Starting phenix.real_space_refine
on Wed May 14 21:38:37 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8vmn_43360/05_2025/8vmn_43360.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8vmn_43360/05_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_43360/05_2025/8vmn_43360.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8vmn_43360/05_2025/8vmn_43360.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8vmn_43360/05_2025/8vmn_43360.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8vmn_43360/05_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-5687/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: 8.60, per 1000 atoms: 0.69
  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: 2.87
  Conformation dependent library (CDL) restraints added in 930.4 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: 5.90
  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: 5.08

  Time building geometry restraints manager: 3.42 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:             12.320
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.160
  Check model and map are aligned:         0.030
  Set scattering table:                    0.150
  Process input model:                     34.790
  Find NCS groups from input model:        0.320
  Set up NCS constraints:                  0.050
  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:2.670
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   50.490
-------------------------------------------------------------------------------
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  : 0.856 
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: 0.3266
  time to fit residues: 53.9149
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  : 1.014 
-------------------------------------------------------------------------------
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 = 46)----------------|
| r_work = 0.3694 r_free = 0.3694 target = 0.095120 restraints weight = 31972.266|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 55)----------------|
| r_work = 0.3734 r_free = 0.3734 target = 0.097303 restraints weight = 16546.926|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3760 r_free = 0.3760 target = 0.098729 restraints weight = 11119.930|
|-----------------------------------------------------------------------------|
r_work (final): 0.3643
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7618
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  : 0.848 
Fit side-chains
   revert: symmetry clash
REVERT: J   88 TYR cc_start: 0.7749 (m-10) cc_final: 0.7412 (m-10)
REVERT: M   39 TYR cc_start: 0.7929 (t80) cc_final: 0.7567 (t80)
REVERT: M  110 GLU cc_start: 0.8084 (mp0) cc_final: 0.7856 (mp0)
REVERT: Q   35 ARG cc_start: 0.7320 (mtp85) cc_final: 0.7068 (mtp180)
REVERT: R   64 GLU cc_start: 0.7935 (tm-30) cc_final: 0.7616 (tt0)
REVERT: S   77 LEU cc_start: 0.8516 (OUTLIER) cc_final: 0.8153 (mp)
  outliers start: 18
  outliers final: 11
  residues processed: 141
  average time/residue: 0.3097
  time to fit residues: 58.3908
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  : 0.933 
-------------------------------------------------------------------------------
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:    0.3980
   chunk 43 optimal weight:    6.9990
   chunk 6 optimal weight:    5.9990
   chunk 19 optimal weight:    0.6980
   chunk 45 optimal weight:    2.9990
   overall best weight:    2.0186

-------------------------------------------------------------------------------
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 = 0.4114 r_free = 0.4114 target = 0.120932 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3639 r_free = 0.3639 target = 0.092018 restraints weight = 32309.725|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3673 r_free = 0.3673 target = 0.093896 restraints weight = 18048.844|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3694 r_free = 0.3694 target = 0.095057 restraints weight = 12553.404|
|-----------------------------------------------------------------------------|
r_work (final): 0.3564
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7724
moved from start:          0.3596

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.050  13403  Z= 0.250
  Angle     :  0.709   7.068  19459  Z= 0.414
  Chirality :  0.042   0.156   2218
  Planarity :  0.005   0.046   1377
  Dihedral  : 33.689 178.879   4273
  Min Nonbonded Distance : 2.077

Molprobity Statistics.
  All-atom Clashscore : 11.72
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.55 %
    Favored  : 96.45 %
  Rotamer:
    Outliers :  4.59 %
    Allowed  : 20.57 %
    Favored  : 74.84 %
  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:  0.75 (0.31), residues: 760
  helix:  1.52 (0.23), residues: 523
  sheet:  None (None), residues: 0
  loop : -1.91 (0.37), residues: 237

