Starting phenix.real_space_refine
on Thu Aug  6 02:21:40 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9zeo_74114/08_2026/9zeo_74114.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9zeo_74114/08_2026/9zeo_74114.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.1
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/9zeo_74114/08_2026/9zeo_74114.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9zeo_74114/08_2026/9zeo_74114.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9zeo_74114/08_2026/9zeo_74114.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9zeo_74114/08_2026/9zeo_74114.cif"
  }
  resolution = 3.1
  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=   0.003 sd=   0.021
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 5
    Type Number    sf(0)   Gaussians
     P     288      5.49       5
     S      18      5.16       5
     C    7188      2.51       5
     N    2415      2.21       5
     O    2986      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 20 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib"
  Total number of atoms: 12895
  Number of models: 1
  Model: ""
    Number of chains: 11
    Chain: "I"
      Number of atoms: 2952
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 145, 2952
          Classifications: {'DNA': 145}
          Modifications used: {'5*END': 1}
          Link IDs: {'rna3p': 144}
    Chain: "J"
      Number of atoms: 2987
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 145, 2987
          Classifications: {'DNA': 145}
          Modifications used: {'5*END': 1}
          Link IDs: {'rna3p': 144}
    Chain: "A"
      Number of atoms: 801
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 97, 801
          Classifications: {'peptide': 97}
          Link IDs: {'PTRANS': 3, 'TRANS': 93}
    Chain: "B"
      Number of atoms: 662
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 83, 662
          Classifications: {'peptide': 83}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 1, 'TRANS': 81}
    Chain: "C"
      Number of atoms: 829
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 108, 829
          Classifications: {'peptide': 108}
          Incomplete info: {'truncation_to_alanine': 1}
          Link IDs: {'PTRANS': 5, 'TRANS': 102}
          Unresolved non-hydrogen bonds: 6
          Unresolved non-hydrogen angles: 7
          Unresolved non-hydrogen dihedrals: 5
          Planarities with less than four sites: {'ARG:plan': 1}
          Unresolved non-hydrogen planarities: 5
    Chain: "D"
      Number of atoms: 744
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 95, 744
          Classifications: {'peptide': 95}
          Modifications used: {'COO': 1}
          Incomplete info: {'truncation_to_alanine': 1}
          Link IDs: {'PTRANS': 2, 'TRANS': 92}
          Unresolved non-hydrogen bonds: 1
          Unresolved non-hydrogen angles: 1
          Unresolved non-hydrogen dihedrals: 1
    Chain: "E"
      Number of atoms: 800
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 97, 800
          Classifications: {'peptide': 97}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 3, 'TRANS': 93}
    Chain: "F"
      Number of atoms: 619
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 78, 619
          Classifications: {'peptide': 78}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 1, 'TRANS': 76}
    Chain: "G"
      Number of atoms: 829
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 108, 829
          Classifications: {'peptide': 108}
          Incomplete info: {'truncation_to_alanine': 1}
          Link IDs: {'PTRANS': 5, 'TRANS': 102}
          Unresolved non-hydrogen bonds: 6
          Unresolved non-hydrogen angles: 7
          Unresolved non-hydrogen dihedrals: 5
          Planarities with less than four sites: {'ARG:plan': 1}
          Unresolved non-hydrogen planarities: 5
    Chain: "H"
      Number of atoms: 733
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 94, 733
          Classifications: {'peptide': 94}
          Link IDs: {'PTRANS': 2, 'TRANS': 91}
    Chain: "K"
      Number of atoms: 939
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 124, 939
          Classifications: {'peptide': 124}
          Incomplete info: {'truncation_to_alanine': 1}
          Link IDs: {'PTRANS': 2, 'TRANS': 121}
          Unresolved non-hydrogen bonds: 7
          Unresolved non-hydrogen angles: 9
          Unresolved non-hydrogen dihedrals: 7
          Planarities with less than four sites: {'PHE:plan': 1}
          Unresolved non-hydrogen planarities: 6
  Time building chain proxies: 2.50, per 1000 atoms: 0.19
  Number of scatterers: 12895
  At special positions: 0
  Unit cell: (126.27, 107.604, 116.388, 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      18     16.00
     P     288     15.00
     O    2986      8.00
     N    2415      7.00
     C    7188      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=1, symmetry=0
    Simple disulfide: pdb=" SG  CYS K  22 " - pdb=" SG  CYS K  96 " distance=2.03

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 0.96
  Conformation dependent library (CDL) restraints added in 391.7 milliseconds
  

  1732 Ramachandran restraints generated.
    866 Oldfield, 0 Emsley, 866 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1632

