Starting phenix.real_space_refine
on Wed Mar  5 18:40:37 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7qwl_14188/03_2025/7qwl_14188.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7qwl_14188/03_2025/7qwl_14188.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.47
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7qwl_14188/03_2025/7qwl_14188.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7qwl_14188/03_2025/7qwl_14188.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7qwl_14188/03_2025/7qwl_14188.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7qwl_14188/03_2025/7qwl_14188.cif"
  }
  resolution = 3.47
  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=   0.004
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 4
    Type Number    sf(0)   Gaussians
     S      21      5.16       5
     C    2082      2.51       5
     N     519      2.21       5
     O     636      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 26 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib"
  Total number of atoms: 3258
  Number of models: 1
  Model: ""
    Number of chains: 3
    Chain: "A"
      Number of atoms: 1086
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 135, 1086
          Classifications: {'peptide': 135}
          Link IDs: {'PTRANS': 2, 'TRANS': 132}
    Chain: "B"
      Number of atoms: 1086
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 135, 1086
          Classifications: {'peptide': 135}
          Link IDs: {'PTRANS': 2, 'TRANS': 132}
    Chain: "C"
      Number of atoms: 1086
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 135, 1086
          Classifications: {'peptide': 135}
          Link IDs: {'PTRANS': 2, 'TRANS': 132}
  Time building chain proxies: 3.02, per 1000 atoms: 0.93
  Number of scatterers: 3258
  At special positions: 0
  Unit cell: (105.8, 98.9, 31.05, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     S      21     16.00
     O     636      8.00
     N     519      7.00
     C    2082      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=3, symmetry=0
    Simple disulfide: pdb=" SG  CYS A 214 " - pdb=" SG  CYS A 253 " distance=2.05
    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: 0.69
  Conformation dependent library (CDL) restraints added in 346.5 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, 50.6% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.56
  Creating SS restraints...
    Processing sheet with id=AA1, first strand: chain 'A' and resid 125 through 126
    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: 6.961A  pdb=" N   VAL A 133 " --> pdb=" O   SER B 134 " (cutoff:3.500A)
      removed outlier: 6.838A  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 142 through 144
    Processing sheet with id=AA5, first strand: chain 'A' and resid 147 through 148
    Processing sheet with id=AA6, first strand: chain 'A' and resid 151 through 156
    Processing sheet with id=AA7, first strand: chain 'A' and resid 165 through 170
      removed outlier: 6.459A  pdb=" N   ILE A 165 " --> pdb=" O   THR B 166 " (cutoff:3.500A)
      removed outlier: 8.297A  pdb=" N   GLN B 168 " --> pdb=" O   ILE A 165 " (cutoff:3.500A)
      removed outlier: 6.847A  pdb=" N   ALA A 167 " --> pdb=" O   GLN B 168 " (cutoff:3.500A)
      removed outlier: 8.696A  pdb=" N   GLN B 170 " --> pdb=" O   ALA A 167 " (cutoff:3.500A)
      removed outlier: 6.844A  pdb=" N   VAL A 169 " --> pdb=" O   GLN B 170 " (cutoff:3.500A)
      removed outlier: 6.334A  pdb=" N   ILE B 165 " --> pdb=" O   THR C 166 " (cutoff:3.500A)
      removed outlier: 8.355A  pdb=" N   GLN C 168 " --> pdb=" O   ILE B 165 " (cutoff:3.500A)
      removed outlier: 6.763A  pdb=" N   ALA B 167 " --> pdb=" O   GLN C 168 " (cutoff:3.500A)
      removed outlier: 8.635A  pdb=" N   GLN C 170 " --> pdb=" O   ALA B 167 " (cutoff:3.500A)
      removed outlier: 6.355A  pdb=" N   VAL B 169 " --> pdb=" O   GLN C 170 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA7
    Processing sheet with id=AA8, first strand: chain 'A' and resid 173 through 175
      removed outlier: 6.412A  pdb=" N   THR A 174 " --> pdb=" O   VAL B 175 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'A' and resid 185 through 187
      removed outlier: 6.464A  pdb=" N   ILE A 186 " --> pdb=" O   ILE B 187 " (cutoff:3.500A)
      removed outlier: 6.459A  pdb=" N   ILE B 186 " --> pdb=" O   ILE C 187 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA9
    Processing sheet with id=AB1, first strand: chain 'A' and resid 190 through 191
    Processing sheet with id=AB2, first strand: chain 'A' and resid 194 through 198
      removed outlier: 8.237A  pdb=" N   ILE A 195 " --> pdb=" O   ASP B 196 " (cutoff:3.500A)
      removed outlier: 7.468A  pdb=" N   THR B 198 " --> pdb=" O   ILE A 195 " (cutoff:3.500A)
      removed outlier: 9.096A  pdb=" N   TYR A 197 " --> pdb=" O   THR B 198 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'A' and resid 201 through 203
      removed outlier: 6.382A  pdb=" N   VAL A 202 " --> pdb=" O   ILE B 203 " (cutoff:3.500A)
    Processing sheet with id=AB4, first strand: chain 'A' and resid 208 through 210
    Processing sheet with id=AB5, first strand: chain 'A' and resid 214 through 218
    Processing sheet with id=AB6, first strand: chain 'A' and resid 221 through 236
      removed outlier: 8.501A  pdb=" N   HIS A 222 " --> pdb=" O   ASN B 223 " (cutoff:3.500A)
      removed outlier: 7.289A  pdb=" N   VAL B 225 " --> pdb=" O   HIS A 222 " (cutoff:3.500A)
      removed outlier: 8.919A  pdb=" N   ILE A 224 " --> pdb=" O   VAL B 225 " (cutoff:3.500A)
      removed outlier: 9.947A  pdb=" N   MET B 227 " --> pdb=" O   ILE A 224 " (cutoff:3.500A)
      removed outlier: 8.914A  pdb=" N   LEU A 226 " --> pdb=" O   MET B 227 " (cutoff:3.500A)
      removed outlier: 9.712A  pdb=" N   GLN B 229 " --> pdb=" O   LEU A 226 " (cutoff:3.500A)
      removed outlier: 6.119A  pdb=" N   MET A 228 " --> pdb=" O   GLN B 229 " (cutoff:3.500A)
      removed outlier: 7.377A  pdb=" N   THR B 231 " --> pdb=" O   MET A 228 " (cutoff:3.500A)
      removed outlier: 6.357A  pdb=" N   VAL A 230 " --> pdb=" O   THR B 231 " (cutoff:3.500A)
      removed outlier: 7.127A  pdb=" N   THR B 233 " --> pdb=" O   VAL A 230 " (cutoff:3.500A)
      removed outlier: 6.987A  pdb=" N   VAL A 232 " --> pdb=" O   THR B 233 " (cutoff:3.500A)
      removed outlier: 10.565A  pdb=" N   THR B 235 " --> pdb=" O   VAL A 232 " (cutoff:3.500A)
      removed outlier: 8.915A  pdb=" N   THR A 234 " --> pdb=" O   THR B 235 " (cutoff:3.500A)
      removed outlier: 8.575A  pdb=" N   HIS B 222 " --> pdb=" O   ASN C 223 " (cutoff:3.500A)
      removed outlier: 7.452A  pdb=" N   VAL C 225 " --> pdb=" O   HIS B 222 " (cutoff:3.500A)
      removed outlier: 8.968A  pdb=" N   ILE B 224 " --> pdb=" O   VAL C 225 " (cutoff:3.500A)
      removed outlier: 9.951A  pdb=" N   MET C 227 " --> pdb=" O   ILE B 224 " (cutoff:3.500A)
      removed outlier: 8.867A  pdb=" N   LEU B 226 " --> pdb=" O   MET C 227 " (cutoff:3.500A)
      removed outlier: 9.641A  pdb=" N   GLN C 229 " --> pdb=" O   LEU B 226 " (cutoff:3.500A)
      removed outlier: 5.947A  pdb=" N   MET B 228 " --> pdb=" O   GLN C 229 " (cutoff:3.500A)
      removed outlier: 7.319A  pdb=" N   THR C 231 " --> pdb=" O   MET B 228 " (cutoff:3.500A)
      removed outlier: 6.094A  pdb=" N   VAL B 230 " --> pdb=" O   THR C 231 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AB6
    Processing sheet with id=AB7, first strand: chain 'A' and resid 221 through 236
      removed outlier: 8.501A  pdb=" N   HIS A 222 " --> pdb=" O   ASN B 223 " (cutoff:3.500A)
      removed outlier: 7.289A  pdb=" N   VAL B 225 " --> pdb=" O   HIS A 222 " (cutoff:3.500A)
      removed outlier: 8.919A  pdb=" N   ILE A 224 " --> pdb=" O   VAL B 225 " (cutoff:3.500A)
      removed outlier: 9.947A  pdb=" N   MET B 227 " --> pdb=" O   ILE A 224 " (cutoff:3.500A)
      removed outlier: 8.914A  pdb=" N   LEU A 226 " --> pdb=" O   MET B 227 " (cutoff:3.500A)
      removed outlier: 9.712A  pdb=" N   GLN B 229 " --> pdb=" O   LEU A 226 " (cutoff:3.500A)
      removed outlier: 6.119A  pdb=" N   MET A 228 " --> pdb=" O   GLN B 229 " (cutoff:3.500A)
      removed outlier: 7.377A  pdb=" N   THR B 231 " --> pdb=" O   MET A 228 " (cutoff:3.500A)
      removed outlier: 6.357A  pdb=" N   VAL A 230 " --> pdb=" O   THR B 231 " (cutoff:3.500A)
      removed outlier: 7.127A  pdb=" N   THR B 233 " --> pdb=" O   VAL A 230 " (cutoff:3.500A)
      removed outlier: 6.987A  pdb=" N   VAL A 232 " --> pdb=" O   THR B 233 " (cutoff:3.500A)
      removed outlier: 10.565A  pdb=" N   THR B 235 " --> pdb=" O   VAL A 232 " (cutoff:3.500A)
      removed outlier: 8.915A  pdb=" N   THR A 234 " --> pdb=" O   THR B 235 " (cutoff:3.500A)
      removed outlier: 8.299A  pdb=" N   TYR C 236 " --> pdb=" O   THR B 233 " (cutoff:3.500A)
      removed outlier: 6.714A  pdb=" N   THR B 235 " --> pdb=" O   TYR C 236 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AB7
    Processing sheet with id=AB8, first strand: chain 'A' and resid 240 through 252
      removed outlier: 6.851A  pdb=" N   VAL A 251 " --> pdb=" O   TYR B 250 " (cutoff:3.500A)
      removed outlier: 6.874A  pdb=" N   ASP B 252 " --> pdb=" O   VAL A 251 " (cutoff:3.500A)
      removed outlier: 6.886A  pdb=" N   VAL B 251 " --> pdb=" O   TYR C 250 " (cutoff:3.500A)
      removed outlier: 6.925A  pdb=" N   ASP C 252 " --> pdb=" O   VAL B 251 " (cutoff:3.500A)

