0.9213 (m-80) cc_final: 0.8912 (m-80)
REVERT: E   25 ASP cc_start: 0.8306 (t70) cc_final: 0.8053 (t0)
REVERT: E   51 ASP cc_start: 0.8648 (m-30) cc_final: 0.8425 (m-30)
REVERT: E  115 ARG cc_start: 0.9049 (mtm180) cc_final: 0.8846 (mtm180)
REVERT: G   17 TYR cc_start: 0.9097 (m-80) cc_final: 0.8839 (m-80)
REVERT: G   25 ASP cc_start: 0.8331 (t70) cc_final: 0.8075 (t0)
REVERT: I   16 ASN cc_start: 0.8802 (t0) cc_final: 0.8473 (t0)
REVERT: I   17 TYR cc_start: 0.9037 (m-80) cc_final: 0.8829 (m-80)
REVERT: I   25 ASP cc_start: 0.8306 (t70) cc_final: 0.8049 (t0)
REVERT: I   51 ASP cc_start: 0.8865 (m-30) cc_final: 0.8423 (m-30)
REVERT: K   25 ASP cc_start: 0.8304 (t70) cc_final: 0.8064 (t0)
REVERT: K  119 LYS cc_start: 0.8946 (tttm) cc_final: 0.8702 (tttt)
REVERT: M   25 ASP cc_start: 0.8329 (t70) cc_final: 0.8070 (t0)
REVERT: O   25 ASP cc_start: 0.8312 (t70) cc_final: 0.8052 (t0)
REVERT: O  115 ARG cc_start: 0.9026 (mtm180) cc_final: 0.8818 (mtm180)
  outliers start: 22
  outliers final: 15
  residues processed: 214
  average time/residue: 0.1080
  time to fit residues: 34.6315
Evaluate side-chains
  213 residues out of total 1424 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 198
  time to evaluate  : 0.472 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  131 SER
Chi-restraints excluded: chain A residue  154 SER
Chi-restraints excluded: chain C residue  131 SER
Chi-restraints excluded: chain C residue  154 SER
Chi-restraints excluded: chain E residue  131 SER
Chi-restraints excluded: chain E residue  154 SER
Chi-restraints excluded: chain G residue  131 SER
Chi-restraints excluded: chain G residue  154 SER
Chi-restraints excluded: chain I residue  154 SER
Chi-restraints excluded: chain K residue  131 SER
Chi-restraints excluded: chain K residue  154 SER
Chi-restraints excluded: chain M residue  131 SER
Chi-restraints excluded: chain M residue  154 SER
Chi-restraints excluded: chain O residue  131 SER
Chi-restraints excluded: chain O residue  154 SER
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 160
   random chunks:
   chunk 158 optimal weight:    1.9990
   chunk 143 optimal weight:    2.9990
   chunk 133 optimal weight:    6.9990
   chunk 80 optimal weight:   10.0000
   chunk 116 optimal weight:    3.9990
   chunk 136 optimal weight:    4.9990
   chunk 37 optimal weight:    6.9990
   chunk 157 optimal weight:    8.9990
   chunk 78 optimal weight:    0.8980
   chunk 152 optimal weight:    3.9990
   chunk 35 optimal weight:    0.9980
   overall best weight:    2.1786

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

Flipped N/Q/H residues before XYZ refinement:
A  16 ASN
A  32 GLN
C  32 GLN
E  16 ASN
E  32 GLN
G  16 ASN
G  32 GLN
I  32 GLN
K  16 ASN
M  16 ASN
M  32 GLN
O  16 ASN
O  32 GLN

Total number of N/Q/H flips: 13

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3078 r_free = 0.3078 target = 0.100827 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.2804 r_free = 0.2804 target = 0.082144 restraints weight = 16596.967|
|-----------------------------------------------------------------------------|
r_work (start): 0.2881 rms_B_bonded: 1.65
r_work: 0.2767 rms_B_bonded: 2.23 restraints_weight: 0.5000
r_work: 0.2622 rms_B_bonded: 3.74 restraints_weight: 0.2500
r_work (final): 0.2622
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8611
moved from start:          0.2392

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.020  13024  Z= 0.139
  Angle     :  0.419   4.492  17776  Z= 0.226
  Chirality :  0.044   0.124   2128
  Planarity :  0.003   0.029   2200
  Dihedral  :  9.838  63.807   2040
  Min Nonbonded Distance : 2.409

