Starting phenix.real_space_refine
on Thu Mar 13 06:35:21 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7o0z_12684/03_2025/7o0z_12684.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7o0z_12684/03_2025/7o0z_12684.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.7
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7o0z_12684/03_2025/7o0z_12684.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7o0z_12684/03_2025/7o0z_12684.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7o0z_12684/03_2025/7o0z_12684.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7o0z_12684/03_2025/7o0z_12684.cif"
  }
  resolution = 3.7
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=  -0.000 sd=   0.003
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      26      5.16       5
     C    5649      2.51       5
     N    1516      2.21       5
     O    1539      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 26 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: 8730
  Number of models: 1
  Model: ""
    Number of chains: 4
    Chain: "B"
      Number of atoms: 2367
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 307, 2367
          Classifications: {'peptide': 307}
          Link IDs: {'PTRANS': 12, 'TRANS': 294}
    Chain: "C"
      Number of atoms: 2367
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 307, 2367
          Classifications: {'peptide': 307}
          Link IDs: {'PTRANS': 12, 'TRANS': 294}
    Chain: "D"
      Number of atoms: 1999
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 264, 1999
          Classifications: {'peptide': 264}
          Link IDs: {'PTRANS': 8, 'TRANS': 255}
          Chain breaks: 2
    Chain: "E"
      Number of atoms: 1997
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 264, 1997
          Classifications: {'peptide': 264}
          Incomplete info: {'truncation_to_alanine': 1}
          Link IDs: {'PTRANS': 8, 'TRANS': 255}
          Chain breaks: 2
          Unresolved non-hydrogen bonds: 1
          Unresolved non-hydrogen angles: 1
          Unresolved non-hydrogen dihedrals: 1
  Time building chain proxies: 5.21, per 1000 atoms: 0.60
  Number of scatterers: 8730
  At special positions: 0
  Unit cell: (84.132, 103.626, 123.12, 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      26     16.00
     O    1539      8.00
     N    1516      7.00
     C    5649      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 2.03
  Conformation dependent library (CDL) restraints added in 1.0 seconds
  

