Starting phenix.real_space_refine
on Fri Jul  3 05:11:40 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8vmn_43360/07_2026/8vmn_43360.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8vmn_43360/07_2026/8vmn_43360.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.5
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/8vmn_43360/07_2026/8vmn_43360.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8vmn_43360/07_2026/8vmn_43360.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/8vmn_43360/07_2026/8vmn_43360.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8vmn_43360/07_2026/8vmn_43360.map"
  }
  resolution = 3.5
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.034
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     314      5.49       5
     S      14      5.16       5
     C    6889      2.51       5
     N    2355      2.21       5
     O    2968      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-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib"
  Total number of atoms: 12540
  Number of models: 1
  Model: ""
    Number of chains: 10
    Chain: "H"
      Number of atoms: 3237
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 157, 3237
          Classifications: {'DNA': 157}
          Link IDs: {'rna3p': 156}
    Chain: "I"
      Number of atoms: 825
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 100, 825
          Classifications: {'peptide': 100}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 4, 'TRANS': 95}
    Chain: "J"
      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: "K"
      Number of atoms: 825
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 108, 825
          Classifications: {'peptide': 108}
          Incomplete info: {'truncation_to_alanine': 1}
          Link IDs: {'PTRANS': 5, 'TRANS': 102}
          Unresolved non-hydrogen bonds: 4
          Unresolved non-hydrogen angles: 4
          Unresolved non-hydrogen dihedrals: 4
    Chain: "M"
      Number of atoms: 736
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 95, 736
          Classifications: {'peptide': 95}
          Incomplete info: {'truncation_to_alanine': 2}
          Link IDs: {'PTRANS': 2, 'TRANS': 92}
          Unresolved non-hydrogen bonds: 8
          Unresolved non-hydrogen angles: 8
          Unresolved non-hydrogen dihedrals: 8
    Chain: "O"
      Number of atoms: 816
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 99, 816
          Classifications: {'peptide': 99}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 4, 'TRANS': 94}
    Chain: "Q"
      Number of atoms: 667
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 87, 667
          Classifications: {'peptide': 87}
          Modifications used: {'COO': 1}
          Incomplete info: {'truncation_to_alanine': 8}
          Link IDs: {'PTRANS': 1, 'TRANS': 85}
          Unresolved non-hydrogen bonds: 37
          Unresolved non-hydrogen angles: 44
          Unresolved non-hydrogen dihedrals: 32
          Unresolved non-hydrogen chiralities: 2
          Planarities with less than four sites: {'ARG:plan': 3, 'HIS:plan': 1}
          Unresolved non-hydrogen planarities: 20
    Chain: "R"
      Number of atoms: 829
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 108, 829
          Classifications: {'peptide': 108}
          Link IDs: {'PTRANS': 5, 'TRANS': 102}
    Chain: "S"
      Number of atoms: 741
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 96, 741
          Classifications: {'peptide': 96}
          Incomplete info: {'truncation_to_alanine': 3}
          Link IDs: {'PTRANS': 2, 'TRANS': 93}
          Unresolved non-hydrogen bonds: 14
          Unresolved non-hydrogen angles: 15
          Unresolved non-hydrogen dihedrals: 13
          Planarities with less than four sites: {'ARG:plan': 1}
          Unresolved non-hydrogen planarities: 5
    Chain: "D"
      Number of atoms: 3202
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 157, 3202
          Classifications: {'DNA': 157}
          Link IDs: {'rna3p': 156}
  Time building chain proxies: 3.02, per 1000 atoms: 0.24
  Number of scatterers: 12540
  At special positions: 0
  Unit cell: (106.64, 141.04, 122.12, 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      14     16.00
     P     314     15.00
     O    2968      8.00
     N    2355      7.00
     C    6889      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 1.05
  Conformation dependent library (CDL) restraints added in 288.2 milliseconds
  

  1520 Ramachandran restraints generated.
    760 Oldfield, 0 Emsley, 760 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1452

  Finding SS restraints...
    Secondary structure from input PDB file:
      34 helices and 7 sheets defined
      69.2% alpha, 1.8% beta
      156 base pairs and 255 stacking pairs defined.
    Time for finding SS restraints: 1.41
  Creating SS restraints...
    Processing helix  chain 'I' and resid 45 through 55
    Processing helix  chain 'I' and resid 63 through 75
      removed outlier: 3.547A  pdb=" N   PHE I  67 " --> pdb=" O   ARG I  63 " (cutoff:3.500A)
    Processing helix  chain 'I' and resid 85 through 114
      removed outlier: 3.676A  pdb=" N   VAL I  89 " --> pdb=" O   GLN I  85 " (cutoff:3.500A)
      removed outlier: 3.646A  pdb=" N   MET I  90 " --> pdb=" O   SER I  86 " (cutoff:3.500A)
    Processing helix  chain 'I' and resid 120 through 131
      removed outlier: 3.535A  pdb=" N   ILE I 124 " --> pdb=" O   MET I 120 " (cutoff:3.500A)
    Processing helix  chain 'J' and resid 24 through 29
      removed outlier: 3.526A  pdb=" N   ILE J  29 " --> pdb=" O   ILE J  26 " (cutoff:3.500A)
    Processing helix  chain 'J' and resid 30 through 42
    Processing helix  chain 'J' and resid 49 through 76
      removed outlier: 3.915A  pdb=" N   GLU J  53 " --> pdb=" O   LEU J  49 " (cutoff:3.500A)
      removed outlier: 3.800A  pdb=" N   ARG J  55 " --> pdb=" O   TYR J  51 " (cutoff:3.500A)
      removed outlier: 3.602A  pdb=" N   VAL J  65 " --> pdb=" O   PHE J  61 " (cutoff:3.500A)
      removed outlier: 4.619A  pdb=" N   ASP J  68 " --> pdb=" O   ASN J  64 " (cutoff:3.500A)
      removed outlier: 3.504A  pdb=" N   ALA J  76 " --> pdb=" O   TYR J  72 " (cutoff:3.500A)
    Processing helix  chain 'J' and resid 82 through 94
    Processing helix  chain 'K' and resid 16 through 22
    Processing helix  chain 'K' and resid 26 through 37
    Processing helix  chain 'K' and resid 45 through 73
      removed outlier: 4.577A  pdb=" N   VAL K  49 " --> pdb=" O   ALA K  45 " (cutoff:3.500A)
    Processing helix  chain 'K' and resid 79 through 88
    Processing helix  chain 'K' and resid 90 through 97
      removed outlier: 3.587A  pdb=" N   LEU K  96 " --> pdb=" O   GLU K  92 " (cutoff:3.500A)
    Processing helix  chain 'M' and resid 34 through 46
    Processing helix  chain 'M' and resid 53 through 81
      removed outlier: 3.869A  pdb=" N   MET M  59 " --> pdb=" O   ALA M  55 " (cutoff:3.500A)
      removed outlier: 3.562A  pdb=" N   GLU M  68 " --> pdb=" O   ASN M  64 " (cutoff:3.500A)
      removed outlier: 3.941A  pdb=" N   GLU M  73 " --> pdb=" O   ARG M  69 " (cutoff:3.500A)
      removed outlier: 3.710A  pdb=" N   ASN M  81 " --> pdb=" O   LEU M  77 " (cutoff:3.500A)
    Processing helix  chain 'M' and resid 87 through 99
      removed outlier: 3.624A  pdb=" N   ILE M  91 " --> pdb=" O   THR M  87 " (cutoff:3.500A)
    Processing helix  chain 'M' and resid 101 through 121
      removed outlier: 4.461A  pdb=" N   SER M 109 " --> pdb=" O   LYS M 105 " (cutoff:3.500A)
      removed outlier: 3.569A  pdb=" N   GLU M 110 " --> pdb=" O   HIS M 106 " (cutoff:3.500A)
      removed outlier: 4.272A  pdb=" N   TYR M 118 " --> pdb=" O   ALA M 114 " (cutoff:3.500A)
      removed outlier: 3.599A  pdb=" N   SER M 120 " --> pdb=" O   THR M 116 " (cutoff:3.500A)
    Processing helix  chain 'O' and resid 44 through 55
      removed outlier: 3.565A  pdb=" N   LEU O  48 " --> pdb=" O   GLY O  44 " (cutoff:3.500A)
    Processing helix  chain 'O' and resid 63 through 76
      removed outlier: 3.622A  pdb=" N   PHE O  67 " --> pdb=" O   ARG O  63 " (cutoff:3.500A)
      removed outlier: 3.659A  pdb=" N   GLN O  76 " --> pdb=" O   ARG O  72 " (cutoff:3.500A)
    Processing helix  chain 'O' and resid 85 through 114
    Processing helix  chain 'O' and resid 120 through 131
      removed outlier: 3.633A  pdb=" N   ILE O 124 " --> pdb=" O   MET O 120 " (cutoff:3.500A)
    Processing helix  chain 'Q' and resid 25 through 29
    Processing helix  chain 'Q' and resid 30 through 42
    Processing helix  chain 'Q' and resid 49 through 77
      removed outlier: 4.254A  pdb=" N   GLU Q  53 " --> pdb=" O   LEU Q  49 " (cutoff:3.500A)
      removed outlier: 3.970A  pdb=" N   ARG Q  55 " --> pdb=" O   TYR Q  51 " (cutoff:3.500A)
      removed outlier: 3.797A  pdb=" N   ASP Q  68 " --> pdb=" O   ASN Q  64 " (cutoff:3.500A)
      removed outlier: 3.559A  pdb=" N   THR Q  73 " --> pdb=" O   ALA Q  69 " (cutoff:3.500A)
    Processing helix  chain 'Q' and resid 82 through 93
      removed outlier: 3.830A  pdb=" N   VAL Q  86 " --> pdb=" O   THR Q  82 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 16 through 22
    Processing helix  chain 'R' and resid 26 through 37
    Processing helix  chain 'R' and resid 45 through 73
      removed outlier: 4.413A  pdb=" N   VAL R  49 " --> pdb=" O   ALA R  45 " (cutoff:3.500A)
      removed outlier: 3.604A  pdb=" N   ALA R  69 " --> pdb=" O   LEU R  65 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 79 through 89
    Processing helix  chain 'R' and resid 90 through 97
    Processing helix  chain 'S' and resid 34 through 44
    Processing helix  chain 'S' and resid 52 through 81
    Processing helix  chain 'S' and resid 87 through 99
    Processing helix  chain 'S' and resid 101 through 121
    Processing sheet with id=AA1, first strand: chain 'I' and resid 83 through 84
      removed outlier: 7.836A  pdb=" N   ARG I  83 " --> pdb=" O   VAL J  81 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA1
    Processing sheet with id=AA2, first strand: chain 'I' and resid 118 through 119
      removed outlier: 3.810A  pdb=" N   ILE I 119 " --> pdb=" O   ARG J  45 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA2
    Processing sheet with id=AA3, first strand: chain 'J' and resid 97 through 98
      removed outlier: 3.618A  pdb=" N   TYR J  98 " --> pdb=" O   THR R 101 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA3
    Processing sheet with id=AA4, first strand: chain 'K' and resid 42 through 43
      removed outlier: 7.732A  pdb=" N   ARG K  42 " --> pdb=" O   ILE M  86 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA4
    Processing sheet with id=AA5, first strand: chain 'K' and resid 101 through 102
      removed outlier: 6.804A  pdb=" N   THR K 101 " --> pdb=" O   TYR Q  98 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA5
    Processing sheet with id=AA6, first strand: chain 'R' and resid 42 through 43
      removed outlier: 7.328A  pdb=" N   ARG R  42 " --> pdb=" O   ILE S  86 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA6
    Processing sheet with id=AA7, first strand: chain 'R' and resid 77 through 78

