Starting phenix.real_space_refine
on Tue Jul 29 07:12:45 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8fy9_29561/07_2025/8fy9_29561.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8fy9_29561/07_2025/8fy9_29561.map

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

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

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8fy9_29561/07_2025/8fy9_29561.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8fy9_29561/07_2025/8fy9_29561.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8fy9_29561/07_2025/8fy9_29561.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8fy9_29561/07_2025/8fy9_29561.cif"
  }
  resolution = 3.1
  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=   0.032
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
  Anisotropic ADP refinement not supported. Converting 611 atoms to isotropic.
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 5
    Type Number    sf(0)   Gaussians
     P      54      5.49       5
     S      30      5.16       5
     C    6628      2.51       5
     N    1942      2.21       5
     O    2088      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 7 residue(s): 0.03s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib"
  Total number of atoms: 10742
  Number of models: 1
  Model: ""
    Number of chains: 8
    Chain: "A"
      Number of atoms: 746
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 93, 746
          Classifications: {'peptide': 93}
          Link IDs: {'PTRANS': 4, 'TRANS': 88}
    Chain: "B"
      Number of atoms: 1865
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 241, 1865
          Classifications: {'peptide': 241}
          Link IDs: {'PTRANS': 8, 'TRANS': 232}
          Chain breaks: 1
    Chain: "C"
      Number of atoms: 2186
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 280, 2186
          Classifications: {'peptide': 280}
          Link IDs: {'PTRANS': 10, 'TRANS': 269}
    Chain: "D"
      Number of atoms: 746
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 93, 746
          Classifications: {'peptide': 93}
          Link IDs: {'PTRANS': 4, 'TRANS': 88}
    Chain: "E"
      Number of atoms: 1865
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 241, 1865
          Classifications: {'peptide': 241}
          Link IDs: {'PTRANS': 8, 'TRANS': 232}
          Chain breaks: 1
    Chain: "F"
      Number of atoms: 2186
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 280, 2186
          Classifications: {'peptide': 280}
          Link IDs: {'PTRANS': 10, 'TRANS': 269}
    Chain: "G"
      Number of atoms: 573
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 28, 573
          Classifications: {'DNA': 28}
          Modifications used: {'5*END': 1}
          Link IDs: {'rna3p': 27}
    Chain: "H"
      Number of atoms: 575
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 28, 575
          Classifications: {'DNA': 28}
          Modifications used: {'5*END': 1}
          Link IDs: {'rna3p': 27}
  Time building chain proxies: 7.23, per 1000 atoms: 0.67
  Number of scatterers: 10742
  At special positions: 0
  Unit cell: (94.775, 90.315, 142.72, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S      30     16.00
     P      54     15.00
     O    2088      8.00
     N    1942      7.00
     C    6628      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 1.4 seconds
  

  2424 Ramachandran restraints generated.
    1212 Oldfield, 0 Emsley, 1212 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2268

