Starting phenix.real_space_refine
on Fri Mar 14 01:27:05 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8gqy_34203/03_2025/8gqy_34203.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8gqy_34203/03_2025/8gqy_34203.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.4
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8gqy_34203/03_2025/8gqy_34203.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8gqy_34203/03_2025/8gqy_34203.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8gqy_34203/03_2025/8gqy_34203.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8gqy_34203/03_2025/8gqy_34203.cif"
  }
  resolution = 3.4
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.004
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      60      5.16       5
     C    6230      2.51       5
     N    1505      2.21       5
     O    1720      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 24 residue(s): 0.03s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib"
  Total number of atoms: 9515
  Number of models: 1
  Model: ""
    Number of chains: 5
    Chain: "A"
      Number of atoms: 1903
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 253, 1903
          Classifications: {'peptide': 253}
          Link IDs: {'PTRANS': 11, 'TRANS': 241}
    Chain: "B"
      Number of atoms: 1903
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 253, 1903
          Classifications: {'peptide': 253}
          Link IDs: {'PTRANS': 11, 'TRANS': 241}
    Chain: "C"
      Number of atoms: 1903
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 253, 1903
          Classifications: {'peptide': 253}
          Link IDs: {'PTRANS': 11, 'TRANS': 241}
    Chain: "D"
      Number of atoms: 1903
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 253, 1903
          Classifications: {'peptide': 253}
          Link IDs: {'PTRANS': 11, 'TRANS': 241}
    Chain: "E"
      Number of atoms: 1903
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 253, 1903
          Classifications: {'peptide': 253}
          Link IDs: {'PTRANS': 11, 'TRANS': 241}
  Time building chain proxies: 6.03, per 1000 atoms: 0.63
  Number of scatterers: 9515
  At special positions: 0
  Unit cell: (88.2, 88.2, 101.7, 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      60     16.00
     O    1720      8.00
     N    1505      7.00
     C    6230      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 2.26
  Conformation dependent library (CDL) restraints added in 1.2 seconds
  

  2510 Ramachandran restraints generated.
    1255 Oldfield, 0 Emsley, 1255 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2310

