Starting phenix.real_space_refine
on Wed Jun  4 14:40:57 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7qwg_14187/06_2025/7qwg_14187.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7qwg_14187/06_2025/7qwg_14187.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.38
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7qwg_14187/06_2025/7qwg_14187.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7qwg_14187/06_2025/7qwg_14187.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7qwg_14187/06_2025/7qwg_14187.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7qwg_14187/06_2025/7qwg_14187.cif"
  }
  resolution = 3.38
  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 28 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: 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: 3.70, per 1000 atoms: 1.14
  Number of scatterers: 3258
  At special positions: 0
  Unit cell: (98.9, 98.9, 34.5, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     S      21     16.00
     O     636      8.00
     N     519      7.00
     C    2082      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=3, symmetry=0
    Simple disulfide: pdb=" SG  CYS A 214 " - pdb=" SG  CYS A 253 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 214 " - pdb=" SG  CYS B 253 " distance=2.03
    Simple disulfide: pdb=" SG  CYS C 214 " - pdb=" SG  CYS C 253 " distance=2.04

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 0.80
  Conformation dependent library (CDL) restraints added in 600.8 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 14 sheets defined
      0.0% alpha, 55.1% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.43
  Creating SS restraints...
    Processing sheet with id=AA1, first strand: chain 'A' and resid 124 through 126
    Processing sheet with id=AA2, first strand: chain 'A' and resid 133 through 139
      removed outlier: 9.102A  pdb=" N   SER A 134 " --> pdb=" O   TYR B 135 " (cutoff:3.500A)
      removed outlier: 10.000A  pdb=" N   VAL B 137 " --> pdb=" O   SER A 134 " (cutoff:3.500A)
      removed outlier: 9.034A  pdb=" N   ASP A 136 " --> pdb=" O   VAL B 137 " (cutoff:3.500A)
      removed outlier: 9.298A  pdb=" N   LYS B 139 " --> pdb=" O   ASP A 136 " (cutoff:3.500A)
      removed outlier: 6.013A  pdb=" N   GLN A 138 " --> pdb=" O   LYS B 139 " (cutoff:3.500A)
      removed outlier: 9.112A  pdb=" N   SER B 134 " --> pdb=" O   TYR C 135 " (cutoff:3.500A)
      removed outlier: 10.098A  pdb=" N   VAL C 137 " --> pdb=" O   SER B 134 " (cutoff:3.500A)
      removed outlier: 9.094A  pdb=" N   ASP B 136 " --> pdb=" O   VAL C 137 " (cutoff:3.500A)
      removed outlier: 9.328A  pdb=" N   LYS C 139 " --> pdb=" O   ASP B 136 " (cutoff:3.500A)
      removed outlier: 6.143A  pdb=" N   GLN B 138 " --> pdb=" O   LYS C 139 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA2
    Processing sheet with id=AA3, first strand: chain 'A' and resid 142 through 143
    Processing sheet with id=AA4, first strand: chain 'A' and resid 147 through 153
    Processing sheet with id=AA5, first strand: chain 'A' and resid 156 through 160
    Processing sheet with id=AA6, first strand: chain 'A' and resid 169 through 175
    Processing sheet with id=AA7, first strand: chain 'A' and resid 185 through 187
      removed outlier: 6.202A  pdb=" N   THR A 185 " --> pdb=" O   ILE B 186 " (cutoff:3.500A)
      removed outlier: 6.322A  pdb=" N   THR B 185 " --> pdb=" O   ILE C 186 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA7
    Processing sheet with id=AA8, first strand: chain 'A' and resid 190 through 191
    Processing sheet with id=AA9, first strand: chain 'A' and resid 194 through 195
    Processing sheet with id=AB1, first strand: chain 'A' and resid 201 through 203
      removed outlier: 6.433A  pdb=" N   VAL A 202 " --> pdb=" O   ILE B 203 " (cutoff:3.500A)
      removed outlier: 6.387A  pdb=" N   VAL B 202 " --> pdb=" O   ILE C 203 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AB1
    Processing sheet with id=AB2, first strand: chain 'A' and resid 208 through 210
    Processing sheet with id=AB3, first strand: chain 'A' and resid 214 through 218
    Processing sheet with id=AB4, first strand: chain 'A' and resid 225 through 230
      removed outlier: 9.034A  pdb=" N   LEU A 226 " --> pdb=" O   MET B 227 " (cutoff:3.500A)
      removed outlier: 9.482A  pdb=" N   GLN B 229 " --> pdb=" O   LEU A 226 " (cutoff:3.500A)
      removed outlier: 5.803A  pdb=" N   MET A 228 " --> pdb=" O   GLN B 229 " (cutoff:3.500A)
      removed outlier: 7.536A  pdb=" N   THR B 231 " --> pdb=" O   MET A 228 " (cutoff:3.500A)
      removed outlier: 6.363A  pdb=" N   VAL A 230 " --> pdb=" O   THR B 231 " (cutoff:3.500A)
      removed outlier: 7.112A  pdb=" N   THR B 233 " --> pdb=" O   VAL A 230 " (cutoff:3.500A)
      removed outlier: 6.655A  pdb=" N   THR A 233 " --> pdb=" O   THR B 234 " (cutoff:3.500A)
      removed outlier: 8.162A  pdb=" N   TYR B 236 " --> pdb=" O   THR A 233 " (cutoff:3.500A)
      removed outlier: 6.318A  pdb=" N   THR A 235 " --> pdb=" O   TYR B 236 " (cutoff:3.500A)
      removed outlier: 8.115A  pdb=" N   GLY B 238 " --> pdb=" O   THR A 235 " (cutoff:3.500A)
      removed outlier: 5.875A  pdb=" N   PHE A 237 " --> pdb=" O   GLY B 238 " (cutoff:3.500A)
      removed outlier: 7.260A  pdb=" N   SER B 240 " --> pdb=" O   PHE A 237 " (cutoff:3.500A)
      removed outlier: 6.678A  pdb=" N   HIS A 239 " --> pdb=" O   SER B 240 " (cutoff:3.500A)
      removed outlier: 8.043A  pdb=" N   GLN B 242 " --> pdb=" O   HIS A 239 " (cutoff:3.500A)
      removed outlier: 6.643A  pdb=" N   GLU A 241 " --> pdb=" O   GLN B 242 " (cutoff:3.500A)
      removed outlier: 8.214A  pdb=" N   SER B 244 " --> pdb=" O   GLU A 241 " (cutoff:3.500A)
      removed outlier: 6.562A  pdb=" N   ILE A 243 " --> pdb=" O   SER B 244 " (cutoff:3.500A)
      removed outlier: 8.344A  pdb=" N   GLU B 246 " --> pdb=" O   ILE A 243 " (cutoff:3.500A)
      removed outlier: 6.641A  pdb=" N   GLN A 245 " --> pdb=" O   GLU B 246 " (cutoff:3.500A)
      removed outlier: 7.993A  pdb=" N   TYR B 248 " --> pdb=" O   GLN A 245 " (cutoff:3.500A)
      removed outlier: 6.433A  pdb=" N   ARG A 247 " --> pdb=" O   TYR B 248 " (cutoff:3.500A)
      removed outlier: 8.225A  pdb=" N   TYR B 250 " --> pdb=" O   ARG A 247 " (cutoff:3.500A)
      removed outlier: 8.813A  pdb=" N   GLN A 249 " --> pdb=" O   TYR B 250 " (cutoff:3.500A)
      removed outlier: 7.200A  pdb=" N   ASP B 252 " --> pdb=" O   GLN A 249 " (cutoff:3.500A)
      removed outlier: 9.149A  pdb=" N   VAL A 251 " --> pdb=" O   ASP B 252 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AB4
    Processing sheet with id=AB5, first strand: chain 'A' and resid 225 through 230
      removed outlier: 9.034A  pdb=" N   LEU A 226 " --> pdb=" O   MET B 227 " (cutoff:3.500A)
      removed outlier: 9.482A  pdb=" N   GLN B 229 " --> pdb=" O   LEU A 226 " (cutoff:3.500A)
      removed outlier: 5.803A  pdb=" N   MET A 228 " --> pdb=" O   GLN B 229 " (cutoff:3.500A)
      removed outlier: 7.536A  pdb=" N   THR B 231 " --> pdb=" O   MET A 228 " (cutoff:3.500A)
      removed outlier: 6.363A  pdb=" N   VAL A 230 " --> pdb=" O   THR B 231 " (cutoff:3.500A)
      removed outlier: 7.112A  pdb=" N   THR B 233 " --> pdb=" O   VAL A 230 " (cutoff:3.500A)
      removed outlier: 6.147A  pdb=" N   VAL B 225 " --> pdb=" O   LEU C 226 " (cutoff:3.500A)
      removed outlier: 7.595A  pdb=" N   MET C 228 " --> pdb=" O   VAL B 225 " (cutoff:3.500A)
      removed outlier: 8.549A  pdb=" N   MET B 227 " --> pdb=" O   MET C 228 " (cutoff:3.500A)
      removed outlier: 6.270A  pdb=" N   VAL C 230 " --> pdb=" O   MET B 227 " (cutoff:3.500A)
      removed outlier: 8.774A  pdb=" N   GLN B 229 " --> pdb=" O   VAL C 230 " (cutoff:3.500A)
      removed outlier: 9.906A  pdb=" N   VAL C 232 " --> pdb=" O   GLN B 229 " (cutoff:3.500A)
      removed outlier: 5.744A  pdb=" N   THR B 231 " --> pdb=" O   VAL C 232 " (cutoff:3.500A)
      removed outlier: 8.377A  pdb=" N   THR C 234 " --> pdb=" O   THR B 231 " (cutoff:3.500A)
      removed outlier: 6.740A  pdb=" N   THR B 233 " --> pdb=" O   THR C 234 " (cutoff:3.500A)
      removed outlier: 8.165A  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: 8.219A  pdb=" N   GLY C 238 " --> pdb=" O   THR B 235 " (cutoff:3.500A)
      removed outlier: 6.070A  pdb=" N   PHE B 237 " --> pdb=" O   GLY C 238 " (cutoff:3.500A)
      removed outlier: 7.354A  pdb=" N   SER C 240 " --> pdb=" O   PHE B 237 " (cutoff:3.500A)
      removed outlier: 6.567A  pdb=" N   HIS B 239 " --> pdb=" O   SER C 240 " (cutoff:3.500A)
      removed outlier: 8.015A  pdb=" N   GLN C 242 " --> pdb=" O   HIS B 239 " (cutoff:3.500A)
      removed outlier: 6.546A  pdb=" N   GLU B 241 " --> pdb=" O   GLN C 242 " (cutoff:3.500A)
      removed outlier: 8.146A  pdb=" N   SER C 244 " --> pdb=" O   GLU B 241 " (cutoff:3.500A)
      removed outlier: 6.433A  pdb=" N   ILE B 243 " --> pdb=" O   SER C 244 " (cutoff:3.500A)
      removed outlier: 8.277A  pdb=" N   GLU C 246 " --> pdb=" O   ILE B 243 " (cutoff:3.500A)
      removed outlier: 6.621A  pdb=" N   GLN B 245 " --> pdb=" O   GLU C 246 " (cutoff:3.500A)
      removed outlier: 7.854A  pdb=" N   TYR C 248 " --> pdb=" O   GLN B 245 " (cutoff:3.500A)
      removed outlier: 6.480A  pdb=" N   ARG B 247 " --> pdb=" O   TYR C 248 " (cutoff:3.500A)
      removed outlier: 8.218A  pdb=" N   TYR C 250 " --> pdb=" O   ARG B 247 " (cutoff:3.500A)
      removed outlier: 8.840A  pdb=" N   GLN B 249 " --> pdb=" O   TYR C 250 " (cutoff:3.500A)
      removed outlier: 7.321A  pdb=" N   ASP C 252 " --> pdb=" O   GLN B 249 " (cutoff:3.500A)
      removed outlier: 9.287A  pdb=" N   VAL B 251 " --> pdb=" O   ASP C 252 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AB5

