Starting phenix.real_space_refine
on Wed Mar 12 19:43:47 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7s8n_24898/03_2025/7s8n_24898.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7s8n_24898/03_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_24898/03_2025/7s8n_24898.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7s8n_24898/03_2025/7s8n_24898.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7s8n_24898/03_2025/7s8n_24898.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7s8n_24898/03_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): 0.03s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/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: 5.48, per 1000 atoms: 0.67
  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 1.1 seconds
  

  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: 0.90
  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: 2.32

  Time building geometry restraints manager: 2.39 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:             0.940
  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:          0.330
  Check model and map are aligned:         0.070
  Set scattering table:                    0.090
  Process input model:                     22.310
  Find NCS groups from input model:        0.120
  Set up NCS constraints:                  0.040
  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:13.940
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   37.850
-------------------------------------------------------------------------------
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   8333  Z= 0.758
  Angle     :  0.896   9.959  11349  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 

*********************** 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  : 0.819 
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: 1.0241
  time to fit residues: 194.4647
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  : 0.820 
-------------------------------------------------------------------------------
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   8333  Z= 0.210
  Angle     :  0.596   7.218  11349  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 

*********************** 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  : 0.895 
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: 1.1157
  time to fit residues: 195.1249
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  : 0.891 
-------------------------------------------------------------------------------
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:    0.2980
   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:    0.7580

-------------------------------------------------------------------------------
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 = 0.3411 r_free = 0.3411 target = 0.108748 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3198 r_free = 0.3198 target = 0.094904 restraints weight = 12294.568|
|-----------------------------------------------------------------------------|
r_work (start): 0.3195 rms_B_bonded: 1.86
r_work: 0.3090 rms_B_bonded: 2.22 restraints_weight: 0.5000
r_work: 0.2955 rms_B_bonded: 3.91 restraints_weight: 0.2500
r_work (final): 0.2955
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7946
moved from start:          0.1742

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   8333  Z= 0.221
  Angle     :  0.571   6.824  11349  Z= 0.303
  Chirality :  0.042   0.133   1323
  Planarity :  0.004   0.040   1426
  Dihedral  :  4.366  28.555   1182
  Min Nonbonded Distance : 2.563

Molprobity Statistics.
  All-atom Clashscore : 2.65
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.36 %
    Favored  : 96.64 %
  Rotamer:
    Outliers :  2.20 %
    Allowed  : 13.06 %
    Favored  : 84.74 %
  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:  0.75 (0.27), residues: 1070
  helix:  2.65 (0.29), residues: 367
  sheet:  0.52 (0.31), residues: 280
  loop : -1.55 (0.28), residues: 423

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 

*********************** 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
  171 residues out of total 937 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 153
  time to evaluate  : 0.806 
Fit side-chains
REVERT: B   10 LYS cc_start: 0.7996 (mtpp) cc_final: 0.7736 (mttm)
REVERT: B  128 ILE cc_start: 0.8436 (tp) cc_final: 0.8217 (tp)
REVERT: C   23 LYS cc_start: 0.8319 (ttpt) cc_final: 0.8016 (ttpt)
REVERT: C   72 SER cc_start: 0.8686 (m) cc_final: 0.8473 (p)
REVERT: E   93 MET cc_start: 0.8430 (ttp) cc_final: 0.8143 (ttt)
REVERT: E  179 ARG cc_start: 0.8673 (OUTLIER) cc_final: 0.6910 (mtp180)
REVERT: E  211 ASP cc_start: 0.7592 (t0) cc_final: 0.7205 (t0)
  outliers start: 18
  outliers final: 8
  residues processed: 159
  average time/residue: 1.1445
  time to fit residues: 193.4143
Evaluate side-chains
  158 residues out of total 937 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 149
  time to evaluate  : 0.910 
-------------------------------------------------------------------------------
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:    1.9990
   chunk 55 optimal weight:    1.9990
   chunk 104 optimal weight:    3.9990
   chunk 105 optimal weight:    5.9990
   chunk 25 optimal weight:    2.9990
   chunk 58 optimal weight:    1.9990
   chunk 90 optimal weight:    0.0870
   chunk 84 optimal weight:    0.5980
   chunk 46 optimal weight:    2.9990
   chunk 13 optimal weight:    0.5980
   chunk 59 optimal weight:    0.0070
   overall best weight:    0.6578

