Starting phenix.real_space_refine
on Tue Mar  3 20:37:11 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/6jbh_9790/03_2026/6jbh_9790.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/6jbh_9790/03_2026/6jbh_9790.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.94
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/6jbh_9790/03_2026/6jbh_9790.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/6jbh_9790/03_2026/6jbh_9790.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/6jbh_9790/03_2026/6jbh_9790.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/6jbh_9790/03_2026/6jbh_9790.cif"
  }
  resolution = 3.94
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.001 sd=   0.012
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      44      5.16       5
     C    5654      2.51       5
     N    1408      2.21       5
     O    1486      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 26 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 8592
  Number of models: 1
  Model: ""
    Number of chains: 4
    Chain: "A"
      Number of atoms: 2075
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 264, 2075
          Classifications: {'peptide': 264}
          Link IDs: {'PTRANS': 7, 'TRANS': 256}
    Chain: "B"
      Number of atoms: 2075
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 264, 2075
          Classifications: {'peptide': 264}
          Link IDs: {'PTRANS': 7, 'TRANS': 256}
    Chain: "C"
      Number of atoms: 2221
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 267, 2221
          Classifications: {'peptide': 267}
          Link IDs: {'PTRANS': 11, 'TRANS': 255}
    Chain: "D"
      Number of atoms: 2221
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 267, 2221
          Classifications: {'peptide': 267}
          Link IDs: {'PTRANS': 11, 'TRANS': 255}
  Time building chain proxies: 1.61, per 1000 atoms: 0.19
  Number of scatterers: 8592
  At special positions: 0
  Unit cell: (93.84, 88.4, 107.44, 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      44     16.00
     O    1486      8.00
     N    1408      7.00
     C    5654      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: 0.83
  Conformation dependent library (CDL) restraints added in 338.2 milliseconds
  

  2108 Ramachandran restraints generated.
    1054 Oldfield, 0 Emsley, 1054 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1988

  Finding SS restraints...
    Secondary structure from input PDB file:
      62 helices and 4 sheets defined
      57.4% alpha, 6.0% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.27
  Creating SS restraints...
    Processing helix  chain 'A' and resid 58 through 62
    Processing helix  chain 'A' and resid 64 through 71
      removed outlier: 3.667A  pdb=" N   ILE A  70 " --> pdb=" O   LEU A  66 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 101 through 114
      removed outlier: 3.670A  pdb=" N   GLU A 107 " --> pdb=" O   ARG A 103 " (cutoff:3.500A)
      removed outlier: 3.686A  pdb=" N   LEU A 111 " --> pdb=" O   GLU A 107 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 118 through 123
    Processing helix  chain 'A' and resid 123 through 132
      removed outlier: 4.060A  pdb=" N   ILE A 127 " --> pdb=" O   MET A 123 " (cutoff:3.500A)
      removed outlier: 3.762A  pdb=" N   ILE A 128 " --> pdb=" O   GLU A 124 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 133 through 139
      removed outlier: 3.575A  pdb=" N   ILE A 137 " --> pdb=" O   GLY A 134 " (cutoff:3.500A)
      removed outlier: 3.752A  pdb=" N   ASP A 138 " --> pdb=" O   LYS A 135 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 140 through 144
    Processing helix  chain 'A' and resid 145 through 157
      removed outlier: 3.871A  pdb=" N   SER A 150 " --> pdb=" O   SER A 146 " (cutoff:3.500A)
      removed outlier: 3.788A  pdb=" N   ALA A 155 " --> pdb=" O   ARG A 151 " (cutoff:3.500A)
      removed outlier: 3.636A  pdb=" N   SER A 157 " --> pdb=" O   GLY A 153 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 178 through 193
      removed outlier: 3.535A  pdb=" N   ASP A 184 " --> pdb=" O   ASP A 180 " (cutoff:3.500A)
      removed outlier: 3.855A  pdb=" N   GLU A 188 " --> pdb=" O   ASP A 184 " (cutoff:3.500A)
      removed outlier: 4.132A  pdb=" N   PHE A 189 " --> pdb=" O   LYS A 185 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 202 through 210
    Processing helix  chain 'A' and resid 229 through 244
      removed outlier: 3.530A  pdb=" N   ALA A 243 " --> pdb=" O   LYS A 239 " (cutoff:3.500A)
      removed outlier: 4.330A  pdb=" N   MET A 244 " --> pdb=" O   GLU A 240 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 251 through 261
    Processing helix  chain 'A' and resid 262 through 264
      No H-bonds generated for 'chain 'A' and resid 262 through 264'
    Processing helix  chain 'B' and resid 58 through 62
    Processing helix  chain 'B' and resid 64 through 71
      removed outlier: 3.667A  pdb=" N   ILE B  70 " --> pdb=" O   LEU B  66 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 101 through 114
      removed outlier: 3.670A  pdb=" N   GLU B 107 " --> pdb=" O   ARG B 103 " (cutoff:3.500A)
      removed outlier: 3.686A  pdb=" N   LEU B 111 " --> pdb=" O   GLU B 107 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 118 through 123
    Processing helix  chain 'B' and resid 123 through 132
      removed outlier: 4.060A  pdb=" N   ILE B 127 " --> pdb=" O   MET B 123 " (cutoff:3.500A)
      removed outlier: 3.762A  pdb=" N   ILE B 128 " --> pdb=" O   GLU B 124 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 133 through 139
      removed outlier: 3.575A  pdb=" N   ILE B 137 " --> pdb=" O   GLY B 134 " (cutoff:3.500A)
      removed outlier: 3.752A  pdb=" N   ASP B 138 " --> pdb=" O   LYS B 135 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 140 through 144
    Processing helix  chain 'B' and resid 145 through 157
      removed outlier: 3.871A  pdb=" N   SER B 150 " --> pdb=" O   SER B 146 " (cutoff:3.500A)
      removed outlier: 3.788A  pdb=" N   ALA B 155 " --> pdb=" O   ARG B 151 " (cutoff:3.500A)
      removed outlier: 3.636A  pdb=" N   SER B 157 " --> pdb=" O   GLY B 153 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 178 through 193
      removed outlier: 3.535A  pdb=" N   ASP B 184 " --> pdb=" O   ASP B 180 " (cutoff:3.500A)
      removed outlier: 3.854A  pdb=" N   GLU B 188 " --> pdb=" O   ASP B 184 " (cutoff:3.500A)
      removed outlier: 4.132A  pdb=" N   PHE B 189 " --> pdb=" O   LYS B 185 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 202 through 210
    Processing helix  chain 'B' and resid 229 through 244
      removed outlier: 3.530A  pdb=" N   ALA B 243 " --> pdb=" O   LYS B 239 " (cutoff:3.500A)
      removed outlier: 4.330A  pdb=" N   MET B 244 " --> pdb=" O   GLU B 240 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 251 through 261
    Processing helix  chain 'B' and resid 262 through 264
      No H-bonds generated for 'chain 'B' and resid 262 through 264'
    Processing helix  chain 'C' and resid 3 through 14
      removed outlier: 3.826A  pdb=" N   VAL C   7 " --> pdb=" O   SER C   3 " (cutoff:3.500A)
      removed outlier: 3.609A  pdb=" N   GLU C  10 " --> pdb=" O   THR C   6 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 14 through 21
    Processing helix  chain 'C' and resid 21 through 30
      removed outlier: 4.530A  pdb=" N   GLU C  25 " --> pdb=" O   LEU C  21 " (cutoff:3.500A)
      removed outlier: 3.880A  pdb=" N   LEU C  26 " --> pdb=" O   SER C  22 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 38 through 56
      removed outlier: 3.993A  pdb=" N   ILE C  42 " --> pdb=" O   LEU C  38 " (cutoff:3.500A)
      Proline residue:  C  44  - end of helix
      removed outlier: 3.707A  pdb=" N   ALA C  49 " --> pdb=" O   MET C  45 " (cutoff:3.500A)
      removed outlier: 3.529A  pdb=" N   ILE C  50 " --> pdb=" O   ILE C  46 " (cutoff:3.500A)
      removed outlier: 3.942A  pdb=" N   TYR C  51 " --> pdb=" O   GLN C  47 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 70 through 76
      removed outlier: 3.745A  pdb=" N   ALA C  76 " --> pdb=" O   LEU C  72 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 77 through 86
      removed outlier: 4.204A  pdb=" N   TRP C  81 " --> pdb=" O   GLY C  77 " (cutoff:3.500A)
      removed outlier: 3.766A  pdb=" N   PHE C  82 " --> pdb=" O   MET C  78 " (cutoff:3.500A)
      removed outlier: 3.944A  pdb=" N   PHE C  83 " --> pdb=" O   THR C  79 " (cutoff:3.500A)
      removed outlier: 3.529A  pdb=" N   VAL C  84 " --> pdb=" O   VAL C  80 " (cutoff:3.500A)
      removed outlier: 4.226A  pdb=" N   GLN C  86 " --> pdb=" O   PHE C  82 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 88 through 93
    Processing helix  chain 'C' and resid 99 through 104
      removed outlier: 4.003A  pdb=" N   GLN C 104 " --> pdb=" O   ARG C 100 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 108 through 112
      removed outlier: 3.534A  pdb=" N   VAL C 111 " --> pdb=" O   PRO C 108 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 113 through 120
      removed outlier: 3.672A  pdb=" N   ILE C 117 " --> pdb=" O   PRO C 113 " (cutoff:3.500A)
      removed outlier: 3.523A  pdb=" N   THR C 118 " --> pdb=" O   THR C 114 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 123 through 128
    Processing helix  chain 'C' and resid 131 through 136
    Processing helix  chain 'C' and resid 149 through 167
      removed outlier: 4.070A  pdb=" N   LEU C 156 " --> pdb=" O   TYR C 152 " (cutoff:3.500A)
      removed outlier: 3.572A  pdb=" N   LEU C 157 " --> pdb=" O   MET C 153 " (cutoff:3.500A)
      removed outlier: 4.931A  pdb=" N   LEU C 165 " --> pdb=" O   VAL C 161 " (cutoff:3.500A)
      removed outlier: 4.361A  pdb=" N   ILE C 166 " --> pdb=" O   SER C 162 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 168 through 175
      removed outlier: 3.592A  pdb=" N   THR C 172 " --> pdb=" O   SER C 168 " (cutoff:3.500A)
      removed outlier: 3.840A  pdb=" N   VAL C 173 " --> pdb=" O   THR C 169 " (cutoff:3.500A)
      removed outlier: 3.899A  pdb=" N   VAL C 174 " --> pdb=" O   LEU C 170 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 176 through 188
      removed outlier: 3.653A  pdb=" N   SER C 183 " --> pdb=" O   MET C 179 " (cutoff:3.500A)
      removed outlier: 4.368A  pdb=" N   ARG C 186 " --> pdb=" O   GLN C 182 " (cutoff:3.500A)
      removed outlier: 3.513A  pdb=" N   LEU C 188 " --> pdb=" O   LEU C 184 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 213 through 223
      removed outlier: 3.909A  pdb=" N   ILE C 217 " --> pdb=" O   PRO C 213 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 232 through 234
      No H-bonds generated for 'chain 'C' and resid 232 through 234'
    Processing helix  chain 'C' and resid 235 through 259
      removed outlier: 4.050A  pdb=" N   VAL C 240 " --> pdb=" O   ALA C 236 " (cutoff:3.500A)
      removed outlier: 4.710A  pdb=" N   TYR C 241 " --> pdb=" O   SER C 237 " (cutoff:3.500A)
      removed outlier: 4.007A  pdb=" N   ILE C 247 " --> pdb=" O   TRP C 243 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 3 through 14
      removed outlier: 3.826A  pdb=" N   VAL D   7 " --> pdb=" O   SER D   3 " (cutoff:3.500A)
      removed outlier: 3.610A  pdb=" N   GLU D  10 " --> pdb=" O   THR D   6 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 14 through 21
    Processing helix  chain 'D' and resid 21 through 30
      removed outlier: 4.530A  pdb=" N   GLU D  25 " --> pdb=" O   LEU D  21 " (cutoff:3.500A)
      removed outlier: 3.880A  pdb=" N   LEU D  26 " --> pdb=" O   SER D  22 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 38 through 56
      removed outlier: 3.993A  pdb=" N   ILE D  42 " --> pdb=" O   LEU D  38 " (cutoff:3.500A)
      Proline residue:  D  44  - end of helix
      removed outlier: 3.707A  pdb=" N   ALA D  49 " --> pdb=" O   MET D  45 " (cutoff:3.500A)
      removed outlier: 3.529A  pdb=" N   ILE D  50 " --> pdb=" O   ILE D  46 " (cutoff:3.500A)
      removed outlier: 3.943A  pdb=" N   TYR D  51 " --> pdb=" O   GLN D  47 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 70 through 76
      removed outlier: 3.745A  pdb=" N   ALA D  76 " --> pdb=" O   LEU D  72 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 77 through 86
      removed outlier: 4.205A  pdb=" N   TRP D  81 " --> pdb=" O   GLY D  77 " (cutoff:3.500A)
      removed outlier: 3.766A  pdb=" N   PHE D  82 " --> pdb=" O   MET D  78 " (cutoff:3.500A)
      removed outlier: 3.945A  pdb=" N   PHE D  83 " --> pdb=" O   THR D  79 " (cutoff:3.500A)
      removed outlier: 3.529A  pdb=" N   VAL D  84 " --> pdb=" O   VAL D  80 " (cutoff:3.500A)
      removed outlier: 4.226A  pdb=" N   GLN D  86 " --> pdb=" O   PHE D  82 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 88 through 93
    Processing helix  chain 'D' and resid 99 through 104
      removed outlier: 4.011A  pdb=" N   GLN D 104 " --> pdb=" O   ARG D 100 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 108 through 112
      removed outlier: 3.534A  pdb=" N   VAL D 111 " --> pdb=" O   PRO D 108 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 113 through 120
      removed outlier: 3.672A  pdb=" N   ILE D 117 " --> pdb=" O   PRO D 113 " (cutoff:3.500A)
      removed outlier: 3.523A  pdb=" N   THR D 118 " --> pdb=" O   THR D 114 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 123 through 128
    Processing helix  chain 'D' and resid 131 through 136
    Processing helix  chain 'D' and resid 149 through 167
      removed outlier: 4.070A  pdb=" N   LEU D 156 " --> pdb=" O   TYR D 152 " (cutoff:3.500A)
      removed outlier: 3.572A  pdb=" N   LEU D 157 " --> pdb=" O   MET D 153 " (cutoff:3.500A)
      removed outlier: 4.930A  pdb=" N   LEU D 165 " --> pdb=" O   VAL D 161 " (cutoff:3.500A)
      removed outlier: 4.361A  pdb=" N   ILE D 166 " --> pdb=" O   SER D 162 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 168 through 175
      removed outlier: 3.592A  pdb=" N   THR D 172 " --> pdb=" O   SER D 168 " (cutoff:3.500A)
      removed outlier: 3.841A  pdb=" N   VAL D 173 " --> pdb=" O   THR D 169 " (cutoff:3.500A)
      removed outlier: 3.899A  pdb=" N   VAL D 174 " --> pdb=" O   LEU D 170 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 176 through 188
      removed outlier: 3.653A  pdb=" N   SER D 183 " --> pdb=" O   MET D 179 " (cutoff:3.500A)
      removed outlier: 4.368A  pdb=" N   ARG D 186 " --> pdb=" O   GLN D 182 " (cutoff:3.500A)
      removed outlier: 3.514A  pdb=" N   LEU D 188 " --> pdb=" O   LEU D 184 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 213 through 223
      removed outlier: 3.908A  pdb=" N   ILE D 217 " --> pdb=" O   PRO D 213 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 232 through 234
      No H-bonds generated for 'chain 'D' and resid 232 through 234'
    Processing helix  chain 'D' and resid 235 through 259
      removed outlier: 4.050A  pdb=" N   VAL D 240 " --> pdb=" O   ALA D 236 " (cutoff:3.500A)
      removed outlier: 4.710A  pdb=" N   TYR D 241 " --> pdb=" O   SER D 237 " (cutoff:3.500A)
      removed outlier: 4.007A  pdb=" N   ILE D 247 " --> pdb=" O   TRP D 243 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 40 through 45
      removed outlier: 5.746A  pdb=" N   ARG A  41 " --> pdb=" O   LYS A  12 " (cutoff:3.500A)
      removed outlier: 7.568A  pdb=" N   LYS A  12 " --> pdb=" O   ARG A  41 " (cutoff:3.500A)
      removed outlier: 7.338A  pdb=" N   PHE A  45 " --> pdb=" O   GLU A   8 " (cutoff:3.500A)
      removed outlier: 5.378A  pdb=" N   GLU A   8 " --> pdb=" O   PHE A  45 " (cutoff:3.500A)
      removed outlier: 6.077A  pdb=" N   ASN A   9 " --> pdb=" O   THR A  80 " (cutoff:3.500A)
      removed outlier: 5.947A  pdb=" N   THR A  80 " --> pdb=" O   ASN A   9 " (cutoff:3.500A)
      removed outlier: 3.605A  pdb=" N   SER A  78 " --> pdb=" O   THR A  11 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 164 through 167
      removed outlier: 6.270A  pdb=" N   VAL A  52 " --> pdb=" O   LYS A 212 " (cutoff:3.500A)
      removed outlier: 7.492A  pdb=" N   LEU A 214 " --> pdb=" O   VAL A  52 " (cutoff:3.500A)
      removed outlier: 6.332A  pdb=" N   GLY A  54 " --> pdb=" O   LEU A 214 " (cutoff:3.500A)
      removed outlier: 7.493A  pdb=" N   LEU A 216 " --> pdb=" O   GLY A  54 " (cutoff:3.500A)
      removed outlier: 7.061A  pdb=" N   ALA A 213 " --> pdb=" O   TYR A 224 " (cutoff:3.500A)
      removed outlier: 5.094A  pdb=" N   TYR A 224 " --> pdb=" O   ALA A 213 " (cutoff:3.500A)
      removed outlier: 4.703A  pdb=" N   TRP A 215 " --> pdb=" O   ARG A 222 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'B' and resid 40 through 45
      removed outlier: 5.746A  pdb=" N   ARG B  41 " --> pdb=" O   LYS B  12 " (cutoff:3.500A)
      removed outlier: 7.569A  pdb=" N   LYS B  12 " --> pdb=" O   ARG B  41 " (cutoff:3.500A)
      removed outlier: 7.338A  pdb=" N   PHE B  45 " --> pdb=" O   GLU B   8 " (cutoff:3.500A)
      removed outlier: 5.379A  pdb=" N   GLU B   8 " --> pdb=" O   PHE B  45 " (cutoff:3.500A)
      removed outlier: 6.075A  pdb=" N   ASN B   9 " --> pdb=" O   THR B  80 " (cutoff:3.500A)
      removed outlier: 5.946A  pdb=" N   THR B  80 " --> pdb=" O   ASN B   9 " (cutoff:3.500A)
      removed outlier: 3.605A  pdb=" N   SER B  78 " --> pdb=" O   THR B  11 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'B' and resid 164 through 167
      removed outlier: 6.271A  pdb=" N   VAL B  52 " --> pdb=" O   LYS B 212 " (cutoff:3.500A)
      removed outlier: 7.492A  pdb=" N   LEU B 214 " --> pdb=" O   VAL B  52 " (cutoff:3.500A)
      removed outlier: 6.332A  pdb=" N   GLY B  54 " --> pdb=" O   LEU B 214 " (cutoff:3.500A)
      removed outlier: 7.494A  pdb=" N   LEU B 216 " --> pdb=" O   GLY B  54 " (cutoff:3.500A)
      removed outlier: 7.061A  pdb=" N   ALA B 213 " --> pdb=" O   TYR B 224 " (cutoff:3.500A)
      removed outlier: 5.093A  pdb=" N   TYR B 224 " --> pdb=" O   ALA B 213 " (cutoff:3.500A)
      removed outlier: 4.703A  pdb=" N   TRP B 215 " --> pdb=" O   ARG B 222 " (cutoff:3.500A)