    55 hydrogen bonds defined for protein.
    165 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: 0.75

  Time building geometry restraints manager: 1.00 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: 850
        1.33 -     1.45: 594
        1.45 -     1.57: 1830
        1.57 -     1.69: 2
        1.69 -     1.81: 36
  Bond restraints: 3312
  Sorted by residual:
  bond pdb=" CA  VAL B 199 "
       pdb=" CB  VAL B 199 "
    ideal  model  delta    sigma   weight residual
    1.537  1.587 -0.049 1.29e-02 6.01e+03 1.47e+01
  bond pdb=" N   SER A 130 "
       pdb=" CA  SER A 130 "
    ideal  model  delta    sigma   weight residual
    1.456  1.491 -0.035 1.23e-02 6.61e+03 8.08e+00
  bond pdb=" CZ  ARG C 247 "
       pdb=" NH2 ARG C 247 "
    ideal  model  delta    sigma   weight residual
    1.330  1.294  0.036 1.30e-02 5.92e+03 7.81e+00
  bond pdb=" CZ  ARG B 247 "
       pdb=" NH2 ARG B 247 "
    ideal  model  delta    sigma   weight residual
    1.330  1.295  0.035 1.30e-02 5.92e+03 7.30e+00
  bond pdb=" N   LYS A 129 "
       pdb=" CA  LYS A 129 "
    ideal  model  delta    sigma   weight residual
    1.455  1.488 -0.033 1.25e-02 6.40e+03 7.01e+00
  ... (remaining 3307 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     3.64: 4018
        3.64 -     7.29: 451
        7.29 -    10.93: 24
       10.93 -    14.57: 9
       14.57 -    18.22: 1
  Bond angle restraints: 4503
  Sorted by residual:
  angle pdb=" N   LYS C 129 "
        pdb=" CA  LYS C 129 "
        pdb=" C   LYS C 129 "
      ideal   model   delta    sigma   weight residual
     112.97  125.45  -12.48 1.06e+00 8.90e-01 1.39e+02
  angle pdb=" N   LYS A 129 "
        pdb=" CA  LYS A 129 "
        pdb=" C   LYS A 129 "
      ideal   model   delta    sigma   weight residual
     112.93  125.98  -13.05 1.12e+00 7.97e-01 1.36e+02
  angle pdb=" N   LYS B 129 "
        pdb=" CA  LYS B 129 "
        pdb=" C   LYS B 129 "
      ideal   model   delta    sigma   weight residual
     113.02  126.71  -13.69 1.20e+00 6.94e-01 1.30e+02
  angle pdb=" CA  VAL A 202 "
        pdb=" CB  VAL A 202 "
        pdb=" CG1 VAL A 202 "
      ideal   model   delta    sigma   weight residual
     110.40  128.62  -18.22 1.70e+00 3.46e-01 1.15e+02
  angle pdb=" N   ASN A 182 "
        pdb=" CA  ASN A 182 "
        pdb=" C   ASN A 182 "
      ideal   model   delta    sigma   weight residual
     111.07  122.20  -11.13 1.07e+00 8.73e-01 1.08e+02
  ... (remaining 4498 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    16.06: 1767
       16.06 -    32.12: 172
       32.12 -    48.18: 38
       48.18 -    64.24: 11
       64.24 -    80.30: 7
  Dihedral angle restraints: 1995
    sinusoidal: 777
      harmonic: 1218
  Sorted by residual:
  dihedral pdb=" C   LYS C 129 "
           pdb=" N   LYS C 129 "
           pdb=" CA  LYS C 129 "
           pdb=" CB  LYS C 129 "
      ideal   model   delta  harmonic     sigma   weight residual
    -122.60 -142.38   19.78     0      2.50e+00 1.60e-01 6.26e+01
  dihedral pdb=" CA  GLU B 246 "
           pdb=" C   GLU B 246 "
           pdb=" N   ARG B 247 "
           pdb=" CA  ARG B 247 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  144.46   35.54     0      5.00e+00 4.00e-02 5.05e+01
  dihedral pdb=" N   LYS C 129 "
           pdb=" C   LYS C 129 "
           pdb=" CA  LYS C 129 "
           pdb=" CB  LYS C 129 "
      ideal   model   delta  harmonic     sigma   weight residual
     122.80  140.27  -17.47     0      2.50e+00 1.60e-01 4.88e+01
  ... (remaining 1992 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.194: 467
       0.194 -    0.388: 67
       0.388 -    0.582: 5
       0.582 -    0.776: 2
       0.776 -    0.970: 2
  Chirality restraints: 543
  Sorted by residual:
  chirality pdb=" CB  VAL A 202 "
            pdb=" CA  VAL A 202 "
            pdb=" CG1 VAL A 202 "
            pdb=" CG2 VAL A 202 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -1.66   -0.97 2.00e-01 2.50e+01 2.35e+01
  chirality pdb=" CA  LYS C 129 "
            pdb=" N   LYS C 129 "
            pdb=" C   LYS C 129 "
            pdb=" CB  LYS C 129 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    1.67    0.84 2.00e-01 2.50e+01 1.77e+01
  chirality pdb=" CB  VAL C 202 "
            pdb=" CA  VAL C 202 "
            pdb=" CG1 VAL C 202 "
            pdb=" CG2 VAL C 202 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -1.97   -0.66 2.00e-01 2.50e+01 1.08e+01
  ... (remaining 540 not shown)

