Starting phenix.real_space_refine
on Sun Apr 27 03:09:45 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/5vrf_8728/04_2025/5vrf_8728.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/5vrf_8728/04_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_8728/04_2025/5vrf_8728.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/5vrf_8728/04_2025/5vrf_8728.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/5vrf_8728/04_2025/5vrf_8728.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/5vrf_8728/04_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-5669/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: 2.97, per 1000 atoms: 0.68
  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: 1.02
  Conformation dependent library (CDL) restraints added in 668.5 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: 0.38
  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: 1.12

  Time building geometry restraints manager: 1.24 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:             0.160
  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:          0.190
  Check model and map are aligned:         0.030
  Set scattering table:                    0.050
  Process input model:                     15.700
  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:2.920
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   19.160
-------------------------------------------------------------------------------
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      :  0.013   0.228   4472  Z= 0.507
  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 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.12539 (  318)
  hydrogen bonds       : angle       8.67153 (  948)
  metal coordination   : bond        0.11177 (   14)
  covalent geometry    : bond        0.01138 ( 4458)
  covalent geometry    : angle       1.27735 ( 6074)

*********************** 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  : 0.518 
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: 0.2639
  time to fit residues: 53.1870
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  : 0.521 
-------------------------------------------------------------------------------
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:   10.0000
   chunk 23 optimal weight:    7.9990
   chunk 14 optimal weight:    9.9990
   chunk 28 optimal weight:   10.0000
   chunk 22 optimal weight:    3.9990
   chunk 43 optimal weight:    8.9990
   chunk 16 optimal weight:    0.8980
   chunk 26 optimal weight:    5.9990
   chunk 32 optimal weight:    0.8980
   chunk 50 optimal weight:   20.0000
   overall best weight:    2.9586

-------------------------------------------------------------------------------
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 = 0.3572 r_free = 0.3572 target = 0.094484 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3042 r_free = 0.3042 target = 0.066840 restraints weight = 12072.432|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3082 r_free = 0.3082 target = 0.068564 restraints weight = 7129.715|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3104 r_free = 0.3104 target = 0.069592 restraints weight = 5057.504|
|-----------------------------------------------------------------------------|
r_work (final): 0.3078
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8407
moved from start:          0.4448

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.037   4472  Z= 0.199
  Angle     :  0.653   7.360   6074  Z= 0.344
  Chirality :  0.039   0.180    730
  Planarity :  0.005   0.046    760
  Dihedral  :  4.548  16.209    606
  Min Nonbonded Distance : 1.991

Molprobity Statistics.
  All-atom Clashscore : 11.57
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.32 %
    Favored  : 97.68 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  4.61 %
    Favored  : 95.39 %
  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: -0.99 (0.32), residues: 560
  helix:  0.21 (0.23), residues: 398
  sheet: -1.01 (0.60), residues: 50
  loop : -3.42 (0.48), residues: 112

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.025   0.002   TRP B 177 
 HIS   0.004   0.001   HIS B 234 
 PHE   0.016   0.002   PHE A 249 
 TYR   0.028   0.002   TYR A 175 
 ARG   0.006   0.001   ARG A 272 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04791 (  318)
  hydrogen bonds       : angle       3.93250 (  948)
  metal coordination   : bond        0.00309 (   14)
  covalent geometry    : bond        0.00432 ( 4458)
  covalent geometry    : angle       0.65339 ( 6074)

