Starting phenix.real_space_refine
on Tue Apr 29 02:25:12 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8zf6_60051/04_2025/8zf6_60051_neut.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8zf6_60051/04_2025/8zf6_60051.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.98
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8zf6_60051/04_2025/8zf6_60051.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8zf6_60051/04_2025/8zf6_60051.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8zf6_60051/04_2025/8zf6_60051_neut.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8zf6_60051/04_2025/8zf6_60051_neut.cif"
  }
  resolution = 2.98
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.001 sd=   0.022
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      53      5.16       5
     C    5264      2.51       5
     N    1438      2.21       5
     O    1529      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 33 residue(s): 0.03s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/chem_data/mon_lib"
  Total number of atoms: 8284
  Number of models: 1
  Model: ""
    Number of chains: 5
    Chain: "A"
      Number of atoms: 1865
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 238, 1865
          Classifications: {'peptide': 238}
          Incomplete info: {'truncation_to_alanine': 27}
          Link IDs: {'PTRANS': 6, 'TRANS': 231}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 108
          Unresolved non-hydrogen angles: 130
          Unresolved non-hydrogen dihedrals: 89
          Unresolved non-hydrogen chiralities: 1
          Planarities with less than four sites: {'TYR:plan': 1, 'GLU:plan': 8, 'ASN:plan1': 1, 'ARG:plan': 3, 'ASP:plan': 6}
          Unresolved non-hydrogen planarities: 75
    Chain: "B"
      Number of atoms: 2484
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 338, 2484
          Classifications: {'peptide': 338}
          Incomplete info: {'truncation_to_alanine': 29}
          Link IDs: {'PTRANS': 5, 'TRANS': 332}
          Unresolved non-hydrogen bonds: 116
          Unresolved non-hydrogen angles: 143
          Unresolved non-hydrogen dihedrals: 89
          Unresolved non-hydrogen chiralities: 6
          Planarities with less than four sites: {'GLN:plan1': 4, 'GLU:plan': 6, 'ARG:plan': 6, 'ASN:plan1': 2, 'ASP:plan': 3}
          Unresolved non-hydrogen planarities: 85
    Chain: "G"
      Number of atoms: 355
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 52, 355
          Classifications: {'peptide': 52}
          Incomplete info: {'truncation_to_alanine': 12}
          Link IDs: {'PTRANS': 4, 'TRANS': 47}
          Unresolved non-hydrogen bonds: 50
          Unresolved non-hydrogen angles: 57
          Unresolved non-hydrogen dihedrals: 43
          Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 3, 'ARG:plan': 2, 'ASP:plan': 1}
          Unresolved non-hydrogen planarities: 29
    Chain: "R"
      Number of atoms: 1888
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 272, 1888
          Classifications: {'peptide': 272}
          Incomplete info: {'truncation_to_alanine': 57}
          Link IDs: {'PCIS': 2, 'PTRANS': 15, 'TRANS': 254}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 228
          Unresolved non-hydrogen angles: 289
          Unresolved non-hydrogen dihedrals: 179
          Unresolved non-hydrogen chiralities: 25
          Planarities with less than four sites: {'GLN:plan1': 1, 'ASP:plan': 3, 'TYR:plan': 1, 'ASN:plan1': 3, 'TRP:plan': 1, 'HIS:plan': 1, 'GLU:plan': 5, 'ARG:plan': 14}
          Unresolved non-hydrogen planarities: 133
    Chain: "S"
      Number of atoms: 1692
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 229, 1692
          Classifications: {'peptide': 229}
          Incomplete info: {'truncation_to_alanine': 19}
          Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 219}
          Chain breaks: 2
          Unresolved non-hydrogen bonds: 66
          Unresolved non-hydrogen angles: 80
          Unresolved non-hydrogen dihedrals: 52
          Unresolved non-hydrogen chiralities: 4
          Planarities with less than four sites: {'GLU:plan': 6, 'ARG:plan': 3, 'ASP:plan': 1}
          Unresolved non-hydrogen planarities: 42
  Time building chain proxies: 5.22, per 1000 atoms: 0.63
  Number of scatterers: 8284
  At special positions: 0
  Unit cell: (86.92, 124.02, 127.2, 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      53     16.00
     O    1529      8.00
     N    1438      7.00
     C    5264      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=2, symmetry=0
    Simple disulfide: pdb=" SG  CYS R  90 " - pdb=" SG  CYS R 168 " distance=2.03
    Simple disulfide: pdb=" SG  CYS S  22 " - pdb=" SG  CYS S  96 " 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: 2.25
  Conformation dependent library (CDL) restraints added in 982.0 milliseconds
  

  2222 Ramachandran restraints generated.
    1111 Oldfield, 0 Emsley, 1111 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2100