  Finding SS restraints...
    Secondary structure from input PDB file:
      35 helices and 12 sheets defined
      60.9% alpha, 6.3% beta
      141 base pairs and 262 stacking pairs defined.
    Time for finding SS restraints: 1.83
  Creating SS restraints...
    Processing helix  chain 'A' and resid 44 through 55
    Processing helix  chain 'A' and resid 63 through 79
      removed outlier: 3.570A  pdb=" N   ARG A  72 " --> pdb=" O   GLN A  68 " (cutoff:3.500A)
      removed outlier: 3.995A  pdb=" N   GLU A  73 " --> pdb=" O   ARG A  69 " (cutoff:3.500A)
      removed outlier: 3.690A  pdb=" N   ILE A  74 " --> pdb=" O   LEU A  70 " (cutoff:3.500A)
      removed outlier: 3.668A  pdb=" N   ASP A  77 " --> pdb=" O   GLU A  73 " (cutoff:3.500A)
      removed outlier: 3.847A  pdb=" N   PHE A  78 " --> pdb=" O   ILE A  74 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 87 through 114
    Processing helix  chain 'A' and resid 120 through 132
      removed outlier: 3.539A  pdb=" N   ILE A 124 " --> pdb=" O   MET A 120 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 25 through 29
    Processing helix  chain 'B' and resid 30 through 42
    Processing helix  chain 'B' and resid 49 through 76
      removed outlier: 4.166A  pdb=" N   GLU B  53 " --> pdb=" O   LEU B  49 " (cutoff:3.500A)
      removed outlier: 3.566A  pdb=" N   ASN B  64 " --> pdb=" O   VAL B  60 " (cutoff:3.500A)
      removed outlier: 3.720A  pdb=" N   VAL B  65 " --> pdb=" O   PHE B  61 " (cutoff:3.500A)
      removed outlier: 4.100A  pdb=" N   ASP B  68 " --> pdb=" O   ASN B  64 " (cutoff:3.500A)
      removed outlier: 3.615A  pdb=" N   ALA B  76 " --> pdb=" O   TYR B  72 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 82 through 93
      removed outlier: 3.699A  pdb=" N   VAL B  86 " --> pdb=" O   THR B  82 " (cutoff:3.500A)
      removed outlier: 3.728A  pdb=" N   GLN B  93 " --> pdb=" O   ALA B  89 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 16 through 21
    Processing helix  chain 'C' and resid 27 through 36
    Processing helix  chain 'C' and resid 45 through 73
      removed outlier: 4.494A  pdb=" N   VAL C  49 " --> pdb=" O   ALA C  45 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 79 through 90
      removed outlier: 3.511A  pdb=" N   ASP C  90 " --> pdb=" O   ALA C  86 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 91 through 97
    Processing helix  chain 'D' and resid 37 through 49
    Processing helix  chain 'D' and resid 55 through 84
      removed outlier: 3.639A  pdb=" N   ASN D  84 " --> pdb=" O   LEU D  80 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 90 through 102
      removed outlier: 3.536A  pdb=" N   ILE D  94 " --> pdb=" O   THR D  90 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 103 through 125
      removed outlier: 3.685A  pdb=" N   HIS D 109 " --> pdb=" O   GLU D 105 " (cutoff:3.500A)
      removed outlier: 3.843A  pdb=" N   SER D 112 " --> pdb=" O   LYS D 108 " (cutoff:3.500A)
      removed outlier: 3.863A  pdb=" N   LYS D 116 " --> pdb=" O   SER D 112 " (cutoff:3.500A)
      removed outlier: 3.546A  pdb=" N   ALA D 117 " --> pdb=" O   GLU D 113 " (cutoff:3.500A)
      removed outlier: 3.560A  pdb=" N   VAL D 118 " --> pdb=" O   GLY D 114 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 44 through 55
    Processing helix  chain 'E' and resid 63 through 76
      removed outlier: 3.622A  pdb=" N   PHE E  67 " --> pdb=" O   ARG E  63 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 87 through 114
    Processing helix  chain 'E' and resid 120 through 132
      removed outlier: 3.530A  pdb=" N   ILE E 124 " --> pdb=" O   MET E 120 " (cutoff:3.500A)
      removed outlier: 3.526A  pdb=" N   GLY E 132 " --> pdb=" O   ARG E 128 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 25 through 29
    Processing helix  chain 'F' and resid 30 through 42
    Processing helix  chain 'F' and resid 50 through 76
      removed outlier: 3.777A  pdb=" N   GLY F  56 " --> pdb=" O   GLU F  52 " (cutoff:3.500A)
      removed outlier: 3.578A  pdb=" N   ARG F  67 " --> pdb=" O   GLU F  63 " (cutoff:3.500A)
      removed outlier: 3.880A  pdb=" N   ASP F  68 " --> pdb=" O   ASN F  64 " (cutoff:3.500A)
      removed outlier: 3.518A  pdb=" N   THR F  71 " --> pdb=" O   ARG F  67 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 82 through 93
      removed outlier: 3.696A  pdb=" N   VAL F  86 " --> pdb=" O   THR F  82 " (cutoff:3.500A)
      removed outlier: 3.669A  pdb=" N   GLN F  93 " --> pdb=" O   ALA F  89 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 16 through 21
      removed outlier: 3.554A  pdb=" N   ALA G  21 " --> pdb=" O   ARG G  17 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 27 through 36
    Processing helix  chain 'G' and resid 45 through 72
      removed outlier: 4.344A  pdb=" N   VAL G  49 " --> pdb=" O   ALA G  45 " (cutoff:3.500A)
      removed outlier: 3.524A  pdb=" N   ALA G  53 " --> pdb=" O   VAL G  49 " (cutoff:3.500A)
      removed outlier: 3.688A  pdb=" N   ILE G  62 " --> pdb=" O   LEU G  58 " (cutoff:3.500A)
      removed outlier: 3.657A  pdb=" N   ARG G  71 " --> pdb=" O   GLY G  67 " (cutoff:3.500A)
      removed outlier: 3.849A  pdb=" N   ASP G  72 " --> pdb=" O   ASN G  68 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 79 through 90
      removed outlier: 3.518A  pdb=" N   LEU G  83 " --> pdb=" O   ILE G  79 " (cutoff:3.500A)
      removed outlier: 3.510A  pdb=" N   ASP G  90 " --> pdb=" O   ALA G  86 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 92 through 97
    Processing helix  chain 'H' and resid 37 through 49
    Processing helix  chain 'H' and resid 55 through 84
      removed outlier: 3.582A  pdb=" N   ASN H  84 " --> pdb=" O   LEU H  80 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 90 through 102
      removed outlier: 3.547A  pdb=" N   ILE H  94 " --> pdb=" O   THR H  90 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 103 through 122
      removed outlier: 3.959A  pdb=" N   HIS H 109 " --> pdb=" O   GLU H 105 " (cutoff:3.500A)
      removed outlier: 3.564A  pdb=" N   SER H 112 " --> pdb=" O   LYS H 108 " (cutoff:3.500A)
    Processing helix  chain 'K' and resid 87 through 91
      removed outlier: 4.091A  pdb=" N   THR K  91 " --> pdb=" O   PRO K  88 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 83 through 84
      removed outlier: 7.293A  pdb=" N   ARG A  83 " --> pdb=" O   VAL B  81 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA1
    Processing sheet with id=AA2, first strand: chain 'A' and resid 118 through 119
    Processing sheet with id=AA3, first strand: chain 'B' and resid 96 through 98
      removed outlier: 6.555A  pdb=" N   THR B  96 " --> pdb=" O   THR G 101 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA3
    Processing sheet with id=AA4, first strand: chain 'C' and resid 77 through 78
    Processing sheet with id=AA5, first strand: chain 'C' and resid 100 through 102
    Processing sheet with id=AA6, first strand: chain 'E' and resid 83 through 84
      removed outlier: 7.173A  pdb=" N   ARG E  83 " --> pdb=" O   VAL F  81 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA6
    Processing sheet with id=AA7, first strand: chain 'E' and resid 118 through 119
    Processing sheet with id=AA8, first strand: chain 'G' and resid 42 through 43
      removed outlier: 7.218A  pdb=" N   ARG G  42 " --> pdb=" O   ILE H  89 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA8
    Processing sheet with id=AA9, first strand: chain 'G' and resid 77 through 78
    Processing sheet with id=AB1, first strand: chain 'K' and resid 3 through 6
    Processing sheet with id=AB2, first strand: chain 'K' and resid 11 through 12
    Processing sheet with id=AB3, first strand: chain 'K' and resid 46 through 50
      removed outlier: 3.834A  pdb=" N   VAL K  48 " --> pdb=" O   TRP K  36 " (cutoff:3.500A)
      removed outlier: 7.196A  pdb=" N   TRP K  36 " --> pdb=" O   VAL K  48 " (cutoff:3.500A)

    386 hydrogen bonds defined for protein.
    1131 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      361 hydrogen bonds
      722 hydrogen bond angles
      0 basepair planarities
      141 basepair parallelities
      262 stacking parallelities
  Total time for adding SS restraints: 2.34

  Time building geometry restraints manager: 1.34 seconds

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

  Histogram of bond lengths:
        1.21 -     1.33: 2641
        1.33 -     1.45: 4448
        1.45 -     1.58: 6018
        1.58 -     1.70: 576
        1.70 -     1.82: 30
  Bond restraints: 13713
  Sorted by residual:
  bond pdb=" C3'  DT J -17 "
       pdb=" O3'  DT J -17 "
    ideal  model  delta    sigma   weight residual
    1.435  1.485 -0.050 1.30e-02 5.92e+03 1.46e+01
  bond pdb=" C3'  DG J  21 "
       pdb=" C2'  DG J  21 "
    ideal  model  delta    sigma   weight residual
    1.516  1.546 -0.030 8.00e-03 1.56e+04 1.42e+01
  bond pdb=" C5'  DG I  47 "
       pdb=" C4'  DG I  47 "
    ideal  model  delta    sigma   weight residual
    1.512  1.536 -0.024 7.00e-03 2.04e+04 1.21e+01
  bond pdb=" C3'  DC I   4 "
       pdb=" C2'  DC I   4 "
    ideal  model  delta    sigma   weight residual
    1.516  1.544 -0.028 8.00e-03 1.56e+04 1.19e+01
  bond pdb=" C3'  DC I   4 "
       pdb=" O3'  DC I   4 "
    ideal  model  delta    sigma   weight residual
    1.435  1.479 -0.044 1.30e-02 5.92e+03 1.13e+01
  ... (remaining 13708 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.17: 18985
        2.17 -     4.34: 718
        4.34 -     6.51: 49
        6.51 -     8.68: 7
        8.68 -    10.86: 2
  Bond angle restraints: 19761
  Sorted by residual:
  angle pdb=" C   ARG B  23 "
        pdb=" N   ASP B  24 "
        pdb=" CA  ASP B  24 "
      ideal   model   delta    sigma   weight residual
     121.54  131.53   -9.99 1.91e+00 2.74e-01 2.74e+01
  angle pdb=" N   GLY D 104 "
        pdb=" CA  GLY D 104 "
        pdb=" C   GLY D 104 "
      ideal   model   delta    sigma   weight residual
     112.50  118.16   -5.66 1.16e+00 7.43e-01 2.38e+01
  angle pdb=" N   VAL G  27 "
        pdb=" CA  VAL G  27 "
        pdb=" C   VAL G  27 "
      ideal   model   delta    sigma   weight residual
     112.96  108.11    4.85 1.00e+00 1.00e+00 2.35e+01
  angle pdb=" O5'  DA I  57 "
        pdb=" C5'  DA I  57 "
        pdb=" C4'  DA I  57 "
      ideal   model   delta    sigma   weight residual
     109.40  113.27   -3.87 8.00e-01 1.56e+00 2.34e+01
  angle pdb=" O5'  DA I -35 "
        pdb=" C5'  DA I -35 "
        pdb=" C4'  DA I -35 "
      ideal   model   delta    sigma   weight residual
     109.40  113.09   -3.69 8.00e-01 1.56e+00 2.12e+01
  ... (remaining 19756 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    35.25: 6094
       35.25 -    70.49: 1366
       70.49 -   105.74: 27
      105.74 -   140.98: 3
      140.98 -   176.23: 2
  Dihedral angle restraints: 7492
    sinusoidal: 4946
      harmonic: 2546
  Sorted by residual:
  dihedral pdb=" CA  GLN K 107 "
           pdb=" C   GLN K 107 "
           pdb=" N   ILE K 108 "
           pdb=" CA  ILE K 108 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  159.72   20.28     0      5.00e+00 4.00e-02 1.64e+01
  dihedral pdb=" C4'  DT J -17 "
           pdb=" C3'  DT J -17 "
           pdb=" O3'  DT J -17 "
           pdb=" P    DT J -16 "
      ideal   model   delta sinusoidal    sigma   weight residual
    -140.00   36.23 -176.23     1      3.50e+01 8.16e-04 1.57e+01
  dihedral pdb=" C4'  DG J  20 "
           pdb=" C3'  DG J  20 "
           pdb=" O3'  DG J  20 "
           pdb=" P    DG J  21 "
      ideal   model   delta sinusoidal    sigma   weight residual
     220.00   74.69  145.31     1      3.50e+01 8.16e-04 1.43e+01
  ... (remaining 7489 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.046: 1499
       0.046 -    0.091: 585
       0.091 -    0.136: 135
       0.136 -    0.182: 12
       0.182 -    0.227: 6
  Chirality restraints: 2237
  Sorted by residual:
  chirality pdb=" CA  ASP B  24 "
            pdb=" N   ASP B  24 "
            pdb=" C   ASP B  24 "
            pdb=" CB  ASP B  24 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.28    0.23 2.00e-01 2.50e+01 1.29e+00
  chirality pdb=" CB  VAL K  29 "
            pdb=" CA  VAL K  29 "
            pdb=" CG1 VAL K  29 "
            pdb=" CG2 VAL K  29 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -2.43   -0.20 2.00e-01 2.50e+01 1.01e+00
  chirality pdb=" C3'  DC I   4 "
            pdb=" C4'  DC I   4 "
            pdb=" O3'  DC I   4 "
            pdb=" C2'  DC I   4 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.73   -2.53   -0.20 2.00e-01 2.50e+01 9.87e-01
  ... (remaining 2234 not shown)

