Starting phenix.real_space_refine
on Wed Mar  5 20:58:48 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7u14_26277/03_2025/7u14_26277.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7u14_26277/03_2025/7u14_26277.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=4.5
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7u14_26277/03_2025/7u14_26277.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7u14_26277/03_2025/7u14_26277.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7u14_26277/03_2025/7u14_26277.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7u14_26277/03_2025/7u14_26277.cif"
  }
  resolution = 4.5
  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    2202      2.51       5
     N     531      2.21       5
     O     702      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 3 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib"
  Total number of atoms: 3456
  Number of models: 1
  Model: ""
    Number of chains: 6
    Chain: "A"
      Number of atoms: 1096
      Number of conformers: 2
      Conformer: "A"
        Number of residues, atoms: 135, 1087
          Classifications: {'peptide': 135}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 2, 'TRANS': 132}
      Conformer: "B"
        Number of residues, atoms: 135, 1087
          Classifications: {'peptide': 135}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 2, 'TRANS': 132}
          bond proxies already assigned to first conformer: 1094
    Chain: "B"
      Number of atoms: 1096
      Number of conformers: 2
      Conformer: "A"
        Number of residues, atoms: 135, 1087
          Classifications: {'peptide': 135}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 2, 'TRANS': 132}
      Conformer: "B"
        Number of residues, atoms: 135, 1087
          Classifications: {'peptide': 135}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 2, 'TRANS': 132}
          bond proxies already assigned to first conformer: 1094
    Chain: "C"
      Number of atoms: 1096
      Number of conformers: 2
      Conformer: "A"
        Number of residues, atoms: 135, 1087
          Classifications: {'peptide': 135}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 2, 'TRANS': 132}
      Conformer: "B"
        Number of residues, atoms: 135, 1087
          Classifications: {'peptide': 135}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 2, 'TRANS': 132}
          bond proxies already assigned to first conformer: 1094
    Chain: "A"
      Number of atoms: 56
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 4, 56
          Unusual residues: {'NAG': 4}
          Classifications: {'undetermined': 4}
          Link IDs: {None: 3}
          Unresolved non-hydrogen bonds: 4
          Unresolved non-hydrogen angles: 8
          Unresolved non-hydrogen dihedrals: 12
          Unresolved non-hydrogen chiralities: 4
    Chain: "B"
      Number of atoms: 56
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 4, 56
          Unusual residues: {'NAG': 4}
          Classifications: {'undetermined': 4}
          Link IDs: {None: 3}
          Unresolved non-hydrogen bonds: 4
          Unresolved non-hydrogen angles: 8
          Unresolved non-hydrogen dihedrals: 12
          Unresolved non-hydrogen chiralities: 4
    Chain: "C"
      Number of atoms: 56
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 4, 56
          Unusual residues: {'NAG': 4}
          Classifications: {'undetermined': 4}
          Link IDs: {None: 3}
          Unresolved non-hydrogen bonds: 4
          Unresolved non-hydrogen angles: 8
          Unresolved non-hydrogen dihedrals: 12
          Unresolved non-hydrogen chiralities: 4
  Time building chain proxies: 4.94, per 1000 atoms: 1.43
  Number of scatterers: 3456
  At special positions: 0
  Unit cell: (98.808, 118.14, 33.294, 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     702      8.00
     N     531      7.00
     C    2202      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=2.04
    Simple disulfide: pdb=" SG  CYS B 214 " - pdb=" SG  CYS B 253 " distance=2.04
    Simple disulfide: pdb=" SG  CYS C 214 " - pdb=" SG  CYS C 253 " distance=2.04

  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
  Links applied
    NAG-ASN
      " NAG A 301 " - " ASN A 183 "
      " NAG A 302 " - " ASN A 151 "
      " NAG A 303 " - " ASN A 145 "
      " NAG A 304 " - " ASN A 164 "
      " NAG B 301 " - " ASN B 183 "
      " NAG B 302 " - " ASN B 151 "
      " NAG B 303 " - " ASN B 145 "
      " NAG B 304 " - " ASN B 164 "
      " NAG C 301 " - " ASN C 183 "
      " NAG C 302 " - " ASN C 151 "
      " NAG C 303 " - " ASN C 145 "
      " NAG C 304 " - " ASN C 164 "
  Time building additional restraints: 0.88
  Conformation dependent library (CDL) restraints added in 906.9 milliseconds
  

  804 Ramachandran restraints generated.
    402 Oldfield, 0 Emsley, 402 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  786

