Starting phenix.real_space_refine
on Fri Jun 13 00:10:04 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8fyc_29564/06_2025/8fyc_29564.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8fyc_29564/06_2025/8fyc_29564.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=4.1
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8fyc_29564/06_2025/8fyc_29564.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8fyc_29564/06_2025/8fyc_29564.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8fyc_29564/06_2025/8fyc_29564.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8fyc_29564/06_2025/8fyc_29564.cif"
  }
  resolution = 4.1
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=  -0.001 sd=   0.017
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     143      5.49       5
     S      34      5.16       5
     C    8774      2.51       5
     N    2623      2.21       5
     O    3001      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 1 residue(s): 0.04s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib"
  Total number of atoms: 14575
  Number of models: 1
  Model: ""
    Number of chains: 11
    Chain: "K"
      Number of atoms: 1314
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 164, 1314
          Classifications: {'peptide': 164}
          Link IDs: {'PTRANS': 3, 'TRANS': 160}
    Chain: "J"
      Number of atoms: 881
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 43, 881
          Classifications: {'DNA': 43}
          Modifications used: {'5*END': 1}
          Link IDs: {'rna3p': 42}
    Chain: "D"
      Number of atoms: 746
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 93, 746
          Classifications: {'peptide': 93}
          Link IDs: {'PTRANS': 4, 'TRANS': 88}
    Chain: "A"
      Number of atoms: 746
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 93, 746
          Classifications: {'peptide': 93}
          Link IDs: {'PTRANS': 4, 'TRANS': 88}
    Chain: "B"
      Number of atoms: 2295
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 292, 2295
          Classifications: {'peptide': 292}
          Link IDs: {'PTRANS': 11, 'TRANS': 280}
    Chain: "C"
      Number of atoms: 2423
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 310, 2423
          Classifications: {'peptide': 310}
          Link IDs: {'PTRANS': 13, 'TRANS': 296}
    Chain: "E"
      Number of atoms: 2295
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 292, 2295
          Classifications: {'peptide': 292}
          Link IDs: {'PTRANS': 11, 'TRANS': 280}
    Chain: "F"
      Number of atoms: 1770
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 231, 1770
          Classifications: {'peptide': 231}
          Link IDs: {'PTRANS': 6, 'TRANS': 224}
          Chain breaks: 1
    Chain: "G"
      Number of atoms: 1187
      Number of conformers: 2
      Conformer: "A"
        Number of residues, atoms: 57, 1165
          Classifications: {'DNA': 57}
          Modifications used: {'5*END': 1}
          Link IDs: {'rna3p': 56}
      Conformer: "B"
        Number of residues, atoms: 57, 1165
          Classifications: {'DNA': 57}
          Modifications used: {'5*END': 1}
          Link IDs: {'rna3p': 56}
          bond proxies already assigned to first conformer: 1279
    Chain: "H"
      Number of atoms: 632
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 31, 632
          Classifications: {'DNA': 31}
          Modifications used: {'5*END': 1}
          Link IDs: {'rna3p': 30}
    Chain: "I"
      Number of atoms: 286
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 14, 286
          Classifications: {'DNA': 14}
          Link IDs: {'rna3p': 13}
  Residues with excluded nonbonded symmetry interactions: 1
    residue:
      pdb=" P  A DG G  29 " occ=0.74
      ... (42 atoms not shown)
      pdb=" C4 B DG G  29 " occ=0.26
  Time building chain proxies: 9.45, per 1000 atoms: 0.65
  Number of scatterers: 14575
  At special positions: 0
  Unit cell: (107.04, 95.89, 157.215, 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      34     16.00
     P     143     15.00
     O    3001      8.00
     N    2623      7.00
     C    8774      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: 3.68
  Conformation dependent library (CDL) restraints added in 1.6 seconds
  

  2918 Ramachandran restraints generated.
    1459 Oldfield, 0 Emsley, 1459 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2724