    60 hydrogen bonds defined for protein.
    180 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: 0.74

  Time building geometry restraints manager: 0.86 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: 938
        1.33 -     1.45: 521
        1.45 -     1.57: 1817
        1.57 -     1.69: 0
        1.69 -     1.81: 36
  Bond restraints: 3312
  Sorted by residual:
  bond pdb=" CB  THR C 215 "
       pdb=" OG1 THR C 215 "
    ideal  model  delta    sigma   weight residual
    1.433  1.387  0.046 1.60e-02 3.91e+03 8.14e+00
  bond pdb=" CZ  ARG B 247 "
       pdb=" NH2 ARG B 247 "
    ideal  model  delta    sigma   weight residual
    1.330  1.294  0.036 1.30e-02 5.92e+03 7.62e+00
  bond pdb=" CZ  ARG C 247 "
       pdb=" NH2 ARG C 247 "
    ideal  model  delta    sigma   weight residual
    1.330  1.295  0.035 1.30e-02 5.92e+03 7.10e+00
  bond pdb=" CZ  ARG C 180 "
       pdb=" NH2 ARG C 180 "
    ideal  model  delta    sigma   weight residual
    1.330  1.297  0.033 1.30e-02 5.92e+03 6.55e+00
  bond pdb=" CZ  ARG A 247 "
       pdb=" NH2 ARG A 247 "
    ideal  model  delta    sigma   weight residual
    1.330  1.297  0.033 1.30e-02 5.92e+03 6.54e+00
  ... (remaining 3307 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.61: 3544
        2.61 -     5.23: 798
        5.23 -     7.84: 147
        7.84 -    10.45: 11
       10.45 -    13.07: 3
  Bond angle restraints: 4503
  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
     109.07  122.14  -13.07 1.52e+00 4.33e-01 7.39e+01
  angle pdb=" N   GLU C 246 "
        pdb=" CA  GLU C 246 "
        pdb=" CB  GLU C 246 "
      ideal   model   delta    sigma   weight residual
     111.66   98.72   12.94 1.67e+00 3.59e-01 6.01e+01
  angle pdb=" OD1 ASN A 164 "
        pdb=" CG  ASN A 164 "
        pdb=" ND2 ASN A 164 "
      ideal   model   delta    sigma   weight residual
     122.60  115.11    7.49 1.00e+00 1.00e+00 5.61e+01
  angle pdb=" OD1 ASN C 164 "
        pdb=" CG  ASN C 164 "
        pdb=" ND2 ASN C 164 "
      ideal   model   delta    sigma   weight residual
     122.60  116.24    6.36 1.00e+00 1.00e+00 4.04e+01
  angle pdb=" C   ILE A 219 "
        pdb=" CA  ILE A 219 "
        pdb=" CB  ILE A 219 "
      ideal   model   delta    sigma   weight residual
     111.06  116.62   -5.56 8.80e-01 1.29e+00 3.99e+01
  ... (remaining 4498 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.01 -    16.07: 1830
       16.07 -    32.13: 122
       32.13 -    48.19: 25
       48.19 -    64.26: 9
       64.26 -    80.32: 9
  Dihedral angle restraints: 1995
    sinusoidal: 777
      harmonic: 1218
  Sorted by residual:
  dihedral pdb=" C   ASN B 183 "
           pdb=" N   ASN B 183 "
           pdb=" CA  ASN B 183 "
           pdb=" CB  ASN B 183 "
      ideal   model   delta  harmonic     sigma   weight residual
    -122.60 -137.49   14.89     0      2.50e+00 1.60e-01 3.55e+01
  dihedral pdb=" CA  ASN B 183 "
           pdb=" C   ASN B 183 "
           pdb=" N   ILE B 184 "
           pdb=" CA  ILE B 184 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -150.77  -29.23     0      5.00e+00 4.00e-02 3.42e+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  151.04   28.96     0      5.00e+00 4.00e-02 3.35e+01
  ... (remaining 1992 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.110: 337
       0.110 -    0.220: 156
       0.220 -    0.329: 38
       0.329 -    0.439: 10
       0.439 -    0.549: 2
  Chirality restraints: 543
  Sorted by residual:
  chirality pdb=" CA  ASN B 183 "
            pdb=" N   ASN B 183 "
            pdb=" C   ASN B 183 "
            pdb=" CB  ASN B 183 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    1.96    0.55 2.00e-01 2.50e+01 7.54e+00
  chirality pdb=" CA  ASN A 183 "
            pdb=" N   ASN A 183 "
            pdb=" C   ASN A 183 "
            pdb=" CB  ASN A 183 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.03    0.48 2.00e-01 2.50e+01 5.68e+00
  chirality pdb=" CA  GLN A 138 "
            pdb=" N   GLN A 138 "
            pdb=" C   GLN A 138 "
            pdb=" CB  GLN A 138 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.08    0.43 2.00e-01 2.50e+01 4.65e+00
  ... (remaining 540 not shown)

