Starting phenix.real_space_refine
on Wed Jul 23 12:02:05 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8j7n_36043/07_2025/8j7n_36043_neut.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8j7n_36043/07_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_36043/07_2025/8j7n_36043.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8j7n_36043/07_2025/8j7n_36043.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8j7n_36043/07_2025/8j7n_36043_neut.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8j7n_36043/07_2025/8j7n_36043_neut.cif"
  }
  resolution = 3.0
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.003
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 4
    Type Number    sf(0)   Gaussians
     S      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): 0.01s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/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:
    C, B
  Time building chain proxies: 5.13, per 1000 atoms: 1.57
  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 C 214 " - pdb=" SG  CYS C 253 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 214 " - pdb=" SG  CYS B 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: 1.15
  Conformation dependent library (CDL) restraints added in 536.7 milliseconds
  

  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: 0.53
  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: 0.87

  Time building geometry restraints manager: 1.40 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: 0.03
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'C'
  selection = chain 'B'
}

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:             13.500
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.130
  Check model and map are aligned:         0.020
  Set scattering table:                    0.040
  Process input model:                     17.220
  Find NCS groups from input model:        0.080
  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:             0.010
  Load rotamer database and sin/cos tables:17.990
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   49.010
-------------------------------------------------------------------------------
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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -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
 HIS   0.006   0.003   HIS A 239 
 PHE   0.005   0.001   PHE C 213 
 TYR   0.024   0.003   TYR A 125 
 ARG   0.004   0.001   ARG B 140 

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

*********************** 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  : 0.375 
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: 1.5160
  time to fit residues: 142.9934
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  : 0.499 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 39
   random chunks:
   chunk 32 optimal weight:    0.9990
   chunk 29 optimal weight:    2.9990
   chunk 16 optimal weight:    6.9990
   chunk 10 optimal weight:    3.9990
   chunk 19 optimal weight:    4.9990
   chunk 15 optimal weight:    6.9990
   chunk 30 optimal weight:    6.9990
   chunk 11 optimal weight:    0.6980
   chunk 18 optimal weight:    2.9990
   chunk 22 optimal weight:   10.0000
   chunk 35 optimal weight:   10.0000
   overall best weight:    2.3388

-------------------------------------------------------------------------------
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 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: 10

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3731 r_free = 0.3731 target = 0.124165 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3572 r_free = 0.3572 target = 0.110673 restraints weight = 4065.221|
|-----------------------------------------------------------------------------|
r_work (start): 0.3582 rms_B_bonded: 1.80
r_work: 0.3496 rms_B_bonded: 1.90 restraints_weight: 0.5000
r_work: 0.3403 rms_B_bonded: 3.25 restraints_weight: 0.2500
r_work (final): 0.3403
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8790
moved from start:          0.1784

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.027   3315  Z= 0.167
  Angle     :  0.626   6.350   4509  Z= 0.345
  Chirality :  0.054   0.185    543
  Planarity :  0.002   0.014    558
  Dihedral  :  6.497  20.218    447
  Min Nonbonded Distance : 2.575

Molprobity Statistics.
  All-atom Clashscore : 5.84
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 10.53 %
    Favored  : 89.47 %
  Rotamer:
    Outliers :  3.44 %
    Allowed  : 11.90 %
    Favored  : 84.66 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -4.83 (0.31), residues: 399
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -3.67 (0.24), residues: 399

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.005   0.002   HIS B 239 
 PHE   0.006   0.001   PHE A 213 
 TYR   0.015   0.002   TYR C 143 
 ARG   0.001   0.000   ARG B 180 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.01797 (   44)
  hydrogen bonds       : angle       5.40767 (  132)
  SS BOND              : bond        0.00234 (    3)
  SS BOND              : angle       0.45670 (    6)
  covalent geometry    : bond        0.00389 ( 3312)
  covalent geometry    : angle       0.62604 ( 4503)