  Planarity restraints: 558
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TYR C 143 "    0.148 2.00e-02 2.50e+03   7.53e-02 1.13e+02
        pdb=" CG  TYR C 143 "   -0.090 2.00e-02 2.50e+03
        pdb=" CD1 TYR C 143 "   -0.065 2.00e-02 2.50e+03
        pdb=" CD2 TYR C 143 "   -0.045 2.00e-02 2.50e+03
        pdb=" CE1 TYR C 143 "   -0.010 2.00e-02 2.50e+03
        pdb=" CE2 TYR C 143 "   -0.030 2.00e-02 2.50e+03
        pdb=" CZ  TYR C 143 "    0.001 2.00e-02 2.50e+03
        pdb=" OH  TYR C 143 "    0.091 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TYR C 248 "    0.135 2.00e-02 2.50e+03   7.28e-02 1.06e+02
        pdb=" CG  TYR C 248 "   -0.046 2.00e-02 2.50e+03
        pdb=" CD1 TYR C 248 "   -0.056 2.00e-02 2.50e+03
        pdb=" CD2 TYR C 248 "   -0.060 2.00e-02 2.50e+03
        pdb=" CE1 TYR C 248 "   -0.042 2.00e-02 2.50e+03
        pdb=" CE2 TYR C 248 "   -0.039 2.00e-02 2.50e+03
        pdb=" CZ  TYR C 248 "   -0.002 2.00e-02 2.50e+03
        pdb=" OH  TYR C 248 "    0.110 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TYR B 143 "    0.125 2.00e-02 2.50e+03   6.60e-02 8.70e+01
        pdb=" CG  TYR B 143 "   -0.044 2.00e-02 2.50e+03
        pdb=" CD1 TYR B 143 "   -0.061 2.00e-02 2.50e+03
        pdb=" CD2 TYR B 143 "   -0.058 2.00e-02 2.50e+03
        pdb=" CE1 TYR B 143 "   -0.030 2.00e-02 2.50e+03
        pdb=" CE2 TYR B 143 "   -0.033 2.00e-02 2.50e+03
        pdb=" CZ  TYR B 143 "    0.010 2.00e-02 2.50e+03
        pdb=" OH  TYR B 143 "    0.090 2.00e-02 2.50e+03
  ... (remaining 555 not shown)

  Histogram of nonbonded interaction distances:
        2.52 -     3.00: 1703
        3.00 -     3.47: 2895
        3.47 -     3.95: 5237
        3.95 -     4.42: 5659
        4.42 -     4.90: 10437
  Nonbonded interactions: 25931
  Sorted by model distance:
  nonbonded pdb=" OE1 GLU A 241 "
            pdb=" OG  SER B 120 "
     model   vdw
     2.525 3.040
  nonbonded pdb=" OE1 GLU B 241 "
            pdb=" OG  SER C 120 "
     model   vdw
     2.528 3.040
  nonbonded pdb=" OD2 ASP A 212 "
            pdb=" OG1 THR A 215 "
     model   vdw
     2.547 3.040
  nonbonded pdb=" N   ASN B 223 "
            pdb=" O   ASN B 223 "
     model   vdw
     2.556 2.496
  nonbonded pdb=" OD2 ASP C 212 "
            pdb=" OG1 THR C 215 "
     model   vdw
     2.567 3.040
  ... (remaining 25926 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:             2.930
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.130
  Check model and map are aligned:         0.030
  Set scattering table:                    0.040
  Process input model:                     14.390
  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:3.070
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   20.720
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7945
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   0.051   3315  Z= 0.747
  Angle     :  2.341  18.216   4509  Z= 1.560
  Chirality :  0.147   0.970    543
  Planarity :  0.014   0.075    558
  Dihedral  : 14.889  80.297   1206
  Min Nonbonded Distance : 2.525

Molprobity Statistics.
  All-atom Clashscore : 0.31
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 10.03 %
    Favored  : 89.97 %
  Rotamer:
    Outliers :  0.26 %
    Allowed  :  4.76 %
    Favored  : 94.97 %
  Cbeta Deviations :  2.56 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.51 %

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: -3.26 (0.31), residues: 399
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.47 (0.24), residues: 399

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.010   0.005   HIS A 222 
 PHE   0.051   0.013   PHE C 237 
 TYR   0.148   0.023   TYR C 143 
 ARG   0.005   0.001   ARG C 247 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.06532 (   55)
  hydrogen bonds       : angle       7.97571 (  165)
  SS BOND              : bond        0.00665 (    3)
  SS BOND              : angle       1.49117 (    6)
  covalent geometry    : bond        0.01244 ( 3312)
  covalent geometry    : angle       2.34145 ( 4503)

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

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

  798 Ramachandran restraints generated.
    399 Oldfield, 0 Emsley, 399 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  798 Ramachandran restraints generated.
    399 Oldfield, 0 Emsley, 399 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  100 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 99
  time to evaluate  : 0.315 
Fit side-chains
REVERT: A  140 ARG cc_start: 0.8099 (mtp85) cc_final: 0.7764 (mtp-110)
REVERT: A  186 ILE cc_start: 0.8656 (mp) cc_final: 0.8405 (mt)
REVERT: B  186 ILE cc_start: 0.8791 (mp) cc_final: 0.8532 (mt)
REVERT: B  210 MET cc_start: 0.8244 (mtm) cc_final: 0.8038 (mtt)
REVERT: C  122 ASP cc_start: 0.8460 (t0) cc_final: 0.8228 (t70)
REVERT: C  140 ARG cc_start: 0.7986 (mtp85) cc_final: 0.7384 (mmt180)
REVERT: C  186 ILE cc_start: 0.8726 (mp) cc_final: 0.8520 (mt)
REVERT: C  210 MET cc_start: 0.8294 (mtm) cc_final: 0.8086 (mtt)
  outliers start: 1
  outliers final: 1
  residues processed: 99
  average time/residue: 0.1818
  time to fit residues: 21.0325
Evaluate side-chains
  79 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 78
  time to evaluate  : 0.358 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  199 VAL
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:    3.9990
   chunk 16 optimal weight:    3.9990
   chunk 10 optimal weight:    1.9990
   chunk 19 optimal weight:    5.9990
   chunk 15 optimal weight:    1.9990
   chunk 30 optimal weight:    0.9990
   chunk 11 optimal weight:    0.7980
   chunk 18 optimal weight:    5.9990
   chunk 22 optimal weight:    1.9990
   chunk 35 optimal weight:    5.9990
   overall best weight:    1.5588

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

Flipped N/Q/H residues before XYZ refinement:
A 245 GLN
C 155 ASN
** 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 = 0.3954 r_free = 0.3954 target = 0.129280 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3745 r_free = 0.3745 target = 0.110521 restraints weight = 4070.361|
|-----------------------------------------------------------------------------|
r_work (start): 0.3755 rms_B_bonded: 2.21
r_work: 0.3646 rms_B_bonded: 2.39 restraints_weight: 0.5000
r_work: 0.3527 rms_B_bonded: 4.08 restraints_weight: 0.2500
r_work (final): 0.3527
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7998
moved from start:          0.2570

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.032   3315  Z= 0.165
  Angle     :  0.747   5.829   4509  Z= 0.422
  Chirality :  0.056   0.153    543
  Planarity :  0.003   0.014    558
  Dihedral  :  8.769  32.343    448
  Min Nonbonded Distance : 2.542

Molprobity Statistics.
  All-atom Clashscore : 7.37
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.77 %
    Favored  : 91.23 %
  Rotamer:
    Outliers :  2.12 %
    Allowed  : 11.90 %
    Favored  : 85.98 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.25 %

