Starting phenix.real_space_refine
on Tue May 13 04:38:08 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9lu9_63392/05_2025/9lu9_63392.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9lu9_63392/05_2025/9lu9_63392.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.3
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/9lu9_63392/05_2025/9lu9_63392.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9lu9_63392/05_2025/9lu9_63392.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9lu9_63392/05_2025/9lu9_63392.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9lu9_63392/05_2025/9lu9_63392.cif"
  }
  resolution = 3.3
  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=   0.001 sd=   0.036
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: 4
    Type Number    sf(0)   Gaussians
     S      52      5.16       5
     C    6363      2.51       5
     N    1619      2.21       5
     O    1824      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 60 residue(s): 0.03s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib"
  Total number of atoms: 9858
  Number of models: 1
  Model: ""
    Number of chains: 8
    Chain: "A"
      Number of atoms: 1669
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 218, 1669
          Classifications: {'peptide': 218}
          Link IDs: {'PTRANS': 9, 'TRANS': 208}
    Chain: "B"
      Number of atoms: 1865
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 246, 1865
          Classifications: {'peptide': 246}
          Link IDs: {'PTRANS': 9, 'TRANS': 236}
    Chain: "C"
      Number of atoms: 1865
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 246, 1865
          Classifications: {'peptide': 246}
          Link IDs: {'PTRANS': 9, 'TRANS': 236}
    Chain: "D"
      Number of atoms: 1865
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 246, 1865
          Classifications: {'peptide': 246}
          Link IDs: {'PTRANS': 9, 'TRANS': 236}
    Chain: "E"
      Number of atoms: 1865
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 246, 1865
          Classifications: {'peptide': 246}
          Link IDs: {'PTRANS': 9, 'TRANS': 236}
    Chain: "F"
      Number of atoms: 372
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 45, 372
          Classifications: {'peptide': 45}
          Link IDs: {'TRANS': 44}
    Chain: "G"
      Number of atoms: 288
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 34, 288
          Classifications: {'peptide': 34}
          Link IDs: {'TRANS': 33}
    Chain: "G"
      Number of atoms: 69
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 69
          Unusual residues: {'AV0': 1}
          Classifications: {'undetermined': 1}
  Time building chain proxies: 6.30, per 1000 atoms: 0.64
  Number of scatterers: 9858
  At special positions: 0
  Unit cell: (91.52, 97.68, 117.92, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     S      52     16.00
     O    1824      8.00
     N    1619      7.00
     C    6363      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: 2.74
  Conformation dependent library (CDL) restraints added in 1.2 seconds
  

  2534 Ramachandran restraints generated.
    1267 Oldfield, 0 Emsley, 1267 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2344

  Finding SS restraints...
    Secondary structure from input PDB file:
      61 helices and 0 sheets defined
      91.7% alpha, 0.0% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.84
  Creating SS restraints...
    Processing helix  chain 'A' and resid 32 through 51
      removed outlier: 3.950A  pdb=" N   GLY A  41 " --> pdb=" O   LEU A  37 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 52 through 57
    Processing helix  chain 'A' and resid 58 through 67
    Processing helix  chain 'A' and resid 72 through 77
    Processing helix  chain 'A' and resid 77 through 91
      removed outlier: 3.828A  pdb=" N   MET A  86 " --> pdb=" O   VAL A  82 " (cutoff:3.500A)
      removed outlier: 3.672A  pdb=" N   ARG A  89 " --> pdb=" O   SER A  85 " (cutoff:3.500A)
      removed outlier: 3.571A  pdb=" N   GLU A  91 " --> pdb=" O   VAL A  87 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 92 through 94
      No H-bonds generated for 'chain 'A' and resid 92 through 94'
    Processing helix  chain 'A' and resid 95 through 100
    Processing helix  chain 'A' and resid 105 through 116
    Processing helix  chain 'A' and resid 120 through 171
      removed outlier: 3.599A  pdb=" N   LEU A 145 " --> pdb=" O   ASN A 141 " (cutoff:3.500A)
      removed outlier: 3.751A  pdb=" N   PHE A 146 " --> pdb=" O   TYR A 142 " (cutoff:3.500A)
      Proline residue:  A 154  - end of helix
      removed outlier: 3.551A  pdb=" N   ILE A 158 " --> pdb=" O   PRO A 154 " (cutoff:3.500A)
      removed outlier: 3.519A  pdb=" N   HIS A 171 " --> pdb=" O   GLN A 167 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 179 through 199
      removed outlier: 3.901A  pdb=" N   ALA A 188 " --> pdb=" O   VAL A 184 " (cutoff:3.500A)
      removed outlier: 4.045A  pdb=" N   THR A 189 " --> pdb=" O   ALA A 185 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 199 through 231
    Processing helix  chain 'A' and resid 233 through 245
      removed outlier: 3.653A  pdb=" N   TYR A 244 " --> pdb=" O   LYS A 240 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 2 through 23
    Processing helix  chain 'B' and resid 26 through 31
      removed outlier: 3.777A  pdb=" N   PHE B  31 " --> pdb=" O   THR B  28 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 32 through 51
    Processing helix  chain 'B' and resid 52 through 68
      removed outlier: 3.762A  pdb=" N   ILE B  56 " --> pdb=" O   PRO B  52 " (cutoff:3.500A)
      Proline residue:  B  60  - end of helix
    Processing helix  chain 'B' and resid 73 through 91
      removed outlier: 3.797A  pdb=" N   VAL B  82 " --> pdb=" O   LEU B  78 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 92 through 94
      No H-bonds generated for 'chain 'B' and resid 92 through 94'
    Processing helix  chain 'B' and resid 95 through 100
      removed outlier: 3.620A  pdb=" N   LYS B  99 " --> pdb=" O   ALA B  95 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 105 through 118
    Processing helix  chain 'B' and resid 120 through 171
      removed outlier: 3.599A  pdb=" N   LEU B 145 " --> pdb=" O   ASN B 141 " (cutoff:3.500A)
      removed outlier: 3.757A  pdb=" N   PHE B 146 " --> pdb=" O   TYR B 142 " (cutoff:3.500A)
      Proline residue:  B 154  - end of helix
      removed outlier: 3.610A  pdb=" N   HIS B 171 " --> pdb=" O   GLN B 167 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 178 through 199
      removed outlier: 3.828A  pdb=" N   ALA B 183 " --> pdb=" O   GLY B 179 " (cutoff:3.500A)
      removed outlier: 3.785A  pdb=" N   ALA B 185 " --> pdb=" O   SER B 181 " (cutoff:3.500A)
      removed outlier: 3.878A  pdb=" N   PHE B 186 " --> pdb=" O   ILE B 182 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 199 through 231
    Processing helix  chain 'B' and resid 233 through 245
      removed outlier: 3.500A  pdb=" N   VAL B 237 " --> pdb=" O   ASN B 233 " (cutoff:3.500A)
      removed outlier: 3.957A  pdb=" N   TYR B 244 " --> pdb=" O   LYS B 240 " (cutoff:3.500A)
      removed outlier: 3.725A  pdb=" N   ILE B 245 " --> pdb=" O   LEU B 241 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 2 through 22
    Processing helix  chain 'C' and resid 26 through 31
    Processing helix  chain 'C' and resid 32 through 51
    Processing helix  chain 'C' and resid 52 through 67
      removed outlier: 3.763A  pdb=" N   ILE C  56 " --> pdb=" O   PRO C  52 " (cutoff:3.500A)
      removed outlier: 3.573A  pdb=" N   LEU C  59 " --> pdb=" O   ARG C  55 " (cutoff:3.500A)
      Proline residue:  C  60  - end of helix
    Processing helix  chain 'C' and resid 73 through 92
    Processing helix  chain 'C' and resid 93 through 100
      removed outlier: 4.027A  pdb=" N   GLU C  97 " --> pdb=" O   VAL C  93 " (cutoff:3.500A)
      removed outlier: 3.605A  pdb=" N   GLN C  98 " --> pdb=" O   LEU C  94 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 105 through 117
    Processing helix  chain 'C' and resid 120 through 171
      removed outlier: 3.588A  pdb=" N   LEU C 145 " --> pdb=" O   ASN C 141 " (cutoff:3.500A)
      removed outlier: 3.778A  pdb=" N   PHE C 146 " --> pdb=" O   TYR C 142 " (cutoff:3.500A)
      Proline residue:  C 154  - end of helix
    Processing helix  chain 'C' and resid 177 through 199
      removed outlier: 3.873A  pdb=" N   SER C 181 " --> pdb=" O   GLN C 177 " (cutoff:3.500A)
      removed outlier: 3.568A  pdb=" N   ALA C 185 " --> pdb=" O   SER C 181 " (cutoff:3.500A)
      removed outlier: 4.011A  pdb=" N   ALA C 188 " --> pdb=" O   VAL C 184 " (cutoff:3.500A)
      removed outlier: 4.060A  pdb=" N   THR C 189 " --> pdb=" O   ALA C 185 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 199 through 231
    Processing helix  chain 'C' and resid 233 through 245
      removed outlier: 3.943A  pdb=" N   TYR C 244 " --> pdb=" O   LYS C 240 " (cutoff:3.500A)
      removed outlier: 3.633A  pdb=" N   ILE C 245 " --> pdb=" O   LEU C 241 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 2 through 24
    Processing helix  chain 'D' and resid 26 through 30
    Processing helix  chain 'D' and resid 32 through 51
    Processing helix  chain 'D' and resid 52 through 68
      removed outlier: 3.730A  pdb=" N   ILE D  56 " --> pdb=" O   PRO D  52 " (cutoff:3.500A)
      Proline residue:  D  60  - end of helix
    Processing helix  chain 'D' and resid 73 through 92
      removed outlier: 3.628A  pdb=" N   TRP D  77 " --> pdb=" O   GLU D  73 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 93 through 101
      removed outlier: 3.710A  pdb=" N   GLU D  97 " --> pdb=" O   VAL D  93 " (cutoff:3.500A)
      removed outlier: 3.598A  pdb=" N   GLN D  98 " --> pdb=" O   LEU D  94 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 105 through 117
    Processing helix  chain 'D' and resid 120 through 169
      removed outlier: 3.613A  pdb=" N   LEU D 145 " --> pdb=" O   ASN D 141 " (cutoff:3.500A)
      removed outlier: 3.729A  pdb=" N   PHE D 146 " --> pdb=" O   TYR D 142 " (cutoff:3.500A)
      Proline residue:  D 154  - end of helix
    Processing helix  chain 'D' and resid 177 through 199
      removed outlier: 3.532A  pdb=" N   ILE D 187 " --> pdb=" O   ALA D 183 " (cutoff:3.500A)
      removed outlier: 4.626A  pdb=" N   ALA D 188 " --> pdb=" O   VAL D 184 " (cutoff:3.500A)
      removed outlier: 4.777A  pdb=" N   THR D 189 " --> pdb=" O   ALA D 185 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 199 through 231
    Processing helix  chain 'D' and resid 233 through 243
      removed outlier: 3.567A  pdb=" N   THR D 243 " --> pdb=" O   LYS D 239 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 2 through 23
      removed outlier: 3.572A  pdb=" N   GLU E  23 " --> pdb=" O   GLY E  19 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 26 through 31
    Processing helix  chain 'E' and resid 32 through 51
    Processing helix  chain 'E' and resid 52 through 67
      removed outlier: 3.741A  pdb=" N   ILE E  56 " --> pdb=" O   PRO E  52 " (cutoff:3.500A)
      Proline residue:  E  60  - end of helix
    Processing helix  chain 'E' and resid 72 through 91
      removed outlier: 4.237A  pdb=" N   GLU E  76 " --> pdb=" O   SER E  72 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 93 through 101
    Processing helix  chain 'E' and resid 105 through 117
    Processing helix  chain 'E' and resid 120 through 171
      removed outlier: 3.593A  pdb=" N   LEU E 145 " --> pdb=" O   ASN E 141 " (cutoff:3.500A)
      removed outlier: 3.664A  pdb=" N   PHE E 146 " --> pdb=" O   TYR E 142 " (cutoff:3.500A)
      Proline residue:  E 154  - end of helix
    Processing helix  chain 'E' and resid 174 through 176
      No H-bonds generated for 'chain 'E' and resid 174 through 176'
    Processing helix  chain 'E' and resid 177 through 199
      removed outlier: 4.904A  pdb=" N   VAL E 184 " --> pdb=" O   PRO E 180 " (cutoff:3.500A)
      removed outlier: 4.153A  pdb=" N   ALA E 185 " --> pdb=" O   SER E 181 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 199 through 231
    Processing helix  chain 'E' and resid 233 through 245
      removed outlier: 3.930A  pdb=" N   TYR E 244 " --> pdb=" O   LYS E 240 " (cutoff:3.500A)
      removed outlier: 3.832A  pdb=" N   ILE E 245 " --> pdb=" O   LEU E 241 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 23 through 47
      removed outlier: 3.747A  pdb=" N   ASP F  30 " --> pdb=" O   ILE F  26 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 49 through 64
      removed outlier: 3.969A  pdb=" N   THR F  63 " --> pdb=" O   SER F  59 " (cutoff:3.500A)
      removed outlier: 3.550A  pdb=" N   PHE F  64 " --> pdb=" O   LEU F  60 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 23 through 53
      removed outlier: 4.368A  pdb=" N   THR G  27 " --> pdb=" O   ARG G  23 " (cutoff:3.500A)
      removed outlier: 3.618A  pdb=" N   ALA G  44 " --> pdb=" O   VAL G  40 " (cutoff:3.500A)

