Starting phenix.real_space_refine
on Sat Aug 23 14:20:52 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8at6_15635/08_2025/8at6_15635.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8at6_15635/08_2025/8at6_15635.map

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

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

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8at6_15635/08_2025/8at6_15635.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8at6_15635/08_2025/8at6_15635.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8at6_15635/08_2025/8at6_15635.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8at6_15635/08_2025/8at6_15635.cif"
  }
  resolution = 3.7
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.002
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      49      5.16       5
     C    8040      2.51       5
     N    2112      2.21       5
     O    2382      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 34 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 12583
  Number of models: 1
  Model: ""
    Number of chains: 6
    Chain: "A"
      Number of atoms: 2284
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 288, 2284
          Classifications: {'peptide': 288}
          Link IDs: {'PCIS': 1, 'PTRANS': 17, 'TRANS': 269}
          Chain breaks: 1
    Chain: "B"
      Number of atoms: 1842
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 227, 1842
          Classifications: {'peptide': 227}
          Link IDs: {'PTRANS': 9, 'TRANS': 217}
    Chain: "C"
      Number of atoms: 2154
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 273, 2154
          Classifications: {'peptide': 273}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 11, 'TRANS': 261}
    Chain: "D"
      Number of atoms: 2313
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 293, 2313
          Classifications: {'peptide': 293}
          Link IDs: {'PCIS': 1, 'PTRANS': 18, 'TRANS': 273}
          Chain breaks: 1
    Chain: "E"
      Number of atoms: 1848
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 228, 1848
          Classifications: {'peptide': 228}
          Link IDs: {'PTRANS': 9, 'TRANS': 218}
    Chain: "F"
      Number of atoms: 2142
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 271, 2142
          Classifications: {'peptide': 271}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 11, 'TRANS': 259}
  Time building chain proxies: 3.24, per 1000 atoms: 0.26
  Number of scatterers: 12583
  At special positions: 0
  Unit cell: (80.3, 115.5, 144.1, 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      49     16.00
     O    2382      8.00
     N    2112      7.00
     C    8040      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 1.02
  Conformation dependent library (CDL) restraints added in 566.9 milliseconds
  
  Enol-peptide restraints added in 715.3 nanoseconds
  

  3128 Ramachandran restraints generated.
    1564 Oldfield, 0 Emsley, 1564 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  3050

