Starting phenix.real_space_refine
on Fri Aug 22 22:47:15 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8g59_29736/08_2025/8g59_29736.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8g59_29736/08_2025/8g59_29736.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.64
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/8g59_29736/08_2025/8g59_29736.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8g59_29736/08_2025/8g59_29736.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/8g59_29736/08_2025/8g59_29736.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8g59_29736/08_2025/8g59_29736.map"
  }
  resolution = 2.64
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.008 sd=   0.088
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 5
    Type Number    sf(0)   Gaussians
     S      58      5.16       5
     C    5503      2.51       5
     N    1444      2.21       5
     O    1577      1.98       5
     F       1      1.80       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model
  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 8583
  Number of models: 1
  Model: ""
    Number of chains: 6
    Chain: "B"
      Number of atoms: 2509
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 335, 2509
          Classifications: {'peptide': 335}
          Modifications used: {'COO': 1}
          Incomplete info: {'truncation_to_alanine': 16}
          Link IDs: {'PTRANS': 5, 'TRANS': 329}
          Unresolved non-hydrogen bonds: 67
          Unresolved non-hydrogen angles: 81
          Unresolved non-hydrogen dihedrals: 53
          Unresolved non-hydrogen chiralities: 1
          Planarities with less than four sites: {'GLN:plan1': 4, 'ARG:plan': 3, 'GLU:plan': 4, 'ASN:plan1': 1, 'ASP:plan': 1}
          Unresolved non-hydrogen planarities: 53
    Chain: "Y"
      Number of atoms: 365
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 53, 365
          Classifications: {'peptide': 53}
          Incomplete info: {'truncation_to_alanine': 10}
          Link IDs: {'PTRANS': 4, 'TRANS': 48}
          Unresolved non-hydrogen bonds: 42
          Unresolved non-hydrogen angles: 47
          Unresolved non-hydrogen dihedrals: 37
          Planarities with less than four sites: {'GLN:plan1': 1, 'ARG:plan': 1, 'GLU:plan': 3}
          Unresolved non-hydrogen planarities: 21
    Chain: "S"
      Number of atoms: 1739
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 230, 1739
          Classifications: {'peptide': 230}
          Incomplete info: {'truncation_to_alanine': 8}
          Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 219}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 32
          Unresolved non-hydrogen angles: 39
          Unresolved non-hydrogen dihedrals: 25
          Unresolved non-hydrogen chiralities: 1
          Planarities with less than four sites: {'ASP:plan': 1, 'GLU:plan': 4, 'ARG:plan': 1}
          Unresolved non-hydrogen planarities: 24
    Chain: "A"
      Number of atoms: 1739
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 219, 1739
          Classifications: {'peptide': 219}
          Modifications used: {'COO': 1}
          Incomplete info: {'truncation_to_alanine': 8}
          Link IDs: {'PTRANS': 2, 'TRANS': 216}
          Chain breaks: 3
          Unresolved non-hydrogen bonds: 33
          Unresolved non-hydrogen angles: 38
          Unresolved non-hydrogen dihedrals: 28
          Unresolved non-hydrogen chiralities: 1
          Planarities with less than four sites: {'GLU:plan': 3, 'ARG:plan': 1}
          Unresolved non-hydrogen planarities: 17
    Chain: "R"
      Number of atoms: 2204
      Number of conformers: 2
      Conformer: "A"
        Number of residues, atoms: 281, 2193
          Classifications: {'peptide': 281}
          Incomplete info: {'truncation_to_alanine': 12}
          Link IDs: {'PTRANS': 11, 'TRANS': 269}
          Chain breaks: 4
          Unresolved non-hydrogen bonds: 48
          Unresolved non-hydrogen angles: 61
          Unresolved non-hydrogen dihedrals: 37
          Unresolved non-hydrogen chiralities: 5
          Planarities with less than four sites: {'ASP:plan': 2, 'HIS:plan': 1, 'ARG:plan': 3, 'GLU:plan': 1}
          Unresolved non-hydrogen planarities: 30
      Conformer: "B"
        Number of residues, atoms: 281, 2193
          Classifications: {'peptide': 281}
          Incomplete info: {'truncation_to_alanine': 12}
          Link IDs: {'PTRANS': 11, 'TRANS': 269}
          Chain breaks: 4
          Unresolved non-hydrogen bonds: 48
          Unresolved non-hydrogen angles: 61
          Unresolved non-hydrogen dihedrals: 37
          Unresolved non-hydrogen chiralities: 5
          Planarities with less than four sites: {'ASP:plan': 2, 'HIS:plan': 1, 'ARG:plan': 3, 'GLU:plan': 1}
          Unresolved non-hydrogen planarities: 30
          bond proxies already assigned to first conformer: 2231
    Chain: "R"
      Number of atoms: 27
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 27
          Unusual residues: {'YN9': 1}
          Classifications: {'undetermined': 1}
  Residues with excluded nonbonded symmetry interactions: 1
    residue:
      pdb=" N  APHE R 115 " occ=0.50
      ... (20 atoms not shown)
      pdb=" CZ BPHE R 115 " occ=0.50
  Time building chain proxies: 2.01, per 1000 atoms: 0.23
  Number of scatterers: 8583
  At special positions: 0
  Unit cell: (105.456, 121.68, 115.596, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S      58     16.00
     F       1      9.00
     O    1577      8.00
     N    1444      7.00
     C    5503      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=2, symmetry=0
    Simple disulfide: pdb=" SG  CYS S 159 " - pdb=" SG  CYS S 229 " distance=2.03
    Simple disulfide: pdb=" SG  CYS R 111 " - pdb=" SG  CYS R 194 " distance=2.04

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 0.54
  Conformation dependent library (CDL) restraints added in 284.2 milliseconds
  
  Enol-peptide restraints added in 476.8 nanoseconds
  

  2190 Ramachandran restraints generated.
    1095 Oldfield, 0 Emsley, 1095 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2102

