Starting phenix.real_space_refine
on Mon Feb 10 23:23:43 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7qvc_14174/02_2025/7qvc_14174.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7qvc_14174/02_2025/7qvc_14174.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.64
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7qvc_14174/02_2025/7qvc_14174.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7qvc_14174/02_2025/7qvc_14174.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7qvc_14174/02_2025/7qvc_14174.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7qvc_14174/02_2025/7qvc_14174.cif"
  }
  resolution = 2.64
  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=   0.001
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    2079      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 10 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/chem_data/mon_lib"
  Total number of atoms: 3255
  Number of models: 1
  Model: ""
    Number of chains: 3
    Chain: "A"
      Number of atoms: 1085
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 135, 1085
          Classifications: {'peptide': 135}
          Link IDs: {'PTRANS': 2, 'TRANS': 132}
    Chain: "B"
      Number of atoms: 1085
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 135, 1085
          Classifications: {'peptide': 135}
          Link IDs: {'PTRANS': 2, 'TRANS': 132}
    Chain: "C"
      Number of atoms: 1085
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 135, 1085
          Classifications: {'peptide': 135}
          Link IDs: {'PTRANS': 2, 'TRANS': 132}
  Time building chain proxies: 2.81, per 1000 atoms: 0.86
  Number of scatterers: 3255
  At special positions: 0
  Unit cell: (101.78, 91.602, 31.988, 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    2079      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=2.05
    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=2.05

  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: 0.70
  Conformation dependent library (CDL) restraints added in 1.6 seconds
  

  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, 60.0% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.57
  Creating SS restraints...
    Processing sheet with id=AA1, first strand: chain 'A' and resid 121 through 126
      removed outlier: 6.736A  pdb=" N   ASP A 122 " --> pdb=" O   ILE B 121 " (cutoff:3.500A)
      removed outlier: 6.738A  pdb=" N   ASP B 122 " --> pdb=" O   ILE C 121 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 129 through 130
    Processing sheet with id=AA3, first strand: chain 'A' and resid 133 through 134
      removed outlier: 6.823A  pdb=" N   VAL A 133 " --> pdb=" O   SER B 134 " (cutoff:3.500A)
      removed outlier: 6.893A  pdb=" N   VAL B 133 " --> pdb=" O   SER C 134 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA3
    Processing sheet with id=AA4, first strand: chain 'A' and resid 137 through 139
      removed outlier: 6.647A  pdb=" N   GLN A 138 " --> pdb=" O   LYS B 139 " (cutoff:3.500A)
      removed outlier: 8.555A  pdb=" N   VAL B 137 " --> pdb=" O   GLN C 138 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA4
    Processing sheet with id=AA5, first strand: chain 'A' and resid 142 through 144
    Processing sheet with id=AA6, first strand: chain 'A' and resid 147 through 153
    Processing sheet with id=AA7, first strand: chain 'A' and resid 156 through 160
    Processing sheet with id=AA8, first strand: chain 'A' and resid 163 through 176
      removed outlier: 6.867A  pdb=" N   ASN A 164 " --> pdb=" O   GLU B 163 " (cutoff:3.500A)
      removed outlier: 6.906A  pdb=" N   ILE B 165 " --> pdb=" O   ASN A 164 " (cutoff:3.500A)
      removed outlier: 6.794A  pdb=" N   THR A 166 " --> pdb=" O   ILE B 165 " (cutoff:3.500A)
      removed outlier: 6.897A  pdb=" N   ASN B 164 " --> pdb=" O   GLU C 163 " (cutoff:3.500A)
      removed outlier: 6.896A  pdb=" N   ILE C 165 " --> pdb=" O   ASN B 164 " (cutoff:3.500A)
      removed outlier: 6.896A  pdb=" N   THR B 166 " --> pdb=" O   ILE C 165 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'A' and resid 180 through 181
    Processing sheet with id=AB1, first strand: chain 'A' and resid 184 through 187
      removed outlier: 6.447A  pdb=" N   ILE A 184 " --> pdb=" O   SER B 185 " (cutoff:3.500A)
      removed outlier: 7.750A  pdb=" N   ILE B 187 " --> pdb=" O   ILE A 184 " (cutoff:3.500A)
      removed outlier: 6.475A  pdb=" N   ILE A 186 " --> pdb=" O   ILE B 187 " (cutoff:3.500A)
      removed outlier: 6.522A  pdb=" N   ILE B 184 " --> pdb=" O   SER C 185 " (cutoff:3.500A)
      removed outlier: 7.816A  pdb=" N   ILE C 187 " --> pdb=" O   ILE B 184 " (cutoff:3.500A)
      removed outlier: 6.509A  pdb=" N   ILE B 186 " --> pdb=" O   ILE C 187 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AB1
    Processing sheet with id=AB2, first strand: chain 'A' and resid 192 through 193
      removed outlier: 6.590A  pdb=" N   MET A 192 " --> pdb=" O   LYS B 193 " (cutoff:3.500A)
      removed outlier: 6.577A  pdb=" N   MET B 192 " --> pdb=" O   LYS C 193 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AB2
    Processing sheet with id=AB3, first strand: chain 'A' and resid 196 through 198
      removed outlier: 6.419A  pdb=" N   TYR A 197 " --> pdb=" O   THR B 198 " (cutoff:3.500A)
      removed outlier: 6.400A  pdb=" N   TYR B 197 " --> pdb=" O   THR C 198 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AB3