  Finding SS restraints...
    Secondary structure from input PDB file:
      28 helices and 14 sheets defined
      37.7% alpha, 23.7% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 1.13
  Creating SS restraints...
    Processing helix  chain 'A' and resid 6 through 38
      removed outlier: 3.639A  pdb=" N   VAL A  36 " --> pdb=" O   LYS A  32 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 52 through 64
    Processing helix  chain 'A' and resid 243 through 249
      removed outlier: 3.615A  pdb=" N   GLN A 246 " --> pdb=" O   LYS A 243 " (cutoff:3.500A)
      removed outlier: 3.731A  pdb=" N   ASN A 249 " --> pdb=" O   GLN A 246 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 265 through 278
    Processing helix  chain 'A' and resid 293 through 304
    Processing helix  chain 'A' and resid 312 through 316
    Processing helix  chain 'A' and resid 331 through 352
      removed outlier: 4.606A  pdb=" N   SER A 352 " --> pdb=" O   ILE A 348 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 370 through 391
    Processing helix  chain 'B' and resid 4 through 25
    Processing helix  chain 'B' and resid 29 through 35
    Processing helix  chain 'G' and resid 12 through 24
      removed outlier: 3.518A  pdb=" N   ASN G  24 " --> pdb=" O   LYS G  20 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 29 through 44
    Processing helix  chain 'R' and resid 18 through 47
      removed outlier: 4.559A  pdb=" N   LEU R  32 " --> pdb=" O   PHE R  28 " (cutoff:3.500A)
      Proline residue:  R  33  - end of helix
    Processing helix  chain 'R' and resid 51 through 79
      removed outlier: 4.125A  pdb=" N   TYR R  55 " --> pdb=" O   GLU R  51 " (cutoff:3.500A)
      Proline residue:  R  71  - end of helix
    Processing helix  chain 'R' and resid 86 through 121
      removed outlier: 4.008A  pdb=" N   TYR R 102 " --> pdb=" O   TYR R  98 " (cutoff:3.500A)
      removed outlier: 3.824A  pdb=" N   ALA R 105 " --> pdb=" O   LEU R 101 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 122 through 125
      removed outlier: 3.915A  pdb=" N   PHE R 125 " --> pdb=" O   PRO R 122 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'R' and resid 122 through 125'
    Processing helix  chain 'R' and resid 129 through 150
      removed outlier: 3.774A  pdb=" N   SER R 133 " --> pdb=" O   ARG R 129 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 151 through 155
      removed outlier: 3.648A  pdb=" N   GLY R 155 " --> pdb=" O   PRO R 152 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 177 through 191
      removed outlier: 3.708A  pdb=" N   ALA R 182 " --> pdb=" O   GLY R 178 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 193 through 209
      removed outlier: 3.588A  pdb=" N   LEU R 209 " --> pdb=" O   LEU R 205 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 216 through 253
      removed outlier: 3.538A  pdb=" N   VAL R 223 " --> pdb=" O   GLU R 219 " (cutoff:3.500A)
      Proline residue:  R 231  - end of helix
      Proline residue:  R 240  - end of helix
    Processing helix  chain 'R' and resid 266 through 284
      Proline residue:  R 273  - end of helix
    Processing helix  chain 'R' and resid 287 through 295
    Processing helix  chain 'S' and resid 28 through 32
    Processing helix  chain 'S' and resid 53 through 56
      removed outlier: 4.226A  pdb=" N   GLY S  56 " --> pdb=" O   SER S  53 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'S' and resid 53 through 56'
    Processing helix  chain 'S' and resid 62 through 65
    Processing helix  chain 'S' and resid 87 through 91
      removed outlier: 3.732A  pdb=" N   ASP S  90 " --> pdb=" O   ARG S  87 " (cutoff:3.500A)
      removed outlier: 4.156A  pdb=" N   THR S  91 " --> pdb=" O   SER S  88 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'S' and resid 87 through 91'
    Processing helix  chain 'S' and resid 220 through 224
      removed outlier: 3.941A  pdb=" N   VAL S 224 " --> pdb=" O   ALA S 221 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 217 through 224
      removed outlier: 4.614A  pdb=" N   VAL A 234 " --> pdb=" O   LEU A  45 " (cutoff:3.500A)
      removed outlier: 7.950A  pdb=" N   GLY A  47 " --> pdb=" O   VAL A 234 " (cutoff:3.500A)
      removed outlier: 3.883A  pdb=" N   ALA A 253 " --> pdb=" O   ARG A  42 " (cutoff:3.500A)
      removed outlier: 6.273A  pdb=" N   ILE A 254 " --> pdb=" O   ILE A 288 " (cutoff:3.500A)
      removed outlier: 7.266A  pdb=" N   PHE A 290 " --> pdb=" O   ILE A 254 " (cutoff:3.500A)
      removed outlier: 6.687A  pdb=" N   PHE A 256 " --> pdb=" O   PHE A 290 " (cutoff:3.500A)
      removed outlier: 6.645A  pdb=" N   ASN A 292 " --> pdb=" O   PHE A 256 " (cutoff:3.500A)
      removed outlier: 6.312A  pdb=" N   VAL A 258 " --> pdb=" O   ASN A 292 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'B' and resid 47 through 51
      removed outlier: 6.581A  pdb=" N   ILE B 338 " --> pdb=" O   ARG B  48 " (cutoff:3.500A)
      removed outlier: 4.426A  pdb=" N   THR B  50 " --> pdb=" O   LEU B 336 " (cutoff:3.500A)
      removed outlier: 6.520A  pdb=" N   LEU B 336 " --> pdb=" O   THR B  50 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'B' and resid 58 through 63
      removed outlier: 3.756A  pdb=" N   ALA B  60 " --> pdb=" O   ALA B  73 " (cutoff:3.500A)
      removed outlier: 3.822A  pdb=" N   LYS B  78 " --> pdb=" O   SER B  74 " (cutoff:3.500A)
      removed outlier: 6.330A  pdb=" N   LEU B  79 " --> pdb=" O   ALA B  92 " (cutoff:3.500A)
      removed outlier: 4.255A  pdb=" N   ALA B  92 " --> pdb=" O   LEU B  79 " (cutoff:3.500A)
      removed outlier: 6.506A  pdb=" N   ILE B  81 " --> pdb=" O   VAL B  90 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'B' and resid 100 through 105
      removed outlier: 6.564A  pdb=" N   GLY B 115 " --> pdb=" O   MET B 101 " (cutoff:3.500A)
      removed outlier: 4.346A  pdb=" N   CYS B 103 " --> pdb=" O   ALA B 113 " (cutoff:3.500A)
      removed outlier: 6.575A  pdb=" N   ALA B 113 " --> pdb=" O   CYS B 103 " (cutoff:3.500A)
      removed outlier: 4.928A  pdb=" N   TYR B 105 " --> pdb=" O   TYR B 111 " (cutoff:3.500A)
      removed outlier: 7.070A  pdb=" N   TYR B 111 " --> pdb=" O   TYR B 105 " (cutoff:3.500A)
      removed outlier: 4.225A  pdb=" N   GLY B 116 " --> pdb=" O   ILE B 120 " (cutoff:3.500A)
      removed outlier: 4.683A  pdb=" N   ILE B 120 " --> pdb=" O   GLY B 116 " (cutoff:3.500A)
      removed outlier: 6.313A  pdb=" N   CYS B 121 " --> pdb=" O   GLU B 138 " (cutoff:3.500A)
      removed outlier: 4.707A  pdb=" N   GLU B 138 " --> pdb=" O   CYS B 121 " (cutoff:3.500A)
      removed outlier: 6.861A  pdb=" N   ILE B 123 " --> pdb=" O   SER B 136 " (cutoff:3.500A)
      removed outlier: 3.712A  pdb=" N   ARG B 134 " --> pdb=" O   ASN B 125 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'B' and resid 146 through 153
      removed outlier: 6.614A  pdb=" N   GLN B 156 " --> pdb=" O   LEU B 152 " (cutoff:3.500A)
      removed outlier: 4.713A  pdb=" N   THR B 165 " --> pdb=" O   SER B 161 " (cutoff:3.500A)
      removed outlier: 6.420A  pdb=" N   ASP B 170 " --> pdb=" O   GLN B 176 " (cutoff:3.500A)
      removed outlier: 6.101A  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: 6.863A  pdb=" N   GLY B 202 " --> pdb=" O   MET B 188 " (cutoff:3.500A)
      removed outlier: 4.461A  pdb=" N   LEU B 190 " --> pdb=" O   VAL B 200 " (cutoff:3.500A)
      removed outlier: 6.881A  pdb=" N   VAL B 200 " --> pdb=" O   LEU B 190 " (cutoff:3.500A)
      removed outlier: 5.180A  pdb=" N   LEU B 192 " --> pdb=" O   LEU B 198 " (cutoff:3.500A)
      removed outlier: 7.332A  pdb=" N   LEU B 198 " --> pdb=" O   LEU B 192 " (cutoff:3.500A)
      removed outlier: 3.745A  pdb=" N   GLN B 220 " --> pdb=" O   LEU B 210 " (cutoff:3.500A)
      removed outlier: 6.918A  pdb=" N   ASP B 212 " --> pdb=" O   CYS B 218 " (cutoff:3.500A)
      removed outlier: 6.517A  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: 6.602A  pdb=" N   GLY B 244 " --> pdb=" O   ASN B 230 " (cutoff:3.500A)
      removed outlier: 4.278A  pdb=" N   ILE B 232 " --> pdb=" O   ALA B 242 " (cutoff:3.500A)
      removed outlier: 6.680A  pdb=" N   ALA B 242 " --> pdb=" O   ILE B 232 " (cutoff:3.500A)
      removed outlier: 4.719A  pdb=" N   PHE B 234 " --> pdb=" O   ALA B 240 " (cutoff:3.500A)
      removed outlier: 6.919A  pdb=" N   ALA B 240 " --> pdb=" O   PHE B 234 " (cutoff:3.500A)
      removed outlier: 3.704A  pdb=" N   MET B 262 " --> pdb=" O   LEU B 252 " (cutoff:3.500A)
      removed outlier: 6.599A  pdb=" N   ASP B 254 " --> pdb=" O   GLU B 260 " (cutoff:3.500A)
      removed outlier: 5.944A  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: 4.388A  pdb=" N   SER B 275 " --> pdb=" O   GLY B 288 " (cutoff:3.500A)
      removed outlier: 6.529A  pdb=" N   ASP B 298 " --> pdb=" O   ARG B 304 " (cutoff:3.500A)
      removed outlier: 6.607A  pdb=" N   ARG B 304 " --> pdb=" O   ASP B 298 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'R' and resid 158 through 159
    Processing sheet with id=AB1, first strand: chain 'S' and resid 3 through 7
    Processing sheet with id=AB2, first strand: chain 'S' and resid 11 through 12
      removed outlier: 3.579A  pdb=" N   GLN S  39 " --> pdb=" O   MET S  93 " (cutoff:3.500A)
      removed outlier: 6.163A  pdb=" N   ARG S  38 " --> pdb=" O   TRP S  47 " (cutoff:3.500A)
      removed outlier: 5.177A  pdb=" N   TRP S  47 " --> pdb=" O   ARG S  38 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'S' and resid 11 through 12
      removed outlier: 4.014A  pdb=" N   PHE S 110 " --> pdb=" O   ARG S  98 " (cutoff:3.500A)
    Processing sheet with id=AB4, first strand: chain 'S' and resid 140 through 142
      removed outlier: 3.539A  pdb=" N   VAL S 155 " --> pdb=" O   ILE S 216 " (cutoff:3.500A)
    Processing sheet with id=AB5, first strand: chain 'S' and resid 194 through 195
      removed outlier: 5.635A  pdb=" N   LEU S 187 " --> pdb=" O   LEU S 178 " (cutoff:3.500A)
      removed outlier: 6.198A  pdb=" N   LEU S 178 " --> pdb=" O   LEU S 187 " (cutoff:3.500A)

    443 hydrogen bonds defined for protein.
    1254 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: 2.47

