Starting phenix.real_space_refine
on Wed Sep 17 04:36:21 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/5vrf_8728/09_2025/5vrf_8728.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/5vrf_8728/09_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_8728/09_2025/5vrf_8728.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/5vrf_8728/09_2025/5vrf_8728.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/5vrf_8728/09_2025/5vrf_8728.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/5vrf_8728/09_2025/5vrf_8728.cif"
  }
  resolution = 4.1
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/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: 1.35, per 1000 atoms: 0.31
  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: 0.38
  Conformation dependent library (CDL) restraints added in 175.1 milliseconds
  
  Enol-peptide restraints added in 476.8 nanoseconds
  
  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: 0.13
  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: 0.59

  Time building geometry restraints manager: 0.52 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: 0.01
Found NCS groups:
ncs_group {
  reference = chain 'B'
  selection = chain 'A'
}

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:             0.140
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.090
  Check model and map are aligned:         0.010
  Set scattering table:                    0.010
  Process input model:                     6.770
  Find NCS groups from input model:        0.030
  Set up NCS constraints:                  0.010
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.420
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:    8.480
-------------------------------------------------------------------------------
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 : 8.74
  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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  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
 ARG   0.008   0.001   ARG B 237 
 TYR   0.039   0.006   TYR A  75 
 PHE   0.032   0.005   PHE B  97 
 TRP   0.012   0.003   TRP B  33 
 HIS   0.013   0.003   HIS B 234 

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

*********************** 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  : 0.206 
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: 0.8383 (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: 0.8508 (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: 0.8388 (t0)
  outliers start: 0
  outliers final: 0
  residues processed: 175
  average time/residue: 0.1226
  time to fit residues: 24.7285
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  : 0.160 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 56
   random chunks:
   chunk 54 optimal weight:    6.9990
   chunk 24 optimal weight:    8.9990
   chunk 48 optimal weight:    6.9990
   chunk 26 optimal weight:    6.9990
   chunk 2 optimal weight:    0.9990
   chunk 16 optimal weight:    0.8980
   chunk 32 optimal weight:    0.7980
   chunk 31 optimal weight:    1.9990
   chunk 25 optimal weight:   10.0000
   chunk 50 optimal weight:   20.0000
   chunk 53 optimal weight:    8.9990
   overall best weight:    2.3386

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

Flipped N/Q/H residues before XYZ refinement:
B  71 HIS
B 163 ASN
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 = 0.3596 r_free = 0.3596 target = 0.095888 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3069 r_free = 0.3069 target = 0.067999 restraints weight = 12182.663|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3108 r_free = 0.3108 target = 0.069757 restraints weight = 7106.526|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3132 r_free = 0.3132 target = 0.070891 restraints weight = 5015.884|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.3147 r_free = 0.3147 target = 0.071599 restraints weight = 4025.087|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.3152 r_free = 0.3152 target = 0.071855 restraints weight = 3529.125|
|-----------------------------------------------------------------------------|
r_work (final): 0.3126
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8357
moved from start:          0.4450

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.027   4472  Z= 0.184
  Angle     :  0.634   7.979   6074  Z= 0.333
  Chirality :  0.038   0.178    730
  Planarity :  0.005   0.044    760
  Dihedral  :  4.493  16.232    606
  Min Nonbonded Distance : 2.035

Molprobity Statistics.
  All-atom Clashscore : 10.44
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.68 %
    Favored  : 97.32 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  5.26 %
    Favored  : 94.74 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.90 (0.32), residues: 560
  helix:  0.27 (0.23), residues: 398
  sheet: -0.82 (0.60), residues: 50
  loop : -3.45 (0.47), residues: 112

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG B 272 
 TYR   0.029   0.002   TYR A 175 
 PHE   0.014   0.002   PHE A 249 
 TRP   0.023   0.002   TRP B 177 
 HIS   0.004   0.001   HIS B 234 

Details of bonding type rmsd
  covalent geometry    : bond        0.00380 ( 4458)
  covalent geometry    : angle       0.63437 ( 6074)
  hydrogen bonds       : bond        0.04638 (  318)
  hydrogen bonds       : angle       3.82165 (  948)
  metal coordination   : bond        0.00293 (   14)

