Starting phenix.real_space_refine
on Wed Jul 30 11:20:09 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8vmn_43360/07_2025/8vmn_43360.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8vmn_43360/07_2025/8vmn_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 {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8vmn_43360/07_2025/8vmn_43360.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8vmn_43360/07_2025/8vmn_43360.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8vmn_43360/07_2025/8vmn_43360.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8vmn_43360/07_2025/8vmn_43360.cif"
  }
  resolution = 3.5
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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): 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/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: 9.13, per 1000 atoms: 0.73
  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: 2.85
  Conformation dependent library (CDL) restraints added in 926.4 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: 6.22
  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: 5.30

  Time building geometry restraints manager: 3.47 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'  DA H  20 "
       pdb=" O3'  DA H  20 "
    ideal  model  delta    sigma   weight residual
    1.422  1.477 -0.055 3.00e-02 1.11e+03 3.35e+00
  bond pdb=" C3'  DC D 185 "
       pdb=" O3'  DC D 185 "
    ideal  model  delta    sigma   weight residual
    1.422  1.473 -0.051 3.00e-02 1.11e+03 2.86e+00
  bond pdb=" CG  PRO R  26 "
       pdb=" CD  PRO R  26 "
    ideal  model  delta    sigma   weight residual
    1.503  1.561 -0.058 3.40e-02 8.65e+02 2.86e+00
  bond pdb=" CB  LYS O  37 "
       pdb=" CG  LYS O  37 "
    ideal  model  delta    sigma   weight residual
    1.520  1.570 -0.050 3.00e-02 1.11e+03 2.82e+00
  bond pdb=" C3'  DG D 161 "
       pdb=" O3'  DG D 161 "
    ideal  model  delta    sigma   weight residual
    1.422  1.470 -0.048 3.00e-02 1.11e+03 2.60e+00
  ... (remaining 13398 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.08: 18993
        2.08 -     4.16: 437
        4.16 -     6.24: 24
        6.24 -     8.33: 3
        8.33 -    10.41: 2
  Bond angle restraints: 19459
  Sorted by residual:
  angle pdb=" CB  LYS O  37 "
        pdb=" CG  LYS O  37 "
        pdb=" CD  LYS O  37 "
      ideal   model   delta    sigma   weight residual
     111.30  121.71  -10.41 2.30e+00 1.89e-01 2.05e+01
  angle pdb=" N   VAL I 117 "
        pdb=" CA  VAL I 117 "
        pdb=" C   VAL I 117 "
      ideal   model   delta    sigma   weight residual
     113.47  109.04    4.43 1.01e+00 9.80e-01 1.93e+01
  angle pdb=" CA  PRO R  26 "
        pdb=" N   PRO R  26 "
        pdb=" CD  PRO R  26 "
      ideal   model   delta    sigma   weight residual
     112.00  106.84    5.16 1.40e+00 5.10e-01 1.36e+01
  angle pdb=" N   GLY R  98 "
        pdb=" CA  GLY R  98 "
        pdb=" C   GLY R  98 "
      ideal   model   delta    sigma   weight residual
     112.73  116.87   -4.14 1.20e+00 6.94e-01 1.19e+01
  angle pdb=" C   THR M  87 "
        pdb=" CA  THR M  87 "
        pdb=" CB  THR M  87 "
      ideal   model   delta    sigma   weight residual
     110.24  116.41   -6.17 1.88e+00 2.83e-01 1.08e+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: 1672
       0.037 -    0.074: 409
       0.074 -    0.110: 105
       0.110 -    0.147: 30
       0.147 -    0.184: 2
  Chirality restraints: 2218
  Sorted by residual:
  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=" CA  PRO R  26 "
            pdb=" N   PRO R  26 "
            pdb=" C   PRO R  26 "
            pdb=" CB  PRO R  26 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.72    2.57    0.15 2.00e-01 2.50e+01 5.80e-01
  chirality pdb=" P    DC D 250 "
            pdb=" OP1  DC D 250 "
            pdb=" OP2  DC D 250 "
            pdb=" O5'  DC D 250 "
    both_signs  ideal   model   delta    sigma   weight residual
      True       2.35   -2.49   -0.15 2.00e-01 2.50e+01 5.29e-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:             6.630
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.570
  Check model and map are aligned:         0.100
  Set scattering table:                    0.120
  Process input model:                     36.210
  Find NCS groups from input model:        0.300
  Set up NCS constraints:                  0.060
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:2.660
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   46.660
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7387
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.071  13403  Z= 0.178
  Angle     :  0.666  10.407  19459  Z= 0.399
  Chirality :  0.036   0.184   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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  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
 HIS   0.009   0.001   HIS R  31 
 PHE   0.015   0.001   PHE J 100 
 TYR   0.033   0.002   TYR M  80 
 ARG   0.007   0.001   ARG I 128 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.13450 (  768)
  hydrogen bonds       : angle       4.91494 ( 1860)
  covalent geometry    : bond        0.00389 (13403)
  covalent geometry    : angle       0.66623 (19459)

