Starting phenix.real_space_refine
on Wed Jun  4 14:29:04 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7qvc_14174/06_2025/7qvc_14174.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7qvc_14174/06_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_14174/06_2025/7qvc_14174.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7qvc_14174/06_2025/7qvc_14174.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7qvc_14174/06_2025/7qvc_14174.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7qvc_14174/06_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-5710/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: 3.21, per 1000 atoms: 0.99
  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: 0.75
  Conformation dependent library (CDL) restraints added in 396.9 milliseconds
  

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

  Finding SS restraints...
    Secondary structure from input PDB file:
      0 helices and 17 sheets defined
      0.0% alpha, 60.0% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.48
  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: 1.08

  Time building geometry restraints manager: 0.92 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:             3.230
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.150
  Check model and map are aligned:         0.020
  Set scattering table:                    0.030
  Process input model:                     13.540
  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:13.600
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   30.690
-------------------------------------------------------------------------------
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   3312  Z= 0.694
  Angle     :  2.094  11.548   4503  Z= 1.352
  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 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.08397 (   80)
  hydrogen bonds       : angle       8.13757 (  240)
  SS BOND              : bond        0.01553 (    3)
  SS BOND              : angle       1.53835 (    6)
  covalent geometry    : bond        0.01204 ( 3309)
  covalent geometry    : angle       2.09490 ( 4497)

*********************** 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  : 0.401 
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: 1.1255
  time to fit residues: 151.4550
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  : 0.414 
-------------------------------------------------------------------------------
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 = 0.4102 r_free = 0.4102 target = 0.139302 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3906 r_free = 0.3906 target = 0.122049 restraints weight = 3572.973|
|-----------------------------------------------------------------------------|
r_work (start): 0.3912 rms_B_bonded: 1.66
r_work: 0.3818 rms_B_bonded: 1.89 restraints_weight: 0.5000
r_work: 0.3720 rms_B_bonded: 3.24 restraints_weight: 0.2500
r_work (final): 0.3720
-------------------------------------------------------------------------------
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   3312  Z= 0.179
  Angle     :  0.781   8.743   4503  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 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02627 (   80)
  hydrogen bonds       : angle       5.41412 (  240)
  SS BOND              : bond        0.00429 (    3)
  SS BOND              : angle       0.80978 (    6)
  covalent geometry    : bond        0.00416 ( 3309)
  covalent geometry    : angle       0.78048 ( 4497)

*********************** 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  : 0.372 
Fit side-chains
REVERT: A  124 LYS cc_start: 0.8828 (mttp) cc_final: 0.7944 (mmtt)
REVERT: A  144 LEU cc_start: 0.8924 (tt) cc_final: 0.8694 (tp)
REVERT: A  163 GLU cc_start: 0.7944 (mt-10) cc_final: 0.7686 (mp0)
REVERT: B  140 ARG cc_start: 0.8362 (mtm180) cc_final: 0.7172 (mtt90)
REVERT: B  180 ARG cc_start: 0.7799 (mtm-85) cc_final: 0.7509 (mtp85)
REVERT: C  140 ARG cc_start: 0.8115 (OUTLIER) cc_final: 0.7676 (mtt90)
REVERT: C  196 ASP cc_start: 0.8278 (t0) cc_final: 0.7844 (m-30)
  outliers start: 20
  outliers final: 10
  residues processed: 106
  average time/residue: 1.2574
  time to fit residues: 136.5561
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  : 0.414 
-------------------------------------------------------------------------------
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:    0.0670
   chunk 5 optimal weight:    1.9990
   chunk 21 optimal weight:    9.9990
   chunk 25 optimal weight:   10.0000
   chunk 14 optimal weight:    4.9990
   chunk 3 optimal weight:    7.9990
   chunk 19 optimal weight:    6.9990
   chunk 13 optimal weight:   10.0000
   chunk 34 optimal weight:    0.9990
   chunk 7 optimal weight:   10.0000
   chunk 8 optimal weight:    5.9990
   overall best weight:    2.8126

