Starting phenix.real_space_refine
on Thu Mar 13 03:29:49 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/6dde_7868/03_2025/6dde_7868_neut.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/6dde_7868/03_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 {
    real_map_files = "/net/cci-nas-00/data/ceres_data/6dde_7868/03_2025/6dde_7868.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/6dde_7868/03_2025/6dde_7868.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/6dde_7868/03_2025/6dde_7868_neut.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/6dde_7868/03_2025/6dde_7868_neut.cif"
  }
  resolution = 3.5
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.027 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): 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/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: {'GLU:plan': 7, 'ASP:plan': 6}
          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: {'GLN:plan1': 2, 'GLU:plan': 1, 'ASN:plan1': 2, 'ARG:plan': 1, 'ASP:plan': 3}
          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: {'GLN:plan1': 1, 'TYR:plan': 1, 'ASN:plan1': 1, 'TRP:plan': 1, 'HIS:plan': 1, 'PHE:plan': 3, 'GLU:plan': 1, 'ARG:plan': 2}
          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: 5.08, per 1000 atoms: 0.60
  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: 2.17
  Conformation dependent library (CDL) restraints added in 967.7 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: 1.08
  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: 2.50

  Time building geometry restraints manager: 2.43 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:             0.980
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.290
  Check model and map are aligned:         0.060
  Set scattering table:                    0.080
  Process input model:                     21.710
  Find NCS groups from input model:        0.090
  Set up NCS constraints:                  0.030
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.010
  Load rotamer database and sin/cos tables:2.850
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   26.110
-------------------------------------------------------------------------------
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      :  0.006   0.078   8664  Z= 0.409
  Angle     :  1.026   9.858  11766  Z= 0.569
  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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -3.56 (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
 TRP   0.041   0.004   TRP B  63 
 HIS   0.011   0.003   HIS E 155 
 PHE   0.028   0.003   PHE B 241 
 TYR   0.030   0.003   TYR E 163 
 ARG   0.018   0.001   ARG B  68 

*********************** 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  : 0.881 
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: 0.2298
  time to fit residues: 110.2049
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  : 0.873 
-------------------------------------------------------------------------------
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 92 optimal weight:    0.9980
   chunk 83 optimal weight:    3.9990
   chunk 46 optimal weight:    0.0970
   chunk 28 optimal weight:    0.9990
   chunk 56 optimal weight:    0.9980
   chunk 44 optimal weight:    1.9990
   chunk 86 optimal weight:    4.9990
   chunk 33 optimal weight:    0.8980
   chunk 52 optimal weight:    1.9990
   chunk 64 optimal weight:    0.9980
   chunk 99 optimal weight:    0.6980
   overall best weight:    0.7378

-------------------------------------------------------------------------------
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 150 ASN
R 230 ASN
R 297 HIS
R 328 ASN

Total number of N/Q/H flips: 14

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4175 r_free = 0.4175 target = 0.171226 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3842 r_free = 0.3842 target = 0.142508 restraints weight = 12948.352|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 41)----------------|
| r_work = 0.3903 r_free = 0.3903 target = 0.147283 restraints weight = 6670.900|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 43)----------------|
| r_work = 0.3943 r_free = 0.3943 target = 0.150419 restraints weight = 4240.639|
|-----------------------------------------------------------------------------|
r_work (final): 0.3970
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7340
moved from start:          0.2951

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.044   8664  Z= 0.224
  Angle     :  0.674  10.576  11766  Z= 0.347
  Chirality :  0.044   0.203   1362
  Planarity :  0.004   0.041   1484
  Dihedral  :  5.581  67.873   1214
  Min Nonbonded Distance : 2.523

Molprobity Statistics.
  All-atom Clashscore : 11.30
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.62 %
    Favored  : 95.38 %
  Rotamer:
    Outliers :  4.04 %
    Allowed  : 17.44 %
    Favored  : 78.52 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.45 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.05 (0.24), residues: 1103
  helix: -0.60 (0.27), residues: 351
  sheet: -1.68 (0.31), residues: 239
  loop : -1.65 (0.27), residues: 513

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.020   0.002   TRP B 169 
 HIS   0.004   0.001   HIS B 183 
 PHE   0.016   0.002   PHE R 241 
 TYR   0.019   0.002   TYR R  75 
 ARG   0.006   0.001   ARG A  21 

*********************** 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
  291 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 256
  time to evaluate  : 0.994 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   14 GLU cc_start: 0.7789 (tm-30) cc_final: 0.7282 (tm-30)
REVERT: A   51 LYS cc_start: 0.8610 (ttmp) cc_final: 0.8192 (tmmt)
REVERT: A  216 GLU cc_start: 0.7858 (pt0) cc_final: 0.7612 (pp20)
REVERT: A  254 CYS cc_start: 0.7955 (OUTLIER) cc_final: 0.7638 (m)
REVERT: A  302 TYR cc_start: 0.8185 (t80) cc_final: 0.7958 (t80)
REVERT: A  341 ASP cc_start: 0.8706 (t70) cc_final: 0.8472 (t0)
REVERT: B   82 TRP cc_start: 0.8954 (m100) cc_final: 0.8728 (m100)
REVERT: B   86 THR cc_start: 0.8450 (p) cc_final: 0.8246 (p)
REVERT: B  117 LEU cc_start: 0.7990 (OUTLIER) cc_final: 0.7335 (tt)
REVERT: B  163 ASP cc_start: 0.7875 (p0) cc_final: 0.7651 (p0)
REVERT: B  280 LYS cc_start: 0.8148 (tmmt) cc_final: 0.7904 (tttt)
REVERT: B  339 TRP cc_start: 0.8780 (m100) cc_final: 0.8222 (m-10)
REVERT: E  115 THR cc_start: 0.8677 (OUTLIER) cc_final: 0.8315 (p)
REVERT: E  130 GLN cc_start: 0.6482 (tp-100) cc_final: 0.5744 (mt0)
REVERT: R  106 TYR cc_start: 0.9039 (m-80) cc_final: 0.8666 (m-10)
REVERT: R  123 PHE cc_start: 0.8331 (OUTLIER) cc_final: 0.7030 (t80)
REVERT: R  161 MET cc_start: 0.8618 (OUTLIER) cc_final: 0.8393 (tpp)
REVERT: R  165 ARG cc_start: 0.8450 (mtt90) cc_final: 0.8204 (mtt90)
REVERT: R  185 LYS cc_start: 0.8622 (ttmp) cc_final: 0.8058 (tptt)
REVERT: R  228 TRP cc_start: 0.7479 (t-100) cc_final: 0.7146 (t-100)
REVERT: R  263 ARG cc_start: 0.8274 (tmt90) cc_final: 0.7849 (tmt170)
REVERT: R  270 GLU cc_start: 0.8150 (tm-30) cc_final: 0.7865 (tm-30)
REVERT: R  298 ILE cc_start: 0.7382 (OUTLIER) cc_final: 0.7166 (pt)
REVERT: R  336 TYR cc_start: 0.7124 (m-10) cc_final: 0.6859 (m-80)
  outliers start: 35
  outliers final: 18
  residues processed: 278
  average time/residue: 0.2299
  time to fit residues: 84.2183
Evaluate side-chains
  248 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 224
  time to evaluate  : 0.910 
-------------------------------------------------------------------------------
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 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 C residue   37 LEU
Chi-restraints excluded: chain E residue  115 THR
Chi-restraints excluded: chain E residue  211 ASP
Chi-restraints excluded: chain E residue  212 VAL
Chi-restraints excluded: chain R residue  120 THR
Chi-restraints excluded: chain R residue  123 PHE
Chi-restraints excluded: chain R residue  154 SER
Chi-restraints excluded: chain R residue  161 MET
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 98 optimal weight:    8.9990
   chunk 92 optimal weight:    0.0030
   chunk 100 optimal weight:    0.4980
   chunk 29 optimal weight:    0.4980
   chunk 81 optimal weight:    2.9990
   chunk 84 optimal weight:    9.9990
   chunk 8 optimal weight:    0.7980
   chunk 99 optimal weight:    2.9990
   chunk 80 optimal weight:    0.5980
   chunk 20 optimal weight:    1.9990
   chunk 14 optimal weight:    0.9990
   overall best weight:    0.4790