  Planarity restraints: 558
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TYR B 135 "   -0.134 2.00e-02 2.50e+03   8.25e-02 1.36e+02
        pdb=" CG  TYR B 135 "    0.020 2.00e-02 2.50e+03
        pdb=" CD1 TYR B 135 "    0.062 2.00e-02 2.50e+03
        pdb=" CD2 TYR B 135 "    0.051 2.00e-02 2.50e+03
        pdb=" CE1 TYR B 135 "    0.055 2.00e-02 2.50e+03
        pdb=" CE2 TYR B 135 "    0.069 2.00e-02 2.50e+03
        pdb=" CZ  TYR B 135 "    0.024 2.00e-02 2.50e+03
        pdb=" OH  TYR B 135 "   -0.146 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TYR A 135 "   -0.129 2.00e-02 2.50e+03   8.01e-02 1.28e+02
        pdb=" CG  TYR A 135 "    0.023 2.00e-02 2.50e+03
        pdb=" CD1 TYR A 135 "    0.061 2.00e-02 2.50e+03
        pdb=" CD2 TYR A 135 "    0.040 2.00e-02 2.50e+03
        pdb=" CE1 TYR A 135 "    0.049 2.00e-02 2.50e+03
        pdb=" CE2 TYR A 135 "    0.072 2.00e-02 2.50e+03
        pdb=" CZ  TYR A 135 "    0.027 2.00e-02 2.50e+03
        pdb=" OH  TYR A 135 "   -0.143 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TYR C 143 "    0.153 2.00e-02 2.50e+03   7.96e-02 1.27e+02
        pdb=" CG  TYR C 143 "   -0.064 2.00e-02 2.50e+03
        pdb=" CD1 TYR C 143 "   -0.075 2.00e-02 2.50e+03
        pdb=" CD2 TYR C 143 "   -0.065 2.00e-02 2.50e+03
        pdb=" CE1 TYR C 143 "   -0.024 2.00e-02 2.50e+03
        pdb=" CE2 TYR C 143 "   -0.036 2.00e-02 2.50e+03
        pdb=" CZ  TYR C 143 "    0.003 2.00e-02 2.50e+03
        pdb=" OH  TYR C 143 "    0.107 2.00e-02 2.50e+03
  ... (remaining 555 not shown)

  Histogram of nonbonded interaction distances:
        2.50 -     2.98: 1602
        2.98 -     3.46: 2809
        3.46 -     3.94: 5234
        3.94 -     4.42: 5555
        4.42 -     4.90: 10249
  Nonbonded interactions: 25449
  Sorted by model distance:
  nonbonded pdb=" OE1 GLU A 161 "
            pdb=" OG  SER B 120 "
     model   vdw
     2.501 3.040
  nonbonded pdb=" OE1 GLU B 161 "
            pdb=" OG  SER C 120 "
     model   vdw
     2.526 3.040
  nonbonded pdb=" OD2 ASP C 212 "
            pdb=" OG1 THR C 215 "
     model   vdw
     2.550 3.040
  nonbonded pdb=" OD2 ASP A 212 "
            pdb=" OG1 THR A 215 "
     model   vdw
     2.559 3.040
  nonbonded pdb=" OD2 ASP B 212 "
            pdb=" OG1 THR B 215 "
     model   vdw
     2.579 3.040
  ... (remaining 25444 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:             2.190
  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:          0.120
  Check model and map are aligned:         0.030
  Set scattering table:                    0.040
  Process input model:                     12.960
  Find NCS groups from input model:        0.100
  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:3.140
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   18.590
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7842
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   0.046   3312  Z= 0.796
  Angle     :  2.274  13.066   4503  Z= 1.512
  Chirality :  0.135   0.549    543
  Planarity :  0.015   0.083    558
  Dihedral  : 13.778  80.320   1206
  Min Nonbonded Distance : 2.501

Molprobity Statistics.
  All-atom Clashscore : 3.69
  Ramachandran Plot:
    Outliers :  0.50 %
    Allowed  : 11.28 %
    Favored  : 88.22 %
  Rotamer:
    Outliers :  1.06 %
    Allowed  :  2.65 %
    Favored  : 96.30 %
  Cbeta Deviations :  3.59 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -3.35 (0.32), residues: 399
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.55 (0.24), residues: 399

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.014   0.004   HIS A 239 
 PHE   0.047   0.013   PHE A 171 
 TYR   0.153   0.031   TYR C 143 
 ARG   0.002   0.001   ARG C 247 

*********************** 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
  106 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 102
  time to evaluate  : 0.384 
Fit side-chains
   revert: symmetry clash
REVERT: A  129 LYS cc_start: 0.7814 (mttt) cc_final: 0.7568 (mtpt)
REVERT: A  241 GLU cc_start: 0.7171 (tt0) cc_final: 0.6929 (tt0)
REVERT: B  122 ASP cc_start: 0.7749 (t0) cc_final: 0.6593 (t0)
REVERT: C  139 LYS cc_start: 0.8698 (mttt) cc_final: 0.8349 (mmmt)
  outliers start: 4
  outliers final: 0
  residues processed: 105
  average time/residue: 0.1623
  time to fit residues: 20.2890
Evaluate side-chains
  69 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 69
  time to evaluate  : 0.391 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 39
   random chunks:
   chunk 32 optimal weight:   20.0000
   chunk 29 optimal weight:    3.9990
   chunk 16 optimal weight:    0.9990
   chunk 10 optimal weight:    0.9980
   chunk 19 optimal weight:    6.9990
   chunk 15 optimal weight:    0.9980
   chunk 30 optimal weight:    3.9990
   chunk 11 optimal weight:    1.9990
   chunk 18 optimal weight:    6.9990
   chunk 22 optimal weight:    2.9990
   chunk 35 optimal weight:    0.5980
   overall best weight:    1.1184

