Starting phenix.real_space_refine
on Wed Jul 30 18:14:18 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8at6_15635/07_2025/8at6_15635.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8at6_15635/07_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_15635/07_2025/8at6_15635.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8at6_15635/07_2025/8at6_15635.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8at6_15635/07_2025/8at6_15635.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8at6_15635/07_2025/8at6_15635.cif"
  }
  resolution = 3.7
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.002
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): 0.04s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/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: 8.52, per 1000 atoms: 0.68
  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: 3.00
  Conformation dependent library (CDL) restraints added in 1.7 seconds
  

  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: 1.42
  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: 3.79

  Time building geometry restraints manager: 3.52 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:             1.890
  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:          0.470
  Check model and map are aligned:         0.090
  Set scattering table:                    0.120
  Process input model:                     31.440
  Find NCS groups from input model:        0.460
  Set up NCS constraints:                  0.060
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:3.150
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   37.690
-------------------------------------------------------------------------------
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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.49 (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
 TRP   0.013   0.001   TRP C  44 
 HIS   0.003   0.001   HIS A 312 
 PHE   0.012   0.001   PHE C  32 
 TYR   0.023   0.001   TYR F 103 
 ARG   0.004   0.000   ARG F  74 

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

*********************** 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  : 1.370 
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: 0.2578
  time to fit residues: 37.8457
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  : 1.554 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 155
   random chunks:
   chunk 130 optimal weight:    0.0010
   chunk 117 optimal weight:    2.9990
   chunk 65 optimal weight:    0.9990
   chunk 40 optimal weight:    0.9990
   chunk 79 optimal weight:    7.9990
   chunk 62 optimal weight:    0.6980
   chunk 121 optimal weight:    1.9990
   chunk 47 optimal weight:    4.9990
   chunk 73 optimal weight:    3.9990
   chunk 90 optimal weight:    0.7980
   chunk 140 optimal weight:    0.7980
   overall best weight:    0.6588

-------------------------------------------------------------------------------
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
C   7 GLN
F 218 ASN
F 220 ASN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3331 r_free = 0.3331 target = 0.069323 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3000 r_free = 0.3000 target = 0.055481 restraints weight = 46900.680|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3043 r_free = 0.3043 target = 0.057178 restraints weight = 26362.223|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3071 r_free = 0.3071 target = 0.058331 restraints weight = 18352.696|
|-----------------------------------------------------------------------------|
r_work (final): 0.3066
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8444
moved from start:          0.0890

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.035  12850  Z= 0.109
  Angle     :  0.532  10.752  17442  Z= 0.279
  Chirality :  0.043   0.170   2038
  Planarity :  0.004   0.056   2221
  Dihedral  :  4.416  56.590   1678
  Min Nonbonded Distance : 2.512

Molprobity Statistics.
  All-atom Clashscore : 5.51
  Ramachandran Plot:
    Outliers :  0.13 %
    Allowed  :  5.24 %
    Favored  : 94.63 %
  Rotamer:
    Outliers :  1.78 %
    Allowed  : 18.34 %
    Favored  : 79.88 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.60 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.74 (0.23), residues: 1564
  helix:  1.68 (0.25), residues: 487
  sheet:  1.45 (0.30), residues: 353
  loop : -0.87 (0.25), residues: 724

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.002   0.000   TRP E 150 
 HIS   0.003   0.001   HIS C  53 
 PHE   0.009   0.001   PHE C 228 
 TYR   0.020   0.001   TYR C  88 
 ARG   0.003   0.000   ARG F  74 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03909 (  475)
  hydrogen bonds       : angle       5.01754 ( 1347)
  covalent geometry    : bond        0.00241 (12850)
  covalent geometry    : angle       0.53245 (17442)

