Starting phenix.real_space_refine
on Wed Jan 15 06:08:04 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8zsj_60417/01_2025/8zsj_60417.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8zsj_60417/01_2025/8zsj_60417.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.8
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8zsj_60417/01_2025/8zsj_60417.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8zsj_60417/01_2025/8zsj_60417.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8zsj_60417/01_2025/8zsj_60417.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8zsj_60417/01_2025/8zsj_60417.cif"
  }
  resolution = 2.8
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


Starting job
===============================================================================
-------------------------------------------------------------------------------
Citation:
*********
Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams
PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography.
Acta Cryst. D74:531-544.

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=  -0.000 sd=   0.024
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 4
    Type Number    sf(0)   Gaussians
     S      60      5.16       5
     C    5166      2.51       5
     N    1390      2.21       5
     O    1502      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 5 residue(s): 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/chem_data/mon_lib"
  Total number of atoms: 8118
  Number of models: 1
  Model: ""
    Number of chains: 6
    Chain: "A"
      Number of atoms: 1889
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 231, 1889
          Classifications: {'peptide': 231}
          Modifications used: {'COO': 1}
          Incomplete info: {'truncation_to_alanine': 1}
          Link IDs: {'PTRANS': 6, 'TRANS': 224}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 3
          Unresolved non-hydrogen angles: 3
          Unresolved non-hydrogen dihedrals: 3
    Chain: "B"
      Number of atoms: 2594
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 338, 2594
          Classifications: {'peptide': 338}
          Incomplete info: {'truncation_to_alanine': 1}
          Link IDs: {'PTRANS': 5, 'TRANS': 332}
          Unresolved non-hydrogen bonds: 6
          Unresolved non-hydrogen angles: 7
          Unresolved non-hydrogen dihedrals: 5
          Planarities with less than four sites: {'ARG:plan': 1}
          Unresolved non-hydrogen planarities: 5
    Chain: "G"
      Number of atoms: 436
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 57, 436
          Classifications: {'peptide': 57}
          Link IDs: {'PTRANS': 4, 'TRANS': 52}
    Chain: "N"
      Number of atoms: 967
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 127, 967
          Classifications: {'peptide': 127}
          Link IDs: {'PTRANS': 5, 'TRANS': 121}
    Chain: "R"
      Number of atoms: 2200
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 282, 2200
          Classifications: {'peptide': 282}
          Incomplete info: {'truncation_to_alanine': 23}
          Link IDs: {'PTRANS': 11, 'TRANS': 270}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 91
          Unresolved non-hydrogen angles: 107
          Unresolved non-hydrogen dihedrals: 80
          Unresolved non-hydrogen chiralities: 3
          Planarities with less than four sites: {'TYR:plan': 1, 'GLU:plan': 4, 'ARG:plan': 3, 'ASN:plan1': 1, 'HIS:plan': 1}
          Unresolved non-hydrogen planarities: 46
    Chain: "R"
      Number of atoms: 32
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 5, 32
          Unusual residues: {'CLR': 1}
          Classifications: {'undetermined': 1, 'water': 4}
          Link IDs: {None: 4}
  Time building chain proxies: 4.87, per 1000 atoms: 0.60
  Number of scatterers: 8118
  At special positions: 0
  Unit cell: (80.704, 99.008, 133.952, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     S      60     16.00
     O    1502      8.00
     N    1390      7.00
     C    5166      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=3, symmetry=0
    Simple disulfide: pdb=" SG  CYS N  22 " - pdb=" SG  CYS N  96 " distance=2.03
    Simple disulfide: pdb=" SG  CYS N  99 " - pdb=" SG  CYS N 107 " distance=2.03
    Simple disulfide: pdb=" SG  CYS R  96 " - pdb=" SG  CYS R 182 " distance=2.03

  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: 1.98
  Conformation dependent library (CDL) restraints added in 981.2 milliseconds
  

  2042 Ramachandran restraints generated.
    1021 Oldfield, 0 Emsley, 1021 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1948

