Starting phenix.real_space_refine
on Sat Jul 26 01:31:44 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7s8n_24898/07_2025/7s8n_24898.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7s8n_24898/07_2025/7s8n_24898.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.9
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7s8n_24898/07_2025/7s8n_24898.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7s8n_24898/07_2025/7s8n_24898.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7s8n_24898/07_2025/7s8n_24898.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7s8n_24898/07_2025/7s8n_24898.cif"
  }
  resolution = 2.9
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.001 sd=   0.026
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 4
    Type Number    sf(0)   Gaussians
     S      53      5.16       5
     C    5232      2.51       5
     N    1386      2.21       5
     O    1483      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 48 residue(s): 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib"
  Total number of atoms: 8154
  Number of models: 1
  Model: ""
    Number of chains: 6
    Chain: "B"
      Number of atoms: 1704
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 221, 1704
          Classifications: {'peptide': 221}
          Incomplete info: {'truncation_to_alanine': 26}
          Link IDs: {'PTRANS': 6, 'TRANS': 214}
          Chain breaks: 2
          Unresolved chain link angles: 2
          Unresolved non-hydrogen bonds: 102
          Unresolved non-hydrogen angles: 124
          Unresolved non-hydrogen dihedrals: 84
          Unresolved non-hydrogen chiralities: 2
          Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 5, 'ARG:plan': 4, 'ASP:plan': 7}
          Unresolved non-hydrogen planarities: 67
    Chain: "C"
      Number of atoms: 2475
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 337, 2475
          Classifications: {'peptide': 337}
          Incomplete info: {'truncation_to_alanine': 32}
          Link IDs: {'PTRANS': 5, 'TRANS': 331}
          Unresolved non-hydrogen bonds: 116
          Unresolved non-hydrogen angles: 142
          Unresolved non-hydrogen dihedrals: 90
          Unresolved non-hydrogen chiralities: 4
          Planarities with less than four sites: {'GLN:plan1': 4, 'GLU:plan': 4, 'ARG:plan': 7, 'ASN:plan1': 1, 'ASP:plan': 6}
          Unresolved non-hydrogen planarities: 88
    Chain: "D"
      Number of atoms: 350
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 51, 350
          Classifications: {'peptide': 51}
          Incomplete info: {'truncation_to_alanine': 12}
          Link IDs: {'PTRANS': 4, 'TRANS': 46}
          Unresolved non-hydrogen bonds: 44
          Unresolved non-hydrogen angles: 52
          Unresolved non-hydrogen dihedrals: 36
          Unresolved non-hydrogen chiralities: 2
          Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 2, 'ARG:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 1}
          Unresolved non-hydrogen planarities: 23
    Chain: "R"
      Number of atoms: 1872
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 250, 1872
          Classifications: {'peptide': 250}
          Incomplete info: {'truncation_to_alanine': 34}
          Link IDs: {'PTRANS': 7, 'TRANS': 242}
          Chain breaks: 2
          Unresolved chain link angles: 1
          Unresolved non-hydrogen bonds: 131
          Unresolved non-hydrogen angles: 163
          Unresolved non-hydrogen dihedrals: 114
          Unresolved non-hydrogen chiralities: 7
          Planarities with less than four sites: {'PHE:plan': 7, 'GLU:plan': 1, 'ARG:plan': 4, 'ASN:plan1': 2, 'ASP:plan': 3}
          Unresolved non-hydrogen planarities: 81
    Chain: "E"
      Number of atoms: 1730
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 231, 1730
          Classifications: {'peptide': 231}
          Incomplete info: {'truncation_to_alanine': 14}
          Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 220}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 47
          Unresolved non-hydrogen angles: 58
          Unresolved non-hydrogen dihedrals: 36
          Unresolved non-hydrogen chiralities: 4
          Planarities with less than four sites: {'GLU:plan': 6, 'ARG:plan': 1}
          Unresolved non-hydrogen planarities: 29
    Chain: "R"
      Number of atoms: 23
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 23
          Unusual residues: {'8IU': 1}
          Classifications: {'undetermined': 1}
  Time building chain proxies: 5.03, per 1000 atoms: 0.62
  Number of scatterers: 8154
  At special positions: 0
  Unit cell: (91.91, 121.03, 128.31, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     S      53     16.00
     O    1483      8.00
     N    1386      7.00
     C    5232      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=2, symmetry=0
    Simple disulfide: pdb=" SG  CYS R 168 " - pdb=" SG  CYS R 180 " distance=2.02
    Simple disulfide: pdb=" SG  CYS E 147 " - pdb=" SG  CYS E 217 " distance=2.05

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 1.99
  Conformation dependent library (CDL) restraints added in 945.4 milliseconds
  

  2140 Ramachandran restraints generated.
    1070 Oldfield, 0 Emsley, 1070 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2030

