Starting phenix.real_space_refine
on Tue Feb 11 08:53:17 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/6lni_0931/02_2025/6lni_0931.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/6lni_0931/02_2025/6lni_0931.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.702
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/6lni_0931/02_2025/6lni_0931.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/6lni_0931/02_2025/6lni_0931.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/6lni_0931/02_2025/6lni_0931.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/6lni_0931/02_2025/6lni_0931.cif"
  }
  resolution = 2.702
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.003
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 4
    Type Number    sf(0)   Gaussians
     S      50      5.16       5
     C    2990      2.51       5
     N     870      2.21       5
     O    1010      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 10 residue(s): 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/chem_data/mon_lib"
  Total number of atoms: 4920
  Number of models: 1
  Model: ""
    Number of chains: 1
    Chain: "A"
      Number of atoms: 492
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 60, 492
          Classifications: {'peptide': 60}
          Link IDs: {'TRANS': 59}
  Restraints were copied for chains:
    C, B, E, D, G, F, I, H, J
  Time building chain proxies: 3.08, per 1000 atoms: 0.63
  Number of scatterers: 4920
  At special positions: 0
  Unit cell: (145.002, 122.694, 44.616, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     S      50     16.00
     O    1010      8.00
     N     870      7.00
     C    2990      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=1, symmetry=0
    Simple disulfide: pdb=" SG  CYS A 179 " - pdb=" SG  CYS A 214 " 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: 1.22
  Conformation dependent library (CDL) restraints added in 533.3 milliseconds
  

  1160 Ramachandran restraints generated.
    580 Oldfield, 0 Emsley, 580 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1160

  Finding SS restraints...
    Secondary structure from input PDB file:
      0 helices and 11 sheets defined
      0.0% alpha, 35.5% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.69
  Creating SS restraints...
    Processing sheet with id=AA1, first strand: chain 'A' and resid 172 through 178
    Processing sheet with id=AA2, first strand: chain 'A' and resid 182 through 185
      removed outlier: 6.240A  pdb=" N   THR A 183 " --> pdb=" O   ILE B 184 " (cutoff:3.500A)
      removed outlier: 6.276A  pdb=" N   THR B 183 " --> pdb=" O   ILE C 184 " (cutoff:3.500A)
      removed outlier: 6.242A  pdb=" N   THR C 183 " --> pdb=" O   ILE D 184 " (cutoff:3.500A)
      removed outlier: 6.262A  pdb=" N   THR D 183 " --> pdb=" O   ILE E 184 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA2
    Processing sheet with id=AA3, first strand: chain 'A' and resid 189 through 192
    Processing sheet with id=AA4, first strand: chain 'A' and resid 197 through 202
      removed outlier: 6.356A  pdb=" N   ASN A 197 " --> pdb=" O   PHE B 198 " (cutoff:3.500A)
      removed outlier: 7.881A  pdb=" N   GLU B 200 " --> pdb=" O   ASN A 197 " (cutoff:3.500A)
      removed outlier: 8.248A  pdb=" N   THR A 199 " --> pdb=" O   GLU B 200 " (cutoff:3.500A)
      removed outlier: 7.653A  pdb=" N   ASP B 202 " --> pdb=" O   THR A 199 " (cutoff:3.500A)
      removed outlier: 9.057A  pdb=" N   THR A 201 " --> pdb=" O   ASP B 202 " (cutoff:3.500A)
      removed outlier: 6.330A  pdb=" N   ASN B 197 " --> pdb=" O   PHE C 198 " (cutoff:3.500A)
      removed outlier: 7.865A  pdb=" N   GLU C 200 " --> pdb=" O   ASN B 197 " (cutoff:3.500A)
      removed outlier: 8.163A  pdb=" N   THR B 199 " --> pdb=" O   GLU C 200 " (cutoff:3.500A)
      removed outlier: 7.569A  pdb=" N   ASP C 202 " --> pdb=" O   THR B 199 " (cutoff:3.500A)
      removed outlier: 8.963A  pdb=" N   THR B 201 " --> pdb=" O   ASP C 202 " (cutoff:3.500A)
      removed outlier: 6.962A  pdb=" N   PHE C 198 " --> pdb=" O   ASN D 197 " (cutoff:3.500A)
      removed outlier: 6.831A  pdb=" N   THR D 199 " --> pdb=" O   PHE C 198 " (cutoff:3.500A)
      removed outlier: 6.986A  pdb=" N   GLU C 200 " --> pdb=" O   THR D 199 " (cutoff:3.500A)
      removed outlier: 6.337A  pdb=" N   ASN D 197 " --> pdb=" O   PHE E 198 " (cutoff:3.500A)
      removed outlier: 7.872A  pdb=" N   GLU E 200 " --> pdb=" O   ASN D 197 " (cutoff:3.500A)
      removed outlier: 8.209A  pdb=" N   THR D 199 " --> pdb=" O   GLU E 200 " (cutoff:3.500A)
      removed outlier: 7.624A  pdb=" N   ASP E 202 " --> pdb=" O   THR D 199 " (cutoff:3.500A)
      removed outlier: 9.019A  pdb=" N   THR D 201 " --> pdb=" O   ASP E 202 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'A' and resid 206 through 210
      removed outlier: 8.802A  pdb=" N   GLU A 207 " --> pdb=" O   ARG B 208 " (cutoff:3.500A)
      removed outlier: 9.950A  pdb=" N   VAL B 210 " --> pdb=" O   GLU A 207 " (cutoff:3.500A)
      removed outlier: 6.124A  pdb=" N   VAL A 209 " --> pdb=" O   VAL B 210 " (cutoff:3.500A)
      removed outlier: 8.754A  pdb=" N   GLU B 207 " --> pdb=" O   ARG C 208 " (cutoff:3.500A)
      removed outlier: 9.904A  pdb=" N   VAL C 210 " --> pdb=" O   GLU B 207 " (cutoff:3.500A)
      removed outlier: 6.086A  pdb=" N   VAL B 209 " --> pdb=" O   VAL C 210 " (cutoff:3.500A)
      removed outlier: 8.765A  pdb=" N   GLU C 207 " --> pdb=" O   ARG D 208 " (cutoff:3.500A)
      removed outlier: 9.920A  pdb=" N   VAL D 210 " --> pdb=" O   GLU C 207 " (cutoff:3.500A)
      removed outlier: 6.092A  pdb=" N   VAL C 209 " --> pdb=" O   VAL D 210 " (cutoff:3.500A)
      removed outlier: 8.780A  pdb=" N   GLU D 207 " --> pdb=" O   ARG E 208 " (cutoff:3.500A)
      removed outlier: 9.939A  pdb=" N   VAL E 210 " --> pdb=" O   GLU D 207 " (cutoff:3.500A)
      removed outlier: 6.108A  pdb=" N   VAL D 209 " --> pdb=" O   VAL E 210 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA5
    Processing sheet with id=AA6, first strand: chain 'A' and resid 223 through 225
      removed outlier: 6.697A  pdb=" N   ALA A 224 " --> pdb=" O   TYR B 225 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA6
    Processing sheet with id=AA7, first strand: chain 'F' and resid 173 through 178
    Processing sheet with id=AA8, first strand: chain 'F' and resid 182 through 185
      removed outlier: 6.258A  pdb=" N   THR F 183 " --> pdb=" O   ILE G 184 " (cutoff:3.500A)
      removed outlier: 6.249A  pdb=" N   THR G 183 " --> pdb=" O   ILE H 184 " (cutoff:3.500A)
      removed outlier: 6.246A  pdb=" N   THR H 183 " --> pdb=" O   ILE I 184 " (cutoff:3.500A)
      removed outlier: 6.260A  pdb=" N   THR I 183 " --> pdb=" O   ILE J 184 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA8
    Processing sheet with id=AA9, first strand: chain 'F' and resid 189 through 192
    Processing sheet with id=AB1, first strand: chain 'F' and resid 197 through 202
      removed outlier: 6.899A  pdb=" N   PHE F 198 " --> pdb=" O   ASN G 197 " (cutoff:3.500A)
      removed outlier: 6.779A  pdb=" N   THR G 199 " --> pdb=" O   PHE F 198 " (cutoff:3.500A)
      removed outlier: 6.939A  pdb=" N   GLU F 200 " --> pdb=" O   THR G 199 " (cutoff:3.500A)
      removed outlier: 6.942A  pdb=" N   PHE G 198 " --> pdb=" O   ASN H 197 " (cutoff:3.500A)
      removed outlier: 6.817A  pdb=" N   THR H 199 " --> pdb=" O   PHE G 198 " (cutoff:3.500A)
      removed outlier: 6.980A  pdb=" N   GLU G 200 " --> pdb=" O   THR H 199 " (cutoff:3.500A)
      removed outlier: 6.968A  pdb=" N   PHE H 198 " --> pdb=" O   ASN I 197 " (cutoff:3.500A)
      removed outlier: 6.837A  pdb=" N   THR I 199 " --> pdb=" O   PHE H 198 " (cutoff:3.500A)
      removed outlier: 6.992A  pdb=" N   GLU H 200 " --> pdb=" O   THR I 199 " (cutoff:3.500A)
      removed outlier: 6.320A  pdb=" N   ASN I 197 " --> pdb=" O   PHE J 198 " (cutoff:3.500A)
      removed outlier: 7.862A  pdb=" N   GLU J 200 " --> pdb=" O   ASN I 197 " (cutoff:3.500A)
      removed outlier: 8.182A  pdb=" N   THR I 199 " --> pdb=" O   GLU J 200 " (cutoff:3.500A)
      removed outlier: 7.608A  pdb=" N   ASP J 202 " --> pdb=" O   THR I 199 " (cutoff:3.500A)
      removed outlier: 8.997A  pdb=" N   THR I 201 " --> pdb=" O   ASP J 202 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'F' and resid 206 through 210
      removed outlier: 8.779A  pdb=" N   GLU F 207 " --> pdb=" O   ARG G 208 " (cutoff:3.500A)
      removed outlier: 9.941A  pdb=" N   VAL G 210 " --> pdb=" O   GLU F 207 " (cutoff:3.500A)
      removed outlier: 6.115A  pdb=" N   VAL F 209 " --> pdb=" O   VAL G 210 " (cutoff:3.500A)
      removed outlier: 8.783A  pdb=" N   GLU G 207 " --> pdb=" O   ARG H 208 " (cutoff:3.500A)
      removed outlier: 9.942A  pdb=" N   VAL H 210 " --> pdb=" O   GLU G 207 " (cutoff:3.500A)
      removed outlier: 6.113A  pdb=" N   VAL G 209 " --> pdb=" O   VAL H 210 " (cutoff:3.500A)
      removed outlier: 8.764A  pdb=" N   GLU H 207 " --> pdb=" O   ARG I 208 " (cutoff:3.500A)
      removed outlier: 9.919A  pdb=" N   VAL I 210 " --> pdb=" O   GLU H 207 " (cutoff:3.500A)
      removed outlier: 6.090A  pdb=" N   VAL H 209 " --> pdb=" O   VAL I 210 " (cutoff:3.500A)
      removed outlier: 8.775A  pdb=" N   GLU I 207 " --> pdb=" O   ARG J 208 " (cutoff:3.500A)
      removed outlier: 9.937A  pdb=" N   VAL J 210 " --> pdb=" O   GLU I 207 " (cutoff:3.500A)
      removed outlier: 6.110A  pdb=" N   VAL I 209 " --> pdb=" O   VAL J 210 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AB2