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: -3.20 (0.32), residues: 399
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.43 (0.24), residues: 399

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.003   0.001   HIS B 222 
 PHE   0.012   0.002   PHE B 171 
 TYR   0.019   0.002   TYR B 197 
 ARG   0.001   0.000   ARG A 180 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02495 (   55)
  hydrogen bonds       : angle       5.89283 (  165)
  SS BOND              : bond        0.00356 (    3)
  SS BOND              : angle       0.83917 (    6)
  covalent geometry    : bond        0.00367 ( 3312)
  covalent geometry    : angle       0.74724 ( 4503)

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

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

  798 Ramachandran restraints generated.
    399 Oldfield, 0 Emsley, 399 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  798 Ramachandran restraints generated.
    399 Oldfield, 0 Emsley, 399 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  91 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 83
  time to evaluate  : 0.337 
Fit side-chains
REVERT: A  140 ARG cc_start: 0.8496 (mtp85) cc_final: 0.7414 (mtp-110)
REVERT: A  141 THR cc_start: 0.8752 (m) cc_final: 0.8523 (p)
REVERT: A  154 ASN cc_start: 0.8947 (t0) cc_final: 0.8602 (t0)
REVERT: A  206 GLU cc_start: 0.8337 (mt-10) cc_final: 0.8001 (tt0)
REVERT: A  210 MET cc_start: 0.8546 (mtt) cc_final: 0.8203 (mtm)
REVERT: B  140 ARG cc_start: 0.7702 (ttm110) cc_final: 0.7393 (ttm110)
REVERT: B  210 MET cc_start: 0.8840 (mtm) cc_final: 0.8601 (mtt)
REVERT: C  140 ARG cc_start: 0.8344 (mtp85) cc_final: 0.7217 (mmt-90)
REVERT: C  206 GLU cc_start: 0.8035 (tt0) cc_final: 0.6840 (tm-30)
  outliers start: 8
  outliers final: 6
  residues processed: 85
  average time/residue: 0.1801
  time to fit residues: 18.1355
Evaluate side-chains
  78 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 72
  time to evaluate  : 0.385 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  212 ASP
Chi-restraints excluded: chain A residue  240 SER
Chi-restraints excluded: chain B residue  142 ILE
Chi-restraints excluded: chain B residue  144 LEU
Chi-restraints excluded: chain B residue  192 MET
Chi-restraints excluded: chain B residue  212 ASP
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 39
   random chunks:
   chunk 25 optimal weight:    1.9990
   chunk 14 optimal weight:   10.0000
   chunk 3 optimal weight:    0.9980
   chunk 19 optimal weight:   10.0000
   chunk 13 optimal weight:    7.9990
   chunk 34 optimal weight:    4.9990
   chunk 7 optimal weight:    7.9990
   chunk 8 optimal weight:    6.9990
   chunk 23 optimal weight:    0.9980
   chunk 17 optimal weight:    7.9990
   chunk 11 optimal weight:    0.0770
   overall best weight:    1.8142

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

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

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3918 r_free = 0.3918 target = 0.125914 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3710 r_free = 0.3710 target = 0.106976 restraints weight = 4044.501|
|-----------------------------------------------------------------------------|
r_work (start): 0.3715 rms_B_bonded: 2.17
r_work: 0.3611 rms_B_bonded: 2.37 restraints_weight: 0.5000
r_work: 0.3497 rms_B_bonded: 4.01 restraints_weight: 0.2500
r_work (final): 0.3497
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8037
moved from start:          0.3207

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.037   3315  Z= 0.162
  Angle     :  0.664   7.520   4509  Z= 0.370
  Chirality :  0.053   0.147    543
  Planarity :  0.002   0.011    558
  Dihedral  :  7.933  27.509    447
  Min Nonbonded Distance : 2.581

Molprobity Statistics.
  All-atom Clashscore : 8.76
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.27 %
    Favored  : 90.73 %
  Rotamer:
    Outliers :  3.97 %
    Allowed  : 13.23 %
    Favored  : 82.80 %
  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: -3.17 (0.33), residues: 399
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.40 (0.25), residues: 399

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.002   0.001   HIS A 239 
 PHE   0.010   0.001   PHE B 171 
 TYR   0.015   0.002   TYR C 143 
 ARG   0.001   0.000   ARG C 180 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02099 (   55)
  hydrogen bonds       : angle       5.41758 (  165)
  SS BOND              : bond        0.00311 (    3)
  SS BOND              : angle       0.64227 (    6)
  covalent geometry    : bond        0.00366 ( 3312)
  covalent geometry    : angle       0.66430 ( 4503)

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

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

  798 Ramachandran restraints generated.
    399 Oldfield, 0 Emsley, 399 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  798 Ramachandran restraints generated.
    399 Oldfield, 0 Emsley, 399 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  92 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 77
  time to evaluate  : 0.370 
Fit side-chains
REVERT: A  141 THR cc_start: 0.8714 (m) cc_final: 0.8444 (p)
REVERT: A  192 MET cc_start: 0.9211 (OUTLIER) cc_final: 0.8988 (mtm)
REVERT: A  205 GLU cc_start: 0.8353 (tp30) cc_final: 0.6853 (mp0)
REVERT: A  206 GLU cc_start: 0.8505 (mt-10) cc_final: 0.8228 (tt0)
REVERT: A  210 MET cc_start: 0.8695 (mtt) cc_final: 0.8350 (mtm)
REVERT: A  247 ARG cc_start: 0.8553 (ptm160) cc_final: 0.8325 (ttt180)
REVERT: B  124 LYS cc_start: 0.8790 (mtpt) cc_final: 0.8509 (mttt)
REVERT: B  210 MET cc_start: 0.8853 (mtm) cc_final: 0.8622 (mtt)
REVERT: C  140 ARG cc_start: 0.8372 (mtp85) cc_final: 0.7171 (mmt-90)
REVERT: C  206 GLU cc_start: 0.8000 (tt0) cc_final: 0.6796 (tm-30)
  outliers start: 15
  outliers final: 10
  residues processed: 85
  average time/residue: 0.1651
  time to fit residues: 16.7755
Evaluate side-chains
  81 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 70
  time to evaluate  : 0.332 
-------------------------------------------------------------------------------
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  192 MET
Chi-restraints excluded: chain A residue  212 ASP
Chi-restraints excluded: chain A residue  229 GLN
Chi-restraints excluded: chain B residue  142 ILE
Chi-restraints excluded: chain B residue  144 LEU
Chi-restraints excluded: chain B residue  153 THR
Chi-restraints excluded: chain B residue  192 MET
Chi-restraints excluded: chain C residue  192 MET
Chi-restraints excluded: chain C residue  229 GLN
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 39
   random chunks:
   chunk 6 optimal weight:    5.9990
   chunk 37 optimal weight:    1.9990
   chunk 36 optimal weight:    2.9990
   chunk 33 optimal weight:    4.9990
   chunk 19 optimal weight:    0.8980
   chunk 38 optimal weight:    2.9990
   chunk 2 optimal weight:    2.9990
   chunk 25 optimal weight:    2.9990
   chunk 1 optimal weight:    1.9990
   chunk 13 optimal weight:    0.9980
   chunk 21 optimal weight:    9.9990
   overall best weight:    1.7786

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

Flipped N/Q/H residues before XYZ refinement:
A 154 ASN
** B 239 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** 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 = 0.3909 r_free = 0.3909 target = 0.125093 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3696 r_free = 0.3696 target = 0.106096 restraints weight = 4096.776|
|-----------------------------------------------------------------------------|
r_work (start): 0.3699 rms_B_bonded: 2.17
r_work: 0.3595 rms_B_bonded: 2.35 restraints_weight: 0.5000
r_work: 0.3482 rms_B_bonded: 3.98 restraints_weight: 0.2500
r_work (final): 0.3482
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8035
moved from start:          0.3530

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.033   3315  Z= 0.156
  Angle     :  0.634   6.176   4509  Z= 0.351
  Chirality :  0.052   0.148    543
  Planarity :  0.002   0.010    558
  Dihedral  :  7.620  26.613    447
  Min Nonbonded Distance : 2.586

Molprobity Statistics.
  All-atom Clashscore : 9.06
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.27 %
    Favored  : 90.73 %
  Rotamer:
    Outliers :  6.08 %
    Allowed  : 15.34 %
    Favored  : 78.57 %
  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: -3.23 (0.34), residues: 399
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.45 (0.26), residues: 399