*********************** 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  : 0.169 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   16 ARG cc_start: 0.8741 (ttp80) cc_final: 0.8487 (ttp80)
REVERT: B  170 LEU cc_start: 0.9459 (tt) cc_final: 0.9235 (tp)
REVERT: B  198 ASP cc_start: 0.8875 (t0) cc_final: 0.8460 (t0)
REVERT: A  105 GLU cc_start: 0.8480 (tm-30) cc_final: 0.8230 (tm-30)
REVERT: A  163 ASN cc_start: 0.9194 (t0) cc_final: 0.8690 (t0)
REVERT: A  198 ASP cc_start: 0.8916 (t0) cc_final: 0.8673 (t0)
REVERT: A  218 GLN cc_start: 0.8186 (tp-100) cc_final: 0.7736 (tm-30)
  outliers start: 0
  outliers final: 0
  residues processed: 136
  average time/residue: 0.0872
  time to fit residues: 14.4179
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  : 0.169 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 56
   random chunks:
   chunk 7 optimal weight:    3.9990
   chunk 49 optimal weight:    4.9990
   chunk 50 optimal weight:    0.4980
   chunk 1 optimal weight:    9.9990
   chunk 26 optimal weight:   10.0000
   chunk 23 optimal weight:   10.0000
   chunk 11 optimal weight:    4.9990
   chunk 30 optimal weight:    0.7980
   chunk 55 optimal weight:    8.9990
   chunk 14 optimal weight:   30.0000
   chunk 46 optimal weight:    0.7980
   overall best weight:    2.2184

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

Flipped N/Q/H residues before XYZ refinement:
** B 145 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 163 ASN
A  71 HIS
** A  88 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 195 GLN
** A 234 HIS ** 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 = 0.3582 r_free = 0.3582 target = 0.095279 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3042 r_free = 0.3042 target = 0.067080 restraints weight = 12269.008|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3080 r_free = 0.3080 target = 0.068762 restraints weight = 7028.452|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3104 r_free = 0.3104 target = 0.069888 restraints weight = 4937.322|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 39)----------------|
| r_work = 0.3118 r_free = 0.3118 target = 0.070590 restraints weight = 3978.864|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 24)----------------|
| r_work = 0.3122 r_free = 0.3122 target = 0.070776 restraints weight = 3499.231|
|-----------------------------------------------------------------------------|
r_work (final): 0.3097
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8368
moved from start:          0.5253

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.024   4472  Z= 0.162
  Angle     :  0.613   7.469   6074  Z= 0.311
  Chirality :  0.038   0.156    730
  Planarity :  0.004   0.040    760
  Dihedral  :  4.204  15.266    606
  Min Nonbonded Distance : 2.151

Molprobity Statistics.
  All-atom Clashscore : 9.64
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.61 %
    Favored  : 98.39 %
  Rotamer:
    Outliers :  0.22 %
    Allowed  :  4.39 %
    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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.52 (0.34), residues: 560
  helix:  1.35 (0.24), residues: 398
  sheet: -0.24 (0.64), residues: 50
  loop : -3.09 (0.52), residues: 112

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG B  16 
 TYR   0.012   0.001   TYR B 175 
 PHE   0.015   0.002   PHE A 101 
 TRP   0.017   0.002   TRP B 177 
 HIS   0.007   0.001   HIS A  73 

Details of bonding type rmsd
  covalent geometry    : bond        0.00346 ( 4458)
  covalent geometry    : angle       0.61303 ( 6074)
  hydrogen bonds       : bond        0.04321 (  318)
  hydrogen bonds       : angle       3.60139 (  948)
  metal coordination   : bond        0.00311 (   14)

*********************** 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
  121 residues out of total 456 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 120
  time to evaluate  : 0.170 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  105 GLU cc_start: 0.8396 (tm-30) cc_final: 0.8196 (tm-30)
REVERT: B  156 TYR cc_start: 0.8521 (m-10) cc_final: 0.7070 (m-10)
REVERT: A  105 GLU cc_start: 0.8507 (tm-30) cc_final: 0.8283 (tm-30)
REVERT: A  156 TYR cc_start: 0.8535 (m-10) cc_final: 0.7356 (m-10)
REVERT: A  163 ASN cc_start: 0.9087 (t0) cc_final: 0.8600 (t0)
REVERT: A  181 ASP cc_start: 0.8563 (t0) cc_final: 0.8317 (t0)
REVERT: A  198 ASP cc_start: 0.8890 (t0) cc_final: 0.8681 (t0)
  outliers start: 1
  outliers final: 0
  residues processed: 120
  average time/residue: 0.0758
  time to fit residues: 11.5098
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  : 0.177 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 56
   random chunks:
   chunk 12 optimal weight:    0.9980
   chunk 45 optimal weight:    0.9990
   chunk 13 optimal weight:   10.0000
   chunk 21 optimal weight:    2.9990
   chunk 27 optimal weight:    4.9990
   chunk 6 optimal weight:    8.9990
   chunk 2 optimal weight:    1.9990
   chunk 55 optimal weight:    7.9990
   chunk 46 optimal weight:    0.9980
   chunk 31 optimal weight:    0.9980
   chunk 19 optimal weight:    1.9990
   overall best weight:    1.1984