  Finding SS restraints...
    Secondary structure from input PDB file:
      89 helices and 0 sheets defined
      82.1% alpha, 0.0% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.93
  Creating SS restraints...
    Processing helix  chain 'A' and resid 5 through 14
      removed outlier: 3.768A  pdb=" N   ALA A  12 " --> pdb=" O   GLY A   8 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 17 through 22
    Processing helix  chain 'A' and resid 31 through 35
    Processing helix  chain 'A' and resid 38 through 45
    Processing helix  chain 'A' and resid 51 through 60
    Processing helix  chain 'A' and resid 61 through 65
    Processing helix  chain 'A' and resid 72 through 77
    Processing helix  chain 'A' and resid 77 through 90
    Processing helix  chain 'A' and resid 98 through 104
    Processing helix  chain 'A' and resid 106 through 119
      removed outlier: 3.891A  pdb=" N   ASP A 111 " --> pdb=" O   PRO A 107 " (cutoff:3.500A)
      removed outlier: 3.588A  pdb=" N   GLY A 119 " --> pdb=" O   MET A 115 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 121 through 125
    Processing helix  chain 'A' and resid 128 through 134
    Processing helix  chain 'A' and resid 140 through 148
      removed outlier: 3.786A  pdb=" N   VAL A 146 " --> pdb=" O   THR A 142 " (cutoff:3.500A)
      removed outlier: 4.133A  pdb=" N   TRP A 147 " --> pdb=" O   GLU A 143 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 149 through 154
    Processing helix  chain 'A' and resid 157 through 173
      removed outlier: 3.739A  pdb=" N   LEU A 163 " --> pdb=" O   MET A 159 " (cutoff:3.500A)
      removed outlier: 3.809A  pdb=" N   GLN A 168 " --> pdb=" O   ILE A 164 " (cutoff:3.500A)
      removed outlier: 4.302A  pdb=" N   MET A 169 " --> pdb=" O   GLY A 165 " (cutoff:3.500A)
      removed outlier: 3.888A  pdb=" N   ASN A 172 " --> pdb=" O   GLN A 168 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 175 through 178
    Processing helix  chain 'A' and resid 179 through 200
      removed outlier: 3.563A  pdb=" N   ALA A 186 " --> pdb=" O   GLY A 182 " (cutoff:3.500A)
      removed outlier: 4.014A  pdb=" N   THR A 189 " --> pdb=" O   VAL A 185 " (cutoff:3.500A)
      removed outlier: 4.545A  pdb=" N   THR A 190 " --> pdb=" O   ALA A 186 " (cutoff:3.500A)
      removed outlier: 3.677A  pdb=" N   GLY A 193 " --> pdb=" O   THR A 189 " (cutoff:3.500A)
      removed outlier: 3.630A  pdb=" N   ALA A 197 " --> pdb=" O   GLY A 193 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 200 through 211
      removed outlier: 4.204A  pdb=" N   LYS A 209 " --> pdb=" O   ALA A 205 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 211 through 231
      removed outlier: 3.550A  pdb=" N   LEU A 217 " --> pdb=" O   ASP A 213 " (cutoff:3.500A)
      removed outlier: 3.552A  pdb=" N   ILE A 223 " --> pdb=" O   LYS A 219 " (cutoff:3.500A)
      removed outlier: 4.126A  pdb=" N   GLU A 224 " --> pdb=" O   THR A 220 " (cutoff:3.500A)
      removed outlier: 3.787A  pdb=" N   LYS A 231 " --> pdb=" O   GLU A 227 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 234 through 247
      removed outlier: 3.775A  pdb=" N   LYS A 239 " --> pdb=" O   PRO A 235 " (cutoff:3.500A)
      removed outlier: 3.567A  pdb=" N   GLN A 240 " --> pdb=" O   ASN A 236 " (cutoff:3.500A)
      removed outlier: 3.596A  pdb=" N   ILE A 244 " --> pdb=" O   GLN A 240 " (cutoff:3.500A)
      removed outlier: 3.869A  pdb=" N   MET A 245 " --> pdb=" O   GLU A 241 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 9 through 24
      removed outlier: 4.032A  pdb=" N   LEU B  15 " --> pdb=" O   ALA B  11 " (cutoff:3.500A)
      removed outlier: 4.213A  pdb=" N   ILE B  16 " --> pdb=" O   ALA B  12 " (cutoff:3.500A)
      removed outlier: 3.758A  pdb=" N   LEU B  17 " --> pdb=" O   PHE B  13 " (cutoff:3.500A)
      removed outlier: 3.632A  pdb=" N   SER B  19 " --> pdb=" O   LEU B  15 " (cutoff:3.500A)
      removed outlier: 4.328A  pdb=" N   ILE B  20 " --> pdb=" O   ILE B  16 " (cutoff:3.500A)
      removed outlier: 4.073A  pdb=" N   GLY B  23 " --> pdb=" O   SER B  19 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 25 through 29
      removed outlier: 3.807A  pdb=" N   ALA B  28 " --> pdb=" O   SER B  25 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 31 through 33
      No H-bonds generated for 'chain 'B' and resid 31 through 33'
    Processing helix  chain 'B' and resid 34 through 39
      removed outlier: 3.991A  pdb=" N   VAL B  38 " --> pdb=" O   SER B  34 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 51 through 60
      removed outlier: 3.591A  pdb=" N   ILE B  56 " --> pdb=" O   LEU B  52 " (cutoff:3.500A)
      removed outlier: 3.657A  pdb=" N   GLY B  58 " --> pdb=" O   ASP B  54 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 72 through 91
      removed outlier: 3.597A  pdb=" N   ILE B  77 " --> pdb=" O   LEU B  73 " (cutoff:3.500A)
      removed outlier: 4.065A  pdb=" N   GLU B  78 " --> pdb=" O   ASN B  74 " (cutoff:3.500A)
      removed outlier: 3.793A  pdb=" N   ILE B  80 " --> pdb=" O   VAL B  76 " (cutoff:3.500A)
      removed outlier: 3.564A  pdb=" N   GLU B  82 " --> pdb=" O   GLU B  78 " (cutoff:3.500A)
      removed outlier: 3.538A  pdb=" N   SER B  85 " --> pdb=" O   GLY B  81 " (cutoff:3.500A)
      removed outlier: 3.548A  pdb=" N   LYS B  86 " --> pdb=" O   GLU B  82 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 92 through 97
      removed outlier: 3.581A  pdb=" N   LEU B  95 " --> pdb=" O   ILE B  92 " (cutoff:3.500A)
      removed outlier: 4.184A  pdb=" N   GLU B  96 " --> pdb=" O   LEU B  93 " (cutoff:3.500A)
      removed outlier: 4.968A  pdb=" N   GLY B  97 " --> pdb=" O   ALA B  94 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 92 through 97'
    Processing helix  chain 'B' and resid 98 through 106
      removed outlier: 3.700A  pdb=" N   GLN B 104 " --> pdb=" O   GLU B 100 " (cutoff:3.500A)
      removed outlier: 3.503A  pdb=" N   LYS B 105 " --> pdb=" O   LEU B 101 " (cutoff:3.500A)
      removed outlier: 3.910A  pdb=" N   ASP B 106 " --> pdb=" O   TYR B 102 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 106 through 119
      removed outlier: 3.892A  pdb=" N   ASP B 111 " --> pdb=" O   PRO B 107 " (cutoff:3.500A)
      removed outlier: 3.629A  pdb=" N   GLY B 119 " --> pdb=" O   MET B 115 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 121 through 130
      removed outlier: 4.452A  pdb=" N   ALA B 127 " --> pdb=" O   ASN B 123 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 130 through 148
      removed outlier: 3.991A  pdb=" N   GLU B 138 " --> pdb=" O   ALA B 134 " (cutoff:3.500A)
      removed outlier: 4.271A  pdb=" N   LYS B 139 " --> pdb=" O   GLN B 135 " (cutoff:3.500A)
      removed outlier: 3.691A  pdb=" N   MET B 140 " --> pdb=" O   LEU B 136 " (cutoff:3.500A)
      removed outlier: 3.769A  pdb=" N   GLU B 143 " --> pdb=" O   LYS B 139 " (cutoff:3.500A)
      removed outlier: 4.004A  pdb=" N   TRP B 147 " --> pdb=" O   GLU B 143 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 149 through 154
    Processing helix  chain 'B' and resid 157 through 172
      removed outlier: 3.600A  pdb=" N   GLN B 168 " --> pdb=" O   ILE B 164 " (cutoff:3.500A)
      removed outlier: 3.940A  pdb=" N   MET B 169 " --> pdb=" O   GLY B 165 " (cutoff:3.500A)
      removed outlier: 4.111A  pdb=" N   ASN B 172 " --> pdb=" O   GLN B 168 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 175 through 178
    Processing helix  chain 'B' and resid 179 through 200
      removed outlier: 3.542A  pdb=" N   VAL B 185 " --> pdb=" O   PRO B 181 " (cutoff:3.500A)
      removed outlier: 3.761A  pdb=" N   THR B 189 " --> pdb=" O   VAL B 185 " (cutoff:3.500A)
      removed outlier: 4.740A  pdb=" N   THR B 190 " --> pdb=" O   ALA B 186 " (cutoff:3.500A)
      removed outlier: 3.926A  pdb=" N   GLY B 193 " --> pdb=" O   THR B 189 " (cutoff:3.500A)
      removed outlier: 3.691A  pdb=" N   LEU B 196 " --> pdb=" O   TYR B 192 " (cutoff:3.500A)
      removed outlier: 3.759A  pdb=" N   ASN B 198 " --> pdb=" O   ALA B 194 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 200 through 211
      removed outlier: 3.726A  pdb=" N   VAL B 204 " --> pdb=" O   PHE B 200 " (cutoff:3.500A)
      removed outlier: 4.102A  pdb=" N   LYS B 209 " --> pdb=" O   ALA B 205 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 211 through 231
      removed outlier: 3.524A  pdb=" N   GLU B 227 " --> pdb=" O   ILE B 223 " (cutoff:3.500A)
      removed outlier: 3.820A  pdb=" N   LYS B 228 " --> pdb=" O   GLU B 224 " (cutoff:3.500A)
      removed outlier: 3.548A  pdb=" N   LYS B 231 " --> pdb=" O   GLU B 227 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 234 through 239
      removed outlier: 3.558A  pdb=" N   LYS B 239 " --> pdb=" O   PRO B 235 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 239 through 247
      removed outlier: 3.758A  pdb=" N   ILE B 244 " --> pdb=" O   GLN B 240 " (cutoff:3.500A)
      removed outlier: 3.641A  pdb=" N   MET B 245 " --> pdb=" O   GLU B 241 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 17 through 24
      removed outlier: 4.125A  pdb=" N   GLY C  23 " --> pdb=" O   SER C  19 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 31 through 33
      No H-bonds generated for 'chain 'C' and resid 31 through 33'
    Processing helix  chain 'C' and resid 34 through 45
      removed outlier: 3.623A  pdb=" N   VAL C  38 " --> pdb=" O   SER C  34 " (cutoff:3.500A)
      removed outlier: 3.553A  pdb=" N   MET C  43 " --> pdb=" O   VAL C  39 " (cutoff:3.500A)
      removed outlier: 3.508A  pdb=" N   ALA C  44 " --> pdb=" O   GLY C  40 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 51 through 60
      removed outlier: 3.516A  pdb=" N   ILE C  56 " --> pdb=" O   LEU C  52 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 61 through 67
      removed outlier: 3.635A  pdb=" N   LEU C  67 " --> pdb=" O   LYS C  63 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 72 through 77
      removed outlier: 3.604A  pdb=" N   ILE C  77 " --> pdb=" O   LEU C  73 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 79 through 91
      removed outlier: 3.502A  pdb=" N   SER C  85 " --> pdb=" O   GLY C  81 " (cutoff:3.500A)
      removed outlier: 3.621A  pdb=" N   LYS C  89 " --> pdb=" O   SER C  85 " (cutoff:3.500A)
      removed outlier: 3.628A  pdb=" N   GLU C  90 " --> pdb=" O   LYS C  86 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 92 through 96
      removed outlier: 3.718A  pdb=" N   GLU C  96 " --> pdb=" O   LEU C  93 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 98 through 106
      removed outlier: 3.978A  pdb=" N   GLN C 104 " --> pdb=" O   GLU C 100 " (cutoff:3.500A)
      removed outlier: 3.575A  pdb=" N   LYS C 105 " --> pdb=" O   LEU C 101 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 106 through 119
      removed outlier: 3.566A  pdb=" N   GLY C 110 " --> pdb=" O   ASP C 106 " (cutoff:3.500A)
      removed outlier: 4.010A  pdb=" N   ASP C 111 " --> pdb=" O   PRO C 107 " (cutoff:3.500A)
      removed outlier: 3.774A  pdb=" N   MET C 115 " --> pdb=" O   ASP C 111 " (cutoff:3.500A)
      removed outlier: 3.565A  pdb=" N   GLY C 119 " --> pdb=" O   MET C 115 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 121 through 135
      removed outlier: 3.525A  pdb=" N   LYS C 126 " --> pdb=" O   ILE C 122 " (cutoff:3.500A)
      removed outlier: 3.562A  pdb=" N   ALA C 127 " --> pdb=" O   ASN C 123 " (cutoff:3.500A)
      removed outlier: 3.540A  pdb=" N   ALA C 129 " --> pdb=" O   ILE C 125 " (cutoff:3.500A)
      removed outlier: 3.783A  pdb=" N   MET C 131 " --> pdb=" O   ALA C 127 " (cutoff:3.500A)
      removed outlier: 3.529A  pdb=" N   GLN C 135 " --> pdb=" O   MET C 131 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 136 through 151
      removed outlier: 3.746A  pdb=" N   THR C 142 " --> pdb=" O   GLU C 138 " (cutoff:3.500A)
      removed outlier: 3.725A  pdb=" N   GLU C 143 " --> pdb=" O   LYS C 139 " (cutoff:3.500A)
      removed outlier: 3.574A  pdb=" N   VAL C 146 " --> pdb=" O   THR C 142 " (cutoff:3.500A)
      removed outlier: 4.327A  pdb=" N   TRP C 147 " --> pdb=" O   GLU C 143 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 157 through 171
      removed outlier: 3.703A  pdb=" N   GLN C 168 " --> pdb=" O   ILE C 164 " (cutoff:3.500A)
      removed outlier: 4.167A  pdb=" N   MET C 169 " --> pdb=" O   GLY C 165 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 175 through 178
    Processing helix  chain 'C' and resid 179 through 200
      removed outlier: 3.614A  pdb=" N   ALA C 186 " --> pdb=" O   GLY C 182 " (cutoff:3.500A)
      removed outlier: 4.092A  pdb=" N   THR C 189 " --> pdb=" O   VAL C 185 " (cutoff:3.500A)
      removed outlier: 4.724A  pdb=" N   THR C 190 " --> pdb=" O   ALA C 186 " (cutoff:3.500A)
      removed outlier: 3.512A  pdb=" N   LEU C 191 " --> pdb=" O   LEU C 187 " (cutoff:3.500A)
      removed outlier: 3.581A  pdb=" N   GLY C 193 " --> pdb=" O   THR C 189 " (cutoff:3.500A)
      removed outlier: 3.647A  pdb=" N   LEU C 196 " --> pdb=" O   TYR C 192 " (cutoff:3.500A)
      removed outlier: 3.625A  pdb=" N   ALA C 197 " --> pdb=" O   GLY C 193 " (cutoff:3.500A)
      removed outlier: 3.517A  pdb=" N   ASN C 198 " --> pdb=" O   ALA C 194 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 200 through 231
      removed outlier: 3.790A  pdb=" N   VAL C 204 " --> pdb=" O   PHE C 200 " (cutoff:3.500A)
      removed outlier: 4.028A  pdb=" N   LYS C 209 " --> pdb=" O   ALA C 205 " (cutoff:3.500A)
      removed outlier: 3.512A  pdb=" N   LYS C 210 " --> pdb=" O   ASN C 206 " (cutoff:3.500A)
      removed outlier: 3.667A  pdb=" N   MET C 214 " --> pdb=" O   LYS C 210 " (cutoff:3.500A)
      removed outlier: 3.704A  pdb=" N   GLU C 215 " --> pdb=" O   ALA C 211 " (cutoff:3.500A)
      removed outlier: 3.881A  pdb=" N   VAL C 218 " --> pdb=" O   MET C 214 " (cutoff:3.500A)
      removed outlier: 3.518A  pdb=" N   LYS C 219 " --> pdb=" O   GLU C 215 " (cutoff:3.500A)
      removed outlier: 3.641A  pdb=" N   GLU C 224 " --> pdb=" O   THR C 220 " (cutoff:3.500A)
      removed outlier: 3.641A  pdb=" N   GLU C 227 " --> pdb=" O   ILE C 223 " (cutoff:3.500A)
      removed outlier: 3.660A  pdb=" N   ILE C 229 " --> pdb=" O   ALA C 225 " (cutoff:3.500A)
      removed outlier: 3.512A  pdb=" N   LYS C 231 " --> pdb=" O   GLU C 227 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 234 through 247
      removed outlier: 3.501A  pdb=" N   VAL C 238 " --> pdb=" O   ASN C 234 " (cutoff:3.500A)
      removed outlier: 3.533A  pdb=" N   LYS C 239 " --> pdb=" O   PRO C 235 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 5 through 10
    Processing helix  chain 'D' and resid 11 through 24
      removed outlier: 3.620A  pdb=" N   LEU D  15 " --> pdb=" O   ALA D  11 " (cutoff:3.500A)
      removed outlier: 3.620A  pdb=" N   LEU D  17 " --> pdb=" O   PHE D  13 " (cutoff:3.500A)
      removed outlier: 3.573A  pdb=" N   SER D  19 " --> pdb=" O   LEU D  15 " (cutoff:3.500A)
      removed outlier: 3.555A  pdb=" N   GLY D  23 " --> pdb=" O   SER D  19 " (cutoff:3.500A)
      removed outlier: 3.683A  pdb=" N   GLY D  24 " --> pdb=" O   ILE D  20 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 31 through 33
      No H-bonds generated for 'chain 'D' and resid 31 through 33'
    Processing helix  chain 'D' and resid 34 through 45
      removed outlier: 3.775A  pdb=" N   VAL D  38 " --> pdb=" O   SER D  34 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 51 through 60
      removed outlier: 3.553A  pdb=" N   ARG D  57 " --> pdb=" O   LYS D  53 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 62 through 67
    Processing helix  chain 'D' and resid 72 through 91
      removed outlier: 3.757A  pdb=" N   ILE D  77 " --> pdb=" O   LEU D  73 " (cutoff:3.500A)
      removed outlier: 3.689A  pdb=" N   GLU D  78 " --> pdb=" O   ASN D  74 " (cutoff:3.500A)
      removed outlier: 3.713A  pdb=" N   GLU D  82 " --> pdb=" O   GLU D  78 " (cutoff:3.500A)
      removed outlier: 3.690A  pdb=" N   SER D  85 " --> pdb=" O   GLY D  81 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 92 through 97
      removed outlier: 4.272A  pdb=" N   GLU D  96 " --> pdb=" O   LEU D  93 " (cutoff:3.500A)
      removed outlier: 5.046A  pdb=" N   GLY D  97 " --> pdb=" O   ALA D  94 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 98 through 104
    Processing helix  chain 'D' and resid 106 through 118
      removed outlier: 3.653A  pdb=" N   GLY D 110 " --> pdb=" O   ASP D 106 " (cutoff:3.500A)
      removed outlier: 3.517A  pdb=" N   MET D 115 " --> pdb=" O   ASP D 111 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 121 through 135
      removed outlier: 3.944A  pdb=" N   ALA D 127 " --> pdb=" O   ASN D 123 " (cutoff:3.500A)
      removed outlier: 3.812A  pdb=" N   MET D 131 " --> pdb=" O   ALA D 127 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 139 through 154
      removed outlier: 3.878A  pdb=" N   GLU D 143 " --> pdb=" O   LYS D 139 " (cutoff:3.500A)
      removed outlier: 3.969A  pdb=" N   TRP D 147 " --> pdb=" O   GLU D 143 " (cutoff:3.500A)
      removed outlier: 3.650A  pdb=" N   ASP D 152 " --> pdb=" O   GLU D 148 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 157 through 172
      removed outlier: 3.561A  pdb=" N   GLY D 165 " --> pdb=" O   GLY D 161 " (cutoff:3.500A)
      removed outlier: 3.701A  pdb=" N   ILE D 167 " --> pdb=" O   LEU D 163 " (cutoff:3.500A)
      removed outlier: 3.610A  pdb=" N   GLN D 168 " --> pdb=" O   ILE D 164 " (cutoff:3.500A)
      removed outlier: 3.674A  pdb=" N   MET D 169 " --> pdb=" O   GLY D 165 " (cutoff:3.500A)
      removed outlier: 3.873A  pdb=" N   LEU D 170 " --> pdb=" O   LEU D 166 " (cutoff:3.500A)
      removed outlier: 3.684A  pdb=" N   ASN D 172 " --> pdb=" O   GLN D 168 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 175 through 178
    Processing helix  chain 'D' and resid 179 through 200
      removed outlier: 3.949A  pdb=" N   THR D 189 " --> pdb=" O   VAL D 185 " (cutoff:3.500A)
      removed outlier: 4.587A  pdb=" N   THR D 190 " --> pdb=" O   ALA D 186 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 202 through 207
    Processing helix  chain 'D' and resid 208 through 231
      removed outlier: 3.532A  pdb=" N   MET D 214 " --> pdb=" O   LYS D 210 " (cutoff:3.500A)
      removed outlier: 3.554A  pdb=" N   LEU D 217 " --> pdb=" O   ASP D 213 " (cutoff:3.500A)
      removed outlier: 3.546A  pdb=" N   VAL D 218 " --> pdb=" O   MET D 214 " (cutoff:3.500A)
      removed outlier: 3.823A  pdb=" N   LYS D 219 " --> pdb=" O   GLU D 215 " (cutoff:3.500A)
      removed outlier: 3.502A  pdb=" N   ILE D 221 " --> pdb=" O   LEU D 217 " (cutoff:3.500A)
      removed outlier: 3.530A  pdb=" N   TYR D 222 " --> pdb=" O   VAL D 218 " (cutoff:3.500A)
      removed outlier: 3.683A  pdb=" N   GLU D 224 " --> pdb=" O   THR D 220 " (cutoff:3.500A)
      removed outlier: 3.813A  pdb=" N   GLU D 227 " --> pdb=" O   ILE D 223 " (cutoff:3.500A)
      removed outlier: 3.610A  pdb=" N   ILE D 229 " --> pdb=" O   ALA D 225 " (cutoff:3.500A)
      removed outlier: 3.977A  pdb=" N   LYS D 231 " --> pdb=" O   GLU D 227 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 234 through 245
      removed outlier: 3.511A  pdb=" N   VAL D 238 " --> pdb=" O   ASN D 234 " (cutoff:3.500A)
      removed outlier: 3.535A  pdb=" N   GLN D 240 " --> pdb=" O   ASN D 236 " (cutoff:3.500A)
      removed outlier: 3.509A  pdb=" N   ILE D 244 " --> pdb=" O   GLN D 240 " (cutoff:3.500A)
      removed outlier: 3.608A  pdb=" N   MET D 245 " --> pdb=" O   GLU D 241 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 5 through 24
      removed outlier: 3.830A  pdb=" N   ALA E  12 " --> pdb=" O   GLY E   8 " (cutoff:3.500A)
      removed outlier: 3.696A  pdb=" N   ILE E  18 " --> pdb=" O   LEU E  14 " (cutoff:3.500A)
      removed outlier: 4.014A  pdb=" N   GLY E  23 " --> pdb=" O   SER E  19 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 31 through 33
      No H-bonds generated for 'chain 'E' and resid 31 through 33'
    Processing helix  chain 'E' and resid 34 through 43
      removed outlier: 4.137A  pdb=" N   VAL E  38 " --> pdb=" O   SER E  34 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 44 through 49
    Processing helix  chain 'E' and resid 51 through 60
      removed outlier: 3.835A  pdb=" N   ARG E  57 " --> pdb=" O   LYS E  53 " (cutoff:3.500A)
      removed outlier: 3.651A  pdb=" N   GLY E  58 " --> pdb=" O   ASP E  54 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 76 through 91
      removed outlier: 3.944A  pdb=" N   ILE E  80 " --> pdb=" O   VAL E  76 " (cutoff:3.500A)
      removed outlier: 3.734A  pdb=" N   GLU E  82 " --> pdb=" O   GLU E  78 " (cutoff:3.500A)
      removed outlier: 4.130A  pdb=" N   SER E  85 " --> pdb=" O   GLY E  81 " (cutoff:3.500A)
      removed outlier: 3.501A  pdb=" N   LYS E  86 " --> pdb=" O   GLU E  82 " (cutoff:3.500A)
      removed outlier: 3.572A  pdb=" N   GLU E  90 " --> pdb=" O   LYS E  86 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 92 through 97
      removed outlier: 3.540A  pdb=" N   LEU E  95 " --> pdb=" O   ILE E  92 " (cutoff:3.500A)
      removed outlier: 4.516A  pdb=" N   GLU E  96 " --> pdb=" O   LEU E  93 " (cutoff:3.500A)
      removed outlier: 4.695A  pdb=" N   GLY E  97 " --> pdb=" O   ALA E  94 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'E' and resid 92 through 97'
    Processing helix  chain 'E' and resid 98 through 106
      removed outlier: 3.651A  pdb=" N   GLN E 104 " --> pdb=" O   GLU E 100 " (cutoff:3.500A)
      removed outlier: 4.040A  pdb=" N   LYS E 105 " --> pdb=" O   LEU E 101 " (cutoff:3.500A)
      removed outlier: 4.399A  pdb=" N   ASP E 106 " --> pdb=" O   TYR E 102 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 106 through 118
      removed outlier: 3.635A  pdb=" N   ARG E 114 " --> pdb=" O   GLY E 110 " (cutoff:3.500A)
      removed outlier: 4.048A  pdb=" N   MET E 115 " --> pdb=" O   ASP E 111 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 121 through 154
      removed outlier: 3.685A  pdb=" N   ALA E 127 " --> pdb=" O   ASN E 123 " (cutoff:3.500A)
      removed outlier: 3.536A  pdb=" N   GLU E 130 " --> pdb=" O   LYS E 126 " (cutoff:3.500A)
      removed outlier: 3.834A  pdb=" N   MET E 131 " --> pdb=" O   ALA E 127 " (cutoff:3.500A)
      removed outlier: 3.967A  pdb=" N   LYS E 139 " --> pdb=" O   GLN E 135 " (cutoff:3.500A)
      removed outlier: 3.782A  pdb=" N   MET E 140 " --> pdb=" O   LEU E 136 " (cutoff:3.500A)
      removed outlier: 3.617A  pdb=" N   THR E 142 " --> pdb=" O   GLU E 138 " (cutoff:3.500A)
      removed outlier: 3.540A  pdb=" N   GLU E 143 " --> pdb=" O   LYS E 139 " (cutoff:3.500A)
      removed outlier: 4.173A  pdb=" N   TRP E 147 " --> pdb=" O   GLU E 143 " (cutoff:3.500A)
      removed outlier: 3.508A  pdb=" N   LYS E 149 " --> pdb=" O   ALA E 145 " (cutoff:3.500A)
      removed outlier: 4.073A  pdb=" N   ASP E 152 " --> pdb=" O   GLU E 148 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 157 through 172
      removed outlier: 3.524A  pdb=" N   LEU E 163 " --> pdb=" O   MET E 159 " (cutoff:3.500A)
      removed outlier: 3.653A  pdb=" N   GLY E 165 " --> pdb=" O   GLY E 161 " (cutoff:3.500A)
      removed outlier: 4.195A  pdb=" N   GLN E 168 " --> pdb=" O   ILE E 164 " (cutoff:3.500A)
      removed outlier: 4.096A  pdb=" N   MET E 169 " --> pdb=" O   GLY E 165 " (cutoff:3.500A)
      removed outlier: 3.869A  pdb=" N   LEU E 170 " --> pdb=" O   LEU E 166 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 179 through 200
      removed outlier: 3.783A  pdb=" N   THR E 189 " --> pdb=" O   VAL E 185 " (cutoff:3.500A)
      removed outlier: 4.514A  pdb=" N   THR E 190 " --> pdb=" O   ALA E 186 " (cutoff:3.500A)
      removed outlier: 3.764A  pdb=" N   GLY E 193 " --> pdb=" O   THR E 189 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 200 through 208
      removed outlier: 3.630A  pdb=" N   VAL E 204 " --> pdb=" O   PHE E 200 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 211 through 228
      removed outlier: 3.654A  pdb=" N   TYR E 222 " --> pdb=" O   VAL E 218 " (cutoff:3.500A)
      removed outlier: 3.730A  pdb=" N   LYS E 228 " --> pdb=" O   GLU E 224 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 235 through 247
      removed outlier: 3.736A  pdb=" N   GLU E 241 " --> pdb=" O   VAL E 237 " (cutoff:3.500A)
      removed outlier: 3.599A  pdb=" N   MET E 245 " --> pdb=" O   GLU E 241 " (cutoff:3.500A)

