Starting phenix.real_space_refine
on Thu Mar  6 01:04:07 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/5vrf_8728/03_2025/5vrf_8728.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/5vrf_8728/03_2025/5vrf_8728.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=4.1
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/5vrf_8728/03_2025/5vrf_8728.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/5vrf_8728/03_2025/5vrf_8728.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/5vrf_8728/03_2025/5vrf_8728.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/5vrf_8728/03_2025/5vrf_8728.cif"
  }
  resolution = 4.1
  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=   0.001 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: 5
    Type Number    sf(0)   Gaussians
     Zn      8      6.06       5
     S       6      5.16       5
     C    2828      2.51       5
     N     736      2.21       5
     O     800      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model
  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib"
  Total number of atoms: 4378
  Number of models: 1
  Model: ""
    Number of chains: 4
    Chain: "B"
      Number of atoms: 2185
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 282, 2185
          Classifications: {'peptide': 282}
          Link IDs: {'PTRANS': 6, 'TRANS': 275}
    Chain: "A"
      Number of atoms: 2185
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 282, 2185
          Classifications: {'peptide': 282}
          Link IDs: {'PTRANS': 6, 'TRANS': 275}
    Chain: "B"
      Number of atoms: 4
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 4, 4
          Unusual residues: {' ZN': 4}
          Classifications: {'undetermined': 4}
          Link IDs: {None: 3}
    Chain: "A"
      Number of atoms: 4
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 4, 4
          Unusual residues: {' ZN': 4}
          Classifications: {'undetermined': 4}
          Link IDs: {None: 3}
  Time building chain proxies: 3.52, per 1000 atoms: 0.80
  Number of scatterers: 4378
  At special positions: 0
  Unit cell: (102.72, 93.09, 93.09, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     Zn      8     29.99
     S       6     16.00
     O     800      8.00
     N     736      7.00
     C    2828      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  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: 1.09
  Conformation dependent library (CDL) restraints added in 565.8 milliseconds
  
  Dynamic metal coordination
    Zn2+ tetrahedral coordination
      pdb="  ZN A 301 "
        pdb="ZN    ZN A 301 " - pdb=" NE2 HIS A 155 "
      pdb="  ZN A 302 "
        pdb="ZN    ZN A 302 " - pdb=" ND1 HIS A  73 "
        pdb="ZN    ZN A 302 " - pdb=" NE2 HIS A  77 "
      pdb="  ZN A 303 "
        pdb="ZN    ZN A 303 " - pdb=" NE2 HIS B 263 "
        pdb="ZN    ZN A 303 " - pdb=" NE2 HIS A 285 "
      pdb="  ZN A 304 "
        pdb="ZN    ZN A 304 " - pdb=" NE2 HIS A 234 "
        pdb="ZN    ZN A 304 " - pdb=" ND1 HIS A 250 "
      pdb="  ZN B 301 "
        pdb="ZN    ZN B 301 " - pdb=" NE2 HIS B 155 "
      pdb="  ZN B 302 "
        pdb="ZN    ZN B 302 " - pdb=" NE2 HIS B  77 "
        pdb="ZN    ZN B 302 " - pdb=" ND1 HIS B  73 "
      pdb="  ZN B 303 "
        pdb="ZN    ZN B 303 " - pdb=" NE2 HIS A 263 "
        pdb="ZN    ZN B 303 " - pdb=" NE2 HIS B 285 "
      pdb="  ZN B 304 "
        pdb="ZN    ZN B 304 " - pdb=" NE2 HIS B 234 "
        pdb="ZN    ZN B 304 " - pdb=" ND1 HIS B 250 "


  1120 Ramachandran restraints generated.
    560 Oldfield, 0 Emsley, 560 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1068