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.012   0.002   HIS I  39 
 PHE   0.015   0.002   PHE S  62 
 TYR   0.039   0.003   TYR M  80 
 ARG   0.005   0.001   ARG K  71 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.09436 (  768)
  hydrogen bonds       : angle       3.54322 ( 1860)
  covalent geometry    : bond        0.00567 (13403)
  covalent geometry    : angle       0.70936 (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
  146 residues out of total 646 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 117
  time to evaluate  : 0.870 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: I  120 MET cc_start: 0.7088 (mtt) cc_final: 0.6869 (mtt)
REVERT: K  112 GLN cc_start: 0.7774 (mm110) cc_final: 0.7326 (mp10)
REVERT: M   68 GLU cc_start: 0.8339 (tp30) cc_final: 0.7773 (tp30)
REVERT: M   73 GLU cc_start: 0.7939 (tp30) cc_final: 0.7667 (tp30)
REVERT: M  117 LYS cc_start: 0.8535 (tptm) cc_final: 0.8268 (mtpt)
REVERT: O   84 PHE cc_start: 0.8626 (OUTLIER) cc_final: 0.8326 (m-80)
REVERT: O  105 GLU cc_start: 0.7646 (mm-30) cc_final: 0.7425 (mm-30)
REVERT: Q   35 ARG cc_start: 0.7439 (mtp85) cc_final: 0.7131 (mtp180)
REVERT: S   77 LEU cc_start: 0.8610 (OUTLIER) cc_final: 0.8193 (mp)
  outliers start: 29
  outliers final: 18
  residues processed: 139
  average time/residue: 0.2961
  time to fit residues: 55.3981
Evaluate side-chains
  127 residues out of total 646 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 107
  time to evaluate  : 0.966 
-------------------------------------------------------------------------------
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 K residue   65 LEU
Chi-restraints excluded: chain K residue   76 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   87 VAL
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:    4.9990
   chunk 15 optimal weight:    2.9990
   chunk 67 optimal weight:    0.9980
   chunk 73 optimal weight:    2.9990
   chunk 63 optimal weight:    0.6980
   chunk 59 optimal weight:    0.5980
   chunk 51 optimal weight:    0.9990
   chunk 79 optimal weight:    0.5980
   chunk 17 optimal weight:    0.8980
   overall best weight:    0.7580

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

Flipped N/Q/H residues before XYZ refinement:
I  85 GLN
** R  31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
R  82 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4030 r_free = 0.4030 target = 0.117691 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.3556 r_free = 0.3556 target = 0.089687 restraints weight = 31754.902|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3594 r_free = 0.3594 target = 0.091729 restraints weight = 17531.291|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 43)----------------|
| r_work = 0.3617 r_free = 0.3617 target = 0.093046 restraints weight = 12071.200|
|-----------------------------------------------------------------------------|
r_work (final): 0.3574
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7635
moved from start:          0.3692

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     :  0.624   5.377  19459  Z= 0.368
  Chirality :  0.037   0.152   2218
  Planarity :  0.004   0.048   1377
  Dihedral  : 33.340 179.881   4273
  Min Nonbonded Distance : 2.066

Molprobity Statistics.
  All-atom Clashscore : 10.20
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.29 %
    Favored  : 96.71 %
  Rotamer:
    Outliers :  3.16 %
    Allowed  : 21.84 %
    Favored  : 75.00 %
  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:  1.32 (0.31), residues: 760
  helix:  1.97 (0.23), residues: 527
  sheet:  None (None), residues: 0
  loop : -1.80 (0.37), residues: 233