  Planarity restraints: 1504
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ILE C  79 "    0.042 5.00e-02 4.00e+02   6.39e-02 6.54e+00
        pdb=" N   PRO C  80 "   -0.111 5.00e-02 4.00e+02
        pdb=" CA  PRO C  80 "    0.033 5.00e-02 4.00e+02
        pdb=" CD  PRO C  80 "    0.035 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ILE G  79 "    0.042 5.00e-02 4.00e+02   6.33e-02 6.41e+00
        pdb=" N   PRO G  80 "   -0.109 5.00e-02 4.00e+02
        pdb=" CA  PRO G  80 "    0.032 5.00e-02 4.00e+02
        pdb=" CD  PRO G  80 "    0.035 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   MET E 120 "    0.036 5.00e-02 4.00e+02   5.43e-02 4.71e+00
        pdb=" N   PRO E 121 "   -0.094 5.00e-02 4.00e+02
        pdb=" CA  PRO E 121 "    0.028 5.00e-02 4.00e+02
        pdb=" CD  PRO E 121 "    0.030 5.00e-02 4.00e+02
  ... (remaining 1501 not shown)

  Histogram of nonbonded interaction distances:
        2.37 -     2.88: 3891
        2.88 -     3.38: 10385
        3.38 -     3.89: 24330
        3.89 -     4.39: 28365
        4.39 -     4.90: 40350
  Nonbonded interactions: 107321
  Sorted by model distance:
  nonbonded pdb=" OG1 THR H  90 "
            pdb=" OE1 GLU H  93 "
     model   vdw
     2.369 3.040
  nonbonded pdb=" NH2 ARG C  32 "
            pdb=" OE2 GLU D  35 "
     model   vdw
     2.390 3.120
  nonbonded pdb=" O   ILE B  50 "
            pdb=" OG1 THR B  54 "
     model   vdw
     2.394 3.040
  nonbonded pdb=" O   LEU A  61 "
            pdb=" NH1 ARG B  36 "
     model   vdw
     2.400 3.120
  nonbonded pdb=" O   THR H 115 "
            pdb=" OG1 THR H 119 "
     model   vdw
     2.404 3.040
  ... (remaining 107316 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.00
Found NCS groups:
ncs_group {
  reference = (chain 'A' and resid 39 through 134)
  selection = (chain 'E' and resid 39 through 134)
}
ncs_group {
  reference = (chain 'B' and resid 25 through 102)
  selection = chain 'F'
}
ncs_group {
  reference = chain 'C'
  selection = chain 'G'
}
ncs_group {
  reference = (chain 'D' and (resid 32 through 124 or (resid 125 and (name N or name CA or nam \ 
e C or name O or name CB or name CG or name CD or name CE or name NZ ))))
  selection = (chain 'H' and ((resid 32 and (name N or name CA or name C or name O or name CB  \ 
)) or resid 33 through 125))
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             1.700
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.140
  Check model and map are aligned:         0.040
  Set scattering table:                    0.020
  Process input model:                     13.090
  Find NCS groups from input model:        0.150
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.010
  Load rotamer database and sin/cos tables:1.210
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   16.380
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8415
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      :  0.006   0.050  13714  Z= 0.542
  Angle     :  0.883  10.855  19763  Z= 0.720
  Chirality :  0.050   0.227   2237
  Planarity :  0.006   0.064   1504
  Dihedral  : 27.019 176.225   5857
  Min Nonbonded Distance : 2.369

Molprobity Statistics.
  All-atom Clashscore : 2.22
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.23 %
    Favored  : 96.77 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.24 %
    Favored  : 98.76 %
  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: -1.45 (0.25), residues: 866
  helix: -0.65 (0.19), residues: 524
  sheet: -1.49 (0.77), residues: 44
  loop : -1.18 (0.32), residues: 298

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.012   0.001   ARG D  79 
 TYR   0.022   0.001   TYR D  37 
 PHE   0.012   0.002   PHE D  65 
 TRP   0.003   0.001   TRP K 114 
 HIS   0.007   0.001   HIS B  75 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00609 /  0.54 (13713)
  covalent geometry    : angle       0.88318 /  0.72 (19761)
  SS BOND              : bond        0.00044 /  0.02 (    1)
  SS BOND              : angle       0.18694 /  0.33 (    2)
  hydrogen bonds       : bond        0.11795 / 13.62 (  747)
  hydrogen bonds       : angle       4.27270 /  5.44 ( 1853)

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

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

  1732 Ramachandran restraints generated.
    866 Oldfield, 0 Emsley, 866 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1732 Ramachandran restraints generated.
    866 Oldfield, 0 Emsley, 866 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  202 residues out of total 730 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 202
  time to evaluate  : 0.358 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   56 LYS cc_start: 0.8699 (ttmm) cc_final: 0.8480 (ttmm)
REVERT: A   79 LYS cc_start: 0.8763 (tttm) cc_final: 0.8558 (ttpp)
REVERT: A   90 MET cc_start: 0.8214 (mmm) cc_final: 0.7980 (mmp)
REVERT: H   35 GLU cc_start: 0.8149 (mm-30) cc_final: 0.7871 (mm-30)
REVERT: H   42 TYR cc_start: 0.8432 (t80) cc_final: 0.8213 (t80)
REVERT: K   81 LEU cc_start: 0.8363 (tp) cc_final: 0.7942 (tt)
REVERT: K   84 ASN cc_start: 0.7976 (m-40) cc_final: 0.7617 (m-40)
  outliers start: 0
  outliers final: 0
  residues processed: 202
  average time/residue: 0.1605
  time to fit residues: 42.9196
Evaluate side-chains
  179 residues out of total 730 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 179
  time to evaluate  : 0.351 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 111
   random chunks:
   chunk 108 optimal weight:    9.9990
   chunk 49 optimal weight:    3.9990
   chunk 97 optimal weight:    4.9990
   chunk 53 optimal weight:    4.9990
   chunk 5 optimal weight:   10.0000
   chunk 33 optimal weight:    2.9990
   chunk 65 optimal weight:    1.9990
   chunk 62 optimal weight:    2.9990
   chunk 51 optimal weight:    4.9990
   chunk 100 optimal weight:   30.0000
   chunk 106 optimal weight:   10.0000
   overall best weight:    3.3990

