Starting phenix.real_space_refine
on Tue Apr 29 11:05:23 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/6jbh_9790/04_2025/6jbh_9790.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/6jbh_9790/04_2025/6jbh_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_9790/04_2025/6jbh_9790.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/6jbh_9790/04_2025/6jbh_9790.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/6jbh_9790/04_2025/6jbh_9790.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/6jbh_9790/04_2025/6jbh_9790.cif"
  }
  resolution = 3.94
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.001 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): 0.03s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/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: 5.60, per 1000 atoms: 0.65
  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: 2.21
  Conformation dependent library (CDL) restraints added in 1.2 seconds
  

  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: 1.05
  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: 2.11

  Time building geometry restraints manager: 2.64 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: 0.04
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:                  0.010
  Normalize map: mean=0, sd=1:             0.980
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.380
  Check model and map are aligned:         0.070
  Set scattering table:                    0.100
  Process input model:                     23.560
  Find NCS groups from input model:        0.150
  Set up NCS constraints:                  0.040
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.010
  Load rotamer database and sin/cos tables:2.910
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   28.220
-------------------------------------------------------------------------------
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 : 6.09
  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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -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
 TRP   0.030   0.004   TRP A 215 
 HIS   0.011   0.002   HIS C 124 
 PHE   0.038   0.003   PHE C 264 
 TYR   0.027   0.003   TYR B  14 
 ARG   0.007   0.001   ARG B  41 

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

*********************** 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  : 0.968 
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: -0.1875 (mpp)
REVERT: A   38 TYR cc_start: 0.8712 (m-80) cc_final: 0.7987 (m-80)
REVERT: A   84 ASP cc_start: 0.7513 (m-30) cc_final: 0.7119 (m-30)
REVERT: A  132 ASP cc_start: 0.8022 (t0) cc_final: 0.7372 (t0)
REVERT: A  186 MET cc_start: 0.9423 (mmt) cc_final: 0.9174 (mmp)
REVERT: A  192 ARG cc_start: 0.8269 (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: 0.8007 (m-80)
REVERT: B  104 GLU cc_start: 0.8728 (mm-30) cc_final: 0.8519 (mm-30)
REVERT: B  107 GLU cc_start: 0.8903 (mt-10) cc_final: 0.8699 (tt0)
REVERT: B  132 ASP cc_start: 0.8004 (t0) cc_final: 0.7437 (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: 0.6927 (t80)
REVERT: C   14 ASN cc_start: 0.9211 (m-40) cc_final: 0.8949 (m-40)
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: 0.8485 (pp30)
REVERT: C  112 ILE cc_start: 0.9700 (tp) cc_final: 0.9488 (mt)
REVERT: C  126 MET cc_start: 0.6721 (tpp) cc_final: 0.5864 (tpp)
REVERT: C  132 PHE cc_start: 0.8268 (m-10) cc_final: 0.7776 (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: 0.8078 (m)
REVERT: C  180 ILE cc_start: 0.9548 (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: 0.7261 (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  126 MET cc_start: 0.7038 (tpp) cc_final: 0.6180 (tpp)
REVERT: D  132 PHE cc_start: 0.8227 (m-10) cc_final: 0.7721 (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: 0.7242 (p0)
  outliers start: 5
  outliers final: 2
  residues processed: 394
  average time/residue: 0.2436
  time to fit residues: 124.7920
Evaluate side-chains
  209 residues out of total 940 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 207
  time to evaluate  : 1.052 
-------------------------------------------------------------------------------
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 87 optimal weight:    0.8980
   chunk 78 optimal weight:    2.9990
   chunk 43 optimal weight:    6.9990
   chunk 26 optimal weight:    8.9990
   chunk 53 optimal weight:    0.9990
   chunk 42 optimal weight:    0.0370
   chunk 81 optimal weight:    3.9990
   chunk 31 optimal weight:    2.9990
   chunk 49 optimal weight:    0.8980
   chunk 60 optimal weight:    0.8980
   chunk 94 optimal weight:    0.8980
   overall best weight:    0.7258

-------------------------------------------------------------------------------
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
D  32 ASN
** D  47 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
D 257 HIS

Total number of N/Q/H flips: 9

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3407 r_free = 0.3407 target = 0.101230 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3083 r_free = 0.3083 target = 0.083045 restraints weight = 22587.054|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3125 r_free = 0.3125 target = 0.085327 restraints weight = 13490.489|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 22)----------------|
| r_work = 0.3153 r_free = 0.3153 target = 0.086856 restraints weight = 9500.437|
|-----------------------------------------------------------------------------|
r_work (final): 0.3149
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8236
moved from start:          0.3350

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.041   8802  Z= 0.163
  Angle     :  0.890  10.623  11918  Z= 0.454
  Chirality :  0.050   0.236   1350
  Planarity :  0.005   0.040   1468
  Dihedral  :  7.514  29.911   1172
  Min Nonbonded Distance : 2.487

Molprobity Statistics.
  All-atom Clashscore : 12.82
  Ramachandran Plot:
    Outliers :  0.19 %
    Allowed  : 14.14 %
    Favored  : 85.67 %
  Rotamer:
    Outliers :  2.77 %
    Allowed  : 16.60 %
    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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -4.66 (0.21), residues: 1054
  helix: -2.65 (0.18), residues: 524
  sheet: -2.73 (0.68), residues: 44
  loop : -3.65 (0.25), residues: 486

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.027   0.002   TRP D  52 
 HIS   0.008   0.001   HIS D 257 
 PHE   0.038   0.002   PHE D  70 
 TYR   0.033   0.002   TYR C 215 
 ARG   0.008   0.001   ARG B  41 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05589 (  300)
  hydrogen bonds       : angle       5.83228 (  852)
  covalent geometry    : bond        0.00351 ( 8802)
  covalent geometry    : angle       0.89005 (11918)