    Processing sheet with id=AB4, first strand: chain 'A' and resid 201 through 206
    Processing sheet with id=AB5, first strand: chain 'A' and resid 209 through 213
    Processing sheet with id=AB6, first strand: chain 'A' and resid 216 through 219
    Processing sheet with id=AB7, first strand: chain 'A' and resid 222 through 228
      removed outlier: 5.995A  pdb=" N   ASN A 223 " --> pdb=" O   ILE B 224 " (cutoff:3.500A)
      removed outlier: 7.496A  pdb=" N   LEU B 226 " --> pdb=" O   ASN A 223 " (cutoff:3.500A)
      removed outlier: 6.259A  pdb=" N   VAL A 225 " --> pdb=" O   LEU B 226 " (cutoff:3.500A)
      removed outlier: 7.750A  pdb=" N   MET B 228 " --> pdb=" O   VAL A 225 " (cutoff:3.500A)
      removed outlier: 6.401A  pdb=" N   MET A 227 " --> pdb=" O   MET B 228 " (cutoff:3.500A)
      removed outlier: 6.230A  pdb=" N   ASN B 223 " --> pdb=" O   ILE C 224 " (cutoff:3.500A)
      removed outlier: 7.651A  pdb=" N   LEU C 226 " --> pdb=" O   ASN B 223 " (cutoff:3.500A)
      removed outlier: 6.360A  pdb=" N   VAL B 225 " --> pdb=" O   LEU C 226 " (cutoff:3.500A)
      removed outlier: 7.859A  pdb=" N   MET C 228 " --> pdb=" O   VAL B 225 " (cutoff:3.500A)
      removed outlier: 6.394A  pdb=" N   MET B 227 " --> pdb=" O   MET C 228 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AB7
    Processing sheet with id=AB8, first strand: chain 'A' and resid 231 through 253
      removed outlier: 5.753A  pdb=" N   THR A 231 " --> pdb=" O   VAL B 232 " (cutoff:3.500A)
      removed outlier: 8.012A  pdb=" N   THR B 234 " --> pdb=" O   THR A 231 " (cutoff:3.500A)
      removed outlier: 6.760A  pdb=" N   THR A 233 " --> pdb=" O   THR B 234 " (cutoff:3.500A)
      removed outlier: 8.118A  pdb=" N   TYR B 236 " --> pdb=" O   THR A 233 " (cutoff:3.500A)
      removed outlier: 6.373A  pdb=" N   THR A 235 " --> pdb=" O   TYR B 236 " (cutoff:3.500A)
      removed outlier: 8.063A  pdb=" N   GLY B 238 " --> pdb=" O   THR A 235 " (cutoff:3.500A)
      removed outlier: 6.014A  pdb=" N   PHE A 237 " --> pdb=" O   GLY B 238 " (cutoff:3.500A)
      removed outlier: 7.457A  pdb=" N   SER B 240 " --> pdb=" O   PHE A 237 " (cutoff:3.500A)
      removed outlier: 6.498A  pdb=" N   HIS A 239 " --> pdb=" O   SER B 240 " (cutoff:3.500A)
      removed outlier: 8.476A  pdb=" N   GLN B 242 " --> pdb=" O   HIS A 239 " (cutoff:3.500A)
      removed outlier: 6.504A  pdb=" N   GLU A 241 " --> pdb=" O   GLN B 242 " (cutoff:3.500A)
      removed outlier: 8.165A  pdb=" N   SER B 244 " --> pdb=" O   GLU A 241 " (cutoff:3.500A)
      removed outlier: 6.476A  pdb=" N   ILE A 243 " --> pdb=" O   SER B 244 " (cutoff:3.500A)
      removed outlier: 8.231A  pdb=" N   GLU B 246 " --> pdb=" O   ILE A 243 " (cutoff:3.500A)
      removed outlier: 6.617A  pdb=" N   GLN A 245 " --> pdb=" O   GLU B 246 " (cutoff:3.500A)
      removed outlier: 7.624A  pdb=" N   TYR B 248 " --> pdb=" O   GLN A 245 " (cutoff:3.500A)
      removed outlier: 6.198A  pdb=" N   ARG A 247 " --> pdb=" O   TYR B 248 " (cutoff:3.500A)
      removed outlier: 7.917A  pdb=" N   TYR B 250 " --> pdb=" O   ARG A 247 " (cutoff:3.500A)
      removed outlier: 8.750A  pdb=" N   GLN A 249 " --> pdb=" O   TYR B 250 " (cutoff:3.500A)
      removed outlier: 7.133A  pdb=" N   ASP B 252 " --> pdb=" O   GLN A 249 " (cutoff:3.500A)
      removed outlier: 9.139A  pdb=" N   VAL A 251 " --> pdb=" O   ASP B 252 " (cutoff:3.500A)
      removed outlier: 5.688A  pdb=" N   THR B 231 " --> pdb=" O   VAL C 232 " (cutoff:3.500A)
      removed outlier: 8.174A  pdb=" N   THR C 234 " --> pdb=" O   THR B 231 " (cutoff:3.500A)
      removed outlier: 6.743A  pdb=" N   THR B 233 " --> pdb=" O   THR C 234 " (cutoff:3.500A)
      removed outlier: 8.049A  pdb=" N   TYR C 236 " --> pdb=" O   THR B 233 " (cutoff:3.500A)
      removed outlier: 6.425A  pdb=" N   THR B 235 " --> pdb=" O   TYR C 236 " (cutoff:3.500A)
      removed outlier: 8.130A  pdb=" N   GLY C 238 " --> pdb=" O   THR B 235 " (cutoff:3.500A)
      removed outlier: 6.017A  pdb=" N   PHE B 237 " --> pdb=" O   GLY C 238 " (cutoff:3.500A)
      removed outlier: 7.467A  pdb=" N   SER C 240 " --> pdb=" O   PHE B 237 " (cutoff:3.500A)
      removed outlier: 6.451A  pdb=" N   HIS B 239 " --> pdb=" O   SER C 240 " (cutoff:3.500A)
      removed outlier: 8.475A  pdb=" N   GLN C 242 " --> pdb=" O   HIS B 239 " (cutoff:3.500A)
      removed outlier: 6.507A  pdb=" N   GLU B 241 " --> pdb=" O   GLN C 242 " (cutoff:3.500A)
      removed outlier: 8.168A  pdb=" N   SER C 244 " --> pdb=" O   GLU B 241 " (cutoff:3.500A)
      removed outlier: 6.419A  pdb=" N   ILE B 243 " --> pdb=" O   SER C 244 " (cutoff:3.500A)
      removed outlier: 8.103A  pdb=" N   GLU C 246 " --> pdb=" O   ILE B 243 " (cutoff:3.500A)
      removed outlier: 6.615A  pdb=" N   GLN B 245 " --> pdb=" O   GLU C 246 " (cutoff:3.500A)
      removed outlier: 7.669A  pdb=" N   TYR C 248 " --> pdb=" O   GLN B 245 " (cutoff:3.500A)
      removed outlier: 6.399A  pdb=" N   ARG B 247 " --> pdb=" O   TYR C 248 " (cutoff:3.500A)
      removed outlier: 7.969A  pdb=" N   TYR C 250 " --> pdb=" O   ARG B 247 " (cutoff:3.500A)
      removed outlier: 8.780A  pdb=" N   GLN B 249 " --> pdb=" O   TYR C 250 " (cutoff:3.500A)
      removed outlier: 6.968A  pdb=" N   ASP C 252 " --> pdb=" O   GLN B 249 " (cutoff:3.500A)
      removed outlier: 9.196A  pdb=" N   VAL B 251 " --> pdb=" O   ASP C 252 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AB8