  Finding SS restraints...
    Secondary structure from input PDB file:
      62 helices and 9 sheets defined
      50.2% alpha, 13.7% beta
      44 base pairs and 103 stacking pairs defined.
    Time for finding SS restraints: 6.83
  Creating SS restraints...
    Processing helix  chain 'K' and resid 171 through 178
    Processing helix  chain 'K' and resid 181 through 189
    Processing helix  chain 'K' and resid 191 through 203
    Processing helix  chain 'K' and resid 212 through 228
      removed outlier: 3.929A  pdb=" N   ASP K 216 " --> pdb=" O   HIS K 212 " (cutoff:3.500A)
    Processing helix  chain 'K' and resid 238 through 246
      removed outlier: 3.922A  pdb=" N   ILE K 242 " --> pdb=" O   ASP K 238 " (cutoff:3.500A)
      removed outlier: 3.939A  pdb=" N   GLU K 246 " --> pdb=" O   ILE K 242 " (cutoff:3.500A)
    Processing helix  chain 'K' and resid 254 through 262
    Processing helix  chain 'K' and resid 271 through 287
    Processing helix  chain 'D' and resid 12 through 19
    Processing helix  chain 'D' and resid 20 through 22
      No H-bonds generated for 'chain 'D' and resid 20 through 22'
    Processing helix  chain 'D' and resid 36 through 51
      removed outlier: 4.057A  pdb=" N   GLU D  41 " --> pdb=" O   SER D  37 " (cutoff:3.500A)
      removed outlier: 4.030A  pdb=" N   TYR D  42 " --> pdb=" O   ARG D  38 " (cutoff:3.500A)
      removed outlier: 3.521A  pdb=" N   MET D  51 " --> pdb=" O   VAL D  47 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 12 through 19
    Processing helix  chain 'A' and resid 20 through 22
      No H-bonds generated for 'chain 'A' and resid 20 through 22'
    Processing helix  chain 'A' and resid 36 through 49
      removed outlier: 3.577A  pdb=" N   GLU A  49 " --> pdb=" O   ARG A  45 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 68 through 77
      removed outlier: 3.755A  pdb=" N   THR B  77 " --> pdb=" O   LEU B  73 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 86 through 89
    Processing helix  chain 'B' and resid 97 through 101
    Processing helix  chain 'B' and resid 102 through 114
    Processing helix  chain 'B' and resid 114 through 129
      removed outlier: 3.532A  pdb=" N   ARG B 120 " --> pdb=" O   ARG B 116 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 140 through 163
      removed outlier: 3.533A  pdb=" N   ARG B 144 " --> pdb=" O   MET B 140 " (cutoff:3.500A)
      removed outlier: 4.205A  pdb=" N   SER B 145 " --> pdb=" O   GLN B 141 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 180 through 205
      removed outlier: 3.938A  pdb=" N   LEU B 196 " --> pdb=" O   ALA B 192 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 219 through 227
    Processing helix  chain 'B' and resid 228 through 230
      No H-bonds generated for 'chain 'B' and resid 228 through 230'
    Processing helix  chain 'B' and resid 233 through 245
    Processing helix  chain 'B' and resid 250 through 265
      removed outlier: 4.337A  pdb=" N   ASP B 265 " --> pdb=" O   ASP B 261 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 266 through 280
      removed outlier: 4.380A  pdb=" N   GLN B 277 " --> pdb=" O   VAL B 273 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 283 through 287
    Processing helix  chain 'B' and resid 298 through 303
      removed outlier: 3.642A  pdb=" N   VAL B 303 " --> pdb=" O   LYS B 299 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 304 through 306
      No H-bonds generated for 'chain 'B' and resid 304 through 306'
    Processing helix  chain 'C' and resid 17 through 21
      removed outlier: 3.883A  pdb=" N   ARG C  21 " --> pdb=" O   VAL C  18 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 51 through 55
    Processing helix  chain 'C' and resid 68 through 77
      removed outlier: 3.897A  pdb=" N   THR C  77 " --> pdb=" O   LEU C  73 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 102 through 114
      removed outlier: 3.910A  pdb=" N   ASN C 114 " --> pdb=" O   GLU C 110 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 114 through 130
      removed outlier: 3.572A  pdb=" N   ARG C 129 " --> pdb=" O   MET C 125 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 139 through 141
      No H-bonds generated for 'chain 'C' and resid 139 through 141'
    Processing helix  chain 'C' and resid 142 through 163
    Processing helix  chain 'C' and resid 180 through 205
      removed outlier: 3.693A  pdb=" N   GLN C 184 " --> pdb=" O   ASP C 180 " (cutoff:3.500A)
      removed outlier: 3.528A  pdb=" N   ALA C 192 " --> pdb=" O   ALA C 188 " (cutoff:3.500A)
      removed outlier: 3.710A  pdb=" N   LEU C 193 " --> pdb=" O   ALA C 189 " (cutoff:3.500A)
      removed outlier: 3.684A  pdb=" N   LEU C 196 " --> pdb=" O   ALA C 192 " (cutoff:3.500A)
      removed outlier: 3.636A  pdb=" N   ALA C 202 " --> pdb=" O   HIS C 198 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 219 through 231
      removed outlier: 3.748A  pdb=" N   TYR C 223 " --> pdb=" O   ARG C 219 " (cutoff:3.500A)
      removed outlier: 4.078A  pdb=" N   LEU C 228 " --> pdb=" O   ASP C 224 " (cutoff:3.500A)
      removed outlier: 4.411A  pdb=" N   TYR C 229 " --> pdb=" O   VAL C 225 " (cutoff:3.500A)
      removed outlier: 4.416A  pdb=" N   ALA C 231 " --> pdb=" O   ASP C 227 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 233 through 245
    Processing helix  chain 'C' and resid 250 through 266
      removed outlier: 3.722A  pdb=" N   ARG C 260 " --> pdb=" O   ARG C 256 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 267 through 281
    Processing helix  chain 'E' and resid 68 through 77
      removed outlier: 4.483A  pdb=" N   LEU E  73 " --> pdb=" O   ARG E  69 " (cutoff:3.500A)
      removed outlier: 3.872A  pdb=" N   LEU E  74 " --> pdb=" O   ALA E  70 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 97 through 101
      removed outlier: 3.799A  pdb=" N   ARG E 100 " --> pdb=" O   ALA E  97 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 102 through 114
      removed outlier: 3.954A  pdb=" N   LYS E 107 " --> pdb=" O   ARG E 103 " (cutoff:3.500A)
      removed outlier: 3.862A  pdb=" N   VAL E 112 " --> pdb=" O   GLN E 108 " (cutoff:3.500A)
      removed outlier: 3.627A  pdb=" N   THR E 113 " --> pdb=" O   ALA E 109 " (cutoff:3.500A)
      removed outlier: 3.793A  pdb=" N   ASN E 114 " --> pdb=" O   GLU E 110 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 114 through 130
    Processing helix  chain 'E' and resid 139 through 162
      removed outlier: 3.761A  pdb=" N   LYS E 160 " --> pdb=" O   ARG E 156 " (cutoff:3.500A)
      removed outlier: 3.574A  pdb=" N   LYS E 161 " --> pdb=" O   GLU E 157 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 180 through 205
      removed outlier: 4.077A  pdb=" N   GLN E 184 " --> pdb=" O   ASP E 180 " (cutoff:3.500A)
      removed outlier: 4.017A  pdb=" N   LEU E 196 " --> pdb=" O   ALA E 192 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 219 through 224
    Processing helix  chain 'E' and resid 226 through 231
      removed outlier: 4.625A  pdb=" N   ALA E 231 " --> pdb=" O   ASP E 227 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 233 through 244
    Processing helix  chain 'E' and resid 250 through 265
      removed outlier: 4.199A  pdb=" N   ASP E 265 " --> pdb=" O   ASP E 261 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 266 through 280
    Processing helix  chain 'E' and resid 298 through 303
    Processing helix  chain 'F' and resid 51 through 53
      No H-bonds generated for 'chain 'F' and resid 51 through 53'
    Processing helix  chain 'F' and resid 68 through 78
      removed outlier: 3.560A  pdb=" N   THR F  77 " --> pdb=" O   LEU F  73 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 102 through 114
      removed outlier: 3.704A  pdb=" N   ASN F 114 " --> pdb=" O   GLU F 110 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 114 through 130
      removed outlier: 3.753A  pdb=" N   GLN F 127 " --> pdb=" O   ARG F 123 " (cutoff:3.500A)
      removed outlier: 4.331A  pdb=" N   MET F 128 " --> pdb=" O   ARG F 124 " (cutoff:3.500A)
      removed outlier: 3.751A  pdb=" N   ARG F 129 " --> pdb=" O   MET F 125 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 183 through 204
    Processing helix  chain 'F' and resid 219 through 226
    Processing helix  chain 'F' and resid 226 through 231
      removed outlier: 4.306A  pdb=" N   ALA F 231 " --> pdb=" O   ASP F 227 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 233 through 244
    Processing helix  chain 'F' and resid 250 through 267
      removed outlier: 3.534A  pdb=" N   ARG F 256 " --> pdb=" O   GLY F 252 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 267 through 280
      removed outlier: 4.024A  pdb=" N   VAL F 273 " --> pdb=" O   LEU F 269 " (cutoff:3.500A)
      removed outlier: 3.753A  pdb=" N   LYS F 274 " --> pdb=" O   LYS F 270 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'K' and resid 161 through 164
      removed outlier: 3.655A  pdb=" N   PHE K 161 " --> pdb=" O   ALA K 150 " (cutoff:3.500A)
      removed outlier: 3.548A  pdb=" N   GLU K 147 " --> pdb=" O   GLU K 134 " (cutoff:3.500A)
      removed outlier: 3.556A  pdb=" N   GLU K 134 " --> pdb=" O   GLU K 147 " (cutoff:3.500A)
      removed outlier: 3.891A  pdb=" N   TYR K 128 " --> pdb=" O   CYS K 153 " (cutoff:3.500A)
      removed outlier: 5.512A  pdb=" N   VAL K 129 " --> pdb=" O   VAL K 209 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'D' and resid 24 through 25
      removed outlier: 4.485A  pdb=" N   ALA D  56 " --> pdb=" O   GLU D  73 " (cutoff:3.500A)
      removed outlier: 3.821A  pdb=" N   GLU D  73 " --> pdb=" O   ALA D  56 " (cutoff:3.500A)
      removed outlier: 3.811A  pdb=" N   PHE D  60 " --> pdb=" O   ASP D  69 " (cutoff:3.500A)
      removed outlier: 3.588A  pdb=" N   ASP D  69 " --> pdb=" O   PHE D  60 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'D' and resid 78 through 81
      removed outlier: 5.591A  pdb=" N   ILE D  88 " --> pdb=" O   ARG C  49 " (cutoff:3.500A)
      removed outlier: 4.515A  pdb=" N   ARG C  49 " --> pdb=" O   ILE D  88 " (cutoff:3.500A)
      removed outlier: 3.618A  pdb=" N   SER C  67 " --> pdb=" O   ILE C  32 " (cutoff:3.500A)
      removed outlier: 6.890A  pdb=" N   ARG C  34 " --> pdb=" O   SER C  67 " (cutoff:3.500A)
      removed outlier: 6.253A  pdb=" N   ALA B  30 " --> pdb=" O   ASP B  65 " (cutoff:3.500A)
      removed outlier: 7.964A  pdb=" N   SER B  67 " --> pdb=" O   ALA B  30 " (cutoff:3.500A)
      removed outlier: 7.215A  pdb=" N   ILE B  32 " --> pdb=" O   SER B  67 " (cutoff:3.500A)
      removed outlier: 3.888A  pdb=" N   GLY B  46 " --> pdb=" O   GLU B  43 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 24 through 27
      removed outlier: 5.679A  pdb=" N   GLU A  25 " --> pdb=" O   VAL A  32 " (cutoff:3.500A)
      removed outlier: 7.295A  pdb=" N   VAL A  32 " --> pdb=" O   GLU A  25 " (cutoff:3.500A)
      removed outlier: 3.762A  pdb=" N   ALA A  27 " --> pdb=" O   VAL A  30 " (cutoff:3.500A)
      removed outlier: 3.608A  pdb=" N   ALA A  56 " --> pdb=" O   GLU A  73 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'A' and resid 78 through 82
      removed outlier: 6.773A  pdb=" N   ARG F  34 " --> pdb=" O   SER F  67 " (cutoff:3.500A)
      removed outlier: 8.208A  pdb=" N   ILE E  32 " --> pdb=" O   SER E  67 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'B' and resid 289 through 291
      removed outlier: 7.773A  pdb=" N   VAL B  57 " --> pdb=" O   ARG B  21 " (cutoff:3.500A)
      removed outlier: 5.576A  pdb=" N   THR B  23 " --> pdb=" O   VAL B  57 " (cutoff:3.500A)
      removed outlier: 6.603A  pdb=" N   LEU B  59 " --> pdb=" O   THR B  23 " (cutoff:3.500A)
      removed outlier: 6.596A  pdb=" N   ILE B  25 " --> pdb=" O   LEU B  59 " (cutoff:3.500A)
      removed outlier: 3.621A  pdb=" N   VAL B  82 " --> pdb=" O   LEU B  58 " (cutoff:3.500A)
      removed outlier: 5.731A  pdb=" N   LEU B  81 " --> pdb=" O   GLY B  95 " (cutoff:3.500A)
      removed outlier: 3.836A  pdb=" N   GLY C  88 " --> pdb=" O   GLY C  85 " (cutoff:3.500A)
      removed outlier: 3.536A  pdb=" N   GLY C  85 " --> pdb=" O   GLY C  88 " (cutoff:3.500A)
      removed outlier: 7.106A  pdb=" N   TRP C  83 " --> pdb=" O   ARG C  90 " (cutoff:3.500A)
      removed outlier: 4.915A  pdb=" N   TYR C  92 " --> pdb=" O   LEU C  81 " (cutoff:3.500A)
      removed outlier: 6.835A  pdb=" N   LEU C  81 " --> pdb=" O   TYR C  92 " (cutoff:3.500A)
      removed outlier: 6.326A  pdb=" N   LEU C  58 " --> pdb=" O   VAL C  82 " (cutoff:3.500A)
      removed outlier: 7.335A  pdb=" N   VAL C  84 " --> pdb=" O   LEU C  58 " (cutoff:3.500A)
      removed outlier: 5.369A  pdb=" N   LEU C  60 " --> pdb=" O   VAL C  84 " (cutoff:3.500A)
      removed outlier: 6.195A  pdb=" N   ILE C  25 " --> pdb=" O   LEU C  59 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'B' and resid 214 through 215
    Processing sheet with id=AA8, first strand: chain 'E' and resid 289 through 292
      removed outlier: 6.293A  pdb=" N   ALA E  22 " --> pdb=" O   GLU E 291 " (cutoff:3.500A)
      removed outlier: 7.785A  pdb=" N   VAL E  57 " --> pdb=" O   ARG E  21 " (cutoff:3.500A)
      removed outlier: 5.745A  pdb=" N   THR E  23 " --> pdb=" O   VAL E  57 " (cutoff:3.500A)
      removed outlier: 6.708A  pdb=" N   LEU E  59 " --> pdb=" O   THR E  23 " (cutoff:3.500A)
      removed outlier: 6.086A  pdb=" N   ILE E  25 " --> pdb=" O   LEU E  59 " (cutoff:3.500A)
      removed outlier: 6.196A  pdb=" N   LEU E  58 " --> pdb=" O   VAL E  82 " (cutoff:3.500A)
      removed outlier: 6.978A  pdb=" N   VAL E  84 " --> pdb=" O   LEU E  58 " (cutoff:3.500A)
      removed outlier: 5.563A  pdb=" N   LEU E  60 " --> pdb=" O   VAL E  84 " (cutoff:3.500A)
      removed outlier: 5.918A  pdb=" N   LEU E  81 " --> pdb=" O   GLY E  95 " (cutoff:3.500A)
      removed outlier: 3.770A  pdb=" N   TYR F  91 " --> pdb=" O   TRP F  83 " (cutoff:3.500A)
      removed outlier: 3.515A  pdb=" N   LEU F  81 " --> pdb=" O   ALA F  93 " (cutoff:3.500A)
      removed outlier: 3.618A  pdb=" N   VAL F  82 " --> pdb=" O   LEU F  58 " (cutoff:3.500A)
      removed outlier: 6.455A  pdb=" N   THR F  23 " --> pdb=" O   VAL F  57 " (cutoff:3.500A)
      removed outlier: 7.345A  pdb=" N   LEU F  59 " --> pdb=" O   THR F  23 " (cutoff:3.500A)
      removed outlier: 6.064A  pdb=" N   ILE F  25 " --> pdb=" O   LEU F  59 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'E' and resid 47 through 48