-------------------------------------------------------------------------------
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 = 0.4108 r_free = 0.4108 target = 0.139191 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3919 r_free = 0.3919 target = 0.122078 restraints weight = 3526.436|
|-----------------------------------------------------------------------------|
r_work (start): 0.3915 rms_B_bonded: 1.65
r_work: 0.3820 rms_B_bonded: 1.84 restraints_weight: 0.5000
r_work: 0.3723 rms_B_bonded: 3.16 restraints_weight: 0.2500
r_work (final): 0.3723
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8608
moved from start:          0.3200

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.039   3312  Z= 0.162
  Angle     :  0.691   8.909   4503  Z= 0.372
  Chirality :  0.057   0.144    540
  Planarity :  0.002   0.014    558
  Dihedral  :  7.087  25.729    447
  Min Nonbonded Distance : 2.550

Molprobity Statistics.
  All-atom Clashscore : 6.92
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.01 %
    Favored  : 94.99 %
  Rotamer:
    Outliers :  3.97 %
    Allowed  : 16.67 %
    Favored  : 79.37 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.13 (0.37), residues: 399
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.61 (0.28), residues: 399

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.003   0.001   HIS C 239 
 PHE   0.012   0.002   PHE B 171 
 TYR   0.022   0.002   TYR C 143 
 ARG   0.006   0.001   ARG C 247 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02152 (   80)
  hydrogen bonds       : angle       4.96586 (  240)
  SS BOND              : bond        0.00294 (    3)
  SS BOND              : angle       0.47852 (    6)
  covalent geometry    : bond        0.00373 ( 3309)
  covalent geometry    : angle       0.69107 ( 4497)

*********************** 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: 15
    poor density    : 96
  time to evaluate  : 0.469 
Fit side-chains
REVERT: A  124 LYS cc_start: 0.8809 (mttp) cc_final: 0.7859 (mmtt)
REVERT: A  140 ARG cc_start: 0.7570 (ttm170) cc_final: 0.6233 (ppt170)
REVERT: B  140 ARG cc_start: 0.8264 (mtm180) cc_final: 0.6981 (mtt90)
REVERT: B  180 ARG cc_start: 0.7781 (mtm-85) cc_final: 0.7501 (mtp85)
REVERT: C  140 ARG cc_start: 0.8196 (OUTLIER) cc_final: 0.7741 (mtt90)
REVERT: C  196 ASP cc_start: 0.8199 (t0) cc_final: 0.7813 (m-30)
  outliers start: 15
  outliers final: 9
  residues processed: 104
  average time/residue: 1.2962
  time to fit residues: 138.1201
Evaluate side-chains
  102 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 92
  time to evaluate  : 0.369 
-------------------------------------------------------------------------------
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 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:   10.0000
   chunk 8 optimal weight:    9.9990
   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:    0.6980
   chunk 36 optimal weight:    0.0070
   chunk 33 optimal weight:    9.9990
   chunk 38 optimal weight:    5.9990
   chunk 2 optimal weight:    7.9990
   overall best weight:    3.5404

-------------------------------------------------------------------------------
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
C 145 ASN
C 164 ASN
C 170 GLN
C 249 GLN

Total number of N/Q/H flips: 8

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4080 r_free = 0.4080 target = 0.137894 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3898 r_free = 0.3898 target = 0.121194 restraints weight = 3616.472|
|-----------------------------------------------------------------------------|
r_work (start): 0.3899 rms_B_bonded: 1.68
r_work: 0.3803 rms_B_bonded: 1.86 restraints_weight: 0.5000
r_work: 0.3705 rms_B_bonded: 3.19 restraints_weight: 0.2500
r_work (final): 0.3705
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8632
moved from start:          0.3453

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.031   3312  Z= 0.191
  Angle     :  0.697   9.738   4503  Z= 0.373
  Chirality :  0.058   0.151    540
  Planarity :  0.002   0.017    558
  Dihedral  :  7.001  26.264    447
  Min Nonbonded Distance : 2.564