  Finding SS restraints...
    Secondary structure from input PDB file:
      27 helices and 13 sheets defined
      37.4% alpha, 23.7% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.19
  Creating SS restraints...
    Processing helix  chain 'B' and resid 6 through 24
    Processing helix  chain 'B' and resid 29 through 35
    Processing helix  chain 'Y' and resid 10 through 24
    Processing helix  chain 'Y' and resid 29 through 44
    Processing helix  chain 'Y' and resid 45 through 48
    Processing helix  chain 'Y' and resid 55 through 59
    Processing helix  chain 'S' and resid 28 through 32
    Processing helix  chain 'S' and resid 87 through 91
      removed outlier: 3.619A  pdb=" N   THR S  91 " --> pdb=" O   SER S  88 " (cutoff:3.500A)
    Processing helix  chain 'S' and resid 220 through 224
      removed outlier: 3.985A  pdb=" N   VAL S 224 " --> pdb=" O   ALA S 221 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 6 through 31
    Processing helix  chain 'A' and resid 45 through 51
    Processing helix  chain 'A' and resid 207 through 216
      removed outlier: 4.388A  pdb=" N   ILE A 212 " --> pdb=" O   LYS A 209 " (cutoff:3.500A)
      removed outlier: 5.773A  pdb=" N   HIS A 213 " --> pdb=" O   LYS A 210 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 228 through 231
      removed outlier: 4.367A  pdb=" N   ASP A 231 " --> pdb=" O   SER A 228 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 228 through 231'
    Processing helix  chain 'A' and resid 241 through 255
    Processing helix  chain 'A' and resid 256 through 260
      removed outlier: 3.940A  pdb=" N   THR A 260 " --> pdb=" O   LYS A 257 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 270 through 279
    Processing helix  chain 'A' and resid 295 through 309
    Processing helix  chain 'A' and resid 335 through 355
    Processing helix  chain 'R' and resid 42 through 70
    Processing helix  chain 'R' and resid 78 through 91
      removed outlier: 3.956A  pdb=" N   ALA R  91 " --> pdb=" O   LEU R  87 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 91 through 101
      removed outlier: 3.628A  pdb=" N   VAL R  95 " --> pdb=" O   ALA R  91 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 109 through 142
      removed outlier: 4.695A  pdb=" N  APHE R 115 " --> pdb=" O   CYS R 111 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 152 through 169
    Processing helix  chain 'R' and resid 171 through 176
      removed outlier: 3.658A  pdb=" N   PHE R 176 " --> pdb=" O   PRO R 172 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 201 through 244
      removed outlier: 3.556A  pdb=" N   TRP R 207 " --> pdb=" O   GLY R 203 " (cutoff:3.500A)
      removed outlier: 3.840A  pdb=" N   VAL R 209 " --> pdb=" O   ILE R 205 " (cutoff:3.500A)
      removed outlier: 5.301A  pdb=" N   VAL R 218 " --> pdb=" O   LEU R 214 " (cutoff:3.500A)
      Proline residue:  R 219  - end of helix
      removed outlier: 3.958A  pdb=" N   ARG R 238 " --> pdb=" O   THR R 234 " (cutoff:3.500A)
      removed outlier: 3.566A  pdb=" N   VAL R 243 " --> pdb=" O   LYS R 239 " (cutoff:3.500A)
      removed outlier: 4.017A  pdb=" N   SER R 244 " --> pdb=" O   ARG R 240 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 248 through 292
      removed outlier: 3.614A  pdb=" N   LEU R 262 " --> pdb=" O   GLN R 258 " (cutoff:3.500A)
      removed outlier: 4.442A  pdb=" N   PHE R 263 " --> pdb=" O   ASP R 259 " (cutoff:3.500A)
      Proline residue:  R 279  - end of helix
    Processing helix  chain 'R' and resid 299 through 321
      removed outlier: 3.903A  pdb=" N   TRP R 305 " --> pdb=" O   SER R 301 " (cutoff:3.500A)
      removed outlier: 3.937A  pdb=" N   ASN R 313 " --> pdb=" O   PHE R 309 " (cutoff:3.500A)
      removed outlier: 4.397A  pdb=" N   SER R 314 " --> pdb=" O   THR R 310 " (cutoff:3.500A)
      removed outlier: 4.036A  pdb=" N   ALA R 315 " --> pdb=" O   PHE R 311 " (cutoff:3.500A)
      Proline residue:  R 318  - end of helix
    Processing sheet with id=AA1, first strand: chain 'B' and resid 47 through 51
      removed outlier: 3.541A  pdb=" N   ARG B  49 " --> pdb=" O   ILE B 338 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'B' and resid 58 through 63
      removed outlier: 3.627A  pdb=" N   ALA B  60 " --> pdb=" O   ALA B  73 " (cutoff:3.500A)
      removed outlier: 3.773A  pdb=" N   SER B  74 " --> pdb=" O   LYS B  78 " (cutoff:3.500A)
      removed outlier: 4.157A  pdb=" N   LYS B  78 " --> pdb=" O   SER B  74 " (cutoff:3.500A)
      removed outlier: 3.617A  pdb=" N   HIS B  91 " --> pdb=" O   ILE B  81 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'B' and resid 100 through 105
      removed outlier: 6.826A  pdb=" N   GLY B 115 " --> pdb=" O   MET B 101 " (cutoff:3.500A)
      removed outlier: 4.444A  pdb=" N   CYS B 103 " --> pdb=" O   ALA B 113 " (cutoff:3.500A)
      removed outlier: 6.474A  pdb=" N   ALA B 113 " --> pdb=" O   CYS B 103 " (cutoff:3.500A)
      removed outlier: 5.165A  pdb=" N   TYR B 105 " --> pdb=" O   TYR B 111 " (cutoff:3.500A)
      removed outlier: 7.203A  pdb=" N   TYR B 111 " --> pdb=" O   TYR B 105 " (cutoff:3.500A)
      removed outlier: 4.261A  pdb=" N   GLY B 116 " --> pdb=" O   ILE B 120 " (cutoff:3.500A)
      removed outlier: 4.840A  pdb=" N   ILE B 120 " --> pdb=" O   GLY B 116 " (cutoff:3.500A)
      removed outlier: 6.605A  pdb=" N   CYS B 121 " --> pdb=" O   GLU B 138 " (cutoff:3.500A)
      removed outlier: 5.003A  pdb=" N   GLU B 138 " --> pdb=" O   CYS B 121 " (cutoff:3.500A)
      removed outlier: 6.911A  pdb=" N   ILE B 123 " --> pdb=" O   SER B 136 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'B' and resid 146 through 153
      removed outlier: 3.600A  pdb=" N   CYS B 148 " --> pdb=" O   SER B 160 " (cutoff:3.500A)
      removed outlier: 7.199A  pdb=" N   GLN B 156 " --> pdb=" O   LEU B 152 " (cutoff:3.500A)
      removed outlier: 4.300A  pdb=" N   THR B 165 " --> pdb=" O   SER B 161 " (cutoff:3.500A)
      removed outlier: 6.227A  pdb=" N   ASP B 170 " --> pdb=" O   GLN B 176 " (cutoff:3.500A)
      removed outlier: 6.001A  pdb=" N   GLN B 176 " --> pdb=" O   ASP B 170 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'B' and resid 187 through 192
      removed outlier: 6.484A  pdb=" N   GLY B 202 " --> pdb=" O   MET B 188 " (cutoff:3.500A)
      removed outlier: 4.679A  pdb=" N   LEU B 190 " --> pdb=" O   VAL B 200 " (cutoff:3.500A)
      removed outlier: 7.043A  pdb=" N   VAL B 200 " --> pdb=" O   LEU B 190 " (cutoff:3.500A)
      removed outlier: 5.133A  pdb=" N   LEU B 192 " --> pdb=" O   LEU B 198 " (cutoff:3.500A)
      removed outlier: 7.125A  pdb=" N   LEU B 198 " --> pdb=" O   LEU B 192 " (cutoff:3.500A)
      removed outlier: 3.632A  pdb=" N   ALA B 203 " --> pdb=" O   SER B 207 " (cutoff:3.500A)
      removed outlier: 4.548A  pdb=" N   SER B 207 " --> pdb=" O   ALA B 203 " (cutoff:3.500A)
      removed outlier: 3.814A  pdb=" N   GLN B 220 " --> pdb=" O   LEU B 210 " (cutoff:3.500A)
      removed outlier: 7.017A  pdb=" N   ASP B 212 " --> pdb=" O   CYS B 218 " (cutoff:3.500A)
      removed outlier: 6.612A  pdb=" N   CYS B 218 " --> pdb=" O   ASP B 212 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'B' and resid 229 through 234
      removed outlier: 3.593A  pdb=" N   SER B 245 " --> pdb=" O   THR B 249 " (cutoff:3.500A)
      removed outlier: 4.499A  pdb=" N   THR B 249 " --> pdb=" O   SER B 245 " (cutoff:3.500A)
      removed outlier: 3.597A  pdb=" N   MET B 262 " --> pdb=" O   LEU B 252 " (cutoff:3.500A)
      removed outlier: 6.464A  pdb=" N   ASP B 254 " --> pdb=" O   GLU B 260 " (cutoff:3.500A)
      removed outlier: 6.395A  pdb=" N   GLU B 260 " --> pdb=" O   ASP B 254 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'B' and resid 273 through 278
      removed outlier: 3.714A  pdb=" N   CYS B 294 " --> pdb=" O   LEU B 308 " (cutoff:3.500A)
      removed outlier: 3.555A  pdb=" N   GLY B 306 " --> pdb=" O   VAL B 296 " (cutoff:3.500A)
      removed outlier: 6.237A  pdb=" N   ASP B 298 " --> pdb=" O   ARG B 304 " (cutoff:3.500A)
      removed outlier: 6.347A  pdb=" N   ARG B 304 " --> pdb=" O   ASP B 298 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'S' and resid 3 through 7
      removed outlier: 3.527A  pdb=" N   SER S  21 " --> pdb=" O   SER S   7 " (cutoff:3.500A)
      removed outlier: 3.682A  pdb=" N   CYS S  22 " --> pdb=" O   LEU S  79 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'S' and resid 11 through 12
      removed outlier: 3.572A  pdb=" N   THR S 115 " --> pdb=" O   TYR S  94 " (cutoff:3.500A)
      removed outlier: 6.800A  pdb=" N   MET S  34 " --> pdb=" O   TYR S  50 " (cutoff:3.500A)
      removed outlier: 4.414A  pdb=" N   TYR S  50 " --> pdb=" O   MET S  34 " (cutoff:3.500A)
      removed outlier: 6.630A  pdb=" N   TRP S  36 " --> pdb=" O   VAL S  48 " (cutoff:3.500A)
      removed outlier: 3.809A  pdb=" N   GLY S  44 " --> pdb=" O   ALA S  40 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'S' and resid 140 through 142
      removed outlier: 3.559A  pdb=" N   ALA S 211 " --> pdb=" O   SER S 208 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'S' and resid 146 through 148
      removed outlier: 3.624A  pdb=" N   ILE S 189 " --> pdb=" O   TRP S 176 " (cutoff:3.500A)
      removed outlier: 6.015A  pdb=" N   LEU S 178 " --> pdb=" O   LEU S 187 " (cutoff:3.500A)
      removed outlier: 5.630A  pdb=" N   LEU S 187 " --> pdb=" O   LEU S 178 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'A' and resid 185 through 190
      removed outlier: 3.697A  pdb=" N   PHE A 189 " --> pdb=" O   PHE A 196 " (cutoff:3.500A)
      removed outlier: 9.010A  pdb=" N   ALA A 220 " --> pdb=" O   GLU A  33 " (cutoff:3.500A)
      removed outlier: 6.792A  pdb=" N   LYS A  35 " --> pdb=" O   ALA A 220 " (cutoff:3.500A)
      removed outlier: 7.581A  pdb=" N   ILE A 222 " --> pdb=" O   LYS A  35 " (cutoff:3.500A)
      removed outlier: 6.370A  pdb=" N   LEU A  37 " --> pdb=" O   ILE A 222 " (cutoff:3.500A)
      removed outlier: 7.703A  pdb=" N   CYS A 224 " --> pdb=" O   LEU A  37 " (cutoff:3.500A)
      removed outlier: 6.885A  pdb=" N   LEU A  39 " --> pdb=" O   CYS A 224 " (cutoff:3.500A)
      removed outlier: 8.796A  pdb=" N   ALA A 226 " --> pdb=" O   LEU A  39 " (cutoff:3.500A)
      removed outlier: 6.340A  pdb=" N   ILE A 221 " --> pdb=" O   ILE A 265 " (cutoff:3.500A)
      removed outlier: 7.078A  pdb=" N   PHE A 267 " --> pdb=" O   ILE A 221 " (cutoff:3.500A)
      removed outlier: 6.237A  pdb=" N   PHE A 223 " --> pdb=" O   PHE A 267 " (cutoff:3.500A)
      removed outlier: 7.180A  pdb=" N   ASN A 269 " --> pdb=" O   PHE A 223 " (cutoff:3.500A)
      removed outlier: 6.768A  pdb=" N   VAL A 225 " --> pdb=" O   ASN A 269 " (cutoff:3.500A)
    Processing sheet with id=AB4, first strand: chain 'R' and resid 177 through 182

    437 hydrogen bonds defined for protein.
    1231 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 1.20