    372 hydrogen bonds defined for protein.
    1104 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      396 hydrogen bonds
      756 hydrogen bond angles
      0 basepair planarities
      156 basepair parallelities
      255 stacking parallelities
  Total time for adding SS restraints: 1.71

  Time building geometry restraints manager: 1.46 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: 2483
        1.33 -     1.45: 4422
        1.45 -     1.57: 5848
        1.57 -     1.69: 626
        1.69 -     1.81: 24
  Bond restraints: 13403
  Sorted by residual:
  bond pdb=" C3'  DC D 261 "
       pdb=" C2'  DC D 261 "
    ideal  model  delta    sigma   weight residual
    1.516  1.546 -0.030 8.00e-03 1.56e+04 1.44e+01
  bond pdb=" C3'  DT D 255 "
       pdb=" C2'  DT D 255 "
    ideal  model  delta    sigma   weight residual
    1.516  1.544 -0.028 8.00e-03 1.56e+04 1.25e+01
  bond pdb=" C3'  DC D 162 "
       pdb=" C2'  DC D 162 "
    ideal  model  delta    sigma   weight residual
    1.516  1.544 -0.028 8.00e-03 1.56e+04 1.20e+01
  bond pdb=" C3'  DT H  16 "
       pdb=" C2'  DT H  16 "
    ideal  model  delta    sigma   weight residual
    1.516  1.544 -0.028 8.00e-03 1.56e+04 1.19e+01
  bond pdb=" C3'  DT H  57 "
       pdb=" C2'  DT H  57 "
    ideal  model  delta    sigma   weight residual
    1.516  1.544 -0.028 8.00e-03 1.56e+04 1.18e+01
  ... (remaining 13398 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.08: 18665
        2.08 -     4.16: 760
        4.16 -     6.24: 29
        6.24 -     8.33: 3
        8.33 -    10.41: 2
  Bond angle restraints: 19459
  Sorted by residual:
  angle pdb=" O4'  DA H  18 "
        pdb=" C4'  DA H  18 "
        pdb=" C3'  DA H  18 "
      ideal   model   delta    sigma   weight residual
     106.00  102.97    3.03 6.00e-01 2.78e+00 2.54e+01
  angle pdb=" O4'  DG H  54 "
        pdb=" C1'  DG H  54 "
        pdb=" N9   DG H  54 "
      ideal   model   delta    sigma   weight residual
     108.00  111.51   -3.51 7.00e-01 2.04e+00 2.51e+01
  angle pdb=" O4'  DA H  35 "
        pdb=" C4'  DA H  35 "
        pdb=" C3'  DA H  35 "
      ideal   model   delta    sigma   weight residual
     106.00  103.13    2.87 6.00e-01 2.78e+00 2.29e+01
  angle pdb=" O4'  DC H  48 "
        pdb=" C4'  DC H  48 "
        pdb=" C3'  DC H  48 "
      ideal   model   delta    sigma   weight residual
     106.00  103.23    2.77 6.00e-01 2.78e+00 2.13e+01
  angle pdb=" O4'  DT H  95 "
        pdb=" C4'  DT H  95 "
        pdb=" C3'  DT H  95 "
      ideal   model   delta    sigma   weight residual
     106.00  103.23    2.77 6.00e-01 2.78e+00 2.13e+01
  ... (remaining 19454 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    35.96: 5750
       35.96 -    71.92: 1411
       71.92 -   107.87: 28
      107.87 -   143.83: 8
      143.83 -   179.79: 25
  Dihedral angle restraints: 7222
    sinusoidal: 4972
      harmonic: 2250
  Sorted by residual:
  dihedral pdb=" C4'  DT D 236 "
           pdb=" C3'  DT D 236 "
           pdb=" O3'  DT D 236 "
           pdb=" P    DA D 237 "
      ideal   model   delta sinusoidal    sigma   weight residual
     220.00   40.21  179.79     1      3.50e+01 8.16e-04 1.57e+01
  dihedral pdb=" C4'  DG D 167 "
           pdb=" C3'  DG D 167 "
           pdb=" O3'  DG D 167 "
           pdb=" P    DG D 168 "
      ideal   model   delta sinusoidal    sigma   weight residual
     220.00   41.08  178.92     1      3.50e+01 8.16e-04 1.57e+01
  dihedral pdb=" C4'  DT D 195 "
           pdb=" C3'  DT D 195 "
           pdb=" O3'  DT D 195 "
           pdb=" P    DC D 196 "
      ideal   model   delta sinusoidal    sigma   weight residual
    -140.00   38.06 -178.06     1      3.50e+01 8.16e-04 1.57e+01
  ... (remaining 7219 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.037: 1381
       0.037 -    0.075: 594
       0.075 -    0.112: 183
       0.112 -    0.149: 47
       0.149 -    0.187: 13
  Chirality restraints: 2218
  Sorted by residual:
  chirality pdb=" C3'  DC D 249 "
            pdb=" C4'  DC D 249 "
            pdb=" O3'  DC D 249 "
            pdb=" C2'  DC D 249 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.73   -2.54   -0.19 2.00e-01 2.50e+01 8.73e-01
  chirality pdb=" CA  MET O  90 "
            pdb=" N   MET O  90 "
            pdb=" C   MET O  90 "
            pdb=" CB  MET O  90 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.33    0.18 2.00e-01 2.50e+01 8.45e-01
  chirality pdb=" C3'  DT D 203 "
            pdb=" C4'  DT D 203 "
            pdb=" O3'  DT D 203 "
            pdb=" C2'  DT D 203 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.73   -2.55   -0.18 2.00e-01 2.50e+01 8.18e-01
  ... (remaining 2215 not shown)

