Starting phenix.real_space_refine
on Fri Aug 22 18:04:38 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8bms_16124/08_2025/8bms_16124.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8bms_16124/08_2025/8bms_16124.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.6
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8bms_16124/08_2025/8bms_16124.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8bms_16124/08_2025/8bms_16124.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8bms_16124/08_2025/8bms_16124.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8bms_16124/08_2025/8bms_16124.cif"
  }
  resolution = 2.6
  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=   0.000 sd=   0.096
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: 6
    Type Number    sf(0)   Gaussians
     P       6      5.49       5
     Mg      2      5.21       5
     S      26      5.16       5
     C    4173      2.51       5
     N    1080      2.21       5
     O    1283      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 4 residue(s): 0.00s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 6570
  Number of models: 1
  Model: ""
    Number of chains: 8
    Chain: "A"
      Number of atoms: 2133
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 278, 2133
          Classifications: {'peptide': 278}
          Link IDs: {'PTRANS': 13, 'TRANS': 264}
          Chain breaks: 1
    Chain: "B"
      Number of atoms: 2183
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 281, 2183
          Classifications: {'peptide': 281}
          Link IDs: {'PTRANS': 14, 'TRANS': 266}
    Chain: "C"
      Number of atoms: 2118
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 263, 2118
          Classifications: {'peptide': 263}
          Link IDs: {'PTRANS': 9, 'TRANS': 253}
    Chain: "A"
      Number of atoms: 32
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 32
          Unusual residues: {' MG': 1, 'ATP': 1}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
    Chain: "B"
      Number of atoms: 32
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 32
          Unusual residues: {' MG': 1, 'ATP': 1}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
    Chain: "A"
      Number of atoms: 35
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 35, 35
          Classifications: {'water': 35}
          Link IDs: {None: 34}
    Chain: "B"
      Number of atoms: 28
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 28, 28
          Classifications: {'water': 28}
          Link IDs: {None: 27}
    Chain: "C"
      Number of atoms: 9
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 9, 9
          Classifications: {'water': 9}
          Link IDs: {None: 8}
  Time building chain proxies: 1.37, per 1000 atoms: 0.21
  Number of scatterers: 6570
  At special positions: 0
  Unit cell: (72.732, 75.24, 122.056, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 6
    Type Number    sf(0)
     S      26     16.00
     P       6     15.00
     Mg      2     11.99
     O    1283      8.00
     N    1080      7.00
     C    4173      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 0.45
  Conformation dependent library (CDL) restraints added in 346.8 milliseconds
  
  Enol-peptide restraints added in 715.3 nanoseconds
  

  1628 Ramachandran restraints generated.
    814 Oldfield, 0 Emsley, 814 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1528

  Finding SS restraints...
    Secondary structure from input PDB file:
      37 helices and 4 sheets defined
      58.3% alpha, 11.7% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.19
  Creating SS restraints...
    Processing helix  chain 'A' and resid 45 through 54
    Processing helix  chain 'A' and resid 78 through 84
      removed outlier: 3.555A  pdb=" N   GLU A  84 " --> pdb=" O   TRP A  80 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 92 through 96
    Processing helix  chain 'A' and resid 101 through 113
      removed outlier: 4.453A  pdb=" N   GLY A 109 " --> pdb=" O   ASP A 105 " (cutoff:3.500A)
      removed outlier: 4.390A  pdb=" N   LEU A 110 " --> pdb=" O   VAL A 106 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 116 through 131
      removed outlier: 3.815A  pdb=" N   LYS A 122 " --> pdb=" O   PRO A 118 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 133 through 137
      removed outlier: 3.937A  pdb=" N   ALA A 137 " --> pdb=" O   ALA A 134 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 145 through 159
      removed outlier: 3.537A  pdb=" N   ILE A 157 " --> pdb=" O   ALA A 153 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 175 through 194
    Processing helix  chain 'A' and resid 203 through 209
      removed outlier: 3.605A  pdb=" N   GLY A 209 " --> pdb=" O   GLU A 205 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 226 through 231
    Processing helix  chain 'A' and resid 233 through 240
    Processing helix  chain 'A' and resid 245 through 257
    Processing helix  chain 'A' and resid 267 through 281
      removed outlier: 3.535A  pdb=" N   LYS A 281 " --> pdb=" O   GLN A 277 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 45 through 54
      removed outlier: 3.742A  pdb=" N   ASN B  54 " --> pdb=" O   MET B  50 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 80 through 86
    Processing helix  chain 'B' and resid 93 through 97
    Processing helix  chain 'B' and resid 102 through 114
      removed outlier: 4.464A  pdb=" N   GLY B 110 " --> pdb=" O   ASP B 106 " (cutoff:3.500A)
      Proline residue:  B 111  - end of helix
    Processing helix  chain 'B' and resid 117 through 132
    Processing helix  chain 'B' and resid 135 through 141
      removed outlier: 3.721A  pdb=" N   ILE B 139 " --> pdb=" O   ASP B 136 " (cutoff:3.500A)
      removed outlier: 4.166A  pdb=" N   GLU B 140 " --> pdb=" O   ASP B 137 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 147 through 161
    Processing helix  chain 'B' and resid 177 through 193
    Processing helix  chain 'B' and resid 204 through 212
      removed outlier: 3.515A  pdb=" N   VAL B 208 " --> pdb=" O   ASN B 204 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 228 through 233
    Processing helix  chain 'B' and resid 235 through 242
    Processing helix  chain 'B' and resid 247 through 260
    Processing helix  chain 'B' and resid 269 through 282
    Processing helix  chain 'C' and resid 14 through 19
      removed outlier: 3.884A  pdb=" N   ARG C  18 " --> pdb=" O   THR C  14 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 20 through 36
      removed outlier: 3.675A  pdb=" N   PHE C  36 " --> pdb=" O   ILE C  32 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 40 through 57
    Processing helix  chain 'C' and resid 61 through 87
      Proline residue:  C  71  - end of helix
    Processing helix  chain 'C' and resid 102 through 130
    Processing helix  chain 'C' and resid 131 through 143
    Processing helix  chain 'C' and resid 144 through 148
    Processing helix  chain 'C' and resid 152 through 184
      removed outlier: 4.165A  pdb=" N   VAL C 167 " --> pdb=" O   ALA C 163 " (cutoff:3.500A)
      Proline residue:  C 168  - end of helix
      removed outlier: 3.608A  pdb=" N   ARG C 184 " --> pdb=" O   ALA C 180 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 192 through 201
    Processing helix  chain 'C' and resid 203 through 225
      removed outlier: 3.558A  pdb=" N   SER C 219 " --> pdb=" O   ALA C 215 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 245 through 261
      removed outlier: 3.887A  pdb=" N   VAL C 249 " --> pdb=" O   ASP C 245 " (cutoff:3.500A)
      removed outlier: 3.547A  pdb=" N   LEU C 255 " --> pdb=" O   TYR C 251 " (cutoff:3.500A)
      removed outlier: 3.707A  pdb=" N   THR C 256 " --> pdb=" O   CYS C 252 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 23 through 30
      removed outlier: 5.636A  pdb=" N   SER A  24 " --> pdb=" O   VAL A  11 " (cutoff:3.500A)
      removed outlier: 7.475A  pdb=" N   VAL A  11 " --> pdb=" O   SER A  24 " (cutoff:3.500A)
      removed outlier: 7.390A  pdb=" N   PHE A  28 " --> pdb=" O   SER A   7 " (cutoff:3.500A)
      removed outlier: 5.130A  pdb=" N   SER A   7 " --> pdb=" O   PHE A  28 " (cutoff:3.500A)
      removed outlier: 7.616A  pdb=" N   ILE A  30 " --> pdb=" O   ILE A   5 " (cutoff:3.500A)
      removed outlier: 5.945A  pdb=" N   ILE A   5 " --> pdb=" O   ILE A  30 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 86 through 89
      removed outlier: 6.668A  pdb=" N   THR A  36 " --> pdb=" O   SER A 199 " (cutoff:3.500A)
      removed outlier: 6.525A  pdb=" N   ASP A 217 " --> pdb=" O   LEU A 221 " (cutoff:3.500A)
      removed outlier: 5.172A  pdb=" N   LEU A 221 " --> pdb=" O   ASP A 217 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'B' and resid 20 through 30
      removed outlier: 6.150A  pdb=" N   TYR B  10 " --> pdb=" O   GLY B  22 " (cutoff:3.500A)
      removed outlier: 4.168A  pdb=" N   ASP B  24 " --> pdb=" O   VAL B   8 " (cutoff:3.500A)
      removed outlier: 6.351A  pdb=" N   VAL B   8 " --> pdb=" O   ASP B  24 " (cutoff:3.500A)
      removed outlier: 6.122A  pdb=" N   LEU B  26 " --> pdb=" O   GLU B   6 " (cutoff:3.500A)
      removed outlier: 3.907A  pdb=" N   GLU B   6 " --> pdb=" O   LEU B  26 " (cutoff:3.500A)
      removed outlier: 6.597A  pdb=" N   PHE B  28 " --> pdb=" O   LYS B   4 " (cutoff:3.500A)
      removed outlier: 4.470A  pdb=" N   LYS B   4 " --> pdb=" O   PHE B  28 " (cutoff:3.500A)
      removed outlier: 4.199A  pdb=" N   VAL B   8 " --> pdb=" O   SER B  61 " (cutoff:3.500A)
      removed outlier: 6.549A  pdb=" N   SER B  61 " --> pdb=" O   VAL B   8 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'B' and resid 87 through 90
      removed outlier: 6.373A  pdb=" N   SER B  88 " --> pdb=" O   CYS B 168 " (cutoff:3.500A)
      removed outlier: 7.763A  pdb=" N   ASP B 170 " --> pdb=" O   SER B  88 " (cutoff:3.500A)
      removed outlier: 6.993A  pdb=" N   ALA B  90 " --> pdb=" O   ASP B 170 " (cutoff:3.500A)
      removed outlier: 6.165A  pdb=" N   ILE B 167 " --> pdb=" O   ILE B 199 " (cutoff:3.500A)
      removed outlier: 7.507A  pdb=" N   VAL B 201 " --> pdb=" O   ILE B 167 " (cutoff:3.500A)
      removed outlier: 6.556A  pdb=" N   LEU B 169 " --> pdb=" O   VAL B 201 " (cutoff:3.500A)
      removed outlier: 6.268A  pdb=" N   PHE B  35 " --> pdb=" O   ASP B 214 " (cutoff:3.500A)
      removed outlier: 7.695A  pdb=" N   LEU B 216 " --> pdb=" O   PHE B  35 " (cutoff:3.500A)
      removed outlier: 6.311A  pdb=" N   ALA B  37 " --> pdb=" O   LEU B 216 " (cutoff:3.500A)
      removed outlier: 7.454A  pdb=" N   LEU B 218 " --> pdb=" O   ALA B  37 " (cutoff:3.500A)
      removed outlier: 6.828A  pdb=" N   VAL B  39 " --> pdb=" O   LEU B 218 " (cutoff:3.500A)
      removed outlier: 3.565A  pdb=" N   LYS B 225 " --> pdb=" O   ALA B 217 " (cutoff:3.500A)
      removed outlier: 6.626A  pdb=" N   GLU B 219 " --> pdb=" O   LEU B 223 " (cutoff:3.500A)
      removed outlier: 5.251A  pdb=" N   LEU B 223 " --> pdb=" O   GLU B 219 " (cutoff:3.500A)