*********************** 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
  128 residues out of total 1461 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 102
  time to evaluate  : 1.481 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  334 ASP cc_start: 0.8332 (OUTLIER) cc_final: 0.8118 (m-30)
REVERT: B  122 SER cc_start: 0.9137 (p) cc_final: 0.8885 (p)
REVERT: C    1 MET cc_start: 0.6794 (tpp) cc_final: 0.6570 (tpt)
REVERT: D  276 ILE cc_start: 0.9113 (mm) cc_final: 0.8910 (mm)
REVERT: E   78 MET cc_start: 0.8008 (ppp) cc_final: 0.7648 (ppp)
  outliers start: 26
  outliers final: 15
  residues processed: 121
  average time/residue: 0.2390
  time to fit residues: 43.1705
Evaluate side-chains
  106 residues out of total 1461 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 90
  time to evaluate  : 1.523 
-------------------------------------------------------------------------------
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   62 THR
Chi-restraints excluded: chain B residue  212 SER
Chi-restraints excluded: chain B residue  229 TYR
Chi-restraints excluded: chain C residue   10 VAL
Chi-restraints excluded: chain C residue  149 GLU
Chi-restraints excluded: chain C residue  219 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  337 THR
Chi-restraints excluded: chain E residue  161 LEU
Chi-restraints excluded: chain E residue  176 THR
Chi-restraints excluded: chain F residue  211 SER
Chi-restraints excluded: chain F residue  216 MET
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 155
   random chunks:
   chunk 32 optimal weight:    3.9990
   chunk 145 optimal weight:    0.9990
   chunk 52 optimal weight:    0.9980
   chunk 7 optimal weight:    5.9990
   chunk 140 optimal weight:    0.7980
   chunk 90 optimal weight:    0.1980
   chunk 5 optimal weight:    0.9980
   chunk 10 optimal weight:    6.9990
   chunk 136 optimal weight:    3.9990
   chunk 30 optimal weight:    5.9990
   chunk 122 optimal weight:    0.9980
   overall best weight:    0.7980

-------------------------------------------------------------------------------
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 = 0.3330 r_free = 0.3330 target = 0.069191 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.2999 r_free = 0.2999 target = 0.055374 restraints weight = 47618.732|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3041 r_free = 0.3041 target = 0.057072 restraints weight = 26739.482|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3070 r_free = 0.3070 target = 0.058238 restraints weight = 18566.670|
|-----------------------------------------------------------------------------|
r_work (final): 0.3065
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8449
moved from start:          0.1050

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= 0.112
  Angle     :  0.513  11.248  17442  Z= 0.269
  Chirality :  0.042   0.224   2038
  Planarity :  0.004   0.055   2221
  Dihedral  :  4.370  57.103   1678
  Min Nonbonded Distance : 2.541

Molprobity Statistics.
  All-atom Clashscore : 6.15
  Ramachandran Plot:
    Outliers :  0.06 %
    Allowed  :  5.24 %
    Favored  : 94.69 %
  Rotamer:
    Outliers :  2.12 %
    Allowed  : 18.62 %
    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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.80 (0.23), residues: 1564
  helix:  1.70 (0.25), residues: 487
  sheet:  1.54 (0.30), residues: 355
  loop : -0.85 (0.25), residues: 722

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP C  44 
 HIS   0.003   0.001   HIS A 312 
 PHE   0.016   0.001   PHE E  72 
 TYR   0.018   0.001   TYR C  88 
 ARG   0.002   0.000   ARG F  74 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03722 (  475)
  hydrogen bonds       : angle       4.85775 ( 1347)
  covalent geometry    : bond        0.00252 (12850)
  covalent geometry    : angle       0.51324 (17442)

*********************** 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
  123 residues out of total 1461 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 92
  time to evaluate  : 1.470 
Fit side-chains
   revert: symmetry clash
REVERT: A  334 ASP cc_start: 0.8303 (OUTLIER) cc_final: 0.8091 (m-30)
REVERT: B   49 LYS cc_start: 0.8492 (mmmt) cc_final: 0.8233 (mmmm)
REVERT: B  122 SER cc_start: 0.9136 (p) cc_final: 0.8895 (p)
REVERT: C    1 MET cc_start: 0.6783 (tpp) cc_final: 0.6500 (tpt)
REVERT: D  276 ILE cc_start: 0.9135 (mm) cc_final: 0.8930 (mm)
REVERT: E   78 MET cc_start: 0.8149 (ppp) cc_final: 0.7941 (ppp)
  outliers start: 31
  outliers final: 19
  residues processed: 119
  average time/residue: 0.2451
  time to fit residues: 44.0707
Evaluate side-chains
  106 residues out of total 1461 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 86
  time to evaluate  : 1.469 
-------------------------------------------------------------------------------
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   62 THR
Chi-restraints excluded: chain B residue  212 SER
Chi-restraints excluded: chain B residue  229 TYR
Chi-restraints excluded: chain C residue   10 VAL
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  337 THR
Chi-restraints excluded: chain D residue  365 LEU
Chi-restraints excluded: chain E residue  118 THR
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=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 155
   random chunks:
   chunk 52 optimal weight:    0.8980
   chunk 47 optimal weight:    4.9990
   chunk 97 optimal weight:    0.8980
   chunk 13 optimal weight:    5.9990
   chunk 1 optimal weight:    0.1980
   chunk 69 optimal weight:    4.9990
   chunk 95 optimal weight:    1.9990
   chunk 32 optimal weight:    0.0980
   chunk 89 optimal weight:    0.9980
   chunk 75 optimal weight:    5.9990
   chunk 139 optimal weight:    1.9990
   overall best weight:    0.6180

