Starting phenix.real_space_refine
on Sat May 24 16:46:29 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8g9s_29877/05_2025/8g9s_29877.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8g9s_29877/05_2025/8g9s_29877.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/8g9s_29877/05_2025/8g9s_29877.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8g9s_29877/05_2025/8g9s_29877.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8g9s_29877/05_2025/8g9s_29877.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8g9s_29877/05_2025/8g9s_29877.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=   0.034
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: 5
    Type Number    sf(0)   Gaussians
     P      42      5.49       5
     S     108      5.16       5
     C   16056      2.51       5
     N    4594      2.21       5
     O    4958      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 188 residue(s): 0.07s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib"
  Total number of atoms: 25758
  Number of models: 1
  Model: ""
    Number of chains: 15
    Chain: "B"
      Number of atoms: 2261
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 283, 2261
          Classifications: {'peptide': 283}
          Link IDs: {'PTRANS': 8, 'TRANS': 274}
    Chain: "C"
      Number of atoms: 2261
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 283, 2261
          Classifications: {'peptide': 283}
          Link IDs: {'PTRANS': 8, 'TRANS': 274}
    Chain: "D"
      Number of atoms: 2261
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 283, 2261
          Classifications: {'peptide': 283}
          Link IDs: {'PTRANS': 8, 'TRANS': 274}
    Chain: "E"
      Number of atoms: 2261
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 283, 2261
          Classifications: {'peptide': 283}
          Link IDs: {'PTRANS': 8, 'TRANS': 274}
    Chain: "F"
      Number of atoms: 2124
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 265, 2124
          Classifications: {'peptide': 265}
          Link IDs: {'PTRANS': 8, 'TRANS': 256}
          Chain breaks: 1
    Chain: "G"
      Number of atoms: 2173
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 271, 2173
          Classifications: {'peptide': 271}
          Link IDs: {'PTRANS': 8, 'TRANS': 262}
          Chain breaks: 1
    Chain: "H"
      Number of atoms: 1007
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 124, 1007
          Classifications: {'peptide': 124}
          Link IDs: {'PTRANS': 4, 'TRANS': 119}
    Chain: "I"
      Number of atoms: 1007
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 124, 1007
          Classifications: {'peptide': 124}
          Link IDs: {'PTRANS': 4, 'TRANS': 119}
    Chain: "J"
      Number of atoms: 1007
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 124, 1007
          Classifications: {'peptide': 124}
          Link IDs: {'PTRANS': 4, 'TRANS': 119}
    Chain: "M"
      Number of atoms: 2110
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 264, 2110
          Classifications: {'peptide': 264}
          Link IDs: {'PTRANS': 8, 'TRANS': 255}
          Chain breaks: 1
    Chain: "N"
      Number of atoms: 1673
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 205, 1673
          Classifications: {'peptide': 205}
          Link IDs: {'PTRANS': 11, 'TRANS': 193}
    Chain: "O"
      Number of atoms: 895
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 42, 895
          Classifications: {'RNA': 42}
          Modifications used: {'rna2p_pur': 9, 'rna2p_pyr': 11, 'rna3p_pur': 12, 'rna3p_pyr': 10}
          Link IDs: {'rna2p': 20, 'rna3p': 21}
    Chain: "K"
      Number of atoms: 3223
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 409, 3223
          Classifications: {'peptide': 409}
          Incomplete info: {'truncation_to_alanine': 2}
          Link IDs: {'PTRANS': 18, 'TRANS': 390}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 7
          Unresolved non-hydrogen angles: 8
          Unresolved non-hydrogen dihedrals: 6
          Planarities with less than four sites: {'ASN:plan1': 1}
          Unresolved non-hydrogen planarities: 3
    Chain: "L"
      Number of atoms: 917
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 114, 917
          Classifications: {'peptide': 114}
          Link IDs: {'PTRANS': 3, 'TRANS': 110}
          Chain breaks: 2
    Chain: "A"
      Number of atoms: 578
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 70, 578
          Classifications: {'peptide': 70}
          Link IDs: {'PTRANS': 2, 'TRANS': 67}
  Time building chain proxies: 14.01, per 1000 atoms: 0.54
  Number of scatterers: 25758
  At special positions: 0
  Unit cell: (120.054, 129.941, 206.21, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S     108     16.00
     P      42     15.00
     O    4958      8.00
     N    4594      7.00
     C   16056      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: 6.68
  Conformation dependent library (CDL) restraints added in 2.9 seconds
  

  6124 Ramachandran restraints generated.
    3062 Oldfield, 0 Emsley, 3062 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  5728