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

Flipped N/Q/H residues before XYZ refinement:
A 347 ASN
B  75 GLN
E 130 GLN
** R 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
R 127 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4195 r_free = 0.4195 target = 0.172936 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3863 r_free = 0.3863 target = 0.144398 restraints weight = 13243.672|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.3924 r_free = 0.3924 target = 0.149214 restraints weight = 6765.544|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3962 r_free = 0.3962 target = 0.152314 restraints weight = 4251.684|
|-----------------------------------------------------------------------------|
r_work (final): 0.3982
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7324
moved from start:          0.3612

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   8664  Z= 0.184
  Angle     :  0.655   8.758  11766  Z= 0.333
  Chirality :  0.043   0.194   1362
  Planarity :  0.004   0.039   1484
  Dihedral  :  5.303  71.399   1214
  Min Nonbonded Distance : 2.393

Molprobity Statistics.
  All-atom Clashscore : 11.84
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.90 %
    Favored  : 95.10 %
  Rotamer:
    Outliers :  4.27 %
    Allowed  : 20.21 %
    Favored  : 75.52 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.45 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.47 (0.25), residues: 1103
  helix:  0.09 (0.28), residues: 355
  sheet: -1.41 (0.31), residues: 237
  loop : -1.45 (0.27), residues: 511

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.019   0.002   TRP B 169 
 HIS   0.005   0.001   HIS B 183 
 PHE   0.016   0.001   PHE R 241 
 TYR   0.024   0.002   TYR R  75 
 ARG   0.006   0.001   ARG A  21 

*********************** 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
  291 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 37
    poor density    : 254
  time to evaluate  : 0.910 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   14 GLU cc_start: 0.7736 (tm-30) cc_final: 0.7276 (tm-30)
REVERT: A   51 LYS cc_start: 0.8623 (ttmp) cc_final: 0.8163 (tmmt)
REVERT: A  228 SER cc_start: 0.7886 (p) cc_final: 0.7299 (m)
REVERT: A  341 ASP cc_start: 0.8692 (t70) cc_final: 0.8479 (t0)
REVERT: A  347 ASN cc_start: 0.9252 (m-40) cc_final: 0.8824 (m-40)
REVERT: B  117 LEU cc_start: 0.7982 (OUTLIER) cc_final: 0.7269 (tt)
REVERT: B  234 PHE cc_start: 0.8791 (OUTLIER) cc_final: 0.8303 (m-10)
REVERT: B  280 LYS cc_start: 0.8244 (tmmt) cc_final: 0.8042 (tmmt)
REVERT: B  308 LEU cc_start: 0.8236 (mp) cc_final: 0.7946 (mp)
REVERT: B  339 TRP cc_start: 0.8759 (m100) cc_final: 0.8176 (m-10)
REVERT: E    6 GLU cc_start: 0.6599 (mp0) cc_final: 0.6370 (mp0)
REVERT: R  106 TYR cc_start: 0.9025 (m-80) cc_final: 0.8449 (m-10)
REVERT: R  161 MET cc_start: 0.8689 (OUTLIER) cc_final: 0.8322 (tpp)
REVERT: R  164 ASP cc_start: 0.8625 (t70) cc_final: 0.8358 (t70)
REVERT: R  185 LYS cc_start: 0.8548 (ttmp) cc_final: 0.8032 (tptt)
REVERT: R  228 TRP cc_start: 0.7502 (t-100) cc_final: 0.7145 (t-100)
REVERT: R  233 LYS cc_start: 0.8209 (mtmm) cc_final: 0.7753 (ttpt)
REVERT: R  263 ARG cc_start: 0.8209 (tmt90) cc_final: 0.7795 (tmt170)
REVERT: R  270 GLU cc_start: 0.8198 (tm-30) cc_final: 0.7914 (tm-30)
REVERT: R  277 ARG cc_start: 0.8512 (tmm-80) cc_final: 0.7943 (tmm-80)
REVERT: R  298 ILE cc_start: 0.7427 (OUTLIER) cc_final: 0.7143 (pt)
REVERT: R  336 TYR cc_start: 0.7202 (m-10) cc_final: 0.6922 (m-10)
  outliers start: 37
  outliers final: 20
  residues processed: 275
  average time/residue: 0.2266
  time to fit residues: 82.2867
Evaluate side-chains
  244 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 220
  time to evaluate  : 0.875 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   34 VAL
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 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  234 PHE
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 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  212 VAL
Chi-restraints excluded: chain R residue  154 SER
Chi-restraints excluded: chain R residue  161 MET
Chi-restraints excluded: chain R residue  176 LEU
Chi-restraints excluded: chain R residue  191 ASN
Chi-restraints excluded: chain R residue  290 ILE
Chi-restraints excluded: chain R residue  293 TRP
Chi-restraints excluded: chain R residue  298 ILE
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 110
   random chunks:
   chunk 2 optimal weight:    4.9990
   chunk 25 optimal weight:    4.9990
   chunk 99 optimal weight:    3.9990
   chunk 42 optimal weight:    2.9990
   chunk 54 optimal weight:    0.9980
   chunk 104 optimal weight:    0.6980
   chunk 97 optimal weight:    0.0980
   chunk 17 optimal weight:    2.9990
   chunk 106 optimal weight:    0.0170
   chunk 82 optimal weight:   10.0000
   chunk 109 optimal weight:    5.9990
   overall best weight:    0.9620

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

Flipped N/Q/H residues before XYZ refinement:
A 306 GLN
B  75 GLN
B 156 GLN
B 230 ASN
E  82 GLN
E 130 GLN
** R 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
R 127 ASN

Total number of N/Q/H flips: 7

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4159 r_free = 0.4159 target = 0.169606 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3816 r_free = 0.3816 target = 0.140744 restraints weight = 13344.327|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 41)----------------|
| r_work = 0.3878 r_free = 0.3878 target = 0.145604 restraints weight = 6907.733|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.3918 r_free = 0.3918 target = 0.148771 restraints weight = 4368.824|
|-----------------------------------------------------------------------------|
r_work (final): 0.3969
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7393
moved from start:          0.4029

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.045   8664  Z= 0.239
  Angle     :  0.669   8.033  11766  Z= 0.337
  Chirality :  0.044   0.293   1362
  Planarity :  0.004   0.039   1484
  Dihedral  :  5.173  70.357   1214
  Min Nonbonded Distance : 2.439

Molprobity Statistics.
  All-atom Clashscore : 12.32
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.26 %
    Favored  : 94.74 %
  Rotamer:
    Outliers :  4.62 %
    Allowed  : 22.40 %
    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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.19 (0.25), residues: 1103
  helix:  0.52 (0.29), residues: 350
  sheet: -1.30 (0.31), residues: 248
  loop : -1.40 (0.28), residues: 505

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.021   0.002   TRP R 133 
 HIS   0.005   0.001   HIS R 319 
 PHE   0.015   0.001   PHE R 241 
 TYR   0.032   0.002   TYR E 178 
 ARG   0.007   0.001   ARG B  49 

