Starting phenix.real_space_refine
on Fri Aug 22 13:24:04 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8j7n_36043/08_2025/8j7n_36043_neut.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8j7n_36043/08_2025/8j7n_36043.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.0
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8j7n_36043/08_2025/8j7n_36043.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8j7n_36043/08_2025/8j7n_36043.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8j7n_36043/08_2025/8j7n_36043_neut.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8j7n_36043/08_2025/8j7n_36043_neut.cif"
  }
  resolution = 3.0
  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=   0.003
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      21      5.16       5
     C    2082      2.51       5
     N     519      2.21       5
     O     636      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 24 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: 3258
  Number of models: 1
  Model: ""
    Number of chains: 1
    Chain: "A"
      Number of atoms: 1086
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 135, 1086
          Classifications: {'peptide': 135}
          Link IDs: {'PTRANS': 2, 'TRANS': 132}
  Restraints were copied for chains:
    B, C
  Time building chain proxies: 0.72, per 1000 atoms: 0.22
  Number of scatterers: 3258
  At special positions: 0
  Unit cell: (95.45, 104.58, 34.86, 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      21     16.00
     O     636      8.00
     N     519      7.00
     C    2082      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=3, symmetry=0
    Simple disulfide: pdb=" SG  CYS A 214 " - pdb=" SG  CYS A 253 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 214 " - pdb=" SG  CYS B 253 " distance=2.03
    Simple disulfide: pdb=" SG  CYS C 214 " - pdb=" SG  CYS C 253 " distance=2.03

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 0.16
  Conformation dependent library (CDL) restraints added in 80.9 milliseconds
  
  Enol-peptide restraints added in 238.4 nanoseconds
  

  798 Ramachandran restraints generated.
    399 Oldfield, 0 Emsley, 399 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  780

  Finding SS restraints...
    Secondary structure from input PDB file:
      0 helices and 17 sheets defined
      0.0% alpha, 40.7% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.15
  Creating SS restraints...
    Processing sheet with id=AA1, first strand: chain 'B' and resid 122 through 126
      removed outlier: 6.344A  pdb=" N   VAL A 123 " --> pdb=" O   LYS B 124 " (cutoff:3.500A)
      removed outlier: 7.597A  pdb=" N   ILE B 126 " --> pdb=" O   VAL A 123 " (cutoff:3.500A)
      removed outlier: 6.020A  pdb=" N   TYR A 125 " --> pdb=" O   ILE B 126 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'B' and resid 129 through 130
      removed outlier: 6.669A  pdb=" N   LYS A 129 " --> pdb=" O   SER B 130 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'B' and resid 133 through 138
      removed outlier: 6.520A  pdb=" N   SER A 134 " --> pdb=" O   TYR B 135 " (cutoff:3.500A)
      removed outlier: 8.035A  pdb=" N   VAL B 137 " --> pdb=" O   SER A 134 " (cutoff:3.500A)
      removed outlier: 6.221A  pdb=" N   ASP A 136 " --> pdb=" O   VAL B 137 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'B' and resid 142 through 144
      removed outlier: 6.463A  pdb=" N   ILE A 142 " --> pdb=" O   TYR B 143 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'B' and resid 147 through 151
      removed outlier: 6.088A  pdb=" N   THR A 147 " --> pdb=" O   ASN B 148 " (cutoff:3.500A)
      removed outlier: 7.425A  pdb=" N   LEU B 150 " --> pdb=" O   THR A 147 " (cutoff:3.500A)
      removed outlier: 6.369A  pdb=" N   THR A 149 " --> pdb=" O   LEU B 150 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'B' and resid 156 through 160
      removed outlier: 6.315A  pdb=" N   TYR A 157 " --> pdb=" O   TYR B 158 " (cutoff:3.500A)
      removed outlier: 7.543A  pdb=" N   VAL B 160 " --> pdb=" O   TYR A 157 " (cutoff:3.500A)
      removed outlier: 6.288A  pdb=" N   SER A 159 " --> pdb=" O   VAL B 160 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'B' and resid 163 through 170
      removed outlier: 6.198A  pdb=" N   ASN A 164 " --> pdb=" O   ILE B 165 " (cutoff:3.500A)
      removed outlier: 7.727A  pdb=" N   ALA B 167 " --> pdb=" O   ASN A 164 " (cutoff:3.500A)
      removed outlier: 6.379A  pdb=" N   THR A 166 " --> pdb=" O   ALA B 167 " (cutoff:3.500A)
      removed outlier: 7.891A  pdb=" N   VAL B 169 " --> pdb=" O   THR A 166 " (cutoff:3.500A)
      removed outlier: 6.322A  pdb=" N   GLN A 168 " --> pdb=" O   VAL B 169 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'B' and resid 173 through 176
      removed outlier: 7.994A  pdb=" N   LYS A 173 " --> pdb=" O   THR B 174 " (cutoff:3.500A)
      removed outlier: 7.504A  pdb=" N   ILE B 176 " --> pdb=" O   LYS A 173 " (cutoff:3.500A)
      removed outlier: 9.071A  pdb=" N   VAL A 175 " --> pdb=" O   ILE B 176 " (cutoff:3.500A)
      removed outlier: 6.787A  pdb=" N   VAL C 175 " --> pdb=" O   THR A 174 " (cutoff:3.500A)
      removed outlier: 6.954A  pdb=" N   ILE A 176 " --> pdb=" O   VAL C 175 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'B' and resid 185 through 187
      removed outlier: 6.755A  pdb=" N   ILE A 186 " --> pdb=" O   ILE B 187 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'B' and resid 192 through 195
      removed outlier: 9.217A  pdb=" N   MET A 192 " --> pdb=" O   LYS B 193 " (cutoff:3.500A)
      removed outlier: 9.408A  pdb=" N   ILE B 195 " --> pdb=" O   MET A 192 " (cutoff:3.500A)
      removed outlier: 5.930A  pdb=" N   GLN A 194 " --> pdb=" O   ILE B 195 " (cutoff:3.500A)
      removed outlier: 6.899A  pdb=" N   LYS A 193 " --> pdb=" O   MET C 192 " (cutoff:3.500A)
      removed outlier: 6.838A  pdb=" N   GLN C 194 " --> pdb=" O   LYS A 193 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'B' and resid 202 through 203
      removed outlier: 6.177A  pdb=" N   VAL A 202 " --> pdb=" O   ILE B 203 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'B' and resid 206 through 207
      removed outlier: 6.581A  pdb=" N   GLU A 206 " --> pdb=" O   MET C 207 " (cutoff:3.500A)
    Processing sheet with id=AB4, first strand: chain 'B' and resid 210 through 213
      removed outlier: 6.878A  pdb=" N   MET A 210 " --> pdb=" O   TYR C 211 " (cutoff:3.500A)
      removed outlier: 7.863A  pdb=" N   PHE C 213 " --> pdb=" O   MET A 210 " (cutoff:3.500A)
      removed outlier: 6.577A  pdb=" N   ASP A 212 " --> pdb=" O   PHE C 213 " (cutoff:3.500A)
    Processing sheet with id=AB5, first strand: chain 'B' and resid 222 through 230
      removed outlier: 6.980A  pdb=" N   ASN B 223 " --> pdb=" O   HIS A 222 " (cutoff:3.500A)
      removed outlier: 6.991A  pdb=" N   ILE A 224 " --> pdb=" O   ASN B 223 " (cutoff:3.500A)
      removed outlier: 6.931A  pdb=" N   VAL B 225 " --> pdb=" O   ILE A 224 " (cutoff:3.500A)
      removed outlier: 6.964A  pdb=" N   LEU A 226 " --> pdb=" O   VAL B 225 " (cutoff:3.500A)
      removed outlier: 6.874A  pdb=" N   MET B 227 " --> pdb=" O   LEU A 226 " (cutoff:3.500A)
      removed outlier: 6.988A  pdb=" N   MET A 228 " --> pdb=" O   MET B 227 " (cutoff:3.500A)
      removed outlier: 6.966A  pdb=" N   GLN B 229 " --> pdb=" O   MET A 228 " (cutoff:3.500A)
      removed outlier: 9.054A  pdb=" N   ASN A 223 " --> pdb=" O   ILE C 224 " (cutoff:3.500A)
      removed outlier: 10.385A  pdb=" N   LEU C 226 " --> pdb=" O   ASN A 223 " (cutoff:3.500A)
      removed outlier: 9.068A  pdb=" N   VAL A 225 " --> pdb=" O   LEU C 226 " (cutoff:3.500A)
      removed outlier: 10.526A  pdb=" N   MET C 228 " --> pdb=" O   VAL A 225 " (cutoff:3.500A)
      removed outlier: 9.226A  pdb=" N   MET A 227 " --> pdb=" O   MET C 228 " (cutoff:3.500A)
      removed outlier: 9.113A  pdb=" N   VAL C 230 " --> pdb=" O   MET A 227 " (cutoff:3.500A)
      removed outlier: 6.052A  pdb=" N   GLN A 229 " --> pdb=" O   VAL C 230 " (cutoff:3.500A)
    Processing sheet with id=AB6, first strand: chain 'B' and resid 236 through 239
      removed outlier: 6.444A  pdb=" N   TYR A 236 " --> pdb=" O   PHE B 237 " (cutoff:3.500A)
      removed outlier: 7.545A  pdb=" N   HIS B 239 " --> pdb=" O   TYR A 236 " (cutoff:3.500A)
      removed outlier: 6.467A  pdb=" N   GLY A 238 " --> pdb=" O   HIS B 239 " (cutoff:3.500A)
    Processing sheet with id=AB7, first strand: chain 'B' and resid 243 through 245
      removed outlier: 6.423A  pdb=" N   SER A 244 " --> pdb=" O   GLN B 245 " (cutoff:3.500A)
    Processing sheet with id=AB8, first strand: chain 'B' and resid 251 through 253
      removed outlier: 6.504A  pdb=" N   ASP A 252 " --> pdb=" O   CYS C 253 " (cutoff:3.500A)