  Finding SS restraints...
    Secondary structure from input PDB file:
      49 helices and 9 sheets defined
      51.1% alpha, 14.8% beta
      11 base pairs and 46 stacking pairs defined.
    Time for finding SS restraints: 3.87
  Creating SS restraints...
    Processing helix  chain 'A' and resid 12 through 19
    Processing helix  chain 'A' and resid 36 through 51
    Processing helix  chain 'B' and resid 68 through 77
    Processing helix  chain 'B' and resid 86 through 89
    Processing helix  chain 'B' and resid 97 through 101
    Processing helix  chain 'B' and resid 102 through 114
      removed outlier: 4.070A  pdb=" N   ASN B 114 " --> pdb=" O   GLU B 110 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 114 through 129
    Processing helix  chain 'B' and resid 182 through 205
    Processing helix  chain 'B' and resid 219 through 230
      removed outlier: 3.616A  pdb=" N   TYR B 223 " --> pdb=" O   ARG B 219 " (cutoff:3.500A)
      removed outlier: 3.768A  pdb=" N   LEU B 228 " --> pdb=" O   ASP B 224 " (cutoff:3.500A)
      removed outlier: 4.097A  pdb=" N   TYR B 229 " --> pdb=" O   VAL B 225 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 233 through 244
    Processing helix  chain 'B' and resid 250 through 264
    Processing helix  chain 'B' and resid 266 through 280
    Processing helix  chain 'B' and resid 298 through 303
    Processing helix  chain 'B' and resid 304 through 306
      No H-bonds generated for 'chain 'B' and resid 304 through 306'
    Processing helix  chain 'C' and resid 17 through 21
      removed outlier: 3.729A  pdb=" N   ARG C  21 " --> pdb=" O   VAL C  18 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 51 through 53
      No H-bonds generated for 'chain 'C' and resid 51 through 53'
    Processing helix  chain 'C' and resid 68 through 78
    Processing helix  chain 'C' and resid 102 through 114
      removed outlier: 3.641A  pdb=" N   ASN C 114 " --> pdb=" O   GLU C 110 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 114 through 130
    Processing helix  chain 'C' and resid 139 through 163
    Processing helix  chain 'C' and resid 180 through 205
    Processing helix  chain 'C' and resid 219 through 231
      removed outlier: 3.954A  pdb=" N   LEU C 228 " --> pdb=" O   ASP C 224 " (cutoff:3.500A)
      removed outlier: 4.094A  pdb=" N   TYR C 229 " --> pdb=" O   VAL C 225 " (cutoff:3.500A)
      removed outlier: 4.416A  pdb=" N   ALA C 231 " --> pdb=" O   ASP C 227 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 233 through 245
    Processing helix  chain 'C' and resid 250 through 267
    Processing helix  chain 'C' and resid 267 through 280
    Processing helix  chain 'D' and resid 12 through 19
    Processing helix  chain 'D' and resid 20 through 22
      No H-bonds generated for 'chain 'D' and resid 20 through 22'
    Processing helix  chain 'D' and resid 36 through 51
    Processing helix  chain 'E' and resid 53 through 55
      No H-bonds generated for 'chain 'E' and resid 53 through 55'
    Processing helix  chain 'E' and resid 67 through 77
    Processing helix  chain 'E' and resid 97 through 101
    Processing helix  chain 'E' and resid 102 through 114
      removed outlier: 3.922A  pdb=" N   ASN E 114 " --> pdb=" O   GLU E 110 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 114 through 129
    Processing helix  chain 'E' and resid 182 through 205
    Processing helix  chain 'E' and resid 219 through 227
    Processing helix  chain 'E' and resid 233 through 245
    Processing helix  chain 'E' and resid 250 through 264
      removed outlier: 3.945A  pdb=" N   LEU E 254 " --> pdb=" O   ASP E 250 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 266 through 280
      removed outlier: 3.748A  pdb=" N   LEU E 280 " --> pdb=" O   LEU E 276 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 17 through 21
      removed outlier: 3.724A  pdb=" N   ARG F  21 " --> pdb=" O   VAL F  18 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 51 through 53
      No H-bonds generated for 'chain 'F' and resid 51 through 53'
    Processing helix  chain 'F' and resid 67 through 78
      removed outlier: 3.868A  pdb=" N   VAL F  71 " --> pdb=" O   SER F  67 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 102 through 114
      removed outlier: 3.760A  pdb=" N   ASN F 114 " --> pdb=" O   GLU F 110 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 114 through 130
    Processing helix  chain 'F' and resid 139 through 163
    Processing helix  chain 'F' and resid 180 through 205
    Processing helix  chain 'F' and resid 219 through 231
      removed outlier: 4.476A  pdb=" N   LEU F 228 " --> pdb=" O   ASP F 224 " (cutoff:3.500A)
      removed outlier: 4.280A  pdb=" N   TYR F 229 " --> pdb=" O   VAL F 225 " (cutoff:3.500A)
      removed outlier: 4.097A  pdb=" N   ALA F 231 " --> pdb=" O   ASP F 227 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 233 through 245
    Processing helix  chain 'F' and resid 250 through 267
    Processing helix  chain 'F' and resid 267 through 280
      removed outlier: 3.745A  pdb=" N   LEU F 280 " --> pdb=" O   LEU F 276 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 24 through 27
      removed outlier: 5.291A  pdb=" N   GLU A  25 " --> pdb=" O   VAL A  32 " (cutoff:3.500A)
      removed outlier: 6.940A  pdb=" N   VAL A  32 " --> pdb=" O   GLU A  25 " (cutoff:3.500A)
      removed outlier: 3.634A  pdb=" N   ALA A  27 " --> pdb=" O   VAL A  30 " (cutoff:3.500A)
      removed outlier: 7.063A  pdb=" N   MET A   3 " --> pdb=" O   ALA A  61 " (cutoff:3.500A)
      removed outlier: 3.966A  pdb=" N   ALA A  61 " --> pdb=" O   MET A   3 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 78 through 81
      removed outlier: 5.277A  pdb=" N   ILE A  88 " --> pdb=" O   ARG F  49 " (cutoff:3.500A)
      removed outlier: 4.154A  pdb=" N   ARG F  49 " --> pdb=" O   ILE A  88 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'B' and resid 289 through 291
      removed outlier: 8.053A  pdb=" N   VAL B  57 " --> pdb=" O   ARG B  21 " (cutoff:3.500A)
      removed outlier: 6.388A  pdb=" N   THR B  23 " --> pdb=" O   VAL B  57 " (cutoff:3.500A)
      removed outlier: 7.196A  pdb=" N   LEU B  59 " --> pdb=" O   THR B  23 " (cutoff:3.500A)
      removed outlier: 6.936A  pdb=" N   ILE B  25 " --> pdb=" O   LEU B  59 " (cutoff:3.500A)
      removed outlier: 6.398A  pdb=" N   LEU B  58 " --> pdb=" O   VAL B  82 " (cutoff:3.500A)
      removed outlier: 6.724A  pdb=" N   VAL B  84 " --> pdb=" O   LEU B  58 " (cutoff:3.500A)
      removed outlier: 6.063A  pdb=" N   LEU B  60 " --> pdb=" O   VAL B  84 " (cutoff:3.500A)
      removed outlier: 6.518A  pdb=" N   TRP C  83 " --> pdb=" O   ARG C  90 " (cutoff:3.500A)
      removed outlier: 4.708A  pdb=" N   TYR C  92 " --> pdb=" O   LEU C  81 " (cutoff:3.500A)
      removed outlier: 6.721A  pdb=" N   LEU C  81 " --> pdb=" O   TYR C  92 " (cutoff:3.500A)
      removed outlier: 6.612A  pdb=" N   THR C  23 " --> pdb=" O   VAL C  57 " (cutoff:3.500A)
      removed outlier: 7.656A  pdb=" N   LEU C  59 " --> pdb=" O   THR C  23 " (cutoff:3.500A)
      removed outlier: 6.272A  pdb=" N   ILE C  25 " --> pdb=" O   LEU C  59 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'B' and resid 39 through 41
      removed outlier: 7.627A  pdb=" N   ALA B  30 " --> pdb=" O   ASP B  65 " (cutoff:3.500A)
      removed outlier: 8.075A  pdb=" N   SER B  67 " --> pdb=" O   ALA B  30 " (cutoff:3.500A)
      removed outlier: 7.527A  pdb=" N   ILE B  32 " --> pdb=" O   SER B  67 " (cutoff:3.500A)
      removed outlier: 6.598A  pdb=" N   ARG C  34 " --> pdb=" O   SER C  67 " (cutoff:3.500A)
      removed outlier: 3.502A  pdb=" N   LYS C  31 " --> pdb=" O   ALA C  42 " (cutoff:3.500A)
      removed outlier: 4.304A  pdb=" N   ARG C  49 " --> pdb=" O   ILE D  88 " (cutoff:3.500A)
      removed outlier: 5.524A  pdb=" N   ILE D  88 " --> pdb=" O   ARG C  49 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'B' and resid 47 through 49
      removed outlier: 3.939A  pdb=" N   ASN B 308 " --> pdb=" O   ARG B  49 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'D' and resid 24 through 27
      removed outlier: 5.588A  pdb=" N   GLU D  25 " --> pdb=" O   VAL D  32 " (cutoff:3.500A)
      removed outlier: 7.223A  pdb=" N   VAL D  32 " --> pdb=" O   GLU D  25 " (cutoff:3.500A)
      removed outlier: 3.972A  pdb=" N   ALA D  27 " --> pdb=" O   VAL D  30 " (cutoff:3.500A)
      removed outlier: 6.932A  pdb=" N   MET D   3 " --> pdb=" O   ALA D  61 " (cutoff:3.500A)
      removed outlier: 3.533A  pdb=" N   ALA D  61 " --> pdb=" O   MET D   3 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'E' and resid 91 through 94
      removed outlier: 6.563A  pdb=" N   TRP E  83 " --> pdb=" O   TYR E  92 " (cutoff:3.500A)
      removed outlier: 4.395A  pdb=" N   SER E  94 " --> pdb=" O   LEU E  81 " (cutoff:3.500A)
      removed outlier: 6.829A  pdb=" N   LEU E  81 " --> pdb=" O   SER E  94 " (cutoff:3.500A)
      removed outlier: 6.310A  pdb=" N   LEU E  58 " --> pdb=" O   VAL E  82 " (cutoff:3.500A)
      removed outlier: 6.636A  pdb=" N   VAL E  84 " --> pdb=" O   LEU E  58 " (cutoff:3.500A)
      removed outlier: 5.847A  pdb=" N   LEU E  60 " --> pdb=" O   VAL E  84 " (cutoff:3.500A)
      removed outlier: 7.613A  pdb=" N   VAL E  57 " --> pdb=" O   ARG E  21 " (cutoff:3.500A)
      removed outlier: 6.188A  pdb=" N   THR E  23 " --> pdb=" O   VAL E  57 " (cutoff:3.500A)
      removed outlier: 7.336A  pdb=" N   LEU E  59 " --> pdb=" O   THR E  23 " (cutoff:3.500A)
      removed outlier: 7.030A  pdb=" N   ILE E  25 " --> pdb=" O   LEU E  59 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'E' and resid 32 through 35
    Processing sheet with id=AA9, first strand: chain 'F' and resid 22 through 27
      removed outlier: 6.349A  pdb=" N   THR F  23 " --> pdb=" O   VAL F  57 " (cutoff:3.500A)
      removed outlier: 7.434A  pdb=" N   LEU F  59 " --> pdb=" O   THR F  23 " (cutoff:3.500A)
      removed outlier: 6.182A  pdb=" N   ILE F  25 " --> pdb=" O   LEU F  59 " (cutoff:3.500A)

    525 hydrogen bonds defined for protein.
    1512 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      28 hydrogen bonds
      56 hydrogen bond angles
      0 basepair planarities
      11 basepair parallelities
      46 stacking parallelities
  Total time for adding SS restraints: 3.66