    79 hydrogen bonds defined for protein.
    237 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: 1.14

  Time building geometry restraints manager: 1.42 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: 1700
        1.34 -     1.46: 947
        1.46 -     1.58: 2253
        1.58 -     1.69: 0
        1.69 -     1.81: 80
  Bond restraints: 4980
  Sorted by residual:
  bond pdb=" CB  CYS B 214 "
       pdb=" SG  CYS B 214 "
    ideal  model  delta    sigma   weight residual
    1.808  1.784  0.024 3.30e-02 9.18e+02 5.40e-01
  bond pdb=" CB  CYS I 214 "
       pdb=" SG  CYS I 214 "
    ideal  model  delta    sigma   weight residual
    1.808  1.784  0.024 3.30e-02 9.18e+02 5.39e-01
  bond pdb=" CB  CYS D 214 "
       pdb=" SG  CYS D 214 "
    ideal  model  delta    sigma   weight residual
    1.808  1.784  0.024 3.30e-02 9.18e+02 5.35e-01
  bond pdb=" CB  CYS C 214 "
       pdb=" SG  CYS C 214 "
    ideal  model  delta    sigma   weight residual
    1.808  1.784  0.024 3.30e-02 9.18e+02 5.31e-01
  bond pdb=" CB  CYS J 214 "
       pdb=" SG  CYS J 214 "
    ideal  model  delta    sigma   weight residual
    1.808  1.784  0.024 3.30e-02 9.18e+02 5.30e-01
  ... (remaining 4975 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     0.75: 5974
        0.75 -     1.50: 601
        1.50 -     2.25: 55
        2.25 -     3.00: 63
        3.00 -     3.75: 17
  Bond angle restraints: 6710
  Sorted by residual:
  angle pdb=" C   ARG H 220 "
        pdb=" N   GLU H 221 "
        pdb=" CA  GLU H 221 "
      ideal   model   delta    sigma   weight residual
     122.08  125.05   -2.97 1.47e+00 4.63e-01 4.09e+00
  angle pdb=" C   ARG D 220 "
        pdb=" N   GLU D 221 "
        pdb=" CA  GLU D 221 "
      ideal   model   delta    sigma   weight residual
     122.08  125.05   -2.97 1.47e+00 4.63e-01 4.09e+00
  angle pdb=" C   ARG F 220 "
        pdb=" N   GLU F 221 "
        pdb=" CA  GLU F 221 "
      ideal   model   delta    sigma   weight residual
     122.08  125.04   -2.96 1.47e+00 4.63e-01 4.07e+00
  angle pdb=" C   ARG J 220 "
        pdb=" N   GLU J 221 "
        pdb=" CA  GLU J 221 "
      ideal   model   delta    sigma   weight residual
     122.08  125.04   -2.96 1.47e+00 4.63e-01 4.05e+00
  angle pdb=" C   ARG B 220 "
        pdb=" N   GLU B 221 "
        pdb=" CA  GLU B 221 "
      ideal   model   delta    sigma   weight residual
     122.08  125.04   -2.96 1.47e+00 4.63e-01 4.05e+00
  ... (remaining 6705 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    13.13: 2532
       13.13 -    26.26: 341
       26.26 -    39.39: 100
       39.39 -    52.52: 40
       52.52 -    65.66: 20
  Dihedral angle restraints: 3033
    sinusoidal: 1253
      harmonic: 1780
  Sorted by residual:
  dihedral pdb=" CA  CYS B 214 "
           pdb=" C   CYS B 214 "
           pdb=" N   ILE B 215 "
           pdb=" CA  ILE B 215 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -161.04  -18.96     0      5.00e+00 4.00e-02 1.44e+01
  dihedral pdb=" CA  CYS G 214 "
           pdb=" C   CYS G 214 "
           pdb=" N   ILE G 215 "
           pdb=" CA  ILE G 215 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -161.05  -18.95     0      5.00e+00 4.00e-02 1.44e+01
  dihedral pdb=" CA  CYS A 214 "
           pdb=" C   CYS A 214 "
           pdb=" N   ILE A 215 "
           pdb=" CA  ILE A 215 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -161.05  -18.95     0      5.00e+00 4.00e-02 1.44e+01
  ... (remaining 3030 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.024: 353
       0.024 -    0.047: 221
       0.047 -    0.071: 89
       0.071 -    0.095: 56
       0.095 -    0.118: 41
  Chirality restraints: 760
  Sorted by residual:
  chirality pdb=" CA  ILE A 182 "
            pdb=" N   ILE A 182 "
            pdb=" C   ILE A 182 "
            pdb=" CB  ILE A 182 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.55   -0.12 2.00e-01 2.50e+01 3.49e-01
  chirality pdb=" CA  ILE H 182 "
            pdb=" N   ILE H 182 "
            pdb=" C   ILE H 182 "
            pdb=" CB  ILE H 182 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.55   -0.12 2.00e-01 2.50e+01 3.38e-01
  chirality pdb=" CA  ILE D 182 "
            pdb=" N   ILE D 182 "
            pdb=" C   ILE D 182 "
            pdb=" CB  ILE D 182 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.55   -0.12 2.00e-01 2.50e+01 3.35e-01
  ... (remaining 757 not shown)