    300 hydrogen bonds defined for protein.
    852 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: 0.96

  Time building geometry restraints manager: 1.05 seconds

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

  Histogram of bond lengths:
        1.22 -     1.33: 2459
        1.33 -     1.45: 1542
        1.45 -     1.57: 4719
        1.57 -     1.69: 0
        1.69 -     1.81: 82
  Bond restraints: 8802
  Sorted by residual:
  bond pdb=" C   ILE C  68 "
       pdb=" N   PRO C  69 "
    ideal  model  delta    sigma   weight residual
    1.331  1.410 -0.079 1.20e-02 6.94e+03 4.29e+01
  bond pdb=" C   ILE D  68 "
       pdb=" N   PRO D  69 "
    ideal  model  delta    sigma   weight residual
    1.331  1.410 -0.078 1.20e-02 6.94e+03 4.28e+01
  bond pdb=" N   ARG C 186 "
       pdb=" CA  ARG C 186 "
    ideal  model  delta    sigma   weight residual
    1.458  1.483 -0.024 1.26e-02 6.30e+03 3.73e+00
  bond pdb=" N   ARG C 175 "
       pdb=" CA  ARG C 175 "
    ideal  model  delta    sigma   weight residual
    1.460  1.488 -0.028 1.48e-02 4.57e+03 3.69e+00
  bond pdb=" N   ARG D 175 "
       pdb=" CA  ARG D 175 "
    ideal  model  delta    sigma   weight residual
    1.460  1.488 -0.028 1.48e-02 4.57e+03 3.63e+00
  ... (remaining 8797 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.45: 11339
        2.45 -     4.91: 449
        4.91 -     7.36: 88
        7.36 -     9.81: 36
        9.81 -    12.27: 6
  Bond angle restraints: 11918
  Sorted by residual:
  angle pdb=" C   ASP A  48 "
        pdb=" N   LYS A  49 "
        pdb=" CA  LYS A  49 "
      ideal   model   delta    sigma   weight residual
     121.54  130.80   -9.26 1.91e+00 2.74e-01 2.35e+01
  angle pdb=" C   ASP B  48 "
        pdb=" N   LYS B  49 "
        pdb=" CA  LYS B  49 "
      ideal   model   delta    sigma   weight residual
     121.54  130.79   -9.25 1.91e+00 2.74e-01 2.35e+01
  angle pdb=" C   ALA A  47 "
        pdb=" N   ASP A  48 "
        pdb=" CA  ASP A  48 "
      ideal   model   delta    sigma   weight residual
     121.54  130.05   -8.51 1.91e+00 2.74e-01 1.99e+01
  angle pdb=" C   ALA B  47 "
        pdb=" N   ASP B  48 "
        pdb=" CA  ASP B  48 "
      ideal   model   delta    sigma   weight residual
     121.54  130.02   -8.48 1.91e+00 2.74e-01 1.97e+01
  angle pdb=" C   ALA B 170 "
        pdb=" N   LEU B 171 "
        pdb=" CA  LEU B 171 "
      ideal   model   delta    sigma   weight residual
     121.54  129.91   -8.37 1.91e+00 2.74e-01 1.92e+01
  ... (remaining 11913 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    15.32: 4674
       15.32 -    30.65: 394
       30.65 -    45.97: 110
       45.97 -    61.30: 11
       61.30 -    76.62: 3
  Dihedral angle restraints: 5192
    sinusoidal: 2090
      harmonic: 3102
  Sorted by residual:
  dihedral pdb=" CD  ARG C 175 "
           pdb=" NE  ARG C 175 "
           pdb=" CZ  ARG C 175 "
           pdb=" NH1 ARG C 175 "
      ideal   model   delta sinusoidal    sigma   weight residual
       0.00   76.62  -76.62     1      1.00e+01 1.00e-02 7.38e+01
  dihedral pdb=" CA  ALA B  87 "
           pdb=" C   ALA B  87 "
           pdb=" N   SER B  88 "
           pdb=" CA  SER B  88 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  142.60   37.40     0      5.00e+00 4.00e-02 5.60e+01
  dihedral pdb=" CA  ALA A  87 "
           pdb=" C   ALA A  87 "
           pdb=" N   SER A  88 "
           pdb=" CA  SER A  88 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  142.63   37.37     0      5.00e+00 4.00e-02 5.59e+01
  ... (remaining 5189 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.048: 759
       0.048 -    0.095: 413
       0.095 -    0.143: 126
       0.143 -    0.191: 42
       0.191 -    0.238: 10
  Chirality restraints: 1350
  Sorted by residual:
  chirality pdb=" CB  ILE C  59 "
            pdb=" CA  ILE C  59 "
            pdb=" CG1 ILE C  59 "
            pdb=" CG2 ILE C  59 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.88   -0.24 2.00e-01 2.50e+01 1.42e+00
  chirality pdb=" CB  ILE D  59 "
            pdb=" CA  ILE D  59 "
            pdb=" CG1 ILE D  59 "
            pdb=" CG2 ILE D  59 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.88   -0.24 2.00e-01 2.50e+01 1.39e+00
  chirality pdb=" CB  VAL A   5 "
            pdb=" CA  VAL A   5 "
            pdb=" CG1 VAL A   5 "
            pdb=" CG2 VAL A   5 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -2.40   -0.23 2.00e-01 2.50e+01 1.27e+00
  ... (remaining 1347 not shown)