    568 hydrogen bonds defined for protein.
    1635 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      104 hydrogen bonds
      196 hydrogen bond angles
      0 basepair planarities
      44 basepair parallelities
      103 stacking parallelities
  Total time for adding SS restraints: 4.94

  Time building geometry restraints manager: 4.34 seconds

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

  Histogram of bond lengths:
        1.19 -     1.32: 2152
        1.32 -     1.44: 4712
        1.44 -     1.57: 7932
        1.57 -     1.69: 286
        1.69 -     1.82: 64
  Bond restraints: 15146
  Sorted by residual:
  bond pdb=" C   ASP E 250 "
       pdb=" O   ASP E 250 "
    ideal  model  delta    sigma   weight residual
    1.234  1.311 -0.077 1.14e-02 7.69e+03 4.55e+01
  bond pdb=" C   SER C 159 "
       pdb=" O   SER C 159 "
    ideal  model  delta    sigma   weight residual
    1.236  1.192  0.044 1.15e-02 7.56e+03 1.47e+01
  bond pdb=" N   THR B 102 "
       pdb=" CA  THR B 102 "
    ideal  model  delta    sigma   weight residual
    1.457  1.495 -0.038 1.06e-02 8.90e+03 1.30e+01
  bond pdb=" N   ILE K 133 "
       pdb=" CA  ILE K 133 "
    ideal  model  delta    sigma   weight residual
    1.457  1.494 -0.037 1.11e-02 8.12e+03 1.10e+01
  bond pdb=" N   VAL E 264 "
       pdb=" CA  VAL E 264 "
    ideal  model  delta    sigma   weight residual
    1.461  1.496 -0.036 1.19e-02 7.06e+03 8.94e+00
  ... (remaining 15141 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.62: 20214
        1.62 -     3.24: 765
        3.24 -     4.86: 100
        4.86 -     6.49: 26
        6.49 -     8.11: 5
  Bond angle restraints: 21110
  Sorted by residual:
  angle pdb=" C   ARG E 260 "
        pdb=" CA  ARG E 260 "
        pdb=" CB  ARG E 260 "
      ideal   model   delta    sigma   weight residual
     110.79  102.68    8.11 1.66e+00 3.63e-01 2.39e+01
  angle pdb=" N   GLU C 147 "
        pdb=" CA  GLU C 147 "
        pdb=" C   GLU C 147 "
      ideal   model   delta    sigma   weight residual
     111.28  105.98    5.30 1.09e+00 8.42e-01 2.36e+01
  angle pdb=" N   SER C 159 "
        pdb=" CA  SER C 159 "
        pdb=" C   SER C 159 "
      ideal   model   delta    sigma   weight residual
     111.07  106.33    4.74 1.07e+00 8.73e-01 1.96e+01
  angle pdb=" N   TYR C 155 "
        pdb=" CA  TYR C 155 "
        pdb=" C   TYR C 155 "
      ideal   model   delta    sigma   weight residual
     111.07  106.47    4.60 1.07e+00 8.73e-01 1.85e+01
  angle pdb=" CA  LYS C 160 "
        pdb=" C   LYS C 160 "
        pdb=" O   LYS C 160 "
      ideal   model   delta    sigma   weight residual
     120.82  116.37    4.45 1.05e+00 9.07e-01 1.79e+01
  ... (remaining 21105 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    35.72: 8083
       35.72 -    71.45: 594
       71.45 -   107.17: 21
      107.17 -   142.90: 4
      142.90 -   178.62: 4
  Dihedral angle restraints: 8706
    sinusoidal: 4458
      harmonic: 4248
  Sorted by residual:
  dihedral pdb=" C   ARG E 260 "
           pdb=" N   ARG E 260 "
           pdb=" CA  ARG E 260 "
           pdb=" CB  ARG E 260 "
      ideal   model   delta  harmonic     sigma   weight residual
    -122.60 -111.60  -11.00     0      2.50e+00 1.60e-01 1.94e+01
  dihedral pdb=" CA  THR C 139 "
           pdb=" C   THR C 139 "
           pdb=" N   MET C 140 "
           pdb=" CA  MET C 140 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -160.20  -19.80     0      5.00e+00 4.00e-02 1.57e+01
  dihedral pdb=" C4'  DA J  31 "
           pdb=" C3'  DA J  31 "
           pdb=" O3'  DA J  31 "
           pdb=" P    DA J  32 "
      ideal   model   delta sinusoidal    sigma   weight residual
     220.00   41.38  178.62     1      3.50e+01 8.16e-04 1.57e+01
  ... (remaining 8703 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.066: 2108
       0.066 -    0.132: 228
       0.132 -    0.199: 32
       0.199 -    0.265: 10
       0.265 -    0.331: 1
  Chirality restraints: 2379
  Sorted by residual:
  chirality pdb=" CA  ARG E 260 "
            pdb=" N   ARG E 260 "
            pdb=" C   ARG E 260 "
            pdb=" CB  ARG E 260 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.84   -0.33 2.00e-01 2.50e+01 2.74e+00
  chirality pdb=" CA  TYR C 155 "
            pdb=" N   TYR C 155 "
            pdb=" C   TYR C 155 "
            pdb=" CB  TYR C 155 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.77   -0.26 2.00e-01 2.50e+01 1.71e+00
  chirality pdb=" CA  LYS F   9 "
            pdb=" N   LYS F   9 "
            pdb=" C   LYS F   9 "
            pdb=" CB  LYS F   9 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.76   -0.25 2.00e-01 2.50e+01 1.59e+00
  ... (remaining 2376 not shown)