  Finding SS restraints...
    Secondary structure from input PDB file:
      0 helices and 12 sheets defined
      0.0% alpha, 60.7% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.49
  Creating SS restraints...
    Processing sheet with id=AA1, first strand: chain 'A' and resid 122 through 124
    Processing sheet with id=AA2, first strand: chain 'A' and resid 129 through 137
      removed outlier: 6.384A  pdb=" N   LYS A 129 " --> pdb=" O   SER B 130 " (cutoff:3.500A)
      removed outlier: 8.140A  pdb=" N   TYR B 132 " --> pdb=" O   LYS A 129 " (cutoff:3.500A)
      removed outlier: 9.038A  pdb=" N   ALA A 131 " --> pdb=" O   TYR B 132 " (cutoff:3.500A)
      removed outlier: 6.228A  pdb=" N   SER B 134 " --> pdb=" O   ALA A 131 " (cutoff:3.500A)
      removed outlier: 9.124A  pdb=" N   VAL A 133 " --> pdb=" O   SER B 134 " (cutoff:3.500A)
      removed outlier: 9.683A  pdb=" N   ASP B 136 " --> pdb=" O   VAL A 133 " (cutoff:3.500A)
      removed outlier: 8.839A  pdb=" N   TYR A 135 " --> pdb=" O   ASP B 136 " (cutoff:3.500A)
      removed outlier: 6.407A  pdb=" N   LYS B 129 " --> pdb=" O   SER C 130 " (cutoff:3.500A)
      removed outlier: 8.166A  pdb=" N   TYR C 132 " --> pdb=" O   LYS B 129 " (cutoff:3.500A)
      removed outlier: 9.050A  pdb=" N   ALA B 131 " --> pdb=" O   TYR C 132 " (cutoff:3.500A)
      removed outlier: 6.240A  pdb=" N   SER C 134 " --> pdb=" O   ALA B 131 " (cutoff:3.500A)
      removed outlier: 9.114A  pdb=" N   VAL B 133 " --> pdb=" O   SER C 134 " (cutoff:3.500A)
      removed outlier: 9.677A  pdb=" N   ASP C 136 " --> pdb=" O   VAL B 133 " (cutoff:3.500A)
      removed outlier: 8.826A  pdb=" N   TYR B 135 " --> pdb=" O   ASP C 136 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA2
    Processing sheet with id=AA3, first strand: chain 'A' and resid 141 through 165
      removed outlier: 6.948A  pdb=" N   ILE A 146 " --> pdb=" O   ASN B 145 " (cutoff:3.500A)
      removed outlier: 6.968A  pdb=" N   THR B 147 " --> pdb=" O   ILE A 146 " (cutoff:3.500A)
      removed outlier: 7.042A  pdb=" N   ASN A 148 " --> pdb=" O   THR B 147 " (cutoff:3.500A)
      removed outlier: 7.018A  pdb=" N   THR B 149 " --> pdb=" O   ASN A 148 " (cutoff:3.500A)
      removed outlier: 7.029A  pdb=" N   LEU A 150 " --> pdb=" O   THR B 149 " (cutoff:3.500A)
      removed outlier: 7.005A  pdb=" N   ASN B 151 " --> pdb=" O   LEU A 150 " (cutoff:3.500A)
      removed outlier: 7.009A  pdb=" N   ILE A 152 " --> pdb=" O   ASN B 151 " (cutoff:3.500A)
      removed outlier: 7.023A  pdb=" N   THR B 153 " --> pdb=" O   ILE A 152 " (cutoff:3.500A)
      removed outlier: 6.960A  pdb=" N   ASN A 154 " --> pdb=" O   THR B 153 " (cutoff:3.500A)
      removed outlier: 7.008A  pdb=" N   ASN B 155 " --> pdb=" O   ASN A 154 " (cutoff:3.500A)
      removed outlier: 7.019A  pdb=" N   ASN A 156 " --> pdb=" O   ASN B 155 " (cutoff:3.500A)
      removed outlier: 7.024A  pdb=" N   TYR B 157 " --> pdb=" O   ASN A 156 " (cutoff:3.500A)
      removed outlier: 7.022A  pdb=" N   TYR A 158 " --> pdb=" O   TYR B 157 " (cutoff:3.500A)
      removed outlier: 7.036A  pdb=" N   SER B 159 " --> pdb=" O   TYR A 158 " (cutoff:3.500A)
      removed outlier: 6.970A  pdb=" N   VAL A 160 " --> pdb=" O   SER B 159 " (cutoff:3.500A)
      removed outlier: 6.981A  pdb=" N   GLU B 161 " --> pdb=" O   VAL A 160 " (cutoff:3.500A)
      removed outlier: 6.946A  pdb=" N   ILE B 146 " --> pdb=" O   ASN C 145 " (cutoff:3.500A)
      removed outlier: 6.958A  pdb=" N   THR C 147 " --> pdb=" O   ILE B 146 " (cutoff:3.500A)
      removed outlier: 7.025A  pdb=" N   ASN B 148 " --> pdb=" O   THR C 147 " (cutoff:3.500A)
      removed outlier: 6.990A  pdb=" N   THR C 149 " --> pdb=" O   ASN B 148 " (cutoff:3.500A)
      removed outlier: 6.996A  pdb=" N   LEU B 150 " --> pdb=" O   THR C 149 " (cutoff:3.500A)
      removed outlier: 6.964A  pdb=" N   ASN C 151 " --> pdb=" O   LEU B 150 " (cutoff:3.500A)
      removed outlier: 6.968A  pdb=" N   ILE B 152 " --> pdb=" O   ASN C 151 " (cutoff:3.500A)
      removed outlier: 6.972A  pdb=" N   THR C 153 " --> pdb=" O   ILE B 152 " (cutoff:3.500A)
      removed outlier: 6.914A  pdb=" N   ASN B 154 " --> pdb=" O   THR C 153 " (cutoff:3.500A)
      removed outlier: 6.951A  pdb=" N   ASN C 155 " --> pdb=" O   ASN B 154 " (cutoff:3.500A)
      removed outlier: 6.966A  pdb=" N   ASN B 156 " --> pdb=" O   ASN C 155 " (cutoff:3.500A)
      removed outlier: 6.960A  pdb=" N   TYR C 157 " --> pdb=" O   ASN B 156 " (cutoff:3.500A)
      removed outlier: 6.963A  pdb=" N   TYR B 158 " --> pdb=" O   TYR C 157 " (cutoff:3.500A)
      removed outlier: 6.968A  pdb=" N   SER C 159 " --> pdb=" O   TYR B 158 " (cutoff:3.500A)
      removed outlier: 6.910A  pdb=" N   VAL B 160 " --> pdb=" O   SER C 159 " (cutoff:3.500A)
      removed outlier: 6.915A  pdb=" N   GLU C 161 " --> pdb=" O   VAL B 160 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 168 through 177
    Processing sheet with id=AA5, first strand: chain 'A' and resid 180 through 181
      removed outlier: 6.575A  pdb=" N   ARG A 180 " --> pdb=" O   LEU B 181 " (cutoff:3.500A)
      removed outlier: 6.570A  pdb=" N   ARG B 180 " --> pdb=" O   LEU C 181 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA5
    Processing sheet with id=AA6, first strand: chain 'A' and resid 184 through 187
      removed outlier: 6.408A  pdb=" N   THR A 185 " --> pdb=" O   ILE B 186 " (cutoff:3.500A)
      removed outlier: 6.430A  pdb=" N   THR B 185 " --> pdb=" O   ILE C 186 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA6
    Processing sheet with id=AA7, first strand: chain 'A' and resid 191 through 198
      removed outlier: 6.775A  pdb=" N   ILE A 195 " --> pdb=" O   GLN B 194 " (cutoff:3.500A)
      removed outlier: 6.910A  pdb=" N   ASP B 196 " --> pdb=" O   ILE A 195 " (cutoff:3.500A)
      removed outlier: 6.982A  pdb=" N   TYR A 197 " --> pdb=" O   ASP B 196 " (cutoff:3.500A)
      removed outlier: 6.965A  pdb=" N   THR B 198 " --> pdb=" O   TYR A 197 " (cutoff:3.500A)
      removed outlier: 6.791A  pdb=" N   ILE B 195 " --> pdb=" O   GLN C 194 " (cutoff:3.500A)
      removed outlier: 6.942A  pdb=" N   ASP C 196 " --> pdb=" O   ILE B 195 " (cutoff:3.500A)
      removed outlier: 7.020A  pdb=" N   TYR B 197 " --> pdb=" O   ASP C 196 " (cutoff:3.500A)
      removed outlier: 7.015A  pdb=" N   THR C 198 " --> pdb=" O   TYR B 197 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'A' and resid 202 through 203
      removed outlier: 6.336A  pdb=" N   VAL A 202 " --> pdb=" O   ILE B 203 " (cutoff:3.500A)
      removed outlier: 6.379A  pdb=" N   VAL B 202 " --> pdb=" O   ILE C 203 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA8
    Processing sheet with id=AA9, first strand: chain 'A' and resid 209 through 219
      removed outlier: 6.973A  pdb=" N   MET A 210 " --> pdb=" O   TYR B 209 " (cutoff:3.500A)
      removed outlier: 6.962A  pdb=" N   TYR B 211 " --> pdb=" O   MET A 210 " (cutoff:3.500A)
      removed outlier: 6.984A  pdb=" N   ASP A 212 " --> pdb=" O   TYR B 211 " (cutoff:3.500A)
      removed outlier: 6.954A  pdb=" N   PHE B 213 " --> pdb=" O   ASP A 212 " (cutoff:3.500A)
      removed outlier: 7.073A  pdb=" N   MET B 210 " --> pdb=" O   TYR C 209 " (cutoff:3.500A)
      removed outlier: 7.050A  pdb=" N   TYR C 211 " --> pdb=" O   MET B 210 " (cutoff:3.500A)
      removed outlier: 7.071A  pdb=" N   ASP B 212 " --> pdb=" O   TYR C 211 " (cutoff:3.500A)
      removed outlier: 7.032A  pdb=" N   PHE C 213 " --> pdb=" O   ASP B 212 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'A' and resid 225 through 228
    Processing sheet with id=AB2, first strand: chain 'A' and resid 233 through 245
      removed outlier: 6.605A  pdb=" N   THR A 234 " --> pdb=" O   THR B 235 " (cutoff:3.500A)
      removed outlier: 8.221A  pdb=" N   PHE B 237 " --> pdb=" O   THR A 234 " (cutoff:3.500A)
      removed outlier: 6.821A  pdb=" N   TYR A 236 " --> pdb=" O   PHE B 237 " (cutoff:3.500A)
      removed outlier: 7.835A  pdb=" N   HIS B 239 " --> pdb=" O   TYR A 236 " (cutoff:3.500A)
      removed outlier: 6.582A  pdb=" N   GLY A 238 " --> pdb=" O   HIS B 239 " (cutoff:3.500A)
      removed outlier: 8.425A  pdb=" N   GLU B 241 " --> pdb=" O   GLY A 238 " (cutoff:3.500A)
      removed outlier: 6.537A  pdb=" N   SER A 240 " --> pdb=" O   GLU B 241 " (cutoff:3.500A)
      removed outlier: 8.297A  pdb=" N   ILE B 243 " --> pdb=" O   SER A 240 " (cutoff:3.500A)
      removed outlier: 6.603A  pdb=" N   GLN A 242 " --> pdb=" O   ILE B 243 " (cutoff:3.500A)
      removed outlier: 8.314A  pdb=" N   GLN B 245 " --> pdb=" O   GLN A 242 " (cutoff:3.500A)
      removed outlier: 6.435A  pdb=" N   SER A 244 " --> pdb=" O   GLN B 245 " (cutoff:3.500A)
      removed outlier: 6.607A  pdb=" N   THR B 234 " --> pdb=" O   THR C 235 " (cutoff:3.500A)
      removed outlier: 8.231A  pdb=" N   PHE C 237 " --> pdb=" O   THR B 234 " (cutoff:3.500A)
      removed outlier: 6.823A  pdb=" N   TYR B 236 " --> pdb=" O   PHE C 237 " (cutoff:3.500A)
      removed outlier: 7.841A  pdb=" N   HIS C 239 " --> pdb=" O   TYR B 236 " (cutoff:3.500A)
      removed outlier: 6.566A  pdb=" N   GLY B 238 " --> pdb=" O   HIS C 239 " (cutoff:3.500A)
      removed outlier: 8.410A  pdb=" N   GLU C 241 " --> pdb=" O   GLY B 238 " (cutoff:3.500A)
      removed outlier: 6.528A  pdb=" N   SER B 240 " --> pdb=" O   GLU C 241 " (cutoff:3.500A)
      removed outlier: 8.296A  pdb=" N   ILE C 243 " --> pdb=" O   SER B 240 " (cutoff:3.500A)
      removed outlier: 6.604A  pdb=" N   GLN B 242 " --> pdb=" O   ILE C 243 " (cutoff:3.500A)
      removed outlier: 8.314A  pdb=" N   GLN C 245 " --> pdb=" O   GLN B 242 " (cutoff:3.500A)
      removed outlier: 6.446A  pdb=" N   SER B 244 " --> pdb=" O   GLN C 245 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AB2
    Processing sheet with id=AB3, first strand: chain 'A' and resid 251 through 253