  Planarity restraints: 1468
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CD  ARG C 175 "   -1.068 9.50e-02 1.11e+02   4.79e-01 1.38e+02
        pdb=" NE  ARG C 175 "    0.064 2.00e-02 2.50e+03
        pdb=" CZ  ARG C 175 "    0.012 2.00e-02 2.50e+03
        pdb=" NH1 ARG C 175 "   -0.008 2.00e-02 2.50e+03
        pdb=" NH2 ARG C 175 "   -0.020 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CD  ARG D 175 "    0.986 9.50e-02 1.11e+02   4.42e-01 1.18e+02
        pdb=" NE  ARG D 175 "   -0.059 2.00e-02 2.50e+03
        pdb=" CZ  ARG D 175 "   -0.011 2.00e-02 2.50e+03
        pdb=" NH1 ARG D 175 "    0.003 2.00e-02 2.50e+03
        pdb=" NH2 ARG D 175 "    0.023 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CD  ARG D 100 "   -0.920 9.50e-02 1.11e+02   4.12e-01 1.03e+02
        pdb=" NE  ARG D 100 "    0.055 2.00e-02 2.50e+03
        pdb=" CZ  ARG D 100 "    0.010 2.00e-02 2.50e+03
        pdb=" NH1 ARG D 100 "   -0.001 2.00e-02 2.50e+03
        pdb=" NH2 ARG D 100 "   -0.024 2.00e-02 2.50e+03
  ... (remaining 1465 not shown)

  Histogram of nonbonded interaction distances:
        2.26 -     2.79: 2191
        2.79 -     3.32: 8165
        3.32 -     3.84: 13283
        3.84 -     4.37: 15766
        4.37 -     4.90: 25436
  Nonbonded interactions: 64841
  Sorted by model distance:
  nonbonded pdb=" OG1 THR D 138 "
            pdb=" O   TYR D 140 "
     model   vdw
     2.260 3.040
  nonbonded pdb=" OG1 THR C 138 "
            pdb=" O   TYR C 140 "
     model   vdw
     2.261 3.040
  nonbonded pdb=" OE1 GLU D 219 "
            pdb=" OH  TYR D 231 "
     model   vdw
     2.267 3.040
  nonbonded pdb=" OE1 GLU C 219 "
            pdb=" OH  TYR C 231 "
     model   vdw
     2.267 3.040
  nonbonded pdb=" OG  SER A  21 "
            pdb=" OE1 GLU A  22 "
     model   vdw
     2.318 3.040
  ... (remaining 64836 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: 0.01
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'B'
}
ncs_group {
  reference = chain 'C'
  selection = chain 'D'
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             0.690
  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:             0.000
  Extract box with map and model:          0.080
  Check model and map are aligned:         0.010
  Set scattering table:                    0.030
  Process input model:                     8.670
  Find NCS groups from input model:        0.060
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.380
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   10.940
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8205
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.007   0.079   8802  Z= 0.326
  Angle     :  1.225  12.267  11918  Z= 0.636
  Chirality :  0.066   0.238   1350
  Planarity :  0.028   0.479   1468
  Dihedral  : 12.504  76.622   3204
  Min Nonbonded Distance : 2.260

Molprobity Statistics.
  All-atom Clashscore : 5.92
  Ramachandran Plot:
    Outliers :  0.19 %
    Allowed  : 14.33 %
    Favored  : 85.48 %
  Rotamer:
    Outliers :  0.53 %
    Allowed  :  8.19 %
    Favored  : 91.28 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.59 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -5.84 (0.18), residues: 1054
  helix: -3.92 (0.13), residues: 498
  sheet: -3.55 (0.55), residues: 46
  loop : -3.87 (0.23), residues: 510

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG B  41 
 TYR   0.027   0.003   TYR B  14 
 PHE   0.038   0.003   PHE C 264 
 TRP   0.030   0.004   TRP A 215 
 HIS   0.011   0.002   HIS C 124 

Details of bonding type rmsd
  covalent geometry    : bond        0.00679 ( 8802)
  covalent geometry    : angle       1.22506 (11918)
  hydrogen bonds       : bond        0.30135 (  300)
  hydrogen bonds       : angle       9.69624 (  852)

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

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

  2108 Ramachandran restraints generated.
    1054 Oldfield, 0 Emsley, 1054 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2108 Ramachandran restraints generated.
    1054 Oldfield, 0 Emsley, 1054 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  397 residues out of total 940 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 392
  time to evaluate  : 0.285 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   27 MET cc_start: -0.1097 (tpp) cc_final: -0.1874 (mpp)
REVERT: A   38 TYR cc_start: 0.8711 (m-80) cc_final: 0.7988 (m-80)
REVERT: A   84 ASP cc_start: 0.7514 (m-30) cc_final: 0.7120 (m-30)
REVERT: A  107 GLU cc_start: 0.8914 (mt-10) cc_final: 0.8636 (tt0)
REVERT: A  132 ASP cc_start: 0.8022 (t0) cc_final: 0.7374 (t0)
REVERT: A  186 MET cc_start: 0.9423 (mmt) cc_final: 0.9174 (mmp)
REVERT: A  192 ARG cc_start: 0.8270 (ttm170) cc_final: 0.8009 (ttm170)
REVERT: A  214 LEU cc_start: 0.9248 (mt) cc_final: 0.9023 (tt)
REVERT: B   27 MET cc_start: -0.1029 (tpp) cc_final: -0.1761 (mpp)
REVERT: B   38 TYR cc_start: 0.8483 (m-80) cc_final: 0.8008 (m-80)
REVERT: B  104 GLU cc_start: 0.8728 (mm-30) cc_final: 0.8505 (mm-30)
REVERT: B  107 GLU cc_start: 0.8904 (mt-10) cc_final: 0.8556 (tt0)
REVERT: B  132 ASP cc_start: 0.8004 (t0) cc_final: 0.7439 (t0)
REVERT: B  214 LEU cc_start: 0.9195 (mt) cc_final: 0.8875 (tt)
REVERT: B  251 GLN cc_start: 0.8215 (tp40) cc_final: 0.7753 (tp40)
REVERT: B  264 PHE cc_start: 0.7159 (t80) cc_final: 0.6926 (t80)
REVERT: C   14 ASN cc_start: 0.9211 (m-40) cc_final: 0.8948 (m-40)
REVERT: C   20 ARG cc_start: 0.8713 (tpm-80) cc_final: 0.8299 (mmm160)
REVERT: C   70 PHE cc_start: 0.6162 (t80) cc_final: 0.5839 (t80)
REVERT: C   86 GLN cc_start: 0.8696 (pp30) cc_final: 0.8480 (pp30)
REVERT: C  112 ILE cc_start: 0.9701 (tp) cc_final: 0.9489 (mt)
REVERT: C  126 MET cc_start: 0.6721 (tpp) cc_final: 0.5865 (tpp)
REVERT: C  132 PHE cc_start: 0.8268 (m-10) cc_final: 0.7778 (m-10)
REVERT: C  136 GLN cc_start: 0.8915 (mt0) cc_final: 0.8385 (mm110)
REVERT: C  142 VAL cc_start: 0.8703 (m) cc_final: 0.8079 (m)
REVERT: C  180 ILE cc_start: 0.9547 (mm) cc_final: 0.9333 (mt)
REVERT: C  259 LYS cc_start: 0.8860 (mmtt) cc_final: 0.8095 (tmtt)
REVERT: C  266 ASP cc_start: 0.8334 (p0) cc_final: 0.7262 (p0)
REVERT: D    6 THR cc_start: 0.9703 (p) cc_final: 0.9380 (p)
REVERT: D   14 ASN cc_start: 0.9254 (m-40) cc_final: 0.9048 (m-40)
REVERT: D   20 ARG cc_start: 0.8794 (tpm-80) cc_final: 0.8410 (mmm160)
REVERT: D  126 MET cc_start: 0.7038 (tpp) cc_final: 0.6180 (tpp)
REVERT: D  132 PHE cc_start: 0.8227 (m-10) cc_final: 0.7722 (m-10)
REVERT: D  136 GLN cc_start: 0.8629 (mt0) cc_final: 0.8344 (mm110)
REVERT: D  142 VAL cc_start: 0.8917 (m) cc_final: 0.8431 (m)
REVERT: D  180 ILE cc_start: 0.9592 (mm) cc_final: 0.9332 (mt)
REVERT: D  266 ASP cc_start: 0.8246 (p0) cc_final: 0.7243 (p0)
  outliers start: 5
  outliers final: 2
  residues processed: 394
  average time/residue: 0.1047
  time to fit residues: 54.0277
Evaluate side-chains
  210 residues out of total 940 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 208
  time to evaluate  : 0.375 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue  186 ARG
Chi-restraints excluded: chain D residue  186 ARG
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 104
   random chunks:
   chunk 49 optimal weight:    0.0070
   chunk 97 optimal weight:    0.7980
   chunk 53 optimal weight:    0.9990
   chunk 5 optimal weight:    1.9990
   chunk 33 optimal weight:    7.9990
   chunk 65 optimal weight:    1.9990
   chunk 62 optimal weight:    0.8980
   chunk 51 optimal weight:    1.9990
   chunk 100 optimal weight:    6.9990
   chunk 38 optimal weight:    3.9990
   chunk 61 optimal weight:    0.9980
   overall best weight:    0.7400

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

Flipped N/Q/H residues before XYZ refinement:
** A 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 187 ASN
A 251 GLN
B 187 ASN
B 251 GLN
C  32 ASN
** C  47 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 104 GLN
C 200 HIS
C 257 HIS
D  32 ASN
** D  47 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
D 257 HIS

Total number of N/Q/H flips: 10

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3404 r_free = 0.3404 target = 0.101049 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3084 r_free = 0.3084 target = 0.083085 restraints weight = 22772.785|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3126 r_free = 0.3126 target = 0.085379 restraints weight = 13492.093|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.3156 r_free = 0.3156 target = 0.086954 restraints weight = 9421.132|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 32)----------------|
| r_work = 0.3174 r_free = 0.3174 target = 0.087966 restraints weight = 7336.753|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.3187 r_free = 0.3187 target = 0.088678 restraints weight = 6208.536|
|-----------------------------------------------------------------------------|
r_work (final): 0.3181
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8205
moved from start:          0.3355

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.044   8802  Z= 0.165
  Angle     :  0.887  10.492  11918  Z= 0.453
  Chirality :  0.049   0.243   1350
  Planarity :  0.006   0.040   1468
  Dihedral  :  7.512  29.800   1172
  Min Nonbonded Distance : 2.486