Molprobity Statistics.
  All-atom Clashscore : 1.80
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.66 %
    Favored  : 98.34 %
  Rotamer:
    Outliers :  1.73 %
    Allowed  : 11.60 %
    Favored  : 86.68 %
  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 are not related in a simple way.
  whole:  1.20 (0.21), residues: 1624
  helix:  1.62 (0.20), residues: 704
  sheet:  1.36 (0.29), residues: 240
  loop : -0.23 (0.24), residues: 680

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A   5 
 TYR   0.004   0.001   TYR O 158 
 PHE   0.010   0.001   PHE C  78 
 TRP   0.002   0.001   TRP I 139 
 HIS   0.003   0.001   HIS O  79 

Details of bonding type rmsd
  covalent geometry    : bond        0.00326 (13024)
  covalent geometry    : angle       0.41922 (17776)
  hydrogen bonds       : bond        0.03401 (  560)
  hydrogen bonds       : angle       5.40049 ( 1680)

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

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

  3248 Ramachandran restraints generated.
    1624 Oldfield, 0 Emsley, 1624 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3248 Ramachandran restraints generated.
    1624 Oldfield, 0 Emsley, 1624 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  218 residues out of total 1424 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 197
  time to evaluate  : 0.462 
Fit side-chains
REVERT: A  119 LYS cc_start: 0.8953 (tttm) cc_final: 0.8708 (tttt)
REVERT: C   16 ASN cc_start: 0.8660 (t0) cc_final: 0.8290 (t0)
REVERT: C   25 ASP cc_start: 0.8282 (t70) cc_final: 0.8019 (t0)
REVERT: C  115 ARG cc_start: 0.9038 (mtm180) cc_final: 0.8836 (mtm180)
REVERT: E   17 TYR cc_start: 0.9186 (m-80) cc_final: 0.8895 (m-80)
REVERT: E   25 ASP cc_start: 0.8250 (t70) cc_final: 0.7994 (t0)
REVERT: E   51 ASP cc_start: 0.8645 (m-30) cc_final: 0.8405 (m-30)
REVERT: G   25 ASP cc_start: 0.8284 (t70) cc_final: 0.8021 (t0)
REVERT: I   16 ASN cc_start: 0.8775 (t0) cc_final: 0.8484 (t0)
REVERT: I   25 ASP cc_start: 0.8261 (t70) cc_final: 0.7999 (t0)
REVERT: I   51 ASP cc_start: 0.8852 (m-30) cc_final: 0.8410 (m-30)
REVERT: K   25 ASP cc_start: 0.8240 (t70) cc_final: 0.7996 (t0)
REVERT: K  119 LYS cc_start: 0.8959 (tttm) cc_final: 0.8718 (tttt)
REVERT: M   25 ASP cc_start: 0.8271 (t70) cc_final: 0.8006 (t0)
REVERT: O   17 TYR cc_start: 0.9080 (m-80) cc_final: 0.8853 (m-80)
REVERT: O   25 ASP cc_start: 0.8267 (t70) cc_final: 0.8001 (t0)
REVERT: O  115 ARG cc_start: 0.9025 (mtm180) cc_final: 0.8821 (mtm180)
  outliers start: 21
  outliers final: 15
  residues processed: 205
  average time/residue: 0.1045
  time to fit residues: 31.8940
Evaluate side-chains
  206 residues out of total 1424 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 191
  time to evaluate  : 0.468 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  131 SER
Chi-restraints excluded: chain A residue  154 SER
Chi-restraints excluded: chain C residue  131 SER
Chi-restraints excluded: chain C residue  154 SER
Chi-restraints excluded: chain E residue  131 SER
Chi-restraints excluded: chain E residue  154 SER
Chi-restraints excluded: chain G residue  131 SER
Chi-restraints excluded: chain G residue  154 SER
Chi-restraints excluded: chain I residue  154 SER
Chi-restraints excluded: chain K residue  131 SER
Chi-restraints excluded: chain K residue  154 SER
Chi-restraints excluded: chain M residue  131 SER
Chi-restraints excluded: chain M residue  154 SER
Chi-restraints excluded: chain O residue  131 SER
Chi-restraints excluded: chain O residue  154 SER
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 160
   random chunks:
   chunk 84 optimal weight:    7.9990
   chunk 65 optimal weight:    2.9990
   chunk 60 optimal weight:   10.0000
   chunk 28 optimal weight:    8.9990
   chunk 155 optimal weight:   10.0000
   chunk 33 optimal weight:    1.9990
   chunk 12 optimal weight:    0.6980
   chunk 137 optimal weight:    6.9990
   chunk 110 optimal weight:    6.9990
   chunk 145 optimal weight:    0.9980
   chunk 100 optimal weight:   10.0000
   overall best weight:    2.7386

