Starting phenix.real_space_refine
on Tue Nov 18 01:57:56 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7s5t_24839/11_2025/7s5t_24839.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7s5t_24839/11_2025/7s5t_24839.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/7s5t_24839/11_2025/7s5t_24839.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7s5t_24839/11_2025/7s5t_24839.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7s5t_24839/11_2025/7s5t_24839.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7s5t_24839/11_2025/7s5t_24839.cif"
  }
  resolution = 3.1
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=  -0.005 sd=   0.065
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 5
    Type Number    sf(0)   Gaussians
     K       2      8.98       5
     S      64      5.16       5
     C    6488      2.51       5
     N    1720      2.21       5
     O    1804      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 92 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5881/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 10078
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "A"
      Number of atoms: 2519
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 321, 2519
          Classifications: {'peptide': 321}
          Link IDs: {'PTRANS': 13, 'TRANS': 307}
    Chain: "A"
      Number of atoms: 2
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 2
          Unusual residues: {'  K': 2}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
  Restraints were copied for chains:
    B, C, D
  Time building chain proxies: 1.88, per 1000 atoms: 0.19
  Number of scatterers: 10078
  At special positions: 0
  Unit cell: (91, 89.7, 122.2, 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)
     K       2     19.00
     S      64     16.00
     O    1804      8.00
     N    1720      7.00
     C    6488      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=4, symmetry=0
    Simple disulfide: pdb=" SG  CYS A 110 " - pdb=" SG  CYS A 142 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 110 " - pdb=" SG  CYS B 142 " distance=2.03
    Simple disulfide: pdb=" SG  CYS C 110 " - pdb=" SG  CYS C 142 " distance=2.03
    Simple disulfide: pdb=" SG  CYS D 110 " - pdb=" SG  CYS D 142 " distance=2.03

  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: 0.92
  Conformation dependent library (CDL) restraints added in 316.7 milliseconds
  

  2552 Ramachandran restraints generated.
    1276 Oldfield, 0 Emsley, 1276 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2416

  Finding SS restraints...
    Secondary structure from input PDB file:
      35 helices and 20 sheets defined
      34.8% alpha, 25.9% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.38
  Creating SS restraints...
    Processing helix  chain 'A' and resid 51 through 57
      removed outlier: 3.783A  pdb=" N   ARG A  54 " --> pdb=" O   GLU A  51 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 58 through 65
      removed outlier: 3.670A  pdb=" N   THR A  62 " --> pdb=" O   ASP A  58 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 67 through 97
    Processing helix  chain 'A' and resid 116 through 129
    Processing helix  chain 'A' and resid 142 through 172
      removed outlier: 3.557A  pdb=" N   ILE A 146 " --> pdb=" O   CYS A 142 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 173 through 179
      removed outlier: 4.042A  pdb=" N   ARG A 176 " --> pdb=" O   GLN A 173 " (cutoff:3.500A)
      removed outlier: 3.851A  pdb=" N   ALA A 178 " --> pdb=" O   HIS A 175 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 271 through 275
      removed outlier: 3.809A  pdb=" N   LEU A 275 " --> pdb=" O   PRO A 272 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 330 through 333
    Processing helix  chain 'A' and resid 346 through 351
    Processing helix  chain 'B' and resid 51 through 57
      removed outlier: 3.783A  pdb=" N   ARG B  54 " --> pdb=" O   GLU B  51 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 58 through 65
      removed outlier: 3.670A  pdb=" N   THR B  62 " --> pdb=" O   ASP B  58 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 67 through 97
    Processing helix  chain 'B' and resid 116 through 129
    Processing helix  chain 'B' and resid 142 through 172
      removed outlier: 3.557A  pdb=" N   ILE B 146 " --> pdb=" O   CYS B 142 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 173 through 179
      removed outlier: 4.042A  pdb=" N   ARG B 176 " --> pdb=" O   GLN B 173 " (cutoff:3.500A)
      removed outlier: 3.850A  pdb=" N   ALA B 178 " --> pdb=" O   HIS B 175 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 271 through 275
      removed outlier: 3.809A  pdb=" N   LEU B 275 " --> pdb=" O   PRO B 272 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 330 through 333
    Processing helix  chain 'B' and resid 346 through 351
    Processing helix  chain 'C' and resid 51 through 57
      removed outlier: 3.784A  pdb=" N   ARG C  54 " --> pdb=" O   GLU C  51 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 58 through 65
      removed outlier: 3.668A  pdb=" N   THR C  62 " --> pdb=" O   ASP C  58 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 67 through 97
    Processing helix  chain 'C' and resid 116 through 129
    Processing helix  chain 'C' and resid 142 through 172
      removed outlier: 3.558A  pdb=" N   ILE C 146 " --> pdb=" O   CYS C 142 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 173 through 179
      removed outlier: 4.042A  pdb=" N   ARG C 176 " --> pdb=" O   GLN C 173 " (cutoff:3.500A)
      removed outlier: 3.851A  pdb=" N   ALA C 178 " --> pdb=" O   HIS C 175 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 330 through 333
    Processing helix  chain 'C' and resid 346 through 351
    Processing helix  chain 'D' and resid 51 through 57
      removed outlier: 3.783A  pdb=" N   ARG D  54 " --> pdb=" O   GLU D  51 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 58 through 65
      removed outlier: 3.669A  pdb=" N   THR D  62 " --> pdb=" O   ASP D  58 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 67 through 97
    Processing helix  chain 'D' and resid 116 through 129
    Processing helix  chain 'D' and resid 142 through 172
      removed outlier: 3.557A  pdb=" N   ILE D 146 " --> pdb=" O   CYS D 142 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 173 through 179
      removed outlier: 4.042A  pdb=" N   ARG D 176 " --> pdb=" O   GLN D 173 " (cutoff:3.500A)
      removed outlier: 3.851A  pdb=" N   ALA D 178 " --> pdb=" O   HIS D 175 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 271 through 275
      removed outlier: 3.810A  pdb=" N   LEU D 275 " --> pdb=" O   PRO D 272 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 330 through 333
    Processing helix  chain 'D' and resid 346 through 351
    Processing sheet with id=AA1, first strand: chain 'A' and resid 181 through 183
    Processing sheet with id=AA2, first strand: chain 'A' and resid 181 through 183
      removed outlier: 6.773A  pdb=" N   ALA A 187 " --> pdb=" O   LEU A 310 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 230 through 238
      removed outlier: 5.064A  pdb=" N   THR A 223 " --> pdb=" O   PRO A 232 " (cutoff:3.500A)
      removed outlier: 4.304A  pdb=" N   MET A 217 " --> pdb=" O   ILE A 238 " (cutoff:3.500A)
      removed outlier: 4.324A  pdb=" N   ALA A 213 " --> pdb=" O   GLU A 288 " (cutoff:3.500A)
      removed outlier: 6.433A  pdb=" N   GLU A 288 " --> pdb=" O   ALA A 213 " (cutoff:3.500A)
      removed outlier: 4.325A  pdb=" N   ILE A 215 " --> pdb=" O   ILE A 286 " (cutoff:3.500A)
      removed outlier: 6.576A  pdb=" N   ILE A 286 " --> pdb=" O   ILE A 215 " (cutoff:3.500A)
      removed outlier: 4.478A  pdb=" N   MET A 217 " --> pdb=" O   ILE A 284 " (cutoff:3.500A)
      removed outlier: 6.660A  pdb=" N   ILE A 284 " --> pdb=" O   MET A 217 " (cutoff:3.500A)
      removed outlier: 4.712A  pdb=" N   VAL A 219 " --> pdb=" O   GLU A 282 " (cutoff:3.500A)
      removed outlier: 6.587A  pdb=" N   GLU A 282 " --> pdb=" O   VAL A 219 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 313 through 315
    Processing sheet with id=AA5, first strand: chain 'A' and resid 319 through 322
    Processing sheet with id=AA6, first strand: chain 'B' and resid 181 through 183
    Processing sheet with id=AA7, first strand: chain 'B' and resid 181 through 183
      removed outlier: 6.773A  pdb=" N   ALA B 187 " --> pdb=" O   LEU B 310 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'B' and resid 230 through 238
      removed outlier: 5.064A  pdb=" N   THR B 223 " --> pdb=" O   PRO B 232 " (cutoff:3.500A)
      removed outlier: 4.304A  pdb=" N   MET B 217 " --> pdb=" O   ILE B 238 " (cutoff:3.500A)
      removed outlier: 4.324A  pdb=" N   ALA B 213 " --> pdb=" O   GLU B 288 " (cutoff:3.500A)
      removed outlier: 6.433A  pdb=" N   GLU B 288 " --> pdb=" O   ALA B 213 " (cutoff:3.500A)
      removed outlier: 4.324A  pdb=" N   ILE B 215 " --> pdb=" O   ILE B 286 " (cutoff:3.500A)
      removed outlier: 6.576A  pdb=" N   ILE B 286 " --> pdb=" O   ILE B 215 " (cutoff:3.500A)
      removed outlier: 4.477A  pdb=" N   MET B 217 " --> pdb=" O   ILE B 284 " (cutoff:3.500A)
      removed outlier: 6.659A  pdb=" N   ILE B 284 " --> pdb=" O   MET B 217 " (cutoff:3.500A)
      removed outlier: 4.711A  pdb=" N   VAL B 219 " --> pdb=" O   GLU B 282 " (cutoff:3.500A)
      removed outlier: 6.587A  pdb=" N   GLU B 282 " --> pdb=" O   VAL B 219 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'B' and resid 313 through 315
    Processing sheet with id=AB1, first strand: chain 'B' and resid 319 through 322
    Processing sheet with id=AB2, first strand: chain 'C' and resid 181 through 183
    Processing sheet with id=AB3, first strand: chain 'C' and resid 181 through 183
      removed outlier: 6.774A  pdb=" N   ALA C 187 " --> pdb=" O   LEU C 310 " (cutoff:3.500A)
    Processing sheet with id=AB4, first strand: chain 'C' and resid 230 through 238
      removed outlier: 5.064A  pdb=" N   THR C 223 " --> pdb=" O   PRO C 232 " (cutoff:3.500A)
      removed outlier: 4.305A  pdb=" N   MET C 217 " --> pdb=" O   ILE C 238 " (cutoff:3.500A)
      removed outlier: 4.324A  pdb=" N   ALA C 213 " --> pdb=" O   GLU C 288 " (cutoff:3.500A)
      removed outlier: 6.433A  pdb=" N   GLU C 288 " --> pdb=" O   ALA C 213 " (cutoff:3.500A)
      removed outlier: 4.325A  pdb=" N   ILE C 215 " --> pdb=" O   ILE C 286 " (cutoff:3.500A)
      removed outlier: 6.576A  pdb=" N   ILE C 286 " --> pdb=" O   ILE C 215 " (cutoff:3.500A)
      removed outlier: 4.478A  pdb=" N   MET C 217 " --> pdb=" O   ILE C 284 " (cutoff:3.500A)
      removed outlier: 6.659A  pdb=" N   ILE C 284 " --> pdb=" O   MET C 217 " (cutoff:3.500A)
      removed outlier: 4.711A  pdb=" N   VAL C 219 " --> pdb=" O   GLU C 282 " (cutoff:3.500A)
      removed outlier: 6.588A  pdb=" N   GLU C 282 " --> pdb=" O   VAL C 219 " (cutoff:3.500A)
    Processing sheet with id=AB5, first strand: chain 'C' and resid 313 through 315
    Processing sheet with id=AB6, first strand: chain 'C' and resid 319 through 322
    Processing sheet with id=AB7, first strand: chain 'D' and resid 181 through 183
    Processing sheet with id=AB8, first strand: chain 'D' and resid 181 through 183
      removed outlier: 6.773A  pdb=" N   ALA D 187 " --> pdb=" O   LEU D 310 " (cutoff:3.500A)
    Processing sheet with id=AB9, first strand: chain 'D' and resid 230 through 238
      removed outlier: 5.064A  pdb=" N   THR D 223 " --> pdb=" O   PRO D 232 " (cutoff:3.500A)
      removed outlier: 4.304A  pdb=" N   MET D 217 " --> pdb=" O   ILE D 238 " (cutoff:3.500A)
      removed outlier: 4.324A  pdb=" N   ALA D 213 " --> pdb=" O   GLU D 288 " (cutoff:3.500A)
      removed outlier: 6.432A  pdb=" N   GLU D 288 " --> pdb=" O   ALA D 213 " (cutoff:3.500A)
      removed outlier: 4.324A  pdb=" N   ILE D 215 " --> pdb=" O   ILE D 286 " (cutoff:3.500A)
      removed outlier: 6.576A  pdb=" N   ILE D 286 " --> pdb=" O   ILE D 215 " (cutoff:3.500A)
      removed outlier: 4.477A  pdb=" N   MET D 217 " --> pdb=" O   ILE D 284 " (cutoff:3.500A)
      removed outlier: 6.660A  pdb=" N   ILE D 284 " --> pdb=" O   MET D 217 " (cutoff:3.500A)
      removed outlier: 4.711A  pdb=" N   VAL D 219 " --> pdb=" O   GLU D 282 " (cutoff:3.500A)
      removed outlier: 6.588A  pdb=" N   GLU D 282 " --> pdb=" O   VAL D 219 " (cutoff:3.500A)
    Processing sheet with id=AC1, first strand: chain 'D' and resid 313 through 315
    Processing sheet with id=AC2, first strand: chain 'D' and resid 319 through 322

