Starting phenix.real_space_refine
on Thu Feb 13 02:47:22 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/6jbh_9790/02_2025/6jbh_9790.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/6jbh_9790/02_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_9790/02_2025/6jbh_9790.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/6jbh_9790/02_2025/6jbh_9790.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/6jbh_9790/02_2025/6jbh_9790.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/6jbh_9790/02_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-5592/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: 5.05, per 1000 atoms: 0.59
  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: 1.81
  Conformation dependent library (CDL) restraints added in 1.0 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: 0.89
  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: 2.00

  Time building geometry restraints manager: 2.17 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:                  0.000
  Normalize map: mean=0, sd=1:             0.490
  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:          0.330
  Check model and map are aligned:         0.060
  Set scattering table:                    0.070
  Process input model:                     20.730
  Find NCS groups from input model:        0.140
  Set up NCS constraints:                  0.030
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:2.780
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   24.640
-------------------------------------------------------------------------------
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= 0.442
  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 

*********************** 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  : 1.062 
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: 0.2458
  time to fit residues: 125.6619
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  : 1.010 
-------------------------------------------------------------------------------
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 = 39)----------------|
| r_work = 0.3084 r_free = 0.3084 target = 0.083054 restraints weight = 22587.054|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 41)----------------|
| r_work = 0.3125 r_free = 0.3125 target = 0.085326 restraints weight = 13491.115|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.3153 r_free = 0.3153 target = 0.086846 restraints weight = 9511.065|
|-----------------------------------------------------------------------------|
r_work (final): 0.3152
-------------------------------------------------------------------------------
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= 0.220
  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 

*********************** 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  : 1.029 
Fit side-chains
REVERT: A   27 MET cc_start: -0.0735 (tpp) cc_final: -0.1387 (mpp)
REVERT: A   38 TYR cc_start: 0.8627 (m-80) cc_final: 0.7976 (m-80)
REVERT: A  251 GLN cc_start: 0.8402 (tp-100) cc_final: 0.7745 (tp-100)
REVERT: B   11 THR cc_start: 0.9161 (m) cc_final: 0.8627 (t)
REVERT: B   27 MET cc_start: -0.1158 (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: 0.7945 (mtmm) cc_final: 0.7675 (mtmm)
REVERT: B  251 GLN cc_start: 0.8552 (tp-100) cc_final: 0.7844 (tp-100)
REVERT: C   38 LEU cc_start: 0.8161 (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: 0.8580 (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: 0.8717 (pp30) cc_final: 0.8432 (pp30)
REVERT: D  126 MET cc_start: 0.6880 (tpp) cc_final: 0.5908 (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: 0.8298 (p0) cc_final: 0.7450 (p0)
  outliers start: 26
  outliers final: 16
  residues processed: 276
  average time/residue: 0.1847
  time to fit residues: 71.2583
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  : 1.036 
-------------------------------------------------------------------------------
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:    0.4980
   chunk 93 optimal weight:    3.9990
   chunk 58 optimal weight:    9.9990
   chunk 92 optimal weight:    9.9990
   chunk 49 optimal weight:    4.9990
   chunk 100 optimal weight:    4.9990
   chunk 27 optimal weight:    0.0270
   chunk 21 optimal weight:    8.9990
   chunk 23 optimal weight:    4.9990
   chunk 37 optimal weight:    0.6980
   overall best weight:    1.2440

-------------------------------------------------------------------------------
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 = 0.3394 r_free = 0.3394 target = 0.099809 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3061 r_free = 0.3061 target = 0.081423 restraints weight = 23253.035|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3104 r_free = 0.3104 target = 0.083725 restraints weight = 13806.830|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3135 r_free = 0.3135 target = 0.085314 restraints weight = 9692.849|
|-----------------------------------------------------------------------------|
r_work (final): 0.3129
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8256
moved from start:          0.4083

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.047   8802  Z= 0.230
  Angle     :  0.845   9.494  11918  Z= 0.422
  Chirality :  0.049   0.252   1350
  Planarity :  0.004   0.031   1468
  Dihedral  :  6.887  27.879   1164
  Min Nonbonded Distance : 2.504

Molprobity Statistics.
  All-atom Clashscore : 11.84
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 14.33 %
    Favored  : 85.67 %
  Rotamer:
    Outliers :  5.32 %
    Allowed  : 18.30 %
    Favored  : 76.38 %
  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: -3.84 (0.23), residues: 1054
  helix: -1.84 (0.20), residues: 520
  sheet: -2.84 (0.67), residues: 46
  loop : -3.34 (0.27), residues: 488

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.021   0.002   TRP C  81 
 HIS   0.005   0.001   HIS C 124 
 PHE   0.020   0.001   PHE D  70 
 TYR   0.029   0.002   TYR C 215 
 ARG   0.006   0.001   ARG A  41 