*********************** 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
  94 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 81
  time to evaluate  : 0.315 
Fit side-chains
REVERT: A  168 GLN cc_start: 0.8974 (mt0) cc_final: 0.8718 (mt0)
REVERT: A  178 LYS cc_start: 0.8387 (OUTLIER) cc_final: 0.8127 (ttpt)
REVERT: B  129 LYS cc_start: 0.9115 (ptpp) cc_final: 0.8886 (ptpt)
REVERT: B  168 GLN cc_start: 0.9029 (mt0) cc_final: 0.8822 (mt0)
REVERT: B  178 LYS cc_start: 0.8461 (OUTLIER) cc_final: 0.8261 (tppt)
REVERT: B  180 ARG cc_start: 0.8218 (ptp-170) cc_final: 0.6024 (pmt-80)
REVERT: B  190 LEU cc_start: 0.8991 (OUTLIER) cc_final: 0.8508 (tt)
REVERT: C  168 GLN cc_start: 0.8780 (mt0) cc_final: 0.8566 (mt0)
REVERT: C  180 ARG cc_start: 0.8064 (ptp-170) cc_final: 0.7774 (ptp90)
REVERT: C  250 TYR cc_start: 0.7761 (t80) cc_final: 0.7491 (t80)
  outliers start: 13
  outliers final: 2
  residues processed: 83
  average time/residue: 2.2585
  time to fit residues: 192.0832
Evaluate side-chains
  79 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 74
  time to evaluate  : 1.079 
-------------------------------------------------------------------------------
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  178 LYS
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 25 optimal weight:    4.9990
   chunk 14 optimal weight:    3.9990
   chunk 3 optimal weight:    7.9990
   chunk 19 optimal weight:    0.9980
   chunk 13 optimal weight:    0.9980
   chunk 34 optimal weight:    0.2980
   chunk 7 optimal weight:    3.9990
   chunk 8 optimal weight:   10.0000
   chunk 23 optimal weight:    3.9990
   chunk 17 optimal weight:    0.0970
   chunk 11 optimal weight:    5.9990
   overall best weight:    1.2780

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

Flipped N/Q/H residues before XYZ refinement:
A 229 GLN
A 239 HIS
B 223 ASN
B 239 HIS

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3777 r_free = 0.3777 target = 0.127634 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3617 r_free = 0.3617 target = 0.113831 restraints weight = 4020.219|
|-----------------------------------------------------------------------------|
r_work (start): 0.3630 rms_B_bonded: 1.82
r_work: 0.3546 rms_B_bonded: 1.94 restraints_weight: 0.5000
r_work: 0.3456 rms_B_bonded: 3.34 restraints_weight: 0.2500
r_work (final): 0.3456
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8756
moved from start:          0.2297

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.017   3315  Z= 0.108
  Angle     :  0.557   6.905   4509  Z= 0.307
  Chirality :  0.053   0.173    543
  Planarity :  0.002   0.011    558
  Dihedral  :  6.049  18.666    447
  Min Nonbonded Distance : 2.564

Molprobity Statistics.
  All-atom Clashscore : 5.99
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.52 %
    Favored  : 90.48 %
  Rotamer:
    Outliers :  3.17 %
    Allowed  : 15.08 %
    Favored  : 81.75 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -4.57 (0.32), residues: 399
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -3.47 (0.24), residues: 399

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.005   0.002   HIS C 239 
 PHE   0.006   0.001   PHE A 213 
 TYR   0.015   0.001   TYR A 250 
 ARG   0.001   0.000   ARG A 247 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.01415 (   44)
  hydrogen bonds       : angle       4.99385 (  132)
  SS BOND              : bond        0.00170 (    3)
  SS BOND              : angle       0.30677 (    6)
  covalent geometry    : bond        0.00244 ( 3312)
  covalent geometry    : angle       0.55750 ( 4503)

*********************** 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
  96 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 84
  time to evaluate  : 0.901 
Fit side-chains
REVERT: A  168 GLN cc_start: 0.8970 (mt0) cc_final: 0.8681 (mt0)
REVERT: A  178 LYS cc_start: 0.8281 (OUTLIER) cc_final: 0.8037 (ttpt)
REVERT: A  208 SER cc_start: 0.8514 (m) cc_final: 0.8296 (t)
REVERT: A  250 TYR cc_start: 0.7369 (t80) cc_final: 0.7020 (t80)
REVERT: B  168 GLN cc_start: 0.8992 (mt0) cc_final: 0.8785 (mt0)
REVERT: B  180 ARG cc_start: 0.8167 (ptp-170) cc_final: 0.5965 (pmt-80)
REVERT: B  190 LEU cc_start: 0.8972 (OUTLIER) cc_final: 0.8482 (tt)
REVERT: C  180 ARG cc_start: 0.7995 (ptp-170) cc_final: 0.5659 (mmp-170)
REVERT: C  250 TYR cc_start: 0.7762 (t80) cc_final: 0.7475 (t80)
  outliers start: 12
  outliers final: 4
  residues processed: 86
  average time/residue: 1.2880
  time to fit residues: 114.0966
Evaluate side-chains
  88 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 82
  time to evaluate  : 0.428 
-------------------------------------------------------------------------------
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
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 6 optimal weight:    9.9990
   chunk 37 optimal weight:    5.9990
   chunk 36 optimal weight:    1.9990
   chunk 33 optimal weight:    5.9990
   chunk 19 optimal weight:    1.9990
   chunk 38 optimal weight:    7.9990
   chunk 2 optimal weight:   10.0000
   chunk 25 optimal weight:    2.9990
   chunk 1 optimal weight:    8.9990
   chunk 13 optimal weight:    7.9990
   chunk 21 optimal weight:    7.9990
   overall best weight:    3.7990