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   0.037   0.002   TYR S  80 
 ARG   0.004   0.000   ARG K  35 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.07679 (  768)
  hydrogen bonds       : angle       3.03612 ( 1860)
  covalent geometry    : bond        0.00384 (13403)
  covalent geometry    : angle       0.62401 (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
  144 residues out of total 646 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 124
  time to evaluate  : 0.944 
Fit side-chains
   revert: symmetry clash
REVERT: I  120 MET cc_start: 0.6689 (mtt) cc_final: 0.6479 (mtt)
REVERT: J   88 TYR cc_start: 0.7787 (m-10) cc_final: 0.7302 (m-10)
REVERT: K   41 GLU cc_start: 0.7748 (tp30) cc_final: 0.7524 (tt0)
REVERT: K   71 ARG cc_start: 0.7866 (tpt90) cc_final: 0.7268 (tmt-80)
REVERT: K  112 GLN cc_start: 0.7616 (mm110) cc_final: 0.7191 (mp10)
REVERT: M   73 GLU cc_start: 0.7899 (tp30) cc_final: 0.7673 (tp30)
REVERT: M  117 LYS cc_start: 0.8629 (tptm) cc_final: 0.8279 (mtpt)
REVERT: O  105 GLU cc_start: 0.7454 (mm-30) cc_final: 0.7078 (mm-30)
REVERT: Q   35 ARG cc_start: 0.7239 (mtp85) cc_final: 0.6886 (mtp180)
REVERT: S   77 LEU cc_start: 0.8203 (OUTLIER) cc_final: 0.7747 (mp)
  outliers start: 20
  outliers final: 12
  residues processed: 134
  average time/residue: 0.3071
  time to fit residues: 55.4257
Evaluate side-chains
  129 residues out of total 646 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 116
  time to evaluate  : 0.941 
-------------------------------------------------------------------------------
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 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   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 27 optimal weight:    3.9990
   chunk 80 optimal weight:    0.4980
   chunk 41 optimal weight:    0.0060
   chunk 28 optimal weight:    0.7980
   chunk 83 optimal weight:    2.9990
   chunk 46 optimal weight:    2.9990
   chunk 29 optimal weight:    0.9980
   chunk 68 optimal weight:    2.9990
   chunk 34 optimal weight:    2.9990
   chunk 96 optimal weight:    3.9990
   chunk 86 optimal weight:    2.9990
   overall best weight:    1.0598

-------------------------------------------------------------------------------
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 = 0.117653 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3556 r_free = 0.3556 target = 0.089439 restraints weight = 31826.333|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 52)----------------|
| r_work = 0.3593 r_free = 0.3593 target = 0.091418 restraints weight = 17651.175|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 45)----------------|
| r_work = 0.3616 r_free = 0.3616 target = 0.092721 restraints weight = 12202.518|
|-----------------------------------------------------------------------------|
r_work (final): 0.3556
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7666
moved from start:          0.3935

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= 0.185
  Angle     :  0.628   5.269  19459  Z= 0.371
  Chirality :  0.038   0.183   2218
  Planarity :  0.004   0.048   1377
  Dihedral  : 33.311 179.461   4271
  Min Nonbonded Distance : 2.060

Molprobity Statistics.
  All-atom Clashscore : 10.20
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.89 %
    Favored  : 97.11 %
  Rotamer:
    Outliers :  3.01 %
    Allowed  : 22.78 %
    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:  1.43 (0.31), residues: 760
  helix:  2.06 (0.23), residues: 527
  sheet:  None (None), residues: 0
  loop : -1.79 (0.38), residues: 233

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   0.037   0.002   TYR S  80 
 ARG   0.006   0.000   ARG K  35 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.07900 (  768)
  hydrogen bonds       : angle       3.06699 ( 1860)
  covalent geometry    : bond        0.00416 (13403)
  covalent geometry    : angle       0.62808 (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
  132 residues out of total 646 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 113
  time to evaluate  : 0.969 
Fit side-chains
   revert: symmetry clash
REVERT: I  120 MET cc_start: 0.6800 (mtt) cc_final: 0.6586 (mtt)
REVERT: K   64 GLU cc_start: 0.8374 (tm-30) cc_final: 0.8128 (tm-30)
REVERT: K   71 ARG cc_start: 0.7871 (tpt90) cc_final: 0.7381 (tmt-80)
REVERT: K  112 GLN cc_start: 0.7659 (mm110) cc_final: 0.7231 (mp10)
REVERT: M   73 GLU cc_start: 0.7830 (tp30) cc_final: 0.7570 (tp30)
REVERT: M  117 LYS cc_start: 0.8618 (tptm) cc_final: 0.8295 (mtpt)
REVERT: O  105 GLU cc_start: 0.7462 (mm-30) cc_final: 0.7086 (mm-30)
REVERT: Q   35 ARG cc_start: 0.7284 (mtp85) cc_final: 0.6931 (mtp180)
REVERT: S   90 GLU cc_start: 0.7096 (mp0) cc_final: 0.6879 (mp0)
  outliers start: 19
  outliers final: 15
  residues processed: 124
  average time/residue: 0.3161
  time to fit residues: 52.8428
Evaluate side-chains
  127 residues out of total 646 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 112
  time to evaluate  : 0.863 
-------------------------------------------------------------------------------
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 J residue   86 VAL
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 O residue   39 HIS
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   87 THR
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 103
   random chunks:
   chunk 67 optimal weight:    2.9990
   chunk 83 optimal weight:    2.9990
   chunk 84 optimal weight:    0.1980
   chunk 74 optimal weight:    4.9990
   chunk 41 optimal weight:    0.8980
   chunk 28 optimal weight:    3.9990
   chunk 23 optimal weight:    0.6980
   chunk 82 optimal weight:    0.6980
   chunk 12 optimal weight:    5.9990
   chunk 20 optimal weight:    0.6980
   chunk 18 optimal weight:    0.8980
   overall best weight:    0.6380