  Time building geometry restraints manager: 2.65 seconds

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

  Histogram of bond lengths:
        1.16 -     1.29: 1338
        1.29 -     1.42: 2329
        1.42 -     1.56: 4729
        1.56 -     1.69: 2
        1.69 -     1.82: 73
  Bond restraints: 8471
  Sorted by residual:
  bond pdb=" C   HIS A 387 "
       pdb=" O   HIS A 387 "
    ideal  model  delta    sigma   weight residual
    1.237  1.156  0.081 1.17e-02 7.31e+03 4.75e+01
  bond pdb=" CA  GLN A 384 "
       pdb=" C   GLN A 384 "
    ideal  model  delta    sigma   weight residual
    1.523  1.435  0.089 1.30e-02 5.92e+03 4.67e+01
  bond pdb=" CA  HIS A 387 "
       pdb=" C   HIS A 387 "
    ideal  model  delta    sigma   weight residual
    1.523  1.437  0.086 1.30e-02 5.92e+03 4.36e+01
  bond pdb=" CA  ALA A  39 "
       pdb=" C   ALA A  39 "
    ideal  model  delta    sigma   weight residual
    1.523  1.439  0.084 1.28e-02 6.10e+03 4.33e+01
  bond pdb=" CA  HIS A 387 "
       pdb=" CB  HIS A 387 "
    ideal  model  delta    sigma   weight residual
    1.528  1.433  0.096 1.56e-02 4.11e+03 3.77e+01
  ... (remaining 8466 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.88: 11177
        1.88 -     3.76: 294
        3.76 -     5.63: 57
        5.63 -     7.51: 16
        7.51 -     9.39: 6
  Bond angle restraints: 11550
  Sorted by residual:
  angle pdb=" N   GLN S 183 "
        pdb=" CA  GLN S 183 "
        pdb=" C   GLN S 183 "
      ideal   model   delta    sigma   weight residual
     110.41  119.80   -9.39 1.23e+00 6.61e-01 5.83e+01
  angle pdb=" C   SER S 184 "
        pdb=" N   PRO S 185 "
        pdb=" CA  PRO S 185 "
      ideal   model   delta    sigma   weight residual
     119.78  125.62   -5.84 1.03e+00 9.43e-01 3.22e+01
  angle pdb=" C   GLN A 384 "
        pdb=" CA  GLN A 384 "
        pdb=" CB  GLN A 384 "
      ideal   model   delta    sigma   weight residual
     110.79  101.75    9.04 1.66e+00 3.63e-01 2.97e+01
  angle pdb=" C   ILE A 382 "
        pdb=" CA  ILE A 382 "
        pdb=" CB  ILE A 382 "
      ideal   model   delta    sigma   weight residual
     112.22  104.81    7.41 1.38e+00 5.25e-01 2.89e+01
  angle pdb=" N   ASP R  81 "
        pdb=" CA  ASP R  81 "
        pdb=" C   ASP R  81 "
      ideal   model   delta    sigma   weight residual
     113.28  121.69   -8.41 1.57e+00 4.06e-01 2.87e+01
  ... (remaining 11545 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    15.47: 4499
       15.47 -    30.95: 351
       30.95 -    46.42: 77
       46.42 -    61.90: 12
       61.90 -    77.37: 7
  Dihedral angle restraints: 4946
    sinusoidal: 1680
      harmonic: 3266
  Sorted by residual:
  dihedral pdb=" C   GLN A 384 "
           pdb=" N   GLN A 384 "
           pdb=" CA  GLN A 384 "
           pdb=" CB  GLN A 384 "
      ideal   model   delta  harmonic     sigma   weight residual
    -122.60 -110.74  -11.86     0      2.50e+00 1.60e-01 2.25e+01
  dihedral pdb=" N   ASP R  81 "
           pdb=" C   ASP R  81 "
           pdb=" CA  ASP R  81 "
           pdb=" CB  ASP R  81 "
      ideal   model   delta  harmonic     sigma   weight residual
     122.80  134.58  -11.78     0      2.50e+00 1.60e-01 2.22e+01
  dihedral pdb=" CA  LEU R 192 "
           pdb=" C   LEU R 192 "
           pdb=" N   LEU R 193 "
           pdb=" CA  LEU R 193 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  158.57   21.43     0      5.00e+00 4.00e-02 1.84e+01
  ... (remaining 4943 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.097: 1225
       0.097 -    0.194: 85
       0.194 -    0.291: 5
       0.291 -    0.388: 4
       0.388 -    0.485: 4
  Chirality restraints: 1323
  Sorted by residual:
  chirality pdb=" CA  ARG A 385 "
            pdb=" N   ARG A 385 "
            pdb=" C   ARG A 385 "
            pdb=" CB  ARG A 385 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.03    0.49 2.00e-01 2.50e+01 5.88e+00
  chirality pdb=" CA  ASP R  81 "
            pdb=" N   ASP R  81 "
            pdb=" C   ASP R  81 "
            pdb=" CB  ASP R  81 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.09    0.42 2.00e-01 2.50e+01 4.40e+00
  chirality pdb=" CA  ILE A 383 "
            pdb=" N   ILE A 383 "
            pdb=" C   ILE A 383 "
            pdb=" CB  ILE A 383 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.02    0.41 2.00e-01 2.50e+01 4.26e+00
  ... (remaining 1320 not shown)

  Planarity restraints: 1483
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   LEU R 230 "   -0.061 5.00e-02 4.00e+02   9.11e-02 1.33e+01
        pdb=" N   PRO R 231 "    0.157 5.00e-02 4.00e+02
        pdb=" CA  PRO R 231 "   -0.047 5.00e-02 4.00e+02
        pdb=" CD  PRO R 231 "   -0.050 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ARG S 180 "   -0.056 5.00e-02 4.00e+02   8.38e-02 1.12e+01
        pdb=" N   PRO S 181 "    0.145 5.00e-02 4.00e+02
        pdb=" CA  PRO S 181 "   -0.044 5.00e-02 4.00e+02
        pdb=" CD  PRO S 181 "   -0.045 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  LYS A  32 "   -0.013 2.00e-02 2.50e+03   2.62e-02 6.87e+00
        pdb=" C   LYS A  32 "    0.045 2.00e-02 2.50e+03
        pdb=" O   LYS A  32 "   -0.017 2.00e-02 2.50e+03
        pdb=" N   ASP A  33 "   -0.015 2.00e-02 2.50e+03
  ... (remaining 1480 not shown)

  Histogram of nonbonded interaction distances:
        2.12 -     2.68: 184
        2.68 -     3.23: 7893
        3.23 -     3.79: 12926
        3.79 -     4.34: 16840
        4.34 -     4.90: 28984
  Nonbonded interactions: 66827
  Sorted by model distance:
  nonbonded pdb=" OG  SER B 331 "
            pdb=" OD1 ASP B 333 "
     model   vdw
     2.120 3.040
  nonbonded pdb=" OH  TYR A 318 "
            pdb=" OD2 ASP A 343 "
     model   vdw
     2.165 3.040
  nonbonded pdb=" OG  SER B 281 "
            pdb=" OD2 ASP G  48 "
     model   vdw
     2.191 3.040
  nonbonded pdb=" OG  SER B 161 "
            pdb=" OD1 ASP B 163 "
     model   vdw
     2.199 3.040
  nonbonded pdb=" NH1 ARG A 238 "
            pdb=" OD1 ASP B 186 "
     model   vdw
     2.259 3.120
  ... (remaining 66822 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:             1.780
  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:          0.330
  Check model and map are aligned:         0.060
  Set scattering table:                    0.090
  Process input model:                     22.870
  Find NCS groups from input model:        0.100
  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:             0.010
  Load rotamer database and sin/cos tables:12.530
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   37.800
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7453
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      :  0.009   0.096   8473  Z= 0.511
  Angle     :  0.799   9.388  11554  Z= 0.460
  Chirality :  0.058   0.485   1323
  Planarity :  0.006   0.091   1483
  Dihedral  : 12.395  77.369   2840
  Min Nonbonded Distance : 2.120

Molprobity Statistics.
  All-atom Clashscore : 8.51
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.68 %
    Favored  : 95.32 %
  Rotamer:
    Outliers :  0.62 %
    Allowed  :  0.87 %
    Favored  : 98.50 %
  Cbeta Deviations :  0.29 %
  Peptide Plane:
    Cis-proline     : 7.50 %
    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: -0.35 (0.25), residues: 1111
  helix:  1.01 (0.27), residues: 382
  sheet: -0.51 (0.31), residues: 269
  loop : -1.05 (0.28), residues: 460

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.002   TRP B  63 
 HIS   0.009   0.002   HIS R 276 
 PHE   0.026   0.002   PHE S  68 
 TYR   0.020   0.002   TYR A 263 
 ARG   0.014   0.001   ARG A 385 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.19138 (  438)
  hydrogen bonds       : angle       6.92190 ( 1254)
  SS BOND              : bond        0.00188 (    2)
  SS BOND              : angle       1.38043 (    4)
  covalent geometry    : bond        0.00915 ( 8471)
  covalent geometry    : angle       0.79893 (11550)

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

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

  2222 Ramachandran restraints generated.
    1111 Oldfield, 0 Emsley, 1111 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2222 Ramachandran restraints generated.
    1111 Oldfield, 0 Emsley, 1111 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  174 residues out of total 945 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 169
  time to evaluate  : 0.815 
Fit side-chains
REVERT: A   14 GLU cc_start: 0.7097 (tt0) cc_final: 0.6860 (tt0)
REVERT: A  381 ASP cc_start: 0.8220 (t0) cc_final: 0.7923 (t0)
REVERT: A  386 MET cc_start: 0.7395 (ttm) cc_final: 0.7164 (ttm)
REVERT: B   33 ILE cc_start: 0.8200 (tt) cc_final: 0.7872 (mt)
REVERT: B  177 THR cc_start: 0.8402 (m) cc_final: 0.8124 (p)
REVERT: B  188 MET cc_start: 0.8683 (mmm) cc_final: 0.8330 (mmm)
REVERT: B  308 LEU cc_start: 0.7854 (mp) cc_final: 0.7515 (mp)
REVERT: S   82 GLN cc_start: 0.8551 (tp40) cc_final: 0.8198 (tm-30)
REVERT: S  183 GLN cc_start: 0.7506 (OUTLIER) cc_final: 0.7268 (mp10)
  outliers start: 5
  outliers final: 2
  residues processed: 173
  average time/residue: 1.1215
  time to fit residues: 206.6222
Evaluate side-chains
  146 residues out of total 945 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 143
  time to evaluate  : 0.828 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   36 VAL
Chi-restraints excluded: chain S residue  181 PRO
Chi-restraints excluded: chain S residue  183 GLN
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 110
   random chunks:
   chunk 92 optimal weight:    0.5980
   chunk 83 optimal weight:    0.9980
   chunk 46 optimal weight:    0.0970
   chunk 28 optimal weight:    1.9990
   chunk 56 optimal weight:    1.9990
   chunk 44 optimal weight:    0.6980
   chunk 86 optimal weight:    0.9990
   chunk 33 optimal weight:    0.5980
   chunk 52 optimal weight:    0.8980
   chunk 64 optimal weight:    0.6980
   chunk 99 optimal weight:    0.5980
   overall best weight:    0.5178