  Planarity restraints: 1377
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C1'  DC D 250 "    0.001 2.00e-02 2.50e+03   2.16e-02 1.05e+01
        pdb=" N1   DC D 250 "   -0.009 2.00e-02 2.50e+03
        pdb=" C2   DC D 250 "    0.056 2.00e-02 2.50e+03
        pdb=" O2   DC D 250 "   -0.027 2.00e-02 2.50e+03
        pdb=" N3   DC D 250 "   -0.014 2.00e-02 2.50e+03
        pdb=" C4   DC D 250 "   -0.003 2.00e-02 2.50e+03
        pdb=" N4   DC D 250 "    0.004 2.00e-02 2.50e+03
        pdb=" C5   DC D 250 "   -0.009 2.00e-02 2.50e+03
        pdb=" C6   DC D 250 "    0.001 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   PHE R  25 "   -0.051 5.00e-02 4.00e+02   7.51e-02 9.03e+00
        pdb=" N   PRO R  26 "    0.130 5.00e-02 4.00e+02
        pdb=" CA  PRO R  26 "   -0.037 5.00e-02 4.00e+02
        pdb=" CD  PRO R  26 "   -0.042 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C1'  DC H 114 "   -0.001 2.00e-02 2.50e+03   1.77e-02 7.02e+00
        pdb=" N1   DC H 114 "   -0.009 2.00e-02 2.50e+03
        pdb=" C2   DC H 114 "    0.044 2.00e-02 2.50e+03
        pdb=" O2   DC H 114 "   -0.024 2.00e-02 2.50e+03
        pdb=" N3   DC H 114 "   -0.004 2.00e-02 2.50e+03
        pdb=" C4   DC H 114 "    0.008 2.00e-02 2.50e+03
        pdb=" N4   DC H 114 "   -0.010 2.00e-02 2.50e+03
        pdb=" C5   DC H 114 "   -0.002 2.00e-02 2.50e+03
        pdb=" C6   DC H 114 "   -0.003 2.00e-02 2.50e+03
  ... (remaining 1374 not shown)

  Histogram of nonbonded interaction distances:
        2.02 -     2.60: 129
        2.60 -     3.17: 9814
        3.17 -     3.75: 22719
        3.75 -     4.32: 28539
        4.32 -     4.90: 41403
  Nonbonded interactions: 102604
  Sorted by model distance:
  nonbonded pdb=" N2   DG H  93 "
            pdb=" O2   DC D 222 "
     model   vdw
     2.024 2.496
  nonbonded pdb=" OG  SER M 109 "
            pdb=" OE1 GLU M 110 "
     model   vdw
     2.038 3.040
  nonbonded pdb=" O2   DC H 154 "
            pdb=" N2   DG D 161 "
     model   vdw
     2.102 2.496
  nonbonded pdb=" O2   DC H 110 "
            pdb=" N2   DG D 205 "
     model   vdw
     2.113 2.496
  nonbonded pdb=" N2   DG H  94 "
            pdb=" O2   DC D 221 "
     model   vdw
     2.121 2.496
  ... (remaining 102599 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 'I' and resid 37 through 135)
  selection = chain 'O'
}
ncs_group {
  reference = (chain 'J' and ((resid 20 through 23 and (name N or name CA or name C or name O  \ 
or name CB )) or resid 24 through 102))
  selection = (chain 'Q' and resid 20 through 102)
}
ncs_group {
  reference = chain 'K'
  selection = (chain 'R' and ((resid 12 through 14 and (name N or name CA or name C or name O  \ 
or name CB )) or resid 15 through 119))
}
ncs_group {
  reference = chain 'M'
  selection = (chain 'S' and resid 28 through 122)
}

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 group one per residue
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:             9.010
  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:             0.020
  Extract box with map and model:          0.260
  Check model and map are aligned:         0.030
  Set scattering table:                    0.050
  Process input model:                     12.310
  Find NCS groups from input model:        0.110
  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:0.980
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   22.790
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7603
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   0.071  13403  Z= 0.530
  Angle     :  0.825  10.407  19459  Z= 0.706
  Chirality :  0.047   0.187   2218
  Planarity :  0.005   0.075   1377
  Dihedral  : 30.827 179.789   5770
  Min Nonbonded Distance : 2.024

Molprobity Statistics.
  All-atom Clashscore : 12.03
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.84 %
    Favored  : 98.16 %
  Rotamer:
    Outliers :  0.63 %
    Allowed  : 25.16 %
    Favored  : 74.21 %
  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:  0.74 (0.31), residues: 760
  helix:  1.49 (0.23), residues: 520
  sheet:  None (None), residues: 0
  loop : -1.82 (0.36), residues: 240

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG I 128 
 TYR   0.033   0.002   TYR M  80 
 PHE   0.015   0.001   PHE J 100 
 HIS   0.009   0.001   HIS R  31 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00584 /  0.53 (13403)
  covalent geometry    : angle       0.82515 /  0.71 (19459)
  hydrogen bonds       : bond        0.13450 / 15.08 (  768)
  hydrogen bonds       : angle       4.91494 /  6.57 ( 1860)

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

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

  1520 Ramachandran restraints generated.
    760 Oldfield, 0 Emsley, 760 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1520 Ramachandran restraints generated.
    760 Oldfield, 0 Emsley, 760 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  126 residues out of total 646 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 122
  time to evaluate  : 0.312 
Fit side-chains
   revert: symmetry clash
REVERT: J   82 THR cc_start: 0.8710 (m) cc_final: 0.8430 (p)
REVERT: M   39 TYR cc_start: 0.7613 (t80) cc_final: 0.7008 (t80)
REVERT: O   37 LYS cc_start: 0.8244 (tppt) cc_final: 0.7526 (mmmm)
  outliers start: 4
  outliers final: 2
  residues processed: 123
  average time/residue: 0.1259
  time to fit residues: 21.1675
Evaluate side-chains
  109 residues out of total 646 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 107
  time to evaluate  : 0.308 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain J residue   62 LEU
Chi-restraints excluded: chain R residue   74 LYS
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 103
   random chunks:
   chunk 49 optimal weight:    2.9990
   chunk 97 optimal weight:    9.9990
   chunk 53 optimal weight:    0.8980
   chunk 5 optimal weight:   10.0000
   chunk 33 optimal weight:    0.0770
   chunk 65 optimal weight:    1.9990
   chunk 62 optimal weight:    1.9990
   chunk 51 optimal weight:    4.9990
   chunk 100 optimal weight:   10.0000
   chunk 38 optimal weight:    4.9990
   chunk 61 optimal weight:    7.9990
   overall best weight:    1.5944

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
I  39 HIS
R  31 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4185 r_free = 0.4185 target = 0.125624 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3731 r_free = 0.3731 target = 0.097287 restraints weight = 32281.729|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3768 r_free = 0.3768 target = 0.099327 restraints weight = 17791.961|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 43)----------------|
| r_work = 0.3792 r_free = 0.3792 target = 0.100662 restraints weight = 12269.119|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 36)----------------|
| r_work = 0.3806 r_free = 0.3806 target = 0.101515 restraints weight = 9895.023|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3813 r_free = 0.3813 target = 0.101910 restraints weight = 8772.272|
|-----------------------------------------------------------------------------|
r_work (final): 0.3718
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7676
moved from start:          0.1204

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.036  13403  Z= 0.198
  Angle     :  0.735   8.344  19459  Z= 0.429
  Chirality :  0.054   0.327   2218
  Planarity :  0.005   0.051   1377
  Dihedral  : 34.051 179.631   4277
  Min Nonbonded Distance : 2.006