  Finding SS restraints...
    Secondary structure from input PDB file:
      25 helices and 13 sheets defined
      36.5% alpha, 23.8% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 1.03
  Creating SS restraints...
    Processing helix  chain 'B' and resid 6 through 31
    Processing helix  chain 'B' and resid 45 through 49
      removed outlier: 3.593A  pdb=" N   THR B  48 " --> pdb=" O   GLY B  45 " (cutoff:3.500A)
      removed outlier: 3.985A  pdb=" N   ILE B  49 " --> pdb=" O   LYS B  46 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 45 through 49'
    Processing helix  chain 'B' and resid 95 through 99
      removed outlier: 3.592A  pdb=" N   GLN B  98 " --> pdb=" O   LYS B  95 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 114 through 116
      No H-bonds generated for 'chain 'B' and resid 114 through 116'
    Processing helix  chain 'B' and resid 117 through 130
      removed outlier: 3.671A  pdb=" N   ALA B 121 " --> pdb=" O   ARG B 117 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 145 through 156
      removed outlier: 3.837A  pdb=" N   LEU B 149 " --> pdb=" O   LYS B 145 " (cutoff:3.500A)
      removed outlier: 3.927A  pdb=" N   GLY B 156 " --> pdb=" O   LYS B 152 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 159 through 163
      removed outlier: 3.586A  pdb=" N   ASP B 162 " --> pdb=" O   LYS B 159 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 164 through 168
    Processing helix  chain 'B' and resid 183 through 202
      removed outlier: 3.601A  pdb=" N   THR B 187 " --> pdb=" O   ASP B 183 " (cutoff:3.500A)
      removed outlier: 3.675A  pdb=" N   ILE B 193 " --> pdb=" O   ALA B 189 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 223 through 243
      removed outlier: 4.024A  pdb=" N   ILE B 227 " --> pdb=" O   ASN B 223 " (cutoff:3.500A)
      removed outlier: 3.679A  pdb=" N   PHE B 228 " --> pdb=" O   ALA B 224 " (cutoff:3.500A)
      removed outlier: 3.538A  pdb=" N   TYR B 243 " --> pdb=" O   ASN B 239 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 5 through 25
      removed outlier: 3.633A  pdb=" N   LYS C  23 " --> pdb=" O   ARG C  19 " (cutoff:3.500A)
      removed outlier: 3.677A  pdb=" N   CYS C  25 " --> pdb=" O   ALA C  21 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 29 through 34
    Processing helix  chain 'D' and resid 12 through 23
    Processing helix  chain 'D' and resid 29 through 44
      removed outlier: 3.567A  pdb=" N   ALA D  33 " --> pdb=" O   LYS D  29 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 45 through 48
      removed outlier: 3.878A  pdb=" N   ASP D  48 " --> pdb=" O   ALA D  45 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'D' and resid 45 through 48'
    Processing helix  chain 'R' and resid 30 through 57
      removed outlier: 4.115A  pdb=" N   VAL R  46 " --> pdb=" O   LEU R  42 " (cutoff:3.500A)
      removed outlier: 4.017A  pdb=" N   GLY R  47 " --> pdb=" O   VAL R  43 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 64 through 95
    Processing helix  chain 'R' and resid 103 through 133
      removed outlier: 4.009A  pdb=" N   LEU R 120 " --> pdb=" O   GLY R 116 " (cutoff:3.500A)
      removed outlier: 3.802A  pdb=" N   SER R 121 " --> pdb=" O   LEU R 117 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 133 through 140
    Processing helix  chain 'R' and resid 144 through 168
    Processing helix  chain 'R' and resid 176 through 211
    Processing helix  chain 'R' and resid 219 through 245
      Proline residue:  R 238  - end of helix
    Processing helix  chain 'R' and resid 245 through 250
    Processing helix  chain 'R' and resid 256 through 280
      Proline residue:  R 262  - end of helix
      Proline residue:  R 276  - end of helix
    Processing helix  chain 'E' and resid 28 through 32
      removed outlier: 3.547A  pdb=" N   SER E  31 " --> pdb=" O   ALA E  28 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'B' and resid 69 through 76
      removed outlier: 3.600A  pdb=" N   PHE B  74 " --> pdb=" O   PHE B  81 " (cutoff:3.500A)
      removed outlier: 5.001A  pdb=" N   VAL B  86 " --> pdb=" O   LEU B  38 " (cutoff:3.500A)
      removed outlier: 7.230A  pdb=" N   ARG B  35 " --> pdb=" O   ALA B 105 " (cutoff:3.500A)
      removed outlier: 8.152A  pdb=" N   ILE B 107 " --> pdb=" O   ARG B  35 " (cutoff:3.500A)
      removed outlier: 6.582A  pdb=" N   LEU B  37 " --> pdb=" O   ILE B 107 " (cutoff:3.500A)
      removed outlier: 7.973A  pdb=" N   VAL B 109 " --> pdb=" O   LEU B  37 " (cutoff:3.500A)
      removed outlier: 7.314A  pdb=" N   LEU B  39 " --> pdb=" O   VAL B 109 " (cutoff:3.500A)
      removed outlier: 9.186A  pdb=" N   ASP B 111 " --> pdb=" O   LEU B  39 " (cutoff:3.500A)
      removed outlier: 6.535A  pdb=" N   ILE B 106 " --> pdb=" O   ILE B 140 " (cutoff:3.500A)
      removed outlier: 7.728A  pdb=" N   PHE B 142 " --> pdb=" O   ILE B 106 " (cutoff:3.500A)
      removed outlier: 6.754A  pdb=" N   PHE B 108 " --> pdb=" O   PHE B 142 " (cutoff:3.500A)
      removed outlier: 7.227A  pdb=" N   ASN B 144 " --> pdb=" O   PHE B 108 " (cutoff:3.500A)
      removed outlier: 6.418A  pdb=" N   VAL B 110 " --> pdb=" O   ASN B 144 " (cutoff:3.500A)
      removed outlier: 7.075A  pdb=" N   VAL B 139 " --> pdb=" O   TYR B 212 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'C' and resid 47 through 51
      removed outlier: 6.660A  pdb=" N   ILE C 338 " --> pdb=" O   ARG C  48 " (cutoff:3.500A)
      removed outlier: 4.497A  pdb=" N   THR C  50 " --> pdb=" O   LEU C 336 " (cutoff:3.500A)
      removed outlier: 6.734A  pdb=" N   LEU C 336 " --> pdb=" O   THR C  50 " (cutoff:3.500A)
      removed outlier: 3.534A  pdb=" N   CYS C 317 " --> pdb=" O   GLY C 330 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'C' and resid 58 through 63
      removed outlier: 3.838A  pdb=" N   ALA C  60 " --> pdb=" O   ALA C  73 " (cutoff:3.500A)
      removed outlier: 3.608A  pdb=" N   LEU C  70 " --> pdb=" O   TRP C  82 " (cutoff:3.500A)
      removed outlier: 3.984A  pdb=" N   LYS C  78 " --> pdb=" O   SER C  74 " (cutoff:3.500A)
      removed outlier: 6.421A  pdb=" N   LEU C  79 " --> pdb=" O   ALA C  92 " (cutoff:3.500A)
      removed outlier: 4.277A  pdb=" N   ALA C  92 " --> pdb=" O   LEU C  79 " (cutoff:3.500A)
      removed outlier: 6.633A  pdb=" N   ILE C  81 " --> pdb=" O   VAL C  90 " (cutoff:3.500A)
      removed outlier: 3.578A  pdb=" N   ASN C  88 " --> pdb=" O   ASP C  83 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'C' and resid 100 through 105
      removed outlier: 6.657A  pdb=" N   CYS C 121 " --> pdb=" O   GLU C 138 " (cutoff:3.500A)
      removed outlier: 4.657A  pdb=" N   GLU C 138 " --> pdb=" O   CYS C 121 " (cutoff:3.500A)
      removed outlier: 6.769A  pdb=" N   ILE C 123 " --> pdb=" O   SER C 136 " (cutoff:3.500A)
      removed outlier: 3.653A  pdb=" N   ARG C 134 " --> pdb=" O   ASN C 125 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'C' and resid 146 through 153
      removed outlier: 3.822A  pdb=" N   CYS C 148 " --> pdb=" O   SER C 160 " (cutoff:3.500A)
      removed outlier: 6.733A  pdb=" N   GLN C 156 " --> pdb=" O   LEU C 152 " (cutoff:3.500A)
      removed outlier: 3.666A  pdb=" N   ILE C 157 " --> pdb=" O   TRP C 169 " (cutoff:3.500A)
      removed outlier: 4.123A  pdb=" N   THR C 165 " --> pdb=" O   SER C 161 " (cutoff:3.500A)
      removed outlier: 3.779A  pdb=" N   THR C 178 " --> pdb=" O   LEU C 168 " (cutoff:3.500A)
      removed outlier: 6.148A  pdb=" N   ASP C 170 " --> pdb=" O   GLN C 176 " (cutoff:3.500A)
      removed outlier: 6.005A  pdb=" N   GLN C 176 " --> pdb=" O   ASP C 170 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'C' and resid 187 through 192
      removed outlier: 6.793A  pdb=" N   GLY C 202 " --> pdb=" O   MET C 188 " (cutoff:3.500A)
      removed outlier: 4.327A  pdb=" N   LEU C 190 " --> pdb=" O   VAL C 200 " (cutoff:3.500A)
      removed outlier: 6.677A  pdb=" N   VAL C 200 " --> pdb=" O   LEU C 190 " (cutoff:3.500A)
      removed outlier: 5.153A  pdb=" N   LEU C 192 " --> pdb=" O   LEU C 198 " (cutoff:3.500A)
      removed outlier: 7.499A  pdb=" N   LEU C 198 " --> pdb=" O   LEU C 192 " (cutoff:3.500A)
      removed outlier: 3.664A  pdb=" N   PHE C 199 " --> pdb=" O   TRP C 211 " (cutoff:3.500A)
      removed outlier: 3.769A  pdb=" N   GLN C 220 " --> pdb=" O   LEU C 210 " (cutoff:3.500A)
      removed outlier: 6.874A  pdb=" N   ASP C 212 " --> pdb=" O   CYS C 218 " (cutoff:3.500A)
      removed outlier: 6.208A  pdb=" N   CYS C 218 " --> pdb=" O   ASP C 212 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'C' and resid 229 through 234
      removed outlier: 3.593A  pdb=" N   ALA C 231 " --> pdb=" O   GLY C 244 " (cutoff:3.500A)
      removed outlier: 6.757A  pdb=" N   CYS C 250 " --> pdb=" O   THR C 263 " (cutoff:3.500A)
      removed outlier: 4.658A  pdb=" N   THR C 263 " --> pdb=" O   CYS C 250 " (cutoff:3.500A)
      removed outlier: 6.844A  pdb=" N   LEU C 252 " --> pdb=" O   LEU C 261 " (cutoff:3.500A)
      removed outlier: 3.590A  pdb=" N   GLN C 259 " --> pdb=" O   ASP C 254 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'C' and resid 273 through 278
      removed outlier: 6.590A  pdb=" N   GLY C 288 " --> pdb=" O   THR C 274 " (cutoff:3.500A)
      removed outlier: 4.353A  pdb=" N   VAL C 276 " --> pdb=" O   LEU C 286 " (cutoff:3.500A)
      removed outlier: 6.770A  pdb=" N   LEU C 286 " --> pdb=" O   VAL C 276 " (cutoff:3.500A)
      removed outlier: 4.797A  pdb=" N   PHE C 278 " --> pdb=" O   LEU C 284 " (cutoff:3.500A)
      removed outlier: 6.889A  pdb=" N   LEU C 284 " --> pdb=" O   PHE C 278 " (cutoff:3.500A)
      removed outlier: 6.810A  pdb=" N   CYS C 294 " --> pdb=" O   VAL C 307 " (cutoff:3.500A)
      removed outlier: 4.681A  pdb=" N   VAL C 307 " --> pdb=" O   CYS C 294 " (cutoff:3.500A)
      removed outlier: 6.597A  pdb=" N   VAL C 296 " --> pdb=" O   ALA C 305 " (cutoff:3.500A)
      removed outlier: 4.014A  pdb=" N   ASP C 303 " --> pdb=" O   ASP C 298 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'E' and resid 3 through 7
      removed outlier: 3.519A  pdb=" N   SER E  25 " --> pdb=" O   GLN E   3 " (cutoff:3.500A)
      removed outlier: 3.593A  pdb=" N   SER E  71 " --> pdb=" O   PHE E  80 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'E' and resid 10 through 12
      removed outlier: 3.876A  pdb=" N   THR E 118 " --> pdb=" O   GLY E  10 " (cutoff:3.500A)
      removed outlier: 6.984A  pdb=" N   MET E  34 " --> pdb=" O   TYR E  50 " (cutoff:3.500A)
      removed outlier: 4.593A  pdb=" N   TYR E  50 " --> pdb=" O   MET E  34 " (cutoff:3.500A)
      removed outlier: 6.672A  pdb=" N   TRP E  36 " --> pdb=" O   VAL E  48 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'E' and resid 134 through 136
      removed outlier: 6.652A  pdb=" N   VAL E 135 " --> pdb=" O   GLU E 234 " (cutoff:3.500A)
      removed outlier: 6.489A  pdb=" N   LEU E 162 " --> pdb=" O   TYR E 178 " (cutoff:3.500A)
      removed outlier: 4.699A  pdb=" N   TYR E 178 " --> pdb=" O   LEU E 162 " (cutoff:3.500A)
      removed outlier: 6.670A  pdb=" N   TRP E 164 " --> pdb=" O   LEU E 176 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'E' and resid 134 through 136
      removed outlier: 6.652A  pdb=" N   VAL E 135 " --> pdb=" O   GLU E 234 " (cutoff:3.500A)
      removed outlier: 4.234A  pdb=" N   THR E 226 " --> pdb=" O   GLN E 219 " (cutoff:3.500A)
    Processing sheet with id=AB4, first strand: chain 'E' and resid 142 through 147