-------------------------------------------------------------------------------
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 = 0.3420 r_free = 0.3420 target = 0.109327 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3207 r_free = 0.3207 target = 0.095469 restraints weight = 12147.695|
|-----------------------------------------------------------------------------|
r_work (start): 0.3205 rms_B_bonded: 1.85
r_work: 0.3101 rms_B_bonded: 2.22 restraints_weight: 0.5000
r_work: 0.2966 rms_B_bonded: 3.90 restraints_weight: 0.2500
r_work (final): 0.2966
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7937
moved from start:          0.1921

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   8333  Z= 0.197
  Angle     :  0.552   6.594  11349  Z= 0.291
  Chirality :  0.042   0.132   1323
  Planarity :  0.004   0.038   1426
  Dihedral  :  4.194  23.585   1182
  Min Nonbonded Distance : 2.576

Molprobity Statistics.
  All-atom Clashscore : 2.84
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.99 %
    Favored  : 97.01 %
  Rotamer:
    Outliers :  2.32 %
    Allowed  : 15.63 %
    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:  0.83 (0.27), residues: 1070
  helix:  2.67 (0.29), residues: 373
  sheet:  0.53 (0.31), residues: 286
  loop : -1.54 (0.29), residues: 411

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP R 243 
 HIS   0.004   0.001   HIS C  54 
 PHE   0.011   0.001   PHE C 151 
 TYR   0.014   0.001   TYR E 178 
 ARG   0.005   0.000   ARG B 194 

*********************** 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
  167 residues out of total 937 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 148
  time to evaluate  : 0.816 
Fit side-chains
REVERT: B   10 LYS cc_start: 0.7937 (mtpp) cc_final: 0.7692 (mttm)
REVERT: B  128 ILE cc_start: 0.8442 (tp) cc_final: 0.8219 (tp)
REVERT: B  195 LYS cc_start: 0.7672 (ttpt) cc_final: 0.7349 (ttpt)
REVERT: C   23 LYS cc_start: 0.8332 (ttpt) cc_final: 0.8009 (ttmm)
REVERT: C   72 SER cc_start: 0.8683 (m) cc_final: 0.8471 (p)
REVERT: C  165 THR cc_start: 0.8449 (OUTLIER) cc_final: 0.8178 (p)
REVERT: E   93 MET cc_start: 0.8430 (ttp) cc_final: 0.8158 (ttt)
REVERT: E  179 ARG cc_start: 0.8651 (OUTLIER) cc_final: 0.6879 (mtp180)
REVERT: E  211 ASP cc_start: 0.7548 (t0) cc_final: 0.7177 (t0)
  outliers start: 19
  outliers final: 9
  residues processed: 156
  average time/residue: 1.1618
  time to fit residues: 192.5991
Evaluate side-chains
  156 residues out of total 937 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 145
  time to evaluate  : 0.841 
-------------------------------------------------------------------------------
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  201 SER
Chi-restraints excluded: chain R residue  207 VAL
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:    0.9980
   chunk 39 optimal weight:    2.9990
   chunk 42 optimal weight:    2.9990
   chunk 9 optimal weight:    1.9990
   chunk 8 optimal weight:    2.9990
   chunk 56 optimal weight:    4.9990
   chunk 54 optimal weight:    1.9990
   chunk 106 optimal weight:    2.9990
   chunk 102 optimal weight:    1.9990
   overall best weight:    1.7988

-------------------------------------------------------------------------------
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 = 0.3348 r_free = 0.3348 target = 0.104663 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3136 r_free = 0.3136 target = 0.091129 restraints weight = 12175.211|
|-----------------------------------------------------------------------------|
r_work (start): 0.3142 rms_B_bonded: 1.86
r_work: 0.3033 rms_B_bonded: 2.21 restraints_weight: 0.5000
r_work: 0.2895 rms_B_bonded: 3.88 restraints_weight: 0.2500
r_work (final): 0.2895
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7988
moved from start:          0.1765