  2252 Ramachandran restraints generated.
    1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2050

  Finding SS restraints...
    Secondary structure from input PDB file:
      50 helices and 7 sheets defined
      59.9% alpha, 8.8% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.89
  Creating SS restraints...
    Processing helix  chain 'B' and resid 39 through 42
      removed outlier: 3.903A  pdb=" N   LYS B  42 " --> pdb=" O   GLY B  39 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 39 through 42'
    Processing helix  chain 'B' and resid 43 through 50
      removed outlier: 3.737A  pdb=" N   LEU B  50 " --> pdb=" O   MET B  46 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 69 through 74
    Processing helix  chain 'B' and resid 90 through 103
      removed outlier: 3.551A  pdb=" N   LEU B  95 " --> pdb=" O   GLY B  91 " (cutoff:3.500A)
      removed outlier: 3.718A  pdb=" N   ARG B 100 " --> pdb=" O   ARG B  96 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 106 through 116
      removed outlier: 4.536A  pdb=" N   ASP B 110 " --> pdb=" O   LEU B 106 " (cutoff:3.500A)
      removed outlier: 4.000A  pdb=" N   GLU B 111 " --> pdb=" O   THR B 107 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 130 through 143
      removed outlier: 3.596A  pdb=" N   LEU B 137 " --> pdb=" O   MET B 133 " (cutoff:3.500A)
      removed outlier: 3.876A  pdb=" N   ALA B 142 " --> pdb=" O   GLY B 138 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 160 through 177
      removed outlier: 3.820A  pdb=" N   GLN B 165 " --> pdb=" O   PRO B 161 " (cutoff:3.500A)
      removed outlier: 3.609A  pdb=" N   ASP B 166 " --> pdb=" O   ILE B 162 " (cutoff:3.500A)
      removed outlier: 3.672A  pdb=" N   LEU B 167 " --> pdb=" O   ALA B 163 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 211 through 219
      removed outlier: 3.507A  pdb=" N   ARG B 216 " --> pdb=" O   LEU B 212 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 234 through 242
      removed outlier: 3.699A  pdb=" N   ARG B 239 " --> pdb=" O   SER B 235 " (cutoff:3.500A)
      removed outlier: 4.977A  pdb=" N   TRP B 240 " --> pdb=" O   TRP B 236 " (cutoff:3.500A)
      removed outlier: 4.077A  pdb=" N   THR B 241 " --> pdb=" O   LEU B 237 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 263 through 269
    Processing helix  chain 'B' and resid 286 through 298
      removed outlier: 3.522A  pdb=" N   MET B 295 " --> pdb=" O   TYR B 291 " (cutoff:3.500A)
      removed outlier: 3.986A  pdb=" N   GLU B 296 " --> pdb=" O   ARG B 292 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 40 through 50
      removed outlier: 3.514A  pdb=" N   THR C  44 " --> pdb=" O   ALA C  40 " (cutoff:3.500A)
      removed outlier: 3.532A  pdb=" N   SER C  45 " --> pdb=" O   GLY C  41 " (cutoff:3.500A)
      removed outlier: 3.602A  pdb=" N   LEU C  50 " --> pdb=" O   MET C  46 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 90 through 103
      removed outlier: 3.660A  pdb=" N   LEU C  95 " --> pdb=" O   GLY C  91 " (cutoff:3.500A)
      removed outlier: 3.520A  pdb=" N   PHE C  98 " --> pdb=" O   THR C  94 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 108 through 116
    Processing helix  chain 'C' and resid 125 through 129
    Processing helix  chain 'C' and resid 130 through 143
      removed outlier: 3.504A  pdb=" N   ALA C 140 " --> pdb=" O   ARG C 136 " (cutoff:3.500A)
      removed outlier: 3.699A  pdb=" N   ALA C 142 " --> pdb=" O   GLY C 138 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 160 through 176
      removed outlier: 3.513A  pdb=" N   GLN C 165 " --> pdb=" O   PRO C 161 " (cutoff:3.500A)
      removed outlier: 3.836A  pdb=" N   TYR C 168 " --> pdb=" O   THR C 164 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 190 through 194
      removed outlier: 3.622A  pdb=" N   ALA C 193 " --> pdb=" O   GLY C 190 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 211 through 219
    Processing helix  chain 'C' and resid 232 through 241
      removed outlier: 4.039A  pdb=" N   TRP C 236 " --> pdb=" O   GLU C 232 " (cutoff:3.500A)
      removed outlier: 3.685A  pdb=" N   ARG C 239 " --> pdb=" O   SER C 235 " (cutoff:3.500A)
      removed outlier: 3.710A  pdb=" N   THR C 241 " --> pdb=" O   LEU C 237 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 267 through 274
      removed outlier: 3.764A  pdb=" N   LEU C 271 " --> pdb=" O   LEU C 267 " (cutoff:3.500A)
      removed outlier: 3.504A  pdb=" N   GLY C 273 " --> pdb=" O   ARG C 269 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 286 through 299
      removed outlier: 4.065A  pdb=" N   ALA C 298 " --> pdb=" O   TYR C 294 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 303 through 307
      removed outlier: 4.256A  pdb=" N   GLY C 306 " --> pdb=" O   ALA C 303 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 3 through 16
      removed outlier: 3.757A  pdb=" N   LYS D  10 " --> pdb=" O   ASN D   6 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 18 through 43
      removed outlier: 3.619A  pdb=" N   ALA D  23 " --> pdb=" O   ARG D  19 " (cutoff:3.500A)
      removed outlier: 3.621A  pdb=" N   LEU D  26 " --> pdb=" O   LEU D  22 " (cutoff:3.500A)
      removed outlier: 3.653A  pdb=" N   SER D  43 " --> pdb=" O   GLY D  39 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 51 through 75
      removed outlier: 3.775A  pdb=" N   ILE D  55 " --> pdb=" O   ILE D  51 " (cutoff:3.500A)
      removed outlier: 3.545A  pdb=" N   SER D  60 " --> pdb=" O   ALA D  56 " (cutoff:3.500A)
      Proline residue:  D  67  - end of helix
      removed outlier: 3.527A  pdb=" N   ALA D  70 " --> pdb=" O   MET D  66 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 78 through 83
    Processing helix  chain 'D' and resid 85 through 91
      removed outlier: 3.598A  pdb=" N   LEU D  89 " --> pdb=" O   GLY D  85 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 98 through 131
      removed outlier: 3.959A  pdb=" N   ILE D 111 " --> pdb=" O   GLY D 107 " (cutoff:3.500A)
      removed outlier: 3.562A  pdb=" N   ILE D 118 " --> pdb=" O   LEU D 114 " (cutoff:3.500A)
      removed outlier: 3.784A  pdb=" N   GLY D 121 " --> pdb=" O   LEU D 117 " (cutoff:3.500A)
      removed outlier: 4.408A  pdb=" N   CYS D 122 " --> pdb=" O   ILE D 118 " (cutoff:3.500A)
      removed outlier: 3.701A  pdb=" N   ALA D 123 " --> pdb=" O   GLY D 119 " (cutoff:3.500A)
      removed outlier: 3.747A  pdb=" N   ILE D 127 " --> pdb=" O   ALA D 123 " (cutoff:3.500A)
      removed outlier: 4.197A  pdb=" N   ALA D 128 " --> pdb=" O   ALA D 124 " (cutoff:3.500A)
      removed outlier: 3.549A  pdb=" N   LEU D 129 " --> pdb=" O   LEU D 125 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 135 through 143
      removed outlier: 3.754A  pdb=" N   LEU D 139 " --> pdb=" O   GLU D 135 " (cutoff:3.500A)
      removed outlier: 4.025A  pdb=" N   PHE D 140 " --> pdb=" O   LEU D 136 " (cutoff:3.500A)
      removed outlier: 4.003A  pdb=" N   TRP D 141 " --> pdb=" O   GLY D 137 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 143 through 168
      removed outlier: 3.875A  pdb=" N   ILE D 148 " --> pdb=" O   GLY D 144 " (cutoff:3.500A)
      removed outlier: 3.870A  pdb=" N   SER D 149 " --> pdb=" O   ARG D 145 " (cutoff:3.500A)
      removed outlier: 3.677A  pdb=" N   THR D 151 " --> pdb=" O   MET D 147 " (cutoff:3.500A)
      removed outlier: 4.705A  pdb=" N   LEU D 152 " --> pdb=" O   ILE D 148 " (cutoff:3.500A)
      removed outlier: 3.739A  pdb=" N   VAL D 156 " --> pdb=" O   LEU D 152 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 170 through 188
      removed outlier: 3.537A  pdb=" N   GLY D 180 " --> pdb=" O   GLY D 176 " (cutoff:3.500A)
      removed outlier: 3.694A  pdb=" N   VAL D 186 " --> pdb=" O   TRP D 182 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 188 through 199
    Processing helix  chain 'D' and resid 209 through 214
      removed outlier: 4.010A  pdb=" N   LEU D 213 " --> pdb=" O   PRO D 210 " (cutoff:3.500A)
      removed outlier: 3.935A  pdb=" N   LEU D 214 " --> pdb=" O   TRP D 211 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 216 through 226
      removed outlier: 3.819A  pdb=" N   ILE D 220 " --> pdb=" O   ASN D 216 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 248 through 273
      removed outlier: 3.967A  pdb=" N   LEU D 254 " --> pdb=" O   ALA D 250 " (cutoff:3.500A)
      removed outlier: 3.893A  pdb=" N   LEU D 256 " --> pdb=" O   LEU D 252 " (cutoff:3.500A)
      removed outlier: 3.894A  pdb=" N   SER D 263 " --> pdb=" O   TRP D 259 " (cutoff:3.500A)
      removed outlier: 3.508A  pdb=" N   LEU D 265 " --> pdb=" O   GLY D 261 " (cutoff:3.500A)
      removed outlier: 4.006A  pdb=" N   ALA D 267 " --> pdb=" O   SER D 263 " (cutoff:3.500A)
      removed outlier: 3.925A  pdb=" N   ARG D 273 " --> pdb=" O   ALA D 269 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 3 through 17
      removed outlier: 4.049A  pdb=" N   LYS E  10 " --> pdb=" O   ASN E   6 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 18 through 41
      removed outlier: 3.526A  pdb=" N   LEU E  22 " --> pdb=" O   ASN E  18 " (cutoff:3.500A)
      removed outlier: 3.507A  pdb=" N   LEU E  38 " --> pdb=" O   GLY E  34 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 51 through 75
      removed outlier: 4.213A  pdb=" N   ALA E  56 " --> pdb=" O   PRO E  52 " (cutoff:3.500A)
      removed outlier: 4.723A  pdb=" N   SER E  57 " --> pdb=" O   ALA E  53 " (cutoff:3.500A)
      removed outlier: 3.519A  pdb=" N   ALA E  62 " --> pdb=" O   LEU E  58 " (cutoff:3.500A)
      removed outlier: 4.026A  pdb=" N   PHE E  64 " --> pdb=" O   SER E  60 " (cutoff:3.500A)
      Proline residue:  E  67  - end of helix
    Processing helix  chain 'E' and resid 78 through 85
      removed outlier: 3.705A  pdb=" N   GLY E  84 " --> pdb=" O   GLY E  80 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 85 through 93
      removed outlier: 3.755A  pdb=" N   THR E  92 " --> pdb=" O   MET E  88 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 97 through 132
      removed outlier: 3.511A  pdb=" N   LEU E 101 " --> pdb=" O   ARG E  97 " (cutoff:3.500A)
      removed outlier: 4.010A  pdb=" N   ILE E 111 " --> pdb=" O   GLY E 107 " (cutoff:3.500A)
      removed outlier: 3.509A  pdb=" N   LEU E 112 " --> pdb=" O   HIS E 108 " (cutoff:3.500A)
      removed outlier: 4.018A  pdb=" N   GLY E 121 " --> pdb=" O   LEU E 117 " (cutoff:3.500A)
      removed outlier: 4.360A  pdb=" N   CYS E 122 " --> pdb=" O   ILE E 118 " (cutoff:3.500A)
      removed outlier: 3.573A  pdb=" N   ALA E 123 " --> pdb=" O   GLY E 119 " (cutoff:3.500A)
      removed outlier: 3.544A  pdb=" N   LEU E 125 " --> pdb=" O   GLY E 121 " (cutoff:3.500A)
      removed outlier: 3.899A  pdb=" N   GLU E 132 " --> pdb=" O   ALA E 128 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 135 through 138
    Processing helix  chain 'E' and resid 139 through 168
      removed outlier: 4.022A  pdb=" N   ARG E 145 " --> pdb=" O   TRP E 141 " (cutoff:3.500A)
      removed outlier: 3.963A  pdb=" N   ILE E 148 " --> pdb=" O   GLY E 144 " (cutoff:3.500A)
      removed outlier: 4.350A  pdb=" N   SER E 149 " --> pdb=" O   ARG E 145 " (cutoff:3.500A)
      removed outlier: 3.774A  pdb=" N   VAL E 156 " --> pdb=" O   LEU E 152 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 170 through 188
      removed outlier: 3.562A  pdb=" N   GLY E 176 " --> pdb=" O   SER E 172 " (cutoff:3.500A)
      removed outlier: 3.526A  pdb=" N   GLY E 180 " --> pdb=" O   GLY E 176 " (cutoff:3.500A)
      removed outlier: 3.625A  pdb=" N   VAL E 186 " --> pdb=" O   TRP E 182 " (cutoff:3.500A)
      removed outlier: 3.567A  pdb=" N   VAL E 188 " --> pdb=" O   LEU E 184 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 190 through 200
      removed outlier: 3.758A  pdb=" N   ALA E 195 " --> pdb=" O   LEU E 191 " (cutoff:3.500A)
      removed outlier: 3.719A  pdb=" N   VAL E 198 " --> pdb=" O   LEU E 194 " (cutoff:3.500A)
      removed outlier: 3.577A  pdb=" N   SER E 200 " --> pdb=" O   LEU E 196 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 209 through 213
      removed outlier: 3.865A  pdb=" N   LEU E 212 " --> pdb=" O   LEU E 209 " (cutoff:3.500A)
      removed outlier: 3.632A  pdb=" N   LEU E 213 " --> pdb=" O   PRO E 210 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'E' and resid 209 through 213'
    Processing helix  chain 'E' and resid 216 through 225
      removed outlier: 3.512A  pdb=" N   ASN E 225 " --> pdb=" O   TYR E 221 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 237 through 245
      removed outlier: 3.659A  pdb=" N   SER E 240 " --> pdb=" O   GLY E 237 " (cutoff:3.500A)
      removed outlier: 3.614A  pdb=" N   LEU E 241 " --> pdb=" O   VAL E 238 " (cutoff:3.500A)
      removed outlier: 3.549A  pdb=" N   GLY E 242 " --> pdb=" O   LEU E 239 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 249 through 272
      removed outlier: 3.508A  pdb=" N   LEU E 254 " --> pdb=" O   ALA E 250 " (cutoff:3.500A)
      removed outlier: 3.994A  pdb=" N   LEU E 256 " --> pdb=" O   LEU E 252 " (cutoff:3.500A)
      removed outlier: 3.679A  pdb=" N   ILE E 260 " --> pdb=" O   LEU E 256 " (cutoff:3.500A)
      removed outlier: 3.758A  pdb=" N   GLY E 261 " --> pdb=" O   LEU E 257 " (cutoff:3.500A)
      removed outlier: 3.788A  pdb=" N   SER E 263 " --> pdb=" O   TRP E 259 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'B' and resid 25 through 26
      removed outlier: 3.771A  pdb=" N   VAL B   4 " --> pdb=" O   LEU B  26 " (cutoff:3.500A)
      removed outlier: 4.182A  pdb=" N   GLN B  59 " --> pdb=" O   GLN B   7 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'B' and resid 9 through 12
      removed outlier: 5.380A  pdb=" N   VAL B   9 " --> pdb=" O   ASP B  21 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'B' and resid 76 through 79
      removed outlier: 6.174A  pdb=" N   LEU B 150 " --> pdb=" O   ILE B 182 " (cutoff:3.500A)
      removed outlier: 7.576A  pdb=" N   CYS B 184 " --> pdb=" O   LEU B 150 " (cutoff:3.500A)
      removed outlier: 6.481A  pdb=" N   LEU B 152 " --> pdb=" O   CYS B 184 " (cutoff:3.500A)
      removed outlier: 6.102A  pdb=" N   LEU B  32 " --> pdb=" O   LEU B 183 " (cutoff:3.500A)
      removed outlier: 6.473A  pdb=" N   GLY B  33 " --> pdb=" O   ALA B 199 " (cutoff:3.500A)
      removed outlier: 6.651A  pdb=" N   LEU B 201 " --> pdb=" O   GLY B  33 " (cutoff:3.500A)
      removed outlier: 5.762A  pdb=" N   PHE B  35 " --> pdb=" O   LEU B 201 " (cutoff:3.500A)
      removed outlier: 6.142A  pdb=" N   ALA B 202 " --> pdb=" O   LEU B 206 " (cutoff:3.500A)
      removed outlier: 4.956A  pdb=" N   LEU B 206 " --> pdb=" O   ALA B 202 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'B' and resid 246 through 250
      removed outlier: 3.576A  pdb=" N   LEU B 250 " --> pdb=" O   SER B 254 " (cutoff:3.500A)
      removed outlier: 3.534A  pdb=" N   SER B 254 " --> pdb=" O   LEU B 250 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'C' and resid 22 through 26
      removed outlier: 5.468A  pdb=" N   LEU C  22 " --> pdb=" O   GLY C   8 " (cutoff:3.500A)
      removed outlier: 3.798A  pdb=" N   VAL C   4 " --> pdb=" O   LEU C  26 " (cutoff:3.500A)
      removed outlier: 3.979A  pdb=" N   GLN C  59 " --> pdb=" O   GLN C   7 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'C' and resid 149 through 153
      removed outlier: 6.468A  pdb=" N   LEU C  32 " --> pdb=" O   LEU C 183 " (cutoff:3.500A)
      removed outlier: 6.345A  pdb=" N   VAL C  31 " --> pdb=" O   ARG C 197 " (cutoff:3.500A)
      removed outlier: 7.715A  pdb=" N   ALA C 199 " --> pdb=" O   VAL C  31 " (cutoff:3.500A)
      removed outlier: 6.255A  pdb=" N   GLY C  33 " --> pdb=" O   ALA C 199 " (cutoff:3.500A)
      removed outlier: 6.978A  pdb=" N   LEU C 201 " --> pdb=" O   GLY C  33 " (cutoff:3.500A)
      removed outlier: 6.074A  pdb=" N   PHE C  35 " --> pdb=" O   LEU C 201 " (cutoff:3.500A)
      removed outlier: 6.148A  pdb=" N   ALA C 202 " --> pdb=" O   LEU C 206 " (cutoff:3.500A)
      removed outlier: 4.856A  pdb=" N   LEU C 206 " --> pdb=" O   ALA C 202 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'C' and resid 248 through 251
      removed outlier: 3.550A  pdb=" N   ARG C 248 " --> pdb=" O   GLU C 256 " (cutoff:3.500A)
      removed outlier: 6.521A  pdb=" N   SER C 254 " --> pdb=" O   LEU C 250 " (cutoff:3.500A)

    432 hydrogen bonds defined for protein.
    1254 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 2.25