  Finding SS restraints...
    Secondary structure from input PDB file:
      27 helices and 10 sheets defined
      43.0% alpha, 20.0% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.87
  Creating SS restraints...
    Processing helix  chain 'A' and resid 12 through 38
      removed outlier: 3.557A  pdb=" N   GLU A  34 " --> pdb=" O   ARG A  30 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 52 through 56
    Processing helix  chain 'A' and resid 95 through 101
      removed outlier: 3.680A  pdb=" N   ASN A 101 " --> pdb=" O   GLN A  98 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 117 through 131
    Processing helix  chain 'A' and resid 145 through 156
    Processing helix  chain 'A' and resid 159 through 164
      removed outlier: 4.245A  pdb=" N   TYR A 163 " --> pdb=" O   LYS A 159 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 165 through 168
    Processing helix  chain 'A' and resid 183 through 204
      removed outlier: 3.756A  pdb=" N   ILE A 200 " --> pdb=" O   GLU A 196 " (cutoff:3.500A)
      removed outlier: 4.032A  pdb=" N   SER A 204 " --> pdb=" O   ILE A 200 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 222 through 243
    Processing helix  chain 'B' and resid 4 through 26
    Processing helix  chain 'B' and resid 29 through 34
    Processing helix  chain 'G' and resid 7 through 24
    Processing helix  chain 'G' and resid 29 through 44
    Processing helix  chain 'N' and resid 28 through 32
      removed outlier: 3.658A  pdb=" N   TYR N  32 " --> pdb=" O   PHE N  29 " (cutoff:3.500A)
    Processing helix  chain 'N' and resid 62 through 65
    Processing helix  chain 'N' and resid 87 through 91
    Processing helix  chain 'R' and resid 23 through 52
      removed outlier: 3.667A  pdb=" N   SER R  28 " --> pdb=" O   ALA R  24 " (cutoff:3.500A)
      removed outlier: 3.827A  pdb=" N   LEU R  29 " --> pdb=" O   SER R  25 " (cutoff:3.500A)
      removed outlier: 4.657A  pdb=" N   LYS R  52 " --> pdb=" O   ILE R  48 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 56 through 86
      Proline residue:  R  78  - end of helix
    Processing helix  chain 'R' and resid 92 through 127
    Processing helix  chain 'R' and resid 130 through 135
    Processing helix  chain 'R' and resid 136 through 161
      Proline residue:  R 151  - end of helix
    Processing helix  chain 'R' and resid 169 through 179
      removed outlier: 3.777A  pdb=" N   TYR R 173 " --> pdb=" O   GLU R 169 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 187 through 199
    Processing helix  chain 'R' and resid 199 through 230
      removed outlier: 3.549A  pdb=" N   ILE R 205 " --> pdb=" O   ILE R 201 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 247 through 274
      removed outlier: 3.631A  pdb=" N   LYS R 251 " --> pdb=" O   ARG R 247 " (cutoff:3.500A)
      Proline residue:  R 266  - end of helix
    Processing helix  chain 'R' and resid 282 through 305
      removed outlier: 3.522A  pdb=" N   ASN R 286 " --> pdb=" O   PRO R 282 " (cutoff:3.500A)
      removed outlier: 3.618A  pdb=" N   TRP R 291 " --> pdb=" O   ASP R 287 " (cutoff:3.500A)
      removed outlier: 3.723A  pdb=" N   SER R 297 " --> pdb=" O   GLY R 293 " (cutoff:3.500A)
      Proline residue:  R 301  - end of helix
    Processing helix  chain 'R' and resid 308 through 318
    Processing sheet with id=AA1, first strand: chain 'A' and resid 69 through 75
      removed outlier: 6.446A  pdb=" N   HIS A  41 " --> pdb=" O   HIS A  82 " (cutoff:3.500A)
      removed outlier: 7.520A  pdb=" N   PHE A  84 " --> pdb=" O   HIS A  41 " (cutoff:3.500A)
      removed outlier: 6.553A  pdb=" N   LEU A  43 " --> pdb=" O   PHE A  84 " (cutoff:3.500A)
      removed outlier: 7.765A  pdb=" N   VAL A  86 " --> pdb=" O   LEU A  43 " (cutoff:3.500A)
      removed outlier: 7.844A  pdb=" N   LEU A  45 " --> pdb=" O   VAL A  86 " (cutoff:3.500A)
      removed outlier: 9.644A  pdb=" N   ALA A 105 " --> pdb=" O   THR A  40 " (cutoff:3.500A)
      removed outlier: 6.885A  pdb=" N   ARG A  42 " --> pdb=" O   ALA A 105 " (cutoff:3.500A)
      removed outlier: 7.860A  pdb=" N   ILE A 107 " --> pdb=" O   ARG A  42 " (cutoff:3.500A)
      removed outlier: 6.480A  pdb=" N   LEU A  44 " --> pdb=" O   ILE A 107 " (cutoff:3.500A)
      removed outlier: 7.363A  pdb=" N   VAL A 109 " --> pdb=" O   LEU A  44 " (cutoff:3.500A)
      removed outlier: 6.927A  pdb=" N   LEU A  46 " --> pdb=" O   VAL A 109 " (cutoff:3.500A)
      removed outlier: 8.611A  pdb=" N   ASP A 111 " --> pdb=" O   LEU A  46 " (cutoff:3.500A)
      removed outlier: 6.439A  pdb=" N   ILE A 106 " --> pdb=" O   ILE A 140 " (cutoff:3.500A)
      removed outlier: 6.996A  pdb=" N   PHE A 142 " --> pdb=" O   ILE A 106 " (cutoff:3.500A)
      removed outlier: 6.443A  pdb=" N   PHE A 108 " --> pdb=" O   PHE A 142 " (cutoff:3.500A)
      removed outlier: 6.721A  pdb=" N   ASN A 144 " --> pdb=" O   PHE A 108 " (cutoff:3.500A)
      removed outlier: 6.174A  pdb=" N   VAL A 110 " --> pdb=" O   ASN A 144 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'B' and resid 47 through 51
      removed outlier: 3.520A  pdb=" N   LEU B 336 " --> pdb=" O   LEU B  51 " (cutoff:3.500A)
      removed outlier: 3.820A  pdb=" N   CYS B 317 " --> pdb=" O   GLY B 330 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'B' and resid 58 through 63
      removed outlier: 3.513A  pdb=" N   ALA B  60 " --> pdb=" O   ALA B  73 " (cutoff:3.500A)
      removed outlier: 3.599A  pdb=" N   SER B  74 " --> pdb=" O   LYS B  78 " (cutoff:3.500A)
      removed outlier: 4.303A  pdb=" N   LYS B  78 " --> pdb=" O   SER B  74 " (cutoff:3.500A)
      removed outlier: 6.367A  pdb=" N   ASP B  83 " --> pdb=" O   LYS B  89 " (cutoff:3.500A)
      removed outlier: 5.873A  pdb=" N   LYS B  89 " --> pdb=" O   ASP B  83 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'B' and resid 100 through 105
      removed outlier: 6.416A  pdb=" N   ASN B 125 " --> pdb=" O   VAL B 135 " (cutoff:3.500A)
      removed outlier: 6.604A  pdb=" N   VAL B 135 " --> pdb=" O   ASN B 125 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'B' and resid 146 through 151
      removed outlier: 6.514A  pdb=" N   ASP B 170 " --> pdb=" O   GLN B 176 " (cutoff:3.500A)
      removed outlier: 6.184A  pdb=" N   GLN B 176 " --> pdb=" O   ASP B 170 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'B' and resid 187 through 192
      removed outlier: 6.697A  pdb=" N   GLY B 202 " --> pdb=" O   MET B 188 " (cutoff:3.500A)
      removed outlier: 4.441A  pdb=" N   LEU B 190 " --> pdb=" O   VAL B 200 " (cutoff:3.500A)
      removed outlier: 6.664A  pdb=" N   VAL B 200 " --> pdb=" O   LEU B 190 " (cutoff:3.500A)
      removed outlier: 5.156A  pdb=" N   LEU B 192 " --> pdb=" O   LEU B 198 " (cutoff:3.500A)
      removed outlier: 7.392A  pdb=" N   LEU B 198 " --> pdb=" O   LEU B 192 " (cutoff:3.500A)
      removed outlier: 4.492A  pdb=" N   SER B 207 " --> pdb=" O   ALA B 203 " (cutoff:3.500A)
      removed outlier: 3.652A  pdb=" N   GLN B 220 " --> pdb=" O   LEU B 210 " (cutoff:3.500A)
      removed outlier: 6.497A  pdb=" N   ASP B 212 " --> pdb=" O   CYS B 218 " (cutoff:3.500A)
      removed outlier: 6.149A  pdb=" N   CYS B 218 " --> pdb=" O   ASP B 212 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'B' and resid 229 through 234
      removed outlier: 6.578A  pdb=" N   GLY B 244 " --> pdb=" O   ASN B 230 " (cutoff:3.500A)
      removed outlier: 4.277A  pdb=" N   ILE B 232 " --> pdb=" O   ALA B 242 " (cutoff:3.500A)
      removed outlier: 6.656A  pdb=" N   ALA B 242 " --> pdb=" O   ILE B 232 " (cutoff:3.500A)
      removed outlier: 4.807A  pdb=" N   PHE B 234 " --> pdb=" O   ALA B 240 " (cutoff:3.500A)
      removed outlier: 7.017A  pdb=" N   ALA B 240 " --> pdb=" O   PHE B 234 " (cutoff:3.500A)
      removed outlier: 3.562A  pdb=" N   MET B 262 " --> pdb=" O   LEU B 252 " (cutoff:3.500A)
      removed outlier: 5.808A  pdb=" N   ASP B 254 " --> pdb=" O   GLU B 260 " (cutoff:3.500A)
      removed outlier: 5.773A  pdb=" N   GLU B 260 " --> pdb=" O   ASP B 254 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'B' and resid 273 through 278
      removed outlier: 6.401A  pdb=" N   GLY B 288 " --> pdb=" O   THR B 274 " (cutoff:3.500A)
      removed outlier: 4.224A  pdb=" N   VAL B 276 " --> pdb=" O   LEU B 286 " (cutoff:3.500A)
      removed outlier: 6.596A  pdb=" N   LEU B 286 " --> pdb=" O   VAL B 276 " (cutoff:3.500A)
      removed outlier: 4.536A  pdb=" N   PHE B 278 " --> pdb=" O   LEU B 284 " (cutoff:3.500A)
      removed outlier: 6.999A  pdb=" N   LEU B 284 " --> pdb=" O   PHE B 278 " (cutoff:3.500A)
      removed outlier: 6.461A  pdb=" N   CYS B 294 " --> pdb=" O   VAL B 307 " (cutoff:3.500A)
      removed outlier: 4.597A  pdb=" N   VAL B 307 " --> pdb=" O   CYS B 294 " (cutoff:3.500A)
      removed outlier: 6.416A  pdb=" N   VAL B 296 " --> pdb=" O   ALA B 305 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'N' and resid 3 through 7
    Processing sheet with id=AB1, first strand: chain 'N' and resid 11 through 12
      removed outlier: 6.976A  pdb=" N   MET N  34 " --> pdb=" O   ASP N  50 " (cutoff:3.500A)
      removed outlier: 4.675A  pdb=" N   ASP N  50 " --> pdb=" O   MET N  34 " (cutoff:3.500A)
      removed outlier: 6.522A  pdb=" N   TRP N  36 " --> pdb=" O   VAL N  48 " (cutoff:3.500A)

    424 hydrogen bonds defined for protein.
    1218 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: 2.29