    80 hydrogen bonds defined for protein.
    240 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: 0.86

  Time building geometry restraints manager: 0.83 seconds

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

  Histogram of bond lengths:
        1.21 -     1.33: 904
        1.33 -     1.45: 541
        1.45 -     1.57: 1828
        1.57 -     1.69: 0
        1.69 -     1.81: 36
  Bond restraints: 3309
  Sorted by residual:
  bond pdb=" CZ  ARG C 247 "
       pdb=" NH2 ARG C 247 "
    ideal  model  delta    sigma   weight residual
    1.330  1.290  0.040 1.30e-02 5.92e+03 9.65e+00
  bond pdb=" CZ  ARG B 247 "
       pdb=" NH2 ARG B 247 "
    ideal  model  delta    sigma   weight residual
    1.330  1.293  0.037 1.30e-02 5.92e+03 8.31e+00
  bond pdb=" CZ  ARG B 180 "
       pdb=" NH2 ARG B 180 "
    ideal  model  delta    sigma   weight residual
    1.330  1.294  0.036 1.30e-02 5.92e+03 7.87e+00
  bond pdb=" CZ  ARG B 140 "
       pdb=" NH2 ARG B 140 "
    ideal  model  delta    sigma   weight residual
    1.330  1.295  0.035 1.30e-02 5.92e+03 7.23e+00
  bond pdb=" CZ  ARG C 247 "
       pdb=" NH1 ARG C 247 "
    ideal  model  delta    sigma   weight residual
    1.323  1.285  0.038 1.40e-02 5.10e+03 7.21e+00
  ... (remaining 3304 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.31: 3458
        2.31 -     4.62: 858
        4.62 -     6.93: 162
        6.93 -     9.24: 17
        9.24 -    11.55: 2
  Bond angle restraints: 4497
  Sorted by residual:
  angle pdb=" N   GLU C 246 "
        pdb=" CA  GLU C 246 "
        pdb=" C   GLU C 246 "
      ideal   model   delta    sigma   weight residual
     108.55  120.10  -11.55 1.62e+00 3.81e-01 5.08e+01
  angle pdb=" CB  ASN A 183 "
        pdb=" CG  ASN A 183 "
        pdb=" ND2 ASN A 183 "
      ideal   model   delta    sigma   weight residual
     116.40  106.12   10.28 1.50e+00 4.44e-01 4.70e+01
  angle pdb=" CA  ASP B 136 "
        pdb=" CB  ASP B 136 "
        pdb=" CG  ASP B 136 "
      ideal   model   delta    sigma   weight residual
     112.60  119.30   -6.70 1.00e+00 1.00e+00 4.48e+01
  angle pdb=" CA  ASP A 136 "
        pdb=" CB  ASP A 136 "
        pdb=" CG  ASP A 136 "
      ideal   model   delta    sigma   weight residual
     112.60  118.07   -5.47 1.00e+00 1.00e+00 2.99e+01
  angle pdb=" CA  ASN A 183 "
        pdb=" CB  ASN A 183 "
        pdb=" CG  ASN A 183 "
      ideal   model   delta    sigma   weight residual
     112.60  117.92   -5.32 1.00e+00 1.00e+00 2.83e+01
  ... (remaining 4492 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.73: 1816
       17.73 -    35.46: 131
       35.46 -    53.19: 27
       53.19 -    70.92: 7
       70.92 -    88.65: 14
  Dihedral angle restraints: 1995
    sinusoidal: 777
      harmonic: 1218
  Sorted by residual:
  dihedral pdb=" CA  ILE C 152 "
           pdb=" C   ILE C 152 "
           pdb=" N   THR C 153 "
           pdb=" CA  THR C 153 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  151.40   28.60     0      5.00e+00 4.00e-02 3.27e+01
  dihedral pdb=" CA  ILE B 152 "
           pdb=" C   ILE B 152 "
           pdb=" N   THR B 153 "
           pdb=" CA  THR B 153 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  151.42   28.58     0      5.00e+00 4.00e-02 3.27e+01
  dihedral pdb=" C   GLN C 138 "
           pdb=" N   GLN C 138 "
           pdb=" CA  GLN C 138 "
           pdb=" CB  GLN C 138 "
      ideal   model   delta  harmonic     sigma   weight residual
    -122.60 -136.80   14.20     0      2.50e+00 1.60e-01 3.23e+01
  ... (remaining 1992 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.108: 353
       0.108 -    0.216: 152
       0.216 -    0.324: 24
       0.324 -    0.432: 6
       0.432 -    0.540: 5
  Chirality restraints: 540
  Sorted by residual:
  chirality pdb=" CA  GLN C 138 "
            pdb=" N   GLN C 138 "
            pdb=" C   GLN C 138 "
            pdb=" CB  GLN C 138 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    1.97    0.54 2.00e-01 2.50e+01 7.30e+00
  chirality pdb=" CA  GLN B 194 "
            pdb=" N   GLN B 194 "
            pdb=" C   GLN B 194 "
            pdb=" CB  GLN B 194 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.02    0.49 2.00e-01 2.50e+01 6.00e+00
  chirality pdb=" CA  THR B 166 "
            pdb=" N   THR B 166 "
            pdb=" C   THR B 166 "
            pdb=" CB  THR B 166 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.53    2.06    0.47 2.00e-01 2.50e+01 5.49e+00
  ... (remaining 537 not shown)

  Planarity restraints: 558
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TYR A 143 "    0.137 2.00e-02 2.50e+03   7.13e-02 1.02e+02
        pdb=" CG  TYR A 143 "   -0.058 2.00e-02 2.50e+03
        pdb=" CD1 TYR A 143 "   -0.065 2.00e-02 2.50e+03
        pdb=" CD2 TYR A 143 "   -0.057 2.00e-02 2.50e+03
        pdb=" CE1 TYR A 143 "   -0.025 2.00e-02 2.50e+03
        pdb=" CE2 TYR A 143 "   -0.035 2.00e-02 2.50e+03
        pdb=" CZ  TYR A 143 "    0.009 2.00e-02 2.50e+03
        pdb=" OH  TYR A 143 "    0.095 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TYR A 250 "   -0.096 2.00e-02 2.50e+03   5.62e-02 6.32e+01
        pdb=" CG  TYR A 250 "    0.011 2.00e-02 2.50e+03
        pdb=" CD1 TYR A 250 "    0.050 2.00e-02 2.50e+03
        pdb=" CD2 TYR A 250 "    0.049 2.00e-02 2.50e+03
        pdb=" CE1 TYR A 250 "    0.038 2.00e-02 2.50e+03
        pdb=" CE2 TYR A 250 "    0.034 2.00e-02 2.50e+03
        pdb=" CZ  TYR A 250 "    0.005 2.00e-02 2.50e+03
        pdb=" OH  TYR A 250 "   -0.092 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TYR B 250 "   -0.084 2.00e-02 2.50e+03   5.28e-02 5.57e+01
        pdb=" CG  TYR B 250 "    0.003 2.00e-02 2.50e+03
        pdb=" CD1 TYR B 250 "    0.043 2.00e-02 2.50e+03
        pdb=" CD2 TYR B 250 "    0.040 2.00e-02 2.50e+03
        pdb=" CE1 TYR B 250 "    0.040 2.00e-02 2.50e+03
        pdb=" CE2 TYR B 250 "    0.039 2.00e-02 2.50e+03
        pdb=" CZ  TYR B 250 "    0.011 2.00e-02 2.50e+03
        pdb=" OH  TYR B 250 "   -0.092 2.00e-02 2.50e+03
  ... (remaining 555 not shown)

  Histogram of nonbonded interaction distances:
        2.52 -     3.00: 1633
        3.00 -     3.47: 2841
        3.47 -     3.95: 5424
        3.95 -     4.42: 5665
        4.42 -     4.90: 10525
  Nonbonded interactions: 26088
  Sorted by model distance:
  nonbonded pdb=" OG  SER B 134 "
            pdb=" OD1 ASP B 136 "
     model   vdw
     2.525 3.040
  nonbonded pdb=" OE2 GLU B 241 "
            pdb=" OG  SER C 120 "
     model   vdw
     2.529 3.040
  nonbonded pdb=" OE2 GLU A 241 "
            pdb=" OG  SER B 120 "
     model   vdw
     2.542 3.040
  nonbonded pdb=" OG  SER C 134 "
            pdb=" OD1 ASP C 136 "
     model   vdw
     2.565 3.040
  nonbonded pdb=" OE2 GLU A 205 "
            pdb=" OG  SER A 208 "
     model   vdw
     2.566 3.040
  ... (remaining 26083 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: 0.01
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'B'
  selection = chain 'C'
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             1.400
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.130
  Check model and map are aligned:         0.030
  Set scattering table:                    0.030
  Process input model:                     12.620
  Find NCS groups from input model:        0.110
  Set up NCS constraints:                  0.010
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:11.410
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   25.750
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8275
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      :  0.012   0.047   3309  Z= 0.788
  Angle     :  2.095  11.548   4497  Z= 1.353
  Chirality :  0.122   0.540    540
  Planarity :  0.013   0.095    558
  Dihedral  : 15.485  88.647   1206
  Min Nonbonded Distance : 2.525

Molprobity Statistics.
  All-atom Clashscore : 0.00
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.76 %
    Favored  : 94.24 %
  Rotamer:
    Outliers :  0.53 %
    Allowed  :  4.50 %
    Favored  : 94.97 %
  Cbeta Deviations :  2.56 %
  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: -2.45 (0.34), residues: 399
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.86 (0.26), residues: 399