*********************** 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
  287 residues out of total 940 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 261
  time to evaluate  : 1.080 
Fit side-chains
REVERT: A   27 MET cc_start: -0.0732 (tpp) cc_final: -0.1387 (mpp)
REVERT: A   38 TYR cc_start: 0.8628 (m-80) cc_final: 0.7976 (m-80)
REVERT: A  251 GLN cc_start: 0.8400 (tp-100) cc_final: 0.7744 (tp-100)
REVERT: B   11 THR cc_start: 0.9161 (m) cc_final: 0.8627 (t)
REVERT: B   27 MET cc_start: -0.1155 (tpp) cc_final: -0.1795 (mpp)
REVERT: B   38 TYR cc_start: 0.8660 (m-80) cc_final: 0.7978 (m-80)
REVERT: B  247 LYS cc_start: 0.7944 (mtmm) cc_final: 0.7675 (mtmm)
REVERT: B  251 GLN cc_start: 0.8550 (tp-100) cc_final: 0.7843 (tp-100)
REVERT: C   38 LEU cc_start: 0.8162 (mm) cc_final: 0.7084 (mm)
REVERT: C  104 GLN cc_start: 0.8937 (mt0) cc_final: 0.8457 (mt0)
REVERT: C  105 MET cc_start: 0.8859 (mpt) cc_final: 0.8291 (mpp)
REVERT: C  136 GLN cc_start: 0.8806 (mt0) cc_final: 0.8317 (mm-40)
REVERT: C  175 ARG cc_start: 0.8123 (ttm110) cc_final: 0.7832 (ttm170)
REVERT: C  182 GLN cc_start: 0.9001 (tt0) cc_final: 0.8764 (tt0)
REVERT: C  219 GLU cc_start: 0.8579 (mm-30) cc_final: 0.8370 (mm-30)
REVERT: C  259 LYS cc_start: 0.8851 (mmtt) cc_final: 0.8189 (tmtt)
REVERT: C  266 ASP cc_start: 0.8292 (p0) cc_final: 0.7566 (p0)
REVERT: D   70 PHE cc_start: 0.6724 (t80) cc_final: 0.6281 (t80)
REVERT: D   86 GLN cc_start: 0.8716 (pp30) cc_final: 0.8432 (pp30)
REVERT: D  126 MET cc_start: 0.6879 (tpp) cc_final: 0.5906 (tpp)
REVERT: D  254 SER cc_start: 0.9624 (OUTLIER) cc_final: 0.9286 (t)
REVERT: D  259 LYS cc_start: 0.8928 (mmtt) cc_final: 0.8338 (tmtt)
REVERT: D  266 ASP cc_start: 0.8299 (p0) cc_final: 0.7451 (p0)
  outliers start: 26
  outliers final: 16
  residues processed: 276
  average time/residue: 0.1829
  time to fit residues: 70.6465
Evaluate side-chains
  225 residues out of total 940 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 208
  time to evaluate  : 0.983 
-------------------------------------------------------------------------------
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 78 optimal weight:    0.9980
   chunk 41 optimal weight:    0.8980
   chunk 93 optimal weight:    3.9990
   chunk 58 optimal weight:    9.9990
   chunk 92 optimal weight:    2.9990
   chunk 49 optimal weight:    4.9990
   chunk 100 optimal weight:    5.9990
   chunk 27 optimal weight:    0.0270
   chunk 21 optimal weight:    8.9990
   chunk 23 optimal weight:    4.9990
   chunk 37 optimal weight:    0.0870
   overall best weight:    1.0018

-------------------------------------------------------------------------------
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  30 ASN
C 200 HIS
** D  47 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
D 200 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3405 r_free = 0.3405 target = 0.100644 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3075 r_free = 0.3075 target = 0.082331 restraints weight = 23226.272|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3118 r_free = 0.3118 target = 0.084622 restraints weight = 13809.661|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.3148 r_free = 0.3148 target = 0.086194 restraints weight = 9733.676|
|-----------------------------------------------------------------------------|
r_work (final): 0.3144
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8245
moved from start:          0.4089

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.049   8802  Z= 0.150
  Angle     :  0.846   9.693  11918  Z= 0.420
  Chirality :  0.049   0.247   1350
  Planarity :  0.004   0.031   1468
  Dihedral  :  6.871  27.955   1164
  Min Nonbonded Distance : 2.504

Molprobity Statistics.
  All-atom Clashscore : 11.55
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 13.95 %
    Favored  : 86.05 %
  Rotamer:
    Outliers :  5.21 %
    Allowed  : 18.19 %
    Favored  : 76.60 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -3.85 (0.23), residues: 1054
  helix: -1.85 (0.20), residues: 520
  sheet: -2.81 (0.67), residues: 46
  loop : -3.35 (0.26), residues: 488

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.020   0.002   TRP C  81 
 HIS   0.005   0.001   HIS C 257 
 PHE   0.021   0.001   PHE D  70 
 TYR   0.029   0.002   TYR C 215 
 ARG   0.005   0.001   ARG A  41 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04159 (  300)
  hydrogen bonds       : angle       5.30725 (  852)
  covalent geometry    : bond        0.00339 ( 8802)
  covalent geometry    : angle       0.84616 (11918)

*********************** 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
  279 residues out of total 940 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 49
    poor density    : 230
  time to evaluate  : 0.910 
Fit side-chains
REVERT: A   27 MET cc_start: -0.0700 (tpp) cc_final: -0.1359 (mpp)
REVERT: A   38 TYR cc_start: 0.8651 (m-80) cc_final: 0.7941 (m-80)
REVERT: A  251 GLN cc_start: 0.8470 (tp-100) cc_final: 0.7853 (tp-100)
REVERT: B    5 VAL cc_start: 0.8347 (OUTLIER) cc_final: 0.8125 (m)
REVERT: B   11 THR cc_start: 0.9183 (m) cc_final: 0.8729 (t)
REVERT: B   16 LEU cc_start: 0.8422 (tm) cc_final: 0.8103 (tm)
REVERT: B   27 MET cc_start: -0.1000 (tpp) cc_final: -0.1789 (mpp)
REVERT: B  139 GLN cc_start: 0.8336 (tp40) cc_final: 0.8133 (mm110)
REVERT: B  247 LYS cc_start: 0.7732 (mtmm) cc_final: 0.7460 (mtmm)
REVERT: B  251 GLN cc_start: 0.8578 (tp-100) cc_final: 0.7946 (tp-100)
REVERT: C  206 GLN cc_start: 0.8585 (tt0) cc_final: 0.8206 (mt0)
REVERT: C  215 TYR cc_start: 0.8909 (t80) cc_final: 0.8579 (t80)
REVERT: C  219 GLU cc_start: 0.8553 (mm-30) cc_final: 0.8054 (mm-30)
REVERT: C  225 LEU cc_start: 0.8604 (OUTLIER) cc_final: 0.8377 (pp)
REVERT: C  259 LYS cc_start: 0.8874 (mmtt) cc_final: 0.8285 (tmtt)
REVERT: C  266 ASP cc_start: 0.8245 (p0) cc_final: 0.7603 (p0)
REVERT: D   86 GLN cc_start: 0.8862 (pp30) cc_final: 0.8561 (pp30)
REVERT: D  165 LEU cc_start: 0.9366 (mp) cc_final: 0.9093 (mp)
REVERT: D  259 LYS cc_start: 0.8894 (mmtt) cc_final: 0.8273 (tmtt)
REVERT: D  266 ASP cc_start: 0.8006 (p0) cc_final: 0.7173 (p0)
  outliers start: 49
  outliers final: 29
  residues processed: 265
  average time/residue: 0.1691
  time to fit residues: 65.8448
Evaluate side-chains
  242 residues out of total 940 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 211
  time to evaluate  : 1.077 
-------------------------------------------------------------------------------
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  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   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 B residue  252 TYR
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   38 LEU
Chi-restraints excluded: chain D residue   79 THR
Chi-restraints excluded: chain D residue   99 ILE
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 9 optimal weight:    5.9990
   chunk 14 optimal weight:    3.9990
   chunk 86 optimal weight:    3.9990
   chunk 80 optimal weight:    0.9980
   chunk 78 optimal weight:    0.8980
   chunk 17 optimal weight:    6.9990
   chunk 43 optimal weight:    0.0570
   chunk 103 optimal weight:    4.9990
   chunk 73 optimal weight:    0.7980
   chunk 26 optimal weight:    8.9990
   chunk 97 optimal weight:    0.8980
   overall best weight:    0.7298