  Finding SS restraints...
    Secondary structure from input PDB file:
      16 helices and 2 sheets defined
      73.8% alpha, 8.5% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.34
  Creating SS restraints...
    Processing helix  chain 'B' and resid 9 through 37
      removed outlier: 3.677A  pdb=" N   LEU B  13 " --> pdb=" O   PHE B   9 " (cutoff:3.500A)
      removed outlier: 3.917A  pdb=" N   LEU B  34 " --> pdb=" O   LEU B  30 " (cutoff:3.500A)
      removed outlier: 4.165A  pdb=" N   TYR B  35 " --> pdb=" O   LEU B  31 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 38 through 66
      removed outlier: 3.659A  pdb=" N   ASP B  47 " --> pdb=" O   ALA B  43 " (cutoff:3.500A)
      removed outlier: 3.541A  pdb=" N   SER B  55 " --> pdb=" O   ASP B  51 " (cutoff:3.500A)
      removed outlier: 3.863A  pdb=" N   ILE B  66 " --> pdb=" O   ILE B  62 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 79 through 109
      removed outlier: 3.880A  pdb=" N   LEU B  83 " --> pdb=" O   LYS B  79 " (cutoff:3.500A)
      removed outlier: 3.705A  pdb=" N   PHE B  91 " --> pdb=" O   ALA B  87 " (cutoff:3.500A)
      removed outlier: 4.196A  pdb=" N   LEU B  98 " --> pdb=" O   GLY B  94 " (cutoff:3.500A)
      removed outlier: 3.739A  pdb=" N   ASN B 109 " --> pdb=" O   GLU B 105 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 115 through 142
      removed outlier: 4.469A  pdb=" N   VAL B 121 " --> pdb=" O   THR B 117 " (cutoff:3.500A)
      removed outlier: 3.849A  pdb=" N   VAL B 122 " --> pdb=" O   LEU B 118 " (cutoff:3.500A)
      removed outlier: 4.417A  pdb=" N   SER B 123 " --> pdb=" O   GLY B 119 " (cutoff:3.500A)
      removed outlier: 3.697A  pdb=" N   ALA B 142 " --> pdb=" O   LYS B 138 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 149 through 174
      removed outlier: 3.882A  pdb=" N   SER B 153 " --> pdb=" O   VAL B 149 " (cutoff:3.500A)
      removed outlier: 3.978A  pdb=" N   PHE B 161 " --> pdb=" O   LYS B 157 " (cutoff:3.500A)
      removed outlier: 3.528A  pdb=" N   VAL B 166 " --> pdb=" O   LEU B 162 " (cutoff:3.500A)
      removed outlier: 3.747A  pdb=" N   LEU B 167 " --> pdb=" O   ASN B 163 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 178 through 208
      removed outlier: 4.047A  pdb=" N   GLY B 182 " --> pdb=" O   TRP B 178 " (cutoff:3.500A)
      removed outlier: 3.514A  pdb=" N   ALA B 185 " --> pdb=" O   ASP B 181 " (cutoff:3.500A)
      removed outlier: 4.034A  pdb=" N   VAL B 186 " --> pdb=" O   GLY B 182 " (cutoff:3.500A)
      removed outlier: 4.244A  pdb=" N   GLN B 205 " --> pdb=" O   TYR B 201 " (cutoff:3.500A)
      removed outlier: 4.253A  pdb=" N   ALA B 206 " --> pdb=" O   ARG B 202 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 213 through 226
      removed outlier: 3.816A  pdb=" N   GLU B 226 " --> pdb=" O   LEU B 222 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 258 through 277
    Processing helix  chain 'A' and resid 9 through 37
      removed outlier: 3.678A  pdb=" N   LEU A  13 " --> pdb=" O   PHE A   9 " (cutoff:3.500A)
      removed outlier: 3.918A  pdb=" N   LEU A  34 " --> pdb=" O   LEU A  30 " (cutoff:3.500A)
      removed outlier: 4.164A  pdb=" N   TYR A  35 " --> pdb=" O   LEU A  31 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 38 through 66
      removed outlier: 3.658A  pdb=" N   ASP A  47 " --> pdb=" O   ALA A  43 " (cutoff:3.500A)
      removed outlier: 3.541A  pdb=" N   SER A  55 " --> pdb=" O   ASP A  51 " (cutoff:3.500A)
      removed outlier: 3.863A  pdb=" N   ILE A  66 " --> pdb=" O   ILE A  62 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 79 through 109
      removed outlier: 3.880A  pdb=" N   LEU A  83 " --> pdb=" O   LYS A  79 " (cutoff:3.500A)
      removed outlier: 3.705A  pdb=" N   PHE A  91 " --> pdb=" O   ALA A  87 " (cutoff:3.500A)
      removed outlier: 4.196A  pdb=" N   LEU A  98 " --> pdb=" O   GLY A  94 " (cutoff:3.500A)
      removed outlier: 3.740A  pdb=" N   ASN A 109 " --> pdb=" O   GLU A 105 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 115 through 142
      removed outlier: 4.469A  pdb=" N   VAL A 121 " --> pdb=" O   THR A 117 " (cutoff:3.500A)
      removed outlier: 3.849A  pdb=" N   VAL A 122 " --> pdb=" O   LEU A 118 " (cutoff:3.500A)
      removed outlier: 4.416A  pdb=" N   SER A 123 " --> pdb=" O   GLY A 119 " (cutoff:3.500A)
      removed outlier: 3.697A  pdb=" N   ALA A 142 " --> pdb=" O   LYS A 138 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 149 through 174
      removed outlier: 3.881A  pdb=" N   SER A 153 " --> pdb=" O   VAL A 149 " (cutoff:3.500A)
      removed outlier: 3.978A  pdb=" N   PHE A 161 " --> pdb=" O   LYS A 157 " (cutoff:3.500A)
      removed outlier: 3.528A  pdb=" N   VAL A 166 " --> pdb=" O   LEU A 162 " (cutoff:3.500A)
      removed outlier: 3.747A  pdb=" N   LEU A 167 " --> pdb=" O   ASN A 163 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 178 through 208
      removed outlier: 4.047A  pdb=" N   GLY A 182 " --> pdb=" O   TRP A 178 " (cutoff:3.500A)
      removed outlier: 3.514A  pdb=" N   ALA A 185 " --> pdb=" O   ASP A 181 " (cutoff:3.500A)
      removed outlier: 4.034A  pdb=" N   VAL A 186 " --> pdb=" O   GLY A 182 " (cutoff:3.500A)
      removed outlier: 4.244A  pdb=" N   GLN A 205 " --> pdb=" O   TYR A 201 " (cutoff:3.500A)
      removed outlier: 4.253A  pdb=" N   ALA A 206 " --> pdb=" O   ARG A 202 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 213 through 226
      removed outlier: 3.817A  pdb=" N   GLU A 226 " --> pdb=" O   LEU A 222 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 258 through 277
    Processing sheet with id=AA1, first strand: chain 'B' and resid 232 through 241
      removed outlier: 5.933A  pdb=" N   LEU B 233 " --> pdb=" O   GLU B 252 " (cutoff:3.500A)
      removed outlier: 7.184A  pdb=" N   GLU B 252 " --> pdb=" O   LEU B 233 " (cutoff:3.500A)
      removed outlier: 4.183A  pdb=" N   ASP B 235 " --> pdb=" O   HIS B 250 " (cutoff:3.500A)
      removed outlier: 7.306A  pdb=" N   VAL B 245 " --> pdb=" O   GLU B 281 " (cutoff:3.500A)
      removed outlier: 8.676A  pdb=" N   ILE B 283 " --> pdb=" O   VAL B 245 " (cutoff:3.500A)
      removed outlier: 6.828A  pdb=" N   ILE B 247 " --> pdb=" O   ILE B 283 " (cutoff:3.500A)
      removed outlier: 8.207A  pdb=" N   HIS B 285 " --> pdb=" O   ILE B 247 " (cutoff:3.500A)
      removed outlier: 6.437A  pdb=" N   PHE B 249 " --> pdb=" O   HIS B 285 " (cutoff:3.500A)
      removed outlier: 7.416A  pdb=" N   ASP B 287 " --> pdb=" O   PHE B 249 " (cutoff:3.500A)
      removed outlier: 5.831A  pdb=" N   LEU B 251 " --> pdb=" O   ASP B 287 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 232 through 241
      removed outlier: 5.933A  pdb=" N   LEU A 233 " --> pdb=" O   GLU A 252 " (cutoff:3.500A)
      removed outlier: 7.184A  pdb=" N   GLU A 252 " --> pdb=" O   LEU A 233 " (cutoff:3.500A)
      removed outlier: 4.182A  pdb=" N   ASP A 235 " --> pdb=" O   HIS A 250 " (cutoff:3.500A)
      removed outlier: 7.306A  pdb=" N   VAL A 245 " --> pdb=" O   GLU A 281 " (cutoff:3.500A)
      removed outlier: 8.677A  pdb=" N   ILE A 283 " --> pdb=" O   VAL A 245 " (cutoff:3.500A)
      removed outlier: 6.828A  pdb=" N   ILE A 247 " --> pdb=" O   ILE A 283 " (cutoff:3.500A)
      removed outlier: 8.208A  pdb=" N   HIS A 285 " --> pdb=" O   ILE A 247 " (cutoff:3.500A)
      removed outlier: 6.437A  pdb=" N   PHE A 249 " --> pdb=" O   HIS A 285 " (cutoff:3.500A)
      removed outlier: 7.417A  pdb=" N   ASP A 287 " --> pdb=" O   PHE A 249 " (cutoff:3.500A)
      removed outlier: 5.831A  pdb=" N   LEU A 251 " --> pdb=" O   ASP A 287 " (cutoff:3.500A)

    318 hydrogen bonds defined for protein.
    948 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 1.18