    447 hydrogen bonds defined for protein.
    1224 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: 1.61

  Time building geometry restraints manager: 1.21 seconds

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

  Histogram of bond lengths:
        1.23 -     1.34: 3272
        1.34 -     1.46: 2071
        1.46 -     1.57: 4857
        1.57 -     1.69: 0
        1.69 -     1.81: 104
  Bond restraints: 10304
  Sorted by residual:
  bond pdb=" CB  GLU D 104 "
       pdb=" CG  GLU D 104 "
    ideal  model  delta    sigma   weight residual
    1.520  1.563 -0.043 3.00e-02 1.11e+03 2.05e+00
  bond pdb=" CB  GLU C 104 "
       pdb=" CG  GLU C 104 "
    ideal  model  delta    sigma   weight residual
    1.520  1.563 -0.043 3.00e-02 1.11e+03 2.04e+00
  bond pdb=" CB  GLU B 104 "
       pdb=" CG  GLU B 104 "
    ideal  model  delta    sigma   weight residual
    1.520  1.563 -0.043 3.00e-02 1.11e+03 2.03e+00
  bond pdb=" CB  GLU A 104 "
       pdb=" CG  GLU A 104 "
    ideal  model  delta    sigma   weight residual
    1.520  1.562 -0.042 3.00e-02 1.11e+03 1.98e+00
  bond pdb=" CG  GLU A 104 "
       pdb=" CD  GLU A 104 "
    ideal  model  delta    sigma   weight residual
    1.516  1.543 -0.027 2.50e-02 1.60e+03 1.16e+00
  ... (remaining 10299 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.29: 13302
        1.29 -     2.58: 580
        2.58 -     3.88: 62
        3.88 -     5.17: 41
        5.17 -     6.46: 23
  Bond angle restraints: 14008
  Sorted by residual:
  angle pdb=" CB  GLU B 104 "
        pdb=" CG  GLU B 104 "
        pdb=" CD  GLU B 104 "
      ideal   model   delta    sigma   weight residual
     112.60  118.72   -6.12 1.70e+00 3.46e-01 1.29e+01
  angle pdb=" CB  GLU C 104 "
        pdb=" CG  GLU C 104 "
        pdb=" CD  GLU C 104 "
      ideal   model   delta    sigma   weight residual
     112.60  118.71   -6.11 1.70e+00 3.46e-01 1.29e+01
  angle pdb=" CB  GLU A 104 "
        pdb=" CG  GLU A 104 "
        pdb=" CD  GLU A 104 "
      ideal   model   delta    sigma   weight residual
     112.60  118.71   -6.11 1.70e+00 3.46e-01 1.29e+01
  angle pdb=" CB  GLU D 104 "
        pdb=" CG  GLU D 104 "
        pdb=" CD  GLU D 104 "
      ideal   model   delta    sigma   weight residual
     112.60  118.71   -6.11 1.70e+00 3.46e-01 1.29e+01
  angle pdb=" CA  GLU C 104 "
        pdb=" CB  GLU C 104 "
        pdb=" CG  GLU C 104 "
      ideal   model   delta    sigma   weight residual
     114.10  120.56   -6.46 2.00e+00 2.50e-01 1.04e+01
  ... (remaining 14003 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    16.98: 5494
       16.98 -    33.95: 446
       33.95 -    50.93: 120
       50.93 -    67.91: 52
       67.91 -    84.88: 16
  Dihedral angle restraints: 6128
    sinusoidal: 2412
      harmonic: 3716
  Sorted by residual:
  dihedral pdb=" CB  CYS A 110 "
           pdb=" SG  CYS A 110 "
           pdb=" SG  CYS A 142 "
           pdb=" CB  CYS A 142 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -86.00  -12.06  -73.94     1      1.00e+01 1.00e-02 6.94e+01
  dihedral pdb=" CB  CYS D 110 "
           pdb=" SG  CYS D 110 "
           pdb=" SG  CYS D 142 "
           pdb=" CB  CYS D 142 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -86.00  -12.07  -73.93     1      1.00e+01 1.00e-02 6.94e+01
  dihedral pdb=" CB  CYS C 110 "
           pdb=" SG  CYS C 110 "
           pdb=" SG  CYS C 142 "
           pdb=" CB  CYS C 142 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -86.00  -12.08  -73.92     1      1.00e+01 1.00e-02 6.94e+01
  ... (remaining 6125 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.029: 834
       0.029 -    0.058: 487
       0.058 -    0.086: 148
       0.086 -    0.115: 145
       0.115 -    0.144: 38
  Chirality restraints: 1652
  Sorted by residual:
  chirality pdb=" CB  ILE B 210 "
            pdb=" CA  ILE B 210 "
            pdb=" CG1 ILE B 210 "
            pdb=" CG2 ILE B 210 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.50    0.14 2.00e-01 2.50e+01 5.17e-01
  chirality pdb=" CB  ILE A 210 "
            pdb=" CA  ILE A 210 "
            pdb=" CG1 ILE A 210 "
            pdb=" CG2 ILE A 210 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.50    0.14 2.00e-01 2.50e+01 5.16e-01
  chirality pdb=" CB  ILE D 210 "
            pdb=" CA  ILE D 210 "
            pdb=" CG1 ILE D 210 "
            pdb=" CG2 ILE D 210 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.50    0.14 2.00e-01 2.50e+01 4.98e-01
  ... (remaining 1649 not shown)

  Planarity restraints: 1764
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   TRP D  68 "    0.026 5.00e-02 4.00e+02   3.88e-02 2.41e+00
        pdb=" N   PRO D  69 "   -0.067 5.00e-02 4.00e+02
        pdb=" CA  PRO D  69 "    0.019 5.00e-02 4.00e+02
        pdb=" CD  PRO D  69 "    0.022 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   TRP B  68 "   -0.026 5.00e-02 4.00e+02   3.85e-02 2.37e+00
        pdb=" N   PRO B  69 "    0.066 5.00e-02 4.00e+02
        pdb=" CA  PRO B  69 "   -0.019 5.00e-02 4.00e+02
        pdb=" CD  PRO B  69 "   -0.022 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   TRP C  68 "   -0.026 5.00e-02 4.00e+02   3.84e-02 2.36e+00
        pdb=" N   PRO C  69 "    0.066 5.00e-02 4.00e+02
        pdb=" CA  PRO C  69 "   -0.019 5.00e-02 4.00e+02
        pdb=" CD  PRO C  69 "   -0.022 5.00e-02 4.00e+02
  ... (remaining 1761 not shown)

  Histogram of nonbonded interaction distances:
        2.25 -     2.83: 3141
        2.83 -     3.41: 10274
        3.41 -     3.98: 19076
        3.98 -     4.56: 26741
        4.56 -     5.14: 40974
  Nonbonded interactions: 100206
  Sorted by model distance:
  nonbonded pdb=" O   PRO C 109 "
            pdb=" OG1 THR C 139 "
     model   vdw
     2.252 3.040
  nonbonded pdb=" O   PRO B 109 "
            pdb=" OG1 THR B 139 "
     model   vdw
     2.252 3.040
  nonbonded pdb=" O   PRO D 109 "
            pdb=" OG1 THR D 139 "
     model   vdw
     2.252 3.040
  nonbonded pdb=" O   PRO A 109 "
            pdb=" OG1 THR A 139 "
     model   vdw
     2.253 3.040
  nonbonded pdb=" OE2 GLU C 140 "
            pdb=" OG  SER D 119 "
     model   vdw
     2.263 3.040
  ... (remaining 100201 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' and resid 32 through 352)
  selection = chain 'B'
  selection = chain 'C'
  selection = chain 'D'
}

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:             3.180
  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:          0.150
  Check model and map are aligned:         0.030
  Set scattering table:                    0.020
  Process input model:                     10.050
  Find NCS groups from input model:        0.190
  Set up NCS constraints:                  0.010
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.330
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   14.970
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8357
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      :  0.005   0.043  10308  Z= 0.235
  Angle     :  0.679   6.459  14016  Z= 0.398
  Chirality :  0.048   0.144   1652
  Planarity :  0.005   0.039   1764
  Dihedral  : 15.459  84.882   3700
  Min Nonbonded Distance : 2.252

Molprobity Statistics.
  All-atom Clashscore : 5.67
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.51 %
    Favored  : 97.49 %
  Rotamer:
    Outliers :  4.68 %
    Allowed  : 16.19 %
    Favored  : 79.14 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.41 (0.19), residues: 1276
  helix: -1.26 (0.21), residues: 396
  sheet: -1.35 (0.31), residues: 256
  loop : -1.87 (0.20), residues: 624

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG D 177 
 TYR   0.007   0.001   TYR A 258 
 PHE   0.015   0.002   PHE B  75 
 TRP   0.006   0.001   TRP B 311 
 HIS   0.003   0.001   HIS D 175 

Details of bonding type rmsd
  covalent geometry    : bond        0.00514 (10304)
  covalent geometry    : angle       0.67748 (14008)
  SS BOND              : bond        0.00228 (    4)
  SS BOND              : angle       1.78093 (    8)
  hydrogen bonds       : bond        0.15100 (  439)
  hydrogen bonds       : angle       5.16719 ( 1224)