*********************** 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
  134 residues out of total 456 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 134
  time to evaluate  : 0.482 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   16 ARG cc_start: 0.8770 (ttp80) cc_final: 0.8528 (ttp80)
REVERT: B   24 THR cc_start: 0.9303 (p) cc_final: 0.9033 (p)
REVERT: B   27 THR cc_start: 0.9532 (m) cc_final: 0.9310 (p)
REVERT: B  105 GLU cc_start: 0.8372 (tm-30) cc_final: 0.8143 (tm-30)
REVERT: B  170 LEU cc_start: 0.9487 (tt) cc_final: 0.9275 (tp)
REVERT: B  198 ASP cc_start: 0.8880 (t0) cc_final: 0.8483 (t0)
REVERT: A   81 GLU cc_start: 0.9112 (pp20) cc_final: 0.8909 (pp20)
REVERT: A  105 GLU cc_start: 0.8534 (tm-30) cc_final: 0.8274 (tm-30)
REVERT: A  163 ASN cc_start: 0.9227 (t0) cc_final: 0.8814 (t0)
REVERT: A  198 ASP cc_start: 0.8948 (t0) cc_final: 0.8701 (t0)
REVERT: A  218 GLN cc_start: 0.8213 (tp-100) cc_final: 0.7789 (tm-30)
  outliers start: 0
  outliers final: 0
  residues processed: 134
  average time/residue: 0.1988
  time to fit residues: 32.3174
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  : 0.485 
-------------------------------------------------------------------------------
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:    0.9980
   chunk 8 optimal weight:    1.9990
   chunk 41 optimal weight:    3.9990
   chunk 50 optimal weight:   50.0000
   chunk 51 optimal weight:    6.9990
   chunk 48 optimal weight:    0.7980
   chunk 11 optimal weight:    0.0010
   chunk 33 optimal weight:    3.9990
   chunk 29 optimal weight:    2.9990
   chunk 2 optimal weight:    0.7980
   chunk 12 optimal weight:    0.9990
   overall best weight:    0.7188

-------------------------------------------------------------------------------
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**
B 195 GLN
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: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3616 r_free = 0.3616 target = 0.097207 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3095 r_free = 0.3095 target = 0.069361 restraints weight = 12182.374|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3134 r_free = 0.3134 target = 0.071118 restraints weight = 6932.689|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 23)----------------|
| r_work = 0.3158 r_free = 0.3158 target = 0.072228 restraints weight = 4813.426|
|-----------------------------------------------------------------------------|
r_work (final): 0.3123
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8325
moved from start:          0.5210

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.358   4472  Z= 0.217
  Angle     :  0.582   7.116   6074  Z= 0.285
  Chirality :  0.036   0.157    730
  Planarity :  0.003   0.034    760
  Dihedral  :  4.135  14.485    606
  Min Nonbonded Distance : 2.151

Molprobity Statistics.
  All-atom Clashscore : 8.28
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.14 %
    Favored  : 97.86 %
  Rotamer:
    Outliers :  0.22 %
    Allowed  :  4.17 %
    Favored  : 95.61 %
  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:  1.50 (0.25), residues: 390
  sheet: -0.14 (0.64), residues: 50
  loop : -3.11 (0.48), residues: 120

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP B 177 
 HIS   0.007   0.001   HIS A  73 
 PHE   0.010   0.001   PHE B 249 
 TYR   0.007   0.001   TYR A 175 
 ARG   0.005   0.001   ARG B  16 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04091 (  318)
  hydrogen bonds       : angle       3.51082 (  948)
  metal coordination   : bond        0.09578 (   14)
  covalent geometry    : bond        0.00249 ( 4458)
  covalent geometry    : angle       0.58222 ( 6074)

*********************** 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
  129 residues out of total 456 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 128
  time to evaluate  : 0.519 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  170 LEU cc_start: 0.9395 (tt) cc_final: 0.9011 (tp)
REVERT: B  181 ASP cc_start: 0.8624 (t0) cc_final: 0.8412 (t0)
REVERT: B  198 ASP cc_start: 0.8855 (t0) cc_final: 0.8653 (t0)
REVERT: B  202 ARG cc_start: 0.8879 (ttm110) cc_final: 0.8623 (ttm110)
REVERT: A  156 TYR cc_start: 0.8518 (m-10) cc_final: 0.7279 (m-10)
REVERT: A  163 ASN cc_start: 0.9073 (t0) cc_final: 0.8605 (t0)
REVERT: A  198 ASP cc_start: 0.8868 (t0) cc_final: 0.8648 (t0)
  outliers start: 1
  outliers final: 0
  residues processed: 128
  average time/residue: 0.1671
  time to fit residues: 26.9414
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  : 0.469 
-------------------------------------------------------------------------------
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:    2.9990
   chunk 31 optimal weight:    0.0980
   chunk 5 optimal weight:    2.9990
   chunk 45 optimal weight:    0.8980
   chunk 25 optimal weight:    0.9990
   chunk 32 optimal weight:    1.9990
   chunk 19 optimal weight:    3.9990
   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:    0.9784