  Finding SS restraints...
    Secondary structure from input PDB file:
      50 helices and 10 sheets defined
      34.4% alpha, 18.3% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.45
  Creating SS restraints...
    Processing helix  chain 'A' and resid 90 through 98
      removed outlier: 3.616A  pdb=" N   GLY A  98 " --> pdb=" O   ASP A  94 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 118 through 136
      removed outlier: 3.714A  pdb=" N   LEU A 122 " --> pdb=" O   PHE A 118 " (cutoff:3.500A)
      removed outlier: 3.607A  pdb=" N   GLY A 130 " --> pdb=" O   PHE A 126 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 157 through 164
      removed outlier: 3.763A  pdb=" N   LEU A 164 " --> pdb=" O   ALA A 161 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 264 through 279
    Processing helix  chain 'A' and resid 298 through 302
    Processing helix  chain 'A' and resid 303 through 321
    Processing helix  chain 'A' and resid 337 through 348
    Processing helix  chain 'A' and resid 358 through 369
    Processing helix  chain 'B' and resid 7 through 17
      removed outlier: 3.771A  pdb=" N   LEU B  11 " --> pdb=" O   ASN B   7 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 35 through 49
    Processing helix  chain 'B' and resid 79 through 90
      removed outlier: 3.531A  pdb=" N   TYR B  90 " --> pdb=" O   GLN B  86 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 113 through 115
      No H-bonds generated for 'chain 'B' and resid 113 through 115'
    Processing helix  chain 'B' and resid 116 through 122
    Processing helix  chain 'B' and resid 156 through 165
    Processing helix  chain 'B' and resid 180 through 190
    Processing helix  chain 'C' and resid 19 through 23
      removed outlier: 4.104A  pdb=" N   PHE C  22 " --> pdb=" O   PRO C  19 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 42 through 55
    Processing helix  chain 'C' and resid 85 through 95
      removed outlier: 3.768A  pdb=" N   PHE C  89 " --> pdb=" O   GLU C  85 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 111 through 117
    Processing helix  chain 'C' and resid 121 through 140
      removed outlier: 3.841A  pdb=" N   ALA C 136 " --> pdb=" O   LYS C 132 " (cutoff:3.500A)
      removed outlier: 3.551A  pdb=" N   ILE C 137 " --> pdb=" O   PHE C 133 " (cutoff:3.500A)
      removed outlier: 3.800A  pdb=" N   ASN C 140 " --> pdb=" O   ALA C 136 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 153 through 158
    Processing helix  chain 'C' and resid 162 through 170
    Processing helix  chain 'C' and resid 170 through 177
      removed outlier: 3.695A  pdb=" N   GLN C 177 " --> pdb=" O   PRO C 173 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 188 through 192
      removed outlier: 4.127A  pdb=" N   ILE C 192 " --> pdb=" O   ILE C 189 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 196 through 201
      removed outlier: 4.214A  pdb=" N   HIS C 200 " --> pdb=" O   ASP C 196 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 201 through 215
      removed outlier: 3.731A  pdb=" N   GLN C 205 " --> pdb=" O   SER C 201 " (cutoff:3.500A)
      removed outlier: 3.663A  pdb=" N   PHE C 207 " --> pdb=" O   ASN C 203 " (cutoff:3.500A)
      removed outlier: 3.643A  pdb=" N   TYR C 208 " --> pdb=" O   LEU C 204 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 90 through 97
    Processing helix  chain 'D' and resid 118 through 140
      removed outlier: 4.000A  pdb=" N   LEU D 122 " --> pdb=" O   PHE D 118 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 157 through 163
      removed outlier: 3.697A  pdb=" N   ALA D 161 " --> pdb=" O   GLN D 158 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 264 through 279
      removed outlier: 3.559A  pdb=" N   ASN D 279 " --> pdb=" O   THR D 275 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 298 through 302
    Processing helix  chain 'D' and resid 303 through 321
    Processing helix  chain 'D' and resid 337 through 348
    Processing helix  chain 'D' and resid 358 through 370
    Processing helix  chain 'E' and resid 7 through 17
    Processing helix  chain 'E' and resid 35 through 49
    Processing helix  chain 'E' and resid 79 through 91
    Processing helix  chain 'E' and resid 113 through 115
      No H-bonds generated for 'chain 'E' and resid 113 through 115'
    Processing helix  chain 'E' and resid 116 through 125
    Processing helix  chain 'E' and resid 156 through 165
    Processing helix  chain 'E' and resid 180 through 190
    Processing helix  chain 'F' and resid 20 through 25
      removed outlier: 3.734A  pdb=" N   GLN F  24 " --> pdb=" O   ALA F  20 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 42 through 56
      removed outlier: 3.606A  pdb=" N   ILE F  46 " --> pdb=" O   PRO F  42 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 86 through 94
    Processing helix  chain 'F' and resid 111 through 117
    Processing helix  chain 'F' and resid 121 through 139
      removed outlier: 3.941A  pdb=" N   ASN F 139 " --> pdb=" O   ALA F 135 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 153 through 158
    Processing helix  chain 'F' and resid 162 through 170
    Processing helix  chain 'F' and resid 170 through 177
      removed outlier: 3.522A  pdb=" N   GLN F 177 " --> pdb=" O   PRO F 173 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 202 through 214
      removed outlier: 4.106A  pdb=" N   PHE F 207 " --> pdb=" O   ASN F 203 " (cutoff:3.500A)
      removed outlier: 3.649A  pdb=" N   TYR F 208 " --> pdb=" O   LEU F 204 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 76 through 77
    Processing sheet with id=AA2, first strand: chain 'A' and resid 256 through 259
      removed outlier: 3.892A  pdb=" N   SER A 290 " --> pdb=" O   SER A 330 " (cutoff:3.500A)
      removed outlier: 6.232A  pdb=" N   VAL A 108 " --> pdb=" O   ALA A 329 " (cutoff:3.500A)
      removed outlier: 7.967A  pdb=" N   ILE A 331 " --> pdb=" O   VAL A 108 " (cutoff:3.500A)
      removed outlier: 6.197A  pdb=" N   VAL A 110 " --> pdb=" O   ILE A 331 " (cutoff:3.500A)
      removed outlier: 8.434A  pdb=" N   ILE A 352 " --> pdb=" O   SER A 107 " (cutoff:3.500A)
      removed outlier: 6.618A  pdb=" N   LEU A 109 " --> pdb=" O   ILE A 352 " (cutoff:3.500A)
      removed outlier: 7.901A  pdb=" N   LEU A 354 " --> pdb=" O   LEU A 109 " (cutoff:3.500A)
      removed outlier: 6.458A  pdb=" N   VAL A 351 " --> pdb=" O   LEU A 384 " (cutoff:3.500A)
      removed outlier: 3.671A  pdb=" N   LEU A 384 " --> pdb=" O   VAL A 351 " (cutoff:3.500A)
      removed outlier: 3.902A  pdb=" N   GLY A 379 " --> pdb=" O   PHE A 404 " (cutoff:3.500A)
      removed outlier: 4.149A  pdb=" N   TRP A 402 " --> pdb=" O   VAL A 381 " (cutoff:3.500A)
      removed outlier: 9.265A  pdb=" N   ILE A 383 " --> pdb=" O   SER A 400 " (cutoff:3.500A)
      removed outlier: 7.689A  pdb=" N   SER A 400 " --> pdb=" O   ILE A 383 " (cutoff:3.500A)
      removed outlier: 8.363A  pdb=" N   LYS A 385 " --> pdb=" O   LEU A 398 " (cutoff:3.500A)
      removed outlier: 9.212A  pdb=" N   LEU A 398 " --> pdb=" O   LYS A 385 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'B' and resid 71 through 74
      removed outlier: 6.345A  pdb=" N   VAL B  56 " --> pdb=" O   ILE B 105 " (cutoff:3.500A)
      removed outlier: 6.646A  pdb=" N   VAL B 104 " --> pdb=" O   VAL B 132 " (cutoff:3.500A)
      removed outlier: 8.534A  pdb=" N   THR B 134 " --> pdb=" O   VAL B 104 " (cutoff:3.500A)
      removed outlier: 7.536A  pdb=" N   ILE B 106 " --> pdb=" O   THR B 134 " (cutoff:3.500A)
      removed outlier: 9.296A  pdb=" N   HIS B 136 " --> pdb=" O   ILE B 106 " (cutoff:3.500A)
      removed outlier: 6.920A  pdb=" N   PHE B  24 " --> pdb=" O   THR B 167 " (cutoff:3.500A)
      removed outlier: 8.073A  pdb=" N   VAL B 169 " --> pdb=" O   PHE B  24 " (cutoff:3.500A)
      removed outlier: 6.200A  pdb=" N   LEU B  26 " --> pdb=" O   VAL B 169 " (cutoff:3.500A)
      removed outlier: 7.593A  pdb=" N   ILE B 171 " --> pdb=" O   LEU B  26 " (cutoff:3.500A)
      removed outlier: 6.540A  pdb=" N   LEU B  28 " --> pdb=" O   ILE B 171 " (cutoff:3.500A)
      removed outlier: 8.435A  pdb=" N   VAL B 173 " --> pdb=" O   LEU B  28 " (cutoff:3.500A)
      removed outlier: 3.832A  pdb=" N   ASP B 172 " --> pdb=" O   GLN B 203 " (cutoff:3.500A)
      removed outlier: 5.112A  pdb=" N   ARG B 210 " --> pdb=" O   ARG B 214 " (cutoff:3.500A)
      removed outlier: 5.421A  pdb=" N   ARG B 214 " --> pdb=" O   ARG B 210 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'C' and resid 103 through 107
      removed outlier: 3.955A  pdb=" N   SER C  81 " --> pdb=" O   LEU C 106 " (cutoff:3.500A)
      removed outlier: 6.885A  pdb=" N   HIS C  76 " --> pdb=" O   ILE C 145 " (cutoff:3.500A)
      removed outlier: 8.272A  pdb=" N   ILE C 147 " --> pdb=" O   HIS C  76 " (cutoff:3.500A)
      removed outlier: 6.300A  pdb=" N   VAL C  78 " --> pdb=" O   ILE C 147 " (cutoff:3.500A)
      removed outlier: 7.932A  pdb=" N   GLU C 149 " --> pdb=" O   VAL C  78 " (cutoff:3.500A)
      removed outlier: 7.122A  pdb=" N   ALA C  80 " --> pdb=" O   GLU C 149 " (cutoff:3.500A)
      removed outlier: 5.568A  pdb=" N   VAL C 180 " --> pdb=" O   THR C 144 " (cutoff:3.500A)
      removed outlier: 7.061A  pdb=" N   LEU C  31 " --> pdb=" O   ILE C 217 " (cutoff:3.500A)
      removed outlier: 8.416A  pdb=" N   LEU C 219 " --> pdb=" O   LEU C  31 " (cutoff:3.500A)
      removed outlier: 6.447A  pdb=" N   PHE C  33 " --> pdb=" O   LEU C 219 " (cutoff:3.500A)
      removed outlier: 7.785A  pdb=" N   LEU C 221 " --> pdb=" O   PHE C  33 " (cutoff:3.500A)
      removed outlier: 6.742A  pdb=" N   THR C  35 " --> pdb=" O   LEU C 221 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'C' and resid 263 through 264
    Processing sheet with id=AA6, first strand: chain 'D' and resid 75 through 77
    Processing sheet with id=AA7, first strand: chain 'D' and resid 256 through 259
      removed outlier: 6.498A  pdb=" N   VAL D 326 " --> pdb=" O   ARG D 285 " (cutoff:3.500A)
      removed outlier: 5.601A  pdb=" N   VAL D 287 " --> pdb=" O   VAL D 326 " (cutoff:3.500A)
      removed outlier: 6.680A  pdb=" N   PHE D 328 " --> pdb=" O   VAL D 287 " (cutoff:3.500A)
      removed outlier: 6.313A  pdb=" N   SER D 330 " --> pdb=" O   PRO D 289 " (cutoff:3.500A)
      removed outlier: 4.461A  pdb=" N   SER D 332 " --> pdb=" O   LEU D 291 " (cutoff:3.500A)
      removed outlier: 3.682A  pdb=" N   ILE D 331 " --> pdb=" O   VAL D 110 " (cutoff:3.500A)
      removed outlier: 6.707A  pdb=" N   LEU D 109 " --> pdb=" O   ILE D 352 " (cutoff:3.500A)
      removed outlier: 7.935A  pdb=" N   LEU D 354 " --> pdb=" O   LEU D 109 " (cutoff:3.500A)
      removed outlier: 7.312A  pdb=" N   GLU D 111 " --> pdb=" O   LEU D 354 " (cutoff:3.500A)
      removed outlier: 6.417A  pdb=" N   VAL D 351 " --> pdb=" O   LEU D 384 " (cutoff:3.500A)
      removed outlier: 3.558A  pdb=" N   LEU D 384 " --> pdb=" O   VAL D 351 " (cutoff:3.500A)
      removed outlier: 3.867A  pdb=" N   GLY D 379 " --> pdb=" O   PHE D 404 " (cutoff:3.500A)
      removed outlier: 4.197A  pdb=" N   TRP D 402 " --> pdb=" O   VAL D 381 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'D' and resid 165 through 167
      removed outlier: 3.550A  pdb=" N   GLY D 166 " --> pdb=" O   ASP D 242 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'E' and resid 71 through 74
      removed outlier: 3.551A  pdb=" N   GLN E  71 " --> pdb=" O   ILE E  55 " (cutoff:3.500A)
      removed outlier: 6.249A  pdb=" N   VAL E  56 " --> pdb=" O   ILE E 105 " (cutoff:3.500A)
      removed outlier: 6.324A  pdb=" N   HIS E 102 " --> pdb=" O   THR E 130 " (cutoff:3.500A)
      removed outlier: 7.719A  pdb=" N   VAL E 132 " --> pdb=" O   HIS E 102 " (cutoff:3.500A)
      removed outlier: 6.036A  pdb=" N   VAL E 104 " --> pdb=" O   VAL E 132 " (cutoff:3.500A)
      removed outlier: 8.054A  pdb=" N   THR E 134 " --> pdb=" O   VAL E 104 " (cutoff:3.500A)
      removed outlier: 7.199A  pdb=" N   ILE E 106 " --> pdb=" O   THR E 134 " (cutoff:3.500A)
      removed outlier: 8.811A  pdb=" N   HIS E 136 " --> pdb=" O   ILE E 106 " (cutoff:3.500A)
      removed outlier: 6.395A  pdb=" N   ILE E  25 " --> pdb=" O   ALA E 133 " (cutoff:3.500A)
      removed outlier: 7.469A  pdb=" N   TYR E 135 " --> pdb=" O   ILE E  25 " (cutoff:3.500A)
      removed outlier: 6.055A  pdb=" N   CYS E  27 " --> pdb=" O   TYR E 135 " (cutoff:3.500A)
      removed outlier: 3.519A  pdb=" N   THR E 167 " --> pdb=" O   PHE E  24 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'F' and resid 103 through 107
      removed outlier: 4.028A  pdb=" N   SER F  81 " --> pdb=" O   LEU F 106 " (cutoff:3.500A)
      removed outlier: 7.510A  pdb=" N   HIS F  76 " --> pdb=" O   ILE F 145 " (cutoff:3.500A)
      removed outlier: 8.700A  pdb=" N   ILE F 147 " --> pdb=" O   HIS F  76 " (cutoff:3.500A)
      removed outlier: 6.551A  pdb=" N   VAL F  78 " --> pdb=" O   ILE F 147 " (cutoff:3.500A)
      removed outlier: 8.345A  pdb=" N   GLU F 149 " --> pdb=" O   VAL F  78 " (cutoff:3.500A)
      removed outlier: 7.541A  pdb=" N   ALA F  80 " --> pdb=" O   GLU F 149 " (cutoff:3.500A)
      removed outlier: 7.305A  pdb=" N   THR F 144 " --> pdb=" O   VAL F 180 " (cutoff:3.500A)
      removed outlier: 8.500A  pdb=" N   ILE F 182 " --> pdb=" O   THR F 144 " (cutoff:3.500A)
      removed outlier: 6.669A  pdb=" N   VAL F 146 " --> pdb=" O   ILE F 182 " (cutoff:3.500A)
      removed outlier: 7.776A  pdb=" N   VAL F 184 " --> pdb=" O   VAL F 146 " (cutoff:3.500A)
      removed outlier: 6.909A  pdb=" N   ILE F 148 " --> pdb=" O   VAL F 184 " (cutoff:3.500A)
      removed outlier: 8.883A  pdb=" N   ASN F 186 " --> pdb=" O   ILE F 148 " (cutoff:3.500A)
      removed outlier: 6.514A  pdb=" N   ASN F  30 " --> pdb=" O   LEU F 181 " (cutoff:3.500A)
      removed outlier: 7.992A  pdb=" N   ILE F 183 " --> pdb=" O   ASN F  30 " (cutoff:3.500A)
      removed outlier: 6.573A  pdb=" N   PHE F  32 " --> pdb=" O   ILE F 183 " (cutoff:3.500A)
      removed outlier: 7.817A  pdb=" N   SER F 185 " --> pdb=" O   PHE F  32 " (cutoff:3.500A)
      removed outlier: 6.578A  pdb=" N   ILE F  34 " --> pdb=" O   SER F 185 " (cutoff:3.500A)
      removed outlier: 4.460A  pdb=" N   ILE F 217 " --> pdb=" O   LEU F  31 " (cutoff:3.500A)
      removed outlier: 3.526A  pdb=" N   PHE F  33 " --> pdb=" O   ILE F 217 " (cutoff:3.500A)
      removed outlier: 3.784A  pdb=" N   SER F 267 " --> pdb=" O   GLU F 264 " (cutoff:3.500A)