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
C  73 ASN
C  84 GLN
** C 104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 112 GLN
D  84 ASN
H  47 GLN
K  13 GLN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3586 r_free = 0.3586 target = 0.077963 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3298 r_free = 0.3298 target = 0.064850 restraints weight = 34158.092|
|-----------------------------------------------------------------------------|
r_work (start): 0.3283 rms_B_bonded: 1.41
r_work: 0.3136 rms_B_bonded: 2.18 restraints_weight: 0.5000
r_work: 0.3017 rms_B_bonded: 3.49 restraints_weight: 0.2500
r_work (final): 0.3017
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8746
moved from start:          0.1492

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.007   0.054  13714  Z= 0.317
  Angle     :  0.754   8.125  19763  Z= 0.425
  Chirality :  0.054   0.260   2237
  Planarity :  0.006   0.056   1504
  Dihedral  : 30.358 174.974   4160
  Min Nonbonded Distance : 2.328

Molprobity Statistics.
  All-atom Clashscore : 5.39
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.46 %
    Favored  : 96.54 %
  Rotamer:
    Outliers :  2.34 %
    Allowed  :  9.09 %
    Favored  : 88.57 %
  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: -0.16 (0.27), residues: 866
  helix:  0.72 (0.22), residues: 533
  sheet: -1.49 (0.69), residues: 50
  loop : -1.31 (0.34), residues: 283

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG E  40 
 TYR   0.012   0.002   TYR C  57 
 PHE   0.014   0.002   PHE D  65 
 TRP   0.015   0.003   TRP K 114 
 HIS   0.007   0.002   HIS H  49 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00657 /  0.32 (13713)
  covalent geometry    : angle       0.75376 /  0.43 (19761)
  SS BOND              : bond        0.01437 /  0.57 (    1)
  SS BOND              : angle       0.57245 /  1.08 (    2)
  hydrogen bonds       : bond        0.07299 /  7.91 (  747)
  hydrogen bonds       : angle       3.36054 /  4.28 ( 1853)

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

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

  1732 Ramachandran restraints generated.
    866 Oldfield, 0 Emsley, 866 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1732 Ramachandran restraints generated.
    866 Oldfield, 0 Emsley, 866 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  195 residues out of total 730 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 178
  time to evaluate  : 0.364 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   79 LYS cc_start: 0.8517 (tttm) cc_final: 0.8288 (ttpp)
REVERT: H   35 GLU cc_start: 0.7778 (mm-30) cc_final: 0.7498 (mm-30)
REVERT: K   36 TRP cc_start: 0.7906 (m100) cc_final: 0.7540 (m-10)
REVERT: K   38 ARG cc_start: 0.7575 (ptm160) cc_final: 0.7359 (ptm160)
REVERT: K   81 LEU cc_start: 0.8485 (tp) cc_final: 0.7680 (tp)
REVERT: K   83 MET cc_start: 0.7961 (mpp) cc_final: 0.7435 (mpp)
REVERT: K   95 TYR cc_start: 0.7689 (m-10) cc_final: 0.7382 (m-10)
REVERT: K  114 TRP cc_start: 0.8571 (m100) cc_final: 0.8268 (m100)
  outliers start: 17
  outliers final: 13
  residues processed: 189
  average time/residue: 0.1701
  time to fit residues: 42.1993
Evaluate side-chains
  185 residues out of total 730 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 172
  time to evaluate  : 0.346 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  112 ILE
Chi-restraints excluded: chain C residue   41 GLU
Chi-restraints excluded: chain D residue   39 VAL
Chi-restraints excluded: chain D residue   71 GLU
Chi-restraints excluded: chain D residue  106 LEU
Chi-restraints excluded: chain D residue  112 SER
Chi-restraints excluded: chain D residue  123 SER
Chi-restraints excluded: chain F residue   25 ASN
Chi-restraints excluded: chain F residue   49 LEU
Chi-restraints excluded: chain G residue   16 THR
Chi-restraints excluded: chain H residue   98 VAL
Chi-restraints excluded: chain H residue  115 THR
Chi-restraints excluded: chain K residue   51 ILE
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 111
   random chunks:
   chunk 85 optimal weight:    2.9990
   chunk 104 optimal weight:    5.9990
   chunk 11 optimal weight:   10.0000
   chunk 27 optimal weight:   10.0000
   chunk 34 optimal weight:    0.6980
   chunk 92 optimal weight:    0.7980
   chunk 55 optimal weight:    0.8980
   chunk 76 optimal weight:    0.8980
   chunk 62 optimal weight:    0.9990
   chunk 4 optimal weight:    9.9990
   chunk 81 optimal weight:    0.7980
   overall best weight:    0.8180

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** K  84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3622 r_free = 0.3622 target = 0.079590 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3345 r_free = 0.3345 target = 0.066702 restraints weight = 34463.974|
|-----------------------------------------------------------------------------|
r_work (start): 0.3330 rms_B_bonded: 1.43
r_work: 0.3187 rms_B_bonded: 2.21 restraints_weight: 0.5000
r_work: 0.3068 rms_B_bonded: 3.57 restraints_weight: 0.2500
r_work (final): 0.3068
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8698
moved from start:          0.1461

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035  13714  Z= 0.148
  Angle     :  0.648   7.185  19763  Z= 0.374
  Chirality :  0.048   0.234   2237
  Planarity :  0.004   0.042   1504
  Dihedral  : 30.417 174.934   4160
  Min Nonbonded Distance : 2.522

Molprobity Statistics.
  All-atom Clashscore : 5.90
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.66 %
    Favored  : 97.34 %
  Rotamer:
    Outliers :  2.20 %
    Allowed  : 10.88 %
    Favored  : 86.91 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.57 (0.28), residues: 866
  helix:  1.39 (0.23), residues: 532
  sheet: -1.21 (0.68), residues: 47
  loop : -1.24 (0.34), residues: 287

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG K  38 
 TYR   0.022   0.001   TYR K 105 
 PHE   0.008   0.001   PHE H  65 
 TRP   0.002   0.000   TRP K  36 
 HIS   0.003   0.000   HIS F  75 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00260 /  0.15 (13713)
  covalent geometry    : angle       0.64822 /  0.37 (19761)
  SS BOND              : bond        0.00676 /  0.27 (    1)
  SS BOND              : angle       1.87940 /  3.75 (    2)
  hydrogen bonds       : bond        0.05095 /  5.46 (  747)
  hydrogen bonds       : angle       3.10702 /  3.91 ( 1853)

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

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

  1732 Ramachandran restraints generated.
    866 Oldfield, 0 Emsley, 866 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1732 Ramachandran restraints generated.
    866 Oldfield, 0 Emsley, 866 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  197 residues out of total 730 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 181
  time to evaluate  : 0.259 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   79 LYS cc_start: 0.8451 (tttm) cc_final: 0.8140 (tttm)
REVERT: H   35 GLU cc_start: 0.7760 (mm-30) cc_final: 0.7480 (mm-30)
REVERT: K   36 TRP cc_start: 0.7888 (m100) cc_final: 0.7557 (m-10)
REVERT: K   81 LEU cc_start: 0.8605 (tp) cc_final: 0.7912 (tp)
REVERT: K   95 TYR cc_start: 0.7746 (m-10) cc_final: 0.7288 (m-10)
  outliers start: 16
  outliers final: 11
  residues processed: 190
  average time/residue: 0.1558
  time to fit residues: 39.4342
Evaluate side-chains
  186 residues out of total 730 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 175
  time to evaluate  : 0.349 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   94 GLU
Chi-restraints excluded: chain B residue   43 VAL
Chi-restraints excluded: chain C residue   41 GLU
Chi-restraints excluded: chain C residue  118 LYS
Chi-restraints excluded: chain D residue   39 VAL
Chi-restraints excluded: chain D residue   71 GLU
Chi-restraints excluded: chain D residue  112 SER
Chi-restraints excluded: chain D residue  123 SER
Chi-restraints excluded: chain F residue   49 LEU
Chi-restraints excluded: chain G residue   16 THR
Chi-restraints excluded: chain H residue   98 VAL
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 111
   random chunks:
   chunk 5 optimal weight:    9.9990
   chunk 12 optimal weight:    9.9990
   chunk 2 optimal weight:   10.0000
   chunk 18 optimal weight:   10.0000
   chunk 89 optimal weight:    0.8980
   chunk 105 optimal weight:    9.9990
   chunk 65 optimal weight:    1.9990
   chunk 98 optimal weight:    5.9990
   chunk 72 optimal weight:    0.8980
   chunk 96 optimal weight:    0.8980
   chunk 30 optimal weight:    0.7980
   overall best weight:    1.0982