    44 hydrogen bonds defined for protein.
    132 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: 0.33

  Time building geometry restraints manager: 0.21 seconds

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

  Histogram of bond lengths:
        1.22 -     1.33: 1015
        1.33 -     1.45: 424
        1.45 -     1.57: 1837
        1.57 -     1.68: 0
        1.68 -     1.80: 36
  Bond restraints: 3312
  Sorted by residual:
  bond pdb=" CB  MET A 228 "
       pdb=" CG  MET A 228 "
    ideal  model  delta    sigma   weight residual
    1.520  1.475  0.045 3.00e-02 1.11e+03 2.24e+00
  bond pdb=" CB  MET C 228 "
       pdb=" CG  MET C 228 "
    ideal  model  delta    sigma   weight residual
    1.520  1.476  0.044 3.00e-02 1.11e+03 2.19e+00
  bond pdb=" CB  MET B 228 "
       pdb=" CG  MET B 228 "
    ideal  model  delta    sigma   weight residual
    1.520  1.476  0.044 3.00e-02 1.11e+03 2.18e+00
  bond pdb=" CB  THR A 235 "
       pdb=" CG2 THR A 235 "
    ideal  model  delta    sigma   weight residual
    1.521  1.476  0.045 3.30e-02 9.18e+02 1.87e+00
  bond pdb=" CB  THR C 235 "
       pdb=" CG2 THR C 235 "
    ideal  model  delta    sigma   weight residual
    1.521  1.477  0.044 3.30e-02 9.18e+02 1.82e+00
  ... (remaining 3307 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.32: 4105
        1.32 -     2.63: 340
        2.63 -     3.95: 40
        3.95 -     5.27: 12
        5.27 -     6.58: 6
  Bond angle restraints: 4503
  Sorted by residual:
  angle pdb=" N   GLU B 246 "
        pdb=" CA  GLU B 246 "
        pdb=" C   GLU B 246 "
      ideal   model   delta    sigma   weight residual
     110.41  114.66   -4.25 1.23e+00 6.61e-01 1.20e+01
  angle pdb=" N   GLU C 246 "
        pdb=" CA  GLU C 246 "
        pdb=" C   GLU C 246 "
      ideal   model   delta    sigma   weight residual
     110.41  114.65   -4.24 1.23e+00 6.61e-01 1.19e+01
  angle pdb=" N   GLU A 246 "
        pdb=" CA  GLU A 246 "
        pdb=" C   GLU A 246 "
      ideal   model   delta    sigma   weight residual
     110.41  114.65   -4.24 1.23e+00 6.61e-01 1.19e+01
  angle pdb=" C   LEU A 144 "
        pdb=" N   ASN A 145 "
        pdb=" CA  ASN A 145 "
      ideal   model   delta    sigma   weight residual
     121.54  128.12   -6.58 1.91e+00 2.74e-01 1.19e+01
  angle pdb=" C   LEU C 144 "
        pdb=" N   ASN C 145 "
        pdb=" CA  ASN C 145 "
      ideal   model   delta    sigma   weight residual
     121.54  128.12   -6.58 1.91e+00 2.74e-01 1.19e+01
  ... (remaining 4498 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    11.51: 1676
       11.51 -    23.01: 239
       23.01 -    34.52: 47
       34.52 -    46.03: 27
       46.03 -    57.53: 6
  Dihedral angle restraints: 1995
    sinusoidal: 777
      harmonic: 1218
  Sorted by residual:
  dihedral pdb=" CA  GLN B 138 "
           pdb=" C   GLN B 138 "
           pdb=" N   LYS B 139 "
           pdb=" CA  LYS B 139 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  158.19   21.81     0      5.00e+00 4.00e-02 1.90e+01
  dihedral pdb=" CA  GLN A 138 "
           pdb=" C   GLN A 138 "
           pdb=" N   LYS A 139 "
           pdb=" CA  LYS A 139 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  158.21   21.79     0      5.00e+00 4.00e-02 1.90e+01
  dihedral pdb=" CA  GLN C 138 "
           pdb=" C   GLN C 138 "
           pdb=" N   LYS C 139 "
           pdb=" CA  LYS C 139 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  158.22   21.78     0      5.00e+00 4.00e-02 1.90e+01
  ... (remaining 1992 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.043: 310
       0.043 -    0.085: 141
       0.085 -    0.128: 83
       0.128 -    0.170: 6
       0.170 -    0.213: 3
  Chirality restraints: 543
  Sorted by residual:
  chirality pdb=" CA  ASN C 145 "
            pdb=" N   ASN C 145 "
            pdb=" C   ASN C 145 "
            pdb=" CB  ASN C 145 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.30    0.21 2.00e-01 2.50e+01 1.13e+00
  chirality pdb=" CA  ASN B 145 "
            pdb=" N   ASN B 145 "
            pdb=" C   ASN B 145 "
            pdb=" CB  ASN B 145 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.30    0.21 2.00e-01 2.50e+01 1.13e+00
  chirality pdb=" CA  ASN A 145 "
            pdb=" N   ASN A 145 "
            pdb=" C   ASN A 145 "
            pdb=" CB  ASN A 145 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.30    0.21 2.00e-01 2.50e+01 1.11e+00
  ... (remaining 540 not shown)