Molprobity Statistics.
  All-atom Clashscore : 12.65
  Ramachandran Plot:
    Outliers :  0.19 %
    Allowed  : 14.14 %
    Favored  : 85.67 %
  Rotamer:
    Outliers :  2.55 %
    Allowed  : 16.81 %
    Favored  : 80.64 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -4.67 (0.21), residues: 1054
  helix: -2.67 (0.18), residues: 532
  sheet: -2.71 (0.68), residues: 44
  loop : -3.63 (0.25), residues: 478

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG B  41 
 TYR   0.036   0.002   TYR C 215 
 PHE   0.039   0.002   PHE D  70 
 TRP   0.027   0.002   TRP D  52 
 HIS   0.007   0.001   HIS D 257 

Details of bonding type rmsd
  covalent geometry    : bond        0.00356 ( 8802)
  covalent geometry    : angle       0.88678 (11918)
  hydrogen bonds       : bond        0.05709 (  300)
  hydrogen bonds       : angle       5.84213 (  852)

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

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

  2108 Ramachandran restraints generated.
    1054 Oldfield, 0 Emsley, 1054 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2108 Ramachandran restraints generated.
    1054 Oldfield, 0 Emsley, 1054 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  286 residues out of total 940 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 262
  time to evaluate  : 0.353 
Fit side-chains
REVERT: A   27 MET cc_start: -0.0574 (tpp) cc_final: -0.1351 (mpp)
REVERT: A   38 TYR cc_start: 0.8631 (m-80) cc_final: 0.7984 (m-80)
REVERT: A  251 GLN cc_start: 0.8272 (tp-100) cc_final: 0.7635 (tp-100)
REVERT: B   11 THR cc_start: 0.9160 (m) cc_final: 0.8611 (t)
REVERT: B   27 MET cc_start: -0.0971 (tpp) cc_final: -0.1760 (mpp)
REVERT: B   38 TYR cc_start: 0.8668 (m-80) cc_final: 0.7991 (m-80)
REVERT: B  247 LYS cc_start: 0.7850 (mtmm) cc_final: 0.7624 (mtmm)
REVERT: B  251 GLN cc_start: 0.8412 (tp-100) cc_final: 0.7730 (tp-100)
REVERT: C   38 LEU cc_start: 0.8132 (mm) cc_final: 0.7052 (mm)
REVERT: C  104 GLN cc_start: 0.8960 (mt0) cc_final: 0.8463 (mt0)
REVERT: C  105 MET cc_start: 0.8862 (mpt) cc_final: 0.8283 (mpp)
REVERT: C  136 GLN cc_start: 0.8796 (mt0) cc_final: 0.8321 (mm-40)
REVERT: C  175 ARG cc_start: 0.8169 (ttm110) cc_final: 0.7882 (ttm170)
REVERT: C  182 GLN cc_start: 0.9008 (tt0) cc_final: 0.8781 (tt0)
REVERT: C  219 GLU cc_start: 0.8550 (mm-30) cc_final: 0.8335 (mm-30)
REVERT: C  259 LYS cc_start: 0.8832 (mmtt) cc_final: 0.8179 (tmtt)
REVERT: C  266 ASP cc_start: 0.8209 (p0) cc_final: 0.7470 (p0)
REVERT: D   70 PHE cc_start: 0.6667 (t80) cc_final: 0.6241 (t80)
REVERT: D   86 GLN cc_start: 0.8727 (pp30) cc_final: 0.8437 (pp30)
REVERT: D  126 MET cc_start: 0.6869 (tpp) cc_final: 0.5889 (tpp)
REVERT: D  254 SER cc_start: 0.9625 (OUTLIER) cc_final: 0.9289 (t)
REVERT: D  259 LYS cc_start: 0.8908 (mmtt) cc_final: 0.8338 (tmtt)
REVERT: D  266 ASP cc_start: 0.8230 (p0) cc_final: 0.7364 (p0)
  outliers start: 24
  outliers final: 16
  residues processed: 275
  average time/residue: 0.0788
  time to fit residues: 30.9679
Evaluate side-chains
  226 residues out of total 940 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 209
  time to evaluate  : 0.340 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   69 ILE
Chi-restraints excluded: chain A residue   89 LEU
Chi-restraints excluded: chain A residue  108 LEU
Chi-restraints excluded: chain A residue  126 ASP
Chi-restraints excluded: chain A residue  133 ILE
Chi-restraints excluded: chain A residue  159 ASN
Chi-restraints excluded: chain B residue   69 ILE
Chi-restraints excluded: chain B residue   89 LEU
Chi-restraints excluded: chain B residue  108 LEU
Chi-restraints excluded: chain B residue  133 ILE
Chi-restraints excluded: chain B residue  159 ASN
Chi-restraints excluded: chain C residue  169 THR
Chi-restraints excluded: chain C residue  228 THR
Chi-restraints excluded: chain D residue   79 THR
Chi-restraints excluded: chain D residue  169 THR
Chi-restraints excluded: chain D residue  228 THR
Chi-restraints excluded: chain D residue  254 SER
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 104
   random chunks:
   chunk 26 optimal weight:    9.9990
   chunk 42 optimal weight:    0.0050
   chunk 73 optimal weight:    0.3980
   chunk 6 optimal weight:    3.9990
   chunk 10 optimal weight:    3.9990
   chunk 64 optimal weight:    3.9990
   chunk 66 optimal weight:    4.9990
   chunk 32 optimal weight:    1.9990
   chunk 102 optimal weight:    1.9990
   chunk 16 optimal weight:    0.1980
   chunk 33 optimal weight:    1.9990
   overall best weight:    0.9198

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

Flipped N/Q/H residues before XYZ refinement:
** B 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C  47 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 200 HIS
D  47 GLN
D 200 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3410 r_free = 0.3410 target = 0.100784 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3080 r_free = 0.3080 target = 0.082518 restraints weight = 22974.052|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3123 r_free = 0.3123 target = 0.084823 restraints weight = 13727.706|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3153 r_free = 0.3153 target = 0.086401 restraints weight = 9680.541|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 35)----------------|
| r_work = 0.3173 r_free = 0.3173 target = 0.087466 restraints weight = 7580.805|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 25)----------------|
| r_work = 0.3187 r_free = 0.3187 target = 0.088202 restraints weight = 6396.973|
|-----------------------------------------------------------------------------|
r_work (final): 0.3188
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8210
moved from start:          0.4091

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042   8802  Z= 0.146
  Angle     :  0.846   9.379  11918  Z= 0.420
  Chirality :  0.049   0.237   1350
  Planarity :  0.004   0.031   1468
  Dihedral  :  6.892  27.778   1164
  Min Nonbonded Distance : 2.504

Molprobity Statistics.
  All-atom Clashscore : 11.67
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 14.42 %
    Favored  : 85.58 %
  Rotamer:
    Outliers :  5.21 %
    Allowed  : 17.66 %
    Favored  : 77.13 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -3.91 (0.23), residues: 1054
  helix: -1.90 (0.20), residues: 516
  sheet: -2.83 (0.66), residues: 46
  loop : -3.37 (0.26), residues: 492

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG A  41 
 TYR   0.027   0.002   TYR C 215 
 PHE   0.019   0.001   PHE D  70 
 TRP   0.021   0.002   TRP C  81 
 HIS   0.004   0.001   HIS C 124 

Details of bonding type rmsd
  covalent geometry    : bond        0.00328 ( 8802)
  covalent geometry    : angle       0.84609 (11918)
  hydrogen bonds       : bond        0.04275 (  300)
  hydrogen bonds       : angle       5.34204 (  852)

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

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

  2108 Ramachandran restraints generated.
    1054 Oldfield, 0 Emsley, 1054 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2108 Ramachandran restraints generated.
    1054 Oldfield, 0 Emsley, 1054 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  278 residues out of total 940 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 49
    poor density    : 229
  time to evaluate  : 0.248 
Fit side-chains
REVERT: A   27 MET cc_start: -0.0579 (tpp) cc_final: -0.1324 (mpp)
REVERT: A   38 TYR cc_start: 0.8646 (m-80) cc_final: 0.7947 (m-80)
REVERT: A  251 GLN cc_start: 0.8399 (tp-100) cc_final: 0.7775 (tp-100)
REVERT: B    5 VAL cc_start: 0.8337 (OUTLIER) cc_final: 0.8114 (m)
REVERT: B   11 THR cc_start: 0.9173 (m) cc_final: 0.8710 (t)
REVERT: B   16 LEU cc_start: 0.8389 (tm) cc_final: 0.8101 (tm)
REVERT: B   27 MET cc_start: -0.0876 (tpp) cc_final: -0.1737 (mpp)
REVERT: B  139 GLN cc_start: 0.8351 (tp40) cc_final: 0.8135 (mm110)
REVERT: B  247 LYS cc_start: 0.7748 (mtmm) cc_final: 0.7414 (mtmm)
REVERT: B  251 GLN cc_start: 0.8485 (tp-100) cc_final: 0.7861 (tp-100)
REVERT: C  206 GLN cc_start: 0.8552 (tt0) cc_final: 0.8202 (mt0)
REVERT: C  215 TYR cc_start: 0.8937 (t80) cc_final: 0.8602 (t80)
REVERT: C  219 GLU cc_start: 0.8534 (mm-30) cc_final: 0.8049 (mm-30)
REVERT: C  225 LEU cc_start: 0.8600 (OUTLIER) cc_final: 0.8375 (pp)
REVERT: C  259 LYS cc_start: 0.8886 (mmtt) cc_final: 0.8162 (tmtt)
REVERT: C  266 ASP cc_start: 0.8189 (p0) cc_final: 0.7547 (p0)
REVERT: D   86 GLN cc_start: 0.8868 (pp30) cc_final: 0.8534 (pp30)
REVERT: D  165 LEU cc_start: 0.9367 (mp) cc_final: 0.9077 (mp)
REVERT: D  259 LYS cc_start: 0.8887 (mmtt) cc_final: 0.8268 (tmtt)
REVERT: D  266 ASP cc_start: 0.8038 (p0) cc_final: 0.7242 (p0)
  outliers start: 49
  outliers final: 27
  residues processed: 265
  average time/residue: 0.0643
  time to fit residues: 25.7378
Evaluate side-chains
  243 residues out of total 940 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 214
  time to evaluate  : 0.316 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   11 THR
Chi-restraints excluded: chain A residue   53 ILE
Chi-restraints excluded: chain A residue   89 LEU
Chi-restraints excluded: chain A residue  108 LEU
Chi-restraints excluded: chain A residue  126 ASP
Chi-restraints excluded: chain A residue  133 ILE
Chi-restraints excluded: chain A residue  159 ASN
Chi-restraints excluded: chain A residue  221 VAL
Chi-restraints excluded: chain A residue  230 ILE
Chi-restraints excluded: chain A residue  252 TYR
Chi-restraints excluded: chain B residue    5 VAL
Chi-restraints excluded: chain B residue   10 VAL
Chi-restraints excluded: chain B residue   69 ILE
Chi-restraints excluded: chain B residue   89 LEU
Chi-restraints excluded: chain B residue  101 THR
Chi-restraints excluded: chain B residue  108 LEU
Chi-restraints excluded: chain B residue  126 ASP
Chi-restraints excluded: chain B residue  133 ILE
Chi-restraints excluded: chain B residue  159 ASN
Chi-restraints excluded: chain B residue  216 LEU
Chi-restraints excluded: chain B residue  230 ILE
Chi-restraints excluded: chain C residue  169 THR
Chi-restraints excluded: chain C residue  225 LEU
Chi-restraints excluded: chain C residue  228 THR
Chi-restraints excluded: chain C residue  254 SER
Chi-restraints excluded: chain D residue   79 THR
Chi-restraints excluded: chain D residue  159 LEU
Chi-restraints excluded: chain D residue  169 THR
Chi-restraints excluded: chain D residue  228 THR
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 104
   random chunks:
   chunk 43 optimal weight:    0.6980
   chunk 10 optimal weight:    0.9990
   chunk 103 optimal weight:    3.9990
   chunk 1 optimal weight:    8.9990
   chunk 89 optimal weight:    2.9990
   chunk 3 optimal weight:    4.9990
   chunk 17 optimal weight:    0.6980
   chunk 96 optimal weight:    0.5980
   chunk 48 optimal weight:    7.9990
   chunk 36 optimal weight:    1.9990
   chunk 53 optimal weight:    0.8980
   overall best weight:    0.7782