    409 hydrogen bonds defined for protein.
    1161 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 2.28

  Time building geometry restraints manager: 2.34 seconds

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

  Histogram of bond lengths:
        1.22 -     1.34: 2615
        1.34 -     1.46: 2011
        1.46 -     1.58: 3634
        1.58 -     1.70: 1
        1.70 -     1.82: 72
  Bond restraints: 8333
  Sorted by residual:
  bond pdb=" C03 8IU R 401 "
       pdb=" C04 8IU R 401 "
    ideal  model  delta    sigma   weight residual
    1.528  1.309  0.219 2.00e-02 2.50e+03 1.19e+02
  bond pdb=" C04 8IU R 401 "
       pdb=" N05 8IU R 401 "
    ideal  model  delta    sigma   weight residual
    1.457  1.647 -0.190 2.00e-02 2.50e+03 9.05e+01
  bond pdb=" C21 8IU R 401 "
       pdb=" N05 8IU R 401 "
    ideal  model  delta    sigma   weight residual
    1.470  1.319  0.151 2.00e-02 2.50e+03 5.67e+01
  bond pdb=" C03 8IU R 401 "
       pdb=" N02 8IU R 401 "
    ideal  model  delta    sigma   weight residual
    1.448  1.546 -0.098 2.00e-02 2.50e+03 2.40e+01
  bond pdb=" N19 8IU R 401 "
       pdb=" N20 8IU R 401 "
    ideal  model  delta    sigma   weight residual
    1.341  1.437 -0.096 2.00e-02 2.50e+03 2.32e+01
  ... (remaining 8328 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.99: 10881
        1.99 -     3.98: 394
        3.98 -     5.98: 52
        5.98 -     7.97: 18
        7.97 -     9.96: 4
  Bond angle restraints: 11349
  Sorted by residual:
  angle pdb=" N   PHE C 234 "
        pdb=" CA  PHE C 234 "
        pdb=" C   PHE C 234 "
      ideal   model   delta    sigma   weight residual
     110.48  116.07   -5.59 1.48e+00 4.57e-01 1.43e+01
  angle pdb=" N   VAL B 219 "
        pdb=" CA  VAL B 219 "
        pdb=" C   VAL B 219 "
      ideal   model   delta    sigma   weight residual
     112.90  110.00    2.90 9.60e-01 1.09e+00 9.15e+00
  angle pdb=" N   LEU R 237 "
        pdb=" CA  LEU R 237 "
        pdb=" C   LEU R 237 "
      ideal   model   delta    sigma   weight residual
     109.81  116.45   -6.64 2.21e+00 2.05e-01 9.04e+00
  angle pdb=" C   GLY R 236 "
        pdb=" N   LEU R 237 "
        pdb=" CA  LEU R 237 "
      ideal   model   delta    sigma   weight residual
     121.80  114.49    7.31 2.44e+00 1.68e-01 8.98e+00
  angle pdb=" CA  CYS E 217 "
        pdb=" CB  CYS E 217 "
        pdb=" SG  CYS E 217 "
      ideal   model   delta    sigma   weight residual
     114.40  120.99   -6.59 2.30e+00 1.89e-01 8.21e+00
  ... (remaining 11344 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.20: 4379
       17.20 -    34.41: 401
       34.41 -    51.61: 59
       51.61 -    68.81: 5
       68.81 -    86.01: 3
  Dihedral angle restraints: 4847
    sinusoidal: 1702
      harmonic: 3145
  Sorted by residual:
  dihedral pdb=" CB  CYS E 147 "
           pdb=" SG  CYS E 147 "
           pdb=" SG  CYS E 217 "
           pdb=" CB  CYS E 217 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00  147.42  -54.42     1      1.00e+01 1.00e-02 4.01e+01
  dihedral pdb=" CA  MET E 128 "
           pdb=" C   MET E 128 "
           pdb=" N   THR E 129 "
           pdb=" CA  THR E 129 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -155.63  -24.37     0      5.00e+00 4.00e-02 2.38e+01
  dihedral pdb=" CA  ASP B 199 "
           pdb=" C   ASP B 199 "
           pdb=" N   ILE B 200 "
           pdb=" CA  ILE B 200 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  157.16   22.84     0      5.00e+00 4.00e-02 2.09e+01
  ... (remaining 4844 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.037: 662
       0.037 -    0.075: 432
       0.075 -    0.112: 169
       0.112 -    0.149: 50
       0.149 -    0.187: 10
  Chirality restraints: 1323
  Sorted by residual:
  chirality pdb=" CA  PRO R 238 "
            pdb=" N   PRO R 238 "
            pdb=" C   PRO R 238 "
            pdb=" CB  PRO R 238 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.72    2.53    0.19 2.00e-01 2.50e+01 8.71e-01
  chirality pdb=" CA  LEU R 237 "
            pdb=" N   LEU R 237 "
            pdb=" C   LEU R 237 "
            pdb=" CB  LEU R 237 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.33    0.18 2.00e-01 2.50e+01 8.05e-01
  chirality pdb=" CG  LEU R 160 "
            pdb=" CB  LEU R 160 "
            pdb=" CD1 LEU R 160 "
            pdb=" CD2 LEU R 160 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.59   -2.75    0.16 2.00e-01 2.50e+01 6.69e-01
  ... (remaining 1320 not shown)

  Planarity restraints: 1426
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  LEU R 233 "    0.011 2.00e-02 2.50e+03   2.26e-02 5.10e+00
        pdb=" C   LEU R 233 "   -0.039 2.00e-02 2.50e+03
        pdb=" O   LEU R 233 "    0.015 2.00e-02 2.50e+03
        pdb=" N   LEU R 234 "    0.013 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   SER E 172 "    0.037 5.00e-02 4.00e+02   5.58e-02 4.97e+00
        pdb=" N   PRO E 173 "   -0.096 5.00e-02 4.00e+02
        pdb=" CA  PRO E 173 "    0.029 5.00e-02 4.00e+02
        pdb=" CD  PRO E 173 "    0.031 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  PHE C 151 "    0.024 2.00e-02 2.50e+03   1.57e-02 4.31e+00
        pdb=" CG  PHE C 151 "   -0.030 2.00e-02 2.50e+03
        pdb=" CD1 PHE C 151 "   -0.006 2.00e-02 2.50e+03
        pdb=" CD2 PHE C 151 "   -0.006 2.00e-02 2.50e+03
        pdb=" CE1 PHE C 151 "    0.005 2.00e-02 2.50e+03
        pdb=" CE2 PHE C 151 "    0.005 2.00e-02 2.50e+03
        pdb=" CZ  PHE C 151 "    0.009 2.00e-02 2.50e+03
  ... (remaining 1423 not shown)

  Histogram of nonbonded interaction distances:
        2.20 -     2.74: 1084
        2.74 -     3.28: 7119
        3.28 -     3.82: 12207
        3.82 -     4.36: 13688
        4.36 -     4.90: 26018
  Nonbonded interactions: 60116
  Sorted by model distance:
  nonbonded pdb=" O   VAL B 198 "
            pdb=" OG  SER B 201 "
     model   vdw
     2.202 3.040
  nonbonded pdb=" OD1 ASP R  75 "
            pdb=" OG  SER R 272 "
     model   vdw
     2.220 3.040
  nonbonded pdb=" O   SER E 106 "
            pdb=" OG  SER E 106 "
     model   vdw
     2.273 3.040
  nonbonded pdb=" ND2 ASN R  48 "
            pdb=" OD2 ASP R  75 "
     model   vdw
     2.331 3.120
  nonbonded pdb=" O   THR C  86 "
            pdb=" OG1 THR C  87 "
     model   vdw
     2.383 3.040
  ... (remaining 60111 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.00
========== WARNING! ============

  No NCS relation were found !!!