  Time building geometry restraints manager: 3.26 seconds

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

  Histogram of bond lengths:
        1.22 -     1.34: 3117
        1.34 -     1.45: 1970
        1.45 -     1.57: 5799
        1.57 -     1.69: 108
        1.69 -     1.81: 58
  Bond restraints: 11052
  Sorted by residual:
  bond pdb=" C3'  DC G   8 "
       pdb=" O3'  DC G   8 "
    ideal  model  delta    sigma   weight residual
    1.422  1.463 -0.041 3.00e-02 1.11e+03 1.83e+00
  bond pdb=" C4'  DG H  24 "
       pdb=" O4'  DG H  24 "
    ideal  model  delta    sigma   weight residual
    1.450  1.432  0.018 2.00e-02 2.50e+03 7.88e-01
  bond pdb=" O4'  DT H   3 "
       pdb=" C1'  DT H   3 "
    ideal  model  delta    sigma   weight residual
    1.414  1.396  0.018 2.00e-02 2.50e+03 7.79e-01
  bond pdb=" C4'  DG G  24 "
       pdb=" O4'  DG G  24 "
    ideal  model  delta    sigma   weight residual
    1.450  1.433  0.017 2.00e-02 2.50e+03 7.62e-01
  bond pdb=" C4'  DC H   2 "
       pdb=" O4'  DC H   2 "
    ideal  model  delta    sigma   weight residual
    1.450  1.433  0.017 2.00e-02 2.50e+03 7.47e-01
  ... (remaining 11047 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.98: 15004
        1.98 -     3.96: 168
        3.96 -     5.94: 18
        5.94 -     7.92: 4
        7.92 -     9.90: 2
  Bond angle restraints: 15196
  Sorted by residual:
  angle pdb=" CB  ARG F 150 "
        pdb=" CG  ARG F 150 "
        pdb=" CD  ARG F 150 "
      ideal   model   delta    sigma   weight residual
     111.30  121.20   -9.90 2.30e+00 1.89e-01 1.85e+01
  angle pdb=" N   GLU C 147 "
        pdb=" CA  GLU C 147 "
        pdb=" CB  GLU C 147 "
      ideal   model   delta    sigma   weight residual
     110.12  115.11   -4.99 1.47e+00 4.63e-01 1.15e+01
  angle pdb=" CA  GLU C 147 "
        pdb=" CB  GLU C 147 "
        pdb=" CG  GLU C 147 "
      ideal   model   delta    sigma   weight residual
     114.10  119.17   -5.07 2.00e+00 2.50e-01 6.44e+00
  angle pdb=" C   GLU C 232 "
        pdb=" N   ILE C 233 "
        pdb=" CA  ILE C 233 "
      ideal   model   delta    sigma   weight residual
     123.16  120.59    2.57 1.06e+00 8.90e-01 5.86e+00
  angle pdb=" CA  GLN F  87 "
        pdb=" CB  GLN F  87 "
        pdb=" CG  GLN F  87 "
      ideal   model   delta    sigma   weight residual
     114.10  118.84   -4.74 2.00e+00 2.50e-01 5.61e+00
  ... (remaining 15191 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    34.42: 6184
       34.42 -    68.83: 314
       68.83 -   103.25: 9
      103.25 -   137.66: 0
      137.66 -   172.08: 1
  Dihedral angle restraints: 6508
    sinusoidal: 2974
      harmonic: 3534
  Sorted by residual:
  dihedral pdb=" CA  ARG E  34 "
           pdb=" C   ARG E  34 "
           pdb=" N   VAL E  35 "
           pdb=" CA  VAL E  35 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  156.58   23.42     0      5.00e+00 4.00e-02 2.19e+01
  dihedral pdb=" C4'  DC G   8 "
           pdb=" C3'  DC G   8 "
           pdb=" O3'  DC G   8 "
           pdb=" P    DT G   9 "
      ideal   model   delta sinusoidal    sigma   weight residual
     220.00   47.92  172.08     1      3.50e+01 8.16e-04 1.56e+01
  dihedral pdb=" CA  ASP D  81 "
           pdb=" CB  ASP D  81 "
           pdb=" CG  ASP D  81 "
           pdb=" OD1 ASP D  81 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -30.00  -89.67   59.67     1      2.00e+01 2.50e-03 1.19e+01
  ... (remaining 6505 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.050: 1428
       0.050 -    0.100: 245
       0.100 -    0.150: 51
       0.150 -    0.199: 1
       0.199 -    0.249: 1
  Chirality restraints: 1726
  Sorted by residual:
  chirality pdb=" CA  ARG F 150 "
            pdb=" N   ARG F 150 "
            pdb=" C   ARG F 150 "
            pdb=" CB  ARG F 150 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.26    0.25 2.00e-01 2.50e+01 1.55e+00
  chirality pdb=" CB  VAL C 191 "
            pdb=" CA  VAL C 191 "
            pdb=" CG1 VAL C 191 "
            pdb=" CG2 VAL C 191 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -2.43   -0.19 2.00e-01 2.50e+01 9.43e-01
  chirality pdb=" CG  LEU F 269 "
            pdb=" CB  LEU F 269 "
            pdb=" CD1 LEU F 269 "
            pdb=" CD2 LEU F 269 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.59   -2.44   -0.15 2.00e-01 2.50e+01 5.38e-01
  ... (remaining 1723 not shown)

  Planarity restraints: 1758
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  HIS E 190 "   -0.010 2.00e-02 2.50e+03   1.45e-02 3.15e+00
        pdb=" CG  HIS E 190 "    0.030 2.00e-02 2.50e+03
        pdb=" ND1 HIS E 190 "   -0.011 2.00e-02 2.50e+03
        pdb=" CD2 HIS E 190 "   -0.011 2.00e-02 2.50e+03
        pdb=" CE1 HIS E 190 "    0.002 2.00e-02 2.50e+03
        pdb=" NE2 HIS E 190 "   -0.000 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  LEU C 143 "   -0.009 2.00e-02 2.50e+03   1.71e-02 2.92e+00
        pdb=" C   LEU C 143 "    0.030 2.00e-02 2.50e+03
        pdb=" O   LEU C 143 "   -0.011 2.00e-02 2.50e+03
        pdb=" N   ARG C 144 "   -0.010 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ASP C 180 "    0.027 5.00e-02 4.00e+02   4.09e-02 2.67e+00
        pdb=" N   PRO C 181 "   -0.071 5.00e-02 4.00e+02
        pdb=" CA  PRO C 181 "    0.021 5.00e-02 4.00e+02
        pdb=" CD  PRO C 181 "    0.023 5.00e-02 4.00e+02
  ... (remaining 1755 not shown)

  Histogram of nonbonded interaction distances:
        2.21 -     2.75: 1127
        2.75 -     3.29: 10426
        3.29 -     3.82: 19078
        3.82 -     4.36: 22169
        4.36 -     4.90: 38034
  Nonbonded interactions: 90834
  Sorted by model distance:
  nonbonded pdb=" O   LEU E 295 "
            pdb=" OH  TYR E 309 "
     model   vdw
     2.209 3.040
  nonbonded pdb=" OH  TYR C 229 "
            pdb=" OD2 ASP C 275 "
     model   vdw
     2.213 3.040
  nonbonded pdb=" OH  TYR F 229 "
            pdb=" OD2 ASP F 275 "
     model   vdw
     2.229 3.040
  nonbonded pdb=" OH  TYR F 126 "
            pdb=" NH2 ARG F 150 "
     model   vdw
     2.231 3.120
  nonbonded pdb=" O   LEU B 295 "
            pdb=" OH  TYR B 309 "
     model   vdw
     2.238 3.040
  ... (remaining 90829 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 'D'
}
ncs_group {
  reference = (chain 'B' and resid 20 through 283)
  selection = (chain 'C' and (resid 20 through 129 or resid 181 through 283))
  selection = (chain 'E' and resid 20 through 283)
  selection = (chain 'F' and (resid 20 through 129 or resid 181 through 283))
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             1.000
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.070
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.450
  Check model and map are aligned:         0.090
  Set scattering table:                    0.120
  Process input model:                     30.930
  Find NCS groups from input model:        0.440
  Set up NCS constraints:                  0.050
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.010
  Load rotamer database and sin/cos tables:2.990
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   36.160
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7476
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      :  0.003   0.041  11052  Z= 0.138
  Angle     :  0.523   9.896  15196  Z= 0.279
  Chirality :  0.039   0.249   1726
  Planarity :  0.004   0.049   1758
  Dihedral  : 17.515 172.077   4240
  Min Nonbonded Distance : 2.209

Molprobity Statistics.
  All-atom Clashscore : 11.22
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.14 %
    Favored  : 96.86 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.40 %
    Favored  : 99.60 %
  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:  0.86 (0.24), residues: 1212
  helix:  2.00 (0.21), residues: 572
  sheet: -0.19 (0.39), residues: 186
  loop : -0.96 (0.28), residues: 454

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP A  44 
 HIS   0.019   0.002   HIS E 190 
 PHE   0.010   0.001   PHE A  89 
 TYR   0.025   0.001   TYR B 126 
 ARG   0.015   0.000   ARG F 150 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.15890 (  553)
  hydrogen bonds       : angle       6.28341 ( 1568)
  covalent geometry    : bond        0.00313 (11052)
  covalent geometry    : angle       0.52313 (15196)

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

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

  2424 Ramachandran restraints generated.
    1212 Oldfield, 0 Emsley, 1212 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2424 Ramachandran restraints generated.
    1212 Oldfield, 0 Emsley, 1212 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  192 residues out of total 998 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 192
  time to evaluate  : 1.159 
Fit side-chains
REVERT: B   24 PHE cc_start: 0.6987 (m-10) cc_final: 0.6238 (m-10)
REVERT: C  120 ARG cc_start: 0.7736 (ttp-110) cc_final: 0.7200 (ttp-110)
REVERT: C  140 MET cc_start: 0.8612 (mpp) cc_final: 0.7969 (mpp)
REVERT: D   57 SER cc_start: 0.8830 (p) cc_final: 0.8535 (p)
REVERT: F  146 HIS cc_start: 0.6869 (m90) cc_final: 0.5941 (m90)
  outliers start: 0
  outliers final: 0
  residues processed: 192
  average time/residue: 0.2458
  time to fit residues: 65.1364
Evaluate side-chains
  166 residues out of total 998 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 166
  time to evaluate  : 1.167 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 126
   random chunks:
   chunk 106 optimal weight:    3.9990
   chunk 95 optimal weight:    0.0370
   chunk 52 optimal weight:    2.9990
   chunk 32 optimal weight:    0.9990
   chunk 64 optimal weight:    0.9980
   chunk 51 optimal weight:    0.9990
   chunk 98 optimal weight:    1.9990
   chunk 38 optimal weight:    2.9990
   chunk 60 optimal weight:    0.1980
   chunk 73 optimal weight:    1.9990
   chunk 114 optimal weight:    0.7980
   overall best weight:    0.6060