*********************** 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
  281 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 40
    poor density    : 241
  time to evaluate  : 0.890 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   14 GLU cc_start: 0.7830 (tm-30) cc_final: 0.7225 (tm-30)
REVERT: A   51 LYS cc_start: 0.8750 (ttmp) cc_final: 0.8267 (tmmt)
REVERT: A  197 LYS cc_start: 0.8417 (mtpt) cc_final: 0.8200 (mtpp)
REVERT: A  228 SER cc_start: 0.7866 (p) cc_final: 0.7384 (m)
REVERT: A  341 ASP cc_start: 0.8694 (t70) cc_final: 0.8450 (t0)
REVERT: A  347 ASN cc_start: 0.9325 (m-40) cc_final: 0.8962 (m-40)
REVERT: B  117 LEU cc_start: 0.8170 (OUTLIER) cc_final: 0.7457 (tt)
REVERT: B  170 ASP cc_start: 0.7172 (t0) cc_final: 0.6963 (t0)
REVERT: B  215 GLU cc_start: 0.6980 (pm20) cc_final: 0.6279 (pm20)
REVERT: B  234 PHE cc_start: 0.8812 (OUTLIER) cc_final: 0.8363 (m-10)
REVERT: B  308 LEU cc_start: 0.8415 (mp) cc_final: 0.7934 (mp)
REVERT: B  339 TRP cc_start: 0.8837 (m100) cc_final: 0.8267 (m-10)
REVERT: R  161 MET cc_start: 0.8725 (tpp) cc_final: 0.8155 (tpp)
REVERT: R  164 ASP cc_start: 0.8638 (t70) cc_final: 0.8348 (t70)
REVERT: R  165 ARG cc_start: 0.8442 (mtt90) cc_final: 0.7735 (mtt90)
REVERT: R  185 LYS cc_start: 0.8658 (ttmp) cc_final: 0.8158 (tptp)
REVERT: R  211 ARG cc_start: 0.6278 (mtt90) cc_final: 0.6004 (mtt180)
REVERT: R  228 TRP cc_start: 0.7474 (t-100) cc_final: 0.7140 (t-100)
REVERT: R  263 ARG cc_start: 0.8227 (tmt90) cc_final: 0.7842 (tmt170)
REVERT: R  277 ARG cc_start: 0.8517 (tmm-80) cc_final: 0.7916 (tmm-80)
REVERT: R  336 TYR cc_start: 0.7166 (m-10) cc_final: 0.6786 (m-10)
  outliers start: 40
  outliers final: 27
  residues processed: 266
  average time/residue: 0.2238
  time to fit residues: 78.8826
Evaluate side-chains
  254 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 225
  time to evaluate  : 0.866 
-------------------------------------------------------------------------------
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 B residue   74 SER
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  181 THR
Chi-restraints excluded: chain B residue  190 LEU
Chi-restraints excluded: chain B residue  234 PHE
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   69 THR
Chi-restraints excluded: chain E residue   86 LEU
Chi-restraints excluded: chain E residue  115 THR
Chi-restraints excluded: chain E residue  146 SER
Chi-restraints excluded: chain E residue  212 VAL
Chi-restraints excluded: chain R residue   78 VAL
Chi-restraints excluded: chain R residue  119 SER
Chi-restraints excluded: chain R residue  154 SER
Chi-restraints excluded: chain R residue  191 ASN
Chi-restraints excluded: chain R residue  290 ILE
Chi-restraints excluded: chain R residue  293 TRP
Chi-restraints excluded: chain R residue  328 ASN
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 36 optimal weight:    1.9990
   chunk 71 optimal weight:    2.9990
   chunk 52 optimal weight:    0.9980
   chunk 51 optimal weight:    5.9990
   chunk 60 optimal weight:    3.9990
   chunk 87 optimal weight:    0.2980
   chunk 99 optimal weight:    3.9990
   chunk 96 optimal weight:    0.0670
   chunk 2 optimal weight:    9.9990
   chunk 103 optimal weight:    0.9990
   chunk 59 optimal weight:    2.9990
   overall best weight:    0.8722

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

Flipped N/Q/H residues before XYZ refinement:
A 306 GLN
B 156 GLN
** 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 = 0.4187 r_free = 0.4187 target = 0.171795 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3893 r_free = 0.3893 target = 0.145371 restraints weight = 13150.348|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3940 r_free = 0.3940 target = 0.150948 restraints weight = 7880.115|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3966 r_free = 0.3966 target = 0.153141 restraints weight = 4250.866|
|-----------------------------------------------------------------------------|
r_work (final): 0.3963
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7330
moved from start:          0.4292

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   8664  Z= 0.221
  Angle     :  0.659   9.263  11766  Z= 0.332
  Chirality :  0.044   0.302   1362
  Planarity :  0.004   0.036   1484
  Dihedral  :  5.098  71.608   1214
  Min Nonbonded Distance : 2.436

Molprobity Statistics.
  All-atom Clashscore : 12.86
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.62 %
    Favored  : 95.38 %
  Rotamer:
    Outliers :  5.43 %
    Allowed  : 22.75 %
    Favored  : 71.82 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.45 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.09 (0.26), residues: 1103
  helix:  0.74 (0.29), residues: 348
  sheet: -1.32 (0.31), residues: 254
  loop : -1.40 (0.28), residues: 501

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.030   0.002   TRP R 133 
 HIS   0.005   0.001   HIS R 319 
 PHE   0.016   0.001   PHE R 241 
 TYR   0.025   0.002   TYR E 178 
 ARG   0.006   0.001   ARG A  21 

*********************** 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
  280 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 47
    poor density    : 233
  time to evaluate  : 0.975 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   14 GLU cc_start: 0.8049 (tm-30) cc_final: 0.7365 (tm-30)
REVERT: A   51 LYS cc_start: 0.8826 (ttmp) cc_final: 0.8282 (tmmt)
REVERT: A  216 GLU cc_start: 0.8416 (OUTLIER) cc_final: 0.8150 (pp20)
REVERT: A  228 SER cc_start: 0.7601 (p) cc_final: 0.7017 (m)
REVERT: A  341 ASP cc_start: 0.8680 (t70) cc_final: 0.8425 (t0)
REVERT: A  347 ASN cc_start: 0.9317 (m-40) cc_final: 0.8967 (m-40)
REVERT: B   59 TYR cc_start: 0.8886 (m-80) cc_final: 0.8624 (m-80)
REVERT: B  117 LEU cc_start: 0.8098 (OUTLIER) cc_final: 0.7780 (tt)
REVERT: B  170 ASP cc_start: 0.7352 (t0) cc_final: 0.6629 (t0)
REVERT: B  172 GLU cc_start: 0.7689 (mp0) cc_final: 0.7475 (mp0)
REVERT: B  234 PHE cc_start: 0.8833 (OUTLIER) cc_final: 0.8474 (m-10)
REVERT: B  339 TRP cc_start: 0.8930 (m100) cc_final: 0.8297 (m-10)
REVERT: C   13 ARG cc_start: 0.8571 (tpp80) cc_final: 0.8055 (mtm110)
REVERT: C   32 LYS cc_start: 0.8462 (mppt) cc_final: 0.8191 (mptt)
REVERT: C   38 MET cc_start: 0.6389 (OUTLIER) cc_final: 0.5979 (ttt)
REVERT: E   98 ARG cc_start: 0.8096 (ttp-110) cc_final: 0.7823 (ttp-110)
REVERT: E  207 LEU cc_start: 0.7012 (OUTLIER) cc_final: 0.6585 (tt)
REVERT: R   78 VAL cc_start: 0.9030 (OUTLIER) cc_final: 0.8797 (t)
REVERT: R  141 LYS cc_start: 0.6093 (pttp) cc_final: 0.5568 (tttt)
REVERT: R  161 MET cc_start: 0.8642 (tpp) cc_final: 0.8134 (tpp)
REVERT: R  164 ASP cc_start: 0.8593 (t70) cc_final: 0.8288 (t70)
REVERT: R  165 ARG cc_start: 0.8482 (mtt90) cc_final: 0.7832 (mtt90)
REVERT: R  185 LYS cc_start: 0.8726 (ttmp) cc_final: 0.8197 (tptp)
REVERT: R  228 TRP cc_start: 0.7564 (t-100) cc_final: 0.7238 (t-100)
REVERT: R  233 LYS cc_start: 0.8287 (mtmm) cc_final: 0.7754 (ttmt)
REVERT: R  263 ARG cc_start: 0.8217 (tmt90) cc_final: 0.7811 (tmt170)
REVERT: R  270 GLU cc_start: 0.8306 (tm-30) cc_final: 0.7520 (tm-30)
REVERT: R  277 ARG cc_start: 0.8525 (tmm-80) cc_final: 0.8195 (tmm-80)
REVERT: R  336 TYR cc_start: 0.7242 (m-10) cc_final: 0.6877 (m-10)
  outliers start: 47
  outliers final: 30
  residues processed: 262
  average time/residue: 0.2197
  time to fit residues: 76.8438
Evaluate side-chains
  248 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 212
  time to evaluate  : 0.861 
-------------------------------------------------------------------------------
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  216 GLU
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 B residue   17 GLN
Chi-restraints excluded: chain B residue   74 SER
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  229 ILE
Chi-restraints excluded: chain B residue  234 PHE
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   38 MET
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  207 LEU
Chi-restraints excluded: chain E residue  212 VAL
Chi-restraints excluded: chain R residue   78 VAL
Chi-restraints excluded: chain R residue  119 SER
Chi-restraints excluded: chain R residue  154 SER
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  328 ASN
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 104 optimal weight:    0.8980
   chunk 46 optimal weight:    0.2980
   chunk 8 optimal weight:    0.8980
   chunk 21 optimal weight:    0.8980
   chunk 37 optimal weight:    0.7980
   chunk 74 optimal weight:    2.9990
   chunk 89 optimal weight:    2.9990
   chunk 35 optimal weight:    0.7980
   chunk 106 optimal weight:    1.9990
   chunk 51 optimal weight:    8.9990
   chunk 7 optimal weight:    0.4980
   overall best weight:    0.6580