    348 hydrogen bonds defined for protein.
    1002 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: 0.90

  Time building geometry restraints manager: 0.63 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: 2078
        1.34 -     1.46: 1013
        1.46 -     1.57: 3479
        1.57 -     1.69: 10
        1.69 -     1.81: 50
  Bond restraints: 6630
  Sorted by residual:
  bond pdb=" CB  ASN B   7 "
       pdb=" CG  ASN B   7 "
    ideal  model  delta    sigma   weight residual
    1.516  1.550 -0.034 2.50e-02 1.60e+03 1.83e+00
  bond pdb=" CG1 ILE C  49 "
       pdb=" CD1 ILE C  49 "
    ideal  model  delta    sigma   weight residual
    1.513  1.465  0.048 3.90e-02 6.57e+02 1.51e+00
  bond pdb=" CA  ASN B   7 "
       pdb=" CB  ASN B   7 "
    ideal  model  delta    sigma   weight residual
    1.529  1.542 -0.013 1.58e-02 4.01e+03 6.59e-01
  bond pdb=" C   VAL C 201 "
       pdb=" N   PRO C 202 "
    ideal  model  delta    sigma   weight residual
    1.337  1.344 -0.007 9.80e-03 1.04e+04 5.69e-01
  bond pdb=" CG1 ILE A  88 "
       pdb=" CD1 ILE A  88 "
    ideal  model  delta    sigma   weight residual
    1.513  1.484  0.029 3.90e-02 6.57e+02 5.60e-01
  ... (remaining 6625 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.47: 8807
        1.47 -     2.93: 144
        2.93 -     4.40: 28
        4.40 -     5.87: 12
        5.87 -     7.33: 3
  Bond angle restraints: 8994
  Sorted by residual:
  angle pdb=" CA  MET C 118 "
        pdb=" CB  MET C 118 "
        pdb=" CG  MET C 118 "
      ideal   model   delta    sigma   weight residual
     114.10  108.83    5.27 2.00e+00 2.50e-01 6.95e+00
  angle pdb=" CA  ASN B   7 "
        pdb=" CB  ASN B   7 "
        pdb=" CG  ASN B   7 "
      ideal   model   delta    sigma   weight residual
     112.60  114.79   -2.19 1.00e+00 1.00e+00 4.82e+00
  angle pdb=" N   VAL C 201 "
        pdb=" CA  VAL C 201 "
        pdb=" C   VAL C 201 "
      ideal   model   delta    sigma   weight residual
     108.88  113.61   -4.73 2.16e+00 2.14e-01 4.79e+00
  angle pdb=" CA  VAL C 201 "
        pdb=" C   VAL C 201 "
        pdb=" N   PRO C 202 "
      ideal   model   delta    sigma   weight residual
     118.88  122.22   -3.34 1.54e+00 4.22e-01 4.70e+00
  angle pdb=" N   PHE A 231 "
        pdb=" CA  PHE A 231 "
        pdb=" C   PHE A 231 "
      ideal   model   delta    sigma   weight residual
     109.81  114.54   -4.73 2.21e+00 2.05e-01 4.58e+00
  ... (remaining 8989 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.47: 3608
       17.47 -    34.94: 311
       34.94 -    52.41: 77
       52.41 -    69.88: 13
       69.88 -    87.35: 10
  Dihedral angle restraints: 4019
    sinusoidal: 1654
      harmonic: 2365
  Sorted by residual:
  dihedral pdb=" CA  ARG B  84 "
           pdb=" C   ARG B  84 "
           pdb=" N   ARG B  85 "
           pdb=" CA  ARG B  85 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  162.84   17.16     0      5.00e+00 4.00e-02 1.18e+01
  dihedral pdb=" CG  ARG C 182 "
           pdb=" CD  ARG C 182 "
           pdb=" NE  ARG C 182 "
           pdb=" CZ  ARG C 182 "
      ideal   model   delta sinusoidal    sigma   weight residual
     180.00  137.23   42.77     2      1.50e+01 4.44e-03 9.84e+00
  dihedral pdb=" CB  GLU B  32 "
           pdb=" CG  GLU B  32 "
           pdb=" CD  GLU B  32 "
           pdb=" OE1 GLU B  32 "
      ideal   model   delta sinusoidal    sigma   weight residual
       0.00   84.98  -84.98     1      3.00e+01 1.11e-03 9.73e+00
  ... (remaining 4016 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.029: 644
       0.029 -    0.059: 225
       0.059 -    0.088: 98
       0.088 -    0.117: 55
       0.117 -    0.147: 12
  Chirality restraints: 1034
  Sorted by residual:
  chirality pdb=" CA  ILE B 167 "
            pdb=" N   ILE B 167 "
            pdb=" C   ILE B 167 "
            pdb=" CB  ILE B 167 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.58   -0.15 2.00e-01 2.50e+01 5.38e-01
  chirality pdb=" CA  ILE A 200 "
            pdb=" N   ILE A 200 "
            pdb=" C   ILE A 200 "
            pdb=" CB  ILE A 200 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.58   -0.14 2.00e-01 2.50e+01 5.12e-01
  chirality pdb=" CA  MET C 118 "
            pdb=" N   MET C 118 "
            pdb=" C   MET C 118 "
            pdb=" CB  MET C 118 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.37    0.14 2.00e-01 2.50e+01 5.04e-01
  ... (remaining 1031 not shown)