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.007   0.056   8333  Z= 0.449
  Angle     :  0.694   8.074  11349  Z= 0.365
  Chirality :  0.048   0.148   1323
  Planarity :  0.005   0.048   1426
  Dihedral  :  4.608  24.179   1182
  Min Nonbonded Distance : 2.578

Molprobity Statistics.
  All-atom Clashscore : 2.77
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.39 %
    Favored  : 95.61 %
  Rotamer:
    Outliers :  3.42 %
    Allowed  : 16.12 %
    Favored  : 80.46 %
  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:  0.69 (0.27), residues: 1070
  helix:  2.43 (0.29), residues: 373
  sheet:  0.69 (0.31), residues: 276
  loop : -1.63 (0.28), residues: 421

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.002   TRP R 243 
 HIS   0.010   0.002   HIS C  54 
 PHE   0.022   0.002   PHE C 151 
 TYR   0.020   0.002   TYR E 178 
 ARG   0.011   0.001   ARG B 194 

*********************** 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
  179 residues out of total 937 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 151
  time to evaluate  : 1.110 
Fit side-chains
REVERT: B   10 LYS cc_start: 0.8273 (mtpp) cc_final: 0.7965 (mttm)
REVERT: B  195 LYS cc_start: 0.7726 (ttpt) cc_final: 0.7339 (ttpt)
REVERT: C   23 LYS cc_start: 0.8360 (ttpt) cc_final: 0.8048 (ttpt)
REVERT: C  165 THR cc_start: 0.8484 (OUTLIER) cc_final: 0.8175 (p)
REVERT: C  256 ARG cc_start: 0.8691 (OUTLIER) cc_final: 0.7105 (mtt180)
REVERT: R  272 SER cc_start: 0.8236 (OUTLIER) cc_final: 0.7923 (t)
REVERT: E    3 GLN cc_start: 0.8550 (mt0) cc_final: 0.8300 (mt0)
REVERT: E   93 MET cc_start: 0.8501 (ttp) cc_final: 0.8223 (ttt)
REVERT: E  179 ARG cc_start: 0.8740 (OUTLIER) cc_final: 0.7371 (mtp180)
REVERT: E  201 THR cc_start: 0.8272 (t) cc_final: 0.8036 (p)
REVERT: E  211 ASP cc_start: 0.7677 (t0) cc_final: 0.7284 (t0)
  outliers start: 28
  outliers final: 15
  residues processed: 163
  average time/residue: 1.3558
  time to fit residues: 235.3085
Evaluate side-chains
  167 residues out of total 937 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 148
  time to evaluate  : 0.918 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   75 GLN
Chi-restraints excluded: chain B residue   79 VAL
Chi-restraints excluded: chain B residue   83 MET
Chi-restraints excluded: chain C residue   18 ILE
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  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  245 LEU
Chi-restraints excluded: chain R residue  272 SER
Chi-restraints excluded: chain R residue  277 ILE
Chi-restraints excluded: chain E residue  128 MET
Chi-restraints excluded: chain E residue  179 ARG
Chi-restraints excluded: chain E residue  181 SER
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 81 optimal weight:    0.4980
   chunk 100 optimal weight:    0.9990
   chunk 21 optimal weight:    0.0470
   chunk 28 optimal weight:    1.9990
   chunk 49 optimal weight:    0.7980
   chunk 51 optimal weight:    0.9980
   chunk 64 optimal weight:    0.9980
   chunk 98 optimal weight:    5.9990
   chunk 65 optimal weight:    0.9980
   chunk 18 optimal weight:    1.9990
   chunk 84 optimal weight:    0.0870
   overall best weight:    0.4856

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

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

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3424 r_free = 0.3424 target = 0.109620 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3212 r_free = 0.3212 target = 0.095791 restraints weight = 12060.655|
|-----------------------------------------------------------------------------|
r_work (start): 0.3213 rms_B_bonded: 1.85
r_work: 0.3110 rms_B_bonded: 2.22 restraints_weight: 0.5000
r_work: 0.2974 rms_B_bonded: 3.90 restraints_weight: 0.2500
r_work (final): 0.2974
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7932
moved from start:          0.2177