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

Flipped N/Q/H residues before XYZ refinement:
A 188 HIS
A 306 GLN
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: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4254 r_free = 0.4254 target = 0.177244 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 27)----------------|
| r_work = 0.3980 r_free = 0.3980 target = 0.151636 restraints weight = 12789.770|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.4028 r_free = 0.4028 target = 0.156222 restraints weight = 7033.590|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.4062 r_free = 0.4062 target = 0.159326 restraints weight = 4111.313|
|-----------------------------------------------------------------------------|
r_work (final): 0.4151
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7224
moved from start:          0.4544

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   8664  Z= 0.194
  Angle     :  0.640   8.784  11766  Z= 0.321
  Chirality :  0.043   0.297   1362
  Planarity :  0.004   0.035   1484
  Dihedral  :  5.016  72.368   1214
  Min Nonbonded Distance : 2.488

Molprobity Statistics.
  All-atom Clashscore : 12.02
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.62 %
    Favored  : 95.38 %
  Rotamer:
    Outliers :  5.08 %
    Allowed  : 23.67 %
    Favored  : 71.25 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.45 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.93 (0.26), residues: 1103
  helix:  1.00 (0.29), residues: 346
  sheet: -1.35 (0.30), residues: 261
  loop : -1.31 (0.29), residues: 496

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.002   TRP R 133 
 HIS   0.004   0.001   HIS R 319 
 PHE   0.016   0.001   PHE R 241 
 TYR   0.022   0.002   TYR E 178 
 ARG   0.006   0.000   ARG A  21 

*********************** 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
  264 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 44
    poor density    : 220
  time to evaluate  : 0.882 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   14 GLU cc_start: 0.8176 (tm-30) cc_final: 0.7471 (tm-30)
REVERT: A   51 LYS cc_start: 0.8876 (ttmp) cc_final: 0.8301 (tmmt)
REVERT: A  216 GLU cc_start: 0.8497 (OUTLIER) cc_final: 0.8210 (pp20)
REVERT: A  228 SER cc_start: 0.7664 (p) cc_final: 0.7034 (m)
REVERT: A  245 GLU cc_start: 0.8436 (tm-30) cc_final: 0.8234 (pt0)
REVERT: A  334 PHE cc_start: 0.8914 (t80) cc_final: 0.8710 (t80)
REVERT: A  347 ASN cc_start: 0.9313 (m-40) cc_final: 0.8902 (m-40)
REVERT: B   59 TYR cc_start: 0.8802 (m-80) cc_final: 0.8358 (m-80)
REVERT: B   75 GLN cc_start: 0.7313 (mt0) cc_final: 0.7042 (mm-40)
REVERT: B  117 LEU cc_start: 0.8010 (OUTLIER) cc_final: 0.7242 (tt)
REVERT: B  234 PHE cc_start: 0.8840 (OUTLIER) cc_final: 0.8488 (m-10)
REVERT: B  280 LYS cc_start: 0.8530 (tmmt) cc_final: 0.8266 (tttt)
REVERT: B  339 TRP cc_start: 0.8978 (m100) cc_final: 0.8220 (m-10)
REVERT: C   18 GLN cc_start: 0.8476 (tp40) cc_final: 0.8197 (tp40)
REVERT: E   71 SER cc_start: 0.8000 (p) cc_final: 0.7648 (t)
REVERT: E   93 MET cc_start: 0.7423 (ttt) cc_final: 0.7140 (ttm)
REVERT: E   98 ARG cc_start: 0.8127 (ttp-110) cc_final: 0.7832 (ttp-110)
REVERT: E  207 LEU cc_start: 0.7010 (OUTLIER) cc_final: 0.6642 (tt)
REVERT: R   78 VAL cc_start: 0.8957 (OUTLIER) cc_final: 0.8689 (t)
REVERT: R  161 MET cc_start: 0.8685 (tpp) cc_final: 0.8164 (tpp)
REVERT: R  164 ASP cc_start: 0.8705 (t70) cc_final: 0.8037 (t70)
REVERT: R  165 ARG cc_start: 0.8519 (mtt90) cc_final: 0.7812 (mtt90)
REVERT: R  179 ARG cc_start: 0.8574 (ptm-80) cc_final: 0.8328 (ptm160)
REVERT: R  185 LYS cc_start: 0.8677 (ttmp) cc_final: 0.8150 (tptp)
REVERT: R  228 TRP cc_start: 0.7570 (t-100) cc_final: 0.7251 (t-100)
REVERT: R  233 LYS cc_start: 0.8321 (mtmm) cc_final: 0.7909 (ttmt)
REVERT: R  263 ARG cc_start: 0.8176 (tmt90) cc_final: 0.7739 (tmt170)
REVERT: R  277 ARG cc_start: 0.8531 (tmm-80) cc_final: 0.8174 (tmm-80)
REVERT: R  336 TYR cc_start: 0.7287 (m-10) cc_final: 0.6946 (m-10)
  outliers start: 44
  outliers final: 31
  residues processed: 248
  average time/residue: 0.2205
  time to fit residues: 72.8470
Evaluate side-chains
  240 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 204
  time to evaluate  : 0.885 
-------------------------------------------------------------------------------
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  216 GLU
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  265 ILE
Chi-restraints excluded: chain A residue  332 VAL
Chi-restraints excluded: chain A residue  335 VAL
Chi-restraints excluded: chain B residue   74 SER
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  181 THR
Chi-restraints excluded: chain B residue  190 LEU
Chi-restraints excluded: chain B residue  229 ILE
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  255 LEU
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 E residue    7 SER
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  146 SER
Chi-restraints excluded: chain E residue  207 LEU
Chi-restraints excluded: chain E residue  212 VAL
Chi-restraints excluded: chain R residue   78 VAL
Chi-restraints excluded: chain R residue  154 SER
Chi-restraints excluded: chain R residue  191 ASN
Chi-restraints excluded: chain R residue  290 ILE
Chi-restraints excluded: chain R residue  293 TRP
Chi-restraints excluded: chain R residue  330 CYS
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 110
   random chunks:
   chunk 89 optimal weight:    0.2980
   chunk 103 optimal weight:    6.9990
   chunk 41 optimal weight:    3.9990
   chunk 29 optimal weight:    3.9990
   chunk 5 optimal weight:    0.0270
   chunk 39 optimal weight:    7.9990
   chunk 1 optimal weight:    1.9990
   chunk 30 optimal weight:    3.9990
   chunk 52 optimal weight:    0.9990
   chunk 72 optimal weight:    0.8980
   chunk 91 optimal weight:    0.9980
   overall best weight:    0.6440