    66 hydrogen bonds defined for protein.
    198 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: 0.94

  Time building geometry restraints manager: 1.08 seconds

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

  Histogram of bond lengths:
        1.21 -     1.34: 1011
        1.34 -     1.46: 629
        1.46 -     1.58: 1840
        1.58 -     1.70: 0
        1.70 -     1.82: 36
  Bond restraints: 3516
  Sorted by residual:
  bond pdb=" C1  NAG A 304 "
       pdb=" O5  NAG A 304 "
    ideal  model  delta    sigma   weight residual
    1.406  1.480 -0.074 2.00e-02 2.50e+03 1.36e+01
  bond pdb=" C1  NAG C 304 "
       pdb=" O5  NAG C 304 "
    ideal  model  delta    sigma   weight residual
    1.406  1.480 -0.074 2.00e-02 2.50e+03 1.36e+01
  bond pdb=" C1  NAG B 304 "
       pdb=" O5  NAG B 304 "
    ideal  model  delta    sigma   weight residual
    1.406  1.480 -0.074 2.00e-02 2.50e+03 1.35e+01
  bond pdb=" CD  GLU A 206 "
       pdb=" OE1 GLU A 206 "
    ideal  model  delta    sigma   weight residual
    1.249  1.214  0.035 1.90e-02 2.77e+03 3.39e+00
  bond pdb=" CB  VAL C 225 "
       pdb=" CG2 VAL C 225 "
    ideal  model  delta    sigma   weight residual
    1.521  1.461  0.060 3.30e-02 9.18e+02 3.33e+00
  ... (remaining 3511 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.69: 4465
        1.69 -     3.38: 260
        3.38 -     5.07: 42
        5.07 -     6.76: 12
        6.76 -     8.45: 9
  Bond angle restraints: 4788
  Sorted by residual:
  angle pdb=" CA  MET C 228 "
        pdb=" CB  MET C 228 "
        pdb=" CG  MET C 228 "
      ideal   model   delta    sigma   weight residual
     114.10  121.52   -7.42 2.00e+00 2.50e-01 1.38e+01
  angle pdb=" CA  MET A 228 "
        pdb=" CB  MET A 228 "
        pdb=" CG  MET A 228 "
      ideal   model   delta    sigma   weight residual
     114.10  121.51   -7.41 2.00e+00 2.50e-01 1.37e+01
  angle pdb=" CA  MET B 228 "
        pdb=" CB  MET B 228 "
        pdb=" CG  MET B 228 "
      ideal   model   delta    sigma   weight residual
     114.10  121.42   -7.32 2.00e+00 2.50e-01 1.34e+01
  angle pdb=" CA  GLU C 205 "
        pdb=" CB  GLU C 205 "
        pdb=" CG  GLU C 205 "
      ideal   model   delta    sigma   weight residual
     114.10  121.18   -7.08 2.00e+00 2.50e-01 1.25e+01
  angle pdb=" CA  GLU B 205 "
        pdb=" CB  GLU B 205 "
        pdb=" CG  GLU B 205 "
      ideal   model   delta    sigma   weight residual
     114.10  121.12   -7.02 2.00e+00 2.50e-01 1.23e+01
  ... (remaining 4783 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    24.61: 2043
       24.61 -    49.21: 178
       49.21 -    73.82: 29
       73.82 -    98.43: 18
       98.43 -   123.04: 3
  Dihedral angle restraints: 2271
    sinusoidal: 1038
      harmonic: 1233
  Sorted by residual:
  dihedral pdb=" CB  CYS C 214 "
           pdb=" SG  CYS C 214 "
           pdb=" SG  CYS C 253 "
           pdb=" CB  CYS C 253 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00   40.17   52.83     1      1.00e+01 1.00e-02 3.80e+01
  dihedral pdb=" CB  CYS A 214 "
           pdb=" SG  CYS A 214 "
           pdb=" SG  CYS A 253 "
           pdb=" CB  CYS A 253 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00   40.18   52.82     1      1.00e+01 1.00e-02 3.80e+01
  dihedral pdb=" CB  CYS B 214 "
           pdb=" SG  CYS B 214 "
           pdb=" SG  CYS B 253 "
           pdb=" CB  CYS B 253 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00   40.24   52.76     1      1.00e+01 1.00e-02 3.79e+01
  ... (remaining 2268 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.078: 477
       0.078 -    0.156: 117
       0.156 -    0.234: 9
       0.234 -    0.312: 0
       0.312 -    0.390: 3
  Chirality restraints: 606
  Sorted by residual:
  chirality pdb=" CB  ILE C 203 "
            pdb=" CA  ILE C 203 "
            pdb=" CG1 ILE C 203 "
            pdb=" CG2 ILE C 203 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.26    0.39 2.00e-01 2.50e+01 3.80e+00
  chirality pdb=" CB  ILE A 203 "
            pdb=" CA  ILE A 203 "
            pdb=" CG1 ILE A 203 "
            pdb=" CG2 ILE A 203 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.26    0.38 2.00e-01 2.50e+01 3.69e+00
  chirality pdb=" CB  ILE B 203 "
            pdb=" CA  ILE B 203 "
            pdb=" CG1 ILE B 203 "
            pdb=" CG2 ILE B 203 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.26    0.38 2.00e-01 2.50e+01 3.66e+00
  ... (remaining 603 not shown)