  Finding SS restraints...
    Secondary structure from input PDB file:
      103 helices and 38 sheets defined
      41.6% alpha, 15.2% beta
      0 base pairs and 5 stacking pairs defined.
    Time for finding SS restraints: 7.91
  Creating SS restraints...
    Processing helix  chain 'B' and resid 42 through 58
      removed outlier: 3.955A  pdb=" N   LEU B  46 " --> pdb=" O   THR B  42 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 72 through 82
    Processing helix  chain 'B' and resid 83 through 89
      removed outlier: 3.530A  pdb=" N   LYS B  89 " --> pdb=" O   ASN B  85 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 90 through 106
      removed outlier: 3.644A  pdb=" N   THR B  95 " --> pdb=" O   LYS B  91 " (cutoff:3.500A)
      removed outlier: 4.708A  pdb=" N   GLU B  96 " --> pdb=" O   GLY B  92 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 106 through 112
    Processing helix  chain 'B' and resid 185 through 193
      removed outlier: 3.714A  pdb=" N   GLN B 191 " --> pdb=" O   HIS B 187 " (cutoff:3.500A)
      removed outlier: 3.898A  pdb=" N   THR B 192 " --> pdb=" O   PHE B 188 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 195 through 208
    Processing helix  chain 'B' and resid 209 through 213
      removed outlier: 3.799A  pdb=" N   HIS B 212 " --> pdb=" O   MET B 209 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 239 through 247
      removed outlier: 4.181A  pdb=" N   LEU B 243 " --> pdb=" O   PRO B 239 " (cutoff:3.500A)
      removed outlier: 4.238A  pdb=" N   ILE B 247 " --> pdb=" O   LEU B 243 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 271 through 275
      removed outlier: 4.098A  pdb=" N   GLU B 274 " --> pdb=" O   LYS B 271 " (cutoff:3.500A)
      removed outlier: 3.753A  pdb=" N   GLU B 275 " --> pdb=" O   ASN B 272 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 271 through 275'
    Processing helix  chain 'C' and resid 42 through 58
      removed outlier: 3.843A  pdb=" N   LEU C  46 " --> pdb=" O   THR C  42 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 72 through 82
    Processing helix  chain 'C' and resid 93 through 106
    Processing helix  chain 'C' and resid 106 through 112
    Processing helix  chain 'C' and resid 186 through 193
      removed outlier: 4.002A  pdb=" N   GLN C 191 " --> pdb=" O   HIS C 187 " (cutoff:3.500A)
      removed outlier: 3.910A  pdb=" N   THR C 192 " --> pdb=" O   PHE C 188 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 195 through 208
    Processing helix  chain 'C' and resid 240 through 245
    Processing helix  chain 'C' and resid 272 through 276
      removed outlier: 3.567A  pdb=" N   THR C 276 " --> pdb=" O   LEU C 273 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 42 through 58
      removed outlier: 3.913A  pdb=" N   LEU D  46 " --> pdb=" O   THR D  42 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 72 through 81
      removed outlier: 3.638A  pdb=" N   ALA D  80 " --> pdb=" O   LEU D  76 " (cutoff:3.500A)
      removed outlier: 3.640A  pdb=" N   HIS D  81 " --> pdb=" O   ILE D  77 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 90 through 106
    Processing helix  chain 'D' and resid 107 through 112
    Processing helix  chain 'D' and resid 188 through 193
      removed outlier: 3.700A  pdb=" N   THR D 192 " --> pdb=" O   PHE D 188 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 195 through 208
      removed outlier: 3.668A  pdb=" N   VAL D 207 " --> pdb=" O   TRP D 203 " (cutoff:3.500A)
      removed outlier: 3.544A  pdb=" N   ASN D 208 " --> pdb=" O   GLN D 204 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 239 through 245
      removed outlier: 3.737A  pdb=" N   LEU D 243 " --> pdb=" O   PRO D 239 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 42 through 58
      removed outlier: 3.931A  pdb=" N   LEU E  46 " --> pdb=" O   THR E  42 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 72 through 84
      removed outlier: 3.725A  pdb=" N   LEU E  76 " --> pdb=" O   ILE E  72 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 85 through 87
      No H-bonds generated for 'chain 'E' and resid 85 through 87'
    Processing helix  chain 'E' and resid 90 through 106
    Processing helix  chain 'E' and resid 106 through 112
    Processing helix  chain 'E' and resid 115 through 119
      removed outlier: 4.169A  pdb=" N   THR E 118 " --> pdb=" O   VAL E 115 " (cutoff:3.500A)
      removed outlier: 3.762A  pdb=" N   GLY E 119 " --> pdb=" O   MET E 116 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'E' and resid 115 through 119'
    Processing helix  chain 'E' and resid 185 through 193
      removed outlier: 4.275A  pdb=" N   ALA E 189 " --> pdb=" O   SER E 185 " (cutoff:3.500A)
      removed outlier: 4.186A  pdb=" N   LYS E 190 " --> pdb=" O   THR E 186 " (cutoff:3.500A)
      removed outlier: 4.424A  pdb=" N   GLN E 191 " --> pdb=" O   HIS E 187 " (cutoff:3.500A)
      removed outlier: 3.651A  pdb=" N   THR E 192 " --> pdb=" O   PHE E 188 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 195 through 208
      removed outlier: 3.846A  pdb=" N   VAL E 207 " --> pdb=" O   TRP E 203 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 209 through 213
    Processing helix  chain 'E' and resid 239 through 246
      removed outlier: 3.728A  pdb=" N   LEU E 243 " --> pdb=" O   PRO E 239 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 260 through 262
      No H-bonds generated for 'chain 'E' and resid 260 through 262'
    Processing helix  chain 'F' and resid 42 through 58
      removed outlier: 3.750A  pdb=" N   LEU F  46 " --> pdb=" O   THR F  42 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 72 through 82
    Processing helix  chain 'F' and resid 93 through 106
    Processing helix  chain 'F' and resid 106 through 112
      removed outlier: 3.571A  pdb=" N   ARG F 110 " --> pdb=" O   TYR F 106 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 185 through 193
    Processing helix  chain 'F' and resid 195 through 208
    Processing helix  chain 'F' and resid 239 through 246
    Processing helix  chain 'G' and resid 42 through 59
    Processing helix  chain 'G' and resid 73 through 82
      removed outlier: 4.100A  pdb=" N   ALA G  80 " --> pdb=" O   LEU G  76 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 90 through 106
      removed outlier: 3.923A  pdb=" N   GLU G  96 " --> pdb=" O   GLY G  92 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 106 through 112
      removed outlier: 3.952A  pdb=" N   ARG G 110 " --> pdb=" O   TYR G 106 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 185 through 193
    Processing helix  chain 'G' and resid 195 through 213
      removed outlier: 3.779A  pdb=" N   VAL G 207 " --> pdb=" O   TRP G 203 " (cutoff:3.500A)
      removed outlier: 5.552A  pdb=" N   PHE G 210 " --> pdb=" O   LEU G 206 " (cutoff:3.500A)
      removed outlier: 4.963A  pdb=" N   ASP G 211 " --> pdb=" O   VAL G 207 " (cutoff:3.500A)
      removed outlier: 3.539A  pdb=" N   ASP G 213 " --> pdb=" O   MET G 209 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 239 through 247
    Processing helix  chain 'H' and resid 9 through 29
    Processing helix  chain 'H' and resid 35 through 47
      removed outlier: 4.567A  pdb=" N   GLY H  42 " --> pdb=" O   ASP H  38 " (cutoff:3.500A)
      removed outlier: 5.301A  pdb=" N   SER H  43 " --> pdb=" O   ARG H  39 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 50 through 65
      removed outlier: 3.505A  pdb=" N   ARG H  57 " --> pdb=" O   GLY H  53 " (cutoff:3.500A)
      Proline residue:  H  60  - end of helix
    Processing helix  chain 'H' and resid 68 through 86
      removed outlier: 3.986A  pdb=" N   HIS H  85 " --> pdb=" O   GLN H  81 " (cutoff:3.500A)
      removed outlier: 4.311A  pdb=" N   CYS H  86 " --> pdb=" O   ILE H  82 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 94 through 113
      removed outlier: 3.612A  pdb=" N   GLN H 110 " --> pdb=" O   TYR H 106 " (cutoff:3.500A)
      removed outlier: 3.695A  pdb=" N   PHE H 111 " --> pdb=" O   HIS H 107 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 116 through 125
      removed outlier: 3.504A  pdb=" N   ALA H 125 " --> pdb=" O   LEU H 121 " (cutoff:3.500A)
    Processing helix  chain 'I' and resid 9 through 29
    Processing helix  chain 'I' and resid 35 through 47
      removed outlier: 5.301A  pdb=" N   GLY I  42 " --> pdb=" O   ASP I  38 " (cutoff:3.500A)
      removed outlier: 5.914A  pdb=" N   SER I  43 " --> pdb=" O   ARG I  39 " (cutoff:3.500A)
    Processing helix  chain 'I' and resid 47 through 66
      removed outlier: 4.770A  pdb=" N   VAL I  51 " --> pdb=" O   THR I  47 " (cutoff:3.500A)
      removed outlier: 3.675A  pdb=" N   THR I  54 " --> pdb=" O   ALA I  50 " (cutoff:3.500A)
      Proline residue:  I  60  - end of helix
    Processing helix  chain 'I' and resid 68 through 84
      removed outlier: 3.910A  pdb=" N   GLU I  84 " --> pdb=" O   ARG I  80 " (cutoff:3.500A)
    Processing helix  chain 'I' and resid 94 through 114
      removed outlier: 3.537A  pdb=" N   ALA I 102 " --> pdb=" O   GLN I  98 " (cutoff:3.500A)
    Processing helix  chain 'I' and resid 116 through 124
    Processing helix  chain 'J' and resid 9 through 29
    Processing helix  chain 'J' and resid 35 through 47
      removed outlier: 4.282A  pdb=" N   ARG J  39 " --> pdb=" O   THR J  35 " (cutoff:3.500A)
      removed outlier: 5.413A  pdb=" N   GLY J  42 " --> pdb=" O   ASP J  38 " (cutoff:3.500A)
      removed outlier: 5.170A  pdb=" N   SER J  43 " --> pdb=" O   ARG J  39 " (cutoff:3.500A)
      removed outlier: 4.646A  pdb=" N   SER J  46 " --> pdb=" O   GLY J  42 " (cutoff:3.500A)
    Processing helix  chain 'J' and resid 47 through 66
      removed outlier: 4.086A  pdb=" N   VAL J  51 " --> pdb=" O   THR J  47 " (cutoff:3.500A)
      removed outlier: 4.812A  pdb=" N   GLY J  53 " --> pdb=" O   ILE J  49 " (cutoff:3.500A)
      removed outlier: 4.242A  pdb=" N   THR J  54 " --> pdb=" O   ALA J  50 " (cutoff:3.500A)
      removed outlier: 3.854A  pdb=" N   LEU J  58 " --> pdb=" O   THR J  54 " (cutoff:3.500A)
      Proline residue:  J  60  - end of helix
    Processing helix  chain 'J' and resid 68 through 84
    Processing helix  chain 'J' and resid 94 through 114
      removed outlier: 3.651A  pdb=" N   ALA J 102 " --> pdb=" O   GLN J  98 " (cutoff:3.500A)
    Processing helix  chain 'J' and resid 116 through 125
    Processing helix  chain 'M' and resid 42 through 58
      removed outlier: 4.022A  pdb=" N   LEU M  46 " --> pdb=" O   THR M  42 " (cutoff:3.500A)
    Processing helix  chain 'M' and resid 95 through 106
    Processing helix  chain 'M' and resid 106 through 112
    Processing helix  chain 'M' and resid 185 through 193
      removed outlier: 3.610A  pdb=" N   ALA M 189 " --> pdb=" O   SER M 185 " (cutoff:3.500A)
      removed outlier: 3.683A  pdb=" N   GLN M 191 " --> pdb=" O   HIS M 187 " (cutoff:3.500A)
    Processing helix  chain 'M' and resid 195 through 208
    Processing helix  chain 'M' and resid 239 through 246
      removed outlier: 3.866A  pdb=" N   LEU M 243 " --> pdb=" O   PRO M 239 " (cutoff:3.500A)
    Processing helix  chain 'M' and resid 260 through 262
      No H-bonds generated for 'chain 'M' and resid 260 through 262'
    Processing helix  chain 'M' and resid 272 through 276
      removed outlier: 3.656A  pdb=" N   THR M 276 " --> pdb=" O   LEU M 273 " (cutoff:3.500A)
    Processing helix  chain 'N' and resid 30 through 42
      removed outlier: 3.635A  pdb=" N   ARG N  35 " --> pdb=" O   PRO N  31 " (cutoff:3.500A)
      removed outlier: 3.532A  pdb=" N   ASN N  36 " --> pdb=" O   ALA N  32 " (cutoff:3.500A)
      removed outlier: 3.742A  pdb=" N   ILE N  41 " --> pdb=" O   ILE N  37 " (cutoff:3.500A)
      removed outlier: 3.639A  pdb=" N   LEU N  42 " --> pdb=" O   LEU N  38 " (cutoff:3.500A)
    Processing helix  chain 'N' and resid 82 through 85
    Processing helix  chain 'N' and resid 117 through 132
    Processing helix  chain 'K' and resid 2 through 16
      removed outlier: 3.572A  pdb=" N   SER K  16 " --> pdb=" O   ARG K  12 " (cutoff:3.500A)
    Processing helix  chain 'K' and resid 243 through 260
    Processing helix  chain 'K' and resid 281 through 290
      removed outlier: 5.401A  pdb=" N   SER K 287 " --> pdb=" O   GLU K 283 " (cutoff:3.500A)
      removed outlier: 5.139A  pdb=" N   MET K 288 " --> pdb=" O   SER K 284 " (cutoff:3.500A)
      removed outlier: 4.522A  pdb=" N   ASN K 290 " --> pdb=" O   ALA K 286 " (cutoff:3.500A)
    Processing helix  chain 'K' and resid 300 through 303
    Processing helix  chain 'K' and resid 304 through 312
      removed outlier: 3.527A  pdb=" N   TYR K 308 " --> pdb=" O   VAL K 304 " (cutoff:3.500A)
      removed outlier: 3.947A  pdb=" N   TYR K 312 " --> pdb=" O   TYR K 308 " (cutoff:3.500A)
    Processing helix  chain 'K' and resid 318 through 322
      removed outlier: 3.908A  pdb=" N   LYS K 322 " --> pdb=" O   PRO K 319 " (cutoff:3.500A)
    Processing helix  chain 'K' and resid 347 through 362
    Processing helix  chain 'K' and resid 376 through 383
    Processing helix  chain 'K' and resid 393 through 408
      removed outlier: 3.629A  pdb=" N   LEU K 397 " --> pdb=" O   LEU K 393 " (cutoff:3.500A)
      removed outlier: 3.566A  pdb=" N   GLN K 400 " --> pdb=" O   ASP K 396 " (cutoff:3.500A)
    Processing helix  chain 'K' and resid 412 through 427
      removed outlier: 3.885A  pdb=" N   LEU K 416 " --> pdb=" O   PRO K 412 " (cutoff:3.500A)
    Processing helix  chain 'K' and resid 432 through 448
    Processing helix  chain 'K' and resid 466 through 486
    Processing helix  chain 'K' and resid 492 through 504
      removed outlier: 6.511A  pdb=" N   GLY K 499 " --> pdb=" O   ASP K 495 " (cutoff:3.500A)
      removed outlier: 6.083A  pdb=" N   SER K 500 " --> pdb=" O   ARG K 496 " (cutoff:3.500A)
    Processing helix  chain 'K' and resid 504 through 523
      removed outlier: 3.837A  pdb=" N   VAL K 508 " --> pdb=" O   THR K 504 " (cutoff:3.500A)
      removed outlier: 4.305A  pdb=" N   GLY K 510 " --> pdb=" O   ILE K 506 " (cutoff:3.500A)
      removed outlier: 4.834A  pdb=" N   THR K 511 " --> pdb=" O   ALA K 507 " (cutoff:3.500A)
      Proline residue:  K 517  - end of helix
    Processing helix  chain 'K' and resid 525 through 541
    Processing helix  chain 'K' and resid 551 through 570
    Processing helix  chain 'K' and resid 573 through 582
      removed outlier: 3.651A  pdb=" N   ALA K 582 " --> pdb=" O   LEU K 578 " (cutoff:3.500A)
    Processing helix  chain 'L' and resid 9 through 29
      removed outlier: 3.784A  pdb=" N   ASN L  29 " --> pdb=" O   GLN L  25 " (cutoff:3.500A)
    Processing helix  chain 'L' and resid 35 through 47
      removed outlier: 6.531A  pdb=" N   GLY L  42 " --> pdb=" O   ASP L  38 " (cutoff:3.500A)
      removed outlier: 6.131A  pdb=" N   SER L  43 " --> pdb=" O   ARG L  39 " (cutoff:3.500A)
    Processing helix  chain 'L' and resid 47 through 66
      removed outlier: 4.051A  pdb=" N   VAL L  51 " --> pdb=" O   THR L  47 " (cutoff:3.500A)
      removed outlier: 4.387A  pdb=" N   GLY L  53 " --> pdb=" O   ILE L  49 " (cutoff:3.500A)
      removed outlier: 4.612A  pdb=" N   THR L  54 " --> pdb=" O   ALA L  50 " (cutoff:3.500A)
      Proline residue:  L  60  - end of helix
    Processing helix  chain 'L' and resid 70 through 85
      removed outlier: 4.194A  pdb=" N   HIS L  85 " --> pdb=" O   GLN L  81 " (cutoff:3.500A)
    Processing helix  chain 'L' and resid 95 through 113
    Processing helix  chain 'L' and resid 116 through 125
    Processing helix  chain 'A' and resid 38 through 52
      removed outlier: 3.542A  pdb=" N   ALA A  42 " --> pdb=" O   THR A  38 " (cutoff:3.500A)
      removed outlier: 4.263A  pdb=" N   GLY A  52 " --> pdb=" O   ASP A  48 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'B' and resid 40 through 41
      removed outlier: 3.604A  pdb=" N   SER B 134 " --> pdb=" O   VAL B  41 " (cutoff:3.500A)
      removed outlier: 5.535A  pdb=" N   LEU B 131 " --> pdb=" O   PHE B 183 " (cutoff:3.500A)
      removed outlier: 7.352A  pdb=" N   PHE B 183 " --> pdb=" O   LEU B 131 " (cutoff:3.500A)
      removed outlier: 5.678A  pdb=" N   PHE B 133 " --> pdb=" O   HIS B 181 " (cutoff:3.500A)
      removed outlier: 4.362A  pdb=" N   HIS B 181 " --> pdb=" O   PHE B 133 " (cutoff:3.500A)
      removed outlier: 3.664A  pdb=" N   TYR B   7 " --> pdb=" O   ILE B 184 " (cutoff:3.500A)
      removed outlier: 6.788A  pdb=" N   ASP B  14 " --> pdb=" O   ALA B 223 " (cutoff:3.500A)
      removed outlier: 5.559A  pdb=" N   ALA B 223 " --> pdb=" O   ASP B  14 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'B' and resid 114 through 115
    Processing sheet with id=AA3, first strand: chain 'B' and resid 145 through 148
      removed outlier: 3.746A  pdb=" N   HIS B 145 " --> pdb=" O   LYS B 170 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'B' and resid 248 through 251
    Processing sheet with id=AA5, first strand: chain 'C' and resid 40 through 41
      removed outlier: 3.629A  pdb=" N   ARG C 135 " --> pdb=" O   ARG C 179 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'C' and resid 40 through 41
      removed outlier: 3.629A  pdb=" N   ARG C 135 " --> pdb=" O   ARG C 179 " (cutoff:3.500A)
      removed outlier: 3.741A  pdb=" N   TYR C   7 " --> pdb=" O   ILE C 184 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'C' and resid 114 through 116
    Processing sheet with id=AA8, first strand: chain 'C' and resid 143 through 144
    Processing sheet with id=AA9, first strand: chain 'C' and resid 247 through 250
    Processing sheet with id=AB1, first strand: chain 'D' and resid 40 through 41
    Processing sheet with id=AB2, first strand: chain 'D' and resid 40 through 41
      removed outlier: 6.533A  pdb=" N   ASP D  14 " --> pdb=" O   ALA D 223 " (cutoff:3.500A)
      removed outlier: 5.320A  pdb=" N   ALA D 223 " --> pdb=" O   ASP D  14 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'D' and resid 114 through 116
    Processing sheet with id=AB4, first strand: chain 'D' and resid 143 through 146
    Processing sheet with id=AB5, first strand: chain 'D' and resid 247 through 251
    Processing sheet with id=AB6, first strand: chain 'E' and resid 32 through 33
      removed outlier: 3.676A  pdb=" N   GLU E  38 " --> pdb=" O   ASP E  33 " (cutoff:3.500A)
      removed outlier: 5.198A  pdb=" N   GLY E  39 " --> pdb=" O   SER E 136 " (cutoff:3.500A)
      removed outlier: 3.794A  pdb=" N   ARG E 135 " --> pdb=" O   ARG E 179 " (cutoff:3.500A)
      removed outlier: 3.811A  pdb=" N   ARG E 179 " --> pdb=" O   ARG E 135 " (cutoff:3.500A)
    Processing sheet with id=AB7, first strand: chain 'E' and resid 129 through 131
    Processing sheet with id=AB8, first strand: chain 'E' and resid 247 through 251
    Processing sheet with id=AB9, first strand: chain 'F' and resid 40 through 41
      removed outlier: 3.583A  pdb=" N   ARG F 135 " --> pdb=" O   ARG F 179 " (cutoff:3.500A)
    Processing sheet with id=AC1, first strand: chain 'F' and resid 40 through 41
      removed outlier: 3.583A  pdb=" N   ARG F 135 " --> pdb=" O   ARG F 179 " (cutoff:3.500A)
      removed outlier: 4.363A  pdb=" N   TYR F   7 " --> pdb=" O   ILE F 184 " (cutoff:3.500A)
      removed outlier: 6.636A  pdb=" N   ARG F   6 " --> pdb=" O   GLU F 230 " (cutoff:3.500A)
      removed outlier: 4.466A  pdb=" N   GLU F 230 " --> pdb=" O   ARG F   6 " (cutoff:3.500A)
      removed outlier: 6.506A  pdb=" N   ASP F   8 " --> pdb=" O   VAL F 228 " (cutoff:3.500A)
      removed outlier: 4.691A  pdb=" N   VAL F 228 " --> pdb=" O   ASP F   8 " (cutoff:3.500A)
      removed outlier: 6.694A  pdb=" N   VAL F  10 " --> pdb=" O   LEU F 226 " (cutoff:3.500A)
      removed outlier: 4.453A  pdb=" N   LEU F 226 " --> pdb=" O   VAL F  10 " (cutoff:3.500A)
      removed outlier: 6.684A  pdb=" N   LEU F  12 " --> pdb=" O   ARG F 224 " (cutoff:3.500A)
      removed outlier: 6.423A  pdb=" N   GLN F 220 " --> pdb=" O   GLN F  16 " (cutoff:3.500A)
    Processing sheet with id=AC2, first strand: chain 'F' and resid 145 through 146
    Processing sheet with id=AC3, first strand: chain 'F' and resid 247 through 250
    Processing sheet with id=AC4, first strand: chain 'G' and resid 40 through 41
    Processing sheet with id=AC5, first strand: chain 'G' and resid 40 through 41
      removed outlier: 6.535A  pdb=" N   ASP G  14 " --> pdb=" O   ALA G 223 " (cutoff:3.500A)
      removed outlier: 5.547A  pdb=" N   ALA G 223 " --> pdb=" O   ASP G  14 " (cutoff:3.500A)
      removed outlier: 7.210A  pdb=" N   GLN G  16 " --> pdb=" O   MET G 221 " (cutoff:3.500A)
      removed outlier: 6.747A  pdb=" N   MET G 221 " --> pdb=" O   GLN G  16 " (cutoff:3.500A)
      removed outlier: 6.930A  pdb=" N   ARG G 224 " --> pdb=" O   GLY G 284 " (cutoff:3.500A)
      removed outlier: 4.886A  pdb=" N   GLY G 284 " --> pdb=" O   ARG G 224 " (cutoff:3.500A)
      removed outlier: 6.662A  pdb=" N   LEU G 226 " --> pdb=" O   LEU G 282 " (cutoff:3.500A)
      removed outlier: 4.074A  pdb=" N   LEU G 282 " --> pdb=" O   LEU G 226 " (cutoff:3.500A)
    Processing sheet with id=AC6, first strand: chain 'G' and resid 145 through 146
    Processing sheet with id=AC7, first strand: chain 'G' and resid 248 through 251
    Processing sheet with id=AC8, first strand: chain 'M' and resid 178 through 183
      removed outlier: 6.929A  pdb=" N   ASP M   8 " --> pdb=" O   VAL M 228 " (cutoff:3.500A)
      removed outlier: 4.915A  pdb=" N   VAL M 228 " --> pdb=" O   ASP M   8 " (cutoff:3.500A)
      removed outlier: 6.844A  pdb=" N   VAL M  10 " --> pdb=" O   LEU M 226 " (cutoff:3.500A)
      removed outlier: 4.632A  pdb=" N   LEU M 226 " --> pdb=" O   VAL M  10 " (cutoff:3.500A)
      removed outlier: 6.642A  pdb=" N   LEU M  12 " --> pdb=" O   ARG M 224 " (cutoff:3.500A)
      removed outlier: 6.866A  pdb=" N   GLN M 220 " --> pdb=" O   GLN M  16 " (cutoff:3.500A)
      removed outlier: 3.693A  pdb=" N   VAL M 228 " --> pdb=" O   ARG M 280 " (cutoff:3.500A)
    Processing sheet with id=AC9, first strand: chain 'M' and resid 114 through 115
    Processing sheet with id=AD1, first strand: chain 'M' and resid 143 through 145
    Processing sheet with id=AD2, first strand: chain 'M' and resid 166 through 167
      removed outlier: 3.583A  pdb=" N   MET M 167 " --> pdb=" O   TYR A  54 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AD2
    Processing sheet with id=AD3, first strand: chain 'M' and resid 248 through 251
    Processing sheet with id=AD4, first strand: chain 'N' and resid 62 through 70
      removed outlier: 6.786A  pdb=" N   ASP N  10 " --> pdb=" O   ASP N  97 " (cutoff:3.500A)
      removed outlier: 6.499A  pdb=" N   ALA N  99 " --> pdb=" O   SER N   8 " (cutoff:3.500A)
      removed outlier: 6.505A  pdb=" N   SER N   8 " --> pdb=" O   ALA N  99 " (cutoff:3.500A)
      removed outlier: 6.811A  pdb=" N   ARG N 101 " --> pdb=" O   GLU N   6 " (cutoff:3.500A)
      removed outlier: 6.746A  pdb=" N   GLU N   6 " --> pdb=" O   ARG N 101 " (cutoff:3.500A)
      removed outlier: 6.851A  pdb=" N   HIS N 103 " --> pdb=" O   ILE N   4 " (cutoff:3.500A)
      removed outlier: 6.863A  pdb=" N   ILE N   4 " --> pdb=" O   HIS N 103 " (cutoff:3.500A)
    Processing sheet with id=AD5, first strand: chain 'N' and resid 62 through 70
      removed outlier: 6.580A  pdb=" N   ARG N 101 " --> pdb=" O   ILE N  54 " (cutoff:3.500A)
      removed outlier: 4.398A  pdb=" N   ILE N  54 " --> pdb=" O   ARG N 101 " (cutoff:3.500A)
      removed outlier: 6.568A  pdb=" N   HIS N 103 " --> pdb=" O   LEU N  52 " (cutoff:3.500A)
    Processing sheet with id=AD6, first strand: chain 'N' and resid 170 through 172
    Processing sheet with id=AD7, first strand: chain 'K' and resid 192 through 194
    Processing sheet with id=AD8, first strand: chain 'K' and resid 210 through 211
    Processing sheet with id=AD9, first strand: chain 'K' and resid 324 through 325
    Processing sheet with id=AE1, first strand: chain 'K' and resid 331 through 332
    Processing sheet with id=AE2, first strand: chain 'A' and resid 20 through 24
      removed outlier: 3.532A  pdb=" N   ILE A  12 " --> pdb=" O   ASP A  65 " (cutoff:3.500A)
      removed outlier: 3.808A  pdb=" N   ASP A  65 " --> pdb=" O   ILE A  12 " (cutoff:3.500A)