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

Flipped N/Q/H residues before XYZ refinement:
A 294 ASN
A 306 GLN
** B 239 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** 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 = 0.4260 r_free = 0.4260 target = 0.177900 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 27)----------------|
| r_work = 0.3989 r_free = 0.3989 target = 0.152352 restraints weight = 12852.559|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.4034 r_free = 0.4034 target = 0.156847 restraints weight = 6843.175|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.4065 r_free = 0.4065 target = 0.159712 restraints weight = 4098.353|
|-----------------------------------------------------------------------------|
r_work (final): 0.4165
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7215
moved from start:          0.4729

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   8664  Z= 0.200
  Angle     :  0.670  10.278  11766  Z= 0.332
  Chirality :  0.043   0.274   1362
  Planarity :  0.003   0.035   1484
  Dihedral  :  4.891  72.814   1212
  Min Nonbonded Distance : 2.500

Molprobity Statistics.
  All-atom Clashscore : 12.14
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.62 %
    Favored  : 95.38 %
  Rotamer:
    Outliers :  5.43 %
    Allowed  : 23.90 %
    Favored  : 70.67 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.45 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.83 (0.26), residues: 1103
  helix:  1.16 (0.29), residues: 346
  sheet: -1.31 (0.30), residues: 261
  loop : -1.31 (0.28), residues: 496

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP R 133 
 HIS   0.003   0.001   HIS R 319 
 PHE   0.016   0.001   PHE R 241 
 TYR   0.020   0.002   TYR E 178 
 ARG   0.006   0.000   ARG A  21 

*********************** 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
  267 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 47
    poor density    : 220
  time to evaluate  : 0.997 
Fit side-chains
   revert: symmetry clash
REVERT: A   14 GLU cc_start: 0.8217 (tm-30) cc_final: 0.7474 (tm-30)
REVERT: A   51 LYS cc_start: 0.8861 (OUTLIER) cc_final: 0.8327 (tmmt)
REVERT: A  216 GLU cc_start: 0.8525 (OUTLIER) cc_final: 0.8233 (pp20)
REVERT: A  228 SER cc_start: 0.7774 (p) cc_final: 0.7163 (m)
REVERT: A  245 GLU cc_start: 0.8524 (tm-30) cc_final: 0.8247 (pt0)
REVERT: A  347 ASN cc_start: 0.9310 (m-40) cc_final: 0.8919 (m-40)
REVERT: B   59 TYR cc_start: 0.8810 (m-80) cc_final: 0.8336 (m-80)
REVERT: B   75 GLN cc_start: 0.7416 (mt0) cc_final: 0.7147 (mm-40)
REVERT: B   78 LYS cc_start: 0.8499 (mmtm) cc_final: 0.8282 (mmtm)
REVERT: B  117 LEU cc_start: 0.8019 (OUTLIER) cc_final: 0.7268 (tt)
REVERT: B  169 TRP cc_start: 0.7684 (OUTLIER) cc_final: 0.6609 (m-90)
REVERT: B  219 ARG cc_start: 0.7572 (ttm-80) cc_final: 0.7104 (mtt90)
REVERT: B  234 PHE cc_start: 0.8853 (OUTLIER) cc_final: 0.8570 (m-10)
REVERT: B  280 LYS cc_start: 0.8561 (tmmt) cc_final: 0.8321 (tttt)
REVERT: B  300 LEU cc_start: 0.8688 (OUTLIER) cc_final: 0.8386 (mp)
REVERT: B  339 TRP cc_start: 0.8996 (m100) cc_final: 0.8282 (m-10)
REVERT: C   18 GLN cc_start: 0.8480 (tp40) cc_final: 0.8229 (tp40)
REVERT: C   21 MET cc_start: 0.7637 (mpp) cc_final: 0.7236 (mpp)
REVERT: C   32 LYS cc_start: 0.8378 (mppt) cc_final: 0.8169 (mptt)
REVERT: E   71 SER cc_start: 0.8050 (p) cc_final: 0.7693 (t)
REVERT: E   98 ARG cc_start: 0.8145 (ttp-110) cc_final: 0.7877 (ttp-110)
REVERT: E  207 LEU cc_start: 0.6926 (OUTLIER) cc_final: 0.6491 (tt)
REVERT: R   78 VAL cc_start: 0.8975 (OUTLIER) cc_final: 0.8714 (t)
REVERT: R  165 ARG cc_start: 0.8539 (mtt90) cc_final: 0.8310 (mtt90)
REVERT: R  185 LYS cc_start: 0.8681 (ttmp) cc_final: 0.8144 (tptp)
REVERT: R  228 TRP cc_start: 0.7566 (t-100) cc_final: 0.7230 (t-100)
REVERT: R  233 LYS cc_start: 0.8317 (mtmm) cc_final: 0.7925 (ttmt)
REVERT: R  263 ARG cc_start: 0.8200 (tmt90) cc_final: 0.7808 (tmt170)
REVERT: R  277 ARG cc_start: 0.8520 (tmm-80) cc_final: 0.8169 (tmm-80)
REVERT: R  336 TYR cc_start: 0.7248 (m-10) cc_final: 0.6919 (m-10)
  outliers start: 47
  outliers final: 32
  residues processed: 247
  average time/residue: 0.2346
  time to fit residues: 77.7490
Evaluate side-chains
  243 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 40
    poor density    : 203
  time to evaluate  : 1.500 
-------------------------------------------------------------------------------
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   51 LYS
Chi-restraints excluded: chain A residue  185 VAL
Chi-restraints excluded: chain A residue  216 GLU
Chi-restraints excluded: chain A residue  227 LEU
Chi-restraints excluded: chain A residue  252 SER
Chi-restraints excluded: chain A residue  254 CYS
Chi-restraints excluded: chain A residue  264 ILE
Chi-restraints excluded: chain A residue  265 ILE
Chi-restraints excluded: chain A residue  332 VAL
Chi-restraints excluded: chain B residue   17 GLN
Chi-restraints excluded: chain B residue   43 ILE
Chi-restraints excluded: chain B residue   74 SER
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  229 ILE
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 B residue  300 LEU
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 E residue  207 LEU
Chi-restraints excluded: chain E residue  212 VAL
Chi-restraints excluded: chain R residue   78 VAL
Chi-restraints excluded: chain R residue  154 SER
Chi-restraints excluded: chain R residue  191 ASN
Chi-restraints excluded: chain R residue  290 ILE
Chi-restraints excluded: chain R residue  293 TRP
Chi-restraints excluded: chain R residue  330 CYS
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 110
   random chunks:
   chunk 96 optimal weight:    3.9990
   chunk 6 optimal weight:    0.8980
   chunk 67 optimal weight:    3.9990
   chunk 20 optimal weight:    1.9990
   chunk 0 optimal weight:   10.0000
   chunk 83 optimal weight:    0.7980
   chunk 51 optimal weight:    6.9990
   chunk 40 optimal weight:    0.9990
   chunk 65 optimal weight:    0.9980
   chunk 26 optimal weight:    2.9990
   chunk 55 optimal weight:    0.9980
   overall best weight:    0.9382