    850 hydrogen bonds defined for protein.
    2529 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 2.94

  Time building geometry restraints manager: 3.13 seconds

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

  Histogram of bond lengths:
        1.20 -     1.33: 2104
        1.33 -     1.46: 3092
        1.46 -     1.59: 4718
        1.59 -     1.72: 0
        1.72 -     1.85: 104
  Bond restraints: 10018
  Sorted by residual:
  bond pdb=" C   PHE B 200 "
       pdb=" O   PHE B 200 "
    ideal  model  delta    sigma   weight residual
    1.237  1.200  0.037 1.16e-02 7.43e+03 9.93e+00
  bond pdb=" CA  ALA D  66 "
       pdb=" CB  ALA D  66 "
    ideal  model  delta    sigma   weight residual
    1.529  1.480  0.048 1.58e-02 4.01e+03 9.39e+00
  bond pdb=" CA  ALA C 153 "
       pdb=" CB  ALA C 153 "
    ideal  model  delta    sigma   weight residual
    1.531  1.491  0.040 1.33e-02 5.65e+03 9.22e+00
  bond pdb=" CA  ALA E 153 "
       pdb=" CB  ALA E 153 "
    ideal  model  delta    sigma   weight residual
    1.531  1.495  0.036 1.33e-02 5.65e+03 7.41e+00
  bond pdb=" CA  ALA D 153 "
       pdb=" CB  ALA D 153 "
    ideal  model  delta    sigma   weight residual
    1.531  1.496  0.036 1.33e-02 5.65e+03 7.20e+00
  ... (remaining 10013 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.16: 12027
        2.16 -     4.32: 1399
        4.32 -     6.48: 141
        6.48 -     8.64: 14
        8.64 -    10.80: 2
  Bond angle restraints: 13583
  Sorted by residual:
  angle pdb=" N   PRO A 104 "
        pdb=" CA  PRO A 104 "
        pdb=" C   PRO A 104 "
      ideal   model   delta    sigma   weight residual
     113.53  102.73   10.80 1.39e+00 5.18e-01 6.04e+01
  angle pdb=" CA  ASP B   2 "
        pdb=" CB  ASP B   2 "
        pdb=" CG  ASP B   2 "
      ideal   model   delta    sigma   weight residual
     112.60  119.45   -6.85 1.00e+00 1.00e+00 4.69e+01
  angle pdb=" CA  ASN C 197 "
        pdb=" CB  ASN C 197 "
        pdb=" CG  ASN C 197 "
      ideal   model   delta    sigma   weight residual
     112.60  106.35    6.25 1.00e+00 1.00e+00 3.90e+01
  angle pdb=" CA  ASP E 133 "
        pdb=" CB  ASP E 133 "
        pdb=" CG  ASP E 133 "
      ideal   model   delta    sigma   weight residual
     112.60  118.21   -5.61 1.00e+00 1.00e+00 3.15e+01
  angle pdb=" CB  GLU C 138 "
        pdb=" CG  GLU C 138 "
        pdb=" CD  GLU C 138 "
      ideal   model   delta    sigma   weight residual
     112.60  121.05   -8.45 1.70e+00 3.46e-01 2.47e+01
  ... (remaining 13578 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    34.92: 5799
       34.92 -    69.84: 273
       69.84 -   104.76: 26
      104.76 -   139.68: 13
      139.68 -   174.61: 1
  Dihedral angle restraints: 6112
    sinusoidal: 2463
      harmonic: 3649
  Sorted by residual:
  dihedral pdb=" CD  ARG C  71 "
           pdb=" NE  ARG C  71 "
           pdb=" CZ  ARG C  71 "
           pdb=" NH1 ARG C  71 "
      ideal   model   delta sinusoidal    sigma   weight residual
       0.00  -72.34   72.34     1      1.00e+01 1.00e-02 6.69e+01
  dihedral pdb=" CD  ARG B 109 "
           pdb=" NE  ARG B 109 "
           pdb=" CZ  ARG B 109 "
           pdb=" NH1 ARG B 109 "
      ideal   model   delta sinusoidal    sigma   weight residual
       0.00   71.76  -71.76     1      1.00e+01 1.00e-02 6.60e+01
  dihedral pdb=" CD  ARG A 125 "
           pdb=" NE  ARG A 125 "
           pdb=" CZ  ARG A 125 "
           pdb=" NH1 ARG A 125 "
      ideal   model   delta sinusoidal    sigma   weight residual
       0.00   65.59  -65.59     1      1.00e+01 1.00e-02 5.63e+01
  ... (remaining 6109 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    1.005: 1646
       1.005 -    2.009: 0
       2.009 -    3.014: 0
       3.014 -    4.018: 0
       4.018 -    5.023: 1
  Chirality restraints: 1647
  Sorted by residual:
  chirality pdb=" C2  AV0 G 401 "
            pdb=" C1  AV0 G 401 "
            pdb=" C3  AV0 G 401 "
            pdb=" O2  AV0 G 401 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.51    2.51   -5.02 2.00e-01 2.50e+01 6.31e+02
  chirality pdb=" CA  ASP E 133 "
            pdb=" N   ASP E 133 "
            pdb=" C   ASP E 133 "
            pdb=" CB  ASP E 133 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    1.97    0.54 2.00e-01 2.50e+01 7.38e+00
  chirality pdb=" CA  ASN C 197 "
            pdb=" N   ASN C 197 "
            pdb=" C   ASN C 197 "
            pdb=" CB  ASN C 197 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.05    0.46 2.00e-01 2.50e+01 5.39e+00
  ... (remaining 1644 not shown)

  Planarity restraints: 1702
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CD  ARG C  71 "   -0.996 9.50e-02 1.11e+02   4.47e-01 1.24e+02
        pdb=" NE  ARG C  71 "    0.071 2.00e-02 2.50e+03
        pdb=" CZ  ARG C  71 "   -0.021 2.00e-02 2.50e+03
        pdb=" NH1 ARG C  71 "    0.005 2.00e-02 2.50e+03
        pdb=" NH2 ARG C  71 "   -0.012 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CD  ARG B 109 "   -0.955 9.50e-02 1.11e+02   4.29e-01 1.17e+02
        pdb=" NE  ARG B 109 "    0.073 2.00e-02 2.50e+03
        pdb=" CZ  ARG B 109 "   -0.033 2.00e-02 2.50e+03
        pdb=" NH1 ARG B 109 "    0.010 2.00e-02 2.50e+03
        pdb=" NH2 ARG B 109 "   -0.008 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CD  ARG A 125 "   -0.916 9.50e-02 1.11e+02   4.11e-01 1.06e+02
        pdb=" NE  ARG A 125 "    0.067 2.00e-02 2.50e+03
        pdb=" CZ  ARG A 125 "   -0.023 2.00e-02 2.50e+03
        pdb=" NH1 ARG A 125 "    0.008 2.00e-02 2.50e+03
        pdb=" NH2 ARG A 125 "   -0.012 2.00e-02 2.50e+03
  ... (remaining 1699 not shown)

  Histogram of nonbonded interaction distances:
        2.26 -     2.79: 1901
        2.79 -     3.32: 10622
        3.32 -     3.85: 16074
        3.85 -     4.37: 18180
        4.37 -     4.90: 30994
  Nonbonded interactions: 77771
  Sorted by model distance:
  nonbonded pdb=" O   SER F  59 "
            pdb=" OG1 THR F  62 "
     model   vdw
     2.265 3.040
  nonbonded pdb=" OD1 ASN D 197 "
            pdb=" NH1 ARG G  23 "
     model   vdw
     2.463 3.120
  nonbonded pdb=" C   THR A 155 "
            pdb=" OG1 THR A 155 "
     model   vdw
     2.468 2.616
  nonbonded pdb=" OAI AV0 G 401 "
            pdb=" OBY AV0 G 401 "
     model   vdw
     2.471 2.432
  nonbonded pdb=" OG1 THR B 161 "
            pdb=" OD1 ASP F  30 "
     model   vdw
     2.502 3.040
  ... (remaining 77766 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.00
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = (chain 'B' and resid 29 through 246)
  selection = (chain 'C' and resid 29 through 246)
  selection = (chain 'D' and resid 29 through 246)
  selection = (chain 'E' and resid 29 through 246)
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             0.890
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.400
  Check model and map are aligned:         0.070
  Set scattering table:                    0.100
  Process input model:                     25.290
  Find NCS groups from input model:        0.420
  Set up NCS constraints:                  0.040
  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:2.960
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   30.180
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8452
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      :  0.009   0.058  10018  Z= 0.610
  Angle     :  1.430  10.799  13583  Z= 0.947
  Chirality :  0.154   5.023   1647
  Planarity :  0.027   0.447   1702
  Dihedral  : 19.981 174.605   3768
  Min Nonbonded Distance : 2.265

Molprobity Statistics.
  All-atom Clashscore : 8.31
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.74 %
    Favored  : 98.26 %
  Rotamer:
    Outliers : 11.48 %
    Allowed  :  8.23 %
    Favored  : 80.29 %
  Cbeta Deviations :  0.26 %
  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: -0.36 (0.21), residues: 1267
  helix:  0.02 (0.14), residues: 1083
  sheet:  None (None), residues: 0
  loop : -0.92 (0.46), residues: 184

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.036   0.008   TRP A  77 
 HIS   0.025   0.006   HIS C 139 
 PHE   0.052   0.011   PHE C  40 
 TYR   0.058   0.011   TYR B  51 
 ARG   0.043   0.007   ARG B 109 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.22822 (  850)
  hydrogen bonds       : angle       8.01649 ( 2529)
  covalent geometry    : bond        0.00940 (10018)
  covalent geometry    : angle       1.43009 (13583)