  Planarity restraints: 591
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TYR C 125 "   -0.027 2.00e-02 2.50e+03   2.67e-02 1.43e+01
        pdb=" CG  TYR C 125 "    0.064 2.00e-02 2.50e+03
        pdb=" CD1 TYR C 125 "   -0.003 2.00e-02 2.50e+03
        pdb=" CD2 TYR C 125 "   -0.025 2.00e-02 2.50e+03
        pdb=" CE1 TYR C 125 "   -0.015 2.00e-02 2.50e+03
        pdb=" CE2 TYR C 125 "    0.006 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 A 125 "   -0.027 2.00e-02 2.50e+03   2.66e-02 1.42e+01
        pdb=" CG  TYR A 125 "    0.064 2.00e-02 2.50e+03
        pdb=" CD1 TYR A 125 "   -0.002 2.00e-02 2.50e+03
        pdb=" CD2 TYR A 125 "   -0.025 2.00e-02 2.50e+03
        pdb=" CE1 TYR A 125 "   -0.016 2.00e-02 2.50e+03
        pdb=" CE2 TYR A 125 "    0.006 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 B 125 "   -0.026 2.00e-02 2.50e+03   2.65e-02 1.41e+01
        pdb=" CG  TYR B 125 "    0.063 2.00e-02 2.50e+03
        pdb=" CD1 TYR B 125 "   -0.003 2.00e-02 2.50e+03
        pdb=" CD2 TYR B 125 "   -0.025 2.00e-02 2.50e+03
        pdb=" CE1 TYR B 125 "   -0.016 2.00e-02 2.50e+03
        pdb=" CE2 TYR B 125 "    0.006 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 588 not shown)

  Histogram of nonbonded interaction distances:
        2.37 -     2.87: 1220
        2.87 -     3.38: 2979
        3.38 -     3.89: 6107
        3.89 -     4.39: 6044
        4.39 -     4.90: 11905
  Nonbonded interactions: 28255
  Sorted by model distance:
  nonbonded pdb=" NZ  LYS C 129 "
            pdb=" OD2 ASP C 136 "
     model   vdw
     2.369 3.120
  nonbonded pdb=" NZ  LYS B 129 "
            pdb=" OD2 ASP B 136 "
     model   vdw
     2.369 3.120
  nonbonded pdb=" NZ  LYS A 129 "
            pdb=" OD2 ASP A 136 "
     model   vdw
     2.370 3.120
  nonbonded pdb=" OH  TYR B 236 "
            pdb=" O   HIS B 239 "
     model   vdw
     2.423 3.040
  nonbonded pdb=" OH  TYR A 236 "
            pdb=" O   HIS A 239 "
     model   vdw
     2.424 3.040
  ... (remaining 28250 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
  Number of NCS constrained groups: 1
  pdb_interpretation.ncs_group {
  reference = chain 'A'
  selection = chain 'C'
  selection = chain 'B'
}
Set refine NCS operators
  NCS operators will be refined.
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=0.50 max=1.00 mean=0.99
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             3.760
  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:          0.120
  Check model and map are aligned:         0.030
  Set scattering table:                    0.030
  Process input model:                     16.800
  Find NCS groups from input model:        0.070
  Set up NCS constraints:                  0.020
  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:3.160
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   24.000
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5068
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      :  0.006   0.074   3516  Z= 0.426
  Angle     :  0.945   8.455   4788  Z= 0.493
  Chirality :  0.066   0.390    606
  Planarity :  0.005   0.028    579
  Dihedral  : 19.585 123.035   1476
  Min Nonbonded Distance : 2.369

Molprobity Statistics.
  All-atom Clashscore : 21.08
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 10.53 %
    Favored  : 89.47 %
  Rotamer:
    Outliers :  6.30 %
    Allowed  :  2.36 %
    Favored  : 91.34 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -3.07 (0.38), residues: 402
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.33 (0.29), residues: 402

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.002   0.001   HIS C 222 
 PHE   0.020   0.004   PHE B 171 
 TYR   0.064   0.004   TYR C 125 
 ARG   0.002   0.000   ARG A 247 

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

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

  804 Ramachandran restraints generated.
    402 Oldfield, 0 Emsley, 402 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  804 Ramachandran restraints generated.
    402 Oldfield, 0 Emsley, 402 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Update NCS operators
********************
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  28 residues out of total 125 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 20
  time to evaluate  : 0.111 
Fit side-chains
REVERT: A  171 PHE cc_start: 0.7517 (t80) cc_final: 0.6047 (p90)
REVERT: A  213 PHE cc_start: 0.6519 (t80) cc_final: 0.4232 (p90)
REVERT: A  222 HIS cc_start: 0.6925 (m-70) cc_final: 0.5425 (p90)
REVERT: A  223 ASN cc_start: 0.4231 (OUTLIER) cc_final: 0.4021 (p0)
  outliers start: 8
  outliers final: 0
  residues processed: 25
  average time/residue: 0.0962
  time to fit residues: 2.8121
Evaluate side-chains
  15 residues out of total 125 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 14
  time to evaluate  : 0.110 
-------------------------------------------------------------------------------
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:    3.9990
   chunk 29 optimal weight:    0.0970
   chunk 16 optimal weight:    9.9990
   chunk 10 optimal weight:    7.9990
   chunk 19 optimal weight:    2.9990
   chunk 15 optimal weight:    3.9990
   chunk 30 optimal weight:    0.0020
   chunk 11 optimal weight:    3.9990
   chunk 18 optimal weight:    0.6980
   chunk 22 optimal weight:    4.9990
   chunk 35 optimal weight:    0.0020
   overall best weight:    0.7596
-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