Molprobity Statistics.
  All-atom Clashscore : 10.92
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.76 %
    Favored  : 97.24 %
  Rotamer:
    Outliers :  3.80 %
    Allowed  : 18.67 %
    Favored  : 77.53 %
  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:  1.01 (0.31), residues: 760
  helix:  1.66 (0.23), residues: 526
  sheet:  None (None), residues: 0
  loop : -1.69 (0.37), residues: 234

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG Q  55 
 TYR   0.025   0.002   TYR M  80 
 PHE   0.012   0.002   PHE S  62 
 HIS   0.006   0.001   HIS R  31 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00363 /  0.20 (13403)
  covalent geometry    : angle       0.73468 /  0.43 (19459)
  hydrogen bonds       : bond        0.09124 /  9.98 (  768)
  hydrogen bonds       : angle       3.50063 /  4.57 ( 1860)

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

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

  1520 Ramachandran restraints generated.
    760 Oldfield, 0 Emsley, 760 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1520 Ramachandran restraints generated.
    760 Oldfield, 0 Emsley, 760 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  142 residues out of total 646 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 118
  time to evaluate  : 0.309 
Fit side-chains
   revert: symmetry clash
REVERT: R   64 GLU cc_start: 0.7850 (tm-30) cc_final: 0.7590 (tt0)
REVERT: S   77 LEU cc_start: 0.8298 (OUTLIER) cc_final: 0.7848 (mp)
  outliers start: 24
  outliers final: 15
  residues processed: 133
  average time/residue: 0.1184
  time to fit residues: 21.6440
Evaluate side-chains
  126 residues out of total 646 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 110
  time to evaluate  : 0.268 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain I residue   46 VAL
Chi-restraints excluded: chain I residue   60 LEU
Chi-restraints excluded: chain J residue   62 LEU
Chi-restraints excluded: chain J residue   86 VAL
Chi-restraints excluded: chain K residue   63 LEU
Chi-restraints excluded: chain M residue   51 ILE
Chi-restraints excluded: chain M residue   85 THR
Chi-restraints excluded: chain M residue  112 THR
Chi-restraints excluded: chain O residue   39 HIS
Chi-restraints excluded: chain Q residue   27 GLN
Chi-restraints excluded: chain Q residue   50 ILE
Chi-restraints excluded: chain R residue   16 THR
Chi-restraints excluded: chain R residue  101 THR
Chi-restraints excluded: chain S residue   53 SER
Chi-restraints excluded: chain S residue   77 LEU
Chi-restraints excluded: chain S residue   87 THR
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 103
   random chunks:
   chunk 51 optimal weight:    2.9990
   chunk 96 optimal weight:    9.9990
   chunk 11 optimal weight:   10.0000
   chunk 77 optimal weight:    0.0270
   chunk 83 optimal weight:    0.9980
   chunk 8 optimal weight:   10.0000
   chunk 65 optimal weight:    0.9980
   chunk 9 optimal weight:   20.0000
   chunk 79 optimal weight:    0.9980
   chunk 39 optimal weight:    1.9990
   chunk 4 optimal weight:    8.9990
   overall best weight:    1.0040

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
R  31 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4200 r_free = 0.4200 target = 0.126482 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3740 r_free = 0.3740 target = 0.097612 restraints weight = 32713.583|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 44)----------------|
| r_work = 0.3780 r_free = 0.3780 target = 0.099848 restraints weight = 16906.645|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3807 r_free = 0.3807 target = 0.101355 restraints weight = 11199.154|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 46)----------------|
| r_work = 0.3823 r_free = 0.3823 target = 0.102276 restraints weight = 8796.171|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 36)----------------|
| r_work = 0.3832 r_free = 0.3832 target = 0.102789 restraints weight = 7696.334|
|-----------------------------------------------------------------------------|
r_work (final): 0.3724
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7703
moved from start:          0.1611

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.044  13403  Z= 0.170
  Angle     :  0.671   8.303  19459  Z= 0.399
  Chirality :  0.051   0.327   2218
  Planarity :  0.004   0.045   1377
  Dihedral  : 33.987 179.692   4273
  Min Nonbonded Distance : 2.002

Molprobity Statistics.
  All-atom Clashscore : 10.07
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.97 %
    Favored  : 98.03 %
  Rotamer:
    Outliers :  2.85 %
    Allowed  : 20.57 %
    Favored  : 76.58 %
  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:  1.30 (0.31), residues: 760
  helix:  1.89 (0.23), residues: 531
  sheet:  None (None), residues: 0
  loop : -1.67 (0.37), residues: 229

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG O 129 
 TYR   0.035   0.002   TYR S  80 
 PHE   0.010   0.001   PHE S  62 
 HIS   0.005   0.001   HIS I  39 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00280 /  0.17 (13403)
  covalent geometry    : angle       0.67115 /  0.40 (19459)
  hydrogen bonds       : bond        0.08091 /  8.95 (  768)
  hydrogen bonds       : angle       3.21837 /  4.15 ( 1860)

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

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

  1520 Ramachandran restraints generated.
    760 Oldfield, 0 Emsley, 760 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1520 Ramachandran restraints generated.
    760 Oldfield, 0 Emsley, 760 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  133 residues out of total 646 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 115
  time to evaluate  : 0.328 
Fit side-chains
REVERT: K   35 ARG cc_start: 0.7914 (mtm-85) cc_final: 0.7671 (mtm-85)
REVERT: M   39 TYR cc_start: 0.7793 (t80) cc_final: 0.7291 (t80)
REVERT: M   76 ARG cc_start: 0.8368 (OUTLIER) cc_final: 0.7672 (ptp-110)
REVERT: R   64 GLU cc_start: 0.7981 (tm-30) cc_final: 0.7629 (tt0)
REVERT: S   77 LEU cc_start: 0.8198 (OUTLIER) cc_final: 0.7782 (mp)
  outliers start: 18
  outliers final: 12
  residues processed: 123
  average time/residue: 0.1195
  time to fit residues: 20.3983
Evaluate side-chains
  123 residues out of total 646 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 109
  time to evaluate  : 0.194 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain J residue   62 LEU
Chi-restraints excluded: chain M residue   49 THR
Chi-restraints excluded: chain M residue   76 ARG
Chi-restraints excluded: chain M residue   85 THR
Chi-restraints excluded: chain M residue  112 THR
Chi-restraints excluded: chain O residue   39 HIS
Chi-restraints excluded: chain Q residue   27 GLN
Chi-restraints excluded: chain Q residue   50 ILE
Chi-restraints excluded: chain Q residue   82 THR
Chi-restraints excluded: chain R residue   16 THR
Chi-restraints excluded: chain R residue   38 ASN
Chi-restraints excluded: chain R residue  101 THR
Chi-restraints excluded: chain S residue   77 LEU
Chi-restraints excluded: chain S residue   87 THR
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 103
   random chunks:
   chunk 10 optimal weight:   20.0000
   chunk 67 optimal weight:    3.9990
   chunk 54 optimal weight:    0.7980
   chunk 60 optimal weight:    2.9990
   chunk 51 optimal weight:    0.9980
   chunk 29 optimal weight:    2.9990
   chunk 47 optimal weight:    1.9990
   chunk 37 optimal weight:    2.9990
   chunk 100 optimal weight:    9.9990
   chunk 21 optimal weight:    2.9990
   chunk 44 optimal weight:    3.9990
   overall best weight:    1.9586

-------------------------------------------------------------------------------
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 = 0.4147 r_free = 0.4147 target = 0.122991 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 53)----------------|
| r_work = 0.3671 r_free = 0.3671 target = 0.093742 restraints weight = 32113.715|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.3711 r_free = 0.3711 target = 0.095877 restraints weight = 16738.887|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 53)----------------|
| r_work = 0.3736 r_free = 0.3736 target = 0.097297 restraints weight = 11262.586|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 33)----------------|
| r_work = 0.3750 r_free = 0.3750 target = 0.098131 restraints weight = 8963.597|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 42)----------------|
| r_work = 0.3759 r_free = 0.3759 target = 0.098645 restraints weight = 7909.923|
|-----------------------------------------------------------------------------|
r_work (final): 0.3647
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7842
moved from start:          0.2322

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.112  13403  Z= 0.224
  Angle     :  0.757   9.935  19459  Z= 0.434
  Chirality :  0.055   0.366   2218
  Planarity :  0.005   0.052   1377
  Dihedral  : 34.032 179.887   4273
  Min Nonbonded Distance : 1.964