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

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

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

  2108 Ramachandran restraints generated.
    1054 Oldfield, 0 Emsley, 1054 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  278 residues out of total 940 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 50
    poor density    : 228
  time to evaluate  : 1.067 
Fit side-chains
REVERT: A   27 MET cc_start: -0.0722 (tpp) cc_final: -0.1468 (mpp)
REVERT: A   38 TYR cc_start: 0.8683 (m-80) cc_final: 0.7966 (m-80)
REVERT: A  251 GLN cc_start: 0.8483 (tp-100) cc_final: 0.7863 (tp-100)
REVERT: B    5 VAL cc_start: 0.8368 (OUTLIER) cc_final: 0.8142 (m)
REVERT: B   11 THR cc_start: 0.9184 (m) cc_final: 0.8739 (t)
REVERT: B   16 LEU cc_start: 0.8449 (tm) cc_final: 0.8129 (tm)
REVERT: B   27 MET cc_start: -0.1034 (tpp) cc_final: -0.1795 (mpp)
REVERT: B  247 LYS cc_start: 0.7751 (mtmm) cc_final: 0.7459 (mtmm)
REVERT: B  251 GLN cc_start: 0.8590 (tp-100) cc_final: 0.7969 (tp-100)
REVERT: C  206 GLN cc_start: 0.8598 (tt0) cc_final: 0.8219 (mt0)
REVERT: C  215 TYR cc_start: 0.8929 (t80) cc_final: 0.8594 (t80)
REVERT: C  219 GLU cc_start: 0.8561 (mm-30) cc_final: 0.8063 (mm-30)
REVERT: C  225 LEU cc_start: 0.8573 (OUTLIER) cc_final: 0.8339 (pp)
REVERT: C  259 LYS cc_start: 0.8890 (mmtt) cc_final: 0.8302 (tmtt)
REVERT: C  266 ASP cc_start: 0.8268 (p0) cc_final: 0.7606 (p0)
REVERT: D   86 GLN cc_start: 0.8879 (pp30) cc_final: 0.8571 (pp30)
REVERT: D  165 LEU cc_start: 0.9367 (mp) cc_final: 0.9077 (mp)
REVERT: D  225 LEU cc_start: 0.8522 (OUTLIER) cc_final: 0.8316 (pp)
REVERT: D  259 LYS cc_start: 0.8912 (mmtt) cc_final: 0.8289 (tmtt)
REVERT: D  266 ASP cc_start: 0.8066 (p0) cc_final: 0.7239 (p0)
  outliers start: 50
  outliers final: 30
  residues processed: 264
  average time/residue: 0.1617
  time to fit residues: 62.3621
Evaluate side-chains
  245 residues out of total 940 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 212
  time to evaluate  : 1.150 
-------------------------------------------------------------------------------
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  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   89 LEU
Chi-restraints excluded: chain B residue  101 THR
Chi-restraints excluded: chain B residue  108 LEU
Chi-restraints excluded: chain B residue  126 ASP
Chi-restraints excluded: chain B residue  133 ILE
Chi-restraints excluded: chain B residue  159 ASN
Chi-restraints excluded: chain B residue  230 ILE
Chi-restraints excluded: chain B residue  252 TYR
Chi-restraints excluded: chain C residue   79 THR
Chi-restraints excluded: chain C residue  159 LEU
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  159 LEU
Chi-restraints excluded: chain D residue  169 THR
Chi-restraints excluded: chain D residue  225 LEU
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:    2.9990
   chunk 78 optimal weight:    4.9990
   chunk 17 optimal weight:    0.0970
   chunk 43 optimal weight:    7.9990
   chunk 103 optimal weight:    4.9990
   chunk 73 optimal weight:    1.9990
   chunk 26 optimal weight:   10.0000
   chunk 97 optimal weight:    0.4980
   overall best weight:    1.9184

-------------------------------------------------------------------------------
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
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 = 0.3357 r_free = 0.3357 target = 0.097471 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 29)----------------|
| r_work = 0.3025 r_free = 0.3025 target = 0.079293 restraints weight = 23303.115|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3067 r_free = 0.3067 target = 0.081538 restraints weight = 13888.920|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.3097 r_free = 0.3097 target = 0.083061 restraints weight = 9774.199|
|-----------------------------------------------------------------------------|
r_work (final): 0.3091
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8295
moved from start:          0.4424

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.049   8802  Z= 0.282
  Angle     :  0.847  10.477  11918  Z= 0.425
  Chirality :  0.050   0.300   1350
  Planarity :  0.004   0.036   1468
  Dihedral  :  6.693  27.008   1164
  Min Nonbonded Distance : 2.416

Molprobity Statistics.
  All-atom Clashscore : 12.42
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 15.65 %
    Favored  : 84.35 %
  Rotamer:
    Outliers :  4.68 %
    Allowed  : 19.04 %
    Favored  : 76.28 %
  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: -3.51 (0.24), residues: 1054
  helix: -1.48 (0.21), residues: 562
  sheet: -2.92 (0.67), residues: 46
  loop : -3.38 (0.28), residues: 446

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.002   TRP D  52 
 HIS   0.005   0.001   HIS C 124 
 PHE   0.014   0.002   PHE D  70 
 TYR   0.023   0.002   TYR C 215 
 ARG   0.004   0.000   ARG D 175 

*********************** 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
  260 residues out of total 940 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 44
    poor density    : 216
  time to evaluate  : 0.955 
Fit side-chains
REVERT: A   16 LEU cc_start: 0.8144 (tm) cc_final: 0.7756 (tm)
REVERT: A   27 MET cc_start: -0.0652 (tpp) cc_final: -0.1404 (mpp)
REVERT: A   38 TYR cc_start: 0.8773 (m-80) cc_final: 0.8493 (m-80)
REVERT: A  251 GLN cc_start: 0.8426 (tp-100) cc_final: 0.7936 (tp-100)
REVERT: A  265 LEU cc_start: 0.7055 (OUTLIER) cc_final: 0.6828 (pp)
REVERT: B   27 MET cc_start: -0.1083 (tpp) cc_final: -0.1866 (mpp)
REVERT: B  247 LYS cc_start: 0.7848 (mtmm) cc_final: 0.7603 (mtmm)
REVERT: B  251 GLN cc_start: 0.8563 (tp-100) cc_final: 0.7960 (tp-100)
REVERT: C  189 LEU cc_start: 0.9295 (OUTLIER) cc_final: 0.9014 (tp)
REVERT: C  206 GLN cc_start: 0.8691 (tt0) cc_final: 0.8290 (mt0)
REVERT: C  215 TYR cc_start: 0.8966 (t80) cc_final: 0.8404 (t80)
REVERT: C  219 GLU cc_start: 0.8722 (mm-30) cc_final: 0.8311 (mm-30)
REVERT: C  225 LEU cc_start: 0.8607 (OUTLIER) cc_final: 0.8344 (pp)
REVERT: C  259 LYS cc_start: 0.8969 (mmtt) cc_final: 0.8322 (tmtt)
REVERT: C  266 ASP cc_start: 0.8315 (p0) cc_final: 0.7717 (p0)
REVERT: D   86 GLN cc_start: 0.8953 (pp30) cc_final: 0.8627 (pp30)
REVERT: D  126 MET cc_start: 0.8113 (ttm) cc_final: 0.7907 (ttp)
REVERT: D  165 LEU cc_start: 0.9375 (mp) cc_final: 0.9161 (mm)
REVERT: D  225 LEU cc_start: 0.8549 (OUTLIER) cc_final: 0.8312 (pp)
REVERT: D  259 LYS cc_start: 0.8921 (mmtt) cc_final: 0.8327 (tmtt)
REVERT: D  266 ASP cc_start: 0.8121 (p0) cc_final: 0.7375 (p0)
  outliers start: 44
  outliers final: 30
  residues processed: 250
  average time/residue: 0.1590
  time to fit residues: 58.4508
Evaluate side-chains
  232 residues out of total 940 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 198
  time to evaluate  : 1.072 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   11 THR
Chi-restraints excluded: chain A residue   65 THR
Chi-restraints excluded: chain A residue   69 ILE
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 A residue  265 LEU
Chi-restraints excluded: chain B residue   10 VAL
Chi-restraints excluded: chain B residue   65 THR
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   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  225 LEU
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  159 LEU
Chi-restraints excluded: chain D residue  169 THR
Chi-restraints excluded: chain D residue  225 LEU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 104
   random chunks:
   chunk 15 optimal weight:    3.9990
   chunk 16 optimal weight:    0.0020
   chunk 32 optimal weight:    2.9990
   chunk 102 optimal weight:    2.9990
   chunk 78 optimal weight:    3.9990
   chunk 89 optimal weight:    1.9990
   chunk 12 optimal weight:    0.8980
   chunk 30 optimal weight:    5.9990
   chunk 58 optimal weight:    8.9990
   chunk 66 optimal weight:    3.9990
   chunk 43 optimal weight:    0.4980
   overall best weight:    1.2792