  Planarity restraints: 558
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TYR A 125 "    0.009 2.00e-02 2.50e+03   1.02e-02 2.09e+00
        pdb=" CG  TYR A 125 "   -0.024 2.00e-02 2.50e+03
        pdb=" CD1 TYR A 125 "    0.004 2.00e-02 2.50e+03
        pdb=" CD2 TYR A 125 "    0.011 2.00e-02 2.50e+03
        pdb=" CE1 TYR A 125 "    0.004 2.00e-02 2.50e+03
        pdb=" CE2 TYR A 125 "   -0.004 2.00e-02 2.50e+03
        pdb=" CZ  TYR A 125 "    0.000 2.00e-02 2.50e+03
        pdb=" OH  TYR A 125 "   -0.000 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TYR C 125 "    0.008 2.00e-02 2.50e+03   1.01e-02 2.05e+00
        pdb=" CG  TYR C 125 "   -0.024 2.00e-02 2.50e+03
        pdb=" CD1 TYR C 125 "    0.004 2.00e-02 2.50e+03
        pdb=" CD2 TYR C 125 "    0.011 2.00e-02 2.50e+03
        pdb=" CE1 TYR C 125 "    0.004 2.00e-02 2.50e+03
        pdb=" CE2 TYR C 125 "   -0.004 2.00e-02 2.50e+03
        pdb=" CZ  TYR C 125 "    0.000 2.00e-02 2.50e+03
        pdb=" OH  TYR C 125 "    0.000 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TYR B 125 "    0.008 2.00e-02 2.50e+03   9.97e-03 1.99e+00
        pdb=" CG  TYR B 125 "   -0.024 2.00e-02 2.50e+03
        pdb=" CD1 TYR B 125 "    0.003 2.00e-02 2.50e+03
        pdb=" CD2 TYR B 125 "    0.011 2.00e-02 2.50e+03
        pdb=" CE1 TYR B 125 "    0.004 2.00e-02 2.50e+03
        pdb=" CE2 TYR B 125 "   -0.003 2.00e-02 2.50e+03
        pdb=" CZ  TYR B 125 "    0.000 2.00e-02 2.50e+03
        pdb=" OH  TYR B 125 "    0.000 2.00e-02 2.50e+03
  ... (remaining 555 not shown)

  Histogram of nonbonded interaction distances:
        2.28 -     2.80: 782
        2.80 -     3.33: 2823
        3.33 -     3.85: 5283
        3.85 -     4.38: 5764
        4.38 -     4.90: 11828
  Nonbonded interactions: 26480
  Sorted by model distance:
  nonbonded pdb=" NE2 GLN B 229 "
            pdb=" O   GLU B 241 "
     model   vdw
     2.276 3.120
  nonbonded pdb=" NE2 GLN C 229 "
            pdb=" O   GLU C 241 "
     model   vdw
     2.276 3.120
  nonbonded pdb=" NE2 GLN A 229 "
            pdb=" O   GLU A 241 "
     model   vdw
     2.276 3.120
  nonbonded pdb=" OG1 THR A 233 "
            pdb=" N   THR A 234 "
     model   vdw
     2.530 3.120
  nonbonded pdb=" OG1 THR B 233 "
            pdb=" N   THR B 234 "
     model   vdw
     2.531 3.120
  ... (remaining 26475 not shown)

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

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             1.930
  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:          0.050
  Check model and map are aligned:         0.000
  Set scattering table:                    0.010
  Process input model:                     3.860
  Find NCS groups from input model:        0.010
  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:5.400
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   11.270
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8667
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      :  0.008   0.045   3315  Z= 0.368
  Angle     :  0.820   6.584   4509  Z= 0.482
  Chirality :  0.058   0.213    543
  Planarity :  0.003   0.012    558
  Dihedral  : 12.258  57.534   1206
  Min Nonbonded Distance : 2.276

Molprobity Statistics.
  All-atom Clashscore : 16.74
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 13.53 %
    Favored  : 86.47 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.38 %
    Favored  : 97.62 %
  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: -5.22 (0.31), residues: 399
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -3.97 (0.23), residues: 399

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG B 140 
 TYR   0.024   0.003   TYR A 125 
 PHE   0.005   0.001   PHE C 213 
 HIS   0.006   0.003   HIS A 239 

Details of bonding type rmsd
  covalent geometry    : bond        0.00845 ( 3312)
  covalent geometry    : angle       0.82000 ( 4503)
  SS BOND              : bond        0.00532 (    3)
  SS BOND              : angle       0.49755 (    6)
  hydrogen bonds       : bond        0.16242 (   44)
  hydrogen bonds       : angle       8.20290 (  132)

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

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

  798 Ramachandran restraints generated.
    399 Oldfield, 0 Emsley, 399 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  798 Ramachandran restraints generated.
    399 Oldfield, 0 Emsley, 399 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  92 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 92
  time to evaluate  : 0.093 
Fit side-chains
REVERT: A  168 GLN cc_start: 0.8781 (mt0) cc_final: 0.8520 (mt0)
REVERT: B  129 LYS cc_start: 0.9171 (ptpp) cc_final: 0.8968 (ptpt)
REVERT: B  168 GLN cc_start: 0.8902 (mt0) cc_final: 0.8673 (mt0)
REVERT: B  180 ARG cc_start: 0.7968 (ptp-170) cc_final: 0.6442 (pmt-80)
REVERT: C  168 GLN cc_start: 0.8790 (mt0) cc_final: 0.8585 (mt0)
REVERT: C  180 ARG cc_start: 0.8061 (ptp-170) cc_final: 0.7838 (ptp-170)
REVERT: C  196 ASP cc_start: 0.8420 (p0) cc_final: 0.8000 (p0)
  outliers start: 0
  outliers final: 0
  residues processed: 92
  average time/residue: 0.5639
  time to fit residues: 53.0635
Evaluate side-chains
  70 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 70
  time to evaluate  : 0.125 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 39
   random chunks:
   chunk 24 optimal weight:    4.9990
   chunk 26 optimal weight:    3.9990
   chunk 2 optimal weight:    3.9990
   chunk 16 optimal weight:    6.9990
   chunk 32 optimal weight:    2.9990
   chunk 31 optimal weight:    4.9990
   chunk 25 optimal weight:    5.9990
   chunk 19 optimal weight:    4.9990
   chunk 30 optimal weight:    2.9990
   chunk 22 optimal weight:   10.0000
   chunk 37 optimal weight:    0.9980
   overall best weight:    2.9988

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

Flipped N/Q/H residues before XYZ refinement:
A 155 ASN
A 156 ASN
A 222 HIS
** A 229 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 239 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 155 ASN
B 156 ASN
B 222 HIS
B 223 ASN
B 229 GLN
** B 239 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
C 156 ASN
C 222 HIS
C 229 GLN

Total number of N/Q/H flips: 11

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3713 r_free = 0.3713 target = 0.122671 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3553 r_free = 0.3553 target = 0.109190 restraints weight = 4108.151|
|-----------------------------------------------------------------------------|
r_work (start): 0.3560 rms_B_bonded: 1.80
r_work: 0.3472 rms_B_bonded: 1.88 restraints_weight: 0.5000
r_work: 0.3379 rms_B_bonded: 3.23 restraints_weight: 0.2500
r_work (final): 0.3379
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8815
moved from start:          0.1775