    495 hydrogen bonds defined for protein.
    1446 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: 2.36

  Time building geometry restraints manager: 2.70 seconds

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

  Histogram of bond lengths:
        1.22 -     1.34: 3007
        1.34 -     1.46: 1035
        1.46 -     1.57: 5493
        1.57 -     1.69: 0
        1.69 -     1.80: 120
  Bond restraints: 9655
  Sorted by residual:
  bond pdb=" C   VAL C  32 "
       pdb=" N   PRO C  33 "
    ideal  model  delta    sigma   weight residual
    1.334  1.348 -0.014 8.40e-03 1.42e+04 2.79e+00
  bond pdb=" C   GLY C 119 "
       pdb=" N   ILE C 120 "
    ideal  model  delta    sigma   weight residual
    1.334  1.318  0.016 1.29e-02 6.01e+03 1.47e+00
  bond pdb=" CG1 ILE D 221 "
       pdb=" CD1 ILE D 221 "
    ideal  model  delta    sigma   weight residual
    1.513  1.467  0.046 3.90e-02 6.57e+02 1.41e+00
  bond pdb=" CG1 ILE E 221 "
       pdb=" CD1 ILE E 221 "
    ideal  model  delta    sigma   weight residual
    1.513  1.474  0.039 3.90e-02 6.57e+02 1.01e+00
  bond pdb=" CB  ASP D 137 "
       pdb=" CG  ASP D 137 "
    ideal  model  delta    sigma   weight residual
    1.516  1.491  0.025 2.50e-02 1.60e+03 9.77e-01
  ... (remaining 9650 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.15: 12148
        1.15 -     2.29: 782
        2.29 -     3.44: 106
        3.44 -     4.59: 25
        4.59 -     5.74: 14
  Bond angle restraints: 13075
  Sorted by residual:
  angle pdb=" C   ASN A  31 "
        pdb=" N   VAL A  32 "
        pdb=" CA  VAL A  32 "
      ideal   model   delta    sigma   weight residual
     120.24  123.93   -3.69 6.30e-01 2.52e+00 3.43e+01
  angle pdb=" N   VAL B   3 "
        pdb=" CA  VAL B   3 "
        pdb=" C   VAL B   3 "
      ideal   model   delta    sigma   weight residual
     111.91  108.15    3.76 8.90e-01 1.26e+00 1.78e+01
  angle pdb=" N   ILE C   7 "
        pdb=" CA  ILE C   7 "
        pdb=" C   ILE C   7 "
      ideal   model   delta    sigma   weight residual
     112.90  108.95    3.95 9.60e-01 1.09e+00 1.69e+01
  angle pdb=" C   VAL A  32 "
        pdb=" CA  VAL A  32 "
        pdb=" CB  VAL A  32 "
      ideal   model   delta    sigma   weight residual
     114.35  110.75    3.60 1.06e+00 8.90e-01 1.15e+01
  angle pdb=" N   VAL A   3 "
        pdb=" CA  VAL A   3 "
        pdb=" C   VAL A   3 "
      ideal   model   delta    sigma   weight residual
     111.91  109.17    2.74 8.90e-01 1.26e+00 9.46e+00
  ... (remaining 13070 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    14.50: 5309
       14.50 -    29.00: 412
       29.00 -    43.49: 126
       43.49 -    57.99: 38
       57.99 -    72.49: 5
  Dihedral angle restraints: 5890
    sinusoidal: 2300
      harmonic: 3590
  Sorted by residual:
  dihedral pdb=" CA  GLN E 135 "
           pdb=" C   GLN E 135 "
           pdb=" N   LEU E 136 "
           pdb=" CA  LEU E 136 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  157.63   22.37     0      5.00e+00 4.00e-02 2.00e+01
  dihedral pdb=" CA  GLN A 135 "
           pdb=" C   GLN A 135 "
           pdb=" N   LEU A 136 "
           pdb=" CA  LEU A 136 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  163.19   16.81     0      5.00e+00 4.00e-02 1.13e+01
  dihedral pdb=" CA  ALA B  46 "
           pdb=" C   ALA B  46 "
           pdb=" N   MET B  47 "
           pdb=" CA  MET B  47 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  163.61   16.39     0      5.00e+00 4.00e-02 1.07e+01
  ... (remaining 5887 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.025: 682
       0.025 -    0.051: 591
       0.051 -    0.076: 265
       0.076 -    0.101: 56
       0.101 -    0.126: 16
  Chirality restraints: 1610
  Sorted by residual:
  chirality pdb=" CB  VAL C   3 "
            pdb=" CA  VAL C   3 "
            pdb=" CG1 VAL C   3 "
            pdb=" CG2 VAL C   3 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -2.50   -0.13 2.00e-01 2.50e+01 3.98e-01
  chirality pdb=" CA  ILE A 120 "
            pdb=" N   ILE A 120 "
            pdb=" C   ILE A 120 "
            pdb=" CB  ILE A 120 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.55   -0.11 2.00e-01 2.50e+01 3.15e-01
  chirality pdb=" CB  VAL B   3 "
            pdb=" CA  VAL B   3 "
            pdb=" CG1 VAL B   3 "
            pdb=" CG2 VAL B   3 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -2.52   -0.11 2.00e-01 2.50e+01 3.11e-01
  ... (remaining 1607 not shown)

  Planarity restraints: 1630
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ILE C 202 "   -0.029 5.00e-02 4.00e+02   4.30e-02 2.96e+00
        pdb=" N   PRO C 203 "    0.074 5.00e-02 4.00e+02
        pdb=" CA  PRO C 203 "   -0.022 5.00e-02 4.00e+02
        pdb=" CD  PRO C 203 "   -0.024 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ILE E 202 "    0.027 5.00e-02 4.00e+02   4.08e-02 2.66e+00
        pdb=" N   PRO E 203 "   -0.071 5.00e-02 4.00e+02
        pdb=" CA  PRO E 203 "    0.020 5.00e-02 4.00e+02
        pdb=" CD  PRO E 203 "    0.023 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ILE B 202 "    0.025 5.00e-02 4.00e+02   3.75e-02 2.25e+00
        pdb=" N   PRO B 203 "   -0.065 5.00e-02 4.00e+02
        pdb=" CA  PRO B 203 "    0.019 5.00e-02 4.00e+02
        pdb=" CD  PRO B 203 "    0.021 5.00e-02 4.00e+02
  ... (remaining 1627 not shown)

  Histogram of nonbonded interaction distances:
        2.12 -     2.67: 123
        2.67 -     3.23: 9442
        3.23 -     3.79: 13488
        3.79 -     4.34: 21454
        4.34 -     4.90: 33480
  Nonbonded interactions: 77987
  Sorted by model distance:
  nonbonded pdb=" O   PHE D  29 "
            pdb=" OH  TYR D 192 "
     model   vdw
     2.117 3.040
  nonbonded pdb=" O   PHE B  29 "
            pdb=" OH  TYR B 192 "
     model   vdw
     2.120 3.040
  nonbonded pdb=" O   PHE A  29 "
            pdb=" OH  TYR A 192 "
     model   vdw
     2.142 3.040
  nonbonded pdb=" O   PHE C  29 "
            pdb=" OH  TYR C 192 "
     model   vdw
     2.143 3.040
  nonbonded pdb=" O   PHE E  29 "
            pdb=" OH  TYR E 192 "
     model   vdw
     2.216 3.040
  ... (remaining 77982 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: 0.02
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'B'
  selection = chain 'C'
  selection = chain 'D'
  selection = chain 'E'
}

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 individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             1.710
  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:         0.070
  Set scattering table:                    0.080
  Process input model:                     23.830
  Find NCS groups from input model:        0.360
  Set up NCS constraints:                  0.040
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:3.030
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   29.460
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8275
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      :  0.005   0.046   9655  Z= 0.324
  Angle     :  0.657   5.736  13075  Z= 0.389
  Chirality :  0.040   0.126   1610
  Planarity :  0.004   0.043   1630
  Dihedral  : 12.578  72.490   3580
  Min Nonbonded Distance : 2.117