    1058 hydrogen bonds defined for protein.
    3009 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      5 stacking parallelities
  Total time for adding SS restraints: 8.12

  Time building geometry restraints manager: 7.79 seconds

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

  Histogram of bond lengths:
        1.21 -     1.33: 6747
        1.33 -     1.45: 5476
        1.45 -     1.57: 13865
        1.57 -     1.70: 83
        1.70 -     1.82: 185
  Bond restraints: 26356
  Sorted by residual:
  bond pdb=" CA  ASP C 213 "
       pdb=" CB  ASP C 213 "
    ideal  model  delta    sigma   weight residual
    1.523  1.489  0.034 1.35e-02 5.49e+03 6.37e+00
  bond pdb=" CG1 ILE M 147 "
       pdb=" CD1 ILE M 147 "
    ideal  model  delta    sigma   weight residual
    1.513  1.427  0.086 3.90e-02 6.57e+02 4.87e+00
  bond pdb=" CA  ASP C   8 "
       pdb=" CB  ASP C   8 "
    ideal  model  delta    sigma   weight residual
    1.534  1.496  0.037 1.72e-02 3.38e+03 4.74e+00
  bond pdb=" CA  GLY B  22 "
       pdb=" C   GLY B  22 "
    ideal  model  delta    sigma   weight residual
    1.520  1.506  0.014 7.30e-03 1.88e+04 3.70e+00
  bond pdb=" CB  VAL C  50 "
       pdb=" CG2 VAL C  50 "
    ideal  model  delta    sigma   weight residual
    1.521  1.460  0.061 3.30e-02 9.18e+02 3.38e+00
  ... (remaining 26351 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.78: 33991
        1.78 -     3.56: 1483
        3.56 -     5.33: 214
        5.33 -     7.11: 34
        7.11 -     8.89: 9
  Bond angle restraints: 35731
  Sorted by residual:
  angle pdb=" C   ARG B 224 "
        pdb=" N   GLY B 225 "
        pdb=" CA  GLY B 225 "
      ideal   model   delta    sigma   weight residual
     122.33  119.18    3.15 7.30e-01 1.88e+00 1.86e+01
  angle pdb=" N   VAL G 258 "
        pdb=" CA  VAL G 258 "
        pdb=" C   VAL G 258 "
      ideal   model   delta    sigma   weight residual
     106.21  109.99   -3.78 1.07e+00 8.73e-01 1.25e+01
  angle pdb=" C   ASP M 157 "
        pdb=" N   ALA M 158 "
        pdb=" CA  ALA M 158 "
      ideal   model   delta    sigma   weight residual
     121.54  128.24   -6.70 1.91e+00 2.74e-01 1.23e+01
  angle pdb=" CB  ARG D 259 "
        pdb=" CG  ARG D 259 "
        pdb=" CD  ARG D 259 "
      ideal   model   delta    sigma   weight residual
     111.30  119.09   -7.79 2.30e+00 1.89e-01 1.15e+01
  angle pdb=" CA  MET E 209 "
        pdb=" CB  MET E 209 "
        pdb=" CG  MET E 209 "
      ideal   model   delta    sigma   weight residual
     114.10  107.56    6.54 2.00e+00 2.50e-01 1.07e+01
  ... (remaining 35726 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    35.76: 15483
       35.76 -    71.53: 345
       71.53 -   107.29: 53
      107.29 -   143.05: 3
      143.05 -   178.81: 3
  Dihedral angle restraints: 15887
    sinusoidal: 6974
      harmonic: 8913
  Sorted by residual:
  dihedral pdb=" O4'   C O  14 "
           pdb=" C1'   C O  14 "
           pdb=" N1    C O  14 "
           pdb=" C2    C O  14 "
      ideal   model   delta sinusoidal    sigma   weight residual
     200.00   42.17  157.83     1      1.50e+01 4.44e-03 8.22e+01
  dihedral pdb=" O4'   C O  38 "
           pdb=" C1'   C O  38 "
           pdb=" N1    C O  38 "
           pdb=" C2    C O  38 "
      ideal   model   delta sinusoidal    sigma   weight residual
     200.00   53.15  146.85     1      1.50e+01 4.44e-03 7.84e+01
  dihedral pdb=" O4'   C O   8 "
           pdb=" C1'   C O   8 "
           pdb=" N1    C O   8 "
           pdb=" C2    C O   8 "
      ideal   model   delta sinusoidal    sigma   weight residual
     200.00   66.11  133.89     1      1.50e+01 4.44e-03 7.22e+01
  ... (remaining 15884 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.063: 3195
       0.063 -    0.125: 605
       0.125 -    0.188: 62
       0.188 -    0.251: 3
       0.251 -    0.314: 1
  Chirality restraints: 3866
  Sorted by residual:
  chirality pdb=" C3'   U O  24 "
            pdb=" C4'   U O  24 "
            pdb=" O3'   U O  24 "
            pdb=" C2'   U O  24 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.74   -2.43   -0.31 2.00e-01 2.50e+01 2.46e+00
  chirality pdb=" CB  THR K 279 "
            pdb=" CA  THR K 279 "
            pdb=" OG1 THR K 279 "
            pdb=" CG2 THR K 279 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.55    2.33    0.22 2.00e-01 2.50e+01 1.26e+00
  chirality pdb=" C1'   C O  31 "
            pdb=" O4'   C O  31 "
            pdb=" C2'   C O  31 "
            pdb=" N1    C O  31 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.47    2.27    0.20 2.00e-01 2.50e+01 9.84e-01
  ... (remaining 3863 not shown)

  Planarity restraints: 4570
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TRP L  77 "   -0.021 2.00e-02 2.50e+03   2.15e-02 1.16e+01
        pdb=" CG  TRP L  77 "    0.058 2.00e-02 2.50e+03
        pdb=" CD1 TRP L  77 "   -0.027 2.00e-02 2.50e+03
        pdb=" CD2 TRP L  77 "    0.000 2.00e-02 2.50e+03
        pdb=" NE1 TRP L  77 "    0.000 2.00e-02 2.50e+03
        pdb=" CE2 TRP L  77 "    0.001 2.00e-02 2.50e+03
        pdb=" CE3 TRP L  77 "   -0.008 2.00e-02 2.50e+03
        pdb=" CZ2 TRP L  77 "    0.001 2.00e-02 2.50e+03
        pdb=" CZ3 TRP L  77 "   -0.002 2.00e-02 2.50e+03
        pdb=" CH2 TRP L  77 "   -0.002 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   THR H  47 "   -0.040 5.00e-02 4.00e+02   6.09e-02 5.94e+00
        pdb=" N   PRO H  48 "    0.105 5.00e-02 4.00e+02
        pdb=" CA  PRO H  48 "   -0.032 5.00e-02 4.00e+02
        pdb=" CD  PRO H  48 "   -0.033 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   GLY D 127 "   -0.040 5.00e-02 4.00e+02   6.01e-02 5.79e+00
        pdb=" N   PRO D 128 "    0.104 5.00e-02 4.00e+02
        pdb=" CA  PRO D 128 "   -0.031 5.00e-02 4.00e+02
        pdb=" CD  PRO D 128 "   -0.033 5.00e-02 4.00e+02
  ... (remaining 4567 not shown)

  Histogram of nonbonded interaction distances:
        2.04 -     2.61: 540
        2.61 -     3.18: 25668
        3.18 -     3.75: 40805
        3.75 -     4.33: 55110
        4.33 -     4.90: 86984
  Nonbonded interactions: 209107
  Sorted by model distance:
  nonbonded pdb=" OG  SER M 195 "
            pdb=" OD1 ASN M 197 "
     model   vdw
     2.037 3.040
  nonbonded pdb=" OD2 ASP B 237 "
            pdb=" OG1 THR B 276 "
     model   vdw
     2.086 3.040
  nonbonded pdb=" NH2 ARG B  51 "
            pdb=" OP1   U O  13 "
     model   vdw
     2.086 3.120
  nonbonded pdb=" NH2 ARG E  51 "
            pdb=" OP1   C O  31 "
     model   vdw
     2.094 3.120
  nonbonded pdb=" OD2 ASP M 237 "
            pdb=" OG1 THR M 276 "
     model   vdw
     2.097 3.040
  ... (remaining 209102 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.00
Found NCS groups:
ncs_group {
  reference = (chain 'B' and (resid 2 through 74 or resid 94 through 148 or resid 167 through  \ 
284))
  selection = (chain 'C' and (resid 2 through 74 or resid 94 through 148 or resid 167 through  \ 
284))
  selection = (chain 'D' and (resid 2 through 74 or resid 94 through 148 or resid 167 through  \ 
284))
  selection = (chain 'E' and (resid 2 through 74 or resid 94 through 148 or resid 167 through  \ 
284))
  selection = (chain 'F' and (resid 2 through 74 or resid 94 through 284))
  selection = (chain 'G' and (resid 2 through 74 or resid 94 through 148 or resid 167 through  \ 
284))
  selection = (chain 'M' and (resid 2 through 148 or resid 167 through 284))
}
ncs_group {
  reference = (chain 'H' and (resid 2 through 67 or resid 70 through 85 or resid 94 through 12 \ 
5))
  selection = (chain 'I' and (resid 2 through 67 or resid 70 through 85 or resid 94 through 12 \ 
5))
  selection = (chain 'J' and (resid 2 through 67 or resid 70 through 85 or resid 94 through 12 \ 
5))
  selection = chain 'L'
}

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:             1.560
  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:             0.030
  Extract box with map and model:          0.940
  Check model and map are aligned:         0.180
  Set scattering table:                    0.230
  Process input model:                     58.040
  Find NCS groups from input model:        1.030
  Set up NCS constraints:                  0.110
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:2.820
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   64.940
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8204
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      :  0.008   0.086  26356  Z= 0.351
  Angle     :  0.851   8.889  35731  Z= 0.488
  Chirality :  0.048   0.314   3866
  Planarity :  0.005   0.061   4570
  Dihedral  : 16.325 178.815  10159
  Min Nonbonded Distance : 2.037

Molprobity Statistics.
  All-atom Clashscore : 24.56
  Ramachandran Plot:
    Outliers :  0.03 %
    Allowed  :  8.52 %
    Favored  : 91.44 %
  Rotamer:
    Outliers :  0.04 %
    Allowed  :  0.57 %
    Favored  : 99.40 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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: -1.55 (0.15), residues: 3062
  helix:  0.42 (0.15), residues: 1116
  sheet: -1.13 (0.21), residues: 585
  loop : -2.25 (0.15), residues: 1361

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.058   0.003   TRP L  77 
 HIS   0.020   0.002   HIS G  62 
 PHE   0.030   0.003   PHE M  11 
 TYR   0.027   0.003   TYR H  12 
 ARG   0.016   0.001   ARG G 280 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.17097 ( 1028)
  hydrogen bonds       : angle       7.56728 ( 3009)
  covalent geometry    : bond        0.00760 (26356)
  covalent geometry    : angle       0.85101 (35731)

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

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

  6124 Ramachandran restraints generated.
    3062 Oldfield, 0 Emsley, 3062 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  6124 Ramachandran restraints generated.
    3062 Oldfield, 0 Emsley, 3062 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  262 residues out of total 2654 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 261
  time to evaluate  : 2.697 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: C  103 CYS cc_start: 0.8560 (m) cc_final: 0.8201 (m)
REVERT: C  272 ASN cc_start: 0.8958 (m110) cc_final: 0.8673 (m-40)
REVERT: D  150 MET cc_start: 0.8868 (tpt) cc_final: 0.8487 (tpp)
REVERT: E  111 THR cc_start: 0.8628 (m) cc_final: 0.8428 (p)
REVERT: E  167 MET cc_start: 0.7910 (mmp) cc_final: 0.7501 (mmm)
REVERT: F  116 MET cc_start: 0.9324 (mpp) cc_final: 0.8326 (mpp)
REVERT: G  116 MET cc_start: 0.9063 (mpp) cc_final: 0.8420 (mpp)
REVERT: H  116 ASP cc_start: 0.9299 (p0) cc_final: 0.8953 (t0)
REVERT: I   25 GLN cc_start: 0.9243 (tm-30) cc_final: 0.8972 (tm-30)
REVERT: I   41 PHE cc_start: 0.9192 (t80) cc_final: 0.8856 (t80)
REVERT: I   68 PHE cc_start: 0.7757 (t80) cc_final: 0.7530 (t80)
REVERT: I   88 ARG cc_start: 0.8786 (tmm-80) cc_final: 0.8550 (ttp80)
REVERT: J   65 LYS cc_start: 0.9026 (ttpp) cc_final: 0.8772 (tttm)
REVERT: N  165 THR cc_start: 0.6275 (p) cc_final: 0.5982 (p)
REVERT: K  300 HIS cc_start: 0.8694 (m90) cc_final: 0.8149 (m-70)
REVERT: K  327 LEU cc_start: 0.9340 (mm) cc_final: 0.8904 (pp)
REVERT: L    9 ASP cc_start: 0.8702 (m-30) cc_final: 0.8480 (m-30)
REVERT: L   56 MET cc_start: 0.8742 (mmp) cc_final: 0.8206 (ttt)
REVERT: A   11 LYS cc_start: 0.8666 (tptt) cc_final: 0.8430 (tppt)
REVERT: A   12 ILE cc_start: 0.8814 (tt) cc_final: 0.8456 (tt)
REVERT: A   22 LYS cc_start: 0.8891 (mppt) cc_final: 0.8667 (mmmt)
REVERT: A   28 GLU cc_start: 0.8426 (mp0) cc_final: 0.8225 (mp0)
REVERT: A   67 LYS cc_start: 0.9501 (pptt) cc_final: 0.9137 (pptt)
  outliers start: 1
  outliers final: 0
  residues processed: 262
  average time/residue: 0.3834
  time to fit residues: 156.5334
Evaluate side-chains
  214 residues out of total 2654 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 214
  time to evaluate  : 2.776 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 309
   random chunks:
   chunk 260 optimal weight:    9.9990
   chunk 234 optimal weight:    0.9990
   chunk 129 optimal weight:   10.0000
   chunk 80 optimal weight:    0.9990
   chunk 157 optimal weight:    3.9990
   chunk 125 optimal weight:    2.9990
   chunk 242 optimal weight:   20.0000
   chunk 93 optimal weight:    5.9990
   chunk 147 optimal weight:   20.0000
   chunk 180 optimal weight:    9.9990
   chunk 280 optimal weight:    7.9990
   overall best weight:    2.9990

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

Flipped N/Q/H residues before XYZ refinement:
B  59 ASN
C  85 ASN
** D  75 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E  21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** G 222 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
H  85 HIS
M 124 GLN
** M 231 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
M 234 ASN
** N 103 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** N 136 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** N 199 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
L  61 HIS
** L  74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3715 r_free = 0.3715 target = 0.083860 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 56)----------------|
| r_work = 0.3133 r_free = 0.3133 target = 0.058745 restraints weight = 99121.736|
|-----------------------------------------------------------------------------|
r_work (start): 0.3071 rms_B_bonded: 4.64
r_work (final): 0.3071
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7959
moved from start:          0.1329