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

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

  2534 Ramachandran restraints generated.
    1267 Oldfield, 0 Emsley, 1267 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2534 Ramachandran restraints generated.
    1267 Oldfield, 0 Emsley, 1267 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  397 residues out of total 1045 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 120
    poor density    : 277
  time to evaluate  : 1.118 
Fit side-chains
REVERT: A   30 LEU cc_start: 0.6769 (OUTLIER) cc_final: 0.6244 (tt)
REVERT: A   68 LYS cc_start: 0.6565 (OUTLIER) cc_final: 0.5924 (pttp)
REVERT: A   70 ASN cc_start: 0.3630 (OUTLIER) cc_final: 0.3279 (p0)
REVERT: A   84 MET cc_start: 0.6276 (OUTLIER) cc_final: 0.6016 (mmm)
REVERT: A   89 ARG cc_start: 0.7038 (OUTLIER) cc_final: 0.6441 (mmm160)
REVERT: A   99 LYS cc_start: 0.3994 (OUTLIER) cc_final: 0.3203 (mtpt)
REVERT: A  239 LYS cc_start: 0.7023 (OUTLIER) cc_final: 0.6766 (tppt)
REVERT: B   64 LYS cc_start: 0.8083 (mttt) cc_final: 0.7732 (tttt)
REVERT: B   90 ARG cc_start: 0.8714 (OUTLIER) cc_final: 0.8200 (mtm-85)
REVERT: B   91 GLU cc_start: 0.6823 (mp0) cc_final: 0.6463 (mp0)
REVERT: B   99 LYS cc_start: 0.8593 (OUTLIER) cc_final: 0.8320 (mmtm)
REVERT: B  109 ARG cc_start: 0.8655 (OUTLIER) cc_final: 0.8431 (ttp80)
REVERT: C   53 MET cc_start: 0.9017 (tpp) cc_final: 0.8617 (tpt)
REVERT: C   70 ASN cc_start: 0.9144 (t0) cc_final: 0.8871 (t0)
REVERT: C  117 ASP cc_start: 0.7917 (m-30) cc_final: 0.7589 (t0)
REVERT: D   32 GLN cc_start: 0.8720 (mm-40) cc_final: 0.8356 (tt0)
REVERT: D   84 MET cc_start: 0.8668 (OUTLIER) cc_final: 0.7967 (mtp)
REVERT: D   98 GLN cc_start: 0.8179 (tm-30) cc_final: 0.7964 (mm-40)
REVERT: D  120 ASP cc_start: 0.8364 (p0) cc_final: 0.8077 (t0)
REVERT: E   26 GLN cc_start: 0.8199 (mm-40) cc_final: 0.7794 (tt0)
REVERT: E   70 ASN cc_start: 0.7632 (t0) cc_final: 0.7336 (m-40)
REVERT: E   83 GLU cc_start: 0.7583 (tt0) cc_final: 0.7094 (tm-30)
REVERT: E  109 ARG cc_start: 0.7037 (ttp80) cc_final: 0.6718 (mtm110)
REVERT: E  171 HIS cc_start: 0.7979 (m90) cc_final: 0.7702 (m90)
REVERT: E  232 ASP cc_start: 0.8138 (m-30) cc_final: 0.7854 (m-30)
  outliers start: 120
  outliers final: 35
  residues processed: 357
  average time/residue: 0.2335
  time to fit residues: 111.8755
Evaluate side-chains
  248 residues out of total 1045 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 46
    poor density    : 202
  time to evaluate  : 1.132 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   30 LEU
Chi-restraints excluded: chain A residue   63 ILE
Chi-restraints excluded: chain A residue   68 LYS
Chi-restraints excluded: chain A residue   70 ASN
Chi-restraints excluded: chain A residue   71 ARG
Chi-restraints excluded: chain A residue   81 ILE
Chi-restraints excluded: chain A residue   83 GLU
Chi-restraints excluded: chain A residue   84 MET
Chi-restraints excluded: chain A residue   89 ARG
Chi-restraints excluded: chain A residue   94 LEU
Chi-restraints excluded: chain A residue   97 GLU
Chi-restraints excluded: chain A residue   99 LYS
Chi-restraints excluded: chain A residue  112 ILE
Chi-restraints excluded: chain A residue  115 VAL
Chi-restraints excluded: chain A residue  123 ILE
Chi-restraints excluded: chain A residue  128 MET
Chi-restraints excluded: chain A residue  156 MET
Chi-restraints excluded: chain A residue  172 LEU
Chi-restraints excluded: chain A residue  176 SER
Chi-restraints excluded: chain A residue  217 VAL
Chi-restraints excluded: chain A residue  237 VAL
Chi-restraints excluded: chain A residue  239 LYS
Chi-restraints excluded: chain A residue  245 ILE
Chi-restraints excluded: chain B residue   78 LEU
Chi-restraints excluded: chain B residue   80 ASP
Chi-restraints excluded: chain B residue   90 ARG
Chi-restraints excluded: chain B residue   97 GLU
Chi-restraints excluded: chain B residue   99 LYS
Chi-restraints excluded: chain B residue  106 ILE
Chi-restraints excluded: chain B residue  109 ARG
Chi-restraints excluded: chain B residue  110 GLU
Chi-restraints excluded: chain B residue  124 VAL
Chi-restraints excluded: chain B residue  172 LEU
Chi-restraints excluded: chain B residue  181 SER
Chi-restraints excluded: chain B residue  182 ILE
Chi-restraints excluded: chain D residue   82 VAL
Chi-restraints excluded: chain D residue   84 MET
Chi-restraints excluded: chain D residue   85 SER
Chi-restraints excluded: chain D residue  102 ASP
Chi-restraints excluded: chain D residue  161 THR
Chi-restraints excluded: chain D residue  216 LEU
Chi-restraints excluded: chain D residue  217 VAL
Chi-restraints excluded: chain E residue  115 VAL
Chi-restraints excluded: chain F residue   25 MET
Chi-restraints excluded: chain F residue   35 LEU
Chi-restraints excluded: chain F residue   54 GLU
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 124
   random chunks:
   chunk 104 optimal weight:    0.4980
   chunk 93 optimal weight:    0.7980
   chunk 52 optimal weight:    2.9990
   chunk 32 optimal weight:    4.9990
   chunk 63 optimal weight:    1.9990
   chunk 50 optimal weight:    0.9980
   chunk 97 optimal weight:    0.9980
   chunk 37 optimal weight:    0.9980
   chunk 59 optimal weight:    0.8980
   chunk 72 optimal weight:    2.9990
   chunk 112 optimal weight:    0.9980
   overall best weight:    0.8380

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

Flipped N/Q/H residues before XYZ refinement:
A  75 ASN
B 103 HIS
B 197 ASN
C 242 ASN
D 121 GLN
D 171 HIS
** E 103 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
E 177 GLN
E 229 GLN

Total number of N/Q/H flips: 8

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3984 r_free = 0.3984 target = 0.162177 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3557 r_free = 0.3557 target = 0.125959 restraints weight = 12219.474|
|-----------------------------------------------------------------------------|
r_work (start): 0.3548 rms_B_bonded: 1.98
r_work: 0.3418 rms_B_bonded: 2.80 restraints_weight: 0.5000
r_work: 0.3268 rms_B_bonded: 4.61 restraints_weight: 0.2500
r_work (final): 0.3268
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8241
moved from start:          0.3313

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028  10018  Z= 0.157
  Angle     :  0.628   8.709  13583  Z= 0.323
  Chirality :  0.041   0.277   1647
  Planarity :  0.005   0.048   1702
  Dihedral  : 12.329 165.004   1587
  Min Nonbonded Distance : 2.380

Molprobity Statistics.
  All-atom Clashscore : 4.78
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.79 %
    Favored  : 99.21 %
  Rotamer:
    Outliers :  4.88 %
    Allowed  : 14.83 %
    Favored  : 80.29 %
  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:  2.35 (0.23), residues: 1267
  helix:  1.96 (0.15), residues: 1107
  sheet:  None (None), residues: 0
  loop : -1.31 (0.44), residues: 160

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.034   0.002   TRP A  77 
 HIS   0.006   0.001   HIS D  54 
 PHE   0.014   0.001   PHE A 107 
 TYR   0.014   0.001   TYR A 244 
 ARG   0.008   0.001   ARG E  57 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05898 (  850)
  hydrogen bonds       : angle       4.69528 ( 2529)
  covalent geometry    : bond        0.00309 (10018)
  covalent geometry    : angle       0.62833 (13583)

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

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

  2534 Ramachandran restraints generated.
    1267 Oldfield, 0 Emsley, 1267 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2534 Ramachandran restraints generated.
    1267 Oldfield, 0 Emsley, 1267 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  270 residues out of total 1045 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 51
    poor density    : 219
  time to evaluate  : 1.051 
Fit side-chains
REVERT: A   73 GLU cc_start: 0.5762 (OUTLIER) cc_final: 0.5002 (tm-30)
REVERT: A   84 MET cc_start: 0.6356 (OUTLIER) cc_final: 0.5745 (mmm)
REVERT: A   86 MET cc_start: 0.5720 (tpt) cc_final: 0.4466 (ttt)
REVERT: A   89 ARG cc_start: 0.7239 (OUTLIER) cc_final: 0.6872 (mmm160)
REVERT: A  133 ASP cc_start: 0.7950 (m-30) cc_final: 0.7733 (m-30)
REVERT: A  167 GLN cc_start: 0.7214 (tm-30) cc_final: 0.6920 (tm-30)
REVERT: A  219 GLU cc_start: 0.8051 (mt-10) cc_final: 0.7846 (mt-10)
REVERT: B   80 ASP cc_start: 0.8451 (OUTLIER) cc_final: 0.8046 (t70)
REVERT: B   90 ARG cc_start: 0.8563 (OUTLIER) cc_final: 0.8184 (mtm-85)
REVERT: B   91 GLU cc_start: 0.6776 (mp0) cc_final: 0.6416 (mp0)
REVERT: B   99 LYS cc_start: 0.8608 (OUTLIER) cc_final: 0.8211 (mmtm)
REVERT: C  218 MET cc_start: 0.8723 (mtt) cc_final: 0.8430 (mtp)
REVERT: C  230 ASN cc_start: 0.8796 (m-40) cc_final: 0.8521 (t0)
REVERT: D   80 ASP cc_start: 0.8831 (m-30) cc_final: 0.8399 (m-30)
REVERT: D   98 GLN cc_start: 0.8064 (tm-30) cc_final: 0.7846 (mp10)
REVERT: E   26 GLN cc_start: 0.7410 (mm-40) cc_final: 0.7159 (tt0)
REVERT: E   57 ARG cc_start: 0.8569 (mtt90) cc_final: 0.8185 (mmm-85)
REVERT: E   83 GLU cc_start: 0.7830 (tt0) cc_final: 0.7097 (tm-30)
REVERT: E  109 ARG cc_start: 0.6823 (ttp80) cc_final: 0.6614 (mtp180)
REVERT: E  214 GLU cc_start: 0.8364 (mm-30) cc_final: 0.8025 (mt-10)
REVERT: F   65 GLN cc_start: 0.6751 (OUTLIER) cc_final: 0.5408 (tm-30)
REVERT: G   45 MET cc_start: 0.8300 (tpp) cc_final: 0.7930 (mmm)
  outliers start: 51
  outliers final: 15
  residues processed: 255
  average time/residue: 0.2233
  time to fit residues: 78.2378
Evaluate side-chains
  217 residues out of total 1045 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 195
  time to evaluate  : 1.133 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   73 GLU
Chi-restraints excluded: chain A residue   83 GLU
Chi-restraints excluded: chain A residue   84 MET
Chi-restraints excluded: chain A residue   89 ARG
Chi-restraints excluded: chain A residue   97 GLU
Chi-restraints excluded: chain A residue  112 ILE
Chi-restraints excluded: chain A residue  172 LEU
Chi-restraints excluded: chain A residue  189 THR
Chi-restraints excluded: chain A residue  237 VAL
Chi-restraints excluded: chain A residue  245 ILE
Chi-restraints excluded: chain B residue   72 SER
Chi-restraints excluded: chain B residue   78 LEU
Chi-restraints excluded: chain B residue   80 ASP
Chi-restraints excluded: chain B residue   90 ARG
Chi-restraints excluded: chain B residue   97 GLU
Chi-restraints excluded: chain B residue   99 LYS
Chi-restraints excluded: chain B residue  117 ASP
Chi-restraints excluded: chain C residue   72 SER
Chi-restraints excluded: chain E residue   87 VAL
Chi-restraints excluded: chain E residue  195 SER
Chi-restraints excluded: chain F residue   35 LEU
Chi-restraints excluded: chain F residue   65 GLN
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 124
   random chunks:
   chunk 28 optimal weight:    2.9990
   chunk 5 optimal weight:    1.9990
   chunk 108 optimal weight:    5.9990
   chunk 102 optimal weight:    4.9990
   chunk 91 optimal weight:    0.9990
   chunk 36 optimal weight:    1.9990
   chunk 58 optimal weight:    4.9990
   chunk 94 optimal weight:    2.9990
   chunk 109 optimal weight:    2.9990
   chunk 118 optimal weight:    3.9990
   chunk 44 optimal weight:    8.9990
   overall best weight:    2.1990