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

Flipped N/Q/H residues before XYZ refinement:
A  16 ASN
E  16 ASN
G  16 ASN
K  16 ASN
M  16 ASN
O  16 ASN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3070 r_free = 0.3070 target = 0.100237 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.2791 r_free = 0.2791 target = 0.081293 restraints weight = 16734.724|
|-----------------------------------------------------------------------------|
r_work (start): 0.2881 rms_B_bonded: 1.70
r_work: 0.2767 rms_B_bonded: 2.26 restraints_weight: 0.5000
r_work: 0.2621 rms_B_bonded: 3.80 restraints_weight: 0.2500
r_work (final): 0.2621
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8604
moved from start:          0.2398

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.022  13024  Z= 0.166
  Angle     :  0.433   4.505  17776  Z= 0.232
  Chirality :  0.045   0.121   2128
  Planarity :  0.003   0.029   2200
  Dihedral  :  9.884  63.822   2040
  Min Nonbonded Distance : 2.387

Molprobity Statistics.
  All-atom Clashscore : 1.88
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.16 %
    Favored  : 97.84 %
  Rotamer:
    Outliers :  1.64 %
    Allowed  : 11.68 %
    Favored  : 86.68 %
  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 are not related in a simple way.
  whole:  1.12 (0.21), residues: 1624
  helix:  1.58 (0.20), residues: 704
  sheet:  1.27 (0.29), residues: 240
  loop : -0.29 (0.24), residues: 680

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG K   5 
 TYR   0.005   0.001   TYR C  17 
 PHE   0.011   0.002   PHE C  78 
 TRP   0.002   0.001   TRP M 139 
 HIS   0.003   0.001   HIS I  79 

Details of bonding type rmsd
  covalent geometry    : bond        0.00394 (13024)
  covalent geometry    : angle       0.43339 (17776)
  hydrogen bonds       : bond        0.03609 (  560)
  hydrogen bonds       : angle       5.48392 ( 1680)

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

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

  3248 Ramachandran restraints generated.
    1624 Oldfield, 0 Emsley, 1624 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3248 Ramachandran restraints generated.
    1624 Oldfield, 0 Emsley, 1624 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  218 residues out of total 1424 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 198
  time to evaluate  : 0.483 
Fit side-chains
REVERT: A   25 ASP cc_start: 0.8311 (t70) cc_final: 0.8061 (t0)
REVERT: A  119 LYS cc_start: 0.8934 (tttm) cc_final: 0.8688 (tttt)
REVERT: C   16 ASN cc_start: 0.8711 (t0) cc_final: 0.8435 (t0)
REVERT: C   25 ASP cc_start: 0.8356 (t70) cc_final: 0.8092 (t0)
REVERT: C  115 ARG cc_start: 0.8996 (mtm180) cc_final: 0.8781 (mtm180)
REVERT: E   17 TYR cc_start: 0.9129 (m-80) cc_final: 0.8789 (m-80)
REVERT: E   25 ASP cc_start: 0.8334 (t70) cc_final: 0.8085 (t0)
REVERT: E   51 ASP cc_start: 0.8645 (m-30) cc_final: 0.8401 (m-30)
REVERT: G   25 ASP cc_start: 0.8327 (t70) cc_final: 0.8078 (t0)
REVERT: I   16 ASN cc_start: 0.8823 (t0) cc_final: 0.8516 (t0)
REVERT: I   17 TYR cc_start: 0.9110 (m-80) cc_final: 0.8797 (m-80)
REVERT: I   25 ASP cc_start: 0.8337 (t70) cc_final: 0.8084 (t0)
REVERT: I   51 ASP cc_start: 0.8770 (m-30) cc_final: 0.8497 (m-30)
REVERT: K   25 ASP cc_start: 0.8326 (t70) cc_final: 0.8086 (t0)
REVERT: K  119 LYS cc_start: 0.8939 (tttm) cc_final: 0.8696 (tttt)
REVERT: M   25 ASP cc_start: 0.8312 (t70) cc_final: 0.8056 (t0)
REVERT: O   25 ASP cc_start: 0.8306 (t70) cc_final: 0.8058 (t0)
REVERT: O  115 ARG cc_start: 0.8989 (mtm180) cc_final: 0.8774 (mtm180)
  outliers start: 20
  outliers final: 14
  residues processed: 206
  average time/residue: 0.1037
  time to fit residues: 31.8905
Evaluate side-chains
  205 residues out of total 1424 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 191
  time to evaluate  : 0.475 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  131 SER
Chi-restraints excluded: chain A residue  154 SER
Chi-restraints excluded: chain C residue  154 SER
Chi-restraints excluded: chain E residue  131 SER
Chi-restraints excluded: chain E residue  154 SER
Chi-restraints excluded: chain G residue  131 SER
Chi-restraints excluded: chain G residue  154 SER
Chi-restraints excluded: chain I residue  154 SER
Chi-restraints excluded: chain K residue  131 SER
Chi-restraints excluded: chain K residue  154 SER
Chi-restraints excluded: chain M residue  131 SER
Chi-restraints excluded: chain M residue  154 SER
Chi-restraints excluded: chain O residue  131 SER
Chi-restraints excluded: chain O residue  154 SER
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 160
   random chunks:
   chunk 108 optimal weight:    0.7980
   chunk 140 optimal weight:   10.0000
   chunk 49 optimal weight:    8.9990
   chunk 6 optimal weight:    5.9990
   chunk 33 optimal weight:    1.9990
   chunk 142 optimal weight:    8.9990
   chunk 145 optimal weight:    5.9990
   chunk 95 optimal weight:    0.0570
   chunk 63 optimal weight:    5.9990
   chunk 97 optimal weight:    8.9990
   chunk 127 optimal weight:    8.9990
   overall best weight:    2.9704