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

Flipped N/Q/H residues before XYZ refinement:
A 306 GLN
B 156 GLN
** B 239 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** 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 = 0.4239 r_free = 0.4239 target = 0.175944 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3963 r_free = 0.3963 target = 0.150365 restraints weight = 12998.183|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.4006 r_free = 0.4006 target = 0.154599 restraints weight = 7103.200|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.4039 r_free = 0.4039 target = 0.157600 restraints weight = 4307.473|
|-----------------------------------------------------------------------------|
r_work (final): 0.4129
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7258
moved from start:          0.4823

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.042   8664  Z= 0.236
  Angle     :  0.672  10.126  11766  Z= 0.337
  Chirality :  0.043   0.262   1362
  Planarity :  0.004   0.035   1484
  Dihedral  :  4.928  72.416   1212
  Min Nonbonded Distance : 2.505

Molprobity Statistics.
  All-atom Clashscore : 12.62
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.81 %
    Favored  : 95.19 %
  Rotamer:
    Outliers :  5.54 %
    Allowed  : 24.36 %
    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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.81 (0.26), residues: 1103
  helix:  1.17 (0.29), residues: 349
  sheet: -1.28 (0.31), residues: 261
  loop : -1.32 (0.28), residues: 493

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.002   TRP R 133 
 HIS   0.005   0.001   HIS B 183 
 PHE   0.015   0.001   PHE R 241 
 TYR   0.025   0.002   TYR R  75 
 ARG   0.006   0.000   ARG A  21 

*********************** 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: 48
    poor density    : 206
  time to evaluate  : 0.936 
Fit side-chains
   revert: symmetry clash
REVERT: A   14 GLU cc_start: 0.8240 (tm-30) cc_final: 0.7507 (tm-30)
REVERT: A   51 LYS cc_start: 0.8895 (ttmp) cc_final: 0.8316 (tmmt)
REVERT: A  216 GLU cc_start: 0.8552 (OUTLIER) cc_final: 0.8251 (pp20)
REVERT: A  228 SER cc_start: 0.7852 (p) cc_final: 0.7261 (m)
REVERT: A  245 GLU cc_start: 0.8538 (tm-30) cc_final: 0.8269 (pt0)
REVERT: A  306 GLN cc_start: 0.8328 (mm-40) cc_final: 0.7802 (mp10)
REVERT: A  347 ASN cc_start: 0.9311 (m-40) cc_final: 0.8936 (m-40)
REVERT: B   34 THR cc_start: 0.7079 (t) cc_final: 0.5582 (p)
REVERT: B   59 TYR cc_start: 0.8812 (m-80) cc_final: 0.8432 (m-80)
REVERT: B   75 GLN cc_start: 0.7499 (mt0) cc_final: 0.7230 (mm-40)
REVERT: B  117 LEU cc_start: 0.8095 (OUTLIER) cc_final: 0.7792 (tt)
REVERT: B  169 TRP cc_start: 0.7600 (OUTLIER) cc_final: 0.6523 (m-90)
REVERT: B  170 ASP cc_start: 0.7453 (t0) cc_final: 0.7186 (t0)
REVERT: B  219 ARG cc_start: 0.7553 (ttm-80) cc_final: 0.7077 (mtt90)
REVERT: B  234 PHE cc_start: 0.8876 (OUTLIER) cc_final: 0.8593 (m-10)
REVERT: B  280 LYS cc_start: 0.8629 (tmmt) cc_final: 0.8378 (tttt)
REVERT: B  300 LEU cc_start: 0.8709 (OUTLIER) cc_final: 0.8196 (mp)
REVERT: B  339 TRP cc_start: 0.9064 (m100) cc_final: 0.8298 (m-10)
REVERT: C   32 LYS cc_start: 0.8417 (mppt) cc_final: 0.8161 (mptt)
REVERT: E   71 SER cc_start: 0.8072 (p) cc_final: 0.7743 (t)
REVERT: E   93 MET cc_start: 0.7484 (ttt) cc_final: 0.7193 (ttm)
REVERT: E  207 LEU cc_start: 0.6928 (OUTLIER) cc_final: 0.6480 (tt)
REVERT: R   78 VAL cc_start: 0.9034 (OUTLIER) cc_final: 0.8798 (t)
REVERT: R   84 PHE cc_start: 0.7604 (t80) cc_final: 0.7355 (t80)
REVERT: R  165 ARG cc_start: 0.8515 (mtt90) cc_final: 0.8287 (mtt90)
REVERT: R  179 ARG cc_start: 0.8470 (ptm-80) cc_final: 0.7983 (ptm160)
REVERT: R  185 LYS cc_start: 0.8702 (ttmp) cc_final: 0.8156 (tptp)
REVERT: R  228 TRP cc_start: 0.7509 (t-100) cc_final: 0.7049 (t-100)
REVERT: R  263 ARG cc_start: 0.8081 (tmt90) cc_final: 0.7692 (tmt170)
REVERT: R  277 ARG cc_start: 0.8515 (tmm-80) cc_final: 0.8170 (tmm-80)
  outliers start: 48
  outliers final: 35
  residues processed: 234
  average time/residue: 0.2525
  time to fit residues: 79.1391
Evaluate side-chains
  239 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 42
    poor density    : 197
  time to evaluate  : 0.970 
-------------------------------------------------------------------------------
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  216 GLU
Chi-restraints excluded: chain A residue  227 LEU
Chi-restraints excluded: chain A residue  252 SER
Chi-restraints excluded: chain A residue  254 CYS
Chi-restraints excluded: chain A residue  264 ILE
Chi-restraints excluded: chain A residue  265 ILE
Chi-restraints excluded: chain A residue  332 VAL
Chi-restraints excluded: chain A residue  335 VAL
Chi-restraints excluded: chain B residue   43 ILE
Chi-restraints excluded: chain B residue   74 SER
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  229 ILE
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  255 LEU
Chi-restraints excluded: chain B residue  263 THR
Chi-restraints excluded: chain B residue  271 CYS
Chi-restraints excluded: chain B residue  300 LEU
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 E residue  207 LEU
Chi-restraints excluded: chain E residue  212 VAL
Chi-restraints excluded: chain R residue   78 VAL
Chi-restraints excluded: chain R residue  154 SER
Chi-restraints excluded: chain R residue  191 ASN
Chi-restraints excluded: chain R residue  242 ILE
Chi-restraints excluded: chain R residue  290 ILE
Chi-restraints excluded: chain R residue  293 TRP
Chi-restraints excluded: chain R residue  328 ASN
Chi-restraints excluded: chain R residue  330 CYS
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 110
   random chunks:
   chunk 36 optimal weight:    5.9990
   chunk 7 optimal weight:    0.7980
   chunk 74 optimal weight:    2.9990
   chunk 11 optimal weight:    0.4980
   chunk 73 optimal weight:    8.9990
   chunk 106 optimal weight:    8.9990
   chunk 99 optimal weight:    3.9990
   chunk 24 optimal weight:    0.0370
   chunk 42 optimal weight:    0.9990
   chunk 15 optimal weight:    2.9990
   chunk 48 optimal weight:    0.9980
   overall best weight:    0.6660