  Time building geometry restraints manager: 1.29 seconds

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

  Histogram of bond lengths:
        1.22 -     1.33: 1251
        1.33 -     1.45: 742
        1.45 -     1.57: 2455
        1.57 -     1.68: 0
        1.68 -     1.80: 10
  Bond restraints: 4458
  Sorted by residual:
  bond pdb=" CZ  TYR B  75 "
       pdb=" OH  TYR B  75 "
    ideal  model  delta    sigma   weight residual
    1.376  1.264  0.112 2.10e-02 2.27e+03 2.86e+01
  bond pdb=" CZ  TYR A  75 "
       pdb=" OH  TYR A  75 "
    ideal  model  delta    sigma   weight residual
    1.376  1.264  0.112 2.10e-02 2.27e+03 2.85e+01
  bond pdb=" CD1 TYR A  75 "
       pdb=" CE1 TYR A  75 "
    ideal  model  delta    sigma   weight residual
    1.382  1.244  0.138 3.00e-02 1.11e+03 2.12e+01
  bond pdb=" CD1 TYR B  75 "
       pdb=" CE1 TYR B  75 "
    ideal  model  delta    sigma   weight residual
    1.382  1.245  0.137 3.00e-02 1.11e+03 2.10e+01
  bond pdb=" CD2 TYR B  75 "
       pdb=" CE2 TYR B  75 "
    ideal  model  delta    sigma   weight residual
    1.382  1.256  0.126 3.00e-02 1.11e+03 1.78e+01
  ... (remaining 4453 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.04: 5614
        2.04 -     4.09: 323
        4.09 -     6.13: 94
        6.13 -     8.17: 35
        8.17 -    10.22: 8
  Bond angle restraints: 6074
  Sorted by residual:
  angle pdb=" NE  ARG B 239 "
        pdb=" CZ  ARG B 239 "
        pdb=" NH1 ARG B 239 "
      ideal   model   delta    sigma   weight residual
     121.50  114.36    7.14 1.00e+00 1.00e+00 5.09e+01
  angle pdb=" NE  ARG A 239 "
        pdb=" CZ  ARG A 239 "
        pdb=" NH1 ARG A 239 "
      ideal   model   delta    sigma   weight residual
     121.50  114.40    7.10 1.00e+00 1.00e+00 5.05e+01
  angle pdb=" NE  ARG B 239 "
        pdb=" CZ  ARG B 239 "
        pdb=" NH2 ARG B 239 "
      ideal   model   delta    sigma   weight residual
     119.20  124.11   -4.91 9.00e-01 1.23e+00 2.97e+01
  angle pdb=" NE  ARG A 239 "
        pdb=" CZ  ARG A 239 "
        pdb=" NH2 ARG A 239 "
      ideal   model   delta    sigma   weight residual
     119.20  124.08   -4.88 9.00e-01 1.23e+00 2.94e+01
  angle pdb=" NE  ARG B  74 "
        pdb=" CZ  ARG B  74 "
        pdb=" NH2 ARG B  74 "
      ideal   model   delta    sigma   weight residual
     119.20  122.74   -3.54 9.00e-01 1.23e+00 1.54e+01
  ... (remaining 6069 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    14.46: 2475
       14.46 -    28.91: 99
       28.91 -    43.37: 46
       43.37 -    57.82: 0
       57.82 -    72.28: 2
  Dihedral angle restraints: 2622
    sinusoidal: 974
      harmonic: 1648
  Sorted by residual:
  dihedral pdb=" CA  PHE B 246 "
           pdb=" C   PHE B 246 "
           pdb=" N   ILE B 247 "
           pdb=" CA  ILE B 247 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -157.31  -22.69     0      5.00e+00 4.00e-02 2.06e+01
  dihedral pdb=" CA  PHE A 246 "
           pdb=" C   PHE A 246 "
           pdb=" N   ILE A 247 "
           pdb=" CA  ILE A 247 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -157.33  -22.67     0      5.00e+00 4.00e-02 2.06e+01
  dihedral pdb=" CA  SER A 203 "
           pdb=" C   SER A 203 "
           pdb=" N   ILE A 204 "
           pdb=" CA  ILE A 204 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -162.03  -17.97     0      5.00e+00 4.00e-02 1.29e+01
  ... (remaining 2619 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.040: 434
       0.040 -    0.079: 188
       0.079 -    0.119: 78
       0.119 -    0.159: 21
       0.159 -    0.198: 9
  Chirality restraints: 730
  Sorted by residual:
  chirality pdb=" CA  GLU A  81 "
            pdb=" N   GLU A  81 "
            pdb=" C   GLU A  81 "
            pdb=" CB  GLU A  81 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.31    0.20 2.00e-01 2.50e+01 9.83e-01
  chirality pdb=" CA  GLU B  81 "
            pdb=" N   GLU B  81 "
            pdb=" C   GLU B  81 "
            pdb=" CB  GLU B  81 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.31    0.20 2.00e-01 2.50e+01 9.76e-01
  chirality pdb=" CB  ILE A 283 "
            pdb=" CA  ILE A 283 "
            pdb=" CG1 ILE A 283 "
            pdb=" CG2 ILE A 283 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.45    0.19 2.00e-01 2.50e+01 9.23e-01
  ... (remaining 727 not shown)

  Planarity restraints: 760
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TYR A  75 "    0.039 2.00e-02 2.50e+03   2.21e-02 9.75e+00
        pdb=" CG  TYR A  75 "   -0.015 2.00e-02 2.50e+03
        pdb=" CD1 TYR A  75 "   -0.022 2.00e-02 2.50e+03
        pdb=" CD2 TYR A  75 "   -0.020 2.00e-02 2.50e+03
        pdb=" CE1 TYR A  75 "   -0.000 2.00e-02 2.50e+03
        pdb=" CE2 TYR A  75 "    0.002 2.00e-02 2.50e+03
        pdb=" CZ  TYR A  75 "   -0.016 2.00e-02 2.50e+03
        pdb=" OH  TYR A  75 "    0.032 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TYR B  75 "   -0.039 2.00e-02 2.50e+03   2.19e-02 9.58e+00
        pdb=" CG  TYR B  75 "    0.015 2.00e-02 2.50e+03
        pdb=" CD1 TYR B  75 "    0.022 2.00e-02 2.50e+03
        pdb=" CD2 TYR B  75 "    0.019 2.00e-02 2.50e+03
        pdb=" CE1 TYR B  75 "    0.000 2.00e-02 2.50e+03
        pdb=" CE2 TYR B  75 "   -0.001 2.00e-02 2.50e+03
        pdb=" CZ  TYR B  75 "    0.016 2.00e-02 2.50e+03
        pdb=" OH  TYR B  75 "   -0.032 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ALA B 132 "    0.014 2.00e-02 2.50e+03   2.80e-02 7.85e+00
        pdb=" C   ALA B 132 "   -0.048 2.00e-02 2.50e+03
        pdb=" O   ALA B 132 "    0.018 2.00e-02 2.50e+03
        pdb=" N   LEU B 133 "    0.016 2.00e-02 2.50e+03
  ... (remaining 757 not shown)

  Histogram of nonbonded interaction distances:
        1.99 -     2.58: 60
        2.58 -     3.16: 3713
        3.16 -     3.74: 6983
        3.74 -     4.32: 8899
        4.32 -     4.90: 14028
  Nonbonded interactions: 33683
  Sorted by model distance:
  nonbonded pdb=" OD2 ASP A 287 "
            pdb="ZN    ZN A 304 "
     model   vdw
     1.994 2.230
  nonbonded pdb=" OD2 ASP B 287 "
            pdb="ZN    ZN B 304 "
     model   vdw
     2.020 2.230
  nonbonded pdb=" OD2 ASP A  47 "
            pdb="ZN    ZN A 301 "
     model   vdw
     2.050 2.230
  nonbonded pdb=" OD1 ASP B 287 "
            pdb="ZN    ZN B 303 "
     model   vdw
     2.053 2.230
  nonbonded pdb=" OD2 ASP B  47 "
            pdb="ZN    ZN B 301 "
     model   vdw
     2.067 2.230
  ... (remaining 33678 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.02
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'B'
}

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 group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             0.200
  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:          0.200
  Check model and map are aligned:         0.030
  Set scattering table:                    0.050
  Process input model:                     16.210
  Find NCS groups from input model:        0.080
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:3.280
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   20.080
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8239
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      :  0.011   0.138   4458  Z= 0.760
  Angle     :  1.277  10.217   6074  Z= 0.650
  Chirality :  0.056   0.198    730
  Planarity :  0.008   0.058    760
  Dihedral  : 10.376  72.280   1554
  Min Nonbonded Distance : 1.994

Molprobity Statistics.
  All-atom Clashscore : 8.85
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.50 %
    Favored  : 97.50 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  4.17 %
    Favored  : 95.83 %
  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: -4.10 (0.25), residues: 560
  helix: -2.45 (0.18), residues: 376
  sheet: -0.79 (0.68), residues: 50
  loop : -3.64 (0.37), residues: 134