-------------------------------------------------------------------------------
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 200 HIS
D  47 GLN
D 200 HIS

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3424 r_free = 0.3424 target = 0.101661 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3096 r_free = 0.3096 target = 0.083297 restraints weight = 23035.880|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3139 r_free = 0.3139 target = 0.085622 restraints weight = 13710.171|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3169 r_free = 0.3169 target = 0.087217 restraints weight = 9644.841|
|-----------------------------------------------------------------------------|
r_work (final): 0.3163
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8224
moved from start:          0.4465

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041   8802  Z= 0.136
  Angle     :  0.823  10.258  11918  Z= 0.407
  Chirality :  0.048   0.268   1350
  Planarity :  0.004   0.032   1468
  Dihedral  :  6.582  26.753   1164
  Min Nonbonded Distance : 2.440

Molprobity Statistics.
  All-atom Clashscore : 11.21
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 14.90 %
    Favored  : 85.10 %
  Rotamer:
    Outliers :  4.15 %
    Allowed  : 20.21 %
    Favored  : 75.64 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -3.42 (0.24), residues: 1054
  helix: -1.35 (0.21), residues: 522
  sheet: -2.87 (0.65), residues: 46
  loop : -3.31 (0.26), residues: 486

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.002   TRP D  52 
 HIS   0.005   0.001   HIS C 257 
 PHE   0.016   0.001   PHE C 242 
 TYR   0.022   0.002   TYR C 215 
 ARG   0.004   0.000   ARG A  41 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03756 (  300)
  hydrogen bonds       : angle       5.23462 (  852)
  covalent geometry    : bond        0.00305 ( 8802)
  covalent geometry    : angle       0.82322 (11918)

*********************** 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
  279 residues out of total 940 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 39
    poor density    : 240
  time to evaluate  : 0.981 
Fit side-chains
REVERT: A   27 MET cc_start: -0.0929 (tpp) cc_final: -0.1717 (mpp)
REVERT: A   38 TYR cc_start: 0.8694 (m-80) cc_final: 0.7931 (m-80)
REVERT: A  152 LEU cc_start: 0.9776 (tp) cc_final: 0.9568 (tt)
REVERT: A  251 GLN cc_start: 0.8466 (tp-100) cc_final: 0.7865 (tp-100)
REVERT: B    5 VAL cc_start: 0.8191 (OUTLIER) cc_final: 0.7935 (m)
REVERT: B   27 MET cc_start: -0.0978 (tpp) cc_final: -0.1719 (mpp)
REVERT: B  139 GLN cc_start: 0.8422 (tp40) cc_final: 0.8218 (mm110)
REVERT: B  251 GLN cc_start: 0.8560 (tp-100) cc_final: 0.7914 (tp-100)
REVERT: C  206 GLN cc_start: 0.8665 (tt0) cc_final: 0.8039 (mt0)
REVERT: C  215 TYR cc_start: 0.8883 (t80) cc_final: 0.8323 (t80)
REVERT: C  219 GLU cc_start: 0.8666 (mm-30) cc_final: 0.8237 (mm-30)
REVERT: C  259 LYS cc_start: 0.8908 (mmtt) cc_final: 0.8266 (tmtt)
REVERT: C  266 ASP cc_start: 0.8231 (p0) cc_final: 0.7693 (p0)
REVERT: D   86 GLN cc_start: 0.8875 (pp30) cc_final: 0.8548 (pp30)
REVERT: D  126 MET cc_start: 0.8047 (ttm) cc_final: 0.7824 (ttp)
REVERT: D  136 GLN cc_start: 0.8639 (mt0) cc_final: 0.8288 (mm110)
REVERT: D  259 LYS cc_start: 0.8877 (mmtt) cc_final: 0.8226 (tmtt)
REVERT: D  266 ASP cc_start: 0.8006 (p0) cc_final: 0.7286 (p0)
  outliers start: 39
  outliers final: 22
  residues processed: 267
  average time/residue: 0.1536
  time to fit residues: 60.3276
Evaluate side-chains
  242 residues out of total 940 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 219
  time to evaluate  : 1.073 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   11 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  216 LEU
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 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 15 optimal weight:    4.9990
   chunk 16 optimal weight:    0.0040
   chunk 32 optimal weight:    0.8980
   chunk 102 optimal weight:    2.9990
   chunk 78 optimal weight:    1.9990
   chunk 89 optimal weight:    4.9990
   chunk 12 optimal weight:    0.6980
   chunk 30 optimal weight:    0.0980
   chunk 58 optimal weight:    0.0980
   chunk 66 optimal weight:    7.9990
   chunk 43 optimal weight:    0.0970
   overall best weight:    0.1990

-------------------------------------------------------------------------------
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 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 123 GLN
C 200 HIS
D  47 GLN
D 200 HIS