  Time building geometry restraints manager: 2.44 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: 2832
        1.34 -     1.46: 1611
        1.46 -     1.57: 4401
        1.57 -     1.69: 0
        1.69 -     1.80: 44
  Bond restraints: 8888
  Sorted by residual:
  bond pdb=" C   LEU D 209 "
       pdb=" N   PRO D 210 "
    ideal  model  delta    sigma   weight residual
    1.337  1.363 -0.026 1.11e-02 8.12e+03 5.66e+00
  bond pdb=" CB  ASN C  38 "
       pdb=" CG  ASN C  38 "
    ideal  model  delta    sigma   weight residual
    1.516  1.565 -0.049 2.50e-02 1.60e+03 3.87e+00
  bond pdb=" C   ILE E  51 "
       pdb=" N   PRO E  52 "
    ideal  model  delta    sigma   weight residual
    1.337  1.355 -0.019 1.06e-02 8.90e+03 3.17e+00
  bond pdb=" CG  LEU C 151 "
       pdb=" CD2 LEU C 151 "
    ideal  model  delta    sigma   weight residual
    1.521  1.464  0.057 3.30e-02 9.18e+02 3.03e+00
  bond pdb=" CA  LEU D 209 "
       pdb=" C   LEU D 209 "
    ideal  model  delta    sigma   weight residual
    1.522  1.544 -0.022 1.26e-02 6.30e+03 2.97e+00
  ... (remaining 8883 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     3.08: 11785
        3.08 -     6.16: 232
        6.16 -     9.25: 36
        9.25 -    12.33: 7
       12.33 -    15.41: 1
  Bond angle restraints: 12061
  Sorted by residual:
  angle pdb=" C   SER B 231 "
        pdb=" N   GLU B 232 "
        pdb=" CA  GLU B 232 "
      ideal   model   delta    sigma   weight residual
     121.54  133.07  -11.53 1.91e+00 2.74e-01 3.65e+01
  angle pdb=" C   GLU B  81 "
        pdb=" N   ASN B  82 "
        pdb=" CA  ASN B  82 "
      ideal   model   delta    sigma   weight residual
     121.54  132.26  -10.72 1.91e+00 2.74e-01 3.15e+01
  angle pdb=" CA  LEU C 188 "
        pdb=" CB  LEU C 188 "
        pdb=" CG  LEU C 188 "
      ideal   model   delta    sigma   weight residual
     116.30  131.71  -15.41 3.50e+00 8.16e-02 1.94e+01
  angle pdb=" C   VAL C 260 "
        pdb=" N   ASN C 261 "
        pdb=" CA  ASN C 261 "
      ideal   model   delta    sigma   weight residual
     124.31  131.61   -7.30 1.67e+00 3.59e-01 1.91e+01
  angle pdb=" C   GLN C 304 "
        pdb=" N   GLU C 305 "
        pdb=" CA  GLU C 305 "
      ideal   model   delta    sigma   weight residual
     121.54  129.86   -8.32 1.91e+00 2.74e-01 1.90e+01
  ... (remaining 12056 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    15.57: 4490
       15.57 -    31.13: 576
       31.13 -    46.70: 157
       46.70 -    62.26: 26
       62.26 -    77.83: 8
  Dihedral angle restraints: 5257
    sinusoidal: 2047
      harmonic: 3210
  Sorted by residual:
  dihedral pdb=" CA  GLU B 232 "
           pdb=" C   GLU B 232 "
           pdb=" N   ARG B 233 "
           pdb=" CA  ARG B 233 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  146.88   33.12     0      5.00e+00 4.00e-02 4.39e+01
  dihedral pdb=" CA  GLU B 305 "
           pdb=" C   GLU B 305 "
           pdb=" N   GLY B 306 "
           pdb=" CA  GLY B 306 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  156.39   23.61     0      5.00e+00 4.00e-02 2.23e+01
  dihedral pdb=" CA  MET E  66 "
           pdb=" C   MET E  66 "
           pdb=" N   PRO E  67 "
           pdb=" CA  PRO E  67 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  156.89   23.11     0      5.00e+00 4.00e-02 2.14e+01
  ... (remaining 5254 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.106: 1327
       0.106 -    0.212: 84
       0.212 -    0.317: 12
       0.317 -    0.423: 1
       0.423 -    0.529: 1
  Chirality restraints: 1425
  Sorted by residual:
  chirality pdb=" CB  ILE E  51 "
            pdb=" CA  ILE E  51 "
            pdb=" CG1 ILE E  51 "
            pdb=" CG2 ILE E  51 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.12    0.53 2.00e-01 2.50e+01 6.99e+00
  chirality pdb=" CB  VAL C 260 "
            pdb=" CA  VAL C 260 "
            pdb=" CG1 VAL C 260 "
            pdb=" CG2 VAL C 260 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -2.29   -0.34 2.00e-01 2.50e+01 2.94e+00
  chirality pdb=" CB  ILE B 200 "
            pdb=" CA  ILE B 200 "
            pdb=" CG1 ILE B 200 "
            pdb=" CG2 ILE B 200 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.37    0.28 2.00e-01 2.50e+01 1.91e+00
  ... (remaining 1422 not shown)

  Planarity restraints: 1520
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   MET E  66 "    0.052 5.00e-02 4.00e+02   7.84e-02 9.83e+00
        pdb=" N   PRO E  67 "   -0.135 5.00e-02 4.00e+02
        pdb=" CA  PRO E  67 "    0.038 5.00e-02 4.00e+02
        pdb=" CD  PRO E  67 "    0.045 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   MET D  66 "   -0.049 5.00e-02 4.00e+02   7.26e-02 8.44e+00
        pdb=" N   PRO D  67 "    0.126 5.00e-02 4.00e+02
        pdb=" CA  PRO D  67 "   -0.035 5.00e-02 4.00e+02
        pdb=" CD  PRO D  67 "   -0.041 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ILE D  51 "   -0.043 5.00e-02 4.00e+02   6.41e-02 6.57e+00
        pdb=" N   PRO D  52 "    0.111 5.00e-02 4.00e+02
        pdb=" CA  PRO D  52 "   -0.031 5.00e-02 4.00e+02
        pdb=" CD  PRO D  52 "   -0.036 5.00e-02 4.00e+02
  ... (remaining 1517 not shown)

  Histogram of nonbonded interaction distances:
        2.32 -     2.84: 2934
        2.84 -     3.35: 7686
        3.35 -     3.87: 15151
        3.87 -     4.38: 16958
        4.38 -     4.90: 27991
  Nonbonded interactions: 70720
  Sorted by model distance:
  nonbonded pdb=" O   ILE D  51 "
            pdb=" OG1 THR D  54 "
     model   vdw
     2.319 3.040
  nonbonded pdb=" O   TRP E 259 "
            pdb=" OG  SER E 263 "
     model   vdw
     2.324 3.040
  nonbonded pdb=" O   ALA D  59 "
            pdb=" OG1 THR D  63 "
     model   vdw
     2.341 3.040
  nonbonded pdb=" O   SER B  90 "
            pdb=" OG1 THR B  94 "
     model   vdw
     2.342 3.040
  nonbonded pdb=" OE1 GLU D  81 "
            pdb=" OG1 THR D  86 "
     model   vdw
     2.342 3.040
  ... (remaining 70715 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
Found NCS groups:
ncs_group {
  reference = chain 'B'
  selection = chain 'C'
}
ncs_group {
  reference = (chain 'D' and (resid 2 through 42 or (resid 43 and (name N or name CA or name C \ 
 or name O or name CB )) or resid 50 through 231 or resid 236 through 274))
  selection = (chain 'E' and (resid 2 through 43 or resid 50 through 274))
}

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 group one per residue
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:             0.510
  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:             0.020
  Extract box with map and model:          0.330
  Check model and map are aligned:         0.070
  Set scattering table:                    0.070
  Process input model:                     21.870
  Find NCS groups from input model:        0.320
  Set up NCS constraints:                  0.030
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:2.930
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   26.150
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8026
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      :  0.007   0.073   8888  Z= 0.478
  Angle     :  1.083  15.411  12061  Z= 0.564
  Chirality :  0.062   0.529   1425
  Planarity :  0.007   0.078   1520
  Dihedral  : 15.074  77.831   3207
  Min Nonbonded Distance : 2.319

Molprobity Statistics.
  All-atom Clashscore : 5.56
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.39 %
    Favored  : 93.61 %
  Rotamer:
    Outliers :  0.44 %
    Allowed  : 13.92 %
    Favored  : 85.64 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.09 %

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: -5.96 (0.16), residues: 1126
  helix: -4.61 (0.08), residues: 633
  sheet: -2.85 (0.39), residues: 114
  loop : -2.56 (0.27), residues: 379

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.002   TRP B 240 
 HIS   0.009   0.002   HIS C  97 
 PHE   0.019   0.002   PHE E 143 
 TYR   0.019   0.002   TYR C  86 
 ARG   0.006   0.001   ARG B 307 

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

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

  2252 Ramachandran restraints generated.
    1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2252 Ramachandran restraints generated.
    1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  141 residues out of total 906 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 137
  time to evaluate  : 1.016 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   42 LYS cc_start: 0.7798 (pttp) cc_final: 0.6941 (ptpp)
REVERT: B   47 LYS cc_start: 0.9761 (mttm) cc_final: 0.9474 (mttp)
REVERT: B  111 GLU cc_start: 0.9282 (mt-10) cc_final: 0.9078 (pt0)
REVERT: C   42 LYS cc_start: 0.9462 (ttpt) cc_final: 0.8466 (ttmm)
REVERT: C   46 MET cc_start: 0.9000 (ttp) cc_final: 0.8780 (ttp)
REVERT: C   47 LYS cc_start: 0.9808 (mttt) cc_final: 0.9423 (mtmm)
REVERT: C   89 LEU cc_start: 0.9567 (mt) cc_final: 0.9103 (tp)
REVERT: C  141 GLN cc_start: 0.9609 (pp30) cc_final: 0.9370 (pp30)
REVERT: C  200 ILE cc_start: 0.9928 (mt) cc_final: 0.9549 (tt)
REVERT: D  147 MET cc_start: 0.9313 (mmt) cc_final: 0.8927 (mmm)
REVERT: D  171 LYS cc_start: 0.9116 (ttpt) cc_final: 0.8836 (tttm)
REVERT: E   76 ASP cc_start: 0.8812 (p0) cc_final: 0.8548 (p0)
REVERT: E   88 MET cc_start: 0.9159 (tpp) cc_final: 0.8780 (tpp)
REVERT: E   97 ARG cc_start: 0.9122 (mtt180) cc_final: 0.7786 (mmm-85)
REVERT: E  147 MET cc_start: 0.9314 (mtt) cc_final: 0.8743 (mmt)
REVERT: E  170 GLU cc_start: 0.8909 (pm20) cc_final: 0.8050 (pm20)
REVERT: E  222 ARG cc_start: 0.9452 (mtm180) cc_final: 0.9225 (mtt-85)
  outliers start: 4
  outliers final: 2
  residues processed: 141
  average time/residue: 0.2294
  time to fit residues: 43.5090
Evaluate side-chains
  91 residues out of total 906 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 89
  time to evaluate  : 0.970 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   83 VAL
Chi-restraints excluded: chain B residue  187 VAL
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 94 optimal weight:    2.9990
   chunk 84 optimal weight:    1.9990
   chunk 47 optimal weight:    6.9990
   chunk 28 optimal weight:    6.9990
   chunk 57 optimal weight:    9.9990
   chunk 45 optimal weight:    3.9990
   chunk 87 optimal weight:    9.9990
   chunk 33 optimal weight:    4.9990
   chunk 53 optimal weight:   10.0000
   chunk 65 optimal weight:    0.9990
   chunk 101 optimal weight:    1.9990
   overall best weight:    2.3990

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

Flipped N/Q/H residues before XYZ refinement:
B 176 GLN
B 194 HIS
** B 263 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
C   2 ASN
C 176 GLN
C 194 HIS
C 270 GLN
D   6 ASN
D 225 ASN
E  99 GLN
E 108 HIS
E 225 ASN