  Planarity restraints: 880
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TYR E 226 "   -0.007 2.00e-02 2.50e+03   4.67e-03 4.36e-01
        pdb=" CG  TYR E 226 "    0.011 2.00e-02 2.50e+03
        pdb=" CD1 TYR E 226 "   -0.001 2.00e-02 2.50e+03
        pdb=" CD2 TYR E 226 "   -0.000 2.00e-02 2.50e+03
        pdb=" CE1 TYR E 226 "   -0.000 2.00e-02 2.50e+03
        pdb=" CE2 TYR E 226 "   -0.001 2.00e-02 2.50e+03
        pdb=" CZ  TYR E 226 "   -0.001 2.00e-02 2.50e+03
        pdb=" OH  TYR E 226 "   -0.001 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TYR A 226 "   -0.007 2.00e-02 2.50e+03   4.64e-03 4.30e-01
        pdb=" CG  TYR A 226 "    0.011 2.00e-02 2.50e+03
        pdb=" CD1 TYR A 226 "   -0.001 2.00e-02 2.50e+03
        pdb=" CD2 TYR A 226 "   -0.000 2.00e-02 2.50e+03
        pdb=" CE1 TYR A 226 "   -0.000 2.00e-02 2.50e+03
        pdb=" CE2 TYR A 226 "   -0.000 2.00e-02 2.50e+03
        pdb=" CZ  TYR A 226 "   -0.001 2.00e-02 2.50e+03
        pdb=" OH  TYR A 226 "   -0.001 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TYR F 226 "    0.007 2.00e-02 2.50e+03   4.63e-03 4.29e-01
        pdb=" CG  TYR F 226 "   -0.011 2.00e-02 2.50e+03
        pdb=" CD1 TYR F 226 "    0.001 2.00e-02 2.50e+03
        pdb=" CD2 TYR F 226 "    0.000 2.00e-02 2.50e+03
        pdb=" CE1 TYR F 226 "   -0.000 2.00e-02 2.50e+03
        pdb=" CE2 TYR F 226 "    0.001 2.00e-02 2.50e+03
        pdb=" CZ  TYR F 226 "    0.001 2.00e-02 2.50e+03
        pdb=" OH  TYR F 226 "    0.001 2.00e-02 2.50e+03
  ... (remaining 877 not shown)

  Histogram of nonbonded interaction distances:
        2.03 -     2.60: 59
        2.60 -     3.18: 3942
        3.18 -     3.75: 6801
        3.75 -     4.33: 10414
        4.33 -     4.90: 18829
  Nonbonded interactions: 40045
  Sorted by model distance:
  nonbonded pdb=" SG  CYS G 179 "
            pdb=" SG  CYS G 214 "
     model   vdw
     2.029 3.760
  nonbonded pdb=" SG  CYS I 179 "
            pdb=" SG  CYS I 214 "
     model   vdw
     2.029 3.760
  nonbonded pdb=" SG  CYS C 179 "
            pdb=" SG  CYS C 214 "
     model   vdw
     2.029 3.760
  nonbonded pdb=" SG  CYS E 179 "
            pdb=" SG  CYS E 214 "
     model   vdw
     2.029 3.760
  nonbonded pdb=" SG  CYS B 179 "
            pdb=" SG  CYS B 214 "
     model   vdw
     2.030 3.760
  ... (remaining 40040 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: 0.04
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'C'
  selection = chain 'B'
  selection = chain 'E'
  selection = chain 'D'
  selection = chain 'G'
  selection = chain 'F'
  selection = chain 'I'
  selection = chain 'H'
  selection = chain 'J'
}

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:             3.740
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.190
  Check model and map are aligned:         0.030
  Set scattering table:                    0.050
  Process input model:                     14.960
  Find NCS groups from input model:        0.110
  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:14.520
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   33.610
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7908
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.024   4980  Z= 0.277
  Angle     :  0.554   3.752   6710  Z= 0.347
  Chirality :  0.044   0.118    760
  Planarity :  0.002   0.006    880
  Dihedral  : 14.813  65.656   1870
  Min Nonbonded Distance : 2.029

Molprobity Statistics.
  All-atom Clashscore : 10.98
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 12.59 %
    Favored  : 87.41 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  5.26 %
    Favored  : 94.74 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -6.05 (0.19), residues: 580
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -4.61 (0.14), residues: 580

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.002   0.001   HIS A 177 
 PHE   0.003   0.001   PHE D 175 
 TYR   0.011   0.001   TYR E 226 
 ARG   0.001   0.000   ARG A 220 

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

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

  1160 Ramachandran restraints generated.
    580 Oldfield, 0 Emsley, 580 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1160 Ramachandran restraints generated.
    580 Oldfield, 0 Emsley, 580 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  182 residues out of total 570 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 182
  time to evaluate  : 0.707 
Fit side-chains
   revert: symmetry clash
REVERT: A  211 GLU cc_start: 0.8065 (tt0) cc_final: 0.7705 (tt0)
REVERT: B  208 ARG cc_start: 0.7155 (mtt180) cc_final: 0.6822 (mtm180)
REVERT: B  211 GLU cc_start: 0.7950 (tt0) cc_final: 0.7719 (tt0)
REVERT: B  228 ARG cc_start: 0.8476 (ttt-90) cc_final: 0.8201 (tmt170)
REVERT: C  221 GLU cc_start: 0.8146 (mp0) cc_final: 0.7895 (mp0)
REVERT: C  228 ARG cc_start: 0.8578 (ttt-90) cc_final: 0.8357 (ttt-90)
REVERT: D  185 LYS cc_start: 0.8411 (tttm) cc_final: 0.8207 (tttt)
REVERT: D  200 GLU cc_start: 0.8024 (mt-10) cc_final: 0.7796 (mt-10)
REVERT: D  228 ARG cc_start: 0.8655 (ttt-90) cc_final: 0.8362 (ttt-90)
REVERT: E  200 GLU cc_start: 0.8297 (mt-10) cc_final: 0.8049 (mt-10)
REVERT: E  221 GLU cc_start: 0.8136 (mp0) cc_final: 0.7746 (mp0)
REVERT: F  211 GLU cc_start: 0.8187 (tt0) cc_final: 0.7834 (tt0)
REVERT: F  228 ARG cc_start: 0.8725 (ttt-90) cc_final: 0.8288 (ttt-90)
REVERT: G  228 ARG cc_start: 0.8704 (ttt-90) cc_final: 0.8326 (ttt-90)
REVERT: H  211 GLU cc_start: 0.7738 (tt0) cc_final: 0.7359 (tt0)
REVERT: H  220 ARG cc_start: 0.7896 (ptt180) cc_final: 0.7549 (ptp-170)
REVERT: H  221 GLU cc_start: 0.8262 (mp0) cc_final: 0.7751 (mp0)
REVERT: I  221 GLU cc_start: 0.8052 (mp0) cc_final: 0.7754 (mp0)
REVERT: J  220 ARG cc_start: 0.7873 (ptt180) cc_final: 0.6738 (mmm160)
  outliers start: 0
  outliers final: 1
  residues processed: 182
  average time/residue: 1.8166
  time to fit residues: 339.2185
Evaluate side-chains
  150 residues out of total 570 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 149
  time to evaluate  : 0.617 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  197 ASN
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 60
   random chunks:
   chunk 50 optimal weight:    4.9990
   chunk 45 optimal weight:    5.9990
   chunk 25 optimal weight:    4.9990
   chunk 15 optimal weight:    5.9990
   chunk 30 optimal weight:    8.9990
   chunk 24 optimal weight:    7.9990
   chunk 47 optimal weight:    4.9990
   chunk 18 optimal weight:    0.9980
   chunk 28 optimal weight:    1.9990
   chunk 35 optimal weight:    0.9990
   chunk 54 optimal weight:    7.9990
   overall best weight:    2.7988