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3461 r_free = 0.3461 target = 0.104028 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3148 r_free = 0.3148 target = 0.085982 restraints weight = 23213.846|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3191 r_free = 0.3191 target = 0.088313 restraints weight = 13698.581|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3220 r_free = 0.3220 target = 0.089938 restraints weight = 9537.199|
|-----------------------------------------------------------------------------|
r_work (final): 0.3219
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8172
moved from start:          0.4869

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041   8802  Z= 0.133
  Angle     :  0.806  10.901  11918  Z= 0.397
  Chirality :  0.047   0.224   1350
  Planarity :  0.004   0.030   1468
  Dihedral  :  6.334  26.001   1164
  Min Nonbonded Distance : 2.411

Molprobity Statistics.
  All-atom Clashscore : 10.17
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 13.66 %
    Favored  : 86.34 %
  Rotamer:
    Outliers :  2.87 %
    Allowed  : 22.02 %
    Favored  : 75.11 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -3.08 (0.25), residues: 1054
  helix: -1.06 (0.22), residues: 528
  sheet: -2.55 (0.65), residues: 46
  loop : -3.18 (0.27), residues: 480

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.002   TRP C  52 
 HIS   0.004   0.001   HIS C 257 
 PHE   0.015   0.001   PHE C 163 
 TYR   0.019   0.002   TYR A 234 
 ARG   0.004   0.000   ARG B  41 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03418 (  300)
  hydrogen bonds       : angle       5.12902 (  852)
  covalent geometry    : bond        0.00283 ( 8802)
  covalent geometry    : angle       0.80571 (11918)

*********************** 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
  279 residues out of total 940 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 252
  time to evaluate  : 0.970 
Fit side-chains
   revert: symmetry clash
REVERT: A    9 ASN cc_start: 0.9040 (m-40) cc_final: 0.8341 (t0)
REVERT: A   27 MET cc_start: -0.0877 (tpp) cc_final: -0.1673 (mpp)
REVERT: A   38 TYR cc_start: 0.8687 (m-80) cc_final: 0.7962 (m-80)
REVERT: A   86 GLN cc_start: 0.6470 (pm20) cc_final: 0.6231 (pm20)
REVERT: A  152 LEU cc_start: 0.9747 (tp) cc_final: 0.9523 (tt)
REVERT: A  251 GLN cc_start: 0.8307 (tp-100) cc_final: 0.7822 (tp-100)
REVERT: A  257 MET cc_start: 0.8504 (mmt) cc_final: 0.8087 (mtt)
REVERT: B   27 MET cc_start: -0.1411 (tpp) cc_final: -0.2298 (mpp)
REVERT: B   86 GLN cc_start: 0.6407 (pm20) cc_final: 0.6168 (pm20)
REVERT: B  152 LEU cc_start: 0.9742 (tp) cc_final: 0.9538 (tt)
REVERT: B  251 GLN cc_start: 0.8524 (tp-100) cc_final: 0.8012 (tp-100)
REVERT: B  264 PHE cc_start: 0.6930 (t80) cc_final: 0.6724 (m-80)
REVERT: C  189 LEU cc_start: 0.9154 (OUTLIER) cc_final: 0.8946 (tp)
REVERT: C  206 GLN cc_start: 0.8594 (tt0) cc_final: 0.8041 (mt0)
REVERT: C  259 LYS cc_start: 0.8880 (mmtt) cc_final: 0.8245 (tmtt)
REVERT: C  266 ASP cc_start: 0.7976 (p0) cc_final: 0.7465 (p0)
REVERT: D   86 GLN cc_start: 0.8813 (pp30) cc_final: 0.8335 (pp30)
REVERT: D  126 MET cc_start: 0.7869 (ttm) cc_final: 0.7618 (ttp)
REVERT: D  206 GLN cc_start: 0.8556 (tt0) cc_final: 0.8060 (mt0)
REVERT: D  219 GLU cc_start: 0.8754 (mm-30) cc_final: 0.8490 (mm-30)
REVERT: D  259 LYS cc_start: 0.8816 (mmtt) cc_final: 0.8212 (tmtt)
REVERT: D  266 ASP cc_start: 0.7860 (p0) cc_final: 0.7239 (p0)
  outliers start: 27
  outliers final: 16
  residues processed: 269
  average time/residue: 0.1699
  time to fit residues: 67.3850
Evaluate side-chains
  232 residues out of total 940 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 215
  time to evaluate  : 1.074 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   11 THR
Chi-restraints excluded: chain A residue  108 LEU
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  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    8 LEU
Chi-restraints excluded: chain D residue   38 LEU
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 5 optimal weight:    2.9990
   chunk 39 optimal weight:    0.9990
   chunk 23 optimal weight:    4.9990
   chunk 8 optimal weight:    2.9990
   chunk 80 optimal weight:    0.9980
   chunk 93 optimal weight:    2.9990
   chunk 65 optimal weight:    0.9990
   chunk 53 optimal weight:    0.9990
   chunk 57 optimal weight:    3.9990
   chunk 9 optimal weight:    3.9990
   chunk 64 optimal weight:    0.9990
   overall best weight:    0.9988

-------------------------------------------------------------------------------
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 139 GLN
C 123 GLN
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 = 0.3434 r_free = 0.3434 target = 0.101965 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3122 r_free = 0.3122 target = 0.084098 restraints weight = 22851.258|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3163 r_free = 0.3163 target = 0.086423 restraints weight = 13440.135|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.3192 r_free = 0.3192 target = 0.088024 restraints weight = 9373.851|
|-----------------------------------------------------------------------------|
r_work (final): 0.3192
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8207
moved from start:          0.4957

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   8802  Z= 0.135
  Angle     :  0.822  13.696  11918  Z= 0.398
  Chirality :  0.048   0.295   1350
  Planarity :  0.004   0.032   1468
  Dihedral  :  6.136  25.702   1164
  Min Nonbonded Distance : 2.500

Molprobity Statistics.
  All-atom Clashscore : 11.78
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 14.42 %
    Favored  : 85.58 %
  Rotamer:
    Outliers :  3.83 %
    Allowed  : 22.55 %
    Favored  : 73.62 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.79 (0.25), residues: 1054
  helix: -0.79 (0.22), residues: 530
  sheet: -2.21 (0.63), residues: 46
  loop : -3.11 (0.28), residues: 478