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.032   3315  Z= 0.204
  Angle     :  0.649   6.359   4509  Z= 0.359
  Chirality :  0.054   0.190    543
  Planarity :  0.002   0.016    558
  Dihedral  :  6.633  20.782    447
  Min Nonbonded Distance : 2.578

Molprobity Statistics.
  All-atom Clashscore : 6.30
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 11.28 %
    Favored  : 88.72 %
  Rotamer:
    Outliers :  3.70 %
    Allowed  : 11.90 %
    Favored  : 84.39 %
  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: -4.83 (0.31), residues: 399
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -3.67 (0.23), residues: 399

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG B 180 
 TYR   0.017   0.002   TYR C 143 
 PHE   0.007   0.001   PHE A 213 
 HIS   0.005   0.002   HIS B 239 

Details of bonding type rmsd
  covalent geometry    : bond        0.00481 ( 3312)
  covalent geometry    : angle       0.64883 ( 4503)
  SS BOND              : bond        0.00279 (    3)
  SS BOND              : angle       0.51976 (    6)
  hydrogen bonds       : bond        0.02142 (   44)
  hydrogen bonds       : angle       5.39756 (  132)

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

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

  798 Ramachandran restraints generated.
    399 Oldfield, 0 Emsley, 399 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  798 Ramachandran restraints generated.
    399 Oldfield, 0 Emsley, 399 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  90 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 76
  time to evaluate  : 0.105 
Fit side-chains
REVERT: A  168 GLN cc_start: 0.8992 (mt0) cc_final: 0.8740 (mt0)
REVERT: A  178 LYS cc_start: 0.8487 (OUTLIER) cc_final: 0.8255 (ttpt)
REVERT: A  208 SER cc_start: 0.8650 (m) cc_final: 0.8438 (m)
REVERT: B  168 GLN cc_start: 0.9032 (mt0) cc_final: 0.8821 (mt0)
REVERT: B  180 ARG cc_start: 0.8227 (ptp-170) cc_final: 0.6042 (pmt-80)
REVERT: B  190 LEU cc_start: 0.8994 (OUTLIER) cc_final: 0.8509 (tt)
REVERT: C  168 GLN cc_start: 0.8803 (mt0) cc_final: 0.8581 (mt0)
  outliers start: 14
  outliers final: 2
  residues processed: 79
  average time/residue: 0.5417
  time to fit residues: 43.7889
Evaluate side-chains
  74 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 70
  time to evaluate  : 0.088 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  178 LYS
Chi-restraints excluded: chain A residue  190 LEU
Chi-restraints excluded: chain B residue  190 LEU
Chi-restraints excluded: chain B residue  217 ILE
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 39
   random chunks:
   chunk 1 optimal weight:    7.9990
   chunk 29 optimal weight:    2.9990
   chunk 38 optimal weight:    1.9990
   chunk 11 optimal weight:    2.9990
   chunk 28 optimal weight:    1.9990
   chunk 20 optimal weight:    6.9990
   chunk 37 optimal weight:    1.9990
   chunk 27 optimal weight:    2.9990
   chunk 36 optimal weight:    1.9990
   chunk 9 optimal weight:    7.9990
   chunk 32 optimal weight:    7.9990
   overall best weight:    2.1990

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

Flipped N/Q/H residues before XYZ refinement:
A 223 ASN
A 229 GLN
** A 239 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 239 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3724 r_free = 0.3724 target = 0.123502 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3561 r_free = 0.3561 target = 0.109600 restraints weight = 4064.050|
|-----------------------------------------------------------------------------|
r_work (start): 0.3580 rms_B_bonded: 1.82
r_work: 0.3492 rms_B_bonded: 1.94 restraints_weight: 0.5000
r_work: 0.3400 rms_B_bonded: 3.32 restraints_weight: 0.2500
r_work (final): 0.3400
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8803
moved from start:          0.2129

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.026   3315  Z= 0.157
  Angle     :  0.595   6.868   4509  Z= 0.329
  Chirality :  0.053   0.181    543
  Planarity :  0.002   0.012    558
  Dihedral  :  6.357  19.491    447
  Min Nonbonded Distance : 2.562

Molprobity Statistics.
  All-atom Clashscore : 5.99
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 11.28 %
    Favored  : 88.72 %
  Rotamer:
    Outliers :  3.44 %
    Allowed  : 15.34 %
    Favored  : 81.22 %
  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: -4.59 (0.31), residues: 399
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -3.49 (0.24), residues: 399

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG B 247 
 TYR   0.015   0.002   TYR A 143 
 PHE   0.006   0.001   PHE A 213 
 HIS   0.005   0.002   HIS C 239 

Details of bonding type rmsd
  covalent geometry    : bond        0.00365 ( 3312)
  covalent geometry    : angle       0.59525 ( 4503)
  SS BOND              : bond        0.00225 (    3)
  SS BOND              : angle       0.39853 (    6)
  hydrogen bonds       : bond        0.01631 (   44)
  hydrogen bonds       : angle       5.02702 (  132)

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

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

  798 Ramachandran restraints generated.
    399 Oldfield, 0 Emsley, 399 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  798 Ramachandran restraints generated.
    399 Oldfield, 0 Emsley, 399 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  93 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 80
  time to evaluate  : 0.119 
Fit side-chains
REVERT: A  168 GLN cc_start: 0.8961 (mt0) cc_final: 0.8676 (mt0)
REVERT: A  178 LYS cc_start: 0.8361 (OUTLIER) cc_final: 0.8110 (ttpt)
REVERT: A  208 SER cc_start: 0.8632 (m) cc_final: 0.8347 (t)
REVERT: B  168 GLN cc_start: 0.9029 (mt0) cc_final: 0.8828 (mt0)
REVERT: B  180 ARG cc_start: 0.8196 (ptp-170) cc_final: 0.6011 (pmt-80)
REVERT: B  190 LEU cc_start: 0.9005 (OUTLIER) cc_final: 0.8522 (tt)
REVERT: C  250 TYR cc_start: 0.7802 (t80) cc_final: 0.7583 (t80)
  outliers start: 13
  outliers final: 5
  residues processed: 83
  average time/residue: 0.5035
  time to fit residues: 42.7841
Evaluate side-chains
  82 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 75
  time to evaluate  : 0.074 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  178 LYS
Chi-restraints excluded: chain A residue  190 LEU
Chi-restraints excluded: chain B residue  134 SER
Chi-restraints excluded: chain B residue  190 LEU
Chi-restraints excluded: chain B residue  217 ILE
Chi-restraints excluded: chain C residue  144 LEU
Chi-restraints excluded: chain C residue  190 LEU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 39
   random chunks:
   chunk 22 optimal weight:    5.9990
   chunk 16 optimal weight:    2.9990
   chunk 27 optimal weight:    6.9990
   chunk 11 optimal weight:    5.9990
   chunk 2 optimal weight:    7.9990
   chunk 33 optimal weight:    3.9990
   chunk 10 optimal weight:    8.9990
   chunk 12 optimal weight:    9.9990
   chunk 19 optimal weight:    0.7980
   chunk 38 optimal weight:    1.9990
   chunk 34 optimal weight:   10.0000
   overall best weight:    3.1588

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

Flipped N/Q/H residues before XYZ refinement:
** A 239 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 239 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
C 168 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3685 r_free = 0.3685 target = 0.120272 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3522 r_free = 0.3522 target = 0.106541 restraints weight = 4098.640|
|-----------------------------------------------------------------------------|
r_work (start): 0.3539 rms_B_bonded: 1.79
r_work: 0.3453 rms_B_bonded: 1.88 restraints_weight: 0.5000
r_work: 0.3363 rms_B_bonded: 3.22 restraints_weight: 0.2500
r_work (final): 0.3363
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8828
moved from start:          0.2200