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.003   TRP B  33 
 HIS   0.013   0.003   HIS B 234 
 PHE   0.032   0.005   PHE B  97 
 TYR   0.039   0.006   TYR A  75 
 ARG   0.008   0.001   ARG B 237 

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

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

  1120 Ramachandran restraints generated.
    560 Oldfield, 0 Emsley, 560 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1120 Ramachandran restraints generated.
    560 Oldfield, 0 Emsley, 560 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  175 residues out of total 456 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 175
  time to evaluate  : 0.432 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  105 GLU cc_start: 0.8605 (tm-30) cc_final: 0.8382 (tp30)
REVERT: B  194 GLN cc_start: 0.8654 (tm-30) cc_final: 0.8355 (tm-30)
REVERT: B  198 ASP cc_start: 0.8854 (t0) cc_final: 0.8515 (t0)
REVERT: A   81 GLU cc_start: 0.9060 (pp20) cc_final: 0.8507 (pp20)
REVERT: A  105 GLU cc_start: 0.8651 (tm-30) cc_final: 0.8321 (tm-30)
REVERT: A  198 ASP cc_start: 0.8769 (t0) cc_final: 0.8389 (t0)
  outliers start: 0
  outliers final: 0
  residues processed: 175
  average time/residue: 0.2563
  time to fit residues: 51.5964
Evaluate side-chains
  90 residues out of total 456 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 90
  time to evaluate  : 0.476 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 56
   random chunks:
   chunk 47 optimal weight:    2.9990
   chunk 42 optimal weight:    6.9990
   chunk 23 optimal weight:    7.9990
   chunk 14 optimal weight:    8.9990
   chunk 28 optimal weight:   10.0000
   chunk 22 optimal weight:    7.9990
   chunk 43 optimal weight:    1.9990
   chunk 16 optimal weight:    0.8980
   chunk 26 optimal weight:    8.9990
   chunk 32 optimal weight:    0.7980
   chunk 50 optimal weight:   20.0000
   overall best weight:    2.7386

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

Flipped N/Q/H residues before XYZ refinement:
B  71 HIS
B 115 ASN
** B 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 205 GLN
A  71 HIS
A 115 ASN
A 195 GLN
A 205 GLN

Total number of N/Q/H flips: 7

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3583 r_free = 0.3583 target = 0.095152 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3057 r_free = 0.3057 target = 0.067516 restraints weight = 12057.274|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3096 r_free = 0.3096 target = 0.069272 restraints weight = 7072.554|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3121 r_free = 0.3121 target = 0.070412 restraints weight = 4986.848|
|-----------------------------------------------------------------------------|
r_work (final): 0.3090
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8389
moved from start:          0.4383

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.032   4458  Z= 0.265
  Angle     :  0.648   7.140   6074  Z= 0.340
  Chirality :  0.038   0.177    730
  Planarity :  0.005   0.045    760
  Dihedral  :  4.535  15.845    606
  Min Nonbonded Distance : 2.023

Molprobity Statistics.
  All-atom Clashscore : 11.01
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.32 %
    Favored  : 97.68 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  5.04 %
    Favored  : 94.96 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.91 (0.32), residues: 560
  helix:  0.25 (0.23), residues: 394
  sheet: -0.97 (0.60), residues: 50
  loop : -3.18 (0.49), residues: 116

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.023   0.002   TRP B 177 
 HIS   0.004   0.001   HIS B 234 
 PHE   0.016   0.002   PHE A 249 
 TYR   0.029   0.002   TYR A 175 
 ARG   0.006   0.001   ARG B  16 

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

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

  1120 Ramachandran restraints generated.
    560 Oldfield, 0 Emsley, 560 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1120 Ramachandran restraints generated.
    560 Oldfield, 0 Emsley, 560 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  136 residues out of total 456 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 136
  time to evaluate  : 0.447 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   16 ARG cc_start: 0.8763 (ttp80) cc_final: 0.8518 (ttp80)
REVERT: B   24 THR cc_start: 0.9291 (p) cc_final: 0.9018 (p)
REVERT: B   27 THR cc_start: 0.9532 (m) cc_final: 0.9301 (p)
REVERT: B  105 GLU cc_start: 0.8335 (tm-30) cc_final: 0.8124 (tm-30)
REVERT: B  170 LEU cc_start: 0.9475 (tt) cc_final: 0.9261 (tp)
REVERT: B  198 ASP cc_start: 0.8887 (t0) cc_final: 0.8494 (t0)
REVERT: A   81 GLU cc_start: 0.9120 (pp20) cc_final: 0.8907 (pp20)
REVERT: A  105 GLU cc_start: 0.8534 (tm-30) cc_final: 0.8276 (tm-30)
REVERT: A  163 ASN cc_start: 0.9216 (t0) cc_final: 0.8757 (t0)
REVERT: A  198 ASP cc_start: 0.8961 (t0) cc_final: 0.8707 (t0)
REVERT: A  218 GLN cc_start: 0.8196 (tp-100) cc_final: 0.7763 (tm-30)
  outliers start: 0
  outliers final: 0
  residues processed: 136
  average time/residue: 0.1939
  time to fit residues: 31.9247
Evaluate side-chains
  100 residues out of total 456 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 100
  time to evaluate  : 0.468 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 56
   random chunks:
   chunk 9 optimal weight:    0.9990
   chunk 8 optimal weight:    0.9990
   chunk 41 optimal weight:    5.9990
   chunk 50 optimal weight:    3.9990
   chunk 51 optimal weight:    0.8980
   chunk 48 optimal weight:    3.9990
   chunk 11 optimal weight:    1.9990
   chunk 33 optimal weight:    0.9980
   chunk 29 optimal weight:    5.9990
   chunk 2 optimal weight:    0.8980
   chunk 12 optimal weight:    0.9990
   overall best weight:    0.9584

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

Flipped N/Q/H residues before XYZ refinement:
** B 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A  71 HIS
** A  88 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 195 GLN
A 234 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3628 r_free = 0.3628 target = 0.098101 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3066 r_free = 0.3066 target = 0.068179 restraints weight = 12155.841|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3105 r_free = 0.3105 target = 0.069970 restraints weight = 7058.449|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3131 r_free = 0.3131 target = 0.071146 restraints weight = 4998.428|
|-----------------------------------------------------------------------------|
r_work (final): 0.3104
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8350
moved from start:          0.5242

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.021   4458  Z= 0.163
  Angle     :  0.579   7.187   6074  Z= 0.286
  Chirality :  0.036   0.165    730
  Planarity :  0.003   0.034    760
  Dihedral  :  4.122  14.310    606
  Min Nonbonded Distance : 2.118

Molprobity Statistics.
  All-atom Clashscore : 7.83
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.61 %
    Favored  : 98.39 %
  Rotamer:
    Outliers :  0.22 %
    Allowed  :  3.73 %
    Favored  : 96.05 %
  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:  0.61 (0.34), residues: 560
  helix:  1.49 (0.25), residues: 388
  sheet: -0.10 (0.66), residues: 50
  loop : -3.01 (0.48), residues: 122

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP B 177 
 HIS   0.004   0.001   HIS A  77 
 PHE   0.010   0.001   PHE A 249 
 TYR   0.006   0.001   TYR A 175 
 ARG   0.005   0.001   ARG B  16 