    475 hydrogen bonds defined for protein.
    1347 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 1.83

  Time building geometry restraints manager: 1.39 seconds

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

  Histogram of bond lengths:
        1.22 -     1.34: 4074
        1.34 -     1.46: 2820
        1.46 -     1.58: 5872
        1.58 -     1.70: 0
        1.70 -     1.82: 84
  Bond restraints: 12850
  Sorted by residual:
  bond pdb=" CA  SER F  65 "
       pdb=" C   SER F  65 "
    ideal  model  delta    sigma   weight residual
    1.523  1.501  0.022 1.41e-02 5.03e+03 2.44e+00
  bond pdb=" N   SER D 114 "
       pdb=" CA  SER D 114 "
    ideal  model  delta    sigma   weight residual
    1.457  1.475 -0.017 1.29e-02 6.01e+03 1.80e+00
  bond pdb=" CA  THR D 115 "
       pdb=" C   THR D 115 "
    ideal  model  delta    sigma   weight residual
    1.523  1.540 -0.017 1.34e-02 5.57e+03 1.66e+00
  bond pdb=" CA  ASN E 110 "
       pdb=" C   ASN E 110 "
    ideal  model  delta    sigma   weight residual
    1.523  1.505  0.018 1.41e-02 5.03e+03 1.60e+00
  bond pdb=" CB  GLN A 274 "
       pdb=" CG  GLN A 274 "
    ideal  model  delta    sigma   weight residual
    1.520  1.556 -0.036 3.00e-02 1.11e+03 1.43e+00
  ... (remaining 12845 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.45: 17247
        2.45 -     4.90: 169
        4.90 -     7.36: 20
        7.36 -     9.81: 4
        9.81 -    12.26: 2
  Bond angle restraints: 17442
  Sorted by residual:
  angle pdb=" CA  ARG F  74 "
        pdb=" CB  ARG F  74 "
        pdb=" CG  ARG F  74 "
      ideal   model   delta    sigma   weight residual
     114.10  122.86   -8.76 2.00e+00 2.50e-01 1.92e+01
  angle pdb=" N   SER D 114 "
        pdb=" CA  SER D 114 "
        pdb=" C   SER D 114 "
      ideal   model   delta    sigma   weight residual
     110.80  120.13   -9.33 2.13e+00 2.20e-01 1.92e+01
  angle pdb=" CB  MET C  45 "
        pdb=" CG  MET C  45 "
        pdb=" SD  MET C  45 "
      ideal   model   delta    sigma   weight residual
     112.70  124.96  -12.26 3.00e+00 1.11e-01 1.67e+01
  angle pdb=" N   THR D 115 "
        pdb=" CA  THR D 115 "
        pdb=" C   THR D 115 "
      ideal   model   delta    sigma   weight residual
     110.80  117.98   -7.18 2.13e+00 2.20e-01 1.14e+01
  angle pdb=" CA  LEU E  18 "
        pdb=" CB  LEU E  18 "
        pdb=" CG  LEU E  18 "
      ideal   model   delta    sigma   weight residual
     116.30  128.05  -11.75 3.50e+00 8.16e-02 1.13e+01
  ... (remaining 17437 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.81: 6800
       17.81 -    35.63: 802
       35.63 -    53.44: 158
       53.44 -    71.25: 37
       71.25 -    89.07: 17
  Dihedral angle restraints: 7814
    sinusoidal: 3142
      harmonic: 4672
  Sorted by residual:
  dihedral pdb=" CA  ASP E 149 "
           pdb=" C   ASP E 149 "
           pdb=" N   TRP E 150 "
           pdb=" CA  TRP E 150 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -156.00  -24.00     0      5.00e+00 4.00e-02 2.30e+01
  dihedral pdb=" CA  PRO A 387 "
           pdb=" C   PRO A 387 "
           pdb=" N   VAL A 388 "
           pdb=" CA  VAL A 388 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -158.85  -21.15     0      5.00e+00 4.00e-02 1.79e+01
  dihedral pdb=" CA  HIS F  84 "
           pdb=" C   HIS F  84 "
           pdb=" N   GLU F  85 "
           pdb=" CA  GLU F  85 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -160.75  -19.25     0      5.00e+00 4.00e-02 1.48e+01
  ... (remaining 7811 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.038: 1430
       0.038 -    0.077: 426
       0.077 -    0.115: 152
       0.115 -    0.154: 25
       0.154 -    0.192: 5
  Chirality restraints: 2038
  Sorted by residual:
  chirality pdb=" CG  LEU F 157 "
            pdb=" CB  LEU F 157 "
            pdb=" CD1 LEU F 157 "
            pdb=" CD2 LEU F 157 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.59   -2.40   -0.19 2.00e-01 2.50e+01 9.23e-01
  chirality pdb=" CA  ILE A 352 "
            pdb=" N   ILE A 352 "
            pdb=" C   ILE A 352 "
            pdb=" CB  ILE A 352 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.61   -0.18 2.00e-01 2.50e+01 7.80e-01
  chirality pdb=" CG  LEU E 161 "
            pdb=" CB  LEU E 161 "
            pdb=" CD1 LEU E 161 "
            pdb=" CD2 LEU E 161 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.59   -2.42   -0.17 2.00e-01 2.50e+01 7.55e-01
  ... (remaining 2035 not shown)

  Planarity restraints: 2221
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   LEU A 386 "   -0.036 5.00e-02 4.00e+02   5.50e-02 4.83e+00
        pdb=" N   PRO A 387 "    0.095 5.00e-02 4.00e+02
        pdb=" CA  PRO A 387 "   -0.028 5.00e-02 4.00e+02
        pdb=" CD  PRO A 387 "   -0.030 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ILE B 147 "    0.033 5.00e-02 4.00e+02   5.14e-02 4.23e+00
        pdb=" N   PRO B 148 "   -0.089 5.00e-02 4.00e+02
        pdb=" CA  PRO B 148 "    0.027 5.00e-02 4.00e+02
        pdb=" CD  PRO B 148 "    0.028 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   LEU D 386 "   -0.034 5.00e-02 4.00e+02   5.10e-02 4.16e+00
        pdb=" N   PRO D 387 "    0.088 5.00e-02 4.00e+02
        pdb=" CA  PRO D 387 "   -0.026 5.00e-02 4.00e+02
        pdb=" CD  PRO D 387 "   -0.028 5.00e-02 4.00e+02
  ... (remaining 2218 not shown)

  Histogram of nonbonded interaction distances:
        2.22 -     2.76: 2039
        2.76 -     3.29: 12461
        3.29 -     3.83: 20324
        3.83 -     4.36: 23167
        4.36 -     4.90: 40328
  Nonbonded interactions: 98319
  Sorted by model distance:
  nonbonded pdb=" OE2 GLU A 112 "
            pdb=" OG1 THR A 116 "
     model   vdw
     2.222 3.040
  nonbonded pdb=" N   GLU F  85 "
            pdb=" OE1 GLU F  85 "
     model   vdw
     2.223 3.120
  nonbonded pdb=" NH2 ARG C  74 "
            pdb=" O   THR C 142 "
     model   vdw
     2.234 3.120
  nonbonded pdb=" O   GLY A 374 "
            pdb=" NZ  LYS A 405 "
     model   vdw
     2.241 3.120
  nonbonded pdb=" O   PRO C 223 "
            pdb=" NH2 ARG E 192 "
     model   vdw
     2.244 3.120
  ... (remaining 98314 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.00
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = (chain 'D' and (resid 66 through 169 or resid 233 through 416))
}
ncs_group {
  reference = chain 'B'
  selection = (chain 'E' and resid 6 through 232)
}
ncs_group {
  reference = (chain 'C' and resid 3 through 273)
  selection = chain 'F'
}

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=0.00 max=1.00 mean=0.99
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:             2.980
  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:          0.190
  Check model and map are aligned:         0.040
  Set scattering table:                    0.030
  Process input model:                     12.780
  Find NCS groups from input model:        0.240
  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:1.130
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   17.440
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8474
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      :  0.003   0.037  12850  Z= 0.163
  Angle     :  0.641  12.260  17442  Z= 0.356
  Chirality :  0.043   0.192   2038
  Planarity :  0.004   0.055   2221
  Dihedral  : 16.248  89.068   4764
  Min Nonbonded Distance : 2.222