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

Flipped N/Q/H residues before XYZ refinement:
** A 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 233 GLN
** B 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 260 GLN
C  30 ASN
** C  47 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 123 GLN
C 200 HIS
** D  47 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
D 200 HIS

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3422 r_free = 0.3422 target = 0.101495 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 29)----------------|
| r_work = 0.3091 r_free = 0.3091 target = 0.083065 restraints weight = 23394.757|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3134 r_free = 0.3134 target = 0.085375 restraints weight = 13969.571|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3163 r_free = 0.3163 target = 0.086930 restraints weight = 9833.799|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 40)----------------|
| r_work = 0.3184 r_free = 0.3184 target = 0.088008 restraints weight = 7709.233|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3196 r_free = 0.3196 target = 0.088699 restraints weight = 6516.040|
|-----------------------------------------------------------------------------|
r_work (final): 0.3196
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8202
moved from start:          0.4415

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.055   8802  Z= 0.141
  Angle     :  0.816  10.980  11918  Z= 0.405
  Chirality :  0.049   0.280   1350
  Planarity :  0.004   0.032   1468
  Dihedral  :  6.585  26.334   1164
  Min Nonbonded Distance : 2.426

Molprobity Statistics.
  All-atom Clashscore : 11.27
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 14.52 %
    Favored  : 85.48 %
  Rotamer:
    Outliers :  3.72 %
    Allowed  : 20.96 %
    Favored  : 75.32 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -3.47 (0.24), residues: 1054
  helix: -1.43 (0.21), residues: 536
  sheet: -2.83 (0.66), residues: 46
  loop : -3.32 (0.27), residues: 472

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A  41 
 TYR   0.026   0.002   TYR D 215 
 PHE   0.016   0.001   PHE C 242 
 TRP   0.016   0.002   TRP C  52 
 HIS   0.003   0.001   HIS C 124 

Details of bonding type rmsd
  covalent geometry    : bond        0.00317 ( 8802)
  covalent geometry    : angle       0.81615 (11918)
  hydrogen bonds       : bond        0.03748 (  300)
  hydrogen bonds       : angle       5.22521 (  852)

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

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

  2108 Ramachandran restraints generated.
    1054 Oldfield, 0 Emsley, 1054 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2108 Ramachandran restraints generated.
    1054 Oldfield, 0 Emsley, 1054 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  270 residues out of total 940 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 235
  time to evaluate  : 0.331 
Fit side-chains
REVERT: A   27 MET cc_start: -0.0804 (tpp) cc_final: -0.1665 (mpp)
REVERT: A   38 TYR cc_start: 0.8686 (m-80) cc_final: 0.7934 (m-80)
REVERT: A  152 LEU cc_start: 0.9778 (tp) cc_final: 0.9568 (tt)
REVERT: A  251 GLN cc_start: 0.8370 (tp-100) cc_final: 0.7773 (tp-100)
REVERT: B    5 VAL cc_start: 0.8195 (OUTLIER) cc_final: 0.7939 (m)
REVERT: B   27 MET cc_start: -0.0828 (tpp) cc_final: -0.1690 (mpp)
REVERT: B  139 GLN cc_start: 0.8445 (tp40) cc_final: 0.8215 (mm110)
REVERT: B  247 LYS cc_start: 0.7735 (mtmm) cc_final: 0.7484 (mtmm)
REVERT: B  251 GLN cc_start: 0.8479 (tp-100) cc_final: 0.7857 (tp-100)
REVERT: C  206 GLN cc_start: 0.8615 (tt0) cc_final: 0.8010 (mt0)
REVERT: C  215 TYR cc_start: 0.8943 (t80) cc_final: 0.8407 (t80)
REVERT: C  219 GLU cc_start: 0.8685 (mm-30) cc_final: 0.8239 (mm-30)
REVERT: C  225 LEU cc_start: 0.8390 (OUTLIER) cc_final: 0.8159 (pp)
REVERT: C  259 LYS cc_start: 0.8886 (mmtt) cc_final: 0.8260 (tmtt)
REVERT: C  266 ASP cc_start: 0.8131 (p0) cc_final: 0.7584 (p0)
REVERT: D   86 GLN cc_start: 0.8843 (pp30) cc_final: 0.8515 (pp30)
REVERT: D  136 GLN cc_start: 0.8619 (mt0) cc_final: 0.8291 (mm110)
REVERT: D  259 LYS cc_start: 0.8855 (mmtt) cc_final: 0.8222 (tmtt)
REVERT: D  266 ASP cc_start: 0.7876 (p0) cc_final: 0.7163 (p0)
  outliers start: 35
  outliers final: 23
  residues processed: 260
  average time/residue: 0.0690
  time to fit residues: 26.7893
Evaluate side-chains
  241 residues out of total 940 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 216
  time to evaluate  : 0.340 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   11 THR
Chi-restraints excluded: chain A residue  101 THR
Chi-restraints excluded: chain A residue  108 LEU
Chi-restraints excluded: chain A residue  126 ASP
Chi-restraints excluded: chain A residue  133 ILE
Chi-restraints excluded: chain A residue  159 ASN
Chi-restraints excluded: chain A residue  221 VAL
Chi-restraints excluded: chain A residue  230 ILE
Chi-restraints excluded: chain A residue  252 TYR
Chi-restraints excluded: chain B residue    5 VAL
Chi-restraints excluded: chain B residue   69 ILE
Chi-restraints excluded: chain B residue  101 THR
Chi-restraints excluded: chain B residue  108 LEU
Chi-restraints excluded: chain B residue  126 ASP
Chi-restraints excluded: chain B residue  133 ILE
Chi-restraints excluded: chain B residue  159 ASN
Chi-restraints excluded: chain B residue  230 ILE
Chi-restraints excluded: chain C residue  114 THR
Chi-restraints excluded: chain C residue  169 THR
Chi-restraints excluded: chain C residue  225 LEU
Chi-restraints excluded: chain D residue   38 LEU
Chi-restraints excluded: chain D residue   48 ILE
Chi-restraints excluded: chain D residue   79 THR
Chi-restraints excluded: chain D residue  169 THR
Chi-restraints excluded: chain D residue  228 THR
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 104
   random chunks:
   chunk 16 optimal weight:    0.0070
   chunk 53 optimal weight:    0.7980
   chunk 45 optimal weight:    2.9990
   chunk 5 optimal weight:    1.9990
   chunk 12 optimal weight:    0.7980
   chunk 2 optimal weight:    2.9990
   chunk 18 optimal weight:    2.9990
   chunk 89 optimal weight:    4.9990
   chunk 65 optimal weight:    0.9980
   chunk 98 optimal weight:    2.9990
   chunk 72 optimal weight:    0.9990
   overall best weight:    0.7200

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

Flipped N/Q/H residues before XYZ refinement:
** A 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 260 GLN
** B 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C  47 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 200 HIS
D 200 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3435 r_free = 0.3435 target = 0.102322 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3108 r_free = 0.3108 target = 0.083833 restraints weight = 22996.907|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3149 r_free = 0.3149 target = 0.086116 restraints weight = 13793.763|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3178 r_free = 0.3178 target = 0.087722 restraints weight = 9739.246|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3196 r_free = 0.3196 target = 0.088707 restraints weight = 7645.828|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 38)----------------|
| r_work = 0.3212 r_free = 0.3212 target = 0.089541 restraints weight = 6527.261|
|-----------------------------------------------------------------------------|
r_work (final): 0.3211
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8192
moved from start:          0.4740

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   8802  Z= 0.135
  Angle     :  0.819  10.480  11918  Z= 0.403
  Chirality :  0.048   0.228   1350
  Planarity :  0.004   0.032   1468
  Dihedral  :  6.433  32.379   1164
  Min Nonbonded Distance : 2.499

Molprobity Statistics.
  All-atom Clashscore : 11.44
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 14.33 %
    Favored  : 85.67 %
  Rotamer:
    Outliers :  3.51 %
    Allowed  : 22.45 %
    Favored  : 74.04 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.10 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -3.08 (0.25), residues: 1054
  helix: -1.07 (0.22), residues: 526
  sheet: -2.65 (0.65), residues: 46
  loop : -3.16 (0.27), residues: 482

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG C 175 
 TYR   0.022   0.002   TYR D 215 
 PHE   0.015   0.001   PHE C 163 
 TRP   0.014   0.002   TRP C  81 
 HIS   0.005   0.001   HIS D 235 

Details of bonding type rmsd
  covalent geometry    : bond        0.00303 ( 8802)
  covalent geometry    : angle       0.81878 (11918)
  hydrogen bonds       : bond        0.03524 (  300)
  hydrogen bonds       : angle       5.15678 (  852)

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

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

  2108 Ramachandran restraints generated.
    1054 Oldfield, 0 Emsley, 1054 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2108 Ramachandran restraints generated.
    1054 Oldfield, 0 Emsley, 1054 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  262 residues out of total 940 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 229
  time to evaluate  : 0.336 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   27 MET cc_start: -0.0751 (tpp) cc_final: -0.1631 (mpp)
REVERT: A   38 TYR cc_start: 0.8718 (m-80) cc_final: 0.7949 (m-80)
REVERT: A   86 GLN cc_start: 0.6521 (pm20) cc_final: 0.6233 (pm20)
REVERT: A  152 LEU cc_start: 0.9771 (tp) cc_final: 0.9564 (tt)
REVERT: A  251 GLN cc_start: 0.8283 (tp-100) cc_final: 0.7680 (tp-100)
REVERT: B    5 VAL cc_start: 0.8092 (OUTLIER) cc_final: 0.7872 (m)
REVERT: B   27 MET cc_start: -0.1338 (tpp) cc_final: -0.2293 (mpp)
REVERT: B  139 GLN cc_start: 0.8502 (tp40) cc_final: 0.8293 (mm-40)
REVERT: B  251 GLN cc_start: 0.8445 (tp-100) cc_final: 0.7910 (tp-100)
REVERT: C   30 ASN cc_start: 0.6509 (t0) cc_final: 0.6129 (t0)
REVERT: C  189 LEU cc_start: 0.9214 (OUTLIER) cc_final: 0.8970 (tp)
REVERT: C  206 GLN cc_start: 0.8591 (tt0) cc_final: 0.8024 (mt0)
REVERT: C  259 LYS cc_start: 0.8876 (mmtt) cc_final: 0.8266 (tmtt)
REVERT: C  266 ASP cc_start: 0.7976 (p0) cc_final: 0.7448 (p0)
REVERT: D   47 GLN cc_start: 0.9379 (tm-30) cc_final: 0.8772 (tm-30)
REVERT: D   86 GLN cc_start: 0.8847 (pp30) cc_final: 0.8528 (pp30)
REVERT: D  259 LYS cc_start: 0.8840 (mmtt) cc_final: 0.8231 (tmtt)
REVERT: D  266 ASP cc_start: 0.7878 (p0) cc_final: 0.7226 (p0)
  outliers start: 33
  outliers final: 22
  residues processed: 251
  average time/residue: 0.0709
  time to fit residues: 26.4645
Evaluate side-chains
  240 residues out of total 940 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 216
  time to evaluate  : 0.249 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   11 THR
Chi-restraints excluded: chain A residue  101 THR
Chi-restraints excluded: chain A residue  108 LEU
Chi-restraints excluded: chain A residue  126 ASP
Chi-restraints excluded: chain A residue  133 ILE
Chi-restraints excluded: chain A residue  159 ASN
Chi-restraints excluded: chain A residue  221 VAL
Chi-restraints excluded: chain A residue  230 ILE
Chi-restraints excluded: chain A residue  252 TYR
Chi-restraints excluded: chain B residue    5 VAL
Chi-restraints excluded: chain B residue   10 VAL
Chi-restraints excluded: chain B residue  101 THR
Chi-restraints excluded: chain B residue  108 LEU
Chi-restraints excluded: chain B residue  126 ASP
Chi-restraints excluded: chain B residue  133 ILE
Chi-restraints excluded: chain B residue  159 ASN
Chi-restraints excluded: chain B residue  230 ILE
Chi-restraints excluded: chain B residue  252 TYR
Chi-restraints excluded: chain C residue  114 THR
Chi-restraints excluded: chain C residue  169 THR
Chi-restraints excluded: chain C residue  189 LEU
Chi-restraints excluded: chain D residue   38 LEU
Chi-restraints excluded: chain D residue   79 THR
Chi-restraints excluded: chain D residue  169 THR
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 104
   random chunks:
   chunk 73 optimal weight:    0.9980
   chunk 62 optimal weight:    5.9990
   chunk 63 optimal weight:    0.6980
   chunk 27 optimal weight:    5.9990
   chunk 38 optimal weight:    6.9990
   chunk 35 optimal weight:    5.9990
   chunk 97 optimal weight:    4.9990
   chunk 57 optimal weight:    0.1980
   chunk 87 optimal weight:    0.9990
   chunk 68 optimal weight:    2.9990
   chunk 29 optimal weight:    1.9990
   overall best weight:    0.9784

