Starting phenix.real_space_refine
on Fri May  9 17:19:23 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8j7n_36043/05_2025/8j7n_36043_neut.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8j7n_36043/05_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_36043/05_2025/8j7n_36043.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8j7n_36043/05_2025/8j7n_36043.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8j7n_36043/05_2025/8j7n_36043_neut.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8j7n_36043/05_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-5687/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: 2.47, per 1000 atoms: 0.76
  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: 0.81
  Conformation dependent library (CDL) restraints added in 405.7 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: 0.60
  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: 0.77

  Time building geometry restraints manager: 0.97 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: 0.02
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:             1.370
  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:          0.150
  Check model and map are aligned:         0.030
  Set scattering table:                    0.040
  Process input model:                     12.940
  Find NCS groups from input model:        0.060
  Set up NCS constraints:                  0.000
  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:10.060
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   24.650
-------------------------------------------------------------------------------
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  : 0.360 
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: 1.2607
  time to fit residues: 118.8065
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  : 0.375 
-------------------------------------------------------------------------------
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 = 0.110674 restraints weight = 4065.026|
|-----------------------------------------------------------------------------|
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: 0.3404 rms_B_bonded: 3.25 restraints_weight: 0.2500
r_work (final): 0.3404
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8790
moved from start:          0.1785

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       5.40766 (  132)
  SS BOND              : bond        0.00234 (    3)
  SS BOND              : angle       0.45672 (    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  : 0.348 
Fit side-chains
REVERT: A  168 GLN cc_start: 0.8974 (mt0) cc_final: 0.8718 (mt0)
REVERT: A  178 LYS cc_start: 0.8390 (OUTLIER) cc_final: 0.8129 (ttpt)
REVERT: B  129 LYS cc_start: 0.9115 (ptpp) cc_final: 0.8885 (ptpt)
REVERT: B  168 GLN cc_start: 0.9029 (mt0) cc_final: 0.8823 (mt0)
REVERT: B  178 LYS cc_start: 0.8463 (OUTLIER) cc_final: 0.8262 (tppt)
REVERT: B  180 ARG cc_start: 0.8216 (ptp-170) cc_final: 0.6025 (pmt-80)
REVERT: B  190 LEU cc_start: 0.8993 (OUTLIER) cc_final: 0.8509 (tt)
REVERT: C  168 GLN cc_start: 0.8781 (mt0) cc_final: 0.8566 (mt0)
REVERT: C  180 ARG cc_start: 0.8064 (ptp-170) cc_final: 0.7775 (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: 1.2742
  time to fit residues: 108.5204
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  : 0.356 
-------------------------------------------------------------------------------
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:    8.9990
   chunk 19 optimal weight:    0.8980
   chunk 13 optimal weight:    4.9990
   chunk 34 optimal weight:    9.9990
   chunk 7 optimal weight:    4.9990
   chunk 8 optimal weight:   10.0000
   chunk 23 optimal weight:    0.7980
   chunk 17 optimal weight:    1.9990
   chunk 11 optimal weight:    5.9990
   overall best weight:    2.5386

-------------------------------------------------------------------------------
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 ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 239 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 223 ASN
** 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 = 0.3709 r_free = 0.3709 target = 0.122341 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3545 r_free = 0.3545 target = 0.108430 restraints weight = 4045.999|
|-----------------------------------------------------------------------------|
r_work (start): 0.3562 rms_B_bonded: 1.81
r_work: 0.3477 rms_B_bonded: 1.92 restraints_weight: 0.5000
r_work: 0.3386 rms_B_bonded: 3.27 restraints_weight: 0.2500
r_work (final): 0.3386
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8810
moved from start:          0.2062

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.028   3315  Z= 0.175
  Angle     :  0.607   6.782   4509  Z= 0.337
  Chirality :  0.053   0.187    543
  Planarity :  0.002   0.012    558
  Dihedral  :  6.412  19.748    447
  Min Nonbonded Distance : 2.563