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

Flipped N/Q/H residues before XYZ refinement:
A 256 ASN
** B 239 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** 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 = 0.4179 r_free = 0.4179 target = 0.171345 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3892 r_free = 0.3892 target = 0.145414 restraints weight = 13317.538|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3928 r_free = 0.3928 target = 0.150178 restraints weight = 7710.009|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3946 r_free = 0.3946 target = 0.151588 restraints weight = 4768.315|
|-----------------------------------------------------------------------------|
r_work (final): 0.4119
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7346
moved from start:          0.4940

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.045   8664  Z= 0.204
  Angle     :  0.671  10.179  11766  Z= 0.334
  Chirality :  0.043   0.246   1362
  Planarity :  0.004   0.035   1484
  Dihedral  :  4.923  73.409   1212
  Min Nonbonded Distance : 2.540

Molprobity Statistics.
  All-atom Clashscore : 12.32
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.62 %
    Favored  : 95.38 %
  Rotamer:
    Outliers :  5.31 %
    Allowed  : 25.06 %
    Favored  : 69.63 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.45 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.72 (0.26), residues: 1103
  helix:  1.27 (0.29), residues: 347
  sheet: -1.27 (0.31), residues: 265
  loop : -1.25 (0.29), residues: 491

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP B  82 
 HIS   0.006   0.001   HIS B 183 
 PHE   0.015   0.001   PHE R 241 
 TYR   0.023   0.001   TYR R  75 
 ARG   0.007   0.001   ARG A  21 

*********************** 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
  249 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 46
    poor density    : 203
  time to evaluate  : 2.114 
Fit side-chains
REVERT: A   14 GLU cc_start: 0.8057 (tm-30) cc_final: 0.7299 (tm-30)
REVERT: A   51 LYS cc_start: 0.8860 (ttmp) cc_final: 0.8284 (tmmt)
REVERT: A  216 GLU cc_start: 0.8508 (OUTLIER) cc_final: 0.8226 (pp20)
REVERT: A  228 SER cc_start: 0.7910 (p) cc_final: 0.7412 (m)
REVERT: A  347 ASN cc_start: 0.9266 (m-40) cc_final: 0.8892 (m-40)
REVERT: B   34 THR cc_start: 0.6930 (t) cc_final: 0.5308 (p)
REVERT: B   59 TYR cc_start: 0.8728 (m-80) cc_final: 0.8376 (m-80)
REVERT: B  117 LEU cc_start: 0.7996 (OUTLIER) cc_final: 0.7705 (tt)
REVERT: B  169 TRP cc_start: 0.7426 (OUTLIER) cc_final: 0.6775 (m-90)
REVERT: B  219 ARG cc_start: 0.7425 (ttm-80) cc_final: 0.7126 (mtt90)
REVERT: B  280 LYS cc_start: 0.8477 (tmmt) cc_final: 0.8201 (tttt)
REVERT: B  300 LEU cc_start: 0.8681 (OUTLIER) cc_final: 0.8188 (mp)
REVERT: B  339 TRP cc_start: 0.8965 (m100) cc_final: 0.8333 (m-10)
REVERT: C   21 MET cc_start: 0.7557 (mpp) cc_final: 0.7015 (mtm)
REVERT: C   32 LYS cc_start: 0.8471 (mppt) cc_final: 0.8211 (mptt)
REVERT: E   98 ARG cc_start: 0.8119 (ttp-110) cc_final: 0.7865 (ttp-110)
REVERT: E  152 SER cc_start: 0.8068 (t) cc_final: 0.7715 (p)
REVERT: E  207 LEU cc_start: 0.6808 (OUTLIER) cc_final: 0.6284 (tt)
REVERT: R   78 VAL cc_start: 0.9063 (OUTLIER) cc_final: 0.8837 (t)
REVERT: R   84 PHE cc_start: 0.7537 (t80) cc_final: 0.7296 (t80)
REVERT: R  164 ASP cc_start: 0.8497 (t70) cc_final: 0.7948 (t70)
REVERT: R  165 ARG cc_start: 0.8496 (mtt90) cc_final: 0.8171 (mtt90)
REVERT: R  179 ARG cc_start: 0.8449 (ptm-80) cc_final: 0.8080 (ptm160)
REVERT: R  185 LYS cc_start: 0.8680 (ttmp) cc_final: 0.8143 (tptp)
REVERT: R  228 TRP cc_start: 0.7478 (t-100) cc_final: 0.7099 (t-100)
REVERT: R  233 LYS cc_start: 0.8382 (mtmm) cc_final: 0.8015 (ttmm)
REVERT: R  243 MET cc_start: 0.8512 (tpt) cc_final: 0.8246 (tmm)
REVERT: R  263 ARG cc_start: 0.8153 (tmt90) cc_final: 0.7784 (tmt170)
REVERT: R  277 ARG cc_start: 0.8470 (tmm-80) cc_final: 0.8142 (tmm-80)
REVERT: R  336 TYR cc_start: 0.7245 (m-10) cc_final: 0.6888 (m-10)
  outliers start: 46
  outliers final: 31
  residues processed: 233
  average time/residue: 0.2213
  time to fit residues: 68.8698
Evaluate side-chains
  233 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 37
    poor density    : 196
  time to evaluate  : 0.856 
-------------------------------------------------------------------------------
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  227 LEU
Chi-restraints excluded: chain A residue  252 SER
Chi-restraints excluded: chain A residue  254 CYS
Chi-restraints excluded: chain A residue  256 ASN
Chi-restraints excluded: chain A residue  264 ILE
Chi-restraints excluded: chain A residue  332 VAL
Chi-restraints excluded: chain A residue  335 VAL
Chi-restraints excluded: chain B residue   43 ILE
Chi-restraints excluded: chain B residue   74 SER
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  229 ILE
Chi-restraints excluded: chain B residue  255 LEU
Chi-restraints excluded: chain B residue  263 THR
Chi-restraints excluded: chain B residue  271 CYS
Chi-restraints excluded: chain B residue  300 LEU
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 E residue  207 LEU
Chi-restraints excluded: chain E residue  212 VAL
Chi-restraints excluded: chain R residue   78 VAL
Chi-restraints excluded: chain R residue  154 SER
Chi-restraints excluded: chain R residue  191 ASN
Chi-restraints excluded: chain R residue  290 ILE
Chi-restraints excluded: chain R residue  293 TRP
Chi-restraints excluded: chain R residue  330 CYS
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 110
   random chunks:
   chunk 59 optimal weight:    3.9990
   chunk 76 optimal weight:    0.9980
   chunk 6 optimal weight:    0.7980
   chunk 94 optimal weight:    1.9990
   chunk 74 optimal weight:    0.9980
   chunk 70 optimal weight:    0.9980
   chunk 85 optimal weight:    5.9990
   chunk 58 optimal weight:    0.0030
   chunk 33 optimal weight:    0.0170
   chunk 107 optimal weight:    2.9990
   chunk 0 optimal weight:    7.9990
   overall best weight:    0.5628

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

Flipped N/Q/H residues before XYZ refinement:
B 183 HIS
** B 239 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
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 = 0.4129 r_free = 0.4129 target = 0.170496 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3837 r_free = 0.3837 target = 0.144238 restraints weight = 13174.617|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3877 r_free = 0.3877 target = 0.148761 restraints weight = 7231.910|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3894 r_free = 0.3894 target = 0.150358 restraints weight = 4224.344|
|-----------------------------------------------------------------------------|
r_work (final): 0.4027
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7304
moved from start:          0.5098

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.044   8664  Z= 0.198
  Angle     :  0.679  10.618  11766  Z= 0.338
  Chirality :  0.044   0.351   1362
  Planarity :  0.004   0.035   1484
  Dihedral  :  4.977  73.639   1212
  Min Nonbonded Distance : 2.528