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

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

  1120 Ramachandran restraints generated.
    560 Oldfield, 0 Emsley, 560 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1120 Ramachandran restraints generated.
    560 Oldfield, 0 Emsley, 560 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  128 residues out of total 456 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 127
  time to evaluate  : 0.510 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  170 LEU cc_start: 0.9399 (tt) cc_final: 0.9018 (tp)
REVERT: B  181 ASP cc_start: 0.8622 (t0) cc_final: 0.8409 (t0)
REVERT: A  156 TYR cc_start: 0.8545 (m-10) cc_final: 0.7253 (m-10)
REVERT: A  163 ASN cc_start: 0.9075 (t0) cc_final: 0.8598 (t0)
REVERT: A  198 ASP cc_start: 0.8864 (t0) cc_final: 0.8650 (t0)
  outliers start: 1
  outliers final: 0
  residues processed: 127
  average time/residue: 0.1649
  time to fit residues: 26.2120
Evaluate side-chains
  100 residues out of total 456 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 100
  time to evaluate  : 0.584 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 56
   random chunks:
   chunk 44 optimal weight:    0.9980
   chunk 31 optimal weight:    0.0170
   chunk 5 optimal weight:    2.9990
   chunk 45 optimal weight:    0.9990
   chunk 25 optimal weight:    9.9990
   chunk 32 optimal weight:    1.9990
   chunk 19 optimal weight:    2.9990
   chunk 23 optimal weight:    5.9990
   chunk 2 optimal weight:    0.8980
   chunk 28 optimal weight:   10.0000
   chunk 29 optimal weight:    8.9990
   overall best weight:    0.9822

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

Flipped N/Q/H residues before XYZ refinement:
B 163 ASN
A 286 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3629 r_free = 0.3629 target = 0.097528 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3096 r_free = 0.3096 target = 0.069298 restraints weight = 12348.929|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 42)----------------|
| r_work = 0.3134 r_free = 0.3134 target = 0.071083 restraints weight = 6945.066|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3158 r_free = 0.3158 target = 0.072233 restraints weight = 4837.217|
|-----------------------------------------------------------------------------|
r_work (final): 0.3130
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8312
moved from start:          0.5575

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.024   4458  Z= 0.167
  Angle     :  0.578   7.994   6074  Z= 0.283
  Chirality :  0.037   0.161    730
  Planarity :  0.003   0.035    760
  Dihedral  :  3.994  13.704    606
  Min Nonbonded Distance : 2.121

Molprobity Statistics.
  All-atom Clashscore : 7.71
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.79 %
    Favored  : 98.21 %
  Rotamer:
    Outliers :  0.22 %
    Allowed  :  4.61 %
    Favored  : 95.18 %
  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:  1.32 (0.35), residues: 560
  helix:  2.01 (0.25), residues: 386
  sheet:  0.24 (0.65), residues: 50
  loop : -2.67 (0.52), residues: 124

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP B 177 
 HIS   0.003   0.001   HIS A  77 
 PHE   0.011   0.001   PHE A 249 
 TYR   0.018   0.001   TYR B 156 
 ARG   0.011   0.001   ARG B  63 

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

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

  1120 Ramachandran restraints generated.
    560 Oldfield, 0 Emsley, 560 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1120 Ramachandran restraints generated.
    560 Oldfield, 0 Emsley, 560 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  118 residues out of total 456 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 117
  time to evaluate  : 0.493 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  105 GLU cc_start: 0.8569 (tm-30) cc_final: 0.8328 (tm-30)
REVERT: B  156 TYR cc_start: 0.8669 (m-10) cc_final: 0.6924 (m-10)
REVERT: B  170 LEU cc_start: 0.9367 (tt) cc_final: 0.9077 (tp)
REVERT: B  198 ASP cc_start: 0.8837 (t70) cc_final: 0.8608 (t0)
REVERT: A  163 ASN cc_start: 0.9038 (t0) cc_final: 0.8514 (t0)
  outliers start: 1
  outliers final: 0
  residues processed: 118
  average time/residue: 0.1657
  time to fit residues: 24.4481
Evaluate side-chains
  98 residues out of total 456 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 98
  time to evaluate  : 0.441 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 56
   random chunks:
   chunk 32 optimal weight:    3.9990
   chunk 21 optimal weight:    6.9990
   chunk 19 optimal weight:    1.9990
   chunk 11 optimal weight:    7.9990
   chunk 52 optimal weight:    2.9990
   chunk 43 optimal weight:    7.9990
   chunk 49 optimal weight:   10.0000
   chunk 22 optimal weight:    0.0970
   chunk 1 optimal weight:   10.0000
   chunk 26 optimal weight:    9.9990
   chunk 35 optimal weight:   10.0000
   overall best weight:    3.2186

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

Flipped N/Q/H residues before XYZ refinement:
B 163 ASN
** A 145 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 195 GLN
** A 286 GLN ** 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 = 0.3569 r_free = 0.3569 target = 0.094547 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.2993 r_free = 0.2993 target = 0.065139 restraints weight = 12464.154|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3030 r_free = 0.3030 target = 0.066853 restraints weight = 7413.445|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3053 r_free = 0.3053 target = 0.067938 restraints weight = 5339.704|
|-----------------------------------------------------------------------------|
r_work (final): 0.3030
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8449
moved from start:          0.5890

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.032   4458  Z= 0.281
  Angle     :  0.646   7.337   6074  Z= 0.328
  Chirality :  0.039   0.171    730
  Planarity :  0.004   0.041    760
  Dihedral  :  4.148  13.155    606
  Min Nonbonded Distance : 2.057

Molprobity Statistics.
  All-atom Clashscore : 10.10
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.79 %
    Favored  : 98.21 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.63 %
    Favored  : 97.37 %
  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:  1.42 (0.35), residues: 560
  helix:  2.02 (0.25), residues: 394
  sheet:  0.38 (0.66), residues: 50
  loop : -2.80 (0.53), residues: 116

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.023   0.002   TRP B 177 
 HIS   0.004   0.001   HIS A  73 
 PHE   0.013   0.002   PHE B 249 
 TYR   0.009   0.002   TYR B 156 
 ARG   0.005   0.001   ARG B  63 

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

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

  1120 Ramachandran restraints generated.
    560 Oldfield, 0 Emsley, 560 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1120 Ramachandran restraints generated.
    560 Oldfield, 0 Emsley, 560 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  113 residues out of total 456 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 113
  time to evaluate  : 0.459 
Fit side-chains
   revert: symmetry clash
REVERT: B  137 GLN cc_start: 0.8435 (tt0) cc_final: 0.7607 (tt0)
REVERT: B  152 ASP cc_start: 0.7554 (t0) cc_final: 0.5839 (t70)
REVERT: B  156 TYR cc_start: 0.8091 (m-10) cc_final: 0.7427 (m-10)
REVERT: B  170 LEU cc_start: 0.9543 (tt) cc_final: 0.9283 (tp)
REVERT: B  173 SER cc_start: 0.9167 (m) cc_final: 0.8867 (p)
REVERT: A   93 MET cc_start: 0.8813 (mmm) cc_final: 0.8513 (mmm)
REVERT: A  105 GLU cc_start: 0.8543 (tm-30) cc_final: 0.8306 (tm-30)
REVERT: A  137 GLN cc_start: 0.8811 (tt0) cc_final: 0.7388 (tt0)
REVERT: A  156 TYR cc_start: 0.8599 (m-10) cc_final: 0.7459 (m-10)
REVERT: A  198 ASP cc_start: 0.8775 (t70) cc_final: 0.8416 (t0)
  outliers start: 0
  outliers final: 0
  residues processed: 113
  average time/residue: 0.1770
  time to fit residues: 25.6585
Evaluate side-chains
  95 residues out of total 456 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 95
  time to evaluate  : 0.522 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 56
   random chunks:
   chunk 1 optimal weight:    9.9990
   chunk 21 optimal weight:    6.9990
   chunk 13 optimal weight:   10.0000
   chunk 19 optimal weight:    1.9990
   chunk 0 optimal weight:   10.0000
   chunk 24 optimal weight:    3.9990
   chunk 37 optimal weight:    1.9990
   chunk 15 optimal weight:    6.9990
   chunk 33 optimal weight:    5.9990
   chunk 22 optimal weight:    0.0980
   chunk 49 optimal weight:    6.9990
   overall best weight:    2.8188