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

Flipped N/Q/H residues before XYZ refinement:
A 223 ASN
C 168 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3662 r_free = 0.3662 target = 0.118478 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3493 r_free = 0.3493 target = 0.104662 restraints weight = 4137.182|
|-----------------------------------------------------------------------------|
r_work (start): 0.3511 rms_B_bonded: 1.78
r_work: 0.3426 rms_B_bonded: 1.88 restraints_weight: 0.5000
r_work: 0.3337 rms_B_bonded: 3.20 restraints_weight: 0.2500
r_work (final): 0.3337
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8849
moved from start:          0.2240

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.035   3315  Z= 0.244
  Angle     :  0.656   6.678   4509  Z= 0.366
  Chirality :  0.055   0.201    543
  Planarity :  0.002   0.014    558
  Dihedral  :  6.555  19.177    447
  Min Nonbonded Distance : 2.574

Molprobity Statistics.
  All-atom Clashscore : 6.45
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 11.03 %
    Favored  : 88.97 %
  Rotamer:
    Outliers :  4.76 %
    Allowed  : 15.08 %
    Favored  : 80.16 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -4.43 (0.32), residues: 399
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -3.37 (0.24), residues: 399

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.005   0.002   HIS C 239 
 PHE   0.007   0.001   PHE A 213 
 TYR   0.020   0.002   TYR C 158 
 ARG   0.001   0.000   ARG B 180 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.01769 (   44)
  hydrogen bonds       : angle       4.98171 (  132)
  SS BOND              : bond        0.00269 (    3)
  SS BOND              : angle       0.59331 (    6)
  covalent geometry    : bond        0.00577 ( 3312)
  covalent geometry    : angle       0.65593 ( 4503)

*********************** 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
  96 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 78
  time to evaluate  : 0.380 
Fit side-chains
REVERT: A  168 GLN cc_start: 0.8989 (mt0) cc_final: 0.8702 (mt0)
REVERT: A  178 LYS cc_start: 0.8516 (OUTLIER) cc_final: 0.8270 (ttpt)
REVERT: B  168 GLN cc_start: 0.9055 (mt0) cc_final: 0.8853 (mt0)
REVERT: B  180 ARG cc_start: 0.8247 (ptp-170) cc_final: 0.6085 (pmt-80)
REVERT: B  190 LEU cc_start: 0.8945 (OUTLIER) cc_final: 0.8478 (tt)
REVERT: C  180 ARG cc_start: 0.8103 (ptp-170) cc_final: 0.7800 (ptp90)
REVERT: C  246 GLU cc_start: 0.8660 (mt-10) cc_final: 0.8043 (mm-30)
  outliers start: 18
  outliers final: 6
  residues processed: 83
  average time/residue: 1.3611
  time to fit residues: 115.7209
Evaluate side-chains
  84 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 76
  time to evaluate  : 0.390 
-------------------------------------------------------------------------------
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
Chi-restraints excluded: chain C residue  250 TYR
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 39
   random chunks:
   chunk 2 optimal weight:    1.9990
   chunk 36 optimal weight:    2.9990
   chunk 3 optimal weight:    7.9990
   chunk 7 optimal weight:    5.9990
   chunk 5 optimal weight:   10.0000
   chunk 9 optimal weight:    8.9990
   chunk 26 optimal weight:    3.9990
   chunk 12 optimal weight:    5.9990
   chunk 27 optimal weight:    1.9990
   chunk 24 optimal weight:    0.0020
   chunk 19 optimal weight:    8.9990
   overall best weight:    2.1996

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3703 r_free = 0.3703 target = 0.121711 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3543 r_free = 0.3543 target = 0.107952 restraints weight = 4091.289|
|-----------------------------------------------------------------------------|
r_work (start): 0.3543 rms_B_bonded: 1.80
r_work: 0.3458 rms_B_bonded: 1.90 restraints_weight: 0.5000
r_work: 0.3367 rms_B_bonded: 3.26 restraints_weight: 0.2500
r_work (final): 0.3367
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8799
moved from start:          0.2491

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.023   3315  Z= 0.158
  Angle     :  0.598   6.655   4509  Z= 0.333
  Chirality :  0.054   0.185    543
  Planarity :  0.002   0.012    558
  Dihedral  :  6.230  18.583    447
  Min Nonbonded Distance : 2.523