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

Flipped N/Q/H residues before XYZ refinement:
B 115 ASN
** B 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 234 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3613 r_free = 0.3613 target = 0.097259 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.3062 r_free = 0.3062 target = 0.068176 restraints weight = 12079.149|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.3098 r_free = 0.3098 target = 0.069901 restraints weight = 7141.840|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3121 r_free = 0.3121 target = 0.070997 restraints weight = 5097.062|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 32)----------------|
| r_work = 0.3133 r_free = 0.3133 target = 0.071606 restraints weight = 4147.850|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 39)----------------|
| r_work = 0.3142 r_free = 0.3142 target = 0.072055 restraints weight = 3691.802|
|-----------------------------------------------------------------------------|
r_work (final): 0.3125
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8351
moved from start:          0.5615

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.024   4472  Z= 0.127
  Angle     :  0.584   7.994   6074  Z= 0.287
  Chirality :  0.036   0.169    730
  Planarity :  0.003   0.037    760
  Dihedral  :  4.003  14.031    606
  Min Nonbonded Distance : 2.115

Molprobity Statistics.
  All-atom Clashscore : 8.85
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.32 %
    Favored  : 97.68 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  3.95 %
    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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.23 (0.35), residues: 560
  helix:  1.94 (0.25), residues: 390
  sheet:  0.13 (0.65), residues: 50
  loop : -2.83 (0.52), residues: 120

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG B  16 
 TYR   0.015   0.001   TYR B 175 
 PHE   0.010   0.001   PHE B 249 
 TRP   0.015   0.001   TRP A 178 
 HIS   0.003   0.001   HIS A  77 

Details of bonding type rmsd
  covalent geometry    : bond        0.00273 ( 4458)
  covalent geometry    : angle       0.58362 ( 6074)
  hydrogen bonds       : bond        0.03986 (  318)
  hydrogen bonds       : angle       3.30038 (  948)
  metal coordination   : bond        0.00108 (   14)

*********************** 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: 0
    poor density    : 118
  time to evaluate  : 0.140 
Fit side-chains
   revert: symmetry clash
REVERT: B  152 ASP cc_start: 0.6850 (t0) cc_final: 0.5695 (t70)
REVERT: B  156 TYR cc_start: 0.7800 (m-10) cc_final: 0.7138 (m-10)
REVERT: B  198 ASP cc_start: 0.8723 (t70) cc_final: 0.8505 (t0)
REVERT: A   93 MET cc_start: 0.8838 (mmm) cc_final: 0.8509 (mmm)
REVERT: A  105 GLU cc_start: 0.8459 (tm-30) cc_final: 0.8199 (tm-30)
REVERT: A  163 ASN cc_start: 0.8994 (t0) cc_final: 0.8628 (t0)
REVERT: A  181 ASP cc_start: 0.8417 (t0) cc_final: 0.8187 (t0)
REVERT: A  218 GLN cc_start: 0.8479 (tp-100) cc_final: 0.8048 (tm-30)
  outliers start: 0
  outliers final: 0
  residues processed: 118
  average time/residue: 0.0715
  time to fit residues: 10.6424
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  : 0.173 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 56
   random chunks:
   chunk 12 optimal weight:    0.9990
   chunk 32 optimal weight:    6.9990
   chunk 7 optimal weight:    0.5980
   chunk 34 optimal weight:    8.9990
   chunk 2 optimal weight:    0.9980
   chunk 52 optimal weight:    0.9990
   chunk 9 optimal weight:    1.9990
   chunk 23 optimal weight:    6.9990
   chunk 21 optimal weight:    4.9990
   chunk 1 optimal weight:    2.9990
   chunk 45 optimal weight:    1.9990
   overall best weight:    1.1186

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

Flipped N/Q/H residues before XYZ refinement:
B 163 ASN
A 137 GLN
A 195 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3634 r_free = 0.3634 target = 0.098885 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3072 r_free = 0.3072 target = 0.068845 restraints weight = 12496.761|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 43)----------------|
| r_work = 0.3110 r_free = 0.3110 target = 0.070691 restraints weight = 7285.566|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3132 r_free = 0.3132 target = 0.071751 restraints weight = 5148.150|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.3148 r_free = 0.3148 target = 0.072539 restraints weight = 4198.449|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 44)----------------|
| r_work = 0.3158 r_free = 0.3158 target = 0.072996 restraints weight = 3688.646|
|-----------------------------------------------------------------------------|
r_work (final): 0.3131
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8340
moved from start:          0.5968