Total number of N/Q/H flips: 11

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3163 r_free = 0.3163 target = 0.053358 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.2835 r_free = 0.2835 target = 0.042244 restraints weight = 46088.467|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.2876 r_free = 0.2876 target = 0.043697 restraints weight = 24452.149|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.2904 r_free = 0.2904 target = 0.044720 restraints weight = 15853.045|
|-----------------------------------------------------------------------------|
r_work (final): 0.2894
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8096
moved from start:          0.2251

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.043   8888  Z= 0.219
  Angle     :  0.674   8.622  12061  Z= 0.347
  Chirality :  0.042   0.210   1425
  Planarity :  0.005   0.039   1520
  Dihedral  :  5.299  33.456   1234
  Min Nonbonded Distance : 2.472

Molprobity Statistics.
  All-atom Clashscore : 9.38
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.71 %
    Favored  : 95.29 %
  Rotamer:
    Outliers :  1.99 %
    Allowed  : 19.01 %
    Favored  : 79.01 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.09 %

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: -3.60 (0.21), residues: 1126
  helix: -2.21 (0.16), residues: 644
  sheet: -2.44 (0.43), residues: 104
  loop : -2.32 (0.29), residues: 378

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.038   0.001   TRP E 259 
 HIS   0.003   0.001   HIS C  37 
 PHE   0.011   0.001   PHE D 157 
 TYR   0.017   0.001   TYR B 293 
 ARG   0.003   0.000   ARG B 248 

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

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

  2252 Ramachandran restraints generated.
    1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2252 Ramachandran restraints generated.
    1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  126 residues out of total 906 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 108
  time to evaluate  : 1.122 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   42 LYS cc_start: 0.7517 (pttp) cc_final: 0.7173 (pttm)
REVERT: B   47 LYS cc_start: 0.9766 (mttm) cc_final: 0.9496 (mttp)
REVERT: B   89 LEU cc_start: 0.9310 (OUTLIER) cc_final: 0.8924 (tt)
REVERT: C   42 LYS cc_start: 0.9495 (ttpt) cc_final: 0.8606 (ttmt)
REVERT: C   47 LYS cc_start: 0.9813 (mttt) cc_final: 0.9503 (mtmm)
REVERT: C   89 LEU cc_start: 0.9622 (mt) cc_final: 0.9090 (tp)
REVERT: D   11 GLU cc_start: 0.9403 (mm-30) cc_final: 0.9007 (mm-30)
REVERT: D   81 GLU cc_start: 0.8713 (mm-30) cc_final: 0.8321 (mm-30)
REVERT: D  146 PHE cc_start: 0.8998 (OUTLIER) cc_final: 0.8625 (t80)
REVERT: D  147 MET cc_start: 0.9221 (mmt) cc_final: 0.8851 (mmp)
REVERT: D  221 TYR cc_start: 0.8983 (t80) cc_final: 0.8377 (t80)
REVERT: E   76 ASP cc_start: 0.8855 (p0) cc_final: 0.8634 (p0)
REVERT: E   81 GLU cc_start: 0.8691 (mm-30) cc_final: 0.8483 (mt-10)
REVERT: E   83 GLU cc_start: 0.9062 (mm-30) cc_final: 0.8786 (mm-30)
REVERT: E   88 MET cc_start: 0.9183 (tpp) cc_final: 0.8880 (tpp)
REVERT: E  147 MET cc_start: 0.9321 (mtt) cc_final: 0.8880 (mtp)
REVERT: E  170 GLU cc_start: 0.8450 (pm20) cc_final: 0.7785 (pm20)
  outliers start: 18
  outliers final: 8
  residues processed: 122
  average time/residue: 0.1878
  time to fit residues: 32.7237
Evaluate side-chains
  95 residues out of total 906 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 85
  time to evaluate  : 1.036 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   13 TYR
Chi-restraints excluded: chain B residue   83 VAL
Chi-restraints excluded: chain B residue   89 LEU
Chi-restraints excluded: chain B residue  187 VAL
Chi-restraints excluded: chain D residue   55 ILE
Chi-restraints excluded: chain D residue  146 PHE
Chi-restraints excluded: chain D residue  251 VAL
Chi-restraints excluded: chain D residue  260 ILE
Chi-restraints excluded: chain E residue   51 ILE
Chi-restraints excluded: chain E residue  100 ILE
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 57 optimal weight:   20.0000
   chunk 85 optimal weight:    3.9990
   chunk 63 optimal weight:    9.9990
   chunk 83 optimal weight:    2.9990
   chunk 30 optimal weight:   10.0000
   chunk 82 optimal weight:    0.5980
   chunk 0 optimal weight:   10.0000
   chunk 15 optimal weight:    2.9990
   chunk 95 optimal weight:    0.3980
   chunk 75 optimal weight:    9.9990
   chunk 81 optimal weight:   10.0000
   overall best weight:    2.1986

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

Flipped N/Q/H residues before XYZ refinement:
B 135 GLN
B 263 HIS
C  38 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3160 r_free = 0.3160 target = 0.053361 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.2830 r_free = 0.2830 target = 0.042108 restraints weight = 47108.181|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.2871 r_free = 0.2871 target = 0.043565 restraints weight = 25049.252|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.2898 r_free = 0.2898 target = 0.044560 restraints weight = 16258.762|
|-----------------------------------------------------------------------------|
r_work (final): 0.2890
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8108
moved from start:          0.2753

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   8888  Z= 0.199
  Angle     :  0.636   9.308  12061  Z= 0.318
  Chirality :  0.042   0.196   1425
  Planarity :  0.004   0.035   1520
  Dihedral  :  4.826  31.843   1234
  Min Nonbonded Distance : 2.457

Molprobity Statistics.
  All-atom Clashscore : 9.44
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.60 %
    Favored  : 94.40 %
  Rotamer:
    Outliers :  2.98 %
    Allowed  : 21.33 %
    Favored  : 75.69 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.09 %

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: -1.98 (0.24), residues: 1126
  helix: -0.62 (0.20), residues: 645
  sheet: -2.17 (0.45), residues: 104
  loop : -2.06 (0.31), residues: 377

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.024   0.001   TRP E 259 
 HIS   0.004   0.001   HIS C 194 
 PHE   0.013   0.001   PHE D 157 
 TYR   0.014   0.001   TYR B 293 
 ARG   0.003   0.000   ARG B 248 

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

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

  2252 Ramachandran restraints generated.
    1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2252 Ramachandran restraints generated.
    1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  128 residues out of total 906 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 101
  time to evaluate  : 0.909 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   42 LYS cc_start: 0.7492 (pttp) cc_final: 0.7170 (pttm)
REVERT: B   47 LYS cc_start: 0.9780 (mttm) cc_final: 0.9513 (mttp)
REVERT: B   89 LEU cc_start: 0.9251 (OUTLIER) cc_final: 0.8852 (tt)
REVERT: B  133 MET cc_start: 0.9387 (mtm) cc_final: 0.8998 (mtm)
REVERT: B  215 LEU cc_start: 0.9825 (mt) cc_final: 0.9620 (mt)
REVERT: C   38 ASN cc_start: 0.7757 (OUTLIER) cc_final: 0.7469 (p0)
REVERT: C   42 LYS cc_start: 0.9553 (ttpt) cc_final: 0.8760 (ttmt)
REVERT: C   47 LYS cc_start: 0.9819 (mttt) cc_final: 0.9541 (mtmm)
REVERT: C   89 LEU cc_start: 0.9575 (mt) cc_final: 0.9073 (tp)
REVERT: C  133 MET cc_start: 0.9252 (mtm) cc_final: 0.8617 (ptp)
REVERT: C  295 MET cc_start: 0.9423 (mmm) cc_final: 0.9122 (mmm)
REVERT: D   11 GLU cc_start: 0.9413 (mm-30) cc_final: 0.9097 (mm-30)
REVERT: D   58 LEU cc_start: 0.9706 (OUTLIER) cc_final: 0.9490 (mm)
REVERT: D   68 LEU cc_start: 0.9559 (tp) cc_final: 0.9359 (tt)
REVERT: D   81 GLU cc_start: 0.8685 (mm-30) cc_final: 0.8320 (mm-30)
REVERT: D  146 PHE cc_start: 0.8889 (OUTLIER) cc_final: 0.8585 (t80)
REVERT: D  147 MET cc_start: 0.9213 (mmt) cc_final: 0.8857 (mmm)
REVERT: D  221 TYR cc_start: 0.9141 (t80) cc_final: 0.8384 (t80)
REVERT: E   11 GLU cc_start: 0.9263 (mm-30) cc_final: 0.8513 (mm-30)
REVERT: E   76 ASP cc_start: 0.8892 (p0) cc_final: 0.8643 (p0)
REVERT: E   83 GLU cc_start: 0.9086 (mm-30) cc_final: 0.8869 (mt-10)
REVERT: E   97 ARG cc_start: 0.8801 (mtt180) cc_final: 0.8380 (mmm-85)
REVERT: E  147 MET cc_start: 0.9297 (mtt) cc_final: 0.8861 (mtp)
REVERT: E  170 GLU cc_start: 0.8346 (pm20) cc_final: 0.7606 (pm20)
  outliers start: 27
  outliers final: 14
  residues processed: 121
  average time/residue: 0.1732
  time to fit residues: 31.0186
Evaluate side-chains
  102 residues out of total 906 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 84
  time to evaluate  : 0.990 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   83 VAL
Chi-restraints excluded: chain B residue   89 LEU
Chi-restraints excluded: chain B residue  187 VAL
Chi-restraints excluded: chain C residue   38 ASN
Chi-restraints excluded: chain C residue   48 LEU
Chi-restraints excluded: chain D residue   55 ILE
Chi-restraints excluded: chain D residue   58 LEU
Chi-restraints excluded: chain D residue  146 PHE
Chi-restraints excluded: chain D residue  152 LEU
Chi-restraints excluded: chain D residue  214 LEU
Chi-restraints excluded: chain D residue  247 VAL
Chi-restraints excluded: chain D residue  251 VAL
Chi-restraints excluded: chain D residue  260 ILE
Chi-restraints excluded: chain E residue   51 ILE
Chi-restraints excluded: chain E residue   86 THR
Chi-restraints excluded: chain E residue  100 ILE
Chi-restraints excluded: chain E residue  151 THR
Chi-restraints excluded: chain E residue  266 LEU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 34 optimal weight:    8.9990
   chunk 81 optimal weight:    6.9990
   chunk 2 optimal weight:   10.0000
   chunk 76 optimal weight:    6.9990
   chunk 97 optimal weight:    7.9990
   chunk 26 optimal weight:   20.0000
   chunk 57 optimal weight:    6.9990
   chunk 111 optimal weight:    7.9990
   chunk 77 optimal weight:    0.8980
   chunk 75 optimal weight:    5.9990
   chunk 60 optimal weight:    8.9990
   overall best weight:    5.5788

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

Flipped N/Q/H residues before XYZ refinement:
B  59 GLN
C  38 ASN
C 214 GLN
C 263 HIS

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3104 r_free = 0.3104 target = 0.051399 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.2761 r_free = 0.2761 target = 0.040239 restraints weight = 48554.166|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.2801 r_free = 0.2801 target = 0.041602 restraints weight = 26110.092|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.2831 r_free = 0.2831 target = 0.042566 restraints weight = 17166.975|
|-----------------------------------------------------------------------------|
r_work (final): 0.2822
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8182
moved from start:          0.3056