  Planarity restraints: 1127
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   PHE A 231 "   -0.038 5.00e-02 4.00e+02   5.72e-02 5.24e+00
        pdb=" N   PRO A 232 "    0.099 5.00e-02 4.00e+02
        pdb=" CA  PRO A 232 "   -0.029 5.00e-02 4.00e+02
        pdb=" CD  PRO A 232 "   -0.032 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   GLY B 110 "   -0.028 5.00e-02 4.00e+02   4.22e-02 2.85e+00
        pdb=" N   PRO B 111 "    0.073 5.00e-02 4.00e+02
        pdb=" CA  PRO B 111 "   -0.022 5.00e-02 4.00e+02
        pdb=" CD  PRO B 111 "   -0.024 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   THR B  72 "    0.025 5.00e-02 4.00e+02   3.84e-02 2.36e+00
        pdb=" N   PRO B  73 "   -0.066 5.00e-02 4.00e+02
        pdb=" CA  PRO B  73 "    0.019 5.00e-02 4.00e+02
        pdb=" CD  PRO B  73 "    0.022 5.00e-02 4.00e+02
  ... (remaining 1124 not shown)

  Histogram of nonbonded interaction distances:
        1.96 -     2.55: 54
        2.55 -     3.13: 5081
        3.13 -     3.72: 10515
        3.72 -     4.31: 15344
        4.31 -     4.90: 25482
  Nonbonded interactions: 56476
  Sorted by model distance:
  nonbonded pdb=" O2B ATP A 301 "
            pdb="MG    MG A 302 "
     model   vdw
     1.956 2.170
  nonbonded pdb=" OG  SER B  47 "
            pdb="MG    MG B 302 "
     model   vdw
     1.958 2.170
  nonbonded pdb=" OE1 GLN A  91 "
            pdb="MG    MG A 302 "
     model   vdw
     1.991 2.170
  nonbonded pdb=" OE1 GLN B  92 "
            pdb="MG    MG B 302 "
     model   vdw
     2.028 2.170
  nonbonded pdb=" OG  SER A  47 "
            pdb="MG    MG A 302 "
     model   vdw
     2.043 2.170
  ... (remaining 56471 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
========== WARNING! ============

  No NCS relation were found !!!

================================

Found NCS groups:
  found none.
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:             3.240
  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:          0.060
  Check model and map are aligned:         0.010
  Set scattering table:                    0.010
  Process input model:                     6.560
  Find NCS groups from input model:        0.040
  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:6.060
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   15.990
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8121
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.048   6630  Z= 0.115
  Angle     :  0.522   7.334   8994  Z= 0.270
  Chirality :  0.041   0.147   1034
  Planarity :  0.004   0.057   1127
  Dihedral  : 14.825  87.345   2491
  Min Nonbonded Distance : 1.956

Molprobity Statistics.
  All-atom Clashscore : 6.19
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.21 %
    Favored  : 97.79 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.00 %
    Favored  : 100.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.83 (0.29), residues: 814
  helix:  1.57 (0.25), residues: 452
  sheet: -0.80 (0.52), residues: 74
  loop : -0.66 (0.35), residues: 288

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B 181 
 TYR   0.008   0.001   TYR B 162 
 PHE   0.011   0.001   PHE C  50 
 TRP   0.009   0.001   TRP B 128 
 HIS   0.002   0.000   HIS A  10 

Details of bonding type rmsd
  covalent geometry    : bond        0.00270 ( 6630)
  covalent geometry    : angle       0.52218 ( 8994)
  hydrogen bonds       : bond        0.14816 (  348)
  hydrogen bonds       : angle       5.51961 ( 1002)

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

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

  1628 Ramachandran restraints generated.
    814 Oldfield, 0 Emsley, 814 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1628 Ramachandran restraints generated.
    814 Oldfield, 0 Emsley, 814 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  114 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 114
  time to evaluate  : 0.274 
Fit side-chains
REVERT: A  180 GLU cc_start: 0.7829 (tt0) cc_final: 0.7373 (tt0)
REVERT: A  184 ASP cc_start: 0.8172 (m-30) cc_final: 0.7873 (m-30)
REVERT: C  106 LEU cc_start: 0.5436 (tt) cc_final: 0.4988 (tm)
  outliers start: 0
  outliers final: 1
  residues processed: 114
  average time/residue: 0.5017
  time to fit residues: 60.0081
Evaluate side-chains
  91 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 90
  time to evaluate  : 0.251 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue  189 ASN
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 81
   random chunks:
   chunk 49 optimal weight:    1.9990
   chunk 53 optimal weight:    1.9990
   chunk 5 optimal weight:    0.4980
   chunk 33 optimal weight:    2.9990
   chunk 65 optimal weight:    6.9990
   chunk 62 optimal weight:    6.9990
   chunk 51 optimal weight:    0.8980
   chunk 38 optimal weight:    2.9990
   chunk 61 optimal weight:    0.6980
   chunk 45 optimal weight:    0.5980
   chunk 74 optimal weight:    1.9990
   overall best weight:    0.9382

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

Flipped N/Q/H residues before XYZ refinement:
A  10 HIS
B 243 HIS
C 181 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3819 r_free = 0.3819 target = 0.160403 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3436 r_free = 0.3436 target = 0.121957 restraints weight = 6386.711|
|-----------------------------------------------------------------------------|
r_work (start): 0.3396 rms_B_bonded: 1.63
r_work: 0.3216 rms_B_bonded: 2.31 restraints_weight: 0.5000
r_work: 0.3085 rms_B_bonded: 3.76 restraints_weight: 0.2500
r_work (final): 0.3085
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8160
moved from start:          0.1040

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.061   6630  Z= 0.187
  Angle     :  0.594   7.758   8994  Z= 0.302
  Chirality :  0.044   0.142   1034
  Planarity :  0.005   0.062   1127
  Dihedral  : 10.141  86.232    941
  Min Nonbonded Distance : 1.882

Molprobity Statistics.
  All-atom Clashscore : 5.43
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.21 %
    Favored  : 97.79 %
  Rotamer:
    Outliers :  2.29 %
    Allowed  :  8.14 %
    Favored  : 89.57 %
  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 aren not related in a simple way.
  whole:  0.95 (0.29), residues: 814
  helix:  1.59 (0.24), residues: 448
  sheet: -0.56 (0.54), residues: 73
  loop : -0.48 (0.34), residues: 293

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B 181 
 TYR   0.014   0.001   TYR C 251 
 PHE   0.014   0.001   PHE B  93 
 TRP   0.013   0.001   TRP A  80 
 HIS   0.007   0.001   HIS A  10 

Details of bonding type rmsd
  covalent geometry    : bond        0.00460 ( 6630)
  covalent geometry    : angle       0.59361 ( 8994)
  hydrogen bonds       : bond        0.04354 (  348)
  hydrogen bonds       : angle       4.55908 ( 1002)

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

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

  1628 Ramachandran restraints generated.
    814 Oldfield, 0 Emsley, 814 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1628 Ramachandran restraints generated.
    814 Oldfield, 0 Emsley, 814 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  111 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 95
  time to evaluate  : 0.251 
Fit side-chains
REVERT: A   62 LEU cc_start: 0.7997 (OUTLIER) cc_final: 0.7753 (mm)
REVERT: A  180 GLU cc_start: 0.8131 (tt0) cc_final: 0.7610 (tt0)
REVERT: A  184 ASP cc_start: 0.8260 (m-30) cc_final: 0.7891 (m-30)
REVERT: A  264 GLU cc_start: 0.7389 (OUTLIER) cc_final: 0.7157 (mt-10)
REVERT: B    4 LYS cc_start: 0.8171 (ttpt) cc_final: 0.7964 (ttpt)
REVERT: B   82 ASP cc_start: 0.7581 (t0) cc_final: 0.7121 (m-30)
REVERT: C  208 PHE cc_start: 0.6465 (OUTLIER) cc_final: 0.5994 (t80)
  outliers start: 16
  outliers final: 5
  residues processed: 102
  average time/residue: 0.5400
  time to fit residues: 57.9582
Evaluate side-chains
  99 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 91
  time to evaluate  : 0.256 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   62 LEU
Chi-restraints excluded: chain A residue  264 GLU
Chi-restraints excluded: chain B residue    6 GLU
Chi-restraints excluded: chain B residue   94 SER
Chi-restraints excluded: chain B residue  136 ASP
Chi-restraints excluded: chain B residue  167 ILE
Chi-restraints excluded: chain C residue  193 LEU
Chi-restraints excluded: chain C residue  208 PHE
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 81
   random chunks:
   chunk 56 optimal weight:    0.9990
   chunk 68 optimal weight:    1.9990
   chunk 14 optimal weight:    0.9980
   chunk 12 optimal weight:    0.6980
   chunk 19 optimal weight:    1.9990
   chunk 21 optimal weight:    1.9990
   chunk 43 optimal weight:    0.9990
   chunk 53 optimal weight:    4.9990
   chunk 27 optimal weight:    0.8980
   chunk 32 optimal weight:    0.2980
   chunk 45 optimal weight:    2.9990
   overall best weight:    0.7782