  Time building geometry restraints manager: 2.30 seconds

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

  Histogram of bond lengths:
        1.18 -     1.31: 1314
        1.31 -     1.43: 2289
        1.43 -     1.56: 4604
        1.56 -     1.69: 0
        1.69 -     1.81: 87
  Bond restraints: 8294
  Sorted by residual:
  bond pdb=" C   CYS B 294 "
       pdb=" O   CYS B 294 "
    ideal  model  delta    sigma   weight residual
    1.235  1.179  0.056 1.28e-02 6.10e+03 1.94e+01
  bond pdb=" CA  LEU B 308 "
       pdb=" C   LEU B 308 "
    ideal  model  delta    sigma   weight residual
    1.528  1.485  0.043 1.04e-02 9.25e+03 1.72e+01
  bond pdb=" C   LEU B 210 "
       pdb=" O   LEU B 210 "
    ideal  model  delta    sigma   weight residual
    1.236  1.188  0.048 1.22e-02 6.72e+03 1.52e+01
  bond pdb=" CA  LEU B 210 "
       pdb=" C   LEU B 210 "
    ideal  model  delta    sigma   weight residual
    1.524  1.480  0.044 1.23e-02 6.61e+03 1.29e+01
  bond pdb=" CA  GLU A  92 "
       pdb=" CB  GLU A  92 "
    ideal  model  delta    sigma   weight residual
    1.528  1.482  0.046 1.35e-02 5.49e+03 1.16e+01
  ... (remaining 8289 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.08: 10983
        2.08 -     4.17: 242
        4.17 -     6.25: 21
        6.25 -     8.34: 2
        8.34 -    10.42: 3
  Bond angle restraints: 11251
  Sorted by residual:
  angle pdb=" N   PHE A  70 "
        pdb=" CA  PHE A  70 "
        pdb=" C   PHE A  70 "
      ideal   model   delta    sigma   weight residual
     110.30  100.05   10.25 1.50e+00 4.44e-01 4.67e+01
  angle pdb=" C   PHE A  70 "
        pdb=" CA  PHE A  70 "
        pdb=" CB  PHE A  70 "
      ideal   model   delta    sigma   weight residual
     110.06  118.15   -8.09 1.39e+00 5.18e-01 3.39e+01
  angle pdb=" N   VAL A  57 "
        pdb=" CA  VAL A  57 "
        pdb=" C   VAL A  57 "
      ideal   model   delta    sigma   weight residual
     112.17  107.42    4.75 9.50e-01 1.11e+00 2.50e+01
  angle pdb=" N   GLU R 170 "
        pdb=" CA  GLU R 170 "
        pdb=" C   GLU R 170 "
      ideal   model   delta    sigma   weight residual
     111.71  106.56    5.15 1.15e+00 7.56e-01 2.01e+01
  angle pdb=" N   GLY R 167 "
        pdb=" CA  GLY R 167 "
        pdb=" C   GLY R 167 "
      ideal   model   delta    sigma   weight residual
     115.64  109.53    6.11 1.46e+00 4.69e-01 1.75e+01
  ... (remaining 11246 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    16.07: 4484
       16.07 -    32.13: 371
       32.13 -    48.20: 85
       48.20 -    64.27: 15
       64.27 -    80.34: 8
  Dihedral angle restraints: 4963
    sinusoidal: 1949
      harmonic: 3014
  Sorted by residual:
  dihedral pdb=" CA  HIS R  50 "
           pdb=" C   HIS R  50 "
           pdb=" N   PHE R  51 "
           pdb=" CA  PHE R  51 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -155.62  -24.38     0      5.00e+00 4.00e-02 2.38e+01
  dihedral pdb=" CB  CYS N  22 "
           pdb=" SG  CYS N  22 "
           pdb=" SG  CYS N  96 "
           pdb=" CB  CYS N  96 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00   53.06   39.94     1      1.00e+01 1.00e-02 2.24e+01
  dihedral pdb=" CG  ARG N  67 "
           pdb=" CD  ARG N  67 "
           pdb=" NE  ARG N  67 "
           pdb=" CZ  ARG N  67 "
      ideal   model   delta sinusoidal    sigma   weight residual
      90.00  131.74  -41.74     2      1.50e+01 4.44e-03 9.45e+00
  ... (remaining 4960 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.067: 1063
       0.067 -    0.133: 178
       0.133 -    0.200: 21
       0.200 -    0.266: 3
       0.266 -    0.333: 1
  Chirality restraints: 1266
  Sorted by residual:
  chirality pdb=" CA  THR N  91 "
            pdb=" N   THR N  91 "
            pdb=" C   THR N  91 "
            pdb=" CB  THR N  91 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.53    2.19    0.33 2.00e-01 2.50e+01 2.77e+00
  chirality pdb=" CA  ASP R 287 "
            pdb=" N   ASP R 287 "
            pdb=" C   ASP R 287 "
            pdb=" CB  ASP R 287 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.29    0.22 2.00e-01 2.50e+01 1.22e+00
  chirality pdb=" CA  VAL A  57 "
            pdb=" N   VAL A  57 "
            pdb=" C   VAL A  57 "
            pdb=" CB  VAL A  57 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.66   -0.22 2.00e-01 2.50e+01 1.21e+00
  ... (remaining 1263 not shown)

  Planarity restraints: 1429
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CD  ARG R  83 "    0.418 9.50e-02 1.11e+02   1.88e-01 2.15e+01
        pdb=" NE  ARG R  83 "   -0.025 2.00e-02 2.50e+03
        pdb=" CZ  ARG R  83 "   -0.004 2.00e-02 2.50e+03
        pdb=" NH1 ARG R  83 "   -0.004 2.00e-02 2.50e+03
        pdb=" NH2 ARG R  83 "    0.014 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   TYR R 308 "    0.071 5.00e-02 4.00e+02   1.07e-01 1.83e+01
        pdb=" N   PRO R 309 "   -0.185 5.00e-02 4.00e+02
        pdb=" CA  PRO R 309 "    0.056 5.00e-02 4.00e+02
        pdb=" CD  PRO R 309 "    0.057 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CD  ARG R 312 "    0.383 9.50e-02 1.11e+02   1.72e-01 1.80e+01
        pdb=" NE  ARG R 312 "   -0.022 2.00e-02 2.50e+03
        pdb=" CZ  ARG R 312 "   -0.005 2.00e-02 2.50e+03
        pdb=" NH1 ARG R 312 "   -0.003 2.00e-02 2.50e+03
        pdb=" NH2 ARG R 312 "    0.013 2.00e-02 2.50e+03
  ... (remaining 1426 not shown)

  Histogram of nonbonded interaction distances:
        2.22 -     2.75: 1105
        2.75 -     3.29: 7970
        3.29 -     3.83: 14027
        3.83 -     4.36: 17110
        4.36 -     4.90: 29488
  Nonbonded interactions: 69700
  Sorted by model distance:
  nonbonded pdb=" OG  SER N   7 "
            pdb=" OG  SER N  21 "
     model   vdw
     2.216 3.040
  nonbonded pdb=" O   ILE B  58 "
            pdb=" OG  SER B 316 "
     model   vdw
     2.231 3.040
  nonbonded pdb=" OG1 THR R  56 "
            pdb=" OD1 ASN R  59 "
     model   vdw
     2.253 3.040
  nonbonded pdb=" OG  SER B 227 "
            pdb=" O   PRO N 100 "
     model   vdw
     2.272 3.040
  nonbonded pdb=" OD2 ASP R 103 "
            pdb=" O   HOH R 501 "
     model   vdw
     2.273 3.040
  ... (remaining 69695 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: 0.00
========== WARNING! ============

  No NCS relation were found !!!

================================

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             2.270
  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:          0.310
  Check model and map are aligned:         0.060
  Set scattering table:                    0.070
  Process input model:                     20.880
  Find NCS groups from input model:        0.070
  Set up NCS constraints:                  0.030
  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:12.340
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   36.040
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8060
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      :  0.005   0.056   8294  Z= 0.324
  Angle     :  0.684  10.422  11251  Z= 0.444
  Chirality :  0.051   0.333   1266
  Planarity :  0.011   0.188   1429
  Dihedral  : 12.911  80.336   3006
  Min Nonbonded Distance : 2.216

Molprobity Statistics.
  All-atom Clashscore : 8.42
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.43 %
    Favored  : 96.57 %
  Rotamer:
    Outliers :  0.12 %
    Allowed  :  1.16 %
    Favored  : 98.73 %
  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:  0.88 (0.27), residues: 1021
  helix:  2.24 (0.25), residues: 387
  sheet: -0.06 (0.35), residues: 215
  loop : -0.62 (0.31), residues: 419

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.002   TRP R 291 
 HIS   0.004   0.001   HIS R  63 
 PHE   0.018   0.001   PHE R  91 
 TYR   0.010   0.001   TYR R 308 
 ARG   0.016   0.001   ARG A 237 

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

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

  2042 Ramachandran restraints generated.
    1021 Oldfield, 0 Emsley, 1021 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2042 Ramachandran restraints generated.
    1021 Oldfield, 0 Emsley, 1021 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  179 residues out of total 890 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 178
  time to evaluate  : 0.917 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   15 ASP cc_start: 0.7879 (m-30) cc_final: 0.7586 (m-30)
REVERT: N   53 GLN cc_start: 0.8750 (mp10) cc_final: 0.8533 (mp10)
REVERT: R   95 PHE cc_start: 0.7456 (t80) cc_final: 0.7231 (t80)
REVERT: R  302 MET cc_start: 0.7989 (mtt) cc_final: 0.7758 (mtp)
  outliers start: 1
  outliers final: 1
  residues processed: 178
  average time/residue: 1.3836
  time to fit residues: 259.3331
Evaluate side-chains
  142 residues out of total 890 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 141
  time to evaluate  : 0.943 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue  184 VAL
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 101
   random chunks:
   chunk 85 optimal weight:    0.5980
   chunk 76 optimal weight:    2.9990
   chunk 42 optimal weight:    4.9990
   chunk 26 optimal weight:    4.9990
   chunk 51 optimal weight:    0.0470
   chunk 40 optimal weight:    2.9990
   chunk 79 optimal weight:    5.9990
   chunk 30 optimal weight:    1.9990
   chunk 48 optimal weight:    0.5980
   chunk 58 optimal weight:    4.9990
   chunk 91 optimal weight:    0.9980
   overall best weight:    0.8480