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

Flipped N/Q/H residues before XYZ refinement:
A  48 GLN
C 146 HIS
D  48 GLN
** E 190 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4041 r_free = 0.4041 target = 0.170261 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3594 r_free = 0.3594 target = 0.129375 restraints weight = 12374.901|
|-----------------------------------------------------------------------------|
r_work (start): 0.3604 rms_B_bonded: 2.22
r_work: 0.3476 rms_B_bonded: 3.05 restraints_weight: 0.5000
r_work: 0.3328 rms_B_bonded: 4.95 restraints_weight: 0.2500
r_work (final): 0.3328
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7654
moved from start:          0.1171

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042  11052  Z= 0.141
  Angle     :  0.533  10.743  15196  Z= 0.293
  Chirality :  0.041   0.146   1726
  Planarity :  0.004   0.042   1758
  Dihedral  : 18.261 177.610   1978
  Min Nonbonded Distance : 2.472

Molprobity Statistics.
  All-atom Clashscore : 10.36
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.56 %
    Favored  : 97.44 %
  Rotamer:
    Outliers :  1.40 %
    Allowed  :  7.72 %
    Favored  : 90.88 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.02 (0.24), residues: 1212
  helix:  2.03 (0.21), residues: 582
  sheet:  0.04 (0.40), residues: 182
  loop : -0.86 (0.28), residues: 448

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP A  44 
 HIS   0.011   0.001   HIS E  29 
 PHE   0.014   0.001   PHE C 212 
 TYR   0.011   0.001   TYR C 229 
 ARG   0.004   0.000   ARG D  63 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04158 (  553)
  hydrogen bonds       : angle       4.44096 ( 1568)
  covalent geometry    : bond        0.00311 (11052)
  covalent geometry    : angle       0.53297 (15196)

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

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

  2424 Ramachandran restraints generated.
    1212 Oldfield, 0 Emsley, 1212 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2424 Ramachandran restraints generated.
    1212 Oldfield, 0 Emsley, 1212 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  196 residues out of total 998 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 182
  time to evaluate  : 1.032 
Fit side-chains
REVERT: B   24 PHE cc_start: 0.7040 (m-10) cc_final: 0.6790 (m-10)
REVERT: C  120 ARG cc_start: 0.7798 (ttp-110) cc_final: 0.7473 (ttp-110)
REVERT: C  140 MET cc_start: 0.8782 (mpp) cc_final: 0.8094 (mpp)
REVERT: C  147 GLU cc_start: 0.7262 (mp0) cc_final: 0.6476 (mp0)
REVERT: D    9 LYS cc_start: 0.8100 (ptmm) cc_final: 0.7817 (ptmt)
REVERT: E   36 ASP cc_start: 0.7733 (p0) cc_final: 0.7518 (p0)
REVERT: E  115 GLU cc_start: 0.5135 (tp30) cc_final: 0.4865 (tp30)
REVERT: E  227 ASP cc_start: 0.8755 (OUTLIER) cc_final: 0.8101 (t70)
REVERT: F  140 MET cc_start: 0.7735 (mmm) cc_final: 0.7435 (tpt)
REVERT: F  250 ASP cc_start: 0.8350 (t0) cc_final: 0.8025 (t0)
  outliers start: 14
  outliers final: 11
  residues processed: 189
  average time/residue: 0.2215
  time to fit residues: 59.3996
Evaluate side-chains
  170 residues out of total 998 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 158
  time to evaluate  : 1.105 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   35 VAL
Chi-restraints excluded: chain B residue  102 THR
Chi-restraints excluded: chain C residue   13 SER
Chi-restraints excluded: chain C residue  215 THR
Chi-restraints excluded: chain C residue  264 VAL
Chi-restraints excluded: chain D residue   26 ILE
Chi-restraints excluded: chain D residue   30 VAL
Chi-restraints excluded: chain E residue  186 LEU
Chi-restraints excluded: chain E residue  227 ASP
Chi-restraints excluded: chain F residue  187 SER
Chi-restraints excluded: chain F residue  215 THR
Chi-restraints excluded: chain F residue  265 ASP
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 126
   random chunks:
   chunk 52 optimal weight:    0.8980
   chunk 25 optimal weight:    0.0000
   chunk 121 optimal weight:    0.0970
   chunk 34 optimal weight:    0.7980
   chunk 5 optimal weight:    3.9990
   chunk 15 optimal weight:    1.9990
   chunk 45 optimal weight:    6.9990
   chunk 20 optimal weight:   10.0000
   chunk 64 optimal weight:    0.9990
   chunk 122 optimal weight:    2.9990
   chunk 41 optimal weight:    0.5980
   overall best weight:    0.4782

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

Flipped N/Q/H residues before XYZ refinement:
C 146 HIS
D  48 GLN
F 183 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4056 r_free = 0.4056 target = 0.171442 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3611 r_free = 0.3611 target = 0.130925 restraints weight = 12486.068|
|-----------------------------------------------------------------------------|
r_work (start): 0.3613 rms_B_bonded: 2.25
r_work: 0.3478 rms_B_bonded: 3.12 restraints_weight: 0.5000
r_work (final): 0.3478
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7527
moved from start:          0.1502

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039  11052  Z= 0.125
  Angle     :  0.492   7.547  15196  Z= 0.271
  Chirality :  0.039   0.146   1726
  Planarity :  0.003   0.038   1758
  Dihedral  : 18.166 173.330   1978
  Min Nonbonded Distance : 2.458

Molprobity Statistics.
  All-atom Clashscore : 9.61
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.56 %
    Favored  : 97.44 %
  Rotamer:
    Outliers :  2.00 %
    Allowed  : 10.82 %
    Favored  : 87.17 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.12 (0.24), residues: 1212
  helix:  2.14 (0.21), residues: 582
  sheet:  0.07 (0.40), residues: 182
  loop : -0.83 (0.28), residues: 448

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP B 296 
 HIS   0.007   0.001   HIS E  29 
 PHE   0.011   0.001   PHE D  89 
 TYR   0.011   0.001   TYR F 126 
 ARG   0.003   0.000   ARG D  63 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03527 (  553)
  hydrogen bonds       : angle       4.15885 ( 1568)
  covalent geometry    : bond        0.00276 (11052)
  covalent geometry    : angle       0.49197 (15196)

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

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

  2424 Ramachandran restraints generated.
    1212 Oldfield, 0 Emsley, 1212 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2424 Ramachandran restraints generated.
    1212 Oldfield, 0 Emsley, 1212 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  192 residues out of total 998 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 172
  time to evaluate  : 1.235 
Fit side-chains
REVERT: C  120 ARG cc_start: 0.7727 (ttp-110) cc_final: 0.7507 (ttp-110)
REVERT: C  140 MET cc_start: 0.8564 (mpp) cc_final: 0.7972 (mpp)
REVERT: C  147 GLU cc_start: 0.7136 (mt-10) cc_final: 0.6333 (mp0)
REVERT: D    9 LYS cc_start: 0.8074 (ptmm) cc_final: 0.7798 (ptmt)
REVERT: D   82 TYR cc_start: 0.7631 (m-80) cc_final: 0.7372 (m-80)
REVERT: E  115 GLU cc_start: 0.4960 (tp30) cc_final: 0.4700 (tp30)
REVERT: E  119 LEU cc_start: 0.7976 (tp) cc_final: 0.7770 (tp)
REVERT: F  140 MET cc_start: 0.7778 (mmm) cc_final: 0.7443 (mmm)
REVERT: F  146 HIS cc_start: 0.6733 (m170) cc_final: 0.6335 (m90)
  outliers start: 20
  outliers final: 16
  residues processed: 181
  average time/residue: 0.2450
  time to fit residues: 63.0884
Evaluate side-chains
  177 residues out of total 998 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 161
  time to evaluate  : 1.056 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   26 ILE
Chi-restraints excluded: chain A residue   71 LEU
Chi-restraints excluded: chain A residue   80 ILE
Chi-restraints excluded: chain B residue   35 VAL
Chi-restraints excluded: chain B residue  102 THR
Chi-restraints excluded: chain C residue   13 SER
Chi-restraints excluded: chain C residue  146 HIS
Chi-restraints excluded: chain C residue  215 THR
Chi-restraints excluded: chain C residue  264 VAL
Chi-restraints excluded: chain D residue   26 ILE
Chi-restraints excluded: chain D residue   30 VAL
Chi-restraints excluded: chain D residue   57 SER
Chi-restraints excluded: chain E residue  186 LEU
Chi-restraints excluded: chain E residue  207 SER
Chi-restraints excluded: chain F residue  187 SER
Chi-restraints excluded: chain F residue  215 THR
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 126
   random chunks:
   chunk 66 optimal weight:    0.9980
   chunk 71 optimal weight:    2.9990
   chunk 47 optimal weight:   20.0000
   chunk 41 optimal weight:    0.3980
   chunk 19 optimal weight:    4.9990
   chunk 58 optimal weight:    4.9990
   chunk 45 optimal weight:    2.9990
   chunk 88 optimal weight:    0.0670
   chunk 67 optimal weight:    2.9990
   chunk 33 optimal weight:    7.9990
   chunk 64 optimal weight:    0.7980
   overall best weight:    1.0520