  Time building geometry restraints manager: 0.69 seconds

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

  Histogram of bond lengths:
        1.12 -     1.26: 1365
        1.26 -     1.40: 2177
        1.40 -     1.53: 4857
        1.53 -     1.67: 280
        1.67 -     1.81: 84
  Bond restraints: 8763
  Sorted by residual:
  bond pdb=" C   PHE R 260 "
       pdb=" O   PHE R 260 "
    ideal  model  delta    sigma   weight residual
    1.233  1.117  0.116 1.46e-02 4.69e+03 6.29e+01
  bond pdb=" N   GLN R 258 "
       pdb=" CA  GLN R 258 "
    ideal  model  delta    sigma   weight residual
    1.458  1.383  0.074 1.33e-02 5.65e+03 3.12e+01
  bond pdb=" N   ASP R 259 "
       pdb=" CA  ASP R 259 "
    ideal  model  delta    sigma   weight residual
    1.456  1.393  0.063 1.18e-02 7.18e+03 2.84e+01
  bond pdb=" C   ARG R  36 "
       pdb=" O   ARG R  36 "
    ideal  model  delta    sigma   weight residual
    1.235  1.172  0.063 1.25e-02 6.40e+03 2.54e+01
  bond pdb=" C1  YN9 R 401 "
       pdb=" C3  YN9 R 401 "
    ideal  model  delta    sigma   weight residual
    1.481  1.581 -0.100 2.00e-02 2.50e+03 2.50e+01
  ... (remaining 8758 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.34: 11696
        2.34 -     4.67: 178
        4.67 -     7.01: 27
        7.01 -     9.35: 5
        9.35 -    11.68: 4
  Bond angle restraints: 11910
  Sorted by residual:
  angle pdb=" N   PHE R 260 "
        pdb=" CA  PHE R 260 "
        pdb=" C   PHE R 260 "
      ideal   model   delta    sigma   weight residual
     114.04  102.67   11.37 1.24e+00 6.50e-01 8.41e+01
  angle pdb=" C   ALA R  91 "
        pdb=" N   ILE R  92 "
        pdb=" CA  ILE R  92 "
      ideal   model   delta    sigma   weight residual
     120.24  124.87   -4.63 6.30e-01 2.52e+00 5.39e+01
  angle pdb=" N   ILE R  89 "
        pdb=" CA  ILE R  89 "
        pdb=" C   ILE R  89 "
      ideal   model   delta    sigma   weight residual
     110.62  117.17   -6.55 1.02e+00 9.61e-01 4.13e+01
  angle pdb=" N   LEU A 358 "
        pdb=" CA  LEU A 358 "
        pdb=" C   LEU A 358 "
      ideal   model   delta    sigma   weight residual
     111.36  118.33   -6.97 1.09e+00 8.42e-01 4.09e+01
  angle pdb=" C   ASP R 259 "
        pdb=" CA  ASP R 259 "
        pdb=" CB  ASP R 259 "
      ideal   model   delta    sigma   weight residual
     110.94  120.06   -9.12 1.65e+00 3.67e-01 3.05e+01
  ... (remaining 11905 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    15.94: 4695
       15.94 -    31.87: 368
       31.87 -    47.81: 62
       47.81 -    63.75: 16
       63.75 -    79.68: 7
  Dihedral angle restraints: 5148
    sinusoidal: 1904
      harmonic: 3244
  Sorted by residual:
  dihedral pdb=" C   ASP R 259 "
           pdb=" N   ASP R 259 "
           pdb=" CA  ASP R 259 "
           pdb=" CB  ASP R 259 "
      ideal   model   delta  harmonic     sigma   weight residual
    -122.60 -144.58   21.98     0      2.50e+00 1.60e-01 7.73e+01
  dihedral pdb=" N   ASP R 259 "
           pdb=" C   ASP R 259 "
           pdb=" CA  ASP R 259 "
           pdb=" CB  ASP R 259 "
      ideal   model   delta  harmonic     sigma   weight residual
     122.80  142.49  -19.69     0      2.50e+00 1.60e-01 6.21e+01
  dihedral pdb=" CB  CYS R 111 "
           pdb=" SG  CYS R 111 "
           pdb=" SG  CYS R 194 "
           pdb=" CB  CYS R 194 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00   27.64   65.36     1      1.00e+01 1.00e-02 5.60e+01
  ... (remaining 5145 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.197: 1389
       0.197 -    0.394: 3
       0.394 -    0.591: 0
       0.591 -    0.788: 0
       0.788 -    0.985: 1
  Chirality restraints: 1393
  Sorted by residual:
  chirality pdb=" CA  ASP R 259 "
            pdb=" N   ASP R 259 "
            pdb=" C   ASP R 259 "
            pdb=" CB  ASP R 259 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    1.53    0.99 2.00e-01 2.50e+01 2.43e+01
  chirality pdb=" CA  ARG R 254 "
            pdb=" N   ARG R 254 "
            pdb=" C   ARG R 254 "
            pdb=" CB  ARG R 254 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.18    0.33 2.00e-01 2.50e+01 2.67e+00
  chirality pdb=" CA  GLN R 258 "
            pdb=" N   GLN R 258 "
            pdb=" C   GLN R 258 "
            pdb=" CB  GLN R 258 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.23    0.28 2.00e-01 2.50e+01 1.91e+00
  ... (remaining 1390 not shown)

  Planarity restraints: 1491
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  GLN R 257 "   -0.028 2.00e-02 2.50e+03   5.65e-02 3.19e+01
        pdb=" C   GLN R 257 "    0.098 2.00e-02 2.50e+03
        pdb=" O   GLN R 257 "   -0.037 2.00e-02 2.50e+03
        pdb=" N   GLN R 258 "   -0.033 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ASP S  74 "   -0.075 5.00e-02 4.00e+02   1.12e-01 2.01e+01
        pdb=" N   PRO S  75 "    0.194 5.00e-02 4.00e+02
        pdb=" CA  PRO S  75 "   -0.058 5.00e-02 4.00e+02
        pdb=" CD  PRO S  75 "   -0.061 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   TRP R 299 "    0.040 5.00e-02 4.00e+02   6.13e-02 6.01e+00
        pdb=" N   PRO R 300 "   -0.106 5.00e-02 4.00e+02
        pdb=" CA  PRO R 300 "    0.032 5.00e-02 4.00e+02
        pdb=" CD  PRO R 300 "    0.034 5.00e-02 4.00e+02
  ... (remaining 1488 not shown)

  Histogram of nonbonded interaction distances:
        1.93 -     2.52: 57
        2.52 -     3.12: 6315
        3.12 -     3.71: 13279
        3.71 -     4.31: 19213
        4.31 -     4.90: 32205
  Nonbonded interactions: 71069
  Sorted by model distance:
  nonbonded pdb=" NH2 ARG R 238 "
            pdb=" OD2 ASP R 259 "
     model   vdw
     1.930 3.120
  nonbonded pdb=" O   CYS R  60 "
            pdb=" CD2 LEU R  64 "
     model   vdw
     1.953 3.460
  nonbonded pdb=" O   ALA A  41 "
            pdb=" OG  SER A  44 "
     model   vdw
     2.183 3.040
  nonbonded pdb=" OG  SER B 331 "
            pdb=" OD1 ASP B 333 "
     model   vdw
     2.222 3.040
  nonbonded pdb=" O   CYS A 254 "
            pdb=" NZ  LYS A 317 "
     model   vdw
     2.255 3.120
  ... (remaining 71064 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=0.50 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:             0.440
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.090
  Check model and map are aligned:         0.020
  Set scattering table:                    0.010
  Process input model:                     7.580
  Find NCS groups from input model:        0.030
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:8.540
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   16.740
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7237
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.116   8765  Z= 0.293
  Angle     :  0.731  11.682  11914  Z= 0.431
  Chirality :  0.053   0.985   1393
  Planarity :  0.006   0.112   1491
  Dihedral  : 12.174  79.684   3040
  Min Nonbonded Distance : 1.930

Molprobity Statistics.
  All-atom Clashscore : 10.26
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  :  3.85 %
    Favored  : 96.06 %
  Rotamer:
    Outliers :  0.22 %
    Allowed  :  0.88 %
    Favored  : 98.90 %
  Cbeta Deviations :  0.10 %
  Peptide Plane:
    Cis-proline     : 3.12 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.15 (0.25), residues: 1095
  helix:  0.23 (0.25), residues: 387
  sheet:  0.39 (0.30), residues: 301
  loop : -0.65 (0.30), residues: 407

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG R  36 
 TYR   0.017   0.001   TYR A 302 
 PHE   0.016   0.001   PHE R 311 
 TRP   0.020   0.001   TRP B  63 
 HIS   0.004   0.001   HIS R 251 

Details of bonding type rmsd
  covalent geometry    : bond        0.00524 ( 8763)
  covalent geometry    : angle       0.72755 (11910)
  SS BOND              : bond        0.00460 (    2)
  SS BOND              : angle       4.13992 (    4)
  hydrogen bonds       : bond        0.19869 (  437)
  hydrogen bonds       : angle       7.15701 ( 1231)

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

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

  2190 Ramachandran restraints generated.
    1095 Oldfield, 0 Emsley, 1095 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2190 Ramachandran restraints generated.
    1095 Oldfield, 0 Emsley, 1095 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  161 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 159
  time to evaluate  : 0.279 
Fit side-chains
   revert: symmetry clash
REVERT: B  209 LYS cc_start: 0.9253 (mttm) cc_final: 0.9006 (mttp)
REVERT: R  165 TYR cc_start: 0.7006 (t80) cc_final: 0.6178 (t80)
  outliers start: 2
  outliers final: 1
  residues processed: 161
  average time/residue: 0.6901
  time to fit residues: 116.4525
Evaluate side-chains
  135 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 134
  time to evaluate  : 0.332 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue  259 ASP
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 110
   random chunks:
   chunk 108 optimal weight:    0.7980
   chunk 49 optimal weight:    7.9990
   chunk 97 optimal weight:    0.8980
   chunk 53 optimal weight:    7.9990
   chunk 5 optimal weight:    9.9990
   chunk 33 optimal weight:    8.9990
   chunk 65 optimal weight:    1.9990
   chunk 62 optimal weight:    0.9990
   chunk 51 optimal weight:   30.0000
   chunk 100 optimal weight:    0.9980
   chunk 106 optimal weight:    0.6980
   overall best weight:    0.8782