*********************** 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  : 1.033 
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: 0.7525 (mmmm)
  outliers start: 4
  outliers final: 2
  residues processed: 123
  average time/residue: 0.3247
  time to fit residues: 53.9657
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  : 0.931 
-------------------------------------------------------------------------------
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 86 optimal weight:    3.9990
   chunk 78 optimal weight:    3.9990
   chunk 43 optimal weight:    3.9990
   chunk 26 optimal weight:    1.9990
   chunk 52 optimal weight:    3.9990
   chunk 41 optimal weight:    3.9990
   chunk 80 optimal weight:    0.8980
   chunk 31 optimal weight:    0.9980
   chunk 49 optimal weight:    2.9990
   chunk 60 optimal weight:    0.5980
   chunk 93 optimal weight:    6.9990
   overall best weight:    1.4984

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

Flipped N/Q/H residues before XYZ refinement:
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 = 0.4165 r_free = 0.4165 target = 0.124196 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3694 r_free = 0.3694 target = 0.095121 restraints weight = 31972.096|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.3734 r_free = 0.3734 target = 0.097290 restraints weight = 16567.644|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 51)----------------|
| r_work = 0.3759 r_free = 0.3759 target = 0.098741 restraints weight = 11137.090|
|-----------------------------------------------------------------------------|
r_work (final): 0.3643
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7616
moved from start:          0.2146

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.050  13403  Z= 0.220
  Angle     :  0.687   7.112  19459  Z= 0.400
  Chirality :  0.040   0.175   2218
  Planarity :  0.005   0.051   1377
  Dihedral  : 33.730 179.701   4277
  Min Nonbonded Distance : 1.983

Molprobity Statistics.
  All-atom Clashscore : 11.10
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.68 %
    Favored  : 96.32 %
  Rotamer:
    Outliers :  2.85 %
    Allowed  : 21.04 %
    Favored  : 76.11 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.07 (0.31), residues: 760
  helix:  1.70 (0.23), residues: 528
  sheet:  None (None), residues: 0
  loop : -1.69 (0.38), residues: 232

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.006   0.002   HIS R  31 
 PHE   0.014   0.002   PHE S  62 
 TYR   0.038   0.002   TYR Q  88 
 ARG   0.006   0.001   ARG Q  55 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.08453 (  768)
  hydrogen bonds       : angle       3.38840 ( 1860)
  covalent geometry    : bond        0.00496 (13403)
  covalent geometry    : angle       0.68700 (19459)

*********************** 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
  145 residues out of total 646 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 127
  time to evaluate  : 1.037 
Fit side-chains
   revert: symmetry clash
REVERT: J   88 TYR cc_start: 0.7745 (m-10) cc_final: 0.7409 (m-10)
REVERT: M   39 TYR cc_start: 0.7923 (t80) cc_final: 0.7561 (t80)
REVERT: M  110 GLU cc_start: 0.8085 (mp0) cc_final: 0.7856 (mp0)
REVERT: Q   35 ARG cc_start: 0.7320 (mtp85) cc_final: 0.7067 (mtp180)
REVERT: R   64 GLU cc_start: 0.7938 (tm-30) cc_final: 0.7617 (tt0)
REVERT: S   77 LEU cc_start: 0.8513 (OUTLIER) cc_final: 0.8151 (mp)
  outliers start: 18
  outliers final: 11
  residues processed: 141
  average time/residue: 0.3295
  time to fit residues: 61.7101
Evaluate side-chains
  119 residues out of total 646 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 107
  time to evaluate  : 0.868 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain I residue   46 VAL
Chi-restraints excluded: chain J residue   62 LEU
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   38 ASN
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 95 optimal weight:    3.9990
   chunk 34 optimal weight:    3.9990
   chunk 85 optimal weight:    1.9990
   chunk 100 optimal weight:    5.9990
   chunk 15 optimal weight:    3.9990
   chunk 99 optimal weight:    3.9990
   chunk 58 optimal weight:    0.7980
   chunk 43 optimal weight:    8.9990
   chunk 6 optimal weight:    5.9990
   chunk 19 optimal weight:    0.3980
   chunk 45 optimal weight:    0.0470
   overall best weight:    1.4482

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

Flipped N/Q/H residues before XYZ refinement:
** R  31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** 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 = 0.4151 r_free = 0.4151 target = 0.123216 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3685 r_free = 0.3685 target = 0.094572 restraints weight = 32355.333|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3721 r_free = 0.3721 target = 0.096531 restraints weight = 17862.059|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 47)----------------|
| r_work = 0.3744 r_free = 0.3744 target = 0.097814 restraints weight = 12353.757|
|-----------------------------------------------------------------------------|
r_work (final): 0.3610
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7635
moved from start:          0.3115

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.051  13403  Z= 0.209
  Angle     :  0.658   7.223  19459  Z= 0.386
  Chirality :  0.039   0.149   2218
  Planarity :  0.005   0.046   1377
  Dihedral  : 33.537 179.846   4273
  Min Nonbonded Distance : 2.086