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

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

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3642 r_free = 0.3642 target = 0.098630 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3081 r_free = 0.3081 target = 0.068908 restraints weight = 12342.146|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 44)----------------|
| r_work = 0.3118 r_free = 0.3118 target = 0.070699 restraints weight = 7115.319|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3141 r_free = 0.3141 target = 0.071812 restraints weight = 5045.509|
|-----------------------------------------------------------------------------|
r_work (final): 0.3115
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8349
moved from start:          0.5609

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.023   4472  Z= 0.118
  Angle     :  0.573   7.647   6074  Z= 0.280
  Chirality :  0.036   0.170    730
  Planarity :  0.003   0.035    760
  Dihedral  :  3.982  13.826    606
  Min Nonbonded Distance : 2.128

Molprobity Statistics.
  All-atom Clashscore : 7.49
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.79 %
    Favored  : 98.21 %
  Rotamer:
    Outliers :  0.22 %
    Allowed  :  4.17 %
    Favored  : 95.61 %
  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:  1.35 (0.35), residues: 560
  helix:  2.03 (0.25), residues: 386
  sheet:  0.29 (0.66), residues: 50
  loop : -2.69 (0.52), residues: 124

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP A 178 
 HIS   0.003   0.001   HIS A  73 
 PHE   0.010   0.001   PHE B 249 
 TYR   0.013   0.001   TYR B 102 
 ARG   0.004   0.001   ARG B  16 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03874 (  318)
  hydrogen bonds       : angle       3.23706 (  948)
  metal coordination   : bond        0.00173 (   14)
  covalent geometry    : bond        0.00246 ( 4458)
  covalent geometry    : angle       0.57307 ( 6074)

*********************** 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
  122 residues out of total 456 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 121
  time to evaluate  : 0.543 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  156 TYR cc_start: 0.8671 (m-10) cc_final: 0.8444 (m-10)
REVERT: B  198 ASP cc_start: 0.8807 (t0) cc_final: 0.8531 (t0)
REVERT: B  202 ARG cc_start: 0.8880 (ttm110) cc_final: 0.8451 (ttm110)
REVERT: A  163 ASN cc_start: 0.9000 (t0) cc_final: 0.8515 (t0)
  outliers start: 1
  outliers final: 1
  residues processed: 122
  average time/residue: 0.2018
  time to fit residues: 30.5222
Evaluate side-chains
  101 residues out of total 456 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 100
  time to evaluate  : 0.538 
-------------------------------------------------------------------------------
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:    0.9980
   chunk 21 optimal weight:    5.9990
   chunk 19 optimal weight:    0.8980
   chunk 11 optimal weight:    2.9990
   chunk 52 optimal weight:    9.9990
   chunk 43 optimal weight:    0.7980
   chunk 49 optimal weight:    6.9990
   chunk 22 optimal weight:    0.6980
   chunk 1 optimal weight:    9.9990
   chunk 26 optimal weight:    7.9990
   chunk 35 optimal weight:    0.9980
   overall best weight:    0.8780

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

Flipped N/Q/H residues before XYZ refinement:
B 163 ASN
A 195 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3651 r_free = 0.3651 target = 0.098961 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3086 r_free = 0.3086 target = 0.069074 restraints weight = 12530.383|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3123 r_free = 0.3123 target = 0.070856 restraints weight = 7102.119|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3147 r_free = 0.3147 target = 0.072038 restraints weight = 5011.478|
|-----------------------------------------------------------------------------|
r_work (final): 0.3123
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8326
moved from start:          0.5817

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.025   4472  Z= 0.120
  Angle     :  0.587   6.962   6074  Z= 0.287
  Chirality :  0.036   0.161    730
  Planarity :  0.004   0.038    760
  Dihedral  :  3.877  13.724    606
  Min Nonbonded Distance : 2.127