Molprobity Statistics.
  All-atom Clashscore : 6.30
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 11.78 %
    Favored  : 88.22 %
  Rotamer:
    Outliers :  3.70 %
    Allowed  : 14.81 %
    Favored  : 81.48 %
  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: -4.61 (0.31), residues: 399
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -3.50 (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   0.017   0.002   TYR A 250 
 ARG   0.001   0.000   ARG B 247 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.01693 (   44)
  hydrogen bonds       : angle       5.01131 (  132)
  SS BOND              : bond        0.00237 (    3)
  SS BOND              : angle       0.44258 (    6)
  covalent geometry    : bond        0.00410 ( 3312)
  covalent geometry    : angle       0.60745 ( 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
  92 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 78
  time to evaluate  : 0.356 
Fit side-chains
REVERT: A  168 GLN cc_start: 0.8971 (mt0) cc_final: 0.8709 (mt0)
REVERT: A  178 LYS cc_start: 0.8371 (OUTLIER) cc_final: 0.8124 (ttpt)
REVERT: A  250 TYR cc_start: 0.7710 (t80) cc_final: 0.7183 (t80)
REVERT: B  168 GLN cc_start: 0.9032 (mt0) cc_final: 0.8822 (mt0)
REVERT: B  180 ARG cc_start: 0.8201 (ptp-170) cc_final: 0.6047 (pmt-80)
REVERT: B  190 LEU cc_start: 0.9012 (OUTLIER) cc_final: 0.8523 (tt)
REVERT: C  180 ARG cc_start: 0.8065 (ptp-170) cc_final: 0.7772 (ptp90)
  outliers start: 14
  outliers final: 6
  residues processed: 81
  average time/residue: 1.3131
  time to fit residues: 109.0230
Evaluate side-chains
  79 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 71
  time to evaluate  : 0.401 
-------------------------------------------------------------------------------
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  138 GLN
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:   10.0000
   chunk 37 optimal weight:    3.9990
   chunk 36 optimal weight:    2.9990
   chunk 33 optimal weight:    7.9990
   chunk 19 optimal weight:    1.9990
   chunk 38 optimal weight:    4.9990
   chunk 2 optimal weight:    6.9990
   chunk 25 optimal weight:    4.9990
   chunk 1 optimal weight:    7.9990
   chunk 13 optimal weight:    7.9990
   chunk 21 optimal weight:    8.9990
   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 229 GLN ** 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 = 0.3669 r_free = 0.3669 target = 0.118785 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3505 r_free = 0.3505 target = 0.105049 restraints weight = 4133.939|
|-----------------------------------------------------------------------------|
r_work (start): 0.3525 rms_B_bonded: 1.81
r_work: 0.3436 rms_B_bonded: 1.90 restraints_weight: 0.5000
r_work: 0.3344 rms_B_bonded: 3.24 restraints_weight: 0.2500
r_work (final): 0.3344
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8849
moved from start:          0.2144

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.036   3315  Z= 0.246
  Angle     :  0.654   6.606   4509  Z= 0.365
  Chirality :  0.054   0.198    543
  Planarity :  0.002   0.014    558
  Dihedral  :  6.657  20.491    447
  Min Nonbonded Distance : 2.571

