Starting phenix.real_space_refine
on Mon Nov 17 21:05:06 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/6dde_7868/11_2025/6dde_7868_neut.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/6dde_7868/11_2025/6dde_7868.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.5
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/6dde_7868/11_2025/6dde_7868_neut.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/6dde_7868/11_2025/6dde_7868_neut.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/6dde_7868/11_2025/6dde_7868.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/6dde_7868/11_2025/6dde_7868.map"
  }
  resolution = 3.5
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.027 sd=   0.613
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      60      5.16       5
     C    5416      2.51       5
     N    1457      2.21       5
     O    1556      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 15 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5881/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 8489
  Number of models: 1
  Model: ""
    Number of chains: 8
    Chain: "A"
      Number of atoms: 1679
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 217, 1679
          Classifications: {'peptide': 217}
          Modifications used: {'COO': 1}
          Incomplete info: {'truncation_to_alanine': 21}
          Link IDs: {'PTRANS': 2, 'TRANS': 214}
          Chain breaks: 2
          Unresolved non-hydrogen bonds: 72
          Unresolved non-hydrogen angles: 89
          Unresolved non-hydrogen dihedrals: 55
          Unresolved non-hydrogen chiralities: 4
          Planarities with less than four sites: {'ASP:plan': 6, 'GLU:plan': 7}
          Unresolved non-hydrogen planarities: 46
    Chain: "B"
      Number of atoms: 2547
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 336, 2547
          Classifications: {'peptide': 336}
          Modifications used: {'COO': 1}
          Incomplete info: {'truncation_to_alanine': 11}
          Link IDs: {'PTRANS': 5, 'TRANS': 330}
          Unresolved non-hydrogen bonds: 37
          Unresolved non-hydrogen angles: 46
          Unresolved non-hydrogen dihedrals: 28
          Planarities with less than four sites: {'ASP:plan': 3, 'GLN:plan1': 2, 'ASN:plan1': 2, 'GLU:plan': 1, 'ARG:plan': 1}
          Unresolved non-hydrogen planarities: 32
    Chain: "C"
      Number of atoms: 381
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 53, 381
          Classifications: {'peptide': 53}
          Incomplete info: {'truncation_to_alanine': 7}
          Link IDs: {'PTRANS': 4, 'TRANS': 48}
          Unresolved non-hydrogen bonds: 26
          Unresolved non-hydrogen angles: 31
          Unresolved non-hydrogen dihedrals: 21
          Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 2, 'ASP:plan': 2}
          Unresolved non-hydrogen planarities: 18
    Chain: "E"
      Number of atoms: 1748
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 232, 1748
          Classifications: {'peptide': 232}
          Incomplete info: {'truncation_to_alanine': 13}
          Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 221}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 35
          Unresolved non-hydrogen angles: 43
          Unresolved non-hydrogen dihedrals: 27
          Unresolved non-hydrogen chiralities: 1
          Planarities with less than four sites: {'GLU:plan': 5, 'ASP:plan': 2}
          Unresolved non-hydrogen planarities: 26
    Chain: "R"
      Number of atoms: 2097
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 281, 2097
          Classifications: {'peptide': 281}
          Incomplete info: {'truncation_to_alanine': 50}
          Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 270}
          Unresolved non-hydrogen bonds: 165
          Unresolved non-hydrogen angles: 209
          Unresolved non-hydrogen dihedrals: 139
          Unresolved non-hydrogen chiralities: 23
          Planarities with less than four sites: {'ARG:plan': 2, 'ASN:plan1': 1, 'GLN:plan1': 1, 'PHE:plan': 3, 'HIS:plan': 1, 'TRP:plan': 1, 'TYR:plan': 1, 'GLU:plan': 1}
          Unresolved non-hydrogen planarities: 60
    Chain: "D"
      Number of atoms: 12
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 12
          Classifications: {'peptide': 1}
    Chain: "D"
      Number of atoms: 21
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 3, 21
          Classifications: {'peptide': 3}
          Modifications used: {'PEPT-D': 1}
          Link IDs: {'TRANS': 2}
          Unresolved non-hydrogen bonds: 1
          Unresolved non-hydrogen angles: 2
          Planarities with less than four sites: {'MEA:plan-2': 1}
          Unresolved non-hydrogen planarities: 1
    Chain: "D"
      Number of atoms: 4
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 4
          Unusual residues: {'ETA': 1}
          Classifications: {'undetermined': 1}
  Time building chain proxies: 2.21, per 1000 atoms: 0.26
  Number of scatterers: 8489
  At special positions: 0
  Unit cell: (100.88, 118.56, 112.32, 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      60     16.00
     O    1556      8.00
     N    1457      7.00
     C    5416      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=3, symmetry=0
    Simple disulfide: pdb=" SG  CYS E  22 " - pdb=" SG  CYS E  96 " distance=2.04
    Simple disulfide: pdb=" SG  CYS E 147 " - pdb=" SG  CYS E 217 " distance=2.70
    Simple disulfide: pdb=" SG  CYS R 140 " - pdb=" SG  CYS R 217 " distance=2.03

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=1, symmetry=0
  Links applied
    TRANS
      " DAL D   2 " - " TYR D   1 "
  Number of additional bonds: simple=1, symmetry=0
  Coordination:
  Other bonds:
  Time building additional restraints: 0.67
  Conformation dependent library (CDL) restraints added in 466.1 milliseconds
  

  2206 Ramachandran restraints generated.
    1103 Oldfield, 0 Emsley, 1103 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
    Skipped
      Input residue name is d-peptide
        pdb=" CB  DAL D   2 "
  Number of C-beta restraints generated:  2102

  Finding SS restraints...
    Secondary structure from input PDB file:
      26 helices and 16 sheets defined
      35.1% alpha, 23.6% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.35
  Creating SS restraints...
    Processing helix  chain 'A' and resid 8 through 33
      removed outlier: 3.834A  pdb=" N   ALA A  12 " --> pdb=" O   GLU A   8 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 207 through 216
      removed outlier: 3.989A  pdb=" N   ILE A 212 " --> pdb=" O   LYS A 209 " (cutoff:3.500A)
      removed outlier: 5.855A  pdb=" N   HIS A 213 " --> pdb=" O   LYS A 210 " (cutoff:3.500A)
      removed outlier: 3.730A  pdb=" N   GLU A 216 " --> pdb=" O   HIS A 213 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 242 through 255
    Processing helix  chain 'A' and resid 256 through 260
      removed outlier: 4.191A  pdb=" N   THR A 260 " --> pdb=" O   LYS A 257 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 270 through 275
    Processing helix  chain 'A' and resid 282 through 286
      removed outlier: 3.648A  pdb=" N   ILE A 285 " --> pdb=" O   PRO A 282 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 295 through 309
      removed outlier: 3.723A  pdb=" N   ALA A 300 " --> pdb=" O   TYR A 296 " (cutoff:3.500A)
      removed outlier: 5.502A  pdb=" N   ALA A 301 " --> pdb=" O   GLU A 297 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 330 through 352
      removed outlier: 3.529A  pdb=" N   LYS A 345 " --> pdb=" O   ASP A 341 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 6 through 25
      removed outlier: 3.710A  pdb=" N   ARG B  22 " --> pdb=" O   ILE B  18 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 11 through 24
      removed outlier: 4.109A  pdb=" N   ASN C  24 " --> pdb=" O   LYS C  20 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 29 through 33
    Processing helix  chain 'C' and resid 34 through 43
    Processing helix  chain 'E' and resid 28 through 32
    Processing helix  chain 'E' and resid 87 through 91
    Processing helix  chain 'R' and resid 67 through 97
      removed outlier: 4.307A  pdb=" N   ALA R  73 " --> pdb=" O   ILE R  69 " (cutoff:3.500A)
      removed outlier: 4.346A  pdb=" N   VAL R  78 " --> pdb=" O   LEU R  74 " (cutoff:3.500A)
      removed outlier: 4.091A  pdb=" N   CYS R  79 " --> pdb=" O   TYR R  75 " (cutoff:3.500A)
      removed outlier: 3.528A  pdb=" N   THR R  97 " --> pdb=" O   ILE R  93 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 102 through 120
      removed outlier: 3.589A  pdb=" N   TYR R 106 " --> pdb=" O   ALA R 102 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 120 through 125
      removed outlier: 4.160A  pdb=" N   GLN R 124 " --> pdb=" O   THR R 120 " (cutoff:3.500A)
      removed outlier: 4.078A  pdb=" N   SER R 125 " --> pdb=" O   LEU R 121 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'R' and resid 120 through 125'
    Processing helix  chain 'R' and resid 126 through 128
      No H-bonds generated for 'chain 'R' and resid 126 through 128'
    Processing helix  chain 'R' and resid 136 through 171
      removed outlier: 4.077A  pdb=" N   LYS R 141 " --> pdb=" O   ASN R 137 " (cutoff:3.500A)
      removed outlier: 5.220A  pdb=" N   ILE R 142 " --> pdb=" O   ILE R 138 " (cutoff:3.500A)
      removed outlier: 3.892A  pdb=" N   PHE R 152 " --> pdb=" O   TYR R 148 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 171 through 179
      removed outlier: 3.758A  pdb=" N   ASP R 177 " --> pdb=" O   VAL R 173 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 180 through 205
      removed outlier: 3.764A  pdb=" N   ILE R 198 " --> pdb=" O   LEU R 194 " (cutoff:3.500A)
      Proline residue:  R 201  - end of helix
    Processing helix  chain 'R' and resid 227 through 241
      removed outlier: 3.662A  pdb=" N   LEU R 231 " --> pdb=" O   TYR R 227 " (cutoff:3.500A)
      removed outlier: 3.776A  pdb=" N   LEU R 232 " --> pdb=" O   TRP R 228 " (cutoff:3.500A)
      removed outlier: 3.543A  pdb=" N   LYS R 233 " --> pdb=" O   GLU R 229 " (cutoff:3.500A)
      removed outlier: 3.807A  pdb=" N   ILE R 234 " --> pdb=" O   ASN R 230 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 241 through 260
      removed outlier: 4.180A  pdb=" N   VAL R 250 " --> pdb=" O   LEU R 246 " (cutoff:3.500A)
      removed outlier: 3.580A  pdb=" N   TYR R 252 " --> pdb=" O   ILE R 248 " (cutoff:3.500A)
      removed outlier: 4.378A  pdb=" N   MET R 255 " --> pdb=" O   CYS R 251 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 269 through 294
    Processing helix  chain 'R' and resid 294 through 306
      removed outlier: 3.764A  pdb=" N   VAL R 300 " --> pdb=" O   ILE R 296 " (cutoff:3.500A)
      removed outlier: 3.810A  pdb=" N   ILE R 301 " --> pdb=" O   HIS R 297 " (cutoff:3.500A)
      removed outlier: 3.902A  pdb=" N   ALA R 304 " --> pdb=" O   VAL R 300 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 313 through 339
      removed outlier: 3.686A  pdb=" N   SER R 317 " --> pdb=" O   PHE R 313 " (cutoff:3.500A)
      removed outlier: 4.180A  pdb=" N   ASN R 328 " --> pdb=" O   LEU R 324 " (cutoff:3.500A)
      removed outlier: 4.445A  pdb=" N   SER R 329 " --> pdb=" O   GLY R 325 " (cutoff:3.500A)
      Proline residue:  R 333  - end of helix
      removed outlier: 3.837A  pdb=" N   PHE R 338 " --> pdb=" O   VAL R 334 " (cutoff:3.500A)
      removed outlier: 3.709A  pdb=" N   LEU R 339 " --> pdb=" O   LEU R 335 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 186 through 190
      removed outlier: 7.082A  pdb=" N   LYS A  35 " --> pdb=" O   ALA A 220 " (cutoff:3.500A)
      removed outlier: 7.992A  pdb=" N   ILE A 222 " --> pdb=" O   LYS A  35 " (cutoff:3.500A)
      removed outlier: 6.518A  pdb=" N   LEU A  37 " --> pdb=" O   ILE A 222 " (cutoff:3.500A)
      removed outlier: 7.366A  pdb=" N   CYS A 224 " --> pdb=" O   LEU A  37 " (cutoff:3.500A)
      removed outlier: 6.714A  pdb=" N   LEU A  39 " --> pdb=" O   CYS A 224 " (cutoff:3.500A)
      removed outlier: 8.856A  pdb=" N   ALA A 226 " --> pdb=" O   LEU A  39 " (cutoff:3.500A)
      removed outlier: 7.487A  pdb=" N   ASN A 269 " --> pdb=" O   PHE A 223 " (cutoff:3.500A)
      removed outlier: 7.308A  pdb=" N   VAL A 225 " --> pdb=" O   ASN A 269 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 186 through 190
      removed outlier: 7.082A  pdb=" N   LYS A  35 " --> pdb=" O   ALA A 220 " (cutoff:3.500A)
      removed outlier: 7.992A  pdb=" N   ILE A 222 " --> pdb=" O   LYS A  35 " (cutoff:3.500A)
      removed outlier: 6.518A  pdb=" N   LEU A  37 " --> pdb=" O   ILE A 222 " (cutoff:3.500A)
      removed outlier: 7.366A  pdb=" N   CYS A 224 " --> pdb=" O   LEU A  37 " (cutoff:3.500A)
      removed outlier: 6.714A  pdb=" N   LEU A  39 " --> pdb=" O   CYS A 224 " (cutoff:3.500A)
      removed outlier: 8.856A  pdb=" N   ALA A 226 " --> pdb=" O   LEU A  39 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'B' and resid 47 through 51
      removed outlier: 6.823A  pdb=" N   ILE B 338 " --> pdb=" O   ARG B  48 " (cutoff:3.500A)
      removed outlier: 4.853A  pdb=" N   THR B  50 " --> pdb=" O   LEU B 336 " (cutoff:3.500A)
      removed outlier: 6.346A  pdb=" N   LEU B 336 " --> pdb=" O   THR B  50 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'B' and resid 62 through 63
      removed outlier: 3.636A  pdb=" N   HIS B  62 " --> pdb=" O   VAL B  71 " (cutoff:3.500A)
      removed outlier: 4.237A  pdb=" N   LEU B  70 " --> pdb=" O   TRP B  82 " (cutoff:3.500A)
      removed outlier: 6.353A  pdb=" N   LEU B  79 " --> pdb=" O   ALA B  92 " (cutoff:3.500A)
      removed outlier: 4.735A  pdb=" N   ALA B  92 " --> pdb=" O   LEU B  79 " (cutoff:3.500A)
      removed outlier: 6.608A  pdb=" N   ILE B  81 " --> pdb=" O   VAL B  90 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'B' and resid 104 through 105
      removed outlier: 3.529A  pdb=" N   VAL B 112 " --> pdb=" O   TYR B 124 " (cutoff:3.500A)
      removed outlier: 3.529A  pdb=" N   ILE B 123 " --> pdb=" O   ARG B 137 " (cutoff:3.500A)
      removed outlier: 3.615A  pdb=" N   ARG B 137 " --> pdb=" O   ILE B 123 " (cutoff:3.500A)
      removed outlier: 6.445A  pdb=" N   ASN B 125 " --> pdb=" O   VAL B 135 " (cutoff:3.500A)
      removed outlier: 5.986A  pdb=" N   VAL B 135 " --> pdb=" O   ASN B 125 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'B' and resid 146 through 151
      removed outlier: 3.690A  pdb=" N   CYS B 148 " --> pdb=" O   SER B 160 " (cutoff:3.500A)
      removed outlier: 3.812A  pdb=" N   ILE B 157 " --> pdb=" O   TRP B 169 " (cutoff:3.500A)
      removed outlier: 3.589A  pdb=" N   ALA B 167 " --> pdb=" O   THR B 159 " (cutoff:3.500A)
      removed outlier: 3.628A  pdb=" N   THR B 165 " --> pdb=" O   SER B 161 " (cutoff:3.500A)
      removed outlier: 7.024A  pdb=" N   ASP B 170 " --> pdb=" O   GLN B 176 " (cutoff:3.500A)
      removed outlier: 6.483A  pdb=" N   GLN B 176 " --> pdb=" O   ASP B 170 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'B' and resid 189 through 191
      removed outlier: 3.809A  pdb=" N   GLN B 220 " --> pdb=" O   LEU B 210 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'B' and resid 229 through 234
      removed outlier: 3.563A  pdb=" N   ALA B 231 " --> pdb=" O   GLY B 244 " (cutoff:3.500A)
      removed outlier: 6.338A  pdb=" N   ASP B 254 " --> pdb=" O   GLU B 260 " (cutoff:3.500A)
      removed outlier: 6.012A  pdb=" N   GLU B 260 " --> pdb=" O   ASP B 254 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'B' and resid 273 through 278
      removed outlier: 3.569A  pdb=" N   SER B 275 " --> pdb=" O   GLY B 288 " (cutoff:3.500A)
      removed outlier: 6.512A  pdb=" N   VAL B 296 " --> pdb=" O   ALA B 305 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'B' and resid 315 through 320
      removed outlier: 6.937A  pdb=" N   GLY B 330 " --> pdb=" O   SER B 316 " (cutoff:3.500A)
      removed outlier: 4.198A  pdb=" N   LEU B 318 " --> pdb=" O   ALA B 328 " (cutoff:3.500A)
      removed outlier: 5.987A  pdb=" N   ALA B 328 " --> pdb=" O   LEU B 318 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'E' and resid 3 through 7
    Processing sheet with id=AB3, first strand: chain 'E' and resid 10 through 12
      removed outlier: 3.653A  pdb=" N   ALA E  92 " --> pdb=" O   LEU E 117 " (cutoff:3.500A)
      removed outlier: 6.589A  pdb=" N   MET E  34 " --> pdb=" O   TYR E  50 " (cutoff:3.500A)
      removed outlier: 4.306A  pdb=" N   TYR E  50 " --> pdb=" O   MET E  34 " (cutoff:3.500A)
      removed outlier: 6.539A  pdb=" N   TRP E  36 " --> pdb=" O   VAL E  48 " (cutoff:3.500A)
    Processing sheet with id=AB4, first strand: chain 'E' and resid 10 through 12
      removed outlier: 3.653A  pdb=" N   ALA E  92 " --> pdb=" O   LEU E 117 " (cutoff:3.500A)
      removed outlier: 4.317A  pdb=" N   PHE E 110 " --> pdb=" O   ARG E  98 " (cutoff:3.500A)
    Processing sheet with id=AB5, first strand: chain 'E' and resid 128 through 129
      removed outlier: 3.538A  pdb=" N   ARG E 148 " --> pdb=" O   THR E 129 " (cutoff:3.500A)
      removed outlier: 3.532A  pdb=" N   ALA E 199 " --> pdb=" O   SER E 196 " (cutoff:3.500A)
    Processing sheet with id=AB6, first strand: chain 'E' and resid 134 through 136
      removed outlier: 6.728A  pdb=" N   LEU E 162 " --> pdb=" O   TYR E 178 " (cutoff:3.500A)
      removed outlier: 5.017A  pdb=" N   TYR E 178 " --> pdb=" O   LEU E 162 " (cutoff:3.500A)
      removed outlier: 6.816A  pdb=" N   TRP E 164 " --> pdb=" O   LEU E 176 " (cutoff:3.500A)
    Processing sheet with id=AB7, first strand: chain 'E' and resid 134 through 136
      removed outlier: 3.796A  pdb=" N   THR E 226 " --> pdb=" O   GLN E 219 " (cutoff:3.500A)