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.003   0.001   HIS C 239 
 PHE   0.009   0.001   PHE B 171 
 TYR   0.015   0.002   TYR C 143 
 ARG   0.004   0.000   ARG A 140 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.01925 (   55)
  hydrogen bonds       : angle       5.23550 (  165)
  SS BOND              : bond        0.00257 (    3)
  SS BOND              : angle       0.55124 (    6)
  covalent geometry    : bond        0.00351 ( 3312)
  covalent geometry    : angle       0.63379 ( 4503)

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

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

  798 Ramachandran restraints generated.
    399 Oldfield, 0 Emsley, 399 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  798 Ramachandran restraints generated.
    399 Oldfield, 0 Emsley, 399 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  94 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 71
  time to evaluate  : 0.454 
Fit side-chains
REVERT: A  122 ASP cc_start: 0.8678 (t0) cc_final: 0.8445 (t0)
REVERT: A  124 LYS cc_start: 0.5990 (mmtt) cc_final: 0.4582 (mttt)
REVERT: A  141 THR cc_start: 0.8755 (m) cc_final: 0.8533 (p)
REVERT: A  148 ASN cc_start: 0.8092 (t0) cc_final: 0.7784 (t0)
REVERT: A  161 GLU cc_start: 0.8173 (OUTLIER) cc_final: 0.7871 (tt0)
REVERT: A  205 GLU cc_start: 0.8437 (tp30) cc_final: 0.6778 (mp0)
REVERT: A  210 MET cc_start: 0.8760 (mtt) cc_final: 0.8458 (mtm)
REVERT: A  247 ARG cc_start: 0.8561 (ptm160) cc_final: 0.8356 (ttt180)
REVERT: B  124 LYS cc_start: 0.8976 (mtpt) cc_final: 0.8595 (mttt)
REVERT: B  210 MET cc_start: 0.8868 (mtm) cc_final: 0.8621 (mtt)
REVERT: C  140 ARG cc_start: 0.8378 (mtp85) cc_final: 0.7086 (mmt180)
REVERT: C  184 ILE cc_start: 0.6365 (OUTLIER) cc_final: 0.6148 (mp)
REVERT: C  206 GLU cc_start: 0.8016 (tt0) cc_final: 0.6829 (tm-30)
  outliers start: 23
  outliers final: 14
  residues processed: 81
  average time/residue: 0.1637
  time to fit residues: 15.8778
Evaluate side-chains
  83 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 67
  time to evaluate  : 0.335 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  133 VAL
Chi-restraints excluded: chain A residue  144 LEU
Chi-restraints excluded: chain A residue  149 THR
Chi-restraints excluded: chain A residue  161 GLU
Chi-restraints excluded: chain A residue  212 ASP
Chi-restraints excluded: chain A residue  229 GLN
Chi-restraints excluded: chain B residue  142 ILE
Chi-restraints excluded: chain B residue  144 LEU
Chi-restraints excluded: chain B residue  153 THR
Chi-restraints excluded: chain B residue  192 MET
Chi-restraints excluded: chain C residue  184 ILE
Chi-restraints excluded: chain C residue  192 MET
Chi-restraints excluded: chain C residue  227 MET
Chi-restraints excluded: chain C residue  228 MET
Chi-restraints excluded: chain C residue  229 GLN
Chi-restraints excluded: chain C residue  247 ARG
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 39
   random chunks:
   chunk 2 optimal weight:    1.9990
   chunk 36 optimal weight:    6.9990
   chunk 3 optimal weight:    6.9990
   chunk 7 optimal weight:    5.9990
   chunk 5 optimal weight:    4.9990
   chunk 9 optimal weight:    5.9990
   chunk 26 optimal weight:    0.8980
   chunk 12 optimal weight:    3.9990
   chunk 27 optimal weight:    5.9990
   chunk 24 optimal weight:    7.9990
   chunk 19 optimal weight:   10.0000
   overall best weight:    3.5788

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

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

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3812 r_free = 0.3812 target = 0.118358 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 25)----------------|
| r_work = 0.3591 r_free = 0.3591 target = 0.099504 restraints weight = 4237.345|
|-----------------------------------------------------------------------------|
r_work (start): 0.3599 rms_B_bonded: 2.19
r_work: 0.3498 rms_B_bonded: 2.31 restraints_weight: 0.5000
r_work: 0.3382 rms_B_bonded: 3.90 restraints_weight: 0.2500
r_work (final): 0.3382
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8124
moved from start:          0.3663

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.046   3315  Z= 0.277
  Angle     :  0.704   5.880   4509  Z= 0.395
  Chirality :  0.054   0.148    543
  Planarity :  0.003   0.011    558
  Dihedral  :  8.081  28.302    447
  Min Nonbonded Distance : 2.580

Molprobity Statistics.
  All-atom Clashscore : 9.98
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 11.53 %
    Favored  : 88.47 %
  Rotamer:
    Outliers :  5.29 %
    Allowed  : 16.93 %
    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: -3.48 (0.33), residues: 399
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.64 (0.25), residues: 399

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.005   0.001   HIS C 239 
 PHE   0.013   0.002   PHE B 171 
 TYR   0.020   0.002   TYR C 143 
 ARG   0.003   0.001   ARG A 140 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02185 (   55)
  hydrogen bonds       : angle       5.29519 (  165)
  SS BOND              : bond        0.00270 (    3)
  SS BOND              : angle       0.89705 (    6)
  covalent geometry    : bond        0.00629 ( 3312)
  covalent geometry    : angle       0.70416 ( 4503)

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

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

  798 Ramachandran restraints generated.
    399 Oldfield, 0 Emsley, 399 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  798 Ramachandran restraints generated.
    399 Oldfield, 0 Emsley, 399 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  94 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 74
  time to evaluate  : 0.374 
Fit side-chains
REVERT: A  124 LYS cc_start: 0.6253 (mmtt) cc_final: 0.4717 (mttt)
REVERT: A  129 LYS cc_start: 0.8571 (mttt) cc_final: 0.8279 (mtpp)
REVERT: A  141 THR cc_start: 0.8705 (m) cc_final: 0.8469 (p)
REVERT: A  148 ASN cc_start: 0.8329 (t0) cc_final: 0.7953 (t0)
REVERT: A  205 GLU cc_start: 0.8566 (tp30) cc_final: 0.6783 (mp0)
REVERT: A  210 MET cc_start: 0.8801 (mtt) cc_final: 0.8544 (mtm)
REVERT: B  124 LYS cc_start: 0.9034 (mtpt) cc_final: 0.8682 (mttt)
REVERT: B  210 MET cc_start: 0.8759 (mtm) cc_final: 0.8500 (mtt)
REVERT: C  140 ARG cc_start: 0.8423 (mtp85) cc_final: 0.8064 (mtt90)
REVERT: C  206 GLU cc_start: 0.8035 (tt0) cc_final: 0.6868 (tm-30)
  outliers start: 20
  outliers final: 16
  residues processed: 83
  average time/residue: 0.1770
  time to fit residues: 17.3750
Evaluate side-chains
  86 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 70
  time to evaluate  : 0.370 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  133 VAL
Chi-restraints excluded: chain A residue  144 LEU
Chi-restraints excluded: chain A residue  145 ASN
Chi-restraints excluded: chain A residue  149 THR
Chi-restraints excluded: chain A residue  212 ASP
Chi-restraints excluded: chain A residue  229 GLN
Chi-restraints excluded: chain A residue  234 THR
Chi-restraints excluded: chain B residue  144 LEU
Chi-restraints excluded: chain B residue  153 THR
Chi-restraints excluded: chain B residue  192 MET
Chi-restraints excluded: chain C residue  184 ILE
Chi-restraints excluded: chain C residue  192 MET
Chi-restraints excluded: chain C residue  227 MET
Chi-restraints excluded: chain C residue  228 MET
Chi-restraints excluded: chain C residue  229 GLN
Chi-restraints excluded: chain C residue  247 ARG
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 39
   random chunks:
   chunk 26 optimal weight:    3.9990
   chunk 21 optimal weight:   10.0000
   chunk 15 optimal weight:    5.9990
   chunk 24 optimal weight:    4.9990
   chunk 27 optimal weight:    5.9990
   chunk 10 optimal weight:    1.9990
   chunk 12 optimal weight:    3.9990
   chunk 25 optimal weight:    3.9990
   chunk 22 optimal weight:    2.9990
   chunk 34 optimal weight:    4.9990
   chunk 33 optimal weight:    1.9990
   overall best weight:    2.9990