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.032   3315  Z= 0.209
  Angle     :  0.625   6.717   4509  Z= 0.347
  Chirality :  0.054   0.193    543
  Planarity :  0.002   0.013    558
  Dihedral  :  6.491  19.714    447
  Min Nonbonded Distance : 2.571

Molprobity Statistics.
  All-atom Clashscore : 6.91
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 11.28 %
    Favored  : 88.72 %
  Rotamer:
    Outliers :  5.03 %
    Allowed  : 15.08 %
    Favored  : 79.89 %
  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: -4.45 (0.32), residues: 399
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -3.39 (0.24), residues: 399

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG B 180 
 TYR   0.018   0.002   TYR A 143 
 PHE   0.006   0.001   PHE A 213 
 HIS   0.005   0.002   HIS C 239 

Details of bonding type rmsd
  covalent geometry    : bond        0.00494 ( 3312)
  covalent geometry    : angle       0.62530 ( 4503)
  SS BOND              : bond        0.00239 (    3)
  SS BOND              : angle       0.53159 (    6)
  hydrogen bonds       : bond        0.01674 (   44)
  hydrogen bonds       : angle       4.95978 (  132)

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

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

  798 Ramachandran restraints generated.
    399 Oldfield, 0 Emsley, 399 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  798 Ramachandran restraints generated.
    399 Oldfield, 0 Emsley, 399 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  98 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 79
  time to evaluate  : 0.125 
Fit side-chains
REVERT: A  168 GLN cc_start: 0.8984 (mt0) cc_final: 0.8706 (mt0)
REVERT: A  178 LYS cc_start: 0.8479 (OUTLIER) cc_final: 0.8240 (ttpt)
REVERT: A  208 SER cc_start: 0.8617 (m) cc_final: 0.8333 (t)
REVERT: B  168 GLN cc_start: 0.9046 (mt0) cc_final: 0.8845 (mt0)
REVERT: B  180 ARG cc_start: 0.8207 (ptp-170) cc_final: 0.6040 (pmt-80)
REVERT: B  190 LEU cc_start: 0.8952 (OUTLIER) cc_final: 0.8498 (tt)
  outliers start: 19
  outliers final: 6
  residues processed: 83
  average time/residue: 0.4818
  time to fit residues: 41.0552
Evaluate side-chains
  80 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 72
  time to evaluate  : 0.125 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  178 LYS
Chi-restraints excluded: chain A residue  190 LEU
Chi-restraints excluded: chain A residue  192 MET
Chi-restraints excluded: chain B residue  134 SER
Chi-restraints excluded: chain B residue  190 LEU
Chi-restraints excluded: chain B residue  217 ILE
Chi-restraints excluded: chain C residue  144 LEU
Chi-restraints excluded: chain C residue  190 LEU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 39
   random chunks:
   chunk 22 optimal weight:    6.9990
   chunk 5 optimal weight:    9.9990
   chunk 17 optimal weight:    2.9990
   chunk 25 optimal weight:    4.9990
   chunk 6 optimal weight:    6.9990
   chunk 20 optimal weight:    4.9990
   chunk 37 optimal weight:    3.9990
   chunk 9 optimal weight:    8.9990
   chunk 24 optimal weight:    1.9990
   chunk 32 optimal weight:    0.9980
   chunk 18 optimal weight:    6.9990
   overall best weight:    2.9988

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

Flipped N/Q/H residues before XYZ refinement:
** A 239 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 239 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
C 168 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3687 r_free = 0.3687 target = 0.120492 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3523 r_free = 0.3523 target = 0.106789 restraints weight = 4064.046|
|-----------------------------------------------------------------------------|
r_work (start): 0.3552 rms_B_bonded: 1.80
r_work: 0.3456 rms_B_bonded: 1.91 restraints_weight: 0.5000
r_work: 0.3364 rms_B_bonded: 3.29 restraints_weight: 0.2500
r_work (final): 0.3364
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8832
moved from start:          0.2362

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.030   3315  Z= 0.200
  Angle     :  0.627   6.619   4509  Z= 0.347
  Chirality :  0.054   0.193    543
  Planarity :  0.002   0.013    558
  Dihedral  :  6.416  19.087    447
  Min Nonbonded Distance : 2.542

Molprobity Statistics.
  All-atom Clashscore : 6.61
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 11.53 %
    Favored  : 88.47 %
  Rotamer:
    Outliers :  4.76 %
    Allowed  : 17.46 %
    Favored  : 77.78 %
  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: -4.33 (0.32), residues: 399
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -3.29 (0.25), residues: 399

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG B 180 
 TYR   0.018   0.002   TYR C 158 
 PHE   0.007   0.001   PHE A 213 
 HIS   0.005   0.002   HIS C 239 

Details of bonding type rmsd
  covalent geometry    : bond        0.00471 ( 3312)
  covalent geometry    : angle       0.62725 ( 4503)
  SS BOND              : bond        0.00223 (    3)
  SS BOND              : angle       0.50740 (    6)
  hydrogen bonds       : bond        0.01702 (   44)
  hydrogen bonds       : angle       4.94138 (  132)

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

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

  798 Ramachandran restraints generated.
    399 Oldfield, 0 Emsley, 399 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  798 Ramachandran restraints generated.
    399 Oldfield, 0 Emsley, 399 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  96 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 78
  time to evaluate  : 0.134 
Fit side-chains
REVERT: A  168 GLN cc_start: 0.8987 (mt0) cc_final: 0.8716 (mt0)
REVERT: A  178 LYS cc_start: 0.8458 (OUTLIER) cc_final: 0.8189 (ttpt)
REVERT: A  208 SER cc_start: 0.8603 (m) cc_final: 0.8344 (t)
REVERT: B  168 GLN cc_start: 0.9062 (mt0) cc_final: 0.8861 (mt0)
REVERT: B  180 ARG cc_start: 0.8201 (ptp-170) cc_final: 0.5977 (pmt-80)
REVERT: B  190 LEU cc_start: 0.8964 (OUTLIER) cc_final: 0.8511 (tt)
REVERT: C  180 ARG cc_start: 0.8130 (ptp90) cc_final: 0.5712 (mmp-170)
  outliers start: 18
  outliers final: 6
  residues processed: 84
  average time/residue: 0.4850
  time to fit residues: 41.8279
Evaluate side-chains
  81 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 73
  time to evaluate  : 0.109 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  178 LYS
Chi-restraints excluded: chain A residue  190 LEU
Chi-restraints excluded: chain A residue  192 MET
Chi-restraints excluded: chain B residue  134 SER
Chi-restraints excluded: chain B residue  190 LEU
Chi-restraints excluded: chain B residue  217 ILE
Chi-restraints excluded: chain C residue  144 LEU
Chi-restraints excluded: chain C residue  190 LEU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 39
   random chunks:
   chunk 17 optimal weight:    3.9990
   chunk 36 optimal weight:    0.7980
   chunk 0 optimal weight:   10.0000
   chunk 8 optimal weight:    9.9990
   chunk 16 optimal weight:    3.9990
   chunk 9 optimal weight:    7.9990
   chunk 18 optimal weight:    6.9990
   chunk 28 optimal weight:    8.9990
   chunk 38 optimal weight:    2.9990
   chunk 31 optimal weight:    8.9990
   chunk 19 optimal weight:    2.9990
   overall best weight:    2.9588