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

Flipped N/Q/H residues before XYZ refinement:
D  48 GLN
F 184 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4027 r_free = 0.4027 target = 0.168735 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3597 r_free = 0.3597 target = 0.129493 restraints weight = 12442.380|
|-----------------------------------------------------------------------------|
r_work (start): 0.3606 rms_B_bonded: 2.28
r_work: 0.3449 rms_B_bonded: 3.08 restraints_weight: 0.5000
r_work: 0.3303 rms_B_bonded: 4.95 restraints_weight: 0.2500
r_work (final): 0.3303
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7694
moved from start:          0.1587

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.043  11052  Z= 0.163
  Angle     :  0.519  12.078  15196  Z= 0.281
  Chirality :  0.040   0.145   1726
  Planarity :  0.003   0.037   1758
  Dihedral  : 18.243 173.244   1978
  Min Nonbonded Distance : 2.466

Molprobity Statistics.
  All-atom Clashscore : 8.99
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.14 %
    Favored  : 96.86 %
  Rotamer:
    Outliers :  2.20 %
    Allowed  : 13.83 %
    Favored  : 83.97 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.11 (0.24), residues: 1212
  helix:  2.14 (0.21), residues: 582
  sheet:  0.04 (0.40), residues: 182
  loop : -0.86 (0.28), residues: 448

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP E  83 
 HIS   0.016   0.002   HIS C 146 
 PHE   0.022   0.001   PHE F 176 
 TYR   0.010   0.001   TYR F 223 
 ARG   0.004   0.000   ARG D  63 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03563 (  553)
  hydrogen bonds       : angle       4.11900 ( 1568)
  covalent geometry    : bond        0.00378 (11052)
  covalent geometry    : angle       0.51950 (15196)

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

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

  2424 Ramachandran restraints generated.
    1212 Oldfield, 0 Emsley, 1212 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2424 Ramachandran restraints generated.
    1212 Oldfield, 0 Emsley, 1212 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  195 residues out of total 998 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 173
  time to evaluate  : 1.176 
Fit side-chains
REVERT: C  120 ARG cc_start: 0.7712 (ttp-110) cc_final: 0.7500 (ttp-110)
REVERT: C  140 MET cc_start: 0.8418 (mpp) cc_final: 0.7864 (mpp)
REVERT: D    9 LYS cc_start: 0.8091 (ptmm) cc_final: 0.7822 (ptmt)
REVERT: E  115 GLU cc_start: 0.5075 (tp30) cc_final: 0.4789 (tp30)
REVERT: F  140 MET cc_start: 0.7716 (mmm) cc_final: 0.7339 (mmm)
REVERT: F  146 HIS cc_start: 0.6662 (m170) cc_final: 0.6361 (m90)
REVERT: F  176 PHE cc_start: 0.5448 (t80) cc_final: 0.5165 (t80)
REVERT: F  250 ASP cc_start: 0.8372 (t0) cc_final: 0.7912 (t0)
  outliers start: 22
  outliers final: 18
  residues processed: 186
  average time/residue: 0.2433
  time to fit residues: 63.8038
Evaluate side-chains
  181 residues out of total 998 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 163
  time to evaluate  : 1.172 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    9 LYS
Chi-restraints excluded: chain A residue   23 MET
Chi-restraints excluded: chain A residue   26 ILE
Chi-restraints excluded: chain A residue   71 LEU
Chi-restraints excluded: chain B residue   35 VAL
Chi-restraints excluded: chain B residue  102 THR
Chi-restraints excluded: chain B residue  199 SER
Chi-restraints excluded: chain C residue   13 SER
Chi-restraints excluded: chain C residue  215 THR
Chi-restraints excluded: chain C residue  228 LEU
Chi-restraints excluded: chain C residue  264 VAL
Chi-restraints excluded: chain D residue   26 ILE
Chi-restraints excluded: chain D residue   30 VAL
Chi-restraints excluded: chain D residue   57 SER
Chi-restraints excluded: chain E residue  186 LEU
Chi-restraints excluded: chain E residue  207 SER
Chi-restraints excluded: chain F residue  187 SER
Chi-restraints excluded: chain F residue  215 THR
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 126
   random chunks:
   chunk 40 optimal weight:    1.9990
   chunk 64 optimal weight:    0.5980
   chunk 21 optimal weight:    0.6980
   chunk 125 optimal weight:    4.9990
   chunk 27 optimal weight:    0.5980
   chunk 102 optimal weight:    0.0980
   chunk 108 optimal weight:    0.7980
   chunk 47 optimal weight:   20.0000
   chunk 103 optimal weight:    5.9990
   chunk 115 optimal weight:    0.9980
   chunk 84 optimal weight:    4.9990
   overall best weight:    0.5580

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

Flipped N/Q/H residues before XYZ refinement:
C 146 HIS
D  48 GLN
F 184 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4048 r_free = 0.4048 target = 0.170568 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3603 r_free = 0.3603 target = 0.130123 restraints weight = 12406.762|
|-----------------------------------------------------------------------------|
r_work (start): 0.3606 rms_B_bonded: 2.23
r_work: 0.3469 rms_B_bonded: 3.09 restraints_weight: 0.5000
r_work (final): 0.3469
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7538
moved from start:          0.1740

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040  11052  Z= 0.125
  Angle     :  0.489   7.473  15196  Z= 0.269
  Chirality :  0.039   0.146   1726
  Planarity :  0.003   0.035   1758
  Dihedral  : 18.194 173.086   1978
  Min Nonbonded Distance : 2.465

Molprobity Statistics.
  All-atom Clashscore : 9.70
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.56 %
    Favored  : 97.44 %
  Rotamer:
    Outliers :  1.90 %
    Allowed  : 14.73 %
    Favored  : 83.37 %
  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:  1.21 (0.24), residues: 1212
  helix:  2.25 (0.21), residues: 582
  sheet:  0.03 (0.39), residues: 182
  loop : -0.81 (0.28), residues: 448

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP D  44 
 HIS   0.008   0.001   HIS E  29 
 PHE   0.014   0.001   PHE F 176 
 TYR   0.010   0.001   TYR C 223 
 ARG   0.005   0.000   ARG C 150 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03269 (  553)
  hydrogen bonds       : angle       4.04012 ( 1568)
  covalent geometry    : bond        0.00280 (11052)
  covalent geometry    : angle       0.48934 (15196)