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

Flipped N/Q/H residues before XYZ refinement:
A 230 HIS
R  45 GLN
S  39 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3562 r_free = 0.3562 target = 0.120078 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3332 r_free = 0.3332 target = 0.105006 restraints weight = 12528.618|
|-----------------------------------------------------------------------------|
r_work (start): 0.3328 rms_B_bonded: 1.75
r_work: 0.3230 rms_B_bonded: 2.17 restraints_weight: 0.5000
r_work: 0.3096 rms_B_bonded: 3.80 restraints_weight: 0.2500
r_work (final): 0.3096
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7901
moved from start:          0.2068

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.050   8473  Z= 0.173
  Angle     :  0.638   8.701  11554  Z= 0.331
  Chirality :  0.044   0.154   1323
  Planarity :  0.005   0.061   1483
  Dihedral  :  5.061  52.647   1225
  Min Nonbonded Distance : 2.507

Molprobity Statistics.
  All-atom Clashscore : 6.01
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.06 %
    Favored  : 96.94 %
  Rotamer:
    Outliers :  2.25 %
    Allowed  : 10.61 %
    Favored  : 87.14 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 7.50 %
    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:  0.09 (0.25), residues: 1111
  helix:  1.60 (0.27), residues: 377
  sheet: -0.42 (0.30), residues: 273
  loop : -0.88 (0.28), residues: 461

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.020   0.002   TRP B 169 
 HIS   0.007   0.001   HIS A  41 
 PHE   0.021   0.002   PHE S  68 
 TYR   0.019   0.002   TYR S 190 
 ARG   0.005   0.001   ARG S  18 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04613 (  438)
  hydrogen bonds       : angle       5.03426 ( 1254)
  SS BOND              : bond        0.00214 (    2)
  SS BOND              : angle       1.49665 (    4)
  covalent geometry    : bond        0.00409 ( 8471)
  covalent geometry    : angle       0.63787 (11550)

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

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

  2222 Ramachandran restraints generated.
    1111 Oldfield, 0 Emsley, 1111 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2222 Ramachandran restraints generated.
    1111 Oldfield, 0 Emsley, 1111 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  167 residues out of total 945 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 149
  time to evaluate  : 1.298 
Fit side-chains
REVERT: A   33 ASP cc_start: 0.8045 (m-30) cc_final: 0.7763 (m-30)
REVERT: A  219 GLU cc_start: 0.7237 (tm-30) cc_final: 0.6930 (tm-30)
REVERT: A  381 ASP cc_start: 0.8260 (t0) cc_final: 0.7919 (t70)
REVERT: B  188 MET cc_start: 0.8939 (mmm) cc_final: 0.8522 (mmm)
REVERT: R   83 TRP cc_start: 0.5274 (t-100) cc_final: 0.4132 (t-100)
REVERT: S   82 GLN cc_start: 0.8714 (tp40) cc_final: 0.8435 (mm-40)
REVERT: S  180 ARG cc_start: 0.7324 (mtt90) cc_final: 0.7047 (mtt180)
  outliers start: 18
  outliers final: 8
  residues processed: 155
  average time/residue: 1.6991
  time to fit residues: 280.5692
Evaluate side-chains
  145 residues out of total 945 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 137
  time to evaluate  : 0.976 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   36 VAL
Chi-restraints excluded: chain A residue  258 VAL
Chi-restraints excluded: chain A residue  262 ASP
Chi-restraints excluded: chain B residue  135 VAL
Chi-restraints excluded: chain B residue  228 ASP
Chi-restraints excluded: chain B residue  314 ARG
Chi-restraints excluded: chain S residue   63 THR
Chi-restraints excluded: chain S residue  183 GLN
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 110
   random chunks:
   chunk 96 optimal weight:    0.9990
   chunk 51 optimal weight:    1.9990
   chunk 67 optimal weight:    1.9990
   chunk 66 optimal weight:    2.9990
   chunk 105 optimal weight:    1.9990
   chunk 101 optimal weight:    0.0870
   chunk 108 optimal weight:    1.9990
   chunk 102 optimal weight:    1.9990
   chunk 23 optimal weight:    0.7980
   chunk 8 optimal weight:    0.7980
   chunk 30 optimal weight:    1.9990
   overall best weight:    0.9362

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

Flipped N/Q/H residues before XYZ refinement:
A 294 GLN
A 390 GLN
S  39 GLN
S 179 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3494 r_free = 0.3494 target = 0.113185 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3260 r_free = 0.3260 target = 0.098215 restraints weight = 12705.866|
|-----------------------------------------------------------------------------|
r_work (start): 0.3271 rms_B_bonded: 1.74
r_work: 0.3171 rms_B_bonded: 2.15 restraints_weight: 0.5000
r_work: 0.3036 rms_B_bonded: 3.75 restraints_weight: 0.2500
r_work (final): 0.3036
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7967
moved from start:          0.2776

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.064   8473  Z= 0.252
  Angle     :  0.688   9.067  11554  Z= 0.353
  Chirality :  0.046   0.140   1323
  Planarity :  0.005   0.057   1483
  Dihedral  :  5.318  55.676   1222
  Min Nonbonded Distance : 2.486

Molprobity Statistics.
  All-atom Clashscore : 6.01
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.69 %
    Favored  : 96.31 %
  Rotamer:
    Outliers :  3.62 %
    Allowed  : 13.36 %
    Favored  : 83.02 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 7.50 %
    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: -0.07 (0.25), residues: 1111
  helix:  1.41 (0.26), residues: 386
  sheet: -0.49 (0.31), residues: 268
  loop : -0.97 (0.27), residues: 457

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.002   TRP B 169 
 HIS   0.011   0.002   HIS A 230 
 PHE   0.021   0.002   PHE R 107 
 TYR   0.021   0.002   TYR A 263 
 ARG   0.007   0.001   ARG R 225 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04988 (  438)
  hydrogen bonds       : angle       4.98994 ( 1254)
  SS BOND              : bond        0.00126 (    2)
  SS BOND              : angle       1.68443 (    4)
  covalent geometry    : bond        0.00616 ( 8471)
  covalent geometry    : angle       0.68706 (11550)

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

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

  2222 Ramachandran restraints generated.
    1111 Oldfield, 0 Emsley, 1111 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2222 Ramachandran restraints generated.
    1111 Oldfield, 0 Emsley, 1111 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  174 residues out of total 945 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 145
  time to evaluate  : 0.934 
Fit side-chains
REVERT: A   38 ARG cc_start: 0.7519 (mtp-110) cc_final: 0.7305 (mtt90)
REVERT: A   40 THR cc_start: 0.8910 (t) cc_final: 0.8503 (m)
REVERT: A  381 ASP cc_start: 0.8287 (t0) cc_final: 0.7980 (t70)
REVERT: B   33 ILE cc_start: 0.8193 (tt) cc_final: 0.7875 (mt)
REVERT: B  188 MET cc_start: 0.8950 (mmm) cc_final: 0.8589 (mmm)
REVERT: B  217 MET cc_start: 0.8565 (OUTLIER) cc_final: 0.7854 (pmt)
REVERT: B  304 ARG cc_start: 0.8169 (ttp80) cc_final: 0.7891 (ttp-170)
REVERT: S    5 VAL cc_start: 0.8269 (OUTLIER) cc_final: 0.8039 (t)
  outliers start: 29
  outliers final: 13
  residues processed: 155
  average time/residue: 1.3210
  time to fit residues: 216.6864
Evaluate side-chains
  158 residues out of total 945 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 143
  time to evaluate  : 0.860 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   36 VAL
Chi-restraints excluded: chain A residue  258 VAL
Chi-restraints excluded: chain A residue  262 ASP
Chi-restraints excluded: chain A residue  299 GLU
Chi-restraints excluded: chain A residue  390 GLN
Chi-restraints excluded: chain B residue  135 VAL
Chi-restraints excluded: chain B residue  217 MET
Chi-restraints excluded: chain G residue   24 ASN
Chi-restraints excluded: chain R residue  188 LEU
Chi-restraints excluded: chain S residue    5 VAL
Chi-restraints excluded: chain S residue   63 THR
Chi-restraints excluded: chain S residue  141 THR
Chi-restraints excluded: chain S residue  183 GLN
Chi-restraints excluded: chain S residue  213 THR
Chi-restraints excluded: chain S residue  245 LEU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 110
   random chunks:
   chunk 41 optimal weight:    1.9990
   chunk 58 optimal weight:    2.9990
   chunk 104 optimal weight:    0.6980
   chunk 43 optimal weight:    0.5980
   chunk 64 optimal weight:    0.0870
   chunk 48 optimal weight:    0.8980
   chunk 62 optimal weight:    0.3980
   chunk 103 optimal weight:    0.4980
   chunk 46 optimal weight:    0.5980
   chunk 82 optimal weight:    0.5980
   chunk 75 optimal weight:    0.0980
   overall best weight:    0.3358