Molprobity Statistics.
  All-atom Clashscore : 6.76
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.77 %
    Favored  : 90.23 %
  Rotamer:
    Outliers :  4.76 %
    Allowed  : 16.67 %
    Favored  : 78.57 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -4.28 (0.32), residues: 399
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -3.26 (0.25), residues: 399

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.005   0.002   HIS C 239 
 PHE   0.006   0.001   PHE A 213 
 TYR   0.016   0.002   TYR A 143 
 ARG   0.001   0.000   ARG A 140 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.01532 (   44)
  hydrogen bonds       : angle       4.93312 (  132)
  SS BOND              : bond        0.00180 (    3)
  SS BOND              : angle       0.40084 (    6)
  covalent geometry    : bond        0.00365 ( 3312)
  covalent geometry    : angle       0.59778 ( 4503)

*********************** 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
  98 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 80
  time to evaluate  : 0.375 
Fit side-chains
REVERT: A  168 GLN cc_start: 0.8950 (mt0) cc_final: 0.8641 (mt0)
REVERT: A  178 LYS cc_start: 0.8338 (OUTLIER) cc_final: 0.8000 (ttpt)
REVERT: B  178 LYS cc_start: 0.8263 (OUTLIER) cc_final: 0.7637 (ttmt)
REVERT: B  180 ARG cc_start: 0.8193 (ptp-170) cc_final: 0.6007 (pmt-80)
REVERT: B  190 LEU cc_start: 0.8917 (OUTLIER) cc_final: 0.8453 (tt)
REVERT: C  250 TYR cc_start: 0.8209 (OUTLIER) cc_final: 0.7846 (t80)
  outliers start: 18
  outliers final: 6
  residues processed: 83
  average time/residue: 1.2492
  time to fit residues: 106.3082
Evaluate side-chains
  85 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 75
  time to evaluate  : 0.344 
-------------------------------------------------------------------------------
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  178 LYS
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  250 TYR
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 39
   random chunks:
   chunk 26 optimal weight:    7.9990
   chunk 21 optimal weight:    2.9990
   chunk 15 optimal weight:    9.9990
   chunk 24 optimal weight:    0.9990
   chunk 27 optimal weight:    0.8980
   chunk 10 optimal weight:    8.9990
   chunk 12 optimal weight:    0.9990
   chunk 25 optimal weight:    0.8980
   chunk 22 optimal weight:    9.9990
   chunk 34 optimal weight:   10.0000
   chunk 33 optimal weight:    2.9990
   overall best weight:    1.3586

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3758 r_free = 0.3758 target = 0.125902 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3603 r_free = 0.3603 target = 0.112110 restraints weight = 4144.636|
|-----------------------------------------------------------------------------|
r_work (start): 0.3606 rms_B_bonded: 1.81
r_work: 0.3522 rms_B_bonded: 1.94 restraints_weight: 0.5000
r_work: 0.3432 rms_B_bonded: 3.33 restraints_weight: 0.2500
r_work (final): 0.3432
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8755
moved from start:          0.2696

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.018   3315  Z= 0.115
  Angle     :  0.560   6.615   4509  Z= 0.309
  Chirality :  0.053   0.172    543
  Planarity :  0.002   0.012    558
  Dihedral  :  5.917  17.950    447
  Min Nonbonded Distance : 2.566

Molprobity Statistics.
  All-atom Clashscore : 5.68
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 10.53 %
    Favored  : 89.47 %
  Rotamer:
    Outliers :  3.97 %
    Allowed  : 17.72 %
    Favored  : 78.31 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -4.16 (0.33), residues: 399
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -3.16 (0.25), residues: 399

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.005   0.001   HIS C 239 
 PHE   0.005   0.001   PHE A 213 
 TYR   0.014   0.001   TYR A 250 
 ARG   0.001   0.000   ARG B 140 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.01342 (   44)
  hydrogen bonds       : angle       4.87207 (  132)
  SS BOND              : bond        0.00155 (    3)
  SS BOND              : angle       0.30848 (    6)
  covalent geometry    : bond        0.00259 ( 3312)
  covalent geometry    : angle       0.55993 ( 4503)