Molprobity Statistics.
  All-atom Clashscore : 7.54
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.51 %
    Favored  : 95.49 %
  Rotamer:
    Outliers :  5.56 %
    Allowed  : 16.67 %
    Favored  : 77.78 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.15 (0.37), residues: 399
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.63 (0.28), residues: 399

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.002   0.001   HIS C 239 
 PHE   0.011   0.003   PHE B 237 
 TYR   0.021   0.002   TYR B 143 
 ARG   0.004   0.001   ARG C 247 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02201 (   80)
  hydrogen bonds       : angle       4.90345 (  240)
  SS BOND              : bond        0.00310 (    3)
  SS BOND              : angle       0.55565 (    6)
  covalent geometry    : bond        0.00436 ( 3309)
  covalent geometry    : angle       0.69738 ( 4497)

*********************** 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
  115 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 94
  time to evaluate  : 0.351 
Fit side-chains
REVERT: A  124 LYS cc_start: 0.8838 (mttp) cc_final: 0.7929 (mmtt)
REVERT: A  140 ARG cc_start: 0.7594 (ttm170) cc_final: 0.6124 (ppt170)
REVERT: A  144 LEU cc_start: 0.9113 (tt) cc_final: 0.8901 (tp)
REVERT: B  140 ARG cc_start: 0.8251 (mtm180) cc_final: 0.7001 (mtt90)
REVERT: B  180 ARG cc_start: 0.7756 (mtm-85) cc_final: 0.7479 (mtp85)
REVERT: C  140 ARG cc_start: 0.8184 (OUTLIER) cc_final: 0.7687 (mtt90)
REVERT: C  196 ASP cc_start: 0.8205 (t0) cc_final: 0.7818 (m-30)
  outliers start: 21
  outliers final: 11
  residues processed: 107
  average time/residue: 1.1883
  time to fit residues: 130.5540
Evaluate side-chains
  105 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 93
  time to evaluate  : 0.391 
-------------------------------------------------------------------------------
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 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
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:   10.0000
   chunk 25 optimal weight:   10.0000
   chunk 34 optimal weight:   10.0000
   chunk 2 optimal weight:    0.0370
   chunk 36 optimal weight:    0.0980
   chunk 3 optimal weight:    4.9990
   chunk 7 optimal weight:    9.9990
   chunk 5 optimal weight:    9.9990
   overall best weight:    3.6264

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

Flipped N/Q/H residues before XYZ refinement:
A 249 GLN
B 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 = 0.4074 r_free = 0.4074 target = 0.137150 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3892 r_free = 0.3892 target = 0.120477 restraints weight = 3593.659|
|-----------------------------------------------------------------------------|
r_work (start): 0.3889 rms_B_bonded: 1.69
r_work: 0.3791 rms_B_bonded: 1.87 restraints_weight: 0.5000
r_work: 0.3691 rms_B_bonded: 3.18 restraints_weight: 0.2500
r_work (final): 0.3691
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8635
moved from start:          0.3565

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.036   3312  Z= 0.196
  Angle     :  0.680   8.509   4503  Z= 0.367
  Chirality :  0.057   0.143    540
  Planarity :  0.003   0.017    558
  Dihedral  :  6.919  25.353    447
  Min Nonbonded Distance : 2.555

Molprobity Statistics.
  All-atom Clashscore : 7.38
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.26 %
    Favored  : 95.74 %
  Rotamer:
    Outliers :  5.56 %
    Allowed  : 18.25 %
    Favored  : 76.19 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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: -2.23 (0.36), residues: 399
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.69 (0.28), residues: 399

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.002   0.001   HIS A 239 
 PHE   0.011   0.003   PHE B 237 
 TYR   0.020   0.002   TYR B 143 
 ARG   0.002   0.000   ARG C 247 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02103 (   80)
  hydrogen bonds       : angle       4.84236 (  240)
  SS BOND              : bond        0.00291 (    3)
  SS BOND              : angle       0.67888 (    6)
  covalent geometry    : bond        0.00448 ( 3309)
  covalent geometry    : angle       0.67998 ( 4497)