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

Flipped N/Q/H residues before XYZ refinement:
** A 239 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 239 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
C 168 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3694 r_free = 0.3694 target = 0.120608 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3527 r_free = 0.3527 target = 0.106935 restraints weight = 4057.475|
|-----------------------------------------------------------------------------|
r_work (start): 0.3544 rms_B_bonded: 1.79
r_work: 0.3456 rms_B_bonded: 1.90 restraints_weight: 0.5000
r_work: 0.3365 rms_B_bonded: 3.24 restraints_weight: 0.2500
r_work (final): 0.3365
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8823
moved from start:          0.2406

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.031   3315  Z= 0.198
  Angle     :  0.630   6.564   4509  Z= 0.348
  Chirality :  0.054   0.192    543
  Planarity :  0.002   0.013    558
  Dihedral  :  6.382  18.940    447
  Min Nonbonded Distance : 2.567

Molprobity Statistics.
  All-atom Clashscore : 6.30
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 11.53 %
    Favored  : 88.47 %
  Rotamer:
    Outliers :  4.50 %
    Allowed  : 17.72 %
    Favored  : 77.78 %
  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: -4.26 (0.33), residues: 399
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -3.24 (0.25), residues: 399

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A 180 
 TYR   0.018   0.002   TYR A 143 
 PHE   0.006   0.001   PHE A 213 
 HIS   0.005   0.002   HIS C 239 

Details of bonding type rmsd
  covalent geometry    : bond        0.00467 ( 3312)
  covalent geometry    : angle       0.63024 ( 4503)
  SS BOND              : bond        0.00222 (    3)
  SS BOND              : angle       0.47392 (    6)
  hydrogen bonds       : bond        0.01682 (   44)
  hydrogen bonds       : angle       4.97470 (  132)

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

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

  798 Ramachandran restraints generated.
    399 Oldfield, 0 Emsley, 399 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  798 Ramachandran restraints generated.
    399 Oldfield, 0 Emsley, 399 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  93 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 76
  time to evaluate  : 0.144 
Fit side-chains
REVERT: A  168 GLN cc_start: 0.8989 (mt0) cc_final: 0.8729 (mt0)
REVERT: A  178 LYS cc_start: 0.8466 (OUTLIER) cc_final: 0.8188 (ttpt)
REVERT: A  180 ARG cc_start: 0.8025 (ptp-170) cc_final: 0.7526 (mtp85)
REVERT: A  208 SER cc_start: 0.8590 (m) cc_final: 0.8354 (t)
REVERT: B  180 ARG cc_start: 0.8233 (ptp-170) cc_final: 0.6078 (pmt-80)
REVERT: B  190 LEU cc_start: 0.8947 (OUTLIER) cc_final: 0.8488 (tt)
REVERT: C  139 LYS cc_start: 0.9152 (mttt) cc_final: 0.8870 (mttp)
REVERT: C  180 ARG cc_start: 0.8158 (ptp90) cc_final: 0.5687 (mmp-170)
  outliers start: 17
  outliers final: 7
  residues processed: 80
  average time/residue: 0.5387
  time to fit residues: 44.1394
Evaluate side-chains
  79 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 70
  time to evaluate  : 0.134 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  142 ILE
Chi-restraints excluded: chain A residue  178 LYS
Chi-restraints excluded: chain A residue  190 LEU
Chi-restraints excluded: chain A residue  192 MET
Chi-restraints excluded: chain B residue  134 SER
Chi-restraints excluded: chain B residue  190 LEU
Chi-restraints excluded: chain B residue  217 ILE
Chi-restraints excluded: chain C residue  144 LEU
Chi-restraints excluded: chain C residue  190 LEU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 39
   random chunks:
   chunk 34 optimal weight:   10.0000
   chunk 22 optimal weight:    4.9990
   chunk 10 optimal weight:    6.9990
   chunk 14 optimal weight:    3.9990
   chunk 31 optimal weight:    7.9990
   chunk 1 optimal weight:    3.9990
   chunk 28 optimal weight:    6.9990
   chunk 16 optimal weight:    1.9990
   chunk 25 optimal weight:    4.9990
   chunk 36 optimal weight:    5.9990
   chunk 32 optimal weight:    6.9990
   overall best weight:    3.9990

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

Flipped N/Q/H residues before XYZ refinement:
B 168 GLN
** B 239 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
C 168 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3675 r_free = 0.3675 target = 0.118740 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3504 r_free = 0.3504 target = 0.104958 restraints weight = 4152.691|
|-----------------------------------------------------------------------------|
r_work (start): 0.3514 rms_B_bonded: 1.82
r_work: 0.3425 rms_B_bonded: 1.91 restraints_weight: 0.5000
r_work: 0.3332 rms_B_bonded: 3.26 restraints_weight: 0.2500
r_work (final): 0.3332
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8848
moved from start:          0.2389

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.041   3315  Z= 0.259
  Angle     :  0.677   6.489   4509  Z= 0.376
  Chirality :  0.055   0.199    543
  Planarity :  0.002   0.014    558
  Dihedral  :  6.600  19.826    447
  Min Nonbonded Distance : 2.535

Molprobity Statistics.
  All-atom Clashscore : 7.07
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 11.28 %
    Favored  : 88.72 %
  Rotamer:
    Outliers :  4.50 %
    Allowed  : 17.46 %
    Favored  : 78.04 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -4.21 (0.33), residues: 399
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -3.20 (0.25), residues: 399

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG B 180 
 TYR   0.024   0.002   TYR C 158 
 PHE   0.007   0.001   PHE A 213 
 HIS   0.005   0.002   HIS C 239 

Details of bonding type rmsd
  covalent geometry    : bond        0.00615 ( 3312)
  covalent geometry    : angle       0.67707 ( 4503)
  SS BOND              : bond        0.00252 (    3)
  SS BOND              : angle       0.54946 (    6)
  hydrogen bonds       : bond        0.01877 (   44)
  hydrogen bonds       : angle       5.01669 (  132)

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

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

  798 Ramachandran restraints generated.
    399 Oldfield, 0 Emsley, 399 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  798 Ramachandran restraints generated.
    399 Oldfield, 0 Emsley, 399 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  85 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 68
  time to evaluate  : 0.096 
Fit side-chains
REVERT: A  168 GLN cc_start: 0.8987 (mt0) cc_final: 0.8705 (mt0)
REVERT: A  178 LYS cc_start: 0.8510 (OUTLIER) cc_final: 0.8270 (ttpt)
REVERT: A  180 ARG cc_start: 0.8080 (ptp-170) cc_final: 0.7582 (mtp85)
REVERT: A  208 SER cc_start: 0.8583 (m) cc_final: 0.8333 (t)
REVERT: B  180 ARG cc_start: 0.8242 (ptp-170) cc_final: 0.6013 (pmt-80)
REVERT: B  190 LEU cc_start: 0.8933 (OUTLIER) cc_final: 0.8481 (tt)
REVERT: C  139 LYS cc_start: 0.9170 (mttt) cc_final: 0.8865 (mttp)
REVERT: C  180 ARG cc_start: 0.8232 (ptp90) cc_final: 0.5776 (mmp-170)
REVERT: C  228 MET cc_start: 0.8921 (OUTLIER) cc_final: 0.8618 (mtm)
  outliers start: 17
  outliers final: 8
  residues processed: 76
  average time/residue: 0.5329
  time to fit residues: 41.4897
Evaluate side-chains
  78 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 67
  time to evaluate  : 0.075 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  142 ILE
Chi-restraints excluded: chain A residue  178 LYS
Chi-restraints excluded: chain A residue  190 LEU
Chi-restraints excluded: chain A residue  192 MET
Chi-restraints excluded: chain A residue  240 SER
Chi-restraints excluded: chain B residue  134 SER
Chi-restraints excluded: chain B residue  190 LEU
Chi-restraints excluded: chain B residue  217 ILE
Chi-restraints excluded: chain C residue  144 LEU
Chi-restraints excluded: chain C residue  190 LEU
Chi-restraints excluded: chain C residue  228 MET
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 39
   random chunks:
   chunk 32 optimal weight:    0.9990
   chunk 21 optimal weight:    8.9990
   chunk 11 optimal weight:    3.9990
   chunk 19 optimal weight:    4.9990
   chunk 37 optimal weight:    3.9990
   chunk 29 optimal weight:    4.9990
   chunk 38 optimal weight:    5.9990
   chunk 22 optimal weight:    9.9990
   chunk 35 optimal weight:    0.8980
   chunk 34 optimal weight:    4.9990
   chunk 26 optimal weight:    4.9990
   overall best weight:    2.9788