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.002   TRP C  81 
 HIS   0.004   0.001   HIS C 257 
 PHE   0.017   0.001   PHE C 242 
 TYR   0.015   0.002   TYR D 238 
 ARG   0.002   0.000   ARG A  41 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03312 (  300)
  hydrogen bonds       : angle       4.92596 (  852)
  covalent geometry    : bond        0.00304 ( 8802)
  covalent geometry    : angle       0.82175 (11918)

*********************** 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
  258 residues out of total 940 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 222
  time to evaluate  : 1.079 
Fit side-chains
   revert: symmetry clash
REVERT: A    9 ASN cc_start: 0.9077 (m-40) cc_final: 0.8385 (t0)
REVERT: A   27 MET cc_start: -0.0976 (tpp) cc_final: -0.1988 (mpp)
REVERT: A   38 TYR cc_start: 0.8800 (m-80) cc_final: 0.8060 (m-80)
REVERT: A   86 GLN cc_start: 0.6533 (pm20) cc_final: 0.6261 (pm20)
REVERT: A  152 LEU cc_start: 0.9764 (tp) cc_final: 0.9545 (tt)
REVERT: A  247 LYS cc_start: 0.7858 (mtmm) cc_final: 0.7574 (mtmm)
REVERT: A  251 GLN cc_start: 0.8284 (tp-100) cc_final: 0.7777 (tp-100)
REVERT: A  257 MET cc_start: 0.8497 (mmt) cc_final: 0.8113 (mtt)
REVERT: B   27 MET cc_start: -0.1338 (tpp) cc_final: -0.2395 (mpp)
REVERT: B   86 GLN cc_start: 0.6565 (pm20) cc_final: 0.6280 (pm20)
REVERT: B  152 LEU cc_start: 0.9764 (tp) cc_final: 0.9529 (tt)
REVERT: B  251 GLN cc_start: 0.8523 (tp-100) cc_final: 0.8123 (tp-100)
REVERT: C  189 LEU cc_start: 0.9278 (OUTLIER) cc_final: 0.9034 (tp)
REVERT: C  206 GLN cc_start: 0.8636 (tt0) cc_final: 0.8134 (mt0)
REVERT: C  259 LYS cc_start: 0.8899 (mmtt) cc_final: 0.8288 (tmtt)
REVERT: C  266 ASP cc_start: 0.8001 (p0) cc_final: 0.7489 (p0)
REVERT: D   47 GLN cc_start: 0.9409 (tm-30) cc_final: 0.9112 (tm-30)
REVERT: D   86 GLN cc_start: 0.8842 (pp30) cc_final: 0.8330 (pp30)
REVERT: D  206 GLN cc_start: 0.8530 (tt0) cc_final: 0.8056 (mt0)
REVERT: D  219 GLU cc_start: 0.8745 (mm-30) cc_final: 0.8522 (mm-30)
REVERT: D  259 LYS cc_start: 0.8842 (mmtt) cc_final: 0.8251 (tmtt)
REVERT: D  266 ASP cc_start: 0.7970 (p0) cc_final: 0.7270 (p0)
  outliers start: 36
  outliers final: 22
  residues processed: 243
  average time/residue: 0.1708
  time to fit residues: 60.0050
Evaluate side-chains
  233 residues out of total 940 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 210
  time to evaluate  : 1.050 
-------------------------------------------------------------------------------
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  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  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 57 optimal weight:    3.9990
   chunk 91 optimal weight:    0.8980
   chunk 37 optimal weight:    1.9990
   chunk 44 optimal weight:    2.9990
   chunk 47 optimal weight:    1.9990
   chunk 101 optimal weight:    4.9990
   chunk 84 optimal weight:    8.9990
   chunk 32 optimal weight:    0.6980
   chunk 59 optimal weight:    3.9990
   chunk 74 optimal weight:    0.0870
   chunk 86 optimal weight:    0.2980
   overall best weight:    0.7960

-------------------------------------------------------------------------------
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 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 = 0.3437 r_free = 0.3437 target = 0.102265 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3124 r_free = 0.3124 target = 0.084343 restraints weight = 23146.598|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3165 r_free = 0.3165 target = 0.086631 restraints weight = 13642.301|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3194 r_free = 0.3194 target = 0.088206 restraints weight = 9514.303|
|-----------------------------------------------------------------------------|
r_work (final): 0.3190
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8198
moved from start:          0.5170

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   8802  Z= 0.131
  Angle     :  0.828  12.985  11918  Z= 0.400
  Chirality :  0.048   0.215   1350
  Planarity :  0.004   0.031   1468
  Dihedral  :  6.069  25.866   1164
  Min Nonbonded Distance : 2.492

Molprobity Statistics.
  All-atom Clashscore : 11.21
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 14.23 %
    Favored  : 85.77 %
  Rotamer:
    Outliers :  3.40 %
    Allowed  : 23.72 %
    Favored  : 72.87 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.63 (0.25), residues: 1054
  helix: -0.65 (0.22), residues: 530
  sheet: -1.67 (0.69), residues: 46
  loop : -3.09 (0.28), residues: 478

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.002   TRP C  81 
 HIS   0.003   0.001   HIS C 124 
 PHE   0.011   0.001   PHE C 163 
 TYR   0.018   0.002   TYR C 151 
 ARG   0.005   0.000   ARG B 250 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03273 (  300)
  hydrogen bonds       : angle       4.91552 (  852)
  covalent geometry    : bond        0.00296 ( 8802)
  covalent geometry    : angle       0.82789 (11918)