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

Flipped N/Q/H residues before XYZ refinement:
C  76 HIS
F  91 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3341 r_free = 0.3341 target = 0.069706 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3011 r_free = 0.3011 target = 0.055904 restraints weight = 46818.813|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3054 r_free = 0.3054 target = 0.057622 restraints weight = 26297.361|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3082 r_free = 0.3082 target = 0.058782 restraints weight = 18252.656|
|-----------------------------------------------------------------------------|
r_work (final): 0.3076
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8437
moved from start:          0.1243

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= 0.100
  Angle     :  0.514  11.164  17442  Z= 0.266
  Chirality :  0.042   0.210   2038
  Planarity :  0.004   0.056   2221
  Dihedral  :  4.335  56.048   1678
  Min Nonbonded Distance : 2.570

Molprobity Statistics.
  All-atom Clashscore : 5.83
  Ramachandran Plot:
    Outliers :  0.13 %
    Allowed  :  5.24 %
    Favored  : 94.63 %
  Rotamer:
    Outliers :  2.12 %
    Allowed  : 18.62 %
    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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.81 (0.23), residues: 1564
  helix:  1.68 (0.25), residues: 493
  sheet:  1.66 (0.30), residues: 354
  loop : -0.90 (0.25), residues: 717

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP C  44 
 HIS   0.003   0.001   HIS F  36 
 PHE   0.014   0.001   PHE E  72 
 TYR   0.016   0.001   TYR C  88 
 ARG   0.005   0.000   ARG C  74 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03400 (  475)
  hydrogen bonds       : angle       4.69994 ( 1347)
  covalent geometry    : bond        0.00223 (12850)
  covalent geometry    : angle       0.51393 (17442)

*********************** 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
  121 residues out of total 1461 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 90
  time to evaluate  : 1.447 
Fit side-chains
   revert: symmetry clash
REVERT: B   49 LYS cc_start: 0.8515 (mmmt) cc_final: 0.8284 (mmmm)
REVERT: B  122 SER cc_start: 0.9144 (p) cc_final: 0.8910 (p)
REVERT: C    1 MET cc_start: 0.6769 (tpp) cc_final: 0.6483 (tpt)
REVERT: C  216 MET cc_start: 0.8500 (OUTLIER) cc_final: 0.7621 (ppp)
REVERT: D  276 ILE cc_start: 0.9125 (mm) cc_final: 0.8922 (mm)
REVERT: E   78 MET cc_start: 0.8212 (ppp) cc_final: 0.7777 (ppp)
  outliers start: 31
  outliers final: 20
  residues processed: 115
  average time/residue: 0.2233
  time to fit residues: 39.3403
Evaluate side-chains
  107 residues out of total 1461 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 86
  time to evaluate  : 1.500 
-------------------------------------------------------------------------------
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   69 CYS
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  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  337 THR
Chi-restraints excluded: chain E residue  118 THR
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 84 optimal weight:    9.9990
   chunk 48 optimal weight:    0.3980
   chunk 71 optimal weight:    3.9990
   chunk 16 optimal weight:    0.0870
   chunk 5 optimal weight:    0.8980
   chunk 37 optimal weight:    0.7980
   chunk 17 optimal weight:    1.9990
   chunk 74 optimal weight:    0.1980
   chunk 139 optimal weight:    0.8980
   chunk 7 optimal weight:    7.9990
   chunk 122 optimal weight:    0.9990
   overall best weight:    0.4758

-------------------------------------------------------------------------------
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 = 0.3353 r_free = 0.3353 target = 0.070268 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3025 r_free = 0.3025 target = 0.056475 restraints weight = 46742.443|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3068 r_free = 0.3068 target = 0.058218 restraints weight = 26103.849|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3097 r_free = 0.3097 target = 0.059397 restraints weight = 18052.682|
|-----------------------------------------------------------------------------|
r_work (final): 0.3092
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8419
moved from start:          0.1421