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.017   0.005   HIS B 239 
 PHE   0.032   0.010   PHE A 171 
 TYR   0.137   0.025   TYR A 143 
 ARG   0.002   0.000   ARG A 180 

*********************** 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
  131 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 129
  time to evaluate  : 0.366 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  124 LYS cc_start: 0.8619 (mttp) cc_final: 0.7767 (mmpt)
REVERT: A  190 LEU cc_start: 0.9097 (mp) cc_final: 0.8874 (mm)
REVERT: B  234 THR cc_start: 0.8258 (t) cc_final: 0.8021 (m)
  outliers start: 2
  outliers final: 1
  residues processed: 131
  average time/residue: 1.0631
  time to fit residues: 143.2791
Evaluate side-chains
  86 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 85
  time to evaluate  : 0.369 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  136 ASP
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 39
   random chunks:
   chunk 32 optimal weight:    8.9990
   chunk 29 optimal weight:    6.9990
   chunk 16 optimal weight:    5.9990
   chunk 10 optimal weight:    0.9990
   chunk 19 optimal weight:    0.9990
   chunk 15 optimal weight:    5.9990
   chunk 30 optimal weight:    5.9990
   chunk 11 optimal weight:    0.9980
   chunk 18 optimal weight:    5.9990
   chunk 22 optimal weight:    6.9990
   chunk 35 optimal weight:   20.0000
   overall best weight:    2.9988

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

Flipped N/Q/H residues before XYZ refinement:
A 145 ASN
A 151 ASN
A 182 ASN
A 242 GLN
B 145 ASN
B 182 ASN
B 194 GLN
C 138 GLN
C 145 ASN
C 182 ASN
C 249 GLN

Total number of N/Q/H flips: 11

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4099 r_free = 0.4099 target = 0.138520 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3905 r_free = 0.3905 target = 0.121248 restraints weight = 3577.498|
|-----------------------------------------------------------------------------|
r_work (start): 0.3911 rms_B_bonded: 1.66
r_work: 0.3816 rms_B_bonded: 1.88 restraints_weight: 0.5000
r_work: 0.3718 rms_B_bonded: 3.24 restraints_weight: 0.2500
r_work (final): 0.3718
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8602
moved from start:          0.2584

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.040   3309  Z= 0.274
  Angle     :  0.780   8.743   4497  Z= 0.420
  Chirality :  0.059   0.160    540
  Planarity :  0.003   0.028    558
  Dihedral  :  7.513  31.432    449
  Min Nonbonded Distance : 2.523

Molprobity Statistics.
  All-atom Clashscore : 5.85
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.76 %
    Favored  : 95.24 %
  Rotamer:
    Outliers :  5.29 %
    Allowed  : 13.76 %
    Favored  : 80.95 %
  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: -2.12 (0.36), residues: 399
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.60 (0.28), residues: 399

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.004   0.001   HIS B 239 
 PHE   0.013   0.003   PHE B 213 
 TYR   0.024   0.002   TYR C 143 
 ARG   0.002   0.001   ARG B 180 

*********************** 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
  114 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 94
  time to evaluate  : 0.398 
Fit side-chains
REVERT: A  124 LYS cc_start: 0.8828 (mttp) cc_final: 0.7943 (mmtt)
REVERT: A  144 LEU cc_start: 0.8926 (tt) cc_final: 0.8695 (tp)
REVERT: A  163 GLU cc_start: 0.7942 (mt-10) cc_final: 0.7682 (mp0)
REVERT: B  140 ARG cc_start: 0.8362 (mtm180) cc_final: 0.7175 (mtt90)
REVERT: B  180 ARG cc_start: 0.7800 (mtm-85) cc_final: 0.7510 (mtp85)
REVERT: C  140 ARG cc_start: 0.8114 (OUTLIER) cc_final: 0.7671 (mtt90)
REVERT: C  196 ASP cc_start: 0.8276 (t0) cc_final: 0.7844 (m-30)
  outliers start: 20
  outliers final: 10
  residues processed: 106
  average time/residue: 1.2395
  time to fit residues: 134.8075
Evaluate side-chains
  97 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 86
  time to evaluate  : 0.390 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  141 THR
Chi-restraints excluded: chain A residue  149 THR
Chi-restraints excluded: chain A residue  194 GLN
Chi-restraints excluded: chain A residue  201 THR
Chi-restraints excluded: chain B residue  141 THR
Chi-restraints excluded: chain B residue  149 THR
Chi-restraints excluded: chain B residue  201 THR
Chi-restraints excluded: chain C residue  140 ARG
Chi-restraints excluded: chain C residue  141 THR
Chi-restraints excluded: chain C residue  166 THR
Chi-restraints excluded: chain C residue  201 THR
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 39
   random chunks:
   chunk 36 optimal weight:    0.0370
   chunk 5 optimal weight:    5.9990
   chunk 21 optimal weight:    9.9990
   chunk 25 optimal weight:    9.9990
   chunk 14 optimal weight:    6.9990
   chunk 3 optimal weight:    7.9990
   chunk 19 optimal weight:    9.9990
   chunk 13 optimal weight:    9.9990
   chunk 34 optimal weight:    0.9980
   chunk 7 optimal weight:    9.9990
   chunk 8 optimal weight:    5.9990
   overall best weight:    4.0064

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

Flipped N/Q/H residues before XYZ refinement:
C 249 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4071 r_free = 0.4071 target = 0.136275 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3881 r_free = 0.3881 target = 0.119405 restraints weight = 3590.486|
|-----------------------------------------------------------------------------|
r_work (start): 0.3885 rms_B_bonded: 1.67
r_work: 0.3788 rms_B_bonded: 1.87 restraints_weight: 0.5000
r_work: 0.3691 rms_B_bonded: 3.19 restraints_weight: 0.2500
r_work (final): 0.3691
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8642
moved from start:          0.3223

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.041   3309  Z= 0.317
  Angle     :  0.727   9.280   4497  Z= 0.392
  Chirality :  0.059   0.152    540
  Planarity :  0.003   0.016    558
  Dihedral  :  7.274  26.271    447
  Min Nonbonded Distance : 2.544

Molprobity Statistics.
  All-atom Clashscore : 7.38
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.01 %
    Favored  : 94.99 %
  Rotamer:
    Outliers :  4.23 %
    Allowed  : 15.87 %
    Favored  : 79.89 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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: -2.17 (0.37), residues: 399
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.65 (0.28), residues: 399

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.003   0.001   HIS C 239 
 PHE   0.013   0.003   PHE B 237 
 TYR   0.023   0.002   TYR C 143 
 ARG   0.005   0.001   ARG C 247 