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

Flipped N/Q/H residues before XYZ refinement:
A 390 GLN
B 237 ASN
B 239 ASN
** R  58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** R 276 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
S  39 GLN
S 179 GLN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3526 r_free = 0.3526 target = 0.115466 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3298 r_free = 0.3298 target = 0.100881 restraints weight = 12714.729|
|-----------------------------------------------------------------------------|
r_work (start): 0.3308 rms_B_bonded: 1.67
r_work: 0.3213 rms_B_bonded: 2.09 restraints_weight: 0.5000
r_work: 0.3083 rms_B_bonded: 3.66 restraints_weight: 0.2500
r_work (final): 0.3083
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7918
moved from start:          0.2938

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038   8473  Z= 0.131
  Angle     :  0.577   8.522  11554  Z= 0.297
  Chirality :  0.042   0.131   1323
  Planarity :  0.005   0.053   1483
  Dihedral  :  4.915  56.711   1222
  Min Nonbonded Distance : 2.483

Molprobity Statistics.
  All-atom Clashscore : 5.69
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.70 %
    Favored  : 97.30 %
  Rotamer:
    Outliers :  3.25 %
    Allowed  : 15.98 %
    Favored  : 80.77 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 7.50 %
    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:  0.30 (0.25), residues: 1111
  helix:  1.92 (0.27), residues: 377
  sheet: -0.40 (0.31), residues: 268
  loop : -0.83 (0.27), residues: 466

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.001   TRP B 169 
 HIS   0.010   0.001   HIS A 230 
 PHE   0.014   0.001   PHE A 222 
 TYR   0.021   0.001   TYR R 275 
 ARG   0.007   0.000   ARG R 225 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03952 (  438)
  hydrogen bonds       : angle       4.72078 ( 1254)
  SS BOND              : bond        0.00299 (    2)
  SS BOND              : angle       1.19607 (    4)
  covalent geometry    : bond        0.00302 ( 8471)
  covalent geometry    : angle       0.57692 (11550)

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

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

  2222 Ramachandran restraints generated.
    1111 Oldfield, 0 Emsley, 1111 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2222 Ramachandran restraints generated.
    1111 Oldfield, 0 Emsley, 1111 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  176 residues out of total 945 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 150
  time to evaluate  : 0.898 
Fit side-chains
REVERT: A   38 ARG cc_start: 0.7427 (mtp-110) cc_final: 0.7219 (mtt90)
REVERT: A  381 ASP cc_start: 0.8276 (t0) cc_final: 0.7974 (t70)
REVERT: B   17 GLN cc_start: 0.8277 (tm-30) cc_final: 0.7790 (tt0)
REVERT: B   33 ILE cc_start: 0.8205 (tt) cc_final: 0.7915 (mt)
REVERT: B  188 MET cc_start: 0.8895 (mmm) cc_final: 0.8488 (mmm)
REVERT: R   83 TRP cc_start: 0.5353 (t-100) cc_final: 0.4611 (t-100)
REVERT: R  276 HIS cc_start: 0.8127 (OUTLIER) cc_final: 0.7848 (m-70)
REVERT: S    5 VAL cc_start: 0.8260 (OUTLIER) cc_final: 0.8045 (t)
REVERT: S   80 PHE cc_start: 0.8659 (m-80) cc_final: 0.8333 (m-80)
REVERT: S  183 GLN cc_start: 0.7936 (OUTLIER) cc_final: 0.7481 (mm-40)
  outliers start: 26
  outliers final: 8
  residues processed: 161
  average time/residue: 1.2463
  time to fit residues: 212.6858
Evaluate side-chains
  154 residues out of total 945 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 143
  time to evaluate  : 0.914 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   36 VAL
Chi-restraints excluded: chain A residue  258 VAL
Chi-restraints excluded: chain A residue  262 ASP
Chi-restraints excluded: chain B residue  135 VAL
Chi-restraints excluded: chain G residue   38 MET
Chi-restraints excluded: chain R residue  276 HIS
Chi-restraints excluded: chain S residue    5 VAL
Chi-restraints excluded: chain S residue   63 THR
Chi-restraints excluded: chain S residue  166 LEU
Chi-restraints excluded: chain S residue  183 GLN
Chi-restraints excluded: chain S residue  213 THR
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 110
   random chunks:
   chunk 9 optimal weight:    1.9990
   chunk 105 optimal weight:    0.9980
   chunk 71 optimal weight:    0.6980
   chunk 6 optimal weight:    0.4980
   chunk 95 optimal weight:    0.6980
   chunk 87 optimal weight:    0.0980
   chunk 61 optimal weight:    0.1980
   chunk 49 optimal weight:    1.9990
   chunk 90 optimal weight:    0.8980
   chunk 20 optimal weight:    1.9990
   chunk 24 optimal weight:    0.9980
   overall best weight:    0.4380

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

Flipped N/Q/H residues before XYZ refinement:
A  35 GLN
** R  58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
R 276 HIS
S  39 GLN
S 179 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3528 r_free = 0.3528 target = 0.115618 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3298 r_free = 0.3298 target = 0.100704 restraints weight = 12571.460|
|-----------------------------------------------------------------------------|
r_work (start): 0.3312 rms_B_bonded: 1.72
r_work: 0.3216 rms_B_bonded: 2.15 restraints_weight: 0.5000
r_work: 0.3083 rms_B_bonded: 3.76 restraints_weight: 0.2500
r_work (final): 0.3083
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7924
moved from start:          0.3086

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042   8473  Z= 0.145
  Angle     :  0.586   8.901  11554  Z= 0.299
  Chirality :  0.042   0.130   1323
  Planarity :  0.005   0.052   1483
  Dihedral  :  4.834  56.253   1222
  Min Nonbonded Distance : 2.549

Molprobity Statistics.
  All-atom Clashscore : 5.38
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.42 %
    Favored  : 96.58 %
  Rotamer:
    Outliers :  2.87 %
    Allowed  : 17.48 %
    Favored  : 79.65 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 7.50 %
    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:  0.42 (0.25), residues: 1111
  helix:  1.95 (0.27), residues: 383
  sheet: -0.18 (0.32), residues: 261
  loop : -0.83 (0.27), residues: 467

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.001   TRP B 169 
 HIS   0.003   0.001   HIS A 357 
 PHE   0.014   0.001   PHE R 107 
 TYR   0.021   0.001   TYR R 275 
 ARG   0.008   0.001   ARG R 225 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03948 (  438)
  hydrogen bonds       : angle       4.61493 ( 1254)
  SS BOND              : bond        0.00214 (    2)
  SS BOND              : angle       1.19044 (    4)
  covalent geometry    : bond        0.00344 ( 8471)
  covalent geometry    : angle       0.58535 (11550)

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

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

  2222 Ramachandran restraints generated.
    1111 Oldfield, 0 Emsley, 1111 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2222 Ramachandran restraints generated.
    1111 Oldfield, 0 Emsley, 1111 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  175 residues out of total 945 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 152
  time to evaluate  : 0.936 
Fit side-chains
REVERT: A   38 ARG cc_start: 0.7491 (mtp-110) cc_final: 0.7207 (mtt90)
REVERT: A  221 LYS cc_start: 0.8508 (OUTLIER) cc_final: 0.8286 (tppp)
REVERT: A  381 ASP cc_start: 0.8262 (t0) cc_final: 0.7946 (t70)
REVERT: B   17 GLN cc_start: 0.8290 (tm-30) cc_final: 0.7850 (tt0)
REVERT: B   33 ILE cc_start: 0.8191 (tt) cc_final: 0.7910 (mt)
REVERT: B  188 MET cc_start: 0.8877 (mmm) cc_final: 0.8593 (mmm)
REVERT: B  258 ASP cc_start: 0.7645 (t70) cc_final: 0.7361 (t0)
REVERT: R   83 TRP cc_start: 0.5276 (t-100) cc_final: 0.4632 (t-100)
REVERT: S    5 VAL cc_start: 0.8253 (OUTLIER) cc_final: 0.8039 (t)
REVERT: S   80 PHE cc_start: 0.8659 (m-80) cc_final: 0.8309 (m-80)
REVERT: S  183 GLN cc_start: 0.7816 (OUTLIER) cc_final: 0.7372 (mm-40)
  outliers start: 23
  outliers final: 10
  residues processed: 162
  average time/residue: 1.3306
  time to fit residues: 228.6111
Evaluate side-chains
  156 residues out of total 945 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 143
  time to evaluate  : 0.837 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   36 VAL
Chi-restraints excluded: chain A residue  221 LYS
Chi-restraints excluded: chain A residue  258 VAL
Chi-restraints excluded: chain A residue  262 ASP
Chi-restraints excluded: chain A residue  266 LEU
Chi-restraints excluded: chain B residue  135 VAL
Chi-restraints excluded: chain B residue  137 ARG
Chi-restraints excluded: chain G residue   38 MET
Chi-restraints excluded: chain S residue    5 VAL
Chi-restraints excluded: chain S residue   63 THR
Chi-restraints excluded: chain S residue  166 LEU
Chi-restraints excluded: chain S residue  183 GLN
Chi-restraints excluded: chain S residue  213 THR
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 110
   random chunks:
   chunk 39 optimal weight:    0.0170
   chunk 67 optimal weight:    0.9990
   chunk 28 optimal weight:    0.8980
   chunk 87 optimal weight:    0.8980
   chunk 100 optimal weight:    0.0980
   chunk 57 optimal weight:    0.9980
   chunk 33 optimal weight:    0.9980
   chunk 22 optimal weight:    0.5980
   chunk 50 optimal weight:    1.9990
   chunk 108 optimal weight:    1.9990
   chunk 3 optimal weight:    0.9980
   overall best weight:    0.5018