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
B  75 HIS
C  73 ASN
D  84 ASN
** F  75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** H  84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3629 r_free = 0.3629 target = 0.079931 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 64)----------------|
| r_work = 0.3353 r_free = 0.3353 target = 0.067052 restraints weight = 34508.572|
|-----------------------------------------------------------------------------|
r_work (start): 0.3339 rms_B_bonded: 1.52
r_work: 0.3197 rms_B_bonded: 2.22 restraints_weight: 0.5000
r_work: 0.3079 rms_B_bonded: 3.57 restraints_weight: 0.2500
r_work (final): 0.3079
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8691
moved from start:          0.1576

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032  13714  Z= 0.149
  Angle     :  0.611   7.762  19763  Z= 0.355
  Chirality :  0.046   0.254   2237
  Planarity :  0.004   0.038   1504
  Dihedral  : 30.459 174.240   4160
  Min Nonbonded Distance : 2.524

Molprobity Statistics.
  All-atom Clashscore : 5.39
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.12 %
    Favored  : 96.88 %
  Rotamer:
    Outliers :  2.34 %
    Allowed  : 12.12 %
    Favored  : 85.54 %
  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:  1.05 (0.29), residues: 866
  helix:  1.79 (0.23), residues: 531
  sheet: -0.81 (0.74), residues: 47
  loop : -1.12 (0.34), residues: 288

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG K  72 
 TYR   0.022   0.001   TYR K 105 
 PHE   0.008   0.001   PHE H  65 
 TRP   0.002   0.000   TRP K 114 
 HIS   0.004   0.001   HIS F  75 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00265 /  0.15 (13713)
  covalent geometry    : angle       0.61088 /  0.35 (19761)
  SS BOND              : bond        0.00334 /  0.13 (    1)
  SS BOND              : angle       1.53545 /  3.06 (    2)
  hydrogen bonds       : bond        0.04743 /  5.13 (  747)
  hydrogen bonds       : angle       2.93681 /  3.66 ( 1853)

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

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

  1732 Ramachandran restraints generated.
    866 Oldfield, 0 Emsley, 866 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1732 Ramachandran restraints generated.
    866 Oldfield, 0 Emsley, 866 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  193 residues out of total 730 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 176
  time to evaluate  : 0.350 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   79 LYS cc_start: 0.8450 (tttm) cc_final: 0.8117 (tttm)
REVERT: H   35 GLU cc_start: 0.7735 (mm-30) cc_final: 0.7396 (mm-30)
REVERT: K   36 TRP cc_start: 0.7876 (m100) cc_final: 0.7554 (m-10)
REVERT: K   38 ARG cc_start: 0.7864 (ptm160) cc_final: 0.7491 (ptm160)
REVERT: K   59 TYR cc_start: 0.7687 (m-10) cc_final: 0.7388 (m-10)
REVERT: K   81 LEU cc_start: 0.8702 (tp) cc_final: 0.7661 (tp)
REVERT: K   95 TYR cc_start: 0.7933 (m-10) cc_final: 0.7492 (m-10)
  outliers start: 17
  outliers final: 13
  residues processed: 184
  average time/residue: 0.1565
  time to fit residues: 38.3221
Evaluate side-chains
  183 residues out of total 730 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 170
  time to evaluate  : 0.343 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   94 GLU
Chi-restraints excluded: chain B residue   43 VAL
Chi-restraints excluded: chain C residue   16 THR
Chi-restraints excluded: chain C residue  118 LYS
Chi-restraints excluded: chain D residue   39 VAL
Chi-restraints excluded: chain D residue   71 GLU
Chi-restraints excluded: chain D residue  106 LEU
Chi-restraints excluded: chain D residue  112 SER
Chi-restraints excluded: chain D residue  123 SER
Chi-restraints excluded: chain F residue   25 ASN
Chi-restraints excluded: chain F residue   49 LEU
Chi-restraints excluded: chain F residue   63 GLU
Chi-restraints excluded: chain G residue   16 THR
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 111
   random chunks:
   chunk 41 optimal weight:    2.9990
   chunk 15 optimal weight:   10.0000
   chunk 19 optimal weight:   10.0000
   chunk 33 optimal weight:    1.9990
   chunk 53 optimal weight:    4.9990
   chunk 40 optimal weight:    0.7980
   chunk 16 optimal weight:    9.9990
   chunk 58 optimal weight:    2.9990
   chunk 30 optimal weight:    5.9990
   chunk 62 optimal weight:    3.9990
   chunk 6 optimal weight:   10.0000
   overall best weight:    2.5588

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
B  75 HIS
C  73 ASN
D  47 GLN
D  84 ASN
E 125 GLN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3586 r_free = 0.3586 target = 0.078019 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 59)----------------|
| r_work = 0.3302 r_free = 0.3302 target = 0.064999 restraints weight = 34266.561|
|-----------------------------------------------------------------------------|
r_work (start): 0.3288 rms_B_bonded: 1.48
r_work: 0.3144 rms_B_bonded: 2.18 restraints_weight: 0.5000
r_work: 0.3025 rms_B_bonded: 3.48 restraints_weight: 0.2500
r_work (final): 0.3025
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8744
moved from start:          0.1842

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.039  13714  Z= 0.240
  Angle     :  0.675   7.597  19763  Z= 0.382
  Chirality :  0.049   0.270   2237
  Planarity :  0.004   0.040   1504
  Dihedral  : 30.599 175.967   4160
  Min Nonbonded Distance : 2.341

Molprobity Statistics.
  All-atom Clashscore : 4.66
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.35 %
    Favored  : 96.65 %
  Rotamer:
    Outliers :  2.07 %
    Allowed  : 13.50 %
    Favored  : 84.44 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z 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:  0.94 (0.29), residues: 866
  helix:  1.72 (0.23), residues: 531
  sheet: -0.50 (0.79), residues: 47
  loop : -1.28 (0.34), residues: 288

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG K  72 
 TYR   0.016   0.001   TYR K 105 
 PHE   0.013   0.002   PHE D  65 
 TRP   0.003   0.001   TRP K  36 
 HIS   0.007   0.001   HIS F  75 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00486 /  0.24 (13713)
  covalent geometry    : angle       0.67449 /  0.38 (19761)
  SS BOND              : bond        0.00031 /  0.01 (    1)
  SS BOND              : angle       2.18868 /  4.37 (    2)
  hydrogen bonds       : bond        0.06316 /  6.85 (  747)
  hydrogen bonds       : angle       3.02327 /  3.80 ( 1853)

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

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

  1732 Ramachandran restraints generated.
    866 Oldfield, 0 Emsley, 866 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1732 Ramachandran restraints generated.
    866 Oldfield, 0 Emsley, 866 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  191 residues out of total 730 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 176
  time to evaluate  : 0.342 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: K   34 MET cc_start: 0.7516 (mpp) cc_final: 0.7154 (mpp)
REVERT: K   36 TRP cc_start: 0.7900 (m100) cc_final: 0.7587 (m-10)
REVERT: K   59 TYR cc_start: 0.7852 (m-10) cc_final: 0.7262 (m-10)
REVERT: K   81 LEU cc_start: 0.8739 (tp) cc_final: 0.7969 (tp)
REVERT: K   95 TYR cc_start: 0.8002 (m-10) cc_final: 0.7493 (m-10)
  outliers start: 15
  outliers final: 15
  residues processed: 183
  average time/residue: 0.1399
  time to fit residues: 33.7934
Evaluate side-chains
  187 residues out of total 730 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 172
  time to evaluate  : 0.344 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   94 GLU
Chi-restraints excluded: chain B residue   43 VAL
Chi-restraints excluded: chain C residue   16 THR
Chi-restraints excluded: chain C residue  118 LYS
Chi-restraints excluded: chain D residue   39 VAL
Chi-restraints excluded: chain D residue   71 GLU
Chi-restraints excluded: chain D residue  106 LEU
Chi-restraints excluded: chain D residue  112 SER
Chi-restraints excluded: chain D residue  123 SER
Chi-restraints excluded: chain F residue   49 LEU
Chi-restraints excluded: chain F residue   63 GLU
Chi-restraints excluded: chain G residue   16 THR
Chi-restraints excluded: chain H residue   98 VAL
Chi-restraints excluded: chain H residue  115 THR
Chi-restraints excluded: chain K residue   80 TYR
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 111
   random chunks:
   chunk 76 optimal weight:    0.6980
   chunk 106 optimal weight:    0.8980
   chunk 19 optimal weight:    9.9990
   chunk 51 optimal weight:    0.9980
   chunk 69 optimal weight:    4.9990
   chunk 108 optimal weight:    7.9990
   chunk 72 optimal weight:    1.9990
   chunk 50 optimal weight:    0.9980
   chunk 91 optimal weight:    0.9980
   chunk 27 optimal weight:   10.0000
   chunk 104 optimal weight:    4.9990
   overall best weight:    0.9180