*********************** 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
  111 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 95
  time to evaluate  : 0.362 
Fit side-chains
REVERT: A  124 LYS cc_start: 0.8844 (mttp) cc_final: 0.7921 (mmtt)
REVERT: A  140 ARG cc_start: 0.7611 (ttm170) cc_final: 0.6278 (ppt170)
REVERT: B  140 ARG cc_start: 0.8291 (mtm180) cc_final: 0.7032 (mtt90)
REVERT: B  180 ARG cc_start: 0.7783 (mtm-85) cc_final: 0.7533 (mtp85)
REVERT: C  140 ARG cc_start: 0.8239 (OUTLIER) cc_final: 0.7759 (mtt90)
REVERT: C  196 ASP cc_start: 0.8230 (t0) cc_final: 0.7809 (m-30)
  outliers start: 16
  outliers final: 10
  residues processed: 105
  average time/residue: 1.2313
  time to fit residues: 132.7010
Evaluate side-chains
  101 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 90
  time to evaluate  : 0.482 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  141 THR
Chi-restraints excluded: chain A residue  149 THR
Chi-restraints excluded: chain A residue  194 GLN
Chi-restraints excluded: chain A residue  201 THR
Chi-restraints excluded: chain B residue  141 THR
Chi-restraints excluded: chain B residue  201 THR
Chi-restraints excluded: chain B residue  208 SER
Chi-restraints excluded: chain C residue  140 ARG
Chi-restraints excluded: chain C residue  141 THR
Chi-restraints excluded: chain C residue  166 THR
Chi-restraints excluded: chain C residue  201 THR
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 39
   random chunks:
   chunk 19 optimal weight:    9.9990
   chunk 8 optimal weight:   10.0000
   chunk 14 optimal weight:    9.9990
   chunk 29 optimal weight:    3.9990
   chunk 16 optimal weight:    6.9990
   chunk 6 optimal weight:    6.9990
   chunk 37 optimal weight:    0.0050
   chunk 36 optimal weight:    9.9990
   chunk 33 optimal weight:    9.9990
   chunk 38 optimal weight:    5.9990
   chunk 2 optimal weight:    0.9990
   overall best weight:    3.6002

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

Flipped N/Q/H residues before XYZ refinement:
A 170 GLN
A 249 GLN
B 164 ASN
B 170 GLN
B 194 GLN
C 145 ASN
C 164 ASN
C 170 GLN
C 249 GLN

Total number of N/Q/H flips: 9

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4071 r_free = 0.4071 target = 0.135804 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3885 r_free = 0.3885 target = 0.118998 restraints weight = 3617.010|
|-----------------------------------------------------------------------------|
r_work (start): 0.3890 rms_B_bonded: 1.69
r_work: 0.3795 rms_B_bonded: 1.88 restraints_weight: 0.5000
r_work: 0.3696 rms_B_bonded: 3.22 restraints_weight: 0.2500
r_work (final): 0.3696
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8637
moved from start:          0.3489

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.030   3309  Z= 0.293
  Angle     :  0.695  10.073   4497  Z= 0.373
  Chirality :  0.057   0.149    540
  Planarity :  0.002   0.017    558
  Dihedral  :  7.049  26.472    447
  Min Nonbonded Distance : 2.565

Molprobity Statistics.
  All-atom Clashscore : 7.08
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.26 %
    Favored  : 95.74 %
  Rotamer:
    Outliers :  5.82 %
    Allowed  : 16.67 %
    Favored  : 77.51 %
  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: -2.19 (0.37), residues: 399
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.66 (0.28), residues: 399

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.002   0.001   HIS C 239 
 PHE   0.012   0.003   PHE B 237 
 TYR   0.021   0.002   TYR B 143 
 ARG   0.004   0.001   ARG C 247 

*********************** 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
  111 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 89
  time to evaluate  : 0.369 
Fit side-chains
REVERT: A  124 LYS cc_start: 0.8850 (mttp) cc_final: 0.7927 (mmtt)
REVERT: B  140 ARG cc_start: 0.8244 (mtm180) cc_final: 0.7150 (mtt90)
REVERT: B  180 ARG cc_start: 0.7739 (mtm-85) cc_final: 0.7454 (mtp85)
REVERT: B  253 CYS cc_start: 0.7881 (OUTLIER) cc_final: 0.7179 (m)
REVERT: C  140 ARG cc_start: 0.8178 (OUTLIER) cc_final: 0.7670 (mtt90)
REVERT: C  196 ASP cc_start: 0.8232 (t0) cc_final: 0.7817 (m-30)
  outliers start: 22
  outliers final: 11
  residues processed: 104
  average time/residue: 1.1849
  time to fit residues: 126.5373
Evaluate side-chains
  102 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 89
  time to evaluate  : 0.302 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  141 THR
Chi-restraints excluded: chain A residue  149 THR
Chi-restraints excluded: chain A residue  201 THR
Chi-restraints excluded: chain B residue  141 THR
Chi-restraints excluded: chain B residue  153 THR
Chi-restraints excluded: chain B residue  201 THR
Chi-restraints excluded: chain B residue  208 SER
Chi-restraints excluded: chain B residue  253 CYS
Chi-restraints excluded: chain C residue  140 ARG
Chi-restraints excluded: chain C residue  141 THR
Chi-restraints excluded: chain C residue  166 THR
Chi-restraints excluded: chain C residue  201 THR
Chi-restraints excluded: chain C residue  233 THR
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 39
   random chunks:
   chunk 15 optimal weight:    9.9990
   chunk 28 optimal weight:    2.9990
   chunk 0 optimal weight:   10.0000
   chunk 8 optimal weight:    9.9990
   chunk 25 optimal weight:    3.9990
   chunk 34 optimal weight:    9.9990
   chunk 2 optimal weight:    4.9990
   chunk 36 optimal weight:    7.9990
   chunk 3 optimal weight:    5.9990
   chunk 7 optimal weight:    9.9990
   chunk 5 optimal weight:   10.0000
   overall best weight:    5.1990

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

Flipped N/Q/H residues before XYZ refinement:
A 154 ASN
A 249 GLN
** B 239 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
C 249 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4038 r_free = 0.4038 target = 0.132473 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3852 r_free = 0.3852 target = 0.115801 restraints weight = 3627.817|
|-----------------------------------------------------------------------------|
r_work (start): 0.3851 rms_B_bonded: 1.71
r_work: 0.3749 rms_B_bonded: 1.90 restraints_weight: 0.5000
r_work: 0.3646 rms_B_bonded: 3.25 restraints_weight: 0.2500
r_work (final): 0.3646
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8657
moved from start:          0.3604

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.040   3309  Z= 0.396
  Angle     :  0.728   8.804   4497  Z= 0.394
  Chirality :  0.058   0.153    540
  Planarity :  0.003   0.019    558
  Dihedral  :  7.136  26.149    447
  Min Nonbonded Distance : 2.568

Molprobity Statistics.
  All-atom Clashscore : 8.92
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.51 %
    Favored  : 95.49 %
  Rotamer:
    Outliers :  6.88 %
    Allowed  : 17.46 %
    Favored  : 75.66 %
  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: -2.30 (0.36), residues: 399
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.75 (0.28), residues: 399

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.003   0.001   HIS A 239 
 PHE   0.012   0.003   PHE B 171 
 TYR   0.023   0.002   TYR B 143 
 ARG   0.004   0.001   ARG C 247 