*********************** 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
  113 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 92
  time to evaluate  : 0.367 
Fit side-chains
REVERT: A  124 LYS cc_start: 0.8854 (mttp) cc_final: 0.7953 (mmtt)
REVERT: B  140 ARG cc_start: 0.8265 (mtm180) cc_final: 0.7184 (mtt90)
REVERT: B  180 ARG cc_start: 0.7770 (mtm-85) cc_final: 0.7502 (mtp85)
REVERT: C  140 ARG cc_start: 0.8194 (OUTLIER) cc_final: 0.7687 (mtt90)
REVERT: C  196 ASP cc_start: 0.8217 (t0) cc_final: 0.7830 (m-30)
  outliers start: 21
  outliers final: 11
  residues processed: 105
  average time/residue: 1.1943
  time to fit residues: 128.6884
Evaluate side-chains
  103 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 91
  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 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 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=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 39
   random chunks:
   chunk 7 optimal weight:    0.2980
   chunk 21 optimal weight:   20.0000
   chunk 22 optimal weight:    6.9990
   chunk 25 optimal weight:    4.9990
   chunk 6 optimal weight:   10.0000
   chunk 8 optimal weight:    4.9990
   chunk 10 optimal weight:    3.9990
   chunk 17 optimal weight:    7.9990
   chunk 18 optimal weight:    5.9990
   chunk 29 optimal weight:    5.9990
   chunk 38 optimal weight:    0.0570
   overall best weight:    2.8704

-------------------------------------------------------------------------------
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 = 0.4100 r_free = 0.4100 target = 0.139749 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3917 r_free = 0.3917 target = 0.123122 restraints weight = 3641.465|
|-----------------------------------------------------------------------------|
r_work (start): 0.3916 rms_B_bonded: 1.69
r_work: 0.3820 rms_B_bonded: 1.87 restraints_weight: 0.5000
r_work: 0.3720 rms_B_bonded: 3.22 restraints_weight: 0.2500
r_work (final): 0.3720
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8624
moved from start:          0.3679

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.033   3312  Z= 0.166
  Angle     :  0.656   8.718   4503  Z= 0.353
  Chirality :  0.056   0.139    540
  Planarity :  0.002   0.016    558
  Dihedral  :  6.776  25.600    447
  Min Nonbonded Distance : 2.567

Molprobity Statistics.
  All-atom Clashscore : 7.69
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.51 %
    Favored  : 95.49 %
  Rotamer:
    Outliers :  5.82 %
    Allowed  : 19.58 %
    Favored  : 74.60 %
  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: -2.24 (0.36), residues: 399
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.70 (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 237 
 TYR   0.019   0.002   TYR B 143 
 ARG   0.003   0.001   ARG B 140 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.01964 (   80)
  hydrogen bonds       : angle       4.64455 (  240)
  SS BOND              : bond        0.00275 (    3)
  SS BOND              : angle       0.52283 (    6)
  covalent geometry    : bond        0.00380 ( 3309)
  covalent geometry    : angle       0.65637 ( 4497)