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

Flipped N/Q/H residues before XYZ refinement:
B  26 GLN
E 113 GLN
E 177 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3916 r_free = 0.3916 target = 0.155097 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3478 r_free = 0.3478 target = 0.118658 restraints weight = 12763.505|
|-----------------------------------------------------------------------------|
r_work (start): 0.3472 rms_B_bonded: 1.98
r_work: 0.3344 rms_B_bonded: 2.79 restraints_weight: 0.5000
r_work: 0.3199 rms_B_bonded: 4.59 restraints_weight: 0.2500
r_work (final): 0.3199
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8424
moved from start:          0.3795

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.040  10018  Z= 0.194
  Angle     :  0.613   7.734  13583  Z= 0.318
  Chirality :  0.040   0.167   1647
  Planarity :  0.004   0.049   1702
  Dihedral  :  9.875 162.178   1517
  Min Nonbonded Distance : 2.372

Molprobity Statistics.
  All-atom Clashscore : 4.88
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.34 %
    Favored  : 98.66 %
  Rotamer:
    Outliers :  4.59 %
    Allowed  : 17.03 %
    Favored  : 78.37 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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:  2.65 (0.23), residues: 1267
  helix:  2.20 (0.15), residues: 1106
  sheet:  None (None), residues: 0
  loop : -1.57 (0.42), residues: 161

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.032   0.002   TRP A  77 
 HIS   0.005   0.001   HIS B  54 
 PHE   0.022   0.002   PHE A 107 
 TYR   0.010   0.001   TYR A  51 
 ARG   0.005   0.001   ARG D  90 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.06194 (  850)
  hydrogen bonds       : angle       4.57823 ( 2529)
  covalent geometry    : bond        0.00456 (10018)
  covalent geometry    : angle       0.61316 (13583)

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

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

  2534 Ramachandran restraints generated.
    1267 Oldfield, 0 Emsley, 1267 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2534 Ramachandran restraints generated.
    1267 Oldfield, 0 Emsley, 1267 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  245 residues out of total 1045 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 48
    poor density    : 197
  time to evaluate  : 0.981 
Fit side-chains
REVERT: A   73 GLU cc_start: 0.5735 (OUTLIER) cc_final: 0.4858 (tm-30)
REVERT: A   84 MET cc_start: 0.6300 (OUTLIER) cc_final: 0.5528 (tpp)
REVERT: A   86 MET cc_start: 0.5935 (tpt) cc_final: 0.4739 (ttt)
REVERT: A   89 ARG cc_start: 0.7431 (OUTLIER) cc_final: 0.6732 (mmm160)
REVERT: A  107 PHE cc_start: 0.8090 (t80) cc_final: 0.7861 (t80)
REVERT: A  218 MET cc_start: 0.8001 (mmt) cc_final: 0.7646 (mmt)
REVERT: A  219 GLU cc_start: 0.8038 (mt-10) cc_final: 0.7785 (mt-10)
REVERT: B   22 TRP cc_start: 0.7825 (t60) cc_final: 0.6973 (t-100)
REVERT: B   80 ASP cc_start: 0.8562 (OUTLIER) cc_final: 0.8144 (t70)
REVERT: B   90 ARG cc_start: 0.8601 (OUTLIER) cc_final: 0.8092 (mtm-85)
REVERT: B   91 GLU cc_start: 0.6893 (OUTLIER) cc_final: 0.6573 (mp0)
REVERT: B   94 LEU cc_start: 0.7745 (pt) cc_final: 0.7428 (mp)
REVERT: B   99 LYS cc_start: 0.8660 (OUTLIER) cc_final: 0.8316 (mmtm)
REVERT: B  227 SER cc_start: 0.8854 (OUTLIER) cc_final: 0.8415 (t)
REVERT: D   53 MET cc_start: 0.8187 (tpt) cc_final: 0.7786 (tpt)
REVERT: D   89 ARG cc_start: 0.7422 (ttm-80) cc_final: 0.6841 (ttp80)
REVERT: D   98 GLN cc_start: 0.8040 (tm-30) cc_final: 0.7785 (mp10)
REVERT: D  167 GLN cc_start: 0.8319 (tm-30) cc_final: 0.8114 (tm-30)
REVERT: E   26 GLN cc_start: 0.7565 (mm-40) cc_final: 0.7330 (tt0)
REVERT: E   83 GLU cc_start: 0.7780 (tt0) cc_final: 0.7268 (tm-30)
REVERT: E  181 SER cc_start: 0.8489 (m) cc_final: 0.8288 (m)
REVERT: F   64 PHE cc_start: 0.7562 (m-80) cc_final: 0.7327 (m-80)
REVERT: F   65 GLN cc_start: 0.6793 (OUTLIER) cc_final: 0.5515 (tm-30)
  outliers start: 48
  outliers final: 25
  residues processed: 231
  average time/residue: 0.2262
  time to fit residues: 71.3380
Evaluate side-chains
  216 residues out of total 1045 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 182
  time to evaluate  : 1.100 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   73 GLU
Chi-restraints excluded: chain A residue   83 GLU
Chi-restraints excluded: chain A residue   84 MET
Chi-restraints excluded: chain A residue   89 ARG
Chi-restraints excluded: chain A residue  112 ILE
Chi-restraints excluded: chain A residue  172 LEU
Chi-restraints excluded: chain A residue  189 THR
Chi-restraints excluded: chain A residue  217 VAL
Chi-restraints excluded: chain A residue  236 LEU
Chi-restraints excluded: chain A residue  245 ILE
Chi-restraints excluded: chain B residue   14 VAL
Chi-restraints excluded: chain B residue   28 THR
Chi-restraints excluded: chain B residue   63 ILE
Chi-restraints excluded: chain B residue   78 LEU
Chi-restraints excluded: chain B residue   80 ASP
Chi-restraints excluded: chain B residue   84 MET
Chi-restraints excluded: chain B residue   90 ARG
Chi-restraints excluded: chain B residue   91 GLU
Chi-restraints excluded: chain B residue   97 GLU
Chi-restraints excluded: chain B residue   99 LYS
Chi-restraints excluded: chain B residue  117 ASP
Chi-restraints excluded: chain B residue  227 SER
Chi-restraints excluded: chain C residue   22 TRP
Chi-restraints excluded: chain C residue  106 ILE
Chi-restraints excluded: chain C residue  195 SER
Chi-restraints excluded: chain D residue   28 THR
Chi-restraints excluded: chain D residue   34 THR
Chi-restraints excluded: chain D residue  115 VAL
Chi-restraints excluded: chain E residue   87 VAL
Chi-restraints excluded: chain E residue  124 VAL
Chi-restraints excluded: chain E residue  195 SER
Chi-restraints excluded: chain E residue  243 THR
Chi-restraints excluded: chain F residue   35 LEU
Chi-restraints excluded: chain F residue   65 GLN
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 124
   random chunks:
   chunk 50 optimal weight:    0.4980
   chunk 55 optimal weight:    4.9990
   chunk 11 optimal weight:    2.9990
   chunk 62 optimal weight:    6.9990
   chunk 22 optimal weight:    0.9980
   chunk 70 optimal weight:    3.9990
   chunk 87 optimal weight:    1.9990
   chunk 44 optimal weight:    6.9990
   chunk 99 optimal weight:    1.9990
   chunk 113 optimal weight:    0.6980
   chunk 8 optimal weight:   10.0000
   overall best weight:    1.2384

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

Flipped N/Q/H residues before XYZ refinement:
** E 103 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 = 0.4008 r_free = 0.4008 target = 0.160864 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3602 r_free = 0.3602 target = 0.125650 restraints weight = 12653.360|
|-----------------------------------------------------------------------------|
r_work (start): 0.3568 rms_B_bonded: 1.91
r_work: 0.3452 rms_B_bonded: 2.69 restraints_weight: 0.5000
r_work: 0.3315 rms_B_bonded: 4.45 restraints_weight: 0.2500
r_work (final): 0.3315
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8355
moved from start:          0.4277

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029  10018  Z= 0.143
  Angle     :  0.538   7.329  13583  Z= 0.276
  Chirality :  0.037   0.140   1647
  Planarity :  0.004   0.047   1702
  Dihedral  :  9.192 161.177   1513
  Min Nonbonded Distance : 2.424

Molprobity Statistics.
  All-atom Clashscore : 4.88
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.26 %
    Favored  : 98.74 %
  Rotamer:
    Outliers :  3.06 %
    Allowed  : 18.76 %
    Favored  : 78.18 %
  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:  3.08 (0.24), residues: 1267
  helix:  2.47 (0.15), residues: 1109
  sheet:  None (None), residues: 0
  loop : -1.36 (0.43), residues: 158

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.034   0.001   TRP A  77 
 HIS   0.004   0.001   HIS D  54 
 PHE   0.014   0.001   PHE A 107 
 TYR   0.013   0.001   TYR E  51 
 ARG   0.006   0.000   ARG E  57 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05079 (  850)
  hydrogen bonds       : angle       4.22034 ( 2529)
  covalent geometry    : bond        0.00308 (10018)
  covalent geometry    : angle       0.53760 (13583)