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.044  26356  Z= 0.204
  Angle     :  0.674   7.760  35731  Z= 0.364
  Chirality :  0.045   0.283   3866
  Planarity :  0.005   0.100   4570
  Dihedral  : 13.817 169.546   4057
  Min Nonbonded Distance : 2.432

Molprobity Statistics.
  All-atom Clashscore : 15.11
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.72 %
    Favored  : 94.28 %
  Rotamer:
    Outliers :  0.83 %
    Allowed  :  7.84 %
    Favored  : 91.33 %
  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: -1.01 (0.15), residues: 3062
  helix:  0.86 (0.15), residues: 1171
  sheet: -0.75 (0.23), residues: 527
  loop : -2.04 (0.15), residues: 1364

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.026   0.002   TRP L  77 
 HIS   0.006   0.001   HIS F 187 
 PHE   0.025   0.002   PHE H 111 
 TYR   0.016   0.002   TYR K 250 
 ARG   0.008   0.001   ARG K 278 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05167 ( 1028)
  hydrogen bonds       : angle       5.66727 ( 3009)
  covalent geometry    : bond        0.00450 (26356)
  covalent geometry    : angle       0.67440 (35731)

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

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

  6124 Ramachandran restraints generated.
    3062 Oldfield, 0 Emsley, 3062 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  6124 Ramachandran restraints generated.
    3062 Oldfield, 0 Emsley, 3062 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  279 residues out of total 2654 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 257
  time to evaluate  : 2.765 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: C  103 CYS cc_start: 0.8651 (m) cc_final: 0.8278 (m)
REVERT: C  167 MET cc_start: 0.8889 (mmm) cc_final: 0.8341 (mmp)
REVERT: C  255 VAL cc_start: 0.8743 (m) cc_final: 0.8512 (p)
REVERT: D  150 MET cc_start: 0.8951 (tpt) cc_final: 0.8676 (tpp)
REVERT: E  150 MET cc_start: 0.9252 (tpp) cc_final: 0.9000 (tpp)
REVERT: E  209 MET cc_start: 0.6781 (ttm) cc_final: 0.6114 (tpt)
REVERT: F  116 MET cc_start: 0.9375 (mpp) cc_final: 0.8371 (mpp)
REVERT: F  141 MET cc_start: 0.8398 (mpp) cc_final: 0.8194 (mpp)
REVERT: F  209 MET cc_start: 0.8046 (ttp) cc_final: 0.7702 (tmm)
REVERT: H   77 TRP cc_start: 0.8562 (t60) cc_final: 0.8185 (t60)
REVERT: H   87 GLN cc_start: 0.7849 (pp30) cc_final: 0.7644 (pp30)
REVERT: H   89 PHE cc_start: 0.7761 (OUTLIER) cc_final: 0.6917 (t80)
REVERT: I   55 LEU cc_start: 0.9450 (mt) cc_final: 0.9220 (mt)
REVERT: I   68 PHE cc_start: 0.7866 (t80) cc_final: 0.7392 (t80)
REVERT: I   88 ARG cc_start: 0.8881 (tmm-80) cc_final: 0.8532 (ttp80)
REVERT: I  106 TYR cc_start: 0.9221 (m-80) cc_final: 0.9006 (m-80)
REVERT: N  171 MET cc_start: 0.8904 (tpp) cc_final: 0.8669 (tpt)
REVERT: K  300 HIS cc_start: 0.8643 (m90) cc_final: 0.8141 (m-70)
REVERT: K  327 LEU cc_start: 0.9389 (mm) cc_final: 0.8783 (pp)
REVERT: L    9 ASP cc_start: 0.8706 (m-30) cc_final: 0.8481 (m-30)
REVERT: L   18 PHE cc_start: 0.8860 (OUTLIER) cc_final: 0.8590 (t80)
REVERT: L   40 TYR cc_start: 0.9156 (m-80) cc_final: 0.8912 (m-80)
REVERT: A   24 TYR cc_start: 0.9056 (m-80) cc_final: 0.8851 (m-80)
  outliers start: 22
  outliers final: 11
  residues processed: 267
  average time/residue: 0.3809
  time to fit residues: 159.0740
Evaluate side-chains
  229 residues out of total 2654 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 216
  time to evaluate  : 2.951 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue  147 ILE
Chi-restraints excluded: chain D residue  147 ILE
Chi-restraints excluded: chain H residue    6 ASN
Chi-restraints excluded: chain H residue   51 VAL
Chi-restraints excluded: chain H residue   89 PHE
Chi-restraints excluded: chain I residue   36 ILE
Chi-restraints excluded: chain N residue   98 VAL
Chi-restraints excluded: chain K residue  312 TYR
Chi-restraints excluded: chain K residue  363 MET
Chi-restraints excluded: chain L residue   18 PHE
Chi-restraints excluded: chain A residue   34 GLU
Chi-restraints excluded: chain A residue   38 THR
Chi-restraints excluded: chain A residue   68 ILE
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 309
   random chunks:
   chunk 285 optimal weight:    6.9990
   chunk 127 optimal weight:    9.9990
   chunk 290 optimal weight:    6.9990
   chunk 33 optimal weight:    4.9990
   chunk 82 optimal weight:    7.9990
   chunk 107 optimal weight:   10.0000
   chunk 284 optimal weight:    0.9990
   chunk 28 optimal weight:    3.9990
   chunk 131 optimal weight:    9.9990
   chunk 67 optimal weight:    7.9990
   chunk 171 optimal weight:    3.9990
   overall best weight:    4.1990

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

Flipped N/Q/H residues before XYZ refinement:
C  85 ASN
D  75 ASN
E  21 ASN
F  74 ASN
** G 222 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** H  62 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** H  94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
M 130 GLN
** N 103 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** K 518 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** L  74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3684 r_free = 0.3684 target = 0.079116 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 61)----------------|
| r_work = 0.3098 r_free = 0.3098 target = 0.054541 restraints weight = 107029.665|
|-----------------------------------------------------------------------------|
r_work (start): 0.3087 rms_B_bonded: 4.58
r_work (final): 0.3087
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8053
moved from start:          0.1672

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.056  26356  Z= 0.260
  Angle     :  0.692   7.758  35731  Z= 0.372
  Chirality :  0.045   0.300   3866
  Planarity :  0.005   0.098   4570
  Dihedral  : 13.776 169.608   4057
  Min Nonbonded Distance : 2.422

Molprobity Statistics.
  All-atom Clashscore : 16.10
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.76 %
    Favored  : 93.24 %
  Rotamer:
    Outliers :  1.51 %
    Allowed  : 12.67 %
    Favored  : 85.82 %
  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: -0.99 (0.15), residues: 3062
  helix:  0.90 (0.15), residues: 1174
  sheet: -0.81 (0.22), residues: 539
  loop : -2.04 (0.15), residues: 1349

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.002   TRP C 203 
 HIS   0.008   0.001   HIS F 187 
 PHE   0.028   0.002   PHE H 111 
 TYR   0.027   0.002   TYR N 139 
 ARG   0.006   0.001   ARG E  51 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05171 ( 1028)
  hydrogen bonds       : angle       5.56696 ( 3009)
  covalent geometry    : bond        0.00572 (26356)
  covalent geometry    : angle       0.69162 (35731)

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

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

  6124 Ramachandran restraints generated.
    3062 Oldfield, 0 Emsley, 3062 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  6124 Ramachandran restraints generated.
    3062 Oldfield, 0 Emsley, 3062 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  270 residues out of total 2654 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 40
    poor density    : 230
  time to evaluate  : 2.641 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: D   77 ILE cc_start: 0.9241 (OUTLIER) cc_final: 0.9033 (tt)
REVERT: D  150 MET cc_start: 0.9067 (tpt) cc_final: 0.8704 (tpp)
REVERT: D  271 LYS cc_start: 0.9499 (tppt) cc_final: 0.9259 (tppt)
REVERT: E  150 MET cc_start: 0.9166 (tpp) cc_final: 0.8473 (tpp)
REVERT: E  167 MET cc_start: 0.7752 (mmm) cc_final: 0.7505 (mmm)
REVERT: E  221 MET cc_start: 0.8278 (mtm) cc_final: 0.8052 (mtm)
REVERT: F  116 MET cc_start: 0.9391 (mpp) cc_final: 0.8438 (mpp)
REVERT: F  141 MET cc_start: 0.8350 (mpp) cc_final: 0.8085 (mpp)
REVERT: F  209 MET cc_start: 0.8359 (ttp) cc_final: 0.7819 (tmm)
REVERT: G  178 TYR cc_start: 0.8583 (m-80) cc_final: 0.8261 (m-80)
REVERT: H   87 GLN cc_start: 0.7931 (pp30) cc_final: 0.7693 (pp30)
REVERT: H   89 PHE cc_start: 0.8033 (OUTLIER) cc_final: 0.7284 (t80)
REVERT: I   39 ARG cc_start: 0.8981 (mtp180) cc_final: 0.8717 (ttp-170)
REVERT: I   40 TYR cc_start: 0.8730 (m-10) cc_final: 0.8500 (m-10)
REVERT: I   65 LYS cc_start: 0.9303 (pptt) cc_final: 0.9047 (pptt)
REVERT: I   68 PHE cc_start: 0.7814 (t80) cc_final: 0.7549 (t80)
REVERT: I   88 ARG cc_start: 0.8731 (tmm-80) cc_final: 0.8389 (ttp80)
REVERT: J   68 PHE cc_start: 0.8281 (OUTLIER) cc_final: 0.8023 (m-80)
REVERT: M   31 ARG cc_start: 0.7568 (OUTLIER) cc_final: 0.6852 (mtt-85)
REVERT: N  171 MET cc_start: 0.8864 (tpp) cc_final: 0.8619 (tpt)
REVERT: K  300 HIS cc_start: 0.8631 (m90) cc_final: 0.7810 (m-70)
REVERT: K  327 LEU cc_start: 0.9337 (mm) cc_final: 0.8736 (pp)
REVERT: L   56 MET cc_start: 0.8450 (mmp) cc_final: 0.7933 (ttt)
  outliers start: 40
  outliers final: 23
  residues processed: 253
  average time/residue: 0.3751
  time to fit residues: 149.4949
Evaluate side-chains
  241 residues out of total 2654 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 214
  time to evaluate  : 3.010 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  125 VAL
Chi-restraints excluded: chain B residue  131 LEU
Chi-restraints excluded: chain B residue  273 LEU
Chi-restraints excluded: chain C residue  147 ILE
Chi-restraints excluded: chain D residue   56 MET
Chi-restraints excluded: chain D residue   77 ILE
Chi-restraints excluded: chain D residue  147 ILE
Chi-restraints excluded: chain E residue   42 THR
Chi-restraints excluded: chain F residue  227 TYR
Chi-restraints excluded: chain H residue   51 VAL
Chi-restraints excluded: chain H residue   89 PHE
Chi-restraints excluded: chain H residue   92 HIS
Chi-restraints excluded: chain I residue   51 VAL
Chi-restraints excluded: chain J residue   61 HIS
Chi-restraints excluded: chain J residue   68 PHE
Chi-restraints excluded: chain M residue   31 ARG
Chi-restraints excluded: chain N residue   98 VAL
Chi-restraints excluded: chain K residue  250 TYR
Chi-restraints excluded: chain K residue  279 THR
Chi-restraints excluded: chain K residue  312 TYR
Chi-restraints excluded: chain K residue  363 MET
Chi-restraints excluded: chain L residue   35 THR
Chi-restraints excluded: chain L residue   58 LEU
Chi-restraints excluded: chain A residue   12 ILE
Chi-restraints excluded: chain A residue   34 GLU
Chi-restraints excluded: chain A residue   38 THR
Chi-restraints excluded: chain A residue   68 ILE
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 309
   random chunks:
   chunk 167 optimal weight:    6.9990
   chunk 250 optimal weight:   10.0000
   chunk 18 optimal weight:    0.8980
   chunk 180 optimal weight:    6.9990
   chunk 46 optimal weight:    0.8980
   chunk 290 optimal weight:    5.9990
   chunk 10 optimal weight:    0.9990
   chunk 112 optimal weight:    1.9990
   chunk 39 optimal weight:    1.9990
   chunk 71 optimal weight:   20.0000
   chunk 195 optimal weight:    9.9990
   overall best weight:    1.3586

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

Flipped N/Q/H residues before XYZ refinement:
** B  81 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
C  85 ASN
F 234 ASN
** H  62 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** H  92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** H  94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** M 222 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** N 103 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** N 136 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** N 199 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
K 518 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3746 r_free = 0.3746 target = 0.081622 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 62)----------------|
| r_work = 0.3179 r_free = 0.3179 target = 0.056937 restraints weight = 105274.057|
|-----------------------------------------------------------------------------|
r_work (start): 0.3094 rms_B_bonded: 4.71
r_work (final): 0.3094
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7996
moved from start:          0.2180

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033  26356  Z= 0.124
  Angle     :  0.579  10.698  35731  Z= 0.308
  Chirality :  0.042   0.232   3866
  Planarity :  0.004   0.069   4570
  Dihedral  : 13.566 165.623   4057
  Min Nonbonded Distance : 2.404

Molprobity Statistics.
  All-atom Clashscore : 12.00
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.93 %
    Favored  : 95.07 %
  Rotamer:
    Outliers :  1.70 %
    Allowed  : 14.97 %
    Favored  : 83.33 %
  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: -0.60 (0.15), residues: 3062
  helix:  1.20 (0.16), residues: 1189
  sheet: -0.51 (0.22), residues: 525
  loop : -1.87 (0.16), residues: 1348

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP N  43 
 HIS   0.006   0.001   HIS H  92 
 PHE   0.028   0.001   PHE H 111 
 TYR   0.021   0.001   TYR N 139 
 ARG   0.010   0.000   ARG H  80 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04015 ( 1028)
  hydrogen bonds       : angle       4.94031 ( 3009)
  covalent geometry    : bond        0.00268 (26356)
  covalent geometry    : angle       0.57886 (35731)