Molprobity Statistics.
  All-atom Clashscore : 7.37
  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:  1.60 (0.35), residues: 560
  helix:  2.16 (0.25), residues: 388
  sheet:  0.69 (0.69), residues: 50
  loop : -2.60 (0.53), residues: 122

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.001   TRP A 178 
 HIS   0.002   0.001   HIS A  77 
 PHE   0.011   0.001   PHE A 101 
 TYR   0.016   0.001   TYR B 175 
 ARG   0.015   0.001   ARG B  63 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03939 (  318)
  hydrogen bonds       : angle       3.18054 (  948)
  metal coordination   : bond        0.00075 (   14)
  covalent geometry    : bond        0.00253 ( 4458)
  covalent geometry    : angle       0.58739 ( 6074)

*********************** 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
  117 residues out of total 456 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 117
  time to evaluate  : 0.520 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  156 TYR cc_start: 0.8705 (m-10) cc_final: 0.8481 (m-10)
REVERT: A   16 ARG cc_start: 0.8721 (ptm160) cc_final: 0.8404 (ptp90)
REVERT: A   93 MET cc_start: 0.8872 (mmm) cc_final: 0.8521 (mmm)
REVERT: A  156 TYR cc_start: 0.8638 (m-10) cc_final: 0.7450 (m-10)
REVERT: A  163 ASN cc_start: 0.8958 (t0) cc_final: 0.8675 (t0)
REVERT: A  198 ASP cc_start: 0.8784 (t70) cc_final: 0.8364 (t0)
REVERT: A  202 ARG cc_start: 0.8904 (ttm110) cc_final: 0.8689 (ttm110)
  outliers start: 0
  outliers final: 0
  residues processed: 117
  average time/residue: 0.1709
  time to fit residues: 24.9467
Evaluate side-chains
  102 residues out of total 456 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 102
  time to evaluate  : 0.476 
-------------------------------------------------------------------------------
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:    4.9990
   chunk 21 optimal weight:    1.9990
   chunk 13 optimal weight:    1.9990
   chunk 19 optimal weight:    2.9990
   chunk 0 optimal weight:    0.9990
   chunk 24 optimal weight:    3.9990
   chunk 37 optimal weight:    0.8980
   chunk 15 optimal weight:    5.9990
   chunk 33 optimal weight:    0.9980
   chunk 22 optimal weight:    7.9990
   chunk 49 optimal weight:    6.9990
   overall best weight:    1.3786

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

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

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3624 r_free = 0.3624 target = 0.097975 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3071 r_free = 0.3071 target = 0.068673 restraints weight = 12551.559|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3109 r_free = 0.3109 target = 0.070460 restraints weight = 7277.932|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3131 r_free = 0.3131 target = 0.071572 restraints weight = 5158.620|
|-----------------------------------------------------------------------------|
r_work (final): 0.3115
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8364
moved from start:          0.6033

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.025   4472  Z= 0.126
  Angle     :  0.588   6.957   6074  Z= 0.290
  Chirality :  0.037   0.175    730
  Planarity :  0.004   0.042    760
  Dihedral  :  3.817  13.447    606
  Min Nonbonded Distance : 2.154

Molprobity Statistics.
  All-atom Clashscore : 8.28
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.25 %
    Favored  : 98.75 %
  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:  1.93 (0.36), residues: 560
  helix:  2.41 (0.25), residues: 388
  sheet:  0.91 (0.68), residues: 50
  loop : -2.55 (0.54), residues: 122

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.001   TRP B 177 
 HIS   0.002   0.001   HIS A  77 
 PHE   0.010   0.001   PHE B 249 
 TYR   0.008   0.001   TYR A 175 
 ARG   0.007   0.001   ARG B  63 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03835 (  318)
  hydrogen bonds       : angle       3.16662 (  948)
  metal coordination   : bond        0.00113 (   14)
  covalent geometry    : bond        0.00272 ( 4458)
  covalent geometry    : angle       0.58791 ( 6074)