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.053   8888  Z= 0.387
  Angle     :  0.761   8.280  12061  Z= 0.377
  Chirality :  0.044   0.204   1425
  Planarity :  0.004   0.042   1520
  Dihedral  :  4.862  30.814   1234
  Min Nonbonded Distance : 2.426

Molprobity Statistics.
  All-atom Clashscore : 12.36
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.48 %
    Favored  : 93.52 %
  Rotamer:
    Outliers :  4.86 %
    Allowed  : 21.99 %
    Favored  : 73.15 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.09 %

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 (0.25), residues: 1126
  helix:  0.14 (0.20), residues: 648
  sheet: -2.15 (0.44), residues: 114
  loop : -1.68 (0.33), residues: 364

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.025   0.001   TRP E 259 
 HIS   0.005   0.001   HIS C 194 
 PHE   0.015   0.002   PHE D 157 
 TYR   0.022   0.002   TYR E  93 
 ARG   0.002   0.000   ARG C 173 

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

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

  2252 Ramachandran restraints generated.
    1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2252 Ramachandran restraints generated.
    1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  125 residues out of total 906 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 44
    poor density    : 81
  time to evaluate  : 0.939 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   42 LYS cc_start: 0.7517 (pttp) cc_final: 0.7047 (tptm)
REVERT: B   47 LYS cc_start: 0.9785 (mttm) cc_final: 0.9493 (mttp)
REVERT: B   59 GLN cc_start: 0.8820 (OUTLIER) cc_final: 0.8200 (pp30)
REVERT: B   89 LEU cc_start: 0.9198 (OUTLIER) cc_final: 0.8759 (tt)
REVERT: B  133 MET cc_start: 0.9450 (mtm) cc_final: 0.9150 (mtm)
REVERT: C   38 ASN cc_start: 0.8083 (OUTLIER) cc_final: 0.7822 (p0)
REVERT: C   42 LYS cc_start: 0.9597 (ttpt) cc_final: 0.8929 (ttmm)
REVERT: C   43 THR cc_start: 0.9700 (OUTLIER) cc_final: 0.9445 (p)
REVERT: C   47 LYS cc_start: 0.9841 (mttt) cc_final: 0.9566 (mtmm)
REVERT: C   89 LEU cc_start: 0.9491 (mt) cc_final: 0.9254 (tp)
REVERT: D   11 GLU cc_start: 0.9419 (mm-30) cc_final: 0.9069 (mm-30)
REVERT: D   81 GLU cc_start: 0.8732 (mm-30) cc_final: 0.8304 (mm-30)
REVERT: D  146 PHE cc_start: 0.8952 (OUTLIER) cc_final: 0.8630 (t80)
REVERT: D  147 MET cc_start: 0.9333 (mmt) cc_final: 0.8945 (mmp)
REVERT: D  221 TYR cc_start: 0.9070 (t80) cc_final: 0.8381 (t80)
REVERT: E   11 GLU cc_start: 0.9245 (mm-30) cc_final: 0.8509 (tp30)
REVERT: E   76 ASP cc_start: 0.8960 (p0) cc_final: 0.8672 (p0)
REVERT: E   83 GLU cc_start: 0.9051 (mm-30) cc_final: 0.8811 (mt-10)
REVERT: E   97 ARG cc_start: 0.8815 (mtt180) cc_final: 0.7866 (mmm-85)
REVERT: E  147 MET cc_start: 0.9358 (mtt) cc_final: 0.9006 (mtp)
REVERT: E  223 LEU cc_start: 0.9673 (OUTLIER) cc_final: 0.9420 (mm)
  outliers start: 44
  outliers final: 27
  residues processed: 117
  average time/residue: 0.1668
  time to fit residues: 29.0327
Evaluate side-chains
  108 residues out of total 906 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 75
  time to evaluate  : 0.926 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   13 TYR
Chi-restraints excluded: chain B residue   31 VAL
Chi-restraints excluded: chain B residue   34 LEU
Chi-restraints excluded: chain B residue   59 GLN
Chi-restraints excluded: chain B residue   83 VAL
Chi-restraints excluded: chain B residue   84 THR
Chi-restraints excluded: chain B residue   89 LEU
Chi-restraints excluded: chain B residue  187 VAL
Chi-restraints excluded: chain B residue  191 VAL
Chi-restraints excluded: chain B residue  263 HIS
Chi-restraints excluded: chain C residue   38 ASN
Chi-restraints excluded: chain C residue   43 THR
Chi-restraints excluded: chain C residue   48 LEU
Chi-restraints excluded: chain C residue   83 VAL
Chi-restraints excluded: chain D residue   55 ILE
Chi-restraints excluded: chain D residue   65 LEU
Chi-restraints excluded: chain D residue   92 THR
Chi-restraints excluded: chain D residue  117 LEU
Chi-restraints excluded: chain D residue  146 PHE
Chi-restraints excluded: chain D residue  214 LEU
Chi-restraints excluded: chain D residue  236 MET
Chi-restraints excluded: chain D residue  247 VAL
Chi-restraints excluded: chain D residue  251 VAL
Chi-restraints excluded: chain E residue   51 ILE
Chi-restraints excluded: chain E residue   72 LEU
Chi-restraints excluded: chain E residue   86 THR
Chi-restraints excluded: chain E residue   92 THR
Chi-restraints excluded: chain E residue  100 ILE
Chi-restraints excluded: chain E residue  110 LEU
Chi-restraints excluded: chain E residue  151 THR
Chi-restraints excluded: chain E residue  156 VAL
Chi-restraints excluded: chain E residue  223 LEU
Chi-restraints excluded: chain E residue  266 LEU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 107 optimal weight:    5.9990
   chunk 59 optimal weight:    8.9990
   chunk 13 optimal weight:    0.9990
   chunk 80 optimal weight:    8.9990
   chunk 61 optimal weight:    9.9990
   chunk 28 optimal weight:    9.9990
   chunk 74 optimal weight:    0.9990
   chunk 82 optimal weight:   30.0000
   chunk 49 optimal weight:    5.9990
   chunk 104 optimal weight:    4.9990
   chunk 38 optimal weight:    0.9990
   overall best weight:    2.7990

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

Flipped N/Q/H residues before XYZ refinement:
C  38 ASN
C  82 ASN
C 263 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3136 r_free = 0.3136 target = 0.052491 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.2801 r_free = 0.2801 target = 0.041320 restraints weight = 47530.136|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.2841 r_free = 0.2841 target = 0.042737 restraints weight = 25296.752|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.2869 r_free = 0.2869 target = 0.043705 restraints weight = 16506.641|
|-----------------------------------------------------------------------------|
r_work (final): 0.2861
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8141
moved from start:          0.3229

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.044   8888  Z= 0.232
  Angle     :  0.652   9.155  12061  Z= 0.321
  Chirality :  0.043   0.247   1425
  Planarity :  0.004   0.048   1520
  Dihedral  :  4.751  31.041   1234
  Min Nonbonded Distance : 2.283

Molprobity Statistics.
  All-atom Clashscore : 11.80
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.04 %
    Favored  : 93.96 %
  Rotamer:
    Outliers :  3.98 %
    Allowed  : 23.54 %
    Favored  : 72.49 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.09 %

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: -0.87 (0.25), residues: 1126
  helix:  0.35 (0.21), residues: 649
  sheet: -2.02 (0.45), residues: 114
  loop : -1.65 (0.34), residues: 363

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.024   0.001   TRP E 259 
 HIS   0.005   0.001   HIS C 194 
 PHE   0.012   0.001   PHE D 157 
 TYR   0.023   0.002   TYR E  93 
 ARG   0.001   0.000   ARG E  17 

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

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

  2252 Ramachandran restraints generated.
    1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2252 Ramachandran restraints generated.
    1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  123 residues out of total 906 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 87
  time to evaluate  : 1.032 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   47 LYS cc_start: 0.9779 (mttm) cc_final: 0.9440 (mttp)
REVERT: B   89 LEU cc_start: 0.9193 (OUTLIER) cc_final: 0.8779 (tt)
REVERT: B  133 MET cc_start: 0.9401 (mtm) cc_final: 0.9185 (mtm)
REVERT: B  261 ASN cc_start: 0.8503 (OUTLIER) cc_final: 0.8079 (p0)
REVERT: C   38 ASN cc_start: 0.7983 (OUTLIER) cc_final: 0.7743 (p0)
REVERT: C   42 LYS cc_start: 0.9600 (ttpt) cc_final: 0.8956 (ttmt)
REVERT: C   43 THR cc_start: 0.9675 (OUTLIER) cc_final: 0.9278 (p)
REVERT: C   47 LYS cc_start: 0.9834 (mttt) cc_final: 0.9592 (mttp)
REVERT: C   89 LEU cc_start: 0.9466 (mt) cc_final: 0.9220 (tp)
REVERT: C  133 MET cc_start: 0.9338 (mtm) cc_final: 0.8615 (ptp)
REVERT: C  295 MET cc_start: 0.9376 (mmm) cc_final: 0.9128 (mmm)
REVERT: D   11 GLU cc_start: 0.9413 (mm-30) cc_final: 0.9035 (mm-30)
REVERT: D   81 GLU cc_start: 0.8655 (mm-30) cc_final: 0.8223 (mm-30)
REVERT: D   83 GLU cc_start: 0.9034 (mm-30) cc_final: 0.8515 (mt-10)
REVERT: D  146 PHE cc_start: 0.8904 (OUTLIER) cc_final: 0.8675 (t80)
REVERT: D  147 MET cc_start: 0.9305 (mmt) cc_final: 0.9025 (mmp)
REVERT: D  221 TYR cc_start: 0.9105 (t80) cc_final: 0.8396 (t80)
REVERT: E   11 GLU cc_start: 0.9236 (mm-30) cc_final: 0.8448 (tp30)
REVERT: E   76 ASP cc_start: 0.8870 (p0) cc_final: 0.8579 (p0)
REVERT: E   83 GLU cc_start: 0.9046 (mm-30) cc_final: 0.8807 (mt-10)
REVERT: E   97 ARG cc_start: 0.8725 (mtt180) cc_final: 0.7867 (mmm-85)
REVERT: E  147 MET cc_start: 0.9367 (mtt) cc_final: 0.8996 (mtp)
REVERT: E  170 GLU cc_start: 0.8247 (pm20) cc_final: 0.7487 (pm20)
REVERT: E  223 LEU cc_start: 0.9635 (OUTLIER) cc_final: 0.9355 (mm)
  outliers start: 36
  outliers final: 23
  residues processed: 115
  average time/residue: 0.1807
  time to fit residues: 30.6809
Evaluate side-chains
  106 residues out of total 906 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 77
  time to evaluate  : 0.935 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   83 VAL
Chi-restraints excluded: chain B residue   84 THR
Chi-restraints excluded: chain B residue   89 LEU
Chi-restraints excluded: chain B residue  187 VAL
Chi-restraints excluded: chain B residue  191 VAL
Chi-restraints excluded: chain B residue  261 ASN
Chi-restraints excluded: chain B residue  263 HIS
Chi-restraints excluded: chain C residue   38 ASN
Chi-restraints excluded: chain C residue   43 THR
Chi-restraints excluded: chain C residue   48 LEU
Chi-restraints excluded: chain C residue   72 VAL
Chi-restraints excluded: chain C residue   83 VAL
Chi-restraints excluded: chain D residue   55 ILE
Chi-restraints excluded: chain D residue   65 LEU
Chi-restraints excluded: chain D residue   92 THR
Chi-restraints excluded: chain D residue  146 PHE
Chi-restraints excluded: chain D residue  214 LEU
Chi-restraints excluded: chain D residue  247 VAL
Chi-restraints excluded: chain D residue  251 VAL
Chi-restraints excluded: chain E residue   51 ILE
Chi-restraints excluded: chain E residue   72 LEU
Chi-restraints excluded: chain E residue   92 THR
Chi-restraints excluded: chain E residue  100 ILE
Chi-restraints excluded: chain E residue  110 LEU
Chi-restraints excluded: chain E residue  145 ARG
Chi-restraints excluded: chain E residue  151 THR
Chi-restraints excluded: chain E residue  156 VAL
Chi-restraints excluded: chain E residue  223 LEU
Chi-restraints excluded: chain E residue  266 LEU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 105 optimal weight:   20.0000
   chunk 98 optimal weight:    0.0770
   chunk 23 optimal weight:   10.0000
   chunk 58 optimal weight:    8.9990
   chunk 3 optimal weight:    9.9990
   chunk 104 optimal weight:    4.9990
   chunk 56 optimal weight:   20.0000
   chunk 35 optimal weight:    6.9990
   chunk 16 optimal weight:    6.9990
   chunk 24 optimal weight:   30.0000
   chunk 85 optimal weight:    1.9990
   overall best weight:    4.2146