    402 hydrogen bonds defined for protein.
    1110 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 1.57

  Time building geometry restraints manager: 0.97 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: 2712
        1.34 -     1.46: 2067
        1.46 -     1.58: 3798
        1.58 -     1.70: 0
        1.70 -     1.82: 87
  Bond restraints: 8664
  Sorted by residual:
  bond pdb=" C   THR E 138 "
       pdb=" N   PRO E 139 "
    ideal  model  delta    sigma   weight residual
    1.332  1.375 -0.044 1.34e-02 5.57e+03 1.06e+01
  bond pdb=" O   ETA D   5 "
       pdb=" CB  ETA D   5 "
    ideal  model  delta    sigma   weight residual
    1.413  1.459 -0.046 2.00e-02 2.50e+03 5.35e+00
  bond pdb=" C   ASP E  74 "
       pdb=" N   PRO E  75 "
    ideal  model  delta    sigma   weight residual
    1.335  1.363 -0.028 1.36e-02 5.41e+03 4.16e+00
  bond pdb=" N   GLU E 210 "
       pdb=" CA  GLU E 210 "
    ideal  model  delta    sigma   weight residual
    1.457  1.483 -0.025 1.29e-02 6.01e+03 3.85e+00
  bond pdb=" CG  LEU A 227 "
       pdb=" CD2 LEU A 227 "
    ideal  model  delta    sigma   weight residual
    1.521  1.461  0.060 3.30e-02 9.18e+02 3.31e+00
  ... (remaining 8659 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.97: 11086
        1.97 -     3.94: 577
        3.94 -     5.92: 63
        5.92 -     7.89: 27
        7.89 -     9.86: 13
  Bond angle restraints: 11766
  Sorted by residual:
  angle pdb=" N   ILE B  33 "
        pdb=" CA  ILE B  33 "
        pdb=" C   ILE B  33 "
      ideal   model   delta    sigma   weight residual
     111.91  106.14    5.77 8.90e-01 1.26e+00 4.20e+01
  angle pdb=" CA  ARG E 206 "
        pdb=" CB  ARG E 206 "
        pdb=" CG  ARG E 206 "
      ideal   model   delta    sigma   weight residual
     114.10  123.60   -9.50 2.00e+00 2.50e-01 2.26e+01
  angle pdb=" N   GLY B 131 "
        pdb=" CA  GLY B 131 "
        pdb=" C   GLY B 131 "
      ideal   model   delta    sigma   weight residual
     111.45  116.63   -5.18 1.23e+00 6.61e-01 1.77e+01
  angle pdb=" N   THR E 116 "
        pdb=" CA  THR E 116 "
        pdb=" C   THR E 116 "
      ideal   model   delta    sigma   weight residual
     109.24  102.47    6.77 1.63e+00 3.76e-01 1.73e+01
  angle pdb=" C   ARG E 179 "
        pdb=" N   MET E 180 "
        pdb=" CA  MET E 180 "
      ideal   model   delta    sigma   weight residual
     121.54  129.40   -7.86 1.91e+00 2.74e-01 1.69e+01
  ... (remaining 11761 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    15.14: 4770
       15.14 -    30.28: 253
       30.28 -    45.41: 69
       45.41 -    60.55: 9
       60.55 -    75.69: 4
  Dihedral angle restraints: 5105
    sinusoidal: 1846
      harmonic: 3259
  Sorted by residual:
  dihedral pdb=" CA  LEU B  30 "
           pdb=" C   LEU B  30 "
           pdb=" N   SER B  31 "
           pdb=" CA  SER B  31 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  151.47   28.53     0      5.00e+00 4.00e-02 3.26e+01
  dihedral pdb=" CA  TRP B 169 "
           pdb=" C   TRP B 169 "
           pdb=" N   ASP B 170 "
           pdb=" CA  ASP B 170 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  153.38   26.62     0      5.00e+00 4.00e-02 2.83e+01
  dihedral pdb=" CA  SER R 268 "
           pdb=" C   SER R 268 "
           pdb=" N   LYS R 269 "
           pdb=" CA  LYS R 269 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -153.66  -26.34     0      5.00e+00 4.00e-02 2.78e+01
  ... (remaining 5102 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.051: 931
       0.051 -    0.102: 312
       0.102 -    0.153: 90
       0.153 -    0.204: 24
       0.204 -    0.255: 5
  Chirality restraints: 1362
  Sorted by residual:
  chirality pdb=" CA  VAL E  12 "
            pdb=" N   VAL E  12 "
            pdb=" C   VAL E  12 "
            pdb=" CB  VAL E  12 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.70   -0.25 2.00e-01 2.50e+01 1.62e+00
  chirality pdb=" CB  ILE E 100 "
            pdb=" CA  ILE E 100 "
            pdb=" CG1 ILE E 100 "
            pdb=" CG2 ILE E 100 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.40    0.24 2.00e-01 2.50e+01 1.48e+00
  chirality pdb=" CB  ILE R 308 "
            pdb=" CA  ILE R 308 "
            pdb=" CG1 ILE R 308 "
            pdb=" CG2 ILE R 308 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.42    0.22 2.00e-01 2.50e+01 1.24e+00
  ... (remaining 1359 not shown)

  Planarity restraints: 1485
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ALA E  61 "   -0.013 2.00e-02 2.50e+03   2.60e-02 6.76e+00
        pdb=" C   ALA E  61 "    0.045 2.00e-02 2.50e+03
        pdb=" O   ALA E  61 "   -0.017 2.00e-02 2.50e+03
        pdb=" N   ASP E  62 "   -0.015 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TRP B  63 "    0.014 2.00e-02 2.50e+03   1.61e-02 6.48e+00
        pdb=" CG  TRP B  63 "   -0.041 2.00e-02 2.50e+03
        pdb=" CD1 TRP B  63 "    0.025 2.00e-02 2.50e+03
        pdb=" CD2 TRP B  63 "   -0.002 2.00e-02 2.50e+03
        pdb=" NE1 TRP B  63 "   -0.000 2.00e-02 2.50e+03
        pdb=" CE2 TRP B  63 "   -0.003 2.00e-02 2.50e+03
        pdb=" CE3 TRP B  63 "    0.002 2.00e-02 2.50e+03
        pdb=" CZ2 TRP B  63 "   -0.003 2.00e-02 2.50e+03
        pdb=" CZ3 TRP B  63 "    0.009 2.00e-02 2.50e+03
        pdb=" CH2 TRP B  63 "    0.001 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ASP C  48 "    0.041 5.00e-02 4.00e+02   6.18e-02 6.11e+00
        pdb=" N   PRO C  49 "   -0.107 5.00e-02 4.00e+02
        pdb=" CA  PRO C  49 "    0.032 5.00e-02 4.00e+02
        pdb=" CD  PRO C  49 "    0.034 5.00e-02 4.00e+02
  ... (remaining 1482 not shown)

  Histogram of nonbonded interaction distances:
        2.24 -     2.77: 1755
        2.77 -     3.31: 7700
        3.31 -     3.84: 14166
        3.84 -     4.37: 15799
        4.37 -     4.90: 27949
  Nonbonded interactions: 67369
  Sorted by model distance:
  nonbonded pdb=" OH  TYR A 230 "
            pdb=" O   LYS A 277 "
     model   vdw
     2.242 3.040
  nonbonded pdb=" OG1 THR B  34 "
            pdb=" O   LEU B 300 "
     model   vdw
     2.251 3.040
  nonbonded pdb=" N   THR B 143 "
            pdb=" OD2 ASP B 163 "
     model   vdw
     2.265 3.120
  nonbonded pdb=" OG  SER B  74 "
            pdb=" OD1 ASP B  76 "
     model   vdw
     2.269 3.040
  nonbonded pdb=" OH  TYR A 320 "
            pdb=" OD2 ASP A 341 "
     model   vdw
     2.290 3.040
  ... (remaining 67364 not shown)

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

  No NCS relation were found !!!