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

Flipped N/Q/H residues before XYZ refinement:
** A 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 260 GLN
** B 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C  47 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 200 HIS
D 200 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3424 r_free = 0.3424 target = 0.101850 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3096 r_free = 0.3096 target = 0.083368 restraints weight = 23088.067|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3138 r_free = 0.3138 target = 0.085661 restraints weight = 13802.746|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3168 r_free = 0.3168 target = 0.087269 restraints weight = 9713.411|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3186 r_free = 0.3186 target = 0.088264 restraints weight = 7605.966|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.3199 r_free = 0.3199 target = 0.088995 restraints weight = 6468.184|
|-----------------------------------------------------------------------------|
r_work (final): 0.3196
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8199
moved from start:          0.4911

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.046   8802  Z= 0.136
  Angle     :  0.809  12.139  11918  Z= 0.399
  Chirality :  0.049   0.314   1350
  Planarity :  0.004   0.032   1468
  Dihedral  :  6.241  30.186   1164
  Min Nonbonded Distance : 2.499

Molprobity Statistics.
  All-atom Clashscore : 11.96
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 14.90 %
    Favored  : 85.10 %
  Rotamer:
    Outliers :  4.36 %
    Allowed  : 22.34 %
    Favored  : 73.30 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.10 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.84 (0.25), residues: 1054
  helix: -0.89 (0.22), residues: 536
  sheet: -2.26 (0.64), residues: 46
  loop : -3.09 (0.28), residues: 472

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B  41 
 TYR   0.018   0.002   TYR C 151 
 PHE   0.015   0.001   PHE C 242 
 TRP   0.015   0.002   TRP C  81 
 HIS   0.003   0.001   HIS D 124 

Details of bonding type rmsd
  covalent geometry    : bond        0.00309 ( 8802)
  covalent geometry    : angle       0.80935 (11918)
  hydrogen bonds       : bond        0.03428 (  300)
  hydrogen bonds       : angle       5.07505 (  852)

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

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

  2108 Ramachandran restraints generated.
    1054 Oldfield, 0 Emsley, 1054 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2108 Ramachandran restraints generated.
    1054 Oldfield, 0 Emsley, 1054 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  263 residues out of total 940 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 41
    poor density    : 222
  time to evaluate  : 0.305 
Fit side-chains
REVERT: A    9 ASN cc_start: 0.9087 (m-40) cc_final: 0.8372 (t0)
REVERT: A   27 MET cc_start: -0.0925 (tpp) cc_final: -0.1939 (mpp)
REVERT: A   38 TYR cc_start: 0.8839 (m-80) cc_final: 0.8081 (m-80)
REVERT: A   86 GLN cc_start: 0.6689 (pm20) cc_final: 0.6420 (pm20)
REVERT: A  152 LEU cc_start: 0.9770 (tp) cc_final: 0.9561 (tt)
REVERT: A  251 GLN cc_start: 0.8232 (tp-100) cc_final: 0.7715 (tp-100)
REVERT: B   27 MET cc_start: -0.1364 (tpp) cc_final: -0.2407 (mpp)
REVERT: B   86 GLN cc_start: 0.6549 (pm20) cc_final: 0.6292 (pm20)
REVERT: B  251 GLN cc_start: 0.8477 (tp-100) cc_final: 0.7962 (tp-100)
REVERT: B  264 PHE cc_start: 0.7159 (t80) cc_final: 0.6824 (m-80)
REVERT: C   38 LEU cc_start: 0.7859 (mm) cc_final: 0.7593 (mm)
REVERT: C  126 MET cc_start: 0.7945 (ptm) cc_final: 0.7407 (ptm)
REVERT: C  189 LEU cc_start: 0.9248 (OUTLIER) cc_final: 0.8996 (tp)
REVERT: C  206 GLN cc_start: 0.8625 (tt0) cc_final: 0.8118 (mt0)
REVERT: C  259 LYS cc_start: 0.8883 (mmtt) cc_final: 0.8270 (tmtt)
REVERT: C  266 ASP cc_start: 0.7945 (p0) cc_final: 0.7426 (p0)
REVERT: D   40 GLU cc_start: 0.7685 (pm20) cc_final: 0.7483 (pm20)
REVERT: D   86 GLN cc_start: 0.8861 (pp30) cc_final: 0.8526 (pp30)
REVERT: D  206 GLN cc_start: 0.8629 (tt0) cc_final: 0.8269 (tm-30)
REVERT: D  219 GLU cc_start: 0.8755 (mm-30) cc_final: 0.8418 (mm-30)
REVERT: D  259 LYS cc_start: 0.8841 (mmtt) cc_final: 0.8306 (tmtt)
REVERT: D  266 ASP cc_start: 0.7826 (p0) cc_final: 0.7172 (p0)
  outliers start: 41
  outliers final: 26
  residues processed: 247
  average time/residue: 0.0677
  time to fit residues: 25.1249
Evaluate side-chains
  240 residues out of total 940 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 213
  time to evaluate  : 0.223 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   11 THR
Chi-restraints excluded: chain A residue  101 THR
Chi-restraints excluded: chain A residue  108 LEU
Chi-restraints excluded: chain A residue  126 ASP
Chi-restraints excluded: chain A residue  133 ILE
Chi-restraints excluded: chain A residue  159 ASN
Chi-restraints excluded: chain A residue  221 VAL
Chi-restraints excluded: chain A residue  252 TYR
Chi-restraints excluded: chain B residue   10 VAL
Chi-restraints excluded: chain B residue   16 LEU
Chi-restraints excluded: chain B residue  101 THR
Chi-restraints excluded: chain B residue  108 LEU
Chi-restraints excluded: chain B residue  126 ASP
Chi-restraints excluded: chain B residue  133 ILE
Chi-restraints excluded: chain B residue  159 ASN
Chi-restraints excluded: chain B residue  230 ILE
Chi-restraints excluded: chain B residue  252 TYR
Chi-restraints excluded: chain C residue   79 THR
Chi-restraints excluded: chain C residue  114 THR
Chi-restraints excluded: chain C residue  169 THR
Chi-restraints excluded: chain C residue  189 LEU
Chi-restraints excluded: chain C residue  192 THR
Chi-restraints excluded: chain D residue    8 LEU
Chi-restraints excluded: chain D residue   38 LEU
Chi-restraints excluded: chain D residue   79 THR
Chi-restraints excluded: chain D residue  169 THR
Chi-restraints excluded: chain D residue  192 THR
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 104
   random chunks:
   chunk 42 optimal weight:    1.9990
   chunk 90 optimal weight:    4.9990
   chunk 70 optimal weight:    2.9990
   chunk 96 optimal weight:    1.9990
   chunk 67 optimal weight:    0.8980
   chunk 60 optimal weight:    2.9990
   chunk 28 optimal weight:    0.0170
   chunk 87 optimal weight:    0.9990
   chunk 27 optimal weight:    4.9990
   chunk 73 optimal weight:    0.3980
   chunk 80 optimal weight:    0.9990
   overall best weight:    0.6622

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

Flipped N/Q/H residues before XYZ refinement:
** A 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C  47 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 200 HIS
D 200 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3447 r_free = 0.3447 target = 0.103132 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3121 r_free = 0.3121 target = 0.084751 restraints weight = 23063.119|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3164 r_free = 0.3164 target = 0.087066 restraints weight = 13762.026|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3190 r_free = 0.3190 target = 0.088535 restraints weight = 9667.117|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 37)----------------|
| r_work = 0.3213 r_free = 0.3213 target = 0.089728 restraints weight = 7636.022|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.3224 r_free = 0.3224 target = 0.090361 restraints weight = 6413.942|
|-----------------------------------------------------------------------------|
r_work (final): 0.3223
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8176
moved from start:          0.5144

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.046   8802  Z= 0.131
  Angle     :  0.817  11.426  11918  Z= 0.401
  Chirality :  0.048   0.227   1350
  Planarity :  0.004   0.030   1468
  Dihedral  :  6.132  28.266   1164
  Min Nonbonded Distance : 2.502

Molprobity Statistics.
  All-atom Clashscore : 11.55
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 14.61 %
    Favored  : 85.39 %
  Rotamer:
    Outliers :  3.51 %
    Allowed  : 23.09 %
    Favored  : 73.40 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.64 (0.26), residues: 1054
  helix: -0.67 (0.23), residues: 522
  sheet: -1.78 (0.68), residues: 46
  loop : -3.05 (0.28), residues: 486

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG B 250 
 TYR   0.016   0.002   TYR B 234 
 PHE   0.015   0.001   PHE C 242 
 TRP   0.014   0.002   TRP C  81 
 HIS   0.004   0.001   HIS D 124 

Details of bonding type rmsd
  covalent geometry    : bond        0.00295 ( 8802)
  covalent geometry    : angle       0.81741 (11918)
  hydrogen bonds       : bond        0.03313 (  300)
  hydrogen bonds       : angle       5.05306 (  852)