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= 0.090
  Angle     :  0.498  12.055  17442  Z= 0.257
  Chirality :  0.042   0.189   2038
  Planarity :  0.004   0.056   2221
  Dihedral  :  4.205  54.200   1678
  Min Nonbonded Distance : 2.578

Molprobity Statistics.
  All-atom Clashscore : 5.31
  Ramachandran Plot:
    Outliers :  0.06 %
    Allowed  :  5.12 %
    Favored  : 94.82 %
  Rotamer:
    Outliers :  1.98 %
    Allowed  : 19.37 %
    Favored  : 78.64 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.60 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.90 (0.23), residues: 1564
  helix:  1.77 (0.25), residues: 492
  sheet:  1.74 (0.30), residues: 354
  loop : -0.87 (0.24), residues: 718

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.004   0.001   TRP D 416 
 HIS   0.003   0.001   HIS F  36 
 PHE   0.013   0.001   PHE E  72 
 TYR   0.017   0.001   TYR C  88 
 ARG   0.004   0.000   ARG C  74 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03163 (  475)
  hydrogen bonds       : angle       4.55399 ( 1347)
  covalent geometry    : bond        0.00200 (12850)
  covalent geometry    : angle       0.49751 (17442)

*********************** 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
  128 residues out of total 1461 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 99
  time to evaluate  : 1.423 
Fit side-chains
   revert: symmetry clash
REVERT: A  334 ASP cc_start: 0.8145 (OUTLIER) cc_final: 0.7930 (m-30)
REVERT: B  122 SER cc_start: 0.9191 (p) cc_final: 0.8945 (p)
REVERT: C    1 MET cc_start: 0.6765 (tpp) cc_final: 0.6438 (tpt)
REVERT: C  216 MET cc_start: 0.8458 (OUTLIER) cc_final: 0.7550 (ppp)
REVERT: D  276 ILE cc_start: 0.9134 (mm) cc_final: 0.8932 (mm)
REVERT: E   78 MET cc_start: 0.8233 (ppp) cc_final: 0.7751 (ppp)
REVERT: E  214 ARG cc_start: 0.8424 (ttm-80) cc_final: 0.8152 (ttm-80)
  outliers start: 29
  outliers final: 22
  residues processed: 120
  average time/residue: 0.2278
  time to fit residues: 41.3582
Evaluate side-chains
  113 residues out of total 1461 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 89
  time to evaluate  : 1.538 
-------------------------------------------------------------------------------
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  126 SER
Chi-restraints excluded: chain B residue  212 SER
Chi-restraints excluded: chain C residue   10 VAL
Chi-restraints excluded: chain C residue  133 PHE
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  238 ASN
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  216 MET
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 121 optimal weight:    1.9990
   chunk 30 optimal weight:    2.9990
   chunk 107 optimal weight:    0.8980
   chunk 41 optimal weight:    2.9990
   chunk 53 optimal weight:    3.9990
   chunk 42 optimal weight:    0.9980
   chunk 144 optimal weight:    3.9990
   chunk 19 optimal weight:    0.9980
   chunk 49 optimal weight:    4.9990
   chunk 98 optimal weight:    0.5980
   chunk 48 optimal weight:    1.9990
   overall best weight:    1.0982

-------------------------------------------------------------------------------
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 = 0.3323 r_free = 0.3323 target = 0.068868 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.2990 r_free = 0.2990 target = 0.055014 restraints weight = 47759.047|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3032 r_free = 0.3032 target = 0.056732 restraints weight = 26828.969|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3061 r_free = 0.3061 target = 0.057886 restraints weight = 18621.049|
|-----------------------------------------------------------------------------|
r_work (final): 0.3056
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8458
moved from start:          0.1419

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= 0.133
  Angle     :  0.533  10.801  17442  Z= 0.275
  Chirality :  0.042   0.233   2038
  Planarity :  0.004   0.057   2221
  Dihedral  :  4.382  58.736   1678
  Min Nonbonded Distance : 2.518

Molprobity Statistics.
  All-atom Clashscore : 5.83
  Ramachandran Plot:
    Outliers :  0.06 %
    Allowed  :  5.75 %
    Favored  : 94.18 %
  Rotamer:
    Outliers :  2.19 %
    Allowed  : 19.71 %
    Favored  : 78.10 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.60 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.90 (0.23), residues: 1564
  helix:  1.77 (0.25), residues: 487
  sheet:  1.67 (0.30), residues: 354
  loop : -0.82 (0.25), residues: 723