*********************** 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
  114 residues out of total 456 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 114
  time to evaluate  : 0.544 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  137 GLN cc_start: 0.8222 (tt0) cc_final: 0.6754 (tt0)
REVERT: B  156 TYR cc_start: 0.8649 (m-10) cc_final: 0.7150 (m-10)
REVERT: A   93 MET cc_start: 0.8787 (mmm) cc_final: 0.8425 (mmm)
REVERT: A  163 ASN cc_start: 0.8985 (t0) cc_final: 0.8703 (t0)
REVERT: A  198 ASP cc_start: 0.8751 (t70) cc_final: 0.8334 (t0)
  outliers start: 0
  outliers final: 0
  residues processed: 114
  average time/residue: 0.1768
  time to fit residues: 25.4074
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  : 0.475 
-------------------------------------------------------------------------------
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:    2.9990
   chunk 14 optimal weight:   30.0000
   chunk 48 optimal weight:    6.9990
   chunk 20 optimal weight:    0.4980
   chunk 46 optimal weight:    0.8980
   chunk 49 optimal weight:    6.9990
   chunk 22 optimal weight:    8.9990
   chunk 40 optimal weight:    3.9990
   chunk 6 optimal weight:    6.9990
   chunk 47 optimal weight:    1.9990
   chunk 0 optimal weight:   10.0000
   overall best weight:    2.0786

-------------------------------------------------------------------------------
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 145 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 174 GLN
** A 218 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 = 0.3590 r_free = 0.3590 target = 0.095951 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3049 r_free = 0.3049 target = 0.067824 restraints weight = 12650.272|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3086 r_free = 0.3086 target = 0.069616 restraints weight = 7119.590|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.3109 r_free = 0.3109 target = 0.070752 restraints weight = 4945.266|
|-----------------------------------------------------------------------------|
r_work (final): 0.3082
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8351
moved from start:          0.6155

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   4472  Z= 0.153
  Angle     :  0.629   7.003   6074  Z= 0.311
  Chirality :  0.038   0.172    730
  Planarity :  0.004   0.035    760
  Dihedral  :  3.940  15.786    606
  Min Nonbonded Distance : 2.069

Molprobity Statistics.
  All-atom Clashscore : 9.08
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.25 %
    Favored  : 98.75 %
  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:  1.98 (0.36), residues: 560
  helix:  2.46 (0.25), residues: 390
  sheet:  0.99 (0.69), residues: 50
  loop : -2.69 (0.54), residues: 120

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.020   0.002   TRP A 178 
 HIS   0.003   0.001   HIS A 234 
 PHE   0.012   0.001   PHE B 249 
 TYR   0.008   0.001   TYR A 175 
 ARG   0.004   0.001   ARG B  63 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04012 (  318)
  hydrogen bonds       : angle       3.28953 (  948)
  metal coordination   : bond        0.00179 (   14)
  covalent geometry    : bond        0.00334 ( 4458)
  covalent geometry    : angle       0.62899 ( 6074)

*********************** 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
  113 residues out of total 456 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 113
  time to evaluate  : 0.483 
Fit side-chains
   revert: symmetry clash
REVERT: B  194 GLN cc_start: 0.8536 (tm-30) cc_final: 0.8242 (tm-30)
REVERT: B  195 GLN cc_start: 0.8911 (tt0) cc_final: 0.8571 (tt0)
REVERT: A  105 GLU cc_start: 0.8604 (tm-30) cc_final: 0.8330 (tm-30)
REVERT: A  163 ASN cc_start: 0.9042 (t0) cc_final: 0.8724 (t160)
REVERT: A  198 ASP cc_start: 0.8804 (t70) cc_final: 0.8297 (t0)
  outliers start: 0
  outliers final: 0
  residues processed: 113
  average time/residue: 0.1633
  time to fit residues: 23.2063
Evaluate side-chains
  94 residues out of total 456 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 94
  time to evaluate  : 0.501 
-------------------------------------------------------------------------------
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:    4.9990
   chunk 37 optimal weight:    0.9980
   chunk 20 optimal weight:   10.0000
   chunk 21 optimal weight:    6.9990
   chunk 23 optimal weight:    0.8980
   chunk 5 optimal weight:    2.9990
   chunk 41 optimal weight:    6.9990
   chunk 47 optimal weight:    2.9990
   chunk 8 optimal weight:    0.8980
   chunk 55 optimal weight:    3.9990
   chunk 11 optimal weight:    0.9980
   overall best weight:    1.3582