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.023   4472  Z= 0.125
  Angle     :  0.580   6.954   6074  Z= 0.287
  Chirality :  0.037   0.161    730
  Planarity :  0.003   0.034    760
  Dihedral  :  3.925  13.931    606
  Min Nonbonded Distance : 2.077

Molprobity Statistics.
  All-atom Clashscore : 7.83
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.79 %
    Favored  : 98.21 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.85 %
    Favored  : 97.15 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.56 (0.35), residues: 560
  helix:  2.16 (0.25), residues: 390
  sheet:  0.67 (0.68), residues: 50
  loop : -2.81 (0.52), residues: 120

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.011   0.001   ARG B  63 
 TYR   0.008   0.001   TYR B 156 
 PHE   0.017   0.001   PHE A 101 
 TRP   0.014   0.001   TRP B 177 
 HIS   0.002   0.001   HIS A  77 

Details of bonding type rmsd
  covalent geometry    : bond        0.00259 ( 4458)
  covalent geometry    : angle       0.57984 ( 6074)
  hydrogen bonds       : bond        0.04049 (  318)
  hydrogen bonds       : angle       3.26050 (  948)
  metal coordination   : bond        0.00089 (   14)

*********************** 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  : 0.217 
Fit side-chains
   revert: symmetry clash
REVERT: B  152 ASP cc_start: 0.7323 (t0) cc_final: 0.5837 (t70)
REVERT: B  156 TYR cc_start: 0.7926 (m-10) cc_final: 0.7192 (m-10)
REVERT: B  173 SER cc_start: 0.9080 (m) cc_final: 0.8849 (p)
REVERT: B  198 ASP cc_start: 0.8708 (t70) cc_final: 0.8507 (t0)
REVERT: A   93 MET cc_start: 0.8785 (mmm) cc_final: 0.8330 (mmm)
REVERT: A  105 GLU cc_start: 0.8408 (tm-30) cc_final: 0.8121 (tm-30)
REVERT: A  163 ASN cc_start: 0.8957 (t0) cc_final: 0.8628 (t0)
REVERT: A  198 ASP cc_start: 0.8719 (t70) cc_final: 0.8394 (t0)
  outliers start: 0
  outliers final: 0
  residues processed: 117
  average time/residue: 0.0711
  time to fit residues: 10.6411
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  : 0.164 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 56
   random chunks:
   chunk 51 optimal weight:    6.9990
   chunk 35 optimal weight:    7.9990
   chunk 44 optimal weight:    4.9990
   chunk 47 optimal weight:    0.4980
   chunk 54 optimal weight:    9.9990
   chunk 15 optimal weight:    5.9990
   chunk 16 optimal weight:    5.9990
   chunk 46 optimal weight:    0.8980
   chunk 53 optimal weight:    0.2980
   chunk 8 optimal weight:    0.7980
   chunk 21 optimal weight:    5.9990
   overall best weight:    1.4982

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

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

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3621 r_free = 0.3621 target = 0.098246 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3059 r_free = 0.3059 target = 0.068471 restraints weight = 12829.595|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3097 r_free = 0.3097 target = 0.070267 restraints weight = 7587.279|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.3120 r_free = 0.3120 target = 0.071395 restraints weight = 5420.932|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 26)----------------|
| r_work = 0.3133 r_free = 0.3133 target = 0.072009 restraints weight = 4408.361|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 24)----------------|
| r_work = 0.3137 r_free = 0.3137 target = 0.072186 restraints weight = 3922.244|
|-----------------------------------------------------------------------------|
r_work (final): 0.3116
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8374
moved from start:          0.6116

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= 0.135
  Angle     :  0.603   6.877   6074  Z= 0.299
  Chirality :  0.037   0.171    730
  Planarity :  0.004   0.043    760
  Dihedral  :  3.937  13.554    606
  Min Nonbonded Distance : 2.000

Molprobity Statistics.
  All-atom Clashscore : 8.17
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.43 %
    Favored  : 98.57 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.75 %
    Favored  : 98.25 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.83 (0.36), residues: 560
  helix:  2.37 (0.25), residues: 390
  sheet:  0.86 (0.70), residues: 50
  loop : -2.83 (0.52), residues: 120

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG B  63 
 TYR   0.006   0.001   TYR B 102 
 PHE   0.013   0.001   PHE A 101 
 TRP   0.012   0.001   TRP B 177 
 HIS   0.003   0.001   HIS A  77 

Details of bonding type rmsd
  covalent geometry    : bond        0.00290 ( 4458)
  covalent geometry    : angle       0.60280 ( 6074)
  hydrogen bonds       : bond        0.03988 (  318)
  hydrogen bonds       : angle       3.25738 (  948)
  metal coordination   : bond        0.00122 (   14)