-------------------------------------------------------------------------------
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 = 0.4057 r_free = 0.4057 target = 0.119253 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3581 r_free = 0.3581 target = 0.090877 restraints weight = 32271.177|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 41)----------------|
| r_work = 0.3620 r_free = 0.3620 target = 0.093021 restraints weight = 17065.758|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 46)----------------|
| r_work = 0.3645 r_free = 0.3645 target = 0.094463 restraints weight = 11507.174|
|-----------------------------------------------------------------------------|
r_work (final): 0.3586
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7606
moved from start:          0.4074

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.053  13403  Z= 0.165
  Angle     :  0.606   5.685  19459  Z= 0.359
  Chirality :  0.037   0.154   2218
  Planarity :  0.004   0.050   1377
  Dihedral  : 33.169 179.829   4271
  Min Nonbonded Distance : 2.069

Molprobity Statistics.
  All-atom Clashscore : 9.67
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.89 %
    Favored  : 97.11 %
  Rotamer:
    Outliers :  2.37 %
    Allowed  : 24.84 %
    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 (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:  1.67 (0.31), residues: 760
  helix:  2.23 (0.23), residues: 528
  sheet:  None (None), residues: 0
  loop : -1.67 (0.38), residues: 232

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.004   0.001   HIS I  39 
 PHE   0.007   0.001   PHE S  62 
 TYR   0.017   0.001   TYR S  80 
 ARG   0.006   0.000   ARG K  35 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.07320 (  768)
  hydrogen bonds       : angle       2.89976 ( 1860)
  covalent geometry    : bond        0.00365 (13403)
  covalent geometry    : angle       0.60645 (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: 15
    poor density    : 118
  time to evaluate  : 0.871 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: J   88 TYR cc_start: 0.7702 (m-10) cc_final: 0.7482 (m-10)
REVERT: K   64 GLU cc_start: 0.8374 (tm-30) cc_final: 0.8079 (tm-30)
REVERT: M   43 LYS cc_start: 0.7200 (tppt) cc_final: 0.6540 (ptpt)
REVERT: M   73 GLU cc_start: 0.7820 (tp30) cc_final: 0.7618 (tp30)
REVERT: M  117 LYS cc_start: 0.8588 (tptm) cc_final: 0.8250 (mtpt)
REVERT: O   50 GLU cc_start: 0.8423 (mp0) cc_final: 0.8143 (mp0)
REVERT: O  105 GLU cc_start: 0.7382 (mm-30) cc_final: 0.7098 (mm-30)
REVERT: S   90 GLU cc_start: 0.7051 (mp0) cc_final: 0.6826 (mp0)
  outliers start: 15
  outliers final: 11
  residues processed: 127
  average time/residue: 0.3085
  time to fit residues: 52.4207
Evaluate side-chains
  121 residues out of total 646 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 110
  time to evaluate  : 0.854 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain I residue   60 LEU
Chi-restraints excluded: chain I residue   65 LEU
Chi-restraints excluded: chain K residue   15 LYS
Chi-restraints excluded: chain K residue   16 THR
Chi-restraints excluded: chain O residue   39 HIS
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   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:    6.9990
   chunk 46 optimal weight:    2.9990
   chunk 29 optimal weight:    0.9980
   chunk 52 optimal weight:    1.9990
   chunk 18 optimal weight:    0.9990
   chunk 26 optimal weight:    0.8980
   chunk 20 optimal weight:    0.5980
   chunk 65 optimal weight:    1.9990
   chunk 27 optimal weight:    0.7980
   overall best weight:    0.8582