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

Flipped N/Q/H residues before XYZ refinement:
A 173 ASN
A 174 ASN
A 177 HIS
A 187 HIS
A 227 GLN
B 173 ASN
B 174 ASN
B 177 HIS
B 217 GLN
C 173 ASN
C 174 ASN
C 177 HIS
C 187 HIS
D 173 ASN
D 174 ASN
D 177 HIS
E 173 ASN
E 174 ASN
E 187 HIS
F 173 ASN
F 174 ASN
F 187 HIS
G 173 ASN
G 174 ASN
G 177 HIS
G 187 HIS
H 173 ASN
H 174 ASN
H 177 HIS
I 173 ASN
I 174 ASN
I 177 HIS
I 187 HIS
J 173 ASN
J 174 ASN
J 187 HIS

Total number of N/Q/H flips: 36

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3960 r_free = 0.3960 target = 0.122324 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3688 r_free = 0.3688 target = 0.103752 restraints weight = 5334.045|
|-----------------------------------------------------------------------------|
r_work (start): 0.3697 rms_B_bonded: 2.11
r_work: 0.3533 rms_B_bonded: 2.19 restraints_weight: 0.5000
r_work: 0.3387 rms_B_bonded: 3.62 restraints_weight: 0.2500
r_work (final): 0.3387
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8499
moved from start:          0.2261

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.007   0.037   4980  Z= 0.486
  Angle     :  0.635   7.289   6710  Z= 0.374
  Chirality :  0.047   0.112    760
  Planarity :  0.003   0.031    880
  Dihedral  :  6.112  41.305    652
  Min Nonbonded Distance : 2.594

Molprobity Statistics.
  All-atom Clashscore : 6.26
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 13.62 %
    Favored  : 86.38 %
  Rotamer:
    Outliers :  2.28 %
    Allowed  : 20.35 %
    Favored  : 77.37 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -4.96 (0.23), residues: 580
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -3.78 (0.18), residues: 580

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.003   0.001   HIS D 177 
 PHE   0.009   0.001   PHE F 175 
 TYR   0.016   0.002   TYR D 226 
 ARG   0.008   0.001   ARG J 228 

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

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

  1160 Ramachandran restraints generated.
    580 Oldfield, 0 Emsley, 580 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1160 Ramachandran restraints generated.
    580 Oldfield, 0 Emsley, 580 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  158 residues out of total 570 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 145
  time to evaluate  : 0.611 
Fit side-chains
REVERT: A  228 ARG cc_start: 0.9177 (ttt-90) cc_final: 0.8907 (ttt-90)
REVERT: D  200 GLU cc_start: 0.8679 (mt-10) cc_final: 0.8472 (mt-10)
REVERT: D  228 ARG cc_start: 0.9003 (ttt-90) cc_final: 0.8688 (ttt-90)
REVERT: G  221 GLU cc_start: 0.8439 (mp0) cc_final: 0.8228 (mp0)
REVERT: G  228 ARG cc_start: 0.9004 (ttt-90) cc_final: 0.8642 (ttt-90)
REVERT: H  208 ARG cc_start: 0.8017 (mtt180) cc_final: 0.7788 (mtm180)
REVERT: H  211 GLU cc_start: 0.8667 (tt0) cc_final: 0.8411 (tt0)
REVERT: I  221 GLU cc_start: 0.8502 (mp0) cc_final: 0.8178 (mp0)
REVERT: J  220 ARG cc_start: 0.8381 (ptt180) cc_final: 0.6767 (mmm160)
  outliers start: 13
  outliers final: 7
  residues processed: 148
  average time/residue: 2.0286
  time to fit residues: 306.9585
Evaluate side-chains
  146 residues out of total 570 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 139
  time to evaluate  : 0.539 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  185 LYS
Chi-restraints excluded: chain B residue  197 ASN
Chi-restraints excluded: chain D residue  192 THR
Chi-restraints excluded: chain F residue  197 ASN
Chi-restraints excluded: chain F residue  223 GLN
Chi-restraints excluded: chain G residue  197 ASN
Chi-restraints excluded: chain J residue  192 THR
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 60
   random chunks:
   chunk 51 optimal weight:    3.9990
   chunk 10 optimal weight:    0.6980
   chunk 27 optimal weight:    0.9990
   chunk 15 optimal weight:    4.9990
   chunk 25 optimal weight:    2.9990
   chunk 57 optimal weight:    0.8980
   chunk 26 optimal weight:    0.0010
   chunk 3 optimal weight:    3.9990
   chunk 53 optimal weight:    3.9990
   chunk 20 optimal weight:    0.8980
   chunk 2 optimal weight:    2.9990
   overall best weight:    0.6988

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

Flipped N/Q/H residues before XYZ refinement:
E 172 GLN
J 172 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4067 r_free = 0.4067 target = 0.130614 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3803 r_free = 0.3803 target = 0.111955 restraints weight = 5183.722|
|-----------------------------------------------------------------------------|
r_work (start): 0.3814 rms_B_bonded: 2.14
r_work: 0.3658 rms_B_bonded: 2.20 restraints_weight: 0.5000
r_work: 0.3515 rms_B_bonded: 3.67 restraints_weight: 0.2500
r_work (final): 0.3515
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8387
moved from start:          0.2507

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.028   4980  Z= 0.155
  Angle     :  0.458   4.827   6710  Z= 0.270
  Chirality :  0.043   0.116    760
  Planarity :  0.002   0.038    880
  Dihedral  :  5.173  35.930    652
  Min Nonbonded Distance : 2.631

Molprobity Statistics.
  All-atom Clashscore : 6.79
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.62 %
    Favored  : 91.38 %
  Rotamer:
    Outliers :  2.11 %
    Allowed  : 23.68 %
    Favored  : 74.21 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -4.31 (0.27), residues: 580
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -3.27 (0.20), residues: 580

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.001   0.000   HIS A 177 
 PHE   0.003   0.001   PHE F 175 
 TYR   0.009   0.001   TYR B 226 
 ARG   0.008   0.001   ARG E 228 

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

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

  1160 Ramachandran restraints generated.
    580 Oldfield, 0 Emsley, 580 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1160 Ramachandran restraints generated.
    580 Oldfield, 0 Emsley, 580 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  158 residues out of total 570 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 146
  time to evaluate  : 0.666 
Fit side-chains
REVERT: A  220 ARG cc_start: 0.8548 (ptt-90) cc_final: 0.8300 (ptt90)
REVERT: D  228 ARG cc_start: 0.9005 (ttt-90) cc_final: 0.8745 (ttt-90)
REVERT: E  212 GLN cc_start: 0.8952 (pt0) cc_final: 0.8734 (pt0)
REVERT: G  228 ARG cc_start: 0.8942 (ttt-90) cc_final: 0.8395 (ttt-90)
REVERT: H  211 GLU cc_start: 0.8518 (tt0) cc_final: 0.8215 (tt0)
REVERT: I  221 GLU cc_start: 0.8465 (mt-10) cc_final: 0.8216 (mp0)
REVERT: J  196 GLU cc_start: 0.8571 (tt0) cc_final: 0.8001 (mp0)
REVERT: J  220 ARG cc_start: 0.8267 (ptt180) cc_final: 0.6415 (mmm160)
  outliers start: 12
  outliers final: 2
  residues processed: 148
  average time/residue: 1.9346
  time to fit residues: 293.0740
Evaluate side-chains
  137 residues out of total 570 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 135
  time to evaluate  : 0.735 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain D residue  192 THR
Chi-restraints excluded: chain J residue  192 THR
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 60
   random chunks:
   chunk 22 optimal weight:    5.9990
   chunk 50 optimal weight:    4.9990
   chunk 48 optimal weight:    7.9990
   chunk 38 optimal weight:    3.9990
   chunk 33 optimal weight:    2.9990
   chunk 20 optimal weight:    3.9990
   chunk 13 optimal weight:    4.9990
   chunk 2 optimal weight:    3.9990
   chunk 52 optimal weight:    4.9990
   chunk 49 optimal weight:    0.8980
   chunk 44 optimal weight:    1.9990
   overall best weight:    2.7788