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   8333  Z= 0.169
  Angle     :  0.527   6.400  11349  Z= 0.280
  Chirality :  0.041   0.137   1323
  Planarity :  0.004   0.038   1426
  Dihedral  :  4.101  22.903   1182
  Min Nonbonded Distance : 2.559

Molprobity Statistics.
  All-atom Clashscore : 2.96
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.43 %
    Favored  : 97.57 %
  Rotamer:
    Outliers :  2.56 %
    Allowed  : 17.83 %
    Favored  : 79.61 %
  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:  2.90 (0.29), residues: 363
  sheet:  0.78 (0.31), residues: 288
  loop : -1.47 (0.28), residues: 419

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP C  63 
 HIS   0.004   0.001   HIS C  54 
 PHE   0.011   0.001   PHE C 241 
 TYR   0.010   0.001   TYR E 178 
 ARG   0.003   0.000   ARG B  32 

*********************** 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
  175 residues out of total 937 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 154
  time to evaluate  : 0.806 
Fit side-chains
REVERT: B   10 LYS cc_start: 0.7895 (mtpp) cc_final: 0.7649 (mttm)
REVERT: B  195 LYS cc_start: 0.7734 (ttpt) cc_final: 0.7329 (ttpt)
REVERT: C   23 LYS cc_start: 0.8349 (ttpt) cc_final: 0.8035 (ttpt)
REVERT: C   72 SER cc_start: 0.8689 (m) cc_final: 0.8485 (p)
REVERT: C  165 THR cc_start: 0.8436 (OUTLIER) cc_final: 0.8208 (p)
REVERT: C  256 ARG cc_start: 0.8664 (OUTLIER) cc_final: 0.7167 (mtt180)
REVERT: R   55 LEU cc_start: 0.8288 (mt) cc_final: 0.7996 (mt)
REVERT: R  272 SER cc_start: 0.8154 (OUTLIER) cc_final: 0.7929 (t)
REVERT: E    3 GLN cc_start: 0.8507 (mt0) cc_final: 0.8281 (mt0)
REVERT: E   93 MET cc_start: 0.8449 (ttp) cc_final: 0.8183 (ttt)
REVERT: E  179 ARG cc_start: 0.8607 (OUTLIER) cc_final: 0.6836 (mtp180)
REVERT: E  211 ASP cc_start: 0.7493 (t0) cc_final: 0.7137 (t0)
  outliers start: 21
  outliers final: 10
  residues processed: 161
  average time/residue: 1.1516
  time to fit residues: 197.0199
Evaluate side-chains
  163 residues out of total 937 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 149
  time to evaluate  : 0.882 
-------------------------------------------------------------------------------
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  256 ARG
Chi-restraints excluded: chain C residue  270 ILE
Chi-restraints excluded: chain R residue  201 SER
Chi-restraints excluded: chain R residue  245 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  179 ARG
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 66 optimal weight:    0.4980
   chunk 21 optimal weight:    0.9980
   chunk 100 optimal weight:    0.6980
   chunk 4 optimal weight:    2.9990
   chunk 104 optimal weight:    1.9990
   chunk 65 optimal weight:    1.9990
   chunk 42 optimal weight:    3.9990
   chunk 43 optimal weight:    0.2980
   chunk 28 optimal weight:    2.9990
   chunk 90 optimal weight:    0.7980
   chunk 97 optimal weight:    2.9990
   overall best weight:    0.6580

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

Flipped N/Q/H residues before XYZ refinement:
B 101 ASN
B 116 ASN
B 144 ASN
C 340 ASN
** R 275 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3411 r_free = 0.3411 target = 0.108766 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3197 r_free = 0.3197 target = 0.094821 restraints weight = 12171.714|
|-----------------------------------------------------------------------------|
r_work (start): 0.3197 rms_B_bonded: 1.92
r_work: 0.3088 rms_B_bonded: 2.30 restraints_weight: 0.5000
r_work: 0.2949 rms_B_bonded: 4.05 restraints_weight: 0.2500
r_work (final): 0.2949
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7918
moved from start:          0.2228

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   8333  Z= 0.193
  Angle     :  0.545   6.845  11349  Z= 0.288
  Chirality :  0.041   0.132   1323
  Planarity :  0.004   0.057   1426
  Dihedral  :  4.066  22.910   1182
  Min Nonbonded Distance : 2.599