*********************** 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
  260 residues out of total 940 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 228
  time to evaluate  : 1.056 
Fit side-chains
   revert: symmetry clash
REVERT: A    9 ASN cc_start: 0.9077 (m-40) cc_final: 0.8398 (t0)
REVERT: A   27 MET cc_start: -0.0949 (tpp) cc_final: -0.2005 (mpp)
REVERT: A   38 TYR cc_start: 0.8813 (m-80) cc_final: 0.8059 (m-80)
REVERT: A   86 GLN cc_start: 0.6332 (pm20) cc_final: 0.6085 (pm20)
REVERT: A  152 LEU cc_start: 0.9760 (tp) cc_final: 0.9559 (tt)
REVERT: A  251 GLN cc_start: 0.8334 (tp-100) cc_final: 0.7837 (tp-100)
REVERT: A  257 MET cc_start: 0.8501 (mmt) cc_final: 0.8127 (mtt)
REVERT: B   27 MET cc_start: -0.1331 (tpp) cc_final: -0.2408 (mpp)
REVERT: B   86 GLN cc_start: 0.6757 (pm20) cc_final: 0.6274 (pm20)
REVERT: B  251 GLN cc_start: 0.8538 (tp-100) cc_final: 0.8144 (tp-100)
REVERT: C  189 LEU cc_start: 0.9205 (OUTLIER) cc_final: 0.8969 (tp)
REVERT: C  206 GLN cc_start: 0.8612 (tt0) cc_final: 0.8110 (mt0)
REVERT: C  215 TYR cc_start: 0.8862 (t80) cc_final: 0.8517 (t80)
REVERT: C  259 LYS cc_start: 0.8906 (mmtt) cc_final: 0.8315 (tmtt)
REVERT: C  266 ASP cc_start: 0.7975 (p0) cc_final: 0.7514 (p0)
REVERT: D   47 GLN cc_start: 0.9463 (tm-30) cc_final: 0.9190 (tm-30)
REVERT: D   86 GLN cc_start: 0.8842 (pp30) cc_final: 0.8173 (pp30)
REVERT: D  206 GLN cc_start: 0.8526 (tt0) cc_final: 0.8067 (mt0)
REVERT: D  215 TYR cc_start: 0.8981 (t80) cc_final: 0.8304 (t80)
REVERT: D  219 GLU cc_start: 0.8750 (mm-30) cc_final: 0.8261 (mm-30)
REVERT: D  259 LYS cc_start: 0.8885 (mmtt) cc_final: 0.8238 (tmtt)
REVERT: D  266 ASP cc_start: 0.7838 (p0) cc_final: 0.7091 (p0)
  outliers start: 32
  outliers final: 24
  residues processed: 249
  average time/residue: 0.1571
  time to fit residues: 57.4452
Evaluate side-chains
  238 residues out of total 940 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 213
  time to evaluate  : 0.969 
-------------------------------------------------------------------------------
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  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  101 THR
Chi-restraints excluded: chain B residue  133 ILE
Chi-restraints excluded: chain B residue  159 ASN
Chi-restraints excluded: chain B residue  221 VAL
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 D residue    8 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 0 optimal weight:    9.9990
   chunk 3 optimal weight:    5.9990
   chunk 10 optimal weight:    2.9990
   chunk 89 optimal weight:    3.9990
   chunk 21 optimal weight:    7.9990
   chunk 76 optimal weight:    0.9990
   chunk 34 optimal weight:    7.9990
   chunk 37 optimal weight:    0.5980
   chunk 53 optimal weight:    4.9990
   chunk 29 optimal weight:    5.9990
   chunk 66 optimal weight:    8.9990
   overall best weight:    2.7188

-------------------------------------------------------------------------------
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 124 HIS
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 = 0.3353 r_free = 0.3353 target = 0.097176 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3022 r_free = 0.3022 target = 0.078831 restraints weight = 23837.014|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.3063 r_free = 0.3063 target = 0.081007 restraints weight = 14271.726|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3091 r_free = 0.3091 target = 0.082523 restraints weight = 10107.888|
|-----------------------------------------------------------------------------|
r_work (final): 0.3088
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8320
moved from start:          0.5135

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.054   8802  Z= 0.248
  Angle     :  0.900  12.395  11918  Z= 0.443
  Chirality :  0.050   0.234   1350
  Planarity :  0.004   0.035   1468
  Dihedral  :  6.173  25.199   1164
  Min Nonbonded Distance : 2.454

Molprobity Statistics.
  All-atom Clashscore : 13.74
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 15.65 %
    Favored  : 84.35 %
  Rotamer:
    Outliers :  3.83 %
    Allowed  : 24.68 %
    Favored  : 71.49 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.74 (0.25), residues: 1054
  helix: -0.72 (0.22), residues: 548
  sheet: -1.50 (0.73), residues: 46
  loop : -3.29 (0.28), residues: 460

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.019   0.002   TRP C  81 
 HIS   0.007   0.001   HIS D 124 
 PHE   0.012   0.002   PHE D 107 
 TYR   0.025   0.002   TYR C  96 
 ARG   0.005   0.001   ARG C 175 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03760 (  300)
  hydrogen bonds       : angle       4.98453 (  852)
  covalent geometry    : bond        0.00556 ( 8802)
  covalent geometry    : angle       0.89952 (11918)

*********************** 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
  240 residues out of total 940 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 204
  time to evaluate  : 1.067 
Fit side-chains
REVERT: A    9 ASN cc_start: 0.9147 (m-40) cc_final: 0.8449 (t0)
REVERT: A   27 MET cc_start: -0.1070 (tpp) cc_final: -0.2059 (mpp)
REVERT: A   38 TYR cc_start: 0.8904 (m-80) cc_final: 0.8504 (m-80)
REVERT: A  251 GLN cc_start: 0.8281 (tp-100) cc_final: 0.7899 (tp-100)
REVERT: A  257 MET cc_start: 0.8575 (mmt) cc_final: 0.8249 (mtt)
REVERT: B   27 MET cc_start: -0.1101 (tpp) cc_final: -0.2256 (mpp)
REVERT: B   84 ASP cc_start: 0.7220 (OUTLIER) cc_final: 0.7007 (m-30)
REVERT: B  251 GLN cc_start: 0.8607 (tp-100) cc_final: 0.8193 (tp-100)
REVERT: C  124 HIS cc_start: 0.8793 (OUTLIER) cc_final: 0.8405 (m90)
REVERT: C  189 LEU cc_start: 0.9361 (OUTLIER) cc_final: 0.9120 (tp)
REVERT: C  259 LYS cc_start: 0.8982 (mmtt) cc_final: 0.8383 (tmtt)
REVERT: C  266 ASP cc_start: 0.8162 (p0) cc_final: 0.7598 (p0)
REVERT: D   14 ASN cc_start: 0.9228 (m-40) cc_final: 0.8955 (m-40)
REVERT: D   86 GLN cc_start: 0.8777 (pp30) cc_final: 0.8496 (pp30)
REVERT: D  219 GLU cc_start: 0.8661 (mm-30) cc_final: 0.8226 (mm-30)
REVERT: D  259 LYS cc_start: 0.8986 (mmtt) cc_final: 0.8510 (tmtt)
REVERT: D  266 ASP cc_start: 0.8035 (p0) cc_final: 0.7375 (p0)
  outliers start: 36
  outliers final: 28
  residues processed: 232
  average time/residue: 0.1613
  time to fit residues: 54.8041
Evaluate side-chains
  230 residues out of total 940 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 199
  time to evaluate  : 1.019 
-------------------------------------------------------------------------------
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   69 ILE
Chi-restraints excluded: chain B residue   84 ASP
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  221 VAL
Chi-restraints excluded: chain B residue  230 ILE
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  124 HIS
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  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 16 optimal weight:    0.3980
   chunk 45 optimal weight:    0.8980
   chunk 98 optimal weight:    4.9990
   chunk 47 optimal weight:    6.9990
   chunk 60 optimal weight:    0.7980
   chunk 101 optimal weight:    2.9990
   chunk 69 optimal weight:    4.9990
   chunk 20 optimal weight:    5.9990
   chunk 61 optimal weight:    0.6980
   chunk 75 optimal weight:    4.9990
   chunk 42 optimal weight:    1.9990
   overall best weight:    0.9582