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

Flipped N/Q/H residues before XYZ refinement:
A 227 GLN
B 187 HIS
D 223 GLN
I 174 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3967 r_free = 0.3967 target = 0.122870 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3687 r_free = 0.3687 target = 0.104004 restraints weight = 5292.302|
|-----------------------------------------------------------------------------|
r_work (start): 0.3696 rms_B_bonded: 2.15
r_work: 0.3534 rms_B_bonded: 2.19 restraints_weight: 0.5000
r_work: 0.3388 rms_B_bonded: 3.61 restraints_weight: 0.2500
r_work (final): 0.3388
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8492
moved from start:          0.2715

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.007   0.036   4980  Z= 0.476
  Angle     :  0.598   5.869   6710  Z= 0.354
  Chirality :  0.046   0.110    760
  Planarity :  0.003   0.018    880
  Dihedral  :  5.853  20.891    650
  Min Nonbonded Distance : 2.596

Molprobity Statistics.
  All-atom Clashscore : 7.00
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 13.62 %
    Favored  : 86.38 %
  Rotamer:
    Outliers :  4.39 %
    Allowed  : 21.75 %
    Favored  : 73.86 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -4.34 (0.26), residues: 580
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -3.30 (0.20), residues: 580

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.003   0.001   HIS A 177 
 PHE   0.009   0.002   PHE F 175 
 TYR   0.017   0.002   TYR D 226 
 ARG   0.007   0.000   ARG F 228 

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

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

  1160 Ramachandran restraints generated.
    580 Oldfield, 0 Emsley, 580 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1160 Ramachandran restraints generated.
    580 Oldfield, 0 Emsley, 580 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  173 residues out of total 570 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 148
  time to evaluate  : 0.575 
Fit side-chains
REVERT: A  228 ARG cc_start: 0.9186 (ttt-90) cc_final: 0.8853 (ttt-90)
REVERT: D  205 MET cc_start: 0.8759 (OUTLIER) cc_final: 0.8460 (ttt)
REVERT: D  228 ARG cc_start: 0.9009 (ttt-90) cc_final: 0.8681 (ttt-90)
REVERT: F  211 GLU cc_start: 0.8495 (tt0) cc_final: 0.8173 (tt0)
REVERT: F  221 GLU cc_start: 0.8322 (OUTLIER) cc_final: 0.7759 (mp0)
REVERT: G  221 GLU cc_start: 0.8576 (mt-10) cc_final: 0.8324 (mt-10)
REVERT: G  228 ARG cc_start: 0.9032 (ttt-90) cc_final: 0.8626 (ttt-90)
REVERT: H  211 GLU cc_start: 0.8658 (tt0) cc_final: 0.8409 (tt0)
REVERT: H  221 GLU cc_start: 0.8584 (mt-10) cc_final: 0.8236 (mt-10)
REVERT: J  220 ARG cc_start: 0.8359 (ptt180) cc_final: 0.6841 (mmm160)
  outliers start: 25
  outliers final: 10
  residues processed: 156
  average time/residue: 2.2007
  time to fit residues: 351.1856
Evaluate side-chains
  154 residues out of total 570 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 142
  time to evaluate  : 0.628 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  185 LYS
Chi-restraints excluded: chain B residue  197 ASN
Chi-restraints excluded: chain C residue  197 ASN
Chi-restraints excluded: chain C residue  204 LYS
Chi-restraints excluded: chain D residue  192 THR
Chi-restraints excluded: chain D residue  205 MET
Chi-restraints excluded: chain E residue  215 ILE
Chi-restraints excluded: chain F residue  197 ASN
Chi-restraints excluded: chain F residue  221 GLU
Chi-restraints excluded: chain F residue  223 GLN
Chi-restraints excluded: chain G residue  197 ASN
Chi-restraints excluded: chain J residue  192 THR
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 60
   random chunks:
   chunk 47 optimal weight:    4.9990
   chunk 14 optimal weight:    1.9990
   chunk 42 optimal weight:   10.0000
   chunk 40 optimal weight:    1.9990
   chunk 0 optimal weight:    8.9990
   chunk 51 optimal weight:    3.9990
   chunk 45 optimal weight:    0.9980
   chunk 1 optimal weight:    1.9990
   chunk 53 optimal weight:    0.8980
   chunk 27 optimal weight:    2.9990
   chunk 9 optimal weight:    2.9990
   overall best weight:    1.5786

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

Flipped N/Q/H residues before XYZ refinement:
E 172 GLN
F 172 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4022 r_free = 0.4022 target = 0.126336 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3747 r_free = 0.3747 target = 0.107473 restraints weight = 5191.191|
|-----------------------------------------------------------------------------|
r_work (start): 0.3758 rms_B_bonded: 2.15
r_work: 0.3599 rms_B_bonded: 2.20 restraints_weight: 0.5000
r_work: 0.3453 rms_B_bonded: 3.65 restraints_weight: 0.2500
r_work (final): 0.3453
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8441
moved from start:          0.2730

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.032   4980  Z= 0.285
  Angle     :  0.523   4.994   6710  Z= 0.311
  Chirality :  0.044   0.122    760
  Planarity :  0.002   0.037    880
  Dihedral  :  5.445  18.156    650
  Min Nonbonded Distance : 2.617

Molprobity Statistics.
  All-atom Clashscore : 6.58
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.62 %
    Favored  : 91.38 %
  Rotamer:
    Outliers :  3.68 %
    Allowed  : 25.79 %
    Favored  : 70.53 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -4.04 (0.27), residues: 580
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -3.07 (0.20), residues: 580

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.002   0.001   HIS A 177 
 PHE   0.006   0.001   PHE F 175 
 TYR   0.012   0.001   TYR D 226 
 ARG   0.009   0.000   ARG F 228 