*********************** 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  : 0.163 
Fit side-chains
   revert: symmetry clash
REVERT: B  152 ASP cc_start: 0.7453 (t0) cc_final: 0.5775 (t70)
REVERT: B  156 TYR cc_start: 0.8018 (m-10) cc_final: 0.7449 (m-10)
REVERT: B  173 SER cc_start: 0.9136 (m) cc_final: 0.8848 (p)
REVERT: B  181 ASP cc_start: 0.8523 (t0) cc_final: 0.8178 (t0)
REVERT: A  105 GLU cc_start: 0.8347 (tm-30) cc_final: 0.8057 (tm-30)
REVERT: A  163 ASN cc_start: 0.8952 (t0) cc_final: 0.8633 (t0)
REVERT: A  198 ASP cc_start: 0.8730 (t70) cc_final: 0.8321 (t0)
  outliers start: 0
  outliers final: 0
  residues processed: 114
  average time/residue: 0.0721
  time to fit residues: 10.4646
Evaluate side-chains
  96 residues out of total 456 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 96
  time to evaluate  : 0.184 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 56
   random chunks:
   chunk 36 optimal weight:    1.9990
   chunk 23 optimal weight:    0.0170
   chunk 39 optimal weight:    0.8980
   chunk 3 optimal weight:    0.6980
   chunk 25 optimal weight:    1.9990
   chunk 16 optimal weight:    0.7980
   chunk 12 optimal weight:    0.9990
   chunk 9 optimal weight:    0.9980
   chunk 14 optimal weight:   30.0000
   chunk 17 optimal weight:    3.9990
   chunk 50 optimal weight:    9.9990
   overall best weight:    0.6818

-------------------------------------------------------------------------------
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  71 HIS
A  88 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3648 r_free = 0.3648 target = 0.099315 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3099 r_free = 0.3099 target = 0.069796 restraints weight = 12760.472|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 44)----------------|
| r_work = 0.3137 r_free = 0.3137 target = 0.071692 restraints weight = 7224.793|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3159 r_free = 0.3159 target = 0.072803 restraints weight = 5012.399|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 31)----------------|
| r_work = 0.3176 r_free = 0.3176 target = 0.073653 restraints weight = 4052.968|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.3183 r_free = 0.3183 target = 0.074040 restraints weight = 3536.123|
|-----------------------------------------------------------------------------|
r_work (final): 0.3172
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8298
moved from start:          0.6373

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.028   4472  Z= 0.117
  Angle     :  0.595   6.997   6074  Z= 0.287
  Chirality :  0.037   0.172    730
  Planarity :  0.003   0.032    760
  Dihedral  :  3.832  13.492    606
  Min Nonbonded Distance : 2.012

Molprobity Statistics.
  All-atom Clashscore : 7.83
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.61 %
    Favored  : 98.39 %
  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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.04 (0.36), residues: 560
  helix:  2.51 (0.25), residues: 390
  sheet:  1.07 (0.72), residues: 50
  loop : -2.71 (0.53), residues: 120

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG A 219 
 TYR   0.006   0.001   TYR A   7 
 PHE   0.011   0.001   PHE A 101 
 TRP   0.008   0.001   TRP B 177 
 HIS   0.002   0.000   HIS A  77 

Details of bonding type rmsd
  covalent geometry    : bond        0.00247 ( 4458)
  covalent geometry    : angle       0.59484 ( 6074)
  hydrogen bonds       : bond        0.03719 (  318)
  hydrogen bonds       : angle       3.16363 (  948)
  metal coordination   : bond        0.00072 (   14)

*********************** 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
  122 residues out of total 456 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 122
  time to evaluate  : 0.179 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  152 ASP cc_start: 0.7503 (t0) cc_final: 0.6098 (t70)
REVERT: B  156 TYR cc_start: 0.7973 (m-10) cc_final: 0.7506 (m-10)
REVERT: B  173 SER cc_start: 0.9115 (m) cc_final: 0.8855 (p)
REVERT: B  181 ASP cc_start: 0.8587 (t0) cc_final: 0.8247 (t0)
REVERT: B  198 ASP cc_start: 0.8819 (t0) cc_final: 0.8607 (t0)
REVERT: B  202 ARG cc_start: 0.8925 (ttm110) cc_final: 0.8665 (ttm110)
REVERT: A  105 GLU cc_start: 0.8434 (tm-30) cc_final: 0.8105 (tm-30)
REVERT: A  163 ASN cc_start: 0.8953 (t0) cc_final: 0.8620 (t0)
REVERT: A  198 ASP cc_start: 0.8712 (t70) cc_final: 0.8345 (t0)
  outliers start: 0
  outliers final: 0
  residues processed: 122
  average time/residue: 0.0776
  time to fit residues: 11.8338
Evaluate side-chains
  104 residues out of total 456 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 104
  time to evaluate  : 0.179 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 56
   random chunks:
   chunk 42 optimal weight:    9.9990
   chunk 24 optimal weight:   20.0000
   chunk 43 optimal weight:    6.9990
   chunk 15 optimal weight:    5.9990
   chunk 8 optimal weight:    2.9990
   chunk 22 optimal weight:   40.0000
   chunk 18 optimal weight:    3.9990
   chunk 0 optimal weight:   10.0000
   chunk 54 optimal weight:    9.9990
   chunk 27 optimal weight:    9.9990
   chunk 17 optimal weight:    1.9990
   overall best weight:    4.3990