Molprobity Statistics.
  All-atom Clashscore : 9.66
  Ramachandran Plot:
    Outliers :  0.32 %
    Allowed  :  5.88 %
    Favored  : 93.80 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  : 20.74 %
    Favored  : 79.26 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.60 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.49 (0.23), residues: 1564
  helix:  1.45 (0.25), residues: 483
  sheet:  1.25 (0.30), residues: 350
  loop : -0.95 (0.24), residues: 731

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG F  74 
 TYR   0.023   0.001   TYR F 103 
 PHE   0.012   0.001   PHE C  32 
 TRP   0.013   0.001   TRP C  44 
 HIS   0.003   0.001   HIS A 312 

Details of bonding type rmsd
  covalent geometry    : bond        0.00340 (12850)
  covalent geometry    : angle       0.64138 (17442)
  hydrogen bonds       : bond        0.17692 (  475)
  hydrogen bonds       : angle       6.61128 ( 1347)

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

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

  3128 Ramachandran restraints generated.
    1564 Oldfield, 0 Emsley, 1564 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3128 Ramachandran restraints generated.
    1564 Oldfield, 0 Emsley, 1564 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  99 residues out of total 1461 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 99
  time to evaluate  : 0.540 
Fit side-chains
   revert: symmetry clash
REVERT: B   86 GLN cc_start: 0.8312 (tm-30) cc_final: 0.7849 (tm-30)
REVERT: C    1 MET cc_start: 0.6978 (tpp) cc_final: 0.6716 (tpt)
REVERT: E  214 ARG cc_start: 0.8152 (tpp80) cc_final: 0.7926 (ttm-80)
  outliers start: 0
  outliers final: 0
  residues processed: 99
  average time/residue: 0.1246
  time to fit residues: 18.1155
Evaluate side-chains
  96 residues out of total 1461 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 96
  time to evaluate  : 0.511 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 155
   random chunks:
   chunk 98 optimal weight:    2.9990
   chunk 107 optimal weight:    0.0370
   chunk 10 optimal weight:    7.9990
   chunk 66 optimal weight:    3.9990
   chunk 130 optimal weight:    0.0010
   chunk 124 optimal weight:    0.0870
   chunk 103 optimal weight:    0.7980
   chunk 77 optimal weight:    9.9990
   chunk 122 optimal weight:    0.4980
   chunk 91 optimal weight:    3.9990
   chunk 149 optimal weight:    0.5980
   overall best weight:    0.2442

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

Flipped N/Q/H residues before XYZ refinement:
A 146 ASN
A 263 GLN
B 223 ASN
F 218 ASN
F 220 ASN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3346 r_free = 0.3346 target = 0.070025 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3019 r_free = 0.3019 target = 0.056241 restraints weight = 46779.239|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3062 r_free = 0.3062 target = 0.057962 restraints weight = 26240.369|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 41)----------------|
| r_work = 0.3090 r_free = 0.3090 target = 0.059134 restraints weight = 18219.320|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 34)----------------|
| r_work = 0.3110 r_free = 0.3110 target = 0.059926 restraints weight = 14359.605|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3119 r_free = 0.3119 target = 0.060336 restraints weight = 12264.505|
|-----------------------------------------------------------------------------|
r_work (final): 0.3116
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8400
moved from start:          0.0915

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.039  12850  Z= 0.098
  Angle     :  0.529  10.981  17442  Z= 0.278
  Chirality :  0.043   0.171   2038
  Planarity :  0.004   0.056   2221
  Dihedral  :  4.309  55.412   1678
  Min Nonbonded Distance : 2.514

Molprobity Statistics.
  All-atom Clashscore : 5.27
  Ramachandran Plot:
    Outliers :  0.13 %
    Allowed  :  4.73 %
    Favored  : 95.14 %
  Rotamer:
    Outliers :  1.16 %
    Allowed  : 18.41 %
    Favored  : 80.42 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.60 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.82 (0.23), residues: 1564
  helix:  1.74 (0.25), residues: 486
  sheet:  1.54 (0.30), residues: 350
  loop : -0.83 (0.25), residues: 728

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG C  74 
 TYR   0.019   0.001   TYR C  88 
 PHE   0.009   0.001   PHE C 228 
 TRP   0.002   0.000   TRP E 150 
 HIS   0.004   0.001   HIS C  53 

Details of bonding type rmsd
  covalent geometry    : bond        0.00207 (12850)
  covalent geometry    : angle       0.52902 (17442)
  hydrogen bonds       : bond        0.03929 (  475)
  hydrogen bonds       : angle       5.00013 ( 1347)

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

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

  3128 Ramachandran restraints generated.
    1564 Oldfield, 0 Emsley, 1564 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3128 Ramachandran restraints generated.
    1564 Oldfield, 0 Emsley, 1564 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  123 residues out of total 1461 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 106
  time to evaluate  : 0.661 
Fit side-chains
   revert: symmetry clash
REVERT: A  334 ASP cc_start: 0.8336 (OUTLIER) cc_final: 0.8123 (m-30)
REVERT: B  122 SER cc_start: 0.9104 (p) cc_final: 0.8856 (p)
REVERT: C    1 MET cc_start: 0.6787 (tpp) cc_final: 0.6572 (tpt)
REVERT: D  276 ILE cc_start: 0.9080 (mm) cc_final: 0.8880 (mm)
REVERT: E   78 MET cc_start: 0.8025 (ppp) cc_final: 0.7682 (ppp)
  outliers start: 17
  outliers final: 8
  residues processed: 118
  average time/residue: 0.1125
  time to fit residues: 19.8157
Evaluate side-chains
  102 residues out of total 1461 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 93
  time to evaluate  : 0.591 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  159 MET
Chi-restraints excluded: chain A residue  334 ASP
Chi-restraints excluded: chain B residue  229 TYR
Chi-restraints excluded: chain C residue   10 VAL
Chi-restraints excluded: chain D residue   86 THR
Chi-restraints excluded: chain D residue  159 MET
Chi-restraints excluded: chain D residue  247 LEU
Chi-restraints excluded: chain E residue  161 LEU
Chi-restraints excluded: chain F residue  211 SER
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 155
   random chunks:
   chunk 130 optimal weight:    4.9990
   chunk 97 optimal weight:    0.9990
   chunk 95 optimal weight:    0.9980
   chunk 24 optimal weight:    2.9990
   chunk 25 optimal weight:    0.9990
   chunk 37 optimal weight:    0.0570
   chunk 74 optimal weight:    5.9990
   chunk 56 optimal weight:    0.3980
   chunk 113 optimal weight:    0.0170
   chunk 151 optimal weight:    6.9990
   chunk 49 optimal weight:    7.9990
   overall best weight:    0.4938

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

Flipped N/Q/H residues before XYZ refinement:
F  91 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3350 r_free = 0.3350 target = 0.070131 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3023 r_free = 0.3023 target = 0.056341 restraints weight = 47397.583|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3066 r_free = 0.3066 target = 0.058069 restraints weight = 26455.003|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3095 r_free = 0.3095 target = 0.059250 restraints weight = 18306.184|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 33)----------------|
| r_work = 0.3114 r_free = 0.3114 target = 0.060040 restraints weight = 14418.170|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3123 r_free = 0.3123 target = 0.060456 restraints weight = 12292.651|
|-----------------------------------------------------------------------------|
r_work (final): 0.3119
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8399
moved from start:          0.1134

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.038  12850  Z= 0.095
  Angle     :  0.505  12.007  17442  Z= 0.263
  Chirality :  0.042   0.219   2038
  Planarity :  0.004   0.055   2221
  Dihedral  :  4.230  57.163   1678
  Min Nonbonded Distance : 2.548

Molprobity Statistics.
  All-atom Clashscore : 5.59
  Ramachandran Plot:
    Outliers :  0.13 %
    Allowed  :  4.80 %
    Favored  : 95.08 %
  Rotamer:
    Outliers :  1.71 %
    Allowed  : 18.07 %
    Favored  : 80.22 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.60 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.89 (0.23), residues: 1564
  helix:  1.76 (0.25), residues: 486
  sheet:  1.66 (0.30), residues: 354
  loop : -0.82 (0.24), residues: 724

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG F  74 
 TYR   0.017   0.001   TYR C  88 
 PHE   0.016   0.001   PHE E  72 
 TRP   0.002   0.000   TRP C  44 
 HIS   0.003   0.001   HIS A 312 

Details of bonding type rmsd
  covalent geometry    : bond        0.00210 (12850)
  covalent geometry    : angle       0.50488 (17442)
  hydrogen bonds       : bond        0.03482 (  475)
  hydrogen bonds       : angle       4.77053 ( 1347)