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

Flipped N/Q/H residues before XYZ refinement:
A  35 GLN
B  75 GLN
B 220 GLN
** R  58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
S 179 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3522 r_free = 0.3522 target = 0.115197 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3293 r_free = 0.3293 target = 0.100313 restraints weight = 12701.732|
|-----------------------------------------------------------------------------|
r_work (start): 0.3304 rms_B_bonded: 1.73
r_work: 0.3208 rms_B_bonded: 2.15 restraints_weight: 0.5000
r_work: 0.3074 rms_B_bonded: 3.77 restraints_weight: 0.2500
r_work (final): 0.3074
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7932
moved from start:          0.3221

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.041   8473  Z= 0.155
  Angle     :  0.591   8.637  11554  Z= 0.302
  Chirality :  0.042   0.131   1323
  Planarity :  0.004   0.051   1483
  Dihedral  :  4.858  56.264   1222
  Min Nonbonded Distance : 2.454

Molprobity Statistics.
  All-atom Clashscore : 5.76
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.33 %
    Favored  : 96.67 %
  Rotamer:
    Outliers :  2.75 %
    Allowed  : 18.98 %
    Favored  : 78.28 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 7.50 %
    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:  0.47 (0.25), residues: 1111
  helix:  2.01 (0.26), residues: 384
  sheet: -0.21 (0.32), residues: 261
  loop : -0.80 (0.27), residues: 466

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.002   TRP B 169 
 HIS   0.009   0.001   HIS A 230 
 PHE   0.014   0.002   PHE R 107 
 TYR   0.022   0.002   TYR R 275 
 ARG   0.009   0.001   ARG R 225 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03954 (  438)
  hydrogen bonds       : angle       4.59967 ( 1254)
  SS BOND              : bond        0.00228 (    2)
  SS BOND              : angle       1.18766 (    4)
  covalent geometry    : bond        0.00371 ( 8471)
  covalent geometry    : angle       0.59049 (11550)

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

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

  2222 Ramachandran restraints generated.
    1111 Oldfield, 0 Emsley, 1111 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2222 Ramachandran restraints generated.
    1111 Oldfield, 0 Emsley, 1111 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  166 residues out of total 945 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 144
  time to evaluate  : 0.815 
Fit side-chains
REVERT: A   38 ARG cc_start: 0.7531 (mtp-110) cc_final: 0.7229 (mtt90)
REVERT: A  368 ASP cc_start: 0.7472 (m-30) cc_final: 0.7153 (t0)
REVERT: A  381 ASP cc_start: 0.8239 (t0) cc_final: 0.7940 (t70)
REVERT: B   17 GLN cc_start: 0.8303 (tm-30) cc_final: 0.7873 (tt0)
REVERT: B   33 ILE cc_start: 0.8193 (tt) cc_final: 0.7921 (mt)
REVERT: B  156 GLN cc_start: 0.8998 (mt0) cc_final: 0.8775 (mt0)
REVERT: B  188 MET cc_start: 0.8870 (mmm) cc_final: 0.8589 (mmm)
REVERT: B  217 MET cc_start: 0.8593 (OUTLIER) cc_final: 0.8248 (pmt)
REVERT: S    5 VAL cc_start: 0.8252 (OUTLIER) cc_final: 0.8048 (t)
REVERT: S  183 GLN cc_start: 0.7906 (OUTLIER) cc_final: 0.7495 (mm-40)
  outliers start: 22
  outliers final: 11
  residues processed: 155
  average time/residue: 1.2786
  time to fit residues: 209.8949
Evaluate side-chains
  157 residues out of total 945 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 143
  time to evaluate  : 0.953 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    5 LEU
Chi-restraints excluded: chain A residue   36 VAL
Chi-restraints excluded: chain A residue  258 VAL
Chi-restraints excluded: chain A residue  266 LEU
Chi-restraints excluded: chain B residue  135 VAL
Chi-restraints excluded: chain B residue  217 MET
Chi-restraints excluded: chain G residue   37 LEU
Chi-restraints excluded: chain R residue  169 TYR
Chi-restraints excluded: chain R residue  214 SER
Chi-restraints excluded: chain S residue    5 VAL
Chi-restraints excluded: chain S residue   63 THR
Chi-restraints excluded: chain S residue  166 LEU
Chi-restraints excluded: chain S residue  183 GLN
Chi-restraints excluded: chain S residue  213 THR
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 110
   random chunks:
   chunk 80 optimal weight:    0.3980
   chunk 82 optimal weight:    0.0970
   chunk 29 optimal weight:    0.8980
   chunk 31 optimal weight:    0.5980
   chunk 54 optimal weight:    1.9990
   chunk 9 optimal weight:    0.8980
   chunk 11 optimal weight:    0.6980
   chunk 12 optimal weight:    0.9990
   chunk 52 optimal weight:    0.9980
   chunk 107 optimal weight:    0.6980
   chunk 84 optimal weight:    0.5980
   overall best weight:    0.4778

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

Flipped N/Q/H residues before XYZ refinement:
A  35 GLN
B 239 ASN
** R  58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
R 276 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3524 r_free = 0.3524 target = 0.115325 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.3297 r_free = 0.3297 target = 0.100512 restraints weight = 12635.251|
|-----------------------------------------------------------------------------|
r_work (start): 0.3308 rms_B_bonded: 1.72
r_work: 0.3213 rms_B_bonded: 2.14 restraints_weight: 0.5000
r_work: 0.3081 rms_B_bonded: 3.74 restraints_weight: 0.2500
r_work (final): 0.3081
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7927
moved from start:          0.3328

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.038   8473  Z= 0.150
  Angle     :  0.585   8.268  11554  Z= 0.298
  Chirality :  0.042   0.129   1323
  Planarity :  0.004   0.051   1483
  Dihedral  :  4.856  57.074   1222
  Min Nonbonded Distance : 2.544

Molprobity Statistics.
  All-atom Clashscore : 5.44
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.42 %
    Favored  : 96.58 %
  Rotamer:
    Outliers :  2.87 %
    Allowed  : 20.35 %
    Favored  : 76.78 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 7.50 %
    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:  0.49 (0.25), residues: 1111
  helix:  2.06 (0.27), residues: 384
  sheet: -0.23 (0.32), residues: 262
  loop : -0.80 (0.27), residues: 465

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.002   TRP B 169 
 HIS   0.009   0.001   HIS A 230 
 PHE   0.014   0.002   PHE R 107 
 TYR   0.024   0.002   TYR B  85 
 ARG   0.009   0.001   ARG R 225 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03872 (  438)
  hydrogen bonds       : angle       4.55043 ( 1254)
  SS BOND              : bond        0.00191 (    2)
  SS BOND              : angle       1.17413 (    4)
  covalent geometry    : bond        0.00359 ( 8471)
  covalent geometry    : angle       0.58445 (11550)

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

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

  2222 Ramachandran restraints generated.
    1111 Oldfield, 0 Emsley, 1111 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2222 Ramachandran restraints generated.
    1111 Oldfield, 0 Emsley, 1111 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  170 residues out of total 945 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 147
  time to evaluate  : 0.821 
Fit side-chains
REVERT: A   38 ARG cc_start: 0.7563 (mtp-110) cc_final: 0.7277 (mtt90)
REVERT: A  368 ASP cc_start: 0.7529 (m-30) cc_final: 0.7200 (t0)
REVERT: A  381 ASP cc_start: 0.8230 (t0) cc_final: 0.7943 (t70)
REVERT: B   17 GLN cc_start: 0.8296 (tm-30) cc_final: 0.7880 (tt0)
REVERT: B   33 ILE cc_start: 0.8207 (tt) cc_final: 0.7948 (mt)
REVERT: B  156 GLN cc_start: 0.8990 (mt0) cc_final: 0.8761 (mt0)
REVERT: B  188 MET cc_start: 0.8856 (mmm) cc_final: 0.8568 (mmm)
REVERT: S  180 ARG cc_start: 0.7373 (mtt90) cc_final: 0.7035 (mtt180)
REVERT: S  183 GLN cc_start: 0.7884 (OUTLIER) cc_final: 0.7494 (mm-40)
  outliers start: 23
  outliers final: 11
  residues processed: 157
  average time/residue: 1.3238
  time to fit residues: 219.5490
Evaluate side-chains
  152 residues out of total 945 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 140
  time to evaluate  : 0.889 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    5 LEU
Chi-restraints excluded: chain A residue   36 VAL
Chi-restraints excluded: chain A residue  258 VAL
Chi-restraints excluded: chain A residue  262 ASP
Chi-restraints excluded: chain A residue  266 LEU
Chi-restraints excluded: chain B residue  135 VAL
Chi-restraints excluded: chain G residue   38 MET
Chi-restraints excluded: chain R residue  214 SER
Chi-restraints excluded: chain S residue   63 THR
Chi-restraints excluded: chain S residue  166 LEU
Chi-restraints excluded: chain S residue  183 GLN
Chi-restraints excluded: chain S residue  213 THR
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 110
   random chunks:
   chunk 101 optimal weight:    3.9990
   chunk 44 optimal weight:    0.7980
   chunk 47 optimal weight:    0.9980
   chunk 49 optimal weight:    0.0980
   chunk 5 optimal weight:    0.2980
   chunk 8 optimal weight:    0.9980
   chunk 58 optimal weight:    0.7980
   chunk 11 optimal weight:    0.5980
   chunk 22 optimal weight:    0.5980
   chunk 1 optimal weight:    0.5980
   chunk 64 optimal weight:    0.0040
   overall best weight:    0.3192