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

Flipped N/Q/H residues before XYZ refinement:
A  10 HIS
B  77 ASN
B 226 HIS
B 243 HIS
C 189 ASN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3824 r_free = 0.3824 target = 0.160819 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3440 r_free = 0.3440 target = 0.122258 restraints weight = 6341.032|
|-----------------------------------------------------------------------------|
r_work (start): 0.3402 rms_B_bonded: 1.61
r_work: 0.3222 rms_B_bonded: 2.31 restraints_weight: 0.5000
r_work: 0.3093 rms_B_bonded: 3.74 restraints_weight: 0.2500
r_work (final): 0.3093
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8154
moved from start:          0.1119

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.055   6630  Z= 0.161
  Angle     :  0.554   7.371   8994  Z= 0.282
  Chirality :  0.043   0.147   1034
  Planarity :  0.005   0.060   1127
  Dihedral  :  9.965  86.055    939
  Min Nonbonded Distance : 1.885

Molprobity Statistics.
  All-atom Clashscore : 5.65
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.09 %
    Favored  : 97.91 %
  Rotamer:
    Outliers :  2.71 %
    Allowed  :  9.86 %
    Favored  : 87.43 %
  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 aren not related in a simple way.
  whole:  1.07 (0.29), residues: 814
  helix:  1.68 (0.24), residues: 447
  sheet: -0.56 (0.54), residues: 73
  loop : -0.41 (0.34), residues: 294

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B 181 
 TYR   0.011   0.001   TYR C 251 
 PHE   0.013   0.001   PHE A 231 
 TRP   0.012   0.001   TRP B 128 
 HIS   0.006   0.001   HIS A  10 

Details of bonding type rmsd
  covalent geometry    : bond        0.00398 ( 6630)
  covalent geometry    : angle       0.55356 ( 8994)
  hydrogen bonds       : bond        0.03998 (  348)
  hydrogen bonds       : angle       4.41430 ( 1002)

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

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

  1628 Ramachandran restraints generated.
    814 Oldfield, 0 Emsley, 814 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1628 Ramachandran restraints generated.
    814 Oldfield, 0 Emsley, 814 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  111 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 92
  time to evaluate  : 0.280 
Fit side-chains
REVERT: A   62 LEU cc_start: 0.8070 (OUTLIER) cc_final: 0.7818 (mm)
REVERT: A  173 MET cc_start: 0.8937 (mtm) cc_final: 0.8683 (mtt)
REVERT: A  180 GLU cc_start: 0.8132 (tt0) cc_final: 0.7676 (tt0)
REVERT: A  184 ASP cc_start: 0.8226 (m-30) cc_final: 0.7890 (m-30)
REVERT: A  264 GLU cc_start: 0.7396 (OUTLIER) cc_final: 0.7167 (mt-10)
REVERT: B    4 LYS cc_start: 0.8202 (ttpt) cc_final: 0.7997 (ttpt)
REVERT: B   82 ASP cc_start: 0.7560 (t0) cc_final: 0.7106 (m-30)
REVERT: C   52 LEU cc_start: 0.6998 (OUTLIER) cc_final: 0.6658 (mt)
REVERT: C  208 PHE cc_start: 0.6482 (OUTLIER) cc_final: 0.6014 (t80)
REVERT: C  231 GLU cc_start: 0.7780 (OUTLIER) cc_final: 0.7287 (tm-30)
  outliers start: 19
  outliers final: 9
  residues processed: 98
  average time/residue: 0.5795
  time to fit residues: 59.7628
Evaluate side-chains
  102 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 88
  time to evaluate  : 0.261 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    6 ILE
Chi-restraints excluded: chain A residue   62 LEU
Chi-restraints excluded: chain A residue   66 SER
Chi-restraints excluded: chain A residue  236 MET
Chi-restraints excluded: chain A residue  264 GLU
Chi-restraints excluded: chain B residue    6 GLU
Chi-restraints excluded: chain B residue   94 SER
Chi-restraints excluded: chain B residue  136 ASP
Chi-restraints excluded: chain B residue  167 ILE
Chi-restraints excluded: chain C residue   52 LEU
Chi-restraints excluded: chain C residue  193 LEU
Chi-restraints excluded: chain C residue  208 PHE
Chi-restraints excluded: chain C residue  231 GLU
Chi-restraints excluded: chain C residue  259 MET
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 81
   random chunks:
   chunk 46 optimal weight:    1.9990
   chunk 43 optimal weight:    0.7980
   chunk 24 optimal weight:    0.9980
   chunk 3 optimal weight:    2.9990
   chunk 26 optimal weight:    0.8980
   chunk 34 optimal weight:    0.3980
   chunk 18 optimal weight:    0.9980
   chunk 13 optimal weight:    0.0770
   chunk 19 optimal weight:    0.9990
   chunk 45 optimal weight:    0.6980
   chunk 15 optimal weight:    0.5980
   overall best weight:    0.5138

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

Flipped N/Q/H residues before XYZ refinement:
A  10 HIS
B 243 HIS
C 189 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3829 r_free = 0.3829 target = 0.161582 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3454 r_free = 0.3454 target = 0.123556 restraints weight = 6466.603|
|-----------------------------------------------------------------------------|
r_work (start): 0.3417 rms_B_bonded: 1.64
r_work: 0.3242 rms_B_bonded: 2.31 restraints_weight: 0.5000
r_work: 0.3114 rms_B_bonded: 3.74 restraints_weight: 0.2500
r_work (final): 0.3114
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8129
moved from start:          0.1236

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041   6630  Z= 0.126
  Angle     :  0.512   7.495   8994  Z= 0.262
  Chirality :  0.042   0.143   1034
  Planarity :  0.005   0.061   1127
  Dihedral  :  9.705  85.943    939
  Min Nonbonded Distance : 1.878

Molprobity Statistics.
  All-atom Clashscore : 5.04
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.72 %
    Favored  : 98.28 %
  Rotamer:
    Outliers :  2.43 %
    Allowed  : 11.86 %
    Favored  : 85.71 %
  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 aren not related in a simple way.
  whole:  1.19 (0.29), residues: 814
  helix:  1.83 (0.24), residues: 454
  sheet: -0.71 (0.54), residues: 74
  loop : -0.44 (0.36), residues: 286

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG B 181 
 TYR   0.010   0.001   TYR C 251 
 PHE   0.010   0.001   PHE A 231 
 TRP   0.012   0.001   TRP B 128 
 HIS   0.006   0.001   HIS A  10 

Details of bonding type rmsd
  covalent geometry    : bond        0.00303 ( 6630)
  covalent geometry    : angle       0.51153 ( 8994)
  hydrogen bonds       : bond        0.03481 (  348)
  hydrogen bonds       : angle       4.26130 ( 1002)