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

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

  3128 Ramachandran restraints generated.
    1564 Oldfield, 0 Emsley, 1564 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3128 Ramachandran restraints generated.
    1564 Oldfield, 0 Emsley, 1564 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  120 residues out of total 1461 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 95
  time to evaluate  : 0.551 
Fit side-chains
   revert: symmetry clash
REVERT: A  334 ASP cc_start: 0.8157 (OUTLIER) cc_final: 0.7937 (m-30)
REVERT: B  122 SER cc_start: 0.9118 (p) cc_final: 0.8873 (p)
REVERT: D  276 ILE cc_start: 0.9111 (mm) cc_final: 0.8908 (mm)
REVERT: D  389 PHE cc_start: 0.8264 (m-80) cc_final: 0.8058 (m-80)
REVERT: E   78 MET cc_start: 0.8145 (ppp) cc_final: 0.7839 (ppp)
  outliers start: 25
  outliers final: 16
  residues processed: 115
  average time/residue: 0.1145
  time to fit residues: 19.6133
Evaluate side-chains
  110 residues out of total 1461 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 93
  time to evaluate  : 0.527 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  159 MET
Chi-restraints excluded: chain A residue  334 ASP
Chi-restraints excluded: chain B residue   34 THR
Chi-restraints excluded: chain B residue   62 THR
Chi-restraints excluded: chain B residue  212 SER
Chi-restraints excluded: chain C residue   10 VAL
Chi-restraints excluded: chain C residue  219 LEU
Chi-restraints excluded: chain C residue  221 LEU
Chi-restraints excluded: chain D residue   75 VAL
Chi-restraints excluded: chain D residue   86 THR
Chi-restraints excluded: chain D residue  247 LEU
Chi-restraints excluded: chain E residue  161 LEU
Chi-restraints excluded: chain E residue  176 THR
Chi-restraints excluded: chain E residue  223 ASN
Chi-restraints excluded: chain F residue    4 VAL
Chi-restraints excluded: chain F residue  211 SER
Chi-restraints excluded: chain F residue  255 VAL
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 155
   random chunks:
   chunk 74 optimal weight:    0.6980
   chunk 63 optimal weight:    0.9990
   chunk 12 optimal weight:    0.6980
   chunk 19 optimal weight:    3.9990
   chunk 139 optimal weight:    0.0970
   chunk 94 optimal weight:    1.9990
   chunk 95 optimal weight:    2.9990
   chunk 34 optimal weight:    0.0770
   chunk 37 optimal weight:    7.9990
   chunk 130 optimal weight:    4.9990
   chunk 82 optimal weight:    4.9990
   overall best weight:    0.5138

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

Flipped N/Q/H residues before XYZ refinement:
C  76 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3353 r_free = 0.3353 target = 0.070211 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3024 r_free = 0.3024 target = 0.056400 restraints weight = 47190.579|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3067 r_free = 0.3067 target = 0.058136 restraints weight = 26294.215|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3096 r_free = 0.3096 target = 0.059322 restraints weight = 18113.095|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 32)----------------|
| r_work = 0.3115 r_free = 0.3115 target = 0.060119 restraints weight = 14216.753|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3127 r_free = 0.3127 target = 0.060622 restraints weight = 12123.956|
|-----------------------------------------------------------------------------|
r_work (final): 0.3125
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8392
moved from start:          0.1314

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.033  12850  Z= 0.092
  Angle     :  0.503  11.658  17442  Z= 0.260
  Chirality :  0.041   0.158   2038
  Planarity :  0.004   0.056   2221
  Dihedral  :  4.175  53.877   1678
  Min Nonbonded Distance : 2.580

Molprobity Statistics.
  All-atom Clashscore : 5.31
  Ramachandran Plot:
    Outliers :  0.13 %
    Allowed  :  5.18 %
    Favored  : 94.69 %
  Rotamer:
    Outliers :  2.19 %
    Allowed  : 18.34 %
    Favored  : 79.47 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.60 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.89 (0.23), residues: 1564
  helix:  1.71 (0.25), residues: 492
  sheet:  1.75 (0.30), residues: 354
  loop : -0.84 (0.25), residues: 718

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG F  74 
 TYR   0.017   0.001   TYR C  88 
 PHE   0.014   0.001   PHE E  72 
 TRP   0.020   0.001   TRP C  44 
 HIS   0.003   0.001   HIS F  36 

Details of bonding type rmsd
  covalent geometry    : bond        0.00206 (12850)
  covalent geometry    : angle       0.50337 (17442)
  hydrogen bonds       : bond        0.03261 (  475)
  hydrogen bonds       : angle       4.62794 ( 1347)

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

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

  3128 Ramachandran restraints generated.
    1564 Oldfield, 0 Emsley, 1564 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3128 Ramachandran restraints generated.
    1564 Oldfield, 0 Emsley, 1564 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  127 residues out of total 1461 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 95
  time to evaluate  : 0.551 
Fit side-chains
   revert: symmetry clash
REVERT: A  334 ASP cc_start: 0.8120 (OUTLIER) cc_final: 0.7903 (m-30)
REVERT: B  122 SER cc_start: 0.9119 (p) cc_final: 0.8873 (p)
REVERT: D  389 PHE cc_start: 0.8238 (m-80) cc_final: 0.8006 (m-80)
REVERT: E   78 MET cc_start: 0.8206 (ppp) cc_final: 0.7790 (ppp)
  outliers start: 32
  outliers final: 19
  residues processed: 119
  average time/residue: 0.1192
  time to fit residues: 21.0859
Evaluate side-chains
  112 residues out of total 1461 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 92
  time to evaluate  : 0.621 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  159 MET
Chi-restraints excluded: chain A residue  334 ASP
Chi-restraints excluded: chain B residue   34 THR
Chi-restraints excluded: chain B residue   62 THR
Chi-restraints excluded: chain B residue   69 CYS
Chi-restraints excluded: chain B residue  212 SER
Chi-restraints excluded: chain C residue   10 VAL
Chi-restraints excluded: chain C residue  157 LEU
Chi-restraints excluded: chain C residue  219 LEU
Chi-restraints excluded: chain C residue  221 LEU
Chi-restraints excluded: chain D residue   75 VAL
Chi-restraints excluded: chain D residue   86 THR
Chi-restraints excluded: chain D residue  247 LEU
Chi-restraints excluded: chain E residue  161 LEU
Chi-restraints excluded: chain E residue  176 THR
Chi-restraints excluded: chain E residue  223 ASN
Chi-restraints excluded: chain F residue    4 VAL
Chi-restraints excluded: chain F residue  199 VAL
Chi-restraints excluded: chain F residue  211 SER
Chi-restraints excluded: chain F residue  255 VAL
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 155
   random chunks:
   chunk 127 optimal weight:    0.0010
   chunk 148 optimal weight:    0.9990
   chunk 0 optimal weight:   10.0000
   chunk 56 optimal weight:    0.9980
   chunk 120 optimal weight:    0.0470
   chunk 123 optimal weight:    0.4980
   chunk 121 optimal weight:    0.5980
   chunk 15 optimal weight:    0.7980
   chunk 35 optimal weight:    1.9990
   chunk 106 optimal weight:    1.9990
   chunk 16 optimal weight:    2.9990
   overall best weight:    0.3884

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

Flipped N/Q/H residues before XYZ refinement:
A 113 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3365 r_free = 0.3365 target = 0.070702 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3039 r_free = 0.3039 target = 0.056942 restraints weight = 47094.284|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3082 r_free = 0.3082 target = 0.058686 restraints weight = 26331.049|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3111 r_free = 0.3111 target = 0.059881 restraints weight = 18181.590|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 37)----------------|
| r_work = 0.3130 r_free = 0.3130 target = 0.060690 restraints weight = 14284.837|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3142 r_free = 0.3142 target = 0.061202 restraints weight = 12153.472|
|-----------------------------------------------------------------------------|
r_work (final): 0.3139
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8378
moved from start:          0.1515

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.033  12850  Z= 0.087
  Angle     :  0.497  11.078  17442  Z= 0.257
  Chirality :  0.041   0.159   2038
  Planarity :  0.004   0.056   2221
  Dihedral  :  4.112  55.233   1678
  Min Nonbonded Distance : 2.582

Molprobity Statistics.
  All-atom Clashscore : 5.19
  Ramachandran Plot:
    Outliers :  0.06 %
    Allowed  :  5.05 %
    Favored  : 94.88 %
  Rotamer:
    Outliers :  1.78 %
    Allowed  : 19.23 %
    Favored  : 78.99 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.60 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.98 (0.23), residues: 1564
  helix:  1.85 (0.25), residues: 489
  sheet:  1.80 (0.30), residues: 354
  loop : -0.83 (0.24), residues: 721

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG F  74 
 TYR   0.020   0.001   TYR F 103 
 PHE   0.013   0.001   PHE E  72 
 TRP   0.009   0.001   TRP C  44 
 HIS   0.003   0.000   HIS A 312 

Details of bonding type rmsd
  covalent geometry    : bond        0.00192 (12850)
  covalent geometry    : angle       0.49713 (17442)
  hydrogen bonds       : bond        0.03068 (  475)
  hydrogen bonds       : angle       4.51237 ( 1347)