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

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Update NCS operators
********************
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.5305 r_free = 0.5305 target = 0.356147 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 24)----------------|
| r_work = 0.5356 r_free = 0.5356 target = 0.314463 restraints weight = 12035.388|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.5378 r_free = 0.5378 target = 0.314625 restraints weight = 7303.774|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 45)----------------|
| r_work = 0.5416 r_free = 0.5416 target = 0.312154 restraints weight = 5288.473|
|-----------------------------------------------------------------------------|
r_work (final): 0.5229
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.5229
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.5229 r_free = 0.5229    target_work(ls_wunit_k1) = 0.338         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.5237 r_free = 0.5237    target_work(ls_wunit_k1) = 0.338         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        9 |
|-----------------------------------------------------------------------------|
r_final: 0.5237
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5021
moved from start:          0.2447

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042   3516  Z= 0.233
  Angle     :  0.786   8.334   4788  Z= 0.405
  Chirality :  0.068   0.478    606
  Planarity :  0.003   0.020    579
  Dihedral  : 14.107 102.115    711
  Min Nonbonded Distance : 2.485

Molprobity Statistics.
  All-atom Clashscore : 16.26
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.77 %
    Favored  : 93.23 %
  Rotamer:
    Outliers :  0.79 %
    Allowed  :  4.72 %
    Favored  : 94.49 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -3.33 (0.37), residues: 402
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.53 (0.28), residues: 402

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.004   0.002   HIS C 222 
 PHE   0.010   0.002   PHE A 237 
 TYR   0.009   0.001   TYR A 143 
 ARG   0.001   0.000   ARG A 247 

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

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

  536 Ramachandran restraints generated.
    268 Oldfield, 0 Emsley, 268 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  536 Ramachandran restraints generated.
    268 Oldfield, 0 Emsley, 268 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Update NCS operators
********************
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  22 residues out of total 125 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 21
  time to evaluate  : 0.123 
Fit side-chains
REVERT: C  171 PHE cc_start: 0.7782 (t80) cc_final: 0.5495 (p90)
REVERT: C  207 MET cc_start: 0.3175 (ptm) cc_final: 0.2765 (tpt)
REVERT: C  222 HIS cc_start: 0.6762 (m-70) cc_final: 0.5546 (p90)
  outliers start: 1
  outliers final: 0
  residues processed: 21
  average time/residue: 0.0729
  time to fit residues: 1.9262
Evaluate side-chains
  14 residues out of total 125 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 14
  time to evaluate  : 0.124 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 39
   random chunks:
   chunk 32 optimal weight:   20.0000
   chunk 19 optimal weight:    0.8980
   chunk 38 optimal weight:    5.9990
   chunk 33 optimal weight:    0.0170
   chunk 4 optimal weight:    0.5980
   chunk 12 optimal weight:    5.9990
   chunk 0 optimal weight:    9.9990
   chunk 28 optimal weight:    0.0970
   chunk 34 optimal weight:    9.9990
   chunk 7 optimal weight:    0.0170
   chunk 16 optimal weight:    0.0980
   overall best weight:    0.1654
-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

Flipped N/Q/H residues before XYZ refinement:
C 168 GLN
C 222 HIS
C 239 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
Update NCS operators
********************
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.5349 r_free = 0.5349 target = 0.361634 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 28)----------------|
| r_work = 0.5401 r_free = 0.5401 target = 0.316923 restraints weight = 7815.611|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.5432 r_free = 0.5432 target = 0.317241 restraints weight = 7296.493|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.5451 r_free = 0.5451 target = 0.315171 restraints weight = 5845.151|
|-----------------------------------------------------------------------------|
r_work (final): 0.5262
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.5261
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.5261 r_free = 0.5261    target_work(ls_wunit_k1) = 0.342         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        9 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.5261 r_free = 0.5261    target_work(ls_wunit_k1) = 0.342         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        9 |
|-----------------------------------------------------------------------------|
r_final: 0.5261
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.4983
moved from start:          0.3319

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.040   3516  Z= 0.239
  Angle     :  0.780   8.140   4788  Z= 0.397
  Chirality :  0.064   0.373    606
  Planarity :  0.003   0.022    579
  Dihedral  : 13.427 103.220    711
  Min Nonbonded Distance : 2.584

Molprobity Statistics.
  All-atom Clashscore : 18.46
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.27 %
    Favored  : 91.73 %
  Rotamer:
    Outliers :  0.79 %
    Allowed  :  2.36 %
    Favored  : 96.85 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -3.41 (0.37), residues: 402
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.59 (0.28), residues: 402

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.006   0.003   HIS B 222 
 PHE   0.010   0.002   PHE A 237 
 TYR   0.011   0.001   TYR B 143 
 ARG   0.000   0.000   ARG B 180 

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

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

  536 Ramachandran restraints generated.
    268 Oldfield, 0 Emsley, 268 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  536 Ramachandran restraints generated.
    268 Oldfield, 0 Emsley, 268 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Update NCS operators
********************
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  24 residues out of total 125 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 23
  time to evaluate  : 0.119 
Fit side-chains
REVERT: C  140 ARG cc_start: 0.7247 (tpt90) cc_final: 0.5804 (tmt170)
REVERT: C  222 HIS cc_start: 0.6982 (m170) cc_final: 0.5706 (p90)
REVERT: C  229 GLN cc_start: 0.6822 (tt0) cc_final: 0.5033 (mp10)
  outliers start: 1
  outliers final: 0
  residues processed: 24
  average time/residue: 0.1145
  time to fit residues: 3.1426
Evaluate side-chains
  13 residues out of total 125 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 13
  time to evaluate  : 0.111 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 39
   random chunks:
   chunk 12 optimal weight:    8.9990
   chunk 8 optimal weight:    0.7980
   chunk 6 optimal weight:    0.9990
   chunk 34 optimal weight:    0.7980
   chunk 9 optimal weight:    8.9990
   chunk 25 optimal weight:    0.0040
   chunk 28 optimal weight:    8.9990
   chunk 26 optimal weight:    8.9990
   chunk 7 optimal weight:    8.9990
   chunk 13 optimal weight:    9.9990
   chunk 10 optimal weight:    0.0980
   overall best weight:    0.5394
-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

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

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
Update NCS operators
********************
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.5328 r_free = 0.5328 target = 0.362868 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 29)----------------|
| r_work = 0.5400 r_free = 0.5400 target = 0.308693 restraints weight = 14936.593|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 43)----------------|
| r_work = 0.5454 r_free = 0.5454 target = 0.306217 restraints weight = 6625.126|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.5458 r_free = 0.5458 target = 0.305109 restraints weight = 5241.467|
|-----------------------------------------------------------------------------|
r_work (final): 0.5237
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.5237
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.5237 r_free = 0.5237    target_work(ls_wunit_k1) = 0.336         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        9 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.5237 r_free = 0.5237    target_work(ls_wunit_k1) = 0.336         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        9 |
|-----------------------------------------------------------------------------|
r_final: 0.5237
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5066
moved from start:          0.3710