Molprobity Statistics.
  All-atom Clashscore : 7.07
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 11.28 %
    Favored  : 88.72 %
  Rotamer:
    Outliers :  5.03 %
    Allowed  : 15.61 %
    Favored  : 79.37 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -4.45 (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
 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 B 180 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.01789 (   44)
  hydrogen bonds       : angle       4.98173 (  132)
  SS BOND              : bond        0.00265 (    3)
  SS BOND              : angle       0.55191 (    6)
  covalent geometry    : bond        0.00582 ( 3312)
  covalent geometry    : angle       0.65399 ( 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
  94 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 75
  time to evaluate  : 0.377 
Fit side-chains
REVERT: A  168 GLN cc_start: 0.8985 (mt0) cc_final: 0.8702 (mt0)
REVERT: A  178 LYS cc_start: 0.8530 (OUTLIER) cc_final: 0.8295 (ttpt)
REVERT: B  168 GLN cc_start: 0.9056 (mt0) cc_final: 0.8854 (mt0)
REVERT: B  180 ARG cc_start: 0.8219 (ptp-170) cc_final: 0.6034 (pmt-80)
REVERT: B  190 LEU cc_start: 0.8957 (OUTLIER) cc_final: 0.8494 (tt)
REVERT: C  180 ARG cc_start: 0.8128 (ptp-170) cc_final: 0.7825 (ptp90)
  outliers start: 19
  outliers final: 6
  residues processed: 80
  average time/residue: 1.2867
  time to fit residues: 105.5045
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  : 0.386 
-------------------------------------------------------------------------------
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 2 optimal weight:    2.9990
   chunk 36 optimal weight:    0.9990
   chunk 3 optimal weight:    3.9990
   chunk 7 optimal weight:    3.9990
   chunk 5 optimal weight:    9.9990
   chunk 9 optimal weight:    7.9990
   chunk 26 optimal weight:    3.9990
   chunk 12 optimal weight:    3.9990
   chunk 27 optimal weight:    2.9990
   chunk 24 optimal weight:    0.6980
   chunk 19 optimal weight:    0.0570
   overall best weight:    1.5504

-------------------------------------------------------------------------------
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 239 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3752 r_free = 0.3752 target = 0.125281 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3591 r_free = 0.3591 target = 0.111633 restraints weight = 4073.429|
|-----------------------------------------------------------------------------|
r_work (start): 0.3609 rms_B_bonded: 1.81
r_work: 0.3527 rms_B_bonded: 1.93 restraints_weight: 0.5000
r_work: 0.3438 rms_B_bonded: 3.31 restraints_weight: 0.2500
r_work (final): 0.3438
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8776
moved from start:          0.2522

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.019   3315  Z= 0.122
  Angle     :  0.577   6.695   4509  Z= 0.317
  Chirality :  0.053   0.176    543
  Planarity :  0.002   0.012    558
  Dihedral  :  6.115  18.948    447
  Min Nonbonded Distance : 2.532

Molprobity Statistics.
  All-atom Clashscore : 5.68
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.27 %
    Favored  : 90.73 %
  Rotamer:
    Outliers :  4.23 %
    Allowed  : 17.99 %
    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 (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: -4.30 (0.32), residues: 399
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -3.27 (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   0.001   TYR C 250 
 ARG   0.001   0.000   ARG B 140 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.01382 (   44)
  hydrogen bonds       : angle       4.90504 (  132)
  SS BOND              : bond        0.00164 (    3)
  SS BOND              : angle       0.34097 (    6)
  covalent geometry    : bond        0.00278 ( 3312)
  covalent geometry    : angle       0.57774 ( 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
  99 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 83
  time to evaluate  : 0.386 
Fit side-chains
REVERT: A  168 GLN cc_start: 0.8959 (mt0) cc_final: 0.8663 (mt0)
REVERT: B  168 GLN cc_start: 0.8997 (mt0) cc_final: 0.8790 (mt0)
REVERT: B  180 ARG cc_start: 0.8196 (ptp-170) cc_final: 0.6004 (pmt-80)
REVERT: B  190 LEU cc_start: 0.8972 (OUTLIER) cc_final: 0.8507 (tt)
REVERT: C  178 LYS cc_start: 0.8388 (OUTLIER) cc_final: 0.8167 (ttpt)
REVERT: C  246 GLU cc_start: 0.8579 (mt-10) cc_final: 0.7973 (mm-30)
REVERT: C  250 TYR cc_start: 0.8006 (OUTLIER) cc_final: 0.7715 (t80)
  outliers start: 16
  outliers final: 5
  residues processed: 85
  average time/residue: 1.1821
  time to fit residues: 103.1797
Evaluate side-chains
  86 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 78
  time to evaluate  : 0.384 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  190 LEU
Chi-restraints excluded: chain A residue  228 MET
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  178 LYS
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:    1.9990
   chunk 21 optimal weight:    7.9990
   chunk 15 optimal weight:    9.9990
   chunk 24 optimal weight:    8.9990
   chunk 27 optimal weight:    7.9990
   chunk 10 optimal weight:    8.9990
   chunk 12 optimal weight:    6.9990
   chunk 25 optimal weight:    3.9990
   chunk 22 optimal weight:   10.0000
   chunk 34 optimal weight:    9.9990
   chunk 33 optimal weight:    4.9990
   overall best weight:    5.1990