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

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             0.720
  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:          0.300
  Check model and map are aligned:         0.060
  Set scattering table:                    0.070
  Process input model:                     21.220
  Find NCS groups from input model:        0.170
  Set up NCS constraints:                  0.030
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:11.620
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   34.200
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7669
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      :  0.012   0.219   8335  Z= 0.489
  Angle     :  0.896   9.959  11353  Z= 0.478
  Chirality :  0.056   0.187   1323
  Planarity :  0.005   0.056   1426
  Dihedral  : 13.071  86.015   2811
  Min Nonbonded Distance : 2.202

Molprobity Statistics.
  All-atom Clashscore : 4.10
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.14 %
    Favored  : 94.86 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.37 %
    Favored  : 99.63 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.12 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.33 (0.25), residues: 1070
  helix:  1.55 (0.28), residues: 362
  sheet:  0.01 (0.31), residues: 256
  loop : -1.89 (0.26), residues: 452

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.023   0.003   TRP R 243 
 HIS   0.016   0.003   HIS C  54 
 PHE   0.033   0.003   PHE C 235 
 TYR   0.016   0.003   TYR E 163 
 ARG   0.012   0.001   ARG B 117 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.20548 (  407)
  hydrogen bonds       : angle       6.10520 ( 1161)
  SS BOND              : bond        0.01589 (    2)
  SS BOND              : angle       1.25109 (    4)
  covalent geometry    : bond        0.01159 ( 8333)
  covalent geometry    : angle       0.89552 (11349)

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

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

  2140 Ramachandran restraints generated.
    1070 Oldfield, 0 Emsley, 1070 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2140 Ramachandran restraints generated.
    1070 Oldfield, 0 Emsley, 1070 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  178 residues out of total 937 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 178
  time to evaluate  : 0.788 
Fit side-chains
REVERT: B   10 LYS cc_start: 0.7929 (mtpp) cc_final: 0.7682 (mtmm)
REVERT: B   35 ARG cc_start: 0.8364 (mtp85) cc_final: 0.8138 (mtp85)
REVERT: B   80 ASN cc_start: 0.8131 (m-40) cc_final: 0.7897 (m110)
REVERT: B  128 ILE cc_start: 0.8210 (tp) cc_final: 0.7948 (tp)
REVERT: C   23 LYS cc_start: 0.8191 (ttpt) cc_final: 0.7814 (ttpt)
REVERT: C  219 ARG cc_start: 0.7047 (mtt180) cc_final: 0.6801 (mtt90)
REVERT: C  291 ASP cc_start: 0.7896 (p0) cc_final: 0.7674 (p0)
REVERT: R   55 LEU cc_start: 0.8354 (mt) cc_final: 0.8107 (mt)
REVERT: E    3 GLN cc_start: 0.7989 (mt0) cc_final: 0.7766 (mt0)
REVERT: E  185 SER cc_start: 0.8242 (m) cc_final: 0.7962 (p)
  outliers start: 0
  outliers final: 0
  residues processed: 178
  average time/residue: 1.2771
  time to fit residues: 242.2670
Evaluate side-chains
  157 residues out of total 937 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 157
  time to evaluate  : 1.243 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 91 optimal weight:    0.5980
   chunk 81 optimal weight:    0.8980
   chunk 45 optimal weight:    0.6980
   chunk 27 optimal weight:    0.8980
   chunk 55 optimal weight:    0.8980
   chunk 43 optimal weight:    0.9990
   chunk 84 optimal weight:    0.7980
   chunk 32 optimal weight:    0.3980
   chunk 51 optimal weight:    0.8980
   chunk 63 optimal weight:    0.9980
   chunk 98 optimal weight:    6.9990
   overall best weight:    0.6780

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

Flipped N/Q/H residues before XYZ refinement:
B  75 GLN
B 101 ASN
C 340 ASN
** R 275 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3411 r_free = 0.3411 target = 0.108682 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3198 r_free = 0.3198 target = 0.094924 restraints weight = 12081.170|
|-----------------------------------------------------------------------------|
r_work (start): 0.3197 rms_B_bonded: 1.86
r_work: 0.3090 rms_B_bonded: 2.23 restraints_weight: 0.5000
r_work: 0.2953 rms_B_bonded: 3.92 restraints_weight: 0.2500
r_work (final): 0.2953
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7940
moved from start:          0.1412

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   8335  Z= 0.149
  Angle     :  0.596   7.218  11353  Z= 0.319
  Chirality :  0.043   0.140   1323
  Planarity :  0.004   0.041   1426
  Dihedral  :  4.684  31.538   1182
  Min Nonbonded Distance : 2.527

Molprobity Statistics.
  All-atom Clashscore : 2.65
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.08 %
    Favored  : 96.92 %
  Rotamer:
    Outliers :  1.95 %
    Allowed  :  8.91 %
    Favored  : 89.13 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.12 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.46 (0.26), residues: 1070
  helix:  2.35 (0.29), residues: 366
  sheet:  0.32 (0.30), residues: 279
  loop : -1.62 (0.28), residues: 425

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP E  47 
 HIS   0.005   0.001   HIS C  54 
 PHE   0.013   0.001   PHE C 151 
 TYR   0.012   0.001   TYR E 178 
 ARG   0.008   0.000   ARG B  32 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.06792 (  407)
  hydrogen bonds       : angle       4.60809 ( 1161)
  SS BOND              : bond        0.01036 (    2)
  SS BOND              : angle       0.93070 (    4)
  covalent geometry    : bond        0.00322 ( 8333)
  covalent geometry    : angle       0.59578 (11349)

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

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

  2140 Ramachandran restraints generated.
    1070 Oldfield, 0 Emsley, 1070 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2140 Ramachandran restraints generated.
    1070 Oldfield, 0 Emsley, 1070 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  176 residues out of total 937 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 160
  time to evaluate  : 0.891 
Fit side-chains
REVERT: B   10 LYS cc_start: 0.8023 (mtpp) cc_final: 0.7723 (mttm)
REVERT: B   35 ARG cc_start: 0.8728 (mtp85) cc_final: 0.8512 (mtp85)
REVERT: B  128 ILE cc_start: 0.8411 (tp) cc_final: 0.8177 (tp)
REVERT: C   23 LYS cc_start: 0.8299 (ttpt) cc_final: 0.8023 (ttmm)
REVERT: E   93 MET cc_start: 0.8434 (OUTLIER) cc_final: 0.8117 (ttt)
  outliers start: 16
  outliers final: 7
  residues processed: 164
  average time/residue: 1.1161
  time to fit residues: 195.0880
Evaluate side-chains
  157 residues out of total 937 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 149
  time to evaluate  : 0.906 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  160 ILE
Chi-restraints excluded: chain C residue   18 ILE
Chi-restraints excluded: chain C residue  243 THR
Chi-restraints excluded: chain C residue  270 ILE
Chi-restraints excluded: chain R residue  201 SER
Chi-restraints excluded: chain R residue  207 VAL
Chi-restraints excluded: chain R residue  277 ILE
Chi-restraints excluded: chain E residue   93 MET
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 101 optimal weight:    0.0270
   chunk 6 optimal weight:    2.9990
   chunk 13 optimal weight:    3.9990
   chunk 104 optimal weight:    4.9990
   chunk 49 optimal weight:    0.9990
   chunk 53 optimal weight:    0.7980
   chunk 58 optimal weight:    4.9990
   chunk 64 optimal weight:    0.8980
   chunk 1 optimal weight:    1.9990
   chunk 100 optimal weight:    0.9980
   chunk 75 optimal weight:    0.7980
   overall best weight:    0.7038

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

Flipped N/Q/H residues before XYZ refinement:
B 101 ASN
C 340 ASN
** R 275 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3409 r_free = 0.3409 target = 0.108638 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3195 r_free = 0.3195 target = 0.094728 restraints weight = 12314.862|
|-----------------------------------------------------------------------------|
r_work (start): 0.3200 rms_B_bonded: 1.87
r_work: 0.3094 rms_B_bonded: 2.25 restraints_weight: 0.5000
r_work: 0.2957 rms_B_bonded: 3.93 restraints_weight: 0.2500
r_work (final): 0.2957
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7936
moved from start:          0.1770

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   8335  Z= 0.144
  Angle     :  0.564   6.700  11353  Z= 0.300
  Chirality :  0.042   0.132   1323
  Planarity :  0.004   0.040   1426
  Dihedral  :  4.336  28.269   1182
  Min Nonbonded Distance : 2.563

Molprobity Statistics.
  All-atom Clashscore : 2.58
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.36 %
    Favored  : 96.64 %
  Rotamer:
    Outliers :  2.20 %
    Allowed  : 13.19 %
    Favored  : 84.62 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.12 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.76 (0.27), residues: 1070
  helix:  2.66 (0.29), residues: 367
  sheet:  0.44 (0.31), residues: 284
  loop : -1.51 (0.28), residues: 419

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP R 243 
 HIS   0.005   0.001   HIS C  54 
 PHE   0.013   0.001   PHE C 151 
 TYR   0.014   0.001   TYR E 178 
 ARG   0.005   0.000   ARG B  32 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.06150 (  407)
  hydrogen bonds       : angle       4.34685 ( 1161)
  SS BOND              : bond        0.01115 (    2)
  SS BOND              : angle       0.77897 (    4)
  covalent geometry    : bond        0.00321 ( 8333)
  covalent geometry    : angle       0.56432 (11349)

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

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

  2140 Ramachandran restraints generated.
    1070 Oldfield, 0 Emsley, 1070 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2140 Ramachandran restraints generated.
    1070 Oldfield, 0 Emsley, 1070 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  173 residues out of total 937 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 155
  time to evaluate  : 0.885 
Fit side-chains
REVERT: B   10 LYS cc_start: 0.7956 (mtpp) cc_final: 0.7695 (mttm)
REVERT: B  128 ILE cc_start: 0.8427 (tp) cc_final: 0.8205 (tp)
REVERT: C   23 LYS cc_start: 0.8308 (ttpt) cc_final: 0.8006 (ttpt)
REVERT: C   72 SER cc_start: 0.8691 (m) cc_final: 0.8469 (p)
REVERT: E   93 MET cc_start: 0.8429 (ttp) cc_final: 0.8138 (ttt)
REVERT: E  179 ARG cc_start: 0.8662 (OUTLIER) cc_final: 0.6879 (mtp180)
REVERT: E  211 ASP cc_start: 0.7588 (t0) cc_final: 0.7202 (t0)
  outliers start: 18
  outliers final: 8
  residues processed: 161
  average time/residue: 1.2580
  time to fit residues: 215.5941
Evaluate side-chains
  159 residues out of total 937 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 150
  time to evaluate  : 0.833 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   75 GLN
Chi-restraints excluded: chain C residue   18 ILE
Chi-restraints excluded: chain C residue  135 VAL
Chi-restraints excluded: chain R residue  201 SER
Chi-restraints excluded: chain R residue  207 VAL
Chi-restraints excluded: chain R residue  246 ILE
Chi-restraints excluded: chain R residue  250 TRP
Chi-restraints excluded: chain R residue  277 ILE
Chi-restraints excluded: chain E residue  179 ARG
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 106 optimal weight:    0.9980
   chunk 55 optimal weight:    2.9990
   chunk 104 optimal weight:    1.9990
   chunk 105 optimal weight:    4.9990
   chunk 25 optimal weight:    2.9990
   chunk 58 optimal weight:    0.9990
   chunk 90 optimal weight:    0.6980
   chunk 84 optimal weight:    0.2980
   chunk 46 optimal weight:    2.9990
   chunk 13 optimal weight:    0.0060
   chunk 59 optimal weight:    2.9990
   overall best weight:    0.5998