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

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

  2552 Ramachandran restraints generated.
    1276 Oldfield, 0 Emsley, 1276 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2552 Ramachandran restraints generated.
    1276 Oldfield, 0 Emsley, 1276 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  224 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 52
    poor density    : 172
  time to evaluate  : 0.439 
Fit side-chains
   revert: symmetry clash
REVERT: A   39 LYS cc_start: 0.8968 (mmtm) cc_final: 0.8742 (mtmm)
REVERT: A   47 LYS cc_start: 0.8461 (mtpp) cc_final: 0.8228 (mtpp)
REVERT: A  332 LYS cc_start: 0.9210 (mttt) cc_final: 0.8944 (mtpp)
REVERT: B  110 CYS cc_start: 0.6924 (OUTLIER) cc_final: 0.6448 (m)
REVERT: B  137 MET cc_start: 0.9032 (ptt) cc_final: 0.8364 (ptm)
REVERT: B  169 MET cc_start: 0.8866 (ttm) cc_final: 0.8451 (ttm)
REVERT: B  185 LYS cc_start: 0.8927 (ttpp) cc_final: 0.8659 (ttpt)
REVERT: B  222 LYS cc_start: 0.9133 (ttmt) cc_final: 0.8628 (ttpp)
REVERT: B  225 SER cc_start: 0.8256 (OUTLIER) cc_final: 0.7555 (p)
REVERT: C   67 LYS cc_start: 0.7945 (mttp) cc_final: 0.7209 (mmmt)
REVERT: C   88 MET cc_start: 0.7668 (mtt) cc_final: 0.7462 (mtt)
REVERT: C  102 PRO cc_start: 0.7896 (Cg_endo) cc_final: 0.7666 (Cg_exo)
REVERT: C  185 LYS cc_start: 0.8762 (ttpp) cc_final: 0.8477 (tptt)
REVERT: C  240 MET cc_start: 0.9007 (ttp) cc_final: 0.8788 (ttp)
REVERT: C  304 TYR cc_start: 0.9174 (m-80) cc_final: 0.8871 (m-80)
REVERT: D   47 LYS cc_start: 0.8207 (mtpp) cc_final: 0.7880 (mmtt)
REVERT: D   67 LYS cc_start: 0.7763 (mttp) cc_final: 0.7460 (mtmt)
REVERT: D  102 PRO cc_start: 0.7467 (Cg_endo) cc_final: 0.7149 (Cg_exo)
REVERT: D  199 MET cc_start: 0.9054 (mtm) cc_final: 0.8827 (mtp)
REVERT: D  217 MET cc_start: 0.8874 (mtm) cc_final: 0.8635 (mtm)
  outliers start: 52
  outliers final: 27
  residues processed: 215
  average time/residue: 0.1128
  time to fit residues: 33.5263
Evaluate side-chains
  161 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 132
  time to evaluate  : 0.400 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  104 GLU
Chi-restraints excluded: chain A residue  115 HIS
Chi-restraints excluded: chain A residue  118 SER
Chi-restraints excluded: chain A residue  202 VAL
Chi-restraints excluded: chain A residue  236 VAL
Chi-restraints excluded: chain A residue  334 ASP
Chi-restraints excluded: chain A residue  350 ASP
Chi-restraints excluded: chain B residue  110 CYS
Chi-restraints excluded: chain B residue  115 HIS
Chi-restraints excluded: chain B residue  118 SER
Chi-restraints excluded: chain B residue  225 SER
Chi-restraints excluded: chain B residue  236 VAL
Chi-restraints excluded: chain B residue  331 SER
Chi-restraints excluded: chain B residue  334 ASP
Chi-restraints excluded: chain C residue  110 CYS
Chi-restraints excluded: chain C residue  115 HIS
Chi-restraints excluded: chain C residue  118 SER
Chi-restraints excluded: chain C residue  202 VAL
Chi-restraints excluded: chain C residue  236 VAL
Chi-restraints excluded: chain C residue  331 SER
Chi-restraints excluded: chain C residue  334 ASP
Chi-restraints excluded: chain C residue  337 VAL
Chi-restraints excluded: chain D residue  110 CYS
Chi-restraints excluded: chain D residue  118 SER
Chi-restraints excluded: chain D residue  202 VAL
Chi-restraints excluded: chain D residue  236 VAL
Chi-restraints excluded: chain D residue  331 SER
Chi-restraints excluded: chain D residue  334 ASP
Chi-restraints excluded: chain D residue  337 VAL
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 128
   random chunks:
   chunk 98 optimal weight:    1.9990
   chunk 107 optimal weight:    2.9990
   chunk 10 optimal weight:    2.9990
   chunk 66 optimal weight:    2.9990
   chunk 124 optimal weight:    1.9990
   chunk 103 optimal weight:    5.9990
   chunk 77 optimal weight:    1.9990
   chunk 122 optimal weight:    0.7980
   chunk 91 optimal weight:    1.9990
   chunk 55 optimal weight:    0.0040
   chunk 35 optimal weight:    2.9990
   overall best weight:    1.3598

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

Flipped N/Q/H residues before XYZ refinement:
A  48 ASN
A 160 ASN
A 218 GLN
A 234 HIS
A 276 HIS
A 277 HIS
B  48 ASN
B 218 GLN
B 276 HIS
** B 348 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C  41 ASN
C 218 GLN
C 234 HIS
** C 348 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
D  48 ASN
D 218 GLN
D 264 ASN
D 276 HIS
** D 348 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 16

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3076 r_free = 0.3076 target = 0.088263 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.2902 r_free = 0.2902 target = 0.077785 restraints weight = 16373.462|
|-----------------------------------------------------------------------------|
r_work (start): 0.2900 rms_B_bonded: 2.02
r_work: 0.2808 rms_B_bonded: 2.14 restraints_weight: 0.5000
r_work: 0.2688 rms_B_bonded: 3.69 restraints_weight: 0.2500
r_work (final): 0.2688
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8663
moved from start:          0.1566

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.066  10308  Z= 0.248
  Angle     :  0.563   7.200  14016  Z= 0.303
  Chirality :  0.046   0.129   1652
  Planarity :  0.004   0.033   1764
  Dihedral  :  6.899  75.624   1403
  Min Nonbonded Distance : 2.519

Molprobity Statistics.
  All-atom Clashscore : 5.53
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.12 %
    Favored  : 97.88 %
  Rotamer:
    Outliers :  3.51 %
    Allowed  : 15.92 %
    Favored  : 80.58 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.88 (0.22), residues: 1276
  helix:  0.66 (0.25), residues: 400
  sheet: -1.14 (0.30), residues: 252
  loop : -1.12 (0.23), residues: 624

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B 136 
 TYR   0.008   0.001   TYR A 268 
 PHE   0.017   0.002   PHE A 117 
 TRP   0.009   0.001   TRP C 311 
 HIS   0.003   0.001   HIS C 193 

Details of bonding type rmsd
  covalent geometry    : bond        0.00574 (10304)
  covalent geometry    : angle       0.56165 (14008)
  SS BOND              : bond        0.00544 (    4)
  SS BOND              : angle       1.75119 (    8)
  hydrogen bonds       : bond        0.04611 (  439)
  hydrogen bonds       : angle       4.34459 ( 1224)

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

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

  2552 Ramachandran restraints generated.
    1276 Oldfield, 0 Emsley, 1276 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2552 Ramachandran restraints generated.
    1276 Oldfield, 0 Emsley, 1276 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  184 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 39
    poor density    : 145
  time to evaluate  : 0.401 
Fit side-chains
REVERT: A   67 LYS cc_start: 0.8575 (mttp) cc_final: 0.7899 (mmmt)
REVERT: A   77 MET cc_start: 0.8895 (OUTLIER) cc_final: 0.8538 (mpp)
REVERT: A  160 ASN cc_start: 0.8942 (m-40) cc_final: 0.8639 (m110)
REVERT: A  247 ASN cc_start: 0.9018 (p0) cc_final: 0.8709 (p0)
REVERT: A  332 LYS cc_start: 0.9291 (mttt) cc_final: 0.9065 (mtpp)
REVERT: B   47 LYS cc_start: 0.8611 (mtpp) cc_final: 0.8205 (mmmt)
REVERT: B   67 LYS cc_start: 0.8420 (mttp) cc_final: 0.8040 (mtpt)
REVERT: B  137 MET cc_start: 0.9435 (ptt) cc_final: 0.8933 (ptm)
REVERT: B  160 ASN cc_start: 0.8930 (m-40) cc_final: 0.8700 (m-40)
REVERT: B  169 MET cc_start: 0.9112 (ttm) cc_final: 0.8719 (ttm)
REVERT: B  185 LYS cc_start: 0.9160 (ttpp) cc_final: 0.8833 (ttpt)
REVERT: B  222 LYS cc_start: 0.9355 (ttmt) cc_final: 0.9043 (ttpp)
REVERT: C   67 LYS cc_start: 0.8481 (mttp) cc_final: 0.7730 (mmmt)
REVERT: C  185 LYS cc_start: 0.9073 (ttpp) cc_final: 0.8631 (tptt)
REVERT: C  207 LYS cc_start: 0.8990 (tptm) cc_final: 0.8754 (tptt)
REVERT: C  251 LEU cc_start: 0.9093 (tp) cc_final: 0.8874 (tp)
REVERT: C  304 TYR cc_start: 0.9415 (m-80) cc_final: 0.9107 (m-80)
REVERT: C  334 ASP cc_start: 0.9108 (OUTLIER) cc_final: 0.8515 (m-30)
REVERT: D   32 ARG cc_start: 0.6636 (mmt90) cc_final: 0.6065 (mmt90)
REVERT: D   47 LYS cc_start: 0.8621 (mtpp) cc_final: 0.8247 (mmtm)
REVERT: D   57 GLN cc_start: 0.8537 (mt0) cc_final: 0.8109 (mm-40)
REVERT: D   67 LYS cc_start: 0.8391 (mttp) cc_final: 0.8031 (mtmt)
REVERT: D   93 ILE cc_start: 0.9429 (mm) cc_final: 0.9208 (mt)
REVERT: D  199 MET cc_start: 0.9375 (mtm) cc_final: 0.9110 (mtp)
REVERT: D  278 HIS cc_start: 0.7713 (OUTLIER) cc_final: 0.7180 (m-70)
REVERT: D  305 LEU cc_start: 0.9252 (OUTLIER) cc_final: 0.8911 (mm)
REVERT: D  338 LYS cc_start: 0.8596 (mtpp) cc_final: 0.7923 (tptt)
  outliers start: 39
  outliers final: 21
  residues processed: 179
  average time/residue: 0.1292
  time to fit residues: 30.9046
Evaluate side-chains
  159 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 134
  time to evaluate  : 0.396 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   77 MET
Chi-restraints excluded: chain A residue  115 HIS
Chi-restraints excluded: chain A residue  140 GLU
Chi-restraints excluded: chain A residue  236 VAL
Chi-restraints excluded: chain A residue  334 ASP
Chi-restraints excluded: chain A residue  349 LEU
Chi-restraints excluded: chain A residue  350 ASP
Chi-restraints excluded: chain B residue  115 HIS
Chi-restraints excluded: chain B residue  200 LEU
Chi-restraints excluded: chain B residue  236 VAL
Chi-restraints excluded: chain B residue  334 ASP
Chi-restraints excluded: chain C residue  115 HIS
Chi-restraints excluded: chain C residue  140 GLU
Chi-restraints excluded: chain C residue  236 VAL
Chi-restraints excluded: chain C residue  288 GLU
Chi-restraints excluded: chain C residue  305 LEU
Chi-restraints excluded: chain C residue  334 ASP
Chi-restraints excluded: chain C residue  337 VAL
Chi-restraints excluded: chain D residue  140 GLU
Chi-restraints excluded: chain D residue  200 LEU
Chi-restraints excluded: chain D residue  236 VAL
Chi-restraints excluded: chain D residue  238 ILE
Chi-restraints excluded: chain D residue  278 HIS
Chi-restraints excluded: chain D residue  305 LEU
Chi-restraints excluded: chain D residue  334 ASP
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 128
   random chunks:
   chunk 87 optimal weight:    6.9990
   chunk 109 optimal weight:    2.9990
   chunk 101 optimal weight:    0.7980
   chunk 98 optimal weight:    1.9990
   chunk 118 optimal weight:    0.8980
   chunk 29 optimal weight:    2.9990
   chunk 1 optimal weight:    1.9990
   chunk 113 optimal weight:    0.0670
   chunk 66 optimal weight:    1.9990
   chunk 91 optimal weight:    1.9990
   chunk 18 optimal weight:    0.7980
   overall best weight:    0.9120