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

Flipped N/Q/H residues before XYZ refinement:
B 163 ASN
** B 218 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 = 0.3613 r_free = 0.3613 target = 0.097747 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3056 r_free = 0.3056 target = 0.068525 restraints weight = 12583.639|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3094 r_free = 0.3094 target = 0.070366 restraints weight = 7282.233|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3119 r_free = 0.3119 target = 0.071538 restraints weight = 5111.502|
|-----------------------------------------------------------------------------|
r_work (final): 0.3104
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8346
moved from start:          0.6357

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   4472  Z= 0.134
  Angle     :  0.633   6.985   6074  Z= 0.310
  Chirality :  0.038   0.170    730
  Planarity :  0.004   0.050    760
  Dihedral  :  3.921  14.558    606
  Min Nonbonded Distance : 2.046

Molprobity Statistics.
  All-atom Clashscore : 8.62
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.25 %
    Favored  : 98.75 %
  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:  1.98 (0.36), residues: 560
  helix:  2.43 (0.25), residues: 390
  sheet:  1.06 (0.68), residues: 50
  loop : -2.61 (0.55), residues: 120

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP A 178 
 HIS   0.002   0.001   HIS A 234 
 PHE   0.015   0.001   PHE A 101 
 TYR   0.010   0.001   TYR A   7 
 ARG   0.013   0.001   ARG A 202 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03968 (  318)
  hydrogen bonds       : angle       3.23484 (  948)
  metal coordination   : bond        0.00110 (   14)
  covalent geometry    : bond        0.00291 ( 4458)
  covalent geometry    : angle       0.63285 ( 6074)

*********************** 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
  119 residues out of total 456 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 119
  time to evaluate  : 0.525 
Fit side-chains
   revert: symmetry clash
REVERT: B  194 GLN cc_start: 0.8436 (tm-30) cc_final: 0.8138 (tm-30)
REVERT: B  195 GLN cc_start: 0.8850 (tt0) cc_final: 0.8499 (tt0)
REVERT: B  198 ASP cc_start: 0.8790 (t70) cc_final: 0.8584 (t0)
REVERT: A  105 GLU cc_start: 0.8542 (tm-30) cc_final: 0.8242 (tm-30)
REVERT: A  163 ASN cc_start: 0.8952 (t0) cc_final: 0.8710 (t0)
REVERT: A  198 ASP cc_start: 0.8816 (t70) cc_final: 0.8456 (t0)
  outliers start: 0
  outliers final: 0
  residues processed: 119
  average time/residue: 0.1685
  time to fit residues: 25.3908
Evaluate side-chains
  107 residues out of total 456 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 107
  time to evaluate  : 0.488 
-------------------------------------------------------------------------------
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:    1.9990
   chunk 6 optimal weight:   20.0000
   chunk 44 optimal weight:    0.2980
   chunk 53 optimal weight:    0.1980
   chunk 4 optimal weight:    3.9990
   chunk 10 optimal weight:    0.8980
   chunk 20 optimal weight:    0.8980
   chunk 25 optimal weight:    7.9990
   chunk 34 optimal weight:    8.9990
   chunk 12 optimal weight:    0.9980
   overall best weight:    0.6580

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

Flipped N/Q/H residues before XYZ refinement:
B 163 ASN
B 218 GLN
A  71 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3630 r_free = 0.3630 target = 0.098385 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3104 r_free = 0.3104 target = 0.070369 restraints weight = 12486.809|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3140 r_free = 0.3140 target = 0.072167 restraints weight = 6986.006|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3161 r_free = 0.3161 target = 0.073218 restraints weight = 4844.188|
|-----------------------------------------------------------------------------|
r_work (final): 0.3142
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8302
moved from start:          0.6552