  Planarity restraints: 2203
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  SER C 159 "   -0.025 2.00e-02 2.50e+03   5.06e-02 2.56e+01
        pdb=" C   SER C 159 "    0.087 2.00e-02 2.50e+03
        pdb=" O   SER C 159 "   -0.033 2.00e-02 2.50e+03
        pdb=" N   LYS C 160 "   -0.030 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  GLN E 249 "   -0.019 2.00e-02 2.50e+03   3.88e-02 1.51e+01
        pdb=" C   GLN E 249 "    0.067 2.00e-02 2.50e+03
        pdb=" O   GLN E 249 "   -0.025 2.00e-02 2.50e+03
        pdb=" N   ASP E 250 "   -0.022 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ASP E 250 "    0.014 2.00e-02 2.50e+03   2.83e-02 8.02e+00
        pdb=" C   ASP E 250 "   -0.049 2.00e-02 2.50e+03
        pdb=" O   ASP E 250 "    0.018 2.00e-02 2.50e+03
        pdb=" N   ILE E 251 "    0.017 2.00e-02 2.50e+03
  ... (remaining 2200 not shown)

  Histogram of nonbonded interaction distances:
        2.20 -     2.74: 1245
        2.74 -     3.28: 15722
        3.28 -     3.82: 27656
        3.82 -     4.36: 31538
        4.36 -     4.90: 48790
  Nonbonded interactions: 124951
  Sorted by model distance:
  nonbonded pdb=" O   GLY D  17 "
            pdb=" OG1 THR D  20 "
     model   vdw
     2.196 3.040
  nonbonded pdb=" OH  TYR E 223 "
            pdb=" N2   DG G  27 "
     model   vdw
     2.229 3.120
  nonbonded pdb=" NH1 ARG E  34 "
            pdb=" O   ARG E  69 "
     model   vdw
     2.229 3.120
  nonbonded pdb=" OH  TYR C 229 "
            pdb=" OD2 ASP C 275 "
     model   vdw
     2.231 3.040
  nonbonded pdb=" O   ARG C 256 "
            pdb=" OG1 THR C 259 "
     model   vdw
     2.233 3.040
  ... (remaining 124946 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 'A'
  selection = chain 'D'
}
ncs_group {
  reference = chain 'B'
  selection = (chain 'C' and resid 20 through 311)
  selection = chain 'E'
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=0.26 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             0.830
  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:             0.020
  Extract box with map and model:          0.550
  Check model and map are aligned:         0.100
  Set scattering table:                    0.140
  Process input model:                     39.910
  Find NCS groups from input model:        0.370
  Set up NCS constraints:                  0.070
  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:2.940
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   44.930
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7526
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      :  0.004   0.077  15146  Z= 0.252
  Angle     :  0.684   8.108  21110  Z= 0.429
  Chirality :  0.046   0.331   2379
  Planarity :  0.004   0.051   2203
  Dihedral  : 20.674 178.623   5982
  Min Nonbonded Distance : 2.196

Molprobity Statistics.
  All-atom Clashscore : 18.87
  Ramachandran Plot:
    Outliers :  0.07 %
    Allowed  :  3.22 %
    Favored  : 96.71 %
  Rotamer:
    Outliers :  0.25 %
    Allowed  :  1.16 %
    Favored  : 98.60 %
  Cbeta Deviations :  0.15 %
  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 (0.21), residues: 1459
  helix:  0.48 (0.21), residues: 624
  sheet: -0.95 (0.34), residues: 211
  loop : -1.00 (0.23), residues: 624

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.002   TRP A  44 
 HIS   0.005   0.001   HIS E  29 
 PHE   0.019   0.001   PHE K 224 
 TYR   0.012   0.001   TYR F  91 
 ARG   0.006   0.000   ARG F 116 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.29180 (  672)
  hydrogen bonds       : angle       8.80156 ( 1831)
  covalent geometry    : bond        0.00400 (15146)
  covalent geometry    : angle       0.68358 (21110)

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

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

  2918 Ramachandran restraints generated.
    1459 Oldfield, 0 Emsley, 1459 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2918 Ramachandran restraints generated.
    1459 Oldfield, 0 Emsley, 1459 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  304 residues out of total 1210 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 301
  time to evaluate  : 1.354 
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: K  271 ARG cc_start: 0.7809 (mtt180) cc_final: 0.7533 (mmt180)
REVERT: D   69 ASP cc_start: 0.8191 (t70) cc_final: 0.7957 (t70)
REVERT: A   49 GLU cc_start: 0.8822 (mm-30) cc_final: 0.8269 (mt-10)
REVERT: B   81 LEU cc_start: 0.8752 (tt) cc_final: 0.8506 (tt)
REVERT: B   86 GLU cc_start: 0.8038 (tp30) cc_final: 0.7831 (tp30)
REVERT: B  141 GLN cc_start: 0.9381 (tm-30) cc_final: 0.8875 (tm-30)
REVERT: B  163 ASN cc_start: 0.8846 (m-40) cc_final: 0.8543 (m-40)
REVERT: B  217 HIS cc_start: 0.9200 (t-90) cc_final: 0.8844 (t70)
REVERT: C  156 ARG cc_start: 0.9251 (mtt180) cc_final: 0.8567 (tpp80)
REVERT: C  197 VAL cc_start: 0.8996 (t) cc_final: 0.8762 (p)
REVERT: C  253 GLN cc_start: 0.7502 (tm-30) cc_final: 0.7148 (tp40)
REVERT: C  282 ILE cc_start: 0.9182 (mm) cc_final: 0.8981 (mm)
REVERT: C  295 LEU cc_start: 0.9372 (mm) cc_final: 0.9144 (mm)
REVERT: E   69 ARG cc_start: 0.7745 (tpm170) cc_final: 0.7099 (tpm170)
REVERT: E  272 MET cc_start: 0.9143 (mpp) cc_final: 0.8934 (mpp)
REVERT: F  114 ASN cc_start: 0.9107 (m110) cc_final: 0.8903 (t0)
REVERT: F  125 MET cc_start: 0.8866 (ttt) cc_final: 0.8263 (tmm)
REVERT: F  190 HIS cc_start: 0.7674 (m170) cc_final: 0.7453 (m-70)
  outliers start: 3
  outliers final: 0
  residues processed: 301
  average time/residue: 0.2972
  time to fit residues: 126.6924
Evaluate side-chains
  223 residues out of total 1210 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 223
  time to evaluate  : 1.534 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 159
   random chunks:
   chunk 134 optimal weight:   10.0000
   chunk 120 optimal weight:    0.0050
   chunk 66 optimal weight:    1.9990
   chunk 41 optimal weight:    9.9990
   chunk 81 optimal weight:    3.9990
   chunk 64 optimal weight:    8.9990
   chunk 124 optimal weight:   10.0000
   chunk 48 optimal weight:    5.9990
   chunk 75 optimal weight:    6.9990
   chunk 92 optimal weight:    8.9990
   chunk 144 optimal weight:    0.7980
   overall best weight:    2.5600

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

Flipped N/Q/H residues before XYZ refinement:
K 222 GLN
K 287 ASN
** B 183 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 190 HIS
** B 198 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 142 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 214 HIS
** E 253 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
F  33 ASN
F 127 GLN
F 183 ASN
F 184 GLN

Total number of N/Q/H flips: 8

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3974 r_free = 0.3974 target = 0.098872 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3479 r_free = 0.3479 target = 0.076661 restraints weight = 72097.592|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 43)----------------|
| r_work = 0.3538 r_free = 0.3538 target = 0.078698 restraints weight = 42901.435|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3568 r_free = 0.3568 target = 0.079951 restraints weight = 30322.927|
|-----------------------------------------------------------------------------|
r_work (final): 0.3542
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3542
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3542 r_free = 0.3542    target_work(ls_wunit_k1) = 0.079         |
| occupancies: max = 1.00  min = 0.26   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3540 r_free = 0.3540    target_work(ls_wunit_k1) = 0.079         |
| occupancies: max = 1.00  min = 0.34   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3540
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7548
moved from start:          0.1842

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.040  15146  Z= 0.209
  Angle     :  0.651   6.938  21110  Z= 0.368
  Chirality :  0.043   0.160   2379
  Planarity :  0.005   0.046   2203
  Dihedral  : 23.969 179.272   3215
  Min Nonbonded Distance : 2.182