Molprobity Statistics.
  All-atom Clashscore : 7.22
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.59 %
    Favored  : 96.41 %
  Rotamer:
    Outliers :  5.67 %
    Allowed  :  9.25 %
    Favored  : 85.07 %
  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: -7.14 (0.13), residues: 1255
  helix: -4.90 (0.06), residues: 985
  sheet:  None (None), residues: 0
  loop : -2.58 (0.29), residues: 270

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.002   TRP C 147 
 HIS   0.001   0.000   HIS B   0 
 PHE   0.008   0.001   PHE A  55 
 TYR   0.007   0.001   TYR D 222 
 ARG   0.002   0.000   ARG D  88 

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

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

  2510 Ramachandran restraints generated.
    1255 Oldfield, 0 Emsley, 1255 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2510 Ramachandran restraints generated.
    1255 Oldfield, 0 Emsley, 1255 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  259 residues out of total 1005 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 57
    poor density    : 202
  time to evaluate  : 0.948 
Fit side-chains
REVERT: A   53 LYS cc_start: 0.8001 (mmtp) cc_final: 0.7725 (mmtm)
REVERT: A   62 ILE cc_start: 0.8002 (OUTLIER) cc_final: 0.7749 (mt)
REVERT: A  217 LEU cc_start: 0.8636 (OUTLIER) cc_final: 0.8386 (tt)
REVERT: B   43 MET cc_start: 0.8434 (mmm) cc_final: 0.8227 (mtt)
REVERT: B   88 ARG cc_start: 0.7484 (ttm-80) cc_final: 0.7038 (ttt90)
REVERT: B  159 MET cc_start: 0.7673 (tmm) cc_final: 0.7107 (ptm)
REVERT: C    2 ASP cc_start: 0.7499 (OUTLIER) cc_final: 0.7252 (t70)
REVERT: C   69 LYS cc_start: 0.8806 (OUTLIER) cc_final: 0.8522 (mttt)
REVERT: C  118 ASP cc_start: 0.7258 (m-30) cc_final: 0.6909 (m-30)
REVERT: C  206 ASN cc_start: 0.8825 (t0) cc_final: 0.8569 (t0)
REVERT: C  249 GLU cc_start: 0.6967 (tm-30) cc_final: 0.6738 (tm-30)
REVERT: D   95 LEU cc_start: 0.6075 (OUTLIER) cc_final: 0.5490 (mp)
REVERT: D  115 MET cc_start: 0.8292 (mtp) cc_final: 0.8026 (mtt)
REVERT: E   86 LYS cc_start: 0.8200 (tptt) cc_final: 0.7976 (tptm)
REVERT: E  139 LYS cc_start: 0.8839 (mmtp) cc_final: 0.8288 (mttt)
  outliers start: 57
  outliers final: 20
  residues processed: 246
  average time/residue: 0.1802
  time to fit residues: 63.7057
Evaluate side-chains
  179 residues out of total 1005 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 154
  time to evaluate  : 1.106 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   -1 VAL
Chi-restraints excluded: chain A residue   62 ILE
Chi-restraints excluded: chain A residue   67 LEU
Chi-restraints excluded: chain A residue  137 ASP
Chi-restraints excluded: chain A residue  217 LEU
Chi-restraints excluded: chain A residue  221 ILE
Chi-restraints excluded: chain A residue  237 VAL
Chi-restraints excluded: chain B residue   59 VAL
Chi-restraints excluded: chain B residue   67 LEU
Chi-restraints excluded: chain B residue  122 ILE
Chi-restraints excluded: chain C residue    1 MET
Chi-restraints excluded: chain C residue    2 ASP
Chi-restraints excluded: chain C residue   59 VAL
Chi-restraints excluded: chain C residue   67 LEU
Chi-restraints excluded: chain C residue   69 LYS
Chi-restraints excluded: chain C residue  121 ASP
Chi-restraints excluded: chain C residue  226 ILE
Chi-restraints excluded: chain D residue   22 ILE
Chi-restraints excluded: chain D residue   67 LEU
Chi-restraints excluded: chain D residue   95 LEU
Chi-restraints excluded: chain D residue  121 ASP
Chi-restraints excluded: chain D residue  157 PHE
Chi-restraints excluded: chain E residue   -1 VAL
Chi-restraints excluded: chain E residue  159 MET
Chi-restraints excluded: chain E residue  228 LYS
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 125
   random chunks:
   chunk 105 optimal weight:    0.6980
   chunk 94 optimal weight:    0.6980
   chunk 52 optimal weight:    3.9990
   chunk 32 optimal weight:    1.9990
   chunk 63 optimal weight:    1.9990
   chunk 50 optimal weight:    6.9990
   chunk 97 optimal weight:    0.9980
   chunk 37 optimal weight:    1.9990
   chunk 59 optimal weight:    5.9990
   chunk 72 optimal weight:    0.9980
   chunk 113 optimal weight:    0.6980
   overall best weight:    0.8180

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

Flipped N/Q/H residues before XYZ refinement:
B 198 ASN
C 168 GLN
C 198 ASN
C 240 GLN
D 198 ASN
D 240 GLN
E 104 GLN
E 198 ASN
E 240 GLN

Total number of N/Q/H flips: 9

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3496 r_free = 0.3496 target = 0.131651 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3213 r_free = 0.3213 target = 0.109429 restraints weight = 11209.529|
|-----------------------------------------------------------------------------|
r_work (start): 0.3046 rms_B_bonded: 1.51
r_work: 0.2923 rms_B_bonded: 2.22 restraints_weight: 0.5000
r_work: 0.2789 rms_B_bonded: 3.75 restraints_weight: 0.2500
r_work (final): 0.2789
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8375
moved from start:          0.1903

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.064   9655  Z= 0.221
  Angle     :  0.647  10.427  13075  Z= 0.335
  Chirality :  0.039   0.121   1610
  Planarity :  0.006   0.035   1630
  Dihedral  :  8.132  59.737   1351
  Min Nonbonded Distance : 2.510

Molprobity Statistics.
  All-atom Clashscore : 5.64
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.07 %
    Favored  : 97.93 %
  Rotamer:
    Outliers :  3.68 %
    Allowed  : 14.73 %
    Favored  : 81.59 %
  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: -5.51 (0.16), residues: 1255
  helix: -3.61 (0.11), residues: 1040
  sheet:  None (None), residues: 0
  loop : -2.07 (0.31), residues: 215

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.002   TRP E 147 
 HIS   0.001   0.000   HIS B   0 
 PHE   0.007   0.001   PHE D  66 
 TYR   0.008   0.001   TYR C 192 
 ARG   0.005   0.001   ARG D  57 

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

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

  2510 Ramachandran restraints generated.
    1255 Oldfield, 0 Emsley, 1255 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2510 Ramachandran restraints generated.
    1255 Oldfield, 0 Emsley, 1255 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  192 residues out of total 1005 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 37
    poor density    : 155
  time to evaluate  : 1.091 
Fit side-chains
REVERT: A   53 LYS cc_start: 0.8174 (mmtp) cc_final: 0.7796 (mmtm)
REVERT: A  217 LEU cc_start: 0.8393 (OUTLIER) cc_final: 0.8145 (tt)
REVERT: B  159 MET cc_start: 0.8191 (tmm) cc_final: 0.7833 (ptm)
REVERT: B  221 ILE cc_start: 0.8256 (OUTLIER) cc_final: 0.7742 (mp)
REVERT: B  236 ASN cc_start: 0.8482 (m-40) cc_final: 0.7921 (m-40)
REVERT: C    2 ASP cc_start: 0.7766 (OUTLIER) cc_final: 0.7358 (t70)
REVERT: C   43 MET cc_start: 0.8733 (OUTLIER) cc_final: 0.8362 (mmt)
REVERT: C   69 LYS cc_start: 0.8977 (OUTLIER) cc_final: 0.8693 (mttt)
REVERT: C  112 MET cc_start: 0.8347 (ttp) cc_final: 0.8101 (ttp)
REVERT: C  118 ASP cc_start: 0.7198 (m-30) cc_final: 0.6790 (m-30)
REVERT: C  138 GLU cc_start: 0.8286 (mm-30) cc_final: 0.7237 (tt0)
REVERT: C  206 ASN cc_start: 0.9011 (t0) cc_final: 0.8576 (t0)
REVERT: C  249 GLU cc_start: 0.6861 (tm-30) cc_final: 0.6653 (tm-30)
REVERT: E  139 LYS cc_start: 0.8884 (mmtp) cc_final: 0.8287 (mttt)
  outliers start: 37
  outliers final: 19
  residues processed: 185
  average time/residue: 0.1794
  time to fit residues: 49.1928
Evaluate side-chains
  163 residues out of total 1005 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 139
  time to evaluate  : 1.070 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   -1 VAL
Chi-restraints excluded: chain A residue   67 LEU
Chi-restraints excluded: chain A residue  112 MET
Chi-restraints excluded: chain A residue  137 ASP
Chi-restraints excluded: chain A residue  217 LEU
Chi-restraints excluded: chain A residue  237 VAL
Chi-restraints excluded: chain B residue    9 ILE
Chi-restraints excluded: chain B residue   59 VAL
Chi-restraints excluded: chain B residue   67 LEU
Chi-restraints excluded: chain B residue  198 ASN
Chi-restraints excluded: chain B residue  221 ILE
Chi-restraints excluded: chain C residue    2 ASP
Chi-restraints excluded: chain C residue   43 MET
Chi-restraints excluded: chain C residue   59 VAL
Chi-restraints excluded: chain C residue   67 LEU
Chi-restraints excluded: chain C residue   69 LYS
Chi-restraints excluded: chain C residue  226 ILE
Chi-restraints excluded: chain C residue  229 ILE
Chi-restraints excluded: chain D residue   22 ILE
Chi-restraints excluded: chain D residue   67 LEU
Chi-restraints excluded: chain D residue  157 PHE
Chi-restraints excluded: chain E residue  159 MET
Chi-restraints excluded: chain E residue  223 ILE
Chi-restraints excluded: chain E residue  228 LYS
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 125
   random chunks:
   chunk 22 optimal weight:    0.7980
   chunk 107 optimal weight:    0.0670
   chunk 63 optimal weight:    5.9990
   chunk 84 optimal weight:    0.7980
   chunk 54 optimal weight:    3.9990
   chunk 53 optimal weight:    0.0470
   chunk 37 optimal weight:    2.9990
   chunk 17 optimal weight:    0.0980
   chunk 66 optimal weight:    3.9990
   chunk 124 optimal weight:    0.5980
   chunk 3 optimal weight:    0.9980
   overall best weight:    0.3216

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

Flipped N/Q/H residues before XYZ refinement:
B 198 ASN
C 198 ASN
** E 198 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3446 r_free = 0.3446 target = 0.128241 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3162 r_free = 0.3162 target = 0.105823 restraints weight = 11156.987|
|-----------------------------------------------------------------------------|
r_work (start): 0.3085 rms_B_bonded: 1.50
r_work: 0.2965 rms_B_bonded: 2.20 restraints_weight: 0.5000
r_work: 0.2832 rms_B_bonded: 3.72 restraints_weight: 0.2500
r_work (final): 0.2832
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8315
moved from start:          0.2438

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.044   9655  Z= 0.148
  Angle     :  0.528   7.929  13075  Z= 0.273
  Chirality :  0.038   0.112   1610
  Planarity :  0.004   0.031   1630
  Dihedral  :  6.874  59.274   1335
  Min Nonbonded Distance : 2.580

Molprobity Statistics.
  All-atom Clashscore : 5.39
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.99 %
    Favored  : 98.01 %
  Rotamer:
    Outliers :  3.68 %
    Allowed  : 16.12 %
    Favored  : 80.20 %
  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: -3.93 (0.20), residues: 1255
  helix: -2.45 (0.14), residues: 1010
  sheet:  None (None), residues: 0
  loop : -2.10 (0.30), residues: 245

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP C 147 
 HIS   0.001   0.000   HIS B   0 
 PHE   0.006   0.001   PHE A 200 
 TYR   0.009   0.001   TYR A 222 
 ARG   0.002   0.000   ARG E  88 