-------------------------------------------------------------------------------
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

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4031 r_free = 0.4031 target = 0.117628 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3549 r_free = 0.3549 target = 0.089282 restraints weight = 32169.199|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 52)----------------|
| r_work = 0.3586 r_free = 0.3586 target = 0.091298 restraints weight = 17795.712|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 56)----------------|
| r_work = 0.3610 r_free = 0.3610 target = 0.092649 restraints weight = 12273.903|
|-----------------------------------------------------------------------------|
r_work (final): 0.3564
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7647
moved from start:          0.4351

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= 0.174
  Angle     :  0.614   6.298  19459  Z= 0.363
  Chirality :  0.037   0.153   2218
  Planarity :  0.004   0.049   1377
  Dihedral  : 33.112 178.909   4271
  Min Nonbonded Distance : 2.066

Molprobity Statistics.
  All-atom Clashscore : 10.38
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.16 %
    Favored  : 96.84 %
  Rotamer:
    Outliers :  2.85 %
    Allowed  : 25.32 %
    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:  1.67 (0.31), residues: 760
  helix:  2.21 (0.23), residues: 528
  sheet:  None (None), residues: 0
  loop : -1.62 (0.38), residues: 232

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   0.032   0.002   TYR S  80 
 ARG   0.005   0.000   ARG K  35 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.07610 (  768)
  hydrogen bonds       : angle       2.97160 ( 1860)
  covalent geometry    : bond        0.00388 (13403)
  covalent geometry    : angle       0.61423 (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
  130 residues out of total 646 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 112
  time to evaluate  : 0.884 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: K   64 GLU cc_start: 0.8386 (tm-30) cc_final: 0.8050 (tm-30)
REVERT: K   71 ARG cc_start: 0.7812 (tpt90) cc_final: 0.7438 (tmt-80)
REVERT: M   43 LYS cc_start: 0.7240 (tppt) cc_final: 0.6563 (ptpt)
REVERT: M   73 GLU cc_start: 0.7899 (tp30) cc_final: 0.7660 (tp30)
REVERT: M  117 LYS cc_start: 0.8576 (tptm) cc_final: 0.8247 (mtpt)
REVERT: O   37 LYS cc_start: 0.8139 (tppt) cc_final: 0.7773 (mmmm)
REVERT: O  105 GLU cc_start: 0.7453 (mm-30) cc_final: 0.7189 (mm-30)
REVERT: S   90 GLU cc_start: 0.7192 (mp0) cc_final: 0.6912 (mp0)
  outliers start: 18
  outliers final: 15
  residues processed: 125
  average time/residue: 0.3127
  time to fit residues: 52.5048
Evaluate side-chains
  123 residues out of total 646 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 108
  time to evaluate  : 0.838 
-------------------------------------------------------------------------------
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  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 O residue   39 HIS
Chi-restraints excluded: chain O residue  118 THR
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   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:    3.9990
   chunk 27 optimal weight:    2.9990
   chunk 83 optimal weight:    2.9990
   chunk 77 optimal weight:    2.9990
   chunk 16 optimal weight:    0.6980
   chunk 6 optimal weight:    5.9990
   chunk 53 optimal weight:    2.9990
   chunk 25 optimal weight:    3.9990
   chunk 44 optimal weight:    2.9990
   chunk 35 optimal weight:    2.9990
   chunk 99 optimal weight:    5.9990
   overall best weight:    2.5388