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

Flipped N/Q/H residues before XYZ refinement:
B 101 ASN
C 340 ASN
** R 275 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3427 r_free = 0.3427 target = 0.109838 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3215 r_free = 0.3215 target = 0.095995 restraints weight = 12162.155|
|-----------------------------------------------------------------------------|
r_work (start): 0.3212 rms_B_bonded: 1.85
r_work: 0.3108 rms_B_bonded: 2.22 restraints_weight: 0.5000
r_work: 0.2973 rms_B_bonded: 3.91 restraints_weight: 0.2500
r_work (final): 0.2973
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7931
moved from start:          0.1978

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   8335  Z= 0.130
  Angle     :  0.540   6.601  11353  Z= 0.285
  Chirality :  0.042   0.131   1323
  Planarity :  0.004   0.038   1426
  Dihedral  :  4.131  23.023   1182
  Min Nonbonded Distance : 2.587

Molprobity Statistics.
  All-atom Clashscore : 2.46
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.99 %
    Favored  : 97.01 %
  Rotamer:
    Outliers :  2.44 %
    Allowed  : 15.51 %
    Favored  : 82.05 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.12 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.89 (0.27), residues: 1070
  helix:  2.74 (0.29), residues: 373
  sheet:  0.56 (0.31), residues: 286
  loop : -1.51 (0.29), residues: 411

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP R 190 
 HIS   0.005   0.001   HIS C  54 
 PHE   0.011   0.001   PHE C 151 
 TYR   0.013   0.001   TYR E 178 
 ARG   0.005   0.000   ARG B 194 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05604 (  407)
  hydrogen bonds       : angle       4.17931 ( 1161)
  SS BOND              : bond        0.01029 (    2)
  SS BOND              : angle       0.82071 (    4)
  covalent geometry    : bond        0.00283 ( 8333)
  covalent geometry    : angle       0.54002 (11349)

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

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

  2140 Ramachandran restraints generated.
    1070 Oldfield, 0 Emsley, 1070 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2140 Ramachandran restraints generated.
    1070 Oldfield, 0 Emsley, 1070 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  169 residues out of total 937 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 149
  time to evaluate  : 0.898 
Fit side-chains
REVERT: B   10 LYS cc_start: 0.7900 (mtpp) cc_final: 0.7662 (mttm)
REVERT: B  128 ILE cc_start: 0.8459 (tp) cc_final: 0.8233 (tp)
REVERT: B  195 LYS cc_start: 0.7666 (ttpt) cc_final: 0.7454 (ttpt)
REVERT: C   23 LYS cc_start: 0.8327 (ttpt) cc_final: 0.8001 (ttmm)
REVERT: C   72 SER cc_start: 0.8682 (m) cc_final: 0.8474 (p)
REVERT: C  165 THR cc_start: 0.8447 (OUTLIER) cc_final: 0.8180 (p)
REVERT: E   93 MET cc_start: 0.8430 (ttp) cc_final: 0.8161 (ttt)
REVERT: E  179 ARG cc_start: 0.8625 (OUTLIER) cc_final: 0.6826 (mtp180)
REVERT: E  211 ASP cc_start: 0.7519 (t0) cc_final: 0.7147 (t0)
  outliers start: 20
  outliers final: 9
  residues processed: 156
  average time/residue: 1.1820
  time to fit residues: 195.3759
Evaluate side-chains
  160 residues out of total 937 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 149
  time to evaluate  : 0.896 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   28 GLU
Chi-restraints excluded: chain B residue   75 GLN
Chi-restraints excluded: chain C residue  135 VAL
Chi-restraints excluded: chain C residue  146 LEU
Chi-restraints excluded: chain C residue  165 THR
Chi-restraints excluded: chain C residue  270 ILE
Chi-restraints excluded: chain R residue  109 MET
Chi-restraints excluded: chain R residue  201 SER
Chi-restraints excluded: chain R residue  234 LEU
Chi-restraints excluded: chain R residue  277 ILE
Chi-restraints excluded: chain E residue  179 ARG
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 37 optimal weight:    3.9990
   chunk 51 optimal weight:    1.9990
   chunk 76 optimal weight:    0.9990
   chunk 39 optimal weight:    2.9990
   chunk 42 optimal weight:    2.9990
   chunk 9 optimal weight:    2.9990
   chunk 8 optimal weight:    0.6980
   chunk 56 optimal weight:    0.0970
   chunk 54 optimal weight:    3.9990
   chunk 106 optimal weight:    2.9990
   chunk 102 optimal weight:    1.9990
   overall best weight:    1.1584

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

Flipped N/Q/H residues before XYZ refinement:
B 101 ASN
C 259 GLN
C 340 ASN
** R 275 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3384 r_free = 0.3384 target = 0.106910 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3170 r_free = 0.3170 target = 0.093117 restraints weight = 12134.772|
|-----------------------------------------------------------------------------|
r_work (start): 0.3167 rms_B_bonded: 1.91
r_work: 0.3058 rms_B_bonded: 2.28 restraints_weight: 0.5000
r_work: 0.2920 rms_B_bonded: 3.99 restraints_weight: 0.2500
r_work (final): 0.2920
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7947
moved from start:          0.1911

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.045   8335  Z= 0.192
  Angle     :  0.611   7.110  11353  Z= 0.321
  Chirality :  0.044   0.133   1323
  Planarity :  0.004   0.049   1426
  Dihedral  :  4.324  23.082   1182
  Min Nonbonded Distance : 2.588

Molprobity Statistics.
  All-atom Clashscore : 2.96
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.36 %
    Favored  : 96.64 %
  Rotamer:
    Outliers :  2.81 %
    Allowed  : 16.48 %
    Favored  : 80.71 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.12 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.92 (0.27), residues: 1070
  helix:  2.68 (0.29), residues: 373
  sheet:  0.80 (0.31), residues: 281
  loop : -1.58 (0.28), residues: 416

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.002   TRP R 243 
 HIS   0.007   0.002   HIS E  35 
 PHE   0.016   0.002   PHE C 151 
 TYR   0.017   0.002   TYR E 178 
 ARG   0.011   0.000   ARG B 194 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.06855 (  407)
  hydrogen bonds       : angle       4.31879 ( 1161)
  SS BOND              : bond        0.01392 (    2)
  SS BOND              : angle       1.07078 (    4)
  covalent geometry    : bond        0.00458 ( 8333)
  covalent geometry    : angle       0.61116 (11349)

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

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

  2140 Ramachandran restraints generated.
    1070 Oldfield, 0 Emsley, 1070 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2140 Ramachandran restraints generated.
    1070 Oldfield, 0 Emsley, 1070 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  173 residues out of total 937 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 150
  time to evaluate  : 0.799 
Fit side-chains
REVERT: B   10 LYS cc_start: 0.8087 (mtpp) cc_final: 0.7809 (mttm)
REVERT: B  195 LYS cc_start: 0.7755 (ttpt) cc_final: 0.7408 (ttpt)
REVERT: C   23 LYS cc_start: 0.8320 (ttpt) cc_final: 0.7955 (ttmm)
REVERT: C   72 SER cc_start: 0.8715 (m) cc_final: 0.8466 (p)
REVERT: C  165 THR cc_start: 0.8459 (OUTLIER) cc_final: 0.8151 (p)
REVERT: C  256 ARG cc_start: 0.8650 (OUTLIER) cc_final: 0.7120 (mtt180)
REVERT: R  272 SER cc_start: 0.8229 (OUTLIER) cc_final: 0.7929 (t)
REVERT: E    3 GLN cc_start: 0.8538 (mt0) cc_final: 0.8282 (mt0)
REVERT: E   93 MET cc_start: 0.8492 (ttp) cc_final: 0.8202 (ttt)
REVERT: E  179 ARG cc_start: 0.8639 (OUTLIER) cc_final: 0.7026 (mtp180)
REVERT: E  211 ASP cc_start: 0.7616 (t0) cc_final: 0.7228 (t0)
  outliers start: 23
  outliers final: 10
  residues processed: 158
  average time/residue: 1.1541
  time to fit residues: 193.6058
Evaluate side-chains
  161 residues out of total 937 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 147
  time to evaluate  : 0.873 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   75 GLN
Chi-restraints excluded: chain C residue  135 VAL
Chi-restraints excluded: chain C residue  146 LEU
Chi-restraints excluded: chain C residue  165 THR
Chi-restraints excluded: chain C residue  256 ARG
Chi-restraints excluded: chain C residue  270 ILE
Chi-restraints excluded: chain C residue  321 THR
Chi-restraints excluded: chain R residue  201 SER
Chi-restraints excluded: chain R residue  207 VAL
Chi-restraints excluded: chain R residue  272 SER
Chi-restraints excluded: chain R residue  277 ILE
Chi-restraints excluded: chain E residue   78 THR
Chi-restraints excluded: chain E residue  128 MET
Chi-restraints excluded: chain E residue  179 ARG
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 81 optimal weight:    1.9990
   chunk 100 optimal weight:    0.8980
   chunk 21 optimal weight:    0.9990
   chunk 28 optimal weight:    1.9990
   chunk 49 optimal weight:    1.9990
   chunk 51 optimal weight:    0.5980
   chunk 64 optimal weight:    0.8980
   chunk 98 optimal weight:    4.9990
   chunk 65 optimal weight:    0.5980
   chunk 18 optimal weight:    1.9990
   chunk 84 optimal weight:    0.1980
   overall best weight:    0.6380