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

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as 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:             1.300
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.010
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.150
  Check model and map are aligned:         0.020
  Set scattering table:                    0.030
  Process input model:                     10.140
  Find NCS groups from input model:        0.040
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.960
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   13.670
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7241
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      :  0.010   0.673   8669  Z= 0.474
  Angle     :  1.055  24.760  11775  Z= 0.581
  Chirality :  0.059   0.255   1362
  Planarity :  0.006   0.062   1484
  Dihedral  : 10.869  75.688   2991
  Min Nonbonded Distance : 2.242

Molprobity Statistics.
  All-atom Clashscore : 6.97
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  :  6.89 %
    Favored  : 93.02 %
  Rotamer:
    Outliers :  0.46 %
    Allowed  :  6.00 %
    Favored  : 93.53 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.45 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -3.56 (0.21), residues: 1103
  helix: -2.51 (0.20), residues: 348
  sheet: -2.14 (0.29), residues: 256
  loop : -2.22 (0.25), residues: 499

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.018   0.001   ARG B  68 
 TYR   0.030   0.003   TYR E 163 
 PHE   0.028   0.003   PHE B 241 
 TRP   0.041   0.004   TRP B  63 
 HIS   0.011   0.003   HIS E 155 

Details of bonding type rmsd
  covalent geometry    : bond        0.00636 ( 8664)
  covalent geometry    : angle       1.02633 (11766)
  SS BOND              : bond        0.38853 (    3)
  SS BOND              : angle      10.88787 (    6)
  hydrogen bonds       : bond        0.14558 (  383)
  hydrogen bonds       : angle       7.60947 ( 1110)
  Misc. bond           : bond        0.09878 (    1)
  link_TRANS           : bond        0.00251 (    1)
  link_TRANS           : angle       0.43157 (    3)

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

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

  2206 Ramachandran restraints generated.
    1103 Oldfield, 0 Emsley, 1103 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2206 Ramachandran restraints generated.
    1103 Oldfield, 0 Emsley, 1103 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  366 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 362
  time to evaluate  : 0.355 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   14 GLU cc_start: 0.7172 (tm-30) cc_final: 0.6898 (tm-30)
REVERT: A  309 ASP cc_start: 0.7384 (t0) cc_final: 0.7153 (t0)
REVERT: A  341 ASP cc_start: 0.8439 (t70) cc_final: 0.8170 (t0)
REVERT: B   86 THR cc_start: 0.8060 (p) cc_final: 0.7552 (p)
REVERT: B  163 ASP cc_start: 0.7499 (p0) cc_final: 0.7240 (p0)
REVERT: B  221 THR cc_start: 0.8150 (m) cc_final: 0.7823 (m)
REVERT: B  339 TRP cc_start: 0.8617 (m100) cc_final: 0.8210 (m100)
REVERT: E    7 SER cc_start: 0.8095 (p) cc_final: 0.7554 (t)
REVERT: E  130 GLN cc_start: 0.6596 (tp40) cc_final: 0.6065 (mt0)
REVERT: R  112 LEU cc_start: 0.9102 (tp) cc_final: 0.8888 (tt)
REVERT: R  145 SER cc_start: 0.8369 (t) cc_final: 0.7708 (m)
REVERT: R  228 TRP cc_start: 0.7285 (t-100) cc_final: 0.7051 (t-100)
REVERT: R  261 SER cc_start: 0.8665 (m) cc_final: 0.8283 (t)
REVERT: R  263 ARG cc_start: 0.8061 (tmt90) cc_final: 0.7791 (tpt90)
REVERT: R  270 GLU cc_start: 0.8079 (tm-30) cc_final: 0.7597 (tm-30)
  outliers start: 4
  outliers final: 1
  residues processed: 365
  average time/residue: 0.1135
  time to fit residues: 54.4417
Evaluate side-chains
  234 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 233
  time to evaluate  : 0.305 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  168 LEU
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 110
   random chunks:
   chunk 108 optimal weight:    0.7980
   chunk 49 optimal weight:    0.8980
   chunk 97 optimal weight:    0.0980
   chunk 53 optimal weight:    0.5980
   chunk 5 optimal weight:    0.9980
   chunk 33 optimal weight:    2.9990
   chunk 65 optimal weight:    0.8980
   chunk 62 optimal weight:    0.6980
   chunk 51 optimal weight:    9.9990
   chunk 100 optimal weight:    5.9990
   chunk 106 optimal weight:    4.9990
   overall best weight:    0.6180

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

Flipped N/Q/H residues before XYZ refinement:
A 241 ASN
A 347 ASN
B 110 ASN
B 295 ASN
E 130 GLN
E 171 GLN
E 174 GLN
E 182 ASN
R  86 ASN
** R 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
R 127 ASN
R 230 ASN
R 297 HIS
R 328 ASN

Total number of N/Q/H flips: 13

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4187 r_free = 0.4187 target = 0.172364 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3856 r_free = 0.3856 target = 0.143685 restraints weight = 12992.240|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.3917 r_free = 0.3917 target = 0.148501 restraints weight = 6684.259|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 41)----------------|
| r_work = 0.3957 r_free = 0.3957 target = 0.151640 restraints weight = 4226.028|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 27)----------------|
| r_work = 0.3979 r_free = 0.3979 target = 0.153586 restraints weight = 3025.502|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 46)----------------|
| r_work = 0.4000 r_free = 0.4000 target = 0.155090 restraints weight = 2369.579|
|-----------------------------------------------------------------------------|
r_work (final): 0.4043
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7269
moved from start:          0.3038

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039   8669  Z= 0.141
  Angle     :  0.665  10.747  11775  Z= 0.342
  Chirality :  0.043   0.201   1362
  Planarity :  0.004   0.041   1484
  Dihedral  :  5.538  69.171   1214
  Min Nonbonded Distance : 2.524

Molprobity Statistics.
  All-atom Clashscore : 11.06
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.35 %
    Favored  : 95.65 %
  Rotamer:
    Outliers :  3.93 %
    Allowed  : 17.78 %
    Favored  : 78.29 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.45 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.05 (0.24), residues: 1103
  helix: -0.49 (0.27), residues: 347
  sheet: -1.72 (0.31), residues: 239
  loop : -1.71 (0.26), residues: 517

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG A  21 
 TYR   0.019   0.002   TYR R  75 
 PHE   0.016   0.002   PHE R 241 
 TRP   0.019   0.002   TRP B 169 
 HIS   0.004   0.001   HIS B 183 

Details of bonding type rmsd
  covalent geometry    : bond        0.00317 ( 8664)
  covalent geometry    : angle       0.66458 (11766)
  SS BOND              : bond        0.01456 (    3)
  SS BOND              : angle       1.15250 (    6)
  hydrogen bonds       : bond        0.03596 (  383)
  hydrogen bonds       : angle       5.39557 ( 1110)
  Misc. bond           : bond        0.00010 (    1)
  link_TRANS           : bond        0.00062 (    1)
  link_TRANS           : angle       0.32653 (    3)

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

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

  2206 Ramachandran restraints generated.
    1103 Oldfield, 0 Emsley, 1103 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2206 Ramachandran restraints generated.
    1103 Oldfield, 0 Emsley, 1103 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  297 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 263
  time to evaluate  : 0.339 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   14 GLU cc_start: 0.7687 (tm-30) cc_final: 0.7192 (tm-30)
REVERT: A   51 LYS cc_start: 0.8577 (ttmp) cc_final: 0.8183 (tmmt)
REVERT: A  309 ASP cc_start: 0.7590 (t0) cc_final: 0.7364 (t0)
REVERT: A  341 ASP cc_start: 0.8715 (t70) cc_final: 0.8494 (t0)
REVERT: B   74 SER cc_start: 0.8984 (p) cc_final: 0.8334 (t)
REVERT: B   82 TRP cc_start: 0.8930 (m100) cc_final: 0.8686 (m100)
REVERT: B  117 LEU cc_start: 0.7978 (OUTLIER) cc_final: 0.7309 (tt)
REVERT: B  163 ASP cc_start: 0.7858 (p0) cc_final: 0.7616 (p0)
REVERT: B  280 LYS cc_start: 0.8091 (tmmt) cc_final: 0.7852 (tttt)
REVERT: B  339 TRP cc_start: 0.8761 (m100) cc_final: 0.8196 (m-10)
REVERT: E  115 THR cc_start: 0.8637 (OUTLIER) cc_final: 0.8245 (p)
REVERT: E  130 GLN cc_start: 0.6305 (tp-100) cc_final: 0.5606 (mt0)
REVERT: R  145 SER cc_start: 0.8158 (t) cc_final: 0.7465 (p)
REVERT: R  165 ARG cc_start: 0.8421 (mtt90) cc_final: 0.8176 (mtt90)
REVERT: R  185 LYS cc_start: 0.8580 (ttmp) cc_final: 0.8044 (tptt)
REVERT: R  228 TRP cc_start: 0.7474 (t-100) cc_final: 0.7141 (t-100)
REVERT: R  263 ARG cc_start: 0.8273 (tmt90) cc_final: 0.7862 (tmt170)
REVERT: R  270 GLU cc_start: 0.8153 (tm-30) cc_final: 0.7867 (tm-30)
REVERT: R  298 ILE cc_start: 0.7387 (OUTLIER) cc_final: 0.7166 (pt)
REVERT: R  336 TYR cc_start: 0.7154 (m-10) cc_final: 0.6927 (m-80)
  outliers start: 34
  outliers final: 18
  residues processed: 286
  average time/residue: 0.1105
  time to fit residues: 41.9368
Evaluate side-chains
  248 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 227
  time to evaluate  : 0.361 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   34 VAL
Chi-restraints excluded: chain A residue   44 SER
Chi-restraints excluded: chain A residue  227 LEU
Chi-restraints excluded: chain A residue  254 CYS
Chi-restraints excluded: chain B residue  117 LEU
Chi-restraints excluded: chain B residue  148 CYS
Chi-restraints excluded: chain B residue  168 LEU
Chi-restraints excluded: chain B residue  181 THR
Chi-restraints excluded: chain B residue  189 SER
Chi-restraints excluded: chain B residue  190 LEU
Chi-restraints excluded: chain C residue   16 VAL
Chi-restraints excluded: chain E residue  115 THR
Chi-restraints excluded: chain E residue  212 VAL
Chi-restraints excluded: chain E residue  217 CYS
Chi-restraints excluded: chain R residue  119 SER
Chi-restraints excluded: chain R residue  120 THR
Chi-restraints excluded: chain R residue  154 SER
Chi-restraints excluded: chain R residue  245 VAL
Chi-restraints excluded: chain R residue  290 ILE
Chi-restraints excluded: chain R residue  298 ILE
Chi-restraints excluded: chain R residue  330 CYS
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 110
   random chunks:
   chunk 5 optimal weight:    4.9990
   chunk 56 optimal weight:    0.5980
   chunk 91 optimal weight:    7.9990
   chunk 69 optimal weight:    1.9990
   chunk 18 optimal weight:    4.9990
   chunk 83 optimal weight:    1.9990
   chunk 64 optimal weight:    1.9990
   chunk 109 optimal weight:    6.9990
   chunk 49 optimal weight:    5.9990
   chunk 10 optimal weight:    4.9990
   chunk 77 optimal weight:    3.9990
   overall best weight:    2.1188

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

Flipped N/Q/H residues before XYZ refinement:
A 306 GLN
A 347 ASN
B  88 ASN
B 340 ASN
** R 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
R 150 ASN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4102 r_free = 0.4102 target = 0.164402 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3785 r_free = 0.3785 target = 0.136659 restraints weight = 13145.310|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3820 r_free = 0.3820 target = 0.140705 restraints weight = 7472.472|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3840 r_free = 0.3840 target = 0.142293 restraints weight = 4544.534|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 27)----------------|
| r_work = 0.3843 r_free = 0.3843 target = 0.142586 restraints weight = 3825.200|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3854 r_free = 0.3854 target = 0.143557 restraints weight = 3558.973|
|-----------------------------------------------------------------------------|
r_work (final): 0.4013
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7393
moved from start:          0.3802