-------------------------------------------------------------------------------
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 = 0.3971 r_free = 0.3971 target = 0.113615 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 60)----------------|
| r_work = 0.3469 r_free = 0.3469 target = 0.084941 restraints weight = 32286.092|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 45)----------------|
| r_work = 0.3505 r_free = 0.3505 target = 0.086841 restraints weight = 17876.025|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 57)----------------|
| r_work = 0.3528 r_free = 0.3528 target = 0.088098 restraints weight = 12402.230|
|-----------------------------------------------------------------------------|
r_work (final): 0.3475
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7806
moved from start:          0.4927

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.007   0.049  13403  Z= 0.283
  Angle     :  0.728   6.437  19459  Z= 0.424
  Chirality :  0.043   0.157   2218
  Planarity :  0.005   0.043   1377
  Dihedral  : 33.410 179.887   4271
  Min Nonbonded Distance : 2.033

Molprobity Statistics.
  All-atom Clashscore : 11.01
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.87 %
    Favored  : 95.13 %
  Rotamer:
    Outliers :  3.96 %
    Allowed  : 24.53 %
    Favored  : 71.52 %
  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:  0.82 (0.30), residues: 760
  helix:  1.59 (0.23), residues: 526
  sheet:  None (None), residues: 0
  loop : -1.97 (0.36), residues: 234

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.010   0.002   HIS I  39 
 PHE   0.014   0.002   PHE S  62 
 TYR   0.068   0.003   TYR S  80 
 ARG   0.006   0.001   ARG K  35 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.09800 (  768)
  hydrogen bonds       : angle       3.54869 ( 1860)
  covalent geometry    : bond        0.00651 (13403)
  covalent geometry    : angle       0.72750 (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
  130 residues out of total 646 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 105
  time to evaluate  : 0.858 
Fit side-chains
   revert: symmetry clash
REVERT: K   71 ARG cc_start: 0.8173 (tpt90) cc_final: 0.7904 (tmt-80)
REVERT: K   75 LYS cc_start: 0.8670 (ttmm) cc_final: 0.8349 (ttmm)
REVERT: M   76 ARG cc_start: 0.8287 (OUTLIER) cc_final: 0.8014 (ptp-110)
REVERT: M  117 LYS cc_start: 0.8658 (tptm) cc_final: 0.8308 (mtpt)
REVERT: O   50 GLU cc_start: 0.8554 (mp0) cc_final: 0.8314 (mp0)
REVERT: O  105 GLU cc_start: 0.7755 (mm-30) cc_final: 0.7483 (mm-30)
REVERT: S   90 GLU cc_start: 0.7386 (mp0) cc_final: 0.7179 (mp0)
  outliers start: 25
  outliers final: 21
  residues processed: 122
  average time/residue: 0.3298
  time to fit residues: 53.8798
Evaluate side-chains
  125 residues out of total 646 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 103
  time to evaluate  : 1.003 
-------------------------------------------------------------------------------
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   71 VAL
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   76 ARG
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  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:    0.7980
   chunk 51 optimal weight:    2.9990
   chunk 86 optimal weight:    1.9990
   chunk 91 optimal weight:    4.9990
   chunk 47 optimal weight:    0.9980
   chunk 79 optimal weight:    2.9990
   chunk 84 optimal weight:    0.1980
   chunk 94 optimal weight:    5.9990
   chunk 71 optimal weight:    0.7980
   chunk 96 optimal weight:    3.9990
   chunk 8 optimal weight:    3.9990
   overall best weight:    0.9582

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

Flipped N/Q/H residues before XYZ refinement:
M 106 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 = 0.4023 r_free = 0.4023 target = 0.117119 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 61)----------------|
| r_work = 0.3546 r_free = 0.3546 target = 0.089010 restraints weight = 31746.196|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3582 r_free = 0.3582 target = 0.090978 restraints weight = 17347.395|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 45)----------------|
| r_work = 0.3604 r_free = 0.3604 target = 0.092276 restraints weight = 11955.398|
|-----------------------------------------------------------------------------|
r_work (final): 0.3544
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7679
moved from start:          0.4865

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= 0.181
  Angle     :  0.641   6.673  19459  Z= 0.378
  Chirality :  0.038   0.153   2218
  Planarity :  0.004   0.048   1377
  Dihedral  : 33.198 179.956   4271
  Min Nonbonded Distance : 2.061