*********************** 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
  116 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 94
  time to evaluate  : 0.405 
Fit side-chains
REVERT: A  124 LYS cc_start: 0.8853 (mttp) cc_final: 0.7898 (mmtt)
REVERT: B  140 ARG cc_start: 0.8280 (mtm180) cc_final: 0.7098 (mtt90)
REVERT: B  144 LEU cc_start: 0.8842 (OUTLIER) cc_final: 0.8541 (tt)
REVERT: B  180 ARG cc_start: 0.7773 (mtm-85) cc_final: 0.7510 (mtp85)
REVERT: C  196 ASP cc_start: 0.8215 (t0) cc_final: 0.7850 (m-30)
  outliers start: 22
  outliers final: 14
  residues processed: 108
  average time/residue: 1.0937
  time to fit residues: 121.5099
Evaluate side-chains
  109 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 94
  time to evaluate  : 0.379 
-------------------------------------------------------------------------------
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 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:   10.0000
   chunk 30 optimal weight:   10.0000
   chunk 16 optimal weight:    6.9990
   chunk 38 optimal weight:    1.9990
   chunk 4 optimal weight:    5.9990
   chunk 21 optimal weight:    9.9990
   chunk 2 optimal weight:    6.9990
   chunk 18 optimal weight:    8.9990
   chunk 1 optimal weight:    0.7980
   chunk 3 optimal weight:    5.9990
   chunk 15 optimal weight:    5.9990
   overall best weight:    4.1588

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

Flipped N/Q/H residues before XYZ refinement:
A 151 ASN
A 154 ASN
** 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 = 0.4067 r_free = 0.4067 target = 0.136187 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3880 r_free = 0.3880 target = 0.119654 restraints weight = 3568.903|
|-----------------------------------------------------------------------------|
r_work (start): 0.3889 rms_B_bonded: 1.64
r_work: 0.3796 rms_B_bonded: 1.82 restraints_weight: 0.5000
r_work: 0.3697 rms_B_bonded: 3.13 restraints_weight: 0.2500
r_work (final): 0.3697
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8645
moved from start:          0.3668

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.032   3312  Z= 0.219
  Angle     :  0.691   8.472   4503  Z= 0.372
  Chirality :  0.057   0.147    540
  Planarity :  0.003   0.017    558
  Dihedral  :  6.852  25.963    447
  Min Nonbonded Distance : 2.563

Molprobity Statistics.
  All-atom Clashscore : 8.77
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.26 %
    Favored  : 95.74 %
  Rotamer:
    Outliers :  5.82 %
    Allowed  : 20.37 %
    Favored  : 73.81 %
  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 (0.37), 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   0.004   0.001   HIS B 239 
 PHE   0.012   0.003   PHE B 171 
 TYR   0.021   0.002   TYR B 143 
 ARG   0.003   0.001   ARG C 247 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02059 (   80)
  hydrogen bonds       : angle       4.61450 (  240)
  SS BOND              : bond        0.00304 (    3)
  SS BOND              : angle       0.66279 (    6)
  covalent geometry    : bond        0.00502 ( 3309)
  covalent geometry    : angle       0.69095 ( 4497)

*********************** 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
  110 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 88
  time to evaluate  : 0.398 
Fit side-chains
REVERT: A  124 LYS cc_start: 0.8862 (mttp) cc_final: 0.7969 (mmtt)
REVERT: B  140 ARG cc_start: 0.8308 (mtm180) cc_final: 0.7126 (mtt90)
REVERT: B  144 LEU cc_start: 0.8889 (OUTLIER) cc_final: 0.8557 (tt)
REVERT: B  180 ARG cc_start: 0.7778 (mtm-85) cc_final: 0.7522 (mtp85)
REVERT: C  196 ASP cc_start: 0.8256 (t0) cc_final: 0.7865 (m-30)
  outliers start: 22
  outliers final: 15
  residues processed: 103
  average time/residue: 1.1702
  time to fit residues: 123.8081
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  : 0.387 
-------------------------------------------------------------------------------
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 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
Chi-restraints excluded: chain C residue  234 THR
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 39
   random chunks:
   chunk 2 optimal weight:    5.9990
   chunk 5 optimal weight:   10.0000
   chunk 15 optimal weight:    5.9990
   chunk 23 optimal weight:    0.7980
   chunk 24 optimal weight:    7.9990
   chunk 26 optimal weight:    2.9990
   chunk 34 optimal weight:    3.9990
   chunk 32 optimal weight:   10.0000
   chunk 36 optimal weight:    0.1980
   chunk 25 optimal weight:    4.9990
   chunk 18 optimal weight:    5.9990
   overall best weight:    2.5986