-------------------------------------------------------------------------------
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 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 = 0.3373 r_free = 0.3373 target = 0.098516 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3046 r_free = 0.3046 target = 0.080402 restraints weight = 23278.009|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 25)----------------|
| r_work = 0.3088 r_free = 0.3088 target = 0.082638 restraints weight = 13820.919|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.3117 r_free = 0.3117 target = 0.084181 restraints weight = 9724.896|
|-----------------------------------------------------------------------------|
r_work (final): 0.3112
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8275
moved from start:          0.4681

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.046   8802  Z= 0.222
  Angle     :  0.827  11.131  11918  Z= 0.411
  Chirality :  0.048   0.213   1350
  Planarity :  0.004   0.034   1468
  Dihedral  :  6.530  27.267   1164
  Min Nonbonded Distance : 2.502

Molprobity Statistics.
  All-atom Clashscore : 11.55
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 14.80 %
    Favored  : 85.20 %
  Rotamer:
    Outliers :  4.36 %
    Allowed  : 20.32 %
    Favored  : 75.32 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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: -3.05 (0.25), residues: 1054
  helix: -1.08 (0.22), residues: 542
  sheet: -2.72 (0.67), residues: 46
  loop : -3.13 (0.29), residues: 466

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   0.042   0.001   PHE C  70 
 TYR   0.019   0.002   TYR C 215 
 ARG   0.005   0.000   ARG A  41 

*********************** 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
  257 residues out of total 940 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 41
    poor density    : 216
  time to evaluate  : 0.972 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   16 LEU cc_start: 0.8246 (OUTLIER) cc_final: 0.7925 (tm)
REVERT: A   27 MET cc_start: -0.1052 (tpp) cc_final: -0.2020 (mpp)
REVERT: A   38 TYR cc_start: 0.8923 (m-80) cc_final: 0.8515 (m-80)
REVERT: A  251 GLN cc_start: 0.8392 (tp-100) cc_final: 0.7898 (tp-100)
REVERT: B   27 MET cc_start: -0.1341 (tpp) cc_final: -0.2297 (mpp)
REVERT: B   86 GLN cc_start: 0.6933 (pm20) cc_final: 0.6622 (pm20)
REVERT: B  251 GLN cc_start: 0.8567 (tp-100) cc_final: 0.7971 (tp-100)
REVERT: C  189 LEU cc_start: 0.9260 (OUTLIER) cc_final: 0.9025 (tp)
REVERT: C  225 LEU cc_start: 0.8482 (OUTLIER) cc_final: 0.8243 (pp)
REVERT: C  259 LYS cc_start: 0.8954 (mmtt) cc_final: 0.8313 (tmtt)
REVERT: C  266 ASP cc_start: 0.8172 (p0) cc_final: 0.7561 (p0)
REVERT: D   47 GLN cc_start: 0.9415 (OUTLIER) cc_final: 0.8824 (tm-30)
REVERT: D   86 GLN cc_start: 0.8832 (pp30) cc_final: 0.8536 (pp30)
REVERT: D  165 LEU cc_start: 0.9432 (mp) cc_final: 0.9222 (mm)
REVERT: D  259 LYS cc_start: 0.8896 (mmtt) cc_final: 0.8317 (tmtt)
REVERT: D  266 ASP cc_start: 0.8046 (p0) cc_final: 0.7291 (p0)
  outliers start: 41
  outliers final: 25
  residues processed: 247
  average time/residue: 0.1677
  time to fit residues: 59.5836
Evaluate side-chains
  232 residues out of total 940 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 203
  time to evaluate  : 0.944 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   11 THR
Chi-restraints excluded: chain A residue   16 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   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  114 THR
Chi-restraints excluded: chain C residue  169 THR
Chi-restraints excluded: chain C residue  189 LEU
Chi-restraints excluded: chain C residue  192 THR
Chi-restraints excluded: chain C residue  225 LEU
Chi-restraints excluded: chain D residue   47 GLN
Chi-restraints excluded: chain D residue   79 THR
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=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 104
   random chunks:
   chunk 5 optimal weight:    1.9990
   chunk 39 optimal weight:    2.9990
   chunk 23 optimal weight:    4.9990
   chunk 8 optimal weight:    0.0040
   chunk 80 optimal weight:    6.9990
   chunk 93 optimal weight:    0.8980
   chunk 65 optimal weight:    0.3980
   chunk 53 optimal weight:    1.9990
   chunk 57 optimal weight:    0.0010
   chunk 9 optimal weight:    2.9990
   chunk 64 optimal weight:    0.3980
   overall best weight:    0.3398