Molprobity Statistics.
  All-atom Clashscore : 10.07
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.37 %
    Favored  : 97.63 %
  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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.15 (0.31), residues: 760
  helix:  1.82 (0.23), residues: 525
  sheet:  None (None), residues: 0
  loop : -1.76 (0.38), residues: 235

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.008   0.001   HIS I  39 
 PHE   0.012   0.001   PHE S  62 
 TYR   0.032   0.002   TYR M  80 
 ARG   0.009   0.001   ARG K  71 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.08415 (  768)
  hydrogen bonds       : angle       3.29245 ( 1860)
  covalent geometry    : bond        0.00472 (13403)
  covalent geometry    : angle       0.65799 (19459)

*********************** 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
  142 residues out of total 646 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 117
  time to evaluate  : 1.868 
Fit side-chains
   revert: symmetry clash
REVERT: M   48 ASP cc_start: 0.8246 (p0) cc_final: 0.7997 (p0)
REVERT: M   73 GLU cc_start: 0.7886 (tp30) cc_final: 0.7601 (tp30)
REVERT: M   76 ARG cc_start: 0.8378 (OUTLIER) cc_final: 0.8036 (ptp-110)
REVERT: M  117 LYS cc_start: 0.8495 (tptm) cc_final: 0.8216 (mtpt)
REVERT: O   84 PHE cc_start: 0.8581 (OUTLIER) cc_final: 0.8302 (m-80)
REVERT: O  105 GLU cc_start: 0.7468 (mm-30) cc_final: 0.7176 (mm-30)
REVERT: Q   35 ARG cc_start: 0.7455 (mtp85) cc_final: 0.7168 (mtp180)
REVERT: S   77 LEU cc_start: 0.8437 (OUTLIER) cc_final: 0.8002 (mp)
  outliers start: 25
  outliers final: 16
  residues processed: 134
  average time/residue: 0.3463
  time to fit residues: 62.6118
Evaluate side-chains
  128 residues out of total 646 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 109
  time to evaluate  : 0.980 
-------------------------------------------------------------------------------
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 J residue   62 LEU
Chi-restraints excluded: chain K residue   63 LEU
Chi-restraints excluded: chain M residue   76 ARG
Chi-restraints excluded: chain M residue   85 THR
Chi-restraints excluded: chain O residue   39 HIS
Chi-restraints excluded: chain O residue   84 PHE
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  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=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 103
   random chunks:
   chunk 92 optimal weight:    4.9990
   chunk 14 optimal weight:    6.9990
   chunk 100 optimal weight:    5.9990
   chunk 15 optimal weight:    3.9990
   chunk 67 optimal weight:    0.9980
   chunk 73 optimal weight:    2.9990
   chunk 63 optimal weight:    0.9990
   chunk 59 optimal weight:    0.7980
   chunk 51 optimal weight:    3.9990
   chunk 79 optimal weight:    0.1980
   chunk 17 optimal weight:    0.9990
   overall best weight:    0.7984

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

Flipped N/Q/H residues before XYZ refinement:
** R  31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
R  82 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4040 r_free = 0.4040 target = 0.118336 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3567 r_free = 0.3567 target = 0.090291 restraints weight = 31846.864|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 43)----------------|
| r_work = 0.3605 r_free = 0.3605 target = 0.092344 restraints weight = 17566.594|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3628 r_free = 0.3628 target = 0.093646 restraints weight = 12099.287|
|-----------------------------------------------------------------------------|
r_work (final): 0.3585
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7617
moved from start:          0.3401

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.052  13403  Z= 0.174
  Angle     :  0.620   5.409  19459  Z= 0.366
  Chirality :  0.037   0.155   2218
  Planarity :  0.004   0.048   1377
  Dihedral  : 33.308 179.832   4273
  Min Nonbonded Distance : 2.066

Molprobity Statistics.
  All-atom Clashscore : 10.16
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.29 %
    Favored  : 96.71 %
  Rotamer:
    Outliers :  3.64 %
    Allowed  : 20.41 %
    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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.45 (0.31), residues: 760
  helix:  2.04 (0.23), residues: 528
  sheet:  None (None), residues: 0
  loop : -1.71 (0.38), residues: 232

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.005   0.001   HIS I  39 
 PHE   0.008   0.001   PHE S  62 
 TYR   0.033   0.002   TYR S  80 
 ARG   0.004   0.000   ARG K  35 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.07589 (  768)
  hydrogen bonds       : angle       3.01392 ( 1860)
  covalent geometry    : bond        0.00386 (13403)
  covalent geometry    : angle       0.62048 (19459)