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

Flipped N/Q/H residues before XYZ refinement:
B  75 GLN
B 268 ASN
B 340 ASN
S 179 GLN
S 186 GLN
A 188 HIS
A 204 GLN
A 357 ASN
R 189 GLN

Total number of N/Q/H flips: 9

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4183 r_free = 0.4183 target = 0.157244 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 61)----------------|
| r_work = 0.3773 r_free = 0.3773 target = 0.122396 restraints weight = 16487.095|
|-----------------------------------------------------------------------------|
r_work (start): 0.3691 rms_B_bonded: 2.28
r_work: 0.3590 rms_B_bonded: 2.36 restraints_weight: 0.5000
r_work: 0.3437 rms_B_bonded: 3.96 restraints_weight: 0.2500
r_work (final): 0.3437
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3442
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3442 r_free = 0.3442    target_work(ls_wunit_k1) = 0.103         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3442 r_free = 0.3442    target_work(ls_wunit_k1) = 0.103         |
| occupancies: max = 1.00  min = 0.45   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3442
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7576
moved from start:          0.1496

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.048   8765  Z= 0.147
  Angle     :  0.633  10.620  11914  Z= 0.324
  Chirality :  0.043   0.142   1393
  Planarity :  0.005   0.074   1491
  Dihedral  :  5.223  59.323   1212
  Min Nonbonded Distance : 2.433

Molprobity Statistics.
  All-atom Clashscore : 7.08
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.75 %
    Favored  : 96.25 %
  Rotamer:
    Outliers :  1.43 %
    Allowed  : 10.35 %
    Favored  : 88.22 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.12 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.48 (0.26), residues: 1095
  helix:  1.05 (0.27), residues: 376
  sheet:  0.52 (0.31), residues: 297
  loop : -0.38 (0.31), residues: 422

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG B 129 
 TYR   0.015   0.001   TYR S 190 
 PHE   0.015   0.001   PHE R 263 
 TRP   0.019   0.001   TRP B 169 
 HIS   0.004   0.001   HIS A 195 

Details of bonding type rmsd
  covalent geometry    : bond        0.00327 ( 8763)
  covalent geometry    : angle       0.62962 (11910)
  SS BOND              : bond        0.01003 (    2)
  SS BOND              : angle       3.62327 (    4)
  hydrogen bonds       : bond        0.04374 (  437)
  hydrogen bonds       : angle       5.21139 ( 1231)

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

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

  2190 Ramachandran restraints generated.
    1095 Oldfield, 0 Emsley, 1095 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2190 Ramachandran restraints generated.
    1095 Oldfield, 0 Emsley, 1095 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  159 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 146
  time to evaluate  : 0.218 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  228 ASP cc_start: 0.8179 (m-30) cc_final: 0.7481 (p0)
REVERT: B  254 ASP cc_start: 0.8033 (t0) cc_final: 0.7702 (t0)
REVERT: A  200 ASP cc_start: 0.8192 (m-30) cc_final: 0.7985 (m-30)
REVERT: A  248 LYS cc_start: 0.8349 (mppt) cc_final: 0.7931 (mppt)
REVERT: R  155 ARG cc_start: 0.6032 (ptm-80) cc_final: 0.5559 (mtp-110)
REVERT: R  165 TYR cc_start: 0.7943 (t80) cc_final: 0.6523 (t80)
REVERT: R  240 ARG cc_start: 0.7586 (OUTLIER) cc_final: 0.6238 (ptt90)
REVERT: R  298 ILE cc_start: 0.8043 (OUTLIER) cc_final: 0.7795 (mp)
  outliers start: 13
  outliers final: 2
  residues processed: 149
  average time/residue: 0.6896
  time to fit residues: 107.7018
Evaluate side-chains
  126 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 122
  time to evaluate  : 0.325 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   78 LYS
Chi-restraints excluded: chain S residue  144 THR
Chi-restraints excluded: chain R residue  240 ARG
Chi-restraints excluded: chain R residue  298 ILE
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 110
   random chunks:
   chunk 58 optimal weight:    6.9990
   chunk 69 optimal weight:    5.9990
   chunk 88 optimal weight:    0.8980
   chunk 67 optimal weight:    1.9990
   chunk 22 optimal weight:    7.9990
   chunk 97 optimal weight:    1.9990
   chunk 0 optimal weight:   40.0000
   chunk 91 optimal weight:    1.9990
   chunk 12 optimal weight:    3.9990
   chunk 2 optimal weight:    7.9990
   chunk 61 optimal weight:    0.9980
   overall best weight:    1.5786

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

Flipped N/Q/H residues before XYZ refinement:
B  75 GLN
B 230 ASN
B 259 GLN
B 268 ASN
B 340 ASN
S 179 GLN
S 194 ASN
A 306 GLN

Total number of N/Q/H flips: 8

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4154 r_free = 0.4154 target = 0.155078 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3784 r_free = 0.3784 target = 0.122126 restraints weight = 23884.628|
|-----------------------------------------------------------------------------|
r_work (start): 0.3668 rms_B_bonded: 3.21
r_work: 0.3499 rms_B_bonded: 2.79 restraints_weight: 0.5000
r_work: 0.3331 rms_B_bonded: 4.63 restraints_weight: 0.2500
r_work (final): 0.3331
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3341
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3341 r_free = 0.3341    target_work(ls_wunit_k1) = 0.097         |
| occupancies: max = 1.00  min = 0.45   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3341 r_free = 0.3341    target_work(ls_wunit_k1) = 0.097         |
| occupancies: max = 1.00  min = 0.44   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3341
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7620
moved from start:          0.1829

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.044   8765  Z= 0.180
  Angle     :  0.624  10.277  11914  Z= 0.319
  Chirality :  0.044   0.141   1393
  Planarity :  0.005   0.063   1491
  Dihedral  :  4.894  47.431   1210
  Min Nonbonded Distance : 2.529

Molprobity Statistics.
  All-atom Clashscore : 7.31
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.12 %
    Favored  : 95.88 %
  Rotamer:
    Outliers :  1.87 %
    Allowed  : 13.22 %
    Favored  : 84.91 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.12 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.48 (0.26), residues: 1095
  helix:  0.96 (0.27), residues: 383
  sheet:  0.70 (0.31), residues: 284
  loop : -0.44 (0.31), residues: 428

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.011   0.001   ARG R 261 
 TYR   0.012   0.002   TYR S 190 
 PHE   0.012   0.002   PHE R 177 
 TRP   0.021   0.002   TRP R 104 
 HIS   0.005   0.001   HIS A 188 

Details of bonding type rmsd
  covalent geometry    : bond        0.00422 ( 8763)
  covalent geometry    : angle       0.62079 (11910)
  SS BOND              : bond        0.00378 (    2)
  SS BOND              : angle       3.46689 (    4)
  hydrogen bonds       : bond        0.04325 (  437)
  hydrogen bonds       : angle       4.96812 ( 1231)

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

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

  2190 Ramachandran restraints generated.
    1095 Oldfield, 0 Emsley, 1095 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2190 Ramachandran restraints generated.
    1095 Oldfield, 0 Emsley, 1095 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  149 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 132
  time to evaluate  : 0.210 
Fit side-chains
   revert: symmetry clash
REVERT: B   78 LYS cc_start: 0.8415 (OUTLIER) cc_final: 0.7787 (mptm)
REVERT: B  228 ASP cc_start: 0.8210 (m-30) cc_final: 0.7809 (p0)
REVERT: B  254 ASP cc_start: 0.8078 (t0) cc_final: 0.7574 (t0)
REVERT: B  259 GLN cc_start: 0.7951 (OUTLIER) cc_final: 0.7714 (mt0)
REVERT: S   46 GLU cc_start: 0.8482 (tt0) cc_final: 0.8048 (tt0)
REVERT: S  109 ASP cc_start: 0.7816 (m-30) cc_final: 0.7614 (m-30)
REVERT: A  240 MET cc_start: 0.6506 (ptt) cc_final: 0.6134 (ptp)
REVERT: A  248 LYS cc_start: 0.8266 (mppt) cc_final: 0.7794 (mppt)
REVERT: A  306 GLN cc_start: 0.7053 (mt0) cc_final: 0.6819 (mt0)
REVERT: A  309 ASP cc_start: 0.8167 (m-30) cc_final: 0.7770 (m-30)
REVERT: A  354 LYS cc_start: 0.8173 (tppt) cc_final: 0.7971 (mmpt)
REVERT: R  155 ARG cc_start: 0.6072 (ptm-80) cc_final: 0.5572 (mtp-110)
REVERT: R  165 TYR cc_start: 0.8161 (t80) cc_final: 0.6546 (t80)
REVERT: R  298 ILE cc_start: 0.8162 (OUTLIER) cc_final: 0.7794 (mp)
  outliers start: 17
  outliers final: 6
  residues processed: 138
  average time/residue: 0.7041
  time to fit residues: 102.0509
Evaluate side-chains
  140 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 131
  time to evaluate  : 0.268 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   78 LYS
Chi-restraints excluded: chain B residue  259 GLN
Chi-restraints excluded: chain Y residue   41 CYS
Chi-restraints excluded: chain S residue   22 CYS
Chi-restraints excluded: chain S residue  144 THR
Chi-restraints excluded: chain S residue  146 SER
Chi-restraints excluded: chain R residue   49 LEU
Chi-restraints excluded: chain R residue  141 VAL
Chi-restraints excluded: chain R residue  298 ILE
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 110
   random chunks:
   chunk 31 optimal weight:    0.0570
   chunk 98 optimal weight:    2.9990
   chunk 78 optimal weight:    9.9990
   chunk 41 optimal weight:    1.9990
   chunk 84 optimal weight:    1.9990
   chunk 29 optimal weight:    6.9990
   chunk 107 optimal weight:    0.9980
   chunk 24 optimal weight:    6.9990
   chunk 81 optimal weight:    0.6980
   chunk 56 optimal weight:    0.0970
   chunk 37 optimal weight:    8.9990
   overall best weight:    0.7698