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

Flipped N/Q/H residues before XYZ refinement:
A 131 ASN
B  17 GLN
B  44 GLN
B 237 ASN
B 239 ASN
B 259 GLN
B 340 ASN
N   3 GLN
N  39 GLN
N  77 ASN

Total number of N/Q/H flips: 10

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3848 r_free = 0.3848 target = 0.149973 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.3473 r_free = 0.3473 target = 0.115068 restraints weight = 10272.018|
|-----------------------------------------------------------------------------|
r_work (start): 0.3414 rms_B_bonded: 2.52
r_work: 0.3275 rms_B_bonded: 3.04 restraints_weight: 0.5000
r_work: 0.3136 rms_B_bonded: 4.86 restraints_weight: 0.2500
r_work (final): 0.3136
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8168
moved from start:          0.1484

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038   8294  Z= 0.227
  Angle     :  0.546  10.230  11251  Z= 0.291
  Chirality :  0.042   0.159   1266
  Planarity :  0.005   0.073   1429
  Dihedral  :  4.318  27.525   1191
  Min Nonbonded Distance : 2.560

Molprobity Statistics.
  All-atom Clashscore : 6.98
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.45 %
    Favored  : 97.55 %
  Rotamer:
    Outliers :  1.73 %
    Allowed  : 11.45 %
    Favored  : 86.82 %
  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:  1.05 (0.27), residues: 1021
  helix:  2.40 (0.25), residues: 389
  sheet: -0.01 (0.35), residues: 212
  loop : -0.54 (0.31), residues: 420

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.002   TRP B 169 
 HIS   0.005   0.001   HIS R  63 
 PHE   0.013   0.001   PHE R  51 
 TYR   0.012   0.001   TYR A 115 
 ARG   0.007   0.000   ARG A 199 

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

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

  2042 Ramachandran restraints generated.
    1021 Oldfield, 0 Emsley, 1021 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2042 Ramachandran restraints generated.
    1021 Oldfield, 0 Emsley, 1021 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  165 residues out of total 890 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 150
  time to evaluate  : 0.845 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   15 ASP cc_start: 0.7760 (m-30) cc_final: 0.7368 (m-30)
REVERT: A   35 LYS cc_start: 0.8692 (ttpt) cc_final: 0.8386 (ptpt)
REVERT: A  151 GLU cc_start: 0.8081 (tp30) cc_final: 0.7860 (tp30)
REVERT: B   59 TYR cc_start: 0.8667 (m-80) cc_final: 0.8245 (m-80)
REVERT: B   75 GLN cc_start: 0.8155 (tt0) cc_final: 0.7917 (tt0)
REVERT: B  134 ARG cc_start: 0.7282 (OUTLIER) cc_final: 0.6748 (ptm160)
REVERT: N   37 VAL cc_start: 0.8828 (OUTLIER) cc_final: 0.8595 (m)
REVERT: N   53 GLN cc_start: 0.8570 (mp10) cc_final: 0.8186 (mp10)
REVERT: R  262 ILE cc_start: 0.8375 (OUTLIER) cc_final: 0.7938 (mp)
REVERT: R  302 MET cc_start: 0.8386 (mtt) cc_final: 0.8007 (mtp)
  outliers start: 15
  outliers final: 4
  residues processed: 154
  average time/residue: 1.4189
  time to fit residues: 230.5374
Evaluate side-chains
  147 residues out of total 890 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 140
  time to evaluate  : 0.945 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  118 ASP
Chi-restraints excluded: chain B residue  134 ARG
Chi-restraints excluded: chain N residue   37 VAL
Chi-restraints excluded: chain N residue   59 SER
Chi-restraints excluded: chain R residue  184 VAL
Chi-restraints excluded: chain R residue  262 ILE
Chi-restraints excluded: chain R residue  315 LEU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 101
   random chunks:
   chunk 0 optimal weight:   10.0000
   chunk 17 optimal weight:    0.6980
   chunk 36 optimal weight:    2.9990
   chunk 49 optimal weight:    0.9990
   chunk 56 optimal weight:    9.9990
   chunk 78 optimal weight:    0.9980
   chunk 40 optimal weight:    2.9990
   chunk 94 optimal weight:    0.8980
   chunk 97 optimal weight:    2.9990
   chunk 84 optimal weight:    1.9990
   chunk 74 optimal weight:    1.9990
   overall best weight:    1.1184

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

Flipped N/Q/H residues before XYZ refinement:
A  80 ASN
B  17 GLN
B  44 GLN
B  75 GLN
B 237 ASN
B 259 GLN
N  39 GLN
N  77 ASN
R 296 ASN

Total number of N/Q/H flips: 9

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3834 r_free = 0.3834 target = 0.148656 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3452 r_free = 0.3452 target = 0.113390 restraints weight = 10488.229|
|-----------------------------------------------------------------------------|
r_work (start): 0.3392 rms_B_bonded: 2.54
r_work: 0.3257 rms_B_bonded: 3.05 restraints_weight: 0.5000
r_work: 0.3121 rms_B_bonded: 4.85 restraints_weight: 0.2500
r_work (final): 0.3121
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8173
moved from start:          0.1798

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.042   8294  Z= 0.263
  Angle     :  0.544   9.938  11251  Z= 0.289
  Chirality :  0.042   0.146   1266
  Planarity :  0.005   0.062   1429
  Dihedral  :  4.385  30.893   1191
  Min Nonbonded Distance : 2.568

Molprobity Statistics.
  All-atom Clashscore : 6.49
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.13 %
    Favored  : 96.87 %
  Rotamer:
    Outliers :  2.20 %
    Allowed  : 14.57 %
    Favored  : 83.24 %
  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:  1.02 (0.27), residues: 1021
  helix:  2.30 (0.25), residues: 397
  sheet: -0.13 (0.33), residues: 217
  loop : -0.45 (0.32), residues: 407

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.002   TRP B  82 
 HIS   0.004   0.001   HIS A 214 
 PHE   0.017   0.002   PHE R  91 
 TYR   0.017   0.001   TYR N  60 
 ARG   0.007   0.000   ARG A  94 

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

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

  2042 Ramachandran restraints generated.
    1021 Oldfield, 0 Emsley, 1021 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2042 Ramachandran restraints generated.
    1021 Oldfield, 0 Emsley, 1021 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  162 residues out of total 890 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 143
  time to evaluate  : 0.936 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   14 GLU cc_start: 0.7128 (pm20) cc_final: 0.6893 (pm20)
REVERT: A   15 ASP cc_start: 0.7801 (m-30) cc_final: 0.7412 (m-30)
REVERT: A  151 GLU cc_start: 0.8169 (tp30) cc_final: 0.7853 (tp30)
REVERT: B   19 ARG cc_start: 0.7608 (ttp-110) cc_final: 0.7350 (ttp-110)
REVERT: B  134 ARG cc_start: 0.7275 (OUTLIER) cc_final: 0.6731 (ptm160)
REVERT: B  219 ARG cc_start: 0.8318 (mtt-85) cc_final: 0.7818 (mtp85)
REVERT: B  325 MET cc_start: 0.8499 (tpp) cc_final: 0.7972 (mmm)
REVERT: N   37 VAL cc_start: 0.8847 (t) cc_final: 0.8579 (m)
REVERT: N   53 GLN cc_start: 0.8552 (mp10) cc_final: 0.8203 (mp10)
REVERT: R  262 ILE cc_start: 0.8336 (OUTLIER) cc_final: 0.7888 (mp)
REVERT: R  302 MET cc_start: 0.8351 (mtt) cc_final: 0.7972 (mtp)
  outliers start: 19
  outliers final: 5
  residues processed: 150
  average time/residue: 1.3998
  time to fit residues: 221.1929
Evaluate side-chains
  143 residues out of total 890 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 136
  time to evaluate  : 0.836 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   49 ASP
Chi-restraints excluded: chain B residue   23 LYS
Chi-restraints excluded: chain B residue   29 THR
Chi-restraints excluded: chain B residue  118 ASP
Chi-restraints excluded: chain B residue  134 ARG
Chi-restraints excluded: chain N residue   59 SER
Chi-restraints excluded: chain R residue  262 ILE
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 101
   random chunks:
   chunk 1 optimal weight:    1.9990
   chunk 58 optimal weight:    6.9990
   chunk 67 optimal weight:    2.9990
   chunk 79 optimal weight:    0.0070
   chunk 0 optimal weight:    2.9990
   chunk 38 optimal weight:    0.9990
   chunk 35 optimal weight:    0.9990
   chunk 64 optimal weight:    0.9990
   chunk 25 optimal weight:    0.7980
   chunk 13 optimal weight:    1.9990
   chunk 37 optimal weight:    0.9990
   overall best weight:    0.7604