-------------------------------------------------------------------------------
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 = 0.3651 r_free = 0.3651 target = 0.116943 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3481 r_free = 0.3481 target = 0.103081 restraints weight = 4204.924|
|-----------------------------------------------------------------------------|
r_work (start): 0.3492 rms_B_bonded: 1.83
r_work: 0.3404 rms_B_bonded: 1.91 restraints_weight: 0.5000
r_work: 0.3312 rms_B_bonded: 3.22 restraints_weight: 0.2500
r_work (final): 0.3312
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8872
moved from start:          0.2355

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.008   0.043   3315  Z= 0.323
  Angle     :  0.717   6.295   4509  Z= 0.399
  Chirality :  0.057   0.210    543
  Planarity :  0.003   0.013    558
  Dihedral  :  6.777  21.010    447
  Min Nonbonded Distance : 2.575

Molprobity Statistics.
  All-atom Clashscore : 8.29
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 11.53 %
    Favored  : 88.47 %
  Rotamer:
    Outliers :  5.03 %
    Allowed  : 19.05 %
    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 (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: -4.25 (0.33), residues: 399
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -3.23 (0.25), residues: 399

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.006   0.002   HIS C 239 
 PHE   0.007   0.001   PHE A 213 
 TYR   0.031   0.003   TYR C 158 
 ARG   0.002   0.000   ARG B 180 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02010 (   44)
  hydrogen bonds       : angle       5.04635 (  132)
  SS BOND              : bond        0.00242 (    3)
  SS BOND              : angle       0.70769 (    6)
  covalent geometry    : bond        0.00769 ( 3312)
  covalent geometry    : angle       0.71662 ( 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
  91 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 72
  time to evaluate  : 0.414 
Fit side-chains
REVERT: A  168 GLN cc_start: 0.8990 (mt0) cc_final: 0.8759 (mt0)
REVERT: B  168 GLN cc_start: 0.9064 (mt0) cc_final: 0.8846 (mt0)
REVERT: B  180 ARG cc_start: 0.8276 (ptp-170) cc_final: 0.6046 (pmt-80)
REVERT: B  190 LEU cc_start: 0.8940 (OUTLIER) cc_final: 0.8478 (tt)
REVERT: C  250 TYR cc_start: 0.8523 (OUTLIER) cc_final: 0.7940 (t80)
  outliers start: 19
  outliers final: 6
  residues processed: 82
  average time/residue: 1.2078
  time to fit residues: 101.6894
Evaluate side-chains
  78 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 70
  time to evaluate  : 0.395 
-------------------------------------------------------------------------------
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  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=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 39
   random chunks:
   chunk 22 optimal weight:    7.9990
   chunk 19 optimal weight:    5.9990
   chunk 17 optimal weight:    1.9990
   chunk 9 optimal weight:   10.0000
   chunk 24 optimal weight:    0.8980
   chunk 4 optimal weight:    0.9990
   chunk 7 optimal weight:    2.9990
   chunk 25 optimal weight:    2.9990
   chunk 31 optimal weight:    6.9990
   chunk 35 optimal weight:    6.9990
   chunk 18 optimal weight:    0.9990
   overall best weight:    1.5788