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.057   8669  Z= 0.281
  Angle     :  0.756   8.669  11775  Z= 0.389
  Chirality :  0.046   0.216   1362
  Planarity :  0.005   0.043   1484
  Dihedral  :  5.637  65.581   1214
  Min Nonbonded Distance : 2.469

Molprobity Statistics.
  All-atom Clashscore : 13.94
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.07 %
    Favored  : 93.93 %
  Rotamer:
    Outliers :  6.24 %
    Allowed  : 18.59 %
    Favored  : 75.17 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.45 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.62 (0.25), residues: 1103
  helix: -0.03 (0.28), residues: 351
  sheet: -1.67 (0.31), residues: 249
  loop : -1.41 (0.28), residues: 503

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG E  38 
 TYR   0.029   0.003   TYR E  94 
 PHE   0.018   0.002   PHE B 241 
 TRP   0.027   0.003   TRP B 169 
 HIS   0.007   0.002   HIS B 183 

Details of bonding type rmsd
  covalent geometry    : bond        0.00645 ( 8664)
  covalent geometry    : angle       0.75510 (11766)
  SS BOND              : bond        0.00748 (    3)
  SS BOND              : angle       1.76106 (    6)
  hydrogen bonds       : bond        0.03749 (  383)
  hydrogen bonds       : angle       5.33233 ( 1110)
  Misc. bond           : bond        0.00002 (    1)
  link_TRANS           : bond        0.00190 (    1)
  link_TRANS           : angle       0.24144 (    3)

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

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

  2206 Ramachandran restraints generated.
    1103 Oldfield, 0 Emsley, 1103 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2206 Ramachandran restraints generated.
    1103 Oldfield, 0 Emsley, 1103 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  292 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 54
    poor density    : 238
  time to evaluate  : 0.314 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   14 GLU cc_start: 0.8202 (tm-30) cc_final: 0.7625 (tm-30)
REVERT: A   18 MET cc_start: 0.8046 (tpp) cc_final: 0.7741 (tpp)
REVERT: A  216 GLU cc_start: 0.8166 (pp20) cc_final: 0.7704 (pp20)
REVERT: A  302 TYR cc_start: 0.7926 (t80) cc_final: 0.7427 (t80)
REVERT: A  341 ASP cc_start: 0.8786 (t70) cc_final: 0.8418 (t0)
REVERT: A  347 ASN cc_start: 0.9431 (m-40) cc_final: 0.9036 (m-40)
REVERT: B   23 LYS cc_start: 0.7485 (tptt) cc_final: 0.7093 (mptt)
REVERT: B   34 THR cc_start: 0.7179 (t) cc_final: 0.6083 (p)
REVERT: B  102 THR cc_start: 0.9027 (t) cc_final: 0.8697 (m)
REVERT: B  117 LEU cc_start: 0.8451 (OUTLIER) cc_final: 0.7814 (tt)
REVERT: B  230 ASN cc_start: 0.8205 (m110) cc_final: 0.7859 (m110)
REVERT: B  296 VAL cc_start: 0.9348 (t) cc_final: 0.9135 (m)
REVERT: B  339 TRP cc_start: 0.9043 (m100) cc_final: 0.8303 (m-10)
REVERT: E  206 ARG cc_start: 0.8305 (OUTLIER) cc_final: 0.8016 (mmp80)
REVERT: E  211 ASP cc_start: 0.6978 (OUTLIER) cc_final: 0.6736 (t0)
REVERT: R  106 TYR cc_start: 0.8825 (m-80) cc_final: 0.8559 (m-10)
REVERT: R  161 MET cc_start: 0.9009 (OUTLIER) cc_final: 0.8736 (tpp)
REVERT: R  164 ASP cc_start: 0.8773 (t70) cc_final: 0.8482 (t70)
REVERT: R  170 CYS cc_start: 0.7552 (t) cc_final: 0.7334 (t)
REVERT: R  185 LYS cc_start: 0.8732 (ttmp) cc_final: 0.8110 (tptt)
REVERT: R  228 TRP cc_start: 0.7534 (t-100) cc_final: 0.7189 (t-100)
REVERT: R  263 ARG cc_start: 0.8317 (tmt90) cc_final: 0.7782 (tmt170)
REVERT: R  270 GLU cc_start: 0.8294 (tm-30) cc_final: 0.8036 (tm-30)
  outliers start: 54
  outliers final: 35
  residues processed: 269
  average time/residue: 0.1130
  time to fit residues: 40.0382
Evaluate side-chains
  264 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 39
    poor density    : 225
  time to evaluate  : 0.314 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   34 VAL
Chi-restraints excluded: chain A residue   44 SER
Chi-restraints excluded: chain A residue  227 LEU
Chi-restraints excluded: chain A residue  254 CYS
Chi-restraints excluded: chain A residue  264 ILE
Chi-restraints excluded: chain A residue  332 VAL
Chi-restraints excluded: chain B residue   18 ILE
Chi-restraints excluded: chain B residue  117 LEU
Chi-restraints excluded: chain B residue  148 CYS
Chi-restraints excluded: chain B residue  168 LEU
Chi-restraints excluded: chain B residue  181 THR
Chi-restraints excluded: chain B residue  190 LEU
Chi-restraints excluded: chain B residue  262 MET
Chi-restraints excluded: chain B residue  263 THR
Chi-restraints excluded: chain B residue  271 CYS
Chi-restraints excluded: chain C residue   16 VAL
Chi-restraints excluded: chain C residue   37 LEU
Chi-restraints excluded: chain E residue    7 SER
Chi-restraints excluded: chain E residue   69 THR
Chi-restraints excluded: chain E residue  115 THR
Chi-restraints excluded: chain E residue  146 SER
Chi-restraints excluded: chain E residue  206 ARG
Chi-restraints excluded: chain E residue  211 ASP
Chi-restraints excluded: chain E residue  233 LEU
Chi-restraints excluded: chain R residue   78 VAL
Chi-restraints excluded: chain R residue  119 SER
Chi-restraints excluded: chain R residue  120 THR
Chi-restraints excluded: chain R residue  154 SER
Chi-restraints excluded: chain R residue  155 ILE
Chi-restraints excluded: chain R residue  158 LEU
Chi-restraints excluded: chain R residue  161 MET
Chi-restraints excluded: chain R residue  163 VAL
Chi-restraints excluded: chain R residue  191 ASN
Chi-restraints excluded: chain R residue  266 SER
Chi-restraints excluded: chain R residue  290 ILE
Chi-restraints excluded: chain R residue  293 TRP
Chi-restraints excluded: chain R residue  298 ILE
Chi-restraints excluded: chain R residue  328 ASN
Chi-restraints excluded: chain R residue  330 CYS
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 110
   random chunks:
   chunk 108 optimal weight:    8.9990
   chunk 53 optimal weight:    0.7980
   chunk 37 optimal weight:    1.9990
   chunk 50 optimal weight:    0.9990
   chunk 21 optimal weight:    0.9980
   chunk 24 optimal weight:    0.5980
   chunk 57 optimal weight:    0.8980
   chunk 4 optimal weight:    5.9990
   chunk 13 optimal weight:    0.6980
   chunk 88 optimal weight:    0.9980
   chunk 16 optimal weight:    0.8980
   overall best weight:    0.7780

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

Flipped N/Q/H residues before XYZ refinement:
B 156 GLN
** E 219 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** R 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4162 r_free = 0.4162 target = 0.169252 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3808 r_free = 0.3808 target = 0.139754 restraints weight = 13329.284|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 41)----------------|
| r_work = 0.3874 r_free = 0.3874 target = 0.144734 restraints weight = 6649.113|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3915 r_free = 0.3915 target = 0.148007 restraints weight = 4139.099|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3941 r_free = 0.3941 target = 0.150117 restraints weight = 2926.720|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 44)----------------|
| r_work = 0.3960 r_free = 0.3960 target = 0.151553 restraints weight = 2267.269|
|-----------------------------------------------------------------------------|
r_work (final): 0.4124
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7223
moved from start:          0.4078

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   8669  Z= 0.144
  Angle     :  0.651   7.756  11775  Z= 0.334
  Chirality :  0.044   0.277   1362
  Planarity :  0.004   0.037   1484
  Dihedral  :  5.307  71.252   1214
  Min Nonbonded Distance : 2.433

Molprobity Statistics.
  All-atom Clashscore : 12.26
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.35 %
    Favored  : 94.65 %
  Rotamer:
    Outliers :  4.73 %
    Allowed  : 22.29 %
    Favored  : 72.98 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.45 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.30 (0.25), residues: 1103
  helix:  0.40 (0.28), residues: 353
  sheet: -1.46 (0.31), residues: 244
  loop : -1.39 (0.28), residues: 506

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG B 137 
 TYR   0.021   0.002   TYR R  75 
 PHE   0.018   0.001   PHE A 223 
 TRP   0.019   0.002   TRP R 133 
 HIS   0.004   0.001   HIS B 183 

Details of bonding type rmsd
  covalent geometry    : bond        0.00331 ( 8664)
  covalent geometry    : angle       0.65108 (11766)
  SS BOND              : bond        0.00423 (    3)
  SS BOND              : angle       0.84529 (    6)
  hydrogen bonds       : bond        0.03286 (  383)
  hydrogen bonds       : angle       4.96213 ( 1110)
  Misc. bond           : bond        0.00014 (    1)
  link_TRANS           : bond        0.00124 (    1)
  link_TRANS           : angle       0.30732 (    3)

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

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

  2206 Ramachandran restraints generated.
    1103 Oldfield, 0 Emsley, 1103 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2206 Ramachandran restraints generated.
    1103 Oldfield, 0 Emsley, 1103 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  292 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 41
    poor density    : 251
  time to evaluate  : 0.404 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   14 GLU cc_start: 0.8172 (tm-30) cc_final: 0.7498 (tm-30)
REVERT: A  306 GLN cc_start: 0.8573 (mm-40) cc_final: 0.8327 (mm-40)
REVERT: A  334 PHE cc_start: 0.8934 (t80) cc_final: 0.8612 (t80)
REVERT: A  341 ASP cc_start: 0.8857 (t70) cc_final: 0.8521 (t0)
REVERT: A  347 ASN cc_start: 0.9364 (m-40) cc_final: 0.8977 (m-40)
REVERT: B   34 THR cc_start: 0.6977 (t) cc_final: 0.5756 (p)
REVERT: B   59 TYR cc_start: 0.8801 (m-80) cc_final: 0.8408 (m-80)
REVERT: B   75 GLN cc_start: 0.7091 (mm-40) cc_final: 0.6006 (mt0)
REVERT: B  117 LEU cc_start: 0.8245 (OUTLIER) cc_final: 0.7891 (tt)
REVERT: B  230 ASN cc_start: 0.8116 (m110) cc_final: 0.7445 (m110)
REVERT: B  234 PHE cc_start: 0.8938 (OUTLIER) cc_final: 0.8190 (m-80)
REVERT: B  300 LEU cc_start: 0.8675 (tt) cc_final: 0.8288 (tt)
REVERT: B  339 TRP cc_start: 0.9060 (m100) cc_final: 0.8258 (m-10)
REVERT: C   32 LYS cc_start: 0.8563 (mttp) cc_final: 0.8243 (mptt)
REVERT: R   75 TYR cc_start: 0.7182 (t80) cc_final: 0.6819 (t80)
REVERT: R  161 MET cc_start: 0.9150 (OUTLIER) cc_final: 0.8874 (tpp)
REVERT: R  164 ASP cc_start: 0.8938 (t70) cc_final: 0.8589 (t70)
REVERT: R  185 LYS cc_start: 0.8708 (ttmp) cc_final: 0.8162 (tptp)
REVERT: R  228 TRP cc_start: 0.7508 (t-100) cc_final: 0.7140 (t-100)
REVERT: R  258 ARG cc_start: 0.8521 (tpt90) cc_final: 0.8306 (tpt170)
REVERT: R  263 ARG cc_start: 0.8292 (tmt90) cc_final: 0.7778 (tmt170)
REVERT: R  270 GLU cc_start: 0.8289 (tm-30) cc_final: 0.7687 (tm-30)
REVERT: R  277 ARG cc_start: 0.8440 (tmm-80) cc_final: 0.7801 (tmm-80)
REVERT: R  336 TYR cc_start: 0.7149 (m-10) cc_final: 0.6854 (m-10)
  outliers start: 41
  outliers final: 24
  residues processed: 276
  average time/residue: 0.1132
  time to fit residues: 41.3299
Evaluate side-chains
  249 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 222
  time to evaluate  : 0.275 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   34 VAL
Chi-restraints excluded: chain A residue   44 SER
Chi-restraints excluded: chain A residue  185 VAL
Chi-restraints excluded: chain A residue  227 LEU
Chi-restraints excluded: chain A residue  254 CYS
Chi-restraints excluded: chain B residue  117 LEU
Chi-restraints excluded: chain B residue  148 CYS
Chi-restraints excluded: chain B residue  164 THR
Chi-restraints excluded: chain B residue  168 LEU
Chi-restraints excluded: chain B residue  181 THR
Chi-restraints excluded: chain B residue  190 LEU
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  271 CYS
Chi-restraints excluded: chain C residue   16 VAL
Chi-restraints excluded: chain E residue    7 SER
Chi-restraints excluded: chain E residue   69 THR
Chi-restraints excluded: chain E residue  115 THR
Chi-restraints excluded: chain E residue  146 SER
Chi-restraints excluded: chain R residue  154 SER
Chi-restraints excluded: chain R residue  155 ILE
Chi-restraints excluded: chain R residue  161 MET
Chi-restraints excluded: chain R residue  191 ASN
Chi-restraints excluded: chain R residue  217 CYS
Chi-restraints excluded: chain R residue  290 ILE
Chi-restraints excluded: chain R residue  293 TRP
Chi-restraints excluded: chain R residue  298 ILE
Chi-restraints excluded: chain R residue  330 CYS
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 110
   random chunks:
   chunk 48 optimal weight:    0.6980
   chunk 41 optimal weight:    0.0980
   chunk 62 optimal weight:    0.5980
   chunk 92 optimal weight:    0.7980
   chunk 24 optimal weight:    2.9990
   chunk 20 optimal weight:    1.9990
   chunk 63 optimal weight:    0.8980
   chunk 104 optimal weight:    0.0870
   chunk 95 optimal weight:   10.0000
   chunk 4 optimal weight:    1.9990
   chunk 73 optimal weight:    0.7980
   overall best weight:    0.4558