*********************** 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
  101 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 86
  time to evaluate  : 0.364 
Fit side-chains
REVERT: A  168 GLN cc_start: 0.8899 (mt0) cc_final: 0.8559 (mt0)
REVERT: B  178 LYS cc_start: 0.8153 (OUTLIER) cc_final: 0.7549 (ttmt)
REVERT: B  180 ARG cc_start: 0.8103 (ptp-170) cc_final: 0.5910 (pmt-80)
REVERT: B  190 LEU cc_start: 0.8945 (OUTLIER) cc_final: 0.8491 (tt)
REVERT: C  180 ARG cc_start: 0.8029 (ptp-170) cc_final: 0.5555 (mmp-170)
REVERT: C  246 GLU cc_start: 0.8574 (mt-10) cc_final: 0.7911 (mm-30)
REVERT: C  250 TYR cc_start: 0.8041 (OUTLIER) cc_final: 0.7677 (t80)
  outliers start: 15
  outliers final: 4
  residues processed: 89
  average time/residue: 1.1887
  time to fit residues: 108.5976
Evaluate side-chains
  86 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 79
  time to evaluate  : 0.352 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  190 LEU
Chi-restraints excluded: chain B residue  134 SER
Chi-restraints excluded: chain B residue  178 LYS
Chi-restraints excluded: chain B residue  190 LEU
Chi-restraints excluded: chain B residue  217 ILE
Chi-restraints excluded: chain C residue  190 LEU
Chi-restraints excluded: chain C residue  250 TYR
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 39
   random chunks:
   chunk 22 optimal weight:    3.9990
   chunk 19 optimal weight:    3.9990
   chunk 17 optimal weight:    1.9990
   chunk 9 optimal weight:    5.9990
   chunk 24 optimal weight:    0.0050
   chunk 4 optimal weight:    9.9990
   chunk 7 optimal weight:   10.0000
   chunk 25 optimal weight:    5.9990
   chunk 31 optimal weight:   10.0000
   chunk 35 optimal weight:    9.9990
   chunk 18 optimal weight:    3.9990
   overall best weight:    2.8002

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

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

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3703 r_free = 0.3703 target = 0.121223 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3535 r_free = 0.3535 target = 0.107477 restraints weight = 4051.182|
|-----------------------------------------------------------------------------|
r_work (start): 0.3550 rms_B_bonded: 1.80
r_work: 0.3468 rms_B_bonded: 1.90 restraints_weight: 0.5000
r_work: 0.3377 rms_B_bonded: 3.27 restraints_weight: 0.2500
r_work (final): 0.3377
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8819
moved from start:          0.2593

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= 0.189
  Angle     :  0.609   6.411   4509  Z= 0.340
  Chirality :  0.054   0.186    543
  Planarity :  0.002   0.013    558
  Dihedral  :  6.187  17.965    447
  Min Nonbonded Distance : 2.562

Molprobity Statistics.
  All-atom Clashscore : 7.53
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 11.78 %
    Favored  : 88.22 %
  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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -4.16 (0.33), residues: 399
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -3.16 (0.25), residues: 399

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.005   0.002   HIS C 239 
 PHE   0.006   0.001   PHE A 213 
 TYR   0.019   0.002   TYR C 158 
 ARG   0.001   0.000   ARG A 140 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.01636 (   44)
  hydrogen bonds       : angle       4.93625 (  132)
  SS BOND              : bond        0.00217 (    3)
  SS BOND              : angle       0.42355 (    6)
  covalent geometry    : bond        0.00447 ( 3312)
  covalent geometry    : angle       0.60910 ( 4503)

*********************** 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
  89 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 72
  time to evaluate  : 0.363 
Fit side-chains
REVERT: A  168 GLN cc_start: 0.8934 (mt0) cc_final: 0.8625 (mt0)
REVERT: A  217 ILE cc_start: 0.8789 (OUTLIER) cc_final: 0.8357 (mt)
REVERT: B  178 LYS cc_start: 0.8318 (OUTLIER) cc_final: 0.7730 (ttmt)
REVERT: B  180 ARG cc_start: 0.8190 (ptp-170) cc_final: 0.6032 (pmt-80)
REVERT: B  190 LEU cc_start: 0.8898 (OUTLIER) cc_final: 0.8449 (tt)
REVERT: C  180 ARG cc_start: 0.8175 (ptp-170) cc_final: 0.5710 (mmp-170)
REVERT: C  250 TYR cc_start: 0.8353 (OUTLIER) cc_final: 0.7873 (t80)
  outliers start: 17
  outliers final: 6
  residues processed: 79
  average time/residue: 1.2788
  time to fit residues: 103.5517
Evaluate side-chains
  76 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 66
  time to evaluate  : 0.345 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  190 LEU
Chi-restraints excluded: chain A residue  192 MET
Chi-restraints excluded: chain A residue  217 ILE
Chi-restraints excluded: chain B residue  134 SER
Chi-restraints excluded: chain B residue  178 LYS
Chi-restraints excluded: chain B residue  190 LEU
Chi-restraints excluded: chain B residue  232 VAL
Chi-restraints excluded: chain C residue  144 LEU
Chi-restraints excluded: chain C residue  190 LEU
Chi-restraints excluded: chain C residue  250 TYR
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 39
   random chunks:
   chunk 26 optimal weight:    8.9990
   chunk 9 optimal weight:    9.9990
   chunk 15 optimal weight:    0.8980
   chunk 28 optimal weight:    8.9990
   chunk 6 optimal weight:    3.9990
   chunk 38 optimal weight:    6.9990
   chunk 10 optimal weight:    2.9990
   chunk 34 optimal weight:    7.9990
   chunk 37 optimal weight:    3.9990
   chunk 20 optimal weight:    4.9990
   chunk 29 optimal weight:    1.9990
   overall best weight:    2.7788