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

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

  1628 Ramachandran restraints generated.
    814 Oldfield, 0 Emsley, 814 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1628 Ramachandran restraints generated.
    814 Oldfield, 0 Emsley, 814 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  110 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 93
  time to evaluate  : 0.235 
Fit side-chains
REVERT: A   62 LEU cc_start: 0.8098 (OUTLIER) cc_final: 0.7831 (mm)
REVERT: A  180 GLU cc_start: 0.8134 (tt0) cc_final: 0.7657 (tt0)
REVERT: A  184 ASP cc_start: 0.8239 (m-30) cc_final: 0.7912 (m-30)
REVERT: A  218 ASP cc_start: 0.8425 (OUTLIER) cc_final: 0.8224 (m-30)
REVERT: A  264 GLU cc_start: 0.7370 (OUTLIER) cc_final: 0.7137 (mt-10)
REVERT: B    4 LYS cc_start: 0.8181 (ttpt) cc_final: 0.7974 (ttpt)
REVERT: B   82 ASP cc_start: 0.7551 (t0) cc_final: 0.7075 (m-30)
REVERT: B  118 GLU cc_start: 0.7371 (mm-30) cc_final: 0.7113 (mp0)
REVERT: C  208 PHE cc_start: 0.6443 (OUTLIER) cc_final: 0.6016 (t80)
REVERT: C  231 GLU cc_start: 0.7785 (OUTLIER) cc_final: 0.7298 (tm-30)
  outliers start: 17
  outliers final: 6
  residues processed: 100
  average time/residue: 0.4998
  time to fit residues: 52.6477
Evaluate side-chains
  99 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 88
  time to evaluate  : 0.291 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    6 ILE
Chi-restraints excluded: chain A residue   62 LEU
Chi-restraints excluded: chain A residue  218 ASP
Chi-restraints excluded: chain A residue  236 MET
Chi-restraints excluded: chain A residue  264 GLU
Chi-restraints excluded: chain B residue   94 SER
Chi-restraints excluded: chain B residue  136 ASP
Chi-restraints excluded: chain B residue  167 ILE
Chi-restraints excluded: chain C residue  193 LEU
Chi-restraints excluded: chain C residue  208 PHE
Chi-restraints excluded: chain C residue  231 GLU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 81
   random chunks:
   chunk 80 optimal weight:    3.9990
   chunk 37 optimal weight:    0.9980
   chunk 0 optimal weight:    3.9990
   chunk 47 optimal weight:    0.6980
   chunk 38 optimal weight:    0.9990
   chunk 76 optimal weight:    2.9990
   chunk 77 optimal weight:    1.9990
   chunk 58 optimal weight:    0.9990
   chunk 23 optimal weight:    0.9980
   chunk 15 optimal weight:    0.8980
   chunk 35 optimal weight:    0.1980
   overall best weight:    0.7580

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

Flipped N/Q/H residues before XYZ refinement:
A  10 HIS
B 243 HIS
C 181 GLN
C 189 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3824 r_free = 0.3824 target = 0.160793 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3442 r_free = 0.3442 target = 0.122425 restraints weight = 6412.639|
|-----------------------------------------------------------------------------|
r_work (start): 0.3402 rms_B_bonded: 1.63
r_work: 0.3226 rms_B_bonded: 2.31 restraints_weight: 0.5000
r_work: 0.3097 rms_B_bonded: 3.73 restraints_weight: 0.2500
r_work (final): 0.3097
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8154
moved from start:          0.1282

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.053   6630  Z= 0.157
  Angle     :  0.547   7.467   8994  Z= 0.277
  Chirality :  0.043   0.147   1034
  Planarity :  0.005   0.062   1127
  Dihedral  :  9.851  85.171    939
  Min Nonbonded Distance : 1.864

Molprobity Statistics.
  All-atom Clashscore : 5.43
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.72 %
    Favored  : 98.28 %
  Rotamer:
    Outliers :  2.86 %
    Allowed  : 12.57 %
    Favored  : 84.57 %
  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 aren not related in a simple way.
  whole:  1.10 (0.29), residues: 814
  helix:  1.75 (0.24), residues: 454
  sheet: -0.73 (0.53), residues: 74
  loop : -0.47 (0.36), residues: 286

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG B 181 
 TYR   0.011   0.001   TYR C 251 
 PHE   0.012   0.001   PHE A 231 
 TRP   0.012   0.001   TRP B 128 
 HIS   0.005   0.001   HIS A  10 

Details of bonding type rmsd
  covalent geometry    : bond        0.00389 ( 6630)
  covalent geometry    : angle       0.54731 ( 8994)
  hydrogen bonds       : bond        0.03735 (  348)
  hydrogen bonds       : angle       4.29969 ( 1002)

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

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

  1628 Ramachandran restraints generated.
    814 Oldfield, 0 Emsley, 814 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1628 Ramachandran restraints generated.
    814 Oldfield, 0 Emsley, 814 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  111 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 91
  time to evaluate  : 0.270 
Fit side-chains
REVERT: A   62 LEU cc_start: 0.8136 (OUTLIER) cc_final: 0.7841 (mm)
REVERT: A  180 GLU cc_start: 0.8143 (tt0) cc_final: 0.7685 (tt0)
REVERT: A  184 ASP cc_start: 0.8228 (m-30) cc_final: 0.7900 (m-30)
REVERT: A  218 ASP cc_start: 0.8448 (OUTLIER) cc_final: 0.8237 (m-30)
REVERT: A  264 GLU cc_start: 0.7383 (OUTLIER) cc_final: 0.7131 (mt-10)
REVERT: B   82 ASP cc_start: 0.7565 (t0) cc_final: 0.7090 (m-30)
REVERT: B  118 GLU cc_start: 0.7395 (mm-30) cc_final: 0.7138 (mp0)
REVERT: C  208 PHE cc_start: 0.6493 (OUTLIER) cc_final: 0.6057 (t80)
REVERT: C  231 GLU cc_start: 0.7782 (OUTLIER) cc_final: 0.7294 (tm-30)
  outliers start: 20
  outliers final: 6
  residues processed: 100
  average time/residue: 0.5899
  time to fit residues: 61.9806
Evaluate side-chains
  103 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 92
  time to evaluate  : 0.271 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    6 ILE
Chi-restraints excluded: chain A residue   62 LEU
Chi-restraints excluded: chain A residue   66 SER
Chi-restraints excluded: chain A residue  218 ASP
Chi-restraints excluded: chain A residue  264 GLU
Chi-restraints excluded: chain B residue    6 GLU
Chi-restraints excluded: chain B residue   94 SER
Chi-restraints excluded: chain B residue  136 ASP
Chi-restraints excluded: chain B residue  167 ILE
Chi-restraints excluded: chain C residue  208 PHE
Chi-restraints excluded: chain C residue  231 GLU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 81
   random chunks:
   chunk 0 optimal weight:    2.9990
   chunk 55 optimal weight:    1.9990
   chunk 49 optimal weight:    0.9980
   chunk 34 optimal weight:    0.8980
   chunk 76 optimal weight:    3.9990
   chunk 52 optimal weight:    3.9990
   chunk 53 optimal weight:    0.8980
   chunk 58 optimal weight:    1.9990
   chunk 48 optimal weight:    0.7980
   chunk 8 optimal weight:    0.9990
   chunk 64 optimal weight:    0.9990
   overall best weight:    0.9182

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

Flipped N/Q/H residues before XYZ refinement:
A  10 HIS
B 243 HIS
C 189 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3816 r_free = 0.3816 target = 0.160274 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3432 r_free = 0.3432 target = 0.121784 restraints weight = 6388.261|
|-----------------------------------------------------------------------------|
r_work (start): 0.3397 rms_B_bonded: 1.54
r_work: 0.3214 rms_B_bonded: 2.29 restraints_weight: 0.5000
r_work: 0.3085 rms_B_bonded: 3.71 restraints_weight: 0.2500
r_work (final): 0.3085
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8162
moved from start:          0.1365

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.060   6630  Z= 0.179
  Angle     :  0.568   7.371   8994  Z= 0.286
  Chirality :  0.044   0.156   1034
  Planarity :  0.005   0.062   1127
  Dihedral  :  9.987  84.603    939
  Min Nonbonded Distance : 1.852

Molprobity Statistics.
  All-atom Clashscore : 5.73
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.97 %
    Favored  : 98.03 %
  Rotamer:
    Outliers :  3.14 %
    Allowed  : 12.71 %
    Favored  : 84.14 %
  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 aren not related in a simple way.
  whole:  1.00 (0.29), residues: 814
  helix:  1.67 (0.24), residues: 455
  sheet: -0.75 (0.54), residues: 74
  loop : -0.52 (0.35), residues: 285

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.000   ARG B 181 
 TYR   0.013   0.001   TYR C 251 
 PHE   0.013   0.001   PHE A 231 
 TRP   0.011   0.001   TRP B 128 
 HIS   0.005   0.001   HIS A  10 

Details of bonding type rmsd
  covalent geometry    : bond        0.00445 ( 6630)
  covalent geometry    : angle       0.56790 ( 8994)
  hydrogen bonds       : bond        0.03895 (  348)
  hydrogen bonds       : angle       4.34123 ( 1002)