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

Flipped N/Q/H residues before XYZ refinement:
A  16 ASN
A  32 GLN
C  32 GLN
E  16 ASN
G  16 ASN
K  16 ASN
M  16 ASN
O  16 ASN

Total number of N/Q/H flips: 8

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3069 r_free = 0.3069 target = 0.100079 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.2790 r_free = 0.2790 target = 0.081173 restraints weight = 16811.425|
|-----------------------------------------------------------------------------|
r_work (start): 0.2845 rms_B_bonded: 1.70
r_work: 0.2731 rms_B_bonded: 2.25 restraints_weight: 0.5000
r_work: 0.2584 rms_B_bonded: 3.79 restraints_weight: 0.2500
r_work (final): 0.2584
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8606
moved from start:          0.2418

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.023  13024  Z= 0.177
  Angle     :  0.440   4.502  17776  Z= 0.236
  Chirality :  0.045   0.122   2128
  Planarity :  0.003   0.029   2200
  Dihedral  :  9.893  63.830   2040
  Min Nonbonded Distance : 2.417

Molprobity Statistics.
  All-atom Clashscore : 2.00
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.97 %
    Favored  : 98.03 %
  Rotamer:
    Outliers :  1.64 %
    Allowed  : 11.51 %
    Favored  : 86.84 %
  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 are not related in a simple way.
  whole:  1.06 (0.21), residues: 1624
  helix:  1.56 (0.20), residues: 704
  sheet:  1.18 (0.29), residues: 240
  loop : -0.34 (0.24), residues: 680

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG E  67 
 TYR   0.006   0.001   TYR O  17 
 PHE   0.012   0.002   PHE C  78 
 TRP   0.002   0.001   TRP I 139 
 HIS   0.003   0.001   HIS M  79 

Details of bonding type rmsd
  covalent geometry    : bond        0.00422 (13024)
  covalent geometry    : angle       0.44001 (17776)
  hydrogen bonds       : bond        0.03664 (  560)
  hydrogen bonds       : angle       5.50998 ( 1680)