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   3516  Z= 0.217
  Angle     :  0.786   9.794   4788  Z= 0.400
  Chirality :  0.073   0.636    606
  Planarity :  0.003   0.029    579
  Dihedral  : 12.950 101.600    711
  Min Nonbonded Distance : 2.595

Molprobity Statistics.
  All-atom Clashscore : 15.24
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.52 %
    Favored  : 92.48 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.36 %
    Favored  : 97.64 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -3.29 (0.37), residues: 402
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.50 (0.28), residues: 402

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.001   0.000   HIS C 239 
 PHE   0.008   0.001   PHE B 237 
 TYR   0.010   0.001   TYR C 143 
 ARG   0.000   0.000   ARG B 180 

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

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

  536 Ramachandran restraints generated.
    268 Oldfield, 0 Emsley, 268 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  536 Ramachandran restraints generated.
    268 Oldfield, 0 Emsley, 268 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Update NCS operators
********************
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  20 residues out of total 125 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 20
  time to evaluate  : 0.111 
Fit side-chains
REVERT: C  140 ARG cc_start: 0.7308 (tpt90) cc_final: 0.5785 (tmt170)
  outliers start: 0
  outliers final: 0
  residues processed: 20
  average time/residue: 0.1094
  time to fit residues: 2.5836
Evaluate side-chains
  12 residues out of total 125 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 12
  time to evaluate  : 0.118 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 39
   random chunks:
   chunk 1 optimal weight:    1.9990
   chunk 4 optimal weight:    9.9990
   chunk 29 optimal weight:    0.9990
   chunk 12 optimal weight:    7.9990
   chunk 11 optimal weight:    6.9990
   chunk 5 optimal weight:    0.3980
   chunk 22 optimal weight:   20.0000
   chunk 16 optimal weight:    0.9980
   chunk 2 optimal weight:    0.0270
   chunk 14 optimal weight:    0.0050
   chunk 31 optimal weight:    0.3980
   overall best weight:    0.3652
-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

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

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
Update NCS operators
********************
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.5303 r_free = 0.5303 target = 0.362854 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 24)----------------|
| r_work = 0.5359 r_free = 0.5359 target = 0.318233 restraints weight = 7812.294|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 42)----------------|
| r_work = 0.5407 r_free = 0.5407 target = 0.313194 restraints weight = 6235.629|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 62)----------------|
| r_work = 0.5495 r_free = 0.5495 target = 0.310499 restraints weight = 4644.122|
|-----------------------------------------------------------------------------|
r_work (final): 0.5243
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.5243
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.5243 r_free = 0.5243    target_work(ls_wunit_k1) = 0.344         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        9 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.5243 r_free = 0.5243    target_work(ls_wunit_k1) = 0.344         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        9 |
|-----------------------------------------------------------------------------|
r_final: 0.5243
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5004
moved from start:          0.4124

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.054   3516  Z= 0.265
  Angle     :  0.823  10.029   4788  Z= 0.416
  Chirality :  0.080   0.761    606
  Planarity :  0.003   0.025    579
  Dihedral  : 12.808 100.852    711
  Min Nonbonded Distance : 2.599

Molprobity Statistics.
  All-atom Clashscore : 16.12
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.52 %
    Favored  : 92.48 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.57 %
    Favored  : 98.43 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -3.51 (0.37), residues: 402
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.67 (0.29), residues: 402

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.001   0.001   HIS A 222 
 PHE   0.008   0.001   PHE B 237 
 TYR   0.009   0.001   TYR A 143 
 ARG   0.000   0.000   ARG A 180 

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

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

  536 Ramachandran restraints generated.
    268 Oldfield, 0 Emsley, 268 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  536 Ramachandran restraints generated.
    268 Oldfield, 0 Emsley, 268 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Update NCS operators
********************
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  21 residues out of total 125 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 21
  time to evaluate  : 0.111 
Fit side-chains
REVERT: C  140 ARG cc_start: 0.7169 (tpt90) cc_final: 0.5701 (tmt170)
REVERT: C  229 GLN cc_start: 0.6827 (tt0) cc_final: 0.5768 (mp10)
  outliers start: 0
  outliers final: 0
  residues processed: 21
  average time/residue: 0.1013
  time to fit residues: 2.5007
Evaluate side-chains
  13 residues out of total 125 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 13
  time to evaluate  : 0.115 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 39
   random chunks:
   chunk 1 optimal weight:    0.0570
   chunk 36 optimal weight:    0.6980
   chunk 10 optimal weight:    0.6980
   chunk 25 optimal weight:    5.9990
   chunk 22 optimal weight:   20.0000
   chunk 28 optimal weight:    0.1980
   chunk 12 optimal weight:    4.9990
   chunk 29 optimal weight:    0.0010
   chunk 2 optimal weight:    0.1980
   chunk 9 optimal weight:   20.0000
   chunk 32 optimal weight:    8.9990
   overall best weight:    0.2304
-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

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

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
Update NCS operators
********************
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.5318 r_free = 0.5318 target = 0.366272 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.5471 r_free = 0.5471 target = 0.308830 restraints weight = 5603.229|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.5472 r_free = 0.5472 target = 0.311262 restraints weight = 6239.580|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.5481 r_free = 0.5481 target = 0.311525 restraints weight = 4882.416|
|-----------------------------------------------------------------------------|
r_work (final): 0.5228
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.5229
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.5229 r_free = 0.5229    target_work(ls_wunit_k1) = 0.342         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        9 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.5229 r_free = 0.5229    target_work(ls_wunit_k1) = 0.342         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        9 |
|-----------------------------------------------------------------------------|
r_final: 0.5229
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.4998
moved from start:          0.4423

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042   3516  Z= 0.226
  Angle     :  0.779  10.860   4788  Z= 0.389
  Chirality :  0.085   0.861    606
  Planarity :  0.003   0.029    579
  Dihedral  : 12.545  99.337    711
  Min Nonbonded Distance : 2.603

Molprobity Statistics.
  All-atom Clashscore : 15.82
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.52 %
    Favored  : 92.48 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.00 %
    Favored  : 100.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -3.63 (0.37), residues: 402
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.76 (0.28), residues: 402

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.001   0.001   HIS A 222 
 PHE   0.007   0.001   PHE B 237 
 TYR   0.009   0.001   TYR B 143 
 ARG   0.000   0.000   ARG A 180 