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

Flipped N/Q/H residues before XYZ refinement:
B 220 GLN
R  58 ASN
R 276 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3541 r_free = 0.3541 target = 0.116497 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3315 r_free = 0.3315 target = 0.101696 restraints weight = 12783.807|
|-----------------------------------------------------------------------------|
r_work (start): 0.3326 rms_B_bonded: 1.74
r_work: 0.3230 rms_B_bonded: 2.17 restraints_weight: 0.5000
r_work: 0.3097 rms_B_bonded: 3.80 restraints_weight: 0.2500
r_work (final): 0.3097
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7908
moved from start:          0.3374

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   8473  Z= 0.124
  Angle     :  0.569   7.930  11554  Z= 0.288
  Chirality :  0.041   0.128   1323
  Planarity :  0.005   0.057   1483
  Dihedral  :  4.750  57.832   1222
  Min Nonbonded Distance : 2.538

Molprobity Statistics.
  All-atom Clashscore : 5.69
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.06 %
    Favored  : 96.94 %
  Rotamer:
    Outliers :  2.12 %
    Allowed  : 20.85 %
    Favored  : 77.03 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 7.50 %
    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:  0.58 (0.25), residues: 1111
  helix:  2.20 (0.26), residues: 384
  sheet: -0.24 (0.32), residues: 264
  loop : -0.76 (0.28), residues: 463

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.001   TRP B 169 
 HIS   0.008   0.001   HIS A 230 
 PHE   0.012   0.001   PHE A 222 
 TYR   0.023   0.001   TYR R 275 
 ARG   0.010   0.001   ARG R 225 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03623 (  438)
  hydrogen bonds       : angle       4.45501 ( 1254)
  SS BOND              : bond        0.00256 (    2)
  SS BOND              : angle       0.89343 (    4)
  covalent geometry    : bond        0.00288 ( 8471)
  covalent geometry    : angle       0.56931 (11550)

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

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

  2222 Ramachandran restraints generated.
    1111 Oldfield, 0 Emsley, 1111 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2222 Ramachandran restraints generated.
    1111 Oldfield, 0 Emsley, 1111 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  161 residues out of total 945 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 144
  time to evaluate  : 0.815 
Fit side-chains
REVERT: A   38 ARG cc_start: 0.7547 (mtp-110) cc_final: 0.7220 (mtt90)
REVERT: A  368 ASP cc_start: 0.7439 (m-30) cc_final: 0.7111 (t0)
REVERT: A  381 ASP cc_start: 0.8241 (t0) cc_final: 0.7946 (t70)
REVERT: B   17 GLN cc_start: 0.8293 (tm-30) cc_final: 0.7905 (tt0)
REVERT: B   33 ILE cc_start: 0.8184 (tt) cc_final: 0.7920 (mt)
REVERT: B  156 GLN cc_start: 0.8952 (mt0) cc_final: 0.8741 (mt0)
REVERT: B  188 MET cc_start: 0.8816 (mmm) cc_final: 0.8529 (mmm)
REVERT: B  219 ARG cc_start: 0.8241 (OUTLIER) cc_final: 0.7821 (mtt-85)
REVERT: B  259 GLN cc_start: 0.7213 (tt0) cc_final: 0.7001 (mt0)
REVERT: R   46 VAL cc_start: 0.6917 (t) cc_final: 0.6672 (p)
REVERT: R   83 TRP cc_start: 0.5188 (t-100) cc_final: 0.4805 (t-100)
REVERT: S  180 ARG cc_start: 0.7356 (mtt90) cc_final: 0.7000 (mtt180)
REVERT: S  183 GLN cc_start: 0.7743 (OUTLIER) cc_final: 0.7344 (mm-40)
  outliers start: 17
  outliers final: 10
  residues processed: 152
  average time/residue: 1.4795
  time to fit residues: 237.8753
Evaluate side-chains
  155 residues out of total 945 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 143
  time to evaluate  : 1.126 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    5 LEU
Chi-restraints excluded: chain A residue   36 VAL
Chi-restraints excluded: chain A residue  258 VAL
Chi-restraints excluded: chain A residue  262 ASP
Chi-restraints excluded: chain A residue  266 LEU
Chi-restraints excluded: chain B residue  135 VAL
Chi-restraints excluded: chain B residue  219 ARG
Chi-restraints excluded: chain G residue   38 MET
Chi-restraints excluded: chain R residue  214 SER
Chi-restraints excluded: chain S residue  166 LEU
Chi-restraints excluded: chain S residue  183 GLN
Chi-restraints excluded: chain S residue  213 THR
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 110
   random chunks:
   chunk 49 optimal weight:    0.8980
   chunk 92 optimal weight:    1.9990
   chunk 76 optimal weight:    0.5980
   chunk 98 optimal weight:    0.7980
   chunk 103 optimal weight:    0.8980
   chunk 95 optimal weight:    0.5980
   chunk 10 optimal weight:    0.9980
   chunk 16 optimal weight:    0.3980
   chunk 46 optimal weight:    0.0970
   chunk 18 optimal weight:    0.3980
   chunk 24 optimal weight:    0.9990
   overall best weight:    0.4178

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

Flipped N/Q/H residues before XYZ refinement:
B 220 GLN
R 276 HIS
S  82 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3533 r_free = 0.3533 target = 0.115980 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3306 r_free = 0.3306 target = 0.101128 restraints weight = 12858.573|
|-----------------------------------------------------------------------------|
r_work (start): 0.3318 rms_B_bonded: 1.74
r_work: 0.3222 rms_B_bonded: 2.16 restraints_weight: 0.5000
r_work: 0.3088 rms_B_bonded: 3.79 restraints_weight: 0.2500
r_work (final): 0.3088
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7917
moved from start:          0.3452

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   8473  Z= 0.141
  Angle     :  0.585   7.834  11554  Z= 0.296
  Chirality :  0.042   0.146   1323
  Planarity :  0.005   0.051   1483
  Dihedral  :  4.791  59.005   1222
  Min Nonbonded Distance : 2.501

Molprobity Statistics.
  All-atom Clashscore : 6.26
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.51 %
    Favored  : 96.49 %
  Rotamer:
    Outliers :  2.50 %
    Allowed  : 21.10 %
    Favored  : 76.40 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 7.50 %
    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:  0.54 (0.25), residues: 1111
  helix:  2.16 (0.26), residues: 384
  sheet: -0.25 (0.32), residues: 261
  loop : -0.79 (0.28), residues: 466

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.002   TRP B 169 
 HIS   0.007   0.001   HIS A 230 
 PHE   0.013   0.001   PHE A 222 
 TYR   0.022   0.001   TYR R 275 
 ARG   0.010   0.001   ARG R 225 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03767 (  438)
  hydrogen bonds       : angle       4.45443 ( 1254)
  SS BOND              : bond        0.00194 (    2)
  SS BOND              : angle       1.00489 (    4)
  covalent geometry    : bond        0.00336 ( 8471)
  covalent geometry    : angle       0.58441 (11550)