-------------------------------------------------------------------------------
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 = 0.3751 r_free = 0.3751 target = 0.125050 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3592 r_free = 0.3592 target = 0.111193 restraints weight = 4008.626|
|-----------------------------------------------------------------------------|
r_work (start): 0.3598 rms_B_bonded: 1.81
r_work: 0.3513 rms_B_bonded: 1.94 restraints_weight: 0.5000
r_work: 0.3424 rms_B_bonded: 3.32 restraints_weight: 0.2500
r_work (final): 0.3424
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8775
moved from start:          0.2699

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   3315  Z= 0.130
  Angle     :  0.597   6.637   4509  Z= 0.330
  Chirality :  0.054   0.173    543
  Planarity :  0.002   0.012    558
  Dihedral  :  6.123  19.555    447
  Min Nonbonded Distance : 2.535

Molprobity Statistics.
  All-atom Clashscore : 6.14
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.52 %
    Favored  : 91.48 %
  Rotamer:
    Outliers :  2.91 %
    Allowed  : 20.11 %
    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: -4.16 (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
 HIS   0.005   0.001   HIS C 239 
 PHE   0.007   0.001   PHE A 213 
 TYR   0.015   0.001   TYR C 250 
 ARG   0.001   0.000   ARG C 180 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.01340 (   44)
  hydrogen bonds       : angle       4.91188 (  132)
  SS BOND              : bond        0.00208 (    3)
  SS BOND              : angle       0.22699 (    6)
  covalent geometry    : bond        0.00296 ( 3312)
  covalent geometry    : angle       0.59751 ( 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
  91 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 80
  time to evaluate  : 0.365 
Fit side-chains
REVERT: A  168 GLN cc_start: 0.8909 (mt0) cc_final: 0.8610 (mt0)
REVERT: A  180 ARG cc_start: 0.7918 (ptp-170) cc_final: 0.7355 (mtm180)
REVERT: B  178 LYS cc_start: 0.8206 (OUTLIER) cc_final: 0.7714 (ttmt)
REVERT: B  180 ARG cc_start: 0.8182 (ptp-170) cc_final: 0.6003 (pmt-80)
REVERT: B  190 LEU cc_start: 0.8978 (OUTLIER) cc_final: 0.8512 (tt)
REVERT: C  180 ARG cc_start: 0.8072 (ptp90) cc_final: 0.5626 (mmp-170)
REVERT: C  246 GLU cc_start: 0.8559 (mt-10) cc_final: 0.7937 (mm-30)
REVERT: C  250 TYR cc_start: 0.8115 (OUTLIER) cc_final: 0.7479 (t80)
  outliers start: 11
  outliers final: 5
  residues processed: 82
  average time/residue: 1.2115
  time to fit residues: 101.9565
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  : 0.355 
-------------------------------------------------------------------------------
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 C residue  144 LEU
Chi-restraints excluded: chain C residue  190 LEU
Chi-restraints excluded: chain C residue  217 ILE
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:    9.9990
   chunk 9 optimal weight:    9.9990
   chunk 15 optimal weight:    0.0770
   chunk 28 optimal weight:    6.9990
   chunk 6 optimal weight:    6.9990
   chunk 38 optimal weight:    0.7980
   chunk 10 optimal weight:    7.9990
   chunk 34 optimal weight:    0.0770
   chunk 37 optimal weight:    3.9990
   chunk 20 optimal weight:    1.9990
   chunk 29 optimal weight:    7.9990
   overall best weight:    1.3900