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
D  47 GLN
E 125 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3611 r_free = 0.3611 target = 0.079164 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 54)----------------|
| r_work = 0.3334 r_free = 0.3334 target = 0.066228 restraints weight = 34173.511|
|-----------------------------------------------------------------------------|
r_work (start): 0.3318 rms_B_bonded: 1.46
r_work: 0.3175 rms_B_bonded: 2.19 restraints_weight: 0.5000
r_work: 0.3057 rms_B_bonded: 3.54 restraints_weight: 0.2500
r_work (final): 0.3057
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8712
moved from start:          0.1840

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036  13714  Z= 0.145
  Angle     :  0.638   8.841  19763  Z= 0.364
  Chirality :  0.047   0.243   2237
  Planarity :  0.004   0.047   1504
  Dihedral  : 30.613 175.187   4160
  Min Nonbonded Distance : 2.528

Molprobity Statistics.
  All-atom Clashscore : 5.26
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.12 %
    Favored  : 96.88 %
  Rotamer:
    Outliers :  1.79 %
    Allowed  : 14.88 %
    Favored  : 83.33 %
  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:  1.21 (0.29), residues: 866
  helix:  1.93 (0.23), residues: 531
  sheet: -0.54 (0.76), residues: 47
  loop : -1.13 (0.34), residues: 288

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.014   0.000   ARG K  72 
 TYR   0.019   0.001   TYR C  57 
 PHE   0.014   0.001   PHE K  68 
 TRP   0.002   0.001   TRP K  36 
 HIS   0.005   0.001   HIS F  75 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00259 /  0.15 (13713)
  covalent geometry    : angle       0.63748 /  0.36 (19761)
  SS BOND              : bond        0.00850 /  0.34 (    1)
  SS BOND              : angle       1.69123 /  3.38 (    2)
  hydrogen bonds       : bond        0.05059 /  5.44 (  747)
  hydrogen bonds       : angle       2.94513 /  3.66 ( 1853)

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

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

  1732 Ramachandran restraints generated.
    866 Oldfield, 0 Emsley, 866 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1732 Ramachandran restraints generated.
    866 Oldfield, 0 Emsley, 866 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  191 residues out of total 730 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 178
  time to evaluate  : 0.392 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: K   34 MET cc_start: 0.7855 (mpp) cc_final: 0.6773 (mpp)
REVERT: K   36 TRP cc_start: 0.7957 (m100) cc_final: 0.7596 (m-10)
REVERT: K   59 TYR cc_start: 0.7780 (m-10) cc_final: 0.7323 (m-10)
REVERT: K   81 LEU cc_start: 0.8727 (tp) cc_final: 0.7768 (tp)
REVERT: K   83 MET cc_start: 0.7558 (mpp) cc_final: 0.7001 (mpp)
REVERT: K   95 TYR cc_start: 0.7997 (m-10) cc_final: 0.7457 (m-10)
  outliers start: 13
  outliers final: 12
  residues processed: 184
  average time/residue: 0.1466
  time to fit residues: 35.7219
Evaluate side-chains
  185 residues out of total 730 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 173
  time to evaluate  : 0.252 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   94 GLU
Chi-restraints excluded: chain B residue   43 VAL
Chi-restraints excluded: chain C residue   16 THR
Chi-restraints excluded: chain C residue  118 LYS
Chi-restraints excluded: chain D residue   39 VAL
Chi-restraints excluded: chain D residue   71 GLU
Chi-restraints excluded: chain D residue  106 LEU
Chi-restraints excluded: chain D residue  112 SER
Chi-restraints excluded: chain F residue   49 LEU
Chi-restraints excluded: chain F residue   63 GLU
Chi-restraints excluded: chain G residue   16 THR
Chi-restraints excluded: chain K residue   80 TYR
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 111
   random chunks:
   chunk 79 optimal weight:    2.9990
   chunk 12 optimal weight:   10.0000
   chunk 66 optimal weight:    0.7980
   chunk 95 optimal weight:    6.9990
   chunk 53 optimal weight:    4.9990
   chunk 45 optimal weight:    0.9980
   chunk 18 optimal weight:    9.9990
   chunk 78 optimal weight:    0.5980
   chunk 35 optimal weight:    2.9990
   chunk 30 optimal weight:    0.6980
   chunk 15 optimal weight:    9.9990
   overall best weight:    1.2182

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
D  47 GLN
H  84 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3616 r_free = 0.3616 target = 0.079390 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 65)----------------|
| r_work = 0.3339 r_free = 0.3339 target = 0.066484 restraints weight = 34173.869|
|-----------------------------------------------------------------------------|
r_work (start): 0.3324 rms_B_bonded: 1.52
r_work: 0.3183 rms_B_bonded: 2.20 restraints_weight: 0.5000
r_work: 0.3067 rms_B_bonded: 3.51 restraints_weight: 0.2500
r_work (final): 0.3067
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8704
moved from start:          0.1864

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028  13714  Z= 0.152
  Angle     :  0.628   6.977  19763  Z= 0.359
  Chirality :  0.046   0.254   2237
  Planarity :  0.004   0.037   1504
  Dihedral  : 30.605 174.187   4160
  Min Nonbonded Distance : 2.493

Molprobity Statistics.
  All-atom Clashscore : 5.30
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.00 %
    Favored  : 97.00 %
  Rotamer:
    Outliers :  2.07 %
    Allowed  : 14.74 %
    Favored  : 83.20 %
  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:  1.34 (0.29), residues: 866
  helix:  2.00 (0.23), residues: 531
  sheet: -0.36 (0.77), residues: 47
  loop : -1.05 (0.35), residues: 288

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG D  79 
 TYR   0.016   0.001   TYR C  57 
 PHE   0.015   0.001   PHE K  68 
 TRP   0.004   0.001   TRP K  36 
 HIS   0.005   0.001   HIS F  75 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00276 /  0.15 (13713)
  covalent geometry    : angle       0.62771 /  0.36 (19761)
  SS BOND              : bond        0.00390 /  0.16 (    1)
  SS BOND              : angle       2.12625 /  4.25 (    2)
  hydrogen bonds       : bond        0.04866 /  5.24 (  747)
  hydrogen bonds       : angle       2.87803 /  3.59 ( 1853)

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

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

  1732 Ramachandran restraints generated.
    866 Oldfield, 0 Emsley, 866 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1732 Ramachandran restraints generated.
    866 Oldfield, 0 Emsley, 866 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  190 residues out of total 730 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 175
  time to evaluate  : 0.347 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: K   34 MET cc_start: 0.7235 (mpp) cc_final: 0.6932 (mpp)
REVERT: K   36 TRP cc_start: 0.7905 (m100) cc_final: 0.7617 (m-10)
REVERT: K   38 ARG cc_start: 0.7782 (ptm160) cc_final: 0.7566 (ptm160)
REVERT: K   59 TYR cc_start: 0.7850 (m-10) cc_final: 0.7309 (m-10)
REVERT: K   72 ARG cc_start: 0.7483 (ptm160) cc_final: 0.6163 (ttm-80)
REVERT: K   81 LEU cc_start: 0.8718 (tp) cc_final: 0.7919 (tp)
REVERT: K   83 MET cc_start: 0.7830 (mpp) cc_final: 0.7249 (mpp)
REVERT: K   95 TYR cc_start: 0.8070 (m-10) cc_final: 0.7530 (m-10)
  outliers start: 15
  outliers final: 13
  residues processed: 182
  average time/residue: 0.1378
  time to fit residues: 33.6599
Evaluate side-chains
  184 residues out of total 730 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 171
  time to evaluate  : 0.266 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   94 GLU
Chi-restraints excluded: chain B residue   43 VAL
Chi-restraints excluded: chain C residue   16 THR
Chi-restraints excluded: chain C residue  118 LYS
Chi-restraints excluded: chain D residue   39 VAL
Chi-restraints excluded: chain D residue   71 GLU
Chi-restraints excluded: chain D residue  106 LEU
Chi-restraints excluded: chain D residue  112 SER
Chi-restraints excluded: chain D residue  123 SER
Chi-restraints excluded: chain F residue   49 LEU
Chi-restraints excluded: chain F residue   63 GLU
Chi-restraints excluded: chain G residue   16 THR
Chi-restraints excluded: chain K residue   80 TYR
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 111
   random chunks:
   chunk 79 optimal weight:    0.6980
   chunk 22 optimal weight:   10.0000
   chunk 6 optimal weight:    9.9990
   chunk 52 optimal weight:    0.8980
   chunk 96 optimal weight:    0.7980
   chunk 29 optimal weight:    0.8980
   chunk 23 optimal weight:   10.0000
   chunk 2 optimal weight:   10.0000
   chunk 9 optimal weight:   10.0000
   chunk 4 optimal weight:    9.9990
   chunk 71 optimal weight:    4.9990
   overall best weight:    1.6582