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

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

  2510 Ramachandran restraints generated.
    1255 Oldfield, 0 Emsley, 1255 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2510 Ramachandran restraints generated.
    1255 Oldfield, 0 Emsley, 1255 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  183 residues out of total 1005 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 37
    poor density    : 146
  time to evaluate  : 1.031 
Fit side-chains
REVERT: A   53 LYS cc_start: 0.8170 (mmtp) cc_final: 0.7828 (mmtm)
REVERT: B    7 ILE cc_start: 0.8415 (tt) cc_final: 0.7931 (pt)
REVERT: B  122 ILE cc_start: 0.7991 (OUTLIER) cc_final: 0.7780 (mp)
REVERT: B  159 MET cc_start: 0.8169 (tmm) cc_final: 0.7734 (ptm)
REVERT: B  172 ASN cc_start: 0.6532 (m-40) cc_final: 0.4959 (p0)
REVERT: B  183 MET cc_start: 0.8026 (tpt) cc_final: 0.7666 (tpp)
REVERT: B  221 ILE cc_start: 0.8207 (OUTLIER) cc_final: 0.7781 (mp)
REVERT: C    2 ASP cc_start: 0.7687 (OUTLIER) cc_final: 0.7365 (t70)
REVERT: C   43 MET cc_start: 0.8534 (OUTLIER) cc_final: 0.8192 (mmt)
REVERT: C  118 ASP cc_start: 0.7199 (m-30) cc_final: 0.6861 (m-30)
REVERT: C  138 GLU cc_start: 0.8099 (mm-30) cc_final: 0.7189 (tt0)
REVERT: C  206 ASN cc_start: 0.8980 (t0) cc_final: 0.8439 (t0)
REVERT: C  249 GLU cc_start: 0.6822 (tm-30) cc_final: 0.6617 (tm-30)
REVERT: D  159 MET cc_start: 0.8341 (tmm) cc_final: 0.7873 (ttt)
REVERT: E  137 ASP cc_start: 0.8359 (t0) cc_final: 0.8051 (t0)
  outliers start: 37
  outliers final: 20
  residues processed: 172
  average time/residue: 0.2377
  time to fit residues: 61.2861
Evaluate side-chains
  157 residues out of total 1005 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 133
  time to evaluate  : 1.331 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   -1 VAL
Chi-restraints excluded: chain A residue    1 MET
Chi-restraints excluded: chain A residue   67 LEU
Chi-restraints excluded: chain A residue  112 MET
Chi-restraints excluded: chain A residue  137 ASP
Chi-restraints excluded: chain A residue  142 THR
Chi-restraints excluded: chain A residue  179 LEU
Chi-restraints excluded: chain A residue  237 VAL
Chi-restraints excluded: chain B residue    9 ILE
Chi-restraints excluded: chain B residue   67 LEU
Chi-restraints excluded: chain B residue  122 ILE
Chi-restraints excluded: chain B residue  221 ILE
Chi-restraints excluded: chain C residue    2 ASP
Chi-restraints excluded: chain C residue   43 MET
Chi-restraints excluded: chain C residue   67 LEU
Chi-restraints excluded: chain C residue  198 ASN
Chi-restraints excluded: chain C residue  226 ILE
Chi-restraints excluded: chain D residue   67 LEU
Chi-restraints excluded: chain D residue  113 ILE
Chi-restraints excluded: chain D residue  169 MET
Chi-restraints excluded: chain E residue   67 LEU
Chi-restraints excluded: chain E residue  189 THR
Chi-restraints excluded: chain E residue  221 ILE
Chi-restraints excluded: chain E residue  228 LYS
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 125
   random chunks:
   chunk 94 optimal weight:    2.9990
   chunk 20 optimal weight:    0.8980
   chunk 114 optimal weight:    0.9990
   chunk 67 optimal weight:    1.9990
   chunk 51 optimal weight:    2.9990
   chunk 48 optimal weight:    0.0870
   chunk 34 optimal weight:    0.0060
   chunk 12 optimal weight:    3.9990
   chunk 19 optimal weight:    0.9980
   chunk 103 optimal weight:    2.9990
   chunk 68 optimal weight:    1.9990
   overall best weight:    0.5976

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

Flipped N/Q/H residues before XYZ refinement:
B 198 ASN
** E 198 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3541 r_free = 0.3541 target = 0.135988 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3260 r_free = 0.3260 target = 0.113418 restraints weight = 11022.366|
|-----------------------------------------------------------------------------|
r_work (start): 0.3068 rms_B_bonded: 1.53
r_work: 0.2945 rms_B_bonded: 2.24 restraints_weight: 0.5000
r_work: 0.2810 rms_B_bonded: 3.79 restraints_weight: 0.2500
r_work (final): 0.2810
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8316
moved from start:          0.2608

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.044   9655  Z= 0.163
  Angle     :  0.509   6.501  13075  Z= 0.260
  Chirality :  0.038   0.114   1610
  Planarity :  0.004   0.033   1630
  Dihedral  :  6.230  59.724   1320
  Min Nonbonded Distance : 2.571

Molprobity Statistics.
  All-atom Clashscore : 4.98
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.31 %
    Favored  : 97.69 %
  Rotamer:
    Outliers :  3.28 %
    Allowed  : 16.02 %
    Favored  : 80.70 %
  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: -3.12 (0.21), residues: 1255
  helix: -1.85 (0.15), residues: 1000
  sheet:  None (None), residues: 0
  loop : -2.04 (0.30), residues: 255

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP C 147 
 HIS   0.001   0.000   HIS E   0 
 PHE   0.007   0.001   PHE A 200 
 TYR   0.006   0.001   TYR A 222 
 ARG   0.001   0.000   ARG E  88 

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

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

  2510 Ramachandran restraints generated.
    1255 Oldfield, 0 Emsley, 1255 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2510 Ramachandran restraints generated.
    1255 Oldfield, 0 Emsley, 1255 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  172 residues out of total 1005 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 139
  time to evaluate  : 1.052 
Fit side-chains
REVERT: A   53 LYS cc_start: 0.8135 (mmtp) cc_final: 0.7806 (mmtm)
REVERT: A  106 ASP cc_start: 0.8396 (p0) cc_final: 0.8083 (p0)
REVERT: B    7 ILE cc_start: 0.8504 (OUTLIER) cc_final: 0.8001 (pt)
REVERT: B  122 ILE cc_start: 0.7991 (OUTLIER) cc_final: 0.7780 (mp)
REVERT: B  159 MET cc_start: 0.8209 (tmm) cc_final: 0.7710 (ptm)
REVERT: B  183 MET cc_start: 0.8037 (tpt) cc_final: 0.7718 (tpp)
REVERT: B  221 ILE cc_start: 0.8218 (OUTLIER) cc_final: 0.7783 (mp)
REVERT: C    2 ASP cc_start: 0.7690 (OUTLIER) cc_final: 0.7351 (t70)
REVERT: C   43 MET cc_start: 0.8468 (tpp) cc_final: 0.8132 (mmt)
REVERT: C   69 LYS cc_start: 0.8996 (OUTLIER) cc_final: 0.8776 (mttt)
REVERT: C  138 GLU cc_start: 0.8097 (mm-30) cc_final: 0.7210 (tt0)
REVERT: C  206 ASN cc_start: 0.8982 (t0) cc_final: 0.8411 (t0)
REVERT: C  223 ILE cc_start: 0.8423 (OUTLIER) cc_final: 0.7824 (mp)
REVERT: D   90 GLU cc_start: 0.8440 (mp0) cc_final: 0.8075 (mt-10)
REVERT: D  159 MET cc_start: 0.8353 (tmm) cc_final: 0.7901 (ttt)
REVERT: D  227 GLU cc_start: 0.7908 (tt0) cc_final: 0.7604 (tt0)
REVERT: E  136 LEU cc_start: 0.8607 (tt) cc_final: 0.8355 (tp)
REVERT: E  137 ASP cc_start: 0.8407 (t0) cc_final: 0.8096 (t0)
REVERT: E  241 GLU cc_start: 0.8040 (mt-10) cc_final: 0.7794 (mt-10)
  outliers start: 33
  outliers final: 20
  residues processed: 163
  average time/residue: 0.1742
  time to fit residues: 42.5367
Evaluate side-chains
  162 residues out of total 1005 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 136
  time to evaluate  : 1.044 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   -1 VAL
Chi-restraints excluded: chain A residue    1 MET
Chi-restraints excluded: chain A residue   67 LEU
Chi-restraints excluded: chain A residue  112 MET
Chi-restraints excluded: chain A residue  137 ASP
Chi-restraints excluded: chain A residue  237 VAL
Chi-restraints excluded: chain B residue    7 ILE
Chi-restraints excluded: chain B residue    9 ILE
Chi-restraints excluded: chain B residue   67 LEU
Chi-restraints excluded: chain B residue  122 ILE
Chi-restraints excluded: chain B residue  187 LEU
Chi-restraints excluded: chain B residue  221 ILE
Chi-restraints excluded: chain C residue    2 ASP
Chi-restraints excluded: chain C residue   67 LEU
Chi-restraints excluded: chain C residue   69 LYS
Chi-restraints excluded: chain C residue  198 ASN
Chi-restraints excluded: chain C residue  223 ILE
Chi-restraints excluded: chain C residue  226 ILE
Chi-restraints excluded: chain D residue   67 LEU
Chi-restraints excluded: chain D residue  113 ILE
Chi-restraints excluded: chain D residue  169 MET
Chi-restraints excluded: chain E residue   -1 VAL
Chi-restraints excluded: chain E residue   67 LEU
Chi-restraints excluded: chain E residue  159 MET
Chi-restraints excluded: chain E residue  221 ILE
Chi-restraints excluded: chain E residue  228 LYS
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 125
   random chunks:
   chunk 110 optimal weight:    2.9990
   chunk 111 optimal weight:    0.6980
   chunk 64 optimal weight:    0.9980
   chunk 66 optimal weight:    0.6980
   chunk 30 optimal weight:    0.9980
   chunk 8 optimal weight:    0.9990
   chunk 83 optimal weight:    0.9990
   chunk 89 optimal weight:    1.9990
   chunk 35 optimal weight:    2.9990
   chunk 11 optimal weight:    5.9990
   chunk 87 optimal weight:    2.9990
   overall best weight:    0.8782

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

Flipped N/Q/H residues before XYZ refinement:
C 198 ASN
D 198 ASN
** E 198 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3422 r_free = 0.3422 target = 0.126552 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3134 r_free = 0.3134 target = 0.104054 restraints weight = 11088.932|
|-----------------------------------------------------------------------------|
r_work (start): 0.3059 rms_B_bonded: 1.48
r_work: 0.2946 rms_B_bonded: 2.10 restraints_weight: 0.5000
r_work: 0.2815 rms_B_bonded: 3.55 restraints_weight: 0.2500
r_work (final): 0.2815
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8320
moved from start:          0.2732

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.045   9655  Z= 0.194
  Angle     :  0.512   5.338  13075  Z= 0.261
  Chirality :  0.039   0.113   1610
  Planarity :  0.004   0.033   1630
  Dihedral  :  6.183  59.896   1320
  Min Nonbonded Distance : 2.571

Molprobity Statistics.
  All-atom Clashscore : 4.98
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.31 %
    Favored  : 97.69 %
  Rotamer:
    Outliers :  4.38 %
    Allowed  : 16.12 %
    Favored  : 79.50 %
  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: -2.51 (0.22), residues: 1255
  helix: -1.42 (0.16), residues: 1000
  sheet:  None (None), residues: 0
  loop : -1.84 (0.31), residues: 255

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP C 147 
 HIS   0.001   0.000   HIS B   0 
 PHE   0.009   0.001   PHE E 157 
 TYR   0.007   0.001   TYR D 222 
 ARG   0.001   0.000   ARG C  57 

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

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

  2510 Ramachandran restraints generated.
    1255 Oldfield, 0 Emsley, 1255 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2510 Ramachandran restraints generated.
    1255 Oldfield, 0 Emsley, 1255 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  188 residues out of total 1005 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 44
    poor density    : 144
  time to evaluate  : 1.172 
Fit side-chains
REVERT: A   53 LYS cc_start: 0.8115 (mmtp) cc_final: 0.7780 (mmtm)
REVERT: A  106 ASP cc_start: 0.8385 (p0) cc_final: 0.8056 (p0)
REVERT: B    7 ILE cc_start: 0.8539 (OUTLIER) cc_final: 0.8199 (tt)
REVERT: B   88 ARG cc_start: 0.7478 (ttm-80) cc_final: 0.7059 (ttt90)
REVERT: B  122 ILE cc_start: 0.7962 (OUTLIER) cc_final: 0.7722 (mp)
REVERT: B  159 MET cc_start: 0.8260 (tmm) cc_final: 0.7711 (ptm)
REVERT: B  221 ILE cc_start: 0.8222 (OUTLIER) cc_final: 0.7727 (mp)
REVERT: B  236 ASN cc_start: 0.8109 (m-40) cc_final: 0.7895 (m-40)
REVERT: C    2 ASP cc_start: 0.7660 (OUTLIER) cc_final: 0.7344 (t70)
REVERT: C   43 MET cc_start: 0.8425 (tpp) cc_final: 0.8079 (mmt)
REVERT: C   69 LYS cc_start: 0.9019 (OUTLIER) cc_final: 0.8755 (mttt)
REVERT: C   89 LYS cc_start: 0.8125 (tptt) cc_final: 0.7701 (mptt)
REVERT: C  206 ASN cc_start: 0.9020 (t0) cc_final: 0.8430 (t0)
REVERT: C  223 ILE cc_start: 0.8438 (OUTLIER) cc_final: 0.7811 (mp)
REVERT: D   90 GLU cc_start: 0.8493 (mp0) cc_final: 0.8173 (mt-10)
REVERT: D  159 MET cc_start: 0.8363 (tmm) cc_final: 0.7901 (ttt)
REVERT: D  227 GLU cc_start: 0.7916 (tt0) cc_final: 0.7685 (tt0)
REVERT: E   17 LEU cc_start: 0.8520 (OUTLIER) cc_final: 0.8282 (tp)
REVERT: E  136 LEU cc_start: 0.8574 (tt) cc_final: 0.8363 (tp)
REVERT: E  137 ASP cc_start: 0.8441 (t0) cc_final: 0.8119 (t0)
REVERT: E  228 LYS cc_start: 0.7821 (OUTLIER) cc_final: 0.7460 (mttt)
  outliers start: 44
  outliers final: 25
  residues processed: 177
  average time/residue: 0.1997
  time to fit residues: 52.4765
Evaluate side-chains
  173 residues out of total 1005 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 140
  time to evaluate  : 1.033 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   -1 VAL
Chi-restraints excluded: chain A residue    1 MET
Chi-restraints excluded: chain A residue   67 LEU
Chi-restraints excluded: chain A residue  112 MET
Chi-restraints excluded: chain A residue  137 ASP
Chi-restraints excluded: chain A residue  142 THR
Chi-restraints excluded: chain A residue  179 LEU
Chi-restraints excluded: chain A residue  221 ILE
Chi-restraints excluded: chain A residue  226 ILE
Chi-restraints excluded: chain A residue  237 VAL
Chi-restraints excluded: chain B residue    7 ILE
Chi-restraints excluded: chain B residue    9 ILE
Chi-restraints excluded: chain B residue   67 LEU
Chi-restraints excluded: chain B residue  122 ILE
Chi-restraints excluded: chain B residue  187 LEU
Chi-restraints excluded: chain B residue  221 ILE
Chi-restraints excluded: chain C residue    2 ASP
Chi-restraints excluded: chain C residue   67 LEU
Chi-restraints excluded: chain C residue   69 LYS
Chi-restraints excluded: chain C residue  223 ILE
Chi-restraints excluded: chain C residue  226 ILE
Chi-restraints excluded: chain D residue   22 ILE
Chi-restraints excluded: chain D residue   67 LEU
Chi-restraints excluded: chain D residue   88 ARG
Chi-restraints excluded: chain D residue  113 ILE
Chi-restraints excluded: chain D residue  185 VAL
Chi-restraints excluded: chain D residue  198 ASN
Chi-restraints excluded: chain E residue   -1 VAL
Chi-restraints excluded: chain E residue   17 LEU
Chi-restraints excluded: chain E residue   67 LEU
Chi-restraints excluded: chain E residue  159 MET
Chi-restraints excluded: chain E residue  221 ILE
Chi-restraints excluded: chain E residue  228 LYS
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 125
   random chunks:
   chunk 73 optimal weight:    4.9990
   chunk 19 optimal weight:    2.9990
   chunk 44 optimal weight:    1.9990
   chunk 26 optimal weight:    1.9990
   chunk 32 optimal weight:    0.0040
   chunk 11 optimal weight:    0.8980
   chunk 29 optimal weight:    0.0770
   chunk 25 optimal weight:    5.9990
   chunk 67 optimal weight:    6.9990
   chunk 51 optimal weight:    0.9990
   chunk 58 optimal weight:    2.9990
   overall best weight:    0.7954