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

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

  2108 Ramachandran restraints generated.
    1054 Oldfield, 0 Emsley, 1054 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2108 Ramachandran restraints generated.
    1054 Oldfield, 0 Emsley, 1054 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  273 residues out of total 940 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 240
  time to evaluate  : 0.288 
Fit side-chains
REVERT: A    9 ASN cc_start: 0.9091 (m-40) cc_final: 0.8391 (t0)
REVERT: A   27 MET cc_start: -0.0888 (tpp) cc_final: -0.1941 (mpp)
REVERT: A   38 TYR cc_start: 0.8848 (m-80) cc_final: 0.8558 (m-80)
REVERT: A   86 GLN cc_start: 0.6399 (pm20) cc_final: 0.6155 (pm20)
REVERT: A  152 LEU cc_start: 0.9766 (tp) cc_final: 0.9564 (tt)
REVERT: A  251 GLN cc_start: 0.8236 (tp-100) cc_final: 0.7751 (tp-100)
REVERT: A  257 MET cc_start: 0.8519 (mmt) cc_final: 0.8141 (mtt)
REVERT: B   27 MET cc_start: -0.1305 (tpp) cc_final: -0.2402 (mpp)
REVERT: B   86 GLN cc_start: 0.6510 (pm20) cc_final: 0.6217 (pm20)
REVERT: B  152 LEU cc_start: 0.9772 (tp) cc_final: 0.9571 (tt)
REVERT: B  251 GLN cc_start: 0.8432 (tp-100) cc_final: 0.7912 (tp-100)
REVERT: C  189 LEU cc_start: 0.9190 (OUTLIER) cc_final: 0.8983 (tp)
REVERT: C  206 GLN cc_start: 0.8583 (tt0) cc_final: 0.8107 (mt0)
REVERT: C  215 TYR cc_start: 0.8880 (t80) cc_final: 0.8569 (t80)
REVERT: C  259 LYS cc_start: 0.8872 (mmtt) cc_final: 0.8254 (tmtt)
REVERT: C  266 ASP cc_start: 0.7961 (p0) cc_final: 0.7498 (p0)
REVERT: D   47 GLN cc_start: 0.9481 (tm-30) cc_final: 0.9193 (tm-30)
REVERT: D   86 GLN cc_start: 0.8841 (pp30) cc_final: 0.8154 (pp30)
REVERT: D  206 GLN cc_start: 0.8544 (tt0) cc_final: 0.8212 (tm-30)
REVERT: D  219 GLU cc_start: 0.8802 (mm-30) cc_final: 0.8513 (mm-30)
REVERT: D  259 LYS cc_start: 0.8906 (mmtt) cc_final: 0.8275 (tmtt)
REVERT: D  266 ASP cc_start: 0.7719 (p0) cc_final: 0.6938 (p0)
  outliers start: 33
  outliers final: 25
  residues processed: 261
  average time/residue: 0.0659
  time to fit residues: 25.8884
Evaluate side-chains
  244 residues out of total 940 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 218
  time to evaluate  : 0.331 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   11 THR
Chi-restraints excluded: chain A residue  101 THR
Chi-restraints excluded: chain A residue  108 LEU
Chi-restraints excluded: chain A residue  126 ASP
Chi-restraints excluded: chain A residue  133 ILE
Chi-restraints excluded: chain A residue  159 ASN
Chi-restraints excluded: chain A residue  221 VAL
Chi-restraints excluded: chain A residue  252 TYR
Chi-restraints excluded: chain B residue   10 VAL
Chi-restraints excluded: chain B residue   89 LEU
Chi-restraints excluded: chain B residue  108 LEU
Chi-restraints excluded: chain B residue  126 ASP
Chi-restraints excluded: chain B residue  133 ILE
Chi-restraints excluded: chain B residue  159 ASN
Chi-restraints excluded: chain B residue  230 ILE
Chi-restraints excluded: chain B residue  252 TYR
Chi-restraints excluded: chain C residue  114 THR
Chi-restraints excluded: chain C residue  169 THR
Chi-restraints excluded: chain C residue  189 LEU
Chi-restraints excluded: chain C residue  192 THR
Chi-restraints excluded: chain C residue  254 SER
Chi-restraints excluded: chain D residue    8 LEU
Chi-restraints excluded: chain D residue   38 LEU
Chi-restraints excluded: chain D residue  111 VAL
Chi-restraints excluded: chain D residue  169 THR
Chi-restraints excluded: chain D residue  192 THR
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 104
   random chunks:
   chunk 24 optimal weight:    1.9990
   chunk 85 optimal weight:    5.9990
   chunk 49 optimal weight:    0.8980
   chunk 16 optimal weight:    0.5980
   chunk 73 optimal weight:    6.9990
   chunk 76 optimal weight:    0.8980
   chunk 19 optimal weight:    2.9990
   chunk 51 optimal weight:    9.9990
   chunk 69 optimal weight:    5.9990
   chunk 72 optimal weight:    0.8980
   chunk 50 optimal weight:    7.9990
   overall best weight:    1.0582

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

Flipped N/Q/H residues before XYZ refinement:
** A 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 260 GLN
** C  47 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 124 HIS
C 200 HIS
D 200 HIS

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3427 r_free = 0.3427 target = 0.102030 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3107 r_free = 0.3107 target = 0.083794 restraints weight = 22700.128|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3149 r_free = 0.3149 target = 0.086089 restraints weight = 13557.260|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 22)----------------|
| r_work = 0.3177 r_free = 0.3177 target = 0.087646 restraints weight = 9535.036|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.3198 r_free = 0.3198 target = 0.088795 restraints weight = 7447.304|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 31)----------------|
| r_work = 0.3210 r_free = 0.3210 target = 0.089497 restraints weight = 6239.277|
|-----------------------------------------------------------------------------|
r_work (final): 0.3208
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8189
moved from start:          0.5247

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   8802  Z= 0.144
  Angle     :  0.840  14.635  11918  Z= 0.409
  Chirality :  0.048   0.234   1350
  Planarity :  0.004   0.029   1468
  Dihedral  :  6.065  28.277   1164
  Min Nonbonded Distance : 2.481

Molprobity Statistics.
  All-atom Clashscore : 12.30
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 14.42 %
    Favored  : 85.58 %
  Rotamer:
    Outliers :  3.51 %
    Allowed  : 24.57 %
    Favored  : 71.91 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.62 (0.26), residues: 1054
  helix: -0.62 (0.22), residues: 530
  sheet: -1.33 (0.74), residues: 46
  loop : -3.16 (0.28), residues: 478

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG B 250 
 TYR   0.015   0.002   TYR A  14 
 PHE   0.020   0.001   PHE B 264 
 TRP   0.016   0.002   TRP C  81 
 HIS   0.004   0.001   HIS C 124 

Details of bonding type rmsd
  covalent geometry    : bond        0.00324 ( 8802)
  covalent geometry    : angle       0.84001 (11918)
  hydrogen bonds       : bond        0.03267 (  300)
  hydrogen bonds       : angle       4.98484 (  852)

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

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

  2108 Ramachandran restraints generated.
    1054 Oldfield, 0 Emsley, 1054 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2108 Ramachandran restraints generated.
    1054 Oldfield, 0 Emsley, 1054 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  251 residues out of total 940 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 218
  time to evaluate  : 0.292 
Fit side-chains
   revert: symmetry clash
REVERT: A    9 ASN cc_start: 0.9132 (m-40) cc_final: 0.8425 (t0)
REVERT: A   27 MET cc_start: -0.0866 (tpp) cc_final: -0.1953 (mpp)
REVERT: A   38 TYR cc_start: 0.8960 (m-80) cc_final: 0.8551 (m-80)
REVERT: A   86 GLN cc_start: 0.6354 (pm20) cc_final: 0.6002 (pm20)
REVERT: A  251 GLN cc_start: 0.8207 (tp-100) cc_final: 0.7835 (tp-100)
REVERT: A  257 MET cc_start: 0.8514 (mmt) cc_final: 0.8152 (mtt)
REVERT: B   27 MET cc_start: -0.0980 (tpp) cc_final: -0.2197 (mpp)
REVERT: B  251 GLN cc_start: 0.8440 (tp-100) cc_final: 0.8046 (tp-100)
REVERT: C   27 LYS cc_start: 0.8906 (tttp) cc_final: 0.8689 (tttm)
REVERT: C   30 ASN cc_start: 0.6300 (t0) cc_final: 0.6017 (t0)
REVERT: C  189 LEU cc_start: 0.9172 (OUTLIER) cc_final: 0.8945 (tp)
REVERT: C  206 GLN cc_start: 0.8567 (tt0) cc_final: 0.8099 (mt0)
REVERT: C  266 ASP cc_start: 0.7872 (p0) cc_final: 0.7326 (p0)
REVERT: D   47 GLN cc_start: 0.9541 (tm-30) cc_final: 0.9283 (tm-30)
REVERT: D   86 GLN cc_start: 0.8802 (pp30) cc_final: 0.8459 (pp30)
REVERT: D  206 GLN cc_start: 0.8626 (tt0) cc_final: 0.8351 (tm-30)
REVERT: D  219 GLU cc_start: 0.8716 (mm-30) cc_final: 0.8513 (mm-30)
REVERT: D  259 LYS cc_start: 0.8924 (mmtt) cc_final: 0.8295 (tmtt)
REVERT: D  266 ASP cc_start: 0.7758 (p0) cc_final: 0.6996 (p0)
  outliers start: 33
  outliers final: 26
  residues processed: 241
  average time/residue: 0.0639
  time to fit residues: 23.4142
Evaluate side-chains
  237 residues out of total 940 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 210
  time to evaluate  : 0.258 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   11 THR
Chi-restraints excluded: chain A residue   89 LEU
Chi-restraints excluded: chain A residue  101 THR
Chi-restraints excluded: chain A residue  108 LEU
Chi-restraints excluded: chain A residue  126 ASP
Chi-restraints excluded: chain A residue  159 ASN
Chi-restraints excluded: chain A residue  221 VAL
Chi-restraints excluded: chain A residue  252 TYR
Chi-restraints excluded: chain B residue   10 VAL
Chi-restraints excluded: chain B residue   89 LEU
Chi-restraints excluded: chain B residue  101 THR
Chi-restraints excluded: chain B residue  108 LEU
Chi-restraints excluded: chain B residue  126 ASP
Chi-restraints excluded: chain B residue  133 ILE
Chi-restraints excluded: chain B residue  159 ASN
Chi-restraints excluded: chain B residue  230 ILE
Chi-restraints excluded: chain B residue  252 TYR
Chi-restraints excluded: chain C residue  114 THR
Chi-restraints excluded: chain C residue  169 THR
Chi-restraints excluded: chain C residue  189 LEU
Chi-restraints excluded: chain C residue  192 THR
Chi-restraints excluded: chain C residue  254 SER
Chi-restraints excluded: chain D residue    8 LEU
Chi-restraints excluded: chain D residue   38 LEU
Chi-restraints excluded: chain D residue  111 VAL
Chi-restraints excluded: chain D residue  169 THR
Chi-restraints excluded: chain D residue  192 THR
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 104
   random chunks:
   chunk 2 optimal weight:    0.0270
   chunk 6 optimal weight:    0.6980
   chunk 13 optimal weight:    3.9990
   chunk 21 optimal weight:    0.9980
   chunk 36 optimal weight:    0.8980
   chunk 41 optimal weight:    0.9990
   chunk 11 optimal weight:    2.9990
   chunk 16 optimal weight:    6.9990
   chunk 1 optimal weight:    6.9990
   chunk 12 optimal weight:    0.0170
   chunk 58 optimal weight:    0.0980
   overall best weight:    0.3476

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

Flipped N/Q/H residues before XYZ refinement:
** A 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 233 GLN
** C  47 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 200 HIS
D 200 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3472 r_free = 0.3472 target = 0.104750 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3151 r_free = 0.3151 target = 0.086285 restraints weight = 22701.292|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 21)----------------|
| r_work = 0.3195 r_free = 0.3195 target = 0.088636 restraints weight = 13699.251|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3224 r_free = 0.3224 target = 0.090244 restraints weight = 9632.146|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 31)----------------|
| r_work = 0.3242 r_free = 0.3242 target = 0.091265 restraints weight = 7516.350|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 41)----------------|
| r_work = 0.3257 r_free = 0.3257 target = 0.092122 restraints weight = 6354.344|
|-----------------------------------------------------------------------------|
r_work (final): 0.3255
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8144
moved from start:          0.5483

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.052   8802  Z= 0.131
  Angle     :  0.862  14.534  11918  Z= 0.411
  Chirality :  0.048   0.203   1350
  Planarity :  0.004   0.026   1468
  Dihedral  :  5.987  27.511   1164
  Min Nonbonded Distance : 2.395

Molprobity Statistics.
  All-atom Clashscore : 11.27
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 14.52 %
    Favored  : 85.48 %
  Rotamer:
    Outliers :  3.19 %
    Allowed  : 25.74 %
    Favored  : 71.06 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.53 (0.26), residues: 1054
  helix: -0.57 (0.23), residues: 530
  sheet: -0.96 (0.78), residues: 46
  loop : -3.14 (0.28), residues: 478

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG B 250 
 TYR   0.023   0.001   TYR D 151 
 PHE   0.015   0.001   PHE C 242 
 TRP   0.016   0.001   TRP C  81 
 HIS   0.004   0.001   HIS C 124 

Details of bonding type rmsd
  covalent geometry    : bond        0.00294 ( 8802)
  covalent geometry    : angle       0.86197 (11918)
  hydrogen bonds       : bond        0.03281 (  300)
  hydrogen bonds       : angle       5.03655 (  852)