-------------------------------------------------------------------------------
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 124 HIS
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 = 0.3398 r_free = 0.3398 target = 0.099790 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3068 r_free = 0.3068 target = 0.081333 restraints weight = 23406.093|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 23)----------------|
| r_work = 0.3111 r_free = 0.3111 target = 0.083611 restraints weight = 13918.319|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3140 r_free = 0.3140 target = 0.085169 restraints weight = 9765.383|
|-----------------------------------------------------------------------------|
r_work (final): 0.3143
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8257
moved from start:          0.5308

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.079   8802  Z= 0.146
  Angle     :  0.876  12.884  11918  Z= 0.425
  Chirality :  0.048   0.196   1350
  Planarity :  0.004   0.032   1468
  Dihedral  :  6.178  25.798   1164
  Min Nonbonded Distance : 2.456

Molprobity Statistics.
  All-atom Clashscore : 12.19
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 14.23 %
    Favored  : 85.77 %
  Rotamer:
    Outliers :  3.19 %
    Allowed  : 26.06 %
    Favored  : 70.74 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.67 (0.26), residues: 1054
  helix: -0.64 (0.22), residues: 548
  sheet: -1.27 (0.76), residues: 46
  loop : -3.32 (0.27), residues: 460

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.002   TRP C  81 
 HIS   0.005   0.001   HIS D 124 
 PHE   0.012   0.001   PHE C 163 
 TYR   0.014   0.002   TYR D 151 
 ARG   0.006   0.000   ARG B 258 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03599 (  300)
  hydrogen bonds       : angle       5.03174 (  852)
  covalent geometry    : bond        0.00338 ( 8802)
  covalent geometry    : angle       0.87552 (11918)

*********************** 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
  246 residues out of total 940 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 216
  time to evaluate  : 1.068 
Fit side-chains
   revert: symmetry clash
REVERT: A    9 ASN cc_start: 0.9145 (m-40) cc_final: 0.8444 (t0)
REVERT: A   27 MET cc_start: -0.1064 (tpp) cc_final: -0.2027 (mpp)
REVERT: A   38 TYR cc_start: 0.8945 (m-80) cc_final: 0.8479 (m-80)
REVERT: A  251 GLN cc_start: 0.8293 (tp-100) cc_final: 0.7823 (tp-100)
REVERT: A  257 MET cc_start: 0.8544 (mmt) cc_final: 0.8157 (mtt)
REVERT: B   27 MET cc_start: -0.1119 (tpp) cc_final: -0.2251 (mpp)
REVERT: B  251 GLN cc_start: 0.8633 (tp-100) cc_final: 0.8094 (tp-100)
REVERT: B  257 MET cc_start: 0.8995 (mtm) cc_final: 0.8297 (mmt)
REVERT: C   34 TYR cc_start: 0.7205 (OUTLIER) cc_final: 0.6702 (p90)
REVERT: C  266 ASP cc_start: 0.8101 (p0) cc_final: 0.7561 (p0)
REVERT: D   47 GLN cc_start: 0.9536 (tm-30) cc_final: 0.9183 (tm-30)
REVERT: D   86 GLN cc_start: 0.8807 (pp30) cc_final: 0.8466 (pp30)
REVERT: D  206 GLN cc_start: 0.8664 (tt0) cc_final: 0.8318 (mt0)
REVERT: D  215 TYR cc_start: 0.9035 (t80) cc_final: 0.8716 (t80)
REVERT: D  219 GLU cc_start: 0.8815 (mm-30) cc_final: 0.8401 (mm-30)
REVERT: D  259 LYS cc_start: 0.8959 (mmtt) cc_final: 0.8464 (tmtt)
REVERT: D  266 ASP cc_start: 0.7932 (p0) cc_final: 0.7220 (p0)
  outliers start: 30
  outliers final: 23
  residues processed: 235
  average time/residue: 0.1559
  time to fit residues: 54.3959
Evaluate side-chains
  235 residues out of total 940 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 211
  time to evaluate  : 0.966 
-------------------------------------------------------------------------------
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  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  221 VAL
Chi-restraints excluded: chain B residue  230 ILE
Chi-restraints excluded: chain B residue  252 TYR
Chi-restraints excluded: chain C residue   34 TYR
Chi-restraints excluded: chain C residue   72 LEU
Chi-restraints excluded: chain C residue  169 THR
Chi-restraints excluded: chain C residue  192 THR
Chi-restraints excluded: chain C residue  204 LEU
Chi-restraints excluded: chain D residue    8 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 5 optimal weight:    0.9990
   chunk 23 optimal weight:    0.5980
   chunk 35 optimal weight:    1.9990
   chunk 44 optimal weight:    2.9990
   chunk 36 optimal weight:    0.6980
   chunk 81 optimal weight:    6.9990
   chunk 13 optimal weight:    4.9990
   chunk 52 optimal weight:    5.9990
   chunk 83 optimal weight:    4.9990
   chunk 11 optimal weight:    0.8980
   chunk 55 optimal weight:    6.9990
   overall best weight:    1.0384

-------------------------------------------------------------------------------
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 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 = 0.3407 r_free = 0.3407 target = 0.100422 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3080 r_free = 0.3080 target = 0.082081 restraints weight = 23188.720|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3123 r_free = 0.3123 target = 0.084380 restraints weight = 13849.160|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3152 r_free = 0.3152 target = 0.085980 restraints weight = 9702.522|
|-----------------------------------------------------------------------------|
r_work (final): 0.3154
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8246
moved from start:          0.5462