*********************** 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
  115 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 89
  time to evaluate  : 0.338 
Fit side-chains
REVERT: A  124 LYS cc_start: 0.8869 (mttp) cc_final: 0.7933 (mmtt)
REVERT: B  140 ARG cc_start: 0.8283 (mtm180) cc_final: 0.7107 (mtt90)
REVERT: B  144 LEU cc_start: 0.8863 (OUTLIER) cc_final: 0.8537 (tt)
REVERT: B  180 ARG cc_start: 0.7771 (mtm-85) cc_final: 0.7502 (mtp85)
REVERT: B  253 CYS cc_start: 0.7906 (OUTLIER) cc_final: 0.7240 (m)
REVERT: C  140 ARG cc_start: 0.8165 (OUTLIER) cc_final: 0.7625 (mtt90)
REVERT: C  196 ASP cc_start: 0.8288 (t0) cc_final: 0.7820 (m-30)
  outliers start: 26
  outliers final: 14
  residues processed: 107
  average time/residue: 1.2412
  time to fit residues: 136.1234
Evaluate side-chains
  106 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 89
  time to evaluate  : 0.340 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  141 THR
Chi-restraints excluded: chain A residue  149 THR
Chi-restraints excluded: chain A residue  201 THR
Chi-restraints excluded: chain A residue  208 SER
Chi-restraints excluded: chain B residue  141 THR
Chi-restraints excluded: chain B residue  144 LEU
Chi-restraints excluded: chain B residue  153 THR
Chi-restraints excluded: chain B residue  194 GLN
Chi-restraints excluded: chain B residue  201 THR
Chi-restraints excluded: chain B residue  208 SER
Chi-restraints excluded: chain B residue  253 CYS
Chi-restraints excluded: chain C residue  140 ARG
Chi-restraints excluded: chain C residue  141 THR
Chi-restraints excluded: chain C residue  166 THR
Chi-restraints excluded: chain C residue  201 THR
Chi-restraints excluded: chain C residue  208 SER
Chi-restraints excluded: chain C residue  233 THR
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 39
   random chunks:
   chunk 7 optimal weight:    0.9980
   chunk 21 optimal weight:   10.0000
   chunk 22 optimal weight:    5.9990
   chunk 25 optimal weight:    6.9990
   chunk 6 optimal weight:    7.9990
   chunk 8 optimal weight:    4.9990
   chunk 10 optimal weight:    4.9990
   chunk 17 optimal weight:    8.9990
   chunk 18 optimal weight:    8.9990
   chunk 29 optimal weight:    4.9990
   chunk 38 optimal weight:    4.9990
   overall best weight:    4.1988

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

Flipped N/Q/H residues before XYZ refinement:
A 249 GLN
** B 239 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
C 249 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4053 r_free = 0.4053 target = 0.135816 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3871 r_free = 0.3871 target = 0.119615 restraints weight = 3714.871|
|-----------------------------------------------------------------------------|
r_work (start): 0.3880 rms_B_bonded: 1.68
r_work: 0.3787 rms_B_bonded: 1.85 restraints_weight: 0.5000
r_work: 0.3688 rms_B_bonded: 3.17 restraints_weight: 0.2500
r_work (final): 0.3688
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8660
moved from start:          0.3690

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.040   3309  Z= 0.333
  Angle     :  0.697   7.992   4497  Z= 0.377
  Chirality :  0.057   0.147    540
  Planarity :  0.003   0.019    558
  Dihedral  :  7.026  26.693    447
  Min Nonbonded Distance : 2.583

Molprobity Statistics.
  All-atom Clashscore : 7.38
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.26 %
    Favored  : 95.74 %
  Rotamer:
    Outliers :  6.61 %
    Allowed  : 18.52 %
    Favored  : 74.87 %
  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: -2.32 (0.36), residues: 399
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.76 (0.28), residues: 399

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.004   0.001   HIS B 239 
 PHE   0.011   0.003   PHE B 237 
 TYR   0.022   0.002   TYR B 143 
 ARG   0.003   0.000   ARG C 247 

*********************** 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
  114 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 89
  time to evaluate  : 0.340 
Fit side-chains
REVERT: A  124 LYS cc_start: 0.8857 (mttp) cc_final: 0.7976 (mmtt)
REVERT: B  140 ARG cc_start: 0.8342 (mtm180) cc_final: 0.7197 (mtt90)
REVERT: B  144 LEU cc_start: 0.8913 (OUTLIER) cc_final: 0.8601 (tt)
REVERT: B  180 ARG cc_start: 0.7781 (mtm-85) cc_final: 0.7522 (mtp85)
REVERT: B  253 CYS cc_start: 0.7853 (OUTLIER) cc_final: 0.7203 (m)
REVERT: C  140 ARG cc_start: 0.8214 (OUTLIER) cc_final: 0.7736 (mtt90)
REVERT: C  196 ASP cc_start: 0.8246 (t0) cc_final: 0.7849 (m-30)
  outliers start: 25
  outliers final: 14
  residues processed: 107
  average time/residue: 1.1721
  time to fit residues: 128.7636
Evaluate side-chains
  106 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 89
  time to evaluate  : 0.415 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  141 THR
Chi-restraints excluded: chain A residue  149 THR
Chi-restraints excluded: chain A residue  201 THR
Chi-restraints excluded: chain A residue  208 SER
Chi-restraints excluded: chain B residue  141 THR
Chi-restraints excluded: chain B residue  144 LEU
Chi-restraints excluded: chain B residue  153 THR
Chi-restraints excluded: chain B residue  194 GLN
Chi-restraints excluded: chain B residue  201 THR
Chi-restraints excluded: chain B residue  208 SER
Chi-restraints excluded: chain B residue  253 CYS
Chi-restraints excluded: chain C residue  140 ARG
Chi-restraints excluded: chain C residue  141 THR
Chi-restraints excluded: chain C residue  166 THR
Chi-restraints excluded: chain C residue  201 THR
Chi-restraints excluded: chain C residue  208 SER
Chi-restraints excluded: chain C residue  233 THR
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 39
   random chunks:
   chunk 32 optimal weight:    5.9990
   chunk 30 optimal weight:    9.9990
   chunk 16 optimal weight:    5.9990
   chunk 38 optimal weight:    5.9990
   chunk 4 optimal weight:    0.0040
   chunk 21 optimal weight:   10.0000
   chunk 2 optimal weight:    4.9990
   chunk 18 optimal weight:    8.9990
   chunk 1 optimal weight:    0.7980
   chunk 3 optimal weight:    5.9990
   chunk 15 optimal weight:    4.9990
   overall best weight:    3.3598

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

Flipped N/Q/H residues before XYZ refinement:
A 151 ASN
A 249 GLN
B 194 GLN
C 249 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4074 r_free = 0.4074 target = 0.137122 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3893 r_free = 0.3893 target = 0.120958 restraints weight = 3584.509|
|-----------------------------------------------------------------------------|
r_work (start): 0.3904 rms_B_bonded: 1.67
r_work: 0.3811 rms_B_bonded: 1.82 restraints_weight: 0.5000
r_work: 0.3713 rms_B_bonded: 3.14 restraints_weight: 0.2500
r_work (final): 0.3713
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8643
moved from start:          0.3727

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.036   3309  Z= 0.279
  Angle     :  0.673   7.404   4497  Z= 0.364
  Chirality :  0.056   0.148    540
  Planarity :  0.002   0.018    558
  Dihedral  :  6.882  26.066    447
  Min Nonbonded Distance : 2.596

Molprobity Statistics.
  All-atom Clashscore : 7.69
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.51 %
    Favored  : 95.49 %
  Rotamer:
    Outliers :  6.35 %
    Allowed  : 20.37 %
    Favored  : 73.28 %
  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: -2.28 (0.36), residues: 399
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.73 (0.28), residues: 399

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.003   0.001   HIS B 239 
 PHE   0.011   0.003   PHE B 171 
 TYR   0.020   0.002   TYR B 143 
 ARG   0.003   0.000   ARG C 247 