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

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

  2534 Ramachandran restraints generated.
    1267 Oldfield, 0 Emsley, 1267 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2534 Ramachandran restraints generated.
    1267 Oldfield, 0 Emsley, 1267 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  235 residues out of total 1045 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 203
  time to evaluate  : 0.989 
Fit side-chains
REVERT: A   73 GLU cc_start: 0.5590 (OUTLIER) cc_final: 0.4771 (tm-30)
REVERT: A   84 MET cc_start: 0.6923 (OUTLIER) cc_final: 0.5811 (tpp)
REVERT: A   86 MET cc_start: 0.5729 (tpt) cc_final: 0.4541 (ttt)
REVERT: A   89 ARG cc_start: 0.7501 (OUTLIER) cc_final: 0.6718 (mmm160)
REVERT: B   22 TRP cc_start: 0.7832 (t60) cc_final: 0.6913 (t-100)
REVERT: B   80 ASP cc_start: 0.8525 (OUTLIER) cc_final: 0.8188 (t70)
REVERT: B   90 ARG cc_start: 0.8359 (OUTLIER) cc_final: 0.8114 (mtm-85)
REVERT: B   91 GLU cc_start: 0.6803 (mp0) cc_final: 0.6565 (mp0)
REVERT: B   94 LEU cc_start: 0.7882 (pt) cc_final: 0.7507 (mp)
REVERT: B   99 LYS cc_start: 0.8655 (OUTLIER) cc_final: 0.8303 (mmtm)
REVERT: B  227 SER cc_start: 0.8761 (OUTLIER) cc_final: 0.8300 (t)
REVERT: D   53 MET cc_start: 0.7923 (tpt) cc_final: 0.7585 (tpt)
REVERT: D   89 ARG cc_start: 0.7340 (ttm-80) cc_final: 0.6860 (ttp80)
REVERT: D   98 GLN cc_start: 0.8048 (tm-30) cc_final: 0.7812 (mp10)
REVERT: D  167 GLN cc_start: 0.8243 (tm-30) cc_final: 0.8006 (tm-30)
REVERT: E   26 GLN cc_start: 0.7436 (mm-40) cc_final: 0.7127 (tt0)
REVERT: E   83 GLU cc_start: 0.7765 (tt0) cc_final: 0.7287 (tm-30)
REVERT: E   89 ARG cc_start: 0.7180 (OUTLIER) cc_final: 0.5556 (ttp-110)
REVERT: E  181 SER cc_start: 0.8285 (m) cc_final: 0.8071 (m)
REVERT: E  191 TYR cc_start: 0.8902 (m-10) cc_final: 0.8558 (m-10)
REVERT: F   64 PHE cc_start: 0.7481 (m-80) cc_final: 0.7238 (m-80)
  outliers start: 32
  outliers final: 20
  residues processed: 223
  average time/residue: 0.2294
  time to fit residues: 71.2578
Evaluate side-chains
  218 residues out of total 1045 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 190
  time to evaluate  : 0.979 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   73 GLU
Chi-restraints excluded: chain A residue   84 MET
Chi-restraints excluded: chain A residue   89 ARG
Chi-restraints excluded: chain A residue  148 SER
Chi-restraints excluded: chain A residue  172 LEU
Chi-restraints excluded: chain A residue  189 THR
Chi-restraints excluded: chain A residue  236 LEU
Chi-restraints excluded: chain A residue  245 ILE
Chi-restraints excluded: chain B residue   28 THR
Chi-restraints excluded: chain B residue   72 SER
Chi-restraints excluded: chain B residue   78 LEU
Chi-restraints excluded: chain B residue   80 ASP
Chi-restraints excluded: chain B residue   90 ARG
Chi-restraints excluded: chain B residue   97 GLU
Chi-restraints excluded: chain B residue   99 LYS
Chi-restraints excluded: chain B residue  227 SER
Chi-restraints excluded: chain C residue   22 TRP
Chi-restraints excluded: chain C residue   72 SER
Chi-restraints excluded: chain C residue  106 ILE
Chi-restraints excluded: chain C residue  195 SER
Chi-restraints excluded: chain C residue  242 ASN
Chi-restraints excluded: chain D residue   28 THR
Chi-restraints excluded: chain E residue   87 VAL
Chi-restraints excluded: chain E residue   89 ARG
Chi-restraints excluded: chain E residue  115 VAL
Chi-restraints excluded: chain E residue  172 LEU
Chi-restraints excluded: chain E residue  243 THR
Chi-restraints excluded: chain F residue   25 MET
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 124
   random chunks:
   chunk 95 optimal weight:    0.7980
   chunk 62 optimal weight:    8.9990
   chunk 19 optimal weight:    5.9990
   chunk 96 optimal weight:    1.9990
   chunk 45 optimal weight:    0.0020
   chunk 108 optimal weight:    0.1980
   chunk 58 optimal weight:    4.9990
   chunk 111 optimal weight:    1.9990
   chunk 8 optimal weight:    7.9990
   chunk 71 optimal weight:    3.9990
   chunk 72 optimal weight:    0.1980
   overall best weight:    0.6390

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

Flipped N/Q/H residues before XYZ refinement:
** C 197 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
E 197 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4041 r_free = 0.4041 target = 0.164007 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3649 r_free = 0.3649 target = 0.129034 restraints weight = 12637.607|
|-----------------------------------------------------------------------------|
r_work (start): 0.3589 rms_B_bonded: 1.94
r_work: 0.3472 rms_B_bonded: 2.72 restraints_weight: 0.5000
r_work: 0.3334 rms_B_bonded: 4.50 restraints_weight: 0.2500
r_work (final): 0.3334
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8305
moved from start:          0.4675

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.029  10018  Z= 0.121
  Angle     :  0.501   7.911  13583  Z= 0.256
  Chirality :  0.036   0.130   1647
  Planarity :  0.004   0.048   1702
  Dihedral  :  8.644 160.325   1506
  Min Nonbonded Distance : 2.443

Molprobity Statistics.
  All-atom Clashscore : 4.68
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.42 %
    Favored  : 98.58 %
  Rotamer:
    Outliers :  3.16 %
    Allowed  : 20.38 %
    Favored  : 76.46 %
  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:  3.33 (0.24), residues: 1267
  helix:  2.63 (0.16), residues: 1102
  sheet:  None (None), residues: 0
  loop : -1.01 (0.44), residues: 165

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.031   0.001   TRP A  77 
 HIS   0.003   0.001   HIS D  54 
 PHE   0.018   0.001   PHE A 107 
 TYR   0.010   0.001   TYR E  51 
 ARG   0.006   0.000   ARG B  57 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04463 (  850)
  hydrogen bonds       : angle       4.00840 ( 2529)
  covalent geometry    : bond        0.00237 (10018)
  covalent geometry    : angle       0.50148 (13583)

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

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

  2534 Ramachandran restraints generated.
    1267 Oldfield, 0 Emsley, 1267 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2534 Ramachandran restraints generated.
    1267 Oldfield, 0 Emsley, 1267 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  236 residues out of total 1045 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 203
  time to evaluate  : 1.006 
Fit side-chains
REVERT: A   73 GLU cc_start: 0.5635 (OUTLIER) cc_final: 0.4888 (tm-30)
REVERT: A   86 MET cc_start: 0.5806 (tpt) cc_final: 0.4674 (ttt)
REVERT: A   89 ARG cc_start: 0.7440 (OUTLIER) cc_final: 0.6621 (mmm160)
REVERT: B   22 TRP cc_start: 0.7728 (t60) cc_final: 0.6836 (t-100)
REVERT: B   26 GLN cc_start: 0.8021 (tm-30) cc_final: 0.7024 (tm-30)
REVERT: B   80 ASP cc_start: 0.8460 (OUTLIER) cc_final: 0.8124 (t70)
REVERT: B   90 ARG cc_start: 0.8355 (OUTLIER) cc_final: 0.8050 (mtm-85)
REVERT: B   91 GLU cc_start: 0.6844 (OUTLIER) cc_final: 0.6610 (mp0)
REVERT: B   94 LEU cc_start: 0.7864 (pt) cc_final: 0.7532 (mp)
REVERT: B   99 LYS cc_start: 0.8651 (OUTLIER) cc_final: 0.8279 (mmtm)
REVERT: B  113 GLN cc_start: 0.8300 (tp40) cc_final: 0.7832 (tm-30)
REVERT: B  227 SER cc_start: 0.8619 (OUTLIER) cc_final: 0.8155 (t)
REVERT: D   80 ASP cc_start: 0.8952 (m-30) cc_final: 0.8631 (t0)
REVERT: D   98 GLN cc_start: 0.8073 (tm-30) cc_final: 0.7772 (mp10)
REVERT: E   26 GLN cc_start: 0.7294 (mm-40) cc_final: 0.6932 (tt0)
REVERT: E   83 GLU cc_start: 0.7696 (tt0) cc_final: 0.7172 (tm-30)
REVERT: E  181 SER cc_start: 0.8143 (m) cc_final: 0.7921 (m)
REVERT: E  191 TYR cc_start: 0.8882 (m-10) cc_final: 0.8545 (m-10)
REVERT: E  236 LEU cc_start: 0.7680 (OUTLIER) cc_final: 0.7454 (tp)
REVERT: G   48 LEU cc_start: 0.8506 (tp) cc_final: 0.8139 (mt)
  outliers start: 33
  outliers final: 17
  residues processed: 226
  average time/residue: 0.2171
  time to fit residues: 67.8259
Evaluate side-chains
  219 residues out of total 1045 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 194
  time to evaluate  : 1.071 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   73 GLU
Chi-restraints excluded: chain A residue   89 ARG
Chi-restraints excluded: chain A residue  172 LEU
Chi-restraints excluded: chain A residue  189 THR
Chi-restraints excluded: chain A residue  236 LEU
Chi-restraints excluded: chain A residue  245 ILE
Chi-restraints excluded: chain B residue   28 THR
Chi-restraints excluded: chain B residue   72 SER
Chi-restraints excluded: chain B residue   78 LEU
Chi-restraints excluded: chain B residue   80 ASP
Chi-restraints excluded: chain B residue   90 ARG
Chi-restraints excluded: chain B residue   91 GLU
Chi-restraints excluded: chain B residue   97 GLU
Chi-restraints excluded: chain B residue   99 LYS
Chi-restraints excluded: chain B residue  227 SER
Chi-restraints excluded: chain C residue   22 TRP
Chi-restraints excluded: chain C residue   72 SER
Chi-restraints excluded: chain C residue  106 ILE
Chi-restraints excluded: chain C residue  191 TYR
Chi-restraints excluded: chain C residue  195 SER
Chi-restraints excluded: chain D residue   28 THR
Chi-restraints excluded: chain E residue   87 VAL
Chi-restraints excluded: chain E residue  115 VAL
Chi-restraints excluded: chain E residue  195 SER
Chi-restraints excluded: chain E residue  236 LEU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 124
   random chunks:
   chunk 117 optimal weight:    0.5980
   chunk 42 optimal weight:    0.9990
   chunk 35 optimal weight:    0.7980
   chunk 113 optimal weight:    4.9990
   chunk 95 optimal weight:    3.9990
   chunk 15 optimal weight:    0.8980
   chunk 71 optimal weight:    5.9990
   chunk 119 optimal weight:    0.6980
   chunk 37 optimal weight:    0.9990
   chunk 9 optimal weight:    0.4980
   chunk 26 optimal weight:    3.9990
   overall best weight:    0.6980

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

Flipped N/Q/H residues before XYZ refinement:
B 197 ASN
** C 197 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3994 r_free = 0.3994 target = 0.162635 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3585 r_free = 0.3585 target = 0.126703 restraints weight = 12473.917|
|-----------------------------------------------------------------------------|
r_work (start): 0.3580 rms_B_bonded: 1.98
r_work: 0.3450 rms_B_bonded: 2.83 restraints_weight: 0.5000
r_work: 0.3307 rms_B_bonded: 4.68 restraints_weight: 0.2500
r_work (final): 0.3307
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8291
moved from start:          0.4896

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.049  10018  Z= 0.121
  Angle     :  0.520   9.495  13583  Z= 0.258
  Chirality :  0.036   0.131   1647
  Planarity :  0.004   0.049   1702
  Dihedral  :  8.491 158.969   1503
  Min Nonbonded Distance : 2.435