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= 0.147
  Angle     :  0.874  12.798  11918  Z= 0.421
  Chirality :  0.048   0.192   1350
  Planarity :  0.004   0.026   1468
  Dihedral  :  6.057  25.000   1164
  Min Nonbonded Distance : 2.441

Molprobity Statistics.
  All-atom Clashscore : 12.36
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 15.28 %
    Favored  : 84.72 %
  Rotamer:
    Outliers :  2.66 %
    Allowed  : 27.13 %
    Favored  : 70.21 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.58 (0.26), residues: 1054
  helix: -0.55 (0.23), residues: 538
  sheet: -1.04 (0.80), residues: 46
  loop : -3.27 (0.28), residues: 470

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.002   TRP C  81 
 HIS   0.005   0.001   HIS C 124 
 PHE   0.011   0.001   PHE C 264 
 TYR   0.020   0.002   TYR C 215 
 ARG   0.005   0.000   ARG B 250 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03465 (  300)
  hydrogen bonds       : angle       5.06098 (  852)
  covalent geometry    : bond        0.00342 ( 8802)
  covalent geometry    : angle       0.87398 (11918)

********************** 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
  242 residues out of total 940 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 217
  time to evaluate  : 0.970 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A    9 ASN cc_start: 0.9140 (m-40) cc_final: 0.8493 (t0)
REVERT: A   27 MET cc_start: -0.0844 (tpp) cc_final: -0.1877 (mpp)
REVERT: A   38 TYR cc_start: 0.8919 (m-80) cc_final: 0.8414 (m-80)
REVERT: A  251 GLN cc_start: 0.8314 (tp-100) cc_final: 0.7954 (tp-100)
REVERT: A  257 MET cc_start: 0.8526 (mmt) cc_final: 0.8142 (mtt)
REVERT: B   27 MET cc_start: -0.1072 (tpp) cc_final: -0.2232 (mpp)
REVERT: B  123 MET cc_start: 0.8821 (ptp) cc_final: 0.8158 (pmm)
REVERT: B  251 GLN cc_start: 0.8622 (tp-100) cc_final: 0.8202 (tp-100)
REVERT: B  257 MET cc_start: 0.9028 (mtm) cc_final: 0.8328 (mmt)
REVERT: C   52 TRP cc_start: 0.9330 (t60) cc_final: 0.9014 (t60)
REVERT: C   53 PHE cc_start: 0.7985 (t80) cc_final: 0.7491 (t80)
REVERT: C  266 ASP cc_start: 0.8082 (p0) cc_final: 0.7560 (p0)
REVERT: D   47 GLN cc_start: 0.9541 (tm-30) cc_final: 0.9202 (tm-30)
REVERT: D   86 GLN cc_start: 0.8772 (pp30) cc_final: 0.8248 (pp30)
REVERT: D  126 MET cc_start: 0.8258 (ttp) cc_final: 0.7979 (ttm)
REVERT: D  206 GLN cc_start: 0.8611 (tt0) cc_final: 0.8354 (tm-30)
REVERT: D  259 LYS cc_start: 0.8963 (mmtt) cc_final: 0.8447 (tmtt)
REVERT: D  266 ASP cc_start: 0.7947 (p0) cc_final: 0.7216 (p0)
  outliers start: 25
  outliers final: 23
  residues processed: 231
  average time/residue: 0.1694
  time to fit residues: 58.0598
Evaluate side-chains
  234 residues out of total 940 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 211
  time to evaluate  : 0.965 
-------------------------------------------------------------------------------
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  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  221 VAL
Chi-restraints excluded: chain B residue  230 ILE
Chi-restraints excluded: chain B residue  252 TYR
Chi-restraints excluded: chain C residue   72 LEU
Chi-restraints excluded: chain C residue  169 THR
Chi-restraints excluded: chain C residue  192 THR
Chi-restraints excluded: chain C residue  204 LEU
Chi-restraints excluded: chain D residue    8 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 46 optimal weight:    1.9990
   chunk 93 optimal weight:    0.9980
   chunk 83 optimal weight:    3.9990
   chunk 99 optimal weight:    0.0270
   chunk 7 optimal weight:    4.9990
   chunk 33 optimal weight:    0.9990
   chunk 72 optimal weight:   20.0000
   chunk 29 optimal weight:    3.9990
   chunk 10 optimal weight:    0.4980
   chunk 28 optimal weight:    0.0370
   chunk 47 optimal weight:    0.6980
   overall best weight:    0.4516

-------------------------------------------------------------------------------
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 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 = 0.3446 r_free = 0.3446 target = 0.102765 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3120 r_free = 0.3120 target = 0.084263 restraints weight = 23325.504|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3163 r_free = 0.3163 target = 0.086606 restraints weight = 14036.707|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3192 r_free = 0.3192 target = 0.088225 restraints weight = 9865.941|
|-----------------------------------------------------------------------------|
r_work (final): 0.3188
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8206
moved from start:          0.5618

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.061   8802  Z= 0.133
  Angle     :  0.879  13.317  11918  Z= 0.420
  Chirality :  0.047   0.191   1350
  Planarity :  0.004   0.028   1468
  Dihedral  :  6.006  25.119   1164
  Min Nonbonded Distance : 2.444

Molprobity Statistics.
  All-atom Clashscore : 11.32
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 14.42 %
    Favored  : 85.58 %
  Rotamer:
    Outliers :  2.66 %
    Allowed  : 26.91 %
    Favored  : 70.43 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.50 (0.26), residues: 1054
  helix: -0.51 (0.23), residues: 538
  sheet: -0.84 (0.84), residues: 46
  loop : -3.21 (0.28), residues: 470

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP C  52 
 HIS   0.005   0.001   HIS C 124 
 PHE   0.011   0.001   PHE C 163 
 TYR   0.014   0.002   TYR D 151 
 ARG   0.005   0.000   ARG B 250 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03343 (  300)
  hydrogen bonds       : angle       5.13451 (  852)
  covalent geometry    : bond        0.00299 ( 8802)
  covalent geometry    : angle       0.87905 (11918)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2823.88 seconds
wall clock time: 49 minutes 42.53 seconds (2982.53 seconds total)