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

Flipped N/Q/H residues before XYZ refinement:
** A 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 260 GLN
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 = 0.3418 r_free = 0.3418 target = 0.101271 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3101 r_free = 0.3101 target = 0.083444 restraints weight = 22629.125|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 23)----------------|
| r_work = 0.3144 r_free = 0.3144 target = 0.085746 restraints weight = 13372.595|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3174 r_free = 0.3174 target = 0.087335 restraints weight = 9302.822|
|-----------------------------------------------------------------------------|
r_work (final): 0.3174
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8214
moved from start:          0.4938

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.043   8802  Z= 0.185
  Angle     :  0.812  12.400  11918  Z= 0.399
  Chirality :  0.048   0.307   1350
  Planarity :  0.004   0.030   1468
  Dihedral  :  6.341  26.836   1164
  Min Nonbonded Distance : 2.500

Molprobity Statistics.
  All-atom Clashscore : 11.84
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 14.61 %
    Favored  : 85.39 %
  Rotamer:
    Outliers :  3.51 %
    Allowed  : 22.66 %
    Favored  : 73.83 %
  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: -2.91 (0.25), residues: 1054
  helix: -0.94 (0.22), residues: 542
  sheet: -2.42 (0.67), residues: 46
  loop : -3.12 (0.29), residues: 466

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.002   TRP C  52 
 HIS   0.004   0.001   HIS C 257 
 PHE   0.018   0.001   PHE C 242 
 TYR   0.016   0.002   TYR A 234 
 ARG   0.006   0.000   ARG A  41 

*********************** 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
  265 residues out of total 940 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 232
  time to evaluate  : 0.926 
Fit side-chains
   revert: symmetry clash
REVERT: A    9 ASN cc_start: 0.9102 (m-40) cc_final: 0.8396 (t0)
REVERT: A   16 LEU cc_start: 0.8485 (OUTLIER) cc_final: 0.8276 (tm)
REVERT: A   27 MET cc_start: -0.0987 (tpp) cc_final: -0.1966 (mpp)
REVERT: A   38 TYR cc_start: 0.8866 (m-80) cc_final: 0.7858 (m-80)
REVERT: A   86 GLN cc_start: 0.6874 (pm20) cc_final: 0.6343 (pm20)
REVERT: A  251 GLN cc_start: 0.8327 (tp-100) cc_final: 0.7711 (tp-100)
REVERT: B   27 MET cc_start: -0.1546 (tpp) cc_final: -0.2536 (mpp)
REVERT: B   86 GLN cc_start: 0.6693 (pm20) cc_final: 0.6392 (pm20)
REVERT: B  251 GLN cc_start: 0.8513 (tp-100) cc_final: 0.7990 (tp-100)
REVERT: C  206 GLN cc_start: 0.8585 (tt0) cc_final: 0.8114 (mm-40)
REVERT: C  259 LYS cc_start: 0.8909 (mmtt) cc_final: 0.8312 (tmtt)
REVERT: C  266 ASP cc_start: 0.8041 (p0) cc_final: 0.7473 (p0)
REVERT: D   47 GLN cc_start: 0.9257 (OUTLIER) cc_final: 0.9024 (tm-30)
REVERT: D   86 GLN cc_start: 0.8812 (pp30) cc_final: 0.8497 (pp30)
REVERT: D  165 LEU cc_start: 0.9420 (mp) cc_final: 0.9194 (mm)
REVERT: D  206 GLN cc_start: 0.8617 (tt0) cc_final: 0.8376 (tm-30)
REVERT: D  219 GLU cc_start: 0.8775 (mm-30) cc_final: 0.8472 (mm-30)
REVERT: D  225 LEU cc_start: 0.8395 (OUTLIER) cc_final: 0.8155 (pp)
REVERT: D  259 LYS cc_start: 0.8924 (mmtt) cc_final: 0.8262 (tmtt)
REVERT: D  266 ASP cc_start: 0.7923 (p0) cc_final: 0.7172 (p0)
  outliers start: 33
  outliers final: 21
  residues processed: 252
  average time/residue: 0.1868
  time to fit residues: 67.5350
Evaluate side-chains
  230 residues out of total 940 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 206
  time to evaluate  : 1.018 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   11 THR
Chi-restraints excluded: chain A residue   16 LEU
Chi-restraints excluded: chain A residue  108 LEU
Chi-restraints excluded: chain A residue  126 ASP
Chi-restraints excluded: chain A residue  133 ILE
Chi-restraints excluded: chain A residue  159 ASN
Chi-restraints excluded: chain A residue  221 VAL
Chi-restraints excluded: chain A residue  230 ILE
Chi-restraints excluded: chain A residue  252 TYR
Chi-restraints excluded: chain B residue   89 LEU
Chi-restraints excluded: chain B residue  101 THR
Chi-restraints excluded: chain B residue  108 LEU
Chi-restraints excluded: chain B residue  126 ASP
Chi-restraints excluded: chain B residue  133 ILE
Chi-restraints excluded: chain B residue  159 ASN
Chi-restraints excluded: chain B residue  230 ILE
Chi-restraints excluded: chain B residue  252 TYR
Chi-restraints excluded: chain C residue  114 THR
Chi-restraints excluded: chain C residue  169 THR
Chi-restraints excluded: chain D residue    8 LEU
Chi-restraints excluded: chain D residue   47 GLN
Chi-restraints excluded: chain D residue  111 VAL
Chi-restraints excluded: chain D residue  169 THR
Chi-restraints excluded: chain D residue  225 LEU
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:    4.9990
   chunk 37 optimal weight:    5.9990
   chunk 44 optimal weight:    2.9990
   chunk 47 optimal weight:    0.0570
   chunk 101 optimal weight:    0.8980
   chunk 84 optimal weight:    6.9990
   chunk 32 optimal weight:    0.9980
   chunk 59 optimal weight:    0.3980
   chunk 74 optimal weight:    0.0570
   chunk 86 optimal weight:    0.8980
   overall best weight:    0.4616

-------------------------------------------------------------------------------
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  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 = 0.3408 r_free = 0.3408 target = 0.101076 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3079 r_free = 0.3079 target = 0.082933 restraints weight = 23096.548|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3121 r_free = 0.3121 target = 0.085232 restraints weight = 13290.655|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3151 r_free = 0.3151 target = 0.086858 restraints weight = 9144.659|
|-----------------------------------------------------------------------------|
r_work (final): 0.3144
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8198
moved from start:          0.5180