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

Flipped N/Q/H residues before XYZ refinement:
B 156 GLN
C  18 GLN
** E 219 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** R 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4196 r_free = 0.4196 target = 0.172260 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3895 r_free = 0.3895 target = 0.145263 restraints weight = 13316.440|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3931 r_free = 0.3931 target = 0.149764 restraints weight = 7068.814|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3949 r_free = 0.3949 target = 0.151281 restraints weight = 4137.694|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.3963 r_free = 0.3963 target = 0.152514 restraints weight = 3501.383|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3965 r_free = 0.3965 target = 0.152720 restraints weight = 3134.296|
|-----------------------------------------------------------------------------|
r_work (final): 0.3954
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7333
moved from start:          0.4434

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   8669  Z= 0.122
  Angle     :  0.639   8.021  11775  Z= 0.323
  Chirality :  0.043   0.263   1362
  Planarity :  0.004   0.035   1484
  Dihedral  :  5.131  72.939   1214
  Min Nonbonded Distance : 2.450

Molprobity Statistics.
  All-atom Clashscore : 11.66
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.62 %
    Favored  : 95.38 %
  Rotamer:
    Outliers :  5.20 %
    Allowed  : 22.52 %
    Favored  : 72.29 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.45 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.06 (0.26), residues: 1103
  helix:  0.71 (0.29), residues: 353
  sheet: -1.40 (0.30), residues: 267
  loop : -1.26 (0.29), residues: 483

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG A  21 
 TYR   0.031   0.002   TYR E 178 
 PHE   0.016   0.001   PHE A 223 
 TRP   0.030   0.001   TRP R 133 
 HIS   0.004   0.001   HIS B 183 

Details of bonding type rmsd
  covalent geometry    : bond        0.00270 ( 8664)
  covalent geometry    : angle       0.63897 (11766)
  SS BOND              : bond        0.01152 (    3)
  SS BOND              : angle       0.69104 (    6)
  hydrogen bonds       : bond        0.03133 (  383)
  hydrogen bonds       : angle       4.79063 ( 1110)
  Misc. bond           : bond        0.00035 (    1)
  link_TRANS           : bond        0.00204 (    1)
  link_TRANS           : angle       0.33952 (    3)

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

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

  2206 Ramachandran restraints generated.
    1103 Oldfield, 0 Emsley, 1103 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2206 Ramachandran restraints generated.
    1103 Oldfield, 0 Emsley, 1103 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  291 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 45
    poor density    : 246
  time to evaluate  : 0.352 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   14 GLU cc_start: 0.7934 (tm-30) cc_final: 0.7235 (tm-30)
REVERT: A   51 LYS cc_start: 0.8831 (ttmp) cc_final: 0.8232 (tmmt)
REVERT: A  216 GLU cc_start: 0.8298 (OUTLIER) cc_final: 0.8069 (pp20)
REVERT: A  228 SER cc_start: 0.7467 (p) cc_final: 0.6962 (m)
REVERT: A  334 PHE cc_start: 0.8870 (t80) cc_final: 0.8550 (t80)
REVERT: A  347 ASN cc_start: 0.9264 (m-40) cc_final: 0.8884 (m-40)
REVERT: B   51 LEU cc_start: 0.8910 (mt) cc_final: 0.8471 (mt)
REVERT: B   59 TYR cc_start: 0.8729 (m-80) cc_final: 0.8302 (m-80)
REVERT: B   75 GLN cc_start: 0.6883 (mm-40) cc_final: 0.6005 (mt0)
REVERT: B   82 TRP cc_start: 0.9050 (m100) cc_final: 0.8586 (m100)
REVERT: B  117 LEU cc_start: 0.7903 (OUTLIER) cc_final: 0.7576 (tt)
REVERT: B  169 TRP cc_start: 0.7685 (OUTLIER) cc_final: 0.6509 (m-90)
REVERT: B  234 PHE cc_start: 0.8881 (OUTLIER) cc_final: 0.8261 (m-80)
REVERT: B  280 LYS cc_start: 0.8354 (tmmt) cc_final: 0.8081 (tttt)
REVERT: B  339 TRP cc_start: 0.8945 (m100) cc_final: 0.8272 (m-10)
REVERT: C   32 LYS cc_start: 0.8517 (mttp) cc_final: 0.8210 (mptt)
REVERT: E   72 ARG cc_start: 0.7619 (mtp180) cc_final: 0.6690 (mtp180)
REVERT: E  207 LEU cc_start: 0.6975 (OUTLIER) cc_final: 0.6555 (tt)
REVERT: R  164 ASP cc_start: 0.8644 (t70) cc_final: 0.8342 (t70)
REVERT: R  185 LYS cc_start: 0.8692 (ttmp) cc_final: 0.8140 (tptp)
REVERT: R  228 TRP cc_start: 0.7545 (t-100) cc_final: 0.7224 (t-100)
REVERT: R  263 ARG cc_start: 0.8195 (tmt90) cc_final: 0.7795 (tmt170)
REVERT: R  336 TYR cc_start: 0.7205 (m-10) cc_final: 0.6936 (m-10)
  outliers start: 45
  outliers final: 27
  residues processed: 269
  average time/residue: 0.1069
  time to fit residues: 38.5458
Evaluate side-chains
  255 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 223
  time to evaluate  : 0.391 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   34 VAL
Chi-restraints excluded: chain A residue  216 GLU
Chi-restraints excluded: chain A residue  224 CYS
Chi-restraints excluded: chain A residue  227 LEU
Chi-restraints excluded: chain A residue  254 CYS
Chi-restraints excluded: chain A residue  265 ILE
Chi-restraints excluded: chain B residue   17 GLN
Chi-restraints excluded: chain B residue  117 LEU
Chi-restraints excluded: chain B residue  164 THR
Chi-restraints excluded: chain B residue  168 LEU
Chi-restraints excluded: chain B residue  169 TRP
Chi-restraints excluded: chain B residue  181 THR
Chi-restraints excluded: chain B residue  190 LEU
Chi-restraints excluded: chain B residue  215 GLU
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  255 LEU
Chi-restraints excluded: chain B residue  271 CYS
Chi-restraints excluded: chain C residue   16 VAL
Chi-restraints excluded: chain E residue   69 THR
Chi-restraints excluded: chain E residue   86 LEU
Chi-restraints excluded: chain E residue  115 THR
Chi-restraints excluded: chain E residue  207 LEU
Chi-restraints excluded: chain R residue  154 SER
Chi-restraints excluded: chain R residue  155 ILE
Chi-restraints excluded: chain R residue  191 ASN
Chi-restraints excluded: chain R residue  217 CYS
Chi-restraints excluded: chain R residue  266 SER
Chi-restraints excluded: chain R residue  275 LEU
Chi-restraints excluded: chain R residue  290 ILE
Chi-restraints excluded: chain R residue  293 TRP
Chi-restraints excluded: chain R residue  298 ILE
Chi-restraints excluded: chain R residue  330 CYS
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 110
   random chunks:
   chunk 23 optimal weight:    0.0670
   chunk 73 optimal weight:    1.9990
   chunk 44 optimal weight:    0.5980
   chunk 59 optimal weight:    0.5980
   chunk 49 optimal weight:    3.9990
   chunk 1 optimal weight:    1.9990
   chunk 22 optimal weight:    1.9990
   chunk 107 optimal weight:    0.9980
   chunk 74 optimal weight:    2.9990
   chunk 93 optimal weight:    3.9990
   chunk 31 optimal weight:    0.7980
   overall best weight:    0.6118

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

Flipped N/Q/H residues before XYZ refinement:
B 183 HIS
** E 219 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** R 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4194 r_free = 0.4194 target = 0.172494 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3903 r_free = 0.3903 target = 0.146115 restraints weight = 13232.706|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3938 r_free = 0.3938 target = 0.150664 restraints weight = 8042.369|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3961 r_free = 0.3961 target = 0.152617 restraints weight = 4513.212|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.3959 r_free = 0.3959 target = 0.152442 restraints weight = 4011.809|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3964 r_free = 0.3964 target = 0.152867 restraints weight = 3624.506|
|-----------------------------------------------------------------------------|
r_work (final): 0.3955
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7330
moved from start:          0.4688

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039   8669  Z= 0.130
  Angle     :  0.653   8.467  11775  Z= 0.326
  Chirality :  0.043   0.230   1362
  Planarity :  0.004   0.035   1484
  Dihedral  :  5.084  76.777   1214
  Min Nonbonded Distance : 2.517

Molprobity Statistics.
  All-atom Clashscore : 11.78
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.53 %
    Favored  : 95.47 %
  Rotamer:
    Outliers :  4.50 %
    Allowed  : 24.13 %
    Favored  : 71.36 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.45 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.93 (0.26), residues: 1103
  helix:  0.92 (0.29), residues: 348
  sheet: -1.26 (0.31), residues: 266
  loop : -1.31 (0.29), residues: 489

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG A  21 
 TYR   0.024   0.002   TYR R  75 
 PHE   0.029   0.001   PHE E 200 
 TRP   0.017   0.002   TRP R 133 
 HIS   0.005   0.001   HIS B 183 

Details of bonding type rmsd
  covalent geometry    : bond        0.00301 ( 8664)
  covalent geometry    : angle       0.65327 (11766)
  SS BOND              : bond        0.00369 (    3)
  SS BOND              : angle       0.92954 (    6)
  hydrogen bonds       : bond        0.03109 (  383)
  hydrogen bonds       : angle       4.80138 ( 1110)
  Misc. bond           : bond        0.00028 (    1)
  link_TRANS           : bond        0.00227 (    1)
  link_TRANS           : angle       0.11919 (    3)