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

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

  1628 Ramachandran restraints generated.
    814 Oldfield, 0 Emsley, 814 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1628 Ramachandran restraints generated.
    814 Oldfield, 0 Emsley, 814 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  118 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 96
  time to evaluate  : 0.259 
Fit side-chains
REVERT: A   62 LEU cc_start: 0.8131 (OUTLIER) cc_final: 0.7800 (mm)
REVERT: A   63 ASP cc_start: 0.8063 (p0) cc_final: 0.7862 (p0)
REVERT: A  180 GLU cc_start: 0.8144 (tt0) cc_final: 0.7712 (tt0)
REVERT: A  184 ASP cc_start: 0.8233 (m-30) cc_final: 0.7901 (m-30)
REVERT: A  218 ASP cc_start: 0.8478 (OUTLIER) cc_final: 0.8232 (m-30)
REVERT: A  264 GLU cc_start: 0.7368 (OUTLIER) cc_final: 0.7042 (mt-10)
REVERT: B   82 ASP cc_start: 0.7595 (t0) cc_final: 0.7096 (m-30)
REVERT: B  118 GLU cc_start: 0.7375 (mm-30) cc_final: 0.7085 (mp0)
REVERT: B  120 GLU cc_start: 0.8033 (mt-10) cc_final: 0.7665 (mt-10)
REVERT: B  214 ASP cc_start: 0.7860 (OUTLIER) cc_final: 0.7470 (t70)
REVERT: C   87 MET cc_start: 0.4328 (mtt) cc_final: 0.4044 (pp-130)
REVERT: C  208 PHE cc_start: 0.6467 (OUTLIER) cc_final: 0.6011 (t80)
REVERT: C  231 GLU cc_start: 0.7781 (OUTLIER) cc_final: 0.7238 (tm-30)
  outliers start: 22
  outliers final: 10
  residues processed: 106
  average time/residue: 0.5565
  time to fit residues: 61.9833
Evaluate side-chains
  106 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 90
  time to evaluate  : 0.238 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    6 ILE
Chi-restraints excluded: chain A residue   62 LEU
Chi-restraints excluded: chain A residue   66 SER
Chi-restraints excluded: chain A residue  218 ASP
Chi-restraints excluded: chain A residue  236 MET
Chi-restraints excluded: chain A residue  264 GLU
Chi-restraints excluded: chain B residue    6 GLU
Chi-restraints excluded: chain B residue   94 SER
Chi-restraints excluded: chain B residue  136 ASP
Chi-restraints excluded: chain B residue  163 GLU
Chi-restraints excluded: chain B residue  167 ILE
Chi-restraints excluded: chain B residue  214 ASP
Chi-restraints excluded: chain C residue  193 LEU
Chi-restraints excluded: chain C residue  208 PHE
Chi-restraints excluded: chain C residue  231 GLU
Chi-restraints excluded: chain C residue  260 ILE
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 81
   random chunks:
   chunk 74 optimal weight:    2.9990
   chunk 62 optimal weight:    2.9990
   chunk 4 optimal weight:    0.7980
   chunk 2 optimal weight:    0.6980
   chunk 72 optimal weight:    1.9990
   chunk 46 optimal weight:    1.9990
   chunk 30 optimal weight:    0.9990
   chunk 58 optimal weight:    1.9990
   chunk 33 optimal weight:    0.7980
   chunk 47 optimal weight:    0.7980
   chunk 41 optimal weight:    0.7980
   overall best weight:    0.7780

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

Flipped N/Q/H residues before XYZ refinement:
A  10 HIS
B 243 HIS
C 189 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3820 r_free = 0.3820 target = 0.160745 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3437 r_free = 0.3437 target = 0.122162 restraints weight = 6342.991|
|-----------------------------------------------------------------------------|
r_work (start): 0.3401 rms_B_bonded: 1.58
r_work: 0.3222 rms_B_bonded: 2.29 restraints_weight: 0.5000
r_work: 0.3093 rms_B_bonded: 3.73 restraints_weight: 0.2500
r_work (final): 0.3093
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8154
moved from start:          0.1379

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.058   6630  Z= 0.161
  Angle     :  0.558   7.757   8994  Z= 0.282
  Chirality :  0.044   0.160   1034
  Planarity :  0.005   0.060   1127
  Dihedral  :  9.886  84.610    939
  Min Nonbonded Distance : 1.855

Molprobity Statistics.
  All-atom Clashscore : 5.65
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.09 %
    Favored  : 97.91 %
  Rotamer:
    Outliers :  3.00 %
    Allowed  : 13.43 %
    Favored  : 83.57 %
  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 aren not related in a simple way.
  whole:  1.03 (0.29), residues: 814
  helix:  1.71 (0.24), residues: 455
  sheet: -0.78 (0.53), residues: 74
  loop : -0.53 (0.36), residues: 285

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG B 181 
 TYR   0.012   0.001   TYR C 251 
 PHE   0.012   0.001   PHE A 231 
 TRP   0.012   0.001   TRP B 128 
 HIS   0.006   0.001   HIS A  10 

Details of bonding type rmsd
  covalent geometry    : bond        0.00401 ( 6630)
  covalent geometry    : angle       0.55801 ( 8994)
  hydrogen bonds       : bond        0.03775 (  348)
  hydrogen bonds       : angle       4.34311 ( 1002)

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

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

  1628 Ramachandran restraints generated.
    814 Oldfield, 0 Emsley, 814 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1628 Ramachandran restraints generated.
    814 Oldfield, 0 Emsley, 814 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  110 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 89
  time to evaluate  : 0.306 
Fit side-chains
REVERT: A   62 LEU cc_start: 0.8129 (OUTLIER) cc_final: 0.7806 (mm)
REVERT: A  180 GLU cc_start: 0.8136 (tt0) cc_final: 0.7689 (tt0)
REVERT: A  184 ASP cc_start: 0.8233 (m-30) cc_final: 0.7889 (m-30)
REVERT: A  218 ASP cc_start: 0.8452 (OUTLIER) cc_final: 0.8197 (m-30)
REVERT: A  264 GLU cc_start: 0.7328 (OUTLIER) cc_final: 0.7004 (mt-10)
REVERT: B    6 GLU cc_start: 0.7429 (OUTLIER) cc_final: 0.7141 (pp20)
REVERT: B   82 ASP cc_start: 0.7568 (t0) cc_final: 0.7086 (m-30)
REVERT: B  118 GLU cc_start: 0.7417 (mm-30) cc_final: 0.7128 (mp0)
REVERT: B  214 ASP cc_start: 0.7877 (OUTLIER) cc_final: 0.7506 (t70)
REVERT: C   87 MET cc_start: 0.4124 (mtt) cc_final: 0.3877 (pp-130)
REVERT: C  208 PHE cc_start: 0.6501 (OUTLIER) cc_final: 0.6068 (t80)
REVERT: C  231 GLU cc_start: 0.7772 (OUTLIER) cc_final: 0.7227 (tm-30)
  outliers start: 21
  outliers final: 9
  residues processed: 100
  average time/residue: 0.5684
  time to fit residues: 59.7989
Evaluate side-chains
  103 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 87
  time to evaluate  : 0.180 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    6 ILE
Chi-restraints excluded: chain A residue   62 LEU
Chi-restraints excluded: chain A residue   66 SER
Chi-restraints excluded: chain A residue  218 ASP
Chi-restraints excluded: chain A residue  236 MET
Chi-restraints excluded: chain A residue  264 GLU
Chi-restraints excluded: chain B residue    6 GLU
Chi-restraints excluded: chain B residue   94 SER
Chi-restraints excluded: chain B residue  136 ASP
Chi-restraints excluded: chain B residue  163 GLU
Chi-restraints excluded: chain B residue  167 ILE
Chi-restraints excluded: chain B residue  214 ASP
Chi-restraints excluded: chain C residue  193 LEU
Chi-restraints excluded: chain C residue  205 VAL
Chi-restraints excluded: chain C residue  208 PHE
Chi-restraints excluded: chain C residue  231 GLU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 81
   random chunks:
   chunk 20 optimal weight:    0.0870
   chunk 18 optimal weight:    0.9980
   chunk 26 optimal weight:    0.7980
   chunk 67 optimal weight:    3.9990
   chunk 35 optimal weight:    1.9990
   chunk 19 optimal weight:    0.9980
   chunk 32 optimal weight:    4.9990
   chunk 46 optimal weight:    0.6980
   chunk 15 optimal weight:    0.6980
   chunk 80 optimal weight:    2.9990
   chunk 73 optimal weight:    2.9990
   overall best weight:    0.6558