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

Flipped N/Q/H residues before XYZ refinement:
B  75 GLN
B 268 ASN
B 340 ASN
S 179 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4175 r_free = 0.4175 target = 0.156653 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3807 r_free = 0.3807 target = 0.123154 restraints weight = 24107.220|
|-----------------------------------------------------------------------------|
r_work (start): 0.3696 rms_B_bonded: 3.13
r_work: 0.3542 rms_B_bonded: 2.76 restraints_weight: 0.5000
r_work: 0.3370 rms_B_bonded: 4.66 restraints_weight: 0.2500
r_work (final): 0.3370
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3381
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3381 r_free = 0.3381    target_work(ls_wunit_k1) = 0.100         |
| occupancies: max = 1.00  min = 0.44   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3381 r_free = 0.3381    target_work(ls_wunit_k1) = 0.100         |
| occupancies: max = 1.00  min = 0.45   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3381
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7591
moved from start:          0.2034

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   8765  Z= 0.122
  Angle     :  0.566   9.122  11914  Z= 0.289
  Chirality :  0.042   0.140   1393
  Planarity :  0.005   0.059   1491
  Dihedral  :  4.521  40.884   1210
  Min Nonbonded Distance : 2.567

Molprobity Statistics.
  All-atom Clashscore : 6.08
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.66 %
    Favored  : 96.34 %
  Rotamer:
    Outliers :  1.87 %
    Allowed  : 14.76 %
    Favored  : 83.37 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.12 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.66 (0.26), residues: 1095
  helix:  1.27 (0.27), residues: 384
  sheet:  0.63 (0.31), residues: 292
  loop : -0.38 (0.31), residues: 419

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG B 129 
 TYR   0.012   0.001   TYR S 190 
 PHE   0.019   0.001   PHE R 263 
 TRP   0.017   0.001   TRP B 169 
 HIS   0.004   0.001   HIS A 188 

Details of bonding type rmsd
  covalent geometry    : bond        0.00276 ( 8763)
  covalent geometry    : angle       0.56411 (11910)
  SS BOND              : bond        0.00287 (    2)
  SS BOND              : angle       2.50804 (    4)
  hydrogen bonds       : bond        0.03626 (  437)
  hydrogen bonds       : angle       4.70195 ( 1231)

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

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

  2190 Ramachandran restraints generated.
    1095 Oldfield, 0 Emsley, 1095 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2190 Ramachandran restraints generated.
    1095 Oldfield, 0 Emsley, 1095 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  166 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 149
  time to evaluate  : 0.283 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   52 ARG cc_start: 0.8670 (OUTLIER) cc_final: 0.8344 (mtp85)
REVERT: B  201 SER cc_start: 0.8504 (m) cc_final: 0.8123 (p)
REVERT: B  228 ASP cc_start: 0.8168 (m-30) cc_final: 0.7876 (p0)
REVERT: B  254 ASP cc_start: 0.8041 (t0) cc_final: 0.7547 (t0)
REVERT: B  259 GLN cc_start: 0.7959 (mt0) cc_final: 0.7650 (mt0)
REVERT: S   39 GLN cc_start: 0.8810 (tt0) cc_final: 0.8595 (tt0)
REVERT: S   46 GLU cc_start: 0.8495 (tt0) cc_final: 0.8089 (tt0)
REVERT: S  109 ASP cc_start: 0.7860 (m-30) cc_final: 0.7642 (m-30)
REVERT: A  186 GLU cc_start: 0.7894 (tm-30) cc_final: 0.7619 (tm-30)
REVERT: A  240 MET cc_start: 0.6394 (ptt) cc_final: 0.6003 (ptp)
REVERT: A  306 GLN cc_start: 0.7047 (mt0) cc_final: 0.6798 (mt0)
REVERT: A  309 ASP cc_start: 0.8193 (m-30) cc_final: 0.7776 (m-30)
REVERT: R  155 ARG cc_start: 0.5901 (ptm-80) cc_final: 0.5479 (mtp-110)
REVERT: R  165 TYR cc_start: 0.8130 (t80) cc_final: 0.6523 (t80)
REVERT: R  240 ARG cc_start: 0.7649 (OUTLIER) cc_final: 0.6264 (ptt90)
REVERT: R  298 ILE cc_start: 0.8105 (OUTLIER) cc_final: 0.7821 (mp)
  outliers start: 17
  outliers final: 4
  residues processed: 155
  average time/residue: 0.6116
  time to fit residues: 99.7660
Evaluate side-chains
  142 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 135
  time to evaluate  : 0.225 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   52 ARG
Chi-restraints excluded: chain Y residue   41 CYS
Chi-restraints excluded: chain S residue   22 CYS
Chi-restraints excluded: chain S residue  144 THR
Chi-restraints excluded: chain S residue  146 SER
Chi-restraints excluded: chain R residue  240 ARG
Chi-restraints excluded: chain R residue  298 ILE
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 110
   random chunks:
   chunk 84 optimal weight:    0.9990
   chunk 102 optimal weight:    3.9990
   chunk 60 optimal weight:    9.9990
   chunk 29 optimal weight:    7.9990
   chunk 48 optimal weight:    4.9990
   chunk 1 optimal weight:    7.9990
   chunk 33 optimal weight:    6.9990
   chunk 73 optimal weight:    0.2980
   chunk 52 optimal weight:    0.8980
   chunk 100 optimal weight:    0.7980
   chunk 66 optimal weight:    3.9990
   overall best weight:    1.3984

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

Flipped N/Q/H residues before XYZ refinement:
B  75 GLN
B 268 ASN
B 340 ASN
S  77 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4177 r_free = 0.4177 target = 0.148903 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3786 r_free = 0.3786 target = 0.114488 restraints weight = 31522.229|
|-----------------------------------------------------------------------------|
r_work (start): 0.3668 rms_B_bonded: 3.22
r_work: 0.3486 rms_B_bonded: 2.93 restraints_weight: 0.5000
r_work: 0.3317 rms_B_bonded: 4.83 restraints_weight: 0.2500
r_work (final): 0.3317
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3330
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3330 r_free = 0.3330    target_work(ls_wunit_k1) = 0.097         |
| occupancies: max = 1.00  min = 0.45   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3330 r_free = 0.3330    target_work(ls_wunit_k1) = 0.097         |
| occupancies: max = 1.00  min = 0.45   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3330
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7646
moved from start:          0.2160

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.041   8765  Z= 0.160
  Angle     :  0.592  10.610  11914  Z= 0.301
  Chirality :  0.043   0.145   1393
  Planarity :  0.005   0.059   1491
  Dihedral  :  4.669  42.158   1210
  Min Nonbonded Distance : 2.570

Molprobity Statistics.
  All-atom Clashscore : 6.67
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.94 %
    Favored  : 96.06 %
  Rotamer:
    Outliers :  2.09 %
    Allowed  : 16.19 %
    Favored  : 81.72 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.12 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.62 (0.26), residues: 1095
  helix:  1.24 (0.27), residues: 384
  sheet:  0.61 (0.30), residues: 292
  loop : -0.41 (0.31), residues: 419

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG B 129 
 TYR   0.011   0.001   TYR S 190 
 PHE   0.018   0.001   PHE R 260 
 TRP   0.020   0.002   TRP R 104 
 HIS   0.004   0.001   HIS A 188 

Details of bonding type rmsd
  covalent geometry    : bond        0.00374 ( 8763)
  covalent geometry    : angle       0.58935 (11910)
  SS BOND              : bond        0.00311 (    2)
  SS BOND              : angle       2.93651 (    4)
  hydrogen bonds       : bond        0.03955 (  437)
  hydrogen bonds       : angle       4.71080 ( 1231)

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

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

  2190 Ramachandran restraints generated.
    1095 Oldfield, 0 Emsley, 1095 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2190 Ramachandran restraints generated.
    1095 Oldfield, 0 Emsley, 1095 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  155 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 136
  time to evaluate  : 0.319 
Fit side-chains
   revert: symmetry clash
REVERT: B   52 ARG cc_start: 0.8665 (OUTLIER) cc_final: 0.8368 (mtp85)
REVERT: B  228 ASP cc_start: 0.8214 (m-30) cc_final: 0.7934 (p0)
REVERT: B  254 ASP cc_start: 0.8046 (t0) cc_final: 0.7502 (t0)
REVERT: B  262 MET cc_start: 0.8567 (OUTLIER) cc_final: 0.7866 (ptm)
REVERT: S   46 GLU cc_start: 0.8425 (tt0) cc_final: 0.8028 (tt0)
REVERT: S  109 ASP cc_start: 0.7818 (m-30) cc_final: 0.7610 (m-30)
REVERT: A  240 MET cc_start: 0.6480 (ptt) cc_final: 0.6029 (ptp)
REVERT: A  248 LYS cc_start: 0.8340 (mppt) cc_final: 0.7905 (mtmm)
REVERT: A  306 GLN cc_start: 0.7204 (mt0) cc_final: 0.6932 (mt0)
REVERT: A  309 ASP cc_start: 0.8229 (m-30) cc_final: 0.7817 (m-30)
REVERT: A  356 TYR cc_start: 0.7780 (m-10) cc_final: 0.7556 (m-10)
REVERT: R  155 ARG cc_start: 0.6042 (ptm-80) cc_final: 0.5635 (mtp-110)
REVERT: R  165 TYR cc_start: 0.8206 (t80) cc_final: 0.6572 (t80)
REVERT: R  178 ARG cc_start: 0.8228 (OUTLIER) cc_final: 0.7473 (mmp80)
REVERT: R  240 ARG cc_start: 0.7687 (OUTLIER) cc_final: 0.6243 (ptt90)
REVERT: R  298 ILE cc_start: 0.8184 (OUTLIER) cc_final: 0.7848 (mp)
  outliers start: 19
  outliers final: 6
  residues processed: 145
  average time/residue: 0.8203
  time to fit residues: 124.3761
Evaluate side-chains
  148 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 137
  time to evaluate  : 0.346 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   52 ARG
Chi-restraints excluded: chain B residue  262 MET
Chi-restraints excluded: chain B residue  317 CYS
Chi-restraints excluded: chain Y residue   41 CYS
Chi-restraints excluded: chain S residue   22 CYS
Chi-restraints excluded: chain S residue  144 THR
Chi-restraints excluded: chain S residue  146 SER
Chi-restraints excluded: chain R residue   49 LEU
Chi-restraints excluded: chain R residue  178 ARG
Chi-restraints excluded: chain R residue  240 ARG
Chi-restraints excluded: chain R residue  298 ILE
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 110
   random chunks:
   chunk 28 optimal weight:    2.9990
   chunk 58 optimal weight:    9.9990
   chunk 103 optimal weight:    0.8980
   chunk 101 optimal weight:    1.9990
   chunk 22 optimal weight:    9.9990
   chunk 56 optimal weight:    2.9990
   chunk 98 optimal weight:    0.0020
   chunk 40 optimal weight:    0.9990
   chunk 18 optimal weight:    4.9990
   chunk 17 optimal weight:    6.9990
   chunk 8 optimal weight:    4.9990
   overall best weight:    1.3794