Molprobity Statistics.
  All-atom Clashscore : 3.02
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.18 %
    Favored  : 96.82 %
  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:  1.16 (0.27), residues: 1070
  helix:  2.95 (0.29), residues: 367
  sheet:  0.80 (0.31), residues: 288
  loop : -1.37 (0.28), residues: 415

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP R 243 
 HIS   0.004   0.001   HIS E  35 
 PHE   0.012   0.001   PHE C 151 
 TYR   0.014   0.001   TYR E  95 
 ARG   0.014   0.000   ARG B 194 

*********************** 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: 20
    poor density    : 150
  time to evaluate  : 0.890 
Fit side-chains
REVERT: B   10 LYS cc_start: 0.7891 (mtpp) cc_final: 0.7633 (mttm)
REVERT: B   15 ARG cc_start: 0.8490 (ttt90) cc_final: 0.8214 (ttm-80)
REVERT: B  195 LYS cc_start: 0.7699 (ttpt) cc_final: 0.7377 (ttpt)
REVERT: C   23 LYS cc_start: 0.8306 (ttpt) cc_final: 0.7930 (ttmm)
REVERT: C   72 SER cc_start: 0.8706 (m) cc_final: 0.8462 (p)
REVERT: C  165 THR cc_start: 0.8425 (OUTLIER) cc_final: 0.8174 (p)
REVERT: R  272 SER cc_start: 0.8265 (OUTLIER) cc_final: 0.8008 (t)
REVERT: E    3 GLN cc_start: 0.8546 (mt0) cc_final: 0.8286 (mt0)
REVERT: E   93 MET cc_start: 0.8460 (ttp) cc_final: 0.8168 (ttt)
REVERT: E  179 ARG cc_start: 0.8567 (OUTLIER) cc_final: 0.6831 (mtp180)
REVERT: E  211 ASP cc_start: 0.7552 (t0) cc_final: 0.7190 (t0)
  outliers start: 20
  outliers final: 10
  residues processed: 158
  average time/residue: 1.3153
  time to fit residues: 220.2196
Evaluate side-chains
  157 residues out of total 937 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 144
  time to evaluate  : 0.879 
-------------------------------------------------------------------------------
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  270 ILE
Chi-restraints excluded: chain C residue  321 THR
Chi-restraints excluded: chain R residue  201 SER
Chi-restraints excluded: chain R residue  209 ILE
Chi-restraints excluded: chain R residue  245 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  179 ARG
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 32 optimal weight:    0.0970
   chunk 2 optimal weight:    0.4980
   chunk 22 optimal weight:    5.9990
   chunk 69 optimal weight:    0.5980
   chunk 101 optimal weight:    0.8980
   chunk 6 optimal weight:    0.3980
   chunk 47 optimal weight:    1.9990
   chunk 68 optimal weight:    0.9980
   chunk 63 optimal weight:    0.9990
   chunk 39 optimal weight:    1.9990
   chunk 9 optimal weight:    0.9990
   overall best weight:    0.4978

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

Flipped N/Q/H residues before XYZ refinement:
B 101 ASN
B 116 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 = 0.3431 r_free = 0.3431 target = 0.110136 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3217 r_free = 0.3217 target = 0.096052 restraints weight = 12356.523|
|-----------------------------------------------------------------------------|
r_work (start): 0.3220 rms_B_bonded: 1.94
r_work: 0.3112 rms_B_bonded: 2.33 restraints_weight: 0.5000
r_work: 0.2974 rms_B_bonded: 4.09 restraints_weight: 0.2500
r_work (final): 0.2974
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7901
moved from start:          0.2416

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   8333  Z= 0.161
  Angle     :  0.520   7.002  11349  Z= 0.274
  Chirality :  0.041   0.129   1323
  Planarity :  0.004   0.036   1426
  Dihedral  :  3.917  22.877   1182
  Min Nonbonded Distance : 2.579

Molprobity Statistics.
  All-atom Clashscore : 2.96
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.80 %
    Favored  : 97.20 %
  Rotamer:
    Outliers :  2.20 %
    Allowed  : 18.80 %
    Favored  : 79.00 %
  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: 365
  sheet:  0.80 (0.31), residues: 288
  loop : -1.30 (0.28), residues: 417