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

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

  2222 Ramachandran restraints generated.
    1111 Oldfield, 0 Emsley, 1111 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2222 Ramachandran restraints generated.
    1111 Oldfield, 0 Emsley, 1111 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  161 residues out of total 945 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 141
  time to evaluate  : 0.878 
Fit side-chains
REVERT: A   38 ARG cc_start: 0.7572 (mtp-110) cc_final: 0.7249 (mtt90)
REVERT: A  381 ASP cc_start: 0.8238 (t0) cc_final: 0.7951 (t70)
REVERT: B   17 GLN cc_start: 0.8284 (tm-30) cc_final: 0.7894 (tt0)
REVERT: B   33 ILE cc_start: 0.8193 (tt) cc_final: 0.7925 (mt)
REVERT: B  156 GLN cc_start: 0.8940 (mt0) cc_final: 0.8738 (mt0)
REVERT: B  188 MET cc_start: 0.8822 (mmm) cc_final: 0.8422 (mmm)
REVERT: B  219 ARG cc_start: 0.8211 (OUTLIER) cc_final: 0.7813 (mtt-85)
REVERT: R   46 VAL cc_start: 0.6908 (t) cc_final: 0.6658 (p)
REVERT: R   83 TRP cc_start: 0.5245 (t-100) cc_final: 0.4749 (t-100)
REVERT: S  180 ARG cc_start: 0.7354 (mtt90) cc_final: 0.7031 (mtt180)
REVERT: S  183 GLN cc_start: 0.7735 (OUTLIER) cc_final: 0.7356 (mm-40)
  outliers start: 20
  outliers final: 11
  residues processed: 151
  average time/residue: 1.5420
  time to fit residues: 246.0068
Evaluate side-chains
  150 residues out of total 945 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 137
  time to evaluate  : 0.925 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    5 LEU
Chi-restraints excluded: chain A residue   36 VAL
Chi-restraints excluded: chain A residue  258 VAL
Chi-restraints excluded: chain A residue  262 ASP
Chi-restraints excluded: chain A residue  266 LEU
Chi-restraints excluded: chain B residue  135 VAL
Chi-restraints excluded: chain B residue  219 ARG
Chi-restraints excluded: chain G residue   38 MET
Chi-restraints excluded: chain R residue  214 SER
Chi-restraints excluded: chain S residue   63 THR
Chi-restraints excluded: chain S residue  166 LEU
Chi-restraints excluded: chain S residue  183 GLN
Chi-restraints excluded: chain S residue  213 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 110
   random chunks:
   chunk 41 optimal weight:    0.5980
   chunk 60 optimal weight:    0.0670
   chunk 108 optimal weight:    0.6980
   chunk 76 optimal weight:    2.9990
   chunk 47 optimal weight:    0.7980
   chunk 34 optimal weight:    0.7980
   chunk 68 optimal weight:    2.9990
   chunk 9 optimal weight:    0.9990
   chunk 65 optimal weight:    0.5980
   chunk 99 optimal weight:    0.8980
   chunk 96 optimal weight:    0.5980
   overall best weight:    0.5118

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

Flipped N/Q/H residues before XYZ refinement:
A  35 GLN
R 276 HIS
S  82 GLN
S 186 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3525 r_free = 0.3525 target = 0.115282 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3297 r_free = 0.3297 target = 0.100453 restraints weight = 12746.233|
|-----------------------------------------------------------------------------|
r_work (start): 0.3308 rms_B_bonded: 1.74
r_work: 0.3211 rms_B_bonded: 2.16 restraints_weight: 0.5000
r_work: 0.3078 rms_B_bonded: 3.78 restraints_weight: 0.2500
r_work (final): 0.3078
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7926
moved from start:          0.3478

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.037   8473  Z= 0.159
  Angle     :  0.601   7.780  11554  Z= 0.305
  Chirality :  0.042   0.161   1323
  Planarity :  0.005   0.050   1483
  Dihedral  :  4.910  59.470   1222
  Min Nonbonded Distance : 2.453

Molprobity Statistics.
  All-atom Clashscore : 6.32
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.33 %
    Favored  : 96.67 %
  Rotamer:
    Outliers :  2.37 %
    Allowed  : 21.72 %
    Favored  : 75.91 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 7.50 %
    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:  0.55 (0.25), residues: 1111
  helix:  2.12 (0.26), residues: 384
  sheet: -0.14 (0.32), residues: 265
  loop : -0.82 (0.28), residues: 462

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.002   TRP B 169 
 HIS   0.012   0.001   HIS A 230 
 PHE   0.014   0.002   PHE R 107 
 TYR   0.024   0.002   TYR R 275 
 ARG   0.010   0.001   ARG R 225 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03903 (  438)
  hydrogen bonds       : angle       4.50229 ( 1254)
  SS BOND              : bond        0.00214 (    2)
  SS BOND              : angle       1.08706 (    4)
  covalent geometry    : bond        0.00384 ( 8471)
  covalent geometry    : angle       0.60032 (11550)

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

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

  2222 Ramachandran restraints generated.
    1111 Oldfield, 0 Emsley, 1111 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2222 Ramachandran restraints generated.
    1111 Oldfield, 0 Emsley, 1111 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  160 residues out of total 945 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 141
  time to evaluate  : 0.898 
Fit side-chains
REVERT: A   38 ARG cc_start: 0.7558 (mtp-110) cc_final: 0.7223 (mtt90)
REVERT: A  381 ASP cc_start: 0.8234 (t0) cc_final: 0.7949 (t70)
REVERT: B   17 GLN cc_start: 0.8288 (tm-30) cc_final: 0.7908 (tt0)
REVERT: B   33 ILE cc_start: 0.8204 (tt) cc_final: 0.7936 (mt)
REVERT: B  156 GLN cc_start: 0.8943 (mt0) cc_final: 0.8732 (mt0)
REVERT: B  188 MET cc_start: 0.8815 (mmm) cc_final: 0.8422 (mmm)
REVERT: B  219 ARG cc_start: 0.8201 (OUTLIER) cc_final: 0.7784 (mtt-85)
REVERT: R   46 VAL cc_start: 0.6739 (t) cc_final: 0.6501 (p)
REVERT: R   83 TRP cc_start: 0.5168 (t-100) cc_final: 0.4729 (t-100)
REVERT: S  180 ARG cc_start: 0.7365 (mtt90) cc_final: 0.7056 (mtt180)
REVERT: S  183 GLN cc_start: 0.7745 (OUTLIER) cc_final: 0.7406 (mm-40)
  outliers start: 19
  outliers final: 12
  residues processed: 149
  average time/residue: 1.4480
  time to fit residues: 228.2743
Evaluate side-chains
  154 residues out of total 945 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 140
  time to evaluate  : 0.851 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    5 LEU
Chi-restraints excluded: chain A residue   36 VAL
Chi-restraints excluded: chain A residue  258 VAL
Chi-restraints excluded: chain A residue  262 ASP
Chi-restraints excluded: chain A residue  266 LEU
Chi-restraints excluded: chain B residue  135 VAL
Chi-restraints excluded: chain B residue  219 ARG
Chi-restraints excluded: chain G residue   38 MET
Chi-restraints excluded: chain R residue  214 SER
Chi-restraints excluded: chain S residue    6 GLU
Chi-restraints excluded: chain S residue   63 THR
Chi-restraints excluded: chain S residue  166 LEU
Chi-restraints excluded: chain S residue  183 GLN
Chi-restraints excluded: chain S residue  213 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 110
   random chunks:
   chunk 15 optimal weight:    1.9990
   chunk 80 optimal weight:    0.5980
   chunk 31 optimal weight:    1.9990
   chunk 0 optimal weight:    1.9990
   chunk 83 optimal weight:    0.5980
   chunk 23 optimal weight:    0.5980
   chunk 13 optimal weight:    0.5980
   chunk 17 optimal weight:    0.1980
   chunk 56 optimal weight:    0.5980
   chunk 21 optimal weight:    0.9980
   chunk 9 optimal weight:    0.7980
   overall best weight:    0.5180

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

Flipped N/Q/H residues before XYZ refinement:
B 110 ASN
** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
R 276 HIS
S  82 GLN
S 186 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 = 0.114989 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3292 r_free = 0.3292 target = 0.100181 restraints weight = 12887.686|
|-----------------------------------------------------------------------------|
r_work (start): 0.3304 rms_B_bonded: 1.75
r_work: 0.3208 rms_B_bonded: 2.16 restraints_weight: 0.5000
r_work: 0.3075 rms_B_bonded: 3.78 restraints_weight: 0.2500
r_work (final): 0.3075
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7929
moved from start:          0.3549

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.038   8473  Z= 0.161
  Angle     :  0.604   7.668  11554  Z= 0.307
  Chirality :  0.042   0.167   1323
  Planarity :  0.005   0.050   1483
  Dihedral  :  4.941  57.882   1222
  Min Nonbonded Distance : 2.434

Molprobity Statistics.
  All-atom Clashscore : 6.26
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.51 %
    Favored  : 96.49 %
  Rotamer:
    Outliers :  2.12 %
    Allowed  : 22.47 %
    Favored  : 75.41 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 7.50 %
    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:  0.54 (0.25), residues: 1111
  helix:  2.08 (0.26), residues: 384
  sheet: -0.07 (0.31), residues: 270
  loop : -0.85 (0.28), residues: 457

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.002   TRP B 332 
 HIS   0.009   0.001   HIS A 230 
 PHE   0.013   0.002   PHE R 107 
 TYR   0.023   0.002   TYR R 275 
 ARG   0.009   0.001   ARG R 225 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03927 (  438)
  hydrogen bonds       : angle       4.51382 ( 1254)
  SS BOND              : bond        0.00193 (    2)
  SS BOND              : angle       1.10181 (    4)
  covalent geometry    : bond        0.00387 ( 8471)
  covalent geometry    : angle       0.60369 (11550)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 7019.35 seconds
wall clock time: 123 minutes 14.03 seconds (7394.03 seconds total)