Molprobity Statistics.
  All-atom Clashscore : 16.90
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.36 %
    Favored  : 96.64 %
  Rotamer:
    Outliers :  0.08 %
    Allowed  :  6.86 %
    Favored  : 93.06 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.75 (0.21), residues: 1459
  helix:  0.44 (0.19), residues: 665
  sheet: -1.27 (0.33), residues: 216
  loop : -1.18 (0.24), residues: 578

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.002   TRP D  44 
 HIS   0.006   0.001   HIS E  29 
 PHE   0.020   0.002   PHE K 202 
 TYR   0.018   0.002   TYR B 194 
 ARG   0.007   0.001   ARG C 169 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.07178 (  672)
  hydrogen bonds       : angle       5.36543 ( 1831)
  covalent geometry    : bond        0.00444 (15146)
  covalent geometry    : angle       0.65103 (21110)

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

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

  2918 Ramachandran restraints generated.
    1459 Oldfield, 0 Emsley, 1459 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2918 Ramachandran restraints generated.
    1459 Oldfield, 0 Emsley, 1459 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  274 residues out of total 1210 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 273
  time to evaluate  : 1.312 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: K  271 ARG cc_start: 0.7973 (mtt180) cc_final: 0.7585 (mmt180)
REVERT: D   69 ASP cc_start: 0.8402 (t70) cc_final: 0.8172 (t70)
REVERT: B  125 MET cc_start: 0.8653 (mpp) cc_final: 0.8413 (mpp)
REVERT: B  134 ASP cc_start: 0.9114 (m-30) cc_final: 0.8591 (t0)
REVERT: B  141 GLN cc_start: 0.9389 (tm-30) cc_final: 0.9106 (tm-30)
REVERT: B  217 HIS cc_start: 0.9193 (t-90) cc_final: 0.8836 (t70)
REVERT: C   81 LEU cc_start: 0.8829 (mm) cc_final: 0.8617 (mm)
REVERT: C  156 ARG cc_start: 0.8891 (mtt180) cc_final: 0.8672 (tpp80)
REVERT: C  282 ILE cc_start: 0.9114 (mm) cc_final: 0.8763 (mm)
REVERT: E   83 TRP cc_start: 0.8409 (m-90) cc_final: 0.7661 (m-90)
REVERT: E  272 MET cc_start: 0.9147 (mpp) cc_final: 0.8864 (mpp)
REVERT: F   15 LEU cc_start: 0.9284 (mt) cc_final: 0.9047 (mt)
REVERT: F   19 GLU cc_start: 0.8428 (mm-30) cc_final: 0.7939 (mm-30)
  outliers start: 1
  outliers final: 1
  residues processed: 274
  average time/residue: 0.2643
  time to fit residues: 105.3390
Evaluate side-chains
  207 residues out of total 1210 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 206
  time to evaluate  : 1.337 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 159
   random chunks:
   chunk 68 optimal weight:    1.9990
   chunk 114 optimal weight:    5.9990
   chunk 94 optimal weight:    0.8980
   chunk 66 optimal weight:    6.9990
   chunk 131 optimal weight:    0.7980
   chunk 112 optimal weight:    0.8980
   chunk 26 optimal weight:    5.9990
   chunk 13 optimal weight:   10.0000
   chunk 11 optimal weight:    0.0870
   chunk 72 optimal weight:    2.9990
   chunk 142 optimal weight:    6.9990
   overall best weight:    0.9360

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

Flipped N/Q/H residues before XYZ refinement:
K 186 GLN
K 212 HIS
K 237 HIS
** B 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 183 ASN
** B 190 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 198 HIS
** C 142 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 146 HIS
C 253 GLN
F 184 GLN

Total number of N/Q/H flips: 8

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4023 r_free = 0.4023 target = 0.101676 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3535 r_free = 0.3535 target = 0.079349 restraints weight = 71297.834|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.3597 r_free = 0.3597 target = 0.081496 restraints weight = 40903.898|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3627 r_free = 0.3627 target = 0.082805 restraints weight = 28790.554|
|-----------------------------------------------------------------------------|
r_work (final): 0.3604
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3604
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3604 r_free = 0.3604    target_work(ls_wunit_k1) = 0.082         |
| occupancies: max = 1.00  min = 0.34   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3604 r_free = 0.3604    target_work(ls_wunit_k1) = 0.082         |
| occupancies: max = 1.00  min = 0.28   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3604
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7469
moved from start:          0.2541

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039  15146  Z= 0.148
  Angle     :  0.605   6.618  21110  Z= 0.334
  Chirality :  0.041   0.170   2379
  Planarity :  0.004   0.050   2203
  Dihedral  : 24.140 179.818   3215
  Min Nonbonded Distance : 2.174

Molprobity Statistics.
  All-atom Clashscore : 14.36
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.02 %
    Favored  : 96.98 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  5.04 %
    Favored  : 94.96 %
  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: -0.65 (0.21), residues: 1459
  helix:  0.54 (0.19), residues: 677
  sheet: -1.15 (0.33), residues: 214
  loop : -1.24 (0.24), residues: 568

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.037   0.002   TRP B  83 
 HIS   0.007   0.001   HIS F 217 
 PHE   0.018   0.002   PHE K 202 
 TYR   0.019   0.002   TYR F  91 
 ARG   0.012   0.001   ARG A  77 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05799 (  672)
  hydrogen bonds       : angle       4.76052 ( 1831)
  covalent geometry    : bond        0.00322 (15146)
  covalent geometry    : angle       0.60524 (21110)

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

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

  2918 Ramachandran restraints generated.
    1459 Oldfield, 0 Emsley, 1459 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2918 Ramachandran restraints generated.
    1459 Oldfield, 0 Emsley, 1459 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  277 residues out of total 1210 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 277
  time to evaluate  : 1.465 
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: K  271 ARG cc_start: 0.8123 (mtt180) cc_final: 0.7722 (mmt180)
REVERT: D   38 ARG cc_start: 0.8513 (tmm-80) cc_final: 0.8163 (tmm-80)
REVERT: D   41 GLU cc_start: 0.8506 (mp0) cc_final: 0.7997 (mp0)
REVERT: D   69 ASP cc_start: 0.8402 (t70) cc_final: 0.8062 (t70)
REVERT: B  134 ASP cc_start: 0.9055 (m-30) cc_final: 0.8501 (t0)
REVERT: B  163 ASN cc_start: 0.8976 (m-40) cc_final: 0.8696 (m-40)
REVERT: B  210 LEU cc_start: 0.8878 (mm) cc_final: 0.8652 (mm)
REVERT: B  217 HIS cc_start: 0.9205 (t-90) cc_final: 0.8847 (t70)
REVERT: C  282 ILE cc_start: 0.9117 (mm) cc_final: 0.8864 (mm)
REVERT: E   69 ARG cc_start: 0.7305 (tpm170) cc_final: 0.7076 (tpm170)
REVERT: F   15 LEU cc_start: 0.9187 (mt) cc_final: 0.8963 (mt)
  outliers start: 0
  outliers final: 0
  residues processed: 277
  average time/residue: 0.2603
  time to fit residues: 106.0226
Evaluate side-chains
  215 residues out of total 1210 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 215
  time to evaluate  : 1.509 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 159
   random chunks:
   chunk 100 optimal weight:   20.0000
   chunk 1 optimal weight:    6.9990
   chunk 21 optimal weight:    2.9990
   chunk 35 optimal weight:   10.0000
   chunk 42 optimal weight:   20.0000
   chunk 111 optimal weight:   10.0000
   chunk 5 optimal weight:   20.0000
   chunk 26 optimal weight:    5.9990
   chunk 53 optimal weight:    7.9990
   chunk 153 optimal weight:   10.0000
   chunk 89 optimal weight:   10.0000
   overall best weight:    6.7992

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

Flipped N/Q/H residues before XYZ refinement:
** K 212 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
K 222 GLN
** D  48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A  34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 190 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 142 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 146 HIS
C 183 ASN
** C 184 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 217 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
C 253 GLN
F  33 ASN
** F 184 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 = 0.3887 r_free = 0.3887 target = 0.093675 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3379 r_free = 0.3379 target = 0.071804 restraints weight = 74885.163|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3434 r_free = 0.3434 target = 0.073610 restraints weight = 45507.077|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.3465 r_free = 0.3465 target = 0.074839 restraints weight = 32776.107|
|-----------------------------------------------------------------------------|
r_work (final): 0.3433
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3433
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3433 r_free = 0.3433    target_work(ls_wunit_k1) = 0.074         |
| occupancies: max = 1.00  min = 0.28   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3433 r_free = 0.3433    target_work(ls_wunit_k1) = 0.074         |
| occupancies: max = 1.00  min = 0.18   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3433
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7684
moved from start:          0.3044