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

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

  1160 Ramachandran restraints generated.
    580 Oldfield, 0 Emsley, 580 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1160 Ramachandran restraints generated.
    580 Oldfield, 0 Emsley, 580 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  164 residues out of total 570 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 143
  time to evaluate  : 0.568 
Fit side-chains
REVERT: A  220 ARG cc_start: 0.8588 (ptt-90) cc_final: 0.8345 (ptt90)
REVERT: A  228 ARG cc_start: 0.9162 (ttt-90) cc_final: 0.8838 (ttt-90)
REVERT: D  228 ARG cc_start: 0.9033 (ttt-90) cc_final: 0.8658 (ttt-90)
REVERT: F  221 GLU cc_start: 0.8264 (OUTLIER) cc_final: 0.7745 (mp0)
REVERT: F  223 GLN cc_start: 0.8735 (OUTLIER) cc_final: 0.8500 (mp-120)
REVERT: G  208 ARG cc_start: 0.8303 (mtp85) cc_final: 0.7834 (mtm110)
REVERT: G  221 GLU cc_start: 0.8455 (mt-10) cc_final: 0.8252 (mt-10)
REVERT: G  228 ARG cc_start: 0.9000 (ttt-90) cc_final: 0.8484 (ttt-90)
REVERT: H  211 GLU cc_start: 0.8648 (tt0) cc_final: 0.8341 (tt0)
REVERT: I  221 GLU cc_start: 0.8511 (mt-10) cc_final: 0.8167 (mp0)
REVERT: J  196 GLU cc_start: 0.8552 (tt0) cc_final: 0.7977 (mp0)
REVERT: J  220 ARG cc_start: 0.8270 (ptt180) cc_final: 0.6415 (mmm160)
  outliers start: 21
  outliers final: 9
  residues processed: 151
  average time/residue: 2.1274
  time to fit residues: 328.2641
Evaluate side-chains
  152 residues out of total 570 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 141
  time to evaluate  : 0.602 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  185 LYS
Chi-restraints excluded: chain B residue  214 CYS
Chi-restraints excluded: chain C residue  197 ASN
Chi-restraints excluded: chain C residue  204 LYS
Chi-restraints excluded: chain D residue  192 THR
Chi-restraints excluded: chain E residue  215 ILE
Chi-restraints excluded: chain F residue  197 ASN
Chi-restraints excluded: chain F residue  221 GLU
Chi-restraints excluded: chain F residue  223 GLN
Chi-restraints excluded: chain G residue  197 ASN
Chi-restraints excluded: chain J residue  192 THR
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 60
   random chunks:
   chunk 16 optimal weight:    0.7980
   chunk 34 optimal weight:    3.9990
   chunk 5 optimal weight:    2.9990
   chunk 31 optimal weight:    0.9980
   chunk 55 optimal weight:    0.2980
   chunk 36 optimal weight:   10.0000
   chunk 11 optimal weight:    1.9990
   chunk 19 optimal weight:    3.9990
   chunk 20 optimal weight:    0.7980
   chunk 24 optimal weight:    9.9990
   chunk 26 optimal weight:    0.7980
   overall best weight:    0.7380

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

Flipped N/Q/H residues before XYZ refinement:
E 172 GLN
F 172 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4061 r_free = 0.4061 target = 0.128773 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3802 r_free = 0.3802 target = 0.110529 restraints weight = 5301.731|
|-----------------------------------------------------------------------------|
r_work (start): 0.3831 rms_B_bonded: 2.12
r_work: 0.3674 rms_B_bonded: 2.21 restraints_weight: 0.5000
r_work: 0.3534 rms_B_bonded: 3.68 restraints_weight: 0.2500
r_work (final): 0.3534
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8391
moved from start:          0.2848

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.024   4980  Z= 0.156
  Angle     :  0.456   4.713   6710  Z= 0.269
  Chirality :  0.044   0.147    760
  Planarity :  0.002   0.036    880
  Dihedral  :  4.896  16.451    650
  Min Nonbonded Distance : 2.620

Molprobity Statistics.
  All-atom Clashscore : 6.58
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 11.72 %
    Favored  : 88.28 %
  Rotamer:
    Outliers :  3.86 %
    Allowed  : 27.19 %
    Favored  : 68.95 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -3.78 (0.28), residues: 580
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.87 (0.22), residues: 580

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.001   0.000   HIS A 177 
 PHE   0.003   0.001   PHE F 175 
 TYR   0.009   0.001   TYR B 226 
 ARG   0.008   0.000   ARG F 228 

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

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

  1160 Ramachandran restraints generated.
    580 Oldfield, 0 Emsley, 580 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1160 Ramachandran restraints generated.
    580 Oldfield, 0 Emsley, 580 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  165 residues out of total 570 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 143
  time to evaluate  : 1.103 
Fit side-chains
REVERT: A  220 ARG cc_start: 0.8533 (ptt-90) cc_final: 0.8245 (ptt90)
REVERT: A  228 ARG cc_start: 0.9106 (ttt-90) cc_final: 0.8842 (ttt-90)
REVERT: B  220 ARG cc_start: 0.8348 (ptt90) cc_final: 0.8026 (ptt-90)
REVERT: B  221 GLU cc_start: 0.8409 (OUTLIER) cc_final: 0.7967 (mp0)
REVERT: C  221 GLU cc_start: 0.8341 (OUTLIER) cc_final: 0.8043 (mp0)
REVERT: D  228 ARG cc_start: 0.9002 (ttt-90) cc_final: 0.8615 (ttt-90)
REVERT: F  211 GLU cc_start: 0.8355 (tt0) cc_final: 0.8063 (tt0)
REVERT: F  223 GLN cc_start: 0.8657 (OUTLIER) cc_final: 0.8432 (mp-120)
REVERT: G  208 ARG cc_start: 0.8340 (mtp85) cc_final: 0.7876 (mtm110)
REVERT: G  228 ARG cc_start: 0.9053 (ttt-90) cc_final: 0.8607 (ttt-90)
REVERT: H  211 GLU cc_start: 0.8560 (tt0) cc_final: 0.8286 (tt0)
REVERT: I  221 GLU cc_start: 0.8463 (mt-10) cc_final: 0.8194 (mp0)
REVERT: J  196 GLU cc_start: 0.8524 (tt0) cc_final: 0.8006 (mp0)
REVERT: J  220 ARG cc_start: 0.8248 (ptt180) cc_final: 0.6436 (mmm160)
  outliers start: 22
  outliers final: 6
  residues processed: 159
  average time/residue: 1.9386
  time to fit residues: 315.5909
Evaluate side-chains
  148 residues out of total 570 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 139
  time to evaluate  : 0.871 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  185 LYS
Chi-restraints excluded: chain A residue  193 THR
Chi-restraints excluded: chain A residue  214 CYS
Chi-restraints excluded: chain B residue  214 CYS
Chi-restraints excluded: chain B residue  221 GLU
Chi-restraints excluded: chain C residue  221 GLU
Chi-restraints excluded: chain D residue  192 THR
Chi-restraints excluded: chain F residue  223 GLN
Chi-restraints excluded: chain J residue  192 THR
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 60
   random chunks:
   chunk 51 optimal weight:    5.9990
   chunk 39 optimal weight:    4.9990
   chunk 44 optimal weight:    3.9990
   chunk 43 optimal weight:    5.9990
   chunk 2 optimal weight:    3.9990
   chunk 34 optimal weight:    2.9990
   chunk 55 optimal weight:    0.8980
   chunk 45 optimal weight:    0.8980
   chunk 40 optimal weight:    0.9990
   chunk 19 optimal weight:    3.9990
   chunk 21 optimal weight:    4.9990
   overall best weight:    1.9586

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

Flipped N/Q/H residues before XYZ refinement:
E 172 GLN
E 212 GLN
F 172 GLN
I 172 GLN
I 174 ASN
J 172 GLN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4011 r_free = 0.4011 target = 0.125654 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3732 r_free = 0.3732 target = 0.106430 restraints weight = 5220.399|
|-----------------------------------------------------------------------------|
r_work (start): 0.3728 rms_B_bonded: 2.16
r_work: 0.3573 rms_B_bonded: 2.21 restraints_weight: 0.5000
r_work: 0.3428 rms_B_bonded: 3.67 restraints_weight: 0.2500
r_work (final): 0.3428
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8453
moved from start:          0.2885

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.027   4980  Z= 0.350
  Angle     :  0.559   5.454   6710  Z= 0.332
  Chirality :  0.046   0.174    760
  Planarity :  0.003   0.037    880
  Dihedral  :  5.552  17.999    650
  Min Nonbonded Distance : 2.616

Molprobity Statistics.
  All-atom Clashscore : 7.83
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 12.24 %
    Favored  : 87.76 %
  Rotamer:
    Outliers :  4.39 %
    Allowed  : 27.54 %
    Favored  : 68.07 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -3.85 (0.27), residues: 580
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.93 (0.21), residues: 580

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.002   0.001   HIS A 177 
 PHE   0.007   0.001   PHE F 175 
 TYR   0.014   0.002   TYR G 226 
 ARG   0.010   0.001   ARG C 228 