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

Flipped N/Q/H residues before XYZ refinement:
** B 239 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
C 168 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3699 r_free = 0.3699 target = 0.120940 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3531 r_free = 0.3531 target = 0.107163 restraints weight = 4177.874|
|-----------------------------------------------------------------------------|
r_work (start): 0.3541 rms_B_bonded: 1.82
r_work: 0.3452 rms_B_bonded: 1.93 restraints_weight: 0.5000
r_work: 0.3361 rms_B_bonded: 3.30 restraints_weight: 0.2500
r_work (final): 0.3361
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8825
moved from start:          0.2474

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.030   3315  Z= 0.200
  Angle     :  0.636   6.624   4509  Z= 0.354
  Chirality :  0.054   0.192    543
  Planarity :  0.002   0.015    558
  Dihedral  :  6.439  19.267    447
  Min Nonbonded Distance : 2.493

Molprobity Statistics.
  All-atom Clashscore : 7.07
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 11.03 %
    Favored  : 88.97 %
  Rotamer:
    Outliers :  5.03 %
    Allowed  : 17.20 %
    Favored  : 77.78 %
  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: -4.16 (0.33), residues: 399
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -3.17 (0.25), residues: 399

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG B 140 
 TYR   0.019   0.002   TYR B 143 
 PHE   0.007   0.001   PHE A 213 
 HIS   0.006   0.002   HIS C 239 

Details of bonding type rmsd
  covalent geometry    : bond        0.00472 ( 3312)
  covalent geometry    : angle       0.63644 ( 4503)
  SS BOND              : bond        0.00244 (    3)
  SS BOND              : angle       0.44735 (    6)
  hydrogen bonds       : bond        0.01717 (   44)
  hydrogen bonds       : angle       4.97348 (  132)

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

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

  798 Ramachandran restraints generated.
    399 Oldfield, 0 Emsley, 399 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  798 Ramachandran restraints generated.
    399 Oldfield, 0 Emsley, 399 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  96 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 77
  time to evaluate  : 0.134 
Fit side-chains
REVERT: A  168 GLN cc_start: 0.8990 (mt0) cc_final: 0.8716 (mt0)
REVERT: A  178 LYS cc_start: 0.8491 (OUTLIER) cc_final: 0.8157 (ttpt)
REVERT: A  180 ARG cc_start: 0.8034 (ptp-170) cc_final: 0.7527 (mtp85)
REVERT: A  208 SER cc_start: 0.8577 (m) cc_final: 0.8358 (t)
REVERT: B  178 LYS cc_start: 0.8420 (OUTLIER) cc_final: 0.7899 (ttmt)
REVERT: B  180 ARG cc_start: 0.8230 (ptp-170) cc_final: 0.6028 (pmt-80)
REVERT: B  190 LEU cc_start: 0.8923 (OUTLIER) cc_final: 0.8473 (tt)
REVERT: C  180 ARG cc_start: 0.8166 (ptp90) cc_final: 0.5707 (mmp-170)
  outliers start: 19
  outliers final: 10
  residues processed: 82
  average time/residue: 0.5197
  time to fit residues: 43.6888
Evaluate side-chains
  86 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 73
  time to evaluate  : 0.124 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  142 ILE
Chi-restraints excluded: chain A residue  178 LYS
Chi-restraints excluded: chain A residue  190 LEU
Chi-restraints excluded: chain A residue  192 MET
Chi-restraints excluded: chain B residue  134 SER
Chi-restraints excluded: chain B residue  142 ILE
Chi-restraints excluded: chain B residue  178 LYS
Chi-restraints excluded: chain B residue  190 LEU
Chi-restraints excluded: chain B residue  192 MET
Chi-restraints excluded: chain B residue  217 ILE
Chi-restraints excluded: chain C residue  144 LEU
Chi-restraints excluded: chain C residue  190 LEU
Chi-restraints excluded: chain C residue  228 MET
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 39
   random chunks:
   chunk 1 optimal weight:    3.9990
   chunk 30 optimal weight:    0.2980
   chunk 12 optimal weight:    5.9990
   chunk 38 optimal weight:    1.9990
   chunk 35 optimal weight:    0.8980
   chunk 19 optimal weight:    4.9990
   chunk 25 optimal weight:    6.9990
   chunk 34 optimal weight:    9.9990
   chunk 14 optimal weight:    5.9990
   chunk 5 optimal weight:    8.9990
   chunk 21 optimal weight:    0.8980
   overall best weight:    1.6184

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

Flipped N/Q/H residues before XYZ refinement:
A 239 HIS
B 239 HIS
C 168 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3762 r_free = 0.3762 target = 0.125803 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3599 r_free = 0.3599 target = 0.111976 restraints weight = 4069.013|
|-----------------------------------------------------------------------------|
r_work (start): 0.3614 rms_B_bonded: 1.80
r_work: 0.3527 rms_B_bonded: 1.94 restraints_weight: 0.5000
r_work: 0.3438 rms_B_bonded: 3.33 restraints_weight: 0.2500
r_work (final): 0.3438
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8779
moved from start:          0.2686

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.027   3315  Z= 0.131
  Angle     :  0.595   6.749   4509  Z= 0.328
  Chirality :  0.054   0.181    543
  Planarity :  0.002   0.014    558
  Dihedral  :  6.092  17.962    447
  Min Nonbonded Distance : 2.562

Molprobity Statistics.
  All-atom Clashscore : 6.30
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 10.03 %
    Favored  : 89.97 %
  Rotamer:
    Outliers :  3.44 %
    Allowed  : 18.78 %
    Favored  : 77.78 %
  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: -4.10 (0.33), residues: 399
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -3.12 (0.25), residues: 399

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG B 140 
 TYR   0.019   0.002   TYR C 250 
 PHE   0.007   0.001   PHE A 213 
 HIS   0.005   0.002   HIS C 239 

Details of bonding type rmsd
  covalent geometry    : bond        0.00301 ( 3312)
  covalent geometry    : angle       0.59540 ( 4503)
  SS BOND              : bond        0.00210 (    3)
  SS BOND              : angle       0.31750 (    6)
  hydrogen bonds       : bond        0.01457 (   44)
  hydrogen bonds       : angle       4.91033 (  132)