*********************** 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
  142 residues out of total 646 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 119
  time to evaluate  : 1.073 
Fit side-chains
   revert: symmetry clash
REVERT: I  105 GLU cc_start: 0.7715 (tt0) cc_final: 0.7499 (tt0)
REVERT: K   41 GLU cc_start: 0.7745 (tp30) cc_final: 0.7517 (tt0)
REVERT: M   73 GLU cc_start: 0.7900 (tp30) cc_final: 0.7675 (tp30)
REVERT: M  117 LYS cc_start: 0.8597 (tptm) cc_final: 0.8249 (mtpt)
REVERT: O  105 GLU cc_start: 0.7445 (mm-30) cc_final: 0.7095 (mm-30)
REVERT: Q   35 ARG cc_start: 0.7329 (mtp85) cc_final: 0.7001 (mtp180)
  outliers start: 23
  outliers final: 14
  residues processed: 132
  average time/residue: 0.4025
  time to fit residues: 72.9642
Evaluate side-chains
  127 residues out of total 646 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 113
  time to evaluate  : 1.121 
-------------------------------------------------------------------------------
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   86 VAL
Chi-restraints excluded: chain K residue   15 LYS
Chi-restraints excluded: chain K residue   16 THR
Chi-restraints excluded: chain K residue   65 LEU
Chi-restraints excluded: chain M residue   85 THR
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   87 THR
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 103
   random chunks:
   chunk 27 optimal weight:    2.9990
   chunk 80 optimal weight:    0.8980
   chunk 41 optimal weight:    3.9990
   chunk 28 optimal weight:    0.0000
   chunk 83 optimal weight:    0.9990
   chunk 46 optimal weight:    2.9990
   chunk 29 optimal weight:    1.9990
   chunk 68 optimal weight:    1.9990
   chunk 34 optimal weight:    4.9990
   chunk 96 optimal weight:    3.9990
   chunk 86 optimal weight:    0.9990
   overall best weight:    0.9790

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

Flipped N/Q/H residues before XYZ refinement:
M  92 GLN
** R  31 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 = 0.4042 r_free = 0.4042 target = 0.118193 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 55)----------------|
| r_work = 0.3566 r_free = 0.3566 target = 0.089975 restraints weight = 31919.644|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 46)----------------|
| r_work = 0.3602 r_free = 0.3602 target = 0.091953 restraints weight = 17612.506|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 55)----------------|
| r_work = 0.3625 r_free = 0.3625 target = 0.093280 restraints weight = 12219.261|
|-----------------------------------------------------------------------------|
r_work (final): 0.3569
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7644
moved from start:          0.3747

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.051  13403  Z= 0.180
  Angle     :  0.620   5.327  19459  Z= 0.366
  Chirality :  0.038   0.171   2218
  Planarity :  0.004   0.046   1377
  Dihedral  : 33.265 178.966   4271
  Min Nonbonded Distance : 2.059

Molprobity Statistics.
  All-atom Clashscore : 10.47
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.76 %
    Favored  : 97.24 %
  Rotamer:
    Outliers :  2.69 %
    Allowed  : 23.10 %
    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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.48 (0.31), residues: 760
  helix:  2.08 (0.23), residues: 528
  sheet:  None (None), residues: 0
  loop : -1.73 (0.38), residues: 232

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.006   0.001   HIS I  39 
 PHE   0.010   0.001   PHE S  62 
 TYR   0.040   0.002   TYR Q  88 
 ARG   0.005   0.000   ARG K  35 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.07774 (  768)
  hydrogen bonds       : angle       3.06488 ( 1860)
  covalent geometry    : bond        0.00402 (13403)
  covalent geometry    : angle       0.62039 (19459)

*********************** 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
  131 residues out of total 646 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 114
  time to evaluate  : 0.919 
Fit side-chains
   revert: symmetry clash
REVERT: K   64 GLU cc_start: 0.8396 (tm-30) cc_final: 0.8081 (tm-30)
REVERT: K   71 ARG cc_start: 0.7857 (tpt90) cc_final: 0.7401 (tpt-90)
REVERT: M   48 ASP cc_start: 0.8254 (p0) cc_final: 0.7982 (p0)
REVERT: M   73 GLU cc_start: 0.7846 (tp30) cc_final: 0.7615 (tp30)
REVERT: M  117 LYS cc_start: 0.8556 (tptm) cc_final: 0.8235 (mtpt)
REVERT: O  105 GLU cc_start: 0.7435 (mm-30) cc_final: 0.7081 (mm-30)
REVERT: Q   35 ARG cc_start: 0.7278 (mtp85) cc_final: 0.6958 (mtp180)
  outliers start: 17
  outliers final: 12
  residues processed: 125
  average time/residue: 0.3373
  time to fit residues: 56.1341
Evaluate side-chains
  122 residues out of total 646 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 110
  time to evaluate  : 1.022 
-------------------------------------------------------------------------------
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 K residue   16 THR
Chi-restraints excluded: chain M residue   85 THR
Chi-restraints excluded: chain O residue   39 HIS
Chi-restraints excluded: chain Q residue   27 GLN
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=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 103
   random chunks:
   chunk 67 optimal weight:    3.9990
   chunk 83 optimal weight:    0.9980
   chunk 84 optimal weight:    2.9990
   chunk 74 optimal weight:    4.9990
   chunk 41 optimal weight:    0.9990
   chunk 28 optimal weight:    1.9990
   chunk 23 optimal weight:    0.8980
   chunk 82 optimal weight:    0.9990
   chunk 12 optimal weight:    5.9990
   chunk 20 optimal weight:    0.8980
   chunk 18 optimal weight:    0.9980
   overall best weight:    0.9582