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039   8802  Z= 0.182
  Angle     :  0.823  12.061  11918  Z= 0.398
  Chirality :  0.047   0.220   1350
  Planarity :  0.004   0.026   1468
  Dihedral  :  6.200  26.205   1164
  Min Nonbonded Distance : 2.484

Molprobity Statistics.
  All-atom Clashscore : 11.73
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 14.14 %
    Favored  : 85.86 %
  Rotamer:
    Outliers :  4.57 %
    Allowed  : 22.87 %
    Favored  : 72.55 %
  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: -2.76 (0.25), residues: 1054
  helix: -0.84 (0.22), residues: 542
  sheet: -1.94 (0.69), residues: 46
  loop : -3.08 (0.29), residues: 466

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP C  52 
 HIS   0.003   0.001   HIS C 124 
 PHE   0.011   0.001   PHE C 163 
 TYR   0.019   0.002   TYR C 215 
 ARG   0.004   0.000   ARG A  41 

*********************** 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
  276 residues out of total 940 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 43
    poor density    : 233
  time to evaluate  : 0.991 
Fit side-chains
   revert: symmetry clash
REVERT: A    9 ASN cc_start: 0.9124 (m-40) cc_final: 0.8427 (t0)
REVERT: A   16 LEU cc_start: 0.8477 (OUTLIER) cc_final: 0.8233 (tm)
REVERT: A   27 MET cc_start: -0.1101 (tpp) cc_final: -0.2011 (mpp)
REVERT: A   38 TYR cc_start: 0.8960 (m-80) cc_final: 0.8094 (m-80)
REVERT: A   41 ARG cc_start: 0.7619 (mtp85) cc_final: 0.7317 (mtp85)
REVERT: A   86 GLN cc_start: 0.6755 (pm20) cc_final: 0.6250 (pm20)
REVERT: A  251 GLN cc_start: 0.8416 (tp-100) cc_final: 0.7903 (tp-100)
REVERT: A  257 MET cc_start: 0.8727 (mmt) cc_final: 0.8192 (mtt)
REVERT: B   27 MET cc_start: -0.1335 (tpp) cc_final: -0.2349 (mpp)
REVERT: B   84 ASP cc_start: 0.6738 (OUTLIER) cc_final: 0.6308 (m-30)
REVERT: B   86 GLN cc_start: 0.6597 (pm20) cc_final: 0.6300 (pm20)
REVERT: B  251 GLN cc_start: 0.8573 (tp-100) cc_final: 0.8117 (tp-100)
REVERT: C  189 LEU cc_start: 0.9218 (OUTLIER) cc_final: 0.9016 (tp)
REVERT: C  206 GLN cc_start: 0.8648 (tt0) cc_final: 0.8175 (mm-40)
REVERT: C  225 LEU cc_start: 0.8481 (OUTLIER) cc_final: 0.8182 (pp)
REVERT: C  259 LYS cc_start: 0.8919 (mmtt) cc_final: 0.8263 (tmtt)
REVERT: C  266 ASP cc_start: 0.8059 (p0) cc_final: 0.7574 (p0)
REVERT: D    9 MET cc_start: 0.8544 (mmm) cc_final: 0.8329 (mmt)
REVERT: D   47 GLN cc_start: 0.9537 (OUTLIER) cc_final: 0.9242 (tm-30)
REVERT: D   86 GLN cc_start: 0.8902 (pp30) cc_final: 0.8199 (pp30)
REVERT: D  165 LEU cc_start: 0.9450 (mp) cc_final: 0.9192 (mm)
REVERT: D  206 GLN cc_start: 0.8687 (tt0) cc_final: 0.8178 (mt0)
REVERT: D  219 GLU cc_start: 0.8860 (mm-30) cc_final: 0.8523 (mm-30)
REVERT: D  225 LEU cc_start: 0.8316 (OUTLIER) cc_final: 0.8080 (pp)
REVERT: D  259 LYS cc_start: 0.8954 (mmtt) cc_final: 0.8250 (tmtt)
REVERT: D  266 ASP cc_start: 0.8053 (p0) cc_final: 0.7343 (p0)
  outliers start: 43
  outliers final: 22
  residues processed: 262
  average time/residue: 0.1714
  time to fit residues: 64.9799
Evaluate side-chains
  246 residues out of total 940 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 218
  time to evaluate  : 0.916 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   11 THR
Chi-restraints excluded: chain A residue   16 LEU
Chi-restraints excluded: chain A residue   53 ILE
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   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  133 ILE
Chi-restraints excluded: chain B residue  159 ASN
Chi-restraints excluded: chain B residue  230 ILE
Chi-restraints excluded: chain B residue  252 TYR
Chi-restraints excluded: chain C residue  114 THR
Chi-restraints excluded: chain C residue  169 THR
Chi-restraints excluded: chain C residue  189 LEU
Chi-restraints excluded: chain C residue  192 THR
Chi-restraints excluded: chain C residue  225 LEU
Chi-restraints excluded: chain D residue    8 LEU
Chi-restraints excluded: chain D residue   47 GLN
Chi-restraints excluded: chain D residue  111 VAL
Chi-restraints excluded: chain D residue  169 THR
Chi-restraints excluded: chain D residue  192 THR
Chi-restraints excluded: chain D residue  225 LEU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 104
   random chunks:
   chunk 0 optimal weight:   10.0000
   chunk 3 optimal weight:    3.9990
   chunk 10 optimal weight:    0.8980
   chunk 89 optimal weight:    1.9990
   chunk 21 optimal weight:    4.9990
   chunk 76 optimal weight:    1.9990
   chunk 34 optimal weight:    7.9990
   chunk 37 optimal weight:    1.9990
   chunk 53 optimal weight:    0.8980
   chunk 29 optimal weight:    7.9990
   chunk 66 optimal weight:    6.9990
   overall best weight:    1.5586

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

Flipped N/Q/H residues before XYZ refinement:
** A 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 260 GLN
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 = 0.3374 r_free = 0.3374 target = 0.098800 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3039 r_free = 0.3039 target = 0.080759 restraints weight = 23235.565|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3081 r_free = 0.3081 target = 0.083012 restraints weight = 13348.712|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3111 r_free = 0.3111 target = 0.084571 restraints weight = 9178.736|
|-----------------------------------------------------------------------------|
r_work (final): 0.3104
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8243
moved from start:          0.5187