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   0.011   0.001   PHE R  64 
 TYR   0.013   0.001   TYR B 163 
 ARG   0.008   0.000   ARG B 194 

*********************** 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
  166 residues out of total 937 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 148
  time to evaluate  : 1.030 
Fit side-chains
REVERT: B   10 LYS cc_start: 0.7725 (mtpp) cc_final: 0.7480 (mttm)
REVERT: B  195 LYS cc_start: 0.7654 (ttpt) cc_final: 0.7259 (ttpt)
REVERT: C   23 LYS cc_start: 0.8293 (ttpt) cc_final: 0.7920 (ttmm)
REVERT: C   72 SER cc_start: 0.8712 (m) cc_final: 0.8458 (p)
REVERT: C  165 THR cc_start: 0.8416 (OUTLIER) cc_final: 0.8180 (p)
REVERT: R  272 SER cc_start: 0.8275 (OUTLIER) cc_final: 0.8030 (t)
REVERT: E   51 ILE cc_start: 0.8477 (OUTLIER) cc_final: 0.8061 (tp)
REVERT: E   78 THR cc_start: 0.8333 (OUTLIER) cc_final: 0.7993 (t)
REVERT: E   93 MET cc_start: 0.8451 (ttp) cc_final: 0.8174 (ttt)
REVERT: E  179 ARG cc_start: 0.8482 (OUTLIER) cc_final: 0.6763 (mtp180)
REVERT: E  211 ASP cc_start: 0.7519 (t0) cc_final: 0.7146 (t0)
  outliers start: 18
  outliers final: 9
  residues processed: 155
  average time/residue: 1.2020
  time to fit residues: 197.8137
Evaluate side-chains
  157 residues out of total 937 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 143
  time to evaluate  : 0.896 
-------------------------------------------------------------------------------
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  270 ILE
Chi-restraints excluded: chain C residue  321 THR
Chi-restraints excluded: chain R residue  201 SER
Chi-restraints excluded: chain R residue  234 LEU
Chi-restraints excluded: chain R residue  245 LEU
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  179 ARG
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 68 optimal weight:    0.8980
   chunk 88 optimal weight:    3.9990
   chunk 98 optimal weight:    3.9990
   chunk 62 optimal weight:    0.7980
   chunk 10 optimal weight:    1.9990
   chunk 4 optimal weight:    2.9990
   chunk 71 optimal weight:    0.0000
   chunk 50 optimal weight:    0.9990
   chunk 7 optimal weight:    0.9980
   chunk 99 optimal weight:    4.9990
   chunk 48 optimal weight:    0.0970
   overall best weight:    0.5582

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

Flipped N/Q/H residues before XYZ refinement:
B 101 ASN
B 116 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 = 0.3426 r_free = 0.3426 target = 0.109866 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3215 r_free = 0.3215 target = 0.095973 restraints weight = 12401.309|
|-----------------------------------------------------------------------------|
r_work (start): 0.3215 rms_B_bonded: 1.89
r_work: 0.3110 rms_B_bonded: 2.27 restraints_weight: 0.5000
r_work: 0.2974 rms_B_bonded: 4.00 restraints_weight: 0.2500
r_work (final): 0.2974
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7922
moved from start:          0.2437

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   8333  Z= 0.171
  Angle     :  0.529   7.277  11349  Z= 0.278
  Chirality :  0.041   0.132   1323
  Planarity :  0.004   0.063   1426
  Dihedral  :  3.923  23.076   1182
  Min Nonbonded Distance : 2.589

Molprobity Statistics.
  All-atom Clashscore : 3.28
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.90 %
    Favored  : 97.10 %
  Rotamer:
    Outliers :  2.32 %
    Allowed  : 19.54 %
    Favored  : 78.14 %
  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:  3.11 (0.29), residues: 367
  sheet:  0.81 (0.31), residues: 288
  loop : -1.30 (0.28), residues: 415

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP C 339 
 HIS   0.003   0.001   HIS E  35 
 PHE   0.012   0.001   PHE C 151 
 TYR   0.012   0.001   TYR E 178 
 ARG   0.016   0.000   ARG B 194 