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

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

  2108 Ramachandran restraints generated.
    1054 Oldfield, 0 Emsley, 1054 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2108 Ramachandran restraints generated.
    1054 Oldfield, 0 Emsley, 1054 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  267 residues out of total 940 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 237
  time to evaluate  : 0.279 
Fit side-chains
REVERT: A    9 ASN cc_start: 0.9085 (m-40) cc_final: 0.8454 (t0)
REVERT: A   27 MET cc_start: -0.0876 (tpp) cc_final: -0.2005 (mpp)
REVERT: A   38 TYR cc_start: 0.8896 (m-80) cc_final: 0.8507 (m-80)
REVERT: A  251 GLN cc_start: 0.8147 (tp-100) cc_final: 0.7790 (tp-100)
REVERT: A  257 MET cc_start: 0.8451 (mmt) cc_final: 0.8068 (mtt)
REVERT: B   27 MET cc_start: -0.0914 (tpp) cc_final: -0.2163 (mpp)
REVERT: B  251 GLN cc_start: 0.8380 (tp-100) cc_final: 0.8000 (tp-100)
REVERT: C   27 LYS cc_start: 0.8847 (tttp) cc_final: 0.8540 (tttm)
REVERT: C   30 ASN cc_start: 0.6734 (t0) cc_final: 0.6339 (t0)
REVERT: C   52 TRP cc_start: 0.9338 (t60) cc_final: 0.9008 (t60)
REVERT: C  206 GLN cc_start: 0.8498 (tt0) cc_final: 0.8045 (mt0)
REVERT: C  266 ASP cc_start: 0.7678 (p0) cc_final: 0.7075 (p0)
REVERT: D   47 GLN cc_start: 0.9536 (tm-30) cc_final: 0.9292 (tm-30)
REVERT: D   53 PHE cc_start: 0.7855 (t80) cc_final: 0.7308 (t80)
REVERT: D  206 GLN cc_start: 0.8581 (tt0) cc_final: 0.8292 (tm-30)
REVERT: D  259 LYS cc_start: 0.8907 (mmtt) cc_final: 0.8266 (tmtt)
REVERT: D  266 ASP cc_start: 0.7746 (p0) cc_final: 0.6954 (p0)
  outliers start: 30
  outliers final: 22
  residues processed: 255
  average time/residue: 0.0603
  time to fit residues: 23.7489
Evaluate side-chains
  245 residues out of total 940 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 223
  time to evaluate  : 0.277 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  101 THR
Chi-restraints excluded: chain A residue  108 LEU
Chi-restraints excluded: chain A residue  159 ASN
Chi-restraints excluded: chain A residue  221 VAL
Chi-restraints excluded: chain A residue  252 TYR
Chi-restraints excluded: chain B residue   10 VAL
Chi-restraints excluded: chain B residue  101 THR
Chi-restraints excluded: chain B residue  108 LEU
Chi-restraints excluded: chain B residue  133 ILE
Chi-restraints excluded: chain B residue  159 ASN
Chi-restraints excluded: chain B residue  230 ILE
Chi-restraints excluded: chain B residue  233 GLN
Chi-restraints excluded: chain B residue  252 TYR
Chi-restraints excluded: chain C residue    8 LEU
Chi-restraints excluded: chain C residue   79 THR
Chi-restraints excluded: chain C residue  114 THR
Chi-restraints excluded: chain C residue  169 THR
Chi-restraints excluded: chain C residue  192 THR
Chi-restraints excluded: chain D residue   18 ILE
Chi-restraints excluded: chain D residue   38 LEU
Chi-restraints excluded: chain D residue  169 THR
Chi-restraints excluded: chain D residue  192 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 104
   random chunks:
   chunk 64 optimal weight:    0.6980
   chunk 96 optimal weight:    2.9990
   chunk 19 optimal weight:    4.9990
   chunk 17 optimal weight:    6.9990
   chunk 77 optimal weight:    2.9990
   chunk 69 optimal weight:    6.9990
   chunk 28 optimal weight:    0.0050
   chunk 74 optimal weight:    5.9990
   chunk 90 optimal weight:    0.4980
   chunk 21 optimal weight:    4.9990
   chunk 93 optimal weight:    3.9990
   overall best weight:    1.4398

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

Flipped N/Q/H residues before XYZ refinement:
** A 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 233 GLN
** C  47 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 200 HIS
D 200 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3423 r_free = 0.3423 target = 0.101856 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3102 r_free = 0.3102 target = 0.083526 restraints weight = 23059.541|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3143 r_free = 0.3143 target = 0.085772 restraints weight = 13896.065|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3171 r_free = 0.3171 target = 0.087352 restraints weight = 9817.520|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 36)----------------|
| r_work = 0.3191 r_free = 0.3191 target = 0.088453 restraints weight = 7688.326|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3203 r_free = 0.3203 target = 0.089144 restraints weight = 6476.256|
|-----------------------------------------------------------------------------|
r_work (final): 0.3201
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8199
moved from start:          0.5456

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.083   8802  Z= 0.169
  Angle     :  0.901  15.224  11918  Z= 0.435
  Chirality :  0.049   0.309   1350
  Planarity :  0.004   0.028   1468
  Dihedral  :  5.915  26.069   1164
  Min Nonbonded Distance : 2.415

Molprobity Statistics.
  All-atom Clashscore : 12.01
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 15.18 %
    Favored  : 84.82 %
  Rotamer:
    Outliers :  2.77 %
    Allowed  : 27.34 %
    Favored  : 69.89 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.52 (0.26), residues: 1054
  helix: -0.55 (0.23), residues: 542
  sheet: -0.87 (0.80), residues: 46
  loop : -3.22 (0.28), residues: 466

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG B 250 
 TYR   0.016   0.002   TYR A  14 
 PHE   0.012   0.001   PHE C 242 
 TRP   0.019   0.002   TRP C  81 
 HIS   0.006   0.001   HIS C 124 

Details of bonding type rmsd
  covalent geometry    : bond        0.00396 ( 8802)
  covalent geometry    : angle       0.90113 (11918)
  hydrogen bonds       : bond        0.03621 (  300)
  hydrogen bonds       : angle       5.11386 (  852)

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

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

  2108 Ramachandran restraints generated.
    1054 Oldfield, 0 Emsley, 1054 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2108 Ramachandran restraints generated.
    1054 Oldfield, 0 Emsley, 1054 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  243 residues out of total 940 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 217
  time to evaluate  : 0.340 
Fit side-chains
   revert: symmetry clash
REVERT: A    9 ASN cc_start: 0.9115 (m-40) cc_final: 0.8465 (t0)
REVERT: A   27 MET cc_start: -0.0818 (tpp) cc_final: -0.1893 (mpp)
REVERT: A   38 TYR cc_start: 0.8943 (m-80) cc_final: 0.8511 (m-80)
REVERT: A   41 ARG cc_start: 0.7477 (mtp85) cc_final: 0.7277 (mtp85)
REVERT: A  251 GLN cc_start: 0.8237 (tp-100) cc_final: 0.7882 (tp-100)
REVERT: A  257 MET cc_start: 0.8497 (mmt) cc_final: 0.8100 (mtt)
REVERT: B   27 MET cc_start: -0.0988 (tpp) cc_final: -0.2224 (mpp)
REVERT: B  123 MET cc_start: 0.8791 (ptp) cc_final: 0.8196 (pmm)
REVERT: B  148 MET cc_start: 0.8933 (mtm) cc_final: 0.8730 (mtm)
REVERT: B  251 GLN cc_start: 0.8441 (tp-100) cc_final: 0.8083 (tp-100)
REVERT: C   27 LYS cc_start: 0.8840 (tttp) cc_final: 0.8583 (tttm)
REVERT: C   52 TRP cc_start: 0.9302 (t60) cc_final: 0.8992 (t60)
REVERT: C  206 GLN cc_start: 0.8566 (tt0) cc_final: 0.8130 (mt0)
REVERT: C  266 ASP cc_start: 0.7787 (p0) cc_final: 0.7164 (p0)
REVERT: D   53 PHE cc_start: 0.7843 (t80) cc_final: 0.7282 (t80)
REVERT: D  203 HIS cc_start: 0.8077 (t-90) cc_final: 0.7621 (p-80)
REVERT: D  259 LYS cc_start: 0.8937 (mmtt) cc_final: 0.8444 (tmtt)
REVERT: D  266 ASP cc_start: 0.7812 (p0) cc_final: 0.7007 (p0)
  outliers start: 26
  outliers final: 23
  residues processed: 234
  average time/residue: 0.0668
  time to fit residues: 23.6722
Evaluate side-chains
  238 residues out of total 940 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 215
  time to evaluate  : 0.329 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   89 LEU
Chi-restraints excluded: chain A residue  101 THR
Chi-restraints excluded: chain A residue  108 LEU
Chi-restraints excluded: chain A residue  159 ASN
Chi-restraints excluded: chain A residue  221 VAL
Chi-restraints excluded: chain A residue  252 TYR
Chi-restraints excluded: chain B residue   10 VAL
Chi-restraints excluded: chain B residue   89 LEU
Chi-restraints excluded: chain B residue  101 THR
Chi-restraints excluded: chain B residue  108 LEU
Chi-restraints excluded: chain B residue  133 ILE
Chi-restraints excluded: chain B residue  159 ASN
Chi-restraints excluded: chain B residue  230 ILE
Chi-restraints excluded: chain B residue  233 GLN
Chi-restraints excluded: chain B residue  252 TYR
Chi-restraints excluded: chain C residue   72 LEU
Chi-restraints excluded: chain C residue   79 THR
Chi-restraints excluded: chain C residue  114 THR
Chi-restraints excluded: chain C residue  169 THR
Chi-restraints excluded: chain C residue  192 THR
Chi-restraints excluded: chain D residue   38 LEU
Chi-restraints excluded: chain D residue  169 THR
Chi-restraints excluded: chain D residue  192 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 104
   random chunks:
   chunk 65 optimal weight:    0.9990
   chunk 44 optimal weight:    0.9980
   chunk 39 optimal weight:    0.9990
   chunk 84 optimal weight:    5.9990
   chunk 12 optimal weight:    2.9990
   chunk 16 optimal weight:    0.5980
   chunk 91 optimal weight:    2.9990
   chunk 79 optimal weight:    0.6980
   chunk 22 optimal weight:    1.9990
   chunk 6 optimal weight:    2.9990
   chunk 52 optimal weight:    5.9990
   overall best weight:    0.8584

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

Flipped N/Q/H residues before XYZ refinement:
** A 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 233 GLN
** C  47 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 200 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3443 r_free = 0.3443 target = 0.102958 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3118 r_free = 0.3118 target = 0.084452 restraints weight = 23230.205|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3159 r_free = 0.3159 target = 0.086713 restraints weight = 14069.727|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3185 r_free = 0.3185 target = 0.088195 restraints weight = 9948.678|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 39)----------------|
| r_work = 0.3208 r_free = 0.3208 target = 0.089381 restraints weight = 7851.581|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.3220 r_free = 0.3220 target = 0.090079 restraints weight = 6590.252|
|-----------------------------------------------------------------------------|
r_work (final): 0.3216
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8183
moved from start:          0.5545

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.076   8802  Z= 0.144
  Angle     :  0.881  15.296  11918  Z= 0.422
  Chirality :  0.048   0.251   1350
  Planarity :  0.004   0.027   1468
  Dihedral  :  5.905  27.861   1164
  Min Nonbonded Distance : 2.309

Molprobity Statistics.
  All-atom Clashscore : 11.15
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 14.61 %
    Favored  : 85.39 %
  Rotamer:
    Outliers :  2.66 %
    Allowed  : 27.66 %
    Favored  : 69.68 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.51 (0.26), residues: 1054
  helix: -0.55 (0.23), residues: 552
  sheet: -0.76 (0.80), residues: 46
  loop : -3.25 (0.28), residues: 456

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG B 250 
 TYR   0.019   0.002   TYR C 215 
 PHE   0.020   0.001   PHE B 264 
 TRP   0.017   0.002   TRP C  81 
 HIS   0.006   0.001   HIS C 124 

Details of bonding type rmsd
  covalent geometry    : bond        0.00334 ( 8802)
  covalent geometry    : angle       0.88067 (11918)
  hydrogen bonds       : bond        0.03466 (  300)
  hydrogen bonds       : angle       5.13813 (  852)
Origin is already at (0, 0, 0), no shifts will be applied

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Job complete
usr+sys time: 1345.69 seconds
wall clock time: 23 minutes 56.17 seconds (1436.17 seconds total)