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

Flipped N/Q/H residues before XYZ refinement:
C  25 ASN
C  38 ASN
C 263 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3121 r_free = 0.3121 target = 0.051950 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.2786 r_free = 0.2786 target = 0.040862 restraints weight = 47702.126|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 22)----------------|
| r_work = 0.2825 r_free = 0.2825 target = 0.042248 restraints weight = 25457.613|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.2852 r_free = 0.2852 target = 0.043185 restraints weight = 16675.210|
|-----------------------------------------------------------------------------|
r_work (final): 0.2848
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8170
moved from start:          0.3351

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.045   8888  Z= 0.302
  Angle     :  0.688  10.645  12061  Z= 0.340
  Chirality :  0.043   0.204   1425
  Planarity :  0.004   0.049   1520
  Dihedral  :  4.697  30.783   1234
  Min Nonbonded Distance : 2.459

Molprobity Statistics.
  All-atom Clashscore : 12.13
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.39 %
    Favored  : 93.61 %
  Rotamer:
    Outliers :  4.53 %
    Allowed  : 23.65 %
    Favored  : 71.82 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.09 %

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: -0.66 (0.26), residues: 1126
  helix:  0.53 (0.21), residues: 652
  sheet: -1.96 (0.46), residues: 112
  loop : -1.60 (0.34), residues: 362

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.022   0.001   TRP E 259 
 HIS   0.005   0.001   HIS C 194 
 PHE   0.012   0.001   PHE D 157 
 TYR   0.023   0.002   TYR E  93 
 ARG   0.002   0.000   ARG B 269 

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

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

  2252 Ramachandran restraints generated.
    1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2252 Ramachandran restraints generated.
    1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  118 residues out of total 906 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 41
    poor density    : 77
  time to evaluate  : 0.946 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   47 LYS cc_start: 0.9782 (mttm) cc_final: 0.9439 (mttp)
REVERT: B   89 LEU cc_start: 0.9192 (OUTLIER) cc_final: 0.8756 (tt)
REVERT: B  261 ASN cc_start: 0.8582 (OUTLIER) cc_final: 0.8179 (p0)
REVERT: C   38 ASN cc_start: 0.7995 (OUTLIER) cc_final: 0.7762 (p0)
REVERT: C   42 LYS cc_start: 0.9605 (ttpt) cc_final: 0.9000 (ttmt)
REVERT: C   43 THR cc_start: 0.9684 (OUTLIER) cc_final: 0.9393 (p)
REVERT: C   47 LYS cc_start: 0.9834 (mttt) cc_final: 0.9516 (mtmm)
REVERT: C  133 MET cc_start: 0.9348 (mtm) cc_final: 0.8687 (ptp)
REVERT: C  295 MET cc_start: 0.9366 (mmm) cc_final: 0.9132 (mmm)
REVERT: D   11 GLU cc_start: 0.9382 (mm-30) cc_final: 0.9003 (mm-30)
REVERT: D   81 GLU cc_start: 0.8695 (mm-30) cc_final: 0.8162 (mm-30)
REVERT: D   83 GLU cc_start: 0.9037 (mm-30) cc_final: 0.8540 (mt-10)
REVERT: D  147 MET cc_start: 0.9350 (mmt) cc_final: 0.9084 (mmp)
REVERT: D  221 TYR cc_start: 0.9114 (t80) cc_final: 0.8421 (t80)
REVERT: E   11 GLU cc_start: 0.9224 (mm-30) cc_final: 0.8471 (tp30)
REVERT: E   76 ASP cc_start: 0.8939 (p0) cc_final: 0.8629 (p0)
REVERT: E   81 GLU cc_start: 0.9108 (mm-30) cc_final: 0.8635 (mm-30)
REVERT: E   83 GLU cc_start: 0.9038 (mm-30) cc_final: 0.8826 (mt-10)
REVERT: E   88 MET cc_start: 0.9024 (tpp) cc_final: 0.8818 (tpp)
REVERT: E   97 ARG cc_start: 0.8718 (mtt180) cc_final: 0.7828 (mmm-85)
REVERT: E  147 MET cc_start: 0.9379 (mtt) cc_final: 0.9006 (mtp)
REVERT: E  223 LEU cc_start: 0.9635 (OUTLIER) cc_final: 0.9349 (mm)
  outliers start: 41
  outliers final: 27
  residues processed: 111
  average time/residue: 0.1800
  time to fit residues: 29.5264
Evaluate side-chains
  107 residues out of total 906 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 75
  time to evaluate  : 0.946 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   83 VAL
Chi-restraints excluded: chain B residue   84 THR
Chi-restraints excluded: chain B residue   86 TYR
Chi-restraints excluded: chain B residue   89 LEU
Chi-restraints excluded: chain B residue  187 VAL
Chi-restraints excluded: chain B residue  191 VAL
Chi-restraints excluded: chain B residue  261 ASN
Chi-restraints excluded: chain B residue  263 HIS
Chi-restraints excluded: chain C residue   38 ASN
Chi-restraints excluded: chain C residue   43 THR
Chi-restraints excluded: chain C residue   48 LEU
Chi-restraints excluded: chain C residue   72 VAL
Chi-restraints excluded: chain C residue   83 VAL
Chi-restraints excluded: chain D residue   55 ILE
Chi-restraints excluded: chain D residue   65 LEU
Chi-restraints excluded: chain D residue   92 THR
Chi-restraints excluded: chain D residue  100 ILE
Chi-restraints excluded: chain D residue  117 LEU
Chi-restraints excluded: chain D residue  214 LEU
Chi-restraints excluded: chain D residue  247 VAL
Chi-restraints excluded: chain D residue  251 VAL
Chi-restraints excluded: chain E residue    4 VAL
Chi-restraints excluded: chain E residue   12 LEU
Chi-restraints excluded: chain E residue   51 ILE
Chi-restraints excluded: chain E residue   72 LEU
Chi-restraints excluded: chain E residue   92 THR
Chi-restraints excluded: chain E residue  100 ILE
Chi-restraints excluded: chain E residue  110 LEU
Chi-restraints excluded: chain E residue  151 THR
Chi-restraints excluded: chain E residue  156 VAL
Chi-restraints excluded: chain E residue  223 LEU
Chi-restraints excluded: chain E residue  266 LEU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 19 optimal weight:    4.9990
   chunk 52 optimal weight:    4.9990
   chunk 6 optimal weight:    7.9990
   chunk 102 optimal weight:    7.9990
   chunk 45 optimal weight:    7.9990
   chunk 88 optimal weight:   10.0000
   chunk 43 optimal weight:    0.9990
   chunk 53 optimal weight:   20.0000
   chunk 7 optimal weight:    0.9990
   chunk 10 optimal weight:    5.9990
   chunk 58 optimal weight:    2.9990
   overall best weight:    2.9990

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

Flipped N/Q/H residues before XYZ refinement:
** C 263 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3139 r_free = 0.3139 target = 0.052611 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.2803 r_free = 0.2803 target = 0.041391 restraints weight = 47854.347|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.2843 r_free = 0.2843 target = 0.042800 restraints weight = 25413.023|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.2870 r_free = 0.2870 target = 0.043758 restraints weight = 16608.964|
|-----------------------------------------------------------------------------|
r_work (final): 0.2863
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8151
moved from start:          0.3471

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.039   8888  Z= 0.238
  Angle     :  0.665   9.942  12061  Z= 0.323
  Chirality :  0.043   0.203   1425
  Planarity :  0.004   0.050   1520
  Dihedral  :  4.646  30.762   1234
  Min Nonbonded Distance : 2.472

Molprobity Statistics.
  All-atom Clashscore : 11.51
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.22 %
    Favored  : 93.78 %
  Rotamer:
    Outliers :  3.54 %
    Allowed  : 24.42 %
    Favored  : 72.04 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.09 %

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: -0.53 (0.26), residues: 1126
  helix:  0.65 (0.21), residues: 655
  sheet: -1.89 (0.46), residues: 112
  loop : -1.58 (0.34), residues: 359

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.025   0.001   TRP E 259 
 HIS   0.005   0.001   HIS C 194 
 PHE   0.015   0.001   PHE D 120 
 TYR   0.020   0.002   TYR B  86 
 ARG   0.002   0.000   ARG B 307 