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

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

  6124 Ramachandran restraints generated.
    3062 Oldfield, 0 Emsley, 3062 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  6124 Ramachandran restraints generated.
    3062 Oldfield, 0 Emsley, 3062 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  295 residues out of total 2654 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 45
    poor density    : 250
  time to evaluate  : 2.993 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: C   46 LEU cc_start: 0.8230 (OUTLIER) cc_final: 0.7996 (tt)
REVERT: C  167 MET cc_start: 0.8913 (mmm) cc_final: 0.8284 (mmp)
REVERT: C  209 MET cc_start: 0.8645 (tpp) cc_final: 0.8423 (tpp)
REVERT: D   77 ILE cc_start: 0.9203 (OUTLIER) cc_final: 0.8976 (tt)
REVERT: D  271 LYS cc_start: 0.9495 (tppt) cc_final: 0.9242 (tppt)
REVERT: E  125 VAL cc_start: 0.9316 (OUTLIER) cc_final: 0.8951 (m)
REVERT: E  167 MET cc_start: 0.7570 (mmm) cc_final: 0.7286 (mmm)
REVERT: E  221 MET cc_start: 0.8275 (mtm) cc_final: 0.8020 (mtm)
REVERT: F  116 MET cc_start: 0.9476 (mpp) cc_final: 0.8660 (mpp)
REVERT: F  209 MET cc_start: 0.8258 (ttp) cc_final: 0.7850 (tmm)
REVERT: G  116 MET cc_start: 0.8934 (mpp) cc_final: 0.8187 (mpp)
REVERT: G  178 TYR cc_start: 0.8599 (m-80) cc_final: 0.8213 (m-80)
REVERT: G  221 MET cc_start: 0.5182 (ptt) cc_final: 0.4916 (ptt)
REVERT: H   77 TRP cc_start: 0.8565 (t60) cc_final: 0.8365 (t60)
REVERT: H   89 PHE cc_start: 0.8015 (OUTLIER) cc_final: 0.7218 (t80)
REVERT: I   39 ARG cc_start: 0.8990 (mtp180) cc_final: 0.8688 (ttp-170)
REVERT: I   55 LEU cc_start: 0.9494 (mt) cc_final: 0.9252 (mt)
REVERT: I   65 LYS cc_start: 0.9193 (pptt) cc_final: 0.8701 (ptmm)
REVERT: I   88 ARG cc_start: 0.8798 (tmm-80) cc_final: 0.8445 (ttp80)
REVERT: J   22 GLU cc_start: 0.9406 (tm-30) cc_final: 0.9064 (tm-30)
REVERT: J   68 PHE cc_start: 0.7895 (OUTLIER) cc_final: 0.7620 (m-80)
REVERT: N   81 LEU cc_start: 0.8839 (OUTLIER) cc_final: 0.8535 (mm)
REVERT: N  171 MET cc_start: 0.9067 (tpp) cc_final: 0.8867 (tpt)
REVERT: K  300 HIS cc_start: 0.8550 (m90) cc_final: 0.7943 (m-70)
REVERT: K  325 PHE cc_start: 0.7987 (OUTLIER) cc_final: 0.7760 (t80)
REVERT: K  327 LEU cc_start: 0.9292 (mm) cc_final: 0.8890 (pp)
  outliers start: 45
  outliers final: 23
  residues processed: 281
  average time/residue: 0.3780
  time to fit residues: 167.6850
Evaluate side-chains
  248 residues out of total 2654 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 218
  time to evaluate  : 2.851 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  131 LEU
Chi-restraints excluded: chain C residue   46 LEU
Chi-restraints excluded: chain C residue  103 CYS
Chi-restraints excluded: chain C residue  147 ILE
Chi-restraints excluded: chain D residue   77 ILE
Chi-restraints excluded: chain D residue  147 ILE
Chi-restraints excluded: chain E residue  125 VAL
Chi-restraints excluded: chain F residue  227 TYR
Chi-restraints excluded: chain H residue   51 VAL
Chi-restraints excluded: chain H residue   63 LEU
Chi-restraints excluded: chain H residue   89 PHE
Chi-restraints excluded: chain H residue   92 HIS
Chi-restraints excluded: chain I residue   51 VAL
Chi-restraints excluded: chain J residue   68 PHE
Chi-restraints excluded: chain M residue  258 VAL
Chi-restraints excluded: chain M residue  276 THR
Chi-restraints excluded: chain N residue   81 LEU
Chi-restraints excluded: chain N residue   98 VAL
Chi-restraints excluded: chain N residue  139 TYR
Chi-restraints excluded: chain N residue  165 THR
Chi-restraints excluded: chain N residue  204 VAL
Chi-restraints excluded: chain K residue  250 TYR
Chi-restraints excluded: chain K residue  279 THR
Chi-restraints excluded: chain K residue  312 TYR
Chi-restraints excluded: chain K residue  325 PHE
Chi-restraints excluded: chain K residue  570 PHE
Chi-restraints excluded: chain L residue   58 LEU
Chi-restraints excluded: chain A residue   34 GLU
Chi-restraints excluded: chain A residue   38 THR
Chi-restraints excluded: chain A residue   68 ILE
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 309
   random chunks:
   chunk 280 optimal weight:    5.9990
   chunk 196 optimal weight:    6.9990
   chunk 66 optimal weight:    0.8980
   chunk 44 optimal weight:    7.9990
   chunk 182 optimal weight:    4.9990
   chunk 85 optimal weight:    5.9990
   chunk 157 optimal weight:   10.0000
   chunk 254 optimal weight:   10.0000
   chunk 303 optimal weight:    8.9990
   chunk 278 optimal weight:    6.9990
   chunk 135 optimal weight:    6.9990
   overall best weight:    4.9788

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

Flipped N/Q/H residues before XYZ refinement:
** B 187 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
E  35 GLN
** F 212 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
F 234 ASN
** H  62 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** H  97 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
H 123 ASN
** N 103 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
K 518 HIS
** L  74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3677 r_free = 0.3677 target = 0.078685 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 68)----------------|
| r_work = 0.3082 r_free = 0.3082 target = 0.054071 restraints weight = 107578.568|
|-----------------------------------------------------------------------------|
r_work (start): 0.3076 rms_B_bonded: 4.57
r_work: 0.2937 rms_B_bonded: 4.98 restraints_weight: 0.5000
r_work (final): 0.2937
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8125
moved from start:          0.2051

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.007   0.067  26356  Z= 0.296
  Angle     :  0.707   9.306  35731  Z= 0.376
  Chirality :  0.045   0.304   3866
  Planarity :  0.005   0.106   4570
  Dihedral  : 13.674 169.697   4057
  Min Nonbonded Distance : 2.427

Molprobity Statistics.
  All-atom Clashscore : 16.10
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.89 %
    Favored  : 93.11 %
  Rotamer:
    Outliers :  2.64 %
    Allowed  : 15.99 %
    Favored  : 81.37 %
  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: -0.84 (0.15), residues: 3062
  helix:  1.09 (0.15), residues: 1179
  sheet: -0.87 (0.22), residues: 558
  loop : -1.97 (0.16), residues: 1325

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.002   TRP C 203 
 HIS   0.009   0.001   HIS E 187 
 PHE   0.027   0.002   PHE M  11 
 TYR   0.034   0.002   TYR N 139 
 ARG   0.007   0.001   ARG E  51 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04942 ( 1028)
  hydrogen bonds       : angle       5.40017 ( 3009)
  covalent geometry    : bond        0.00652 (26356)
  covalent geometry    : angle       0.70729 (35731)

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

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

  6124 Ramachandran restraints generated.
    3062 Oldfield, 0 Emsley, 3062 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  6124 Ramachandran restraints generated.
    3062 Oldfield, 0 Emsley, 3062 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  289 residues out of total 2654 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 70
    poor density    : 219
  time to evaluate  : 2.785 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: C   46 LEU cc_start: 0.8721 (OUTLIER) cc_final: 0.8307 (tt)
REVERT: C  167 MET cc_start: 0.9014 (mmm) cc_final: 0.8502 (mmm)
REVERT: D  271 LYS cc_start: 0.9538 (tppt) cc_final: 0.9297 (tppt)
REVERT: E  167 MET cc_start: 0.7936 (mmm) cc_final: 0.7654 (mmm)
REVERT: E  209 MET cc_start: 0.7937 (tpp) cc_final: 0.7689 (tpp)
REVERT: F  116 MET cc_start: 0.9395 (mpp) cc_final: 0.8348 (mpp)
REVERT: F  209 MET cc_start: 0.8228 (ttp) cc_final: 0.7793 (tmm)
REVERT: G  178 TYR cc_start: 0.8759 (m-80) cc_final: 0.8374 (m-80)
REVERT: H   89 PHE cc_start: 0.7948 (OUTLIER) cc_final: 0.6940 (t80)
REVERT: I   41 PHE cc_start: 0.9090 (t80) cc_final: 0.8877 (t80)
REVERT: I   65 LYS cc_start: 0.9093 (OUTLIER) cc_final: 0.8677 (ptmm)
REVERT: I   88 ARG cc_start: 0.8773 (tmm-80) cc_final: 0.8425 (tmm-80)
REVERT: J   57 ARG cc_start: 0.9248 (mtp85) cc_final: 0.8280 (mtt-85)
REVERT: J   68 PHE cc_start: 0.7834 (OUTLIER) cc_final: 0.7609 (m-80)
REVERT: M   31 ARG cc_start: 0.7853 (OUTLIER) cc_final: 0.7073 (mtt-85)
REVERT: N   81 LEU cc_start: 0.8955 (OUTLIER) cc_final: 0.8694 (mm)
REVERT: K    1 MET cc_start: 0.7804 (tpt) cc_final: 0.7600 (tpt)
REVERT: K   11 GLN cc_start: 0.9360 (OUTLIER) cc_final: 0.8990 (mt0)
REVERT: K  300 HIS cc_start: 0.8722 (m90) cc_final: 0.8304 (m-70)
REVERT: L   40 TYR cc_start: 0.9255 (OUTLIER) cc_final: 0.8891 (m-80)
REVERT: L   56 MET cc_start: 0.8428 (mmp) cc_final: 0.7860 (ttt)
  outliers start: 70
  outliers final: 43
  residues processed: 275
  average time/residue: 0.3608
  time to fit residues: 157.4600
Evaluate side-chains
  262 residues out of total 2654 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 51
    poor density    : 211
  time to evaluate  : 2.733 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  125 VAL
Chi-restraints excluded: chain B residue  131 LEU
Chi-restraints excluded: chain B residue  273 LEU
Chi-restraints excluded: chain C residue   15 VAL
Chi-restraints excluded: chain C residue   46 LEU
Chi-restraints excluded: chain C residue  103 CYS
Chi-restraints excluded: chain C residue  147 ILE
Chi-restraints excluded: chain C residue  203 TRP
Chi-restraints excluded: chain D residue   54 ILE
Chi-restraints excluded: chain D residue  147 ILE
Chi-restraints excluded: chain E residue   42 THR
Chi-restraints excluded: chain F residue   86 VAL
Chi-restraints excluded: chain F residue  222 ASN
Chi-restraints excluded: chain F residue  227 TYR
Chi-restraints excluded: chain G residue   12 LEU
Chi-restraints excluded: chain G residue   73 LEU
Chi-restraints excluded: chain G residue  228 VAL
Chi-restraints excluded: chain H residue   51 VAL
Chi-restraints excluded: chain H residue   89 PHE
Chi-restraints excluded: chain H residue   92 HIS
Chi-restraints excluded: chain I residue   49 ILE
Chi-restraints excluded: chain I residue   51 VAL
Chi-restraints excluded: chain I residue   65 LYS
Chi-restraints excluded: chain J residue   36 ILE
Chi-restraints excluded: chain J residue   59 LEU
Chi-restraints excluded: chain J residue   61 HIS
Chi-restraints excluded: chain J residue   68 PHE
Chi-restraints excluded: chain M residue   31 ARG
Chi-restraints excluded: chain M residue  115 VAL
Chi-restraints excluded: chain M residue  147 ILE
Chi-restraints excluded: chain M residue  150 MET
Chi-restraints excluded: chain M residue  258 VAL
Chi-restraints excluded: chain M residue  276 THR
Chi-restraints excluded: chain N residue   15 THR
Chi-restraints excluded: chain N residue   21 VAL
Chi-restraints excluded: chain N residue   81 LEU
Chi-restraints excluded: chain N residue   98 VAL
Chi-restraints excluded: chain N residue  139 TYR
Chi-restraints excluded: chain N residue  165 THR
Chi-restraints excluded: chain N residue  201 VAL
Chi-restraints excluded: chain N residue  204 VAL
Chi-restraints excluded: chain K residue   11 GLN
Chi-restraints excluded: chain K residue  250 TYR
Chi-restraints excluded: chain K residue  279 THR
Chi-restraints excluded: chain K residue  312 TYR
Chi-restraints excluded: chain K residue  363 MET
Chi-restraints excluded: chain K residue  570 PHE
Chi-restraints excluded: chain L residue   40 TYR
Chi-restraints excluded: chain L residue   58 LEU
Chi-restraints excluded: chain A residue   38 THR
Chi-restraints excluded: chain A residue   68 ILE
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 309
   random chunks:
   chunk 55 optimal weight:    4.9990
   chunk 194 optimal weight:    7.9990
   chunk 31 optimal weight:    0.9980
   chunk 84 optimal weight:    3.9990
   chunk 215 optimal weight:    6.9990
   chunk 285 optimal weight:    0.0670
   chunk 266 optimal weight:    7.9990
   chunk 15 optimal weight:    0.8980
   chunk 262 optimal weight:    9.9990
   chunk 230 optimal weight:    1.9990
   chunk 181 optimal weight:    1.9990
   overall best weight:    1.1922

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

Flipped N/Q/H residues before XYZ refinement:
** B  81 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 187 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
D 272 ASN
E  28 ASN
F  16 GLN
** F  81 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
F 212 HIS
F 234 ASN
** H  62 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
M 222 ASN
N 103 HIS
** N 136 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** N 199 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
K 518 HIS

Total number of N/Q/H flips: 8

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3746 r_free = 0.3746 target = 0.081629 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 80)----------------|
| r_work = 0.3177 r_free = 0.3177 target = 0.056889 restraints weight = 105505.227|
|-----------------------------------------------------------------------------|
r_work (start): 0.3164 rms_B_bonded: 4.75
r_work (final): 0.3164
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7987
moved from start:          0.2521

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036  26356  Z= 0.122
  Angle     :  0.589  14.012  35731  Z= 0.309
  Chirality :  0.042   0.303   3866
  Planarity :  0.004   0.069   4570
  Dihedral  : 13.473 165.372   4057
  Min Nonbonded Distance : 2.220

Molprobity Statistics.
  All-atom Clashscore : 12.24
  Ramachandran Plot:
    Outliers :  0.03 %
    Allowed  :  4.83 %
    Favored  : 95.13 %
  Rotamer:
    Outliers :  2.34 %
    Allowed  : 16.74 %
    Favored  : 80.92 %
  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: -0.49 (0.15), residues: 3062
  helix:  1.34 (0.16), residues: 1181
  sheet: -0.47 (0.23), residues: 515
  loop : -1.82 (0.16), residues: 1366

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP H  77 
 HIS   0.006   0.001   HIS H  92 
 PHE   0.017   0.001   PHE H 101 
 TYR   0.021   0.001   TYR N 139 
 ARG   0.008   0.000   ARG H  80 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03802 ( 1028)
  hydrogen bonds       : angle       4.79174 ( 3009)
  covalent geometry    : bond        0.00265 (26356)
  covalent geometry    : angle       0.58938 (35731)