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

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

  1160 Ramachandran restraints generated.
    580 Oldfield, 0 Emsley, 580 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1160 Ramachandran restraints generated.
    580 Oldfield, 0 Emsley, 580 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  166 residues out of total 570 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 141
  time to evaluate  : 0.561 
Fit side-chains
REVERT: A  228 ARG cc_start: 0.9186 (ttt-90) cc_final: 0.8900 (ttt-90)
REVERT: D  228 ARG cc_start: 0.9049 (ttt-90) cc_final: 0.8722 (ttt-90)
REVERT: G  208 ARG cc_start: 0.8376 (mtp85) cc_final: 0.7915 (mtm110)
REVERT: G  228 ARG cc_start: 0.9088 (ttt-90) cc_final: 0.8619 (ttt-90)
REVERT: H  211 GLU cc_start: 0.8685 (tt0) cc_final: 0.8425 (tt0)
REVERT: J  220 ARG cc_start: 0.8287 (ptt180) cc_final: 0.6617 (mmm160)
  outliers start: 25
  outliers final: 11
  residues processed: 153
  average time/residue: 2.1586
  time to fit residues: 337.4129
Evaluate side-chains
  151 residues out of total 570 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 140
  time to evaluate  : 0.612 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  185 LYS
Chi-restraints excluded: chain A residue  193 THR
Chi-restraints excluded: chain A residue  214 CYS
Chi-restraints excluded: chain B residue  197 ASN
Chi-restraints excluded: chain C residue  197 ASN
Chi-restraints excluded: chain C residue  204 LYS
Chi-restraints excluded: chain C residue  214 CYS
Chi-restraints excluded: chain D residue  192 THR
Chi-restraints excluded: chain F residue  197 ASN
Chi-restraints excluded: chain G residue  197 ASN
Chi-restraints excluded: chain J residue  192 THR
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 60
   random chunks:
   chunk 39 optimal weight:    3.9990
   chunk 18 optimal weight:   10.0000
   chunk 21 optimal weight:    3.9990
   chunk 34 optimal weight:    0.1980
   chunk 36 optimal weight:   10.0000
   chunk 19 optimal weight:    1.9990
   chunk 57 optimal weight:    3.9990
   chunk 14 optimal weight:    3.9990
   chunk 44 optimal weight:    2.9990
   chunk 33 optimal weight:    0.8980
   chunk 0 optimal weight:    8.9990
   overall best weight:    2.0186

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

Flipped N/Q/H residues before XYZ refinement:
E 172 GLN
F 172 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4010 r_free = 0.4010 target = 0.125802 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3732 r_free = 0.3732 target = 0.106546 restraints weight = 5306.231|
|-----------------------------------------------------------------------------|
r_work (start): 0.3728 rms_B_bonded: 2.17
r_work: 0.3572 rms_B_bonded: 2.23 restraints_weight: 0.5000
r_work: 0.3428 rms_B_bonded: 3.69 restraints_weight: 0.2500
r_work (final): 0.3428
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8460
moved from start:          0.2896

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.039   4980  Z= 0.362
  Angle     :  0.586   6.859   6710  Z= 0.346
  Chirality :  0.047   0.171    760
  Planarity :  0.003   0.030    880
  Dihedral  :  5.721  18.097    650
  Min Nonbonded Distance : 2.590

Molprobity Statistics.
  All-atom Clashscore : 7.83
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 10.52 %
    Favored  : 89.48 %
  Rotamer:
    Outliers :  3.68 %
    Allowed  : 28.95 %
    Favored  : 67.37 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -3.82 (0.27), residues: 580
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.91 (0.21), residues: 580

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.002   0.001   HIS A 177 
 PHE   0.008   0.001   PHE F 175 
 TYR   0.014   0.002   TYR G 226 
 ARG   0.008   0.000   ARG F 228 

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

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

  1160 Ramachandran restraints generated.
    580 Oldfield, 0 Emsley, 580 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1160 Ramachandran restraints generated.
    580 Oldfield, 0 Emsley, 580 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  161 residues out of total 570 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 140
  time to evaluate  : 0.673 
Fit side-chains
REVERT: A  228 ARG cc_start: 0.9190 (ttt-90) cc_final: 0.8899 (ttt-90)
REVERT: D  228 ARG cc_start: 0.9062 (ttt-90) cc_final: 0.8716 (ttt-90)
REVERT: F  211 GLU cc_start: 0.8425 (tt0) cc_final: 0.8148 (tt0)
REVERT: G  208 ARG cc_start: 0.8347 (mtp85) cc_final: 0.7858 (mtm110)
REVERT: G  221 GLU cc_start: 0.8434 (mt-10) cc_final: 0.8232 (mp0)
REVERT: G  228 ARG cc_start: 0.9100 (ttt-90) cc_final: 0.8622 (ttt-90)
REVERT: H  211 GLU cc_start: 0.8714 (tt0) cc_final: 0.8402 (tt0)
REVERT: I  220 ARG cc_start: 0.8484 (ptp90) cc_final: 0.8134 (ptp90)
REVERT: J  220 ARG cc_start: 0.8374 (ptt180) cc_final: 0.6392 (mmm160)
  outliers start: 21
  outliers final: 9
  residues processed: 151
  average time/residue: 2.0123
  time to fit residues: 311.8655
Evaluate side-chains
  148 residues out of total 570 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 139
  time to evaluate  : 0.595 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  193 THR
Chi-restraints excluded: chain A residue  214 CYS
Chi-restraints excluded: chain C residue  197 ASN
Chi-restraints excluded: chain C residue  204 LYS
Chi-restraints excluded: chain C residue  214 CYS
Chi-restraints excluded: chain D residue  192 THR
Chi-restraints excluded: chain F residue  197 ASN
Chi-restraints excluded: chain G residue  197 ASN
Chi-restraints excluded: chain J residue  192 THR
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 60
   random chunks:
   chunk 7 optimal weight:    3.9990
   chunk 42 optimal weight:   10.0000
   chunk 5 optimal weight:    3.9990
   chunk 11 optimal weight:    0.8980
   chunk 22 optimal weight:    0.5980
   chunk 4 optimal weight:    1.9990
   chunk 52 optimal weight:    1.9990
   chunk 39 optimal weight:    6.9990
   chunk 19 optimal weight:    0.7980
   chunk 20 optimal weight:    0.7980
   chunk 49 optimal weight:    1.9990
   overall best weight:    1.0182

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

Flipped N/Q/H residues before XYZ refinement:
F 172 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4077 r_free = 0.4077 target = 0.129796 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3801 r_free = 0.3801 target = 0.110882 restraints weight = 5113.526|
|-----------------------------------------------------------------------------|
r_work (start): 0.3801 rms_B_bonded: 2.13
r_work: 0.3650 rms_B_bonded: 2.20 restraints_weight: 0.5000
r_work: 0.3505 rms_B_bonded: 3.66 restraints_weight: 0.2500
r_work (final): 0.3505
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8396
moved from start:          0.2955

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   4980  Z= 0.207
  Angle     :  0.531   5.758   6710  Z= 0.310
  Chirality :  0.046   0.164    760
  Planarity :  0.002   0.033    880
  Dihedral  :  5.422  17.871    650
  Min Nonbonded Distance : 2.596

Molprobity Statistics.
  All-atom Clashscore : 8.35
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 10.00 %
    Favored  : 90.00 %
  Rotamer:
    Outliers :  2.46 %
    Allowed  : 29.82 %
    Favored  : 67.72 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -3.70 (0.28), residues: 580
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.81 (0.22), residues: 580

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.001   0.000   HIS A 177 
 PHE   0.005   0.001   PHE F 175 
 TYR   0.009   0.001   TYR B 226 
 ARG   0.008   0.000   ARG F 228 