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.008   0.059  15146  Z= 0.388
  Angle     :  0.811  11.455  21110  Z= 0.443
  Chirality :  0.047   0.198   2379
  Planarity :  0.006   0.061   2203
  Dihedral  : 24.571 172.764   3215
  Min Nonbonded Distance : 1.997

Molprobity Statistics.
  All-atom Clashscore : 26.05
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.00 %
    Favored  : 95.00 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  6.94 %
    Favored  : 93.06 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.38 (0.20), residues: 1459
  helix: -0.14 (0.19), residues: 673
  sheet: -1.59 (0.32), residues: 212
  loop : -1.44 (0.24), residues: 574

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.020   0.003   TRP B  83 
 HIS   0.007   0.001   HIS E  29 
 PHE   0.026   0.003   PHE K 224 
 TYR   0.036   0.003   TYR E 229 
 ARG   0.009   0.001   ARG D  77 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.08322 (  672)
  hydrogen bonds       : angle       5.37725 ( 1831)
  covalent geometry    : bond        0.00834 (15146)
  covalent geometry    : angle       0.81118 (21110)

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

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

  2918 Ramachandran restraints generated.
    1459 Oldfield, 0 Emsley, 1459 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2918 Ramachandran restraints generated.
    1459 Oldfield, 0 Emsley, 1459 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  248 residues out of total 1210 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 248
  time to evaluate  : 1.356 
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: K  158 GLU cc_start: 0.6712 (mp0) cc_final: 0.6462 (mp0)
REVERT: K  271 ARG cc_start: 0.8222 (mtt180) cc_final: 0.7782 (mmt180)
REVERT: D   41 GLU cc_start: 0.8539 (mp0) cc_final: 0.7714 (mp0)
REVERT: D   63 ARG cc_start: 0.8263 (mmt180) cc_final: 0.7679 (mmm160)
REVERT: D   69 ASP cc_start: 0.8611 (t70) cc_final: 0.8068 (t70)
REVERT: A   20 THR cc_start: 0.9142 (p) cc_final: 0.8893 (t)
REVERT: B  125 MET cc_start: 0.8599 (mpp) cc_final: 0.8382 (mpp)
REVERT: B  217 HIS cc_start: 0.9183 (t-90) cc_final: 0.8863 (t70)
REVERT: C  141 GLN cc_start: 0.8960 (mp10) cc_final: 0.8723 (mp10)
REVERT: C  184 GLN cc_start: 0.9197 (pm20) cc_final: 0.8830 (pm20)
REVERT: C  282 ILE cc_start: 0.9210 (mm) cc_final: 0.8851 (mm)
REVERT: E  272 MET cc_start: 0.8929 (mpp) cc_final: 0.8620 (mpp)
REVERT: F   15 LEU cc_start: 0.9393 (mt) cc_final: 0.9164 (mt)
REVERT: F  198 HIS cc_start: 0.8465 (t70) cc_final: 0.8200 (t-90)
  outliers start: 0
  outliers final: 0
  residues processed: 248
  average time/residue: 0.2648
  time to fit residues: 95.9143
Evaluate side-chains
  198 residues out of total 1210 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 198
  time to evaluate  : 1.417 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 159
   random chunks:
   chunk 152 optimal weight:    6.9990
   chunk 22 optimal weight:    0.8980
   chunk 73 optimal weight:    5.9990
   chunk 21 optimal weight:    0.9990
   chunk 100 optimal weight:   10.0000
   chunk 52 optimal weight:    0.0170
   chunk 153 optimal weight:    8.9990
   chunk 2 optimal weight:   20.0000
   chunk 128 optimal weight:    0.9990
   chunk 4 optimal weight:   30.0000
   chunk 32 optimal weight:    2.9990
   overall best weight:    1.1824

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

Flipped N/Q/H residues before XYZ refinement:
** K 212 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 190 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 142 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 146 HIS
** C 217 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
F  33 ASN
F 184 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4001 r_free = 0.4001 target = 0.100549 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3483 r_free = 0.3483 target = 0.077232 restraints weight = 90018.569|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 45)----------------|
| r_work = 0.3546 r_free = 0.3546 target = 0.079607 restraints weight = 48653.026|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.3583 r_free = 0.3583 target = 0.081181 restraints weight = 32920.932|
|-----------------------------------------------------------------------------|
r_work (final): 0.3563
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3563
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3563 r_free = 0.3563    target_work(ls_wunit_k1) = 0.080         |
| occupancies: max = 1.00  min = 0.18   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3562 r_free = 0.3562    target_work(ls_wunit_k1) = 0.080         |
| occupancies: max = 1.00  min = 0.31   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3562
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7532
moved from start:          0.3178

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039  15146  Z= 0.161
  Angle     :  0.631   6.765  21110  Z= 0.345
  Chirality :  0.042   0.174   2379
  Planarity :  0.004   0.055   2203
  Dihedral  : 24.556 177.751   3215
  Min Nonbonded Distance : 2.148

Molprobity Statistics.
  All-atom Clashscore : 17.26
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.88 %
    Favored  : 97.12 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.89 %
    Favored  : 97.11 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.95 (0.21), residues: 1459
  helix:  0.33 (0.19), residues: 673
  sheet: -1.48 (0.31), residues: 217
  loop : -1.33 (0.24), residues: 569

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.050   0.003   TRP B  83 
 HIS   0.006   0.001   HIS E  29 
 PHE   0.022   0.002   PHE K 224 
 TYR   0.031   0.002   TYR E 229 
 ARG   0.015   0.001   ARG C 156 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05490 (  672)
  hydrogen bonds       : angle       4.66192 ( 1831)
  covalent geometry    : bond        0.00349 (15146)
  covalent geometry    : angle       0.63083 (21110)

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

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

  2918 Ramachandran restraints generated.
    1459 Oldfield, 0 Emsley, 1459 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2918 Ramachandran restraints generated.
    1459 Oldfield, 0 Emsley, 1459 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  276 residues out of total 1210 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 276
  time to evaluate  : 2.587 
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: K  192 GLU cc_start: 0.7599 (pt0) cc_final: 0.7288 (mt-10)
REVERT: K  220 LEU cc_start: 0.6409 (tt) cc_final: 0.6195 (tt)
REVERT: K  271 ARG cc_start: 0.8321 (mtt180) cc_final: 0.7861 (mmt180)
REVERT: D   38 ARG cc_start: 0.8591 (tmm-80) cc_final: 0.8132 (tmm-80)
REVERT: D   41 GLU cc_start: 0.8519 (mp0) cc_final: 0.7745 (mp0)
REVERT: D   69 ASP cc_start: 0.8438 (t70) cc_final: 0.8049 (t70)
REVERT: A   20 THR cc_start: 0.9121 (p) cc_final: 0.8869 (t)
REVERT: A   49 GLU cc_start: 0.8839 (mm-30) cc_final: 0.8163 (pt0)
REVERT: A   77 ARG cc_start: 0.8515 (mtt90) cc_final: 0.8030 (mtt-85)
REVERT: B   84 VAL cc_start: 0.8097 (m) cc_final: 0.7029 (m)
REVERT: B  134 ASP cc_start: 0.9132 (m-30) cc_final: 0.8463 (t0)
REVERT: B  163 ASN cc_start: 0.9033 (m-40) cc_final: 0.8800 (m-40)
REVERT: B  217 HIS cc_start: 0.9146 (t-90) cc_final: 0.8764 (t70)
REVERT: C   81 LEU cc_start: 0.8807 (mm) cc_final: 0.8604 (mm)
REVERT: C  184 GLN cc_start: 0.9165 (pm20) cc_final: 0.8939 (pm20)
REVERT: C  282 ILE cc_start: 0.9124 (mm) cc_final: 0.8820 (mm)
REVERT: E   90 ARG cc_start: 0.7598 (ttm110) cc_final: 0.7177 (mtm110)
REVERT: E  272 MET cc_start: 0.9032 (mpp) cc_final: 0.8809 (mpp)
REVERT: F   15 LEU cc_start: 0.9228 (mt) cc_final: 0.9015 (mt)
REVERT: F  128 MET cc_start: 0.7486 (pmm) cc_final: 0.7285 (pmm)
  outliers start: 0
  outliers final: 0
  residues processed: 276
  average time/residue: 0.3610
  time to fit residues: 143.2486
Evaluate side-chains
  216 residues out of total 1210 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 216
  time to evaluate  : 1.558 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 159
   random chunks:
   chunk 87 optimal weight:    4.9990
   chunk 126 optimal weight:    8.9990
   chunk 11 optimal weight:    9.9990
   chunk 43 optimal weight:    6.9990
   chunk 89 optimal weight:    6.9990
   chunk 48 optimal weight:    1.9990
   chunk 151 optimal weight:    6.9990
   chunk 82 optimal weight:    3.9990
   chunk 155 optimal weight:    6.9990
   chunk 60 optimal weight:   20.0000
   chunk 0 optimal weight:   30.0000
   overall best weight:    4.9990