-------------------------------------------------------------------------------
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 ** both conformations clash, **PLEASE CHECK MANUALLY**
B 163 ASN
A  71 HIS
** A  88 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 174 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3521 r_free = 0.3521 target = 0.092483 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.2938 r_free = 0.2938 target = 0.063101 restraints weight = 12555.261|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.2975 r_free = 0.2975 target = 0.064804 restraints weight = 7527.161|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.2998 r_free = 0.2998 target = 0.065916 restraints weight = 5414.671|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 33)----------------|
| r_work = 0.3012 r_free = 0.3012 target = 0.066594 restraints weight = 4410.199|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3019 r_free = 0.3019 target = 0.066896 restraints weight = 3905.054|
|-----------------------------------------------------------------------------|
r_work (final): 0.3000
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8451
moved from start:          0.6523

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.054   4472  Z= 0.266
  Angle     :  0.752   8.880   6074  Z= 0.380
  Chirality :  0.042   0.169    730
  Planarity :  0.004   0.041    760
  Dihedral  :  4.395  14.748    606
  Min Nonbonded Distance : 1.886

Molprobity Statistics.
  All-atom Clashscore : 13.27
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.14 %
    Favored  : 97.86 %
  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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.59 (0.35), residues: 560
  helix:  2.18 (0.25), residues: 402
  sheet:  0.60 (0.67), residues: 50
  loop : -3.30 (0.50), residues: 108

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG A  16 
 TYR   0.027   0.002   TYR B 175 
 PHE   0.022   0.002   PHE A 101 
 TRP   0.020   0.002   TRP A  10 
 HIS   0.006   0.002   HIS B 234 

Details of bonding type rmsd
  covalent geometry    : bond        0.00585 ( 4458)
  covalent geometry    : angle       0.75160 ( 6074)
  hydrogen bonds       : bond        0.04835 (  318)
  hydrogen bonds       : angle       3.68344 (  948)
  metal coordination   : bond        0.00363 (   14)

*********************** 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
  109 residues out of total 456 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 109
  time to evaluate  : 0.201 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  181 ASP cc_start: 0.8782 (t0) cc_final: 0.8361 (t0)
REVERT: B  194 GLN cc_start: 0.8563 (tm-30) cc_final: 0.8257 (tm-30)
REVERT: B  195 GLN cc_start: 0.8857 (tt0) cc_final: 0.8520 (tt0)
REVERT: B  214 GLU cc_start: 0.8007 (tp30) cc_final: 0.7799 (tm-30)
REVERT: A   81 GLU cc_start: 0.9067 (pp20) cc_final: 0.8867 (pp20)
REVERT: A  105 GLU cc_start: 0.8751 (tm-30) cc_final: 0.8271 (tm-30)
REVERT: A  163 ASN cc_start: 0.9178 (t0) cc_final: 0.8949 (t160)
REVERT: A  198 ASP cc_start: 0.8841 (t70) cc_final: 0.8344 (t0)
  outliers start: 0
  outliers final: 0
  residues processed: 109
  average time/residue: 0.0796
  time to fit residues: 10.8382
Evaluate side-chains
  87 residues out of total 456 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 87
  time to evaluate  : 0.172 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 56
   random chunks:
   chunk 15 optimal weight:    5.9990
   chunk 5 optimal weight:    2.9990
   chunk 54 optimal weight:    7.9990
   chunk 16 optimal weight:    4.9990
   chunk 28 optimal weight:   10.0000
   chunk 23 optimal weight:    3.9990
   chunk 2 optimal weight:    0.7980
   chunk 25 optimal weight:    1.9990
   chunk 44 optimal weight:    0.9990
   chunk 46 optimal weight:    4.9990
   chunk 27 optimal weight:   10.0000
   overall best weight:    2.1588