-------------------------------------------------------------------------------
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 = 0.3772 r_free = 0.3772 target = 0.126684 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3610 r_free = 0.3610 target = 0.112551 restraints weight = 3983.772|
|-----------------------------------------------------------------------------|
r_work (start): 0.3620 rms_B_bonded: 1.88
r_work: 0.3524 rms_B_bonded: 2.02 restraints_weight: 0.5000
r_work: 0.3432 rms_B_bonded: 3.47 restraints_weight: 0.2500
r_work (final): 0.3432
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8764
moved from start:          0.2841

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.020   3315  Z= 0.119
  Angle     :  0.577   6.690   4509  Z= 0.319
  Chirality :  0.053   0.176    543
  Planarity :  0.002   0.013    558
  Dihedral  :  5.911  18.993    447
  Min Nonbonded Distance : 2.568

Molprobity Statistics.
  All-atom Clashscore : 6.45
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.77 %
    Favored  : 90.23 %
  Rotamer:
    Outliers :  2.12 %
    Allowed  : 21.43 %
    Favored  : 76.46 %
  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: -4.08 (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
 HIS   0.005   0.001   HIS C 239 
 PHE   0.007   0.001   PHE A 213 
 TYR   0.016   0.002   TYR C 250 
 ARG   0.001   0.000   ARG A 140 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.01292 (   44)
  hydrogen bonds       : angle       4.85121 (  132)
  SS BOND              : bond        0.00222 (    3)
  SS BOND              : angle       0.23732 (    6)
  covalent geometry    : bond        0.00270 ( 3312)
  covalent geometry    : angle       0.57707 ( 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
  91 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 83
  time to evaluate  : 0.370 
Fit side-chains
REVERT: A  168 GLN cc_start: 0.8897 (mt0) cc_final: 0.8558 (mt0)
REVERT: A  180 ARG cc_start: 0.7932 (ptp-170) cc_final: 0.7422 (mtp85)
REVERT: B  178 LYS cc_start: 0.8141 (OUTLIER) cc_final: 0.7638 (ttmt)
REVERT: B  180 ARG cc_start: 0.8157 (ptp-170) cc_final: 0.5949 (pmt-80)
REVERT: B  190 LEU cc_start: 0.8926 (OUTLIER) cc_final: 0.8457 (tt)
REVERT: B  212 ASP cc_start: 0.9253 (m-30) cc_final: 0.8942 (m-30)
REVERT: C  180 ARG cc_start: 0.8074 (ptp90) cc_final: 0.5608 (mmp-170)
REVERT: C  250 TYR cc_start: 0.8065 (OUTLIER) cc_final: 0.7440 (t80)
  outliers start: 8
  outliers final: 3
  residues processed: 84
  average time/residue: 1.2151
  time to fit residues: 104.8788
Evaluate side-chains
  83 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 77
  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 C residue  190 LEU
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:    0.7980
   chunk 38 optimal weight:    8.9990
   chunk 1 optimal weight:    7.9990
   chunk 29 optimal weight:    4.9990
   chunk 26 optimal weight:    6.9990
   chunk 32 optimal weight:    1.9990
   chunk 18 optimal weight:    1.9990
   chunk 11 optimal weight:    4.9990
   overall best weight:    2.3588

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

Flipped N/Q/H residues before XYZ refinement:
C 138 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 = 0.3734 r_free = 0.3734 target = 0.123396 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3564 r_free = 0.3564 target = 0.109553 restraints weight = 4084.117|
|-----------------------------------------------------------------------------|
r_work (start): 0.3579 rms_B_bonded: 1.80
r_work: 0.3497 rms_B_bonded: 1.91 restraints_weight: 0.5000
r_work: 0.3410 rms_B_bonded: 3.26 restraints_weight: 0.2500
r_work (final): 0.3410
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8806
moved from start:          0.2754

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.044   3315  Z= 0.171
  Angle     :  0.642   8.564   4509  Z= 0.348
  Chirality :  0.054   0.189    543
  Planarity :  0.002   0.014    558
  Dihedral  :  6.145  19.542    447
  Min Nonbonded Distance : 2.559