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

Flipped N/Q/H residues before XYZ refinement:
A 249 GLN
B 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 = 0.4100 r_free = 0.4100 target = 0.139247 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3918 r_free = 0.3918 target = 0.123128 restraints weight = 3565.750|
|-----------------------------------------------------------------------------|
r_work (start): 0.3928 rms_B_bonded: 1.65
r_work: 0.3840 rms_B_bonded: 1.81 restraints_weight: 0.5000
r_work: 0.3744 rms_B_bonded: 3.12 restraints_weight: 0.2500
r_work (final): 0.3744
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8619
moved from start:          0.3753

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.037   3312  Z= 0.155
  Angle     :  0.654   9.274   4503  Z= 0.348
  Chirality :  0.056   0.146    540
  Planarity :  0.002   0.016    558
  Dihedral  :  6.685  26.260    447
  Min Nonbonded Distance : 2.570

Molprobity Statistics.
  All-atom Clashscore : 7.08
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.51 %
    Favored  : 95.49 %
  Rotamer:
    Outliers :  4.76 %
    Allowed  : 21.43 %
    Favored  : 73.81 %
  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: -2.25 (0.36), residues: 399
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.70 (0.28), residues: 399

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.003   0.001   HIS B 239 
 PHE   0.010   0.002   PHE B 237 
 TYR   0.018   0.002   TYR C 143 
 ARG   0.003   0.000   ARG C 247 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.01864 (   80)
  hydrogen bonds       : angle       4.58959 (  240)
  SS BOND              : bond        0.00246 (    3)
  SS BOND              : angle       0.60386 (    6)
  covalent geometry    : bond        0.00357 ( 3309)
  covalent geometry    : angle       0.65402 ( 4497)

*********************** 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
  114 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 96
  time to evaluate  : 0.370 
Fit side-chains
REVERT: A  124 LYS cc_start: 0.8827 (mttp) cc_final: 0.7966 (mmtt)
REVERT: B  140 ARG cc_start: 0.8348 (mtm180) cc_final: 0.7163 (mtt90)
REVERT: B  144 LEU cc_start: 0.8889 (OUTLIER) cc_final: 0.8601 (tt)
REVERT: B  180 ARG cc_start: 0.7690 (mtm-85) cc_final: 0.7418 (mtp85)
REVERT: C  196 ASP cc_start: 0.8217 (t0) cc_final: 0.7861 (m-30)
  outliers start: 18
  outliers final: 13
  residues processed: 106
  average time/residue: 1.1254
  time to fit residues: 122.5512
Evaluate side-chains
  110 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 96
  time to evaluate  : 0.379 
-------------------------------------------------------------------------------
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  201 THR
Chi-restraints excluded: chain B residue  208 SER
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
Chi-restraints excluded: chain C residue  234 THR
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 39
   random chunks:
   chunk 21 optimal weight:    8.9990
   chunk 12 optimal weight:    8.9990
   chunk 16 optimal weight:    6.9990
   chunk 33 optimal weight:    0.9990
   chunk 37 optimal weight:    0.7980
   chunk 3 optimal weight:    4.9990
   chunk 19 optimal weight:    2.9990
   chunk 34 optimal weight:    4.9990
   chunk 4 optimal weight:    0.6980
   chunk 35 optimal weight:    8.9990
   chunk 22 optimal weight:    6.9990
   overall best weight:    2.0986

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

Flipped N/Q/H residues before XYZ refinement:
B 164 ASN
B 194 GLN
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 = 0.4112 r_free = 0.4112 target = 0.140552 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3932 r_free = 0.3932 target = 0.124500 restraints weight = 3617.809|
|-----------------------------------------------------------------------------|
r_work (start): 0.3943 rms_B_bonded: 1.67
r_work: 0.3853 rms_B_bonded: 1.83 restraints_weight: 0.5000
r_work: 0.3759 rms_B_bonded: 3.11 restraints_weight: 0.2500
r_work (final): 0.3759
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8612
moved from start:          0.3811