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

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

  3248 Ramachandran restraints generated.
    1624 Oldfield, 0 Emsley, 1624 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3248 Ramachandran restraints generated.
    1624 Oldfield, 0 Emsley, 1624 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  217 residues out of total 1424 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 197
  time to evaluate  : 0.490 
Fit side-chains
REVERT: A   25 ASP cc_start: 0.8360 (t70) cc_final: 0.8109 (t0)
REVERT: A  119 LYS cc_start: 0.8943 (tttm) cc_final: 0.8701 (tttt)
REVERT: C   16 ASN cc_start: 0.8807 (t0) cc_final: 0.8529 (t0)
REVERT: C   25 ASP cc_start: 0.8367 (t70) cc_final: 0.8114 (t0)
REVERT: C  115 ARG cc_start: 0.8993 (mtm180) cc_final: 0.8780 (mtm180)
REVERT: E   17 TYR cc_start: 0.9119 (m-80) cc_final: 0.8776 (m-80)
REVERT: E   25 ASP cc_start: 0.8346 (t70) cc_final: 0.8096 (t0)
REVERT: E   51 ASP cc_start: 0.8639 (m-30) cc_final: 0.8390 (m-30)
REVERT: G   25 ASP cc_start: 0.8384 (t70) cc_final: 0.8126 (t0)
REVERT: I   16 ASN cc_start: 0.8840 (t0) cc_final: 0.8511 (t0)
REVERT: I   17 TYR cc_start: 0.9133 (m-80) cc_final: 0.8807 (m-80)
REVERT: I   25 ASP cc_start: 0.8336 (t70) cc_final: 0.8078 (t0)
REVERT: I   51 ASP cc_start: 0.8775 (m-30) cc_final: 0.8459 (m-30)
REVERT: K   25 ASP cc_start: 0.8332 (t70) cc_final: 0.8094 (t0)
REVERT: K  119 LYS cc_start: 0.8944 (tttm) cc_final: 0.8697 (tttt)
REVERT: M   25 ASP cc_start: 0.8358 (t70) cc_final: 0.8095 (t0)
REVERT: O   25 ASP cc_start: 0.8361 (t70) cc_final: 0.8091 (t0)
REVERT: O  115 ARG cc_start: 0.9002 (mtm180) cc_final: 0.8791 (mtm180)
  outliers start: 20
  outliers final: 14
  residues processed: 205
  average time/residue: 0.1003
  time to fit residues: 30.8442
Evaluate side-chains
  210 residues out of total 1424 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 196
  time to evaluate  : 0.458 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  131 SER
Chi-restraints excluded: chain A residue  154 SER
Chi-restraints excluded: chain C residue  154 SER
Chi-restraints excluded: chain E residue  154 SER
Chi-restraints excluded: chain G residue  131 SER
Chi-restraints excluded: chain G residue  154 SER
Chi-restraints excluded: chain I residue  131 SER
Chi-restraints excluded: chain I residue  154 SER
Chi-restraints excluded: chain K residue  131 SER
Chi-restraints excluded: chain K residue  154 SER
Chi-restraints excluded: chain M residue  131 SER
Chi-restraints excluded: chain M residue  154 SER
Chi-restraints excluded: chain O residue  131 SER
Chi-restraints excluded: chain O residue  154 SER
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 160
   random chunks:
   chunk 49 optimal weight:    8.9990
   chunk 105 optimal weight:    0.8980
   chunk 5 optimal weight:   10.0000
   chunk 118 optimal weight:    0.9990
   chunk 120 optimal weight:   10.0000
   chunk 142 optimal weight:    8.9990
   chunk 15 optimal weight:    8.9990
   chunk 99 optimal weight:    4.9990
   chunk 16 optimal weight:    3.9990
   chunk 4 optimal weight:    7.9990
   chunk 151 optimal weight:    7.9990
   overall best weight:    3.7788

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

Flipped N/Q/H residues before XYZ refinement:
A  16 ASN
C  32 GLN
E  16 ASN
E  32 GLN
G  16 ASN
G  32 GLN
I  32 GLN
K  16 ASN
M  16 ASN
M  32 GLN
O  16 ASN
O  32 GLN

Total number of N/Q/H flips: 12

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3051 r_free = 0.3051 target = 0.098925 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.2775 r_free = 0.2775 target = 0.080308 restraints weight = 16843.339|
|-----------------------------------------------------------------------------|
r_work (start): 0.2845 rms_B_bonded: 1.65
r_work: 0.2727 rms_B_bonded: 2.24 restraints_weight: 0.5000
r_work: 0.2575 rms_B_bonded: 3.77 restraints_weight: 0.2500
r_work (final): 0.2575
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8635
moved from start:          0.2427

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.026  13024  Z= 0.219
  Angle     :  0.464   4.509  17776  Z= 0.248
  Chirality :  0.046   0.127   2128
  Planarity :  0.003   0.031   2200
  Dihedral  :  9.974  63.854   2040
  Min Nonbonded Distance : 2.422

Molprobity Statistics.
  All-atom Clashscore : 1.88
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.16 %
    Favored  : 97.84 %
  Rotamer:
    Outliers :  1.64 %
    Allowed  : 11.60 %
    Favored  : 86.76 %
  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 are not related in a simple way.
  whole:  0.92 (0.21), residues: 1624
  helix:  1.48 (0.20), residues: 704
  sheet:  1.04 (0.29), residues: 240
  loop : -0.43 (0.25), residues: 680

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG I 169 
 TYR   0.006   0.001   TYR O  17 
 PHE   0.013   0.002   PHE C  78 
 TRP   0.002   0.001   TRP C 197 
 HIS   0.004   0.001   HIS C  79 

Details of bonding type rmsd
  covalent geometry    : bond        0.00524 (13024)
  covalent geometry    : angle       0.46383 (17776)
  hydrogen bonds       : bond        0.03969 (  560)
  hydrogen bonds       : angle       5.64987 ( 1680)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2540.78 seconds
wall clock time: 44 minutes 18.75 seconds (2658.75 seconds total)