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

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

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3704 r_free = 0.3704 target = 0.121218 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3537 r_free = 0.3537 target = 0.107184 restraints weight = 4045.279|
|-----------------------------------------------------------------------------|
r_work (start): 0.3553 rms_B_bonded: 1.87
r_work: 0.3456 rms_B_bonded: 1.96 restraints_weight: 0.5000
r_work: 0.3362 rms_B_bonded: 3.38 restraints_weight: 0.2500
r_work (final): 0.3362
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8811
moved from start:          0.2668

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.037   3315  Z= 0.190
  Angle     :  0.626   6.705   4509  Z= 0.346
  Chirality :  0.055   0.182    543
  Planarity :  0.002   0.014    558
  Dihedral  :  6.226  18.257    447
  Min Nonbonded Distance : 2.561

Molprobity Statistics.
  All-atom Clashscore : 7.07
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 11.03 %
    Favored  : 88.97 %
  Rotamer:
    Outliers :  4.50 %
    Allowed  : 18.25 %
    Favored  : 77.25 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -4.12 (0.33), residues: 399
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -3.14 (0.25), residues: 399

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.005   0.002   HIS C 239 
 PHE   0.004   0.001   PHE B 213 
 TYR   0.019   0.002   TYR C 158 
 ARG   0.001   0.000   ARG A 140 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.01626 (   44)
  hydrogen bonds       : angle       4.97464 (  132)
  SS BOND              : bond        0.00216 (    3)
  SS BOND              : angle       0.43885 (    6)
  covalent geometry    : bond        0.00454 ( 3312)
  covalent geometry    : angle       0.62611 ( 4503)

*********************** 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
  88 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 71
  time to evaluate  : 0.376 
Fit side-chains
REVERT: A  168 GLN cc_start: 0.8919 (mt0) cc_final: 0.8599 (mt0)
REVERT: A  180 ARG cc_start: 0.7936 (ptp-170) cc_final: 0.7312 (mtm180)
REVERT: B  178 LYS cc_start: 0.8299 (OUTLIER) cc_final: 0.7692 (ttmt)
REVERT: B  180 ARG cc_start: 0.8219 (ptp-170) cc_final: 0.6045 (pmt-80)
REVERT: B  190 LEU cc_start: 0.8859 (OUTLIER) cc_final: 0.8403 (tt)
REVERT: B  212 ASP cc_start: 0.9236 (m-30) cc_final: 0.8986 (m-30)
REVERT: C  178 LYS cc_start: 0.8584 (OUTLIER) cc_final: 0.8079 (ttmt)
REVERT: C  180 ARG cc_start: 0.8147 (ptp-170) cc_final: 0.5691 (mmp-170)
REVERT: C  250 TYR cc_start: 0.8385 (OUTLIER) cc_final: 0.7852 (t80)
  outliers start: 17
  outliers final: 5
  residues processed: 77
  average time/residue: 1.3581
  time to fit residues: 107.1761
Evaluate side-chains
  76 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 67
  time to evaluate  : 0.379 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  190 LEU
Chi-restraints excluded: chain B residue  134 SER
Chi-restraints excluded: chain B residue  178 LYS
Chi-restraints excluded: chain B residue  190 LEU
Chi-restraints excluded: chain B residue  232 VAL
Chi-restraints excluded: chain C residue  144 LEU
Chi-restraints excluded: chain C residue  178 LYS
Chi-restraints excluded: chain C residue  217 ILE
Chi-restraints excluded: chain C residue  250 TYR
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 39
   random chunks:
   chunk 17 optimal weight:    1.9990
   chunk 16 optimal weight:    8.9990
   chunk 5 optimal weight:    7.9990
   chunk 13 optimal weight:    0.0270
   chunk 38 optimal weight:    6.9990
   chunk 1 optimal weight:    5.9990
   chunk 29 optimal weight:    4.9990
   chunk 26 optimal weight:    8.9990
   chunk 32 optimal weight:    0.4980
   chunk 18 optimal weight:    2.9990
   chunk 11 optimal weight:    0.7980
   overall best weight:    1.2642