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

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

  2206 Ramachandran restraints generated.
    1103 Oldfield, 0 Emsley, 1103 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2206 Ramachandran restraints generated.
    1103 Oldfield, 0 Emsley, 1103 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  286 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 39
    poor density    : 247
  time to evaluate  : 0.263 
Fit side-chains
   revert: symmetry clash
REVERT: A   14 GLU cc_start: 0.8060 (tm-30) cc_final: 0.7322 (tm-30)
REVERT: A   51 LYS cc_start: 0.8768 (ttmp) cc_final: 0.8251 (tmmt)
REVERT: A  216 GLU cc_start: 0.8332 (OUTLIER) cc_final: 0.8112 (pp20)
REVERT: A  228 SER cc_start: 0.7663 (p) cc_final: 0.7083 (m)
REVERT: A  253 ILE cc_start: 0.9089 (OUTLIER) cc_final: 0.8840 (mm)
REVERT: A  334 PHE cc_start: 0.8832 (t80) cc_final: 0.8492 (t80)
REVERT: A  347 ASN cc_start: 0.9271 (m-40) cc_final: 0.8867 (m-40)
REVERT: B   59 TYR cc_start: 0.8750 (m-80) cc_final: 0.8354 (m-80)
REVERT: B   75 GLN cc_start: 0.6894 (mm-40) cc_final: 0.5932 (mt0)
REVERT: B   82 TRP cc_start: 0.9092 (m100) cc_final: 0.8830 (m100)
REVERT: B  117 LEU cc_start: 0.7932 (OUTLIER) cc_final: 0.7630 (tt)
REVERT: B  169 TRP cc_start: 0.7662 (OUTLIER) cc_final: 0.6564 (m-90)
REVERT: B  234 PHE cc_start: 0.8912 (OUTLIER) cc_final: 0.8505 (m-80)
REVERT: B  280 LYS cc_start: 0.8410 (tmmt) cc_final: 0.8152 (tttt)
REVERT: B  339 TRP cc_start: 0.8958 (m100) cc_final: 0.8305 (m-10)
REVERT: C   32 LYS cc_start: 0.8520 (mttp) cc_final: 0.8186 (mptt)
REVERT: E   71 SER cc_start: 0.8027 (p) cc_final: 0.7780 (t)
REVERT: E   72 ARG cc_start: 0.7794 (mtp180) cc_final: 0.6719 (mtp180)
REVERT: E   86 LEU cc_start: 0.6963 (OUTLIER) cc_final: 0.6740 (mp)
REVERT: E   98 ARG cc_start: 0.8086 (ttp-110) cc_final: 0.7803 (ttp-110)
REVERT: E  207 LEU cc_start: 0.7099 (OUTLIER) cc_final: 0.6617 (tt)
REVERT: R  164 ASP cc_start: 0.8656 (t70) cc_final: 0.8429 (t70)
REVERT: R  185 LYS cc_start: 0.8689 (ttmp) cc_final: 0.8145 (tptp)
REVERT: R  228 TRP cc_start: 0.7524 (t-100) cc_final: 0.7071 (t-100)
REVERT: R  233 LYS cc_start: 0.8322 (mtmm) cc_final: 0.7778 (ttmt)
REVERT: R  261 SER cc_start: 0.9024 (m) cc_final: 0.8552 (t)
REVERT: R  263 ARG cc_start: 0.8159 (tmt90) cc_final: 0.7736 (tmt170)
REVERT: R  270 GLU cc_start: 0.8189 (tm-30) cc_final: 0.7341 (tm-30)
REVERT: R  336 TYR cc_start: 0.7195 (m-10) cc_final: 0.6916 (m-10)
  outliers start: 39
  outliers final: 26
  residues processed: 268
  average time/residue: 0.1052
  time to fit residues: 37.7708
Evaluate side-chains
  259 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 226
  time to evaluate  : 0.295 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   18 MET
Chi-restraints excluded: chain A residue   34 VAL
Chi-restraints excluded: chain A residue   44 SER
Chi-restraints excluded: chain A residue  216 GLU
Chi-restraints excluded: chain A residue  224 CYS
Chi-restraints excluded: chain A residue  227 LEU
Chi-restraints excluded: chain A residue  253 ILE
Chi-restraints excluded: chain A residue  254 CYS
Chi-restraints excluded: chain A residue  265 ILE
Chi-restraints excluded: chain A residue  295 THR
Chi-restraints excluded: chain B residue  117 LEU
Chi-restraints excluded: chain B residue  148 CYS
Chi-restraints excluded: chain B residue  164 THR
Chi-restraints excluded: chain B residue  169 TRP
Chi-restraints excluded: chain B residue  181 THR
Chi-restraints excluded: chain B residue  190 LEU
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  255 LEU
Chi-restraints excluded: chain B residue  271 CYS
Chi-restraints excluded: chain C residue   16 VAL
Chi-restraints excluded: chain E residue   69 THR
Chi-restraints excluded: chain E residue   86 LEU
Chi-restraints excluded: chain E residue  115 THR
Chi-restraints excluded: chain E residue  207 LEU
Chi-restraints excluded: chain R residue  154 SER
Chi-restraints excluded: chain R residue  155 ILE
Chi-restraints excluded: chain R residue  191 ASN
Chi-restraints excluded: chain R residue  217 CYS
Chi-restraints excluded: chain R residue  290 ILE
Chi-restraints excluded: chain R residue  293 TRP
Chi-restraints excluded: chain R residue  298 ILE
Chi-restraints excluded: chain R residue  330 CYS
Chi-restraints excluded: chain R residue  331 LEU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 110
   random chunks:
   chunk 28 optimal weight:    0.0470
   chunk 107 optimal weight:    3.9990
   chunk 97 optimal weight:    0.7980
   chunk 54 optimal weight:    4.9990
   chunk 52 optimal weight:    0.7980
   chunk 3 optimal weight:    0.9990
   chunk 68 optimal weight:    1.9990
   chunk 24 optimal weight:    2.9990
   chunk 50 optimal weight:    2.9990
   chunk 42 optimal weight:    3.9990
   chunk 70 optimal weight:    0.6980
   overall best weight:    0.6680

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

Flipped N/Q/H residues before XYZ refinement:
A 188 HIS
A 294 ASN
** B 239 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E 219 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4167 r_free = 0.4167 target = 0.170395 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3875 r_free = 0.3875 target = 0.143853 restraints weight = 13533.642|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3906 r_free = 0.3906 target = 0.147844 restraints weight = 6997.297|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3933 r_free = 0.3933 target = 0.150234 restraints weight = 4616.680|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 24)----------------|
| r_work = 0.3937 r_free = 0.3937 target = 0.150593 restraints weight = 3404.867|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3951 r_free = 0.3951 target = 0.151822 restraints weight = 3425.295|
|-----------------------------------------------------------------------------|
r_work (final): 0.3963
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7344
moved from start:          0.4873

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040   8669  Z= 0.133
  Angle     :  0.641   8.878  11775  Z= 0.323
  Chirality :  0.042   0.157   1362
  Planarity :  0.003   0.035   1484
  Dihedral  :  4.970  74.972   1212
  Min Nonbonded Distance : 2.516

Molprobity Statistics.
  All-atom Clashscore : 11.60
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.71 %
    Favored  : 95.29 %
  Rotamer:
    Outliers :  4.97 %
    Allowed  : 24.48 %
    Favored  : 70.55 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.45 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.86 (0.26), residues: 1103
  helix:  0.97 (0.29), residues: 349
  sheet: -1.24 (0.31), residues: 267
  loop : -1.26 (0.29), residues: 487

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG A  21 
 TYR   0.022   0.002   TYR R  75 
 PHE   0.016   0.001   PHE A 223 
 TRP   0.014   0.001   TRP R 133 
 HIS   0.004   0.001   HIS B 183 

Details of bonding type rmsd
  covalent geometry    : bond        0.00311 ( 8664)
  covalent geometry    : angle       0.64084 (11766)
  SS BOND              : bond        0.00438 (    3)
  SS BOND              : angle       0.87423 (    6)
  hydrogen bonds       : bond        0.03143 (  383)
  hydrogen bonds       : angle       4.73918 ( 1110)
  Misc. bond           : bond        0.00024 (    1)
  link_TRANS           : bond        0.00190 (    1)
  link_TRANS           : angle       0.31008 (    3)

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

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

  2206 Ramachandran restraints generated.
    1103 Oldfield, 0 Emsley, 1103 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2206 Ramachandran restraints generated.
    1103 Oldfield, 0 Emsley, 1103 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  265 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 43
    poor density    : 222
  time to evaluate  : 0.353 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   14 GLU cc_start: 0.7958 (tm-30) cc_final: 0.7176 (tm-30)
REVERT: A   51 LYS cc_start: 0.8778 (ttmp) cc_final: 0.8230 (tmmt)
REVERT: A  198 MET cc_start: 0.8299 (mmp) cc_final: 0.8096 (mmp)
REVERT: A  216 GLU cc_start: 0.8274 (OUTLIER) cc_final: 0.8038 (pp20)
REVERT: A  228 SER cc_start: 0.7691 (p) cc_final: 0.7188 (m)
REVERT: A  245 GLU cc_start: 0.8492 (tm-30) cc_final: 0.8260 (pt0)
REVERT: A  334 PHE cc_start: 0.8809 (t80) cc_final: 0.8486 (t80)
REVERT: A  347 ASN cc_start: 0.9232 (m-40) cc_final: 0.8826 (m-40)
REVERT: B   23 LYS cc_start: 0.7380 (tptt) cc_final: 0.7133 (mptt)
REVERT: B   59 TYR cc_start: 0.8732 (m-80) cc_final: 0.8413 (m-80)
REVERT: B   78 LYS cc_start: 0.8635 (mmtm) cc_final: 0.8218 (mmmm)
REVERT: B   82 TRP cc_start: 0.9082 (m100) cc_final: 0.8692 (m100)
REVERT: B  117 LEU cc_start: 0.7935 (OUTLIER) cc_final: 0.7665 (tt)
REVERT: B  169 TRP cc_start: 0.7642 (OUTLIER) cc_final: 0.6613 (m-90)
REVERT: B  170 ASP cc_start: 0.7414 (t0) cc_final: 0.7013 (t0)
REVERT: B  234 PHE cc_start: 0.8922 (OUTLIER) cc_final: 0.8488 (m-80)
REVERT: B  280 LYS cc_start: 0.8476 (tmmt) cc_final: 0.8216 (tttt)
REVERT: B  339 TRP cc_start: 0.8942 (m100) cc_final: 0.8330 (m-10)
REVERT: C   21 MET cc_start: 0.7617 (mpp) cc_final: 0.7217 (mpp)
REVERT: E   43 LYS cc_start: 0.8431 (mmtm) cc_final: 0.8219 (mptt)
REVERT: E   98 ARG cc_start: 0.8075 (ttp-110) cc_final: 0.7791 (ttp-110)
REVERT: E  207 LEU cc_start: 0.6943 (OUTLIER) cc_final: 0.6467 (tt)
REVERT: R  185 LYS cc_start: 0.8672 (ttmp) cc_final: 0.8151 (tptp)
REVERT: R  228 TRP cc_start: 0.7476 (t-100) cc_final: 0.7068 (t-100)
REVERT: R  261 SER cc_start: 0.9001 (m) cc_final: 0.8596 (t)
REVERT: R  262 VAL cc_start: 0.6612 (t) cc_final: 0.5420 (m)
REVERT: R  263 ARG cc_start: 0.8125 (tmt90) cc_final: 0.7812 (tmt170)
REVERT: R  264 MET cc_start: 0.8178 (tpp) cc_final: 0.7870 (tpt)
REVERT: R  270 GLU cc_start: 0.8105 (tm-30) cc_final: 0.7745 (tm-30)
REVERT: R  336 TYR cc_start: 0.7186 (m-10) cc_final: 0.6929 (m-10)
  outliers start: 43
  outliers final: 29
  residues processed: 251
  average time/residue: 0.1049
  time to fit residues: 35.6427
Evaluate side-chains
  246 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 212
  time to evaluate  : 0.311 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   18 MET
Chi-restraints excluded: chain A residue   34 VAL
Chi-restraints excluded: chain A residue   44 SER
Chi-restraints excluded: chain A residue  216 GLU
Chi-restraints excluded: chain A residue  224 CYS
Chi-restraints excluded: chain A residue  227 LEU
Chi-restraints excluded: chain A residue  254 CYS
Chi-restraints excluded: chain A residue  265 ILE
Chi-restraints excluded: chain B residue   17 GLN
Chi-restraints excluded: chain B residue   79 LEU
Chi-restraints excluded: chain B residue  117 LEU
Chi-restraints excluded: chain B residue  148 CYS
Chi-restraints excluded: chain B residue  164 THR
Chi-restraints excluded: chain B residue  168 LEU
Chi-restraints excluded: chain B residue  169 TRP
Chi-restraints excluded: chain B residue  181 THR
Chi-restraints excluded: chain B residue  190 LEU
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  266 HIS
Chi-restraints excluded: chain B residue  271 CYS
Chi-restraints excluded: chain C residue   16 VAL
Chi-restraints excluded: chain E residue    7 SER
Chi-restraints excluded: chain E residue   69 THR
Chi-restraints excluded: chain E residue  115 THR
Chi-restraints excluded: chain E residue  207 LEU
Chi-restraints excluded: chain R residue  154 SER
Chi-restraints excluded: chain R residue  155 ILE
Chi-restraints excluded: chain R residue  191 ASN
Chi-restraints excluded: chain R residue  217 CYS
Chi-restraints excluded: chain R residue  290 ILE
Chi-restraints excluded: chain R residue  293 TRP
Chi-restraints excluded: chain R residue  298 ILE
Chi-restraints excluded: chain R residue  330 CYS
Chi-restraints excluded: chain R residue  331 LEU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 110
   random chunks:
   chunk 96 optimal weight:    0.9980
   chunk 26 optimal weight:    3.9990
   chunk 20 optimal weight:    0.7980
   chunk 106 optimal weight:    6.9990
   chunk 77 optimal weight:    2.9990
   chunk 100 optimal weight:    0.7980
   chunk 55 optimal weight:    0.7980
   chunk 53 optimal weight:    0.6980
   chunk 14 optimal weight:    0.0980
   chunk 67 optimal weight:    0.6980
   chunk 32 optimal weight:    2.9990
   overall best weight:    0.6180

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

Flipped N/Q/H residues before XYZ refinement:
** B 239 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E 219 GLN ** 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 = 0.4197 r_free = 0.4197 target = 0.172708 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3914 r_free = 0.3914 target = 0.146927 restraints weight = 13253.306|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3942 r_free = 0.3942 target = 0.150732 restraints weight = 7435.853|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 23)----------------|
| r_work = 0.3959 r_free = 0.3959 target = 0.152306 restraints weight = 4564.392|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3963 r_free = 0.3963 target = 0.152586 restraints weight = 4129.234|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3968 r_free = 0.3968 target = 0.153069 restraints weight = 3585.595|
|-----------------------------------------------------------------------------|
r_work (final): 0.4079
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7308
moved from start:          0.5052

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039   8669  Z= 0.130
  Angle     :  0.662   9.878  11775  Z= 0.330
  Chirality :  0.042   0.163   1362
  Planarity :  0.004   0.035   1484
  Dihedral  :  4.932  74.778   1212
  Min Nonbonded Distance : 2.526

Molprobity Statistics.
  All-atom Clashscore : 11.54
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.17 %
    Favored  : 95.83 %
  Rotamer:
    Outliers :  4.50 %
    Allowed  : 25.40 %
    Favored  : 70.09 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.45 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.80 (0.26), residues: 1103
  helix:  0.98 (0.29), residues: 349
  sheet: -1.19 (0.31), residues: 266
  loop : -1.20 (0.29), residues: 488