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

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

  2424 Ramachandran restraints generated.
    1212 Oldfield, 0 Emsley, 1212 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2424 Ramachandran restraints generated.
    1212 Oldfield, 0 Emsley, 1212 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  187 residues out of total 998 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 168
  time to evaluate  : 1.043 
Fit side-chains
REVERT: C  140 MET cc_start: 0.8480 (mpp) cc_final: 0.7909 (mpp)
REVERT: D    9 LYS cc_start: 0.8063 (ptmm) cc_final: 0.7778 (ptmt)
REVERT: E  115 GLU cc_start: 0.4979 (tp30) cc_final: 0.4678 (tp30)
REVERT: E  232 GLU cc_start: 0.7281 (tm-30) cc_final: 0.7050 (pt0)
REVERT: F  140 MET cc_start: 0.7709 (mmm) cc_final: 0.7337 (mmm)
  outliers start: 19
  outliers final: 15
  residues processed: 179
  average time/residue: 0.2277
  time to fit residues: 57.7531
Evaluate side-chains
  179 residues out of total 998 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 164
  time to evaluate  : 1.035 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    9 LYS
Chi-restraints excluded: chain A residue   23 MET
Chi-restraints excluded: chain A residue   26 ILE
Chi-restraints excluded: chain A residue   71 LEU
Chi-restraints excluded: chain B residue   35 VAL
Chi-restraints excluded: chain B residue  102 THR
Chi-restraints excluded: chain C residue   13 SER
Chi-restraints excluded: chain C residue  215 THR
Chi-restraints excluded: chain C residue  228 LEU
Chi-restraints excluded: chain C residue  264 VAL
Chi-restraints excluded: chain D residue   26 ILE
Chi-restraints excluded: chain D residue   30 VAL
Chi-restraints excluded: chain E residue  207 SER
Chi-restraints excluded: chain F residue  187 SER
Chi-restraints excluded: chain F residue  215 THR
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 126
   random chunks:
   chunk 120 optimal weight:    0.7980
   chunk 61 optimal weight:    1.9990
   chunk 97 optimal weight:    0.6980
   chunk 83 optimal weight:    0.9980
   chunk 99 optimal weight:    2.9990
   chunk 88 optimal weight:    1.9990
   chunk 80 optimal weight:    1.9990
   chunk 45 optimal weight:    3.9990
   chunk 0 optimal weight:    4.9990
   chunk 69 optimal weight:    4.9990
   chunk 110 optimal weight:    5.9990
   overall best weight:    1.2984

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

Flipped N/Q/H residues before XYZ refinement:
C 146 HIS
D  48 GLN
E 190 HIS
F 184 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4011 r_free = 0.4011 target = 0.166998 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3550 r_free = 0.3550 target = 0.125928 restraints weight = 12588.375|
|-----------------------------------------------------------------------------|
r_work (start): 0.3552 rms_B_bonded: 2.24
r_work: 0.3416 rms_B_bonded: 3.11 restraints_weight: 0.5000
r_work (final): 0.3416
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7601
moved from start:          0.1801

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.048  11052  Z= 0.185
  Angle     :  0.542  11.519  15196  Z= 0.291
  Chirality :  0.041   0.168   1726
  Planarity :  0.003   0.034   1758
  Dihedral  : 18.360 172.441   1978
  Min Nonbonded Distance : 2.454

Molprobity Statistics.
  All-atom Clashscore : 9.70
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.63 %
    Favored  : 96.37 %
  Rotamer:
    Outliers :  2.51 %
    Allowed  : 15.73 %
    Favored  : 81.76 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.05 (0.24), residues: 1212
  helix:  2.12 (0.21), residues: 582
  sheet: -0.05 (0.39), residues: 182
  loop : -0.90 (0.28), residues: 448

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP E  83 
 HIS   0.011   0.001   HIS E  29 
 PHE   0.011   0.001   PHE B  24 
 TYR   0.011   0.001   TYR F 223 
 ARG   0.006   0.000   ARG D  63 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03595 (  553)
  hydrogen bonds       : angle       4.10006 ( 1568)
  covalent geometry    : bond        0.00436 (11052)
  covalent geometry    : angle       0.54150 (15196)

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

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

  2424 Ramachandran restraints generated.
    1212 Oldfield, 0 Emsley, 1212 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2424 Ramachandran restraints generated.
    1212 Oldfield, 0 Emsley, 1212 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  190 residues out of total 998 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 165
  time to evaluate  : 1.057 
Fit side-chains
REVERT: C  140 MET cc_start: 0.8389 (mpp) cc_final: 0.7748 (mpp)
REVERT: D    9 LYS cc_start: 0.8091 (ptmm) cc_final: 0.7810 (ptmt)
REVERT: F  140 MET cc_start: 0.7797 (mmm) cc_final: 0.7418 (mmm)
REVERT: F  250 ASP cc_start: 0.8313 (t0) cc_final: 0.7837 (t0)
  outliers start: 25
  outliers final: 18
  residues processed: 181
  average time/residue: 0.2369
  time to fit residues: 60.5300
Evaluate side-chains
  175 residues out of total 998 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 157
  time to evaluate  : 1.147 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    9 LYS
Chi-restraints excluded: chain A residue   23 MET
Chi-restraints excluded: chain A residue   26 ILE
Chi-restraints excluded: chain A residue   71 LEU
Chi-restraints excluded: chain B residue   35 VAL
Chi-restraints excluded: chain B residue  102 THR
Chi-restraints excluded: chain B residue  199 SER
Chi-restraints excluded: chain C residue   13 SER
Chi-restraints excluded: chain C residue  215 THR
Chi-restraints excluded: chain C residue  217 HIS
Chi-restraints excluded: chain C residue  228 LEU
Chi-restraints excluded: chain C residue  264 VAL
Chi-restraints excluded: chain D residue   26 ILE
Chi-restraints excluded: chain D residue   30 VAL
Chi-restraints excluded: chain E residue  186 LEU
Chi-restraints excluded: chain E residue  207 SER
Chi-restraints excluded: chain F residue  187 SER
Chi-restraints excluded: chain F residue  215 THR
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 126
   random chunks:
   chunk 106 optimal weight:    3.9990
   chunk 4 optimal weight:    1.9990
   chunk 50 optimal weight:   10.0000
   chunk 44 optimal weight:    4.9990
   chunk 29 optimal weight:    0.8980
   chunk 36 optimal weight:    2.9990
   chunk 46 optimal weight:    0.0770
   chunk 71 optimal weight:    3.9990
   chunk 123 optimal weight:    3.9990
   chunk 112 optimal weight:    5.9990
   chunk 87 optimal weight:    0.9990
   overall best weight:    1.3944

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

Flipped N/Q/H residues before XYZ refinement:
B  29 HIS
C 146 HIS
D  48 GLN
F 184 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3998 r_free = 0.3998 target = 0.165797 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3536 r_free = 0.3536 target = 0.124803 restraints weight = 12776.319|
|-----------------------------------------------------------------------------|
r_work (start): 0.3539 rms_B_bonded: 2.24
r_work: 0.3402 rms_B_bonded: 3.13 restraints_weight: 0.5000
r_work (final): 0.3402
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7615
moved from start:          0.1869

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.052  11052  Z= 0.194
  Angle     :  0.549   7.864  15196  Z= 0.297
  Chirality :  0.042   0.178   1726
  Planarity :  0.003   0.033   1758
  Dihedral  : 18.412 172.043   1978
  Min Nonbonded Distance : 2.463

Molprobity Statistics.
  All-atom Clashscore : 10.17
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.14 %
    Favored  : 96.86 %
  Rotamer:
    Outliers :  2.81 %
    Allowed  : 15.73 %
    Favored  : 81.46 %
  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:  0.95 (0.24), residues: 1212
  helix:  2.05 (0.21), residues: 582
  sheet: -0.16 (0.39), residues: 182
  loop : -0.94 (0.28), residues: 448

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP E  83 
 HIS   0.011   0.001   HIS E  29 
 PHE   0.013   0.001   PHE B  24 
 TYR   0.012   0.001   TYR C 223 
 ARG   0.005   0.000   ARG D  63 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03668 (  553)
  hydrogen bonds       : angle       4.14880 ( 1568)
  covalent geometry    : bond        0.00457 (11052)
  covalent geometry    : angle       0.54906 (15196)