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

Flipped N/Q/H residues before XYZ refinement:
** A 135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E 198 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3539 r_free = 0.3539 target = 0.135696 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3266 r_free = 0.3266 target = 0.113916 restraints weight = 10930.876|
|-----------------------------------------------------------------------------|
r_work (start): 0.3091 rms_B_bonded: 1.43
r_work: 0.2975 rms_B_bonded: 2.02 restraints_weight: 0.5000
r_work: 0.2845 rms_B_bonded: 3.45 restraints_weight: 0.2500
r_work (final): 0.2845
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8302
moved from start:          0.2890

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042   9655  Z= 0.183
  Angle     :  0.508   5.332  13075  Z= 0.260
  Chirality :  0.039   0.113   1610
  Planarity :  0.004   0.036   1630
  Dihedral  :  6.122  59.699   1320
  Min Nonbonded Distance : 2.547

Molprobity Statistics.
  All-atom Clashscore : 5.29
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.23 %
    Favored  : 97.77 %
  Rotamer:
    Outliers :  4.18 %
    Allowed  : 16.52 %
    Favored  : 79.30 %
  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: -2.06 (0.22), residues: 1255
  helix: -1.12 (0.16), residues: 980
  sheet:  None (None), residues: 0
  loop : -1.60 (0.31), residues: 275

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP C 147 
 HIS   0.002   0.000   HIS A   0 
 PHE   0.007   0.001   PHE A 200 
 TYR   0.007   0.001   TYR D 222 
 ARG   0.001   0.000   ARG E  57 

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

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

  2510 Ramachandran restraints generated.
    1255 Oldfield, 0 Emsley, 1255 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2510 Ramachandran restraints generated.
    1255 Oldfield, 0 Emsley, 1255 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  179 residues out of total 1005 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 42
    poor density    : 137
  time to evaluate  : 1.052 
Fit side-chains
REVERT: A   53 LYS cc_start: 0.8106 (mmtp) cc_final: 0.7767 (mmtm)
REVERT: A  106 ASP cc_start: 0.8371 (p0) cc_final: 0.8038 (p0)
REVERT: A  244 ILE cc_start: 0.8347 (OUTLIER) cc_final: 0.8146 (mm)
REVERT: B    7 ILE cc_start: 0.8542 (OUTLIER) cc_final: 0.8199 (tt)
REVERT: B   17 LEU cc_start: 0.8227 (OUTLIER) cc_final: 0.7893 (tp)
REVERT: B   88 ARG cc_start: 0.7523 (ttm-80) cc_final: 0.7149 (ttt90)
REVERT: B  122 ILE cc_start: 0.7997 (OUTLIER) cc_final: 0.7748 (mp)
REVERT: B  159 MET cc_start: 0.8185 (tmm) cc_final: 0.7640 (ptm)
REVERT: B  221 ILE cc_start: 0.8213 (OUTLIER) cc_final: 0.7714 (mp)
REVERT: B  236 ASN cc_start: 0.8088 (m-40) cc_final: 0.7879 (m-40)
REVERT: C    2 ASP cc_start: 0.7683 (OUTLIER) cc_final: 0.7353 (t70)
REVERT: C   17 LEU cc_start: 0.8662 (OUTLIER) cc_final: 0.8405 (tp)
REVERT: C   43 MET cc_start: 0.8408 (tpp) cc_final: 0.8061 (mmt)
REVERT: C   69 LYS cc_start: 0.9030 (OUTLIER) cc_final: 0.8776 (mttt)
REVERT: C   89 LYS cc_start: 0.8123 (tptt) cc_final: 0.7688 (mptt)
REVERT: C  206 ASN cc_start: 0.9013 (t0) cc_final: 0.8489 (t0)
REVERT: C  223 ILE cc_start: 0.8410 (OUTLIER) cc_final: 0.7800 (mp)
REVERT: D   90 GLU cc_start: 0.8485 (OUTLIER) cc_final: 0.8201 (mt-10)
REVERT: D  112 MET cc_start: 0.8430 (ttp) cc_final: 0.8157 (mtp)
REVERT: D  159 MET cc_start: 0.8338 (tmm) cc_final: 0.7860 (ttt)
REVERT: D  198 ASN cc_start: 0.8689 (OUTLIER) cc_final: 0.8380 (t0)
REVERT: D  200 PHE cc_start: 0.8946 (t80) cc_final: 0.8728 (t80)
REVERT: D  227 GLU cc_start: 0.7916 (tt0) cc_final: 0.7618 (tt0)
REVERT: E  136 LEU cc_start: 0.8546 (tt) cc_final: 0.8325 (tp)
REVERT: E  137 ASP cc_start: 0.8448 (t0) cc_final: 0.8124 (t0)
REVERT: E  228 LYS cc_start: 0.7695 (OUTLIER) cc_final: 0.7428 (mttt)
  outliers start: 42
  outliers final: 22
  residues processed: 166
  average time/residue: 0.1794
  time to fit residues: 44.0102
Evaluate side-chains
  167 residues out of total 1005 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 133
  time to evaluate  : 0.971 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   67 LEU
Chi-restraints excluded: chain A residue  137 ASP
Chi-restraints excluded: chain A residue  179 LEU
Chi-restraints excluded: chain A residue  221 ILE
Chi-restraints excluded: chain A residue  237 VAL
Chi-restraints excluded: chain A residue  244 ILE
Chi-restraints excluded: chain B residue    7 ILE
Chi-restraints excluded: chain B residue    9 ILE
Chi-restraints excluded: chain B residue   17 LEU
Chi-restraints excluded: chain B residue   43 MET
Chi-restraints excluded: chain B residue   67 LEU
Chi-restraints excluded: chain B residue  122 ILE
Chi-restraints excluded: chain B residue  221 ILE
Chi-restraints excluded: chain C residue    2 ASP
Chi-restraints excluded: chain C residue   17 LEU
Chi-restraints excluded: chain C residue   67 LEU
Chi-restraints excluded: chain C residue   69 LYS
Chi-restraints excluded: chain C residue  223 ILE
Chi-restraints excluded: chain C residue  226 ILE
Chi-restraints excluded: chain C residue  229 ILE
Chi-restraints excluded: chain D residue   22 ILE
Chi-restraints excluded: chain D residue   67 LEU
Chi-restraints excluded: chain D residue   88 ARG
Chi-restraints excluded: chain D residue   90 GLU
Chi-restraints excluded: chain D residue  113 ILE
Chi-restraints excluded: chain D residue  185 VAL
Chi-restraints excluded: chain D residue  198 ASN
Chi-restraints excluded: chain E residue   -1 VAL
Chi-restraints excluded: chain E residue   32 VAL
Chi-restraints excluded: chain E residue   59 VAL
Chi-restraints excluded: chain E residue   67 LEU
Chi-restraints excluded: chain E residue  221 ILE
Chi-restraints excluded: chain E residue  226 ILE
Chi-restraints excluded: chain E residue  228 LYS
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 125
   random chunks:
   chunk 71 optimal weight:    2.9990
   chunk 15 optimal weight:    0.6980
   chunk 58 optimal weight:    1.9990
   chunk 116 optimal weight:    3.9990
   chunk 115 optimal weight:    0.9980
   chunk 33 optimal weight:    0.8980
   chunk 84 optimal weight:    0.9980
   chunk 112 optimal weight:    0.9990
   chunk 117 optimal weight:    0.6980
   chunk 49 optimal weight:    0.6980
   chunk 38 optimal weight:    0.9980
   overall best weight:    0.7980

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

Flipped N/Q/H residues before XYZ refinement:
** A 135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
D 198 ASN
** E 198 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3544 r_free = 0.3544 target = 0.136252 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3287 r_free = 0.3287 target = 0.115541 restraints weight = 10951.945|
|-----------------------------------------------------------------------------|
r_work (start): 0.3099 rms_B_bonded: 1.31
r_work: 0.2979 rms_B_bonded: 1.93 restraints_weight: 0.5000
r_work: 0.2854 rms_B_bonded: 3.26 restraints_weight: 0.2500
r_work (final): 0.2854
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8299
moved from start:          0.3012

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.055   9655  Z= 0.185
  Angle     :  0.507   8.886  13075  Z= 0.257
  Chirality :  0.038   0.113   1610
  Planarity :  0.004   0.034   1630
  Dihedral  :  6.007  59.218   1319
  Min Nonbonded Distance : 2.565

Molprobity Statistics.
  All-atom Clashscore : 5.44
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.31 %
    Favored  : 97.69 %
  Rotamer:
    Outliers :  4.08 %
    Allowed  : 17.21 %
    Favored  : 78.71 %
  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: -1.65 (0.23), residues: 1255
  helix: -0.79 (0.16), residues: 985
  sheet:  None (None), residues: 0
  loop : -1.60 (0.31), residues: 270

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP C 147 
 HIS   0.002   0.000   HIS A   0 
 PHE   0.010   0.001   PHE E 157 
 TYR   0.007   0.001   TYR D 222 
 ARG   0.001   0.000   ARG E  88 