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   4472  Z= 0.126
  Angle     :  0.647   7.501   6074  Z= 0.317
  Chirality :  0.037   0.166    730
  Planarity :  0.004   0.046    760
  Dihedral  :  3.892  14.807    606
  Min Nonbonded Distance : 2.035

Molprobity Statistics.
  All-atom Clashscore : 8.06
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.79 %
    Favored  : 98.21 %
  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:  1.94 (0.36), residues: 560
  helix:  2.38 (0.25), residues: 390
  sheet:  1.13 (0.69), residues: 50
  loop : -2.57 (0.55), residues: 120

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.021   0.001   TRP A 178 
 HIS   0.001   0.000   HIS A 234 
 PHE   0.014   0.002   PHE B 101 
 TYR   0.009   0.001   TYR A 175 
 ARG   0.012   0.001   ARG A 202 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03920 (  318)
  hydrogen bonds       : angle       3.24725 (  948)
  metal coordination   : bond        0.00062 (   14)
  covalent geometry    : bond        0.00268 ( 4458)
  covalent geometry    : angle       0.64735 ( 6074)

*********************** 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  : 0.522 
Fit side-chains
   revert: symmetry clash
REVERT: B   45 LEU cc_start: 0.9719 (tp) cc_final: 0.9508 (tt)
REVERT: B  102 TYR cc_start: 0.9383 (t80) cc_final: 0.9126 (t80)
REVERT: B  156 TYR cc_start: 0.8263 (m-10) cc_final: 0.7885 (m-10)
REVERT: B  194 GLN cc_start: 0.8417 (tm-30) cc_final: 0.8097 (tm-30)
REVERT: B  195 GLN cc_start: 0.8812 (tt0) cc_final: 0.8454 (tt0)
REVERT: B  198 ASP cc_start: 0.8765 (t70) cc_final: 0.8453 (t0)
REVERT: A    7 TYR cc_start: 0.7353 (t80) cc_final: 0.7131 (t80)
REVERT: A   93 MET cc_start: 0.8963 (mmm) cc_final: 0.8399 (mmm)
REVERT: A  105 GLU cc_start: 0.8447 (tm-30) cc_final: 0.8179 (tm-30)
REVERT: A  163 ASN cc_start: 0.8896 (t0) cc_final: 0.8691 (t0)
REVERT: A  198 ASP cc_start: 0.8760 (t70) cc_final: 0.8416 (t0)
  outliers start: 0
  outliers final: 0
  residues processed: 122
  average time/residue: 0.1685
  time to fit residues: 25.5568
Evaluate side-chains
  106 residues out of total 456 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 106
  time to evaluate  : 0.510 
-------------------------------------------------------------------------------
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:    7.9990
   chunk 2 optimal weight:    1.9990
   chunk 36 optimal weight:    0.8980
   chunk 16 optimal weight:    4.9990
   chunk 9 optimal weight:    0.9980
   chunk 26 optimal weight:    5.9990
   chunk 31 optimal weight:    2.9990
   chunk 12 optimal weight:    0.7980
   chunk 43 optimal weight:    0.9980
   chunk 27 optimal weight:   20.0000
   chunk 28 optimal weight:   10.0000
   overall best weight:    1.1382

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

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

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3625 r_free = 0.3625 target = 0.098612 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3075 r_free = 0.3075 target = 0.069313 restraints weight = 12742.048|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3111 r_free = 0.3111 target = 0.071135 restraints weight = 7284.454|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3134 r_free = 0.3134 target = 0.072274 restraints weight = 5115.870|
|-----------------------------------------------------------------------------|
r_work (final): 0.3121
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8363
moved from start:          0.6730

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   4472  Z= 0.131
  Angle     :  0.648   7.106   6074  Z= 0.318
  Chirality :  0.038   0.170    730
  Planarity :  0.004   0.044    760
  Dihedral  :  3.847  14.222    606
  Min Nonbonded Distance : 2.009

Molprobity Statistics.
  All-atom Clashscore : 8.40
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.43 %
    Favored  : 98.57 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.22 %
    Favored  : 99.78 %
  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:  1.97 (0.36), residues: 560
  helix:  2.38 (0.25), residues: 392
  sheet:  0.95 (0.68), residues: 50
  loop : -2.49 (0.55), residues: 118