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

Flipped N/Q/H residues before XYZ refinement:
A 235 GLN
** B 348 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C  41 ASN
C 276 HIS
** C 348 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
D 235 GLN
D 348 GLN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3077 r_free = 0.3077 target = 0.088355 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.2898 r_free = 0.2898 target = 0.077560 restraints weight = 16482.256|
|-----------------------------------------------------------------------------|
r_work (start): 0.2914 rms_B_bonded: 2.07
r_work: 0.2822 rms_B_bonded: 2.17 restraints_weight: 0.5000
r_work: 0.2702 rms_B_bonded: 3.72 restraints_weight: 0.2500
r_work (final): 0.2702
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8702
moved from start:          0.1842

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.048  10308  Z= 0.177
  Angle     :  0.494   5.851  14016  Z= 0.266
  Chirality :  0.045   0.136   1652
  Planarity :  0.003   0.034   1764
  Dihedral  :  6.045  56.952   1385
  Min Nonbonded Distance : 2.603

Molprobity Statistics.
  All-atom Clashscore : 5.58
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.88 %
    Favored  : 98.12 %
  Rotamer:
    Outliers :  3.69 %
    Allowed  : 16.46 %
    Favored  : 79.86 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.21 (0.23), residues: 1276
  helix:  1.41 (0.27), residues: 400
  sheet: -0.92 (0.31), residues: 252
  loop : -0.78 (0.24), residues: 624

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B 136 
 TYR   0.008   0.001   TYR A 330 
 PHE   0.016   0.001   PHE A  75 
 TRP   0.007   0.001   TRP C 311 
 HIS   0.002   0.001   HIS D 276 

Details of bonding type rmsd
  covalent geometry    : bond        0.00409 (10304)
  covalent geometry    : angle       0.49276 (14008)
  SS BOND              : bond        0.00291 (    4)
  SS BOND              : angle       1.53014 (    8)
  hydrogen bonds       : bond        0.04304 (  439)
  hydrogen bonds       : angle       4.11788 ( 1224)

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

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

  2552 Ramachandran restraints generated.
    1276 Oldfield, 0 Emsley, 1276 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2552 Ramachandran restraints generated.
    1276 Oldfield, 0 Emsley, 1276 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  183 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 41
    poor density    : 142
  time to evaluate  : 0.408 
Fit side-chains
REVERT: A   67 LYS cc_start: 0.8645 (mttp) cc_final: 0.8005 (mmmt)
REVERT: A   77 MET cc_start: 0.8947 (OUTLIER) cc_final: 0.8536 (mpp)
REVERT: B   47 LYS cc_start: 0.8634 (mtpp) cc_final: 0.8286 (mmmt)
REVERT: B   67 LYS cc_start: 0.8591 (mttp) cc_final: 0.8352 (mtpt)
REVERT: B  137 MET cc_start: 0.9435 (ptt) cc_final: 0.8948 (ptm)
REVERT: B  185 LYS cc_start: 0.9116 (ttpp) cc_final: 0.8615 (ttpt)
REVERT: B  258 TYR cc_start: 0.9055 (p90) cc_final: 0.8711 (p90)
REVERT: B  334 ASP cc_start: 0.9090 (OUTLIER) cc_final: 0.8759 (m-30)
REVERT: C   67 LYS cc_start: 0.8603 (mttp) cc_final: 0.7882 (mmmt)
REVERT: C  185 LYS cc_start: 0.9062 (ttpp) cc_final: 0.8673 (tptt)
REVERT: C  207 LYS cc_start: 0.8930 (tptm) cc_final: 0.8603 (tptt)
REVERT: C  304 TYR cc_start: 0.9378 (m-80) cc_final: 0.9178 (m-80)
REVERT: C  334 ASP cc_start: 0.9101 (OUTLIER) cc_final: 0.8587 (m-30)
REVERT: D   32 ARG cc_start: 0.6595 (mmt90) cc_final: 0.6101 (mmt90)
REVERT: D   47 LYS cc_start: 0.8633 (mtpp) cc_final: 0.8390 (mmtm)
REVERT: D   67 LYS cc_start: 0.8512 (mttp) cc_final: 0.8117 (mtmt)
REVERT: D  199 MET cc_start: 0.9378 (mtm) cc_final: 0.9129 (mtp)
REVERT: D  235 GLN cc_start: 0.9285 (OUTLIER) cc_final: 0.9003 (mt0)
REVERT: D  278 HIS cc_start: 0.7679 (OUTLIER) cc_final: 0.7181 (m-70)
REVERT: D  305 LEU cc_start: 0.9310 (OUTLIER) cc_final: 0.9033 (mm)
REVERT: D  338 LYS cc_start: 0.8592 (mtpp) cc_final: 0.7934 (tptt)
  outliers start: 41
  outliers final: 24
  residues processed: 172
  average time/residue: 0.1336
  time to fit residues: 30.5378
Evaluate side-chains
  167 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 137
  time to evaluate  : 0.405 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   44 VAL
Chi-restraints excluded: chain A residue   77 MET
Chi-restraints excluded: chain A residue  115 HIS
Chi-restraints excluded: chain A residue  235 GLN
Chi-restraints excluded: chain A residue  236 VAL
Chi-restraints excluded: chain A residue  334 ASP
Chi-restraints excluded: chain A residue  349 LEU
Chi-restraints excluded: chain A residue  350 ASP
Chi-restraints excluded: chain B residue   44 VAL
Chi-restraints excluded: chain B residue   74 ILE
Chi-restraints excluded: chain B residue  115 HIS
Chi-restraints excluded: chain B residue  200 LEU
Chi-restraints excluded: chain B residue  236 VAL
Chi-restraints excluded: chain B residue  240 MET
Chi-restraints excluded: chain B residue  334 ASP
Chi-restraints excluded: chain B residue  339 VAL
Chi-restraints excluded: chain C residue  115 HIS
Chi-restraints excluded: chain C residue  140 GLU
Chi-restraints excluded: chain C residue  236 VAL
Chi-restraints excluded: chain C residue  288 GLU
Chi-restraints excluded: chain C residue  334 ASP
Chi-restraints excluded: chain D residue  200 LEU
Chi-restraints excluded: chain D residue  235 GLN
Chi-restraints excluded: chain D residue  236 VAL
Chi-restraints excluded: chain D residue  238 ILE
Chi-restraints excluded: chain D residue  278 HIS
Chi-restraints excluded: chain D residue  305 LEU
Chi-restraints excluded: chain D residue  334 ASP
Chi-restraints excluded: chain D residue  337 VAL
Chi-restraints excluded: chain D residue  339 VAL
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 128
   random chunks:
   chunk 94 optimal weight:    0.4980
   chunk 26 optimal weight:    1.9990
   chunk 90 optimal weight:    0.9990
   chunk 122 optimal weight:    0.7980
   chunk 97 optimal weight:    0.0570
   chunk 121 optimal weight:    2.9990
   chunk 53 optimal weight:    1.9990
   chunk 9 optimal weight:    1.9990
   chunk 100 optimal weight:    1.9990
   chunk 115 optimal weight:    0.6980
   chunk 54 optimal weight:    0.9990
   overall best weight:    0.6100

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

Flipped N/Q/H residues before XYZ refinement:
A 160 ASN
** B 348 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C  41 ASN
C 348 GLN
D  43 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3116 r_free = 0.3116 target = 0.091167 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.2938 r_free = 0.2938 target = 0.080349 restraints weight = 16386.480|
|-----------------------------------------------------------------------------|
r_work (start): 0.2942 rms_B_bonded: 2.08
r_work: 0.2847 rms_B_bonded: 2.20 restraints_weight: 0.5000
r_work: 0.2729 rms_B_bonded: 3.76 restraints_weight: 0.2500
r_work (final): 0.2729
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8676
moved from start:          0.1977

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039  10308  Z= 0.134
  Angle     :  0.461   5.195  14016  Z= 0.250
  Chirality :  0.044   0.176   1652
  Planarity :  0.003   0.036   1764
  Dihedral  :  5.705  55.021   1384
  Min Nonbonded Distance : 2.497

Molprobity Statistics.
  All-atom Clashscore : 5.72
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.57 %
    Favored  : 98.43 %
  Rotamer:
    Outliers :  3.24 %
    Allowed  : 16.73 %
    Favored  : 80.04 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.32 (0.24), residues: 1276
  helix:  1.75 (0.27), residues: 400
  sheet: -0.40 (0.35), residues: 220
  loop : -0.50 (0.24), residues: 656

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG B 136 
 TYR   0.006   0.001   TYR A 330 
 PHE   0.014   0.001   PHE D  75 
 TRP   0.006   0.001   TRP B  68 
 HIS   0.002   0.000   HIS D 276 

Details of bonding type rmsd
  covalent geometry    : bond        0.00305 (10304)
  covalent geometry    : angle       0.46035 (14008)
  SS BOND              : bond        0.00246 (    4)
  SS BOND              : angle       1.16039 (    8)
  hydrogen bonds       : bond        0.04144 (  439)
  hydrogen bonds       : angle       4.00426 ( 1224)

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

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

  2552 Ramachandran restraints generated.
    1276 Oldfield, 0 Emsley, 1276 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2552 Ramachandran restraints generated.
    1276 Oldfield, 0 Emsley, 1276 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  182 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 146
  time to evaluate  : 0.400 
Fit side-chains
REVERT: A   67 LYS cc_start: 0.8601 (mttp) cc_final: 0.7940 (mmmt)
REVERT: A   77 MET cc_start: 0.8926 (OUTLIER) cc_final: 0.8490 (mpp)
REVERT: A  160 ASN cc_start: 0.8709 (m-40) cc_final: 0.8256 (m110)
REVERT: A  268 TYR cc_start: 0.9223 (t80) cc_final: 0.8994 (t80)
REVERT: B   47 LYS cc_start: 0.8583 (mtpp) cc_final: 0.8224 (mmmt)
REVERT: B   67 LYS cc_start: 0.8592 (mttp) cc_final: 0.7988 (mmmt)
REVERT: B  137 MET cc_start: 0.9379 (ptt) cc_final: 0.8882 (ptm)
REVERT: B  185 LYS cc_start: 0.9119 (ttpp) cc_final: 0.8611 (ttpt)
REVERT: B  334 ASP cc_start: 0.9130 (OUTLIER) cc_final: 0.8809 (m-30)
REVERT: C   67 LYS cc_start: 0.8596 (mttp) cc_final: 0.7866 (mmmt)
REVERT: C  108 GLU cc_start: 0.8337 (pt0) cc_final: 0.8054 (pt0)
REVERT: C  185 LYS cc_start: 0.9055 (ttpp) cc_final: 0.8689 (tptt)
REVERT: C  207 LYS cc_start: 0.8927 (tptm) cc_final: 0.8598 (tptt)
REVERT: C  334 ASP cc_start: 0.9076 (OUTLIER) cc_final: 0.8598 (m-30)
REVERT: D   47 LYS cc_start: 0.8600 (mtpp) cc_final: 0.8309 (mttm)
REVERT: D   67 LYS cc_start: 0.8475 (mttp) cc_final: 0.8077 (mtmt)
REVERT: D  199 MET cc_start: 0.9369 (mtm) cc_final: 0.9120 (mtp)
REVERT: D  278 HIS cc_start: 0.7632 (OUTLIER) cc_final: 0.7140 (m-70)
REVERT: D  305 LEU cc_start: 0.9332 (OUTLIER) cc_final: 0.9079 (mm)
REVERT: D  338 LYS cc_start: 0.8666 (mtpp) cc_final: 0.7921 (tptt)
  outliers start: 36
  outliers final: 20
  residues processed: 168
  average time/residue: 0.1267
  time to fit residues: 28.3984
Evaluate side-chains
  166 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 141
  time to evaluate  : 0.416 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   44 VAL
Chi-restraints excluded: chain A residue   77 MET
Chi-restraints excluded: chain A residue  115 HIS
Chi-restraints excluded: chain A residue  334 ASP
Chi-restraints excluded: chain A residue  350 ASP
Chi-restraints excluded: chain B residue   44 VAL
Chi-restraints excluded: chain B residue   74 ILE
Chi-restraints excluded: chain B residue  115 HIS
Chi-restraints excluded: chain B residue  200 LEU
Chi-restraints excluded: chain B residue  236 VAL
Chi-restraints excluded: chain B residue  240 MET
Chi-restraints excluded: chain B residue  334 ASP
Chi-restraints excluded: chain C residue  115 HIS
Chi-restraints excluded: chain C residue  140 GLU
Chi-restraints excluded: chain C residue  240 MET
Chi-restraints excluded: chain C residue  288 GLU
Chi-restraints excluded: chain C residue  334 ASP
Chi-restraints excluded: chain C residue  337 VAL
Chi-restraints excluded: chain D residue   59 VAL
Chi-restraints excluded: chain D residue  200 LEU
Chi-restraints excluded: chain D residue  236 VAL
Chi-restraints excluded: chain D residue  238 ILE
Chi-restraints excluded: chain D residue  278 HIS
Chi-restraints excluded: chain D residue  305 LEU
Chi-restraints excluded: chain D residue  334 ASP
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 128
   random chunks:
   chunk 99 optimal weight:    0.6980
   chunk 101 optimal weight:    1.9990
   chunk 25 optimal weight:    2.9990
   chunk 50 optimal weight:    0.5980
   chunk 71 optimal weight:    2.9990
   chunk 24 optimal weight:    4.9990
   chunk 64 optimal weight:    3.9990
   chunk 36 optimal weight:    0.5980
   chunk 61 optimal weight:    2.9990
   chunk 62 optimal weight:    0.5980
   chunk 77 optimal weight:    3.9990
   overall best weight:    0.8982