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

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

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3822 r_free = 0.3822 target = 0.118903 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3600 r_free = 0.3600 target = 0.099801 restraints weight = 4332.453|
|-----------------------------------------------------------------------------|
r_work (start): 0.3597 rms_B_bonded: 2.22
r_work: 0.3493 rms_B_bonded: 2.36 restraints_weight: 0.5000
r_work: 0.3377 rms_B_bonded: 4.00 restraints_weight: 0.2500
r_work (final): 0.3377
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8140
moved from start:          0.3797

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.042   3315  Z= 0.237
  Angle     :  0.675   5.271   4509  Z= 0.379
  Chirality :  0.054   0.146    543
  Planarity :  0.003   0.011    558
  Dihedral  :  7.906  27.928    447
  Min Nonbonded Distance : 2.595

Molprobity Statistics.
  All-atom Clashscore : 8.91
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 10.78 %
    Favored  : 89.22 %
  Rotamer:
    Outliers :  5.29 %
    Allowed  : 16.93 %
    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: -3.59 (0.32), residues: 399
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.73 (0.25), residues: 399

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.005   0.001   HIS C 239 
 PHE   0.012   0.002   PHE B 171 
 TYR   0.019   0.002   TYR C 143 
 ARG   0.003   0.001   ARG A 140 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02195 (   55)
  hydrogen bonds       : angle       5.42369 (  165)
  SS BOND              : bond        0.00270 (    3)
  SS BOND              : angle       0.68403 (    6)
  covalent geometry    : bond        0.00536 ( 3312)
  covalent geometry    : angle       0.67532 ( 4503)

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

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

  798 Ramachandran restraints generated.
    399 Oldfield, 0 Emsley, 399 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  798 Ramachandran restraints generated.
    399 Oldfield, 0 Emsley, 399 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  95 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 75
  time to evaluate  : 0.390 
Fit side-chains
REVERT: A  124 LYS cc_start: 0.6162 (mmtt) cc_final: 0.4756 (mttt)
REVERT: A  129 LYS cc_start: 0.8580 (mttt) cc_final: 0.8271 (mtpp)
REVERT: A  141 THR cc_start: 0.8672 (m) cc_final: 0.8452 (p)
REVERT: A  148 ASN cc_start: 0.8322 (t0) cc_final: 0.7962 (t0)
REVERT: A  181 LEU cc_start: 0.8293 (mp) cc_final: 0.7944 (mt)
REVERT: A  205 GLU cc_start: 0.8477 (tp30) cc_final: 0.6788 (mp0)
REVERT: A  210 MET cc_start: 0.8713 (mtt) cc_final: 0.8498 (mtm)
REVERT: B  124 LYS cc_start: 0.9041 (mtpt) cc_final: 0.8765 (mttt)
REVERT: B  210 MET cc_start: 0.8822 (mtm) cc_final: 0.8558 (mtt)
REVERT: C  140 ARG cc_start: 0.8403 (mtp85) cc_final: 0.8035 (mtt90)
REVERT: C  206 GLU cc_start: 0.8015 (tt0) cc_final: 0.6869 (tm-30)
  outliers start: 20
  outliers final: 19
  residues processed: 83
  average time/residue: 0.1807
  time to fit residues: 17.7408
Evaluate side-chains
  93 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 74
  time to evaluate  : 0.354 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  133 VAL
Chi-restraints excluded: chain A residue  144 LEU
Chi-restraints excluded: chain A residue  145 ASN
Chi-restraints excluded: chain A residue  149 THR
Chi-restraints excluded: chain A residue  212 ASP
Chi-restraints excluded: chain A residue  229 GLN
Chi-restraints excluded: chain A residue  234 THR
Chi-restraints excluded: chain B residue  144 LEU
Chi-restraints excluded: chain B residue  153 THR
Chi-restraints excluded: chain B residue  161 GLU
Chi-restraints excluded: chain B residue  192 MET
Chi-restraints excluded: chain B residue  229 GLN
Chi-restraints excluded: chain C residue  184 ILE
Chi-restraints excluded: chain C residue  192 MET
Chi-restraints excluded: chain C residue  227 MET
Chi-restraints excluded: chain C residue  228 MET
Chi-restraints excluded: chain C residue  229 GLN
Chi-restraints excluded: chain C residue  234 THR
Chi-restraints excluded: chain C residue  247 ARG
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 39
   random chunks:
   chunk 22 optimal weight:    6.9990
   chunk 19 optimal weight:    9.9990
   chunk 17 optimal weight:    6.9990
   chunk 9 optimal weight:    4.9990
   chunk 24 optimal weight:    4.9990
   chunk 4 optimal weight:    1.9990
   chunk 7 optimal weight:    1.9990
   chunk 25 optimal weight:    0.8980
   chunk 31 optimal weight:    8.9990
   chunk 35 optimal weight:    3.9990
   chunk 18 optimal weight:    6.9990
   overall best weight:    2.7788

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

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

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3824 r_free = 0.3824 target = 0.118547 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3608 r_free = 0.3608 target = 0.100030 restraints weight = 4217.221|
|-----------------------------------------------------------------------------|
r_work (start): 0.3614 rms_B_bonded: 2.13
r_work: 0.3512 rms_B_bonded: 2.28 restraints_weight: 0.5000
r_work: 0.3400 rms_B_bonded: 3.88 restraints_weight: 0.2500
r_work (final): 0.3400
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8124
moved from start:          0.3950

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.041   3315  Z= 0.222
  Angle     :  0.659   4.870   4509  Z= 0.371
  Chirality :  0.053   0.147    543
  Planarity :  0.002   0.011    558
  Dihedral  :  7.821  28.010    447
  Min Nonbonded Distance : 2.593

Molprobity Statistics.
  All-atom Clashscore : 8.91
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 11.28 %
    Favored  : 88.72 %
  Rotamer:
    Outliers :  6.08 %
    Allowed  : 17.20 %
    Favored  : 76.72 %
  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: -3.64 (0.33), residues: 399
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.77 (0.25), residues: 399

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.005   0.001   HIS C 239 
 PHE   0.011   0.002   PHE B 171 
 TYR   0.016   0.002   TYR A 197 
 ARG   0.003   0.000   ARG A 140 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02165 (   55)
  hydrogen bonds       : angle       5.36870 (  165)
  SS BOND              : bond        0.00238 (    3)
  SS BOND              : angle       0.75442 (    6)
  covalent geometry    : bond        0.00502 ( 3312)
  covalent geometry    : angle       0.65912 ( 4503)

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

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

  798 Ramachandran restraints generated.
    399 Oldfield, 0 Emsley, 399 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  798 Ramachandran restraints generated.
    399 Oldfield, 0 Emsley, 399 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  94 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 71
  time to evaluate  : 0.380 
Fit side-chains
REVERT: A  124 LYS cc_start: 0.6138 (mmtt) cc_final: 0.4751 (mttt)
REVERT: A  129 LYS cc_start: 0.8603 (mttt) cc_final: 0.8285 (mtpp)
REVERT: A  148 ASN cc_start: 0.8254 (t0) cc_final: 0.7885 (t0)
REVERT: A  181 LEU cc_start: 0.8338 (mp) cc_final: 0.8007 (mt)
REVERT: B  124 LYS cc_start: 0.9024 (mtpt) cc_final: 0.8739 (mttt)
REVERT: B  210 MET cc_start: 0.8812 (mtm) cc_final: 0.8593 (mtt)
REVERT: C  140 ARG cc_start: 0.8410 (mtp85) cc_final: 0.8030 (mtt90)
REVERT: C  206 GLU cc_start: 0.8022 (tt0) cc_final: 0.6842 (tm-30)
  outliers start: 23
  outliers final: 19
  residues processed: 83
  average time/residue: 0.1875
  time to fit residues: 18.3063
Evaluate side-chains
  89 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 70
  time to evaluate  : 0.353 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  133 VAL
Chi-restraints excluded: chain A residue  144 LEU
Chi-restraints excluded: chain A residue  149 THR
Chi-restraints excluded: chain A residue  212 ASP
Chi-restraints excluded: chain A residue  229 GLN
Chi-restraints excluded: chain A residue  230 VAL
Chi-restraints excluded: chain A residue  234 THR
Chi-restraints excluded: chain B residue  144 LEU
Chi-restraints excluded: chain B residue  153 THR
Chi-restraints excluded: chain B residue  192 MET
Chi-restraints excluded: chain B residue  229 GLN
Chi-restraints excluded: chain C residue  184 ILE
Chi-restraints excluded: chain C residue  186 ILE
Chi-restraints excluded: chain C residue  192 MET
Chi-restraints excluded: chain C residue  227 MET
Chi-restraints excluded: chain C residue  228 MET
Chi-restraints excluded: chain C residue  229 GLN
Chi-restraints excluded: chain C residue  234 THR
Chi-restraints excluded: chain C residue  247 ARG
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 39
   random chunks:
   chunk 26 optimal weight:    4.9990
   chunk 9 optimal weight:    5.9990
   chunk 15 optimal weight:    4.9990
   chunk 28 optimal weight:    2.9990
   chunk 6 optimal weight:    6.9990
   chunk 38 optimal weight:    1.9990
   chunk 10 optimal weight:    4.9990
   chunk 34 optimal weight:    8.9990
   chunk 37 optimal weight:    0.9990
   chunk 20 optimal weight:    0.9980
   chunk 29 optimal weight:    0.9990
   overall best weight:    1.5988