*********************** 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
  166 residues out of total 937 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 147
  time to evaluate  : 0.911 
Fit side-chains
REVERT: B   10 LYS cc_start: 0.7802 (mtpp) cc_final: 0.7596 (mttm)
REVERT: B  195 LYS cc_start: 0.7657 (ttpt) cc_final: 0.7352 (ttpt)
REVERT: C   23 LYS cc_start: 0.8362 (ttpt) cc_final: 0.8007 (ttmm)
REVERT: C   72 SER cc_start: 0.8692 (m) cc_final: 0.8471 (p)
REVERT: C  165 THR cc_start: 0.8421 (OUTLIER) cc_final: 0.8195 (p)
REVERT: C  312 ASP cc_start: 0.7961 (t0) cc_final: 0.7738 (t70)
REVERT: R  272 SER cc_start: 0.8259 (OUTLIER) cc_final: 0.8012 (t)
REVERT: E   51 ILE cc_start: 0.8497 (OUTLIER) cc_final: 0.8085 (tp)
REVERT: E   78 THR cc_start: 0.8348 (OUTLIER) cc_final: 0.8033 (t)
REVERT: E   93 MET cc_start: 0.8471 (ttp) cc_final: 0.8206 (ttt)
REVERT: E  179 ARG cc_start: 0.8491 (OUTLIER) cc_final: 0.6685 (mtp180)
REVERT: E  211 ASP cc_start: 0.7508 (t0) cc_final: 0.7143 (t0)
  outliers start: 19
  outliers final: 10
  residues processed: 156
  average time/residue: 1.2095
  time to fit residues: 199.8952
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  : 0.769 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   75 GLN
Chi-restraints excluded: chain B residue  117 ARG
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  234 LEU
Chi-restraints excluded: chain R residue  245 LEU
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:    2.9990
   chunk 87 optimal weight:    2.9990
   chunk 56 optimal weight:    0.4980
   chunk 80 optimal weight:    0.9980
   chunk 27 optimal weight:    4.9990
   chunk 43 optimal weight:    2.9990
   chunk 81 optimal weight:    0.7980
   chunk 45 optimal weight:    0.7980
   chunk 60 optimal weight:    0.8980
   chunk 48 optimal weight:    3.9990
   chunk 3 optimal weight:    0.5980
   overall best weight:    0.7180

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

Flipped N/Q/H residues before XYZ refinement:
B 101 ASN
B 116 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 = 0.108817 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3197 r_free = 0.3197 target = 0.094824 restraints weight = 12160.611|
|-----------------------------------------------------------------------------|
r_work (start): 0.3198 rms_B_bonded: 1.93
r_work: 0.3089 rms_B_bonded: 2.30 restraints_weight: 0.5000
r_work: 0.2952 rms_B_bonded: 4.05 restraints_weight: 0.2500
r_work (final): 0.2952
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7918
moved from start:          0.2392

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038   8333  Z= 0.201
  Angle     :  0.551   7.585  11349  Z= 0.289
  Chirality :  0.042   0.133   1323
  Planarity :  0.004   0.063   1426
  Dihedral  :  4.015  23.658   1182
  Min Nonbonded Distance : 2.586

Molprobity Statistics.
  All-atom Clashscore : 3.09
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.08 %
    Favored  : 96.92 %
  Rotamer:
    Outliers :  2.08 %
    Allowed  : 19.90 %
    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:  1.29 (0.27), residues: 1070
  helix:  3.09 (0.29), residues: 367
  sheet:  0.83 (0.31), residues: 288
  loop : -1.30 (0.28), residues: 415

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP C 339 
 HIS   0.004   0.001   HIS E  35 
 PHE   0.013   0.001   PHE C 151 
 TYR   0.013   0.001   TYR E 178 
 ARG   0.016   0.000   ARG B 194 