Molprobity Statistics.
  All-atom Clashscore : 10.47
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.16 %
    Favored  : 96.84 %
  Rotamer:
    Outliers :  2.69 %
    Allowed  : 25.32 %
    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:  1.24 (0.31), residues: 760
  helix:  1.90 (0.23), residues: 528
  sheet:  None (None), residues: 0
  loop : -1.83 (0.37), residues: 232

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.006   0.001   HIS I  39 
 PHE   0.007   0.001   PHE S  62 
 TYR   0.030   0.002   TYR Q  88 
 ARG   0.007   0.000   ARG K  35 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.07867 (  768)
  hydrogen bonds       : angle       3.08579 ( 1860)
  covalent geometry    : bond        0.00403 (13403)
  covalent geometry    : angle       0.64086 (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
  127 residues out of total 646 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 110
  time to evaluate  : 0.886 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: K   57 TYR cc_start: 0.8833 (t80) cc_final: 0.8612 (t80)
REVERT: K   64 GLU cc_start: 0.8377 (tm-30) cc_final: 0.8026 (tm-30)
REVERT: K   71 ARG cc_start: 0.7826 (tpt90) cc_final: 0.7467 (tmt-80)
REVERT: K   75 LYS cc_start: 0.8365 (ttmm) cc_final: 0.8026 (ttmm)
REVERT: M   43 LYS cc_start: 0.7338 (tppt) cc_final: 0.6615 (ptpt)
REVERT: M  106 HIS cc_start: 0.8387 (OUTLIER) cc_final: 0.8105 (m-70)
REVERT: M  117 LYS cc_start: 0.8629 (tptm) cc_final: 0.8276 (mtpt)
REVERT: O   37 LYS cc_start: 0.8009 (tppt) cc_final: 0.7611 (mmmm)
REVERT: O   84 PHE cc_start: 0.8926 (OUTLIER) cc_final: 0.8670 (m-80)
REVERT: O  105 GLU cc_start: 0.7527 (mm-30) cc_final: 0.7146 (mm-30)
REVERT: S   90 GLU cc_start: 0.7174 (mp0) cc_final: 0.6946 (mp0)
  outliers start: 17
  outliers final: 12
  residues processed: 123
  average time/residue: 0.3251
  time to fit residues: 53.2701
Evaluate side-chains
  122 residues out of total 646 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 108
  time to evaluate  : 0.881 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain I residue   60 LEU
Chi-restraints excluded: chain I residue   65 LEU
Chi-restraints excluded: chain K residue   16 THR
Chi-restraints excluded: chain M residue  106 HIS
Chi-restraints excluded: chain O residue   39 HIS
Chi-restraints excluded: chain O residue   84 PHE
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 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 56 optimal weight:    3.9990
   chunk 55 optimal weight:    0.9980
   chunk 38 optimal weight:    0.8980
   chunk 74 optimal weight:    4.9990
   chunk 22 optimal weight:    4.9990
   chunk 62 optimal weight:    0.9990
   chunk 54 optimal weight:    2.9990
   chunk 97 optimal weight:    5.9990
   chunk 2 optimal weight:    7.9990
   chunk 21 optimal weight:    0.8980
   chunk 63 optimal weight:    0.5980
   overall best weight:    0.8782

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

Flipped N/Q/H residues before XYZ refinement:
M 106 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 = 0.4034 r_free = 0.4034 target = 0.117720 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3555 r_free = 0.3555 target = 0.089552 restraints weight = 31723.636|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 45)----------------|
| r_work = 0.3592 r_free = 0.3592 target = 0.091541 restraints weight = 17280.922|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 55)----------------|
| r_work = 0.3615 r_free = 0.3615 target = 0.092853 restraints weight = 11858.463|
|-----------------------------------------------------------------------------|
r_work (final): 0.3554
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7658
moved from start:          0.4931

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= 0.178
  Angle     :  0.640   7.288  19459  Z= 0.377
  Chirality :  0.038   0.154   2218
  Planarity :  0.004   0.048   1377
  Dihedral  : 33.152 179.782   4271
  Min Nonbonded Distance : 2.068