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

Flipped N/Q/H residues before XYZ refinement:
A 155 ASN
B 155 ASN
B 245 GLN
C 155 ASN
C 223 ASN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4252 r_free = 0.4252 target = 0.134049 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.4034 r_free = 0.4034 target = 0.115508 restraints weight = 3962.641|
|-----------------------------------------------------------------------------|
r_work (start): 0.4049 rms_B_bonded: 2.49
r_work: 0.3928 rms_B_bonded: 2.71 restraints_weight: 0.5000
r_work: 0.3808 rms_B_bonded: 4.55 restraints_weight: 0.2500
r_work (final): 0.3808
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7684
moved from start:          0.3500

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.026   3312  Z= 0.208
  Angle     :  0.746   6.759   4503  Z= 0.411
  Chirality :  0.053   0.146    543
  Planarity :  0.003   0.013    558
  Dihedral  :  8.049  23.491    447
  Min Nonbonded Distance : 2.586

Molprobity Statistics.
  All-atom Clashscore : 6.45
  Ramachandran Plot:
    Outliers :  0.25 %
    Allowed  :  7.27 %
    Favored  : 92.48 %
  Rotamer:
    Outliers :  4.50 %
    Allowed  : 10.05 %
    Favored  : 85.45 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -3.12 (0.34), residues: 399
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.37 (0.26), residues: 399

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.002   0.001   HIS B 239 
 PHE   0.008   0.001   PHE C 237 
 TYR   0.026   0.002   TYR A 143 
 ARG   0.002   0.000   ARG B 140 

*********************** 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
  98 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 81
  time to evaluate  : 0.372 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  241 GLU cc_start: 0.8428 (tt0) cc_final: 0.8094 (tt0)
REVERT: B  150 LEU cc_start: 0.9265 (tp) cc_final: 0.8956 (tp)
REVERT: B  161 GLU cc_start: 0.8800 (tp30) cc_final: 0.8591 (tp30)
REVERT: B  178 LYS cc_start: 0.6973 (OUTLIER) cc_final: 0.6065 (tptp)
REVERT: B  205 GLU cc_start: 0.8269 (mt-10) cc_final: 0.7652 (mm-30)
REVERT: B  207 MET cc_start: 0.8045 (ttt) cc_final: 0.7722 (ttm)
REVERT: C  139 LYS cc_start: 0.8495 (mttt) cc_final: 0.7778 (mmmt)
REVERT: C  178 LYS cc_start: 0.7361 (mttp) cc_final: 0.6548 (tptt)
REVERT: C  183 ASN cc_start: 0.5916 (OUTLIER) cc_final: 0.5637 (t0)
REVERT: C  210 MET cc_start: 0.8159 (mtp) cc_final: 0.7601 (mtt)
  outliers start: 17
  outliers final: 12
  residues processed: 90
  average time/residue: 0.1749
  time to fit residues: 18.5265
Evaluate side-chains
  79 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 65
  time to evaluate  : 0.337 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  160 VAL
Chi-restraints excluded: chain A residue  174 THR
Chi-restraints excluded: chain A residue  178 LYS
Chi-restraints excluded: chain A residue  212 ASP
Chi-restraints excluded: chain A residue  227 MET
Chi-restraints excluded: chain B residue  166 THR
Chi-restraints excluded: chain B residue  178 LYS
Chi-restraints excluded: chain B residue  184 ILE
Chi-restraints excluded: chain B residue  227 MET
Chi-restraints excluded: chain B residue  240 SER
Chi-restraints excluded: chain C residue  141 THR
Chi-restraints excluded: chain C residue  183 ASN
Chi-restraints excluded: chain C residue  192 MET
Chi-restraints excluded: chain C residue  231 THR
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 39
   random chunks:
   chunk 25 optimal weight:    8.9990
   chunk 14 optimal weight:   10.0000
   chunk 3 optimal weight:    0.6980
   chunk 19 optimal weight:   10.0000
   chunk 13 optimal weight:    2.9990
   chunk 34 optimal weight:    8.9990
   chunk 7 optimal weight:    0.0010
   chunk 8 optimal weight:    0.5980
   chunk 23 optimal weight:    4.9990
   chunk 17 optimal weight:    2.9990
   chunk 11 optimal weight:    0.6980
   overall best weight:    0.9988

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

Flipped N/Q/H residues before XYZ refinement:
B 245 GLN
** C 239 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4284 r_free = 0.4284 target = 0.135952 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.4076 r_free = 0.4076 target = 0.117988 restraints weight = 3943.518|
|-----------------------------------------------------------------------------|
r_work (start): 0.4105 rms_B_bonded: 2.46
r_work: 0.3980 rms_B_bonded: 2.74 restraints_weight: 0.5000
r_work: 0.3859 rms_B_bonded: 4.63 restraints_weight: 0.2500
r_work (final): 0.3859
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7671
moved from start:          0.4252

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.025   3312  Z= 0.181
  Angle     :  0.638   5.432   4503  Z= 0.355
  Chirality :  0.052   0.170    543
  Planarity :  0.002   0.012    558
  Dihedral  :  7.226  20.743    447
  Min Nonbonded Distance : 2.580

Molprobity Statistics.
  All-atom Clashscore : 7.99
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.26 %
    Favored  : 94.74 %
  Rotamer:
    Outliers :  6.35 %
    Allowed  : 11.11 %
    Favored  : 82.54 %
  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: -2.89 (0.36), residues: 399
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.20 (0.27), residues: 399

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.002   0.001   HIS B 239 
 PHE   0.004   0.001   PHE A 237 
 TYR   0.019   0.002   TYR C 143 
 ARG   0.002   0.000   ARG B 140 

*********************** 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
  97 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 73
  time to evaluate  : 0.337 
Fit side-chains
   revert: symmetry clash
REVERT: A  222 HIS cc_start: 0.8838 (m-70) cc_final: 0.8604 (m-70)
REVERT: A  241 GLU cc_start: 0.8453 (tt0) cc_final: 0.8198 (tt0)
REVERT: B  150 LEU cc_start: 0.9273 (tp) cc_final: 0.8936 (tp)
REVERT: B  178 LYS cc_start: 0.6905 (OUTLIER) cc_final: 0.5967 (tptp)
REVERT: B  205 GLU cc_start: 0.8357 (mt-10) cc_final: 0.7660 (mm-30)
REVERT: B  207 MET cc_start: 0.7906 (ttt) cc_final: 0.7624 (ttm)
REVERT: B  212 ASP cc_start: 0.9006 (p0) cc_final: 0.8792 (p0)
REVERT: C  139 LYS cc_start: 0.8619 (mttt) cc_final: 0.7890 (mmmt)
REVERT: C  178 LYS cc_start: 0.7269 (mttp) cc_final: 0.6484 (tptt)
REVERT: C  205 GLU cc_start: 0.8127 (mt-10) cc_final: 0.7679 (mm-30)
REVERT: C  210 MET cc_start: 0.7824 (mtp) cc_final: 0.7387 (mtt)
  outliers start: 24
  outliers final: 12
  residues processed: 83
  average time/residue: 0.1751
  time to fit residues: 17.1498
Evaluate side-chains
  77 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 64
  time to evaluate  : 0.345 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  133 VAL
Chi-restraints excluded: chain A residue  149 THR
Chi-restraints excluded: chain A residue  174 THR
Chi-restraints excluded: chain A residue  178 LYS
Chi-restraints excluded: chain B residue  166 THR
Chi-restraints excluded: chain B residue  178 LYS
Chi-restraints excluded: chain B residue  184 ILE
Chi-restraints excluded: chain C residue  140 ARG
Chi-restraints excluded: chain C residue  141 THR
Chi-restraints excluded: chain C residue  180 ARG
Chi-restraints excluded: chain C residue  215 THR
Chi-restraints excluded: chain C residue  231 THR
Chi-restraints excluded: chain C residue  247 ARG
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 39
   random chunks:
   chunk 6 optimal weight:    6.9990
   chunk 37 optimal weight:    3.9990
   chunk 36 optimal weight:    2.9990
   chunk 33 optimal weight:    6.9990
   chunk 19 optimal weight:    0.9980
   chunk 38 optimal weight:    4.9990
   chunk 2 optimal weight:    0.9980
   chunk 25 optimal weight:    5.9990
   chunk 1 optimal weight:    0.0030
   chunk 13 optimal weight:    5.9990
   chunk 21 optimal weight:   10.0000
   overall best weight:    1.7994