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

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

  3128 Ramachandran restraints generated.
    1564 Oldfield, 0 Emsley, 1564 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3128 Ramachandran restraints generated.
    1564 Oldfield, 0 Emsley, 1564 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  130 residues out of total 1461 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 104
  time to evaluate  : 0.538 
Fit side-chains
   revert: symmetry clash
REVERT: B   62 THR cc_start: 0.8026 (OUTLIER) cc_final: 0.7713 (t)
REVERT: B  122 SER cc_start: 0.9164 (p) cc_final: 0.8914 (p)
REVERT: C  216 MET cc_start: 0.8452 (OUTLIER) cc_final: 0.7556 (ppp)
REVERT: D  349 ASP cc_start: 0.8393 (m-30) cc_final: 0.8187 (m-30)
REVERT: E   78 MET cc_start: 0.8207 (ppp) cc_final: 0.7699 (ppp)
REVERT: E  214 ARG cc_start: 0.8363 (ttm-80) cc_final: 0.8148 (mtp85)
  outliers start: 26
  outliers final: 19
  residues processed: 122
  average time/residue: 0.1097
  time to fit residues: 20.1510
Evaluate side-chains
  114 residues out of total 1461 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 93
  time to evaluate  : 0.435 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  159 MET
Chi-restraints excluded: chain B residue   62 THR
Chi-restraints excluded: chain B residue   69 CYS
Chi-restraints excluded: chain B residue  126 SER
Chi-restraints excluded: chain C residue   10 VAL
Chi-restraints excluded: chain C residue   29 HIS
Chi-restraints excluded: chain C residue  157 LEU
Chi-restraints excluded: chain C residue  216 MET
Chi-restraints excluded: chain C residue  219 LEU
Chi-restraints excluded: chain C residue  221 LEU
Chi-restraints excluded: chain D residue   75 VAL
Chi-restraints excluded: chain D residue   86 THR
Chi-restraints excluded: chain D residue  247 LEU
Chi-restraints excluded: chain E residue  146 VAL
Chi-restraints excluded: chain E residue  161 LEU
Chi-restraints excluded: chain E residue  176 THR
Chi-restraints excluded: chain E residue  223 ASN
Chi-restraints excluded: chain F residue    4 VAL
Chi-restraints excluded: chain F residue  199 VAL
Chi-restraints excluded: chain F residue  211 SER
Chi-restraints excluded: chain F residue  255 VAL
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 155
   random chunks:
   chunk 132 optimal weight:    1.9990
   chunk 142 optimal weight:    0.8980
   chunk 140 optimal weight:    2.9990
   chunk 113 optimal weight:    0.4980
   chunk 61 optimal weight:    3.9990
   chunk 54 optimal weight:    1.9990
   chunk 78 optimal weight:    0.0170
   chunk 76 optimal weight:    3.9990
   chunk 154 optimal weight:    4.9990
   chunk 39 optimal weight:    0.5980
   chunk 100 optimal weight:    0.8980
   overall best weight:    0.5818

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3357 r_free = 0.3357 target = 0.070396 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3028 r_free = 0.3028 target = 0.056474 restraints weight = 47173.869|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3072 r_free = 0.3072 target = 0.058225 restraints weight = 26443.454|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3101 r_free = 0.3101 target = 0.059428 restraints weight = 18332.734|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 36)----------------|
| r_work = 0.3118 r_free = 0.3118 target = 0.060182 restraints weight = 14447.741|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 21)----------------|
| r_work = 0.3133 r_free = 0.3133 target = 0.060748 restraints weight = 12397.532|
|-----------------------------------------------------------------------------|
r_work (final): 0.3129
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8389
moved from start:          0.1530

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.033  12850  Z= 0.097
  Angle     :  0.508  10.343  17442  Z= 0.260
  Chirality :  0.041   0.157   2038
  Planarity :  0.004   0.058   2221
  Dihedral  :  4.131  56.129   1678
  Min Nonbonded Distance : 2.574

Molprobity Statistics.
  All-atom Clashscore : 5.19
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.50 %
    Favored  : 94.50 %
  Rotamer:
    Outliers :  1.92 %
    Allowed  : 19.23 %
    Favored  : 78.85 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.60 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.97 (0.23), residues: 1564
  helix:  1.80 (0.25), residues: 492
  sheet:  1.81 (0.30), residues: 353
  loop : -0.82 (0.24), residues: 719

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG C  74 
 TYR   0.020   0.001   TYR F 103 
 PHE   0.012   0.001   PHE E  72 
 TRP   0.009   0.001   TRP E 150 
 HIS   0.003   0.000   HIS F  36 

Details of bonding type rmsd
  covalent geometry    : bond        0.00219 (12850)
  covalent geometry    : angle       0.50793 (17442)
  hydrogen bonds       : bond        0.03136 (  475)
  hydrogen bonds       : angle       4.49555 ( 1347)

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

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

  3128 Ramachandran restraints generated.
    1564 Oldfield, 0 Emsley, 1564 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3128 Ramachandran restraints generated.
    1564 Oldfield, 0 Emsley, 1564 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  125 residues out of total 1461 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 97
  time to evaluate  : 0.537 
Fit side-chains
   revert: symmetry clash
REVERT: B   62 THR cc_start: 0.8048 (OUTLIER) cc_final: 0.7733 (t)
REVERT: B  122 SER cc_start: 0.9163 (p) cc_final: 0.8921 (p)
REVERT: C   68 MET cc_start: 0.7087 (tmm) cc_final: 0.6879 (tmm)
REVERT: C  216 MET cc_start: 0.8465 (OUTLIER) cc_final: 0.7544 (ppp)
REVERT: E   78 MET cc_start: 0.8127 (ppp) cc_final: 0.7645 (ppp)
REVERT: E  214 ARG cc_start: 0.8469 (ttm-80) cc_final: 0.8184 (ttm-80)
  outliers start: 28
  outliers final: 20
  residues processed: 117
  average time/residue: 0.1039
  time to fit residues: 18.8333
Evaluate side-chains
  119 residues out of total 1461 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 97
  time to evaluate  : 0.512 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  159 MET
Chi-restraints excluded: chain B residue   62 THR
Chi-restraints excluded: chain B residue  126 SER
Chi-restraints excluded: chain B residue  212 SER
Chi-restraints excluded: chain C residue   10 VAL
Chi-restraints excluded: chain C residue   69 LEU
Chi-restraints excluded: chain C residue  133 PHE
Chi-restraints excluded: chain C residue  157 LEU
Chi-restraints excluded: chain C residue  216 MET
Chi-restraints excluded: chain C residue  219 LEU
Chi-restraints excluded: chain C residue  221 LEU
Chi-restraints excluded: chain D residue   75 VAL
Chi-restraints excluded: chain D residue   86 THR
Chi-restraints excluded: chain D residue  247 LEU
Chi-restraints excluded: chain D residue  331 ILE
Chi-restraints excluded: chain E residue  161 LEU
Chi-restraints excluded: chain E residue  176 THR
Chi-restraints excluded: chain E residue  223 ASN
Chi-restraints excluded: chain F residue    4 VAL
Chi-restraints excluded: chain F residue  199 VAL
Chi-restraints excluded: chain F residue  211 SER
Chi-restraints excluded: chain F residue  255 VAL
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 155
   random chunks:
   chunk 33 optimal weight:    3.9990
   chunk 24 optimal weight:    4.9990
   chunk 31 optimal weight:    0.6980
   chunk 82 optimal weight:    4.9990
   chunk 22 optimal weight:    1.9990
   chunk 150 optimal weight:    0.0970
   chunk 89 optimal weight:    4.9990
   chunk 45 optimal weight:    0.8980
   chunk 16 optimal weight:    3.9990
   chunk 100 optimal weight:    3.9990
   chunk 51 optimal weight:    1.9990
   overall best weight:    1.1382

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3328 r_free = 0.3328 target = 0.069141 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.2996 r_free = 0.2996 target = 0.055336 restraints weight = 47224.319|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3038 r_free = 0.3038 target = 0.057050 restraints weight = 26568.525|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3067 r_free = 0.3067 target = 0.058205 restraints weight = 18446.063|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3084 r_free = 0.3084 target = 0.058929 restraints weight = 14577.039|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 36)----------------|
| r_work = 0.3099 r_free = 0.3099 target = 0.059473 restraints weight = 12560.250|
|-----------------------------------------------------------------------------|
r_work (final): 0.3095
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8426
moved from start:          0.1436

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031  12850  Z= 0.136
  Angle     :  0.537  11.830  17442  Z= 0.276
  Chirality :  0.042   0.156   2038
  Planarity :  0.004   0.059   2221
  Dihedral  :  4.322  56.670   1678
  Min Nonbonded Distance : 2.513

Molprobity Statistics.
  All-atom Clashscore : 5.55
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.95 %
    Favored  : 94.05 %
  Rotamer:
    Outliers :  1.98 %
    Allowed  : 19.85 %
    Favored  : 78.17 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.60 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.97 (0.23), residues: 1564
  helix:  1.81 (0.25), residues: 487
  sheet:  1.71 (0.30), residues: 354
  loop : -0.76 (0.24), residues: 723

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG C  74 
 TYR   0.020   0.001   TYR F 103 
 PHE   0.012   0.001   PHE E  72 
 TRP   0.021   0.001   TRP C  44 
 HIS   0.004   0.001   HIS A 312 

Details of bonding type rmsd
  covalent geometry    : bond        0.00312 (12850)
  covalent geometry    : angle       0.53740 (17442)
  hydrogen bonds       : bond        0.03523 (  475)
  hydrogen bonds       : angle       4.64399 ( 1347)