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

Flipped N/Q/H residues before XYZ refinement:
B 101 ASN
C 340 ASN
** R 275 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3423 r_free = 0.3423 target = 0.109523 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3208 r_free = 0.3208 target = 0.095613 restraints weight = 12060.746|
|-----------------------------------------------------------------------------|
r_work (start): 0.3207 rms_B_bonded: 1.84
r_work: 0.3103 rms_B_bonded: 2.21 restraints_weight: 0.5000
r_work: 0.2967 rms_B_bonded: 3.89 restraints_weight: 0.2500
r_work (final): 0.2967
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7939
moved from start:          0.2173

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   8335  Z= 0.132
  Angle     :  0.540   7.040  11353  Z= 0.285
  Chirality :  0.042   0.130   1323
  Planarity :  0.004   0.036   1426
  Dihedral  :  4.106  22.662   1182
  Min Nonbonded Distance : 2.576

Molprobity Statistics.
  All-atom Clashscore : 2.65
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.90 %
    Favored  : 97.10 %
  Rotamer:
    Outliers :  2.44 %
    Allowed  : 18.32 %
    Favored  : 79.24 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.12 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.04 (0.27), residues: 1070
  helix:  2.79 (0.29), residues: 373
  sheet:  0.79 (0.31), residues: 283
  loop : -1.46 (0.28), residues: 414

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP C  63 
 HIS   0.004   0.001   HIS E  35 
 PHE   0.011   0.001   PHE C 151 
 TYR   0.012   0.001   TYR B 163 
 ARG   0.004   0.000   ARG B 194 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05630 (  407)
  hydrogen bonds       : angle       4.14324 ( 1161)
  SS BOND              : bond        0.01053 (    2)
  SS BOND              : angle       0.85117 (    4)
  covalent geometry    : bond        0.00291 ( 8333)
  covalent geometry    : angle       0.53994 (11349)

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

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

  2140 Ramachandran restraints generated.
    1070 Oldfield, 0 Emsley, 1070 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2140 Ramachandran restraints generated.
    1070 Oldfield, 0 Emsley, 1070 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  168 residues out of total 937 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 148
  time to evaluate  : 0.786 
Fit side-chains
REVERT: B   10 LYS cc_start: 0.7952 (mtpp) cc_final: 0.7700 (mttm)
REVERT: B  195 LYS cc_start: 0.7716 (ttpt) cc_final: 0.7414 (ttpt)
REVERT: C   23 LYS cc_start: 0.8344 (ttpt) cc_final: 0.8006 (ttmm)
REVERT: C   72 SER cc_start: 0.8682 (m) cc_final: 0.8474 (p)
REVERT: C  165 THR cc_start: 0.8454 (OUTLIER) cc_final: 0.8203 (p)
REVERT: R  272 SER cc_start: 0.8181 (OUTLIER) cc_final: 0.7948 (t)
REVERT: E    3 GLN cc_start: 0.8522 (mt0) cc_final: 0.8287 (mt0)
REVERT: E   93 MET cc_start: 0.8462 (ttp) cc_final: 0.8195 (ttt)
REVERT: E  179 ARG cc_start: 0.8598 (OUTLIER) cc_final: 0.6848 (mtp180)
REVERT: E  211 ASP cc_start: 0.7522 (t0) cc_final: 0.7155 (t0)
  outliers start: 20
  outliers final: 14
  residues processed: 157
  average time/residue: 1.2181
  time to fit residues: 202.5610
Evaluate side-chains
  162 residues out of total 937 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 145
  time to evaluate  : 0.830 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   28 GLU
Chi-restraints excluded: chain B residue   75 GLN
Chi-restraints excluded: chain C residue  135 VAL
Chi-restraints excluded: chain C residue  146 LEU
Chi-restraints excluded: chain C residue  165 THR
Chi-restraints excluded: chain C residue  243 THR
Chi-restraints excluded: chain C residue  270 ILE
Chi-restraints excluded: chain C residue  321 THR
Chi-restraints excluded: chain R residue  201 SER
Chi-restraints excluded: chain R residue  207 VAL
Chi-restraints excluded: chain R residue  234 LEU
Chi-restraints excluded: chain R residue  246 ILE
Chi-restraints excluded: chain R residue  272 SER
Chi-restraints excluded: chain R residue  277 ILE
Chi-restraints excluded: chain E residue   78 THR
Chi-restraints excluded: chain E residue  128 MET
Chi-restraints excluded: chain E residue  179 ARG
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 66 optimal weight:    0.6980
   chunk 21 optimal weight:    0.9990
   chunk 100 optimal weight:    0.6980
   chunk 4 optimal weight:    0.1980
   chunk 104 optimal weight:    2.9990
   chunk 65 optimal weight:    0.6980
   chunk 42 optimal weight:    2.9990
   chunk 43 optimal weight:    2.9990
   chunk 28 optimal weight:    2.9990
   chunk 90 optimal weight:    1.9990
   chunk 97 optimal weight:    0.9990
   overall best weight:    0.6582

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

Flipped N/Q/H residues before XYZ refinement:
B 101 ASN
C 340 ASN
** R 275 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3415 r_free = 0.3415 target = 0.108960 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3201 r_free = 0.3201 target = 0.095048 restraints weight = 12150.777|
|-----------------------------------------------------------------------------|
r_work (start): 0.3198 rms_B_bonded: 1.92
r_work: 0.3092 rms_B_bonded: 2.29 restraints_weight: 0.5000
r_work: 0.2954 rms_B_bonded: 4.03 restraints_weight: 0.2500
r_work (final): 0.2954
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7916
moved from start:          0.2195

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   8335  Z= 0.133
  Angle     :  0.542   7.585  11353  Z= 0.284
  Chirality :  0.041   0.132   1323
  Planarity :  0.004   0.059   1426
  Dihedral  :  4.078  22.813   1182
  Min Nonbonded Distance : 2.594

Molprobity Statistics.
  All-atom Clashscore : 2.96
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.90 %
    Favored  : 97.10 %
  Rotamer:
    Outliers :  2.69 %
    Allowed  : 18.19 %
    Favored  : 79.12 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.12 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.18 (0.27), residues: 1070
  helix:  2.98 (0.29), residues: 367
  sheet:  0.81 (0.31), residues: 283
  loop : -1.34 (0.28), residues: 420

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP C  63 
 HIS   0.004   0.001   HIS E  35 
 PHE   0.012   0.001   PHE C 151 
 TYR   0.013   0.001   TYR E 178 
 ARG   0.013   0.000   ARG B 194 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05615 (  407)
  hydrogen bonds       : angle       4.09419 ( 1161)
  SS BOND              : bond        0.01079 (    2)
  SS BOND              : angle       0.89287 (    4)
  covalent geometry    : bond        0.00297 ( 8333)
  covalent geometry    : angle       0.54224 (11349)