Molprobity Statistics.
  All-atom Clashscore : 11.50
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.95 %
    Favored  : 96.05 %
  Rotamer:
    Outliers :  4.91 %
    Allowed  : 19.15 %
    Favored  : 75.95 %
  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:  0.87 (0.31), residues: 760
  helix:  1.57 (0.23), residues: 529
  sheet:  None (None), residues: 0
  loop : -1.82 (0.38), residues: 231

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG R  35 
 TYR   0.044   0.002   TYR S  80 
 PHE   0.014   0.002   PHE S  62 
 HIS   0.010   0.002   HIS I  39 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00457 /  0.22 (13403)
  covalent geometry    : angle       0.75707 /  0.43 (19459)
  hydrogen bonds       : bond        0.09486 / 10.38 (  768)
  hydrogen bonds       : angle       3.50917 /  4.51 ( 1860)

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

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

  1520 Ramachandran restraints generated.
    760 Oldfield, 0 Emsley, 760 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1520 Ramachandran restraints generated.
    760 Oldfield, 0 Emsley, 760 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  147 residues out of total 646 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 116
  time to evaluate  : 0.333 
Fit side-chains
REVERT: J   92 ARG cc_start: 0.8034 (ttm-80) cc_final: 0.7671 (ttm-80)
REVERT: M   76 ARG cc_start: 0.8359 (OUTLIER) cc_final: 0.7872 (ptp-110)
REVERT: M  102 GLU cc_start: 0.6713 (tm-30) cc_final: 0.6503 (tm-30)
REVERT: Q   35 ARG cc_start: 0.7361 (mtp85) cc_final: 0.7022 (mtp180)
REVERT: S   77 LEU cc_start: 0.8347 (OUTLIER) cc_final: 0.7931 (mp)
  outliers start: 31
  outliers final: 21
  residues processed: 138
  average time/residue: 0.1374
  time to fit residues: 25.6920
Evaluate side-chains
  127 residues out of total 646 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 104
  time to evaluate  : 0.246 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain I residue   46 VAL
Chi-restraints excluded: chain I residue   60 LEU
Chi-restraints excluded: chain I residue   65 LEU
Chi-restraints excluded: chain I residue   71 VAL
Chi-restraints excluded: chain I residue   90 MET
Chi-restraints excluded: chain J residue   62 LEU
Chi-restraints excluded: chain K residue   63 LEU
Chi-restraints excluded: chain M residue   36 ILE
Chi-restraints excluded: chain M residue   76 ARG
Chi-restraints excluded: chain M residue   85 THR
Chi-restraints excluded: chain M residue  112 THR
Chi-restraints excluded: chain O residue   39 HIS
Chi-restraints excluded: chain O residue  107 THR
Chi-restraints excluded: chain Q residue   27 GLN
Chi-restraints excluded: chain Q residue   50 ILE
Chi-restraints excluded: chain Q residue   82 THR
Chi-restraints excluded: chain R residue   16 THR
Chi-restraints excluded: chain R residue   38 ASN
Chi-restraints excluded: chain R residue  101 THR
Chi-restraints excluded: chain S residue   53 SER
Chi-restraints excluded: chain S residue   66 VAL
Chi-restraints excluded: chain S residue   77 LEU
Chi-restraints excluded: chain S residue   87 THR
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 103
   random chunks:
   chunk 44 optimal weight:    1.9990
   chunk 62 optimal weight:    0.6980
   chunk 63 optimal weight:    0.6980
   chunk 76 optimal weight:    1.9990
   chunk 94 optimal weight:   20.0000
   chunk 72 optimal weight:    3.9990
   chunk 16 optimal weight:    0.9990
   chunk 67 optimal weight:    4.9990
   chunk 7 optimal weight:   10.0000
   chunk 39 optimal weight:    3.9990
   chunk 6 optimal weight:   10.0000
   overall best weight:    1.2786

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
I  85 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4161 r_free = 0.4161 target = 0.123911 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.3691 r_free = 0.3691 target = 0.094816 restraints weight = 32172.780|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.3730 r_free = 0.3730 target = 0.096973 restraints weight = 16681.094|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 48)----------------|
| r_work = 0.3755 r_free = 0.3755 target = 0.098402 restraints weight = 11160.534|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3769 r_free = 0.3769 target = 0.099218 restraints weight = 8836.016|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 44)----------------|
| r_work = 0.3779 r_free = 0.3779 target = 0.099783 restraints weight = 7797.517|
|-----------------------------------------------------------------------------|
r_work (final): 0.3674
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7807
moved from start:          0.2559

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039  13403  Z= 0.177
  Angle     :  0.690   8.643  19459  Z= 0.405
  Chirality :  0.052   0.328   2218
  Planarity :  0.004   0.046   1377
  Dihedral  : 33.924 179.672   4273
  Min Nonbonded Distance : 2.002

Molprobity Statistics.
  All-atom Clashscore : 10.69
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.76 %
    Favored  : 97.24 %
  Rotamer:
    Outliers :  3.96 %
    Allowed  : 20.09 %
    Favored  : 75.95 %
  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 (0.31), residues: 760
  helix:  1.86 (0.23), residues: 528
  sheet:  None (None), residues: 0
  loop : -1.81 (0.37), residues: 232

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG R  35 
 TYR   0.041   0.002   TYR S  80 
 PHE   0.010   0.001   PHE S  62 
 HIS   0.006   0.001   HIS I  39 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00309 /  0.18 (13403)
  covalent geometry    : angle       0.69000 /  0.40 (19459)
  hydrogen bonds       : bond        0.08422 /  9.24 (  768)
  hydrogen bonds       : angle       3.28454 /  4.21 ( 1860)

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

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

  1520 Ramachandran restraints generated.
    760 Oldfield, 0 Emsley, 760 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1520 Ramachandran restraints generated.
    760 Oldfield, 0 Emsley, 760 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  138 residues out of total 646 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 113
  time to evaluate  : 0.317 
Fit side-chains
   revert: symmetry clash
REVERT: K   64 GLU cc_start: 0.8323 (tm-30) cc_final: 0.8090 (tm-30)
REVERT: M   39 TYR cc_start: 0.7959 (t80) cc_final: 0.7670 (t80)
REVERT: M  117 LYS cc_start: 0.8512 (tptm) cc_final: 0.8091 (mtpt)
REVERT: Q   35 ARG cc_start: 0.7290 (mtp85) cc_final: 0.6954 (mtp180)
REVERT: R   64 GLU cc_start: 0.8042 (tm-30) cc_final: 0.7671 (tt0)
REVERT: S   77 LEU cc_start: 0.8249 (OUTLIER) cc_final: 0.7815 (mp)
  outliers start: 25
  outliers final: 17
  residues processed: 128
  average time/residue: 0.1275
  time to fit residues: 22.4508
Evaluate side-chains
  127 residues out of total 646 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 109
  time to evaluate  : 0.260 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain I residue   60 LEU
Chi-restraints excluded: chain I residue   90 MET
Chi-restraints excluded: chain J residue   84 MET
Chi-restraints excluded: chain J residue   86 VAL
Chi-restraints excluded: chain M residue   36 ILE
Chi-restraints excluded: chain M residue   85 THR
Chi-restraints excluded: chain M residue  112 THR
Chi-restraints excluded: chain O residue   39 HIS
Chi-restraints excluded: chain O residue   87 SER
Chi-restraints excluded: chain O residue  118 THR
Chi-restraints excluded: chain Q residue   27 GLN
Chi-restraints excluded: chain Q residue   50 ILE
Chi-restraints excluded: chain R residue   16 THR
Chi-restraints excluded: chain R residue   38 ASN
Chi-restraints excluded: chain R residue   62 ILE
Chi-restraints excluded: chain R residue  101 THR
Chi-restraints excluded: chain S residue   77 LEU
Chi-restraints excluded: chain S residue   87 THR
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 103
   random chunks:
   chunk 2 optimal weight:   20.0000
   chunk 96 optimal weight:    9.9990
   chunk 81 optimal weight:    0.5980
   chunk 51 optimal weight:    5.9990
   chunk 72 optimal weight:    4.9990
   chunk 7 optimal weight:   10.0000
   chunk 99 optimal weight:   10.0000
   chunk 36 optimal weight:    2.9990
   chunk 56 optimal weight:    4.9990
   chunk 9 optimal weight:   20.0000
   chunk 22 optimal weight:    4.9990
   overall best weight:    3.7188