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

Flipped N/Q/H residues before XYZ refinement:
** B 348 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C  41 ASN
D  43 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3107 r_free = 0.3107 target = 0.090334 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.2933 r_free = 0.2933 target = 0.079720 restraints weight = 16263.851|
|-----------------------------------------------------------------------------|
r_work (start): 0.2908 rms_B_bonded: 2.05
r_work: 0.2813 rms_B_bonded: 2.17 restraints_weight: 0.5000
r_work: 0.2694 rms_B_bonded: 3.71 restraints_weight: 0.2500
r_work (final): 0.2694
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8609
moved from start:          0.2092

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.049  10308  Z= 0.174
  Angle     :  0.479   5.241  14016  Z= 0.258
  Chirality :  0.045   0.160   1652
  Planarity :  0.003   0.036   1764
  Dihedral  :  5.507  54.670   1382
  Min Nonbonded Distance : 2.511

Molprobity Statistics.
  All-atom Clashscore : 5.82
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.65 %
    Favored  : 98.35 %
  Rotamer:
    Outliers :  3.51 %
    Allowed  : 17.18 %
    Favored  : 79.32 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.39 (0.24), residues: 1276
  helix:  1.79 (0.27), residues: 400
  sheet: -0.34 (0.35), residues: 220
  loop : -0.44 (0.24), residues: 656

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B 136 
 TYR   0.014   0.001   TYR C 268 
 PHE   0.015   0.001   PHE A  75 
 TRP   0.006   0.001   TRP C 311 
 HIS   0.003   0.001   HIS D 276 

Details of bonding type rmsd
  covalent geometry    : bond        0.00404 (10304)
  covalent geometry    : angle       0.47880 (14008)
  SS BOND              : bond        0.00285 (    4)
  SS BOND              : angle       1.16584 (    8)
  hydrogen bonds       : bond        0.04220 (  439)
  hydrogen bonds       : angle       3.98623 ( 1224)

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

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

  2552 Ramachandran restraints generated.
    1276 Oldfield, 0 Emsley, 1276 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2552 Ramachandran restraints generated.
    1276 Oldfield, 0 Emsley, 1276 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  186 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 39
    poor density    : 147
  time to evaluate  : 0.408 
Fit side-chains
REVERT: A   67 LYS cc_start: 0.8440 (mttp) cc_final: 0.7777 (mmmt)
REVERT: A   77 MET cc_start: 0.8889 (OUTLIER) cc_final: 0.8460 (mpp)
REVERT: A  160 ASN cc_start: 0.8804 (m-40) cc_final: 0.8452 (m110)
REVERT: A  268 TYR cc_start: 0.9232 (t80) cc_final: 0.8857 (t80)
REVERT: B   47 LYS cc_start: 0.8488 (mtpp) cc_final: 0.8077 (mmmt)
REVERT: B   67 LYS cc_start: 0.8402 (mttp) cc_final: 0.8118 (mtpt)
REVERT: B  137 MET cc_start: 0.9377 (ptt) cc_final: 0.8843 (ptm)
REVERT: B  185 LYS cc_start: 0.9106 (ttpp) cc_final: 0.8639 (ttpt)
REVERT: B  222 LYS cc_start: 0.9299 (ttmm) cc_final: 0.8896 (ttpp)
REVERT: B  334 ASP cc_start: 0.9117 (OUTLIER) cc_final: 0.8816 (m-30)
REVERT: C   67 LYS cc_start: 0.8444 (mttp) cc_final: 0.7665 (mmmt)
REVERT: C  108 GLU cc_start: 0.8398 (pt0) cc_final: 0.8052 (pt0)
REVERT: C  185 LYS cc_start: 0.9010 (ttpp) cc_final: 0.8542 (tptt)
REVERT: C  207 LYS cc_start: 0.8964 (tptm) cc_final: 0.8584 (tptt)
REVERT: C  304 TYR cc_start: 0.9385 (m-80) cc_final: 0.9130 (m-80)
REVERT: C  334 ASP cc_start: 0.9023 (OUTLIER) cc_final: 0.8602 (m-30)
REVERT: D   47 LYS cc_start: 0.8550 (mtpp) cc_final: 0.8195 (mmtm)
REVERT: D   67 LYS cc_start: 0.8247 (mttp) cc_final: 0.7891 (mtmt)
REVERT: D   93 ILE cc_start: 0.9367 (mm) cc_final: 0.9158 (mt)
REVERT: D  199 MET cc_start: 0.9357 (mtm) cc_final: 0.9079 (mtp)
REVERT: D  278 HIS cc_start: 0.7689 (OUTLIER) cc_final: 0.7321 (m-70)
REVERT: D  305 LEU cc_start: 0.9246 (OUTLIER) cc_final: 0.8924 (mm)
REVERT: D  338 LYS cc_start: 0.8709 (mtpp) cc_final: 0.7912 (tptt)
  outliers start: 39
  outliers final: 26
  residues processed: 173
  average time/residue: 0.1221
  time to fit residues: 28.6578
Evaluate side-chains
  174 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 143
  time to evaluate  : 0.405 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   44 VAL
Chi-restraints excluded: chain A residue   77 MET
Chi-restraints excluded: chain A residue  115 HIS
Chi-restraints excluded: chain A residue  140 GLU
Chi-restraints excluded: chain A residue  199 MET
Chi-restraints excluded: chain A residue  235 GLN
Chi-restraints excluded: chain A residue  236 VAL
Chi-restraints excluded: chain A residue  334 ASP
Chi-restraints excluded: chain A residue  349 LEU
Chi-restraints excluded: chain B residue   44 VAL
Chi-restraints excluded: chain B residue   74 ILE
Chi-restraints excluded: chain B residue  115 HIS
Chi-restraints excluded: chain B residue  200 LEU
Chi-restraints excluded: chain B residue  240 MET
Chi-restraints excluded: chain B residue  334 ASP
Chi-restraints excluded: chain C residue  115 HIS
Chi-restraints excluded: chain C residue  140 GLU
Chi-restraints excluded: chain C residue  236 VAL
Chi-restraints excluded: chain C residue  240 MET
Chi-restraints excluded: chain C residue  288 GLU
Chi-restraints excluded: chain C residue  334 ASP
Chi-restraints excluded: chain C residue  337 VAL
Chi-restraints excluded: chain D residue   59 VAL
Chi-restraints excluded: chain D residue  118 SER
Chi-restraints excluded: chain D residue  200 LEU
Chi-restraints excluded: chain D residue  236 VAL
Chi-restraints excluded: chain D residue  238 ILE
Chi-restraints excluded: chain D residue  278 HIS
Chi-restraints excluded: chain D residue  305 LEU
Chi-restraints excluded: chain D residue  334 ASP
Chi-restraints excluded: chain D residue  337 VAL
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 128
   random chunks:
   chunk 75 optimal weight:    0.3980
   chunk 115 optimal weight:    1.9990
   chunk 32 optimal weight:    0.0670
   chunk 9 optimal weight:    0.9980
   chunk 100 optimal weight:    0.9990
   chunk 67 optimal weight:    3.9990
   chunk 72 optimal weight:    2.9990
   chunk 79 optimal weight:    0.8980
   chunk 99 optimal weight:    1.9990
   chunk 12 optimal weight:    0.5980
   chunk 116 optimal weight:    0.2980
   overall best weight:    0.4518

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

Flipped N/Q/H residues before XYZ refinement:
B 277 HIS
B 348 GLN
C  41 ASN
D 277 HIS

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3128 r_free = 0.3128 target = 0.091443 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.2947 r_free = 0.2947 target = 0.080278 restraints weight = 16271.957|
|-----------------------------------------------------------------------------|
r_work (start): 0.2948 rms_B_bonded: 2.20
r_work: 0.2849 rms_B_bonded: 2.33 restraints_weight: 0.5000
r_work: 0.2727 rms_B_bonded: 3.98 restraints_weight: 0.2500
r_work (final): 0.2727
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8615
moved from start:          0.2231

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.032  10308  Z= 0.112
  Angle     :  0.439   5.182  14016  Z= 0.237
  Chirality :  0.043   0.133   1652
  Planarity :  0.003   0.036   1764
  Dihedral  :  4.983  49.391   1379
  Min Nonbonded Distance : 2.604

Molprobity Statistics.
  All-atom Clashscore : 5.63
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.41 %
    Favored  : 98.59 %
  Rotamer:
    Outliers :  3.42 %
    Allowed  : 17.99 %
    Favored  : 78.60 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.58 (0.24), residues: 1276
  helix:  1.96 (0.27), residues: 400
  sheet: -0.13 (0.35), residues: 216
  loop : -0.38 (0.24), residues: 660

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG C 177 
 TYR   0.011   0.001   TYR D 330 
 PHE   0.014   0.001   PHE A  75 
 TRP   0.005   0.001   TRP B  68 
 HIS   0.003   0.000   HIS D 276 

Details of bonding type rmsd
  covalent geometry    : bond        0.00249 (10304)
  covalent geometry    : angle       0.43823 (14008)
  SS BOND              : bond        0.00210 (    4)
  SS BOND              : angle       0.98096 (    8)
  hydrogen bonds       : bond        0.03956 (  439)
  hydrogen bonds       : angle       3.84209 ( 1224)