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   3312  Z= 0.137
  Angle     :  0.647   9.923   4503  Z= 0.342
  Chirality :  0.055   0.140    540
  Planarity :  0.002   0.015    558
  Dihedral  :  6.569  24.990    447
  Min Nonbonded Distance : 2.582

Molprobity Statistics.
  All-atom Clashscore : 6.61
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.76 %
    Favored  : 95.24 %
  Rotamer:
    Outliers :  5.56 %
    Allowed  : 22.49 %
    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: -2.24 (0.36), residues: 399
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.70 (0.28), residues: 399

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.002   0.001   HIS B 239 
 PHE   0.010   0.002   PHE B 213 
 TYR   0.018   0.002   TYR C 143 
 ARG   0.002   0.000   ARG C 247 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.01822 (   80)
  hydrogen bonds       : angle       4.52923 (  240)
  SS BOND              : bond        0.00218 (    3)
  SS BOND              : angle       0.51545 (    6)
  covalent geometry    : bond        0.00311 ( 3309)
  covalent geometry    : angle       0.64676 ( 4497)

*********************** 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
  118 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 97
  time to evaluate  : 0.391 
Fit side-chains
REVERT: A  124 LYS cc_start: 0.8816 (mttp) cc_final: 0.7930 (mmtt)
REVERT: B  140 ARG cc_start: 0.8349 (mtm180) cc_final: 0.7171 (mtt90)
REVERT: B  180 ARG cc_start: 0.7728 (mtm-85) cc_final: 0.7464 (mtp85)
REVERT: C  196 ASP cc_start: 0.8173 (t0) cc_final: 0.7907 (m-30)
REVERT: C  208 SER cc_start: 0.8964 (p) cc_final: 0.8588 (m)
  outliers start: 21
  outliers final: 13
  residues processed: 110
  average time/residue: 1.1601
  time to fit residues: 131.0275
Evaluate side-chains
  109 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 96
  time to evaluate  : 0.408 
-------------------------------------------------------------------------------
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  153 THR
Chi-restraints excluded: chain B residue  201 THR
Chi-restraints excluded: chain B residue  208 SER
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
Chi-restraints excluded: chain C residue  234 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 39
   random chunks:
   chunk 14 optimal weight:    9.9990
   chunk 27 optimal weight:    6.9990
   chunk 17 optimal weight:    5.9990
   chunk 23 optimal weight:   10.0000
   chunk 31 optimal weight:    4.9990
   chunk 5 optimal weight:    9.9990
   chunk 15 optimal weight:   10.0000
   chunk 6 optimal weight:    6.9990
   chunk 12 optimal weight:    8.9990
   chunk 35 optimal weight:    9.9990
   chunk 22 optimal weight:    5.9990
   overall best weight:    6.1990

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

Flipped N/Q/H residues before XYZ refinement:
B 194 GLN
** B 239 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
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 = 0.4036 r_free = 0.4036 target = 0.133127 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3853 r_free = 0.3853 target = 0.116966 restraints weight = 3629.629|
|-----------------------------------------------------------------------------|
r_work (start): 0.3865 rms_B_bonded: 1.65
r_work: 0.3771 rms_B_bonded: 1.83 restraints_weight: 0.5000
r_work: 0.3674 rms_B_bonded: 3.14 restraints_weight: 0.2500
r_work (final): 0.3674
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8676
moved from start:          0.3737

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.007   0.049   3312  Z= 0.314
  Angle     :  0.772  10.010   4503  Z= 0.414
  Chirality :  0.060   0.190    540
  Planarity :  0.003   0.015    558
  Dihedral  :  7.059  26.886    447
  Min Nonbonded Distance : 2.555