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

Flipped N/Q/H residues before XYZ refinement:
B  17 GLN
B  44 GLN
B 237 ASN
B 259 GLN
N  77 ASN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3844 r_free = 0.3844 target = 0.149593 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3471 r_free = 0.3471 target = 0.114686 restraints weight = 10379.128|
|-----------------------------------------------------------------------------|
r_work (start): 0.3412 rms_B_bonded: 2.52
r_work: 0.3277 rms_B_bonded: 3.04 restraints_weight: 0.5000
r_work: 0.3142 rms_B_bonded: 4.84 restraints_weight: 0.2500
r_work (final): 0.3142
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8159
moved from start:          0.1976

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   8294  Z= 0.203
  Angle     :  0.512   9.964  11251  Z= 0.270
  Chirality :  0.041   0.142   1266
  Planarity :  0.004   0.056   1429
  Dihedral  :  4.185  19.228   1190
  Min Nonbonded Distance : 2.569

Molprobity Statistics.
  All-atom Clashscore : 6.42
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.94 %
    Favored  : 97.06 %
  Rotamer:
    Outliers :  2.43 %
    Allowed  : 15.49 %
    Favored  : 82.08 %
  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:  1.09 (0.27), residues: 1021
  helix:  2.36 (0.25), residues: 397
  sheet: -0.09 (0.33), residues: 217
  loop : -0.43 (0.32), residues: 407

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.002   TRP B  82 
 HIS   0.003   0.001   HIS R  63 
 PHE   0.020   0.001   PHE R  91 
 TYR   0.020   0.001   TYR N  60 
 ARG   0.006   0.000   ARG A 199 

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

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

  2042 Ramachandran restraints generated.
    1021 Oldfield, 0 Emsley, 1021 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2042 Ramachandran restraints generated.
    1021 Oldfield, 0 Emsley, 1021 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  174 residues out of total 890 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 153
  time to evaluate  : 0.920 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   14 GLU cc_start: 0.7146 (pm20) cc_final: 0.6888 (pm20)
REVERT: A   15 ASP cc_start: 0.7807 (m-30) cc_final: 0.7414 (m-30)
REVERT: A   35 LYS cc_start: 0.8553 (ttpt) cc_final: 0.8304 (ptpt)
REVERT: A  151 GLU cc_start: 0.8214 (tp30) cc_final: 0.7832 (tp30)
REVERT: B   75 GLN cc_start: 0.8249 (tt0) cc_final: 0.8013 (tt0)
REVERT: B  134 ARG cc_start: 0.7301 (OUTLIER) cc_final: 0.6737 (ptm160)
REVERT: B  219 ARG cc_start: 0.8301 (mtt-85) cc_final: 0.7789 (mtp85)
REVERT: B  325 MET cc_start: 0.8498 (tpp) cc_final: 0.7978 (mmm)
REVERT: N   37 VAL cc_start: 0.8821 (OUTLIER) cc_final: 0.8581 (m)
REVERT: N   53 GLN cc_start: 0.8533 (mp10) cc_final: 0.8116 (mp10)
REVERT: R  262 ILE cc_start: 0.8345 (OUTLIER) cc_final: 0.7897 (mp)
REVERT: R  302 MET cc_start: 0.8341 (mtt) cc_final: 0.7961 (mtp)
  outliers start: 21
  outliers final: 5
  residues processed: 163
  average time/residue: 1.1618
  time to fit residues: 201.5533
Evaluate side-chains
  149 residues out of total 890 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 141
  time to evaluate  : 0.971 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   23 LYS
Chi-restraints excluded: chain B residue   29 THR
Chi-restraints excluded: chain B residue  134 ARG
Chi-restraints excluded: chain N residue   37 VAL
Chi-restraints excluded: chain N residue   59 SER
Chi-restraints excluded: chain N residue  110 VAL
Chi-restraints excluded: chain R residue  226 ASP
Chi-restraints excluded: chain R residue  262 ILE
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 101
   random chunks:
   chunk 18 optimal weight:    0.6980
   chunk 11 optimal weight:    0.9990
   chunk 9 optimal weight:    0.8980
   chunk 7 optimal weight:    3.9990
   chunk 22 optimal weight:    0.6980
   chunk 12 optimal weight:    0.9980
   chunk 62 optimal weight:    1.9990
   chunk 19 optimal weight:    2.9990
   chunk 87 optimal weight:    9.9990
   chunk 56 optimal weight:    5.9990
   chunk 63 optimal weight:    0.8980
   overall best weight:    0.8380

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

Flipped N/Q/H residues before XYZ refinement:
A  82 HIS
A 131 ASN
B  17 GLN
B  44 GLN
B 237 ASN
B 259 GLN
N  31 ASN
N  77 ASN
R  55 HIS

Total number of N/Q/H flips: 9

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3841 r_free = 0.3841 target = 0.149309 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3466 r_free = 0.3466 target = 0.114400 restraints weight = 10366.456|
|-----------------------------------------------------------------------------|
r_work (start): 0.3409 rms_B_bonded: 2.53
r_work: 0.3274 rms_B_bonded: 3.05 restraints_weight: 0.5000
r_work: 0.3136 rms_B_bonded: 4.88 restraints_weight: 0.2500
r_work (final): 0.3136
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8171
moved from start:          0.2126

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   8294  Z= 0.213
  Angle     :  0.516   9.175  11251  Z= 0.273
  Chirality :  0.041   0.149   1266
  Planarity :  0.004   0.053   1429
  Dihedral  :  4.126  18.297   1190
  Min Nonbonded Distance : 2.536

Molprobity Statistics.
  All-atom Clashscore : 7.05
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.13 %
    Favored  : 96.87 %
  Rotamer:
    Outliers :  2.66 %
    Allowed  : 17.11 %
    Favored  : 80.23 %
  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:  1.14 (0.27), residues: 1021
  helix:  2.42 (0.25), residues: 398
  sheet: -0.08 (0.32), residues: 215
  loop : -0.42 (0.32), residues: 408

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.002   TRP B  82 
 HIS   0.004   0.001   HIS R  63 
 PHE   0.014   0.001   PHE R  91 
 TYR   0.024   0.002   TYR N  60 
 ARG   0.007   0.000   ARG A 199 

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

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

  2042 Ramachandran restraints generated.
    1021 Oldfield, 0 Emsley, 1021 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2042 Ramachandran restraints generated.
    1021 Oldfield, 0 Emsley, 1021 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  169 residues out of total 890 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 146
  time to evaluate  : 0.912 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   14 GLU cc_start: 0.7087 (pm20) cc_final: 0.6788 (pm20)
REVERT: A   15 ASP cc_start: 0.7801 (m-30) cc_final: 0.7431 (m-30)
REVERT: A   21 ARG cc_start: 0.7919 (OUTLIER) cc_final: 0.7550 (ttt180)
REVERT: A  151 GLU cc_start: 0.8220 (tp30) cc_final: 0.7828 (tp30)
REVERT: B   75 GLN cc_start: 0.8299 (tt0) cc_final: 0.8059 (tt0)
REVERT: B  134 ARG cc_start: 0.7319 (OUTLIER) cc_final: 0.6753 (ptm160)
REVERT: B  325 MET cc_start: 0.8501 (tpp) cc_final: 0.7958 (mmm)
REVERT: N   37 VAL cc_start: 0.8811 (OUTLIER) cc_final: 0.8598 (m)
REVERT: N   53 GLN cc_start: 0.8550 (mp10) cc_final: 0.8124 (mp10)
REVERT: R  262 ILE cc_start: 0.8340 (OUTLIER) cc_final: 0.7889 (mp)
REVERT: R  302 MET cc_start: 0.8360 (mtt) cc_final: 0.7985 (mtp)
  outliers start: 23
  outliers final: 13
  residues processed: 159
  average time/residue: 1.2470
  time to fit residues: 210.4729
Evaluate side-chains
  158 residues out of total 890 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 141
  time to evaluate  : 0.942 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   21 ARG
Chi-restraints excluded: chain B residue   23 LYS
Chi-restraints excluded: chain B residue   29 THR
Chi-restraints excluded: chain B residue  114 CYS
Chi-restraints excluded: chain B residue  118 ASP
Chi-restraints excluded: chain B residue  134 ARG
Chi-restraints excluded: chain B residue  146 LEU
Chi-restraints excluded: chain B residue  334 SER
Chi-restraints excluded: chain B residue  336 LEU
Chi-restraints excluded: chain N residue   37 VAL
Chi-restraints excluded: chain N residue   59 SER
Chi-restraints excluded: chain N residue  110 VAL
Chi-restraints excluded: chain R residue   67 THR
Chi-restraints excluded: chain R residue   97 LYS
Chi-restraints excluded: chain R residue  103 ASP
Chi-restraints excluded: chain R residue  226 ASP
Chi-restraints excluded: chain R residue  262 ILE
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 101
   random chunks:
   chunk 59 optimal weight:    4.9990
   chunk 17 optimal weight:    0.7980
   chunk 33 optimal weight:    3.9990
   chunk 34 optimal weight:    0.9980
   chunk 94 optimal weight:    0.6980
   chunk 60 optimal weight:    0.6980
   chunk 13 optimal weight:    0.5980
   chunk 22 optimal weight:    0.6980
   chunk 57 optimal weight:   10.0000
   chunk 100 optimal weight:    0.9980
   chunk 20 optimal weight:    0.9980
   overall best weight:    0.6980