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

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

  536 Ramachandran restraints generated.
    268 Oldfield, 0 Emsley, 268 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  536 Ramachandran restraints generated.
    268 Oldfield, 0 Emsley, 268 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Update NCS operators
********************
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  21 residues out of total 125 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 21
  time to evaluate  : 0.130 
Fit side-chains
REVERT: C  140 ARG cc_start: 0.7207 (tpt90) cc_final: 0.5611 (tmt170)
REVERT: C  206 GLU cc_start: 0.7181 (pm20) cc_final: 0.6819 (mm-30)
  outliers start: 0
  outliers final: 0
  residues processed: 21
  average time/residue: 0.1051
  time to fit residues: 2.5974
Evaluate side-chains
  15 residues out of total 125 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 15
  time to evaluate  : 0.120 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 39
   random chunks:
   chunk 28 optimal weight:    7.9990
   chunk 19 optimal weight:    0.0970
   chunk 0 optimal weight:    9.9990
   chunk 9 optimal weight:   20.0000
   chunk 17 optimal weight:    9.9990
   chunk 33 optimal weight:    6.9990
   chunk 34 optimal weight:    0.2980
   chunk 23 optimal weight:    0.2980
   chunk 37 optimal weight:    4.9990
   chunk 35 optimal weight:   20.0000
   chunk 15 optimal weight:    5.9990
   overall best weight:    2.3382
-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

Flipped N/Q/H residues before XYZ refinement:
** C 168 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
Update NCS operators
********************
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.5228 r_free = 0.5228 target = 0.333461 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.5323 r_free = 0.5323 target = 0.272984 restraints weight = 6062.460|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 24)----------------|
| r_work = 0.5326 r_free = 0.5326 target = 0.272976 restraints weight = 5612.380|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.5328 r_free = 0.5328 target = 0.272926 restraints weight = 5370.313|
|-----------------------------------------------------------------------------|
r_work (final): 0.5123
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.5123
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.5123 r_free = 0.5123    target_work(ls_wunit_k1) = 0.307         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        9 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.5123 r_free = 0.5123    target_work(ls_wunit_k1) = 0.307         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        9 |
|-----------------------------------------------------------------------------|
r_final: 0.5123
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5521
moved from start:          0.5393

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.047   3516  Z= 0.273
  Angle     :  0.824   9.607   4788  Z= 0.413
  Chirality :  0.076   0.656    606
  Planarity :  0.004   0.032    579
  Dihedral  : 13.020 101.896    711
  Min Nonbonded Distance : 2.623

Molprobity Statistics.
  All-atom Clashscore : 17.14
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.77 %
    Favored  : 90.23 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.57 %
    Favored  : 98.43 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -3.73 (0.37), residues: 402
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.83 (0.28), residues: 402

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.003   0.001   HIS C 239 
 PHE   0.007   0.002   PHE A 213 
 TYR   0.015   0.002   TYR C 143 
 ARG   0.001   0.000   ARG A 180 

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

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

  536 Ramachandran restraints generated.
    268 Oldfield, 0 Emsley, 268 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  536 Ramachandran restraints generated.
    268 Oldfield, 0 Emsley, 268 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Update NCS operators
********************
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  18 residues out of total 125 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 18
  time to evaluate  : 0.130 
Fit side-chains
REVERT: C  206 GLU cc_start: 0.7678 (pm20) cc_final: 0.6574 (mm-30)
REVERT: C  228 MET cc_start: 0.6646 (ppp) cc_final: 0.5868 (ptm)
  outliers start: 0
  outliers final: 0
  residues processed: 18
  average time/residue: 0.0692
  time to fit residues: 1.6205
Evaluate side-chains
  14 residues out of total 125 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 14
  time to evaluate  : 0.111 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 39
   random chunks:
   chunk 6 optimal weight:   10.0000
   chunk 25 optimal weight:    3.9990
   chunk 2 optimal weight:    0.6980
   chunk 27 optimal weight:    0.5980
   chunk 5 optimal weight:    5.9990
   chunk 16 optimal weight:   10.0000
   chunk 31 optimal weight:    5.9990
   chunk 24 optimal weight:    8.9990
   chunk 7 optimal weight:    0.0670
   chunk 21 optimal weight:    9.9990
   chunk 8 optimal weight:    9.9990
   overall best weight:    2.2722
-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

Flipped N/Q/H residues before XYZ refinement:
** C 168 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 229 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Update NCS operators
********************
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.5179 r_free = 0.5179 target = 0.329528 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 24)----------------|
| r_work = 0.5226 r_free = 0.5226 target = 0.276544 restraints weight = 8316.346|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 41)----------------|
| r_work = 0.5286 r_free = 0.5286 target = 0.268760 restraints weight = 5362.578|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.5297 r_free = 0.5297 target = 0.267852 restraints weight = 3976.880|
|-----------------------------------------------------------------------------|
r_work (final): 0.5096
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.5096
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.5096 r_free = 0.5096    target_work(ls_wunit_k1) = 0.302         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        9 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.5096 r_free = 0.5096    target_work(ls_wunit_k1) = 0.302         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        9 |
|-----------------------------------------------------------------------------|
r_final: 0.5096
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5545
moved from start:          0.5715

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.060   3516  Z= 0.311
  Angle     :  0.988  19.398   4788  Z= 0.469
  Chirality :  0.071   0.544    606
  Planarity :  0.003   0.028    579
  Dihedral  : 13.077 102.473    711
  Min Nonbonded Distance : 2.569

Molprobity Statistics.
  All-atom Clashscore : 17.00
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.02 %
    Favored  : 90.98 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.57 %
    Favored  : 98.43 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -3.83 (0.37), residues: 402
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.91 (0.28), residues: 402

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.003   0.001   HIS C 239 
 PHE   0.005   0.001   PHE B 237 
 TYR   0.012   0.002   TYR B 143 
 ARG   0.001   0.000   ARG B 247 

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

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

  536 Ramachandran restraints generated.
    268 Oldfield, 0 Emsley, 268 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  536 Ramachandran restraints generated.
    268 Oldfield, 0 Emsley, 268 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Update NCS operators
********************
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  20 residues out of total 125 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 20
  time to evaluate  : 0.135 
Fit side-chains
REVERT: C  228 MET cc_start: 0.6658 (ppp) cc_final: 0.5923 (ptm)
  outliers start: 0
  outliers final: 0
  residues processed: 20
  average time/residue: 0.0929
  time to fit residues: 2.2585
Evaluate side-chains
  15 residues out of total 125 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 15
  time to evaluate  : 0.128 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 39
   random chunks:
   chunk 18 optimal weight:    6.9990
   chunk 32 optimal weight:   20.0000
   chunk 3 optimal weight:    0.0470
   chunk 2 optimal weight:    0.9990
   chunk 4 optimal weight:    0.0870
   chunk 5 optimal weight:    9.9990
   chunk 25 optimal weight:    2.9990
   chunk 6 optimal weight:   20.0000
   chunk 22 optimal weight:    9.9990
   chunk 16 optimal weight:    9.9990
   chunk 13 optimal weight:   10.0000
   overall best weight:    2.2262
-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

Flipped N/Q/H residues before XYZ refinement:
** C 168 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
Update NCS operators
********************
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.5174 r_free = 0.5174 target = 0.328211 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 29)----------------|
| r_work = 0.5246 r_free = 0.5246 target = 0.271794 restraints weight = 12202.737|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 50)----------------|
| r_work = 0.5288 r_free = 0.5288 target = 0.267891 restraints weight = 5720.542|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.5288 r_free = 0.5288 target = 0.267851 restraints weight = 4042.349|
|-----------------------------------------------------------------------------|
r_work (final): 0.5076
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.5076
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.5076 r_free = 0.5076    target_work(ls_wunit_k1) = 0.302         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        9 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.5076 r_free = 0.5076    target_work(ls_wunit_k1) = 0.302         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        9 |
|-----------------------------------------------------------------------------|
r_final: 0.5076
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5636
moved from start:          0.6025