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

Flipped N/Q/H residues before XYZ refinement:
** R  31 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 = 0.4033 r_free = 0.4033 target = 0.117649 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 58)----------------|
| r_work = 0.3539 r_free = 0.3539 target = 0.088893 restraints weight = 32222.346|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 42)----------------|
| r_work = 0.3579 r_free = 0.3579 target = 0.091063 restraints weight = 16761.285|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3605 r_free = 0.3605 target = 0.092511 restraints weight = 11217.432|
|-----------------------------------------------------------------------------|
r_work (final): 0.3553
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7647
moved from start:          0.4083

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.052  13403  Z= 0.178
  Angle     :  0.619   6.655  19459  Z= 0.365
  Chirality :  0.037   0.152   2218
  Planarity :  0.004   0.048   1377
  Dihedral  : 33.184 179.287   4271
  Min Nonbonded Distance : 2.060

Molprobity Statistics.
  All-atom Clashscore : 10.12
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.29 %
    Favored  : 96.71 %
  Rotamer:
    Outliers :  2.85 %
    Allowed  : 24.05 %
    Favored  : 73.10 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.59 (0.31), residues: 760
  helix:  2.16 (0.23), residues: 527
  sheet:  None (None), residues: 0
  loop : -1.68 (0.38), residues: 233

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.006   0.001   HIS I  39 
 PHE   0.009   0.001   PHE S  62 
 TYR   0.044   0.002   TYR Q  88 
 ARG   0.005   0.000   ARG K  35 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.07665 (  768)
  hydrogen bonds       : angle       2.99869 ( 1860)
  covalent geometry    : bond        0.00395 (13403)
  covalent geometry    : angle       0.61853 (19459)

*********************** 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
  133 residues out of total 646 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 115
  time to evaluate  : 0.796 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: K   64 GLU cc_start: 0.8366 (tm-30) cc_final: 0.8052 (tm-30)
REVERT: K   71 ARG cc_start: 0.7806 (tpt90) cc_final: 0.7414 (tpt-90)
REVERT: M   43 LYS cc_start: 0.7266 (tppt) cc_final: 0.6583 (ptpt)
REVERT: M   73 GLU cc_start: 0.7874 (tp30) cc_final: 0.7650 (tp30)
REVERT: M  102 GLU cc_start: 0.6841 (tp30) cc_final: 0.5970 (tp30)
REVERT: M  106 HIS cc_start: 0.8261 (m170) cc_final: 0.8013 (m170)
REVERT: M  117 LYS cc_start: 0.8609 (tptm) cc_final: 0.8246 (mtpt)
REVERT: O   37 LYS cc_start: 0.8171 (tppt) cc_final: 0.7750 (mmtp)
REVERT: O   50 GLU cc_start: 0.8455 (mp0) cc_final: 0.8212 (mp0)
REVERT: O  105 GLU cc_start: 0.7485 (mm-30) cc_final: 0.7233 (mm-30)
  outliers start: 18
  outliers final: 16
  residues processed: 127
  average time/residue: 0.3684
  time to fit residues: 62.6386
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  : 0.990 
-------------------------------------------------------------------------------
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   90 MET
Chi-restraints excluded: chain K residue   15 LYS
Chi-restraints excluded: chain K residue   16 THR
Chi-restraints excluded: chain K residue   65 LEU
Chi-restraints excluded: chain M residue   85 THR
Chi-restraints excluded: chain O residue   39 HIS
Chi-restraints excluded: chain O residue  118 THR
Chi-restraints excluded: chain Q residue   27 GLN
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   87 THR
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 103
   random chunks:
   chunk 12 optimal weight:    5.9990
   chunk 14 optimal weight:    6.9990
   chunk 93 optimal weight:    5.9990
   chunk 46 optimal weight:    2.9990
   chunk 29 optimal weight:    2.9990
   chunk 52 optimal weight:    0.7980
   chunk 18 optimal weight:    0.9980
   chunk 26 optimal weight:    0.9980
   chunk 20 optimal weight:    0.9980
   chunk 65 optimal weight:    3.9990
   chunk 27 optimal weight:    1.9990
   overall best weight:    1.1582

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

Flipped N/Q/H residues before XYZ refinement:
** R  31 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 = 0.4015 r_free = 0.4015 target = 0.116617 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3527 r_free = 0.3527 target = 0.088215 restraints weight = 32121.078|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.3565 r_free = 0.3565 target = 0.090226 restraints weight = 17743.480|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.3588 r_free = 0.3588 target = 0.091527 restraints weight = 12130.783|
|-----------------------------------------------------------------------------|
r_work (final): 0.3547
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7669
moved from start:          0.4364

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.051  13403  Z= 0.188
  Angle     :  0.631   5.352  19459  Z= 0.372
  Chirality :  0.038   0.144   2218
  Planarity :  0.004   0.046   1377
  Dihedral  : 33.192 179.838   4271
  Min Nonbonded Distance : 2.057