Molprobity Statistics.
  All-atom Clashscore : 4.98
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.18 %
    Favored  : 98.82 %
  Rotamer:
    Outliers :  3.16 %
    Allowed  : 20.38 %
    Favored  : 76.46 %
  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:  3.43 (0.24), residues: 1267
  helix:  2.71 (0.16), residues: 1108
  sheet:  None (None), residues: 0
  loop : -1.20 (0.44), residues: 159

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.026   0.001   TRP A  77 
 HIS   0.003   0.000   HIS D  54 
 PHE   0.021   0.001   PHE A 107 
 TYR   0.016   0.001   TYR E  51 
 ARG   0.005   0.000   ARG B  57 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04289 (  850)
  hydrogen bonds       : angle       3.93473 ( 2529)
  covalent geometry    : bond        0.00245 (10018)
  covalent geometry    : angle       0.52002 (13583)

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

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

  2534 Ramachandran restraints generated.
    1267 Oldfield, 0 Emsley, 1267 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2534 Ramachandran restraints generated.
    1267 Oldfield, 0 Emsley, 1267 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  239 residues out of total 1045 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 206
  time to evaluate  : 0.970 
Fit side-chains
   revert: symmetry clash
REVERT: A   73 GLU cc_start: 0.5614 (OUTLIER) cc_final: 0.4943 (tm-30)
REVERT: A   86 MET cc_start: 0.5821 (tpt) cc_final: 0.4816 (ttt)
REVERT: A   89 ARG cc_start: 0.7492 (OUTLIER) cc_final: 0.6564 (mmm160)
REVERT: B   22 TRP cc_start: 0.7683 (t60) cc_final: 0.6783 (t-100)
REVERT: B   26 GLN cc_start: 0.8026 (tm-30) cc_final: 0.6929 (tm-30)
REVERT: B   80 ASP cc_start: 0.8424 (OUTLIER) cc_final: 0.8150 (t70)
REVERT: B   90 ARG cc_start: 0.8244 (OUTLIER) cc_final: 0.7983 (mtm-85)
REVERT: B   91 GLU cc_start: 0.6902 (mp0) cc_final: 0.6624 (mp0)
REVERT: B   94 LEU cc_start: 0.7872 (pt) cc_final: 0.7561 (mp)
REVERT: B   99 LYS cc_start: 0.8613 (OUTLIER) cc_final: 0.8220 (mmtm)
REVERT: B  113 GLN cc_start: 0.8268 (tp40) cc_final: 0.7776 (tm-30)
REVERT: B  227 SER cc_start: 0.8593 (OUTLIER) cc_final: 0.8108 (t)
REVERT: D   80 ASP cc_start: 0.9018 (m-30) cc_final: 0.8639 (t0)
REVERT: D   98 GLN cc_start: 0.8108 (tm-30) cc_final: 0.7737 (mp10)
REVERT: E   26 GLN cc_start: 0.7304 (mm-40) cc_final: 0.7009 (tt0)
REVERT: E   83 GLU cc_start: 0.7560 (tt0) cc_final: 0.7065 (tm-30)
REVERT: E  236 LEU cc_start: 0.7697 (OUTLIER) cc_final: 0.7465 (tp)
  outliers start: 33
  outliers final: 23
  residues processed: 229
  average time/residue: 0.2132
  time to fit residues: 67.4579
Evaluate side-chains
  226 residues out of total 1045 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 196
  time to evaluate  : 0.965 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   73 GLU
Chi-restraints excluded: chain A residue   83 GLU
Chi-restraints excluded: chain A residue   89 ARG
Chi-restraints excluded: chain A residue   97 GLU
Chi-restraints excluded: chain A residue  172 LEU
Chi-restraints excluded: chain A residue  189 THR
Chi-restraints excluded: chain A residue  236 LEU
Chi-restraints excluded: chain A residue  245 ILE
Chi-restraints excluded: chain B residue   28 THR
Chi-restraints excluded: chain B residue   72 SER
Chi-restraints excluded: chain B residue   78 LEU
Chi-restraints excluded: chain B residue   80 ASP
Chi-restraints excluded: chain B residue   90 ARG
Chi-restraints excluded: chain B residue   97 GLU
Chi-restraints excluded: chain B residue   99 LYS
Chi-restraints excluded: chain B residue  205 SER
Chi-restraints excluded: chain B residue  227 SER
Chi-restraints excluded: chain C residue   22 TRP
Chi-restraints excluded: chain C residue   72 SER
Chi-restraints excluded: chain C residue   84 MET
Chi-restraints excluded: chain C residue  106 ILE
Chi-restraints excluded: chain C residue  191 TYR
Chi-restraints excluded: chain C residue  195 SER
Chi-restraints excluded: chain C residue  242 ASN
Chi-restraints excluded: chain D residue   28 THR
Chi-restraints excluded: chain E residue   85 SER
Chi-restraints excluded: chain E residue   87 VAL
Chi-restraints excluded: chain E residue  115 VAL
Chi-restraints excluded: chain E residue  195 SER
Chi-restraints excluded: chain E residue  236 LEU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 124
   random chunks:
   chunk 71 optimal weight:    5.9990
   chunk 31 optimal weight:    0.2980
   chunk 88 optimal weight:    0.9990
   chunk 11 optimal weight:    3.9990
   chunk 7 optimal weight:    0.9990
   chunk 94 optimal weight:    4.9990
   chunk 13 optimal weight:    3.9990
   chunk 26 optimal weight:    0.1980
   chunk 116 optimal weight:    4.9990
   chunk 44 optimal weight:    4.9990
   chunk 102 optimal weight:    8.9990
   overall best weight:    1.2986

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

Flipped N/Q/H residues before XYZ refinement:
A 177 GLN
** C 197 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3962 r_free = 0.3962 target = 0.159310 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3541 r_free = 0.3541 target = 0.122784 restraints weight = 12691.223|
|-----------------------------------------------------------------------------|
r_work (start): 0.3526 rms_B_bonded: 1.99
r_work: 0.3395 rms_B_bonded: 2.83 restraints_weight: 0.5000
r_work: 0.3249 rms_B_bonded: 4.71 restraints_weight: 0.2500
r_work (final): 0.3249
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8346
moved from start:          0.4835

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031  10018  Z= 0.140
  Angle     :  0.536   8.749  13583  Z= 0.271
  Chirality :  0.037   0.134   1647
  Planarity :  0.004   0.051   1702
  Dihedral  :  8.441 157.176   1503
  Min Nonbonded Distance : 2.426

Molprobity Statistics.
  All-atom Clashscore : 4.83
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.50 %
    Favored  : 98.50 %
  Rotamer:
    Outliers :  3.35 %
    Allowed  : 20.67 %
    Favored  : 75.98 %
  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:  3.30 (0.24), residues: 1267
  helix:  2.65 (0.15), residues: 1102
  sheet:  None (None), residues: 0
  loop : -1.31 (0.43), residues: 165

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.024   0.001   TRP A  77 
 HIS   0.004   0.001   HIS D  54 
 PHE   0.022   0.001   PHE A 107 
 TYR   0.011   0.001   TYR E  51 
 ARG   0.005   0.000   ARG B  57 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04743 (  850)
  hydrogen bonds       : angle       4.03768 ( 2529)
  covalent geometry    : bond        0.00309 (10018)
  covalent geometry    : angle       0.53617 (13583)

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

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

  2534 Ramachandran restraints generated.
    1267 Oldfield, 0 Emsley, 1267 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2534 Ramachandran restraints generated.
    1267 Oldfield, 0 Emsley, 1267 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  236 residues out of total 1045 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 201
  time to evaluate  : 1.117 
Fit side-chains
   revert: symmetry clash
REVERT: A   73 GLU cc_start: 0.5639 (OUTLIER) cc_final: 0.4915 (tm-30)
REVERT: A   86 MET cc_start: 0.5712 (tpt) cc_final: 0.4746 (ttt)
REVERT: A   89 ARG cc_start: 0.7541 (OUTLIER) cc_final: 0.6617 (mmm160)
REVERT: B   22 TRP cc_start: 0.7621 (t60) cc_final: 0.6748 (t-100)
REVERT: B   26 GLN cc_start: 0.8042 (tm-30) cc_final: 0.6892 (tm-30)
REVERT: B   90 ARG cc_start: 0.8232 (tpt-90) cc_final: 0.7987 (mtm-85)
REVERT: B   91 GLU cc_start: 0.6951 (OUTLIER) cc_final: 0.6648 (mp0)
REVERT: B   94 LEU cc_start: 0.7929 (pt) cc_final: 0.7620 (mp)
REVERT: B   99 LYS cc_start: 0.8618 (OUTLIER) cc_final: 0.8217 (mmtm)
REVERT: B  113 GLN cc_start: 0.8291 (tp40) cc_final: 0.7786 (tm-30)
REVERT: B  227 SER cc_start: 0.8734 (OUTLIER) cc_final: 0.8264 (t)
REVERT: D   53 MET cc_start: 0.7833 (tpt) cc_final: 0.7447 (tpt)
REVERT: D   80 ASP cc_start: 0.9012 (m-30) cc_final: 0.8550 (m-30)
REVERT: D   98 GLN cc_start: 0.8128 (tm-30) cc_final: 0.7746 (mp10)
REVERT: E   26 GLN cc_start: 0.7453 (mm-40) cc_final: 0.7123 (tt0)
REVERT: E   83 GLU cc_start: 0.7521 (tt0) cc_final: 0.7064 (tm-30)
REVERT: E  191 TYR cc_start: 0.8867 (m-10) cc_final: 0.8571 (m-10)
REVERT: E  236 LEU cc_start: 0.7752 (OUTLIER) cc_final: 0.7485 (tp)
REVERT: F   64 PHE cc_start: 0.7292 (m-80) cc_final: 0.7003 (m-80)
  outliers start: 35
  outliers final: 27
  residues processed: 226
  average time/residue: 0.2119
  time to fit residues: 66.7618
Evaluate side-chains
  230 residues out of total 1045 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 197
  time to evaluate  : 1.025 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   73 GLU
Chi-restraints excluded: chain A residue   83 GLU
Chi-restraints excluded: chain A residue   89 ARG
Chi-restraints excluded: chain A residue   97 GLU
Chi-restraints excluded: chain A residue  172 LEU
Chi-restraints excluded: chain A residue  189 THR
Chi-restraints excluded: chain A residue  236 LEU
Chi-restraints excluded: chain A residue  245 ILE
Chi-restraints excluded: chain B residue   28 THR
Chi-restraints excluded: chain B residue   63 ILE
Chi-restraints excluded: chain B residue   72 SER
Chi-restraints excluded: chain B residue   78 LEU
Chi-restraints excluded: chain B residue   91 GLU
Chi-restraints excluded: chain B residue   97 GLU
Chi-restraints excluded: chain B residue   99 LYS
Chi-restraints excluded: chain B residue  205 SER
Chi-restraints excluded: chain B residue  227 SER
Chi-restraints excluded: chain C residue   22 TRP
Chi-restraints excluded: chain C residue   72 SER
Chi-restraints excluded: chain C residue   84 MET
Chi-restraints excluded: chain C residue  106 ILE
Chi-restraints excluded: chain C residue  195 SER
Chi-restraints excluded: chain C residue  242 ASN
Chi-restraints excluded: chain D residue   28 THR
Chi-restraints excluded: chain D residue   34 THR
Chi-restraints excluded: chain E residue   85 SER
Chi-restraints excluded: chain E residue   87 VAL
Chi-restraints excluded: chain E residue  115 VAL
Chi-restraints excluded: chain E residue  172 LEU
Chi-restraints excluded: chain E residue  195 SER
Chi-restraints excluded: chain E residue  236 LEU
Chi-restraints excluded: chain E residue  243 THR
Chi-restraints excluded: chain F residue   25 MET
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 124
   random chunks:
   chunk 6 optimal weight:    0.7980
   chunk 23 optimal weight:    7.9990
   chunk 67 optimal weight:    2.9990
   chunk 26 optimal weight:    3.9990
   chunk 27 optimal weight:    0.8980
   chunk 121 optimal weight:    0.7980
   chunk 85 optimal weight:    3.9990
   chunk 56 optimal weight:    3.9990
   chunk 53 optimal weight:    2.9990
   chunk 84 optimal weight:    0.9980
   chunk 7 optimal weight:    4.9990
   overall best weight:    1.2982