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

Flipped N/Q/H residues before XYZ refinement:
B  17 GLN
B  44 GLN
B 237 ASN
B 259 GLN
N  77 ASN
R  53 GLN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3849 r_free = 0.3849 target = 0.150044 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3475 r_free = 0.3475 target = 0.115096 restraints weight = 10373.476|
|-----------------------------------------------------------------------------|
r_work (start): 0.3414 rms_B_bonded: 2.52
r_work: 0.3279 rms_B_bonded: 3.05 restraints_weight: 0.5000
r_work: 0.3143 rms_B_bonded: 4.87 restraints_weight: 0.2500
r_work (final): 0.3143
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8161
moved from start:          0.2240

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   8294  Z= 0.191
  Angle     :  0.506   9.365  11251  Z= 0.267
  Chirality :  0.041   0.142   1266
  Planarity :  0.004   0.051   1429
  Dihedral  :  4.076  18.046   1190
  Min Nonbonded Distance : 2.480

Molprobity Statistics.
  All-atom Clashscore : 7.17
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.94 %
    Favored  : 97.06 %
  Rotamer:
    Outliers :  2.77 %
    Allowed  : 17.92 %
    Favored  : 79.31 %
  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:  1.14 (0.27), residues: 1021
  helix:  2.44 (0.25), residues: 398
  sheet: -0.06 (0.32), residues: 216
  loop : -0.44 (0.32), residues: 407

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.002   TRP B  82 
 HIS   0.003   0.001   HIS R  63 
 PHE   0.015   0.001   PHE R  91 
 TYR   0.024   0.001   TYR N  60 
 ARG   0.007   0.000   ARG A 199 

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

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

  2042 Ramachandran restraints generated.
    1021 Oldfield, 0 Emsley, 1021 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2042 Ramachandran restraints generated.
    1021 Oldfield, 0 Emsley, 1021 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  169 residues out of total 890 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 145
  time to evaluate  : 0.920 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   14 GLU cc_start: 0.7136 (pm20) cc_final: 0.6804 (pm20)
REVERT: A   15 ASP cc_start: 0.7806 (m-30) cc_final: 0.7425 (m-30)
REVERT: A  151 GLU cc_start: 0.8196 (tp30) cc_final: 0.7857 (tp30)
REVERT: B   75 GLN cc_start: 0.8272 (tt0) cc_final: 0.8012 (tt0)
REVERT: B  134 ARG cc_start: 0.7310 (OUTLIER) cc_final: 0.6748 (ptm160)
REVERT: B  155 ASN cc_start: 0.8146 (t0) cc_final: 0.7895 (t0)
REVERT: B  325 MET cc_start: 0.8505 (tpp) cc_final: 0.7961 (mmm)
REVERT: N   53 GLN cc_start: 0.8542 (mp10) cc_final: 0.8109 (mp10)
REVERT: R  262 ILE cc_start: 0.8343 (OUTLIER) cc_final: 0.7904 (mp)
REVERT: R  302 MET cc_start: 0.8348 (mtt) cc_final: 0.7967 (mtp)
  outliers start: 24
  outliers final: 11
  residues processed: 155
  average time/residue: 1.2472
  time to fit residues: 204.8478
Evaluate side-chains
  156 residues out of total 890 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 143
  time to evaluate  : 0.914 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   23 LYS
Chi-restraints excluded: chain B residue   29 THR
Chi-restraints excluded: chain B residue  114 CYS
Chi-restraints excluded: chain B residue  118 ASP
Chi-restraints excluded: chain B residue  134 ARG
Chi-restraints excluded: chain B residue  146 LEU
Chi-restraints excluded: chain B residue  334 SER
Chi-restraints excluded: chain N residue   59 SER
Chi-restraints excluded: chain N residue  110 VAL
Chi-restraints excluded: chain R residue   74 CYS
Chi-restraints excluded: chain R residue   97 LYS
Chi-restraints excluded: chain R residue  226 ASP
Chi-restraints excluded: chain R residue  262 ILE
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 101
   random chunks:
   chunk 2 optimal weight:    2.9990
   chunk 89 optimal weight:    5.9990
   chunk 53 optimal weight:    3.9990
   chunk 44 optimal weight:    0.9990
   chunk 71 optimal weight:    0.8980
   chunk 72 optimal weight:    0.5980
   chunk 80 optimal weight:    1.9990
   chunk 82 optimal weight:    0.6980
   chunk 19 optimal weight:    0.0030
   chunk 47 optimal weight:    0.9990
   chunk 84 optimal weight:    0.8980
   overall best weight:    0.6190

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

Flipped N/Q/H residues before XYZ refinement:
B  17 GLN
B  44 GLN
B 237 ASN
B 259 GLN
N  77 ASN
R  53 GLN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3853 r_free = 0.3853 target = 0.150534 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3482 r_free = 0.3482 target = 0.115713 restraints weight = 10402.074|
|-----------------------------------------------------------------------------|
r_work (start): 0.3420 rms_B_bonded: 2.52
r_work: 0.3285 rms_B_bonded: 3.05 restraints_weight: 0.5000
r_work: 0.3150 rms_B_bonded: 4.88 restraints_weight: 0.2500
r_work (final): 0.3150
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8144
moved from start:          0.2344

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   8294  Z= 0.182
  Angle     :  0.502   9.245  11251  Z= 0.265
  Chirality :  0.040   0.141   1266
  Planarity :  0.004   0.051   1429
  Dihedral  :  4.000  17.306   1190
  Min Nonbonded Distance : 2.506

Molprobity Statistics.
  All-atom Clashscore : 6.55
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.74 %
    Favored  : 97.26 %
  Rotamer:
    Outliers :  2.43 %
    Allowed  : 18.50 %
    Favored  : 79.08 %
  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:  1.13 (0.26), residues: 1021
  helix:  2.42 (0.25), residues: 399
  sheet: -0.04 (0.32), residues: 215
  loop : -0.47 (0.32), residues: 407

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.002   TRP B  82 
 HIS   0.003   0.001   HIS R  63 
 PHE   0.011   0.001   PHE A  74 
 TYR   0.015   0.001   TYR N  60 
 ARG   0.009   0.000   ARG A 199 

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

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

  2042 Ramachandran restraints generated.
    1021 Oldfield, 0 Emsley, 1021 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2042 Ramachandran restraints generated.
    1021 Oldfield, 0 Emsley, 1021 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  168 residues out of total 890 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 147
  time to evaluate  : 0.889 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   14 GLU cc_start: 0.7134 (pm20) cc_final: 0.6795 (pm20)
REVERT: A   15 ASP cc_start: 0.7804 (m-30) cc_final: 0.7436 (m-30)
REVERT: A  151 GLU cc_start: 0.8163 (tp30) cc_final: 0.7760 (tp30)
REVERT: B   75 GLN cc_start: 0.8295 (tt0) cc_final: 0.8034 (tt0)
REVERT: B  134 ARG cc_start: 0.7218 (OUTLIER) cc_final: 0.6678 (ptm160)
REVERT: B  155 ASN cc_start: 0.8164 (t0) cc_final: 0.7919 (t0)
REVERT: B  219 ARG cc_start: 0.8284 (mtt-85) cc_final: 0.7781 (mtp85)
REVERT: B  325 MET cc_start: 0.8520 (tpp) cc_final: 0.7981 (mmm)
REVERT: N   43 LYS cc_start: 0.7967 (mtpt) cc_final: 0.7743 (mtpp)
REVERT: N   53 GLN cc_start: 0.8556 (mp10) cc_final: 0.8103 (mp10)
REVERT: R  262 ILE cc_start: 0.8325 (OUTLIER) cc_final: 0.7888 (mp)
REVERT: R  302 MET cc_start: 0.8329 (mtt) cc_final: 0.7927 (mtp)
  outliers start: 21
  outliers final: 14
  residues processed: 160
  average time/residue: 1.2522
  time to fit residues: 212.3059
Evaluate side-chains
  156 residues out of total 890 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 140
  time to evaluate  : 0.897 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   34 GLU
Chi-restraints excluded: chain B residue   23 LYS
Chi-restraints excluded: chain B residue   29 THR
Chi-restraints excluded: chain B residue  114 CYS
Chi-restraints excluded: chain B residue  118 ASP
Chi-restraints excluded: chain B residue  134 ARG
Chi-restraints excluded: chain B residue  146 LEU
Chi-restraints excluded: chain B residue  334 SER
Chi-restraints excluded: chain N residue   59 SER
Chi-restraints excluded: chain N residue   95 TYR
Chi-restraints excluded: chain N residue  110 VAL
Chi-restraints excluded: chain R residue   74 CYS
Chi-restraints excluded: chain R residue   97 LYS
Chi-restraints excluded: chain R residue  103 ASP
Chi-restraints excluded: chain R residue  226 ASP
Chi-restraints excluded: chain R residue  262 ILE
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 101
   random chunks:
   chunk 38 optimal weight:    0.8980
   chunk 100 optimal weight:    0.7980
   chunk 17 optimal weight:    1.9990
   chunk 23 optimal weight:    9.9990
   chunk 2 optimal weight:    4.9990
   chunk 54 optimal weight:    0.9980
   chunk 3 optimal weight:    3.9990
   chunk 82 optimal weight:    0.5980
   chunk 72 optimal weight:    2.9990
   chunk 50 optimal weight:    0.5980
   chunk 98 optimal weight:    1.9990
   overall best weight:    0.7780