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

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

  2252 Ramachandran restraints generated.
    1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2252 Ramachandran restraints generated.
    1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  113 residues out of total 906 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 81
  time to evaluate  : 0.996 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   47 LYS cc_start: 0.9779 (mttm) cc_final: 0.9424 (mttp)
REVERT: B   89 LEU cc_start: 0.9187 (OUTLIER) cc_final: 0.8760 (tt)
REVERT: B  261 ASN cc_start: 0.8535 (OUTLIER) cc_final: 0.8135 (p0)
REVERT: C   42 LYS cc_start: 0.9613 (ttpt) cc_final: 0.9022 (ttmt)
REVERT: C   43 THR cc_start: 0.9667 (OUTLIER) cc_final: 0.9375 (p)
REVERT: C   47 LYS cc_start: 0.9832 (mttt) cc_final: 0.9508 (mtmm)
REVERT: C  133 MET cc_start: 0.9323 (mtm) cc_final: 0.8661 (ptp)
REVERT: D   11 GLU cc_start: 0.9389 (mm-30) cc_final: 0.9003 (mm-30)
REVERT: D   81 GLU cc_start: 0.8684 (mm-30) cc_final: 0.8165 (mm-30)
REVERT: D   83 GLU cc_start: 0.9001 (mm-30) cc_final: 0.8526 (mt-10)
REVERT: D  147 MET cc_start: 0.9387 (mmt) cc_final: 0.9019 (mmp)
REVERT: D  221 TYR cc_start: 0.8965 (t80) cc_final: 0.8429 (t80)
REVERT: E   11 GLU cc_start: 0.9233 (mm-30) cc_final: 0.8478 (tp30)
REVERT: E   76 ASP cc_start: 0.8935 (p0) cc_final: 0.8640 (p0)
REVERT: E   81 GLU cc_start: 0.9094 (mm-30) cc_final: 0.8594 (mm-30)
REVERT: E   83 GLU cc_start: 0.9027 (mm-30) cc_final: 0.8798 (mt-10)
REVERT: E   88 MET cc_start: 0.9021 (tpp) cc_final: 0.8761 (tpp)
REVERT: E   97 ARG cc_start: 0.8661 (mtt180) cc_final: 0.7822 (mmm-85)
REVERT: E  147 MET cc_start: 0.9373 (mtt) cc_final: 0.9001 (mtp)
REVERT: E  223 LEU cc_start: 0.9617 (OUTLIER) cc_final: 0.9386 (mm)
  outliers start: 32
  outliers final: 25
  residues processed: 107
  average time/residue: 0.1803
  time to fit residues: 28.2158
Evaluate side-chains
  104 residues out of total 906 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 75
  time to evaluate  : 0.959 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   83 VAL
Chi-restraints excluded: chain B residue   84 THR
Chi-restraints excluded: chain B residue   86 TYR
Chi-restraints excluded: chain B residue   89 LEU
Chi-restraints excluded: chain B residue  187 VAL
Chi-restraints excluded: chain B residue  191 VAL
Chi-restraints excluded: chain B residue  261 ASN
Chi-restraints excluded: chain B residue  263 HIS
Chi-restraints excluded: chain C residue   43 THR
Chi-restraints excluded: chain C residue   48 LEU
Chi-restraints excluded: chain C residue   72 VAL
Chi-restraints excluded: chain C residue   83 VAL
Chi-restraints excluded: chain D residue   55 ILE
Chi-restraints excluded: chain D residue   65 LEU
Chi-restraints excluded: chain D residue   92 THR
Chi-restraints excluded: chain D residue  117 LEU
Chi-restraints excluded: chain D residue  214 LEU
Chi-restraints excluded: chain D residue  247 VAL
Chi-restraints excluded: chain D residue  251 VAL
Chi-restraints excluded: chain E residue   51 ILE
Chi-restraints excluded: chain E residue   72 LEU
Chi-restraints excluded: chain E residue   92 THR
Chi-restraints excluded: chain E residue  100 ILE
Chi-restraints excluded: chain E residue  110 LEU
Chi-restraints excluded: chain E residue  151 THR
Chi-restraints excluded: chain E residue  156 VAL
Chi-restraints excluded: chain E residue  209 LEU
Chi-restraints excluded: chain E residue  223 LEU
Chi-restraints excluded: chain E residue  266 LEU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 77 optimal weight:    3.9990
   chunk 69 optimal weight:    1.9990
   chunk 48 optimal weight:    7.9990
   chunk 9 optimal weight:    0.9990
   chunk 84 optimal weight:    0.8980
   chunk 67 optimal weight:    9.9990
   chunk 79 optimal weight:    9.9990
   chunk 37 optimal weight:    7.9990
   chunk 42 optimal weight:    7.9990
   chunk 30 optimal weight:   10.0000
   chunk 100 optimal weight:    0.8980
   overall best weight:    1.7586

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

Flipped N/Q/H residues before XYZ refinement:
** C 263 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3170 r_free = 0.3170 target = 0.053604 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.2838 r_free = 0.2838 target = 0.042291 restraints weight = 47763.954|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.2878 r_free = 0.2878 target = 0.043746 restraints weight = 25452.527|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.2905 r_free = 0.2905 target = 0.044738 restraints weight = 16587.764|
|-----------------------------------------------------------------------------|
r_work (final): 0.2897
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8122
moved from start:          0.3619

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   8888  Z= 0.175
  Angle     :  0.626   9.720  12061  Z= 0.302
  Chirality :  0.041   0.194   1425
  Planarity :  0.003   0.047   1520
  Dihedral  :  4.484  31.327   1234
  Min Nonbonded Distance : 2.481

Molprobity Statistics.
  All-atom Clashscore : 10.50
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.77 %
    Favored  : 94.23 %
  Rotamer:
    Outliers :  3.65 %
    Allowed  : 24.97 %
    Favored  : 71.38 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.09 %

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: -0.34 (0.26), residues: 1126
  helix:  0.80 (0.21), residues: 659
  sheet: -1.78 (0.48), residues: 105
  loop : -1.58 (0.33), residues: 362

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.022   0.001   TRP E 259 
 HIS   0.005   0.001   HIS C 194 
 PHE   0.008   0.001   PHE D 157 
 TYR   0.018   0.001   TYR E  93 
 ARG   0.003   0.000   ARG E 145 

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

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

  2252 Ramachandran restraints generated.
    1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2252 Ramachandran restraints generated.
    1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  126 residues out of total 906 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 93
  time to evaluate  : 1.164 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   42 LYS cc_start: 0.7437 (pttp) cc_final: 0.6577 (ptpp)
REVERT: B   89 LEU cc_start: 0.9174 (OUTLIER) cc_final: 0.8766 (tt)
REVERT: B  133 MET cc_start: 0.9384 (mtm) cc_final: 0.9029 (ptp)
REVERT: B  166 ASP cc_start: 0.8910 (p0) cc_final: 0.8167 (p0)
REVERT: B  261 ASN cc_start: 0.8426 (OUTLIER) cc_final: 0.8028 (p0)
REVERT: C   42 LYS cc_start: 0.9622 (ttpt) cc_final: 0.9079 (ttmt)
REVERT: C   43 THR cc_start: 0.9628 (OUTLIER) cc_final: 0.9371 (p)
REVERT: C   47 LYS cc_start: 0.9828 (mttt) cc_final: 0.9499 (mtmm)
REVERT: C  133 MET cc_start: 0.9279 (mtm) cc_final: 0.8611 (ptp)
REVERT: C  295 MET cc_start: 0.9317 (mmm) cc_final: 0.9114 (mmm)
REVERT: D   11 GLU cc_start: 0.9395 (mm-30) cc_final: 0.9003 (mm-30)
REVERT: D   81 GLU cc_start: 0.8671 (mm-30) cc_final: 0.8209 (mm-30)
REVERT: D   83 GLU cc_start: 0.8967 (mm-30) cc_final: 0.8590 (mt-10)
REVERT: D  147 MET cc_start: 0.9402 (mmt) cc_final: 0.9021 (mmp)
REVERT: D  221 TYR cc_start: 0.9017 (t80) cc_final: 0.8781 (t80)
REVERT: E   11 GLU cc_start: 0.9240 (mm-30) cc_final: 0.8522 (tp30)
REVERT: E   76 ASP cc_start: 0.8917 (p0) cc_final: 0.8601 (p0)
REVERT: E   83 GLU cc_start: 0.9015 (mm-30) cc_final: 0.8778 (mt-10)
REVERT: E   88 MET cc_start: 0.9040 (tpp) cc_final: 0.8636 (tpp)
REVERT: E  147 MET cc_start: 0.9344 (mtt) cc_final: 0.9005 (mtp)
REVERT: E  223 LEU cc_start: 0.9594 (OUTLIER) cc_final: 0.9378 (mm)
  outliers start: 33
  outliers final: 22
  residues processed: 120
  average time/residue: 0.1688
  time to fit residues: 30.3893
Evaluate side-chains
  110 residues out of total 906 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 84
  time to evaluate  : 1.062 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   83 VAL
Chi-restraints excluded: chain B residue   84 THR
Chi-restraints excluded: chain B residue   86 TYR
Chi-restraints excluded: chain B residue   89 LEU
Chi-restraints excluded: chain B residue  187 VAL
Chi-restraints excluded: chain B residue  191 VAL
Chi-restraints excluded: chain B residue  261 ASN
Chi-restraints excluded: chain B residue  263 HIS
Chi-restraints excluded: chain C residue   43 THR
Chi-restraints excluded: chain D residue   55 ILE
Chi-restraints excluded: chain D residue   65 LEU
Chi-restraints excluded: chain D residue  100 ILE
Chi-restraints excluded: chain D residue  117 LEU
Chi-restraints excluded: chain D residue  214 LEU
Chi-restraints excluded: chain D residue  247 VAL
Chi-restraints excluded: chain D residue  251 VAL
Chi-restraints excluded: chain E residue    4 VAL
Chi-restraints excluded: chain E residue   51 ILE
Chi-restraints excluded: chain E residue   72 LEU
Chi-restraints excluded: chain E residue   86 THR
Chi-restraints excluded: chain E residue   92 THR
Chi-restraints excluded: chain E residue  100 ILE
Chi-restraints excluded: chain E residue  110 LEU
Chi-restraints excluded: chain E residue  156 VAL
Chi-restraints excluded: chain E residue  223 LEU
Chi-restraints excluded: chain E residue  266 LEU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 70 optimal weight:    0.8980
   chunk 88 optimal weight:    9.9990
   chunk 90 optimal weight:    0.6980
   chunk 92 optimal weight:    4.9990
   chunk 34 optimal weight:    7.9990
   chunk 5 optimal weight:    0.0010
   chunk 26 optimal weight:   10.0000
   chunk 45 optimal weight:    0.7980
   chunk 105 optimal weight:    0.0270
   chunk 12 optimal weight:    6.9990
   chunk 94 optimal weight:    0.6980
   overall best weight:    0.4444

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

Flipped N/Q/H residues before XYZ refinement:
C 263 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3210 r_free = 0.3210 target = 0.054989 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.2881 r_free = 0.2881 target = 0.043577 restraints weight = 46512.032|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.2922 r_free = 0.2922 target = 0.045087 restraints weight = 24559.802|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.2950 r_free = 0.2950 target = 0.046112 restraints weight = 15896.298|
|-----------------------------------------------------------------------------|
r_work (final): 0.2943
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8062
moved from start:          0.3862

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.038   8888  Z= 0.143
  Angle     :  0.646  10.172  12061  Z= 0.302
  Chirality :  0.041   0.181   1425
  Planarity :  0.003   0.043   1520
  Dihedral  :  4.405  31.927   1234
  Min Nonbonded Distance : 2.504

Molprobity Statistics.
  All-atom Clashscore : 10.11
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.24 %
    Favored  : 94.76 %
  Rotamer:
    Outliers :  2.43 %
    Allowed  : 26.41 %
    Favored  : 71.16 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.09 %

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: -0.22 (0.26), residues: 1126
  helix:  0.86 (0.21), residues: 661
  sheet: -1.68 (0.48), residues: 105
  loop : -1.45 (0.34), residues: 360

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.020   0.001   TRP E 259 
 HIS   0.004   0.001   HIS C 194 
 PHE   0.009   0.001   PHE D 157 
 TYR   0.015   0.001   TYR B  86 
 ARG   0.002   0.000   ARG E 145 