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

Flipped N/Q/H residues before XYZ refinement:
A  10 HIS
B 243 HIS
C 189 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3828 r_free = 0.3828 target = 0.161493 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3448 r_free = 0.3448 target = 0.122693 restraints weight = 6396.344|
|-----------------------------------------------------------------------------|
r_work (start): 0.3404 rms_B_bonded: 1.66
r_work: 0.3229 rms_B_bonded: 2.32 restraints_weight: 0.5000
r_work: 0.3098 rms_B_bonded: 3.78 restraints_weight: 0.2500
r_work (final): 0.3098
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8145
moved from start:          0.1410

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.049   6630  Z= 0.145
  Angle     :  0.547   9.607   8994  Z= 0.275
  Chirality :  0.043   0.171   1034
  Planarity :  0.005   0.060   1127
  Dihedral  :  9.794  84.788    939
  Min Nonbonded Distance : 1.857

Molprobity Statistics.
  All-atom Clashscore : 5.20
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.97 %
    Favored  : 98.03 %
  Rotamer:
    Outliers :  2.29 %
    Allowed  : 14.29 %
    Favored  : 83.43 %
  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 aren not related in a simple way.
  whole:  1.11 (0.29), residues: 814
  helix:  1.78 (0.24), residues: 454
  sheet: -0.77 (0.53), residues: 74
  loop : -0.49 (0.36), residues: 286

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.000   ARG B 181 
 TYR   0.012   0.001   TYR C 251 
 PHE   0.011   0.001   PHE A 231 
 TRP   0.012   0.001   TRP B 128 
 HIS   0.006   0.001   HIS A  10 

Details of bonding type rmsd
  covalent geometry    : bond        0.00357 ( 6630)
  covalent geometry    : angle       0.54673 ( 8994)
  hydrogen bonds       : bond        0.03597 (  348)
  hydrogen bonds       : angle       4.30653 ( 1002)

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

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

  1628 Ramachandran restraints generated.
    814 Oldfield, 0 Emsley, 814 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1628 Ramachandran restraints generated.
    814 Oldfield, 0 Emsley, 814 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  110 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 94
  time to evaluate  : 0.273 
Fit side-chains
REVERT: A  179 LYS cc_start: 0.8242 (mtmm) cc_final: 0.7756 (mtpp)
REVERT: A  180 GLU cc_start: 0.8147 (tt0) cc_final: 0.7678 (tt0)
REVERT: A  184 ASP cc_start: 0.8233 (m-30) cc_final: 0.7906 (m-30)
REVERT: A  218 ASP cc_start: 0.8469 (OUTLIER) cc_final: 0.8216 (m-30)
REVERT: A  264 GLU cc_start: 0.7321 (OUTLIER) cc_final: 0.7003 (mt-10)
REVERT: B    6 GLU cc_start: 0.7418 (OUTLIER) cc_final: 0.7135 (pp20)
REVERT: B   82 ASP cc_start: 0.7585 (t0) cc_final: 0.7108 (m-30)
REVERT: B  118 GLU cc_start: 0.7396 (mm-30) cc_final: 0.7068 (mp0)
REVERT: B  120 GLU cc_start: 0.7949 (mt-10) cc_final: 0.7575 (mt-10)
REVERT: B  214 ASP cc_start: 0.7866 (OUTLIER) cc_final: 0.7502 (t70)
REVERT: C  208 PHE cc_start: 0.6478 (OUTLIER) cc_final: 0.6043 (t80)
REVERT: C  231 GLU cc_start: 0.7770 (OUTLIER) cc_final: 0.7229 (tm-30)
  outliers start: 16
  outliers final: 9
  residues processed: 101
  average time/residue: 0.5658
  time to fit residues: 60.2445
Evaluate side-chains
  104 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 89
  time to evaluate  : 0.256 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    6 ILE
Chi-restraints excluded: chain A residue   66 SER
Chi-restraints excluded: chain A residue  218 ASP
Chi-restraints excluded: chain A residue  236 MET
Chi-restraints excluded: chain A residue  264 GLU
Chi-restraints excluded: chain B residue    6 GLU
Chi-restraints excluded: chain B residue   94 SER
Chi-restraints excluded: chain B residue  136 ASP
Chi-restraints excluded: chain B residue  163 GLU
Chi-restraints excluded: chain B residue  167 ILE
Chi-restraints excluded: chain B residue  214 ASP
Chi-restraints excluded: chain C residue  193 LEU
Chi-restraints excluded: chain C residue  205 VAL
Chi-restraints excluded: chain C residue  208 PHE
Chi-restraints excluded: chain C residue  231 GLU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 81
   random chunks:
   chunk 60 optimal weight:    6.9990
   chunk 43 optimal weight:    0.9990
   chunk 6 optimal weight:    0.4980
   chunk 57 optimal weight:    0.7980
   chunk 45 optimal weight:    2.9990
   chunk 41 optimal weight:    0.7980
   chunk 76 optimal weight:    3.9990
   chunk 14 optimal weight:    0.5980
   chunk 66 optimal weight:    1.9990
   chunk 11 optimal weight:    0.9980
   chunk 23 optimal weight:    0.9990
   overall best weight:    0.7380

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

Flipped N/Q/H residues before XYZ refinement:
A  10 HIS
B 243 HIS
C 189 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3826 r_free = 0.3826 target = 0.161210 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3442 r_free = 0.3442 target = 0.122443 restraints weight = 6483.280|
|-----------------------------------------------------------------------------|
r_work (start): 0.3397 rms_B_bonded: 1.62
r_work: 0.3221 rms_B_bonded: 2.31 restraints_weight: 0.5000
r_work: 0.3088 rms_B_bonded: 3.79 restraints_weight: 0.2500
r_work (final): 0.3088
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8151
moved from start:          0.1420

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.052   6630  Z= 0.155
  Angle     :  0.543   7.558   8994  Z= 0.276
  Chirality :  0.043   0.168   1034
  Planarity :  0.005   0.061   1127
  Dihedral  :  9.827  84.680    939
  Min Nonbonded Distance : 1.856

Molprobity Statistics.
  All-atom Clashscore : 5.81
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.97 %
    Favored  : 98.03 %
  Rotamer:
    Outliers :  2.29 %
    Allowed  : 14.43 %
    Favored  : 83.29 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.11 (0.29), residues: 814
  helix:  1.77 (0.24), residues: 455
  sheet: -0.66 (0.53), residues: 73
  loop : -0.50 (0.36), residues: 286

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.000   ARG B 181 
 TYR   0.013   0.001   TYR C 251 
 PHE   0.012   0.001   PHE A 231 
 TRP   0.012   0.001   TRP B 128 
 HIS   0.006   0.001   HIS A  10 

Details of bonding type rmsd
  covalent geometry    : bond        0.00384 ( 6630)
  covalent geometry    : angle       0.54349 ( 8994)
  hydrogen bonds       : bond        0.03663 (  348)
  hydrogen bonds       : angle       4.28986 ( 1002)

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

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

  1628 Ramachandran restraints generated.
    814 Oldfield, 0 Emsley, 814 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1628 Ramachandran restraints generated.
    814 Oldfield, 0 Emsley, 814 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  104 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 88
  time to evaluate  : 0.204 
Fit side-chains
REVERT: A   62 LEU cc_start: 0.8127 (OUTLIER) cc_final: 0.7860 (mm)
REVERT: A  180 GLU cc_start: 0.8157 (tt0) cc_final: 0.7687 (tt0)
REVERT: A  184 ASP cc_start: 0.8245 (m-30) cc_final: 0.7908 (m-30)
REVERT: A  218 ASP cc_start: 0.8474 (OUTLIER) cc_final: 0.8222 (m-30)
REVERT: A  264 GLU cc_start: 0.7314 (OUTLIER) cc_final: 0.6995 (mt-10)
REVERT: B    6 GLU cc_start: 0.7425 (OUTLIER) cc_final: 0.7142 (pp20)
REVERT: B   82 ASP cc_start: 0.7592 (t0) cc_final: 0.7103 (m-30)
REVERT: B  118 GLU cc_start: 0.7412 (mm-30) cc_final: 0.7093 (mp0)
REVERT: B  120 GLU cc_start: 0.7941 (mt-10) cc_final: 0.7608 (mt-10)
REVERT: B  214 ASP cc_start: 0.7886 (OUTLIER) cc_final: 0.7505 (t70)
REVERT: C  208 PHE cc_start: 0.6492 (OUTLIER) cc_final: 0.6065 (t80)
REVERT: C  231 GLU cc_start: 0.7772 (OUTLIER) cc_final: 0.7229 (tm-30)
  outliers start: 16
  outliers final: 9
  residues processed: 96
  average time/residue: 0.5469
  time to fit residues: 55.2617
Evaluate side-chains
  102 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 86
  time to evaluate  : 0.223 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    6 ILE
Chi-restraints excluded: chain A residue   62 LEU
Chi-restraints excluded: chain A residue   66 SER
Chi-restraints excluded: chain A residue  218 ASP
Chi-restraints excluded: chain A residue  236 MET
Chi-restraints excluded: chain A residue  264 GLU
Chi-restraints excluded: chain B residue    6 GLU
Chi-restraints excluded: chain B residue   94 SER
Chi-restraints excluded: chain B residue  136 ASP
Chi-restraints excluded: chain B residue  163 GLU
Chi-restraints excluded: chain B residue  167 ILE
Chi-restraints excluded: chain B residue  214 ASP
Chi-restraints excluded: chain C residue  193 LEU
Chi-restraints excluded: chain C residue  205 VAL
Chi-restraints excluded: chain C residue  208 PHE
Chi-restraints excluded: chain C residue  231 GLU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 81
   random chunks:
   chunk 67 optimal weight:    3.9990
   chunk 30 optimal weight:    0.8980
   chunk 55 optimal weight:    0.6980
   chunk 58 optimal weight:    0.9980
   chunk 57 optimal weight:    0.7980
   chunk 28 optimal weight:    2.9990
   chunk 69 optimal weight:    0.2980
   chunk 6 optimal weight:    0.7980
   chunk 18 optimal weight:    0.7980
   chunk 11 optimal weight:    0.0870
   chunk 49 optimal weight:    1.9990
   overall best weight:    0.5358