********************** 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
  156 residues out of total 937 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 139
  time to evaluate  : 0.788 
Fit side-chains
REVERT: B   10 LYS cc_start: 0.7899 (mtpp) cc_final: 0.7669 (mttm)
REVERT: B   15 ARG cc_start: 0.8502 (ttt90) cc_final: 0.8241 (ttm-80)
REVERT: B  195 LYS cc_start: 0.7682 (ttpt) cc_final: 0.7086 (ttpt)
REVERT: B  199 ASP cc_start: 0.7609 (p0) cc_final: 0.7304 (p0)
REVERT: C   23 LYS cc_start: 0.8334 (ttpt) cc_final: 0.7968 (ttmm)
REVERT: C   72 SER cc_start: 0.8714 (m) cc_final: 0.8458 (p)
REVERT: C  165 THR cc_start: 0.8438 (OUTLIER) cc_final: 0.8156 (p)
REVERT: C  312 ASP cc_start: 0.7957 (t0) cc_final: 0.7728 (t70)
REVERT: R  272 SER cc_start: 0.8266 (OUTLIER) cc_final: 0.7996 (t)
REVERT: E    3 GLN cc_start: 0.8549 (mt0) cc_final: 0.8294 (mt0)
REVERT: E   78 THR cc_start: 0.8338 (OUTLIER) cc_final: 0.8018 (t)
REVERT: E   93 MET cc_start: 0.8467 (ttp) cc_final: 0.8177 (ttt)
REVERT: E  179 ARG cc_start: 0.8508 (OUTLIER) cc_final: 0.6795 (mtp180)
REVERT: E  211 ASP cc_start: 0.7578 (t0) cc_final: 0.7195 (t0)
  outliers start: 17
  outliers final: 9
  residues processed: 147
  average time/residue: 1.2329
  time to fit residues: 192.1670
Evaluate side-chains
  149 residues out of total 937 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 136
  time to evaluate  : 0.807 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   28 GLU
Chi-restraints excluded: chain B residue   75 GLN
Chi-restraints excluded: chain B residue  117 ARG
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   54 LEU
Chi-restraints excluded: chain R residue  201 SER
Chi-restraints excluded: chain R residue  245 LEU
Chi-restraints excluded: chain R residue  272 SER
Chi-restraints excluded: chain E residue   78 THR
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:    0.9990
   chunk 10 optimal weight:    1.9990
   chunk 0 optimal weight:    4.9990
   chunk 62 optimal weight:    0.9990
   chunk 91 optimal weight:    2.9990
   chunk 53 optimal weight:    1.9990
   chunk 89 optimal weight:    0.7980
   chunk 55 optimal weight:    1.9990
   chunk 2 optimal weight:    4.9990
   chunk 13 optimal weight:    3.9990
   chunk 26 optimal weight:    1.9990
   overall best weight:    1.3588

-------------------------------------------------------------------------------
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 ** both conformations clash, **PLEASE CHECK MANUALLY**
B 116 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 = 0.3368 r_free = 0.3368 target = 0.105841 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3152 r_free = 0.3152 target = 0.092065 restraints weight = 12311.278|
|-----------------------------------------------------------------------------|
r_work (start): 0.3153 rms_B_bonded: 1.93
r_work: 0.3042 rms_B_bonded: 2.29 restraints_weight: 0.5000
r_work: 0.2904 rms_B_bonded: 4.00 restraints_weight: 0.2500
r_work (final): 0.2904
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7960
moved from start:          0.2191

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.048   8333  Z= 0.342
  Angle     :  0.633   7.860  11349  Z= 0.333
  Chirality :  0.045   0.148   1323
  Planarity :  0.004   0.069   1426
  Dihedral  :  4.359  23.760   1182
  Min Nonbonded Distance : 2.539

Molprobity Statistics.
  All-atom Clashscore : 3.02
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.49 %
    Favored  : 95.51 %
  Rotamer:
    Outliers :  1.83 %
    Allowed  : 20.63 %
    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:  1.11 (0.27), residues: 1070
  helix:  2.90 (0.29), residues: 367
  sheet:  0.72 (0.31), residues: 291
  loop : -1.36 (0.28), residues: 412

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.002   TRP C 339 
 HIS   0.007   0.002   HIS C  54 
 PHE   0.019   0.002   PHE C 234 
 TYR   0.019   0.002   TYR E 178 
 ARG   0.017   0.001   ARG B 194 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 6533.20 seconds
wall clock time: 112 minutes 49.68 seconds (6769.68 seconds total)