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

Flipped N/Q/H residues before XYZ refinement:
** K 212 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 190 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
C 146 HIS
C 183 ASN
** C 184 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 217 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
C 253 GLN
** F 184 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3922 r_free = 0.3922 target = 0.095804 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3397 r_free = 0.3397 target = 0.072939 restraints weight = 99814.359|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 43)----------------|
| r_work = 0.3459 r_free = 0.3459 target = 0.075139 restraints weight = 53645.655|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3493 r_free = 0.3493 target = 0.076598 restraints weight = 35824.555|
|-----------------------------------------------------------------------------|
r_work (final): 0.3461
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3461
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3461 r_free = 0.3461    target_work(ls_wunit_k1) = 0.075         |
| occupancies: max = 1.00  min = 0.31   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3461 r_free = 0.3461    target_work(ls_wunit_k1) = 0.075         |
| occupancies: max = 1.00  min = 0.29   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3461
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7657
moved from start:          0.3387

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.049  15146  Z= 0.289
  Angle     :  0.706   7.370  21110  Z= 0.388
  Chirality :  0.045   0.176   2379
  Planarity :  0.005   0.057   2203
  Dihedral  : 24.708 174.696   3215
  Min Nonbonded Distance : 2.032

Molprobity Statistics.
  All-atom Clashscore : 23.47
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.46 %
    Favored  : 95.54 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  3.22 %
    Favored  : 96.78 %
  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: -1.24 (0.21), residues: 1459
  helix:  0.08 (0.19), residues: 676
  sheet: -1.62 (0.32), residues: 215
  loop : -1.48 (0.24), residues: 568

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.002   TRP B  83 
 HIS   0.009   0.001   HIS E  29 
 PHE   0.025   0.002   PHE B  24 
 TYR   0.031   0.002   TYR E 229 
 ARG   0.007   0.001   ARG D  77 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.06857 (  672)
  hydrogen bonds       : angle       4.98147 ( 1831)
  covalent geometry    : bond        0.00629 (15146)
  covalent geometry    : angle       0.70592 (21110)

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

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

  2918 Ramachandran restraints generated.
    1459 Oldfield, 0 Emsley, 1459 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2918 Ramachandran restraints generated.
    1459 Oldfield, 0 Emsley, 1459 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  255 residues out of total 1210 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 255
  time to evaluate  : 1.457 
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: K  142 ARG cc_start: 0.6214 (mtt180) cc_final: 0.4270 (mtm180)
REVERT: K  192 GLU cc_start: 0.7550 (pt0) cc_final: 0.7279 (mt-10)
REVERT: K  271 ARG cc_start: 0.8386 (mtt180) cc_final: 0.7888 (mmt180)
REVERT: D   41 GLU cc_start: 0.8506 (mp0) cc_final: 0.7698 (mp0)
REVERT: D   63 ARG cc_start: 0.8290 (mmt180) cc_final: 0.7576 (mmm160)
REVERT: D   69 ASP cc_start: 0.8509 (t70) cc_final: 0.8060 (t70)
REVERT: A   20 THR cc_start: 0.9155 (p) cc_final: 0.8921 (t)
REVERT: A   77 ARG cc_start: 0.8507 (mtt90) cc_final: 0.7833 (mtt90)
REVERT: B  134 ASP cc_start: 0.9062 (m-30) cc_final: 0.8386 (t0)
REVERT: B  163 ASN cc_start: 0.9014 (m-40) cc_final: 0.8798 (m-40)
REVERT: B  217 HIS cc_start: 0.9169 (t-90) cc_final: 0.8896 (t70)
REVERT: C  184 GLN cc_start: 0.9220 (pm20) cc_final: 0.8968 (pm20)
REVERT: E  272 MET cc_start: 0.8927 (mpp) cc_final: 0.8696 (mpp)
REVERT: F  128 MET cc_start: 0.7706 (pmm) cc_final: 0.7505 (pmm)
REVERT: F  198 HIS cc_start: 0.8301 (t-90) cc_final: 0.7914 (t-90)
  outliers start: 0
  outliers final: 0
  residues processed: 255
  average time/residue: 0.3006
  time to fit residues: 112.2173
Evaluate side-chains
  203 residues out of total 1210 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 203
  time to evaluate  : 1.426 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 159
   random chunks:
   chunk 96 optimal weight:    5.9990
   chunk 95 optimal weight:    1.9990
   chunk 108 optimal weight:    9.9990
   chunk 79 optimal weight:    1.9990
   chunk 17 optimal weight:    8.9990
   chunk 86 optimal weight:    0.9980
   chunk 152 optimal weight:    8.9990
   chunk 12 optimal weight:   10.0000
   chunk 78 optimal weight:    3.9990
   chunk 66 optimal weight:   10.0000
   chunk 32 optimal weight:    0.5980
   overall best weight:    1.9186

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

Flipped N/Q/H residues before XYZ refinement:
** K 212 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
C 146 HIS
** C 217 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** F 184 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 = 0.3979 r_free = 0.3979 target = 0.099400 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3486 r_free = 0.3486 target = 0.077401 restraints weight = 70719.078|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 41)----------------|
| r_work = 0.3540 r_free = 0.3540 target = 0.079464 restraints weight = 42444.279|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.3573 r_free = 0.3573 target = 0.080847 restraints weight = 29945.734|
|-----------------------------------------------------------------------------|
r_work (final): 0.3552
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3551
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3551 r_free = 0.3551    target_work(ls_wunit_k1) = 0.080         |
| occupancies: max = 1.00  min = 0.29   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3551 r_free = 0.3551    target_work(ls_wunit_k1) = 0.080         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3551
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7556
moved from start:          0.3488

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.049  15146  Z= 0.173
  Angle     :  0.641   7.782  21110  Z= 0.351
  Chirality :  0.043   0.182   2379
  Planarity :  0.004   0.068   2203
  Dihedral  : 24.724 179.806   3215
  Min Nonbonded Distance : 2.124

Molprobity Statistics.
  All-atom Clashscore : 17.40
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.36 %
    Favored  : 96.64 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.15 %
    Favored  : 97.85 %
  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: -1.06 (0.21), residues: 1459
  helix:  0.23 (0.19), residues: 679
  sheet: -1.49 (0.32), residues: 210
  loop : -1.42 (0.24), residues: 570

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.030   0.002   TRP B  83 
 HIS   0.008   0.001   HIS E  29 
 PHE   0.027   0.002   PHE K 224 
 TYR   0.028   0.002   TYR B 194 
 ARG   0.006   0.001   ARG C 169 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05464 (  672)
  hydrogen bonds       : angle       4.69558 ( 1831)
  covalent geometry    : bond        0.00385 (15146)
  covalent geometry    : angle       0.64133 (21110)