Molprobity Statistics.
  All-atom Clashscore : 6.61
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 10.53 %
    Favored  : 89.47 %
  Rotamer:
    Outliers :  2.65 %
    Allowed  : 20.37 %
    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: -4.07 (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   0.002   HIS C 239 
 PHE   0.004   0.001   PHE A 213 
 TYR   0.023   0.002   TYR A 143 
 ARG   0.001   0.000   ARG A 140 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.01556 (   44)
  hydrogen bonds       : angle       4.90405 (  132)
  SS BOND              : bond        0.00207 (    3)
  SS BOND              : angle       0.39228 (    6)
  covalent geometry    : bond        0.00409 ( 3312)
  covalent geometry    : angle       0.64188 ( 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
  82 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 72
  time to evaluate  : 0.406 
Fit side-chains
REVERT: A  168 GLN cc_start: 0.8914 (mt0) cc_final: 0.8594 (mt0)
REVERT: A  180 ARG cc_start: 0.7981 (ptp-170) cc_final: 0.7507 (mtp85)
REVERT: B  178 LYS cc_start: 0.8294 (OUTLIER) cc_final: 0.7806 (ttmt)
REVERT: B  180 ARG cc_start: 0.8186 (ptp-170) cc_final: 0.6040 (pmt-80)
REVERT: B  190 LEU cc_start: 0.8876 (OUTLIER) cc_final: 0.8428 (tt)
REVERT: B  212 ASP cc_start: 0.9227 (m-30) cc_final: 0.8945 (m-30)
REVERT: C  180 ARG cc_start: 0.8175 (ptp90) cc_final: 0.5780 (mmp-170)
REVERT: C  250 TYR cc_start: 0.8251 (OUTLIER) cc_final: 0.7648 (t80)
  outliers start: 10
  outliers final: 6
  residues processed: 76
  average time/residue: 1.3493
  time to fit residues: 105.0249
Evaluate side-chains
  80 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 71
  time to evaluate  : 0.390 
-------------------------------------------------------------------------------
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  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=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 39
   random chunks:
   chunk 21 optimal weight:    6.9990
   chunk 20 optimal weight:    4.9990
   chunk 33 optimal weight:    4.9990
   chunk 1 optimal weight:    5.9990
   chunk 3 optimal weight:    8.9990
   chunk 26 optimal weight:    0.9980
   chunk 27 optimal weight:    3.9990
   chunk 11 optimal weight:    4.9990
   chunk 36 optimal weight:    1.9990
   chunk 24 optimal weight:    3.9990
   chunk 15 optimal weight:    5.9990
   overall best weight:    3.1988

-------------------------------------------------------------------------------
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 = 0.3695 r_free = 0.3695 target = 0.120468 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3529 r_free = 0.3529 target = 0.106562 restraints weight = 4038.024|
|-----------------------------------------------------------------------------|
r_work (start): 0.3543 rms_B_bonded: 1.85
r_work: 0.3445 rms_B_bonded: 1.95 restraints_weight: 0.5000
r_work: 0.3352 rms_B_bonded: 3.35 restraints_weight: 0.2500
r_work (final): 0.3352
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8824
moved from start:          0.2673

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.038   3315  Z= 0.217
  Angle     :  0.686   8.974   4509  Z= 0.371
  Chirality :  0.056   0.224    543
  Planarity :  0.002   0.016    558
  Dihedral  :  6.404  20.363    447
  Min Nonbonded Distance : 2.545