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
D  47 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3607 r_free = 0.3607 target = 0.078993 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 61)----------------|
| r_work = 0.3327 r_free = 0.3327 target = 0.066003 restraints weight = 34053.943|
|-----------------------------------------------------------------------------|
r_work (start): 0.3314 rms_B_bonded: 1.55
r_work: 0.3171 rms_B_bonded: 2.22 restraints_weight: 0.5000
r_work: 0.3054 rms_B_bonded: 3.54 restraints_weight: 0.2500
r_work (final): 0.3054
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8716
moved from start:          0.1925

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028  13714  Z= 0.178
  Angle     :  0.637   7.213  19763  Z= 0.363
  Chirality :  0.047   0.262   2237
  Planarity :  0.004   0.037   1504
  Dihedral  : 30.615 173.924   4160
  Min Nonbonded Distance : 2.501

Molprobity Statistics.
  All-atom Clashscore : 5.22
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.23 %
    Favored  : 96.77 %
  Rotamer:
    Outliers :  1.93 %
    Allowed  : 15.01 %
    Favored  : 83.06 %
  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:  1.31 (0.29), residues: 866
  helix:  1.96 (0.23), residues: 532
  sheet: -0.26 (0.78), residues: 47
  loop : -1.05 (0.35), residues: 287

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG D  79 
 TYR   0.016   0.001   TYR C  57 
 PHE   0.017   0.002   PHE K  68 
 TRP   0.002   0.001   TRP K 114 
 HIS   0.005   0.001   HIS F  75 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00346 /  0.18 (13713)
  covalent geometry    : angle       0.63700 /  0.36 (19761)
  SS BOND              : bond        0.00404 /  0.16 (    1)
  SS BOND              : angle       2.03985 /  4.08 (    2)
  hydrogen bonds       : bond        0.05192 /  5.60 (  747)
  hydrogen bonds       : angle       2.89026 /  3.62 ( 1853)

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

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

  1732 Ramachandran restraints generated.
    866 Oldfield, 0 Emsley, 866 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1732 Ramachandran restraints generated.
    866 Oldfield, 0 Emsley, 866 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  189 residues out of total 730 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 175
  time to evaluate  : 0.208 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: E  100 LEU cc_start: 0.9183 (OUTLIER) cc_final: 0.8926 (mt)
REVERT: K   36 TRP cc_start: 0.7936 (m100) cc_final: 0.7630 (m-10)
REVERT: K   59 TYR cc_start: 0.7768 (m-10) cc_final: 0.7312 (m-10)
REVERT: K   72 ARG cc_start: 0.7345 (ptm160) cc_final: 0.5871 (ttp80)
REVERT: K   81 LEU cc_start: 0.8735 (tp) cc_final: 0.7999 (tp)
REVERT: K   83 MET cc_start: 0.7926 (mpp) cc_final: 0.7392 (mpp)
REVERT: K   95 TYR cc_start: 0.8113 (m-10) cc_final: 0.7581 (m-10)
  outliers start: 14
  outliers final: 13
  residues processed: 182
  average time/residue: 0.1300
  time to fit residues: 31.4589
Evaluate side-chains
  185 residues out of total 730 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 171
  time to evaluate  : 0.319 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   94 GLU
Chi-restraints excluded: chain B residue   43 VAL
Chi-restraints excluded: chain C residue   16 THR
Chi-restraints excluded: chain C residue  118 LYS
Chi-restraints excluded: chain D residue   39 VAL
Chi-restraints excluded: chain D residue   71 GLU
Chi-restraints excluded: chain D residue  106 LEU
Chi-restraints excluded: chain D residue  112 SER
Chi-restraints excluded: chain D residue  123 SER
Chi-restraints excluded: chain E residue  100 LEU
Chi-restraints excluded: chain F residue   49 LEU
Chi-restraints excluded: chain F residue   63 GLU
Chi-restraints excluded: chain G residue   16 THR
Chi-restraints excluded: chain K residue   80 TYR
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 111
   random chunks:
   chunk 103 optimal weight:    8.9990
   chunk 70 optimal weight:    0.7980
   chunk 82 optimal weight:    0.7980
   chunk 5 optimal weight:   10.0000
   chunk 59 optimal weight:    0.6980
   chunk 50 optimal weight:    0.8980
   chunk 65 optimal weight:    2.9990
   chunk 26 optimal weight:   10.0000
   chunk 54 optimal weight:    0.9980
   chunk 87 optimal weight:    1.9990
   chunk 9 optimal weight:   10.0000
   overall best weight:    0.8380

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
C  73 ASN
D  47 GLN
E 125 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3621 r_free = 0.3621 target = 0.079627 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 61)----------------|
| r_work = 0.3343 r_free = 0.3343 target = 0.066681 restraints weight = 34152.825|
|-----------------------------------------------------------------------------|
r_work (start): 0.3330 rms_B_bonded: 1.52
r_work: 0.3188 rms_B_bonded: 2.22 restraints_weight: 0.5000
r_work: 0.3072 rms_B_bonded: 3.53 restraints_weight: 0.2500
r_work (final): 0.3072
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8697
moved from start:          0.1946

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039  13714  Z= 0.141
  Angle     :  0.635   8.530  19763  Z= 0.363
  Chirality :  0.046   0.247   2237
  Planarity :  0.004   0.090   1504
  Dihedral  : 30.604 173.985   4160
  Min Nonbonded Distance : 2.240

Molprobity Statistics.
  All-atom Clashscore : 5.90
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.00 %
    Favored  : 97.00 %
  Rotamer:
    Outliers :  2.07 %
    Allowed  : 15.56 %
    Favored  : 82.37 %
  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:  1.37 (0.29), residues: 866
  helix:  2.00 (0.23), residues: 532
  sheet: -0.31 (0.78), residues: 47
  loop : -0.98 (0.35), residues: 287

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.000   ARG K  72 
 TYR   0.018   0.001   TYR C  57 
 PHE   0.018   0.001   PHE K  68 
 TRP   0.002   0.001   TRP K 114 
 HIS   0.006   0.001   HIS F  75 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00255 /  0.14 (13713)
  covalent geometry    : angle       0.63428 /  0.36 (19761)
  SS BOND              : bond        0.00514 /  0.21 (    1)
  SS BOND              : angle       1.90477 /  3.80 (    2)
  hydrogen bonds       : bond        0.04724 /  5.08 (  747)
  hydrogen bonds       : angle       2.85994 /  3.57 ( 1853)