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

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

  2140 Ramachandran restraints generated.
    1070 Oldfield, 0 Emsley, 1070 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2140 Ramachandran restraints generated.
    1070 Oldfield, 0 Emsley, 1070 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  170 residues out of total 937 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 148
  time to evaluate  : 0.826 
Fit side-chains
REVERT: B   10 LYS cc_start: 0.7893 (mtpp) cc_final: 0.7647 (mttm)
REVERT: B  195 LYS cc_start: 0.7713 (ttpt) cc_final: 0.7417 (ttpt)
REVERT: C   23 LYS cc_start: 0.8306 (ttpt) cc_final: 0.7925 (ttmm)
REVERT: C   72 SER cc_start: 0.8707 (m) cc_final: 0.8455 (p)
REVERT: C  165 THR cc_start: 0.8438 (OUTLIER) cc_final: 0.8165 (p)
REVERT: R  272 SER cc_start: 0.8211 (OUTLIER) cc_final: 0.7937 (t)
REVERT: E    3 GLN cc_start: 0.8554 (mt0) cc_final: 0.8296 (mt0)
REVERT: E   93 MET cc_start: 0.8466 (ttp) cc_final: 0.8176 (ttt)
REVERT: E  179 ARG cc_start: 0.8556 (OUTLIER) cc_final: 0.6798 (mtp180)
REVERT: E  211 ASP cc_start: 0.7546 (t0) cc_final: 0.7176 (t0)
  outliers start: 22
  outliers final: 13
  residues processed: 158
  average time/residue: 1.1197
  time to fit residues: 188.1628
Evaluate side-chains
  155 residues out of total 937 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 139
  time to evaluate  : 1.271 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   75 GLN
Chi-restraints excluded: chain C residue  135 VAL
Chi-restraints excluded: chain C residue  146 LEU
Chi-restraints excluded: chain C residue  165 THR
Chi-restraints excluded: chain C residue  243 THR
Chi-restraints excluded: chain C residue  270 ILE
Chi-restraints excluded: chain C residue  321 THR
Chi-restraints excluded: chain R residue  201 SER
Chi-restraints excluded: chain R residue  207 VAL
Chi-restraints excluded: chain R residue  234 LEU
Chi-restraints excluded: chain R residue  246 ILE
Chi-restraints excluded: chain R residue  272 SER
Chi-restraints excluded: chain R residue  277 ILE
Chi-restraints excluded: chain E residue   78 THR
Chi-restraints excluded: chain E residue  128 MET
Chi-restraints excluded: chain E residue  179 ARG
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 32 optimal weight:    1.9990
   chunk 2 optimal weight:    0.1980
   chunk 22 optimal weight:    1.9990
   chunk 69 optimal weight:    0.5980
   chunk 101 optimal weight:    0.4980
   chunk 6 optimal weight:    0.9980
   chunk 47 optimal weight:    0.3980
   chunk 68 optimal weight:    0.9980
   chunk 63 optimal weight:    0.6980
   chunk 39 optimal weight:    1.9990
   chunk 9 optimal weight:    0.8980
   overall best weight:    0.4780

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

Flipped N/Q/H residues before XYZ refinement:
B 101 ASN
C 340 ASN
** R 275 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3439 r_free = 0.3439 target = 0.110739 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3225 r_free = 0.3225 target = 0.096573 restraints weight = 12315.620|
|-----------------------------------------------------------------------------|
r_work (start): 0.3223 rms_B_bonded: 1.95
r_work: 0.3116 rms_B_bonded: 2.33 restraints_weight: 0.5000
r_work: 0.2978 rms_B_bonded: 4.10 restraints_weight: 0.2500
r_work (final): 0.2978
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7900
moved from start:          0.2395

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.033   8335  Z= 0.115
  Angle     :  0.516   7.353  11353  Z= 0.271
  Chirality :  0.041   0.129   1323
  Planarity :  0.003   0.039   1426
  Dihedral  :  3.922  22.519   1182
  Min Nonbonded Distance : 2.589

Molprobity Statistics.
  All-atom Clashscore : 2.77
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.62 %
    Favored  : 97.38 %
  Rotamer:
    Outliers :  1.71 %
    Allowed  : 19.41 %
    Favored  : 78.88 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.12 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.28 (0.27), residues: 1070
  helix:  3.09 (0.29), residues: 366
  sheet:  0.82 (0.31), residues: 288
  loop : -1.28 (0.28), residues: 416

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP C  63 
 HIS   0.003   0.001   HIS E  35 
 PHE   0.010   0.001   PHE C 241 
 TYR   0.011   0.001   TYR E 178 
 ARG   0.009   0.000   ARG B 194 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04934 (  407)
  hydrogen bonds       : angle       3.96791 ( 1161)
  SS BOND              : bond        0.00927 (    2)
  SS BOND              : angle       0.80717 (    4)
  covalent geometry    : bond        0.00245 ( 8333)
  covalent geometry    : angle       0.51560 (11349)

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

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

  2140 Ramachandran restraints generated.
    1070 Oldfield, 0 Emsley, 1070 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2140 Ramachandran restraints generated.
    1070 Oldfield, 0 Emsley, 1070 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  161 residues out of total 937 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 147
  time to evaluate  : 1.018 
Fit side-chains
REVERT: B    5 VAL cc_start: 0.8314 (t) cc_final: 0.8031 (t)
REVERT: B   10 LYS cc_start: 0.7699 (mtpp) cc_final: 0.7442 (mttm)
REVERT: B  195 LYS cc_start: 0.7635 (ttpt) cc_final: 0.7434 (ttpt)
REVERT: C   23 LYS cc_start: 0.8293 (ttpt) cc_final: 0.7922 (ttmm)
REVERT: C   72 SER cc_start: 0.8711 (m) cc_final: 0.8444 (p)
REVERT: C  165 THR cc_start: 0.8419 (OUTLIER) cc_final: 0.8188 (p)
REVERT: R  272 SER cc_start: 0.8159 (OUTLIER) cc_final: 0.7912 (t)
REVERT: E    3 GLN cc_start: 0.8559 (mt0) cc_final: 0.8313 (mt0)
REVERT: E   93 MET cc_start: 0.8461 (ttp) cc_final: 0.8191 (ttt)
REVERT: E  179 ARG cc_start: 0.8461 (OUTLIER) cc_final: 0.6733 (mtp180)
REVERT: E  211 ASP cc_start: 0.7497 (t0) cc_final: 0.7127 (t0)
  outliers start: 14
  outliers final: 11
  residues processed: 152
  average time/residue: 1.4446
  time to fit residues: 233.4749
Evaluate side-chains
  158 residues out of total 937 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 144
  time to evaluate  : 0.854 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   28 GLU
Chi-restraints excluded: chain B residue   75 GLN
Chi-restraints excluded: chain C residue  135 VAL
Chi-restraints excluded: chain C residue  146 LEU
Chi-restraints excluded: chain C residue  165 THR
Chi-restraints excluded: chain C residue  243 THR
Chi-restraints excluded: chain C residue  270 ILE
Chi-restraints excluded: chain R residue  201 SER
Chi-restraints excluded: chain R residue  234 LEU
Chi-restraints excluded: chain R residue  272 SER
Chi-restraints excluded: chain R residue  277 ILE
Chi-restraints excluded: chain E residue   78 THR
Chi-restraints excluded: chain E residue  128 MET
Chi-restraints excluded: chain E residue  179 ARG
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 68 optimal weight:    0.5980
   chunk 88 optimal weight:    3.9990
   chunk 98 optimal weight:    3.9990
   chunk 62 optimal weight:    0.8980
   chunk 10 optimal weight:    0.8980
   chunk 4 optimal weight:    2.9990
   chunk 71 optimal weight:    1.9990
   chunk 50 optimal weight:    0.6980
   chunk 7 optimal weight:    0.6980
   chunk 99 optimal weight:    3.9990
   chunk 48 optimal weight:    1.9990
   overall best weight:    0.7580

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

Flipped N/Q/H residues before XYZ refinement:
B 144 ASN
C 340 ASN
** R 275 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3412 r_free = 0.3412 target = 0.108891 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3196 r_free = 0.3196 target = 0.094813 restraints weight = 12376.404|
|-----------------------------------------------------------------------------|
r_work (start): 0.3198 rms_B_bonded: 1.95
r_work: 0.3090 rms_B_bonded: 2.32 restraints_weight: 0.5000
r_work: 0.2952 rms_B_bonded: 4.07 restraints_weight: 0.2500
r_work (final): 0.2952
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7923
moved from start:          0.2302

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038   8335  Z= 0.144
  Angle     :  0.554   7.705  11353  Z= 0.289
  Chirality :  0.042   0.133   1323
  Planarity :  0.004   0.060   1426
  Dihedral  :  4.039  23.004   1182
  Min Nonbonded Distance : 2.596

Molprobity Statistics.
  All-atom Clashscore : 2.96
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.27 %
    Favored  : 96.73 %
  Rotamer:
    Outliers :  2.20 %
    Allowed  : 19.78 %
    Favored  : 78.02 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.12 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.24 (0.27), residues: 1070
  helix:  3.06 (0.29), residues: 367
  sheet:  0.81 (0.31), residues: 288
  loop : -1.33 (0.28), residues: 415

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP C 339 
 HIS   0.005   0.001   HIS E  35 
 PHE   0.014   0.001   PHE C 151 
 TYR   0.014   0.001   TYR E 178 
 ARG   0.017   0.000   ARG B 194 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05688 (  407)
  hydrogen bonds       : angle       4.04260 ( 1161)
  SS BOND              : bond        0.01151 (    2)
  SS BOND              : angle       0.96064 (    4)
  covalent geometry    : bond        0.00329 ( 8333)
  covalent geometry    : angle       0.55345 (11349)