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

Flipped N/Q/H residues before XYZ refinement:
B 163 ASN
** A  88 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 163 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3562 r_free = 0.3562 target = 0.094223 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.2993 r_free = 0.2993 target = 0.065402 restraints weight = 12179.663|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3028 r_free = 0.3028 target = 0.067062 restraints weight = 7194.555|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3047 r_free = 0.3047 target = 0.067953 restraints weight = 5190.359|
|-----------------------------------------------------------------------------|
r_work (final): 0.3027
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8443
moved from start:          0.6131

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.034   4458  Z= 0.252
  Angle     :  0.633   7.864   6074  Z= 0.318
  Chirality :  0.039   0.163    730
  Planarity :  0.004   0.039    760
  Dihedral  :  4.111  13.801    606
  Min Nonbonded Distance : 2.031

Molprobity Statistics.
  All-atom Clashscore : 11.35
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.50 %
    Favored  : 97.50 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  3.51 %
    Favored  : 96.49 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.64 (0.35), residues: 560
  helix:  2.23 (0.25), residues: 390
  sheet:  0.67 (0.68), residues: 50
  loop : -2.82 (0.52), residues: 120

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.002   TRP A 178 
 HIS   0.004   0.001   HIS A 234 
 PHE   0.012   0.001   PHE B 249 
 TYR   0.007   0.001   TYR B 175 
 ARG   0.004   0.001   ARG B  63 

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

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

  1120 Ramachandran restraints generated.
    560 Oldfield, 0 Emsley, 560 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1120 Ramachandran restraints generated.
    560 Oldfield, 0 Emsley, 560 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  113 residues out of total 456 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 113
  time to evaluate  : 0.538 
Fit side-chains
   revert: symmetry clash
REVERT: B   79 LYS cc_start: 0.8741 (ptmt) cc_final: 0.8397 (pttm)
REVERT: B  152 ASP cc_start: 0.7679 (t0) cc_final: 0.5546 (t70)
REVERT: B  156 TYR cc_start: 0.8166 (m-10) cc_final: 0.7550 (m-10)
REVERT: B  170 LEU cc_start: 0.9565 (tt) cc_final: 0.9319 (tp)
REVERT: B  173 SER cc_start: 0.9157 (m) cc_final: 0.8762 (p)
REVERT: B  181 ASP cc_start: 0.8708 (t0) cc_final: 0.8329 (t0)
REVERT: B  194 GLN cc_start: 0.8583 (tm-30) cc_final: 0.8297 (tm-30)
REVERT: B  195 GLN cc_start: 0.8826 (tt0) cc_final: 0.8506 (tt0)
REVERT: B  198 ASP cc_start: 0.8735 (t70) cc_final: 0.8521 (t0)
REVERT: A  105 GLU cc_start: 0.8579 (tm-30) cc_final: 0.8240 (tm-30)
REVERT: A  137 GLN cc_start: 0.8379 (tt0) cc_final: 0.7304 (tt0)
REVERT: A  198 ASP cc_start: 0.8770 (t70) cc_final: 0.8427 (t0)
REVERT: A  214 GLU cc_start: 0.8214 (tp30) cc_final: 0.6805 (tp30)
  outliers start: 0
  outliers final: 0
  residues processed: 113
  average time/residue: 0.2009
  time to fit residues: 28.9508
Evaluate side-chains
  95 residues out of total 456 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 95
  time to evaluate  : 0.513 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 56
   random chunks:
   chunk 51 optimal weight:    1.9990
   chunk 14 optimal weight:   20.0000
   chunk 48 optimal weight:    4.9990
   chunk 20 optimal weight:    6.9990
   chunk 46 optimal weight:    2.9990
   chunk 49 optimal weight:    8.9990
   chunk 22 optimal weight:    0.0570
   chunk 40 optimal weight:    0.9980
   chunk 6 optimal weight:    7.9990
   chunk 47 optimal weight:    0.8980
   chunk 0 optimal weight:   10.0000
   overall best weight:    1.3902

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

Flipped N/Q/H residues before XYZ refinement:
B  88 GLN
B 163 ASN
A 163 ASN
** A 218 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3603 r_free = 0.3603 target = 0.096311 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3033 r_free = 0.3033 target = 0.067121 restraints weight = 12244.792|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.3071 r_free = 0.3071 target = 0.068951 restraints weight = 6947.154|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.3093 r_free = 0.3093 target = 0.070039 restraints weight = 4888.224|
|-----------------------------------------------------------------------------|
r_work (final): 0.3076
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8381
moved from start:          0.6280

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.026   4458  Z= 0.187
  Angle     :  0.621   6.946   6074  Z= 0.303
  Chirality :  0.038   0.159    730
  Planarity :  0.003   0.034    760
  Dihedral  :  3.987  13.664    606
  Min Nonbonded Distance : 2.007

Molprobity Statistics.
  All-atom Clashscore : 9.08
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.96 %
    Favored  : 98.04 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.19 %
    Favored  : 97.81 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.82 (0.36), residues: 560
  helix:  2.39 (0.25), residues: 392
  sheet:  0.75 (0.68), residues: 50
  loop : -2.93 (0.52), residues: 118

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP A 178 
 HIS   0.003   0.001   HIS A 234 
 PHE   0.013   0.001   PHE A 101 
 TYR   0.009   0.001   TYR A 175 
 ARG   0.003   0.000   ARG B  16 