Molprobity Statistics.
  All-atom Clashscore : 10.16
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.42 %
    Favored  : 96.58 %
  Rotamer:
    Outliers :  3.32 %
    Allowed  : 24.05 %
    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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.53 (0.31), residues: 760
  helix:  2.11 (0.23), residues: 527
  sheet:  None (None), residues: 0
  loop : -1.68 (0.38), residues: 233

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.007   0.001   HIS I  39 
 PHE   0.010   0.001   PHE S  62 
 TYR   0.040   0.002   TYR Q  88 
 ARG   0.006   0.000   ARG K  35 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.07974 (  768)
  hydrogen bonds       : angle       3.07115 ( 1860)
  covalent geometry    : bond        0.00422 (13403)
  covalent geometry    : angle       0.63141 (19459)

*********************** 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
  129 residues out of total 646 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 108
  time to evaluate  : 0.939 
Fit side-chains
   revert: symmetry clash
REVERT: K   64 GLU cc_start: 0.8378 (tm-30) cc_final: 0.8017 (tm-30)
REVERT: K   71 ARG cc_start: 0.7868 (tpt90) cc_final: 0.7516 (tmt-80)
REVERT: M   43 LYS cc_start: 0.7130 (tppt) cc_final: 0.6571 (ptpt)
REVERT: M   48 ASP cc_start: 0.8234 (p0) cc_final: 0.7960 (p0)
REVERT: M  117 LYS cc_start: 0.8574 (tptm) cc_final: 0.8308 (mtpt)
REVERT: O  105 GLU cc_start: 0.7474 (mm-30) cc_final: 0.7109 (mm-30)
  outliers start: 21
  outliers final: 17
  residues processed: 122
  average time/residue: 0.3541
  time to fit residues: 57.1207
Evaluate side-chains
  120 residues out of total 646 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 103
  time to evaluate  : 0.883 
-------------------------------------------------------------------------------
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 K residue   16 THR
Chi-restraints excluded: chain M residue   85 THR
Chi-restraints excluded: chain O residue   39 HIS
Chi-restraints excluded: chain O residue  118 THR
Chi-restraints excluded: chain Q residue   27 GLN
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   53 SER
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 38 optimal weight:    0.9990
   chunk 27 optimal weight:    2.9990
   chunk 83 optimal weight:    1.9990
   chunk 77 optimal weight:    2.9990
   chunk 16 optimal weight:    0.7980
   chunk 6 optimal weight:    5.9990
   chunk 53 optimal weight:    3.9990
   chunk 25 optimal weight:    5.9990
   chunk 44 optimal weight:    0.9990
   chunk 35 optimal weight:    0.0980
   chunk 99 optimal weight:    5.9990
   overall best weight:    0.9786

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

Flipped N/Q/H residues before XYZ refinement:
** R  31 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 = 0.4034 r_free = 0.4034 target = 0.117751 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 53)----------------|
| r_work = 0.3548 r_free = 0.3548 target = 0.089320 restraints weight = 32182.644|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3585 r_free = 0.3585 target = 0.091315 restraints weight = 17678.260|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 51)----------------|
| r_work = 0.3608 r_free = 0.3608 target = 0.092616 restraints weight = 12159.408|
|-----------------------------------------------------------------------------|
r_work (final): 0.3534
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7657
moved from start:          0.4526

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.051  13403  Z= 0.179
  Angle     :  0.623   6.060  19459  Z= 0.368
  Chirality :  0.037   0.142   2218
  Planarity :  0.004   0.047   1377
  Dihedral  : 33.113 179.510   4271
  Min Nonbonded Distance : 2.062

Molprobity Statistics.
  All-atom Clashscore : 10.07
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.82 %
    Favored  : 96.18 %
  Rotamer:
    Outliers :  3.32 %
    Allowed  : 24.53 %
    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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.60 (0.31), residues: 760
  helix:  2.14 (0.23), residues: 527
  sheet:  None (None), residues: 0
  loop : -1.60 (0.38), residues: 233

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.006   0.001   HIS I  39 
 PHE   0.008   0.001   PHE S  62 
 TYR   0.038   0.002   TYR Q  88 
 ARG   0.007   0.000   ARG K  35 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.07693 (  768)
  hydrogen bonds       : angle       3.01224 ( 1860)
  covalent geometry    : bond        0.00399 (13403)
  covalent geometry    : angle       0.62344 (19459)