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

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

  6124 Ramachandran restraints generated.
    3062 Oldfield, 0 Emsley, 3062 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  6124 Ramachandran restraints generated.
    3062 Oldfield, 0 Emsley, 3062 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  303 residues out of total 2654 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 62
    poor density    : 241
  time to evaluate  : 2.761 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  209 MET cc_start: 0.8380 (tmm) cc_final: 0.6808 (tmm)
REVERT: C   46 LEU cc_start: 0.8221 (OUTLIER) cc_final: 0.7991 (tt)
REVERT: C   90 GLU cc_start: 0.9568 (tm-30) cc_final: 0.9307 (tm-30)
REVERT: C  167 MET cc_start: 0.8978 (mmm) cc_final: 0.8470 (mmm)
REVERT: D   17 ASP cc_start: 0.8503 (m-30) cc_final: 0.8252 (m-30)
REVERT: D  271 LYS cc_start: 0.9511 (tppt) cc_final: 0.9230 (tppt)
REVERT: E  167 MET cc_start: 0.7387 (mmm) cc_final: 0.7108 (mmm)
REVERT: E  209 MET cc_start: 0.7730 (tpp) cc_final: 0.7361 (tpp)
REVERT: E  221 MET cc_start: 0.8420 (mtm) cc_final: 0.8213 (mtm)
REVERT: F  116 MET cc_start: 0.9495 (mpp) cc_final: 0.8704 (mpp)
REVERT: F  209 MET cc_start: 0.8145 (ttp) cc_final: 0.7778 (tmm)
REVERT: G  116 MET cc_start: 0.8856 (mpp) cc_final: 0.8110 (mpp)
REVERT: G  178 TYR cc_start: 0.8738 (m-80) cc_final: 0.8349 (m-80)
REVERT: H   89 PHE cc_start: 0.7989 (OUTLIER) cc_final: 0.7218 (t80)
REVERT: I   38 ASP cc_start: 0.8738 (OUTLIER) cc_final: 0.8007 (t0)
REVERT: I   39 ARG cc_start: 0.9013 (mtp180) cc_final: 0.8371 (ttm170)
REVERT: I   40 TYR cc_start: 0.8648 (m-10) cc_final: 0.8187 (m-10)
REVERT: I   41 PHE cc_start: 0.9076 (t80) cc_final: 0.8780 (t80)
REVERT: I   55 LEU cc_start: 0.9484 (mt) cc_final: 0.9248 (mt)
REVERT: I   65 LYS cc_start: 0.9169 (OUTLIER) cc_final: 0.8648 (ptmm)
REVERT: I   88 ARG cc_start: 0.8829 (tmm-80) cc_final: 0.8535 (tmm-80)
REVERT: J   57 ARG cc_start: 0.9107 (mtp85) cc_final: 0.8206 (mtt-85)
REVERT: J   68 PHE cc_start: 0.7796 (OUTLIER) cc_final: 0.7458 (m-80)
REVERT: M   31 ARG cc_start: 0.7487 (OUTLIER) cc_final: 0.6908 (mtt-85)
REVERT: N   81 LEU cc_start: 0.8823 (OUTLIER) cc_final: 0.8505 (mm)
REVERT: K   11 GLN cc_start: 0.9421 (OUTLIER) cc_final: 0.9041 (mt0)
REVERT: K  300 HIS cc_start: 0.8509 (m90) cc_final: 0.8136 (m-70)
REVERT: K  325 PHE cc_start: 0.7960 (OUTLIER) cc_final: 0.7662 (t80)
REVERT: L   40 TYR cc_start: 0.9260 (OUTLIER) cc_final: 0.8955 (m-80)
REVERT: L   56 MET cc_start: 0.8394 (mmp) cc_final: 0.7815 (ttt)
  outliers start: 62
  outliers final: 35
  residues processed: 287
  average time/residue: 0.3580
  time to fit residues: 163.0982
Evaluate side-chains
  265 residues out of total 2654 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 45
    poor density    : 220
  time to evaluate  : 2.718 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  125 VAL
Chi-restraints excluded: chain B residue  131 LEU
Chi-restraints excluded: chain B residue  268 VAL
Chi-restraints excluded: chain C residue    3 ILE
Chi-restraints excluded: chain C residue   46 LEU
Chi-restraints excluded: chain C residue  103 CYS
Chi-restraints excluded: chain C residue  147 ILE
Chi-restraints excluded: chain D residue  147 ILE
Chi-restraints excluded: chain F residue   86 VAL
Chi-restraints excluded: chain F residue  222 ASN
Chi-restraints excluded: chain F residue  227 TYR
Chi-restraints excluded: chain G residue  228 VAL
Chi-restraints excluded: chain H residue   51 VAL
Chi-restraints excluded: chain H residue   89 PHE
Chi-restraints excluded: chain H residue   92 HIS
Chi-restraints excluded: chain I residue   38 ASP
Chi-restraints excluded: chain I residue   51 VAL
Chi-restraints excluded: chain I residue   65 LYS
Chi-restraints excluded: chain J residue   59 LEU
Chi-restraints excluded: chain J residue   68 PHE
Chi-restraints excluded: chain M residue   31 ARG
Chi-restraints excluded: chain M residue  115 VAL
Chi-restraints excluded: chain M residue  147 ILE
Chi-restraints excluded: chain M residue  172 THR
Chi-restraints excluded: chain M residue  222 ASN
Chi-restraints excluded: chain M residue  258 VAL
Chi-restraints excluded: chain M residue  268 VAL
Chi-restraints excluded: chain M residue  276 THR
Chi-restraints excluded: chain N residue   21 VAL
Chi-restraints excluded: chain N residue   81 LEU
Chi-restraints excluded: chain N residue  139 TYR
Chi-restraints excluded: chain N residue  165 THR
Chi-restraints excluded: chain N residue  204 VAL
Chi-restraints excluded: chain K residue   11 GLN
Chi-restraints excluded: chain K residue  250 TYR
Chi-restraints excluded: chain K residue  279 THR
Chi-restraints excluded: chain K residue  312 TYR
Chi-restraints excluded: chain K residue  325 PHE
Chi-restraints excluded: chain K residue  363 MET
Chi-restraints excluded: chain K residue  426 GLU
Chi-restraints excluded: chain K residue  570 PHE
Chi-restraints excluded: chain L residue   40 TYR
Chi-restraints excluded: chain L residue   58 LEU
Chi-restraints excluded: chain A residue   38 THR
Chi-restraints excluded: chain A residue   68 ILE
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 309
   random chunks:
   chunk 168 optimal weight:   20.0000
   chunk 161 optimal weight:    9.9990
   chunk 9 optimal weight:    2.9990
   chunk 10 optimal weight:    1.9990
   chunk 240 optimal weight:    0.9990
   chunk 156 optimal weight:    5.9990
   chunk 110 optimal weight:    9.9990
   chunk 122 optimal weight:    4.9990
   chunk 221 optimal weight:   10.0000
   chunk 269 optimal weight:    6.9990
   chunk 231 optimal weight:    4.9990
   overall best weight:    3.1990

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

Flipped N/Q/H residues before XYZ refinement:
** B 187 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** E  21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** F  81 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** H  62 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** H  97 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
H 123 ASN
** M 222 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** N 199 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
K 518 HIS
** L  74 GLN ** 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 = 0.3719 r_free = 0.3719 target = 0.083458 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 59)----------------|
| r_work = 0.3130 r_free = 0.3130 target = 0.058209 restraints weight = 100656.088|
|-----------------------------------------------------------------------------|
r_work (start): 0.3128 rms_B_bonded: 4.67
r_work: 0.2975 rms_B_bonded: 4.99 restraints_weight: 0.5000
r_work (final): 0.2975
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8050
moved from start:          0.2461

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.046  26356  Z= 0.205
  Angle     :  0.645  13.082  35731  Z= 0.337
  Chirality :  0.043   0.269   3866
  Planarity :  0.004   0.045   4570
  Dihedral  : 13.472 166.855   4057
  Min Nonbonded Distance : 2.505

Molprobity Statistics.
  All-atom Clashscore : 14.20
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.88 %
    Favored  : 94.12 %
  Rotamer:
    Outliers :  2.79 %
    Allowed  : 17.04 %
    Favored  : 80.17 %
  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: -0.58 (0.15), residues: 3062
  helix:  1.23 (0.16), residues: 1189
  sheet: -0.58 (0.23), residues: 528
  loop : -1.84 (0.16), residues: 1345

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP H  77 
 HIS   0.006   0.001   HIS G 187 
 PHE   0.028   0.002   PHE H 111 
 TYR   0.030   0.002   TYR N 139 
 ARG   0.006   0.000   ARG H  80 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04323 ( 1028)
  hydrogen bonds       : angle       4.98472 ( 3009)
  covalent geometry    : bond        0.00453 (26356)
  covalent geometry    : angle       0.64475 (35731)

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

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

  6124 Ramachandran restraints generated.
    3062 Oldfield, 0 Emsley, 3062 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  6124 Ramachandran restraints generated.
    3062 Oldfield, 0 Emsley, 3062 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  298 residues out of total 2654 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 74
    poor density    : 224
  time to evaluate  : 3.148 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  209 MET cc_start: 0.8809 (tmm) cc_final: 0.7187 (tmm)
REVERT: C   46 LEU cc_start: 0.8590 (OUTLIER) cc_final: 0.8213 (tt)
REVERT: C  167 MET cc_start: 0.8937 (mmm) cc_final: 0.8533 (mmm)
REVERT: D  150 MET cc_start: 0.8504 (ttt) cc_final: 0.8099 (ttp)
REVERT: D  271 LYS cc_start: 0.9535 (tppt) cc_final: 0.9285 (tppt)
REVERT: D  276 THR cc_start: 0.9012 (OUTLIER) cc_final: 0.8770 (p)
REVERT: E   72 ILE cc_start: 0.7675 (OUTLIER) cc_final: 0.7429 (pt)
REVERT: E  167 MET cc_start: 0.7721 (mmm) cc_final: 0.7483 (mmm)
REVERT: F  116 MET cc_start: 0.9430 (mpp) cc_final: 0.8412 (mpp)
REVERT: F  178 TYR cc_start: 0.9025 (m-80) cc_final: 0.8572 (m-80)
REVERT: G  116 MET cc_start: 0.8729 (mpp) cc_final: 0.7957 (mpp)
REVERT: G  178 TYR cc_start: 0.8858 (m-80) cc_final: 0.8509 (m-80)
REVERT: H   38 ASP cc_start: 0.8991 (OUTLIER) cc_final: 0.8777 (t0)
REVERT: H   87 GLN cc_start: 0.8156 (pp30) cc_final: 0.7949 (pp30)
REVERT: H   89 PHE cc_start: 0.8044 (OUTLIER) cc_final: 0.7173 (t80)
REVERT: I   38 ASP cc_start: 0.8715 (OUTLIER) cc_final: 0.7959 (t0)
REVERT: I   39 ARG cc_start: 0.8914 (mtp180) cc_final: 0.8372 (ttp-170)
REVERT: I   41 PHE cc_start: 0.9086 (t80) cc_final: 0.8767 (t80)
REVERT: I   55 LEU cc_start: 0.9476 (mt) cc_final: 0.9231 (mt)
REVERT: I   65 LYS cc_start: 0.9077 (pptt) cc_final: 0.8485 (ptmm)
REVERT: I   88 ARG cc_start: 0.8800 (tmm-80) cc_final: 0.8482 (tmm-80)
REVERT: I   93 LEU cc_start: 0.9154 (OUTLIER) cc_final: 0.8422 (mp)
REVERT: J   57 ARG cc_start: 0.9215 (mtp85) cc_final: 0.8353 (mtt-85)
REVERT: J   68 PHE cc_start: 0.7664 (OUTLIER) cc_final: 0.7462 (m-80)
REVERT: M   31 ARG cc_start: 0.7754 (OUTLIER) cc_final: 0.7035 (mtt-85)
REVERT: N   81 LEU cc_start: 0.8844 (OUTLIER) cc_final: 0.8535 (mm)
REVERT: N  195 CYS cc_start: 0.9611 (t) cc_final: 0.9396 (p)
REVERT: K   11 GLN cc_start: 0.9362 (OUTLIER) cc_final: 0.8978 (mt0)
REVERT: K  300 HIS cc_start: 0.8692 (m90) cc_final: 0.8389 (m-70)
REVERT: K  325 PHE cc_start: 0.8092 (OUTLIER) cc_final: 0.7788 (t80)
REVERT: L   40 TYR cc_start: 0.9254 (OUTLIER) cc_final: 0.8873 (m-80)
REVERT: L   56 MET cc_start: 0.8454 (mmp) cc_final: 0.7731 (ttt)
  outliers start: 74
  outliers final: 47
  residues processed: 279
  average time/residue: 0.3792
  time to fit residues: 168.6929
Evaluate side-chains
  275 residues out of total 2654 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 60
    poor density    : 215
  time to evaluate  : 2.946 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   15 VAL
Chi-restraints excluded: chain B residue  125 VAL
Chi-restraints excluded: chain B residue  131 LEU
Chi-restraints excluded: chain B residue  268 VAL
Chi-restraints excluded: chain C residue    3 ILE
Chi-restraints excluded: chain C residue   15 VAL
Chi-restraints excluded: chain C residue   46 LEU
Chi-restraints excluded: chain C residue   86 VAL
Chi-restraints excluded: chain C residue  103 CYS
Chi-restraints excluded: chain C residue  147 ILE
Chi-restraints excluded: chain D residue   50 VAL
Chi-restraints excluded: chain D residue   54 ILE
Chi-restraints excluded: chain D residue  147 ILE
Chi-restraints excluded: chain D residue  276 THR
Chi-restraints excluded: chain E residue   42 THR
Chi-restraints excluded: chain E residue   72 ILE
Chi-restraints excluded: chain F residue   86 VAL
Chi-restraints excluded: chain F residue  222 ASN
Chi-restraints excluded: chain F residue  227 TYR
Chi-restraints excluded: chain F residue  268 VAL
Chi-restraints excluded: chain F residue  279 LEU
Chi-restraints excluded: chain G residue   12 LEU
Chi-restraints excluded: chain G residue   73 LEU
Chi-restraints excluded: chain G residue  199 LEU
Chi-restraints excluded: chain G residue  228 VAL
Chi-restraints excluded: chain H residue   38 ASP
Chi-restraints excluded: chain H residue   47 THR
Chi-restraints excluded: chain H residue   51 VAL
Chi-restraints excluded: chain H residue   89 PHE
Chi-restraints excluded: chain H residue   92 HIS
Chi-restraints excluded: chain I residue   38 ASP
Chi-restraints excluded: chain I residue   49 ILE
Chi-restraints excluded: chain I residue   51 VAL
Chi-restraints excluded: chain I residue   93 LEU
Chi-restraints excluded: chain J residue   59 LEU
Chi-restraints excluded: chain J residue   68 PHE
Chi-restraints excluded: chain M residue   31 ARG
Chi-restraints excluded: chain M residue  115 VAL
Chi-restraints excluded: chain M residue  147 ILE
Chi-restraints excluded: chain M residue  258 VAL
Chi-restraints excluded: chain M residue  268 VAL
Chi-restraints excluded: chain M residue  276 THR
Chi-restraints excluded: chain N residue   21 VAL
Chi-restraints excluded: chain N residue   60 ILE
Chi-restraints excluded: chain N residue   81 LEU
Chi-restraints excluded: chain N residue   98 VAL
Chi-restraints excluded: chain N residue  139 TYR
Chi-restraints excluded: chain N residue  204 VAL
Chi-restraints excluded: chain K residue   11 GLN
Chi-restraints excluded: chain K residue  250 TYR
Chi-restraints excluded: chain K residue  279 THR
Chi-restraints excluded: chain K residue  312 TYR
Chi-restraints excluded: chain K residue  325 PHE
Chi-restraints excluded: chain K residue  363 MET
Chi-restraints excluded: chain K residue  426 GLU
Chi-restraints excluded: chain K residue  570 PHE
Chi-restraints excluded: chain L residue   40 TYR
Chi-restraints excluded: chain L residue   58 LEU
Chi-restraints excluded: chain A residue   38 THR
Chi-restraints excluded: chain A residue   68 ILE
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 309
   random chunks:
   chunk 305 optimal weight:    5.9990
   chunk 122 optimal weight:    7.9990
   chunk 80 optimal weight:    0.9980
   chunk 31 optimal weight:    4.9990
   chunk 192 optimal weight:    7.9990
   chunk 195 optimal weight:   20.0000
   chunk 229 optimal weight:    8.9990
   chunk 266 optimal weight:    5.9990
   chunk 46 optimal weight:    3.9990
   chunk 204 optimal weight:    5.9990
   chunk 186 optimal weight:    1.9990
   overall best weight:    3.5988

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

Flipped N/Q/H residues before XYZ refinement:
** B 187 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
D 272 ASN
** E  21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** F  81 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** H  62 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** H  97 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** N 199 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
K 518 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3710 r_free = 0.3710 target = 0.083270 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 53)----------------|
| r_work = 0.3118 r_free = 0.3118 target = 0.057942 restraints weight = 101253.373|
|-----------------------------------------------------------------------------|
r_work (start): 0.3117 rms_B_bonded: 4.70
r_work (final): 0.3117
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8000
moved from start:          0.2505

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.048  26356  Z= 0.225
  Angle     :  0.677  15.067  35731  Z= 0.353
  Chirality :  0.044   0.279   3866
  Planarity :  0.004   0.044   4570
  Dihedral  : 13.490 167.980   4057
  Min Nonbonded Distance : 2.212

Molprobity Statistics.
  All-atom Clashscore : 14.65
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.72 %
    Favored  : 94.28 %
  Rotamer:
    Outliers :  2.98 %
    Allowed  : 17.53 %
    Favored  : 79.49 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.67 (0.15), residues: 3062
  helix:  1.16 (0.16), residues: 1188
  sheet: -0.63 (0.23), residues: 524
  loop : -1.87 (0.16), residues: 1350