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG A  21 
 TYR   0.022   0.002   TYR E 178 
 PHE   0.017   0.001   PHE A 223 
 TRP   0.013   0.002   TRP R 133 
 HIS   0.004   0.001   HIS R 319 

Details of bonding type rmsd
  covalent geometry    : bond        0.00303 ( 8664)
  covalent geometry    : angle       0.66185 (11766)
  SS BOND              : bond        0.00382 (    3)
  SS BOND              : angle       0.80532 (    6)
  hydrogen bonds       : bond        0.03117 (  383)
  hydrogen bonds       : angle       4.68783 ( 1110)
  Misc. bond           : bond        0.00017 (    1)
  link_TRANS           : bond        0.00221 (    1)
  link_TRANS           : angle       0.20409 (    3)

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

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

  2206 Ramachandran restraints generated.
    1103 Oldfield, 0 Emsley, 1103 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2206 Ramachandran restraints generated.
    1103 Oldfield, 0 Emsley, 1103 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  254 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 39
    poor density    : 215
  time to evaluate  : 0.403 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   14 GLU cc_start: 0.8081 (tm-30) cc_final: 0.7267 (tm-30)
REVERT: A   51 LYS cc_start: 0.8875 (ttmp) cc_final: 0.8231 (tmmt)
REVERT: A  216 GLU cc_start: 0.8354 (OUTLIER) cc_final: 0.8142 (pp20)
REVERT: A  228 SER cc_start: 0.7778 (p) cc_final: 0.7244 (m)
REVERT: A  245 GLU cc_start: 0.8607 (tm-30) cc_final: 0.8330 (pt0)
REVERT: A  334 PHE cc_start: 0.8828 (t80) cc_final: 0.8511 (t80)
REVERT: B   23 LYS cc_start: 0.7472 (tptt) cc_final: 0.7137 (mptt)
REVERT: B   51 LEU cc_start: 0.9040 (mp) cc_final: 0.8829 (mp)
REVERT: B   59 TYR cc_start: 0.8743 (m-80) cc_final: 0.8248 (m-80)
REVERT: B   78 LYS cc_start: 0.8601 (mmtm) cc_final: 0.8205 (mmtm)
REVERT: B   82 TRP cc_start: 0.9100 (m100) cc_final: 0.8539 (m100)
REVERT: B   95 LEU cc_start: 0.7656 (pp) cc_final: 0.7340 (pp)
REVERT: B  117 LEU cc_start: 0.7971 (OUTLIER) cc_final: 0.7668 (tt)
REVERT: B  169 TRP cc_start: 0.7572 (OUTLIER) cc_final: 0.6582 (m-90)
REVERT: B  211 TRP cc_start: 0.8460 (m100) cc_final: 0.7883 (m100)
REVERT: B  234 PHE cc_start: 0.8937 (OUTLIER) cc_final: 0.8352 (m-80)
REVERT: B  280 LYS cc_start: 0.8538 (tmmt) cc_final: 0.8260 (tttt)
REVERT: B  339 TRP cc_start: 0.8991 (m100) cc_final: 0.8277 (m-10)
REVERT: E  207 LEU cc_start: 0.7012 (OUTLIER) cc_final: 0.6567 (tt)
REVERT: R  164 ASP cc_start: 0.8451 (OUTLIER) cc_final: 0.8116 (t70)
REVERT: R  179 ARG cc_start: 0.8021 (ptm160) cc_final: 0.7667 (ptm160)
REVERT: R  185 LYS cc_start: 0.8605 (ttmp) cc_final: 0.7993 (tptp)
REVERT: R  228 TRP cc_start: 0.7484 (t-100) cc_final: 0.7042 (t-100)
REVERT: R  233 LYS cc_start: 0.8384 (mtmm) cc_final: 0.7981 (ttmm)
REVERT: R  261 SER cc_start: 0.9091 (m) cc_final: 0.8644 (t)
REVERT: R  262 VAL cc_start: 0.6675 (t) cc_final: 0.5396 (m)
REVERT: R  263 ARG cc_start: 0.8162 (tmt90) cc_final: 0.7763 (tmt170)
REVERT: R  264 MET cc_start: 0.8271 (tpp) cc_final: 0.7992 (tpt)
REVERT: R  270 GLU cc_start: 0.8122 (tm-30) cc_final: 0.7763 (tm-30)
REVERT: R  277 ARG cc_start: 0.8280 (tmm-80) cc_final: 0.7981 (tmm-80)
REVERT: R  329 SER cc_start: 0.9066 (t) cc_final: 0.8819 (p)
REVERT: R  336 TYR cc_start: 0.7134 (m-10) cc_final: 0.6851 (m-10)
  outliers start: 39
  outliers final: 26
  residues processed: 241
  average time/residue: 0.1011
  time to fit residues: 33.0686
Evaluate side-chains
  237 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 205
  time to evaluate  : 0.308 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   18 MET
Chi-restraints excluded: chain A residue   34 VAL
Chi-restraints excluded: chain A residue   44 SER
Chi-restraints excluded: chain A residue  216 GLU
Chi-restraints excluded: chain A residue  224 CYS
Chi-restraints excluded: chain A residue  227 LEU
Chi-restraints excluded: chain A residue  254 CYS
Chi-restraints excluded: chain B residue   79 LEU
Chi-restraints excluded: chain B residue  117 LEU
Chi-restraints excluded: chain B residue  148 CYS
Chi-restraints excluded: chain B residue  164 THR
Chi-restraints excluded: chain B residue  168 LEU
Chi-restraints excluded: chain B residue  169 TRP
Chi-restraints excluded: chain B residue  181 THR
Chi-restraints excluded: chain B residue  190 LEU
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  271 CYS
Chi-restraints excluded: chain C residue   16 VAL
Chi-restraints excluded: chain E residue  115 THR
Chi-restraints excluded: chain E residue  207 LEU
Chi-restraints excluded: chain R residue  154 SER
Chi-restraints excluded: chain R residue  155 ILE
Chi-restraints excluded: chain R residue  164 ASP
Chi-restraints excluded: chain R residue  191 ASN
Chi-restraints excluded: chain R residue  217 CYS
Chi-restraints excluded: chain R residue  242 ILE
Chi-restraints excluded: chain R residue  275 LEU
Chi-restraints excluded: chain R residue  290 ILE
Chi-restraints excluded: chain R residue  293 TRP
Chi-restraints excluded: chain R residue  298 ILE
Chi-restraints excluded: chain R residue  330 CYS
Chi-restraints excluded: chain R residue  331 LEU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 110
   random chunks:
   chunk 40 optimal weight:    0.6980
   chunk 83 optimal weight:    6.9990
   chunk 37 optimal weight:    2.9990
   chunk 73 optimal weight:    5.9990
   chunk 78 optimal weight:    0.8980
   chunk 44 optimal weight:    0.7980
   chunk 5 optimal weight:    0.9990
   chunk 54 optimal weight:    4.9990
   chunk 32 optimal weight:    4.9990
   chunk 75 optimal weight:    0.5980
   chunk 16 optimal weight:    0.8980
   overall best weight:    0.7780

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

Flipped N/Q/H residues before XYZ refinement:
** B 239 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E 219 GLN ** 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 = 0.4240 r_free = 0.4240 target = 0.176089 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 27)----------------|
| r_work = 0.3972 r_free = 0.3972 target = 0.151033 restraints weight = 13043.439|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.4002 r_free = 0.4002 target = 0.154206 restraints weight = 7090.789|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.4034 r_free = 0.4034 target = 0.157095 restraints weight = 4766.408|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 24)----------------|
| r_work = 0.4038 r_free = 0.4038 target = 0.157468 restraints weight = 3415.402|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.4057 r_free = 0.4057 target = 0.159177 restraints weight = 3295.955|
|-----------------------------------------------------------------------------|
r_work (final): 0.4123
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7227
moved from start:          0.5118

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.044   8669  Z= 0.145
  Angle     :  0.672  10.401  11775  Z= 0.337
  Chirality :  0.042   0.169   1362
  Planarity :  0.004   0.046   1484
  Dihedral  :  4.943  73.605   1212
  Min Nonbonded Distance : 2.534

Molprobity Statistics.
  All-atom Clashscore : 11.84
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.90 %
    Favored  : 95.10 %
  Rotamer:
    Outliers :  4.16 %
    Allowed  : 26.79 %
    Favored  : 69.05 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.45 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.74 (0.26), residues: 1103
  helix:  1.02 (0.29), residues: 348
  sheet: -1.02 (0.31), residues: 259
  loop : -1.24 (0.29), residues: 496

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.011   0.001   ARG R 165 
 TYR   0.021   0.002   TYR E 178 
 PHE   0.022   0.001   PHE A 223 
 TRP   0.013   0.002   TRP R 133 
 HIS   0.004   0.001   HIS B 183 

Details of bonding type rmsd
  covalent geometry    : bond        0.00339 ( 8664)
  covalent geometry    : angle       0.67197 (11766)
  SS BOND              : bond        0.00317 (    3)
  SS BOND              : angle       0.87277 (    6)
  hydrogen bonds       : bond        0.03200 (  383)
  hydrogen bonds       : angle       4.67915 ( 1110)
  Misc. bond           : bond        0.00010 (    1)
  link_TRANS           : bond        0.00235 (    1)
  link_TRANS           : angle       0.19032 (    3)

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

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

  2206 Ramachandran restraints generated.
    1103 Oldfield, 0 Emsley, 1103 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2206 Ramachandran restraints generated.
    1103 Oldfield, 0 Emsley, 1103 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  251 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 215
  time to evaluate  : 0.345 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   14 GLU cc_start: 0.8180 (tm-30) cc_final: 0.7372 (tm-30)
REVERT: A   51 LYS cc_start: 0.8834 (ttmp) cc_final: 0.8311 (tmtt)
REVERT: A  216 GLU cc_start: 0.8414 (pp20) cc_final: 0.8207 (pp20)
REVERT: A  228 SER cc_start: 0.7840 (p) cc_final: 0.7265 (m)
REVERT: A  245 GLU cc_start: 0.8608 (tm-30) cc_final: 0.8316 (pt0)
REVERT: A  334 PHE cc_start: 0.8825 (t80) cc_final: 0.8584 (t80)
REVERT: B   23 LYS cc_start: 0.7459 (tptt) cc_final: 0.7127 (mptt)
REVERT: B   51 LEU cc_start: 0.9075 (mp) cc_final: 0.8824 (mp)
REVERT: B   57 LYS cc_start: 0.8314 (ptmt) cc_final: 0.7753 (ptmt)
REVERT: B   59 TYR cc_start: 0.8954 (m-80) cc_final: 0.8517 (m-80)
REVERT: B   78 LYS cc_start: 0.8597 (mmtm) cc_final: 0.8360 (mtpp)
REVERT: B   82 TRP cc_start: 0.9128 (m100) cc_final: 0.8517 (m100)
REVERT: B   95 LEU cc_start: 0.7744 (pp) cc_final: 0.7397 (pp)
REVERT: B  117 LEU cc_start: 0.8097 (OUTLIER) cc_final: 0.7797 (tt)
REVERT: B  169 TRP cc_start: 0.7641 (OUTLIER) cc_final: 0.6561 (m-90)
REVERT: B  211 TRP cc_start: 0.8528 (m100) cc_final: 0.7958 (m100)
REVERT: B  234 PHE cc_start: 0.8993 (OUTLIER) cc_final: 0.8395 (m-80)
REVERT: B  332 TRP cc_start: 0.8663 (m-10) cc_final: 0.8396 (m-10)
REVERT: B  339 TRP cc_start: 0.9033 (m100) cc_final: 0.8396 (m-10)
REVERT: C   21 MET cc_start: 0.7478 (mpp) cc_final: 0.6956 (mtm)
REVERT: E   65 LYS cc_start: 0.8533 (ttmt) cc_final: 0.8329 (tppt)
REVERT: E   98 ARG cc_start: 0.8260 (ttp-110) cc_final: 0.7952 (ttp-110)
REVERT: E  207 LEU cc_start: 0.7057 (OUTLIER) cc_final: 0.6620 (tt)
REVERT: R  161 MET cc_start: 0.8949 (tpp) cc_final: 0.8697 (tpp)
REVERT: R  164 ASP cc_start: 0.8541 (OUTLIER) cc_final: 0.8199 (t70)
REVERT: R  185 LYS cc_start: 0.8590 (ttmp) cc_final: 0.7985 (tptp)
REVERT: R  228 TRP cc_start: 0.7480 (t-100) cc_final: 0.7042 (t-100)
REVERT: R  233 LYS cc_start: 0.8377 (mtmm) cc_final: 0.8005 (ttmm)
REVERT: R  261 SER cc_start: 0.9081 (m) cc_final: 0.8685 (t)
REVERT: R  263 ARG cc_start: 0.8171 (tmt90) cc_final: 0.7812 (tmt170)
REVERT: R  270 GLU cc_start: 0.8165 (tm-30) cc_final: 0.7792 (tm-30)
REVERT: R  277 ARG cc_start: 0.8295 (tmm-80) cc_final: 0.7977 (tmm-80)
REVERT: R  336 TYR cc_start: 0.7188 (m-10) cc_final: 0.6841 (m-10)
  outliers start: 36
  outliers final: 28
  residues processed: 238
  average time/residue: 0.1087
  time to fit residues: 34.7648
Evaluate side-chains
  240 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 207
  time to evaluate  : 0.338 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   18 MET
Chi-restraints excluded: chain A residue   34 VAL
Chi-restraints excluded: chain A residue   44 SER
Chi-restraints excluded: chain A residue  185 VAL
Chi-restraints excluded: chain A residue  224 CYS
Chi-restraints excluded: chain A residue  227 LEU
Chi-restraints excluded: chain A residue  254 CYS
Chi-restraints excluded: chain A residue  295 THR
Chi-restraints excluded: chain B residue   79 LEU
Chi-restraints excluded: chain B residue  117 LEU
Chi-restraints excluded: chain B residue  148 CYS
Chi-restraints excluded: chain B residue  164 THR
Chi-restraints excluded: chain B residue  169 TRP
Chi-restraints excluded: chain B residue  181 THR
Chi-restraints excluded: chain B residue  190 LEU
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  271 CYS
Chi-restraints excluded: chain C residue   16 VAL
Chi-restraints excluded: chain E residue    7 SER
Chi-restraints excluded: chain E residue   86 LEU
Chi-restraints excluded: chain E residue  115 THR
Chi-restraints excluded: chain E residue  207 LEU
Chi-restraints excluded: chain R residue  154 SER
Chi-restraints excluded: chain R residue  155 ILE
Chi-restraints excluded: chain R residue  164 ASP
Chi-restraints excluded: chain R residue  191 ASN
Chi-restraints excluded: chain R residue  217 CYS
Chi-restraints excluded: chain R residue  242 ILE
Chi-restraints excluded: chain R residue  275 LEU
Chi-restraints excluded: chain R residue  293 TRP
Chi-restraints excluded: chain R residue  298 ILE
Chi-restraints excluded: chain R residue  330 CYS
Chi-restraints excluded: chain R residue  331 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 110
   random chunks:
   chunk 85 optimal weight:    5.9990
   chunk 16 optimal weight:    1.9990
   chunk 50 optimal weight:    0.4980
   chunk 77 optimal weight:    0.5980
   chunk 10 optimal weight:    0.9990
   chunk 75 optimal weight:    0.9980
   chunk 62 optimal weight:    1.9990
   chunk 6 optimal weight:    0.7980
   chunk 31 optimal weight:    0.9980
   chunk 54 optimal weight:    4.9990
   chunk 24 optimal weight:    2.9990
   overall best weight:    0.7780