-------------------------------------------------------------------------------
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 = 0.4056 r_free = 0.4056 target = 0.117325 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 54)----------------|
| r_work = 0.3562 r_free = 0.3562 target = 0.088167 restraints weight = 32280.819|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 42)----------------|
| r_work = 0.3597 r_free = 0.3597 target = 0.090020 restraints weight = 17880.196|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 58)----------------|
| r_work = 0.3620 r_free = 0.3620 target = 0.091265 restraints weight = 12584.784|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 36)----------------|
| r_work = 0.3634 r_free = 0.3634 target = 0.092004 restraints weight = 10270.731|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 46)----------------|
| r_work = 0.3642 r_free = 0.3642 target = 0.092452 restraints weight = 9181.611|
|-----------------------------------------------------------------------------|
r_work (final): 0.3551
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7983
moved from start:          0.3528

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.007   0.067  13403  Z= 0.338
  Angle     :  0.908   9.624  19459  Z= 0.508
  Chirality :  0.063   0.444   2218
  Planarity :  0.007   0.052   1377
  Dihedral  : 34.149 179.841   4271
  Min Nonbonded Distance : 1.950

Molprobity Statistics.
  All-atom Clashscore : 14.08
  Ramachandran Plot:
    Outliers :  0.13 %
    Allowed  :  5.26 %
    Favored  : 94.61 %
  Rotamer:
    Outliers :  5.38 %
    Allowed  : 20.09 %
    Favored  : 74.53 %
  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: -0.07 (0.30), residues: 760
  helix:  0.89 (0.22), residues: 524
  sheet:  None (None), residues: 0
  loop : -2.19 (0.37), residues: 236

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG R  35 
 TYR   0.063   0.005   TYR S  80 
 PHE   0.019   0.003   PHE S  62 
 HIS   0.019   0.003   HIS I  39 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00739 /  0.34 (13403)
  covalent geometry    : angle       0.90847 /  0.51 (19459)
  hydrogen bonds       : bond        0.11958 / 13.15 (  768)
  hydrogen bonds       : angle       4.12477 /  5.27 ( 1860)

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

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

  1520 Ramachandran restraints generated.
    760 Oldfield, 0 Emsley, 760 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1520 Ramachandran restraints generated.
    760 Oldfield, 0 Emsley, 760 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  138 residues out of total 646 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 104
  time to evaluate  : 0.417 
Fit side-chains
   revert: symmetry clash
REVERT: K   65 LEU cc_start: 0.7213 (OUTLIER) cc_final: 0.7004 (tt)
REVERT: M   39 TYR cc_start: 0.8044 (OUTLIER) cc_final: 0.7660 (t80)
REVERT: M  117 LYS cc_start: 0.8596 (tptm) cc_final: 0.8257 (mtpt)
REVERT: Q   35 ARG cc_start: 0.7538 (mtp85) cc_final: 0.7173 (mtp180)
REVERT: R   64 GLU cc_start: 0.8017 (tm-30) cc_final: 0.7688 (tt0)
REVERT: S   77 LEU cc_start: 0.8589 (OUTLIER) cc_final: 0.8230 (mp)
  outliers start: 34
  outliers final: 24
  residues processed: 128
  average time/residue: 0.1254
  time to fit residues: 22.3995
Evaluate side-chains
  121 residues out of total 646 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 94
  time to evaluate  : 0.252 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain I residue   46 VAL
Chi-restraints excluded: chain I residue   60 LEU
Chi-restraints excluded: chain I residue   65 LEU
Chi-restraints excluded: chain I residue   90 MET
Chi-restraints excluded: chain I residue  108 ASN
Chi-restraints excluded: chain J residue   84 MET
Chi-restraints excluded: chain K residue   65 LEU
Chi-restraints excluded: chain K residue   76 THR
Chi-restraints excluded: chain M residue   36 ILE
Chi-restraints excluded: chain M residue   39 TYR
Chi-restraints excluded: chain M residue  103 LEU
Chi-restraints excluded: chain M residue  112 THR
Chi-restraints excluded: chain O residue   39 HIS
Chi-restraints excluded: chain O residue   87 SER
Chi-restraints excluded: chain O residue  118 THR
Chi-restraints excluded: chain Q residue   27 GLN
Chi-restraints excluded: chain Q residue   50 ILE
Chi-restraints excluded: chain Q residue   82 THR
Chi-restraints excluded: chain R residue   16 THR
Chi-restraints excluded: chain R residue   38 ASN
Chi-restraints excluded: chain R residue   62 ILE
Chi-restraints excluded: chain R residue   87 VAL
Chi-restraints excluded: chain R residue  101 THR
Chi-restraints excluded: chain S residue   53 SER
Chi-restraints excluded: chain S residue   66 VAL
Chi-restraints excluded: chain S residue   77 LEU
Chi-restraints excluded: chain S residue   87 THR
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 103
   random chunks:
   chunk 37 optimal weight:    1.9990
   chunk 78 optimal weight:    0.4980
   chunk 69 optimal weight:    0.8980
   chunk 18 optimal weight:    0.9990
   chunk 33 optimal weight:    1.9990
   chunk 42 optimal weight:    0.8980
   chunk 26 optimal weight:    0.8980
   chunk 46 optimal weight:    1.9990
   chunk 47 optimal weight:    0.9980
   chunk 48 optimal weight:    3.9990
   chunk 59 optimal weight:    1.9990
   overall best weight:    0.8380

-------------------------------------------------------------------------------
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 = 0.4092 r_free = 0.4092 target = 0.119769 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3613 r_free = 0.3613 target = 0.091006 restraints weight = 31888.001|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3650 r_free = 0.3650 target = 0.092978 restraints weight = 17675.861|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3673 r_free = 0.3673 target = 0.094265 restraints weight = 12219.021|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 37)----------------|
| r_work = 0.3688 r_free = 0.3688 target = 0.095088 restraints weight = 9870.139|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 39)----------------|
| r_work = 0.3696 r_free = 0.3696 target = 0.095555 restraints weight = 8743.437|
|-----------------------------------------------------------------------------|
r_work (final): 0.3635
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7862
moved from start:          0.3432

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041  13403  Z= 0.172
  Angle     :  0.722   8.898  19459  Z= 0.418
  Chirality :  0.054   0.349   2218
  Planarity :  0.004   0.046   1377
  Dihedral  : 33.942 179.276   4271
  Min Nonbonded Distance : 2.071

Molprobity Statistics.
  All-atom Clashscore : 10.56
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.37 %
    Favored  : 97.63 %
  Rotamer:
    Outliers :  3.16 %
    Allowed  : 23.10 %
    Favored  : 73.73 %
  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:  0.80 (0.31), residues: 760
  helix:  1.58 (0.23), residues: 528
  sheet:  None (None), residues: 0
  loop : -2.02 (0.36), residues: 232

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG O 129 
 TYR   0.040   0.002   TYR S  80 
 PHE   0.009   0.001   PHE S  62 
 HIS   0.006   0.001   HIS I  39 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00283 /  0.17 (13403)
  covalent geometry    : angle       0.72181 /  0.42 (19459)
  hydrogen bonds       : bond        0.08976 /  9.83 (  768)
  hydrogen bonds       : angle       3.38409 /  4.35 ( 1860)