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

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

  3128 Ramachandran restraints generated.
    1564 Oldfield, 0 Emsley, 1564 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3128 Ramachandran restraints generated.
    1564 Oldfield, 0 Emsley, 1564 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  125 residues out of total 1461 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 96
  time to evaluate  : 0.536 
Fit side-chains
   revert: symmetry clash
REVERT: B  122 SER cc_start: 0.9190 (p) cc_final: 0.8943 (p)
REVERT: C  216 MET cc_start: 0.8577 (OUTLIER) cc_final: 0.7696 (ppp)
REVERT: E   78 MET cc_start: 0.8112 (ppp) cc_final: 0.7626 (ppp)
  outliers start: 29
  outliers final: 25
  residues processed: 117
  average time/residue: 0.1031
  time to fit residues: 18.7062
Evaluate side-chains
  118 residues out of total 1461 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 92
  time to evaluate  : 0.531 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  159 MET
Chi-restraints excluded: chain A residue  238 ASN
Chi-restraints excluded: chain B residue   62 THR
Chi-restraints excluded: chain B residue   69 CYS
Chi-restraints excluded: chain B residue  126 SER
Chi-restraints excluded: chain B residue  212 SER
Chi-restraints excluded: chain C residue   10 VAL
Chi-restraints excluded: chain C residue   69 LEU
Chi-restraints excluded: chain C residue  133 PHE
Chi-restraints excluded: chain C residue  157 LEU
Chi-restraints excluded: chain C residue  216 MET
Chi-restraints excluded: chain C residue  219 LEU
Chi-restraints excluded: chain C residue  221 LEU
Chi-restraints excluded: chain C residue  224 LEU
Chi-restraints excluded: chain D residue   75 VAL
Chi-restraints excluded: chain D residue   86 THR
Chi-restraints excluded: chain D residue  247 LEU
Chi-restraints excluded: chain D residue  331 ILE
Chi-restraints excluded: chain E residue  146 VAL
Chi-restraints excluded: chain E residue  161 LEU
Chi-restraints excluded: chain E residue  176 THR
Chi-restraints excluded: chain E residue  223 ASN
Chi-restraints excluded: chain F residue    4 VAL
Chi-restraints excluded: chain F residue  199 VAL
Chi-restraints excluded: chain F residue  211 SER
Chi-restraints excluded: chain F residue  255 VAL
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 155
   random chunks:
   chunk 19 optimal weight:    0.9990
   chunk 94 optimal weight:    2.9990
   chunk 108 optimal weight:    1.9990
   chunk 70 optimal weight:    1.9990
   chunk 124 optimal weight:    1.9990
   chunk 42 optimal weight:    0.7980
   chunk 55 optimal weight:    5.9990
   chunk 147 optimal weight:    3.9990
   chunk 113 optimal weight:    0.9980
   chunk 97 optimal weight:    1.9990
   chunk 99 optimal weight:    0.7980
   overall best weight:    1.1184

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3326 r_free = 0.3326 target = 0.068995 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.2990 r_free = 0.2990 target = 0.055109 restraints weight = 47123.980|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3032 r_free = 0.3032 target = 0.056808 restraints weight = 26642.205|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3061 r_free = 0.3061 target = 0.057942 restraints weight = 18627.895|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 40)----------------|
| r_work = 0.3080 r_free = 0.3080 target = 0.058723 restraints weight = 14776.972|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.3092 r_free = 0.3092 target = 0.059212 restraints weight = 12667.363|
|-----------------------------------------------------------------------------|
r_work (final): 0.3090
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8433
moved from start:          0.1467

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032  12850  Z= 0.136
  Angle     :  0.548  11.831  17442  Z= 0.281
  Chirality :  0.042   0.156   2038
  Planarity :  0.004   0.059   2221
  Dihedral  :  4.401  56.686   1678
  Min Nonbonded Distance : 2.532

Molprobity Statistics.
  All-atom Clashscore : 5.95
  Ramachandran Plot:
    Outliers :  0.06 %
    Allowed  :  5.82 %
    Favored  : 94.12 %
  Rotamer:
    Outliers :  1.78 %
    Allowed  : 20.40 %
    Favored  : 77.82 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.60 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.93 (0.23), residues: 1564
  helix:  1.78 (0.25), residues: 487
  sheet:  1.65 (0.30), residues: 354
  loop : -0.76 (0.24), residues: 723

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG E 214 
 TYR   0.019   0.001   TYR C  88 
 PHE   0.012   0.001   PHE E  72 
 TRP   0.015   0.001   TRP C  44 
 HIS   0.003   0.001   HIS A 312 

Details of bonding type rmsd
  covalent geometry    : bond        0.00313 (12850)
  covalent geometry    : angle       0.54802 (17442)
  hydrogen bonds       : bond        0.03512 (  475)
  hydrogen bonds       : angle       4.67173 ( 1347)

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

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

  3128 Ramachandran restraints generated.
    1564 Oldfield, 0 Emsley, 1564 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3128 Ramachandran restraints generated.
    1564 Oldfield, 0 Emsley, 1564 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  119 residues out of total 1461 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 93
  time to evaluate  : 0.551 
Fit side-chains
   revert: symmetry clash
REVERT: B  122 SER cc_start: 0.9164 (p) cc_final: 0.8919 (p)
REVERT: C  216 MET cc_start: 0.8608 (OUTLIER) cc_final: 0.7681 (ppp)
REVERT: E   78 MET cc_start: 0.8190 (ppp) cc_final: 0.7675 (ppp)
  outliers start: 26
  outliers final: 25
  residues processed: 112
  average time/residue: 0.0985
  time to fit residues: 17.3772
Evaluate side-chains
  117 residues out of total 1461 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 91
  time to evaluate  : 0.529 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  159 MET
Chi-restraints excluded: chain A residue  238 ASN
Chi-restraints excluded: chain B residue   62 THR
Chi-restraints excluded: chain B residue   69 CYS
Chi-restraints excluded: chain B residue  126 SER
Chi-restraints excluded: chain B residue  212 SER
Chi-restraints excluded: chain C residue   10 VAL
Chi-restraints excluded: chain C residue   29 HIS
Chi-restraints excluded: chain C residue   69 LEU
Chi-restraints excluded: chain C residue  133 PHE
Chi-restraints excluded: chain C residue  157 LEU
Chi-restraints excluded: chain C residue  216 MET
Chi-restraints excluded: chain C residue  219 LEU
Chi-restraints excluded: chain C residue  221 LEU
Chi-restraints excluded: chain C residue  224 LEU
Chi-restraints excluded: chain D residue   75 VAL
Chi-restraints excluded: chain D residue   86 THR
Chi-restraints excluded: chain D residue  247 LEU
Chi-restraints excluded: chain E residue  146 VAL
Chi-restraints excluded: chain E residue  161 LEU
Chi-restraints excluded: chain E residue  176 THR
Chi-restraints excluded: chain E residue  223 ASN
Chi-restraints excluded: chain F residue    4 VAL
Chi-restraints excluded: chain F residue  199 VAL
Chi-restraints excluded: chain F residue  211 SER
Chi-restraints excluded: chain F residue  255 VAL
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 155
   random chunks:
   chunk 108 optimal weight:    0.7980
   chunk 20 optimal weight:    3.9990
   chunk 88 optimal weight:    3.9990
   chunk 25 optimal weight:    2.9990
   chunk 62 optimal weight:    5.9990
   chunk 137 optimal weight:    0.0770
   chunk 77 optimal weight:   10.0000
   chunk 86 optimal weight:    0.9980
   chunk 18 optimal weight:    1.9990
   chunk 112 optimal weight:    3.9990
   chunk 71 optimal weight:    0.6980
   overall best weight:    0.9140

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3332 r_free = 0.3332 target = 0.069210 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.2994 r_free = 0.2994 target = 0.055149 restraints weight = 47724.171|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 24)----------------|
| r_work = 0.3037 r_free = 0.3037 target = 0.056873 restraints weight = 26991.075|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3065 r_free = 0.3065 target = 0.058036 restraints weight = 18840.967|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 33)----------------|
| r_work = 0.3085 r_free = 0.3085 target = 0.058825 restraints weight = 14894.284|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3096 r_free = 0.3096 target = 0.059290 restraints weight = 12805.627|
|-----------------------------------------------------------------------------|
r_work (final): 0.3092
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8429
moved from start:          0.1508

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033  12850  Z= 0.120
  Angle     :  0.544  11.992  17442  Z= 0.276
  Chirality :  0.042   0.155   2038
  Planarity :  0.004   0.059   2221
  Dihedral  :  4.360  57.125   1678
  Min Nonbonded Distance : 2.511

Molprobity Statistics.
  All-atom Clashscore : 5.63
  Ramachandran Plot:
    Outliers :  0.06 %
    Allowed  :  5.69 %
    Favored  : 94.25 %
  Rotamer:
    Outliers :  2.05 %
    Allowed  : 20.19 %
    Favored  : 77.75 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.60 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.97 (0.23), residues: 1564
  helix:  1.79 (0.25), residues: 488
  sheet:  1.68 (0.30), residues: 352
  loop : -0.72 (0.24), residues: 724

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG E 214 
 TYR   0.019   0.001   TYR F 103 
 PHE   0.011   0.001   PHE E  72 
 TRP   0.015   0.001   TRP C  44 
 HIS   0.003   0.001   HIS A 312 

Details of bonding type rmsd
  covalent geometry    : bond        0.00277 (12850)
  covalent geometry    : angle       0.54404 (17442)
  hydrogen bonds       : bond        0.03389 (  475)
  hydrogen bonds       : angle       4.62221 ( 1347)