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

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

  2140 Ramachandran restraints generated.
    1070 Oldfield, 0 Emsley, 1070 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2140 Ramachandran restraints generated.
    1070 Oldfield, 0 Emsley, 1070 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  156 residues out of total 937 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 138
  time to evaluate  : 0.850 
Fit side-chains
REVERT: B   10 LYS cc_start: 0.7900 (mtpp) cc_final: 0.7658 (mttm)
REVERT: B  195 LYS cc_start: 0.7697 (ttpt) cc_final: 0.7381 (ttpt)
REVERT: C   23 LYS cc_start: 0.8324 (ttpt) cc_final: 0.7953 (ttmm)
REVERT: C   72 SER cc_start: 0.8726 (m) cc_final: 0.8466 (p)
REVERT: C  165 THR cc_start: 0.8442 (OUTLIER) cc_final: 0.8168 (p)
REVERT: R  272 SER cc_start: 0.8205 (OUTLIER) cc_final: 0.7925 (t)
REVERT: E    3 GLN cc_start: 0.8569 (mt0) cc_final: 0.8315 (mt0)
REVERT: E   51 ILE cc_start: 0.8507 (OUTLIER) cc_final: 0.8089 (tp)
REVERT: E   93 MET cc_start: 0.8484 (ttp) cc_final: 0.8213 (ttt)
REVERT: E  179 ARG cc_start: 0.8522 (OUTLIER) cc_final: 0.6886 (mtp180)
REVERT: E  211 ASP cc_start: 0.7538 (t0) cc_final: 0.7170 (t0)
  outliers start: 18
  outliers final: 12
  residues processed: 148
  average time/residue: 1.1915
  time to fit residues: 187.1797
Evaluate side-chains
  154 residues out of total 937 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 138
  time to evaluate  : 0.880 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   18 MET
Chi-restraints excluded: chain B residue   22 ASN
Chi-restraints excluded: chain B residue   28 GLU
Chi-restraints excluded: chain B residue   75 GLN
Chi-restraints excluded: chain C residue  135 VAL
Chi-restraints excluded: chain C residue  146 LEU
Chi-restraints excluded: chain C residue  165 THR
Chi-restraints excluded: chain C residue  321 THR
Chi-restraints excluded: chain R residue  201 SER
Chi-restraints excluded: chain R residue  207 VAL
Chi-restraints excluded: chain R residue  272 SER
Chi-restraints excluded: chain R residue  277 ILE
Chi-restraints excluded: chain E residue   51 ILE
Chi-restraints excluded: chain E residue   78 THR
Chi-restraints excluded: chain E residue  128 MET
Chi-restraints excluded: chain E residue  179 ARG
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 82 optimal weight:    0.8980
   chunk 87 optimal weight:    0.8980
   chunk 56 optimal weight:    0.9980
   chunk 80 optimal weight:    0.9990
   chunk 27 optimal weight:    5.9990
   chunk 43 optimal weight:    1.9990
   chunk 81 optimal weight:    0.4980
   chunk 45 optimal weight:    0.4980
   chunk 60 optimal weight:    0.0980
   chunk 48 optimal weight:    3.9990
   chunk 3 optimal weight:    0.7980
   overall best weight:    0.5580

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

Flipped N/Q/H residues before XYZ refinement:
B 101 ASN
C 340 ASN
** R 275 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3429 r_free = 0.3429 target = 0.110060 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3219 r_free = 0.3219 target = 0.096218 restraints weight = 12155.312|
|-----------------------------------------------------------------------------|
r_work (start): 0.3217 rms_B_bonded: 1.87
r_work: 0.3113 rms_B_bonded: 2.25 restraints_weight: 0.5000
r_work: 0.2978 rms_B_bonded: 3.95 restraints_weight: 0.2500
r_work (final): 0.2978
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7926
moved from start:          0.2421

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   8335  Z= 0.122
  Angle     :  0.530   7.570  11353  Z= 0.277
  Chirality :  0.041   0.132   1323
  Planarity :  0.004   0.061   1426
  Dihedral  :  3.957  23.139   1182
  Min Nonbonded Distance : 2.581

Molprobity Statistics.
  All-atom Clashscore : 2.84
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.99 %
    Favored  : 97.01 %
  Rotamer:
    Outliers :  1.95 %
    Allowed  : 20.02 %
    Favored  : 78.02 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.12 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.28 (0.27), residues: 1070
  helix:  3.10 (0.29), residues: 367
  sheet:  0.83 (0.31), residues: 288
  loop : -1.32 (0.28), residues: 415

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP R 190 
 HIS   0.004   0.001   HIS E  35 
 PHE   0.011   0.001   PHE C 151 
 TYR   0.012   0.001   TYR E 178 
 ARG   0.014   0.000   ARG B 194 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05153 (  407)
  hydrogen bonds       : angle       3.98708 ( 1161)
  SS BOND              : bond        0.00994 (    2)
  SS BOND              : angle       0.84783 (    4)
  covalent geometry    : bond        0.00267 ( 8333)
  covalent geometry    : angle       0.52950 (11349)

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

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

  2140 Ramachandran restraints generated.
    1070 Oldfield, 0 Emsley, 1070 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2140 Ramachandran restraints generated.
    1070 Oldfield, 0 Emsley, 1070 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  160 residues out of total 937 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 144
  time to evaluate  : 0.872 
Fit side-chains
REVERT: B   10 LYS cc_start: 0.7834 (mtpp) cc_final: 0.7624 (mttm)
REVERT: B  195 LYS cc_start: 0.7663 (ttpt) cc_final: 0.7391 (ttpt)
REVERT: C   23 LYS cc_start: 0.8366 (ttpt) cc_final: 0.8019 (ttmm)
REVERT: C   72 SER cc_start: 0.8701 (m) cc_final: 0.8473 (p)
REVERT: C  165 THR cc_start: 0.8434 (OUTLIER) cc_final: 0.8206 (p)
REVERT: C  312 ASP cc_start: 0.7956 (t0) cc_final: 0.7741 (t70)
REVERT: R  272 SER cc_start: 0.8166 (OUTLIER) cc_final: 0.7933 (t)
REVERT: E    3 GLN cc_start: 0.8555 (mt0) cc_final: 0.8324 (mt0)
REVERT: E   51 ILE cc_start: 0.8491 (OUTLIER) cc_final: 0.8069 (tp)
REVERT: E   93 MET cc_start: 0.8467 (ttp) cc_final: 0.8213 (ttt)
REVERT: E  179 ARG cc_start: 0.8498 (OUTLIER) cc_final: 0.6696 (mtp180)
REVERT: E  211 ASP cc_start: 0.7477 (t0) cc_final: 0.7102 (t0)
  outliers start: 16
  outliers final: 11
  residues processed: 150
  average time/residue: 1.2352
  time to fit residues: 196.0660
Evaluate side-chains
  157 residues out of total 937 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 142
  time to evaluate  : 0.803 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   18 MET
Chi-restraints excluded: chain B residue   22 ASN
Chi-restraints excluded: chain B residue   28 GLU
Chi-restraints excluded: chain B residue   75 GLN
Chi-restraints excluded: chain C residue  135 VAL
Chi-restraints excluded: chain C residue  146 LEU
Chi-restraints excluded: chain C residue  165 THR
Chi-restraints excluded: chain C residue  321 THR
Chi-restraints excluded: chain R residue  201 SER
Chi-restraints excluded: chain R residue  272 SER
Chi-restraints excluded: chain R residue  277 ILE
Chi-restraints excluded: chain E residue   51 ILE
Chi-restraints excluded: chain E residue   78 THR
Chi-restraints excluded: chain E residue  128 MET
Chi-restraints excluded: chain E residue  179 ARG
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 70 optimal weight:    0.9980
   chunk 10 optimal weight:    1.9990
   chunk 0 optimal weight:    4.9990
   chunk 62 optimal weight:    1.9990
   chunk 91 optimal weight:    2.9990
   chunk 53 optimal weight:    2.9990
   chunk 89 optimal weight:    0.9980
   chunk 55 optimal weight:    1.9990
   chunk 2 optimal weight:    3.9990
   chunk 13 optimal weight:    2.9990
   chunk 26 optimal weight:    0.9990
   overall best weight:    1.3986

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

Flipped N/Q/H residues before XYZ refinement:
B  43 ASN
B 101 ASN
C 340 ASN
** R 275 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3372 r_free = 0.3372 target = 0.106154 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3157 r_free = 0.3157 target = 0.092336 restraints weight = 12272.130|
|-----------------------------------------------------------------------------|
r_work (start): 0.3157 rms_B_bonded: 1.93
r_work: 0.3047 rms_B_bonded: 2.28 restraints_weight: 0.5000
r_work: 0.2908 rms_B_bonded: 4.00 restraints_weight: 0.2500
r_work (final): 0.2908
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7959
moved from start:          0.2143

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.048   8335  Z= 0.223
  Angle     :  0.637   8.319  11353  Z= 0.335
  Chirality :  0.045   0.133   1323
  Planarity :  0.004   0.039   1426
  Dihedral  :  4.357  23.612   1182
  Min Nonbonded Distance : 2.539

Molprobity Statistics.
  All-atom Clashscore : 2.90
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.39 %
    Favored  : 95.61 %
  Rotamer:
    Outliers :  2.44 %
    Allowed  : 20.02 %
    Favored  : 77.53 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.12 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.09 (0.27), residues: 1070
  helix:  2.87 (0.29), residues: 367
  sheet:  0.86 (0.31), residues: 282
  loop : -1.44 (0.27), residues: 421

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.002   TRP R 243 
 HIS   0.010   0.002   HIS E  35 
 PHE   0.019   0.002   PHE C 234 
 TYR   0.019   0.002   TYR E 178 
 ARG   0.007   0.001   ARG B 194 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.07224 (  407)
  hydrogen bonds       : angle       4.27367 ( 1161)
  SS BOND              : bond        0.01497 (    2)
  SS BOND              : angle       1.19427 (    4)
  covalent geometry    : bond        0.00540 ( 8333)
  covalent geometry    : angle       0.63710 (11349)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 6797.31 seconds
wall clock time: 118 minutes 54.34 seconds (7134.34 seconds total)