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

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

  1520 Ramachandran restraints generated.
    760 Oldfield, 0 Emsley, 760 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1520 Ramachandran restraints generated.
    760 Oldfield, 0 Emsley, 760 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  130 residues out of total 646 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 110
  time to evaluate  : 0.309 
Fit side-chains
   revert: symmetry clash
REVERT: M   48 ASP cc_start: 0.8294 (p0) cc_final: 0.8071 (p0)
REVERT: M  117 LYS cc_start: 0.8537 (tptm) cc_final: 0.8238 (mtpt)
REVERT: O  105 GLU cc_start: 0.7319 (mm-30) cc_final: 0.7008 (mm-30)
REVERT: Q   35 ARG cc_start: 0.7336 (mtp85) cc_final: 0.6989 (mtp180)
REVERT: S   77 LEU cc_start: 0.8380 (OUTLIER) cc_final: 0.7945 (mp)
  outliers start: 20
  outliers final: 16
  residues processed: 122
  average time/residue: 0.1388
  time to fit residues: 23.3262
Evaluate side-chains
  124 residues out of total 646 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 107
  time to evaluate  : 0.328 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain I residue   65 LEU
Chi-restraints excluded: chain I residue   90 MET
Chi-restraints excluded: chain I residue  108 ASN
Chi-restraints excluded: chain J residue   62 LEU
Chi-restraints excluded: chain K residue   16 THR
Chi-restraints excluded: chain M residue   36 ILE
Chi-restraints excluded: chain M residue  112 THR
Chi-restraints excluded: chain O residue   39 HIS
Chi-restraints excluded: chain O residue   87 SER
Chi-restraints excluded: chain O residue  118 THR
Chi-restraints excluded: chain Q residue   50 ILE
Chi-restraints excluded: chain R residue   16 THR
Chi-restraints excluded: chain R residue   38 ASN
Chi-restraints excluded: chain R residue   62 ILE
Chi-restraints excluded: chain R residue  101 THR
Chi-restraints excluded: chain S residue   77 LEU
Chi-restraints excluded: chain S residue   87 THR
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 103
   random chunks:
   chunk 80 optimal weight:    1.9990
   chunk 36 optimal weight:    0.9980
   chunk 27 optimal weight:    2.9990
   chunk 73 optimal weight:    1.9990
   chunk 12 optimal weight:   10.0000
   chunk 72 optimal weight:    0.2980
   chunk 41 optimal weight:    0.7980
   chunk 86 optimal weight:    1.9990
   chunk 24 optimal weight:    0.9990
   chunk 84 optimal weight:    2.9990
   chunk 11 optimal weight:    9.9990
   overall best weight:    1.0184

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** R  82 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4010 r_free = 0.4010 target = 0.116306 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3522 r_free = 0.3522 target = 0.087846 restraints weight = 31781.823|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3559 r_free = 0.3559 target = 0.089836 restraints weight = 17767.514|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3583 r_free = 0.3583 target = 0.091142 restraints weight = 12268.034|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 40)----------------|
| r_work = 0.3597 r_free = 0.3597 target = 0.091931 restraints weight = 9899.034|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.3605 r_free = 0.3605 target = 0.092365 restraints weight = 8798.647|
|-----------------------------------------------------------------------------|
r_work (final): 0.3550
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7865
moved from start:          0.3521

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037  13403  Z= 0.173
  Angle     :  0.706   8.786  19459  Z= 0.411
  Chirality :  0.053   0.332   2218
  Planarity :  0.005   0.049   1377
  Dihedral  : 33.801 179.485   4271
  Min Nonbonded Distance : 2.049

Molprobity Statistics.
  All-atom Clashscore : 10.65
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.95 %
    Favored  : 96.05 %
  Rotamer:
    Outliers :  3.16 %
    Allowed  : 23.10 %
    Favored  : 73.73 %
  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:  1.07 (0.31), residues: 760
  helix:  1.78 (0.23), residues: 528
  sheet:  None (None), residues: 0
  loop : -1.92 (0.37), residues: 232

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG K  35 
 TYR   0.056   0.002   TYR Q  88 
 PHE   0.010   0.001   PHE S  62 
 HIS   0.008   0.001   HIS S  79 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00296 /  0.17 (13403)
  covalent geometry    : angle       0.70601 /  0.41 (19459)
  hydrogen bonds       : bond        0.08628 /  9.40 (  768)
  hydrogen bonds       : angle       3.27328 /  4.20 ( 1860)

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

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

  1520 Ramachandran restraints generated.
    760 Oldfield, 0 Emsley, 760 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1520 Ramachandran restraints generated.
    760 Oldfield, 0 Emsley, 760 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  134 residues out of total 646 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 114
  time to evaluate  : 0.325 
Fit side-chains
REVERT: K   64 GLU cc_start: 0.8320 (tm-30) cc_final: 0.8114 (tm-30)
REVERT: M   48 ASP cc_start: 0.8269 (p0) cc_final: 0.8053 (p0)
REVERT: M   92 GLN cc_start: 0.8321 (OUTLIER) cc_final: 0.8057 (tp-100)
REVERT: M  117 LYS cc_start: 0.8589 (tptm) cc_final: 0.8202 (mtpt)
REVERT: O  105 GLU cc_start: 0.7291 (mm-30) cc_final: 0.6885 (mm-30)
REVERT: Q   35 ARG cc_start: 0.7202 (mtp85) cc_final: 0.6858 (mtp180)
REVERT: S   77 LEU cc_start: 0.8142 (OUTLIER) cc_final: 0.7704 (mp)
  outliers start: 20
  outliers final: 15
  residues processed: 127
  average time/residue: 0.1336
  time to fit residues: 23.0695
Evaluate side-chains
  125 residues out of total 646 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 108
  time to evaluate  : 0.304 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain I residue   60 LEU
Chi-restraints excluded: chain I residue   65 LEU
Chi-restraints excluded: chain I residue   90 MET
Chi-restraints excluded: chain J residue   86 VAL
Chi-restraints excluded: chain K residue   16 THR
Chi-restraints excluded: chain M residue   92 GLN
Chi-restraints excluded: chain M residue  112 THR
Chi-restraints excluded: chain O residue   39 HIS
Chi-restraints excluded: chain O residue   87 SER
Chi-restraints excluded: chain O residue  118 THR
Chi-restraints excluded: chain Q residue   50 ILE
Chi-restraints excluded: chain R residue   16 THR
Chi-restraints excluded: chain R residue   38 ASN
Chi-restraints excluded: chain R residue   62 ILE
Chi-restraints excluded: chain R residue  101 THR
Chi-restraints excluded: chain S residue   77 LEU
Chi-restraints excluded: chain S residue   87 THR
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 103
   random chunks:
   chunk 53 optimal weight:    0.8980
   chunk 15 optimal weight:    0.8980
   chunk 77 optimal weight:    2.9990
   chunk 63 optimal weight:    0.9990
   chunk 0 optimal weight:   20.0000
   chunk 14 optimal weight:   10.0000
   chunk 54 optimal weight:    0.0670
   chunk 45 optimal weight:    0.7980
   chunk 13 optimal weight:   20.0000
   chunk 93 optimal weight:   20.0000
   chunk 23 optimal weight:    0.9990
   overall best weight:    0.7320

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
Q  25 ASN
** R  82 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4027 r_free = 0.4027 target = 0.117350 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3542 r_free = 0.3542 target = 0.088955 restraints weight = 32214.782|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.3580 r_free = 0.3580 target = 0.090945 restraints weight = 17864.263|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 51)----------------|
| r_work = 0.3603 r_free = 0.3603 target = 0.092274 restraints weight = 12340.950|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 43)----------------|
| r_work = 0.3618 r_free = 0.3618 target = 0.093101 restraints weight = 9933.223|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 33)----------------|
| r_work = 0.3625 r_free = 0.3625 target = 0.093526 restraints weight = 8776.703|
|-----------------------------------------------------------------------------|
r_work (final): 0.3583
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7828
moved from start:          0.3608

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.043  13403  Z= 0.160
  Angle     :  0.693   8.726  19459  Z= 0.404
  Chirality :  0.052   0.326   2218
  Planarity :  0.005   0.074   1377
  Dihedral  : 33.743 178.849   4271
  Min Nonbonded Distance : 2.075

Molprobity Statistics.
  All-atom Clashscore : 10.20
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.37 %
    Favored  : 97.63 %
  Rotamer:
    Outliers :  3.16 %
    Allowed  : 24.05 %
    Favored  : 72.78 %
  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 (0.31), residues: 760
  helix:  1.85 (0.23), residues: 529
  sheet:  None (None), residues: 0
  loop : -1.81 (0.37), residues: 231

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.020   0.001   ARG R  35 
 TYR   0.040   0.002   TYR S  80 
 PHE   0.008   0.001   PHE S  62 
 HIS   0.010   0.001   HIS R  31 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00258 /  0.16 (13403)
  covalent geometry    : angle       0.69256 /  0.40 (19459)
  hydrogen bonds       : bond        0.08142 /  8.85 (  768)
  hydrogen bonds       : angle       3.18324 /  4.09 ( 1860)