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

Flipped N/Q/H residues before XYZ refinement:
B 229 GLN
B 245 GLN
** C 239 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4177 r_free = 0.4177 target = 0.127236 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3974 r_free = 0.3974 target = 0.110125 restraints weight = 4212.644|
|-----------------------------------------------------------------------------|
r_work (start): 0.3996 rms_B_bonded: 2.36
r_work: 0.3870 rms_B_bonded: 2.60 restraints_weight: 0.5000
r_work: 0.3752 rms_B_bonded: 4.37 restraints_weight: 0.2500
r_work (final): 0.3752
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7763
moved from start:          0.4615

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.030   3312  Z= 0.247
  Angle     :  0.641   5.437   4503  Z= 0.361
  Chirality :  0.052   0.146    543
  Planarity :  0.002   0.012    558
  Dihedral  :  7.210  21.382    447
  Min Nonbonded Distance : 2.589

Molprobity Statistics.
  All-atom Clashscore : 7.37
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.77 %
    Favored  : 92.23 %
  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: -2.83 (0.37), residues: 399
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.15 (0.28), residues: 399

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.003   0.002   HIS B 239 
 PHE   0.010   0.001   PHE C 237 
 TYR   0.019   0.002   TYR B 143 
 ARG   0.002   0.000   ARG C 140 

*********************** 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
  82 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 62
  time to evaluate  : 0.373 
Fit side-chains
   revert: symmetry clash
REVERT: A  140 ARG cc_start: 0.5249 (ppt170) cc_final: 0.4728 (tmm160)
REVERT: A  241 GLU cc_start: 0.8543 (tt0) cc_final: 0.8308 (tt0)
REVERT: B  178 LYS cc_start: 0.6877 (OUTLIER) cc_final: 0.6054 (tptp)
REVERT: B  205 GLU cc_start: 0.8358 (mt-10) cc_final: 0.7691 (mm-30)
REVERT: B  209 TYR cc_start: 0.8793 (m-80) cc_final: 0.8560 (m-80)
REVERT: C  139 LYS cc_start: 0.8598 (mttt) cc_final: 0.8009 (tppt)
REVERT: C  178 LYS cc_start: 0.7311 (mttp) cc_final: 0.6413 (tptp)
REVERT: C  205 GLU cc_start: 0.8126 (mt-10) cc_final: 0.7708 (mm-30)
REVERT: C  210 MET cc_start: 0.7787 (mtp) cc_final: 0.6931 (mtt)
  outliers start: 20
  outliers final: 16
  residues processed: 73
  average time/residue: 0.1882
  time to fit residues: 16.2071
Evaluate side-chains
  74 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 57
  time to evaluate  : 0.335 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  133 VAL
Chi-restraints excluded: chain A residue  149 THR
Chi-restraints excluded: chain A residue  174 THR
Chi-restraints excluded: chain A residue  178 LYS
Chi-restraints excluded: chain A residue  184 ILE
Chi-restraints excluded: chain B residue  166 THR
Chi-restraints excluded: chain B residue  178 LYS
Chi-restraints excluded: chain B residue  184 ILE
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  180 ARG
Chi-restraints excluded: chain C residue  190 LEU
Chi-restraints excluded: chain C residue  215 THR
Chi-restraints excluded: chain C residue  228 MET
Chi-restraints excluded: chain C residue  231 THR
Chi-restraints excluded: chain C residue  234 THR
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 39
   random chunks:
   chunk 2 optimal weight:    0.5980
   chunk 36 optimal weight:    0.0470
   chunk 3 optimal weight:    5.9990
   chunk 7 optimal weight:    8.9990
   chunk 5 optimal weight:    8.9990
   chunk 9 optimal weight:    4.9990
   chunk 26 optimal weight:    8.9990
   chunk 12 optimal weight:    6.9990
   chunk 27 optimal weight:    7.9990
   chunk 24 optimal weight:    3.9990
   chunk 19 optimal weight:   10.0000
   overall best weight:    3.1284

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

Flipped N/Q/H residues before XYZ refinement:
A 229 GLN
B 245 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 = 0.4055 r_free = 0.4055 target = 0.117242 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3839 r_free = 0.3839 target = 0.100816 restraints weight = 4336.623|
|-----------------------------------------------------------------------------|
r_work (start): 0.3900 rms_B_bonded: 2.29
r_work: 0.3777 rms_B_bonded: 2.49 restraints_weight: 0.5000
r_work: 0.3663 rms_B_bonded: 4.21 restraints_weight: 0.2500
r_work (final): 0.3663
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7838
moved from start:          0.4845

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.032   3312  Z= 0.372
  Angle     :  0.679   4.905   4503  Z= 0.386
  Chirality :  0.053   0.153    543
  Planarity :  0.003   0.014    558
  Dihedral  :  7.491  21.354    447
  Min Nonbonded Distance : 2.590

Molprobity Statistics.
  All-atom Clashscore : 7.99
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.27 %
    Favored  : 91.73 %
  Rotamer:
    Outliers :  5.82 %
    Allowed  : 14.55 %
    Favored  : 79.63 %
  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: -2.88 (0.37), residues: 399
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.19 (0.28), residues: 399

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.005   0.002   HIS B 239 
 PHE   0.013   0.002   PHE C 237 
 TYR   0.026   0.003   TYR B 143 
 ARG   0.002   0.000   ARG C 140 