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

Flipped N/Q/H residues before XYZ refinement:
B 197 ASN
E 197 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3964 r_free = 0.3964 target = 0.159839 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 56)----------------|
| r_work = 0.3533 r_free = 0.3533 target = 0.122642 restraints weight = 12802.202|
|-----------------------------------------------------------------------------|
r_work (start): 0.3517 rms_B_bonded: 2.06
r_work: 0.3384 rms_B_bonded: 2.89 restraints_weight: 0.5000
r_work: 0.3235 rms_B_bonded: 4.79 restraints_weight: 0.2500
r_work (final): 0.3235
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8343
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      :  0.003   0.053  10018  Z= 0.140
  Angle     :  0.538   9.366  13583  Z= 0.271
  Chirality :  0.037   0.137   1647
  Planarity :  0.004   0.051   1702
  Dihedral  :  8.328 156.360   1497
  Min Nonbonded Distance : 2.428

Molprobity Statistics.
  All-atom Clashscore : 4.83
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.74 %
    Favored  : 98.26 %
  Rotamer:
    Outliers :  3.54 %
    Allowed  : 20.86 %
    Favored  : 75.60 %
  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:  3.34 (0.24), residues: 1267
  helix:  2.66 (0.15), residues: 1110
  sheet:  None (None), residues: 0
  loop : -1.39 (0.44), residues: 157

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.023   0.001   TRP A  77 
 HIS   0.004   0.001   HIS D  54 
 PHE   0.013   0.001   PHE A 107 
 TYR   0.012   0.001   TYR E  51 
 ARG   0.005   0.000   ARG B  57 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04734 (  850)
  hydrogen bonds       : angle       4.04611 ( 2529)
  covalent geometry    : bond        0.00311 (10018)
  covalent geometry    : angle       0.53803 (13583)

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

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

  2534 Ramachandran restraints generated.
    1267 Oldfield, 0 Emsley, 1267 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2534 Ramachandran restraints generated.
    1267 Oldfield, 0 Emsley, 1267 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  239 residues out of total 1045 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 37
    poor density    : 202
  time to evaluate  : 1.014 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   73 GLU cc_start: 0.5704 (OUTLIER) cc_final: 0.4974 (tm-30)
REVERT: A   86 MET cc_start: 0.5613 (tpt) cc_final: 0.4627 (ttt)
REVERT: A   89 ARG cc_start: 0.7587 (OUTLIER) cc_final: 0.6654 (mmm160)
REVERT: B   22 TRP cc_start: 0.7628 (t60) cc_final: 0.6761 (t-100)
REVERT: B   26 GLN cc_start: 0.8056 (tm-30) cc_final: 0.6883 (tm-30)
REVERT: B   80 ASP cc_start: 0.8463 (t70) cc_final: 0.8217 (t70)
REVERT: B   91 GLU cc_start: 0.6997 (OUTLIER) cc_final: 0.6787 (mp0)
REVERT: B   94 LEU cc_start: 0.7949 (pt) cc_final: 0.7650 (mp)
REVERT: B   99 LYS cc_start: 0.8623 (OUTLIER) cc_final: 0.8197 (mmtm)
REVERT: B  113 GLN cc_start: 0.8259 (tp40) cc_final: 0.7764 (tm-30)
REVERT: B  227 SER cc_start: 0.8694 (OUTLIER) cc_final: 0.8232 (t)
REVERT: D   53 MET cc_start: 0.7901 (tpt) cc_final: 0.7596 (tpt)
REVERT: D   80 ASP cc_start: 0.9014 (m-30) cc_final: 0.8546 (m-30)
REVERT: D   98 GLN cc_start: 0.8195 (tm-30) cc_final: 0.7752 (mp10)
REVERT: E   26 GLN cc_start: 0.7518 (mm-40) cc_final: 0.7181 (tt0)
REVERT: E   83 GLU cc_start: 0.7528 (tt0) cc_final: 0.6971 (tm-30)
REVERT: E  191 TYR cc_start: 0.8865 (m-10) cc_final: 0.8557 (m-10)
REVERT: E  236 LEU cc_start: 0.7732 (OUTLIER) cc_final: 0.7472 (tp)
REVERT: F   64 PHE cc_start: 0.7278 (m-80) cc_final: 0.7002 (m-80)
  outliers start: 37
  outliers final: 29
  residues processed: 226
  average time/residue: 0.2177
  time to fit residues: 68.5125
Evaluate side-chains
  234 residues out of total 1045 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 199
  time to evaluate  : 0.973 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   73 GLU
Chi-restraints excluded: chain A residue   83 GLU
Chi-restraints excluded: chain A residue   89 ARG
Chi-restraints excluded: chain A residue   97 GLU
Chi-restraints excluded: chain A residue  172 LEU
Chi-restraints excluded: chain A residue  189 THR
Chi-restraints excluded: chain A residue  217 VAL
Chi-restraints excluded: chain A residue  236 LEU
Chi-restraints excluded: chain A residue  245 ILE
Chi-restraints excluded: chain B residue   28 THR
Chi-restraints excluded: chain B residue   63 ILE
Chi-restraints excluded: chain B residue   78 LEU
Chi-restraints excluded: chain B residue   84 MET
Chi-restraints excluded: chain B residue   91 GLU
Chi-restraints excluded: chain B residue   97 GLU
Chi-restraints excluded: chain B residue   99 LYS
Chi-restraints excluded: chain B residue  205 SER
Chi-restraints excluded: chain B residue  227 SER
Chi-restraints excluded: chain C residue   22 TRP
Chi-restraints excluded: chain C residue   72 SER
Chi-restraints excluded: chain C residue   84 MET
Chi-restraints excluded: chain C residue  106 ILE
Chi-restraints excluded: chain C residue  195 SER
Chi-restraints excluded: chain C residue  242 ASN
Chi-restraints excluded: chain D residue   28 THR
Chi-restraints excluded: chain D residue   34 THR
Chi-restraints excluded: chain E residue   85 SER
Chi-restraints excluded: chain E residue   87 VAL
Chi-restraints excluded: chain E residue  115 VAL
Chi-restraints excluded: chain E residue  172 LEU
Chi-restraints excluded: chain E residue  195 SER
Chi-restraints excluded: chain E residue  236 LEU
Chi-restraints excluded: chain E residue  243 THR
Chi-restraints excluded: chain F residue   25 MET
Chi-restraints excluded: chain F residue   35 LEU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 124
   random chunks:
   chunk 66 optimal weight:    4.9990
   chunk 14 optimal weight:    0.7980
   chunk 25 optimal weight:    0.6980
   chunk 76 optimal weight:    2.9990
   chunk 60 optimal weight:    0.7980
   chunk 57 optimal weight:    0.9990
   chunk 23 optimal weight:    5.9990
   chunk 114 optimal weight:    0.9980
   chunk 90 optimal weight:    1.9990
   chunk 37 optimal weight:    0.8980
   chunk 93 optimal weight:    0.0270
   overall best weight:    0.6438

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

Flipped N/Q/H residues before XYZ refinement:
C 197 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4051 r_free = 0.4051 target = 0.167019 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3651 r_free = 0.3651 target = 0.131777 restraints weight = 12558.939|
|-----------------------------------------------------------------------------|
r_work (start): 0.3608 rms_B_bonded: 1.98
r_work: 0.3477 rms_B_bonded: 2.87 restraints_weight: 0.5000
r_work: 0.3328 rms_B_bonded: 4.78 restraints_weight: 0.2500
r_work (final): 0.3328
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8288
moved from start:          0.5151

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.045  10018  Z= 0.119
  Angle     :  0.517   9.923  13583  Z= 0.259
  Chirality :  0.036   0.123   1647
  Planarity :  0.004   0.051   1702
  Dihedral  :  8.206 156.446   1497
  Min Nonbonded Distance : 2.446

Molprobity Statistics.
  All-atom Clashscore : 5.03
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.58 %
    Favored  : 98.42 %
  Rotamer:
    Outliers :  3.54 %
    Allowed  : 20.48 %
    Favored  : 75.98 %
  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:  3.52 (0.24), residues: 1267
  helix:  2.79 (0.16), residues: 1101
  sheet:  None (None), residues: 0
  loop : -1.17 (0.43), residues: 166

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.021   0.001   TRP A  77 
 HIS   0.002   0.001   HIS D  54 
 PHE   0.011   0.001   PHE A 107 
 TYR   0.008   0.001   TYR E  51 
 ARG   0.004   0.000   ARG B  57 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04176 (  850)
  hydrogen bonds       : angle       3.89611 ( 2529)
  covalent geometry    : bond        0.00239 (10018)
  covalent geometry    : angle       0.51711 (13583)