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.067   8802  Z= 0.251
  Angle     :  0.851  14.621  11918  Z= 0.416
  Chirality :  0.048   0.204   1350
  Planarity :  0.004   0.026   1468
  Dihedral  :  6.138  26.489   1164
  Min Nonbonded Distance : 2.495

Molprobity Statistics.
  All-atom Clashscore : 12.36
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 15.28 %
    Favored  : 84.72 %
  Rotamer:
    Outliers :  4.04 %
    Allowed  : 24.26 %
    Favored  : 71.70 %
  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: -2.68 (0.26), residues: 1054
  helix: -0.80 (0.22), residues: 554
  sheet: -1.51 (0.75), residues: 46
  loop : -3.11 (0.29), residues: 454

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.002   TRP C  81 
 HIS   0.005   0.001   HIS C 124 
 PHE   0.017   0.001   PHE C 242 
 TYR   0.031   0.002   TYR C 215 
 ARG   0.004   0.000   ARG A  41 

*********************** 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
  250 residues out of total 940 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 38
    poor density    : 212
  time to evaluate  : 0.976 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A    9 ASN cc_start: 0.9157 (m-40) cc_final: 0.8454 (t0)
REVERT: A   27 MET cc_start: -0.1092 (tpp) cc_final: -0.2057 (mpp)
REVERT: A   38 TYR cc_start: 0.8925 (m-80) cc_final: 0.8563 (m-80)
REVERT: A   41 ARG cc_start: 0.7583 (mtp85) cc_final: 0.7303 (mtp85)
REVERT: A  251 GLN cc_start: 0.8341 (tp-100) cc_final: 0.7927 (tp-100)
REVERT: A  257 MET cc_start: 0.8733 (mmt) cc_final: 0.8231 (mtt)
REVERT: B   27 MET cc_start: -0.1123 (tpp) cc_final: -0.2241 (mpp)
REVERT: B  251 GLN cc_start: 0.8595 (tp-100) cc_final: 0.8162 (tp-100)
REVERT: C  189 LEU cc_start: 0.9238 (OUTLIER) cc_final: 0.9006 (tp)
REVERT: C  206 GLN cc_start: 0.8643 (tt0) cc_final: 0.8159 (mm-40)
REVERT: C  215 TYR cc_start: 0.9011 (t80) cc_final: 0.8753 (t80)
REVERT: C  219 GLU cc_start: 0.8647 (mm-30) cc_final: 0.8359 (mm-30)
REVERT: C  225 LEU cc_start: 0.8524 (OUTLIER) cc_final: 0.8316 (pp)
REVERT: C  266 ASP cc_start: 0.8085 (p0) cc_final: 0.7595 (p0)
REVERT: D   47 GLN cc_start: 0.9574 (tm-30) cc_final: 0.9286 (tm-30)
REVERT: D   86 GLN cc_start: 0.8871 (pp30) cc_final: 0.8512 (pp30)
REVERT: D  165 LEU cc_start: 0.9467 (mp) cc_final: 0.9199 (mm)
REVERT: D  206 GLN cc_start: 0.8709 (tt0) cc_final: 0.8386 (tm-30)
REVERT: D  225 LEU cc_start: 0.8476 (OUTLIER) cc_final: 0.8215 (pp)
REVERT: D  259 LYS cc_start: 0.8985 (mmtt) cc_final: 0.8341 (tmtt)
REVERT: D  266 ASP cc_start: 0.8014 (p0) cc_final: 0.7331 (p0)
  outliers start: 38
  outliers final: 28
  residues processed: 241
  average time/residue: 0.1695
  time to fit residues: 59.4476
Evaluate side-chains
  239 residues out of total 940 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 208
  time to evaluate  : 0.970 
-------------------------------------------------------------------------------
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  252 TYR
Chi-restraints excluded: chain B residue   10 VAL
Chi-restraints excluded: chain B residue   89 LEU
Chi-restraints excluded: chain B residue  101 THR
Chi-restraints excluded: chain B residue  108 LEU
Chi-restraints excluded: chain B residue  126 ASP
Chi-restraints excluded: chain B residue  133 ILE
Chi-restraints excluded: chain B residue  159 ASN
Chi-restraints excluded: chain B residue  230 ILE
Chi-restraints excluded: chain B residue  252 TYR
Chi-restraints excluded: chain C residue  111 VAL
Chi-restraints excluded: chain C residue  114 THR
Chi-restraints excluded: chain C residue  169 THR
Chi-restraints excluded: chain C residue  189 LEU
Chi-restraints excluded: chain C residue  192 THR
Chi-restraints excluded: chain C residue  204 LEU
Chi-restraints excluded: chain C residue  225 LEU
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
Chi-restraints excluded: chain D residue  225 LEU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 104
   random chunks:
   chunk 16 optimal weight:    6.9990
   chunk 45 optimal weight:    0.7980
   chunk 98 optimal weight:    0.8980
   chunk 47 optimal weight:    5.9990
   chunk 60 optimal weight:    2.9990
   chunk 101 optimal weight:    7.9990
   chunk 69 optimal weight:    4.9990
   chunk 20 optimal weight:    5.9990
   chunk 61 optimal weight:    0.5980
   chunk 75 optimal weight:    2.9990
   chunk 42 optimal weight:    0.9990
   overall best weight:    1.2584

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

Flipped N/Q/H residues before XYZ refinement:
** A 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C  47 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 200 HIS
D 124 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 = 0.3377 r_free = 0.3377 target = 0.099116 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3045 r_free = 0.3045 target = 0.081079 restraints weight = 22972.207|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3086 r_free = 0.3086 target = 0.083326 restraints weight = 13255.541|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3116 r_free = 0.3116 target = 0.084911 restraints weight = 9120.080|
|-----------------------------------------------------------------------------|
r_work (final): 0.3110
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8236
moved from start:          0.5361

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.071   8802  Z= 0.227
  Angle     :  0.855  14.051  11918  Z= 0.415
  Chirality :  0.048   0.192   1350
  Planarity :  0.004   0.028   1468
  Dihedral  :  6.100  26.101   1164
  Min Nonbonded Distance : 2.462