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

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

  3128 Ramachandran restraints generated.
    1564 Oldfield, 0 Emsley, 1564 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3128 Ramachandran restraints generated.
    1564 Oldfield, 0 Emsley, 1564 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  124 residues out of total 1461 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 94
  time to evaluate  : 0.519 
Fit side-chains
   revert: symmetry clash
REVERT: B  122 SER cc_start: 0.9170 (p) cc_final: 0.8920 (p)
REVERT: C  216 MET cc_start: 0.8535 (OUTLIER) cc_final: 0.7628 (ppp)
REVERT: D  369 TYR cc_start: 0.8442 (m-80) cc_final: 0.8143 (m-80)
REVERT: E   78 MET cc_start: 0.8214 (ppp) cc_final: 0.7876 (ppp)
  outliers start: 30
  outliers final: 25
  residues processed: 116
  average time/residue: 0.0981
  time to fit residues: 17.9393
Evaluate side-chains
  119 residues out of total 1461 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 93
  time to evaluate  : 0.522 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  159 MET
Chi-restraints excluded: chain A residue  238 ASN
Chi-restraints excluded: chain B residue   62 THR
Chi-restraints excluded: chain B residue   69 CYS
Chi-restraints excluded: chain B residue  126 SER
Chi-restraints excluded: chain B residue  212 SER
Chi-restraints excluded: chain C residue   10 VAL
Chi-restraints excluded: chain C residue   29 HIS
Chi-restraints excluded: chain C residue  133 PHE
Chi-restraints excluded: chain C residue  157 LEU
Chi-restraints excluded: chain C residue  216 MET
Chi-restraints excluded: chain C residue  219 LEU
Chi-restraints excluded: chain C residue  221 LEU
Chi-restraints excluded: chain C residue  224 LEU
Chi-restraints excluded: chain D residue   75 VAL
Chi-restraints excluded: chain D residue   86 THR
Chi-restraints excluded: chain D residue  247 LEU
Chi-restraints excluded: chain E residue  146 VAL
Chi-restraints excluded: chain E residue  161 LEU
Chi-restraints excluded: chain E residue  176 THR
Chi-restraints excluded: chain E residue  223 ASN
Chi-restraints excluded: chain F residue    4 VAL
Chi-restraints excluded: chain F residue  199 VAL
Chi-restraints excluded: chain F residue  211 SER
Chi-restraints excluded: chain F residue  216 MET
Chi-restraints excluded: chain F residue  255 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 155
   random chunks:
   chunk 60 optimal weight:    0.0670
   chunk 149 optimal weight:    0.7980
   chunk 40 optimal weight:    5.9990
   chunk 131 optimal weight:    0.8980
   chunk 86 optimal weight:    2.9990
   chunk 137 optimal weight:    0.9990
   chunk 46 optimal weight:    0.0050
   chunk 47 optimal weight:    1.9990
   chunk 38 optimal weight:    0.6980
   chunk 82 optimal weight:    2.9990
   chunk 147 optimal weight:    0.5980
   overall best weight:    0.4332

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

Flipped N/Q/H residues before XYZ refinement:
A 359 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3351 r_free = 0.3351 target = 0.070065 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3020 r_free = 0.3020 target = 0.056205 restraints weight = 47345.050|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3064 r_free = 0.3064 target = 0.057960 restraints weight = 26497.979|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3093 r_free = 0.3093 target = 0.059142 restraints weight = 18341.670|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 35)----------------|
| r_work = 0.3113 r_free = 0.3113 target = 0.059944 restraints weight = 14463.282|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 32)----------------|
| r_work = 0.3125 r_free = 0.3125 target = 0.060472 restraints weight = 12336.544|
|-----------------------------------------------------------------------------|
r_work (final): 0.3123
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8395
moved from start:          0.1631

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.038  12850  Z= 0.093
  Angle     :  0.541  12.208  17442  Z= 0.272
  Chirality :  0.042   0.157   2038
  Planarity :  0.004   0.063   2221
  Dihedral  :  4.265  56.951   1678
  Min Nonbonded Distance : 2.535

Molprobity Statistics.
  All-atom Clashscore : 5.47
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.50 %
    Favored  : 94.50 %
  Rotamer:
    Outliers :  1.78 %
    Allowed  : 20.26 %
    Favored  : 77.96 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.60 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.99 (0.23), residues: 1564
  helix:  1.78 (0.25), residues: 493
  sheet:  1.77 (0.30), residues: 352
  loop : -0.74 (0.24), residues: 719

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG E 214 
 TYR   0.018   0.001   TYR F 103 
 PHE   0.011   0.001   PHE E  72 
 TRP   0.017   0.001   TRP C  44 
 HIS   0.003   0.001   HIS E  82 

Details of bonding type rmsd
  covalent geometry    : bond        0.00209 (12850)
  covalent geometry    : angle       0.54077 (17442)
  hydrogen bonds       : bond        0.03098 (  475)
  hydrogen bonds       : angle       4.50837 ( 1347)

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

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

  3128 Ramachandran restraints generated.
    1564 Oldfield, 0 Emsley, 1564 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3128 Ramachandran restraints generated.
    1564 Oldfield, 0 Emsley, 1564 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  122 residues out of total 1461 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 96
  time to evaluate  : 0.549 
Fit side-chains
   revert: symmetry clash
REVERT: B  122 SER cc_start: 0.9169 (p) cc_final: 0.8910 (p)
REVERT: C  216 MET cc_start: 0.8540 (OUTLIER) cc_final: 0.7605 (ppp)
REVERT: D  126 PHE cc_start: 0.8391 (t80) cc_final: 0.8132 (t80)
REVERT: D  369 TYR cc_start: 0.8506 (m-80) cc_final: 0.8229 (m-80)
REVERT: E   78 MET cc_start: 0.8224 (ppp) cc_final: 0.7882 (ppp)
  outliers start: 26
  outliers final: 24
  residues processed: 114
  average time/residue: 0.1025
  time to fit residues: 18.1065
Evaluate side-chains
  118 residues out of total 1461 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 93
  time to evaluate  : 0.658 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  159 MET
Chi-restraints excluded: chain A residue  238 ASN
Chi-restraints excluded: chain B residue   62 THR
Chi-restraints excluded: chain B residue  126 SER
Chi-restraints excluded: chain B residue  212 SER
Chi-restraints excluded: chain C residue   10 VAL
Chi-restraints excluded: chain C residue   29 HIS
Chi-restraints excluded: chain C residue  133 PHE
Chi-restraints excluded: chain C residue  157 LEU
Chi-restraints excluded: chain C residue  216 MET
Chi-restraints excluded: chain C residue  219 LEU
Chi-restraints excluded: chain C residue  221 LEU
Chi-restraints excluded: chain C residue  224 LEU
Chi-restraints excluded: chain D residue   75 VAL
Chi-restraints excluded: chain D residue   86 THR
Chi-restraints excluded: chain D residue  247 LEU
Chi-restraints excluded: chain E residue  146 VAL
Chi-restraints excluded: chain E residue  161 LEU
Chi-restraints excluded: chain E residue  176 THR
Chi-restraints excluded: chain E residue  223 ASN
Chi-restraints excluded: chain F residue    4 VAL
Chi-restraints excluded: chain F residue  199 VAL
Chi-restraints excluded: chain F residue  211 SER
Chi-restraints excluded: chain F residue  216 MET
Chi-restraints excluded: chain F residue  255 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 155
   random chunks:
   chunk 54 optimal weight:    0.1980
   chunk 22 optimal weight:    2.9990
   chunk 41 optimal weight:    3.9990
   chunk 131 optimal weight:    0.7980
   chunk 127 optimal weight:    7.9990
   chunk 1 optimal weight:    0.6980
   chunk 51 optimal weight:    1.9990
   chunk 152 optimal weight:    3.9990
   chunk 101 optimal weight:    0.8980
   chunk 104 optimal weight:    3.9990
   chunk 61 optimal weight:    0.5980
   overall best weight:    0.6380

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3344 r_free = 0.3344 target = 0.069762 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3013 r_free = 0.3013 target = 0.055925 restraints weight = 47390.763|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 25)----------------|
| r_work = 0.3057 r_free = 0.3057 target = 0.057650 restraints weight = 26747.730|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3086 r_free = 0.3086 target = 0.058835 restraints weight = 18500.480|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3103 r_free = 0.3103 target = 0.059568 restraints weight = 14557.471|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3117 r_free = 0.3117 target = 0.060132 restraints weight = 12534.642|
|-----------------------------------------------------------------------------|
r_work (final): 0.3115
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8402
moved from start:          0.1672

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.033  12850  Z= 0.102
  Angle     :  0.544  11.889  17442  Z= 0.274
  Chirality :  0.042   0.156   2038
  Planarity :  0.004   0.058   2221
  Dihedral  :  4.239  57.227   1678
  Min Nonbonded Distance : 2.442

Molprobity Statistics.
  All-atom Clashscore : 5.55
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.18 %
    Favored  : 94.82 %
  Rotamer:
    Outliers :  1.78 %
    Allowed  : 20.33 %
    Favored  : 77.89 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.60 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.06 (0.23), residues: 1564
  helix:  1.83 (0.25), residues: 488
  sheet:  1.78 (0.30), residues: 352
  loop : -0.66 (0.25), residues: 724

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG E 214 
 TYR   0.018   0.001   TYR F 103 
 PHE   0.011   0.001   PHE E  72 
 TRP   0.015   0.001   TRP C  44 
 HIS   0.003   0.001   HIS E 227 

Details of bonding type rmsd
  covalent geometry    : bond        0.00235 (12850)
  covalent geometry    : angle       0.54440 (17442)
  hydrogen bonds       : bond        0.03157 (  475)
  hydrogen bonds       : angle       4.49265 ( 1347)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1901.37 seconds
wall clock time: 34 minutes 2.97 seconds (2042.97 seconds total)