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

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

  1732 Ramachandran restraints generated.
    866 Oldfield, 0 Emsley, 866 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1732 Ramachandran restraints generated.
    866 Oldfield, 0 Emsley, 866 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  194 residues out of total 730 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 179
  time to evaluate  : 0.354 
Fit side-chains
   revert: symmetry clash
REVERT: E  100 LEU cc_start: 0.9177 (OUTLIER) cc_final: 0.8920 (mt)
REVERT: G   64 GLU cc_start: 0.8569 (tt0) cc_final: 0.8332 (tt0)
REVERT: K   36 TRP cc_start: 0.7936 (m100) cc_final: 0.7638 (m-10)
REVERT: K   59 TYR cc_start: 0.7755 (m-10) cc_final: 0.7304 (m-10)
REVERT: K   81 LEU cc_start: 0.8738 (tp) cc_final: 0.8012 (tp)
REVERT: K   83 MET cc_start: 0.7774 (mpp) cc_final: 0.7422 (mpp)
REVERT: K   95 TYR cc_start: 0.8091 (m-10) cc_final: 0.7561 (m-10)
  outliers start: 15
  outliers final: 12
  residues processed: 186
  average time/residue: 0.1505
  time to fit residues: 37.2027
Evaluate side-chains
  186 residues out of total 730 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 173
  time to evaluate  : 0.267 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   43 VAL
Chi-restraints excluded: chain C residue   16 THR
Chi-restraints excluded: chain C residue  118 LYS
Chi-restraints excluded: chain D residue   39 VAL
Chi-restraints excluded: chain D residue   71 GLU
Chi-restraints excluded: chain D residue  106 LEU
Chi-restraints excluded: chain D residue  112 SER
Chi-restraints excluded: chain D residue  123 SER
Chi-restraints excluded: chain E residue  100 LEU
Chi-restraints excluded: chain F residue   49 LEU
Chi-restraints excluded: chain F residue   63 GLU
Chi-restraints excluded: chain G residue   16 THR
Chi-restraints excluded: chain K residue   80 TYR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 111
   random chunks:
   chunk 108 optimal weight:    3.9990
   chunk 45 optimal weight:    0.9990
   chunk 64 optimal weight:    0.9980
   chunk 53 optimal weight:    3.9990
   chunk 51 optimal weight:    0.6980
   chunk 50 optimal weight:    0.5980
   chunk 104 optimal weight:    5.9990
   chunk 5 optimal weight:   10.0000
   chunk 36 optimal weight:    0.0980
   chunk 16 optimal weight:   10.0000
   chunk 3 optimal weight:   10.0000
   overall best weight:    0.6782

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
E 125 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3629 r_free = 0.3629 target = 0.079968 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 57)----------------|
| r_work = 0.3353 r_free = 0.3353 target = 0.067077 restraints weight = 34326.291|
|-----------------------------------------------------------------------------|
r_work (start): 0.3338 rms_B_bonded: 1.52
r_work: 0.3197 rms_B_bonded: 2.21 restraints_weight: 0.5000
r_work: 0.3079 rms_B_bonded: 3.56 restraints_weight: 0.2500
r_work (final): 0.3079
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8691
moved from start:          0.1960

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.043  13714  Z= 0.136
  Angle     :  0.628   9.348  19763  Z= 0.360
  Chirality :  0.045   0.247   2237
  Planarity :  0.004   0.076   1504
  Dihedral  : 30.592 173.438   4160
  Min Nonbonded Distance : 2.443

Molprobity Statistics.
  All-atom Clashscore : 6.29
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.12 %
    Favored  : 96.88 %
  Rotamer:
    Outliers :  1.79 %
    Allowed  : 15.84 %
    Favored  : 82.37 %
  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:  1.45 (0.29), residues: 866
  helix:  2.06 (0.23), residues: 532
  sheet: -0.31 (0.75), residues: 47
  loop : -0.93 (0.35), residues: 287

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.000   ARG K  54 
 TYR   0.016   0.001   TYR C  57 
 PHE   0.014   0.001   PHE K  68 
 TRP   0.002   0.001   TRP K 114 
 HIS   0.004   0.001   HIS F  75 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00241 /  0.14 (13713)
  covalent geometry    : angle       0.62722 /  0.36 (19761)
  SS BOND              : bond        0.00130 /  0.05 (    1)
  SS BOND              : angle       2.06631 /  4.13 (    2)
  hydrogen bonds       : bond        0.04517 /  4.86 (  747)
  hydrogen bonds       : angle       2.83086 /  3.53 ( 1853)

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

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

  1732 Ramachandran restraints generated.
    866 Oldfield, 0 Emsley, 866 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1732 Ramachandran restraints generated.
    866 Oldfield, 0 Emsley, 866 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  190 residues out of total 730 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 177
  time to evaluate  : 0.351 
Fit side-chains
   revert: symmetry clash
REVERT: E  100 LEU cc_start: 0.9168 (OUTLIER) cc_final: 0.8914 (mt)
REVERT: G   64 GLU cc_start: 0.8512 (tt0) cc_final: 0.8278 (tt0)
REVERT: K   36 TRP cc_start: 0.7933 (m100) cc_final: 0.7618 (m-10)
REVERT: K   59 TYR cc_start: 0.7769 (m-10) cc_final: 0.7313 (m-10)
REVERT: K   68 PHE cc_start: 0.7881 (m-80) cc_final: 0.7480 (m-10)
REVERT: K   81 LEU cc_start: 0.8711 (tp) cc_final: 0.7933 (tp)
REVERT: K   83 MET cc_start: 0.7968 (mpp) cc_final: 0.7354 (mpp)
REVERT: K   95 TYR cc_start: 0.8108 (m-10) cc_final: 0.7566 (m-10)
  outliers start: 13
  outliers final: 11
  residues processed: 183
  average time/residue: 0.1513
  time to fit residues: 36.5748
Evaluate side-chains
  187 residues out of total 730 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 175
  time to evaluate  : 0.343 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   43 VAL
Chi-restraints excluded: chain C residue   16 THR
Chi-restraints excluded: chain C residue  118 LYS
Chi-restraints excluded: chain D residue   39 VAL
Chi-restraints excluded: chain D residue   71 GLU
Chi-restraints excluded: chain D residue  112 SER
Chi-restraints excluded: chain D residue  123 SER
Chi-restraints excluded: chain E residue  100 LEU
Chi-restraints excluded: chain F residue   49 LEU
Chi-restraints excluded: chain F residue   63 GLU
Chi-restraints excluded: chain G residue   16 THR
Chi-restraints excluded: chain K residue   80 TYR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 111
   random chunks:
   chunk 101 optimal weight:    6.9990
   chunk 79 optimal weight:    3.9990
   chunk 32 optimal weight:    0.6980
   chunk 104 optimal weight:    8.9990
   chunk 38 optimal weight:    0.8980
   chunk 28 optimal weight:    1.9990
   chunk 97 optimal weight:    3.9990
   chunk 55 optimal weight:    2.9990
   chunk 86 optimal weight:    3.9990
   chunk 20 optimal weight:   10.0000
   chunk 7 optimal weight:    9.9990
   overall best weight:    2.1186

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

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3596 r_free = 0.3596 target = 0.078445 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 59)----------------|
| r_work = 0.3314 r_free = 0.3314 target = 0.065449 restraints weight = 34132.433|
|-----------------------------------------------------------------------------|
r_work (start): 0.3298 rms_B_bonded: 1.47
r_work: 0.3154 rms_B_bonded: 2.19 restraints_weight: 0.5000
r_work: 0.3036 rms_B_bonded: 3.50 restraints_weight: 0.2500
r_work (final): 0.3036
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8729
moved from start:          0.2056

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.033  13714  Z= 0.209
  Angle     :  0.668   8.829  19763  Z= 0.377
  Chirality :  0.048   0.266   2237
  Planarity :  0.004   0.040   1504
  Dihedral  : 30.640 174.291   4160
  Min Nonbonded Distance : 2.476

Molprobity Statistics.
  All-atom Clashscore : 5.09
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.35 %
    Favored  : 96.65 %
  Rotamer:
    Outliers :  1.93 %
    Allowed  : 15.56 %
    Favored  : 82.51 %
  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 (0.29), residues: 866
  helix:  1.92 (0.23), residues: 532
  sheet: -0.08 (0.73), residues: 54
  loop : -1.09 (0.35), residues: 280

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG D  79 
 TYR   0.020   0.001   TYR C  57 
 PHE   0.011   0.002   PHE H  65 
 TRP   0.002   0.001   TRP K 114 
 HIS   0.007   0.001   HIS F  75 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00425 /  0.21 (13713)
  covalent geometry    : angle       0.66798 /  0.38 (19761)
  SS BOND              : bond        0.00443 /  0.18 (    1)
  SS BOND              : angle       2.15396 /  4.30 (    2)
  hydrogen bonds       : bond        0.05739 /  6.23 (  747)
  hydrogen bonds       : angle       2.88916 /  3.63 ( 1853)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3180.80 seconds
wall clock time: 54 minutes 59.33 seconds (3299.33 seconds total)