*********************** 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
  114 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 90
  time to evaluate  : 0.376 
Fit side-chains
REVERT: A  124 LYS cc_start: 0.8849 (mttp) cc_final: 0.7968 (mmtt)
REVERT: B  140 ARG cc_start: 0.8336 (mtm180) cc_final: 0.7171 (mtt90)
REVERT: B  144 LEU cc_start: 0.8914 (OUTLIER) cc_final: 0.8617 (tt)
REVERT: B  180 ARG cc_start: 0.7780 (mtm-85) cc_final: 0.7521 (mtp85)
REVERT: B  253 CYS cc_start: 0.7838 (OUTLIER) cc_final: 0.7151 (m)
REVERT: C  196 ASP cc_start: 0.8211 (t0) cc_final: 0.7851 (m-30)
  outliers start: 24
  outliers final: 14
  residues processed: 107
  average time/residue: 1.1508
  time to fit residues: 126.4506
Evaluate side-chains
  106 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 90
  time to evaluate  : 0.402 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  141 THR
Chi-restraints excluded: chain A residue  149 THR
Chi-restraints excluded: chain A residue  201 THR
Chi-restraints excluded: chain A residue  208 SER
Chi-restraints excluded: chain B residue  141 THR
Chi-restraints excluded: chain B residue  144 LEU
Chi-restraints excluded: chain B residue  153 THR
Chi-restraints excluded: chain B residue  194 GLN
Chi-restraints excluded: chain B residue  201 THR
Chi-restraints excluded: chain B residue  208 SER
Chi-restraints excluded: chain B residue  253 CYS
Chi-restraints excluded: chain C residue  141 THR
Chi-restraints excluded: chain C residue  166 THR
Chi-restraints excluded: chain C residue  201 THR
Chi-restraints excluded: chain C residue  208 SER
Chi-restraints excluded: chain C residue  233 THR
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 39
   random chunks:
   chunk 2 optimal weight:    4.9990
   chunk 5 optimal weight:    9.9990
   chunk 15 optimal weight:    5.9990
   chunk 23 optimal weight:    6.9990
   chunk 24 optimal weight:    7.9990
   chunk 26 optimal weight:    9.9990
   chunk 34 optimal weight:    0.9990
   chunk 32 optimal weight:    7.9990
   chunk 36 optimal weight:    3.9990
   chunk 25 optimal weight:    0.9990
   chunk 18 optimal weight:    8.9990
   overall best weight:    3.3990

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

Flipped N/Q/H residues before XYZ refinement:
A 249 GLN
C 194 GLN
C 249 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4083 r_free = 0.4083 target = 0.137858 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3906 r_free = 0.3906 target = 0.121813 restraints weight = 3595.472|
|-----------------------------------------------------------------------------|
r_work (start): 0.3918 rms_B_bonded: 1.63
r_work: 0.3828 rms_B_bonded: 1.81 restraints_weight: 0.5000
r_work: 0.3732 rms_B_bonded: 3.12 restraints_weight: 0.2500
r_work (final): 0.3732
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8645
moved from start:          0.3774

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.037   3309  Z= 0.283
  Angle     :  0.682   9.130   4497  Z= 0.365
  Chirality :  0.056   0.154    540
  Planarity :  0.003   0.019    558
  Dihedral  :  6.861  26.354    447
  Min Nonbonded Distance : 2.549

Molprobity Statistics.
  All-atom Clashscore : 7.69
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.51 %
    Favored  : 95.49 %
  Rotamer:
    Outliers :  5.56 %
    Allowed  : 21.69 %
    Favored  : 72.75 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.29 (0.36), residues: 399
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.74 (0.28), residues: 399

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.003   0.001   HIS B 239 
 PHE   0.012   0.003   PHE B 213 
 TYR   0.021   0.002   TYR A 143 
 ARG   0.003   0.000   ARG C 247 

*********************** 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
  109 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 88
  time to evaluate  : 0.361 
Fit side-chains
REVERT: A  124 LYS cc_start: 0.8821 (mttp) cc_final: 0.7967 (mmtt)
REVERT: B  140 ARG cc_start: 0.8356 (mtm180) cc_final: 0.7190 (mtt90)
REVERT: B  144 LEU cc_start: 0.8911 (OUTLIER) cc_final: 0.8612 (tt)
REVERT: B  180 ARG cc_start: 0.7749 (mtm-85) cc_final: 0.7493 (mtp85)
REVERT: B  253 CYS cc_start: 0.7867 (OUTLIER) cc_final: 0.7148 (m)
REVERT: C  196 ASP cc_start: 0.8221 (t0) cc_final: 0.7882 (m-30)
  outliers start: 21
  outliers final: 14
  residues processed: 103
  average time/residue: 1.2473
  time to fit residues: 131.6698
Evaluate side-chains
  104 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 88
  time to evaluate  : 0.347 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  141 THR
Chi-restraints excluded: chain A residue  149 THR
Chi-restraints excluded: chain A residue  201 THR
Chi-restraints excluded: chain A residue  208 SER
Chi-restraints excluded: chain B residue  141 THR
Chi-restraints excluded: chain B residue  144 LEU
Chi-restraints excluded: chain B residue  153 THR
Chi-restraints excluded: chain B residue  194 GLN
Chi-restraints excluded: chain B residue  201 THR
Chi-restraints excluded: chain B residue  208 SER
Chi-restraints excluded: chain B residue  253 CYS
Chi-restraints excluded: chain C residue  141 THR
Chi-restraints excluded: chain C residue  166 THR
Chi-restraints excluded: chain C residue  201 THR
Chi-restraints excluded: chain C residue  208 SER
Chi-restraints excluded: chain C residue  233 THR
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 39
   random chunks:
   chunk 21 optimal weight:    6.9990
   chunk 12 optimal weight:    2.9990
   chunk 16 optimal weight:    5.9990
   chunk 33 optimal weight:    9.9990
   chunk 37 optimal weight:    8.9990
   chunk 3 optimal weight:    2.9990
   chunk 19 optimal weight:    4.9990
   chunk 34 optimal weight:    5.9990
   chunk 4 optimal weight:    0.1980
   chunk 35 optimal weight:    6.9990
   chunk 22 optimal weight:    5.9990
   overall best weight:    3.4388

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

Flipped N/Q/H residues before XYZ refinement:
A 249 GLN
C 145 ASN
C 194 GLN
C 249 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4083 r_free = 0.4083 target = 0.137898 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3904 r_free = 0.3904 target = 0.121759 restraints weight = 3643.882|
|-----------------------------------------------------------------------------|
r_work (start): 0.3915 rms_B_bonded: 1.66
r_work: 0.3823 rms_B_bonded: 1.83 restraints_weight: 0.5000
r_work: 0.3727 rms_B_bonded: 3.15 restraints_weight: 0.2500
r_work (final): 0.3727
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8647
moved from start:          0.3761

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.036   3309  Z= 0.286
  Angle     :  0.676   8.605   4497  Z= 0.363
  Chirality :  0.056   0.152    540
  Planarity :  0.003   0.018    558
  Dihedral  :  6.813  25.891    447
  Min Nonbonded Distance : 2.558

Molprobity Statistics.
  All-atom Clashscore : 7.38
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.76 %
    Favored  : 95.24 %
  Rotamer:
    Outliers :  5.56 %
    Allowed  : 21.96 %
    Favored  : 72.49 %
  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: -2.28 (0.36), residues: 399
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.73 (0.28), residues: 399

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.003   0.001   HIS B 239 
 PHE   0.013   0.003   PHE B 213 
 TYR   0.020   0.002   TYR A 143 
 ARG   0.002   0.000   ARG C 247 