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP C 203 
 HIS   0.006   0.001   HIS E 187 
 PHE   0.027   0.002   PHE H 111 
 TYR   0.030   0.002   TYR N 139 
 ARG   0.006   0.001   ARG E  51 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04408 ( 1028)
  hydrogen bonds       : angle       5.07642 ( 3009)
  covalent geometry    : bond        0.00499 (26356)
  covalent geometry    : angle       0.67729 (35731)

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

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

  6124 Ramachandran restraints generated.
    3062 Oldfield, 0 Emsley, 3062 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  6124 Ramachandran restraints generated.
    3062 Oldfield, 0 Emsley, 3062 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  297 residues out of total 2654 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 79
    poor density    : 218
  time to evaluate  : 2.734 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  209 MET cc_start: 0.8581 (tmm) cc_final: 0.6952 (tmm)
REVERT: C   46 LEU cc_start: 0.8517 (OUTLIER) cc_final: 0.8146 (tt)
REVERT: C   81 HIS cc_start: 0.8376 (OUTLIER) cc_final: 0.8146 (t-90)
REVERT: C  167 MET cc_start: 0.9013 (mmm) cc_final: 0.8554 (mmm)
REVERT: D  150 MET cc_start: 0.8412 (ttt) cc_final: 0.7906 (ttt)
REVERT: D  271 LYS cc_start: 0.9527 (tppt) cc_final: 0.9240 (tppt)
REVERT: D  276 THR cc_start: 0.8855 (OUTLIER) cc_final: 0.8603 (p)
REVERT: E   72 ILE cc_start: 0.7656 (OUTLIER) cc_final: 0.7372 (pt)
REVERT: E  167 MET cc_start: 0.7366 (mmm) cc_final: 0.6991 (mmm)
REVERT: E  209 MET cc_start: 0.7934 (tpp) cc_final: 0.7631 (tpp)
REVERT: F  116 MET cc_start: 0.9482 (mpp) cc_final: 0.8662 (mpp)
REVERT: F  178 TYR cc_start: 0.8929 (m-80) cc_final: 0.8527 (m-80)
REVERT: F  209 MET cc_start: 0.8263 (tmm) cc_final: 0.7900 (ttp)
REVERT: G  116 MET cc_start: 0.8968 (mpp) cc_final: 0.8261 (mpp)
REVERT: G  178 TYR cc_start: 0.8843 (m-80) cc_final: 0.8513 (m-80)
REVERT: H   38 ASP cc_start: 0.8792 (OUTLIER) cc_final: 0.8476 (t0)
REVERT: H   77 TRP cc_start: 0.8346 (t60) cc_final: 0.7615 (t60)
REVERT: H   87 GLN cc_start: 0.8447 (pp30) cc_final: 0.8209 (pp30)
REVERT: H   89 PHE cc_start: 0.8043 (OUTLIER) cc_final: 0.7320 (t80)
REVERT: I   38 ASP cc_start: 0.8744 (OUTLIER) cc_final: 0.7988 (t0)
REVERT: I   39 ARG cc_start: 0.9000 (mtp180) cc_final: 0.8400 (ttm170)
REVERT: I   40 TYR cc_start: 0.8706 (m-10) cc_final: 0.8280 (m-10)
REVERT: I   41 PHE cc_start: 0.9122 (t80) cc_final: 0.8897 (t80)
REVERT: I   55 LEU cc_start: 0.9509 (mt) cc_final: 0.9274 (mt)
REVERT: I   65 LYS cc_start: 0.9259 (OUTLIER) cc_final: 0.8637 (ptmm)
REVERT: I   88 ARG cc_start: 0.8775 (tmm-80) cc_final: 0.8475 (tmm-80)
REVERT: I   93 LEU cc_start: 0.9281 (OUTLIER) cc_final: 0.8644 (mp)
REVERT: J   27 GLU cc_start: 0.9316 (mm-30) cc_final: 0.8754 (mm-30)
REVERT: J   68 PHE cc_start: 0.7839 (OUTLIER) cc_final: 0.7589 (m-80)
REVERT: M   31 ARG cc_start: 0.7646 (OUTLIER) cc_final: 0.7003 (mtt-85)
REVERT: N   52 LEU cc_start: 0.8085 (OUTLIER) cc_final: 0.7612 (mm)
REVERT: N  195 CYS cc_start: 0.9574 (t) cc_final: 0.9245 (p)
REVERT: K  300 HIS cc_start: 0.8542 (m90) cc_final: 0.8229 (m-70)
REVERT: K  325 PHE cc_start: 0.7987 (OUTLIER) cc_final: 0.7696 (t80)
REVERT: L   40 TYR cc_start: 0.9364 (OUTLIER) cc_final: 0.8813 (m-80)
REVERT: L   56 MET cc_start: 0.8649 (mmp) cc_final: 0.7561 (ttt)
REVERT: L  108 GLU cc_start: 0.7957 (mm-30) cc_final: 0.7713 (mm-30)
  outliers start: 79
  outliers final: 55
  residues processed: 281
  average time/residue: 0.3564
  time to fit residues: 158.9319
Evaluate side-chains
  279 residues out of total 2654 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 69
    poor density    : 210
  time to evaluate  : 2.727 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   15 VAL
Chi-restraints excluded: chain B residue  125 VAL
Chi-restraints excluded: chain B residue  131 LEU
Chi-restraints excluded: chain B residue  268 VAL
Chi-restraints excluded: chain C residue    3 ILE
Chi-restraints excluded: chain C residue   15 VAL
Chi-restraints excluded: chain C residue   46 LEU
Chi-restraints excluded: chain C residue   54 ILE
Chi-restraints excluded: chain C residue   81 HIS
Chi-restraints excluded: chain C residue  103 CYS
Chi-restraints excluded: chain C residue  147 ILE
Chi-restraints excluded: chain D residue   50 VAL
Chi-restraints excluded: chain D residue   54 ILE
Chi-restraints excluded: chain D residue  147 ILE
Chi-restraints excluded: chain D residue  276 THR
Chi-restraints excluded: chain E residue   42 THR
Chi-restraints excluded: chain E residue   72 ILE
Chi-restraints excluded: chain F residue   86 VAL
Chi-restraints excluded: chain F residue  222 ASN
Chi-restraints excluded: chain F residue  227 TYR
Chi-restraints excluded: chain F residue  268 VAL
Chi-restraints excluded: chain F residue  279 LEU
Chi-restraints excluded: chain G residue   12 LEU
Chi-restraints excluded: chain G residue   73 LEU
Chi-restraints excluded: chain G residue  199 LEU
Chi-restraints excluded: chain G residue  228 VAL
Chi-restraints excluded: chain G residue  258 VAL
Chi-restraints excluded: chain H residue   38 ASP
Chi-restraints excluded: chain H residue   51 VAL
Chi-restraints excluded: chain H residue   89 PHE
Chi-restraints excluded: chain H residue   92 HIS
Chi-restraints excluded: chain H residue  124 GLU
Chi-restraints excluded: chain I residue   38 ASP
Chi-restraints excluded: chain I residue   49 ILE
Chi-restraints excluded: chain I residue   51 VAL
Chi-restraints excluded: chain I residue   65 LYS
Chi-restraints excluded: chain I residue   93 LEU
Chi-restraints excluded: chain J residue   59 LEU
Chi-restraints excluded: chain J residue   68 PHE
Chi-restraints excluded: chain M residue   31 ARG
Chi-restraints excluded: chain M residue  115 VAL
Chi-restraints excluded: chain M residue  147 ILE
Chi-restraints excluded: chain M residue  150 MET
Chi-restraints excluded: chain M residue  153 THR
Chi-restraints excluded: chain M residue  172 THR
Chi-restraints excluded: chain M residue  258 VAL
Chi-restraints excluded: chain M residue  268 VAL
Chi-restraints excluded: chain M residue  276 THR
Chi-restraints excluded: chain N residue   19 LEU
Chi-restraints excluded: chain N residue   21 VAL
Chi-restraints excluded: chain N residue   52 LEU
Chi-restraints excluded: chain N residue   60 ILE
Chi-restraints excluded: chain N residue   81 LEU
Chi-restraints excluded: chain N residue   98 VAL
Chi-restraints excluded: chain N residue  139 TYR
Chi-restraints excluded: chain N residue  165 THR
Chi-restraints excluded: chain N residue  204 VAL
Chi-restraints excluded: chain K residue  250 TYR
Chi-restraints excluded: chain K residue  279 THR
Chi-restraints excluded: chain K residue  312 TYR
Chi-restraints excluded: chain K residue  325 PHE
Chi-restraints excluded: chain K residue  363 MET
Chi-restraints excluded: chain K residue  426 GLU
Chi-restraints excluded: chain K residue  570 PHE
Chi-restraints excluded: chain L residue   40 TYR
Chi-restraints excluded: chain L residue   58 LEU
Chi-restraints excluded: chain A residue   12 ILE
Chi-restraints excluded: chain A residue   38 THR
Chi-restraints excluded: chain A residue   68 ILE
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 309
   random chunks:
   chunk 22 optimal weight:    0.8980
   chunk 35 optimal weight:    3.9990
   chunk 50 optimal weight:    0.8980
   chunk 110 optimal weight:    7.9990
   chunk 165 optimal weight:    0.0970
   chunk 89 optimal weight:    7.9990
   chunk 279 optimal weight:   10.0000
   chunk 189 optimal weight:    7.9990
   chunk 251 optimal weight:    4.9990
   chunk 114 optimal weight:    0.9990
   chunk 233 optimal weight:    3.9990
   overall best weight:    1.3782

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

Flipped N/Q/H residues before XYZ refinement:
** B  81 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 187 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
C  85 ASN
** E  21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** F  81 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** H  62 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** H  97 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
M 222 ASN
** N 136 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** N 199 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
K  11 GLN
K 518 HIS

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3751 r_free = 0.3751 target = 0.081747 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 78)----------------|
| r_work = 0.3182 r_free = 0.3182 target = 0.056966 restraints weight = 105603.569|
|-----------------------------------------------------------------------------|
r_work (start): 0.3167 rms_B_bonded: 4.74
r_work (final): 0.3167
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8004
moved from start:          0.2818

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.044  26356  Z= 0.128
  Angle     :  0.621  13.673  35731  Z= 0.319
  Chirality :  0.042   0.226   3866
  Planarity :  0.004   0.043   4570
  Dihedral  : 13.370 164.478   4057
  Min Nonbonded Distance : 2.429

Molprobity Statistics.
  All-atom Clashscore : 12.24
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.13 %
    Favored  : 94.87 %
  Rotamer:
    Outliers :  2.60 %
    Allowed  : 18.06 %
    Favored  : 79.34 %
  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: -0.45 (0.15), residues: 3062
  helix:  1.36 (0.16), residues: 1181
  sheet: -0.50 (0.23), residues: 532
  loop : -1.78 (0.16), residues: 1349

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP D 203 
 HIS   0.006   0.001   HIS H  92 
 PHE   0.029   0.001   PHE H 111 
 TYR   0.021   0.001   TYR N 139 
 ARG   0.005   0.000   ARG H  80 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03716 ( 1028)
  hydrogen bonds       : angle       4.73282 ( 3009)
  covalent geometry    : bond        0.00285 (26356)
  covalent geometry    : angle       0.62117 (35731)

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

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

  6124 Ramachandran restraints generated.
    3062 Oldfield, 0 Emsley, 3062 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  6124 Ramachandran restraints generated.
    3062 Oldfield, 0 Emsley, 3062 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  302 residues out of total 2654 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 69
    poor density    : 233
  time to evaluate  : 2.736 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  209 MET cc_start: 0.8371 (tmm) cc_final: 0.6730 (tmm)
REVERT: C   46 LEU cc_start: 0.8250 (OUTLIER) cc_final: 0.7975 (tt)
REVERT: C   81 HIS cc_start: 0.8293 (OUTLIER) cc_final: 0.8074 (t-90)
REVERT: C  167 MET cc_start: 0.8993 (mmm) cc_final: 0.8561 (mmm)
REVERT: D  271 LYS cc_start: 0.9547 (tppt) cc_final: 0.9225 (tppt)
REVERT: D  276 THR cc_start: 0.8983 (OUTLIER) cc_final: 0.8744 (p)
REVERT: E   72 ILE cc_start: 0.7493 (OUTLIER) cc_final: 0.7222 (pt)
REVERT: E  167 MET cc_start: 0.7357 (mmm) cc_final: 0.7029 (mmm)
REVERT: E  209 MET cc_start: 0.7767 (tpp) cc_final: 0.7455 (tpp)
REVERT: E  221 MET cc_start: 0.8625 (OUTLIER) cc_final: 0.7357 (mtm)
REVERT: F  116 MET cc_start: 0.9524 (mpp) cc_final: 0.8741 (mpp)
REVERT: F  178 TYR cc_start: 0.8927 (m-80) cc_final: 0.8467 (m-80)
REVERT: F  209 MET cc_start: 0.8594 (tmm) cc_final: 0.7875 (ttp)
REVERT: G  116 MET cc_start: 0.9075 (mpp) cc_final: 0.8464 (mpp)
REVERT: G  178 TYR cc_start: 0.8770 (m-80) cc_final: 0.8410 (m-80)
REVERT: G  209 MET cc_start: 0.4142 (mmm) cc_final: 0.3912 (mmm)
REVERT: H   77 TRP cc_start: 0.8429 (t60) cc_final: 0.8016 (t60)
REVERT: H   89 PHE cc_start: 0.8086 (OUTLIER) cc_final: 0.7563 (t80)
REVERT: I   38 ASP cc_start: 0.8678 (OUTLIER) cc_final: 0.7955 (t70)
REVERT: I   39 ARG cc_start: 0.8987 (mtp180) cc_final: 0.8394 (ttm170)
REVERT: I   40 TYR cc_start: 0.8658 (m-10) cc_final: 0.8243 (m-10)
REVERT: I   41 PHE cc_start: 0.9095 (t80) cc_final: 0.8868 (t80)
REVERT: I   55 LEU cc_start: 0.9452 (mt) cc_final: 0.9240 (mt)
REVERT: I   65 LYS cc_start: 0.9187 (OUTLIER) cc_final: 0.8745 (ptmm)
REVERT: I   88 ARG cc_start: 0.8779 (tmm-80) cc_final: 0.8385 (ttp80)
REVERT: I   93 LEU cc_start: 0.9344 (OUTLIER) cc_final: 0.8790 (mp)
REVERT: J   27 GLU cc_start: 0.9352 (mm-30) cc_final: 0.8764 (mm-30)
REVERT: J   41 PHE cc_start: 0.8896 (OUTLIER) cc_final: 0.8572 (m-80)
REVERT: J   68 PHE cc_start: 0.7783 (OUTLIER) cc_final: 0.7482 (m-80)
REVERT: J  106 TYR cc_start: 0.9227 (m-80) cc_final: 0.9003 (m-80)
REVERT: M   31 ARG cc_start: 0.7546 (OUTLIER) cc_final: 0.6926 (mtt-85)
REVERT: N   52 LEU cc_start: 0.8224 (OUTLIER) cc_final: 0.7793 (mm)
REVERT: N   81 LEU cc_start: 0.8830 (OUTLIER) cc_final: 0.8550 (mm)
REVERT: N  166 GLN cc_start: 0.8484 (pm20) cc_final: 0.8274 (pm20)
REVERT: N  195 CYS cc_start: 0.9431 (t) cc_final: 0.9103 (p)
REVERT: K  300 HIS cc_start: 0.8470 (m90) cc_final: 0.8153 (m-70)
REVERT: K  325 PHE cc_start: 0.7912 (OUTLIER) cc_final: 0.7604 (t80)
REVERT: L   40 TYR cc_start: 0.9229 (OUTLIER) cc_final: 0.8963 (m-80)
REVERT: L   56 MET cc_start: 0.8363 (mmp) cc_final: 0.7864 (ttt)
REVERT: L  108 GLU cc_start: 0.7324 (mm-30) cc_final: 0.7117 (mm-30)
  outliers start: 69
  outliers final: 44
  residues processed: 284
  average time/residue: 0.3596
  time to fit residues: 163.4155
Evaluate side-chains
  282 residues out of total 2654 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 60
    poor density    : 222
  time to evaluate  : 3.041 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   15 VAL
Chi-restraints excluded: chain B residue  125 VAL
Chi-restraints excluded: chain B residue  131 LEU
Chi-restraints excluded: chain B residue  268 VAL
Chi-restraints excluded: chain C residue    3 ILE
Chi-restraints excluded: chain C residue   15 VAL
Chi-restraints excluded: chain C residue   46 LEU
Chi-restraints excluded: chain C residue   81 HIS
Chi-restraints excluded: chain C residue  103 CYS
Chi-restraints excluded: chain C residue  147 ILE
Chi-restraints excluded: chain C residue  268 VAL
Chi-restraints excluded: chain D residue  147 ILE
Chi-restraints excluded: chain D residue  276 THR
Chi-restraints excluded: chain E residue   42 THR
Chi-restraints excluded: chain E residue   72 ILE
Chi-restraints excluded: chain E residue  221 MET
Chi-restraints excluded: chain F residue   86 VAL
Chi-restraints excluded: chain F residue  222 ASN
Chi-restraints excluded: chain F residue  227 TYR
Chi-restraints excluded: chain F residue  268 VAL
Chi-restraints excluded: chain G residue  199 LEU
Chi-restraints excluded: chain G residue  228 VAL
Chi-restraints excluded: chain G residue  258 VAL
Chi-restraints excluded: chain H residue   47 THR
Chi-restraints excluded: chain H residue   51 VAL
Chi-restraints excluded: chain H residue   89 PHE
Chi-restraints excluded: chain H residue   92 HIS
Chi-restraints excluded: chain H residue  124 GLU
Chi-restraints excluded: chain I residue   38 ASP
Chi-restraints excluded: chain I residue   51 VAL
Chi-restraints excluded: chain I residue   65 LYS
Chi-restraints excluded: chain I residue   93 LEU
Chi-restraints excluded: chain J residue   41 PHE
Chi-restraints excluded: chain J residue   59 LEU
Chi-restraints excluded: chain J residue   68 PHE
Chi-restraints excluded: chain M residue   31 ARG
Chi-restraints excluded: chain M residue  147 ILE
Chi-restraints excluded: chain M residue  153 THR
Chi-restraints excluded: chain M residue  172 THR
Chi-restraints excluded: chain M residue  222 ASN
Chi-restraints excluded: chain M residue  258 VAL
Chi-restraints excluded: chain M residue  268 VAL
Chi-restraints excluded: chain M residue  276 THR
Chi-restraints excluded: chain N residue   19 LEU
Chi-restraints excluded: chain N residue   21 VAL
Chi-restraints excluded: chain N residue   52 LEU
Chi-restraints excluded: chain N residue   81 LEU
Chi-restraints excluded: chain N residue   98 VAL
Chi-restraints excluded: chain N residue  139 TYR
Chi-restraints excluded: chain N residue  204 VAL
Chi-restraints excluded: chain K residue  250 TYR
Chi-restraints excluded: chain K residue  279 THR
Chi-restraints excluded: chain K residue  312 TYR
Chi-restraints excluded: chain K residue  325 PHE
Chi-restraints excluded: chain K residue  363 MET
Chi-restraints excluded: chain K residue  426 GLU
Chi-restraints excluded: chain K residue  570 PHE
Chi-restraints excluded: chain L residue   40 TYR
Chi-restraints excluded: chain L residue   58 LEU
Chi-restraints excluded: chain A residue   38 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 309
   random chunks:
   chunk 84 optimal weight:    5.9990
   chunk 6 optimal weight:    3.9990
   chunk 185 optimal weight:    0.4980
   chunk 297 optimal weight:   40.0000
   chunk 300 optimal weight:    5.9990
   chunk 197 optimal weight:    3.9990
   chunk 23 optimal weight:   10.0000
   chunk 280 optimal weight:    7.9990
   chunk 210 optimal weight:    9.9990
   chunk 4 optimal weight:    2.9990
   chunk 250 optimal weight:    9.9990
   overall best weight:    3.4988