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP C  44 
 HIS   0.004   0.001   HIS A 312 
 PHE   0.012   0.001   PHE E  72 
 TYR   0.021   0.001   TYR F 103 
 ARG   0.007   0.000   ARG C  74 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03548 (  475)
  hydrogen bonds       : angle       4.67972 ( 1347)
  covalent geometry    : bond        0.00305 (12850)
  covalent geometry    : angle       0.53283 (17442)

*********************** 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
  123 residues out of total 1461 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 91
  time to evaluate  : 1.466 
Fit side-chains
   revert: symmetry clash
REVERT: B  122 SER cc_start: 0.9180 (p) cc_final: 0.8941 (p)
REVERT: C    1 MET cc_start: 0.6817 (tpp) cc_final: 0.6420 (tpt)
REVERT: C  216 MET cc_start: 0.8556 (OUTLIER) cc_final: 0.7662 (ppp)
REVERT: D  276 ILE cc_start: 0.9123 (mm) cc_final: 0.8920 (mm)
REVERT: E   78 MET cc_start: 0.8226 (ppp) cc_final: 0.7700 (ppp)
  outliers start: 32
  outliers final: 25
  residues processed: 117
  average time/residue: 0.2101
  time to fit residues: 38.2479
Evaluate side-chains
  111 residues out of total 1461 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 85
  time to evaluate  : 1.465 
-------------------------------------------------------------------------------
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  152 ASN
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  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  238 ASN
Chi-restraints excluded: chain D residue  247 LEU
Chi-restraints excluded: chain D residue  337 THR
Chi-restraints excluded: chain E residue  118 THR
Chi-restraints excluded: chain E residue  161 LEU
Chi-restraints excluded: chain E residue  176 THR
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 53 optimal weight:    3.9990
   chunk 20 optimal weight:    2.9990
   chunk 144 optimal weight:    1.9990
   chunk 44 optimal weight:    4.9990
   chunk 61 optimal weight:    0.4980
   chunk 12 optimal weight:    4.9990
   chunk 33 optimal weight:    0.6980
   chunk 150 optimal weight:    5.9990
   chunk 153 optimal weight:    0.9980
   chunk 95 optimal weight:    0.7980
   chunk 105 optimal weight:    6.9990
   overall best weight:    0.9982

-------------------------------------------------------------------------------
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 = 0.3324 r_free = 0.3324 target = 0.068911 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.2990 r_free = 0.2990 target = 0.055066 restraints weight = 47444.326|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3033 r_free = 0.3033 target = 0.056790 restraints weight = 26716.118|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3062 r_free = 0.3062 target = 0.057942 restraints weight = 18546.841|
|-----------------------------------------------------------------------------|
r_work (final): 0.3057
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8455
moved from start:          0.1463

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= 0.126
  Angle     :  0.539  11.056  17442  Z= 0.278
  Chirality :  0.042   0.222   2038
  Planarity :  0.004   0.057   2221
  Dihedral  :  4.398  56.677   1678
  Min Nonbonded Distance : 2.540

Molprobity Statistics.
  All-atom Clashscore : 5.83
  Ramachandran Plot:
    Outliers :  0.06 %
    Allowed  :  5.75 %
    Favored  : 94.18 %
  Rotamer:
    Outliers :  1.98 %
    Allowed  : 20.88 %
    Favored  : 77.14 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.60 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.91 (0.23), residues: 1564
  helix:  1.81 (0.25), residues: 485
  sheet:  1.68 (0.30), residues: 353
  loop : -0.83 (0.24), residues: 726

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP C  44 
 HIS   0.003   0.001   HIS A 312 
 PHE   0.012   0.001   PHE E  72 
 TYR   0.019   0.001   TYR C  88 
 ARG   0.007   0.000   ARG E 214 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03475 (  475)
  hydrogen bonds       : angle       4.67684 ( 1347)
  covalent geometry    : bond        0.00287 (12850)
  covalent geometry    : angle       0.53882 (17442)