*********************** 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
  112 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 91
  time to evaluate  : 0.370 
Fit side-chains
REVERT: A  124 LYS cc_start: 0.8824 (mttp) cc_final: 0.7971 (mmtt)
REVERT: B  140 ARG cc_start: 0.8347 (mtm180) cc_final: 0.7191 (mtt90)
REVERT: B  144 LEU cc_start: 0.8918 (OUTLIER) cc_final: 0.8612 (tt)
REVERT: B  180 ARG cc_start: 0.7777 (mtm-85) cc_final: 0.7516 (mtp85)
REVERT: B  253 CYS cc_start: 0.7874 (OUTLIER) cc_final: 0.7113 (m)
REVERT: C  196 ASP cc_start: 0.8203 (t0) cc_final: 0.7874 (m-30)
  outliers start: 21
  outliers final: 15
  residues processed: 105
  average time/residue: 1.2086
  time to fit residues: 130.1926
Evaluate side-chains
  108 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 91
  time to evaluate  : 0.360 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  141 THR
Chi-restraints excluded: chain A residue  149 THR
Chi-restraints excluded: chain A residue  201 THR
Chi-restraints excluded: chain A residue  208 SER
Chi-restraints excluded: chain B residue  141 THR
Chi-restraints excluded: chain B residue  144 LEU
Chi-restraints excluded: chain B residue  153 THR
Chi-restraints excluded: chain B residue  194 GLN
Chi-restraints excluded: chain B residue  201 THR
Chi-restraints excluded: chain B residue  208 SER
Chi-restraints excluded: chain B residue  253 CYS
Chi-restraints excluded: chain C residue  141 THR
Chi-restraints excluded: chain C residue  153 THR
Chi-restraints excluded: chain C residue  166 THR
Chi-restraints excluded: chain C residue  201 THR
Chi-restraints excluded: chain C residue  208 SER
Chi-restraints excluded: chain C residue  233 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 39
   random chunks:
   chunk 14 optimal weight:   10.0000
   chunk 27 optimal weight:    0.0670
   chunk 17 optimal weight:    5.9990
   chunk 23 optimal weight:    1.9990
   chunk 31 optimal weight:    9.9990
   chunk 5 optimal weight:    9.9990
   chunk 15 optimal weight:   10.0000
   chunk 6 optimal weight:    6.9990
   chunk 12 optimal weight:    7.9990
   chunk 35 optimal weight:    9.9990
   chunk 22 optimal weight:   10.0000
   overall best weight:    4.6126

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

Flipped N/Q/H residues before XYZ refinement:
A 249 GLN
B 145 ASN
B 164 ASN
** B 239 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
C 145 ASN
C 194 GLN
C 249 GLN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4061 r_free = 0.4061 target = 0.135989 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3880 r_free = 0.3880 target = 0.119893 restraints weight = 3593.405|
|-----------------------------------------------------------------------------|
r_work (start): 0.3890 rms_B_bonded: 1.64
r_work: 0.3797 rms_B_bonded: 1.82 restraints_weight: 0.5000
r_work: 0.3700 rms_B_bonded: 3.13 restraints_weight: 0.2500
r_work (final): 0.3700
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8662
moved from start:          0.3757

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.039   3309  Z= 0.362
  Angle     :  0.711   7.197   4497  Z= 0.384
  Chirality :  0.057   0.156    540
  Planarity :  0.003   0.018    558
  Dihedral  :  6.925  26.699    447
  Min Nonbonded Distance : 2.554

Molprobity Statistics.
  All-atom Clashscore : 8.31
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.76 %
    Favored  : 95.24 %
  Rotamer:
    Outliers :  5.56 %
    Allowed  : 22.75 %
    Favored  : 71.69 %
  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: -2.34 (0.36), residues: 399
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.78 (0.28), residues: 399

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.004   0.001   HIS B 239 
 PHE   0.017   0.003   PHE B 213 
 TYR   0.022   0.002   TYR A 143 
 ARG   0.002   0.000   ARG C 247 

********************** 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
  110 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 89
  time to evaluate  : 0.363 
Fit side-chains
REVERT: A  124 LYS cc_start: 0.8836 (mttp) cc_final: 0.7978 (mmtt)
REVERT: B  140 ARG cc_start: 0.8366 (mtm180) cc_final: 0.7218 (mtt90)
REVERT: B  144 LEU cc_start: 0.8900 (OUTLIER) cc_final: 0.8585 (tt)
REVERT: B  180 ARG cc_start: 0.7804 (mtm-85) cc_final: 0.7548 (mtp85)
REVERT: B  253 CYS cc_start: 0.7927 (OUTLIER) cc_final: 0.7171 (m)
REVERT: C  196 ASP cc_start: 0.8259 (t0) cc_final: 0.7874 (m-30)
  outliers start: 21
  outliers final: 15
  residues processed: 103
  average time/residue: 1.2961
  time to fit residues: 136.8307
Evaluate side-chains
  106 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 89
  time to evaluate  : 0.387 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  141 THR
Chi-restraints excluded: chain A residue  149 THR
Chi-restraints excluded: chain A residue  201 THR
Chi-restraints excluded: chain A residue  208 SER
Chi-restraints excluded: chain B residue  141 THR
Chi-restraints excluded: chain B residue  144 LEU
Chi-restraints excluded: chain B residue  153 THR
Chi-restraints excluded: chain B residue  194 GLN
Chi-restraints excluded: chain B residue  201 THR
Chi-restraints excluded: chain B residue  208 SER
Chi-restraints excluded: chain B residue  253 CYS
Chi-restraints excluded: chain C residue  141 THR
Chi-restraints excluded: chain C residue  153 THR
Chi-restraints excluded: chain C residue  166 THR
Chi-restraints excluded: chain C residue  201 THR
Chi-restraints excluded: chain C residue  208 SER
Chi-restraints excluded: chain C residue  233 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 39
   random chunks:
   chunk 28 optimal weight:    9.9990
   chunk 22 optimal weight:    9.9990
   chunk 2 optimal weight:    7.9990
   chunk 17 optimal weight:    0.9980
   chunk 23 optimal weight:    5.9990
   chunk 1 optimal weight:    0.7980
   chunk 11 optimal weight:    7.9990
   chunk 26 optimal weight:    0.7980
   chunk 19 optimal weight:   10.0000
   chunk 32 optimal weight:    6.9990
   chunk 25 optimal weight:    2.9990
   overall best weight:    2.3184

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

Flipped N/Q/H residues before XYZ refinement:
B 194 GLN
C 145 ASN
C 194 GLN
C 249 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4106 r_free = 0.4106 target = 0.140523 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 26)----------------|
| r_work = 0.3929 r_free = 0.3929 target = 0.124421 restraints weight = 3525.531|
|-----------------------------------------------------------------------------|
r_work (start): 0.3940 rms_B_bonded: 1.62
r_work: 0.3851 rms_B_bonded: 1.79 restraints_weight: 0.5000
r_work: 0.3756 rms_B_bonded: 3.10 restraints_weight: 0.2500
r_work (final): 0.3756
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8622
moved from start:          0.3874

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028   3309  Z= 0.214
  Angle     :  0.645   7.006   4497  Z= 0.347
  Chirality :  0.055   0.141    540
  Planarity :  0.002   0.019    558
  Dihedral  :  6.648  25.755    447
  Min Nonbonded Distance : 2.568

Molprobity Statistics.
  All-atom Clashscore : 6.92
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.26 %
    Favored  : 94.74 %
  Rotamer:
    Outliers :  4.50 %
    Allowed  : 23.54 %
    Favored  : 71.96 %
  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: -2.28 (0.36), residues: 399
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.73 (0.28), residues: 399

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.002   0.001   HIS B 239 
 PHE   0.013   0.002   PHE B 213 
 TYR   0.017   0.002   TYR C 143 
 ARG   0.001   0.000   ARG C 247 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3388.64 seconds
wall clock time: 60 minutes 37.72 seconds (3637.72 seconds total)