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

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

  2424 Ramachandran restraints generated.
    1212 Oldfield, 0 Emsley, 1212 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2424 Ramachandran restraints generated.
    1212 Oldfield, 0 Emsley, 1212 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  183 residues out of total 998 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 155
  time to evaluate  : 1.170 
Fit side-chains
REVERT: B   40 THR cc_start: 0.8312 (m) cc_final: 0.8040 (m)
REVERT: B  250 ASP cc_start: 0.7631 (t70) cc_final: 0.7408 (t70)
REVERT: C  140 MET cc_start: 0.8368 (mpp) cc_final: 0.7778 (mpp)
REVERT: D    9 LYS cc_start: 0.8087 (ptmm) cc_final: 0.7778 (ptmt)
REVERT: E  115 GLU cc_start: 0.5034 (tp30) cc_final: 0.4830 (tp30)
REVERT: F  140 MET cc_start: 0.7736 (mmm) cc_final: 0.7342 (mmm)
  outliers start: 28
  outliers final: 21
  residues processed: 173
  average time/residue: 0.2276
  time to fit residues: 56.0244
Evaluate side-chains
  178 residues out of total 998 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 157
  time to evaluate  : 1.113 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    9 LYS
Chi-restraints excluded: chain A residue   23 MET
Chi-restraints excluded: chain A residue   26 ILE
Chi-restraints excluded: chain A residue   55 GLU
Chi-restraints excluded: chain A residue   71 LEU
Chi-restraints excluded: chain B residue   35 VAL
Chi-restraints excluded: chain B residue  102 THR
Chi-restraints excluded: chain B residue  199 SER
Chi-restraints excluded: chain C residue   13 SER
Chi-restraints excluded: chain C residue  215 THR
Chi-restraints excluded: chain C residue  217 HIS
Chi-restraints excluded: chain C residue  228 LEU
Chi-restraints excluded: chain C residue  264 VAL
Chi-restraints excluded: chain D residue   26 ILE
Chi-restraints excluded: chain D residue   30 VAL
Chi-restraints excluded: chain D residue   57 SER
Chi-restraints excluded: chain E residue  186 LEU
Chi-restraints excluded: chain E residue  190 HIS
Chi-restraints excluded: chain E residue  207 SER
Chi-restraints excluded: chain F residue  187 SER
Chi-restraints excluded: chain F residue  215 THR
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 126
   random chunks:
   chunk 110 optimal weight:    0.4980
   chunk 97 optimal weight:    0.5980
   chunk 96 optimal weight:    0.6980
   chunk 87 optimal weight:    0.0980
   chunk 20 optimal weight:   10.0000
   chunk 71 optimal weight:    3.9990
   chunk 94 optimal weight:    5.9990
   chunk 66 optimal weight:    0.7980
   chunk 43 optimal weight:    3.9990
   chunk 98 optimal weight:    2.9990
   chunk 53 optimal weight:    0.6980
   overall best weight:    0.5180

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

Flipped N/Q/H residues before XYZ refinement:
B  29 HIS
C 146 HIS
C 183 ASN
D  48 GLN
F 184 GLN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4043 r_free = 0.4043 target = 0.170005 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3597 r_free = 0.3597 target = 0.129542 restraints weight = 12568.814|
|-----------------------------------------------------------------------------|
r_work (start): 0.3600 rms_B_bonded: 2.26
r_work: 0.3464 rms_B_bonded: 3.13 restraints_weight: 0.5000
r_work (final): 0.3464
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7552
moved from start:          0.2007

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041  11052  Z= 0.125
  Angle     :  0.518  13.228  15196  Z= 0.278
  Chirality :  0.040   0.198   1726
  Planarity :  0.003   0.033   1758
  Dihedral  : 18.212 172.156   1978
  Min Nonbonded Distance : 2.480

Molprobity Statistics.
  All-atom Clashscore : 9.80
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.89 %
    Favored  : 97.11 %
  Rotamer:
    Outliers :  2.00 %
    Allowed  : 16.63 %
    Favored  : 81.36 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.15 (0.24), residues: 1212
  helix:  2.23 (0.21), residues: 582
  sheet: -0.12 (0.40), residues: 182
  loop : -0.83 (0.28), residues: 448

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP D  44 
 HIS   0.006   0.001   HIS E  29 
 PHE   0.012   0.001   PHE A  35 
 TYR   0.011   0.001   TYR C 126 
 ARG   0.006   0.000   ARG C 150 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03230 (  553)
  hydrogen bonds       : angle       4.05918 ( 1568)
  covalent geometry    : bond        0.00282 (11052)
  covalent geometry    : angle       0.51812 (15196)

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

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

  2424 Ramachandran restraints generated.
    1212 Oldfield, 0 Emsley, 1212 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2424 Ramachandran restraints generated.
    1212 Oldfield, 0 Emsley, 1212 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  190 residues out of total 998 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 170
  time to evaluate  : 1.058 
Fit side-chains
REVERT: B   40 THR cc_start: 0.8346 (m) cc_final: 0.8052 (m)
REVERT: C  140 MET cc_start: 0.8438 (mpp) cc_final: 0.7825 (mpp)
REVERT: D    9 LYS cc_start: 0.8072 (ptmm) cc_final: 0.7779 (ptmt)
REVERT: E  115 GLU cc_start: 0.4889 (tp30) cc_final: 0.4677 (tp30)
REVERT: F  140 MET cc_start: 0.7743 (mmm) cc_final: 0.7349 (mmm)
REVERT: F  250 ASP cc_start: 0.8329 (t0) cc_final: 0.7873 (t0)
  outliers start: 20
  outliers final: 18
  residues processed: 184
  average time/residue: 0.2826
  time to fit residues: 72.8999
Evaluate side-chains
  174 residues out of total 998 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 156
  time to evaluate  : 1.018 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    9 LYS
Chi-restraints excluded: chain A residue   23 MET
Chi-restraints excluded: chain A residue   26 ILE
Chi-restraints excluded: chain A residue   71 LEU
Chi-restraints excluded: chain B residue   29 HIS
Chi-restraints excluded: chain B residue   35 VAL
Chi-restraints excluded: chain B residue  102 THR
Chi-restraints excluded: chain C residue   13 SER
Chi-restraints excluded: chain C residue  215 THR
Chi-restraints excluded: chain C residue  228 LEU
Chi-restraints excluded: chain C residue  264 VAL
Chi-restraints excluded: chain D residue   26 ILE
Chi-restraints excluded: chain D residue   57 SER
Chi-restraints excluded: chain E residue  190 HIS
Chi-restraints excluded: chain E residue  207 SER
Chi-restraints excluded: chain F residue  187 SER
Chi-restraints excluded: chain F residue  215 THR
Chi-restraints excluded: chain F residue  269 LEU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 126
   random chunks:
   chunk 109 optimal weight:    6.9990
   chunk 73 optimal weight:    0.7980
   chunk 100 optimal weight:    0.5980
   chunk 87 optimal weight:    0.0980
   chunk 41 optimal weight:    0.0270
   chunk 85 optimal weight:    1.9990
   chunk 75 optimal weight:    0.3980
   chunk 99 optimal weight:    3.9990
   chunk 7 optimal weight:    2.9990
   chunk 6 optimal weight:    0.7980
   chunk 86 optimal weight:    2.9990
   overall best weight:    0.3838

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

Flipped N/Q/H residues before XYZ refinement:
B  29 HIS
C 183 ASN
D  48 GLN
F 184 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4060 r_free = 0.4060 target = 0.171667 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3613 r_free = 0.3613 target = 0.130949 restraints weight = 12653.798|
|-----------------------------------------------------------------------------|
r_work (start): 0.3623 rms_B_bonded: 2.29
r_work: 0.3492 rms_B_bonded: 3.11 restraints_weight: 0.5000
r_work (final): 0.3492
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7536
moved from start:          0.2088

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041  11052  Z= 0.118
  Angle     :  0.506   9.074  15196  Z= 0.277
  Chirality :  0.040   0.186   1726
  Planarity :  0.003   0.034   1758
  Dihedral  : 18.187 172.164   1978
  Min Nonbonded Distance : 2.486

Molprobity Statistics.
  All-atom Clashscore : 9.51
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.81 %
    Favored  : 97.19 %
  Rotamer:
    Outliers :  1.90 %
    Allowed  : 16.93 %
    Favored  : 81.16 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.23 (0.24), residues: 1212
  helix:  2.29 (0.21), residues: 582
  sheet: -0.07 (0.40), residues: 182
  loop : -0.80 (0.28), residues: 448

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP D  44 
 HIS   0.005   0.001   HIS E  29 
 PHE   0.021   0.001   PHE A  35 
 TYR   0.010   0.001   TYR F 126 
 ARG   0.008   0.000   ARG D  63 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03161 (  553)
  hydrogen bonds       : angle       4.01617 ( 1568)
  covalent geometry    : bond        0.00263 (11052)
  covalent geometry    : angle       0.50622 (15196)