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

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

  2552 Ramachandran restraints generated.
    1276 Oldfield, 0 Emsley, 1276 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2552 Ramachandran restraints generated.
    1276 Oldfield, 0 Emsley, 1276 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  189 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 38
    poor density    : 151
  time to evaluate  : 0.417 
Fit side-chains
REVERT: A   67 LYS cc_start: 0.8490 (mttp) cc_final: 0.7832 (mmmt)
REVERT: A   77 MET cc_start: 0.8896 (OUTLIER) cc_final: 0.8469 (mpp)
REVERT: A  140 GLU cc_start: 0.8819 (OUTLIER) cc_final: 0.8539 (mp0)
REVERT: A  160 ASN cc_start: 0.8784 (m-40) cc_final: 0.8399 (m110)
REVERT: A  258 TYR cc_start: 0.9167 (p90) cc_final: 0.8579 (p90)
REVERT: A  268 TYR cc_start: 0.9207 (t80) cc_final: 0.8787 (t80)
REVERT: B   47 LYS cc_start: 0.8499 (mtpp) cc_final: 0.8101 (mmmt)
REVERT: B   67 LYS cc_start: 0.8424 (mttp) cc_final: 0.8142 (mtpt)
REVERT: B  137 MET cc_start: 0.9330 (ptt) cc_final: 0.8797 (ptm)
REVERT: B  185 LYS cc_start: 0.9105 (ttpp) cc_final: 0.8724 (ttpt)
REVERT: B  247 ASN cc_start: 0.9231 (p0) cc_final: 0.8699 (p0)
REVERT: C   39 LYS cc_start: 0.9222 (mtmm) cc_final: 0.8955 (mtmm)
REVERT: C   67 LYS cc_start: 0.8496 (mttp) cc_final: 0.7729 (mmmt)
REVERT: C  108 GLU cc_start: 0.8337 (pt0) cc_final: 0.7979 (pt0)
REVERT: C  185 LYS cc_start: 0.9013 (ttpp) cc_final: 0.8599 (tptt)
REVERT: C  207 LYS cc_start: 0.8970 (tptm) cc_final: 0.8578 (tptt)
REVERT: C  209 MET cc_start: 0.8772 (tpp) cc_final: 0.8517 (tpp)
REVERT: C  304 TYR cc_start: 0.9372 (m-80) cc_final: 0.9049 (m-80)
REVERT: C  334 ASP cc_start: 0.8888 (OUTLIER) cc_final: 0.8453 (m-30)
REVERT: C  335 ASN cc_start: 0.9146 (m-40) cc_final: 0.8945 (m110)
REVERT: D   47 LYS cc_start: 0.8558 (mtpp) cc_final: 0.8205 (mmtm)
REVERT: D   67 LYS cc_start: 0.8293 (mttp) cc_final: 0.7554 (tptt)
REVERT: D  199 MET cc_start: 0.9344 (mtm) cc_final: 0.9097 (mtp)
REVERT: D  278 HIS cc_start: 0.7715 (OUTLIER) cc_final: 0.7358 (m-70)
REVERT: D  305 LEU cc_start: 0.9261 (OUTLIER) cc_final: 0.9017 (mm)
REVERT: D  338 LYS cc_start: 0.8670 (mtpp) cc_final: 0.7910 (tptt)
  outliers start: 38
  outliers final: 22
  residues processed: 178
  average time/residue: 0.1204
  time to fit residues: 29.1564
Evaluate side-chains
  171 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 144
  time to evaluate  : 0.417 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   44 VAL
Chi-restraints excluded: chain A residue   77 MET
Chi-restraints excluded: chain A residue  115 HIS
Chi-restraints excluded: chain A residue  140 GLU
Chi-restraints excluded: chain A residue  235 GLN
Chi-restraints excluded: chain A residue  236 VAL
Chi-restraints excluded: chain A residue  334 ASP
Chi-restraints excluded: chain B residue   44 VAL
Chi-restraints excluded: chain B residue   74 ILE
Chi-restraints excluded: chain B residue  115 HIS
Chi-restraints excluded: chain B residue  200 LEU
Chi-restraints excluded: chain B residue  240 MET
Chi-restraints excluded: chain C residue  115 HIS
Chi-restraints excluded: chain C residue  140 GLU
Chi-restraints excluded: chain C residue  235 GLN
Chi-restraints excluded: chain C residue  236 VAL
Chi-restraints excluded: chain C residue  240 MET
Chi-restraints excluded: chain C residue  288 GLU
Chi-restraints excluded: chain C residue  334 ASP
Chi-restraints excluded: chain C residue  337 VAL
Chi-restraints excluded: chain D residue   59 VAL
Chi-restraints excluded: chain D residue  166 SER
Chi-restraints excluded: chain D residue  200 LEU
Chi-restraints excluded: chain D residue  238 ILE
Chi-restraints excluded: chain D residue  278 HIS
Chi-restraints excluded: chain D residue  305 LEU
Chi-restraints excluded: chain D residue  337 VAL
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 128
   random chunks:
   chunk 94 optimal weight:    0.9980
   chunk 51 optimal weight:    0.9990
   chunk 76 optimal weight:    0.8980
   chunk 107 optimal weight:    0.6980
   chunk 93 optimal weight:    0.0980
   chunk 83 optimal weight:    0.1980
   chunk 24 optimal weight:    4.9990
   chunk 52 optimal weight:    0.5980
   chunk 56 optimal weight:    0.7980
   chunk 77 optimal weight:    0.6980
   chunk 42 optimal weight:    3.9990
   overall best weight:    0.4580

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

Flipped N/Q/H residues before XYZ refinement:
C  41 ASN
D 216 HIS
D 235 GLN
D 277 HIS

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3150 r_free = 0.3150 target = 0.092784 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.2979 r_free = 0.2979 target = 0.082149 restraints weight = 15912.523|
|-----------------------------------------------------------------------------|
r_work (start): 0.2960 rms_B_bonded: 2.04
r_work: 0.2867 rms_B_bonded: 2.16 restraints_weight: 0.5000
r_work: 0.2749 rms_B_bonded: 3.73 restraints_weight: 0.2500
r_work (final): 0.2749
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8578
moved from start:          0.2342

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035  10308  Z= 0.112
  Angle     :  0.441   5.181  14016  Z= 0.239
  Chirality :  0.043   0.131   1652
  Planarity :  0.003   0.039   1764
  Dihedral  :  4.652  44.784   1374
  Min Nonbonded Distance : 2.424

Molprobity Statistics.
  All-atom Clashscore : 5.58
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.57 %
    Favored  : 98.43 %
  Rotamer:
    Outliers :  2.88 %
    Allowed  : 18.44 %
    Favored  : 78.69 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.69 (0.24), residues: 1276
  helix:  2.03 (0.27), residues: 400
  sheet: -0.06 (0.35), residues: 216
  loop : -0.31 (0.24), residues: 660

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG D 206 
 TYR   0.008   0.001   TYR D 330 
 PHE   0.014   0.001   PHE D  75 
 TRP   0.004   0.001   TRP C  68 
 HIS   0.003   0.000   HIS D 216 

Details of bonding type rmsd
  covalent geometry    : bond        0.00250 (10304)
  covalent geometry    : angle       0.44101 (14008)
  SS BOND              : bond        0.00213 (    4)
  SS BOND              : angle       0.93977 (    8)
  hydrogen bonds       : bond        0.03919 (  439)
  hydrogen bonds       : angle       3.77777 ( 1224)

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

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

  2552 Ramachandran restraints generated.
    1276 Oldfield, 0 Emsley, 1276 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2552 Ramachandran restraints generated.
    1276 Oldfield, 0 Emsley, 1276 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  180 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 148
  time to evaluate  : 0.522 
Fit side-chains
REVERT: A   77 MET cc_start: 0.8853 (OUTLIER) cc_final: 0.8406 (mpp)
REVERT: A  140 GLU cc_start: 0.8797 (OUTLIER) cc_final: 0.8529 (mp0)
REVERT: A  160 ASN cc_start: 0.8736 (m-40) cc_final: 0.8339 (m110)
REVERT: A  258 TYR cc_start: 0.9146 (p90) cc_final: 0.8549 (p90)
REVERT: A  268 TYR cc_start: 0.9215 (t80) cc_final: 0.8794 (t80)
REVERT: B   47 LYS cc_start: 0.8416 (mtpp) cc_final: 0.8010 (mmmt)
REVERT: B   50 ARG cc_start: 0.6735 (mmt-90) cc_final: 0.6422 (mmp80)
REVERT: B   67 LYS cc_start: 0.8378 (mttp) cc_final: 0.8112 (mtpt)
REVERT: B  137 MET cc_start: 0.9255 (ptt) cc_final: 0.8697 (ptm)
REVERT: B  185 LYS cc_start: 0.9085 (ttpp) cc_final: 0.8692 (ttpt)
REVERT: C   39 LYS cc_start: 0.9226 (mtmm) cc_final: 0.8942 (mtmm)
REVERT: C   67 LYS cc_start: 0.8424 (mttp) cc_final: 0.7473 (tptp)
REVERT: C  108 GLU cc_start: 0.8301 (pt0) cc_final: 0.7925 (pt0)
REVERT: C  185 LYS cc_start: 0.8999 (ttpp) cc_final: 0.8635 (tptt)
REVERT: C  207 LYS cc_start: 0.8969 (tptm) cc_final: 0.8572 (tptt)
REVERT: C  304 TYR cc_start: 0.9348 (m-80) cc_final: 0.9089 (m-80)
REVERT: C  335 ASN cc_start: 0.9160 (m-40) cc_final: 0.8956 (m110)
REVERT: D   47 LYS cc_start: 0.8509 (mtpp) cc_final: 0.8084 (mtpp)
REVERT: D   57 GLN cc_start: 0.8394 (mt0) cc_final: 0.7972 (mm-40)
REVERT: D   67 LYS cc_start: 0.8214 (mttp) cc_final: 0.7472 (tptt)
REVERT: D  199 MET cc_start: 0.9323 (mtm) cc_final: 0.9073 (mtp)
REVERT: D  247 ASN cc_start: 0.9151 (p0) cc_final: 0.8826 (p0)
REVERT: D  278 HIS cc_start: 0.7797 (OUTLIER) cc_final: 0.7455 (m-70)
  outliers start: 32
  outliers final: 24
  residues processed: 170
  average time/residue: 0.1228
  time to fit residues: 28.2388
Evaluate side-chains
  172 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 145
  time to evaluate  : 0.445 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   44 VAL
Chi-restraints excluded: chain A residue   77 MET
Chi-restraints excluded: chain A residue  115 HIS
Chi-restraints excluded: chain A residue  129 VAL
Chi-restraints excluded: chain A residue  140 GLU
Chi-restraints excluded: chain A residue  235 GLN
Chi-restraints excluded: chain A residue  236 VAL
Chi-restraints excluded: chain A residue  334 ASP
Chi-restraints excluded: chain B residue   44 VAL
Chi-restraints excluded: chain B residue   74 ILE
Chi-restraints excluded: chain B residue  115 HIS
Chi-restraints excluded: chain B residue  200 LEU
Chi-restraints excluded: chain B residue  240 MET
Chi-restraints excluded: chain C residue  115 HIS
Chi-restraints excluded: chain C residue  140 GLU
Chi-restraints excluded: chain C residue  235 GLN
Chi-restraints excluded: chain C residue  236 VAL
Chi-restraints excluded: chain C residue  240 MET
Chi-restraints excluded: chain C residue  288 GLU
Chi-restraints excluded: chain C residue  337 VAL
Chi-restraints excluded: chain D residue   59 VAL
Chi-restraints excluded: chain D residue  166 SER
Chi-restraints excluded: chain D residue  200 LEU
Chi-restraints excluded: chain D residue  235 GLN
Chi-restraints excluded: chain D residue  238 ILE
Chi-restraints excluded: chain D residue  278 HIS
Chi-restraints excluded: chain D residue  337 VAL
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 128
   random chunks:
   chunk 106 optimal weight:    3.9990
   chunk 122 optimal weight:    4.9990
   chunk 91 optimal weight:    2.9990
   chunk 74 optimal weight:    1.9990
   chunk 56 optimal weight:    0.6980
   chunk 3 optimal weight:    2.9990
   chunk 12 optimal weight:    0.7980
   chunk 24 optimal weight:    2.9990
   chunk 2 optimal weight:    0.9990
   chunk 15 optimal weight:    0.8980
   chunk 60 optimal weight:    0.6980
   overall best weight:    0.8182