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

Flipped N/Q/H residues before XYZ refinement:
B  17 GLN
B  44 GLN
B  88 ASN
B 237 ASN
B 259 GLN
N  77 ASN
R  53 GLN

Total number of N/Q/H flips: 7

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3850 r_free = 0.3850 target = 0.150162 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 56)----------------|
| r_work = 0.3477 r_free = 0.3477 target = 0.115304 restraints weight = 10526.323|
|-----------------------------------------------------------------------------|
r_work (start): 0.3414 rms_B_bonded: 2.53
r_work: 0.3278 rms_B_bonded: 3.06 restraints_weight: 0.5000
r_work: 0.3141 rms_B_bonded: 4.90 restraints_weight: 0.2500
r_work (final): 0.3141
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8157
moved from start:          0.2369

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   8294  Z= 0.204
  Angle     :  0.519   9.293  11251  Z= 0.272
  Chirality :  0.041   0.139   1266
  Planarity :  0.004   0.050   1429
  Dihedral  :  4.017  17.376   1190
  Min Nonbonded Distance : 2.518

Molprobity Statistics.
  All-atom Clashscore : 6.80
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.84 %
    Favored  : 97.16 %
  Rotamer:
    Outliers :  2.89 %
    Allowed  : 18.50 %
    Favored  : 78.61 %
  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:  1.10 (0.26), residues: 1021
  helix:  2.39 (0.25), residues: 399
  sheet: -0.05 (0.32), residues: 217
  loop : -0.49 (0.32), residues: 405

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.002   TRP B  82 
 HIS   0.003   0.001   HIS R  63 
 PHE   0.014   0.001   PHE R  91 
 TYR   0.025   0.001   TYR N  60 
 ARG   0.008   0.000   ARG A 199 

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

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

  2042 Ramachandran restraints generated.
    1021 Oldfield, 0 Emsley, 1021 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2042 Ramachandran restraints generated.
    1021 Oldfield, 0 Emsley, 1021 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  170 residues out of total 890 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 145
  time to evaluate  : 0.835 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   14 GLU cc_start: 0.7137 (pm20) cc_final: 0.6792 (pm20)
REVERT: A   15 ASP cc_start: 0.7813 (m-30) cc_final: 0.7442 (m-30)
REVERT: A  151 GLU cc_start: 0.8167 (tp30) cc_final: 0.7762 (tp30)
REVERT: B   75 GLN cc_start: 0.8273 (tt0) cc_final: 0.8026 (tt0)
REVERT: B  134 ARG cc_start: 0.7241 (OUTLIER) cc_final: 0.6710 (ptm160)
REVERT: B  155 ASN cc_start: 0.8162 (t0) cc_final: 0.7915 (t0)
REVERT: B  325 MET cc_start: 0.8525 (tpp) cc_final: 0.7984 (mmm)
REVERT: N   43 LYS cc_start: 0.7955 (mtpt) cc_final: 0.7733 (mtpp)
REVERT: N   53 GLN cc_start: 0.8564 (mp10) cc_final: 0.8144 (mp10)
REVERT: R  262 ILE cc_start: 0.8334 (OUTLIER) cc_final: 0.7896 (mp)
REVERT: R  302 MET cc_start: 0.8343 (mtt) cc_final: 0.7970 (mtp)
  outliers start: 25
  outliers final: 13
  residues processed: 158
  average time/residue: 1.2811
  time to fit residues: 213.9734
Evaluate side-chains
  156 residues out of total 890 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 141
  time to evaluate  : 0.979 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   83 MET
Chi-restraints excluded: chain B residue   23 LYS
Chi-restraints excluded: chain B residue   29 THR
Chi-restraints excluded: chain B residue  114 CYS
Chi-restraints excluded: chain B residue  118 ASP
Chi-restraints excluded: chain B residue  134 ARG
Chi-restraints excluded: chain B residue  146 LEU
Chi-restraints excluded: chain B residue  334 SER
Chi-restraints excluded: chain N residue   59 SER
Chi-restraints excluded: chain N residue   95 TYR
Chi-restraints excluded: chain N residue  110 VAL
Chi-restraints excluded: chain R residue   74 CYS
Chi-restraints excluded: chain R residue   97 LYS
Chi-restraints excluded: chain R residue  226 ASP
Chi-restraints excluded: chain R residue  262 ILE
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 101
   random chunks:
   chunk 9 optimal weight:    0.8980
   chunk 52 optimal weight:    0.9990
   chunk 50 optimal weight:    0.1980
   chunk 85 optimal weight:    0.9990
   chunk 12 optimal weight:    0.0980
   chunk 38 optimal weight:    0.4980
   chunk 68 optimal weight:    3.9990
   chunk 17 optimal weight:    0.6980
   chunk 19 optimal weight:    1.9990
   chunk 32 optimal weight:    1.9990
   chunk 56 optimal weight:    2.9990
   overall best weight:    0.4780

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

Flipped N/Q/H residues before XYZ refinement:
B  17 GLN
B  44 GLN
B 259 GLN
N  77 ASN
R  53 GLN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3863 r_free = 0.3863 target = 0.151358 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3492 r_free = 0.3492 target = 0.116593 restraints weight = 10549.972|
|-----------------------------------------------------------------------------|
r_work (start): 0.3437 rms_B_bonded: 2.54
r_work: 0.3301 rms_B_bonded: 3.08 restraints_weight: 0.5000
r_work: 0.3164 rms_B_bonded: 4.93 restraints_weight: 0.2500
r_work (final): 0.3164
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8156
moved from start:          0.2496

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.043   8294  Z= 0.171
  Angle     :  0.515   9.117  11251  Z= 0.271
  Chirality :  0.040   0.140   1266
  Planarity :  0.004   0.049   1429
  Dihedral  :  3.961  17.007   1190
  Min Nonbonded Distance : 2.497

Molprobity Statistics.
  All-atom Clashscore : 6.73
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.74 %
    Favored  : 97.26 %
  Rotamer:
    Outliers :  2.31 %
    Allowed  : 19.77 %
    Favored  : 77.92 %
  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:  1.13 (0.26), residues: 1021
  helix:  2.38 (0.25), residues: 398
  sheet:  0.03 (0.32), residues: 215
  loop : -0.47 (0.32), residues: 408

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.002   TRP B  82 
 HIS   0.005   0.001   HIS R  63 
 PHE   0.011   0.001   PHE A  74 
 TYR   0.018   0.001   TYR N  60 
 ARG   0.014   0.000   ARG N 105 