*********************** 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
  117 residues out of total 1461 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 88
  time to evaluate  : 1.919 
Fit side-chains
   revert: symmetry clash
REVERT: B  122 SER cc_start: 0.9189 (p) cc_final: 0.8939 (p)
REVERT: C    1 MET cc_start: 0.6914 (tpp) cc_final: 0.6499 (tpt)
REVERT: C  216 MET cc_start: 0.8563 (OUTLIER) cc_final: 0.7663 (ppp)
REVERT: E   78 MET cc_start: 0.8214 (ppp) cc_final: 0.7623 (ppp)
  outliers start: 29
  outliers final: 26
  residues processed: 111
  average time/residue: 0.2234
  time to fit residues: 39.7651
Evaluate side-chains
  113 residues out of total 1461 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 86
  time to evaluate  : 1.510 
-------------------------------------------------------------------------------
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  133 PHE
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  133 HIS
Chi-restraints excluded: chain D residue  238 ASN
Chi-restraints excluded: chain D residue  247 LEU
Chi-restraints excluded: chain D residue  337 THR
Chi-restraints excluded: chain E residue  118 THR
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 F residue    4 VAL
Chi-restraints excluded: chain F residue  199 VAL
Chi-restraints excluded: chain F residue  210 SER
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 138 optimal weight:    0.9980
   chunk 153 optimal weight:    0.0870
   chunk 54 optimal weight:    0.9990
   chunk 0 optimal weight:   10.0000
   chunk 38 optimal weight:    2.9990
   chunk 59 optimal weight:    4.9990
   chunk 122 optimal weight:    0.9990
   chunk 4 optimal weight:    0.9990
   chunk 23 optimal weight:    0.8980
   chunk 9 optimal weight:    0.9990
   chunk 72 optimal weight:    2.9990
   overall best weight:    0.7962

-------------------------------------------------------------------------------
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 = 0.3329 r_free = 0.3329 target = 0.069144 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.2997 r_free = 0.2997 target = 0.055336 restraints weight = 47843.871|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3040 r_free = 0.3040 target = 0.057072 restraints weight = 26706.561|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3070 r_free = 0.3070 target = 0.058261 restraints weight = 18439.563|
|-----------------------------------------------------------------------------|
r_work (final): 0.3065
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8446
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      :  0.003   0.033  12850  Z= 0.110
  Angle     :  0.535  10.840  17442  Z= 0.273
  Chirality :  0.042   0.253   2038
  Planarity :  0.004   0.058   2221
  Dihedral  :  4.341  56.611   1678
  Min Nonbonded Distance : 2.544

Molprobity Statistics.
  All-atom Clashscore : 5.87
  Ramachandran Plot:
    Outliers :  0.06 %
    Allowed  :  5.56 %
    Favored  : 94.37 %
  Rotamer:
    Outliers :  2.40 %
    Allowed  : 20.60 %
    Favored  : 77.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.60 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.95 (0.23), residues: 1564
  helix:  1.81 (0.25), residues: 487
  sheet:  1.70 (0.30), residues: 352
  loop : -0.78 (0.24), residues: 725

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP C  44 
 HIS   0.003   0.001   HIS A 312 
 PHE   0.011   0.001   PHE E  72 
 TYR   0.018   0.001   TYR C  88 
 ARG   0.006   0.000   ARG E 214 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03363 (  475)
  hydrogen bonds       : angle       4.63381 ( 1347)
  covalent geometry    : bond        0.00251 (12850)
  covalent geometry    : angle       0.53460 (17442)

*********************** 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
  126 residues out of total 1461 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 91
  time to evaluate  : 1.414 
Fit side-chains
   revert: symmetry clash
REVERT: B  122 SER cc_start: 0.9193 (p) cc_final: 0.8939 (p)
REVERT: C    1 MET cc_start: 0.6924 (tpp) cc_final: 0.6485 (tpt)
REVERT: C  216 MET cc_start: 0.8567 (OUTLIER) cc_final: 0.7665 (ppp)
REVERT: E   78 MET cc_start: 0.8248 (ppp) cc_final: 0.7911 (ppp)
  outliers start: 35
  outliers final: 27
  residues processed: 119
  average time/residue: 0.1937
  time to fit residues: 36.5584
Evaluate side-chains
  116 residues out of total 1461 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 88
  time to evaluate  : 1.386 
-------------------------------------------------------------------------------
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  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  133 HIS
Chi-restraints excluded: chain D residue  238 ASN
Chi-restraints excluded: chain D residue  247 LEU
Chi-restraints excluded: chain D residue  337 THR
Chi-restraints excluded: chain E residue  118 THR
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  210 SER
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 133 optimal weight:    0.9990
   chunk 39 optimal weight:    0.0770
   chunk 9 optimal weight:    5.9990
   chunk 26 optimal weight:    2.9990
   chunk 36 optimal weight:    0.0870
   chunk 139 optimal weight:    0.6980
   chunk 132 optimal weight:    0.6980
   chunk 70 optimal weight:    2.9990
   chunk 47 optimal weight:    0.9990
   chunk 59 optimal weight:    4.9990
   chunk 51 optimal weight:    0.9980
   overall best weight:    0.5116