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

Flipped N/Q/H residues before XYZ refinement:
** B 239 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
C 229 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 = 0.3879 r_free = 0.3879 target = 0.122405 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3667 r_free = 0.3667 target = 0.103940 restraints weight = 4114.876|
|-----------------------------------------------------------------------------|
r_work (start): 0.3668 rms_B_bonded: 2.15
r_work: 0.3566 rms_B_bonded: 2.30 restraints_weight: 0.5000
r_work: 0.3454 rms_B_bonded: 3.94 restraints_weight: 0.2500
r_work (final): 0.3454
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8057
moved from start:          0.4107

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   3315  Z= 0.144
  Angle     :  0.609   4.624   4509  Z= 0.343
  Chirality :  0.052   0.146    543
  Planarity :  0.002   0.010    558
  Dihedral  :  7.430  27.278    447
  Min Nonbonded Distance : 2.588

Molprobity Statistics.
  All-atom Clashscore : 9.68
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.77 %
    Favored  : 90.23 %
  Rotamer:
    Outliers :  5.03 %
    Allowed  : 19.31 %
    Favored  : 75.66 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -3.52 (0.33), residues: 399
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.67 (0.25), residues: 399

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.003   0.001   HIS C 239 
 PHE   0.009   0.001   PHE B 171 
 TYR   0.013   0.002   TYR B 211 
 ARG   0.003   0.000   ARG A 140 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.01909 (   55)
  hydrogen bonds       : angle       5.23918 (  165)
  SS BOND              : bond        0.00234 (    3)
  SS BOND              : angle       0.48220 (    6)
  covalent geometry    : bond        0.00322 ( 3312)
  covalent geometry    : angle       0.60887 ( 4503)

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

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

  798 Ramachandran restraints generated.
    399 Oldfield, 0 Emsley, 399 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  798 Ramachandran restraints generated.
    399 Oldfield, 0 Emsley, 399 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  94 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 75
  time to evaluate  : 0.388 
Fit side-chains
   revert: symmetry clash
REVERT: A  124 LYS cc_start: 0.6067 (mmtt) cc_final: 0.4742 (mttt)
REVERT: A  129 LYS cc_start: 0.8544 (mttt) cc_final: 0.8245 (mtpp)
REVERT: A  148 ASN cc_start: 0.8231 (t0) cc_final: 0.7904 (t0)
REVERT: A  181 LEU cc_start: 0.8261 (mp) cc_final: 0.7910 (mt)
REVERT: A  196 ASP cc_start: 0.8641 (m-30) cc_final: 0.8364 (m-30)
REVERT: B  124 LYS cc_start: 0.9010 (mtpt) cc_final: 0.8709 (mttt)
REVERT: B  210 MET cc_start: 0.8811 (mtm) cc_final: 0.8591 (mtt)
REVERT: C  140 ARG cc_start: 0.8413 (mtp85) cc_final: 0.8023 (mtt90)
REVERT: C  184 ILE cc_start: 0.6168 (OUTLIER) cc_final: 0.5928 (mp)
REVERT: C  206 GLU cc_start: 0.7997 (tt0) cc_final: 0.6834 (tm-30)
  outliers start: 19
  outliers final: 15
  residues processed: 84
  average time/residue: 0.1648
  time to fit residues: 16.5720
Evaluate side-chains
  90 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 74
  time to evaluate  : 0.340 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  144 LEU
Chi-restraints excluded: chain A residue  149 THR
Chi-restraints excluded: chain A residue  212 ASP
Chi-restraints excluded: chain A residue  229 GLN
Chi-restraints excluded: chain A residue  234 THR
Chi-restraints excluded: chain B residue  144 LEU
Chi-restraints excluded: chain B residue  153 THR
Chi-restraints excluded: chain B residue  192 MET
Chi-restraints excluded: chain B residue  229 GLN
Chi-restraints excluded: chain C residue  184 ILE
Chi-restraints excluded: chain C residue  192 MET
Chi-restraints excluded: chain C residue  228 MET
Chi-restraints excluded: chain C residue  229 GLN
Chi-restraints excluded: chain C residue  234 THR
Chi-restraints excluded: chain C residue  244 SER
Chi-restraints excluded: chain C residue  247 ARG
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 39
   random chunks:
   chunk 17 optimal weight:    6.9990
   chunk 16 optimal weight:    5.9990
   chunk 5 optimal weight:    5.9990
   chunk 13 optimal weight:    3.9990
   chunk 38 optimal weight:    2.9990
   chunk 1 optimal weight:    0.5980
   chunk 29 optimal weight:    6.9990
   chunk 26 optimal weight:    2.9990
   chunk 32 optimal weight:    4.9990
   chunk 18 optimal weight:    6.9990
   chunk 11 optimal weight:    4.9990
   overall best weight:    3.1188

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

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

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3814 r_free = 0.3814 target = 0.117746 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3595 r_free = 0.3595 target = 0.099381 restraints weight = 4247.193|
|-----------------------------------------------------------------------------|
r_work (start): 0.3596 rms_B_bonded: 2.15
r_work: 0.3491 rms_B_bonded: 2.29 restraints_weight: 0.5000
r_work: 0.3377 rms_B_bonded: 3.89 restraints_weight: 0.2500
r_work (final): 0.3377
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8125
moved from start:          0.4148

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.040   3315  Z= 0.243
  Angle     :  0.667   5.236   4509  Z= 0.376
  Chirality :  0.053   0.147    543
  Planarity :  0.003   0.012    558
  Dihedral  :  7.705  27.776    447
  Min Nonbonded Distance : 2.579

Molprobity Statistics.
  All-atom Clashscore : 8.45
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 11.03 %
    Favored  : 88.97 %
  Rotamer:
    Outliers :  5.29 %
    Allowed  : 19.58 %
    Favored  : 75.13 %
  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: -3.65 (0.33), residues: 399
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.77 (0.25), residues: 399

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.005   0.001   HIS C 239 
 PHE   0.012   0.002   PHE B 171 
 TYR   0.018   0.002   TYR A 197 
 ARG   0.002   0.000   ARG A 140 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02045 (   55)
  hydrogen bonds       : angle       5.30286 (  165)
  SS BOND              : bond        0.00186 (    3)
  SS BOND              : angle       0.80824 (    6)
  covalent geometry    : bond        0.00553 ( 3312)
  covalent geometry    : angle       0.66723 ( 4503)