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

Flipped N/Q/H residues before XYZ refinement:
B 234 HIS
C  41 ASN
D 216 HIS
D 235 GLN
D 277 HIS

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3135 r_free = 0.3135 target = 0.091773 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.2975 r_free = 0.2975 target = 0.081700 restraints weight = 16105.185|
|-----------------------------------------------------------------------------|
r_work (start): 0.2942 rms_B_bonded: 1.87
r_work: 0.2854 rms_B_bonded: 2.01 restraints_weight: 0.5000
r_work: 0.2740 rms_B_bonded: 3.44 restraints_weight: 0.2500
r_work (final): 0.2740
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8628
moved from start:          0.2346

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.046  10308  Z= 0.159
  Angle     :  0.467   5.242  14016  Z= 0.252
  Chirality :  0.044   0.140   1652
  Planarity :  0.003   0.036   1764
  Dihedral  :  4.667  43.305   1372
  Min Nonbonded Distance : 2.524

Molprobity Statistics.
  All-atom Clashscore : 5.63
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.65 %
    Favored  : 98.35 %
  Rotamer:
    Outliers :  3.06 %
    Allowed  : 17.81 %
    Favored  : 79.14 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.70 (0.24), residues: 1276
  helix:  2.02 (0.27), residues: 400
  sheet: -0.05 (0.35), residues: 216
  loop : -0.29 (0.24), residues: 660

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A 206 
 TYR   0.011   0.001   TYR A 330 
 PHE   0.014   0.001   PHE D  75 
 TRP   0.006   0.001   TRP C 311 
 HIS   0.003   0.001   HIS D 276 

Details of bonding type rmsd
  covalent geometry    : bond        0.00367 (10304)
  covalent geometry    : angle       0.46648 (14008)
  SS BOND              : bond        0.00282 (    4)
  SS BOND              : angle       0.99116 (    8)
  hydrogen bonds       : bond        0.04076 (  439)
  hydrogen bonds       : angle       3.84014 ( 1224)

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

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

  2552 Ramachandran restraints generated.
    1276 Oldfield, 0 Emsley, 1276 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2552 Ramachandran restraints generated.
    1276 Oldfield, 0 Emsley, 1276 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  182 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 148
  time to evaluate  : 0.418 
Fit side-chains
REVERT: A   77 MET cc_start: 0.8868 (OUTLIER) cc_final: 0.8419 (mpp)
REVERT: A  140 GLU cc_start: 0.8762 (OUTLIER) cc_final: 0.8487 (mp0)
REVERT: A  268 TYR cc_start: 0.9212 (t80) cc_final: 0.8790 (t80)
REVERT: B   47 LYS cc_start: 0.8461 (mtpp) cc_final: 0.8067 (mmmt)
REVERT: B   50 ARG cc_start: 0.6789 (mmt-90) cc_final: 0.6483 (mmp80)
REVERT: B   67 LYS cc_start: 0.8432 (mttp) cc_final: 0.8185 (mtpt)
REVERT: B  137 MET cc_start: 0.9325 (ptt) cc_final: 0.8811 (ptm)
REVERT: B  185 LYS cc_start: 0.9080 (ttpp) cc_final: 0.8722 (ttpt)
REVERT: B  247 ASN cc_start: 0.9199 (p0) cc_final: 0.8733 (p0)
REVERT: C   39 LYS cc_start: 0.9188 (mtmm) cc_final: 0.8955 (mtmm)
REVERT: C   67 LYS cc_start: 0.8480 (mttp) cc_final: 0.7559 (tptp)
REVERT: C  108 GLU cc_start: 0.8301 (pt0) cc_final: 0.7963 (pt0)
REVERT: C  185 LYS cc_start: 0.8990 (ttpp) cc_final: 0.8677 (tptt)
REVERT: C  207 LYS cc_start: 0.9043 (tptm) cc_final: 0.8639 (tptt)
REVERT: C  304 TYR cc_start: 0.9340 (m-80) cc_final: 0.9091 (m-80)
REVERT: D   47 LYS cc_start: 0.8550 (mtpp) cc_final: 0.8155 (mtpp)
REVERT: D   67 LYS cc_start: 0.8286 (mttp) cc_final: 0.7574 (tptt)
REVERT: D  199 MET cc_start: 0.9351 (mtm) cc_final: 0.9077 (mtp)
REVERT: D  247 ASN cc_start: 0.9184 (p0) cc_final: 0.8859 (p0)
REVERT: D  278 HIS cc_start: 0.7730 (OUTLIER) cc_final: 0.7385 (m-70)
REVERT: D  305 LEU cc_start: 0.9275 (OUTLIER) cc_final: 0.9009 (mm)
REVERT: D  338 LYS cc_start: 0.8608 (mtpp) cc_final: 0.7903 (tptt)
  outliers start: 34
  outliers final: 25
  residues processed: 173
  average time/residue: 0.1215
  time to fit residues: 28.3549
Evaluate side-chains
  175 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 146
  time to evaluate  : 0.415 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   44 VAL
Chi-restraints excluded: chain A residue   77 MET
Chi-restraints excluded: chain A residue  115 HIS
Chi-restraints excluded: chain A residue  129 VAL
Chi-restraints excluded: chain A residue  140 GLU
Chi-restraints excluded: chain A residue  235 GLN
Chi-restraints excluded: chain A residue  236 VAL
Chi-restraints excluded: chain A residue  334 ASP
Chi-restraints excluded: chain B residue   44 VAL
Chi-restraints excluded: chain B residue   74 ILE
Chi-restraints excluded: chain B residue  115 HIS
Chi-restraints excluded: chain B residue  200 LEU
Chi-restraints excluded: chain B residue  240 MET
Chi-restraints excluded: chain C residue  115 HIS
Chi-restraints excluded: chain C residue  140 GLU
Chi-restraints excluded: chain C residue  235 GLN
Chi-restraints excluded: chain C residue  236 VAL
Chi-restraints excluded: chain C residue  240 MET
Chi-restraints excluded: chain C residue  288 GLU
Chi-restraints excluded: chain C residue  337 VAL
Chi-restraints excluded: chain D residue   59 VAL
Chi-restraints excluded: chain D residue  118 SER
Chi-restraints excluded: chain D residue  166 SER
Chi-restraints excluded: chain D residue  200 LEU
Chi-restraints excluded: chain D residue  235 GLN
Chi-restraints excluded: chain D residue  238 ILE
Chi-restraints excluded: chain D residue  278 HIS
Chi-restraints excluded: chain D residue  305 LEU
Chi-restraints excluded: chain D residue  337 VAL
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 128
   random chunks:
   chunk 11 optimal weight:    0.5980
   chunk 106 optimal weight:    3.9990
   chunk 48 optimal weight:    0.4980
   chunk 122 optimal weight:    1.9990
   chunk 84 optimal weight:    2.9990
   chunk 85 optimal weight:    2.9990
   chunk 30 optimal weight:    0.6980
   chunk 80 optimal weight:    2.9990
   chunk 55 optimal weight:    1.9990
   chunk 107 optimal weight:    0.8980
   chunk 51 optimal weight:    0.0000
   overall best weight:    0.5384

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

Flipped N/Q/H residues before XYZ refinement:
A 160 ASN
C  41 ASN
D 216 HIS
D 235 GLN
D 264 ASN
D 277 HIS

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3133 r_free = 0.3133 target = 0.091492 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 27)----------------|
| r_work = 0.2962 r_free = 0.2962 target = 0.080728 restraints weight = 16201.108|
|-----------------------------------------------------------------------------|
r_work (start): 0.2970 rms_B_bonded: 2.05
r_work: 0.2878 rms_B_bonded: 2.15 restraints_weight: 0.5000
r_work: 0.2760 rms_B_bonded: 3.70 restraints_weight: 0.2500
r_work (final): 0.2760
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8660
moved from start:          0.2421

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036  10308  Z= 0.122
  Angle     :  0.451   5.204  14016  Z= 0.244
  Chirality :  0.044   0.130   1652
  Planarity :  0.003   0.036   1764
  Dihedral  :  4.607  41.425   1372
  Min Nonbonded Distance : 2.508

Molprobity Statistics.
  All-atom Clashscore : 5.53
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.41 %
    Favored  : 98.59 %
  Rotamer:
    Outliers :  2.61 %
    Allowed  : 18.26 %
    Favored  : 79.14 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.72 (0.24), residues: 1276
  helix:  2.06 (0.27), residues: 400
  sheet: -0.07 (0.35), residues: 216
  loop : -0.27 (0.24), residues: 660

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG D 206 
 TYR   0.010   0.001   TYR A 330 
 PHE   0.014   0.001   PHE D  75 
 TRP   0.004   0.001   TRP C 311 
 HIS   0.003   0.001   HIS B 277 

Details of bonding type rmsd
  covalent geometry    : bond        0.00277 (10304)
  covalent geometry    : angle       0.45029 (14008)
  SS BOND              : bond        0.00240 (    4)
  SS BOND              : angle       0.94907 (    8)
  hydrogen bonds       : bond        0.03982 (  439)
  hydrogen bonds       : angle       3.80252 ( 1224)