Molprobity Statistics.
  All-atom Clashscore : 10.87
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.08 %
    Favored  : 95.92 %
  Rotamer:
    Outliers :  2.37 %
    Allowed  : 26.11 %
    Favored  : 71.52 %
  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:  1.35 (0.31), residues: 760
  helix:  1.98 (0.23), residues: 529
  sheet:  None (None), residues: 0
  loop : -1.77 (0.37), residues: 231

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   0.024   0.002   TYR Q  88 
 ARG   0.008   0.000   ARG K  35 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.07748 (  768)
  hydrogen bonds       : angle       3.06160 ( 1860)
  covalent geometry    : bond        0.00396 (13403)
  covalent geometry    : angle       0.64043 (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
  124 residues out of total 646 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 109
  time to evaluate  : 0.995 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: K   57 TYR cc_start: 0.8751 (t80) cc_final: 0.8534 (t80)
REVERT: K   64 GLU cc_start: 0.8408 (tm-30) cc_final: 0.8086 (tm-30)
REVERT: K   71 ARG cc_start: 0.7788 (tpt90) cc_final: 0.7475 (tmt-80)
REVERT: K   75 LYS cc_start: 0.8465 (ttmm) cc_final: 0.8136 (ttmm)
REVERT: M   43 LYS cc_start: 0.7131 (tppt) cc_final: 0.6515 (ptpt)
REVERT: M  117 LYS cc_start: 0.8597 (tptm) cc_final: 0.8339 (mtpt)
REVERT: O   37 LYS cc_start: 0.7857 (tppt) cc_final: 0.7590 (mmmm)
REVERT: O  105 GLU cc_start: 0.7396 (mm-30) cc_final: 0.7153 (mm-30)
  outliers start: 15
  outliers final: 15
  residues processed: 121
  average time/residue: 0.3263
  time to fit residues: 52.9530
Evaluate side-chains
  122 residues out of total 646 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 107
  time to evaluate  : 0.908 
-------------------------------------------------------------------------------
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  106 HIS
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 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 82 optimal weight:    0.8980
   chunk 52 optimal weight:    3.9990
   chunk 46 optimal weight:    0.9980
   chunk 6 optimal weight:    5.9990
   chunk 77 optimal weight:    3.9990
   chunk 75 optimal weight:    0.9990
   chunk 45 optimal weight:    1.9990
   chunk 26 optimal weight:    0.6980
   chunk 35 optimal weight:    0.6980
   chunk 25 optimal weight:    4.9990
   chunk 34 optimal weight:    0.7980
   overall best weight:    0.8180

-------------------------------------------------------------------------------
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 = 0.4015 r_free = 0.4015 target = 0.116753 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3533 r_free = 0.3533 target = 0.088627 restraints weight = 32132.345|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3571 r_free = 0.3571 target = 0.090654 restraints weight = 17589.366|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 54)----------------|
| r_work = 0.3594 r_free = 0.3594 target = 0.091980 restraints weight = 12043.761|
|-----------------------------------------------------------------------------|
r_work (final): 0.3550
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7664
moved from start:          0.4940

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= 0.176
  Angle     :  0.640   7.309  19459  Z= 0.377
  Chirality :  0.037   0.151   2218
  Planarity :  0.004   0.048   1377
  Dihedral  : 33.127 179.764   4271
  Min Nonbonded Distance : 2.070

Molprobity Statistics.
  All-atom Clashscore : 10.43
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.68 %
    Favored  : 96.32 %
  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:  1.38 (0.31), residues: 760
  helix:  1.98 (0.23), residues: 529
  sheet:  None (None), residues: 0
  loop : -1.72 (0.38), residues: 231

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.014   0.001   HIS M 106 
 PHE   0.008   0.001   PHE S  62 
 TYR   0.049   0.002   TYR S  80 
 ARG   0.008   0.000   ARG K  35 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.07644 (  768)
  hydrogen bonds       : angle       3.06911 ( 1860)
  covalent geometry    : bond        0.00392 (13403)
  covalent geometry    : angle       0.64021 (19459)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 4049.95 seconds
wall clock time: 71 minutes 29.20 seconds (4289.20 seconds total)