Molprobity Statistics.
  All-atom Clashscore : 9.54
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.26 %
    Favored  : 94.74 %
  Rotamer:
    Outliers :  4.76 %
    Allowed  : 23.02 %
    Favored  : 72.22 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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   0.005   0.002   HIS B 239 
 PHE   0.021   0.004   PHE B 213 
 TYR   0.023   0.002   TYR B 143 
 ARG   0.003   0.001   ARG B 247 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02313 (   80)
  hydrogen bonds       : angle       4.68210 (  240)
  SS BOND              : bond        0.00376 (    3)
  SS BOND              : angle       1.05373 (    6)
  covalent geometry    : bond        0.00726 ( 3309)
  covalent geometry    : angle       0.77196 ( 4497)

********************** 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: 18
    poor density    : 92
  time to evaluate  : 0.389 
Fit side-chains
REVERT: A  124 LYS cc_start: 0.8837 (mttp) cc_final: 0.7952 (mmtt)
REVERT: B  140 ARG cc_start: 0.8380 (mtm180) cc_final: 0.7228 (mtt90)
REVERT: B  180 ARG cc_start: 0.7788 (mtm-85) cc_final: 0.7534 (mtp85)
REVERT: C  196 ASP cc_start: 0.8277 (t0) cc_final: 0.7848 (m-30)
  outliers start: 18
  outliers final: 14
  residues processed: 103
  average time/residue: 1.2865
  time to fit residues: 135.6757
Evaluate side-chains
  105 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 91
  time to evaluate  : 0.316 
-------------------------------------------------------------------------------
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  153 THR
Chi-restraints excluded: chain B residue  201 THR
Chi-restraints excluded: chain B residue  208 SER
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
Chi-restraints excluded: chain C residue  234 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 39
   random chunks:
   chunk 28 optimal weight:   10.0000
   chunk 22 optimal weight:   10.0000
   chunk 2 optimal weight:    8.9990
   chunk 17 optimal weight:   10.0000
   chunk 23 optimal weight:    1.9990
   chunk 1 optimal weight:    0.6980
   chunk 11 optimal weight:    6.9990
   chunk 26 optimal weight:    6.9990
   chunk 19 optimal weight:    6.9990
   chunk 32 optimal weight:    5.9990
   chunk 25 optimal weight:    6.9990
   overall best weight:    4.5388

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

Flipped N/Q/H residues before XYZ refinement:
B 145 ASN
B 194 GLN
** B 239 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
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 = 0.4063 r_free = 0.4063 target = 0.136020 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3883 r_free = 0.3883 target = 0.120144 restraints weight = 3608.125|
|-----------------------------------------------------------------------------|
r_work (start): 0.3893 rms_B_bonded: 1.62
r_work: 0.3804 rms_B_bonded: 1.80 restraints_weight: 0.5000
r_work: 0.3708 rms_B_bonded: 3.09 restraints_weight: 0.2500
r_work (final): 0.3708
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8658
moved from start:          0.3764

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.041   3312  Z= 0.239
  Angle     :  0.729   9.598   4503  Z= 0.389
  Chirality :  0.058   0.176    540
  Planarity :  0.003   0.017    558
  Dihedral  :  6.971  26.850    447
  Min Nonbonded Distance : 2.555

Molprobity Statistics.
  All-atom Clashscore : 7.84
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.76 %
    Favored  : 95.24 %
  Rotamer:
    Outliers :  4.76 %
    Allowed  : 23.28 %
    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: -2.40 (0.36), residues: 399
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.82 (0.28), residues: 399

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.004   0.002   HIS B 239 
 PHE   0.020   0.003   PHE B 213 
 TYR   0.021   0.002   TYR B 143 
 ARG   0.002   0.000   ARG B 247 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02162 (   80)
  hydrogen bonds       : angle       4.70764 (  240)
  SS BOND              : bond        0.00273 (    3)
  SS BOND              : angle       0.87982 (    6)
  covalent geometry    : bond        0.00551 ( 3309)
  covalent geometry    : angle       0.72909 ( 4497)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3655.11 seconds
wall clock time: 63 minutes 2.49 seconds (3782.49 seconds total)