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

Flipped N/Q/H residues before XYZ refinement:
B  75 GLN
B  88 ASN
B 268 ASN
B 340 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4158 r_free = 0.4158 target = 0.155298 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 62)----------------|
| r_work = 0.3729 r_free = 0.3729 target = 0.119740 restraints weight = 20426.120|
|-----------------------------------------------------------------------------|
r_work (start): 0.3642 rms_B_bonded: 2.52
r_work: 0.3531 rms_B_bonded: 2.56 restraints_weight: 0.5000
r_work: 0.3374 rms_B_bonded: 4.21 restraints_weight: 0.2500
r_work (final): 0.3374
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3381
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3381 r_free = 0.3381    target_work(ls_wunit_k1) = 0.100         |
| occupancies: max = 1.00  min = 0.45   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3381 r_free = 0.3381    target_work(ls_wunit_k1) = 0.100         |
| occupancies: max = 1.00  min = 0.44   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3381
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7640
moved from start:          0.2276

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.041   8765  Z= 0.158
  Angle     :  0.581   8.402  11914  Z= 0.297
  Chirality :  0.043   0.147   1393
  Planarity :  0.005   0.059   1491
  Dihedral  :  4.576  37.929   1210
  Min Nonbonded Distance : 2.533

Molprobity Statistics.
  All-atom Clashscore : 6.61
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.03 %
    Favored  : 95.97 %
  Rotamer:
    Outliers :  2.42 %
    Allowed  : 16.41 %
    Favored  : 81.17 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.12 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.64 (0.26), residues: 1095
  helix:  1.24 (0.27), residues: 384
  sheet:  0.61 (0.31), residues: 292
  loop : -0.38 (0.31), residues: 419

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.001   ARG B 129 
 TYR   0.011   0.001   TYR S 190 
 PHE   0.016   0.001   PHE R 260 
 TRP   0.017   0.001   TRP R 104 
 HIS   0.004   0.001   HIS A 188 

Details of bonding type rmsd
  covalent geometry    : bond        0.00370 ( 8763)
  covalent geometry    : angle       0.57906 (11910)
  SS BOND              : bond        0.00308 (    2)
  SS BOND              : angle       2.90654 (    4)
  hydrogen bonds       : bond        0.03884 (  437)
  hydrogen bonds       : angle       4.68575 ( 1231)

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

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

  2190 Ramachandran restraints generated.
    1095 Oldfield, 0 Emsley, 1095 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2190 Ramachandran restraints generated.
    1095 Oldfield, 0 Emsley, 1095 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  166 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 144
  time to evaluate  : 0.374 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   52 ARG cc_start: 0.8625 (OUTLIER) cc_final: 0.8341 (mtp85)
REVERT: B   78 LYS cc_start: 0.8463 (OUTLIER) cc_final: 0.7833 (mptm)
REVERT: B  201 SER cc_start: 0.8597 (m) cc_final: 0.8280 (p)
REVERT: B  228 ASP cc_start: 0.8198 (m-30) cc_final: 0.7989 (p0)
REVERT: B  254 ASP cc_start: 0.8025 (t0) cc_final: 0.7536 (t0)
REVERT: B  262 MET cc_start: 0.8516 (OUTLIER) cc_final: 0.7966 (ptm)
REVERT: S   46 GLU cc_start: 0.8368 (tt0) cc_final: 0.7974 (tt0)
REVERT: S  109 ASP cc_start: 0.7737 (m-30) cc_final: 0.7528 (m-30)
REVERT: A  240 MET cc_start: 0.6617 (ptt) cc_final: 0.6163 (ptp)
REVERT: A  248 LYS cc_start: 0.8366 (mppt) cc_final: 0.7925 (mtmm)
REVERT: A  306 GLN cc_start: 0.7201 (mt0) cc_final: 0.6973 (mt0)
REVERT: A  309 ASP cc_start: 0.8161 (m-30) cc_final: 0.7728 (m-30)
REVERT: R  155 ARG cc_start: 0.6039 (ptm-80) cc_final: 0.5671 (mtp-110)
REVERT: R  165 TYR cc_start: 0.8118 (t80) cc_final: 0.6528 (t80)
REVERT: R  175 VAL cc_start: 0.8463 (m) cc_final: 0.8109 (p)
REVERT: R  178 ARG cc_start: 0.8137 (OUTLIER) cc_final: 0.7274 (mmp80)
REVERT: R  240 ARG cc_start: 0.7652 (OUTLIER) cc_final: 0.6196 (ptt90)
REVERT: R  298 ILE cc_start: 0.8155 (OUTLIER) cc_final: 0.7853 (mp)
  outliers start: 22
  outliers final: 10
  residues processed: 153
  average time/residue: 0.7736
  time to fit residues: 124.1909
Evaluate side-chains
  148 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 132
  time to evaluate  : 0.338 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   52 ARG
Chi-restraints excluded: chain B residue   78 LYS
Chi-restraints excluded: chain B residue  112 VAL
Chi-restraints excluded: chain B residue  262 MET
Chi-restraints excluded: chain B residue  317 CYS
Chi-restraints excluded: chain Y residue   41 CYS
Chi-restraints excluded: chain S residue   22 CYS
Chi-restraints excluded: chain S residue  144 THR
Chi-restraints excluded: chain S residue  146 SER
Chi-restraints excluded: chain R residue   49 LEU
Chi-restraints excluded: chain R residue   89 ILE
Chi-restraints excluded: chain R residue  141 VAL
Chi-restraints excluded: chain R residue  178 ARG
Chi-restraints excluded: chain R residue  240 ARG
Chi-restraints excluded: chain R residue  298 ILE
Chi-restraints excluded: chain R residue  323 MET
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 110
   random chunks:
   chunk 24 optimal weight:    6.9990
   chunk 5 optimal weight:    4.9990
   chunk 54 optimal weight:   10.0000
   chunk 96 optimal weight:    1.9990
   chunk 105 optimal weight:    0.8980
   chunk 89 optimal weight:    3.9990
   chunk 25 optimal weight:    0.8980
   chunk 69 optimal weight:    3.9990
   chunk 92 optimal weight:    0.7980
   chunk 76 optimal weight:    3.9990
   chunk 62 optimal weight:    0.8980
   overall best weight:    1.0982

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

Flipped N/Q/H residues before XYZ refinement:
B  75 GLN
B 268 ASN
B 340 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4165 r_free = 0.4165 target = 0.155771 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 62)----------------|
| r_work = 0.3730 r_free = 0.3730 target = 0.119656 restraints weight = 24448.873|
|-----------------------------------------------------------------------------|
r_work (start): 0.3643 rms_B_bonded: 2.79
r_work: 0.3524 rms_B_bonded: 2.75 restraints_weight: 0.5000
r_work: 0.3363 rms_B_bonded: 4.50 restraints_weight: 0.2500
r_work (final): 0.3363
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3370
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3370 r_free = 0.3370    target_work(ls_wunit_k1) = 0.099         |
| occupancies: max = 1.00  min = 0.44   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3370 r_free = 0.3370    target_work(ls_wunit_k1) = 0.099         |
| occupancies: max = 1.00  min = 0.44   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3370
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7648
moved from start:          0.2383

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   8765  Z= 0.140
  Angle     :  0.580  10.639  11914  Z= 0.295
  Chirality :  0.042   0.141   1393
  Planarity :  0.005   0.059   1491
  Dihedral  :  4.460  34.872   1210
  Min Nonbonded Distance : 2.526

Molprobity Statistics.
  All-atom Clashscore : 6.37
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.94 %
    Favored  : 96.06 %
  Rotamer:
    Outliers :  2.64 %
    Allowed  : 16.85 %
    Favored  : 80.51 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.12 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.72 (0.26), residues: 1095
  helix:  1.37 (0.27), residues: 384
  sheet:  0.61 (0.31), residues: 292
  loop : -0.37 (0.31), residues: 419

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.001   ARG B 129 
 TYR   0.011   0.001   TYR S 190 
 PHE   0.014   0.001   PHE R 260 
 TRP   0.015   0.001   TRP B 169 
 HIS   0.004   0.001   HIS A 188 

Details of bonding type rmsd
  covalent geometry    : bond        0.00326 ( 8763)
  covalent geometry    : angle       0.57771 (11910)
  SS BOND              : bond        0.00284 (    2)
  SS BOND              : angle       2.57269 (    4)
  hydrogen bonds       : bond        0.03703 (  437)
  hydrogen bonds       : angle       4.63003 ( 1231)