*********************** 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
  80 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 58
  time to evaluate  : 0.381 
Fit side-chains
REVERT: A  122 ASP cc_start: 0.8664 (t0) cc_final: 0.7963 (t0)
REVERT: A  241 GLU cc_start: 0.8615 (tt0) cc_final: 0.8378 (tt0)
REVERT: B  178 LYS cc_start: 0.6951 (OUTLIER) cc_final: 0.5926 (tptp)
REVERT: B  205 GLU cc_start: 0.8376 (mt-10) cc_final: 0.7647 (mm-30)
REVERT: C  139 LYS cc_start: 0.8716 (mttt) cc_final: 0.7835 (mmmt)
REVERT: C  178 LYS cc_start: 0.7408 (mttp) cc_final: 0.6419 (tptp)
REVERT: C  205 GLU cc_start: 0.8210 (mt-10) cc_final: 0.7700 (mm-30)
  outliers start: 22
  outliers final: 18
  residues processed: 73
  average time/residue: 0.1813
  time to fit residues: 15.6419
Evaluate side-chains
  76 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 57
  time to evaluate  : 0.354 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  133 VAL
Chi-restraints excluded: chain A residue  139 LYS
Chi-restraints excluded: chain A residue  149 THR
Chi-restraints excluded: chain A residue  174 THR
Chi-restraints excluded: chain A residue  178 LYS
Chi-restraints excluded: chain A residue  184 ILE
Chi-restraints excluded: chain B residue  166 THR
Chi-restraints excluded: chain B residue  176 ILE
Chi-restraints excluded: chain B residue  178 LYS
Chi-restraints excluded: chain B residue  184 ILE
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  180 ARG
Chi-restraints excluded: chain C residue  190 LEU
Chi-restraints excluded: chain C residue  215 THR
Chi-restraints excluded: chain C residue  228 MET
Chi-restraints excluded: chain C residue  231 THR
Chi-restraints excluded: chain C residue  234 THR
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 39
   random chunks:
   chunk 26 optimal weight:    5.9990
   chunk 21 optimal weight:    8.9990
   chunk 15 optimal weight:   10.0000
   chunk 24 optimal weight:    0.7980
   chunk 27 optimal weight:    8.9990
   chunk 10 optimal weight:    5.9990
   chunk 12 optimal weight:    2.9990
   chunk 25 optimal weight:    0.9990
   chunk 22 optimal weight:    0.9980
   chunk 34 optimal weight:    2.9990
   chunk 33 optimal weight:    0.8980
   overall best weight:    1.3384

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

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

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4196 r_free = 0.4196 target = 0.127682 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3996 r_free = 0.3996 target = 0.111217 restraints weight = 4286.926|
|-----------------------------------------------------------------------------|
r_work (start): 0.4015 rms_B_bonded: 2.34
r_work: 0.3891 rms_B_bonded: 2.57 restraints_weight: 0.5000
r_work: 0.3776 rms_B_bonded: 4.33 restraints_weight: 0.2500
r_work (final): 0.3776
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7758
moved from start:          0.5161

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.026   3312  Z= 0.197
  Angle     :  0.604   5.452   4503  Z= 0.339
  Chirality :  0.051   0.149    543
  Planarity :  0.002   0.013    558
  Dihedral  :  6.978  20.366    447
  Min Nonbonded Distance : 2.599

Molprobity Statistics.
  All-atom Clashscore : 7.68
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.77 %
    Favored  : 92.23 %
  Rotamer:
    Outliers :  5.03 %
    Allowed  : 15.87 %
    Favored  : 79.10 %
  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: -2.91 (0.37), residues: 399
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.21 (0.28), residues: 399

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.004   0.001   HIS C 239 
 PHE   0.012   0.001   PHE C 237 
 TYR   0.020   0.002   TYR B 143 
 ARG   0.001   0.000   ARG C 140 

*********************** 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
  80 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 61
  time to evaluate  : 0.383 
Fit side-chains
   revert: symmetry clash
REVERT: A  122 ASP cc_start: 0.8820 (t0) cc_final: 0.8144 (t0)
REVERT: A  138 GLN cc_start: 0.8656 (tp40) cc_final: 0.7050 (pm20)
REVERT: A  140 ARG cc_start: 0.5466 (ppt170) cc_final: 0.4917 (tmm160)
REVERT: A  241 GLU cc_start: 0.8566 (tt0) cc_final: 0.8348 (tt0)
REVERT: B  178 LYS cc_start: 0.6917 (OUTLIER) cc_final: 0.5923 (tptp)
REVERT: B  205 GLU cc_start: 0.8380 (mt-10) cc_final: 0.7714 (mm-30)
REVERT: C  139 LYS cc_start: 0.8644 (mttt) cc_final: 0.7951 (tppt)
REVERT: C  178 LYS cc_start: 0.7285 (mttp) cc_final: 0.6376 (tptp)
REVERT: C  205 GLU cc_start: 0.8284 (mt-10) cc_final: 0.7807 (mm-30)
  outliers start: 19
  outliers final: 15
  residues processed: 75
  average time/residue: 0.1746
  time to fit residues: 15.5695
Evaluate side-chains
  71 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 55
  time to evaluate  : 0.370 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  133 VAL
Chi-restraints excluded: chain A residue  149 THR
Chi-restraints excluded: chain A residue  174 THR
Chi-restraints excluded: chain A residue  178 LYS
Chi-restraints excluded: chain A residue  184 ILE
Chi-restraints excluded: chain B residue  166 THR
Chi-restraints excluded: chain B residue  178 LYS
Chi-restraints excluded: chain B residue  184 ILE
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  180 ARG
Chi-restraints excluded: chain C residue  190 LEU
Chi-restraints excluded: chain C residue  215 THR
Chi-restraints excluded: chain C residue  228 MET
Chi-restraints excluded: chain C residue  231 THR
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 39
   random chunks:
   chunk 22 optimal weight:    9.9990
   chunk 19 optimal weight:   10.0000
   chunk 17 optimal weight:   10.0000
   chunk 9 optimal weight:    4.9990
   chunk 24 optimal weight:    7.9990
   chunk 4 optimal weight:    3.9990
   chunk 7 optimal weight:    9.9990
   chunk 25 optimal weight:    3.9990
   chunk 31 optimal weight:    9.9990
   chunk 35 optimal weight:    0.8980
   chunk 18 optimal weight:    4.9990
   overall best weight:    3.7788

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4063 r_free = 0.4063 target = 0.117493 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3855 r_free = 0.3855 target = 0.101685 restraints weight = 4422.430|
|-----------------------------------------------------------------------------|
r_work (start): 0.3877 rms_B_bonded: 2.27
r_work: 0.3760 rms_B_bonded: 2.46 restraints_weight: 0.5000
r_work: 0.3643 rms_B_bonded: 4.15 restraints_weight: 0.2500
r_work (final): 0.3643
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7891
moved from start:          0.5101

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.007   0.045   3312  Z= 0.439
  Angle     :  0.696   4.969   4503  Z= 0.396
  Chirality :  0.054   0.140    543
  Planarity :  0.003   0.014    558
  Dihedral  :  7.529  21.668    447
  Min Nonbonded Distance : 2.564

Molprobity Statistics.
  All-atom Clashscore : 7.99
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 10.53 %
    Favored  : 89.47 %
  Rotamer:
    Outliers :  5.03 %
    Allowed  : 15.61 %
    Favored  : 79.37 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -3.09 (0.37), residues: 399
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.34 (0.28), residues: 399

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.005   0.002   HIS B 239 
 PHE   0.014   0.002   PHE C 237 
 TYR   0.024   0.003   TYR B 143 
 ARG   0.003   0.000   ARG C 140 