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

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

  2510 Ramachandran restraints generated.
    1255 Oldfield, 0 Emsley, 1255 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2510 Ramachandran restraints generated.
    1255 Oldfield, 0 Emsley, 1255 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  186 residues out of total 1005 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 41
    poor density    : 145
  time to evaluate  : 0.931 
Fit side-chains
REVERT: A   53 LYS cc_start: 0.8113 (mmtp) cc_final: 0.7766 (mmtm)
REVERT: A  106 ASP cc_start: 0.8369 (p0) cc_final: 0.8031 (p0)
REVERT: A  244 ILE cc_start: 0.8342 (OUTLIER) cc_final: 0.8138 (mm)
REVERT: B    7 ILE cc_start: 0.8572 (OUTLIER) cc_final: 0.8246 (tt)
REVERT: B   17 LEU cc_start: 0.8224 (OUTLIER) cc_final: 0.7891 (tp)
REVERT: B   88 ARG cc_start: 0.7563 (ttm-80) cc_final: 0.7223 (ttt90)
REVERT: B  122 ILE cc_start: 0.8021 (OUTLIER) cc_final: 0.7740 (mp)
REVERT: B  159 MET cc_start: 0.8208 (tmm) cc_final: 0.7653 (ptm)
REVERT: B  221 ILE cc_start: 0.8190 (OUTLIER) cc_final: 0.7725 (mp)
REVERT: B  236 ASN cc_start: 0.8093 (m-40) cc_final: 0.7877 (m-40)
REVERT: C    2 ASP cc_start: 0.7676 (OUTLIER) cc_final: 0.7357 (t70)
REVERT: C   17 LEU cc_start: 0.8645 (OUTLIER) cc_final: 0.8415 (tp)
REVERT: C   43 MET cc_start: 0.8351 (tpp) cc_final: 0.8014 (mmt)
REVERT: C   69 LYS cc_start: 0.9055 (OUTLIER) cc_final: 0.8787 (mttt)
REVERT: C   89 LYS cc_start: 0.8147 (tptt) cc_final: 0.7712 (mptt)
REVERT: C  206 ASN cc_start: 0.8990 (t0) cc_final: 0.8455 (t0)
REVERT: C  223 ILE cc_start: 0.8425 (OUTLIER) cc_final: 0.7798 (mp)
REVERT: D   90 GLU cc_start: 0.8523 (OUTLIER) cc_final: 0.8035 (mt-10)
REVERT: D  112 MET cc_start: 0.8426 (ttp) cc_final: 0.8214 (mtp)
REVERT: D  159 MET cc_start: 0.8312 (tmm) cc_final: 0.7842 (ttt)
REVERT: D  227 GLU cc_start: 0.7887 (tt0) cc_final: 0.7582 (tt0)
REVERT: E  136 LEU cc_start: 0.8536 (tt) cc_final: 0.8335 (tp)
REVERT: E  137 ASP cc_start: 0.8456 (t0) cc_final: 0.8138 (t0)
  outliers start: 41
  outliers final: 23
  residues processed: 174
  average time/residue: 0.1759
  time to fit residues: 45.3974
Evaluate side-chains
  172 residues out of total 1005 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 139
  time to evaluate  : 1.029 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   67 LEU
Chi-restraints excluded: chain A residue  137 ASP
Chi-restraints excluded: chain A residue  142 THR
Chi-restraints excluded: chain A residue  179 LEU
Chi-restraints excluded: chain A residue  221 ILE
Chi-restraints excluded: chain A residue  237 VAL
Chi-restraints excluded: chain A residue  244 ILE
Chi-restraints excluded: chain B residue    7 ILE
Chi-restraints excluded: chain B residue    9 ILE
Chi-restraints excluded: chain B residue   17 LEU
Chi-restraints excluded: chain B residue   43 MET
Chi-restraints excluded: chain B residue   67 LEU
Chi-restraints excluded: chain B residue  122 ILE
Chi-restraints excluded: chain B residue  221 ILE
Chi-restraints excluded: chain C residue    2 ASP
Chi-restraints excluded: chain C residue   17 LEU
Chi-restraints excluded: chain C residue   67 LEU
Chi-restraints excluded: chain C residue   69 LYS
Chi-restraints excluded: chain C residue  223 ILE
Chi-restraints excluded: chain C residue  226 ILE
Chi-restraints excluded: chain C residue  229 ILE
Chi-restraints excluded: chain D residue   22 ILE
Chi-restraints excluded: chain D residue   67 LEU
Chi-restraints excluded: chain D residue   88 ARG
Chi-restraints excluded: chain D residue   90 GLU
Chi-restraints excluded: chain D residue  113 ILE
Chi-restraints excluded: chain D residue  185 VAL
Chi-restraints excluded: chain D residue  198 ASN
Chi-restraints excluded: chain E residue   32 VAL
Chi-restraints excluded: chain E residue   59 VAL
Chi-restraints excluded: chain E residue   67 LEU
Chi-restraints excluded: chain E residue  221 ILE
Chi-restraints excluded: chain E residue  226 ILE
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 125
   random chunks:
   chunk 113 optimal weight:    0.9980
   chunk 71 optimal weight:    1.9990
   chunk 11 optimal weight:    0.9990
   chunk 5 optimal weight:    0.5980
   chunk 82 optimal weight:    5.9990
   chunk 58 optimal weight:    2.9990
   chunk 9 optimal weight:    6.9990
   chunk 114 optimal weight:    0.9980
   chunk 55 optimal weight:    0.6980
   chunk 47 optimal weight:    0.7980
   chunk 123 optimal weight:    4.9990
   overall best weight:    0.8180

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

Flipped N/Q/H residues before XYZ refinement:
** A 135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
D 198 ASN
** E 198 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3546 r_free = 0.3546 target = 0.136506 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3267 r_free = 0.3267 target = 0.114302 restraints weight = 11078.939|
|-----------------------------------------------------------------------------|
r_work (start): 0.3095 rms_B_bonded: 1.49
r_work: 0.2972 rms_B_bonded: 2.13 restraints_weight: 0.5000
r_work: 0.2839 rms_B_bonded: 3.62 restraints_weight: 0.2500
r_work (final): 0.2839
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8304
moved from start:          0.3066

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.047   9655  Z= 0.186
  Angle     :  0.505   8.753  13075  Z= 0.255
  Chirality :  0.039   0.113   1610
  Planarity :  0.004   0.034   1630
  Dihedral  :  5.896  59.069   1315
  Min Nonbonded Distance : 2.534

Molprobity Statistics.
  All-atom Clashscore : 5.79
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.07 %
    Favored  : 97.93 %
  Rotamer:
    Outliers :  4.18 %
    Allowed  : 17.61 %
    Favored  : 78.21 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.43 (0.23), residues: 1255
  helix: -0.63 (0.17), residues: 985
  sheet:  None (None), residues: 0
  loop : -1.55 (0.31), residues: 270

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP C 147 
 HIS   0.001   0.000   HIS E   0 
 PHE   0.007   0.001   PHE A 200 
 TYR   0.006   0.001   TYR D 222 
 ARG   0.001   0.000   ARG E  57 

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

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

  2510 Ramachandran restraints generated.
    1255 Oldfield, 0 Emsley, 1255 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2510 Ramachandran restraints generated.
    1255 Oldfield, 0 Emsley, 1255 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  182 residues out of total 1005 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 42
    poor density    : 140
  time to evaluate  : 1.160 
Fit side-chains
REVERT: A   53 LYS cc_start: 0.8114 (mmtp) cc_final: 0.7779 (mmtm)
REVERT: A  106 ASP cc_start: 0.8385 (p0) cc_final: 0.8054 (p0)
REVERT: A  244 ILE cc_start: 0.8345 (OUTLIER) cc_final: 0.8138 (mm)
REVERT: B    7 ILE cc_start: 0.8578 (OUTLIER) cc_final: 0.8247 (tt)
REVERT: B   17 LEU cc_start: 0.8248 (OUTLIER) cc_final: 0.7905 (tp)
REVERT: B  122 ILE cc_start: 0.7980 (OUTLIER) cc_final: 0.7693 (mp)
REVERT: B  159 MET cc_start: 0.8238 (OUTLIER) cc_final: 0.7692 (ptm)
REVERT: B  221 ILE cc_start: 0.8206 (OUTLIER) cc_final: 0.7748 (mp)
REVERT: B  236 ASN cc_start: 0.8103 (m-40) cc_final: 0.7885 (m-40)
REVERT: C    2 ASP cc_start: 0.7709 (OUTLIER) cc_final: 0.7371 (t70)
REVERT: C   17 LEU cc_start: 0.8655 (OUTLIER) cc_final: 0.8412 (tp)
REVERT: C   43 MET cc_start: 0.8367 (tpp) cc_final: 0.8037 (mmt)
REVERT: C   69 LYS cc_start: 0.9058 (OUTLIER) cc_final: 0.8788 (mttt)
REVERT: C   89 LYS cc_start: 0.8129 (tptt) cc_final: 0.7684 (mptt)
REVERT: C  206 ASN cc_start: 0.9004 (t0) cc_final: 0.8460 (t0)
REVERT: C  223 ILE cc_start: 0.8423 (OUTLIER) cc_final: 0.7793 (mp)
REVERT: C  230 GLN cc_start: 0.6793 (OUTLIER) cc_final: 0.6584 (tt0)
REVERT: D   90 GLU cc_start: 0.8509 (OUTLIER) cc_final: 0.8042 (mt-10)
REVERT: D  159 MET cc_start: 0.8344 (tmm) cc_final: 0.7890 (ttt)
REVERT: D  227 GLU cc_start: 0.7915 (tt0) cc_final: 0.7616 (tt0)
REVERT: E  137 ASP cc_start: 0.8434 (t0) cc_final: 0.8121 (t0)
REVERT: E  224 GLU cc_start: 0.7896 (mm-30) cc_final: 0.7664 (mp0)
  outliers start: 42
  outliers final: 29
  residues processed: 169
  average time/residue: 0.1853
  time to fit residues: 46.3673
Evaluate side-chains
  179 residues out of total 1005 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 41
    poor density    : 138
  time to evaluate  : 1.048 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    1 MET
Chi-restraints excluded: chain A residue   67 LEU
Chi-restraints excluded: chain A residue  112 MET
Chi-restraints excluded: chain A residue  137 ASP
Chi-restraints excluded: chain A residue  142 THR
Chi-restraints excluded: chain A residue  179 LEU
Chi-restraints excluded: chain A residue  221 ILE
Chi-restraints excluded: chain A residue  237 VAL
Chi-restraints excluded: chain A residue  244 ILE
Chi-restraints excluded: chain B residue    7 ILE
Chi-restraints excluded: chain B residue    9 ILE
Chi-restraints excluded: chain B residue   17 LEU
Chi-restraints excluded: chain B residue   43 MET
Chi-restraints excluded: chain B residue   67 LEU
Chi-restraints excluded: chain B residue  122 ILE
Chi-restraints excluded: chain B residue  159 MET
Chi-restraints excluded: chain B residue  221 ILE
Chi-restraints excluded: chain C residue    2 ASP
Chi-restraints excluded: chain C residue   17 LEU
Chi-restraints excluded: chain C residue   67 LEU
Chi-restraints excluded: chain C residue   69 LYS
Chi-restraints excluded: chain C residue  223 ILE
Chi-restraints excluded: chain C residue  226 ILE
Chi-restraints excluded: chain C residue  229 ILE
Chi-restraints excluded: chain C residue  230 GLN
Chi-restraints excluded: chain D residue   22 ILE
Chi-restraints excluded: chain D residue   67 LEU
Chi-restraints excluded: chain D residue   88 ARG
Chi-restraints excluded: chain D residue   90 GLU
Chi-restraints excluded: chain D residue  113 ILE
Chi-restraints excluded: chain D residue  137 ASP
Chi-restraints excluded: chain D residue  185 VAL
Chi-restraints excluded: chain D residue  198 ASN
Chi-restraints excluded: chain D residue  229 ILE
Chi-restraints excluded: chain E residue   -1 VAL
Chi-restraints excluded: chain E residue   21 LEU
Chi-restraints excluded: chain E residue   32 VAL
Chi-restraints excluded: chain E residue   59 VAL
Chi-restraints excluded: chain E residue   67 LEU
Chi-restraints excluded: chain E residue  221 ILE
Chi-restraints excluded: chain E residue  226 ILE
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 125
   random chunks:
   chunk 6 optimal weight:    3.9990
   chunk 10 optimal weight:    0.9990
   chunk 14 optimal weight:    0.9980
   chunk 89 optimal weight:    0.9980
   chunk 70 optimal weight:    0.7980
   chunk 80 optimal weight:    0.6980
   chunk 36 optimal weight:    0.9990
   chunk 1 optimal weight:    0.7980
   chunk 33 optimal weight:    0.9990
   chunk 28 optimal weight:    1.9990
   chunk 62 optimal weight:    3.9990
   overall best weight:    0.8580

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

Flipped N/Q/H residues before XYZ refinement:
** A 135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 206 ASN
D 135 GLN
D 198 ASN
** E 198 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3461 r_free = 0.3461 target = 0.129224 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3175 r_free = 0.3175 target = 0.106510 restraints weight = 10971.353|
|-----------------------------------------------------------------------------|
r_work (start): 0.3055 rms_B_bonded: 1.52
r_work: 0.2940 rms_B_bonded: 2.16 restraints_weight: 0.5000
r_work: 0.2807 rms_B_bonded: 3.67 restraints_weight: 0.2500
r_work (final): 0.2807
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8301
moved from start:          0.3127

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.043   9655  Z= 0.191
  Angle     :  0.507   8.611  13075  Z= 0.256
  Chirality :  0.039   0.113   1610
  Planarity :  0.004   0.034   1630
  Dihedral  :  5.879  59.011   1315
  Min Nonbonded Distance : 2.540

Molprobity Statistics.
  All-atom Clashscore : 5.79
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.15 %
    Favored  : 97.85 %
  Rotamer:
    Outliers :  4.38 %
    Allowed  : 17.61 %
    Favored  : 78.01 %
  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: -1.27 (0.23), residues: 1255
  helix: -0.51 (0.17), residues: 985
  sheet:  None (None), residues: 0
  loop : -1.53 (0.31), residues: 270

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP C 147 
 HIS   0.001   0.000   HIS E   0 
 PHE   0.007   0.001   PHE A 200 
 TYR   0.007   0.001   TYR D 222 
 ARG   0.002   0.000   ARG B  88 