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

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

  798 Ramachandran restraints generated.
    399 Oldfield, 0 Emsley, 399 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  798 Ramachandran restraints generated.
    399 Oldfield, 0 Emsley, 399 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  93 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 80
  time to evaluate  : 0.082 
Fit side-chains
REVERT: A  168 GLN cc_start: 0.8942 (mt0) cc_final: 0.8647 (mt0)
REVERT: A  180 ARG cc_start: 0.8038 (ptp-170) cc_final: 0.7524 (mtp85)
REVERT: A  208 SER cc_start: 0.8566 (m) cc_final: 0.8341 (t)
REVERT: B  178 LYS cc_start: 0.8264 (OUTLIER) cc_final: 0.7787 (ttmt)
REVERT: B  180 ARG cc_start: 0.8177 (ptp-170) cc_final: 0.6011 (pmt-80)
REVERT: B  190 LEU cc_start: 0.8960 (OUTLIER) cc_final: 0.8491 (tt)
REVERT: C  180 ARG cc_start: 0.8141 (ptp90) cc_final: 0.5668 (mmp-170)
  outliers start: 13
  outliers final: 3
  residues processed: 84
  average time/residue: 0.5143
  time to fit residues: 44.3016
Evaluate side-chains
  80 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 75
  time to evaluate  : 0.131 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  190 LEU
Chi-restraints excluded: chain A residue  192 MET
Chi-restraints excluded: chain B residue  178 LYS
Chi-restraints excluded: chain B residue  190 LEU
Chi-restraints excluded: chain C residue  190 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 39
   random chunks:
   chunk 23 optimal weight:    2.9990
   chunk 19 optimal weight:    0.5980
   chunk 12 optimal weight:    6.9990
   chunk 9 optimal weight:    6.9990
   chunk 8 optimal weight:   10.0000
   chunk 15 optimal weight:    0.7980
   chunk 13 optimal weight:    8.9990
   chunk 7 optimal weight:    2.9990
   chunk 10 optimal weight:    7.9990
   chunk 0 optimal weight:    7.9990
   chunk 18 optimal weight:    1.9990
   overall best weight:    1.8786

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

Flipped N/Q/H residues before XYZ refinement:
C 168 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3760 r_free = 0.3760 target = 0.125633 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3598 r_free = 0.3598 target = 0.111856 restraints weight = 4103.923|
|-----------------------------------------------------------------------------|
r_work (start): 0.3623 rms_B_bonded: 1.80
r_work: 0.3532 rms_B_bonded: 1.91 restraints_weight: 0.5000
r_work: 0.3443 rms_B_bonded: 3.28 restraints_weight: 0.2500
r_work (final): 0.3443
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8786
moved from start:          0.2757

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041   3315  Z= 0.146
  Angle     :  0.630   8.565   4509  Z= 0.340
  Chirality :  0.055   0.234    543
  Planarity :  0.002   0.015    558
  Dihedral  :  6.074  18.548    447
  Min Nonbonded Distance : 2.558

Molprobity Statistics.
  All-atom Clashscore : 6.61
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 11.03 %
    Favored  : 88.97 %
  Rotamer:
    Outliers :  1.85 %
    Allowed  : 21.96 %
    Favored  : 76.19 %
  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: -4.07 (0.33), residues: 399
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -3.10 (0.25), residues: 399

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.000   0.000   ARG C 180 
 TYR   0.022   0.002   TYR A 143 
 PHE   0.007   0.001   PHE A 213 
 HIS   0.006   0.001   HIS C 239 

Details of bonding type rmsd
  covalent geometry    : bond        0.00343 ( 3312)
  covalent geometry    : angle       0.63035 ( 4503)
  SS BOND              : bond        0.00204 (    3)
  SS BOND              : angle       0.30320 (    6)
  hydrogen bonds       : bond        0.01492 (   44)
  hydrogen bonds       : angle       4.91861 (  132)

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

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

  798 Ramachandran restraints generated.
    399 Oldfield, 0 Emsley, 399 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  798 Ramachandran restraints generated.
    399 Oldfield, 0 Emsley, 399 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  83 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 76
  time to evaluate  : 0.079 
Fit side-chains
REVERT: A  168 GLN cc_start: 0.8968 (mt0) cc_final: 0.8658 (mt0)
REVERT: A  180 ARG cc_start: 0.8028 (ptp-170) cc_final: 0.7351 (mtm180)
REVERT: A  208 SER cc_start: 0.8558 (m) cc_final: 0.8354 (t)
REVERT: B  178 LYS cc_start: 0.8286 (OUTLIER) cc_final: 0.7804 (ttmt)
REVERT: B  180 ARG cc_start: 0.8170 (ptp-170) cc_final: 0.5986 (pmt-80)
REVERT: B  190 LEU cc_start: 0.8940 (OUTLIER) cc_final: 0.8473 (tt)
REVERT: C  180 ARG cc_start: 0.8152 (ptp90) cc_final: 0.5680 (mmp-170)
  outliers start: 7
  outliers final: 4
  residues processed: 78
  average time/residue: 0.5353
  time to fit residues: 42.7796
Evaluate side-chains
  79 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 73
  time to evaluate  : 0.129 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  190 LEU
Chi-restraints excluded: chain A residue  192 MET
Chi-restraints excluded: chain B residue  178 LYS
Chi-restraints excluded: chain B residue  190 LEU
Chi-restraints excluded: chain C residue  144 LEU
Chi-restraints excluded: chain C residue  190 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 39
   random chunks:
   chunk 15 optimal weight:    1.9990
   chunk 38 optimal weight:    8.9990
   chunk 5 optimal weight:    8.9990
   chunk 14 optimal weight:    3.9990
   chunk 22 optimal weight:    0.9990
   chunk 11 optimal weight:    2.9990
   chunk 34 optimal weight:   10.0000
   chunk 16 optimal weight:    0.6980
   chunk 21 optimal weight:    4.9990
   chunk 2 optimal weight:    5.9990
   chunk 4 optimal weight:    6.9990
   overall best weight:    2.1388

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

Flipped N/Q/H residues before XYZ refinement:
C 168 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3755 r_free = 0.3755 target = 0.125263 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3590 r_free = 0.3590 target = 0.111595 restraints weight = 4115.696|
|-----------------------------------------------------------------------------|
r_work (start): 0.3603 rms_B_bonded: 1.80
r_work: 0.3518 rms_B_bonded: 1.91 restraints_weight: 0.5000
r_work: 0.3430 rms_B_bonded: 3.29 restraints_weight: 0.2500
r_work (final): 0.3430
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8788
moved from start:          0.2759

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.029   3315  Z= 0.157
  Angle     :  0.632   8.617   4509  Z= 0.341
  Chirality :  0.054   0.186    543
  Planarity :  0.002   0.014    558
  Dihedral  :  6.087  19.314    447
  Min Nonbonded Distance : 2.561

Molprobity Statistics.
  All-atom Clashscore : 6.14
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 10.78 %
    Favored  : 89.22 %
  Rotamer:
    Outliers :  2.12 %
    Allowed  : 21.96 %
    Favored  : 75.93 %
  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: -4.04 (0.33), residues: 399
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -3.07 (0.25), residues: 399

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.000   0.000   ARG B 180 
 TYR   0.021   0.002   TYR A 143 
 PHE   0.004   0.001   PHE A 213 
 HIS   0.006   0.002   HIS C 239 

Details of bonding type rmsd
  covalent geometry    : bond        0.00369 ( 3312)
  covalent geometry    : angle       0.63250 ( 4503)
  SS BOND              : bond        0.00211 (    3)
  SS BOND              : angle       0.35090 (    6)
  hydrogen bonds       : bond        0.01567 (   44)
  hydrogen bonds       : angle       4.91479 (  132)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1226.05 seconds
wall clock time: 21 minutes 34.79 seconds (1294.79 seconds total)