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

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

  1120 Ramachandran restraints generated.
    560 Oldfield, 0 Emsley, 560 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1120 Ramachandran restraints generated.
    560 Oldfield, 0 Emsley, 560 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  119 residues out of total 456 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 119
  time to evaluate  : 1.134 
Fit side-chains
   revert: symmetry clash
REVERT: B   79 LYS cc_start: 0.8807 (ptmt) cc_final: 0.8215 (pttm)
REVERT: B  137 GLN cc_start: 0.8420 (tt0) cc_final: 0.7064 (tt0)
REVERT: B  152 ASP cc_start: 0.7716 (t0) cc_final: 0.5765 (t70)
REVERT: B  156 TYR cc_start: 0.8137 (m-10) cc_final: 0.7458 (m-10)
REVERT: B  170 LEU cc_start: 0.9530 (tt) cc_final: 0.9147 (tp)
REVERT: B  173 SER cc_start: 0.9148 (m) cc_final: 0.8784 (p)
REVERT: B  181 ASP cc_start: 0.8720 (t0) cc_final: 0.8321 (t0)
REVERT: B  194 GLN cc_start: 0.8443 (tm-30) cc_final: 0.8161 (tm-30)
REVERT: B  195 GLN cc_start: 0.8851 (tt0) cc_final: 0.8517 (tt0)
REVERT: B  198 ASP cc_start: 0.8828 (t70) cc_final: 0.8614 (t0)
REVERT: A   93 MET cc_start: 0.8909 (mmm) cc_final: 0.8598 (mmm)
REVERT: A  105 GLU cc_start: 0.8464 (tm-30) cc_final: 0.8174 (tm-30)
REVERT: A  137 GLN cc_start: 0.8079 (tt0) cc_final: 0.7428 (tt0)
REVERT: A  198 ASP cc_start: 0.8804 (t70) cc_final: 0.8452 (t0)
  outliers start: 0
  outliers final: 0
  residues processed: 119
  average time/residue: 0.2131
  time to fit residues: 33.6510
Evaluate side-chains
  101 residues out of total 456 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 101
  time to evaluate  : 0.543 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 56
   random chunks:
   chunk 6 optimal weight:    6.9990
   chunk 37 optimal weight:    0.9980
   chunk 20 optimal weight:    4.9990
   chunk 21 optimal weight:    0.2980
   chunk 23 optimal weight:   10.0000
   chunk 5 optimal weight:    8.9990
   chunk 41 optimal weight:    0.9980
   chunk 47 optimal weight:    1.9990
   chunk 8 optimal weight:    0.5980
   chunk 55 optimal weight:    3.9990
   chunk 11 optimal weight:    2.9990
   overall best weight:    0.9782

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

Flipped N/Q/H residues before XYZ refinement:
B  88 GLN
B 163 ASN
** B 286 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A  71 HIS
A 163 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3601 r_free = 0.3601 target = 0.096523 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3045 r_free = 0.3045 target = 0.067665 restraints weight = 12310.577|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3082 r_free = 0.3082 target = 0.069454 restraints weight = 7036.614|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3106 r_free = 0.3106 target = 0.070603 restraints weight = 4945.099|
|-----------------------------------------------------------------------------|
r_work (final): 0.3094
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8364
moved from start:          0.6560

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   4458  Z= 0.178
  Angle     :  0.635   6.933   6074  Z= 0.307
  Chirality :  0.038   0.173    730
  Planarity :  0.003   0.034    760
  Dihedral  :  3.925  13.812    606
  Min Nonbonded Distance : 1.992

Molprobity Statistics.
  All-atom Clashscore : 8.06
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.61 %
    Favored  : 98.39 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.54 %
    Favored  : 98.46 %
  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:  2.03 (0.36), residues: 560
  helix:  2.50 (0.25), residues: 388
  sheet:  1.17 (0.70), residues: 50
  loop : -2.69 (0.52), residues: 122

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP A 178 
 HIS   0.003   0.001   HIS A 234 
 PHE   0.016   0.002   PHE B 101 
 TYR   0.008   0.001   TYR A 175 
 ARG   0.003   0.000   ARG B  16 

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

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

  1120 Ramachandran restraints generated.
    560 Oldfield, 0 Emsley, 560 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1120 Ramachandran restraints generated.
    560 Oldfield, 0 Emsley, 560 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  120 residues out of total 456 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 120
  time to evaluate  : 0.650 
Fit side-chains
   revert: symmetry clash
REVERT: B   79 LYS cc_start: 0.8801 (ptmt) cc_final: 0.8278 (pttm)
REVERT: B  137 GLN cc_start: 0.8524 (tt0) cc_final: 0.7277 (tt0)
REVERT: B  152 ASP cc_start: 0.7725 (t0) cc_final: 0.5712 (t70)
REVERT: B  156 TYR cc_start: 0.8094 (m-10) cc_final: 0.7446 (m-10)
REVERT: B  170 LEU cc_start: 0.9502 (tt) cc_final: 0.9222 (tp)
REVERT: B  173 SER cc_start: 0.9032 (m) cc_final: 0.8678 (p)
REVERT: B  181 ASP cc_start: 0.8616 (t0) cc_final: 0.8179 (t0)
REVERT: B  194 GLN cc_start: 0.8410 (tm-30) cc_final: 0.8111 (tm-30)
REVERT: B  195 GLN cc_start: 0.8795 (tt0) cc_final: 0.8462 (tt0)
REVERT: B  198 ASP cc_start: 0.8741 (t70) cc_final: 0.8438 (t0)
REVERT: A   93 MET cc_start: 0.8872 (mmm) cc_final: 0.8547 (mmm)
REVERT: A  105 GLU cc_start: 0.8454 (tm-30) cc_final: 0.8204 (tm-30)
REVERT: A  137 GLN cc_start: 0.8509 (tt0) cc_final: 0.7715 (tt0)
REVERT: A  198 ASP cc_start: 0.8747 (t70) cc_final: 0.8363 (t0)
  outliers start: 0
  outliers final: 0
  residues processed: 120
  average time/residue: 0.2001
  time to fit residues: 30.5184
Evaluate side-chains
  99 residues out of total 456 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 99
  time to evaluate  : 0.510 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 56
   random chunks:
   chunk 47 optimal weight:    0.9990
   chunk 18 optimal weight:    0.9990
   chunk 6 optimal weight:   10.0000
   chunk 44 optimal weight:    7.9990
   chunk 53 optimal weight:    0.1980
   chunk 4 optimal weight:    6.9990
   chunk 10 optimal weight:    5.9990
   chunk 20 optimal weight:    2.9990
   chunk 25 optimal weight:    3.9990
   chunk 34 optimal weight:    0.9980
   chunk 12 optimal weight:    0.9980
   overall best weight:    0.8384

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

Flipped N/Q/H residues before XYZ refinement:
B  88 GLN
B 163 ASN
** B 286 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A  71 HIS
A 163 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3618 r_free = 0.3618 target = 0.097709 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3067 r_free = 0.3067 target = 0.068826 restraints weight = 12476.834|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 43)----------------|
| r_work = 0.3107 r_free = 0.3107 target = 0.070686 restraints weight = 7012.336|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3132 r_free = 0.3132 target = 0.071872 restraints weight = 4895.202|
|-----------------------------------------------------------------------------|
r_work (final): 0.3120
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8345
moved from start:          0.6738

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   4458  Z= 0.173
  Angle     :  0.654   7.928   6074  Z= 0.309
  Chirality :  0.037   0.169    730
  Planarity :  0.003   0.033    760
  Dihedral  :  3.911  14.058    606
  Min Nonbonded Distance : 2.000

Molprobity Statistics.
  All-atom Clashscore : 8.62
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.43 %
    Favored  : 98.57 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.32 %
    Favored  : 98.68 %
  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:  1.98 (0.36), residues: 560
  helix:  2.44 (0.25), residues: 392
  sheet:  1.28 (0.70), residues: 50
  loop : -2.84 (0.51), residues: 118

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.022   0.001   TRP A 178 
 HIS   0.002   0.001   HIS A 234 
 PHE   0.013   0.001   PHE B 101 
 TYR   0.013   0.001   TYR A   7 
 ARG   0.008   0.001   ARG B 202 