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

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

  2190 Ramachandran restraints generated.
    1095 Oldfield, 0 Emsley, 1095 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2190 Ramachandran restraints generated.
    1095 Oldfield, 0 Emsley, 1095 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  161 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 137
  time to evaluate  : 0.362 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   52 ARG cc_start: 0.8695 (OUTLIER) cc_final: 0.8440 (mtp85)
REVERT: B  201 SER cc_start: 0.8579 (m) cc_final: 0.8278 (p)
REVERT: B  228 ASP cc_start: 0.8150 (m-30) cc_final: 0.7636 (p0)
REVERT: B  254 ASP cc_start: 0.8011 (t0) cc_final: 0.7449 (t0)
REVERT: B  262 MET cc_start: 0.8511 (OUTLIER) cc_final: 0.8008 (ptm)
REVERT: S   46 GLU cc_start: 0.8442 (tt0) cc_final: 0.8063 (tt0)
REVERT: A  240 MET cc_start: 0.6605 (ptt) cc_final: 0.6143 (ptp)
REVERT: A  248 LYS cc_start: 0.8361 (mppt) cc_final: 0.7924 (mtmm)
REVERT: A  283 LEU cc_start: 0.8671 (OUTLIER) cc_final: 0.8406 (tt)
REVERT: A  306 GLN cc_start: 0.7249 (mt0) cc_final: 0.6964 (mt0)
REVERT: A  309 ASP cc_start: 0.8162 (m-30) cc_final: 0.7725 (m-30)
REVERT: R  155 ARG cc_start: 0.6057 (ptm-80) cc_final: 0.5626 (mtp-110)
REVERT: R  165 TYR cc_start: 0.8155 (t80) cc_final: 0.6535 (t80)
REVERT: R  175 VAL cc_start: 0.8450 (m) cc_final: 0.8117 (p)
REVERT: R  178 ARG cc_start: 0.8161 (OUTLIER) cc_final: 0.7360 (mmp80)
REVERT: R  240 ARG cc_start: 0.7694 (OUTLIER) cc_final: 0.6255 (ptt90)
REVERT: R  298 ILE cc_start: 0.8140 (OUTLIER) cc_final: 0.7855 (mp)
  outliers start: 24
  outliers final: 7
  residues processed: 146
  average time/residue: 0.7961
  time to fit residues: 121.8671
Evaluate side-chains
  152 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 139
  time to evaluate  : 0.336 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   52 ARG
Chi-restraints excluded: chain B residue  112 VAL
Chi-restraints excluded: chain B residue  262 MET
Chi-restraints excluded: chain B residue  317 CYS
Chi-restraints excluded: chain Y residue   41 CYS
Chi-restraints excluded: chain S residue   22 CYS
Chi-restraints excluded: chain S residue  144 THR
Chi-restraints excluded: chain S residue  146 SER
Chi-restraints excluded: chain A residue  283 LEU
Chi-restraints excluded: chain R residue   49 LEU
Chi-restraints excluded: chain R residue  178 ARG
Chi-restraints excluded: chain R residue  240 ARG
Chi-restraints excluded: chain R residue  298 ILE
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 110
   random chunks:
   chunk 26 optimal weight:    6.9990
   chunk 44 optimal weight:    0.0020
   chunk 106 optimal weight:    1.9990
   chunk 15 optimal weight:    5.9990
   chunk 17 optimal weight:    0.0010
   chunk 82 optimal weight:    0.0020
   chunk 57 optimal weight:   10.0000
   chunk 69 optimal weight:    3.9990
   chunk 42 optimal weight:    1.9990
   chunk 14 optimal weight:    1.9990
   chunk 100 optimal weight:    0.9980
   overall best weight:    0.6004

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

Flipped N/Q/H residues before XYZ refinement:
B  75 GLN
B 268 ASN
B 340 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4201 r_free = 0.4201 target = 0.150768 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3768 r_free = 0.3768 target = 0.117379 restraints weight = 20071.916|
|-----------------------------------------------------------------------------|
r_work (start): 0.3720 rms_B_bonded: 2.60
r_work: 0.3574 rms_B_bonded: 2.60 restraints_weight: 0.5000
r_work: 0.3419 rms_B_bonded: 4.31 restraints_weight: 0.2500
r_work (final): 0.3419
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3427
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3427 r_free = 0.3427    target_work(ls_wunit_k1) = 0.102         |
| occupancies: max = 1.00  min = 0.44   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3427 r_free = 0.3427    target_work(ls_wunit_k1) = 0.102         |
| occupancies: max = 1.00  min = 0.44   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3427
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7570
moved from start:          0.2471

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   8765  Z= 0.112
  Angle     :  0.562  11.317  11914  Z= 0.285
  Chirality :  0.041   0.138   1393
  Planarity :  0.005   0.059   1491
  Dihedral  :  4.206  29.833   1210
  Min Nonbonded Distance : 2.523

Molprobity Statistics.
  All-atom Clashscore : 6.43
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.66 %
    Favored  : 96.34 %
  Rotamer:
    Outliers :  2.09 %
    Allowed  : 17.18 %
    Favored  : 80.73 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.12 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.90 (0.26), residues: 1095
  helix:  1.61 (0.27), residues: 389
  sheet:  0.62 (0.31), residues: 292
  loop : -0.31 (0.32), residues: 414

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.001   ARG B 129 
 TYR   0.011   0.001   TYR S 190 
 PHE   0.023   0.001   PHE R 263 
 TRP   0.016   0.001   TRP B 169 
 HIS   0.004   0.001   HIS R 112 

Details of bonding type rmsd
  covalent geometry    : bond        0.00253 ( 8763)
  covalent geometry    : angle       0.56043 (11910)
  SS BOND              : bond        0.00260 (    2)
  SS BOND              : angle       2.03555 (    4)
  hydrogen bonds       : bond        0.03340 (  437)
  hydrogen bonds       : angle       4.46543 ( 1231)

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

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

  2190 Ramachandran restraints generated.
    1095 Oldfield, 0 Emsley, 1095 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2190 Ramachandran restraints generated.
    1095 Oldfield, 0 Emsley, 1095 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  170 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 151
  time to evaluate  : 0.361 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   52 ARG cc_start: 0.8572 (OUTLIER) cc_final: 0.8305 (mtp85)
REVERT: B   78 LYS cc_start: 0.8411 (OUTLIER) cc_final: 0.7806 (mptm)
REVERT: B  170 ASP cc_start: 0.8170 (t70) cc_final: 0.7704 (OUTLIER)
REVERT: B  201 SER cc_start: 0.8474 (m) cc_final: 0.8188 (p)
REVERT: B  228 ASP cc_start: 0.8034 (m-30) cc_final: 0.7672 (p0)
REVERT: B  254 ASP cc_start: 0.7947 (t0) cc_final: 0.7583 (t0)
REVERT: B  262 MET cc_start: 0.8477 (OUTLIER) cc_final: 0.7982 (ptm)
REVERT: S   46 GLU cc_start: 0.8353 (tt0) cc_final: 0.7978 (tt0)
REVERT: A  240 MET cc_start: 0.6578 (ptt) cc_final: 0.6176 (ptp)
REVERT: A  248 LYS cc_start: 0.8338 (mppt) cc_final: 0.7900 (mtmm)
REVERT: A  306 GLN cc_start: 0.7213 (mt0) cc_final: 0.6982 (mt0)
REVERT: A  309 ASP cc_start: 0.8115 (m-30) cc_final: 0.7671 (m-30)
REVERT: A  356 TYR cc_start: 0.7912 (m-10) cc_final: 0.7691 (m-10)
REVERT: R  155 ARG cc_start: 0.5918 (ptm-80) cc_final: 0.5510 (mtp-110)
REVERT: R  165 TYR cc_start: 0.8095 (t80) cc_final: 0.6449 (t80)
REVERT: R  175 VAL cc_start: 0.8406 (m) cc_final: 0.8109 (p)
REVERT: R  178 ARG cc_start: 0.7999 (OUTLIER) cc_final: 0.7154 (mmp80)
REVERT: R  240 ARG cc_start: 0.7609 (OUTLIER) cc_final: 0.6270 (ptt90)
REVERT: R  259 ASP cc_start: 0.7002 (m-30) cc_final: 0.6769 (t0)
REVERT: R  298 ILE cc_start: 0.8053 (OUTLIER) cc_final: 0.7795 (mp)
  outliers start: 19
  outliers final: 7
  residues processed: 159
  average time/residue: 0.7792
  time to fit residues: 130.0537
Evaluate side-chains
  146 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 134
  time to evaluate  : 0.397 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   52 ARG
Chi-restraints excluded: chain B residue   78 LYS
Chi-restraints excluded: chain B residue  112 VAL
Chi-restraints excluded: chain B residue  262 MET
Chi-restraints excluded: chain B residue  317 CYS
Chi-restraints excluded: chain Y residue   41 CYS
Chi-restraints excluded: chain S residue   22 CYS
Chi-restraints excluded: chain S residue  144 THR
Chi-restraints excluded: chain S residue  146 SER
Chi-restraints excluded: chain R residue  178 ARG
Chi-restraints excluded: chain R residue  240 ARG
Chi-restraints excluded: chain R residue  298 ILE
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 110
   random chunks:
   chunk 10 optimal weight:    0.0070
   chunk 93 optimal weight:    0.3980
   chunk 11 optimal weight:    0.8980
   chunk 79 optimal weight:    4.9990
   chunk 60 optimal weight:    9.9990
   chunk 107 optimal weight:    0.7980
   chunk 13 optimal weight:    0.9990
   chunk 94 optimal weight:    0.6980
   chunk 80 optimal weight:    3.9990
   chunk 46 optimal weight:    0.0020
   chunk 92 optimal weight:    0.9990
   overall best weight:    0.3806

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

Flipped N/Q/H residues before XYZ refinement:
B  75 GLN
B 340 ASN
A 350 GLN
R 112 HIS