-------------------------------------------------------------------------------
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  88 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 = 0.3565 r_free = 0.3565 target = 0.094479 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.2993 r_free = 0.2993 target = 0.065219 restraints weight = 12609.994|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3031 r_free = 0.3031 target = 0.067007 restraints weight = 7438.927|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3055 r_free = 0.3055 target = 0.068132 restraints weight = 5302.903|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 26)----------------|
| r_work = 0.3066 r_free = 0.3066 target = 0.068639 restraints weight = 4314.709|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3075 r_free = 0.3075 target = 0.069117 restraints weight = 3881.029|
|-----------------------------------------------------------------------------|
r_work (final): 0.3057
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8416
moved from start:          0.6655

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.042   4472  Z= 0.166
  Angle     :  0.676   7.056   6074  Z= 0.335
  Chirality :  0.040   0.262    730
  Planarity :  0.006   0.095    760
  Dihedral  :  4.334  17.602    606
  Min Nonbonded Distance : 1.936

Molprobity Statistics.
  All-atom Clashscore : 11.23
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.96 %
    Favored  : 98.04 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.88 %
    Favored  : 99.12 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.75 (0.35), residues: 560
  helix:  2.32 (0.25), residues: 400
  sheet:  0.72 (0.68), residues: 50
  loop : -3.30 (0.50), residues: 110

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.015   0.001   ARG B  63 
 TYR   0.015   0.002   TYR B 102 
 PHE   0.019   0.002   PHE A 101 
 TRP   0.011   0.001   TRP B 177 
 HIS   0.003   0.001   HIS A 155 

Details of bonding type rmsd
  covalent geometry    : bond        0.00371 ( 4458)
  covalent geometry    : angle       0.67609 ( 6074)
  hydrogen bonds       : bond        0.04482 (  318)
  hydrogen bonds       : angle       3.49264 (  948)
  metal coordination   : bond        0.00198 (   14)

*********************** 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
  114 residues out of total 456 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 114
  time to evaluate  : 0.156 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  173 SER cc_start: 0.9218 (t) cc_final: 0.9017 (p)
REVERT: B  181 ASP cc_start: 0.8523 (t0) cc_final: 0.8299 (t0)
REVERT: B  194 GLN cc_start: 0.8490 (tm-30) cc_final: 0.8187 (tm-30)
REVERT: B  195 GLN cc_start: 0.8807 (tt0) cc_final: 0.8575 (tt0)
REVERT: B  198 ASP cc_start: 0.8733 (t70) cc_final: 0.8526 (t0)
REVERT: A   25 LEU cc_start: 0.9613 (tp) cc_final: 0.9410 (tp)
REVERT: A  105 GLU cc_start: 0.8581 (tm-30) cc_final: 0.8187 (tm-30)
REVERT: A  163 ASN cc_start: 0.9139 (t0) cc_final: 0.8838 (t160)
REVERT: A  198 ASP cc_start: 0.8733 (t70) cc_final: 0.8371 (t0)
  outliers start: 0
  outliers final: 0
  residues processed: 114
  average time/residue: 0.0651
  time to fit residues: 9.6427
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  : 0.203 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 56
   random chunks:
   chunk 5 optimal weight:    0.9980
   chunk 54 optimal weight:    5.9990
   chunk 55 optimal weight:    0.0980
   chunk 4 optimal weight:    0.9990
   chunk 51 optimal weight:    5.9990
   chunk 53 optimal weight:    5.9990
   chunk 11 optimal weight:    2.9990
   chunk 38 optimal weight:    4.9990
   chunk 46 optimal weight:    0.9990
   chunk 19 optimal weight:    2.9990
   chunk 7 optimal weight:    0.7980
   overall best weight:    0.7784

-------------------------------------------------------------------------------
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

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3611 r_free = 0.3611 target = 0.097600 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3055 r_free = 0.3055 target = 0.068403 restraints weight = 12613.348|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3090 r_free = 0.3090 target = 0.070175 restraints weight = 7516.497|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3112 r_free = 0.3112 target = 0.071307 restraints weight = 5327.772|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.3124 r_free = 0.3124 target = 0.071928 restraints weight = 4314.327|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 24)----------------|
| r_work = 0.3131 r_free = 0.3131 target = 0.072289 restraints weight = 3833.461|
|-----------------------------------------------------------------------------|
r_work (final): 0.3119
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8356
moved from start:          0.6875

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   4472  Z= 0.129
  Angle     :  0.670   8.057   6074  Z= 0.322
  Chirality :  0.038   0.191    730
  Planarity :  0.004   0.056    760
  Dihedral  :  4.234  20.685    606
  Min Nonbonded Distance : 2.005