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

Flipped N/Q/H residues before XYZ refinement:
C 115 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3346 r_free = 0.3346 target = 0.069877 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3017 r_free = 0.3017 target = 0.056113 restraints weight = 46901.453|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3060 r_free = 0.3060 target = 0.057821 restraints weight = 26410.107|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3090 r_free = 0.3090 target = 0.059015 restraints weight = 18273.891|
|-----------------------------------------------------------------------------|
r_work (final): 0.3085
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8425
moved from start:          0.1643

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.034  12850  Z= 0.095
  Angle     :  0.544  15.686  17442  Z= 0.273
  Chirality :  0.042   0.238   2038
  Planarity :  0.004   0.058   2221
  Dihedral  :  4.262  58.078   1678
  Min Nonbonded Distance : 2.525

Molprobity Statistics.
  All-atom Clashscore : 5.51
  Ramachandran Plot:
    Outliers :  0.06 %
    Allowed  :  5.18 %
    Favored  : 94.76 %
  Rotamer:
    Outliers :  1.98 %
    Allowed  : 21.29 %
    Favored  : 76.73 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.60 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.02 (0.23), residues: 1564
  helix:  1.85 (0.25), residues: 487
  sheet:  1.76 (0.30), residues: 353
  loop : -0.74 (0.25), residues: 724

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.001   TRP C  44 
 HIS   0.004   0.001   HIS E  82 
 PHE   0.011   0.001   PHE E  72 
 TYR   0.017   0.001   TYR F 103 
 ARG   0.006   0.000   ARG E 214 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03135 (  475)
  hydrogen bonds       : angle       4.54346 ( 1347)
  covalent geometry    : bond        0.00216 (12850)
  covalent geometry    : angle       0.54378 (17442)

*********************** 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
  123 residues out of total 1461 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 94
  time to evaluate  : 1.388 
Fit side-chains
   revert: symmetry clash
REVERT: B  122 SER cc_start: 0.9198 (p) cc_final: 0.8940 (p)
REVERT: C    1 MET cc_start: 0.6879 (tpp) cc_final: 0.6477 (tpt)
REVERT: C  216 MET cc_start: 0.8552 (OUTLIER) cc_final: 0.7660 (ppp)
REVERT: E   78 MET cc_start: 0.8261 (ppp) cc_final: 0.7922 (ppp)
  outliers start: 29
  outliers final: 24
  residues processed: 116
  average time/residue: 0.2150
  time to fit residues: 38.9411
Evaluate side-chains
  117 residues out of total 1461 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 92
  time to evaluate  : 1.535 
-------------------------------------------------------------------------------
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  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  133 HIS
Chi-restraints excluded: chain D residue  238 ASN
Chi-restraints excluded: chain D residue  247 LEU
Chi-restraints excluded: chain E residue  107 ASP
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=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 155
   random chunks:
   chunk 76 optimal weight:    1.9990
   chunk 18 optimal weight:    2.9990
   chunk 47 optimal weight:    0.0570
   chunk 97 optimal weight:    3.9990
   chunk 125 optimal weight:    2.9990
   chunk 111 optimal weight:    3.9990
   chunk 65 optimal weight:    0.6980
   chunk 114 optimal weight:    2.9990
   chunk 107 optimal weight:    0.8980
   chunk 117 optimal weight:    2.9990
   chunk 30 optimal weight:    0.0980
   overall best weight:    0.7500

-------------------------------------------------------------------------------
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 = 0.3339 r_free = 0.3339 target = 0.069533 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 29)----------------|
| r_work = 0.3004 r_free = 0.3004 target = 0.055550 restraints weight = 47400.580|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 25)----------------|
| r_work = 0.3047 r_free = 0.3047 target = 0.057281 restraints weight = 26837.464|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3076 r_free = 0.3076 target = 0.058444 restraints weight = 18696.273|
|-----------------------------------------------------------------------------|
r_work (final): 0.3072
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8441
moved from start:          0.1651