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4216 r_free = 0.4216 target = 0.151811 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3840 r_free = 0.3840 target = 0.119559 restraints weight = 23092.626|
|-----------------------------------------------------------------------------|
r_work (start): 0.3765 rms_B_bonded: 3.02
r_work: 0.3601 rms_B_bonded: 2.65 restraints_weight: 0.5000
r_work: 0.3443 rms_B_bonded: 4.44 restraints_weight: 0.2500
r_work (final): 0.3443
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3447
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3447 r_free = 0.3447    target_work(ls_wunit_k1) = 0.097         |
| occupancies: max = 1.00  min = 0.44   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3447 r_free = 0.3447    target_work(ls_wunit_k1) = 0.097         |
| occupancies: max = 1.00  min = 0.43   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3447
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7600
moved from start:          0.2620

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.032   8765  Z= 0.106
  Angle     :  0.565  11.851  11914  Z= 0.285
  Chirality :  0.041   0.132   1393
  Planarity :  0.005   0.058   1491
  Dihedral  :  4.065  27.329   1210
  Min Nonbonded Distance : 2.529

Molprobity Statistics.
  All-atom Clashscore : 6.25
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.39 %
    Favored  : 96.61 %
  Rotamer:
    Outliers :  1.65 %
    Allowed  : 18.17 %
    Favored  : 80.18 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.12 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.03 (0.26), residues: 1095
  helix:  1.74 (0.27), residues: 394
  sheet:  0.64 (0.31), residues: 292
  loop : -0.26 (0.32), residues: 409

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.001   ARG B 129 
 TYR   0.011   0.001   TYR S 190 
 PHE   0.013   0.001   PHE R 260 
 TRP   0.017   0.001   TRP B 169 
 HIS   0.005   0.001   HIS A 188 

Details of bonding type rmsd
  covalent geometry    : bond        0.00234 ( 8763)
  covalent geometry    : angle       0.56405 (11910)
  SS BOND              : bond        0.00227 (    2)
  SS BOND              : angle       1.79807 (    4)
  hydrogen bonds       : bond        0.03125 (  437)
  hydrogen bonds       : angle       4.34321 ( 1231)

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

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

  2190 Ramachandran restraints generated.
    1095 Oldfield, 0 Emsley, 1095 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2190 Ramachandran restraints generated.
    1095 Oldfield, 0 Emsley, 1095 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  151 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 136
  time to evaluate  : 0.424 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   52 ARG cc_start: 0.8568 (OUTLIER) cc_final: 0.8330 (mtp85)
REVERT: B   78 LYS cc_start: 0.8441 (OUTLIER) cc_final: 0.7865 (mptm)
REVERT: B  170 ASP cc_start: 0.8124 (t70) cc_final: 0.7728 (t70)
REVERT: B  201 SER cc_start: 0.8455 (m) cc_final: 0.8242 (p)
REVERT: B  254 ASP cc_start: 0.7955 (t0) cc_final: 0.7637 (t0)
REVERT: B  262 MET cc_start: 0.8451 (OUTLIER) cc_final: 0.8089 (ptm)
REVERT: S   46 GLU cc_start: 0.8397 (tt0) cc_final: 0.8112 (tt0)
REVERT: S  192 MET cc_start: 0.8908 (ttp) cc_final: 0.8460 (tmm)
REVERT: A  240 MET cc_start: 0.6514 (ptt) cc_final: 0.6050 (ptp)
REVERT: A  306 GLN cc_start: 0.7299 (mt0) cc_final: 0.7010 (mt0)
REVERT: A  309 ASP cc_start: 0.8104 (m-30) cc_final: 0.7668 (m-30)
REVERT: A  356 TYR cc_start: 0.7823 (m-10) cc_final: 0.7608 (m-10)
REVERT: R  155 ARG cc_start: 0.5962 (ptm-80) cc_final: 0.5678 (mtp-110)
REVERT: R  165 TYR cc_start: 0.8053 (t80) cc_final: 0.6485 (t80)
REVERT: R  175 VAL cc_start: 0.8397 (m) cc_final: 0.8142 (p)
REVERT: R  178 ARG cc_start: 0.7904 (OUTLIER) cc_final: 0.7079 (mmp80)
REVERT: R  298 ILE cc_start: 0.8040 (OUTLIER) cc_final: 0.7811 (mp)
  outliers start: 15
  outliers final: 5
  residues processed: 143
  average time/residue: 0.7829
  time to fit residues: 117.4697
Evaluate side-chains
  150 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 140
  time to evaluate  : 0.307 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   52 ARG
Chi-restraints excluded: chain B residue   78 LYS
Chi-restraints excluded: chain B residue  112 VAL
Chi-restraints excluded: chain B residue  262 MET
Chi-restraints excluded: chain B residue  317 CYS
Chi-restraints excluded: chain Y residue   41 CYS
Chi-restraints excluded: chain S residue   22 CYS
Chi-restraints excluded: chain S residue  144 THR
Chi-restraints excluded: chain R residue  178 ARG
Chi-restraints excluded: chain R residue  298 ILE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Traceback (most recent call last):
  File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/command_line/real_space_refine.py", line 9, in <module>
    run_program(real_space_refine.Program)
  File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/iotbx/cli_parser.py", line 999, in run_program
    task.run()
  File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/programs/real_space_refine.py", line 206, in run
    self.rsr_result = rsr_wrappers.run_real_space_refine(
  File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/rsr/wrappers.py", line 52, in __init__
    self._refined = macro_cycle_real_space.run(
  File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__
    self.caller(self.refine_xyz)
  File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 321, in caller
    func()
  File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz
    self.minimization_no_ncs()
  File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 755, in minimization_no_ncs
    ro = mmtbx.refinement.real_space.individual_sites.easy(
  File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 44, in __init__
    self.weight = mmtbx.refinement.real_space.weight.run(
  File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/weight.py", line 84, in __init__
    ro.refine(
  File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 362, in refine
    real_space_result = refinery(
  File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 233, in __init__
    refiner.refine(
  File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 100, in refine
    self.refined = maptbx.real_space_refinement_simple.lbfgs(
  File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/maptbx/real_space_refinement_simple.py", line 168, in __init__
    O.minimizer = scitbx.lbfgs.run(
  File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/scitbx/lbfgs/__init__.py", line 270, in run
    return run_c_plus_plus(
  File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus
    f, g = target_evaluator.compute_functional_and_gradients()
  File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/maptbx/real_space_refinement_simple.py", line 243, in compute_functional_and_gradients
    gr_e = O.geometry_restraints_manager.energies_sites(
  File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1588, in energies_sites
    pair_proxies = self.pair_proxies(
  File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1491, in pair_proxies
    check_bonded_distance_cutoff(sites_frac=sites_frac)
  File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1372, in check_bonded_distance_cutoff
    raise RuntimeError(msg)
RuntimeError: Bond distance > max_reasonable_bond_distance: 67.4339 > 50:
  distance: 57 - 63:  22.344
  distance: 63 - 64:  12.016
  distance: 63 - 196:  19.810
  distance: 64 - 65:   7.269
  distance: 64 - 67:   8.342
  distance: 65 - 66:  25.415
  distance: 65 - 74:   5.976
  distance: 66 - 193:  14.799
  distance: 67 - 68:  10.165
  distance: 68 - 69:  19.585
  distance: 68 - 70:  23.227
  distance: 69 - 71:  29.544
  distance: 70 - 72:  31.484
  distance: 71 - 73:  20.292
  distance: 72 - 73:  27.665
  distance: 74 - 75:  15.321
  distance: 75 - 76:  13.505
  distance: 75 - 78:  17.737
  distance: 76 - 77:  18.984
  distance: 76 - 82:  17.513
  distance: 78 - 79:  15.916
  distance: 79 - 80:  33.195
  distance: 79 - 81:  33.110
  distance: 82 - 83:   6.746
  distance: 82 - 178:   7.991
  distance: 83 - 84:  13.348
  distance: 83 - 86:  19.012
  distance: 84 - 85:   8.255
  distance: 84 - 91:  19.766
  distance: 85 - 175:  17.011
  distance: 86 - 87:  22.767
  distance: 87 - 88:  19.144
  distance: 88 - 89:  25.071
  distance: 88 - 90:  35.532
  distance: 91 - 92:  15.339
  distance: 92 - 93:  20.620
  distance: 92 - 95:   6.237
  distance: 93 - 94:  24.455
  distance: 93 - 102:  23.948
  distance: 95 - 96:  17.470
  distance: 96 - 97:  14.566
  distance: 97 - 98:  22.754
  distance: 98 - 99:  13.818
  distance: 99 - 100:   8.579
  distance: 99 - 101:  12.438
  distance: 102 - 103:  13.865
  distance: 102 - 108:  14.219
  distance: 103 - 104:  13.177
  distance: 103 - 106:  25.687
  distance: 104 - 105:  12.962
  distance: 104 - 109:  29.245
  distance: 107 - 108:  17.803
  distance: 109 - 110:  12.013
  distance: 110 - 111:   5.198
  distance: 111 - 112:  22.642
  distance: 111 - 113:  17.970
  distance: 113 - 114:  11.719
  distance: 114 - 115:  13.100
  distance: 114 - 117:  14.052
  distance: 115 - 116:   7.354
  distance: 115 - 122:  26.438
  distance: 117 - 118:  22.384
  distance: 118 - 119:  15.552
  distance: 119 - 121:   7.073
  distance: 122 - 123:  15.118
  distance: 123 - 124:  49.905
  distance: 123 - 126:  13.792
  distance: 124 - 125:  12.749
  distance: 124 - 128:  37.400
  distance: 128 - 129:  18.088
  distance: 128 - 134:  22.681
  distance: 129 - 130:  12.110
  distance: 129 - 132:  12.859
  distance: 130 - 131:  31.765
  distance: 130 - 135:  27.919
  distance: 132 - 133:  10.083
  distance: 133 - 134:  32.967
  distance: 135 - 136:  19.281
  distance: 136 - 137:   7.642
  distance: 136 - 139:  12.333
  distance: 137 - 138:   4.272
  distance: 137 - 144:  26.131
  distance: 139 - 140:  27.260
  distance: 140 - 141:  20.049