*********************** 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
  74 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 55
  time to evaluate  : 0.391 
Fit side-chains
REVERT: A  124 LYS cc_start: 0.9064 (ptpp) cc_final: 0.6764 (mmmt)
REVERT: B  178 LYS cc_start: 0.6950 (OUTLIER) cc_final: 0.5936 (tptp)
REVERT: B  205 GLU cc_start: 0.8405 (mt-10) cc_final: 0.7710 (mm-30)
REVERT: C  139 LYS cc_start: 0.8872 (mttt) cc_final: 0.7870 (mmmt)
REVERT: C  161 GLU cc_start: 0.8514 (mm-30) cc_final: 0.7717 (mm-30)
REVERT: C  178 LYS cc_start: 0.7331 (mttp) cc_final: 0.6330 (tptt)
REVERT: C  205 GLU cc_start: 0.8248 (mt-10) cc_final: 0.7755 (mm-30)
  outliers start: 19
  outliers final: 18
  residues processed: 66
  average time/residue: 0.1836
  time to fit residues: 14.4239
Evaluate side-chains
  73 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 54
  time to evaluate  : 0.379 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  133 VAL
Chi-restraints excluded: chain A residue  149 THR
Chi-restraints excluded: chain A residue  174 THR
Chi-restraints excluded: chain A residue  178 LYS
Chi-restraints excluded: chain A residue  184 ILE
Chi-restraints excluded: chain B residue  166 THR
Chi-restraints excluded: chain B residue  176 ILE
Chi-restraints excluded: chain B residue  178 LYS
Chi-restraints excluded: chain B residue  184 ILE
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  180 ARG
Chi-restraints excluded: chain C residue  190 LEU
Chi-restraints excluded: chain C residue  215 THR
Chi-restraints excluded: chain C residue  227 MET
Chi-restraints excluded: chain C residue  228 MET
Chi-restraints excluded: chain C residue  231 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 26 optimal weight:    3.9990
   chunk 9 optimal weight:    4.9990
   chunk 15 optimal weight:    5.9990
   chunk 28 optimal weight:    7.9990
   chunk 6 optimal weight:    6.9990
   chunk 38 optimal weight:    1.9990
   chunk 10 optimal weight:    3.9990
   chunk 34 optimal weight:    2.9990
   chunk 37 optimal weight:    2.9990
   chunk 20 optimal weight:    8.9990
   chunk 29 optimal weight:    3.9990
   overall best weight:    3.1990

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

Flipped N/Q/H residues before XYZ refinement:
C 229 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4097 r_free = 0.4097 target = 0.119769 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3890 r_free = 0.3890 target = 0.103836 restraints weight = 4324.558|
|-----------------------------------------------------------------------------|
r_work (start): 0.3910 rms_B_bonded: 2.27
r_work: 0.3795 rms_B_bonded: 2.45 restraints_weight: 0.5000
r_work: 0.3679 rms_B_bonded: 4.15 restraints_weight: 0.2500
r_work (final): 0.3679
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7867
moved from start:          0.5184

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.033   3312  Z= 0.375
  Angle     :  0.675   5.689   4503  Z= 0.383
  Chirality :  0.053   0.144    543
  Planarity :  0.003   0.014    558
  Dihedral  :  7.432  21.209    447
  Min Nonbonded Distance : 2.605

Molprobity Statistics.
  All-atom Clashscore : 8.14
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.77 %
    Favored  : 91.23 %
  Rotamer:
    Outliers :  5.56 %
    Allowed  : 15.61 %
    Favored  : 78.84 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -3.14 (0.37), residues: 399
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.39 (0.28), residues: 399

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.005   0.002   HIS A 239 
 PHE   0.017   0.002   PHE C 237 
 TYR   0.022   0.003   TYR B 143 
 ARG   0.002   0.000   ARG C 140 

*********************** 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
  80 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 59
  time to evaluate  : 0.381 
Fit side-chains
REVERT: A  124 LYS cc_start: 0.9020 (ptpp) cc_final: 0.6701 (mmmt)
REVERT: B  205 GLU cc_start: 0.8384 (mt-10) cc_final: 0.7671 (mm-30)
REVERT: B  209 TYR cc_start: 0.8696 (m-80) cc_final: 0.8361 (m-80)
REVERT: C  139 LYS cc_start: 0.8945 (mttt) cc_final: 0.8072 (tppt)
REVERT: C  161 GLU cc_start: 0.8661 (mm-30) cc_final: 0.7627 (mm-30)
REVERT: C  178 LYS cc_start: 0.7291 (mttp) cc_final: 0.6341 (tptt)
REVERT: C  205 GLU cc_start: 0.8254 (mt-10) cc_final: 0.7749 (mm-30)
  outliers start: 21
  outliers final: 17
  residues processed: 73
  average time/residue: 0.1795
  time to fit residues: 15.6084
Evaluate side-chains
  75 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 58
  time to evaluate  : 0.369 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  133 VAL
Chi-restraints excluded: chain A residue  149 THR
Chi-restraints excluded: chain A residue  174 THR
Chi-restraints excluded: chain A residue  178 LYS
Chi-restraints excluded: chain A residue  184 ILE
Chi-restraints excluded: chain B residue  166 THR
Chi-restraints excluded: chain B residue  176 ILE
Chi-restraints excluded: chain B residue  178 LYS
Chi-restraints excluded: chain B residue  184 ILE
Chi-restraints excluded: chain B residue  231 THR
Chi-restraints excluded: chain C residue  141 THR
Chi-restraints excluded: chain C residue  166 THR
Chi-restraints excluded: chain C residue  190 LEU
Chi-restraints excluded: chain C residue  215 THR
Chi-restraints excluded: chain C residue  228 MET
Chi-restraints excluded: chain C residue  231 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 17 optimal weight:    4.9990
   chunk 16 optimal weight:    5.9990
   chunk 5 optimal weight:    9.9990
   chunk 13 optimal weight:    0.0020
   chunk 38 optimal weight:    2.9990
   chunk 1 optimal weight:    1.9990
   chunk 29 optimal weight:    4.9990
   chunk 26 optimal weight:    6.9990
   chunk 32 optimal weight:    1.9990
   chunk 18 optimal weight:    6.9990
   chunk 11 optimal weight:    4.9990
   overall best weight:    2.3996

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

Flipped N/Q/H residues before XYZ refinement:
B 182 ASN
C 182 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4113 r_free = 0.4113 target = 0.120536 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3903 r_free = 0.3903 target = 0.104370 restraints weight = 4324.994|
|-----------------------------------------------------------------------------|
r_work (start): 0.3892 rms_B_bonded: 2.31
r_work: 0.3774 rms_B_bonded: 2.54 restraints_weight: 0.5000
r_work: 0.3658 rms_B_bonded: 4.29 restraints_weight: 0.2500
r_work (final): 0.3658
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7817
moved from start:          0.5348

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.027   3312  Z= 0.296
  Angle     :  0.642   5.705   4503  Z= 0.363
  Chirality :  0.052   0.144    543
  Planarity :  0.002   0.015    558
  Dihedral  :  7.255  20.878    447
  Min Nonbonded Distance : 2.596

Molprobity Statistics.
  All-atom Clashscore : 7.99
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 10.03 %
    Favored  : 89.97 %
  Rotamer:
    Outliers :  4.76 %
    Allowed  : 16.14 %
    Favored  : 79.10 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -3.14 (0.37), residues: 399
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.39 (0.28), residues: 399

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.004   0.002   HIS A 239 
 PHE   0.017   0.002   PHE C 237 
 TYR   0.017   0.002   TYR B 143 
 ARG   0.002   0.000   ARG C 140 