*********************** 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
  131 residues out of total 646 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 110
  time to evaluate  : 0.872 
Fit side-chains
   revert: symmetry clash
REVERT: K   64 GLU cc_start: 0.8324 (tm-30) cc_final: 0.7939 (tm-30)
REVERT: K   71 ARG cc_start: 0.7788 (tpt90) cc_final: 0.7480 (tpt-90)
REVERT: M   43 LYS cc_start: 0.7262 (tppt) cc_final: 0.6572 (ptpt)
REVERT: M  117 LYS cc_start: 0.8603 (tptm) cc_final: 0.8255 (mtpt)
REVERT: O   37 LYS cc_start: 0.7878 (mmtp) cc_final: 0.7647 (tppt)
REVERT: O   50 GLU cc_start: 0.8473 (mp0) cc_final: 0.8269 (mp0)
REVERT: O  105 GLU cc_start: 0.7478 (mm-30) cc_final: 0.7219 (mm-30)
  outliers start: 21
  outliers final: 19
  residues processed: 125
  average time/residue: 0.3152
  time to fit residues: 52.6200
Evaluate side-chains
  125 residues out of total 646 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 106
  time to evaluate  : 0.954 
-------------------------------------------------------------------------------
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 K residue   15 LYS
Chi-restraints excluded: chain K residue   16 THR
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  118 THR
Chi-restraints excluded: chain Q residue   27 GLN
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   53 SER
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 66 optimal weight:    0.0980
   chunk 51 optimal weight:    4.9990
   chunk 86 optimal weight:    0.8980
   chunk 91 optimal weight:    5.9990
   chunk 47 optimal weight:    3.9990
   chunk 79 optimal weight:    4.9990
   chunk 84 optimal weight:    2.9990
   chunk 94 optimal weight:    6.9990
   chunk 71 optimal weight:    1.9990
   chunk 96 optimal weight:    3.9990
   chunk 8 optimal weight:    3.9990
   overall best weight:    1.9986

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

Flipped N/Q/H residues before XYZ refinement:
Q  25 ASN
** R  31 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 = 0.3972 r_free = 0.3972 target = 0.113858 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3466 r_free = 0.3466 target = 0.085101 restraints weight = 31938.365|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 41)----------------|
| r_work = 0.3504 r_free = 0.3504 target = 0.087044 restraints weight = 17837.609|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 54)----------------|
| r_work = 0.3527 r_free = 0.3527 target = 0.088326 restraints weight = 12369.914|
|-----------------------------------------------------------------------------|
r_work (final): 0.3493
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7767
moved from start:          0.4936

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.049  13403  Z= 0.247
  Angle     :  0.703   6.526  19459  Z= 0.411
  Chirality :  0.041   0.146   2218
  Planarity :  0.005   0.042   1377
  Dihedral  : 33.294 179.872   4271
  Min Nonbonded Distance : 2.044

Molprobity Statistics.
  All-atom Clashscore : 11.41
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.74 %
    Favored  : 95.26 %
  Rotamer:
    Outliers :  3.96 %
    Allowed  : 23.58 %
    Favored  : 72.47 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.07 (0.31), residues: 760
  helix:  1.78 (0.23), residues: 526
  sheet:  None (None), residues: 0
  loop : -1.88 (0.37), residues: 234

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.010   0.001   HIS I  39 
 PHE   0.013   0.002   PHE S  62 
 TYR   0.073   0.003   TYR Q  88 
 ARG   0.007   0.001   ARG K  35 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.09250 (  768)
  hydrogen bonds       : angle       3.42056 ( 1860)
  covalent geometry    : bond        0.00563 (13403)
  covalent geometry    : angle       0.70309 (19459)

*********************** 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: 25
    poor density    : 108
  time to evaluate  : 0.956 
Fit side-chains
   revert: symmetry clash
REVERT: K   71 ARG cc_start: 0.8093 (tpt90) cc_final: 0.7862 (tmt-80)
REVERT: K   75 LYS cc_start: 0.8817 (ttmm) cc_final: 0.8563 (ttmm)
REVERT: M   48 ASP cc_start: 0.8240 (p0) cc_final: 0.7966 (p0)
REVERT: M  117 LYS cc_start: 0.8637 (tptm) cc_final: 0.8367 (mtpt)
REVERT: O   50 GLU cc_start: 0.8339 (mp0) cc_final: 0.8040 (mp0)
REVERT: O  105 GLU cc_start: 0.7631 (mm-30) cc_final: 0.7333 (mm-30)
  outliers start: 25
  outliers final: 20
  residues processed: 125
  average time/residue: 0.3320
  time to fit residues: 55.5424
Evaluate side-chains
  125 residues out of total 646 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 105
  time to evaluate  : 1.024 
-------------------------------------------------------------------------------
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   62 LEU
Chi-restraints excluded: chain K residue   16 THR
Chi-restraints excluded: chain K residue   65 LEU
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  118 THR
Chi-restraints excluded: chain Q residue   27 GLN
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   53 SER
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 56 optimal weight:    0.8980
   chunk 55 optimal weight:    0.9990
   chunk 38 optimal weight:    0.6980
   chunk 74 optimal weight:    0.6980
   chunk 22 optimal weight:    3.9990
   chunk 62 optimal weight:    0.9980
   chunk 54 optimal weight:    0.9980
   chunk 97 optimal weight:    4.9990
   chunk 2 optimal weight:    7.9990
   chunk 21 optimal weight:    0.9980
   chunk 63 optimal weight:    0.3980
   overall best weight:    0.7380