-------------------------------------------------------------------------------
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 = 0.3786 r_free = 0.3786 target = 0.127631 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3627 r_free = 0.3627 target = 0.113559 restraints weight = 4033.506|
|-----------------------------------------------------------------------------|
r_work (start): 0.3636 rms_B_bonded: 1.82
r_work: 0.3545 rms_B_bonded: 1.94 restraints_weight: 0.5000
r_work: 0.3453 rms_B_bonded: 3.37 restraints_weight: 0.2500
r_work (final): 0.3453
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8770
moved from start:          0.2894

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.021   3315  Z= 0.114
  Angle     :  0.568   6.983   4509  Z= 0.313
  Chirality :  0.053   0.173    543
  Planarity :  0.002   0.014    558
  Dihedral  :  5.810  17.715    447
  Min Nonbonded Distance : 2.560

Molprobity Statistics.
  All-atom Clashscore : 6.61
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.77 %
    Favored  : 91.23 %
  Rotamer:
    Outliers :  3.17 %
    Allowed  : 19.58 %
    Favored  : 77.25 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -4.06 (0.33), residues: 399
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -3.09 (0.25), residues: 399

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.005   0.001   HIS C 239 
 PHE   0.004   0.001   PHE B 213 
 TYR   0.017   0.001   TYR A 250 
 ARG   0.001   0.000   ARG A 140 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.01328 (   44)
  hydrogen bonds       : angle       4.99728 (  132)
  SS BOND              : bond        0.00218 (    3)
  SS BOND              : angle       0.26929 (    6)
  covalent geometry    : bond        0.00260 ( 3312)
  covalent geometry    : angle       0.56814 ( 4503)

*********************** 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
  86 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 74
  time to evaluate  : 0.499 
Fit side-chains
REVERT: A  168 GLN cc_start: 0.8885 (mt0) cc_final: 0.8569 (mt0)
REVERT: A  178 LYS cc_start: 0.8283 (ttmt) cc_final: 0.7951 (mtpm)
REVERT: A  180 ARG cc_start: 0.7909 (ptp-170) cc_final: 0.7304 (mtm180)
REVERT: B  178 LYS cc_start: 0.8175 (OUTLIER) cc_final: 0.7908 (mtpm)
REVERT: B  180 ARG cc_start: 0.8180 (ptp-170) cc_final: 0.5965 (pmt-80)
REVERT: B  190 LEU cc_start: 0.8891 (OUTLIER) cc_final: 0.8426 (tt)
REVERT: C  178 LYS cc_start: 0.8329 (OUTLIER) cc_final: 0.7793 (ttmt)
REVERT: C  180 ARG cc_start: 0.8071 (ptp-170) cc_final: 0.5614 (mmp-170)
REVERT: C  250 TYR cc_start: 0.8027 (OUTLIER) cc_final: 0.7577 (t80)
  outliers start: 12
  outliers final: 5
  residues processed: 79
  average time/residue: 1.3710
  time to fit residues: 111.1473
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  : 0.392 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  190 LEU
Chi-restraints excluded: chain B residue  134 SER
Chi-restraints excluded: chain B residue  178 LYS
Chi-restraints excluded: chain B residue  190 LEU
Chi-restraints excluded: chain B residue  232 VAL
Chi-restraints excluded: chain C residue  144 LEU
Chi-restraints excluded: chain C residue  178 LYS
Chi-restraints excluded: chain C residue  190 LEU
Chi-restraints excluded: chain C residue  250 TYR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 39
   random chunks:
   chunk 21 optimal weight:    6.9990
   chunk 20 optimal weight:    7.9990
   chunk 33 optimal weight:   20.0000
   chunk 1 optimal weight:    7.9990
   chunk 3 optimal weight:    8.9990
   chunk 26 optimal weight:    8.9990
   chunk 27 optimal weight:    2.9990
   chunk 11 optimal weight:    5.9990
   chunk 36 optimal weight:    6.9990
   chunk 24 optimal weight:    1.9990
   chunk 15 optimal weight:    5.9990
   overall best weight:    4.7990

-------------------------------------------------------------------------------
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 = 0.3655 r_free = 0.3655 target = 0.117049 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3486 r_free = 0.3486 target = 0.103102 restraints weight = 4094.211|
|-----------------------------------------------------------------------------|
r_work (start): 0.3497 rms_B_bonded: 1.87
r_work: 0.3392 rms_B_bonded: 1.95 restraints_weight: 0.5000
r_work: 0.3298 rms_B_bonded: 3.33 restraints_weight: 0.2500
r_work (final): 0.3298
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8854
moved from start:          0.2587

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.007   0.055   3315  Z= 0.302
  Angle     :  0.714   8.491   4509  Z= 0.395
  Chirality :  0.056   0.210    543
  Planarity :  0.003   0.016    558
  Dihedral  :  6.561  18.447    447
  Min Nonbonded Distance : 2.575