Molprobity Statistics.
  All-atom Clashscore : 9.30
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.96 %
    Favored  : 98.04 %
  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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.84 (0.35), residues: 560
  helix:  2.46 (0.25), residues: 386
  sheet:  0.92 (0.70), residues: 50
  loop : -2.97 (0.48), residues: 124

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.014   0.001   ARG A 202 
 TYR   0.011   0.001   TYR A   7 
 PHE   0.015   0.002   PHE A 101 
 TRP   0.012   0.001   TRP B 178 
 HIS   0.002   0.001   HIS A  77 

Details of bonding type rmsd
  covalent geometry    : bond        0.00279 ( 4458)
  covalent geometry    : angle       0.66965 ( 6074)
  hydrogen bonds       : bond        0.04063 (  318)
  hydrogen bonds       : angle       3.37079 (  948)
  metal coordination   : bond        0.00069 (   14)

********************** 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
  114 residues out of total 456 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 114
  time to evaluate  : 0.166 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B    7 TYR cc_start: 0.7056 (t80) cc_final: 0.6805 (t80)
REVERT: B   79 LYS cc_start: 0.8905 (ptpt) cc_final: 0.8146 (pttp)
REVERT: B  156 TYR cc_start: 0.8174 (m-10) cc_final: 0.7832 (m-10)
REVERT: B  194 GLN cc_start: 0.8444 (tm-30) cc_final: 0.8121 (tm-30)
REVERT: B  195 GLN cc_start: 0.8732 (tt0) cc_final: 0.8346 (tt0)
REVERT: B  198 ASP cc_start: 0.8747 (t70) cc_final: 0.8387 (t0)
REVERT: A  163 ASN cc_start: 0.9003 (t0) cc_final: 0.8652 (t0)
REVERT: A  198 ASP cc_start: 0.8676 (t70) cc_final: 0.8342 (t0)
  outliers start: 0
  outliers final: 0
  residues processed: 114
  average time/residue: 0.0730
  time to fit residues: 10.4617
Evaluate side-chains
  96 residues out of total 456 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 96
  time to evaluate  : 0.186 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 56
   random chunks:
   chunk 7 optimal weight:    0.0170
   chunk 33 optimal weight:    3.9990
   chunk 24 optimal weight:    7.9990
   chunk 8 optimal weight:    0.9990
   chunk 26 optimal weight:    5.9990
   chunk 5 optimal weight:    0.4980
   chunk 42 optimal weight:    9.9990
   chunk 47 optimal weight:    3.9990
   chunk 10 optimal weight:    5.9990
   chunk 54 optimal weight:    3.9990
   chunk 1 optimal weight:    5.9990
   overall best weight:    1.9024

-------------------------------------------------------------------------------
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  88 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3585 r_free = 0.3585 target = 0.096106 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3009 r_free = 0.3009 target = 0.066647 restraints weight = 12777.957|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3048 r_free = 0.3048 target = 0.068462 restraints weight = 7581.342|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3072 r_free = 0.3072 target = 0.069606 restraints weight = 5391.308|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 24)----------------|
| r_work = 0.3086 r_free = 0.3086 target = 0.070245 restraints weight = 4371.694|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 38)----------------|
| r_work = 0.3097 r_free = 0.3097 target = 0.070737 restraints weight = 3878.569|
|-----------------------------------------------------------------------------|
r_work (final): 0.3080
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8380
moved from start:          0.6944

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   4472  Z= 0.156
  Angle     :  0.676   6.878   6074  Z= 0.333
  Chirality :  0.038   0.173    730
  Planarity :  0.005   0.057    760
  Dihedral  :  4.176  19.054    606
  Min Nonbonded Distance : 1.933

Molprobity Statistics.
  All-atom Clashscore : 10.44
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.79 %
    Favored  : 98.21 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.66 %
    Favored  : 99.34 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.96 (0.36), residues: 560
  helix:  2.55 (0.25), residues: 394
  sheet:  0.78 (0.70), residues: 50
  loop : -3.21 (0.49), residues: 116

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.015   0.001   ARG A 202 
 TYR   0.014   0.001   TYR B 175 
 PHE   0.015   0.002   PHE A 101 
 TRP   0.013   0.002   TRP B 178 
 HIS   0.002   0.001   HIS A 234 

Details of bonding type rmsd
  covalent geometry    : bond        0.00350 ( 4458)
  covalent geometry    : angle       0.67607 ( 6074)
  hydrogen bonds       : bond        0.04120 (  318)
  hydrogen bonds       : angle       3.36025 (  948)
  metal coordination   : bond        0.00172 (   14)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 964.15 seconds
wall clock time: 17 minutes 20.72 seconds (1040.72 seconds total)