*********************** 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
  80 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 62
  time to evaluate  : 0.337 
Fit side-chains
   revert: symmetry clash
REVERT: A  124 LYS cc_start: 0.8976 (ptpp) cc_final: 0.6667 (mmmt)
REVERT: A  140 ARG cc_start: 0.5081 (ppt170) cc_final: 0.4399 (tmm160)
REVERT: B  205 GLU cc_start: 0.8357 (mt-10) cc_final: 0.7695 (mm-30)
REVERT: B  209 TYR cc_start: 0.8631 (m-80) cc_final: 0.8290 (m-80)
REVERT: C  139 LYS cc_start: 0.8935 (mttt) cc_final: 0.8037 (tppt)
REVERT: C  178 LYS cc_start: 0.7279 (mttp) cc_final: 0.6314 (tptt)
REVERT: C  205 GLU cc_start: 0.8273 (mt-10) cc_final: 0.7746 (mm-30)
  outliers start: 18
  outliers final: 16
  residues processed: 73
  average time/residue: 0.1753
  time to fit residues: 15.2313
Evaluate side-chains
  76 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 60
  time to evaluate  : 0.395 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  133 VAL
Chi-restraints excluded: chain A residue  149 THR
Chi-restraints excluded: chain A residue  174 THR
Chi-restraints excluded: chain A residue  178 LYS
Chi-restraints excluded: chain A residue  184 ILE
Chi-restraints excluded: chain B residue  166 THR
Chi-restraints excluded: chain B residue  176 ILE
Chi-restraints excluded: chain B residue  178 LYS
Chi-restraints excluded: chain B residue  184 ILE
Chi-restraints excluded: chain C residue  141 THR
Chi-restraints excluded: chain C residue  166 THR
Chi-restraints excluded: chain C residue  190 LEU
Chi-restraints excluded: chain C residue  215 THR
Chi-restraints excluded: chain C residue  228 MET
Chi-restraints excluded: chain C residue  231 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 21 optimal weight:    6.9990
   chunk 20 optimal weight:    8.9990
   chunk 33 optimal weight:    0.9980
   chunk 1 optimal weight:    6.9990
   chunk 3 optimal weight:    3.9990
   chunk 26 optimal weight:    7.9990
   chunk 27 optimal weight:    6.9990
   chunk 11 optimal weight:    3.9990
   chunk 36 optimal weight:    6.9990
   chunk 24 optimal weight:    0.6980
   chunk 15 optimal weight:    6.9990
   overall best weight:    3.3386

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4076 r_free = 0.4076 target = 0.117569 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3859 r_free = 0.3859 target = 0.101327 restraints weight = 4331.013|
|-----------------------------------------------------------------------------|
r_work (start): 0.3891 rms_B_bonded: 2.34
r_work: 0.3777 rms_B_bonded: 2.53 restraints_weight: 0.5000
r_work: 0.3663 rms_B_bonded: 4.24 restraints_weight: 0.2500
r_work (final): 0.3663
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7847
moved from start:          0.5330

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.033   3312  Z= 0.393
  Angle     :  0.682   5.562   4503  Z= 0.386
  Chirality :  0.054   0.145    543
  Planarity :  0.003   0.015    558
  Dihedral  :  7.429  21.092    447
  Min Nonbonded Distance : 2.597

Molprobity Statistics.
  All-atom Clashscore : 7.99
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.77 %
    Favored  : 90.23 %
  Rotamer:
    Outliers :  4.50 %
    Allowed  : 16.40 %
    Favored  : 79.10 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -3.21 (0.37), residues: 399
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.44 (0.28), residues: 399

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.005   0.002   HIS A 239 
 PHE   0.019   0.002   PHE C 237 
 TYR   0.019   0.003   TYR B 143 
 ARG   0.003   0.000   ARG C 140 

********************** 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
  72 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 55
  time to evaluate  : 0.358 
Fit side-chains
REVERT: A  140 ARG cc_start: 0.5229 (ppt170) cc_final: 0.4506 (tmm160)
REVERT: B  205 GLU cc_start: 0.8381 (mt-10) cc_final: 0.7669 (mm-30)
REVERT: B  209 TYR cc_start: 0.8686 (m-80) cc_final: 0.8327 (m-80)
REVERT: C  139 LYS cc_start: 0.9079 (mttt) cc_final: 0.8106 (tppt)
REVERT: C  178 LYS cc_start: 0.7228 (mttp) cc_final: 0.6261 (tptt)
REVERT: C  205 GLU cc_start: 0.8262 (mt-10) cc_final: 0.7753 (mm-30)
  outliers start: 17
  outliers final: 17
  residues processed: 66
  average time/residue: 0.1786
  time to fit residues: 14.2154
Evaluate side-chains
  70 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 53
  time to evaluate  : 0.372 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  133 VAL
Chi-restraints excluded: chain A residue  149 THR
Chi-restraints excluded: chain A residue  174 THR
Chi-restraints excluded: chain A residue  178 LYS
Chi-restraints excluded: chain A residue  184 ILE
Chi-restraints excluded: chain B residue  166 THR
Chi-restraints excluded: chain B residue  176 ILE
Chi-restraints excluded: chain B residue  178 LYS
Chi-restraints excluded: chain B residue  184 ILE
Chi-restraints excluded: chain B residue  231 THR
Chi-restraints excluded: chain C residue  141 THR
Chi-restraints excluded: chain C residue  166 THR
Chi-restraints excluded: chain C residue  190 LEU
Chi-restraints excluded: chain C residue  215 THR
Chi-restraints excluded: chain C residue  228 MET
Chi-restraints excluded: chain C residue  231 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 4 optimal weight:    0.7980
   chunk 36 optimal weight:    1.9990
   chunk 3 optimal weight:    6.9990
   chunk 13 optimal weight:    6.9990
   chunk 0 optimal weight:    0.7980
   chunk 30 optimal weight:    4.9990
   chunk 38 optimal weight:    2.9990
   chunk 7 optimal weight:    8.9990
   chunk 35 optimal weight:    0.9990
   chunk 23 optimal weight:    3.9990
   chunk 19 optimal weight:   10.0000
   overall best weight:    1.5186

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4174 r_free = 0.4174 target = 0.125767 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3982 r_free = 0.3982 target = 0.109848 restraints weight = 4250.094|
|-----------------------------------------------------------------------------|
r_work (start): 0.4000 rms_B_bonded: 2.30
r_work: 0.3883 rms_B_bonded: 2.51 restraints_weight: 0.5000
r_work: 0.3770 rms_B_bonded: 4.27 restraints_weight: 0.2500
r_work (final): 0.3770
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7786
moved from start:          0.5487

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.025   3312  Z= 0.207
  Angle     :  0.605   5.769   4503  Z= 0.342
  Chirality :  0.051   0.143    543
  Planarity :  0.002   0.014    558
  Dihedral  :  6.958  20.325    447
  Min Nonbonded Distance : 2.595

Molprobity Statistics.
  All-atom Clashscore : 7.83
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.52 %
    Favored  : 91.48 %
  Rotamer:
    Outliers :  4.23 %
    Allowed  : 16.93 %
    Favored  : 78.84 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -3.14 (0.37), residues: 399
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.39 (0.29), residues: 399

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.004   0.001   HIS B 239 
 PHE   0.015   0.001   PHE C 237 
 TYR   0.017   0.002   TYR B 143 
 ARG   0.001   0.000   ARG B 247 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1876.21 seconds
wall clock time: 33 minutes 26.54 seconds (2006.54 seconds total)