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

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

  2252 Ramachandran restraints generated.
    1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2252 Ramachandran restraints generated.
    1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  121 residues out of total 906 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 99
  time to evaluate  : 1.422 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   42 LYS cc_start: 0.7372 (pttp) cc_final: 0.6534 (ptpp)
REVERT: B   89 LEU cc_start: 0.9142 (OUTLIER) cc_final: 0.8729 (tt)
REVERT: B  133 MET cc_start: 0.9390 (mtm) cc_final: 0.8969 (ptp)
REVERT: B  166 ASP cc_start: 0.8775 (p0) cc_final: 0.8080 (p0)
REVERT: B  261 ASN cc_start: 0.8222 (OUTLIER) cc_final: 0.7830 (p0)
REVERT: C   42 LYS cc_start: 0.9622 (ttpt) cc_final: 0.8966 (ttmm)
REVERT: C  133 MET cc_start: 0.9295 (mtm) cc_final: 0.8688 (ptp)
REVERT: C  295 MET cc_start: 0.9333 (mmm) cc_final: 0.9123 (mmm)
REVERT: D   11 GLU cc_start: 0.9429 (mm-30) cc_final: 0.9027 (mm-30)
REVERT: D   81 GLU cc_start: 0.8692 (mm-30) cc_final: 0.8236 (mm-30)
REVERT: D   83 GLU cc_start: 0.8953 (mm-30) cc_final: 0.8550 (mt-10)
REVERT: D  147 MET cc_start: 0.9400 (mmt) cc_final: 0.9117 (mmp)
REVERT: D  221 TYR cc_start: 0.9017 (t80) cc_final: 0.8789 (t80)
REVERT: E   11 GLU cc_start: 0.9270 (mm-30) cc_final: 0.8645 (tp30)
REVERT: E   76 ASP cc_start: 0.8890 (p0) cc_final: 0.8540 (p0)
REVERT: E   83 GLU cc_start: 0.9054 (mm-30) cc_final: 0.8849 (mt-10)
REVERT: E   88 MET cc_start: 0.9013 (tpp) cc_final: 0.8714 (tpp)
REVERT: E  147 MET cc_start: 0.9350 (mtt) cc_final: 0.9018 (mtp)
REVERT: E  216 ASN cc_start: 0.8798 (t0) cc_final: 0.8084 (t0)
REVERT: E  223 LEU cc_start: 0.9556 (OUTLIER) cc_final: 0.9350 (mm)
  outliers start: 22
  outliers final: 12
  residues processed: 116
  average time/residue: 0.1980
  time to fit residues: 35.3889
Evaluate side-chains
  106 residues out of total 906 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 91
  time to evaluate  : 1.613 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   83 VAL
Chi-restraints excluded: chain B residue   84 THR
Chi-restraints excluded: chain B residue   89 LEU
Chi-restraints excluded: chain B residue  187 VAL
Chi-restraints excluded: chain B residue  261 ASN
Chi-restraints excluded: chain B residue  263 HIS
Chi-restraints excluded: chain D residue  117 LEU
Chi-restraints excluded: chain D residue  247 VAL
Chi-restraints excluded: chain D residue  251 VAL
Chi-restraints excluded: chain E residue    4 VAL
Chi-restraints excluded: chain E residue   92 THR
Chi-restraints excluded: chain E residue  100 ILE
Chi-restraints excluded: chain E residue  209 LEU
Chi-restraints excluded: chain E residue  223 LEU
Chi-restraints excluded: chain E residue  266 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 66 optimal weight:    0.9990
   chunk 3 optimal weight:   10.0000
   chunk 110 optimal weight:    2.9990
   chunk 24 optimal weight:    2.9990
   chunk 95 optimal weight:    5.9990
   chunk 74 optimal weight:    1.9990
   chunk 49 optimal weight:    8.9990
   chunk 101 optimal weight:    2.9990
   chunk 34 optimal weight:    5.9990
   chunk 92 optimal weight:    2.9990
   chunk 5 optimal weight:    5.9990
   overall best weight:    2.3990

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

Flipped N/Q/H residues before XYZ refinement:
** C  38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 263 HIS
** C 304 GLN ** 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 = 0.3176 r_free = 0.3176 target = 0.053860 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.2840 r_free = 0.2840 target = 0.042412 restraints weight = 47432.112|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 41)----------------|
| r_work = 0.2880 r_free = 0.2880 target = 0.043865 restraints weight = 25344.789|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.2908 r_free = 0.2908 target = 0.044871 restraints weight = 16556.999|
|-----------------------------------------------------------------------------|
r_work (final): 0.2913
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8110
moved from start:          0.3845

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   8888  Z= 0.209
  Angle     :  0.682   9.825  12061  Z= 0.322
  Chirality :  0.042   0.139   1425
  Planarity :  0.003   0.045   1520
  Dihedral  :  4.346  31.581   1234
  Min Nonbonded Distance : 2.497

Molprobity Statistics.
  All-atom Clashscore : 10.84
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.42 %
    Favored  : 94.58 %
  Rotamer:
    Outliers :  1.77 %
    Allowed  : 27.29 %
    Favored  : 70.94 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.09 %

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: -0.04 (0.26), residues: 1126
  helix:  1.04 (0.21), residues: 656
  sheet: -1.80 (0.47), residues: 105
  loop : -1.37 (0.34), residues: 365

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.024   0.001   TRP E 259 
 HIS   0.004   0.001   HIS C 194 
 PHE   0.013   0.001   PHE C  85 
 TYR   0.012   0.001   TYR E 221 
 ARG   0.003   0.000   ARG E 145 

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

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

  2252 Ramachandran restraints generated.
    1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2252 Ramachandran restraints generated.
    1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  102 residues out of total 906 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 86
  time to evaluate  : 1.005 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   42 LYS cc_start: 0.7339 (pttp) cc_final: 0.6995 (pttm)
REVERT: B   89 LEU cc_start: 0.9145 (OUTLIER) cc_final: 0.8718 (tt)
REVERT: B  133 MET cc_start: 0.9365 (mtm) cc_final: 0.8887 (ptp)
REVERT: B  166 ASP cc_start: 0.8876 (p0) cc_final: 0.8172 (p0)
REVERT: B  261 ASN cc_start: 0.8264 (OUTLIER) cc_final: 0.7868 (p0)
REVERT: C   42 LYS cc_start: 0.9597 (ttpt) cc_final: 0.9017 (ttmt)
REVERT: C  133 MET cc_start: 0.9343 (mtm) cc_final: 0.8731 (ptp)
REVERT: C  295 MET cc_start: 0.9348 (mmm) cc_final: 0.9146 (mmm)
REVERT: D   11 GLU cc_start: 0.9435 (mm-30) cc_final: 0.9042 (mm-30)
REVERT: D   81 GLU cc_start: 0.8774 (mm-30) cc_final: 0.8322 (mm-30)
REVERT: D   83 GLU cc_start: 0.8991 (mm-30) cc_final: 0.8569 (mt-10)
REVERT: D  147 MET cc_start: 0.9443 (mmt) cc_final: 0.9083 (mmp)
REVERT: D  221 TYR cc_start: 0.9043 (t80) cc_final: 0.8809 (t80)
REVERT: E   11 GLU cc_start: 0.9286 (mm-30) cc_final: 0.8663 (tp30)
REVERT: E   76 ASP cc_start: 0.8916 (p0) cc_final: 0.8539 (p0)
REVERT: E   83 GLU cc_start: 0.9068 (mm-30) cc_final: 0.8812 (mt-10)
REVERT: E   88 MET cc_start: 0.9127 (tpp) cc_final: 0.8819 (tpp)
REVERT: E   97 ARG cc_start: 0.8523 (mtt180) cc_final: 0.7691 (mmm-85)
REVERT: E  147 MET cc_start: 0.9355 (mtt) cc_final: 0.9030 (mtp)
REVERT: E  216 ASN cc_start: 0.8705 (t0) cc_final: 0.7967 (t0)
REVERT: E  223 LEU cc_start: 0.9580 (OUTLIER) cc_final: 0.9367 (mm)
  outliers start: 16
  outliers final: 13
  residues processed: 99
  average time/residue: 0.1948
  time to fit residues: 28.7645
Evaluate side-chains
  100 residues out of total 906 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 84
  time to evaluate  : 1.245 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   83 VAL
Chi-restraints excluded: chain B residue   84 THR
Chi-restraints excluded: chain B residue   89 LEU
Chi-restraints excluded: chain B residue  187 VAL
Chi-restraints excluded: chain B residue  261 ASN
Chi-restraints excluded: chain B residue  263 HIS
Chi-restraints excluded: chain C residue   22 LEU
Chi-restraints excluded: chain D residue  117 LEU
Chi-restraints excluded: chain D residue  247 VAL
Chi-restraints excluded: chain D residue  251 VAL
Chi-restraints excluded: chain E residue    4 VAL
Chi-restraints excluded: chain E residue   92 THR
Chi-restraints excluded: chain E residue  100 ILE
Chi-restraints excluded: chain E residue  209 LEU
Chi-restraints excluded: chain E residue  223 LEU
Chi-restraints excluded: chain E residue  266 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 14 optimal weight:    3.9990
   chunk 81 optimal weight:    4.9990
   chunk 47 optimal weight:   10.0000
   chunk 77 optimal weight:    2.9990
   chunk 50 optimal weight:    0.3980
   chunk 37 optimal weight:    0.7980
   chunk 36 optimal weight:    3.9990
   chunk 4 optimal weight:    4.9990
   chunk 59 optimal weight:    4.9990
   chunk 68 optimal weight:    0.9990
   chunk 110 optimal weight:    0.9990
   overall best weight:    1.2386

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

Flipped N/Q/H residues before XYZ refinement:
C  38 ASN
C 263 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3199 r_free = 0.3199 target = 0.054650 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.2869 r_free = 0.2869 target = 0.043223 restraints weight = 46992.796|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 21)----------------|
| r_work = 0.2909 r_free = 0.2909 target = 0.044698 restraints weight = 24985.802|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.2938 r_free = 0.2938 target = 0.045727 restraints weight = 16298.884|
|-----------------------------------------------------------------------------|
r_work (final): 0.2941
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8083
moved from start:          0.3961

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.035   8888  Z= 0.161
  Angle     :  0.671  10.021  12061  Z= 0.312
  Chirality :  0.042   0.148   1425
  Planarity :  0.003   0.045   1520
  Dihedral  :  4.345  32.050   1234
  Min Nonbonded Distance : 2.501

Molprobity Statistics.
  All-atom Clashscore : 10.50
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.24 %
    Favored  : 94.76 %
  Rotamer:
    Outliers :  1.99 %
    Allowed  : 27.40 %
    Favored  : 70.61 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.09 %

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: -0.02 (0.26), residues: 1126
  helix:  1.05 (0.21), residues: 659
  sheet: -1.82 (0.46), residues: 105
  loop : -1.34 (0.34), residues: 362

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.020   0.001   TRP E 259 
 HIS   0.004   0.001   HIS C 194 
 PHE   0.010   0.001   PHE D 157 
 TYR   0.017   0.001   TYR E 221 
 ARG   0.002   0.000   ARG E 145 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2481.72 seconds
wall clock time: 44 minutes 54.71 seconds (2694.71 seconds total)