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

Flipped N/Q/H residues before XYZ refinement:
** B 187 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** C  85 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E  21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** F  81 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
G 130 GLN
** G 222 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** H  62 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** H  97 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** N 199 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** K  11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
K 518 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3709 r_free = 0.3709 target = 0.080031 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 71)----------------|
| r_work = 0.3124 r_free = 0.3124 target = 0.055265 restraints weight = 106796.791|
|-----------------------------------------------------------------------------|
r_work (start): 0.3125 rms_B_bonded: 4.64
r_work (final): 0.3125
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8042
moved from start:          0.2697

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.048  26356  Z= 0.220
  Angle     :  0.686  14.267  35731  Z= 0.355
  Chirality :  0.044   0.271   3866
  Planarity :  0.004   0.045   4570
  Dihedral  : 13.439 167.279   4057
  Min Nonbonded Distance : 2.410

Molprobity Statistics.
  All-atom Clashscore : 14.60
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.17 %
    Favored  : 93.83 %
  Rotamer:
    Outliers :  2.45 %
    Allowed  : 18.63 %
    Favored  : 78.92 %
  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: -0.59 (0.15), residues: 3062
  helix:  1.21 (0.16), residues: 1188
  sheet: -0.60 (0.23), residues: 533
  loop : -1.80 (0.16), residues: 1341

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP C 203 
 HIS   0.006   0.001   HIS B 187 
 PHE   0.030   0.002   PHE H 111 
 TYR   0.030   0.002   TYR N 139 
 ARG   0.007   0.001   ARG G 224 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04327 ( 1028)
  hydrogen bonds       : angle       5.00797 ( 3009)
  covalent geometry    : bond        0.00489 (26356)
  covalent geometry    : angle       0.68620 (35731)

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

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

  6124 Ramachandran restraints generated.
    3062 Oldfield, 0 Emsley, 3062 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  6124 Ramachandran restraints generated.
    3062 Oldfield, 0 Emsley, 3062 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  283 residues out of total 2654 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 65
    poor density    : 218
  time to evaluate  : 3.091 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  209 MET cc_start: 0.8541 (tmm) cc_final: 0.6949 (tmm)
REVERT: C   46 LEU cc_start: 0.8545 (OUTLIER) cc_final: 0.8179 (tt)
REVERT: C   81 HIS cc_start: 0.8440 (OUTLIER) cc_final: 0.8166 (t-90)
REVERT: C  167 MET cc_start: 0.9033 (mmm) cc_final: 0.8612 (mmm)
REVERT: D  271 LYS cc_start: 0.9545 (tppt) cc_final: 0.9202 (tppt)
REVERT: D  276 THR cc_start: 0.8934 (OUTLIER) cc_final: 0.8673 (p)
REVERT: E   72 ILE cc_start: 0.7689 (OUTLIER) cc_final: 0.7417 (pt)
REVERT: E  167 MET cc_start: 0.7360 (mmm) cc_final: 0.7019 (mmm)
REVERT: E  209 MET cc_start: 0.7920 (tpp) cc_final: 0.7390 (tpp)
REVERT: E  221 MET cc_start: 0.8464 (OUTLIER) cc_final: 0.7062 (mtm)
REVERT: F  116 MET cc_start: 0.9433 (mpp) cc_final: 0.8519 (mpp)
REVERT: F  178 TYR cc_start: 0.8901 (m-80) cc_final: 0.8462 (m-80)
REVERT: F  209 MET cc_start: 0.8446 (tmm) cc_final: 0.7969 (ttp)
REVERT: G  116 MET cc_start: 0.9069 (mpp) cc_final: 0.8443 (mpp)
REVERT: G  178 TYR cc_start: 0.8740 (m-80) cc_final: 0.8447 (m-80)
REVERT: G  209 MET cc_start: 0.4076 (mmm) cc_final: 0.3850 (mmm)
REVERT: G  214 HIS cc_start: 0.7415 (p-80) cc_final: 0.6590 (m-70)
REVERT: H   77 TRP cc_start: 0.8409 (t60) cc_final: 0.7993 (t60)
REVERT: H   89 PHE cc_start: 0.8131 (OUTLIER) cc_final: 0.7431 (t80)
REVERT: I   38 ASP cc_start: 0.8669 (OUTLIER) cc_final: 0.8028 (t70)
REVERT: I   39 ARG cc_start: 0.8951 (mtp180) cc_final: 0.8694 (mtp180)
REVERT: I   65 LYS cc_start: 0.9239 (OUTLIER) cc_final: 0.8711 (ptmm)
REVERT: I   88 ARG cc_start: 0.8762 (tmm-80) cc_final: 0.8444 (tmm-80)
REVERT: I   93 LEU cc_start: 0.9328 (OUTLIER) cc_final: 0.8770 (mp)
REVERT: J   27 GLU cc_start: 0.9380 (mm-30) cc_final: 0.8831 (mm-30)
REVERT: J   41 PHE cc_start: 0.8940 (OUTLIER) cc_final: 0.8630 (m-80)
REVERT: J   68 PHE cc_start: 0.7880 (OUTLIER) cc_final: 0.7559 (m-80)
REVERT: M   31 ARG cc_start: 0.7607 (OUTLIER) cc_final: 0.6972 (mtt-85)
REVERT: N   52 LEU cc_start: 0.8118 (OUTLIER) cc_final: 0.7641 (mm)
REVERT: N   81 LEU cc_start: 0.8806 (OUTLIER) cc_final: 0.8508 (mm)
REVERT: N  195 CYS cc_start: 0.9514 (t) cc_final: 0.9216 (p)
REVERT: K  300 HIS cc_start: 0.8531 (m90) cc_final: 0.7886 (m-70)
REVERT: K  325 PHE cc_start: 0.7967 (OUTLIER) cc_final: 0.7648 (t80)
REVERT: L   40 TYR cc_start: 0.9280 (OUTLIER) cc_final: 0.8964 (m-80)
REVERT: L   56 MET cc_start: 0.8445 (mmp) cc_final: 0.7803 (ttt)
REVERT: L  108 GLU cc_start: 0.7593 (mm-30) cc_final: 0.7393 (mm-30)
  outliers start: 65
  outliers final: 45
  residues processed: 265
  average time/residue: 0.3667
  time to fit residues: 154.8655
Evaluate side-chains
  276 residues out of total 2654 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 61
    poor density    : 215
  time to evaluate  : 2.784 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   15 VAL
Chi-restraints excluded: chain B residue  125 VAL
Chi-restraints excluded: chain B residue  131 LEU
Chi-restraints excluded: chain B residue  268 VAL
Chi-restraints excluded: chain C residue    3 ILE
Chi-restraints excluded: chain C residue   15 VAL
Chi-restraints excluded: chain C residue   46 LEU
Chi-restraints excluded: chain C residue   81 HIS
Chi-restraints excluded: chain C residue  103 CYS
Chi-restraints excluded: chain C residue  147 ILE
Chi-restraints excluded: chain C residue  203 TRP
Chi-restraints excluded: chain C residue  268 VAL
Chi-restraints excluded: chain D residue  147 ILE
Chi-restraints excluded: chain D residue  276 THR
Chi-restraints excluded: chain E residue   42 THR
Chi-restraints excluded: chain E residue   72 ILE
Chi-restraints excluded: chain E residue  221 MET
Chi-restraints excluded: chain F residue   86 VAL
Chi-restraints excluded: chain F residue  222 ASN
Chi-restraints excluded: chain F residue  227 TYR
Chi-restraints excluded: chain F residue  268 VAL
Chi-restraints excluded: chain G residue   73 LEU
Chi-restraints excluded: chain G residue  199 LEU
Chi-restraints excluded: chain G residue  228 VAL
Chi-restraints excluded: chain G residue  258 VAL
Chi-restraints excluded: chain H residue   47 THR
Chi-restraints excluded: chain H residue   51 VAL
Chi-restraints excluded: chain H residue   89 PHE
Chi-restraints excluded: chain H residue   92 HIS
Chi-restraints excluded: chain I residue   38 ASP
Chi-restraints excluded: chain I residue   49 ILE
Chi-restraints excluded: chain I residue   51 VAL
Chi-restraints excluded: chain I residue   65 LYS
Chi-restraints excluded: chain I residue   93 LEU
Chi-restraints excluded: chain J residue   41 PHE
Chi-restraints excluded: chain J residue   59 LEU
Chi-restraints excluded: chain J residue   68 PHE
Chi-restraints excluded: chain M residue   31 ARG
Chi-restraints excluded: chain M residue  147 ILE
Chi-restraints excluded: chain M residue  153 THR
Chi-restraints excluded: chain M residue  258 VAL
Chi-restraints excluded: chain M residue  268 VAL
Chi-restraints excluded: chain M residue  276 THR
Chi-restraints excluded: chain N residue   19 LEU
Chi-restraints excluded: chain N residue   21 VAL
Chi-restraints excluded: chain N residue   52 LEU
Chi-restraints excluded: chain N residue   81 LEU
Chi-restraints excluded: chain N residue   98 VAL
Chi-restraints excluded: chain N residue  139 TYR
Chi-restraints excluded: chain N residue  204 VAL
Chi-restraints excluded: chain K residue  240 PHE
Chi-restraints excluded: chain K residue  250 TYR
Chi-restraints excluded: chain K residue  279 THR
Chi-restraints excluded: chain K residue  312 TYR
Chi-restraints excluded: chain K residue  325 PHE
Chi-restraints excluded: chain K residue  363 MET
Chi-restraints excluded: chain K residue  426 GLU
Chi-restraints excluded: chain K residue  570 PHE
Chi-restraints excluded: chain L residue   40 TYR
Chi-restraints excluded: chain L residue   58 LEU
Chi-restraints excluded: chain A residue   38 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 309
   random chunks:
   chunk 299 optimal weight:    7.9990
   chunk 302 optimal weight:    9.9990
   chunk 253 optimal weight:    6.9990
   chunk 205 optimal weight:    1.9990
   chunk 307 optimal weight:    6.9990
   chunk 151 optimal weight:    7.9990
   chunk 95 optimal weight:    3.9990
   chunk 277 optimal weight:    0.8980
   chunk 230 optimal weight:    0.8980
   chunk 186 optimal weight:    2.9990
   chunk 180 optimal weight:    8.9990
   overall best weight:    2.1586

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

Flipped N/Q/H residues before XYZ refinement:
** B 187 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
C  85 ASN
** E  21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** F  81 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** G 212 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** G 222 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** H  97 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** N 199 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** K  11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** L  74 GLN ** 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 = 0.3734 r_free = 0.3734 target = 0.081079 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 66)----------------|
| r_work = 0.3159 r_free = 0.3159 target = 0.056244 restraints weight = 106628.851|
|-----------------------------------------------------------------------------|
r_work (start): 0.3144 rms_B_bonded: 4.71
r_work (final): 0.3144
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8027
moved from start:          0.2861

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.043  26356  Z= 0.157
  Angle     :  0.640  13.694  35731  Z= 0.330
  Chirality :  0.043   0.244   3866
  Planarity :  0.004   0.043   4570
  Dihedral  : 13.379 165.780   4057
  Min Nonbonded Distance : 2.248

Molprobity Statistics.
  All-atom Clashscore : 13.33
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.29 %
    Favored  : 94.71 %
  Rotamer:
    Outliers :  2.49 %
    Allowed  : 18.48 %
    Favored  : 79.03 %
  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: -0.49 (0.15), residues: 3062
  helix:  1.32 (0.16), residues: 1174
  sheet: -0.43 (0.23), residues: 517
  loop : -1.80 (0.16), residues: 1371

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP B 203 
 HIS   0.016   0.001   HIS G 212 
 PHE   0.029   0.001   PHE H 111 
 TYR   0.024   0.001   TYR N 139 
 ARG   0.006   0.000   ARG G 224 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03933 ( 1028)
  hydrogen bonds       : angle       4.81868 ( 3009)
  covalent geometry    : bond        0.00350 (26356)
  covalent geometry    : angle       0.64038 (35731)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 12760.50 seconds
wall clock time: 221 minutes 37.83 seconds (13297.83 seconds total)