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

Flipped N/Q/H residues before XYZ refinement:
** A  52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 213 HIS
** B 239 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E 219 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 = 0.4102 r_free = 0.4102 target = 0.168465 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3812 r_free = 0.3812 target = 0.142576 restraints weight = 13216.669|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3845 r_free = 0.3845 target = 0.146469 restraints weight = 6970.691|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3868 r_free = 0.3868 target = 0.148479 restraints weight = 4821.703|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3871 r_free = 0.3871 target = 0.148718 restraints weight = 3479.066|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3877 r_free = 0.3877 target = 0.149191 restraints weight = 3544.430|
|-----------------------------------------------------------------------------|
r_work (final): 0.3946
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7287
moved from start:          0.5213

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.045   8669  Z= 0.144
  Angle     :  0.676  11.966  11775  Z= 0.340
  Chirality :  0.042   0.156   1362
  Planarity :  0.004   0.034   1484
  Dihedral  :  4.982  73.250   1212
  Min Nonbonded Distance : 2.524

Molprobity Statistics.
  All-atom Clashscore : 12.50
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.81 %
    Favored  : 95.19 %
  Rotamer:
    Outliers :  3.81 %
    Allowed  : 26.91 %
    Favored  : 69.28 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.45 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.73 (0.26), residues: 1103
  helix:  0.93 (0.29), residues: 355
  sheet: -0.95 (0.32), residues: 251
  loop : -1.22 (0.29), residues: 497

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG A  21 
 TYR   0.020   0.002   TYR R  75 
 PHE   0.022   0.001   PHE A 223 
 TRP   0.014   0.002   TRP B 297 
 HIS   0.004   0.001   HIS B 183 

Details of bonding type rmsd
  covalent geometry    : bond        0.00341 ( 8664)
  covalent geometry    : angle       0.67646 (11766)
  SS BOND              : bond        0.00366 (    3)
  SS BOND              : angle       0.86825 (    6)
  hydrogen bonds       : bond        0.03181 (  383)
  hydrogen bonds       : angle       4.66358 ( 1110)
  Misc. bond           : bond        0.00006 (    1)
  link_TRANS           : bond        0.00241 (    1)
  link_TRANS           : angle       0.16863 (    3)

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

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

  2206 Ramachandran restraints generated.
    1103 Oldfield, 0 Emsley, 1103 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2206 Ramachandran restraints generated.
    1103 Oldfield, 0 Emsley, 1103 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  245 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 212
  time to evaluate  : 0.359 
Fit side-chains
   revert: symmetry clash
REVERT: A   14 GLU cc_start: 0.8178 (tm-30) cc_final: 0.7362 (tm-30)
REVERT: A   51 LYS cc_start: 0.8755 (ttmp) cc_final: 0.8003 (tmmt)
REVERT: A  216 GLU cc_start: 0.8411 (pp20) cc_final: 0.7995 (pp20)
REVERT: A  228 SER cc_start: 0.7898 (p) cc_final: 0.7422 (m)
REVERT: A  242 ARG cc_start: 0.7671 (mtp180) cc_final: 0.7466 (mtp85)
REVERT: A  334 PHE cc_start: 0.8884 (t80) cc_final: 0.8672 (t80)
REVERT: B   23 LYS cc_start: 0.7480 (tptt) cc_final: 0.7133 (mptt)
REVERT: B   34 THR cc_start: 0.7166 (t) cc_final: 0.5655 (p)
REVERT: B   51 LEU cc_start: 0.9057 (mp) cc_final: 0.8803 (mp)
REVERT: B   57 LYS cc_start: 0.8311 (ptmt) cc_final: 0.7931 (ptmt)
REVERT: B   59 TYR cc_start: 0.8908 (m-80) cc_final: 0.8527 (m-80)
REVERT: B   78 LYS cc_start: 0.8617 (mmtm) cc_final: 0.8411 (mtpp)
REVERT: B   82 TRP cc_start: 0.9088 (m100) cc_final: 0.8535 (m100)
REVERT: B   95 LEU cc_start: 0.7768 (pp) cc_final: 0.7424 (pp)
REVERT: B  117 LEU cc_start: 0.8055 (OUTLIER) cc_final: 0.7747 (tt)
REVERT: B  169 TRP cc_start: 0.7579 (OUTLIER) cc_final: 0.6663 (m-90)
REVERT: B  170 ASP cc_start: 0.7322 (t0) cc_final: 0.6771 (t0)
REVERT: B  211 TRP cc_start: 0.8571 (m100) cc_final: 0.7974 (m100)
REVERT: B  234 PHE cc_start: 0.8991 (OUTLIER) cc_final: 0.8402 (m-80)
REVERT: B  339 TRP cc_start: 0.9040 (m100) cc_final: 0.8426 (m-10)
REVERT: C   21 MET cc_start: 0.7509 (mpp) cc_final: 0.6988 (mtm)
REVERT: E  207 LEU cc_start: 0.6977 (OUTLIER) cc_final: 0.6522 (tt)
REVERT: R  161 MET cc_start: 0.8930 (tpp) cc_final: 0.8678 (tpp)
REVERT: R  185 LYS cc_start: 0.8575 (ttmp) cc_final: 0.7969 (tptp)
REVERT: R  228 TRP cc_start: 0.7493 (t-100) cc_final: 0.7028 (t-100)
REVERT: R  233 LYS cc_start: 0.8359 (mtmm) cc_final: 0.7996 (ttmm)
REVERT: R  261 SER cc_start: 0.9125 (m) cc_final: 0.8707 (t)
REVERT: R  263 ARG cc_start: 0.8081 (tmt90) cc_final: 0.7719 (tmt170)
REVERT: R  270 GLU cc_start: 0.8183 (tm-30) cc_final: 0.7815 (tm-30)
REVERT: R  277 ARG cc_start: 0.8295 (tmm-80) cc_final: 0.7970 (tmm-80)
REVERT: R  336 TYR cc_start: 0.7071 (m-10) cc_final: 0.6672 (m-10)
  outliers start: 33
  outliers final: 26
  residues processed: 234
  average time/residue: 0.1002
  time to fit residues: 31.9349
Evaluate side-chains
  239 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 209
  time to evaluate  : 0.307 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   18 MET
Chi-restraints excluded: chain A residue   34 VAL
Chi-restraints excluded: chain A residue   44 SER
Chi-restraints excluded: chain A residue  185 VAL
Chi-restraints excluded: chain A residue  224 CYS
Chi-restraints excluded: chain A residue  227 LEU
Chi-restraints excluded: chain A residue  254 CYS
Chi-restraints excluded: chain A residue  295 THR
Chi-restraints excluded: chain B residue   79 LEU
Chi-restraints excluded: chain B residue  117 LEU
Chi-restraints excluded: chain B residue  148 CYS
Chi-restraints excluded: chain B residue  164 THR
Chi-restraints excluded: chain B residue  169 TRP
Chi-restraints excluded: chain B residue  181 THR
Chi-restraints excluded: chain B residue  190 LEU
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  255 LEU
Chi-restraints excluded: chain B residue  271 CYS
Chi-restraints excluded: chain C residue   16 VAL
Chi-restraints excluded: chain E residue  115 THR
Chi-restraints excluded: chain E residue  207 LEU
Chi-restraints excluded: chain R residue  154 SER
Chi-restraints excluded: chain R residue  155 ILE
Chi-restraints excluded: chain R residue  191 ASN
Chi-restraints excluded: chain R residue  217 CYS
Chi-restraints excluded: chain R residue  275 LEU
Chi-restraints excluded: chain R residue  293 TRP
Chi-restraints excluded: chain R residue  298 ILE
Chi-restraints excluded: chain R residue  330 CYS
Chi-restraints excluded: chain R residue  331 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 110
   random chunks:
   chunk 31 optimal weight:    0.8980
   chunk 20 optimal weight:    0.9990
   chunk 8 optimal weight:    0.9980
   chunk 100 optimal weight:    4.9990
   chunk 25 optimal weight:    0.7980
   chunk 39 optimal weight:    6.9990
   chunk 61 optimal weight:    0.6980
   chunk 0 optimal weight:   10.0000
   chunk 46 optimal weight:    0.1980
   chunk 77 optimal weight:    5.9990
   chunk 78 optimal weight:    1.9990
   overall best weight:    0.7180

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

Flipped N/Q/H residues before XYZ refinement:
** A  52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 306 GLN
B 230 ASN
** E 219 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4108 r_free = 0.4108 target = 0.168948 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3811 r_free = 0.3811 target = 0.142284 restraints weight = 13193.526|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3847 r_free = 0.3847 target = 0.146512 restraints weight = 7496.867|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3867 r_free = 0.3867 target = 0.148136 restraints weight = 4445.056|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.3891 r_free = 0.3891 target = 0.150314 restraints weight = 3695.364|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3894 r_free = 0.3894 target = 0.150514 restraints weight = 3096.865|
|-----------------------------------------------------------------------------|
r_work (final): 0.3897
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7366
moved from start:          0.5313

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.045   8669  Z= 0.140
  Angle     :  0.690  12.115  11775  Z= 0.343
  Chirality :  0.042   0.157   1362
  Planarity :  0.004   0.033   1484
  Dihedral  :  4.986  73.467   1212
  Min Nonbonded Distance : 2.477

Molprobity Statistics.
  All-atom Clashscore : 12.80
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.99 %
    Favored  : 95.01 %
  Rotamer:
    Outliers :  3.35 %
    Allowed  : 27.94 %
    Favored  : 68.71 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.45 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.68 (0.26), residues: 1103
  helix:  0.97 (0.29), residues: 357
  sheet: -0.98 (0.32), residues: 258
  loop : -1.16 (0.29), residues: 488

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG R 211 
 TYR   0.020   0.002   TYR E 178 
 PHE   0.022   0.001   PHE A 223 
 TRP   0.013   0.002   TRP B 297 
 HIS   0.003   0.001   HIS R 319 

Details of bonding type rmsd
  covalent geometry    : bond        0.00332 ( 8664)
  covalent geometry    : angle       0.68936 (11766)
  SS BOND              : bond        0.00351 (    3)
  SS BOND              : angle       1.46215 (    6)
  hydrogen bonds       : bond        0.03196 (  383)
  hydrogen bonds       : angle       4.66135 ( 1110)
  Misc. bond           : bond        0.00004 (    1)
  link_TRANS           : bond        0.00242 (    1)
  link_TRANS           : angle       0.11789 (    3)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1775.70 seconds
wall clock time: 31 minutes 28.06 seconds (1888.06 seconds total)