Molprobity Statistics.
  All-atom Clashscore : 11.50
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 14.99 %
    Favored  : 85.01 %
  Rotamer:
    Outliers :  3.51 %
    Allowed  : 25.43 %
    Favored  : 71.06 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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: -2.65 (0.26), residues: 1054
  helix: -0.72 (0.22), residues: 556
  sheet: -1.14 (0.80), residues: 46
  loop : -3.22 (0.29), residues: 452

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.002   TRP C  81 
 HIS   0.006   0.001   HIS C 124 
 PHE   0.017   0.001   PHE C 242 
 TYR   0.022   0.002   TYR C 215 
 ARG   0.004   0.000   ARG A  41 

*********************** 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
  249 residues out of total 940 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 216
  time to evaluate  : 0.971 
Fit side-chains
REVERT: A    9 ASN cc_start: 0.9149 (m-40) cc_final: 0.8502 (t0)
REVERT: A   27 MET cc_start: -0.1100 (tpp) cc_final: -0.2074 (mpp)
REVERT: A   38 TYR cc_start: 0.8999 (m-80) cc_final: 0.8542 (m-80)
REVERT: A   41 ARG cc_start: 0.7550 (mtp85) cc_final: 0.7320 (mtp85)
REVERT: A  251 GLN cc_start: 0.8297 (tp-100) cc_final: 0.7902 (tp-100)
REVERT: A  257 MET cc_start: 0.8705 (mmt) cc_final: 0.8213 (mtt)
REVERT: B   27 MET cc_start: -0.1098 (tpp) cc_final: -0.2251 (mpp)
REVERT: B  251 GLN cc_start: 0.8552 (tp-100) cc_final: 0.8139 (tp-100)
REVERT: C   52 TRP cc_start: 0.9341 (t60) cc_final: 0.9033 (t60)
REVERT: C  189 LEU cc_start: 0.9227 (OUTLIER) cc_final: 0.9020 (tp)
REVERT: C  206 GLN cc_start: 0.8601 (tt0) cc_final: 0.8161 (mt0)
REVERT: C  215 TYR cc_start: 0.8949 (t80) cc_final: 0.8558 (t80)
REVERT: C  219 GLU cc_start: 0.8573 (mm-30) cc_final: 0.8006 (mm-30)
REVERT: C  266 ASP cc_start: 0.8145 (p0) cc_final: 0.7625 (p0)
REVERT: D    9 MET cc_start: 0.8658 (mmm) cc_final: 0.8408 (mmt)
REVERT: D   47 GLN cc_start: 0.9506 (tm-30) cc_final: 0.9174 (tm-30)
REVERT: D   86 GLN cc_start: 0.8829 (pp30) cc_final: 0.8459 (pp30)
REVERT: D  165 LEU cc_start: 0.9467 (mp) cc_final: 0.9189 (mm)
REVERT: D  206 GLN cc_start: 0.8656 (tt0) cc_final: 0.8427 (tt0)
REVERT: D  225 LEU cc_start: 0.8449 (OUTLIER) cc_final: 0.8186 (pp)
REVERT: D  259 LYS cc_start: 0.8992 (mmtt) cc_final: 0.8464 (tmtt)
REVERT: D  266 ASP cc_start: 0.7983 (p0) cc_final: 0.7266 (p0)
  outliers start: 33
  outliers final: 25
  residues processed: 241
  average time/residue: 0.1589
  time to fit residues: 56.3925
Evaluate side-chains
  235 residues out of total 940 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 208
  time to evaluate  : 0.947 
-------------------------------------------------------------------------------
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  159 ASN
Chi-restraints excluded: chain A residue  221 VAL
Chi-restraints excluded: chain A residue  252 TYR
Chi-restraints excluded: chain B residue   10 VAL
Chi-restraints excluded: chain B residue   89 LEU
Chi-restraints excluded: chain B residue  101 THR
Chi-restraints excluded: chain B residue  108 LEU
Chi-restraints excluded: chain B residue  133 ILE
Chi-restraints excluded: chain B residue  159 ASN
Chi-restraints excluded: chain B residue  230 ILE
Chi-restraints excluded: chain B residue  252 TYR
Chi-restraints excluded: chain C residue  114 THR
Chi-restraints excluded: chain C residue  169 THR
Chi-restraints excluded: chain C residue  189 LEU
Chi-restraints excluded: chain C residue  192 THR
Chi-restraints excluded: chain C residue  204 LEU
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
Chi-restraints excluded: chain D residue  225 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 104
   random chunks:
   chunk 5 optimal weight:    2.9990
   chunk 23 optimal weight:    1.9990
   chunk 35 optimal weight:    4.9990
   chunk 44 optimal weight:    5.9990
   chunk 36 optimal weight:    0.7980
   chunk 81 optimal weight:    5.9990
   chunk 13 optimal weight:    4.9990
   chunk 52 optimal weight:    5.9990
   chunk 83 optimal weight:    4.9990
   chunk 11 optimal weight:    0.7980
   chunk 55 optimal weight:    5.9990
   overall best weight:    2.3186

-------------------------------------------------------------------------------
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 = 0.3323 r_free = 0.3323 target = 0.095769 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.2978 r_free = 0.2978 target = 0.077382 restraints weight = 23288.163|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.3020 r_free = 0.3020 target = 0.079586 restraints weight = 13592.266|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3050 r_free = 0.3050 target = 0.081131 restraints weight = 9460.990|
|-----------------------------------------------------------------------------|
r_work (final): 0.3049
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8302
moved from start:          0.5375

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.089   8802  Z= 0.334
  Angle     :  0.910  14.464  11918  Z= 0.443
  Chirality :  0.050   0.206   1350
  Planarity :  0.004   0.029   1468
  Dihedral  :  6.181  25.409   1164
  Min Nonbonded Distance : 2.458

Molprobity Statistics.
  All-atom Clashscore : 13.16
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 15.94 %
    Favored  : 84.06 %
  Rotamer:
    Outliers :  3.72 %
    Allowed  : 26.17 %
    Favored  : 70.11 %
  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: -2.77 (0.26), residues: 1054
  helix: -0.76 (0.22), residues: 556
  sheet: -1.13 (0.79), residues: 46
  loop : -3.37 (0.28), residues: 452