Molprobity Statistics.
  All-atom Clashscore : 8.29
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 11.78 %
    Favored  : 88.22 %
  Rotamer:
    Outliers :  3.70 %
    Allowed  : 19.31 %
    Favored  : 76.98 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -4.13 (0.33), residues: 399
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -3.14 (0.25), residues: 399

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.005   0.002   HIS A 239 
 PHE   0.005   0.001   PHE A 213 
 TYR   0.032   0.002   TYR C 158 
 ARG   0.002   0.000   ARG A 180 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02013 (   44)
  hydrogen bonds       : angle       5.07561 (  132)
  SS BOND              : bond        0.00285 (    3)
  SS BOND              : angle       0.61791 (    6)
  covalent geometry    : bond        0.00724 ( 3312)
  covalent geometry    : angle       0.71432 ( 4503)

********************** 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
  81 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 67
  time to evaluate  : 0.390 
Fit side-chains
REVERT: A  168 GLN cc_start: 0.8944 (mt0) cc_final: 0.8663 (mt0)
REVERT: A  180 ARG cc_start: 0.7998 (ptp-170) cc_final: 0.7359 (mtp85)
REVERT: B  178 LYS cc_start: 0.8443 (OUTLIER) cc_final: 0.7879 (ttmt)
REVERT: B  180 ARG cc_start: 0.8252 (ptp-170) cc_final: 0.5996 (pmt-80)
REVERT: B  190 LEU cc_start: 0.8863 (OUTLIER) cc_final: 0.8407 (tt)
REVERT: C  178 LYS cc_start: 0.8693 (OUTLIER) cc_final: 0.8253 (ttmt)
REVERT: C  180 ARG cc_start: 0.8239 (ptp-170) cc_final: 0.8021 (ptp90)
  outliers start: 14
  outliers final: 5
  residues processed: 73
  average time/residue: 1.7381
  time to fit residues: 129.8956
Evaluate side-chains
  72 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 64
  time to evaluate  : 0.383 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  190 LEU
Chi-restraints excluded: chain B residue  134 SER
Chi-restraints excluded: chain B residue  178 LYS
Chi-restraints excluded: chain B residue  190 LEU
Chi-restraints excluded: chain B residue  232 VAL
Chi-restraints excluded: chain C residue  178 LYS
Chi-restraints excluded: chain C residue  190 LEU
Chi-restraints excluded: chain C residue  250 TYR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 39
   random chunks:
   chunk 4 optimal weight:    7.9990
   chunk 36 optimal weight:    0.9990
   chunk 3 optimal weight:    4.9990
   chunk 13 optimal weight:    3.9990
   chunk 0 optimal weight:    7.9990
   chunk 30 optimal weight:    5.9990
   chunk 38 optimal weight:    5.9990
   chunk 7 optimal weight:    2.9990
   chunk 35 optimal weight:    3.9990
   chunk 23 optimal weight:    0.9980
   chunk 19 optimal weight:    6.9990
   overall best weight:    2.5988

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3709 r_free = 0.3709 target = 0.121114 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3541 r_free = 0.3541 target = 0.107045 restraints weight = 4088.414|
|-----------------------------------------------------------------------------|
r_work (start): 0.3555 rms_B_bonded: 1.88
r_work: 0.3457 rms_B_bonded: 1.99 restraints_weight: 0.5000
r_work: 0.3363 rms_B_bonded: 3.41 restraints_weight: 0.2500
r_work (final): 0.3363
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8815
moved from start:          0.2733

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.034   3315  Z= 0.184
  Angle     :  0.649   6.683   4509  Z= 0.357
  Chirality :  0.055   0.194    543
  Planarity :  0.002   0.015    558
  Dihedral  :  6.285  18.265    447
  Min Nonbonded Distance : 2.481

Molprobity Statistics.
  All-atom Clashscore : 8.29
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 10.53 %
    Favored  : 89.47 %
  Rotamer:
    Outliers :  2.91 %
    Allowed  : 19.05 %
    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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -4.11 (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
 HIS   0.005   0.002   HIS C 239 
 PHE   0.005   0.001   PHE A 213 
 TYR   0.020   0.002   TYR B 143 
 ARG   0.001   0.000   ARG A 140 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.01689 (   44)
  hydrogen bonds       : angle       5.11094 (  132)
  SS BOND              : bond        0.00233 (    3)
  SS BOND              : angle       0.36722 (    6)
  covalent geometry    : bond        0.00436 ( 3312)
  covalent geometry    : angle       0.64921 ( 4503)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 4082.21 seconds
wall clock time: 73 minutes 58.37 seconds (4438.37 seconds total)