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

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

  2552 Ramachandran restraints generated.
    1276 Oldfield, 0 Emsley, 1276 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2552 Ramachandran restraints generated.
    1276 Oldfield, 0 Emsley, 1276 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  174 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 145
  time to evaluate  : 0.353 
Fit side-chains
REVERT: A   77 MET cc_start: 0.8884 (OUTLIER) cc_final: 0.8444 (mpp)
REVERT: A  140 GLU cc_start: 0.8722 (OUTLIER) cc_final: 0.8480 (mp0)
REVERT: A  160 ASN cc_start: 0.8585 (m-40) cc_final: 0.8180 (m110)
REVERT: A  268 TYR cc_start: 0.9179 (t80) cc_final: 0.8829 (t80)
REVERT: B   47 LYS cc_start: 0.8515 (mtpp) cc_final: 0.8178 (mmmt)
REVERT: B   50 ARG cc_start: 0.6629 (mmt-90) cc_final: 0.6377 (mmp80)
REVERT: B   67 LYS cc_start: 0.8499 (mttp) cc_final: 0.8278 (mtpt)
REVERT: B  137 MET cc_start: 0.9307 (ptt) cc_final: 0.8827 (ptm)
REVERT: B  185 LYS cc_start: 0.9071 (ttpp) cc_final: 0.8753 (ttpt)
REVERT: B  247 ASN cc_start: 0.9259 (p0) cc_final: 0.8790 (p0)
REVERT: C   39 LYS cc_start: 0.9189 (mtmm) cc_final: 0.8962 (mtmm)
REVERT: C   67 LYS cc_start: 0.8557 (mttp) cc_final: 0.7659 (tptp)
REVERT: C  108 GLU cc_start: 0.8258 (pt0) cc_final: 0.7950 (pt0)
REVERT: C  185 LYS cc_start: 0.9001 (ttpp) cc_final: 0.8693 (tptt)
REVERT: C  207 LYS cc_start: 0.9020 (tptm) cc_final: 0.8625 (tptt)
REVERT: C  304 TYR cc_start: 0.9332 (m-80) cc_final: 0.9077 (m-80)
REVERT: D   32 ARG cc_start: 0.6517 (mmt90) cc_final: 0.6275 (mmt90)
REVERT: D   47 LYS cc_start: 0.8588 (mtpp) cc_final: 0.8207 (mtpp)
REVERT: D   67 LYS cc_start: 0.8432 (mttp) cc_final: 0.7700 (tptt)
REVERT: D  199 MET cc_start: 0.9347 (mtm) cc_final: 0.9090 (mtp)
REVERT: D  247 ASN cc_start: 0.9209 (p0) cc_final: 0.8938 (p0)
REVERT: D  278 HIS cc_start: 0.7773 (OUTLIER) cc_final: 0.7289 (m-70)
REVERT: D  305 LEU cc_start: 0.9311 (OUTLIER) cc_final: 0.9098 (mm)
  outliers start: 29
  outliers final: 23
  residues processed: 166
  average time/residue: 0.1298
  time to fit residues: 28.7007
Evaluate side-chains
  171 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 144
  time to evaluate  : 0.414 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   44 VAL
Chi-restraints excluded: chain A residue   77 MET
Chi-restraints excluded: chain A residue  115 HIS
Chi-restraints excluded: chain A residue  129 VAL
Chi-restraints excluded: chain A residue  140 GLU
Chi-restraints excluded: chain A residue  235 GLN
Chi-restraints excluded: chain A residue  236 VAL
Chi-restraints excluded: chain A residue  334 ASP
Chi-restraints excluded: chain B residue   44 VAL
Chi-restraints excluded: chain B residue   74 ILE
Chi-restraints excluded: chain B residue  115 HIS
Chi-restraints excluded: chain B residue  200 LEU
Chi-restraints excluded: chain B residue  240 MET
Chi-restraints excluded: chain C residue  115 HIS
Chi-restraints excluded: chain C residue  140 GLU
Chi-restraints excluded: chain C residue  235 GLN
Chi-restraints excluded: chain C residue  236 VAL
Chi-restraints excluded: chain C residue  240 MET
Chi-restraints excluded: chain C residue  288 GLU
Chi-restraints excluded: chain D residue   59 VAL
Chi-restraints excluded: chain D residue  166 SER
Chi-restraints excluded: chain D residue  200 LEU
Chi-restraints excluded: chain D residue  235 GLN
Chi-restraints excluded: chain D residue  238 ILE
Chi-restraints excluded: chain D residue  278 HIS
Chi-restraints excluded: chain D residue  305 LEU
Chi-restraints excluded: chain D residue  337 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 128
   random chunks:
   chunk 60 optimal weight:    0.9980
   chunk 23 optimal weight:    0.9990
   chunk 76 optimal weight:    0.9990
   chunk 127 optimal weight:    2.9990
   chunk 93 optimal weight:    3.9990
   chunk 13 optimal weight:    0.8980
   chunk 52 optimal weight:    2.9990
   chunk 68 optimal weight:    2.9990
   chunk 104 optimal weight:    2.9990
   chunk 79 optimal weight:    0.5980
   chunk 19 optimal weight:    1.9990
   overall best weight:    0.8984

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

Flipped N/Q/H residues before XYZ refinement:
C  41 ASN
D 216 HIS
D 235 GLN
D 264 ASN
D 277 HIS

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3112 r_free = 0.3112 target = 0.090166 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.2940 r_free = 0.2940 target = 0.079408 restraints weight = 16160.565|
|-----------------------------------------------------------------------------|
r_work (start): 0.2952 rms_B_bonded: 2.04
r_work: 0.2860 rms_B_bonded: 2.13 restraints_weight: 0.5000
r_work: 0.2742 rms_B_bonded: 3.67 restraints_weight: 0.2500
r_work (final): 0.2742
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8680
moved from start:          0.2402

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.048  10308  Z= 0.171
  Angle     :  0.479   6.130  14016  Z= 0.258
  Chirality :  0.044   0.130   1652
  Planarity :  0.003   0.036   1764
  Dihedral  :  4.682  41.410   1372
  Min Nonbonded Distance : 2.477

Molprobity Statistics.
  All-atom Clashscore : 5.77
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.80 %
    Favored  : 98.20 %
  Rotamer:
    Outliers :  2.97 %
    Allowed  : 18.35 %
    Favored  : 78.69 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.68 (0.24), residues: 1276
  helix:  1.98 (0.27), residues: 400
  sheet: -0.06 (0.35), residues: 216
  loop : -0.28 (0.24), residues: 660

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG D 206 
 TYR   0.010   0.001   TYR A 330 
 PHE   0.014   0.001   PHE A  75 
 TRP   0.006   0.001   TRP C 311 
 HIS   0.003   0.001   HIS D 276 

Details of bonding type rmsd
  covalent geometry    : bond        0.00397 (10304)
  covalent geometry    : angle       0.47889 (14008)
  SS BOND              : bond        0.00298 (    4)
  SS BOND              : angle       0.99644 (    8)
  hydrogen bonds       : bond        0.04116 (  439)
  hydrogen bonds       : angle       3.86381 ( 1224)

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

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

  2552 Ramachandran restraints generated.
    1276 Oldfield, 0 Emsley, 1276 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2552 Ramachandran restraints generated.
    1276 Oldfield, 0 Emsley, 1276 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  181 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 148
  time to evaluate  : 0.391 
Fit side-chains
REVERT: A   77 MET cc_start: 0.8897 (OUTLIER) cc_final: 0.8452 (mpp)
REVERT: A  160 ASN cc_start: 0.8609 (m-40) cc_final: 0.8220 (m110)
REVERT: B   47 LYS cc_start: 0.8530 (mtpp) cc_final: 0.8176 (mmmt)
REVERT: B   50 ARG cc_start: 0.6668 (mmt-90) cc_final: 0.6407 (mmp80)
REVERT: B   67 LYS cc_start: 0.8543 (mttp) cc_final: 0.8325 (mtpt)
REVERT: B  137 MET cc_start: 0.9362 (ptt) cc_final: 0.8867 (ptm)
REVERT: B  185 LYS cc_start: 0.9068 (ttpp) cc_final: 0.8764 (ttpt)
REVERT: B  222 LYS cc_start: 0.9295 (ttmm) cc_final: 0.8915 (ttpp)
REVERT: B  247 ASN cc_start: 0.9259 (p0) cc_final: 0.8776 (p0)
REVERT: C   67 LYS cc_start: 0.8558 (mttp) cc_final: 0.7645 (tptp)
REVERT: C  108 GLU cc_start: 0.8298 (pt0) cc_final: 0.8000 (pt0)
REVERT: C  185 LYS cc_start: 0.9018 (ttpp) cc_final: 0.8724 (tptt)
REVERT: C  207 LYS cc_start: 0.9012 (tptm) cc_final: 0.8608 (mptt)
REVERT: C  304 TYR cc_start: 0.9340 (m-80) cc_final: 0.9140 (m-80)
REVERT: D   47 LYS cc_start: 0.8591 (mtpp) cc_final: 0.8209 (mtpp)
REVERT: D   67 LYS cc_start: 0.8377 (mttp) cc_final: 0.7690 (tptt)
REVERT: D  199 MET cc_start: 0.9363 (mtm) cc_final: 0.9081 (mtp)
REVERT: D  247 ASN cc_start: 0.9243 (p0) cc_final: 0.8964 (p0)
REVERT: D  278 HIS cc_start: 0.7790 (OUTLIER) cc_final: 0.7328 (m-70)
REVERT: D  305 LEU cc_start: 0.9326 (OUTLIER) cc_final: 0.9089 (mm)
REVERT: D  338 LYS cc_start: 0.8561 (mtpp) cc_final: 0.8096 (tptt)
  outliers start: 33
  outliers final: 25
  residues processed: 172
  average time/residue: 0.1226
  time to fit residues: 28.2441
Evaluate side-chains
  171 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 143
  time to evaluate  : 0.364 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   44 VAL
Chi-restraints excluded: chain A residue   77 MET
Chi-restraints excluded: chain A residue  115 HIS
Chi-restraints excluded: chain A residue  129 VAL
Chi-restraints excluded: chain A residue  235 GLN
Chi-restraints excluded: chain A residue  236 VAL
Chi-restraints excluded: chain A residue  334 ASP
Chi-restraints excluded: chain B residue   44 VAL
Chi-restraints excluded: chain B residue   74 ILE
Chi-restraints excluded: chain B residue  115 HIS
Chi-restraints excluded: chain B residue  200 LEU
Chi-restraints excluded: chain B residue  240 MET
Chi-restraints excluded: chain C residue   74 ILE
Chi-restraints excluded: chain C residue  115 HIS
Chi-restraints excluded: chain C residue  140 GLU
Chi-restraints excluded: chain C residue  235 GLN
Chi-restraints excluded: chain C residue  236 VAL
Chi-restraints excluded: chain C residue  240 MET
Chi-restraints excluded: chain C residue  288 GLU
Chi-restraints excluded: chain C residue  337 VAL
Chi-restraints excluded: chain D residue   59 VAL
Chi-restraints excluded: chain D residue  166 SER
Chi-restraints excluded: chain D residue  200 LEU
Chi-restraints excluded: chain D residue  235 GLN
Chi-restraints excluded: chain D residue  238 ILE
Chi-restraints excluded: chain D residue  278 HIS
Chi-restraints excluded: chain D residue  305 LEU
Chi-restraints excluded: chain D residue  337 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 128
   random chunks:
   chunk 75 optimal weight:    0.0980
   chunk 49 optimal weight:    3.9990
   chunk 11 optimal weight:    0.5980
   chunk 38 optimal weight:    1.9990
   chunk 91 optimal weight:    1.9990
   chunk 70 optimal weight:    0.9990
   chunk 47 optimal weight:    3.9990
   chunk 98 optimal weight:    2.9990
   chunk 0 optimal weight:    3.9990
   chunk 64 optimal weight:    1.9990
   chunk 63 optimal weight:    0.8980
   overall best weight:    0.9184

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

Flipped N/Q/H residues before XYZ refinement:
C  41 ASN
** D 216 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
D 235 GLN
D 264 ASN
D 277 HIS

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3128 r_free = 0.3128 target = 0.091391 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.2964 r_free = 0.2964 target = 0.081176 restraints weight = 16214.628|
|-----------------------------------------------------------------------------|
r_work (start): 0.2954 rms_B_bonded: 1.91
r_work: 0.2867 rms_B_bonded: 2.02 restraints_weight: 0.5000
r_work: 0.2753 rms_B_bonded: 3.47 restraints_weight: 0.2500
r_work (final): 0.2753
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8647
moved from start:          0.2436

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.050  10308  Z= 0.174
  Angle     :  0.488   5.810  14016  Z= 0.263
  Chirality :  0.045   0.132   1652
  Planarity :  0.003   0.036   1764
  Dihedral  :  4.720  41.709   1372
  Min Nonbonded Distance : 2.448

Molprobity Statistics.
  All-atom Clashscore : 5.67
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.80 %
    Favored  : 98.20 %
  Rotamer:
    Outliers :  2.88 %
    Allowed  : 18.53 %
    Favored  : 78.60 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.66 (0.24), residues: 1276
  helix:  1.97 (0.27), residues: 400
  sheet: -0.10 (0.35), residues: 216
  loop : -0.29 (0.24), residues: 660

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG D 206 
 TYR   0.010   0.001   TYR A 330 
 PHE   0.014   0.001   PHE A  75 
 TRP   0.006   0.001   TRP C 311 
 HIS   0.003   0.001   HIS D 276 

Details of bonding type rmsd
  covalent geometry    : bond        0.00405 (10304)
  covalent geometry    : angle       0.48790 (14008)
  SS BOND              : bond        0.00306 (    4)
  SS BOND              : angle       1.00842 (    8)
  hydrogen bonds       : bond        0.04158 (  439)
  hydrogen bonds       : angle       3.91211 ( 1224)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2382.49 seconds
wall clock time: 41 minutes 41.88 seconds (2501.88 seconds total)