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= 0.108
  Angle     :  0.549  15.163  17442  Z= 0.277
  Chirality :  0.042   0.253   2038
  Planarity :  0.004   0.058   2221
  Dihedral  :  4.300  60.576   1678
  Min Nonbonded Distance : 2.514

Molprobity Statistics.
  All-atom Clashscore : 5.87
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.56 %
    Favored  : 94.44 %
  Rotamer:
    Outliers :  1.92 %
    Allowed  : 21.29 %
    Favored  : 76.80 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.60 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.98 (0.23), residues: 1564
  helix:  1.78 (0.25), residues: 488
  sheet:  1.73 (0.30), residues: 352
  loop : -0.72 (0.25), residues: 724

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP C  44 
 HIS   0.003   0.001   HIS F  36 
 PHE   0.011   0.001   PHE E  72 
 TYR   0.017   0.001   TYR C  88 
 ARG   0.006   0.000   ARG E 214 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03255 (  475)
  hydrogen bonds       : angle       4.54002 ( 1347)
  covalent geometry    : bond        0.00248 (12850)
  covalent geometry    : angle       0.54929 (17442)

********************** 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
  121 residues out of total 1461 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 93
  time to evaluate  : 1.599 
Fit side-chains
   revert: symmetry clash
REVERT: B  122 SER cc_start: 0.9192 (p) cc_final: 0.8938 (p)
REVERT: C  216 MET cc_start: 0.8555 (OUTLIER) cc_final: 0.7654 (ppp)
REVERT: E   78 MET cc_start: 0.8239 (ppp) cc_final: 0.7889 (ppp)
  outliers start: 28
  outliers final: 26
  residues processed: 115
  average time/residue: 0.2045
  time to fit residues: 37.1020
Evaluate side-chains
  118 residues out of total 1461 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 91
  time to evaluate  : 1.410 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  132 VAL
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  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  133 HIS
Chi-restraints excluded: chain D residue  238 ASN
Chi-restraints excluded: chain D residue  247 LEU
Chi-restraints excluded: chain E residue  107 ASP
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  210 SER
Chi-restraints excluded: chain F residue  211 SER
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 121 optimal weight:    0.8980
   chunk 16 optimal weight:    0.5980
   chunk 97 optimal weight:    3.9990
   chunk 17 optimal weight:    1.9990
   chunk 113 optimal weight:    1.9990
   chunk 154 optimal weight:    6.9990
   chunk 6 optimal weight:    2.9990
   chunk 146 optimal weight:    0.8980
   chunk 34 optimal weight:    0.9980
   chunk 70 optimal weight:    2.9990
   chunk 109 optimal weight:    0.6980
   overall best weight:    0.8180

-------------------------------------------------------------------------------
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 = 0.3334 r_free = 0.3334 target = 0.069298 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3002 r_free = 0.3002 target = 0.055499 restraints weight = 47446.889|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3045 r_free = 0.3045 target = 0.057217 restraints weight = 26656.017|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3074 r_free = 0.3074 target = 0.058391 restraints weight = 18444.957|
|-----------------------------------------------------------------------------|
r_work (final): 0.3070
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8442
moved from start:          0.1645

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= 0.113
  Angle     :  0.556  15.481  17442  Z= 0.280
  Chirality :  0.042   0.254   2038
  Planarity :  0.004   0.058   2221
  Dihedral  :  4.278  55.771   1678
  Min Nonbonded Distance : 2.510

Molprobity Statistics.
  All-atom Clashscore : 5.95
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.56 %
    Favored  : 94.44 %
  Rotamer:
    Outliers :  2.19 %
    Allowed  : 21.22 %
    Favored  : 76.59 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.60 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.97 (0.23), residues: 1564
  helix:  1.76 (0.25), residues: 488
  sheet:  1.71 (0.30), residues: 352
  loop : -0.72 (0.25), residues: 724

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP C  44 
 HIS   0.003   0.001   HIS A 312 
 PHE   0.011   0.001   PHE E  72 
 TYR   0.017   0.001   TYR C  88 
 ARG   0.006   0.000   ARG E 214 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03308 (  475)
  hydrogen bonds       : angle       4.55697 ( 1347)
  covalent geometry    : bond        0.00260 (12850)
  covalent geometry    : angle       0.55639 (17442)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3508.18 seconds
wall clock time: 62 minutes 3.11 seconds (3723.11 seconds total)