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

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

  1160 Ramachandran restraints generated.
    580 Oldfield, 0 Emsley, 580 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1160 Ramachandran restraints generated.
    580 Oldfield, 0 Emsley, 580 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  152 residues out of total 570 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 138
  time to evaluate  : 0.560 
Fit side-chains
REVERT: A  228 ARG cc_start: 0.9152 (ttt-90) cc_final: 0.8835 (ttt-90)
REVERT: D  228 ARG cc_start: 0.9052 (ttt-90) cc_final: 0.8679 (ttt-90)
REVERT: E  220 ARG cc_start: 0.8317 (ptp90) cc_final: 0.8094 (ptp90)
REVERT: F  211 GLU cc_start: 0.8376 (tt0) cc_final: 0.8106 (tt0)
REVERT: G  208 ARG cc_start: 0.8399 (mtp85) cc_final: 0.7934 (mtm110)
REVERT: G  228 ARG cc_start: 0.9058 (ttt-90) cc_final: 0.8550 (ttt-90)
REVERT: H  211 GLU cc_start: 0.8647 (tt0) cc_final: 0.8347 (tt0)
REVERT: H  221 GLU cc_start: 0.8346 (mp0) cc_final: 0.8009 (mp0)
REVERT: J  196 GLU cc_start: 0.8545 (tt0) cc_final: 0.7960 (mp0)
REVERT: J  220 ARG cc_start: 0.8186 (ptt180) cc_final: 0.6260 (mmm160)
  outliers start: 14
  outliers final: 6
  residues processed: 149
  average time/residue: 1.9410
  time to fit residues: 296.0405
Evaluate side-chains
  141 residues out of total 570 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 135
  time to evaluate  : 0.571 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  193 THR
Chi-restraints excluded: chain A residue  214 CYS
Chi-restraints excluded: chain B residue  214 CYS
Chi-restraints excluded: chain D residue  192 THR
Chi-restraints excluded: chain G residue  197 ASN
Chi-restraints excluded: chain J residue  192 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 60
   random chunks:
   chunk 29 optimal weight:    0.9990
   chunk 8 optimal weight:    5.9990
   chunk 50 optimal weight:    3.9990
   chunk 6 optimal weight:    9.9990
   chunk 46 optimal weight:    3.9990
   chunk 42 optimal weight:    9.9990
   chunk 18 optimal weight:    9.9990
   chunk 15 optimal weight:    2.9990
   chunk 17 optimal weight:    6.9990
   chunk 22 optimal weight:    0.7980
   chunk 54 optimal weight:    9.9990
   overall best weight:    2.5588

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

Flipped N/Q/H residues before XYZ refinement:
D 187 HIS
E 212 GLN
F 172 GLN
F 177 HIS

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3998 r_free = 0.3998 target = 0.123533 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 29)----------------|
| r_work = 0.3734 r_free = 0.3734 target = 0.105420 restraints weight = 5419.075|
|-----------------------------------------------------------------------------|
r_work (start): 0.3734 rms_B_bonded: 2.08
r_work: 0.3578 rms_B_bonded: 2.18 restraints_weight: 0.5000
r_work: 0.3429 rms_B_bonded: 3.63 restraints_weight: 0.2500
r_work (final): 0.3429
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8502
moved from start:          0.3019

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.007   0.050   4980  Z= 0.451
  Angle     :  0.660   6.068   6710  Z= 0.386
  Chirality :  0.049   0.170    760
  Planarity :  0.003   0.039    880
  Dihedral  :  6.087  19.564    650
  Min Nonbonded Distance : 2.604

Molprobity Statistics.
  All-atom Clashscore : 9.08
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 13.62 %
    Favored  : 86.38 %
  Rotamer:
    Outliers :  1.75 %
    Allowed  : 31.75 %
    Favored  : 66.49 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -3.86 (0.27), residues: 580
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.93 (0.21), residues: 580

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.003   0.001   HIS A 177 
 PHE   0.009   0.002   PHE F 175 
 TYR   0.015   0.002   TYR G 226 
 ARG   0.011   0.001   ARG F 228 

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

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

  1160 Ramachandran restraints generated.
    580 Oldfield, 0 Emsley, 580 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1160 Ramachandran restraints generated.
    580 Oldfield, 0 Emsley, 580 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  150 residues out of total 570 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 140
  time to evaluate  : 0.542 
Fit side-chains
   revert: symmetry clash
REVERT: A  228 ARG cc_start: 0.9187 (ttt-90) cc_final: 0.8901 (ttt-90)
REVERT: B  221 GLU cc_start: 0.8552 (mp0) cc_final: 0.8242 (mp0)
REVERT: C  221 GLU cc_start: 0.8464 (OUTLIER) cc_final: 0.8179 (mp0)
REVERT: D  228 ARG cc_start: 0.9056 (ttt-90) cc_final: 0.8723 (ttt-90)
REVERT: G  208 ARG cc_start: 0.8484 (mtp85) cc_final: 0.7989 (mtm110)
REVERT: G  228 ARG cc_start: 0.9114 (ttt-90) cc_final: 0.8657 (ttt-90)
REVERT: H  211 GLU cc_start: 0.8745 (tt0) cc_final: 0.8453 (tt0)
REVERT: I  228 ARG cc_start: 0.8755 (ttt-90) cc_final: 0.8548 (ttp80)
REVERT: J  220 ARG cc_start: 0.8274 (ptt180) cc_final: 0.6562 (mmm160)
  outliers start: 10
  outliers final: 6
  residues processed: 148
  average time/residue: 2.0498
  time to fit residues: 310.0918
Evaluate side-chains
  147 residues out of total 570 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 140
  time to evaluate  : 0.569 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  193 THR
Chi-restraints excluded: chain A residue  214 CYS
Chi-restraints excluded: chain C residue  221 GLU
Chi-restraints excluded: chain D residue  192 THR
Chi-restraints excluded: chain G residue  197 ASN
Chi-restraints excluded: chain I residue  208 ARG
Chi-restraints excluded: chain J residue  192 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 60
   random chunks:
   chunk 2 optimal weight:    2.9990
   chunk 41 optimal weight:    4.9990
   chunk 18 optimal weight:    9.9990
   chunk 27 optimal weight:    0.3980
   chunk 50 optimal weight:    1.9990
   chunk 58 optimal weight:    0.7980
   chunk 59 optimal weight:    3.9990
   chunk 3 optimal weight:    1.9990
   chunk 34 optimal weight:    0.3980
   chunk 12 optimal weight:    0.9990
   chunk 49 optimal weight:    2.9990
   overall best weight:    0.9184

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

Flipped N/Q/H residues before XYZ refinement:
E 212 GLN
F 172 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4090 r_free = 0.4090 target = 0.131049 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3814 r_free = 0.3814 target = 0.111892 restraints weight = 5232.436|
|-----------------------------------------------------------------------------|
r_work (start): 0.3804 rms_B_bonded: 2.19
r_work: 0.3652 rms_B_bonded: 2.25 restraints_weight: 0.5000
r_work: 0.3508 rms_B_bonded: 3.75 restraints_weight: 0.2500
r_work (final): 0.3508
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8397
moved from start:          0.3039

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028   4980  Z= 0.207
  Angle     :  0.572   7.097   6710  Z= 0.333
  Chirality :  0.047   0.177    760
  Planarity :  0.003   0.045    880
  Dihedral  :  5.869  25.747    650
  Min Nonbonded Distance : 2.625

Molprobity Statistics.
  All-atom Clashscore : 10.13
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 10.17 %
    Favored  : 89.83 %
  Rotamer:
    Outliers :  1.75 %
    Allowed  : 30.70 %
    Favored  : 67.54 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -3.69 (0.28), residues: 580
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.81 (0.22), residues: 580

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.002   0.000   HIS F 177 
 PHE   0.005   0.001   PHE F 175 
 TYR   0.010   0.001   TYR G 226 
 ARG   0.010   0.001   ARG F 228 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 5965.15 seconds
wall clock time: 105 minutes 55.65 seconds (6355.65 seconds total)