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

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

  1520 Ramachandran restraints generated.
    760 Oldfield, 0 Emsley, 760 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1520 Ramachandran restraints generated.
    760 Oldfield, 0 Emsley, 760 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  133 residues out of total 646 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 113
  time to evaluate  : 0.324 
Fit side-chains
REVERT: K   64 GLU cc_start: 0.8297 (tm-30) cc_final: 0.8075 (tm-30)
REVERT: M   48 ASP cc_start: 0.8275 (p0) cc_final: 0.8064 (p0)
REVERT: M  117 LYS cc_start: 0.8608 (tptm) cc_final: 0.8237 (mtpt)
REVERT: O  105 GLU cc_start: 0.7261 (mm-30) cc_final: 0.6849 (mm-30)
REVERT: Q   35 ARG cc_start: 0.7213 (mtp85) cc_final: 0.6875 (mtp180)
REVERT: S   77 LEU cc_start: 0.8070 (OUTLIER) cc_final: 0.7623 (mp)
  outliers start: 20
  outliers final: 13
  residues processed: 126
  average time/residue: 0.1401
  time to fit residues: 23.9892
Evaluate side-chains
  124 residues out of total 646 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 110
  time to evaluate  : 0.388 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain I residue   90 MET
Chi-restraints excluded: chain I residue  112 ILE
Chi-restraints excluded: chain K residue   15 LYS
Chi-restraints excluded: chain K residue   16 THR
Chi-restraints excluded: chain M residue  112 THR
Chi-restraints excluded: chain O residue   87 SER
Chi-restraints excluded: chain O residue  118 THR
Chi-restraints excluded: chain Q residue   50 ILE
Chi-restraints excluded: chain R residue   16 THR
Chi-restraints excluded: chain R residue   38 ASN
Chi-restraints excluded: chain R residue   62 ILE
Chi-restraints excluded: chain R residue  101 THR
Chi-restraints excluded: chain S residue   77 LEU
Chi-restraints excluded: chain S residue   87 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 103
   random chunks:
   chunk 50 optimal weight:    0.7980
   chunk 7 optimal weight:    9.9990
   chunk 55 optimal weight:    0.9990
   chunk 100 optimal weight:   10.0000
   chunk 98 optimal weight:   10.0000
   chunk 1 optimal weight:   20.0000
   chunk 87 optimal weight:    2.9990
   chunk 80 optimal weight:    0.9990
   chunk 47 optimal weight:    1.9990
   chunk 32 optimal weight:    0.9980
   chunk 53 optimal weight:    0.2980
   overall best weight:    0.8184

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** R  82 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4027 r_free = 0.4027 target = 0.117320 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 53)----------------|
| r_work = 0.3543 r_free = 0.3543 target = 0.088996 restraints weight = 32011.045|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 41)----------------|
| r_work = 0.3580 r_free = 0.3580 target = 0.090986 restraints weight = 17661.098|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 48)----------------|
| r_work = 0.3604 r_free = 0.3604 target = 0.092300 restraints weight = 12253.160|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 38)----------------|
| r_work = 0.3618 r_free = 0.3618 target = 0.093126 restraints weight = 9890.570|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 31)----------------|
| r_work = 0.3625 r_free = 0.3625 target = 0.093554 restraints weight = 8756.819|
|-----------------------------------------------------------------------------|
r_work (final): 0.3570
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7830
moved from start:          0.3690

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040  13403  Z= 0.161
  Angle     :  0.691   8.706  19459  Z= 0.403
  Chirality :  0.052   0.335   2218
  Planarity :  0.004   0.051   1377
  Dihedral  : 33.719 179.138   4271
  Min Nonbonded Distance : 2.061

Molprobity Statistics.
  All-atom Clashscore : 10.16
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.03 %
    Favored  : 96.97 %
  Rotamer:
    Outliers :  1.90 %
    Allowed  : 25.47 %
    Favored  : 72.63 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z 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:  1.24 (0.31), residues: 760
  helix:  1.89 (0.23), residues: 528
  sheet:  None (None), residues: 0
  loop : -1.81 (0.37), residues: 232

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG K  35 
 TYR   0.049   0.002   TYR S  80 
 PHE   0.009   0.001   PHE S  62 
 HIS   0.005   0.001   HIS R  31 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00266 /  0.16 (13403)
  covalent geometry    : angle       0.69053 /  0.40 (19459)
  hydrogen bonds       : bond        0.08141 /  8.80 (  768)
  hydrogen bonds       : angle       3.19920 /  4.09 ( 1860)

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

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

  1520 Ramachandran restraints generated.
    760 Oldfield, 0 Emsley, 760 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1520 Ramachandran restraints generated.
    760 Oldfield, 0 Emsley, 760 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  123 residues out of total 646 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 111
  time to evaluate  : 0.320 
Fit side-chains
REVERT: K   64 GLU cc_start: 0.8303 (tm-30) cc_final: 0.8083 (tm-30)
REVERT: K  112 GLN cc_start: 0.7675 (mm110) cc_final: 0.7069 (mp10)
REVERT: M   48 ASP cc_start: 0.8252 (p0) cc_final: 0.8034 (p0)
REVERT: M  117 LYS cc_start: 0.8613 (tptm) cc_final: 0.8244 (mtpt)
REVERT: O   81 ASP cc_start: 0.7868 (p0) cc_final: 0.7286 (p0)
REVERT: Q   35 ARG cc_start: 0.7222 (mtp85) cc_final: 0.6891 (mtp180)
  outliers start: 12
  outliers final: 12
  residues processed: 117
  average time/residue: 0.1470
  time to fit residues: 23.3645
Evaluate side-chains
  120 residues out of total 646 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 108
  time to evaluate  : 0.317 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain I residue   60 LEU
Chi-restraints excluded: chain I residue   90 MET
Chi-restraints excluded: chain K residue   15 LYS
Chi-restraints excluded: chain K residue   16 THR
Chi-restraints excluded: chain M residue  112 THR
Chi-restraints excluded: chain O residue  118 THR
Chi-restraints excluded: chain Q residue   82 THR
Chi-restraints excluded: chain R residue   16 THR
Chi-restraints excluded: chain R residue   38 ASN
Chi-restraints excluded: chain R residue   62 ILE
Chi-restraints excluded: chain R residue  101 THR
Chi-restraints excluded: chain S residue   87 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 103
   random chunks:
   chunk 76 optimal weight:    2.9990
   chunk 16 optimal weight:    0.0570
   chunk 59 optimal weight:    0.7980
   chunk 89 optimal weight:   20.0000
   chunk 85 optimal weight:    0.7980
   chunk 39 optimal weight:    5.9990
   chunk 48 optimal weight:    0.9980
   chunk 54 optimal weight:    0.9990
   chunk 46 optimal weight:    0.9980
   chunk 58 optimal weight:    0.7980
   chunk 7 optimal weight:   10.0000
   overall best weight:    0.6898

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
R  82 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4044 r_free = 0.4044 target = 0.118404 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.3570 r_free = 0.3570 target = 0.090298 restraints weight = 32028.214|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 47)----------------|
| r_work = 0.3606 r_free = 0.3606 target = 0.092304 restraints weight = 17557.748|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 53)----------------|
| r_work = 0.3630 r_free = 0.3630 target = 0.093659 restraints weight = 12072.913|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 52)----------------|
| r_work = 0.3644 r_free = 0.3644 target = 0.094486 restraints weight = 9666.576|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.3652 r_free = 0.3652 target = 0.094927 restraints weight = 8549.840|
|-----------------------------------------------------------------------------|
r_work (final): 0.3598
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7811
moved from start:          0.3774

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039  13403  Z= 0.156
  Angle     :  0.683   8.635  19459  Z= 0.400
  Chirality :  0.051   0.341   2218
  Planarity :  0.004   0.051   1377
  Dihedral  : 33.690 178.822   4271
  Min Nonbonded Distance : 2.071

Molprobity Statistics.
  All-atom Clashscore : 10.34
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.63 %
    Favored  : 97.37 %
  Rotamer:
    Outliers :  2.37 %
    Allowed  : 25.47 %
    Favored  : 72.15 %
  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 (0.31), residues: 760
  helix:  1.94 (0.23), residues: 527
  sheet:  None (None), residues: 0
  loop : -1.75 (0.37), residues: 233

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG K  35 
 TYR   0.056   0.002   TYR S  80 
 PHE   0.008   0.001   PHE S  62 
 HIS   0.004   0.001   HIS I  39 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00251 /  0.16 (13403)
  covalent geometry    : angle       0.68324 /  0.40 (19459)
  hydrogen bonds       : bond        0.07957 /  8.60 (  768)
  hydrogen bonds       : angle       3.15543 /  4.04 ( 1860)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2190.91 seconds
wall clock time: 38 minutes 26.69 seconds (2306.69 seconds total)