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.001   TRP A 178 
 HIS   0.002   0.000   HIS A 234 
 PHE   0.014   0.001   PHE B 101 
 TYR   0.008   0.001   TYR B 175 
 ARG   0.011   0.001   ARG A 202 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03929 (  318)
  hydrogen bonds       : angle       3.19636 (  948)
  metal coordination   : bond        0.00097 (   14)
  covalent geometry    : bond        0.00290 ( 4458)
  covalent geometry    : angle       0.64846 ( 6074)

********************** 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
  117 residues out of total 456 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 117
  time to evaluate  : 0.488 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   45 LEU cc_start: 0.9744 (tp) cc_final: 0.9518 (tt)
REVERT: B  156 TYR cc_start: 0.8110 (m-10) cc_final: 0.7865 (m-10)
REVERT: B  194 GLN cc_start: 0.8462 (tm-30) cc_final: 0.8138 (tm-30)
REVERT: B  195 GLN cc_start: 0.8746 (tt0) cc_final: 0.8392 (tt0)
REVERT: B  198 ASP cc_start: 0.8699 (t70) cc_final: 0.8451 (t0)
REVERT: A    7 TYR cc_start: 0.7376 (t80) cc_final: 0.7160 (t80)
REVERT: A   93 MET cc_start: 0.8899 (mmm) cc_final: 0.8396 (mmm)
REVERT: A  105 GLU cc_start: 0.8377 (tm-30) cc_final: 0.8128 (tm-30)
REVERT: A  198 ASP cc_start: 0.8710 (t70) cc_final: 0.8385 (t0)
  outliers start: 0
  outliers final: 0
  residues processed: 117
  average time/residue: 0.1595
  time to fit residues: 23.6702
Evaluate side-chains
  102 residues out of total 456 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 102
  time to evaluate  : 0.533 
-------------------------------------------------------------------------------
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:   20.0000
   chunk 15 optimal weight:    9.9990
   chunk 19 optimal weight:    0.9990
   chunk 49 optimal weight:    2.9990
   chunk 50 optimal weight:    4.9990
   chunk 47 optimal weight:    0.9980
   chunk 28 optimal weight:   10.0000
   chunk 42 optimal weight:   20.0000
   chunk 37 optimal weight:    4.9990
   chunk 30 optimal weight:    0.7980
   chunk 27 optimal weight:    5.9990
   overall best weight:    2.1586

-------------------------------------------------------------------------------
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 ** 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 = 0.3574 r_free = 0.3574 target = 0.095348 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3014 r_free = 0.3014 target = 0.066126 restraints weight = 12742.019|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3051 r_free = 0.3051 target = 0.067917 restraints weight = 7327.863|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3073 r_free = 0.3073 target = 0.068951 restraints weight = 5160.792|
|-----------------------------------------------------------------------------|
r_work (final): 0.3058
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8398
moved from start:          0.6767

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.039   4472  Z= 0.163
  Angle     :  0.677   7.305   6074  Z= 0.336
  Chirality :  0.039   0.166    730
  Planarity :  0.004   0.042    760
  Dihedral  :  3.976  14.853    606
  Min Nonbonded Distance : 1.903

Molprobity Statistics.
  All-atom Clashscore : 9.98
  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:  1.85 (0.36), residues: 560
  helix:  2.36 (0.25), residues: 400
  sheet:  0.77 (0.65), residues: 50
  loop : -3.11 (0.52), residues: 110

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.002   TRP A 178 
 HIS   0.003   0.001   HIS A 234 
 PHE   0.015   0.002   PHE B 101 
 TYR   0.017   0.001   TYR B 175 
 ARG   0.011   0.001   ARG A 202 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04178 (  318)
  hydrogen bonds       : angle       3.29562 (  948)
  metal coordination   : bond        0.00185 (   14)
  covalent geometry    : bond        0.00365 ( 4458)
  covalent geometry    : angle       0.67703 ( 6074)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1761.25 seconds
wall clock time: 31 minutes 12.88 seconds (1872.88 seconds total)