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

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

  798 Ramachandran restraints generated.
    399 Oldfield, 0 Emsley, 399 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  798 Ramachandran restraints generated.
    399 Oldfield, 0 Emsley, 399 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  93 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 73
  time to evaluate  : 0.393 
Fit side-chains
REVERT: A  124 LYS cc_start: 0.6306 (mmtt) cc_final: 0.4887 (mttt)
REVERT: A  129 LYS cc_start: 0.8659 (mttt) cc_final: 0.8334 (mtpp)
REVERT: A  148 ASN cc_start: 0.8287 (t0) cc_final: 0.7913 (t0)
REVERT: A  181 LEU cc_start: 0.8389 (mp) cc_final: 0.8033 (mt)
REVERT: B  124 LYS cc_start: 0.9011 (mtpt) cc_final: 0.8774 (mttt)
REVERT: B  210 MET cc_start: 0.8827 (mtm) cc_final: 0.8599 (mtt)
REVERT: C  129 LYS cc_start: 0.8791 (mtpp) cc_final: 0.8428 (ttmt)
REVERT: C  140 ARG cc_start: 0.8434 (mtp85) cc_final: 0.8043 (mtt90)
REVERT: C  206 GLU cc_start: 0.8016 (tt0) cc_final: 0.6824 (tm-30)
  outliers start: 20
  outliers final: 19
  residues processed: 83
  average time/residue: 0.1693
  time to fit residues: 16.7346
Evaluate side-chains
  92 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 73
  time to evaluate  : 0.352 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  133 VAL
Chi-restraints excluded: chain A residue  144 LEU
Chi-restraints excluded: chain A residue  149 THR
Chi-restraints excluded: chain A residue  212 ASP
Chi-restraints excluded: chain A residue  229 GLN
Chi-restraints excluded: chain A residue  234 THR
Chi-restraints excluded: chain B residue  144 LEU
Chi-restraints excluded: chain B residue  153 THR
Chi-restraints excluded: chain B residue  192 MET
Chi-restraints excluded: chain B residue  229 GLN
Chi-restraints excluded: chain C residue  184 ILE
Chi-restraints excluded: chain C residue  192 MET
Chi-restraints excluded: chain C residue  207 MET
Chi-restraints excluded: chain C residue  227 MET
Chi-restraints excluded: chain C residue  228 MET
Chi-restraints excluded: chain C residue  229 GLN
Chi-restraints excluded: chain C residue  234 THR
Chi-restraints excluded: chain C residue  244 SER
Chi-restraints excluded: chain C residue  247 ARG
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 39
   random chunks:
   chunk 21 optimal weight:    7.9990
   chunk 20 optimal weight:    0.9990
   chunk 33 optimal weight:    2.9990
   chunk 1 optimal weight:    0.5980
   chunk 3 optimal weight:    0.2980
   chunk 26 optimal weight:    6.9990
   chunk 27 optimal weight:    3.9990
   chunk 11 optimal weight:    0.0570
   chunk 36 optimal weight:    4.9990
   chunk 24 optimal weight:    0.9980
   chunk 15 optimal weight:    0.8980
   overall best weight:    0.5698

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

Flipped N/Q/H residues before XYZ refinement:
** B 239 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 242 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 229 GLN
** C 239 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 242 GLN ** 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 = 0.3998 r_free = 0.3998 target = 0.130519 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3802 r_free = 0.3802 target = 0.112243 restraints weight = 3983.617|
|-----------------------------------------------------------------------------|
r_work (start): 0.3818 rms_B_bonded: 2.14
r_work: 0.3720 rms_B_bonded: 2.22 restraints_weight: 0.5000
r_work: 0.3605 rms_B_bonded: 3.84 restraints_weight: 0.2500
r_work (final): 0.3605
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7970
moved from start:          0.4468

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.021   3315  Z= 0.099
  Angle     :  0.572   5.429   4509  Z= 0.323
  Chirality :  0.051   0.149    543
  Planarity :  0.002   0.009    558
  Dihedral  :  6.937  26.118    447
  Min Nonbonded Distance : 2.592

Molprobity Statistics.
  All-atom Clashscore : 7.83
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.77 %
    Favored  : 91.23 %
  Rotamer:
    Outliers :  3.70 %
    Allowed  : 21.43 %
    Favored  : 74.87 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -3.35 (0.34), residues: 399
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.54 (0.26), residues: 399

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.003   0.001   HIS B 222 
 PHE   0.009   0.001   PHE B 171 
 TYR   0.011   0.001   TYR B 211 
 ARG   0.003   0.000   ARG A 140 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.01676 (   55)
  hydrogen bonds       : angle       5.24997 (  165)
  SS BOND              : bond        0.00214 (    3)
  SS BOND              : angle       0.31862 (    6)
  covalent geometry    : bond        0.00215 ( 3312)
  covalent geometry    : angle       0.57184 ( 4503)

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

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

  798 Ramachandran restraints generated.
    399 Oldfield, 0 Emsley, 399 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  798 Ramachandran restraints generated.
    399 Oldfield, 0 Emsley, 399 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  86 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 72
  time to evaluate  : 0.380 
Fit side-chains
REVERT: A  124 LYS cc_start: 0.6578 (mmtt) cc_final: 0.5354 (mttt)
REVERT: A  148 ASN cc_start: 0.8128 (t0) cc_final: 0.7896 (t0)
REVERT: A  181 LEU cc_start: 0.8284 (mp) cc_final: 0.7901 (mt)
REVERT: B  124 LYS cc_start: 0.8886 (mtpt) cc_final: 0.8656 (mttt)
REVERT: B  210 MET cc_start: 0.8739 (mtm) cc_final: 0.8499 (mtt)
REVERT: B  229 GLN cc_start: 0.8760 (OUTLIER) cc_final: 0.8418 (mp10)
REVERT: C  140 ARG cc_start: 0.8352 (mtp85) cc_final: 0.7116 (mmt180)
REVERT: C  184 ILE cc_start: 0.6238 (OUTLIER) cc_final: 0.5996 (mp)
REVERT: C  206 GLU cc_start: 0.7910 (tt0) cc_final: 0.6896 (tm-30)
  outliers start: 14
  outliers final: 8
  residues processed: 78
  average time/residue: 0.1675
  time to fit residues: 15.6910
Evaluate side-chains
  83 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 73
  time to evaluate  : 0.392 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  144 LEU
Chi-restraints excluded: chain A residue  212 ASP
Chi-restraints excluded: chain A residue  234 THR
Chi-restraints excluded: chain B residue  144 LEU
Chi-restraints excluded: chain B residue  153 THR
Chi-restraints excluded: chain B residue  192 MET
Chi-restraints excluded: chain B residue  229 GLN
Chi-restraints excluded: chain C residue  184 ILE
Chi-restraints excluded: chain C residue  229 GLN
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:    6.9990
   chunk 36 optimal weight:    0.0170
   chunk 3 optimal weight:    0.9990
   chunk 13 optimal weight:    8.9990
   chunk 0 optimal weight:    0.6980
   chunk 30 optimal weight:    0.4980
   chunk 38 optimal weight:    0.8980
   chunk 7 optimal weight:    5.9990
   chunk 35 optimal weight:    0.8980
   chunk 23 optimal weight:    1.9990
   chunk 19 optimal weight:    9.9990
   overall best weight:    0.6018

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

Flipped N/Q/H residues before XYZ refinement:
** B 239 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 242 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 239 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 242 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4001 r_free = 0.4001 target = 0.131224 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3803 r_free = 0.3803 target = 0.112623 restraints weight = 4016.939|
|-----------------------------------------------------------------------------|
r_work (start): 0.3819 rms_B_bonded: 2.20
r_work: 0.3718 rms_B_bonded: 2.29 restraints_weight: 0.5000
r_work: 0.3604 rms_B_bonded: 3.93 restraints_weight: 0.2500
r_work (final): 0.3604
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7955
moved from start:          0.4545

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.021   3315  Z= 0.092
  Angle     :  0.553   5.711   4509  Z= 0.313
  Chirality :  0.051   0.148    543
  Planarity :  0.002   0.010    558
  Dihedral  :  6.799  24.619    447
  Min Nonbonded Distance : 2.608

Molprobity Statistics.
  All-atom Clashscore : 7.22
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.27 %
    Favored  : 90.73 %
  Rotamer:
    Outliers :  2.65 %
    Allowed  : 22.49 %
    Favored  : 74.87 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -3.23 (0.35), residues: 399
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.45 (0.27), residues: 399

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.002   0.001   HIS B 222 
 PHE   0.007   0.001   PHE B 171 
 TYR   0.011   0.001   TYR C 211 
 ARG   0.003   0.000   ARG A 140 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.01596 (   55)
  hydrogen bonds       : angle       5.11061 (  165)
  SS BOND              : bond        0.00201 (    3)
  SS BOND              : angle       0.32402 (    6)
  covalent geometry    : bond        0.00201 ( 3312)
  covalent geometry    : angle       0.55336 ( 4503)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2120.41 seconds
wall clock time: 37 minutes 17.88 seconds (2237.88 seconds total)