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

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

  2424 Ramachandran restraints generated.
    1212 Oldfield, 0 Emsley, 1212 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2424 Ramachandran restraints generated.
    1212 Oldfield, 0 Emsley, 1212 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  181 residues out of total 998 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 162
  time to evaluate  : 0.911 
Fit side-chains
REVERT: B   40 THR cc_start: 0.8332 (m) cc_final: 0.8080 (m)
REVERT: C  120 ARG cc_start: 0.7585 (ttp-110) cc_final: 0.6827 (tpt170)
REVERT: C  140 MET cc_start: 0.8442 (mpp) cc_final: 0.7810 (mpp)
REVERT: D    9 LYS cc_start: 0.8051 (ptmm) cc_final: 0.7766 (ptmt)
REVERT: E  115 GLU cc_start: 0.4866 (tp30) cc_final: 0.4647 (tp30)
REVERT: F  140 MET cc_start: 0.7743 (mmm) cc_final: 0.7344 (mmm)
REVERT: F  150 ARG cc_start: 0.7751 (ptp-170) cc_final: 0.7542 (ptp-170)
REVERT: F  250 ASP cc_start: 0.8275 (t0) cc_final: 0.7837 (t0)
  outliers start: 19
  outliers final: 16
  residues processed: 174
  average time/residue: 0.3344
  time to fit residues: 84.5074
Evaluate side-chains
  172 residues out of total 998 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 156
  time to evaluate  : 0.945 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    9 LYS
Chi-restraints excluded: chain A residue   23 MET
Chi-restraints excluded: chain A residue   26 ILE
Chi-restraints excluded: chain A residue   71 LEU
Chi-restraints excluded: chain B residue   29 HIS
Chi-restraints excluded: chain B residue   35 VAL
Chi-restraints excluded: chain B residue  102 THR
Chi-restraints excluded: chain C residue  215 THR
Chi-restraints excluded: chain C residue  228 LEU
Chi-restraints excluded: chain C residue  264 VAL
Chi-restraints excluded: chain D residue   26 ILE
Chi-restraints excluded: chain E residue  190 HIS
Chi-restraints excluded: chain E residue  207 SER
Chi-restraints excluded: chain F residue  187 SER
Chi-restraints excluded: chain F residue  215 THR
Chi-restraints excluded: chain F residue  269 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 126
   random chunks:
   chunk 42 optimal weight:    7.9990
   chunk 53 optimal weight:    0.0040
   chunk 76 optimal weight:    3.9990
   chunk 107 optimal weight:    8.9990
   chunk 87 optimal weight:    4.9990
   chunk 18 optimal weight:    0.0670
   chunk 10 optimal weight:    4.9990
   chunk 106 optimal weight:    0.8980
   chunk 54 optimal weight:    2.9990
   chunk 51 optimal weight:    4.9990
   chunk 65 optimal weight:    1.9990
   overall best weight:    1.1934

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

Flipped N/Q/H residues before XYZ refinement:
B  29 HIS
C 183 ASN
D  48 GLN
F 184 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4018 r_free = 0.4018 target = 0.167632 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3560 r_free = 0.3560 target = 0.126761 restraints weight = 12666.510|
|-----------------------------------------------------------------------------|
r_work (start): 0.3571 rms_B_bonded: 2.26
r_work: 0.3437 rms_B_bonded: 3.09 restraints_weight: 0.5000
r_work (final): 0.3437
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7597
moved from start:          0.2080

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.050  11052  Z= 0.179
  Angle     :  0.561  12.700  15196  Z= 0.300
  Chirality :  0.041   0.197   1726
  Planarity :  0.004   0.036   1758
  Dihedral  : 18.361 171.850   1978
  Min Nonbonded Distance : 2.435

Molprobity Statistics.
  All-atom Clashscore : 10.03
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.38 %
    Favored  : 96.62 %
  Rotamer:
    Outliers :  1.90 %
    Allowed  : 17.03 %
    Favored  : 81.06 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.06 (0.24), residues: 1212
  helix:  2.15 (0.21), residues: 582
  sheet: -0.13 (0.40), residues: 182
  loop : -0.89 (0.28), residues: 448

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP E  83 
 HIS   0.011   0.001   HIS B  29 
 PHE   0.018   0.001   PHE A  35 
 TYR   0.011   0.001   TYR F 223 
 ARG   0.008   0.000   ARG C 150 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03525 (  553)
  hydrogen bonds       : angle       4.10211 ( 1568)
  covalent geometry    : bond        0.00418 (11052)
  covalent geometry    : angle       0.56116 (15196)

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

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

  2424 Ramachandran restraints generated.
    1212 Oldfield, 0 Emsley, 1212 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2424 Ramachandran restraints generated.
    1212 Oldfield, 0 Emsley, 1212 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  181 residues out of total 998 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 162
  time to evaluate  : 1.105 
Fit side-chains
REVERT: B   40 THR cc_start: 0.8338 (m) cc_final: 0.8039 (m)
REVERT: B  250 ASP cc_start: 0.7494 (t70) cc_final: 0.7264 (t70)
REVERT: C  140 MET cc_start: 0.8317 (mpp) cc_final: 0.7707 (mpp)
REVERT: C  223 TYR cc_start: 0.7462 (m-80) cc_final: 0.7220 (m-80)
REVERT: C  227 ASP cc_start: 0.8048 (m-30) cc_final: 0.7790 (m-30)
REVERT: D    1 MET cc_start: 0.6936 (mmt) cc_final: 0.6173 (mtm)
REVERT: D    9 LYS cc_start: 0.8083 (ptmm) cc_final: 0.7749 (ptmt)
REVERT: E  115 GLU cc_start: 0.4988 (tp30) cc_final: 0.4774 (tp30)
REVERT: F  140 MET cc_start: 0.7702 (mmm) cc_final: 0.7290 (mmm)
REVERT: F  250 ASP cc_start: 0.8320 (t0) cc_final: 0.7859 (t0)
  outliers start: 19
  outliers final: 18
  residues processed: 175
  average time/residue: 0.2778
  time to fit residues: 67.3586
Evaluate side-chains
  169 residues out of total 998 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 151
  time to evaluate  : 1.001 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    9 LYS
Chi-restraints excluded: chain A residue   23 MET
Chi-restraints excluded: chain A residue   26 ILE
Chi-restraints excluded: chain A residue   71 LEU
Chi-restraints excluded: chain B residue   29 HIS
Chi-restraints excluded: chain B residue   35 VAL
Chi-restraints excluded: chain B residue  102 THR
Chi-restraints excluded: chain C residue   13 SER
Chi-restraints excluded: chain C residue  215 THR
Chi-restraints excluded: chain C residue  228 LEU
Chi-restraints excluded: chain C residue  264 VAL
Chi-restraints excluded: chain D residue   26 ILE
Chi-restraints excluded: chain D residue   57 SER
Chi-restraints excluded: chain E residue  190 HIS
Chi-restraints excluded: chain E residue  207 SER
Chi-restraints excluded: chain F residue  187 SER
Chi-restraints excluded: chain F residue  215 THR
Chi-restraints excluded: chain F residue  269 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 126
   random chunks:
   chunk 60 optimal weight:    2.9990
   chunk 28 optimal weight:    0.9980
   chunk 104 optimal weight:    0.6980
   chunk 47 optimal weight:    9.9990
   chunk 54 optimal weight:    0.5980
   chunk 27 optimal weight:    0.9990
   chunk 125 optimal weight:    4.9990
   chunk 99 optimal weight:    2.9990
   chunk 58 optimal weight:    0.8980
   chunk 79 optimal weight:    0.6980
   chunk 2 optimal weight:    2.9990
   overall best weight:    0.7780

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

Flipped N/Q/H residues before XYZ refinement:
B  29 HIS
C 183 ASN
D  48 GLN
F 184 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4034 r_free = 0.4034 target = 0.169101 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3587 r_free = 0.3587 target = 0.128718 restraints weight = 12437.875|
|-----------------------------------------------------------------------------|
r_work (start): 0.3598 rms_B_bonded: 2.24
r_work: 0.3459 rms_B_bonded: 3.12 restraints_weight: 0.5000
r_work (final): 0.3459
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7568
moved from start:          0.2140

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040  11052  Z= 0.144
  Angle     :  0.532   9.589  15196  Z= 0.288
  Chirality :  0.040   0.194   1726
  Planarity :  0.003   0.036   1758
  Dihedral  : 18.341 172.102   1978
  Min Nonbonded Distance : 2.442

Molprobity Statistics.
  All-atom Clashscore : 9.89
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.97 %
    Favored  : 97.03 %
  Rotamer:
    Outliers :  1.80 %
    Allowed  : 17.33 %
    Favored  : 80.86 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.09 (0.24), residues: 1212
  helix:  2.19 (0.21), residues: 582
  sheet: -0.17 (0.40), residues: 182
  loop : -0.88 (0.28), residues: 448

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP E  83 
 HIS   0.008   0.001   HIS E  29 
 PHE   0.017   0.001   PHE A  35 
 TYR   0.012   0.001   TYR B  26 
 ARG   0.008   0.000   ARG D  63 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03352 (  553)
  hydrogen bonds       : angle       4.09816 ( 1568)
  covalent geometry    : bond        0.00331 (11052)
  covalent geometry    : angle       0.53237 (15196)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 5390.00 seconds
wall clock time: 97 minutes 42.08 seconds (5862.08 seconds total)