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.052   3516  Z= 0.287
  Angle     :  0.935  12.824   4788  Z= 0.451
  Chirality :  0.088   0.927    606
  Planarity :  0.003   0.028    579
  Dihedral  : 13.159 103.261    711
  Min Nonbonded Distance : 2.624

Molprobity Statistics.
  All-atom Clashscore : 15.53
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.77 %
    Favored  : 90.23 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.00 %
    Favored  : 100.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -3.88 (0.37), residues: 402
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.95 (0.28), residues: 402

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.003   0.002   HIS C 239 
 PHE   0.006   0.001   PHE B 237 
 TYR   0.012   0.002   TYR C 143 
 ARG   0.001   0.000   ARG B 247 

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

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

  536 Ramachandran restraints generated.
    268 Oldfield, 0 Emsley, 268 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  536 Ramachandran restraints generated.
    268 Oldfield, 0 Emsley, 268 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Update NCS operators
********************
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  18 residues out of total 125 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 18
  time to evaluate  : 0.126 
Fit side-chains
REVERT: C  207 MET cc_start: 0.2105 (tmm) cc_final: -0.0425 (mmm)
REVERT: C  227 MET cc_start: 0.6346 (tpt) cc_final: 0.6048 (tpp)
REVERT: C  228 MET cc_start: 0.6498 (ppp) cc_final: 0.5835 (ptm)
  outliers start: 0
  outliers final: 0
  residues processed: 18
  average time/residue: 0.0665
  time to fit residues: 1.5803
Evaluate side-chains
  11 residues out of total 125 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 11
  time to evaluate  : 0.127 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 39
   random chunks:
   chunk 0 optimal weight:   10.0000
   chunk 29 optimal weight:    9.9990
   chunk 33 optimal weight:    0.4980
   chunk 6 optimal weight:   10.0000
   chunk 8 optimal weight:    0.0050
   chunk 12 optimal weight:    3.9990
   chunk 14 optimal weight:    4.9990
   chunk 37 optimal weight:    7.9990
   chunk 30 optimal weight:    5.9990
   chunk 9 optimal weight:    6.9990
   chunk 11 optimal weight:    7.9990
   overall best weight:    3.1000
-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
Update NCS operators
********************
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.5163 r_free = 0.5163 target = 0.323138 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 28)----------------|
| r_work = 0.5217 r_free = 0.5217 target = 0.266081 restraints weight = 6212.926|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.5268 r_free = 0.5268 target = 0.259202 restraints weight = 4796.083|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.5282 r_free = 0.5282 target = 0.257580 restraints weight = 3888.291|
|-----------------------------------------------------------------------------|
r_work (final): 0.5072
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.5072
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.5072 r_free = 0.5072    target_work(ls_wunit_k1) = 0.297         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        9 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.5072 r_free = 0.5072    target_work(ls_wunit_k1) = 0.297         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        9 |
|-----------------------------------------------------------------------------|
r_final: 0.5072
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5657
moved from start:          0.6203

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.054   3516  Z= 0.314
  Angle     :  1.067  17.405   4788  Z= 0.518
  Chirality :  0.092   0.860    606
  Planarity :  0.003   0.028    579
  Dihedral  : 13.222 103.691    711
  Min Nonbonded Distance : 2.592

Molprobity Statistics.
  All-atom Clashscore : 15.97
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.02 %
    Favored  : 90.98 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.00 %
    Favored  : 100.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -3.89 (0.37), residues: 402
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.96 (0.28), residues: 402

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.005   0.002   HIS C 239 
 PHE   0.006   0.001   PHE B 237 
 TYR   0.014   0.002   TYR C 143 
 ARG   0.001   0.000   ARG B 247 

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

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

  536 Ramachandran restraints generated.
    268 Oldfield, 0 Emsley, 268 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  536 Ramachandran restraints generated.
    268 Oldfield, 0 Emsley, 268 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Update NCS operators
********************
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  19 residues out of total 125 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 19
  time to evaluate  : 0.127 
Fit side-chains
REVERT: C  206 GLU cc_start: 0.7098 (pm20) cc_final: 0.6881 (mm-30)
REVERT: C  207 MET cc_start: 0.4012 (tmm) cc_final: -0.0737 (mmm)
REVERT: C  227 MET cc_start: 0.6672 (tpt) cc_final: 0.6380 (tpp)
REVERT: C  228 MET cc_start: 0.6635 (ppp) cc_final: 0.6061 (ptm)
  outliers start: 0
  outliers final: 0
  residues processed: 19
  average time/residue: 0.0627
  time to fit residues: 1.5586
Evaluate side-chains
  14 residues out of total 125 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 14
  time to evaluate  : 0.114 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 39
   random chunks:
   chunk 18 optimal weight:    9.9990
   chunk 13 optimal weight:   10.0000
   chunk 30 optimal weight:    6.9990
   chunk 36 optimal weight:    4.9990
   chunk 0 optimal weight:    9.9990
   chunk 10 optimal weight:    4.9990
   chunk 27 optimal weight:    8.9990
   chunk 35 optimal weight:    4.9990
   chunk 1 optimal weight:    8.9990
   chunk 20 optimal weight:    0.9990
   chunk 15 optimal weight:    0.0020
   overall best weight:    3.1996
-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

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

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Update NCS operators
********************
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.5156 r_free = 0.5156 target = 0.316797 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 24)----------------|
| r_work = 0.5195 r_free = 0.5195 target = 0.262973 restraints weight = 12337.646|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.5222 r_free = 0.5222 target = 0.258774 restraints weight = 5574.294|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.5223 r_free = 0.5223 target = 0.258619 restraints weight = 4174.627|
|-----------------------------------------------------------------------------|
r_work (final): 0.5056
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.5056
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.5056 r_free = 0.5056    target_work(ls_wunit_k1) = 0.296         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        9 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.5056 r_free = 0.5056    target_work(ls_wunit_k1) = 0.296         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        9 |
|-----------------------------------------------------------------------------|
r_final: 0.5056
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5680
moved from start:          0.6561

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.065   3516  Z= 0.338
  Angle     :  1.039  11.538   4788  Z= 0.499
  Chirality :  0.084   0.815    606
  Planarity :  0.003   0.028    579
  Dihedral  : 13.370 104.469    711
  Min Nonbonded Distance : 2.563

Molprobity Statistics.
  All-atom Clashscore : 20.37
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.02 %
    Favored  : 90.98 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.00 %
    Favored  : 100.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -3.92 (0.36), residues: 402
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.98 (0.28), residues: 402

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.005   0.002   HIS C 239 
 PHE   0.007   0.001   PHE B 237 
 TYR   0.014   0.002   TYR B 143 
 ARG   0.001   0.000   ARG A 247 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1316.60 seconds
wall clock time: 23 minutes 29.27 seconds (1409.27 seconds total)