Molprobity Statistics.
  All-atom Clashscore : 7.37
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 11.28 %
    Favored  : 88.72 %
  Rotamer:
    Outliers :  3.17 %
    Allowed  : 19.84 %
    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: -4.10 (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
 HIS   0.005   0.002   HIS C 239 
 PHE   0.004   0.001   PHE A 213 
 TYR   0.024   0.002   TYR B 143 
 ARG   0.001   0.000   ARG A 140 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.01704 (   44)
  hydrogen bonds       : angle       4.90644 (  132)
  SS BOND              : bond        0.00237 (    3)
  SS BOND              : angle       0.46969 (    6)
  covalent geometry    : bond        0.00521 ( 3312)
  covalent geometry    : angle       0.68658 ( 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: 12
    poor density    : 69
  time to evaluate  : 0.323 
Fit side-chains
REVERT: A  168 GLN cc_start: 0.8904 (mt0) cc_final: 0.8590 (mt0)
REVERT: A  180 ARG cc_start: 0.7969 (ptp-170) cc_final: 0.7406 (mtp85)
REVERT: B  178 LYS cc_start: 0.8297 (OUTLIER) cc_final: 0.7797 (ttmt)
REVERT: B  180 ARG cc_start: 0.8234 (ptp-170) cc_final: 0.5999 (pmt-80)
REVERT: B  190 LEU cc_start: 0.8865 (OUTLIER) cc_final: 0.8404 (tt)
REVERT: B  212 ASP cc_start: 0.9257 (m-30) cc_final: 0.9015 (m-30)
REVERT: C  180 ARG cc_start: 0.8188 (ptp90) cc_final: 0.5728 (mmp-170)
REVERT: C  250 TYR cc_start: 0.8398 (OUTLIER) cc_final: 0.7749 (t80)
  outliers start: 12
  outliers final: 7
  residues processed: 73
  average time/residue: 1.3321
  time to fit residues: 99.6042
Evaluate side-chains
  77 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 67
  time to evaluate  : 0.387 
-------------------------------------------------------------------------------
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  217 ILE
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:    9.9990
   chunk 36 optimal weight:    2.9990
   chunk 3 optimal weight:    6.9990
   chunk 13 optimal weight:    0.8980
   chunk 0 optimal weight:    4.9990
   chunk 30 optimal weight:    5.9990
   chunk 38 optimal weight:    5.9990
   chunk 7 optimal weight:    5.9990
   chunk 35 optimal weight:    0.9990
   chunk 23 optimal weight:    0.9980
   chunk 19 optimal weight:    5.9990
   overall best weight:    2.1786

-------------------------------------------------------------------------------
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 = 0.3739 r_free = 0.3739 target = 0.123879 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3573 r_free = 0.3573 target = 0.109728 restraints weight = 4063.959|
|-----------------------------------------------------------------------------|
r_work (start): 0.3576 rms_B_bonded: 1.89
r_work: 0.3488 rms_B_bonded: 2.00 restraints_weight: 0.5000
r_work: 0.3396 rms_B_bonded: 3.43 restraints_weight: 0.2500
r_work (final): 0.3396
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8797
moved from start:          0.2813

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.028   3315  Z= 0.160
  Angle     :  0.649   8.720   4509  Z= 0.349
  Chirality :  0.054   0.185    543
  Planarity :  0.002   0.015    558
  Dihedral  :  6.205  19.841    447
  Min Nonbonded Distance : 2.561

Molprobity Statistics.
  All-atom Clashscore : 6.76
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 10.28 %
    Favored  : 89.72 %
  Rotamer:
    Outliers :  2.65 %
    Allowed  : 20.37 %
    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: -4.11 (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   0.004   0.001   PHE A 213 
 TYR   0.021   0.002   TYR A 143 
 ARG   0.001   0.000   ARG A 140 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.01519 (   44)
  hydrogen bonds       : angle       4.93870 (  132)
  SS BOND              : bond        0.00251 (    3)
  SS BOND              : angle       0.30794 (    6)
  covalent geometry    : bond        0.00376 ( 3312)
  covalent geometry    : angle       0.64942 ( 4503)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2953.56 seconds
wall clock time: 51 minutes 37.98 seconds (3097.98 seconds total)