Molprobity Statistics.
  All-atom Clashscore : 11.90
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.62 %
    Favored  : 95.38 %
  Rotamer:
    Outliers :  5.08 %
    Allowed  : 24.60 %
    Favored  : 70.32 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.45 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.65 (0.26), residues: 1103
  helix:  1.18 (0.29), residues: 353
  sheet: -1.07 (0.32), residues: 252
  loop : -1.23 (0.28), residues: 498

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.026   0.002   TRP B  82 
 HIS   0.006   0.001   HIS B 183 
 PHE   0.015   0.001   PHE R 241 
 TYR   0.023   0.002   TYR R  75 
 ARG   0.006   0.000   ARG A  21 

********************** 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
  247 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 44
    poor density    : 203
  time to evaluate  : 0.871 
Fit side-chains
REVERT: A   14 GLU cc_start: 0.8168 (tm-30) cc_final: 0.7361 (tm-30)
REVERT: A   18 MET cc_start: 0.7827 (OUTLIER) cc_final: 0.7518 (ttm)
REVERT: A   51 LYS cc_start: 0.8864 (ttmp) cc_final: 0.8188 (tmmt)
REVERT: A  216 GLU cc_start: 0.8494 (OUTLIER) cc_final: 0.8237 (pp20)
REVERT: A  228 SER cc_start: 0.7918 (p) cc_final: 0.7406 (m)
REVERT: A  347 ASN cc_start: 0.9282 (m-40) cc_final: 0.8900 (m-40)
REVERT: B   34 THR cc_start: 0.6838 (t) cc_final: 0.5164 (p)
REVERT: B   59 TYR cc_start: 0.8799 (m-80) cc_final: 0.8274 (m-80)
REVERT: B   75 GLN cc_start: 0.7324 (mm-40) cc_final: 0.5867 (mt0)
REVERT: B   78 LYS cc_start: 0.8526 (mmtm) cc_final: 0.8174 (mmtm)
REVERT: B  117 LEU cc_start: 0.7993 (OUTLIER) cc_final: 0.7686 (tt)
REVERT: B  169 TRP cc_start: 0.7399 (OUTLIER) cc_final: 0.6794 (m-90)
REVERT: B  219 ARG cc_start: 0.7489 (ttm-80) cc_final: 0.7169 (mtt90)
REVERT: B  280 LYS cc_start: 0.8496 (tmmt) cc_final: 0.8235 (tttt)
REVERT: B  300 LEU cc_start: 0.8683 (OUTLIER) cc_final: 0.8174 (mp)
REVERT: B  339 TRP cc_start: 0.8927 (m100) cc_final: 0.8351 (m-10)
REVERT: C   21 MET cc_start: 0.7555 (mpp) cc_final: 0.6990 (mtm)
REVERT: C   32 LYS cc_start: 0.8414 (mppt) cc_final: 0.8211 (mptt)
REVERT: E   98 ARG cc_start: 0.8216 (ttp-110) cc_final: 0.7976 (ttp-110)
REVERT: E  152 SER cc_start: 0.8163 (t) cc_final: 0.7788 (p)
REVERT: R  164 ASP cc_start: 0.8578 (t70) cc_final: 0.8047 (t70)
REVERT: R  165 ARG cc_start: 0.8524 (mtt90) cc_final: 0.8189 (mtt90)
REVERT: R  179 ARG cc_start: 0.8490 (ptm-80) cc_final: 0.8103 (ptm160)
REVERT: R  185 LYS cc_start: 0.8678 (ttmp) cc_final: 0.8092 (tptp)
REVERT: R  228 TRP cc_start: 0.7492 (t-100) cc_final: 0.7072 (t-100)
REVERT: R  233 LYS cc_start: 0.8368 (mtmm) cc_final: 0.8023 (ttmm)
REVERT: R  243 MET cc_start: 0.8507 (tpt) cc_final: 0.8213 (tmm)
REVERT: R  263 ARG cc_start: 0.8111 (tmt90) cc_final: 0.7713 (tmt170)
REVERT: R  277 ARG cc_start: 0.8452 (tmm-80) cc_final: 0.8144 (tmm-80)
REVERT: R  336 TYR cc_start: 0.7190 (m-10) cc_final: 0.6842 (m-10)
  outliers start: 44
  outliers final: 31
  residues processed: 231
  average time/residue: 0.2126
  time to fit residues: 65.7611
Evaluate side-chains
  231 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 195
  time to evaluate  : 0.862 
-------------------------------------------------------------------------------
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  216 GLU
Chi-restraints excluded: chain A residue  227 LEU
Chi-restraints excluded: chain A residue  252 SER
Chi-restraints excluded: chain A residue  254 CYS
Chi-restraints excluded: chain A residue  295 THR
Chi-restraints excluded: chain A residue  332 VAL
Chi-restraints excluded: chain A residue  335 VAL
Chi-restraints excluded: chain B residue   43 ILE
Chi-restraints excluded: chain B residue   74 SER
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  229 ILE
Chi-restraints excluded: chain B residue  255 LEU
Chi-restraints excluded: chain B residue  263 THR
Chi-restraints excluded: chain B residue  271 CYS
Chi-restraints excluded: chain B residue  300 LEU
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 E residue  212 VAL
Chi-restraints excluded: chain R residue  154 SER
Chi-restraints excluded: chain R residue  191 ASN
Chi-restraints excluded: chain R residue  290 ILE
Chi-restraints excluded: chain R residue  293 TRP
Chi-restraints excluded: chain R residue  330 CYS
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 110
   random chunks:
   chunk 87 optimal weight:    0.9980
   chunk 48 optimal weight:    3.9990
   chunk 33 optimal weight:    2.9990
   chunk 68 optimal weight:    0.4980
   chunk 109 optimal weight:    7.9990
   chunk 97 optimal weight:    2.9990
   chunk 7 optimal weight:    0.9980
   chunk 103 optimal weight:    6.9990
   chunk 65 optimal weight:    0.2980
   chunk 74 optimal weight:    0.9980
   chunk 99 optimal weight:    4.9990
   overall best weight:    0.7580

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

Flipped N/Q/H residues before XYZ refinement:
** 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**
** 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 = 0.4118 r_free = 0.4118 target = 0.169456 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3823 r_free = 0.3823 target = 0.143066 restraints weight = 13471.930|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3863 r_free = 0.3863 target = 0.147586 restraints weight = 7238.431|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3881 r_free = 0.3881 target = 0.149166 restraints weight = 4269.323|
|-----------------------------------------------------------------------------|
r_work (final): 0.4063
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7323
moved from start:          0.5179

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.044   8664  Z= 0.220
  Angle     :  0.709  12.989  11766  Z= 0.347
  Chirality :  0.045   0.475   1362
  Planarity :  0.004   0.035   1484
  Dihedral  :  4.999  73.223   1212
  Min Nonbonded Distance : 2.507

Molprobity Statistics.
  All-atom Clashscore : 12.98
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.81 %
    Favored  : 95.19 %
  Rotamer:
    Outliers :  4.39 %
    Allowed  : 25.75 %
    Favored  : 69.86 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.45 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.61 (0.26), residues: 1103
  helix:  1.27 (0.29), residues: 348
  sheet: -1.06 (0.32), residues: 252
  loop : -1.21 (0.28), residues: 503

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.022   0.002   TRP B  82 
 HIS   0.004   0.001   HIS B 183 
 PHE   0.015   0.001   PHE R 241 
 TYR   0.023   0.002   TYR R  75 
 ARG   0.007   0.000   ARG A  21 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3136.69 seconds
wall clock time: 55 minutes 11.72 seconds (3311.72 seconds total)