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

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

  2534 Ramachandran restraints generated.
    1267 Oldfield, 0 Emsley, 1267 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2534 Ramachandran restraints generated.
    1267 Oldfield, 0 Emsley, 1267 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  238 residues out of total 1045 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 37
    poor density    : 201
  time to evaluate  : 1.083 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   73 GLU cc_start: 0.5733 (OUTLIER) cc_final: 0.4992 (tm-30)
REVERT: A   86 MET cc_start: 0.5686 (tpt) cc_final: 0.4742 (ttt)
REVERT: A   89 ARG cc_start: 0.7497 (OUTLIER) cc_final: 0.6552 (mmm160)
REVERT: B   22 TRP cc_start: 0.7539 (t60) cc_final: 0.6730 (t-100)
REVERT: B   26 GLN cc_start: 0.8017 (tm-30) cc_final: 0.6917 (tm-30)
REVERT: B   80 ASP cc_start: 0.8435 (t70) cc_final: 0.8165 (t70)
REVERT: B   91 GLU cc_start: 0.7132 (OUTLIER) cc_final: 0.6929 (mp0)
REVERT: B   94 LEU cc_start: 0.7929 (pt) cc_final: 0.7669 (mp)
REVERT: B   99 LYS cc_start: 0.8593 (OUTLIER) cc_final: 0.8228 (mmtm)
REVERT: B  113 GLN cc_start: 0.8226 (tp40) cc_final: 0.7816 (tm-30)
REVERT: C  167 GLN cc_start: 0.8910 (tm-30) cc_final: 0.8592 (tm-30)
REVERT: C  226 LEU cc_start: 0.7899 (OUTLIER) cc_final: 0.7615 (mp)
REVERT: D   53 MET cc_start: 0.7706 (tpt) cc_final: 0.7364 (tpt)
REVERT: D   80 ASP cc_start: 0.9004 (m-30) cc_final: 0.8631 (t0)
REVERT: D   98 GLN cc_start: 0.8137 (tm-30) cc_final: 0.7691 (mp10)
REVERT: D  156 MET cc_start: 0.9258 (mmt) cc_final: 0.8845 (mmt)
REVERT: E   26 GLN cc_start: 0.7330 (mm-40) cc_final: 0.7081 (tt0)
REVERT: E   83 GLU cc_start: 0.7567 (tt0) cc_final: 0.7080 (tm-30)
REVERT: E  236 LEU cc_start: 0.7737 (OUTLIER) cc_final: 0.7522 (tp)
REVERT: F   64 PHE cc_start: 0.7229 (m-80) cc_final: 0.6913 (m-80)
  outliers start: 37
  outliers final: 28
  residues processed: 225
  average time/residue: 0.2068
  time to fit residues: 65.4329
Evaluate side-chains
  227 residues out of total 1045 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 193
  time to evaluate  : 1.032 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   73 GLU
Chi-restraints excluded: chain A residue   83 GLU
Chi-restraints excluded: chain A residue   89 ARG
Chi-restraints excluded: chain A residue   93 VAL
Chi-restraints excluded: chain A residue   97 GLU
Chi-restraints excluded: chain A residue  112 ILE
Chi-restraints excluded: chain A residue  172 LEU
Chi-restraints excluded: chain A residue  189 THR
Chi-restraints excluded: chain A residue  217 VAL
Chi-restraints excluded: chain A residue  236 LEU
Chi-restraints excluded: chain A residue  245 ILE
Chi-restraints excluded: chain B residue   28 THR
Chi-restraints excluded: chain B residue   78 LEU
Chi-restraints excluded: chain B residue   91 GLU
Chi-restraints excluded: chain B residue   97 GLU
Chi-restraints excluded: chain B residue   99 LYS
Chi-restraints excluded: chain B residue  205 SER
Chi-restraints excluded: chain B residue  227 SER
Chi-restraints excluded: chain C residue   22 TRP
Chi-restraints excluded: chain C residue   72 SER
Chi-restraints excluded: chain C residue   84 MET
Chi-restraints excluded: chain C residue  106 ILE
Chi-restraints excluded: chain C residue  197 ASN
Chi-restraints excluded: chain C residue  226 LEU
Chi-restraints excluded: chain D residue   28 THR
Chi-restraints excluded: chain D residue   34 THR
Chi-restraints excluded: chain E residue   85 SER
Chi-restraints excluded: chain E residue   87 VAL
Chi-restraints excluded: chain E residue  115 VAL
Chi-restraints excluded: chain E residue  172 LEU
Chi-restraints excluded: chain E residue  195 SER
Chi-restraints excluded: chain E residue  236 LEU
Chi-restraints excluded: chain F residue   25 MET
Chi-restraints excluded: chain F residue   35 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 124
   random chunks:
   chunk 29 optimal weight:    3.9990
   chunk 96 optimal weight:    2.9990
   chunk 54 optimal weight:    0.0370
   chunk 11 optimal weight:    1.9990
   chunk 4 optimal weight:    3.9990
   chunk 67 optimal weight:    4.9990
   chunk 70 optimal weight:    0.9980
   chunk 90 optimal weight:    1.9990
   chunk 60 optimal weight:    0.7980
   chunk 25 optimal weight:    0.9980
   chunk 16 optimal weight:    1.9990
   overall best weight:    0.9660

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

Flipped N/Q/H residues before XYZ refinement:
C 197 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3932 r_free = 0.3932 target = 0.158668 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3490 r_free = 0.3490 target = 0.120979 restraints weight = 12732.338|
|-----------------------------------------------------------------------------|
r_work (start): 0.3462 rms_B_bonded: 2.26
r_work: 0.3327 rms_B_bonded: 3.06 restraints_weight: 0.5000
r_work (final): 0.3327
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7718
moved from start:          0.5140

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.044  10018  Z= 0.128
  Angle     :  0.530   8.796  13583  Z= 0.266
  Chirality :  0.036   0.204   1647
  Planarity :  0.004   0.052   1702
  Dihedral  :  8.170 155.225   1497
  Min Nonbonded Distance : 2.444

Molprobity Statistics.
  All-atom Clashscore : 5.47
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.50 %
    Favored  : 98.50 %
  Rotamer:
    Outliers :  3.25 %
    Allowed  : 21.15 %
    Favored  : 75.60 %
  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:  3.47 (0.24), residues: 1267
  helix:  2.75 (0.15), residues: 1107
  sheet:  None (None), residues: 0
  loop : -1.27 (0.44), residues: 160

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.021   0.001   TRP A  77 
 HIS   0.003   0.001   HIS D  54 
 PHE   0.017   0.001   PHE A 107 
 TYR   0.007   0.001   TYR A  51 
 ARG   0.004   0.000   ARG B  57 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04382 (  850)
  hydrogen bonds       : angle       3.94315 ( 2529)
  covalent geometry    : bond        0.00275 (10018)
  covalent geometry    : angle       0.53027 (13583)

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

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

  2534 Ramachandran restraints generated.
    1267 Oldfield, 0 Emsley, 1267 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2534 Ramachandran restraints generated.
    1267 Oldfield, 0 Emsley, 1267 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  232 residues out of total 1045 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 198
  time to evaluate  : 1.047 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   73 GLU cc_start: 0.5375 (OUTLIER) cc_final: 0.4826 (tm-30)
REVERT: A   86 MET cc_start: 0.5370 (tpt) cc_final: 0.4453 (ttt)
REVERT: A   89 ARG cc_start: 0.7389 (OUTLIER) cc_final: 0.6639 (mmm160)
REVERT: B   22 TRP cc_start: 0.7350 (t60) cc_final: 0.6550 (t-100)
REVERT: B   26 GLN cc_start: 0.7514 (tm-30) cc_final: 0.6251 (tm-30)
REVERT: B   69 PRO cc_start: 0.8442 (Cg_exo) cc_final: 0.8228 (Cg_endo)
REVERT: B   80 ASP cc_start: 0.8278 (t70) cc_final: 0.7991 (t70)
REVERT: B   91 GLU cc_start: 0.6891 (OUTLIER) cc_final: 0.6652 (mp0)
REVERT: B   94 LEU cc_start: 0.7826 (pt) cc_final: 0.7600 (mp)
REVERT: B   99 LYS cc_start: 0.8483 (OUTLIER) cc_final: 0.8074 (mmtm)
REVERT: B  113 GLN cc_start: 0.8005 (tp40) cc_final: 0.7555 (tm-30)
REVERT: B  227 SER cc_start: 0.8228 (OUTLIER) cc_final: 0.7794 (t)
REVERT: C  167 GLN cc_start: 0.8320 (tm-30) cc_final: 0.7917 (tm-30)
REVERT: C  226 LEU cc_start: 0.7128 (OUTLIER) cc_final: 0.6857 (mp)
REVERT: D   53 MET cc_start: 0.7248 (tpt) cc_final: 0.6875 (tpt)
REVERT: D   80 ASP cc_start: 0.8787 (m-30) cc_final: 0.8452 (t0)
REVERT: D   98 GLN cc_start: 0.8099 (tm-30) cc_final: 0.7518 (mp10)
REVERT: E   26 GLN cc_start: 0.7191 (mm-40) cc_final: 0.6791 (tt0)
REVERT: E   83 GLU cc_start: 0.6954 (tt0) cc_final: 0.6469 (tm-30)
REVERT: E  167 GLN cc_start: 0.7623 (tp40) cc_final: 0.7391 (tp-100)
REVERT: E  191 TYR cc_start: 0.8392 (m-10) cc_final: 0.8114 (m-10)
  outliers start: 34
  outliers final: 27
  residues processed: 220
  average time/residue: 0.2057
  time to fit residues: 63.3815
Evaluate side-chains
  228 residues out of total 1045 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 195
  time to evaluate  : 0.963 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   73 GLU
Chi-restraints excluded: chain A residue   83 GLU
Chi-restraints excluded: chain A residue   89 ARG
Chi-restraints excluded: chain A residue   93 VAL
Chi-restraints excluded: chain A residue   97 GLU
Chi-restraints excluded: chain A residue  112 ILE
Chi-restraints excluded: chain A residue  172 LEU
Chi-restraints excluded: chain A residue  189 THR
Chi-restraints excluded: chain A residue  217 VAL
Chi-restraints excluded: chain A residue  236 LEU
Chi-restraints excluded: chain A residue  245 ILE
Chi-restraints excluded: chain B residue   28 THR
Chi-restraints excluded: chain B residue   78 LEU
Chi-restraints excluded: chain B residue   84 MET
Chi-restraints excluded: chain B residue   91 GLU
Chi-restraints excluded: chain B residue   97 GLU
Chi-restraints excluded: chain B residue   99 LYS
Chi-restraints excluded: chain B residue  205 SER
Chi-restraints excluded: chain B residue  227 SER
Chi-restraints excluded: chain C residue   22 TRP
Chi-restraints excluded: chain C residue   84 MET
Chi-restraints excluded: chain C residue  106 ILE
Chi-restraints excluded: chain C residue  195 SER
Chi-restraints excluded: chain C residue  197 ASN
Chi-restraints excluded: chain C residue  226 LEU
Chi-restraints excluded: chain D residue   28 THR
Chi-restraints excluded: chain D residue   34 THR
Chi-restraints excluded: chain E residue   87 VAL
Chi-restraints excluded: chain E residue  110 GLU
Chi-restraints excluded: chain E residue  115 VAL
Chi-restraints excluded: chain E residue  195 SER
Chi-restraints excluded: chain F residue   25 MET
Chi-restraints excluded: chain F residue   35 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 124
   random chunks:
   chunk 17 optimal weight:    0.7980
   chunk 37 optimal weight:    0.7980
   chunk 98 optimal weight:    0.7980
   chunk 121 optimal weight:    4.9990
   chunk 77 optimal weight:    8.9990
   chunk 73 optimal weight:    0.7980
   chunk 107 optimal weight:    1.9990
   chunk 88 optimal weight:    2.9990
   chunk 72 optimal weight:    0.9980
   chunk 53 optimal weight:    0.8980
   chunk 6 optimal weight:    9.9990
   overall best weight:    0.8180

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

Flipped N/Q/H residues before XYZ refinement:
C 197 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4048 r_free = 0.4048 target = 0.166377 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3646 r_free = 0.3646 target = 0.131115 restraints weight = 12624.525|
|-----------------------------------------------------------------------------|
r_work (start): 0.3548 rms_B_bonded: 1.96
r_work: 0.3413 rms_B_bonded: 2.81 restraints_weight: 0.5000
r_work: 0.3271 rms_B_bonded: 4.61 restraints_weight: 0.2500
r_work (final): 0.3271
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8263
moved from start:          0.5228

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030  10018  Z= 0.123
  Angle     :  0.529  10.865  13583  Z= 0.264
  Chirality :  0.036   0.184   1647
  Planarity :  0.004   0.052   1702
  Dihedral  :  8.126 154.578   1497
  Min Nonbonded Distance : 2.452

Molprobity Statistics.
  All-atom Clashscore : 5.67
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.58 %
    Favored  : 98.42 %
  Rotamer:
    Outliers :  2.97 %
    Allowed  : 21.72 %
    Favored  : 75.31 %
  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:  3.51 (0.24), residues: 1267
  helix:  2.78 (0.15), residues: 1107
  sheet:  None (None), residues: 0
  loop : -1.25 (0.44), residues: 160

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.024   0.001   TRP A  77 
 HIS   0.003   0.001   HIS D  54 
 PHE   0.019   0.001   PHE A 107 
 TYR   0.007   0.001   TYR A  51 
 ARG   0.004   0.000   ARG B  57 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04276 (  850)
  hydrogen bonds       : angle       3.91480 ( 2529)
  covalent geometry    : bond        0.00256 (10018)
  covalent geometry    : angle       0.52946 (13583)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 5234.91 seconds
wall clock time: 91 minutes 0.65 seconds (5460.65 seconds total)