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

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

  2510 Ramachandran restraints generated.
    1255 Oldfield, 0 Emsley, 1255 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2510 Ramachandran restraints generated.
    1255 Oldfield, 0 Emsley, 1255 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  182 residues out of total 1005 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 44
    poor density    : 138
  time to evaluate  : 1.081 
Fit side-chains
REVERT: A   53 LYS cc_start: 0.8120 (mmtp) cc_final: 0.7789 (mmtm)
REVERT: A  106 ASP cc_start: 0.8400 (p0) cc_final: 0.8069 (p0)
REVERT: B    7 ILE cc_start: 0.8575 (OUTLIER) cc_final: 0.8240 (tt)
REVERT: B   17 LEU cc_start: 0.8240 (OUTLIER) cc_final: 0.7887 (tp)
REVERT: B  159 MET cc_start: 0.8256 (OUTLIER) cc_final: 0.7714 (ptm)
REVERT: B  221 ILE cc_start: 0.8192 (OUTLIER) cc_final: 0.7728 (mp)
REVERT: B  236 ASN cc_start: 0.8094 (m-40) cc_final: 0.7893 (m-40)
REVERT: C    2 ASP cc_start: 0.7726 (OUTLIER) cc_final: 0.7383 (t70)
REVERT: C   17 LEU cc_start: 0.8667 (OUTLIER) cc_final: 0.8420 (tp)
REVERT: C   43 MET cc_start: 0.8357 (tpp) cc_final: 0.8026 (mmt)
REVERT: C   69 LYS cc_start: 0.9056 (OUTLIER) cc_final: 0.8779 (mttt)
REVERT: C   89 LYS cc_start: 0.8130 (tptt) cc_final: 0.7678 (mptt)
REVERT: C  206 ASN cc_start: 0.8945 (t0) cc_final: 0.8508 (t0)
REVERT: C  223 ILE cc_start: 0.8421 (OUTLIER) cc_final: 0.7786 (mp)
REVERT: C  230 GLN cc_start: 0.6879 (OUTLIER) cc_final: 0.6654 (tt0)
REVERT: D   90 GLU cc_start: 0.8515 (OUTLIER) cc_final: 0.8051 (mt-10)
REVERT: D  159 MET cc_start: 0.8367 (tmm) cc_final: 0.7927 (ttt)
REVERT: D  227 GLU cc_start: 0.7862 (tt0) cc_final: 0.7578 (tt0)
REVERT: E  137 ASP cc_start: 0.8405 (t0) cc_final: 0.8123 (t0)
REVERT: E  224 GLU cc_start: 0.7914 (mm-30) cc_final: 0.7658 (mp0)
  outliers start: 44
  outliers final: 27
  residues processed: 171
  average time/residue: 0.1753
  time to fit residues: 44.6645
Evaluate side-chains
  168 residues out of total 1005 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 37
    poor density    : 131
  time to evaluate  : 1.038 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    1 MET
Chi-restraints excluded: chain A residue   67 LEU
Chi-restraints excluded: chain A residue  112 MET
Chi-restraints excluded: chain A residue  137 ASP
Chi-restraints excluded: chain A residue  142 THR
Chi-restraints excluded: chain A residue  179 LEU
Chi-restraints excluded: chain A residue  221 ILE
Chi-restraints excluded: chain A residue  237 VAL
Chi-restraints excluded: chain B residue    7 ILE
Chi-restraints excluded: chain B residue    9 ILE
Chi-restraints excluded: chain B residue   17 LEU
Chi-restraints excluded: chain B residue   67 LEU
Chi-restraints excluded: chain B residue  159 MET
Chi-restraints excluded: chain B residue  221 ILE
Chi-restraints excluded: chain C residue    2 ASP
Chi-restraints excluded: chain C residue   17 LEU
Chi-restraints excluded: chain C residue   59 VAL
Chi-restraints excluded: chain C residue   67 LEU
Chi-restraints excluded: chain C residue   69 LYS
Chi-restraints excluded: chain C residue  223 ILE
Chi-restraints excluded: chain C residue  226 ILE
Chi-restraints excluded: chain C residue  229 ILE
Chi-restraints excluded: chain C residue  230 GLN
Chi-restraints excluded: chain D residue   22 ILE
Chi-restraints excluded: chain D residue   67 LEU
Chi-restraints excluded: chain D residue   88 ARG
Chi-restraints excluded: chain D residue   90 GLU
Chi-restraints excluded: chain D residue  113 ILE
Chi-restraints excluded: chain D residue  137 ASP
Chi-restraints excluded: chain D residue  185 VAL
Chi-restraints excluded: chain D residue  229 ILE
Chi-restraints excluded: chain E residue   -1 VAL
Chi-restraints excluded: chain E residue   21 LEU
Chi-restraints excluded: chain E residue   32 VAL
Chi-restraints excluded: chain E residue   59 VAL
Chi-restraints excluded: chain E residue   67 LEU
Chi-restraints excluded: chain E residue  221 ILE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 125
   random chunks:
   chunk 15 optimal weight:    0.5980
   chunk 18 optimal weight:    0.9980
   chunk 23 optimal weight:    0.8980
   chunk 13 optimal weight:    6.9990
   chunk 56 optimal weight:    0.8980
   chunk 91 optimal weight:    0.9990
   chunk 79 optimal weight:    3.9990
   chunk 110 optimal weight:    0.0370
   chunk 104 optimal weight:    0.9980
   chunk 90 optimal weight:    0.5980
   chunk 75 optimal weight:    6.9990
   overall best weight:    0.6058

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

Flipped N/Q/H residues before XYZ refinement:
** A 135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 206 ASN
D 198 ASN
** E 198 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3559 r_free = 0.3559 target = 0.137988 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3305 r_free = 0.3305 target = 0.117132 restraints weight = 10954.456|
|-----------------------------------------------------------------------------|
r_work (start): 0.3300 rms_B_bonded: 1.32
r_work: 0.3175 rms_B_bonded: 2.03 restraints_weight: 0.5000
r_work: 0.3050 rms_B_bonded: 3.44 restraints_weight: 0.2500
r_work (final): 0.3050
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8290
moved from start:          0.3243

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039   9655  Z= 0.162
  Angle     :  0.493   8.563  13075  Z= 0.249
  Chirality :  0.038   0.111   1610
  Planarity :  0.003   0.035   1630
  Dihedral  :  5.727  58.794   1315
  Min Nonbonded Distance : 2.525

Molprobity Statistics.
  All-atom Clashscore : 5.95
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.83 %
    Favored  : 98.17 %
  Rotamer:
    Outliers :  3.48 %
    Allowed  : 18.41 %
    Favored  : 78.11 %
  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: -0.97 (0.23), residues: 1255
  helix: -0.29 (0.17), residues: 985
  sheet:  None (None), residues: 0
  loop : -1.47 (0.31), residues: 270

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP C 147 
 HIS   0.001   0.000   HIS E   0 
 PHE   0.010   0.001   PHE E 157 
 TYR   0.007   0.001   TYR D 222 
 ARG   0.001   0.000   ARG B  88 

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

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

  2510 Ramachandran restraints generated.
    1255 Oldfield, 0 Emsley, 1255 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2510 Ramachandran restraints generated.
    1255 Oldfield, 0 Emsley, 1255 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  167 residues out of total 1005 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 132
  time to evaluate  : 1.067 
Fit side-chains
REVERT: A   53 LYS cc_start: 0.8121 (mmtp) cc_final: 0.7783 (mmtm)
REVERT: A  106 ASP cc_start: 0.8373 (p0) cc_final: 0.8052 (p0)
REVERT: B    7 ILE cc_start: 0.8561 (OUTLIER) cc_final: 0.8234 (tt)
REVERT: B   17 LEU cc_start: 0.8178 (OUTLIER) cc_final: 0.7831 (tp)
REVERT: B  159 MET cc_start: 0.8148 (tmm) cc_final: 0.7560 (ptm)
REVERT: B  221 ILE cc_start: 0.8233 (OUTLIER) cc_final: 0.7770 (mp)
REVERT: C    2 ASP cc_start: 0.7642 (OUTLIER) cc_final: 0.7336 (t70)
REVERT: C   17 LEU cc_start: 0.8666 (OUTLIER) cc_final: 0.8424 (tp)
REVERT: C   43 MET cc_start: 0.8304 (tpp) cc_final: 0.7991 (mmt)
REVERT: C   69 LYS cc_start: 0.9085 (OUTLIER) cc_final: 0.8827 (mttt)
REVERT: C   89 LYS cc_start: 0.8132 (tptt) cc_final: 0.7671 (mptt)
REVERT: C  206 ASN cc_start: 0.8956 (t0) cc_final: 0.8424 (t0)
REVERT: C  223 ILE cc_start: 0.8444 (OUTLIER) cc_final: 0.7820 (mp)
REVERT: C  230 GLN cc_start: 0.6915 (OUTLIER) cc_final: 0.6396 (tt0)
REVERT: D   90 GLU cc_start: 0.8540 (mp0) cc_final: 0.8090 (mt-10)
REVERT: D  138 GLU cc_start: 0.8105 (mm-30) cc_final: 0.6640 (mt-10)
REVERT: D  159 MET cc_start: 0.8313 (tmm) cc_final: 0.7857 (ttt)
REVERT: D  227 GLU cc_start: 0.7875 (tt0) cc_final: 0.7590 (tt0)
REVERT: E  137 ASP cc_start: 0.8375 (t0) cc_final: 0.8086 (t0)
REVERT: E  224 GLU cc_start: 0.7949 (mm-30) cc_final: 0.7688 (mp0)
  outliers start: 35
  outliers final: 22
  residues processed: 159
  average time/residue: 0.2278
  time to fit residues: 54.4409
Evaluate side-chains
  164 residues out of total 1005 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 134
  time to evaluate  : 0.971 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   67 LEU
Chi-restraints excluded: chain A residue  112 MET
Chi-restraints excluded: chain A residue  142 THR
Chi-restraints excluded: chain A residue  179 LEU
Chi-restraints excluded: chain A residue  221 ILE
Chi-restraints excluded: chain A residue  237 VAL
Chi-restraints excluded: chain B residue    7 ILE
Chi-restraints excluded: chain B residue    9 ILE
Chi-restraints excluded: chain B residue   17 LEU
Chi-restraints excluded: chain B residue   67 LEU
Chi-restraints excluded: chain B residue  221 ILE
Chi-restraints excluded: chain C residue    2 ASP
Chi-restraints excluded: chain C residue   17 LEU
Chi-restraints excluded: chain C residue   59 VAL
Chi-restraints excluded: chain C residue   67 LEU
Chi-restraints excluded: chain C residue   69 LYS
Chi-restraints excluded: chain C residue  188 ILE
Chi-restraints excluded: chain C residue  223 ILE
Chi-restraints excluded: chain C residue  226 ILE
Chi-restraints excluded: chain C residue  230 GLN
Chi-restraints excluded: chain D residue   67 LEU
Chi-restraints excluded: chain D residue   88 ARG
Chi-restraints excluded: chain D residue  113 ILE
Chi-restraints excluded: chain D residue  137 ASP
Chi-restraints excluded: chain D residue  185 VAL
Chi-restraints excluded: chain D residue  198 ASN
Chi-restraints excluded: chain D residue  229 ILE
Chi-restraints excluded: chain E residue   32 VAL
Chi-restraints excluded: chain E residue   67 LEU
Chi-restraints excluded: chain E residue  221 ILE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 125
   random chunks:
   chunk 86 optimal weight:    0.9990
   chunk 88 optimal weight:    0.2980
   chunk 111 optimal weight:    0.8980
   chunk 87 optimal weight:    0.0030
   chunk 71 optimal weight:    0.0980
   chunk 110 optimal weight:    5.9990
   chunk 59 optimal weight:    4.9990
   chunk 82 optimal weight:    0.8980
   chunk 65 optimal weight:    0.8980
   chunk 76 optimal weight:    0.6980
   chunk 53 optimal weight:    0.1980
   overall best weight:    0.2590

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

Flipped N/Q/H residues before XYZ refinement:
** A 135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 206 ASN
** E 198 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3560 r_free = 0.3560 target = 0.137953 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3311 r_free = 0.3311 target = 0.117644 restraints weight = 10948.414|
|-----------------------------------------------------------------------------|
r_work (start): 0.3121 rms_B_bonded: 1.40
r_work: 0.2992 rms_B_bonded: 1.96 restraints_weight: 0.5000
r_work: 0.2868 rms_B_bonded: 3.30 restraints_weight: 0.2500
r_work (final): 0.2868
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8281
moved from start:          0.3265

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.118   9655  Z= 0.185
  Angle     :  0.900  59.200  13075  Z= 0.542
  Chirality :  0.038   0.162   1610
  Planarity :  0.004   0.037   1630
  Dihedral  :  5.663  58.810   1313
  Min Nonbonded Distance : 2.386

Molprobity Statistics.
  All-atom Clashscore : 6.45
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.83 %
    Favored  : 98.17 %
  Rotamer:
    Outliers :  3.28 %
    Allowed  : 18.81 %
    Favored  : 77.91 %
  Cbeta Deviations :  0.09 %
  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: -0.93 (0.23), residues: 1255
  helix: -0.26 (0.17), residues: 985
  sheet:  None (None), residues: 0
  loop : -1.46 (0.31), residues: 270

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP C 147 
 HIS   0.001   0.000   HIS E   0 
 PHE   0.010   0.001   PHE E 157 
 TYR   0.007   0.001   TYR D 222 
 ARG   0.001   0.000   ARG E  57 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 4266.00 seconds
wall clock time: 76 minutes 50.43 seconds (4610.43 seconds total)