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

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

  2042 Ramachandran restraints generated.
    1021 Oldfield, 0 Emsley, 1021 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2042 Ramachandran restraints generated.
    1021 Oldfield, 0 Emsley, 1021 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  169 residues out of total 890 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 149
  time to evaluate  : 0.865 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   14 GLU cc_start: 0.7127 (pm20) cc_final: 0.6779 (pm20)
REVERT: A   15 ASP cc_start: 0.7795 (m-30) cc_final: 0.7435 (m-30)
REVERT: A  151 GLU cc_start: 0.8170 (tp30) cc_final: 0.7742 (tp30)
REVERT: B   75 GLN cc_start: 0.8285 (tt0) cc_final: 0.8068 (tt0)
REVERT: B  134 ARG cc_start: 0.7203 (OUTLIER) cc_final: 0.6684 (ptm160)
REVERT: B  155 ASN cc_start: 0.8139 (t0) cc_final: 0.7891 (t0)
REVERT: B  325 MET cc_start: 0.8546 (tpp) cc_final: 0.8012 (mmm)
REVERT: N   43 LYS cc_start: 0.7947 (mtpt) cc_final: 0.7722 (mtpp)
REVERT: N   53 GLN cc_start: 0.8564 (mp10) cc_final: 0.8098 (mp10)
REVERT: N   59 SER cc_start: 0.8524 (OUTLIER) cc_final: 0.8196 (p)
REVERT: R  262 ILE cc_start: 0.8362 (OUTLIER) cc_final: 0.7920 (mp)
REVERT: R  302 MET cc_start: 0.8340 (mtt) cc_final: 0.7970 (mtp)
  outliers start: 20
  outliers final: 11
  residues processed: 160
  average time/residue: 1.2280
  time to fit residues: 208.4159
Evaluate side-chains
  156 residues out of total 890 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 142
  time to evaluate  : 1.015 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   23 LYS
Chi-restraints excluded: chain B residue   29 THR
Chi-restraints excluded: chain B residue   35 ASN
Chi-restraints excluded: chain B residue  134 ARG
Chi-restraints excluded: chain B residue  146 LEU
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain N residue   59 SER
Chi-restraints excluded: chain N residue   95 TYR
Chi-restraints excluded: chain N residue  110 VAL
Chi-restraints excluded: chain R residue   74 CYS
Chi-restraints excluded: chain R residue   97 LYS
Chi-restraints excluded: chain R residue  103 ASP
Chi-restraints excluded: chain R residue  226 ASP
Chi-restraints excluded: chain R residue  262 ILE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 101
   random chunks:
   chunk 84 optimal weight:    3.9990
   chunk 31 optimal weight:    1.9990
   chunk 89 optimal weight:    4.9990
   chunk 64 optimal weight:    4.9990
   chunk 30 optimal weight:    0.6980
   chunk 24 optimal weight:    6.9990
   chunk 39 optimal weight:    1.9990
   chunk 23 optimal weight:    5.9990
   chunk 52 optimal weight:    0.9990
   chunk 91 optimal weight:    0.9980
   chunk 90 optimal weight:    0.7980
   overall best weight:    1.0984

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

Flipped N/Q/H residues before XYZ refinement:
A  82 HIS
B  17 GLN
B  44 GLN
B 237 ASN
B 259 GLN
N  39 GLN
N  77 ASN
R  53 GLN

Total number of N/Q/H flips: 8

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3841 r_free = 0.3841 target = 0.149225 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3466 r_free = 0.3466 target = 0.114432 restraints weight = 10425.783|
|-----------------------------------------------------------------------------|
r_work (start): 0.3407 rms_B_bonded: 2.51
r_work: 0.3273 rms_B_bonded: 3.03 restraints_weight: 0.5000
r_work: 0.3138 rms_B_bonded: 4.84 restraints_weight: 0.2500
r_work (final): 0.3138
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8159
moved from start:          0.2456

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.042   8294  Z= 0.255
  Angle     :  0.546   9.134  11251  Z= 0.286
  Chirality :  0.042   0.152   1266
  Planarity :  0.005   0.060   1429
  Dihedral  :  4.079  17.483   1190
  Min Nonbonded Distance : 2.498

Molprobity Statistics.
  All-atom Clashscore : 7.17
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.74 %
    Favored  : 97.26 %
  Rotamer:
    Outliers :  1.73 %
    Allowed  : 20.69 %
    Favored  : 77.57 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.06 (0.26), residues: 1021
  helix:  2.32 (0.25), residues: 399
  sheet: -0.01 (0.32), residues: 217
  loop : -0.50 (0.32), residues: 405

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.002   TRP B  82 
 HIS   0.005   0.001   HIS R  63 
 PHE   0.019   0.001   PHE R  91 
 TYR   0.025   0.002   TYR N  60 
 ARG   0.015   0.000   ARG N 105 

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

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

  2042 Ramachandran restraints generated.
    1021 Oldfield, 0 Emsley, 1021 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2042 Ramachandran restraints generated.
    1021 Oldfield, 0 Emsley, 1021 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  155 residues out of total 890 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 140
  time to evaluate  : 0.881 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   14 GLU cc_start: 0.7127 (pm20) cc_final: 0.6783 (pm20)
REVERT: A   15 ASP cc_start: 0.7819 (m-30) cc_final: 0.7467 (m-30)
REVERT: A  151 GLU cc_start: 0.8204 (tp30) cc_final: 0.7785 (tp30)
REVERT: B   59 TYR cc_start: 0.8604 (m-80) cc_final: 0.8221 (m-80)
REVERT: B   75 GLN cc_start: 0.8267 (tt0) cc_final: 0.8033 (tt0)
REVERT: B  134 ARG cc_start: 0.7258 (OUTLIER) cc_final: 0.6718 (ptm160)
REVERT: B  155 ASN cc_start: 0.8130 (t0) cc_final: 0.7876 (t0)
REVERT: B  262 MET cc_start: 0.8369 (tpt) cc_final: 0.8138 (tpp)
REVERT: B  325 MET cc_start: 0.8524 (tpp) cc_final: 0.7980 (mmm)
REVERT: N   43 LYS cc_start: 0.7950 (mtpt) cc_final: 0.7721 (mtpp)
REVERT: N   53 GLN cc_start: 0.8566 (mp10) cc_final: 0.8083 (mp10)
REVERT: R  262 ILE cc_start: 0.8336 (OUTLIER) cc_final: 0.7901 (mp)
REVERT: R  302 MET cc_start: 0.8365 (mtt) cc_final: 0.8005 (mtp)
  outliers start: 15
  outliers final: 10
  residues processed: 147
  average time/residue: 1.3216
  time to fit residues: 205.2581
Evaluate side-chains
  150 residues out of total 890 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 138
  time to evaluate  : 1.253 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   23 LYS
Chi-restraints excluded: chain B residue   29 THR
Chi-restraints excluded: chain B residue   35 ASN
Chi-restraints excluded: chain B residue  134 ARG
Chi-restraints excluded: chain B residue  146 LEU
Chi-restraints excluded: chain N residue   59 SER
Chi-restraints excluded: chain N residue   95 TYR
Chi-restraints excluded: chain N residue  110 VAL
Chi-restraints excluded: chain R residue   74 CYS
Chi-restraints excluded: chain R residue  103 ASP
Chi-restraints excluded: chain R residue  226 ASP
Chi-restraints excluded: chain R residue  262 ILE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 101
   random chunks:
   chunk 4 optimal weight:    1.9990
   chunk 33 optimal weight:    1.9990
   chunk 0 optimal weight:   10.0000
   chunk 36 optimal weight:    0.0070
   chunk 12 optimal weight:    0.0980
   chunk 32 optimal weight:    0.5980
   chunk 22 optimal weight:    0.9980
   chunk 35 optimal weight:    2.9990
   chunk 5 optimal weight:    2.9990
   chunk 54 optimal weight:    0.5980
   chunk 64 optimal weight:    4.9990
   overall best weight:    0.4598

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

Flipped N/Q/H residues before XYZ refinement:
B  17 GLN
B  44 GLN
B 259 GLN
N  77 ASN
R  53 GLN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3859 r_free = 0.3859 target = 0.150834 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3490 r_free = 0.3490 target = 0.116299 restraints weight = 10481.356|
|-----------------------------------------------------------------------------|
r_work (start): 0.3432 rms_B_bonded: 2.51
r_work: 0.3298 rms_B_bonded: 3.04 restraints_weight: 0.5000
r_work: 0.3163 rms_B_bonded: 4.87 restraints_weight: 0.2500
r_work (final): 0.3163
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8134
moved from start:          0.2507

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.044   8294  Z= 0.175
  Angle     :  0.525   9.211  11251  Z= 0.275
  Chirality :  0.040   0.142   1266
  Planarity :  0.004   0.064   1429
  Dihedral  :  4.028  17.435   1190
  Min Nonbonded Distance : 2.486

Molprobity Statistics.
  All-atom Clashscore : 6.86
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.74 %
    Favored  : 97.26 %
  Rotamer:
    Outliers :  1.85 %
    Allowed  : 20.58 %
    Favored  : 77.57 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.12 (0.26), residues: 1021
  helix:  2.36 (0.25), residues: 399
  sheet:  0.07 (0.32), residues: 213
  loop : -0.49 (0.32), residues: 409

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.002   TRP B  82 
 HIS   0.004   0.001   HIS R  63 
 PHE   0.011   0.001   PHE A  74 
 TYR   0.025   0.001   TYR R 172 
 ARG   0.016   0.000   ARG N 105 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 7424.78 seconds
wall clock time: 132 minutes 13.05 seconds (7933.05 seconds total)