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.021   0.002   TRP C  81 
 HIS   0.008   0.001   HIS C 124 
 PHE   0.014   0.002   PHE C 242 
 TYR   0.021   0.002   TYR A  14 
 ARG   0.003   0.000   ARG A  41 

********************** 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
  232 residues out of total 940 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 197
  time to evaluate  : 0.976 
Fit side-chains
REVERT: A    9 ASN cc_start: 0.9159 (m-40) cc_final: 0.8505 (t0)
REVERT: A   27 MET cc_start: -0.1228 (tpp) cc_final: -0.2247 (mpp)
REVERT: A   38 TYR cc_start: 0.9049 (m-80) cc_final: 0.8477 (m-80)
REVERT: A   41 ARG cc_start: 0.7578 (mtp85) cc_final: 0.7347 (mtp85)
REVERT: A  251 GLN cc_start: 0.8354 (tp-100) cc_final: 0.7960 (tp-100)
REVERT: A  257 MET cc_start: 0.8719 (mmt) cc_final: 0.8265 (mtt)
REVERT: B   27 MET cc_start: -0.1136 (tpp) cc_final: -0.2280 (mpp)
REVERT: B  251 GLN cc_start: 0.8607 (tp-100) cc_final: 0.8218 (tp-100)
REVERT: B  264 PHE cc_start: 0.7120 (t80) cc_final: 0.6887 (m-80)
REVERT: C   52 TRP cc_start: 0.9332 (t60) cc_final: 0.8994 (t60)
REVERT: C  189 LEU cc_start: 0.9310 (OUTLIER) cc_final: 0.9098 (tp)
REVERT: C  206 GLN cc_start: 0.8639 (tt0) cc_final: 0.8171 (mt0)
REVERT: C  266 ASP cc_start: 0.8220 (p0) cc_final: 0.7546 (p0)
REVERT: D   86 GLN cc_start: 0.8884 (pp30) cc_final: 0.8514 (pp30)
REVERT: D  165 LEU cc_start: 0.9480 (mp) cc_final: 0.9210 (mm)
REVERT: D  225 LEU cc_start: 0.8659 (OUTLIER) cc_final: 0.8360 (pp)
REVERT: D  259 LYS cc_start: 0.9025 (mmtt) cc_final: 0.8501 (tmtt)
REVERT: D  266 ASP cc_start: 0.8106 (p0) cc_final: 0.7378 (p0)
  outliers start: 35
  outliers final: 28
  residues processed: 226
  average time/residue: 0.1588
  time to fit residues: 52.7892
Evaluate side-chains
  228 residues out of total 940 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 198
  time to evaluate  : 1.027 
-------------------------------------------------------------------------------
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  159 ASN
Chi-restraints excluded: chain A residue  221 VAL
Chi-restraints excluded: chain A residue  252 TYR
Chi-restraints excluded: chain B residue   10 VAL
Chi-restraints excluded: chain B residue   89 LEU
Chi-restraints excluded: chain B residue  101 THR
Chi-restraints excluded: chain B residue  108 LEU
Chi-restraints excluded: chain B residue  133 ILE
Chi-restraints excluded: chain B residue  159 ASN
Chi-restraints excluded: chain B residue  230 ILE
Chi-restraints excluded: chain B residue  252 TYR
Chi-restraints excluded: chain C residue  114 THR
Chi-restraints excluded: chain C residue  169 THR
Chi-restraints excluded: chain C residue  189 LEU
Chi-restraints excluded: chain C residue  192 THR
Chi-restraints excluded: chain C residue  204 LEU
Chi-restraints excluded: chain C residue  258 LEU
Chi-restraints excluded: chain D residue    8 LEU
Chi-restraints excluded: chain D residue   54 VAL
Chi-restraints excluded: chain D residue  111 VAL
Chi-restraints excluded: chain D residue  157 LEU
Chi-restraints excluded: chain D residue  169 THR
Chi-restraints excluded: chain D residue  192 THR
Chi-restraints excluded: chain D residue  225 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 104
   random chunks:
   chunk 46 optimal weight:    0.8980
   chunk 93 optimal weight:    1.9990
   chunk 83 optimal weight:    5.9990
   chunk 99 optimal weight:    5.9990
   chunk 7 optimal weight:    2.9990
   chunk 33 optimal weight:    0.9990
   chunk 72 optimal weight:   10.0000
   chunk 29 optimal weight:    4.9990
   chunk 10 optimal weight:    0.1980
   chunk 28 optimal weight:    2.9990
   chunk 47 optimal weight:    0.7980
   overall best weight:    0.9784

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

Flipped N/Q/H residues before XYZ refinement:
B 233 GLN
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 = 0.3362 r_free = 0.3362 target = 0.098240 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3024 r_free = 0.3024 target = 0.079862 restraints weight = 23438.266|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3066 r_free = 0.3066 target = 0.082133 restraints weight = 13580.719|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3095 r_free = 0.3095 target = 0.083687 restraints weight = 9387.021|
|-----------------------------------------------------------------------------|
r_work (final): 0.3088
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8247
moved from start:          0.5522

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.070   8802  Z= 0.216
  Angle     :  0.880  14.835  11918  Z= 0.425
  Chirality :  0.049   0.194   1350
  Planarity :  0.004   0.028   1468
  Dihedral  :  6.143  26.873   1164
  Min Nonbonded Distance : 2.360

Molprobity Statistics.
  All-atom Clashscore : 11.67
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 14.52 %
    Favored  : 85.48 %
  Rotamer:
    Outliers :  2.98 %
    Allowed  : 27.13 %
    Favored  : 69.89 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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: -2.61 (0.26), residues: 1054
  helix: -0.63 (0.22), residues: 550
  sheet: -1.06 (0.80), residues: 46
  loop : -3.26 (0.29), residues: 458

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.020   0.002   TRP C  81 
 HIS   0.005   0.001   HIS D 124 
 PHE   0.016   0.001   PHE C 242 
 TYR   0.016   0.002   TYR A  14 
 ARG   0.005   0.000   ARG A  41 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2526.70 seconds
wall clock time: 46 minutes 10.89 seconds (2770.89 seconds total)