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

Flipped N/Q/H residues before XYZ refinement:
A  10 HIS
B 243 HIS
C 189 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3836 r_free = 0.3836 target = 0.162183 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3461 r_free = 0.3461 target = 0.124158 restraints weight = 6323.072|
|-----------------------------------------------------------------------------|
r_work (start): 0.3423 rms_B_bonded: 1.53
r_work: 0.3240 rms_B_bonded: 2.32 restraints_weight: 0.5000
r_work: 0.3112 rms_B_bonded: 3.75 restraints_weight: 0.2500
r_work (final): 0.3112
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8134
moved from start:          0.1456

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.043   6630  Z= 0.130
  Angle     :  0.535  11.219   8994  Z= 0.267
  Chirality :  0.042   0.202   1034
  Planarity :  0.005   0.060   1127
  Dihedral  :  9.677  84.506    939
  Min Nonbonded Distance : 1.861

Molprobity Statistics.
  All-atom Clashscore : 5.27
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.09 %
    Favored  : 97.91 %
  Rotamer:
    Outliers :  2.00 %
    Allowed  : 14.71 %
    Favored  : 83.29 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.21 (0.29), residues: 814
  helix:  1.86 (0.24), residues: 455
  sheet: -0.66 (0.53), residues: 73
  loop : -0.47 (0.36), residues: 286

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.000   ARG B 181 
 TYR   0.011   0.001   TYR C 251 
 PHE   0.011   0.001   PHE A 231 
 TRP   0.012   0.001   TRP B 128 
 HIS   0.007   0.001   HIS A  10 

Details of bonding type rmsd
  covalent geometry    : bond        0.00316 ( 6630)
  covalent geometry    : angle       0.53486 ( 8994)
  hydrogen bonds       : bond        0.03414 (  348)
  hydrogen bonds       : angle       4.25769 ( 1002)

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

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

  1628 Ramachandran restraints generated.
    814 Oldfield, 0 Emsley, 814 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1628 Ramachandran restraints generated.
    814 Oldfield, 0 Emsley, 814 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  100 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 86
  time to evaluate  : 0.294 
Fit side-chains
REVERT: A   62 LEU cc_start: 0.8066 (OUTLIER) cc_final: 0.7838 (mm)
REVERT: A  179 LYS cc_start: 0.8192 (mtmm) cc_final: 0.7718 (mtpp)
REVERT: A  180 GLU cc_start: 0.8140 (tt0) cc_final: 0.7680 (tt0)
REVERT: A  184 ASP cc_start: 0.8248 (m-30) cc_final: 0.7923 (m-30)
REVERT: A  218 ASP cc_start: 0.8453 (OUTLIER) cc_final: 0.8220 (m-30)
REVERT: A  264 GLU cc_start: 0.7342 (OUTLIER) cc_final: 0.7017 (mt-10)
REVERT: B   82 ASP cc_start: 0.7540 (t0) cc_final: 0.7059 (m-30)
REVERT: B  118 GLU cc_start: 0.7398 (mm-30) cc_final: 0.7077 (mp0)
REVERT: B  120 GLU cc_start: 0.7869 (mt-10) cc_final: 0.7511 (mt-10)
REVERT: B  214 ASP cc_start: 0.7843 (OUTLIER) cc_final: 0.7474 (t70)
REVERT: C  208 PHE cc_start: 0.6501 (OUTLIER) cc_final: 0.6078 (t80)
REVERT: C  231 GLU cc_start: 0.7770 (OUTLIER) cc_final: 0.7240 (tm-30)
  outliers start: 14
  outliers final: 8
  residues processed: 91
  average time/residue: 0.5684
  time to fit residues: 54.6332
Evaluate side-chains
  98 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 84
  time to evaluate  : 0.274 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   62 LEU
Chi-restraints excluded: chain A residue   66 SER
Chi-restraints excluded: chain A residue  218 ASP
Chi-restraints excluded: chain A residue  236 MET
Chi-restraints excluded: chain A residue  264 GLU
Chi-restraints excluded: chain B residue   94 SER
Chi-restraints excluded: chain B residue  136 ASP
Chi-restraints excluded: chain B residue  163 GLU
Chi-restraints excluded: chain B residue  167 ILE
Chi-restraints excluded: chain B residue  214 ASP
Chi-restraints excluded: chain C residue  193 LEU
Chi-restraints excluded: chain C residue  205 VAL
Chi-restraints excluded: chain C residue  208 PHE
Chi-restraints excluded: chain C residue  231 GLU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 81
   random chunks:
   chunk 64 optimal weight:    3.9990
   chunk 39 optimal weight:    2.9990
   chunk 27 optimal weight:    0.6980
   chunk 34 optimal weight:    0.7980
   chunk 68 optimal weight:    0.9980
   chunk 63 optimal weight:    0.9990
   chunk 38 optimal weight:    0.9980
   chunk 3 optimal weight:    2.9990
   chunk 47 optimal weight:    1.9990
   chunk 15 optimal weight:    1.9990
   chunk 0 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:
A  10 HIS
B 243 HIS
C 189 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3816 r_free = 0.3816 target = 0.160416 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3434 r_free = 0.3434 target = 0.121949 restraints weight = 6396.828|
|-----------------------------------------------------------------------------|
r_work (start): 0.3399 rms_B_bonded: 1.57
r_work: 0.3217 rms_B_bonded: 2.30 restraints_weight: 0.5000
r_work: 0.3087 rms_B_bonded: 3.73 restraints_weight: 0.2500
r_work (final): 0.3087
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8161
moved from start:          0.1485

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.059   6630  Z= 0.176
  Angle     :  0.588  15.385   8994  Z= 0.289
  Chirality :  0.044   0.186   1034
  Planarity :  0.005   0.062   1127
  Dihedral  :  9.950  83.506    939
  Min Nonbonded Distance : 1.850

Molprobity Statistics.
  All-atom Clashscore : 5.81
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.97 %
    Favored  : 98.03 %
  Rotamer:
    Outliers :  2.71 %
    Allowed  : 13.86 %
    Favored  : 83.43 %
  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 aren not related in a simple way.
  whole:  1.02 (0.29), residues: 814
  helix:  1.69 (0.24), residues: 455
  sheet: -0.75 (0.53), residues: 74
  loop : -0.51 (0.36), residues: 285

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG B 181 
 TYR   0.013   0.001   TYR C 251 
 PHE   0.013   0.001   PHE A 231 
 TRP   0.012   0.001   TRP B 128 
 HIS   0.007   0.001   HIS A  10 

Details of bonding type rmsd
  covalent geometry    : bond        0.00438 ( 6630)
  covalent geometry    : angle       0.58788 ( 8994)
  hydrogen bonds       : bond        0.03811 (  348)
  hydrogen bonds       : angle       4.36088 ( 1002)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2597.95 seconds
wall clock time: 44 minutes 58.32 seconds (2698.32 seconds total)