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

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

  1120 Ramachandran restraints generated.
    560 Oldfield, 0 Emsley, 560 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1120 Ramachandran restraints generated.
    560 Oldfield, 0 Emsley, 560 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  122 residues out of total 456 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 122
  time to evaluate  : 0.482 
Fit side-chains
   revert: symmetry clash
REVERT: B   79 LYS cc_start: 0.8769 (ptmt) cc_final: 0.8161 (pttm)
REVERT: B  137 GLN cc_start: 0.8510 (tt0) cc_final: 0.7264 (tt0)
REVERT: B  152 ASP cc_start: 0.7707 (t0) cc_final: 0.5686 (t70)
REVERT: B  156 TYR cc_start: 0.8114 (m-10) cc_final: 0.7400 (m-10)
REVERT: B  170 LEU cc_start: 0.9488 (tt) cc_final: 0.9125 (tp)
REVERT: B  173 SER cc_start: 0.8974 (m) cc_final: 0.8587 (p)
REVERT: B  181 ASP cc_start: 0.8613 (t0) cc_final: 0.8186 (t0)
REVERT: B  194 GLN cc_start: 0.8415 (tm-30) cc_final: 0.8109 (tm-30)
REVERT: B  195 GLN cc_start: 0.8811 (tt0) cc_final: 0.8447 (tt0)
REVERT: B  198 ASP cc_start: 0.8772 (t70) cc_final: 0.8533 (t0)
REVERT: A   93 MET cc_start: 0.8882 (mmm) cc_final: 0.8552 (mmm)
REVERT: A  105 GLU cc_start: 0.8514 (tm-30) cc_final: 0.8248 (tm-30)
REVERT: A  137 GLN cc_start: 0.8323 (tt0) cc_final: 0.7803 (tt0)
REVERT: A  198 ASP cc_start: 0.8756 (t70) cc_final: 0.8387 (t0)
  outliers start: 0
  outliers final: 0
  residues processed: 122
  average time/residue: 0.1616
  time to fit residues: 25.0934
Evaluate side-chains
  103 residues out of total 456 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 103
  time to evaluate  : 0.599 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 56
   random chunks:
   chunk 52 optimal weight:    5.9990
   chunk 2 optimal weight:    1.9990
   chunk 36 optimal weight:    0.7980
   chunk 16 optimal weight:    5.9990
   chunk 9 optimal weight:    0.9990
   chunk 26 optimal weight:    5.9990
   chunk 31 optimal weight:    5.9990
   chunk 12 optimal weight:    0.9980
   chunk 43 optimal weight:    0.6980
   chunk 27 optimal weight:    9.9990
   chunk 28 optimal weight:   10.0000
   overall best weight:    1.0984

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

Flipped N/Q/H residues before XYZ refinement:
B  71 HIS
B  88 GLN
B 163 ASN
** B 286 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 163 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3610 r_free = 0.3610 target = 0.097163 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3064 r_free = 0.3064 target = 0.068622 restraints weight = 12414.526|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3103 r_free = 0.3103 target = 0.070501 restraints weight = 6961.148|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.3128 r_free = 0.3128 target = 0.071702 restraints weight = 4827.517|
|-----------------------------------------------------------------------------|
r_work (final): 0.3113
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8348
moved from start:          0.6863

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   4458  Z= 0.194
  Angle     :  0.694   9.629   6074  Z= 0.331
  Chirality :  0.039   0.208    730
  Planarity :  0.004   0.038    760
  Dihedral  :  4.002  20.842    606
  Min Nonbonded Distance : 1.974

Molprobity Statistics.
  All-atom Clashscore : 9.53
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.61 %
    Favored  : 98.39 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.44 %
    Favored  : 99.56 %
  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:  2.04 (0.36), residues: 560
  helix:  2.56 (0.25), residues: 386
  sheet:  1.25 (0.70), residues: 50
  loop : -2.82 (0.49), residues: 124

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP A 178 
 HIS   0.002   0.001   HIS A 234 
 PHE   0.013   0.001   PHE B 101 
 TYR   0.022   0.001   TYR B 175 
 ARG   0.008   0.001   ARG B  63 

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

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

  1120 Ramachandran restraints generated.
    560 Oldfield, 0 Emsley, 560 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1120 Ramachandran restraints generated.
    560 Oldfield, 0 Emsley, 560 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  120 residues out of total 456 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 120
  time to evaluate  : 0.488 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   79 LYS cc_start: 0.8741 (ptmt) cc_final: 0.8024 (pttp)
REVERT: B  137 GLN cc_start: 0.8441 (tt0) cc_final: 0.7194 (tt0)
REVERT: B  152 ASP cc_start: 0.7713 (t0) cc_final: 0.5681 (t70)
REVERT: B  156 TYR cc_start: 0.8109 (m-10) cc_final: 0.7429 (m-10)
REVERT: B  170 LEU cc_start: 0.9487 (tt) cc_final: 0.9135 (tp)
REVERT: B  173 SER cc_start: 0.8986 (m) cc_final: 0.8582 (p)
REVERT: B  181 ASP cc_start: 0.8659 (t0) cc_final: 0.8230 (t0)
REVERT: B  194 GLN cc_start: 0.8503 (tm-30) cc_final: 0.8157 (tm-30)
REVERT: B  198 ASP cc_start: 0.8746 (t70) cc_final: 0.8494 (t0)
REVERT: A  105 GLU cc_start: 0.8520 (tm-30) cc_final: 0.8197 (tm-30)
REVERT: A  137 GLN cc_start: 0.8543 (tt0) cc_final: 0.7770 (tt0)
REVERT: A  198 ASP cc_start: 0.8760 (t70) cc_final: 0.8384 (t0)
  outliers start: 0
  outliers final: 0
  residues processed: 120
  average time/residue: 0.1575
  time to fit residues: 23.8639
Evaluate side-chains
  103 residues out of total 456 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 103
  time to evaluate  : 0.473 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 56
   random chunks:
   chunk 6 optimal weight:    0.9980
   chunk 15 optimal weight:    6.9990
   chunk 19 optimal weight:    2.9990
   chunk 49 optimal weight:    3.9990
   chunk 50 optimal weight:    0.8980
   chunk 47 optimal weight:    0.2980
   chunk 28 optimal weight:   10.0000
   chunk 42 optimal weight:    4.9990
   chunk 37 optimal weight:    0.9980
   chunk 30 optimal weight:    4.9990
   chunk 27 optimal weight:    0.0370
   overall best weight:    0.6458

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

Flipped N/Q/H residues before XYZ refinement:
B  88 GLN
B 163 ASN
** B 286 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A  71 HIS
** A  88 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 163 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3633 r_free = 0.3633 target = 0.098904 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3092 r_free = 0.3092 target = 0.069741 restraints weight = 13023.489|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.3131 r_free = 0.3131 target = 0.071612 restraints weight = 7461.711|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 45)----------------|
| r_work = 0.3155 r_free = 0.3155 target = 0.072804 restraints weight = 5244.201|
|-----------------------------------------------------------------------------|
r_work (final): 0.3145
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8344
moved from start:          0.7039

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   4458  Z= 0.175
  Angle     :  0.671   7.040   6074  Z= 0.318
  Chirality :  0.038   0.169    730
  Planarity :  0.003   0.035    760
  Dihedral  :  3.916  20.472    606
  Min Nonbonded Distance : 2.009

Molprobity Statistics.
  All-atom Clashscore : 9.53
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.43 %
    Favored  : 98.57 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.44 %
    Favored  : 99.56 %
  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:  2.05 (0.36), residues: 560
  helix:  2.56 (0.25), residues: 384
  sheet:  1.14 (0.69), residues: 50
  loop : -2.63 (0.50), residues: 126

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP A 178 
 HIS   0.002   0.000   HIS A 234 
 PHE   0.013   0.001   PHE B 101 
 TYR   0.009   0.001   TYR B 175 
 ARG   0.007   0.001   ARG B 202 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1846.22 seconds
wall clock time: 33 minutes 44.32 seconds (2024.32 seconds total)