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

Flipped N/Q/H residues before XYZ refinement:
R  31 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4027 r_free = 0.4027 target = 0.117502 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3542 r_free = 0.3542 target = 0.089093 restraints weight = 31744.440|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3581 r_free = 0.3581 target = 0.091229 restraints weight = 16762.802|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 49)----------------|
| r_work = 0.3606 r_free = 0.3606 target = 0.092620 restraints weight = 11280.540|
|-----------------------------------------------------------------------------|
r_work (final): 0.3564
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7650
moved from start:          0.4896

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.052  13403  Z= 0.174
  Angle     :  0.637   7.617  19459  Z= 0.376
  Chirality :  0.037   0.138   2218
  Planarity :  0.004   0.049   1377
  Dihedral  : 33.118 179.933   4271
  Min Nonbonded Distance : 2.065

Molprobity Statistics.
  All-atom Clashscore : 10.56
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.29 %
    Favored  : 96.71 %
  Rotamer:
    Outliers :  2.22 %
    Allowed  : 25.79 %
    Favored  : 71.99 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.46 (0.31), residues: 760
  helix:  2.05 (0.23), residues: 526
  sheet:  None (None), residues: 0
  loop : -1.67 (0.38), residues: 234

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.005   0.001   HIS I  39 
 PHE   0.006   0.001   PHE S  62 
 TYR   0.071   0.002   TYR Q  88 
 ARG   0.007   0.000   ARG K  35 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.07637 (  768)
  hydrogen bonds       : angle       3.05609 ( 1860)
  covalent geometry    : bond        0.00386 (13403)
  covalent geometry    : angle       0.63680 (19459)

********************** 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
  126 residues out of total 646 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 112
  time to evaluate  : 1.039 
Fit side-chains
   revert: symmetry clash
REVERT: K   64 GLU cc_start: 0.8418 (tm-30) cc_final: 0.8004 (tm-30)
REVERT: K   71 ARG cc_start: 0.7787 (tpt90) cc_final: 0.7413 (tmt-80)
REVERT: K   75 LYS cc_start: 0.8490 (ttmm) cc_final: 0.8244 (ttmm)
REVERT: M   43 LYS cc_start: 0.7321 (tppt) cc_final: 0.6663 (ptpt)
REVERT: M  117 LYS cc_start: 0.8589 (tptm) cc_final: 0.8284 (mtpt)
REVERT: O  105 GLU cc_start: 0.7502 (mm-30) cc_final: 0.7125 (mm-30)
  outliers start: 14
  outliers final: 12
  residues processed: 122
  average time/residue: 0.3339
  time to fit residues: 54.4687
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  : 0.959 
-------------------------------------------------------------------------------
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   90 MET
Chi-restraints excluded: chain K residue   16 THR
Chi-restraints excluded: chain O residue   39 HIS
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 S residue   53 SER
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 82 optimal weight:    0.6980
   chunk 52 optimal weight:    0.0270
   chunk 46 optimal weight:    1.9990
   chunk 6 optimal weight:    5.9990
   chunk 77 optimal weight:    0.9990
   chunk 75 optimal weight:    0.6980
   chunk 45 optimal weight:    0.6980
   chunk 26 optimal weight:    0.9980
   chunk 35 optimal weight:    0.6980
   chunk 25 optimal weight:    3.9990
   chunk 34 optimal weight:    0.0570
   overall best weight:    0.4356

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

Flipped N/Q/H residues before XYZ refinement:
R  31 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4028 r_free = 0.4028 target = 0.117311 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 55)----------------|
| r_work = 0.3528 r_free = 0.3528 target = 0.088295 restraints weight = 32111.908|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 47)----------------|
| r_work = 0.3570 r_free = 0.3570 target = 0.090572 restraints weight = 16115.173|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 53)----------------|
| r_work = 0.3598 r_free = 0.3598 target = 0.092090 restraints weight = 10534.444|
|-----------------------------------------------------------------------------|
r_work (final): 0.3541
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7625
moved from start:          0.4891

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.052  13403  Z= 0.169
  Angle     :  0.638   7.791  19459  Z= 0.376
  Chirality :  0.037   0.143   2218
  Planarity :  0.004   0.050   1377
  Dihedral  : 33.088 179.945   4271
  Min Nonbonded Distance : 2.078

Molprobity Statistics.
  All-atom Clashscore : 10.52
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.03 %
    Favored  : 96.97 %
  Rotamer:
    Outliers :  2.53 %
    Allowed  : 25.63 %
    Favored  : 71.84 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.58 (0.31), residues: 760
  helix:  2.12 (0.23), residues: 524
  sheet:  None (None), residues: 0
  loop : -1.52 (0.38), residues: 236

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.005   0.001   HIS S  79 
 PHE   0.006   0.001   PHE S  62 
 TYR   0.083   0.002   TYR Q  88 
 ARG   0.008   0.000   ARG K  35 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.07409 (  768)
  hydrogen bonds       : angle       3.06338 ( 1860)
  covalent geometry    : bond        0.00370 (13403)
  covalent geometry    : angle       0.63833 (19459)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 4407.29 seconds
wall clock time: 78 minutes 49.24 seconds (4729.24 seconds total)