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

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

  2918 Ramachandran restraints generated.
    1459 Oldfield, 0 Emsley, 1459 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2918 Ramachandran restraints generated.
    1459 Oldfield, 0 Emsley, 1459 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  263 residues out of total 1210 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 263
  time to evaluate  : 1.464 
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: K  142 ARG cc_start: 0.6205 (mtt180) cc_final: 0.4312 (mtm180)
REVERT: K  192 GLU cc_start: 0.7462 (pt0) cc_final: 0.7126 (mt-10)
REVERT: K  220 LEU cc_start: 0.6342 (tt) cc_final: 0.6090 (tt)
REVERT: K  271 ARG cc_start: 0.8440 (mtt180) cc_final: 0.7903 (mmt180)
REVERT: D   38 ARG cc_start: 0.8694 (tmm-80) cc_final: 0.8489 (tmm-80)
REVERT: D   69 ASP cc_start: 0.8459 (t70) cc_final: 0.8187 (t70)
REVERT: A   77 ARG cc_start: 0.8520 (mtt90) cc_final: 0.8023 (mtt-85)
REVERT: B   84 VAL cc_start: 0.8155 (m) cc_final: 0.7292 (m)
REVERT: B  134 ASP cc_start: 0.9147 (m-30) cc_final: 0.8480 (t0)
REVERT: B  163 ASN cc_start: 0.9010 (m-40) cc_final: 0.8797 (m-40)
REVERT: B  217 HIS cc_start: 0.9144 (t-90) cc_final: 0.8838 (t70)
REVERT: C  282 ILE cc_start: 0.9221 (mm) cc_final: 0.8972 (mm)
REVERT: E  272 MET cc_start: 0.8982 (mpp) cc_final: 0.8763 (mpp)
REVERT: F   15 LEU cc_start: 0.9282 (mt) cc_final: 0.8999 (mt)
REVERT: F   19 GLU cc_start: 0.7940 (mm-30) cc_final: 0.7475 (tp30)
REVERT: F  128 MET cc_start: 0.7693 (pmm) cc_final: 0.7492 (pmm)
REVERT: F  270 LYS cc_start: 0.9538 (tptt) cc_final: 0.9284 (mmmt)
  outliers start: 0
  outliers final: 0
  residues processed: 263
  average time/residue: 0.2808
  time to fit residues: 106.5407
Evaluate side-chains
  214 residues out of total 1210 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 214
  time to evaluate  : 1.520 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 159
   random chunks:
   chunk 75 optimal weight:    4.9990
   chunk 65 optimal weight:    9.9990
   chunk 124 optimal weight:    6.9990
   chunk 20 optimal weight:    6.9990
   chunk 71 optimal weight:    0.9980
   chunk 6 optimal weight:   20.0000
   chunk 2 optimal weight:    7.9990
   chunk 123 optimal weight:    1.9990
   chunk 125 optimal weight:    5.9990
   chunk 43 optimal weight:    4.9990
   chunk 154 optimal weight:    8.9990
   overall best weight:    3.7988

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

Flipped N/Q/H residues before XYZ refinement:
** K 212 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
K 287 ASN
C 146 HIS
C 183 ASN
** C 217 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
C 253 GLN
F 184 GLN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3933 r_free = 0.3933 target = 0.096463 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3414 r_free = 0.3414 target = 0.073976 restraints weight = 84760.479|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 41)----------------|
| r_work = 0.3473 r_free = 0.3473 target = 0.075969 restraints weight = 48332.268|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3504 r_free = 0.3504 target = 0.077287 restraints weight = 33501.368|
|-----------------------------------------------------------------------------|
r_work (final): 0.3478
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3478
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3478 r_free = 0.3478    target_work(ls_wunit_k1) = 0.076         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3478 r_free = 0.3478    target_work(ls_wunit_k1) = 0.076         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3478
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7640
moved from start:          0.3684

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.047  15146  Z= 0.242
  Angle     :  0.686   7.970  21110  Z= 0.376
  Chirality :  0.044   0.205   2379
  Planarity :  0.005   0.062   2203
  Dihedral  : 24.787 175.647   3215
  Min Nonbonded Distance : 2.045

Molprobity Statistics.
  All-atom Clashscore : 21.72
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.52 %
    Favored  : 95.48 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.07 %
    Favored  : 97.93 %
  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: -1.24 (0.21), residues: 1459
  helix:  0.08 (0.19), residues: 679
  sheet: -1.57 (0.32), residues: 222
  loop : -1.51 (0.24), residues: 558

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.019   0.002   TRP B  83 
 HIS   0.008   0.001   HIS E  29 
 PHE   0.030   0.002   PHE K 224 
 TYR   0.028   0.002   TYR E 229 
 ARG   0.008   0.001   ARG B 150 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.06318 (  672)
  hydrogen bonds       : angle       4.85289 ( 1831)
  covalent geometry    : bond        0.00532 (15146)
  covalent geometry    : angle       0.68578 (21110)

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

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

  2918 Ramachandran restraints generated.
    1459 Oldfield, 0 Emsley, 1459 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2918 Ramachandran restraints generated.
    1459 Oldfield, 0 Emsley, 1459 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  253 residues out of total 1210 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 253
  time to evaluate  : 1.984 
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: K  142 ARG cc_start: 0.6285 (mtt180) cc_final: 0.4313 (mtm180)
REVERT: K  192 GLU cc_start: 0.7481 (pt0) cc_final: 0.7163 (mt-10)
REVERT: K  220 LEU cc_start: 0.6513 (tt) cc_final: 0.6262 (tt)
REVERT: K  271 ARG cc_start: 0.8459 (mtt180) cc_final: 0.7910 (mmt180)
REVERT: D   38 ARG cc_start: 0.8711 (tmm-80) cc_final: 0.8473 (tmm-80)
REVERT: D   41 GLU cc_start: 0.8420 (mp0) cc_final: 0.8118 (mp0)
REVERT: D   63 ARG cc_start: 0.8243 (mmt180) cc_final: 0.7537 (mmm160)
REVERT: D   69 ASP cc_start: 0.8503 (t70) cc_final: 0.8061 (t70)
REVERT: D   70 PHE cc_start: 0.8185 (m-10) cc_final: 0.7911 (m-10)
REVERT: A   77 ARG cc_start: 0.8447 (mtt90) cc_final: 0.8224 (mtt90)
REVERT: B  217 HIS cc_start: 0.9139 (t-90) cc_final: 0.8885 (t70)
REVERT: C   81 LEU cc_start: 0.8907 (mm) cc_final: 0.8697 (mm)
REVERT: C  277 GLN cc_start: 0.8269 (tp-100) cc_final: 0.8057 (tp-100)
REVERT: E  128 MET cc_start: 0.8850 (tpp) cc_final: 0.8619 (tpp)
REVERT: E  272 MET cc_start: 0.8930 (mpp) cc_final: 0.8700 (mpp)
REVERT: F   15 LEU cc_start: 0.9306 (mt) cc_final: 0.9046 (mt)
REVERT: F   17 ARG cc_start: 0.8412 (mtm-85) cc_final: 0.7852 (ptp-170)
REVERT: F   19 GLU cc_start: 0.8117 (mm-30) cc_final: 0.7638 (tp30)
REVERT: F  128 MET cc_start: 0.7757 (pmm) cc_final: 0.7539 (pmm)
  outliers start: 0
  outliers final: 0
  residues processed: 253
  average time/residue: 0.2857
  time to fit residues: 104.9996
Evaluate side-chains
  205 residues out of total 1210 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 205
  time to evaluate  : 1.444 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 159
   random chunks:
   chunk 56 optimal weight:    0.8980
   chunk 84 optimal weight:    1.9990
   chunk 120 optimal weight:    1.9990
   chunk 112 optimal weight:    1.9990
   chunk 43 optimal weight:    8.9990
   chunk 42 optimal weight:    5.9990
   chunk 37 optimal weight:    1.9990
   chunk 58 optimal weight:    6.9990
   chunk 15 optimal weight:    0.8980
   chunk 55 optimal weight:    0.9990
   chunk 103 optimal weight:    1.9990
   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 142 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 146 HIS
** C 217 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
C 253 GLN
F 184 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3989 r_free = 0.3989 target = 0.099388 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3493 r_free = 0.3493 target = 0.077196 restraints weight = 70734.843|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 42)----------------|
| r_work = 0.3550 r_free = 0.3550 target = 0.079192 restraints weight = 41464.060|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3579 r_free = 0.3579 target = 0.080420 restraints weight = 29345.830|
|-----------------------------------------------------------------------------|
r_work (final): 0.3561
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3561
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3561 r_free = 0.3561    target_work(ls_wunit_k1) = 0.079         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3561 r_free = 0.3561    target_work(ls_wunit_k1) = 0.079         |
| occupancies: max = 1.00  min = 0.31   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3561
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7545
moved from start:          0.3770

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.040  15146  Z= 0.159
  Angle     :  0.649   9.225  21110  Z= 0.352
  Chirality :  0.043   0.186   2379
  Planarity :  0.004   0.057   2203
  Dihedral  : 24.760 179.320   3215
  Min Nonbonded Distance : 2.124

Molprobity Statistics.
  All-atom Clashscore : 17.79
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.77 %
    Favored  : 96.23 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.91 %
    Favored  : 99.09 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.97 (0.21), residues: 1459
  helix:  0.33 (0.20), residues: 676
  sheet: -1.61 (0.31), residues: 226
  loop : -1.31 (0.24), residues: 557

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.002   TRP A  22 
 HIS   0.008   0.001   HIS E  29 
 PHE   0.027   0.002   PHE K 224 
 TYR   0.028   0.002   TYR E 229 
 ARG   0.010   0.001   ARG K 152 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05280 (  672)
  hydrogen bonds       : angle       4.61907 ( 1831)
  covalent geometry    : bond        0.00356 (15146)
  covalent geometry    : angle       0.64855 (21110)

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

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

  2918 Ramachandran restraints generated.
    1459 Oldfield, 0 Emsley, 1459 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2918 Ramachandran restraints generated.
    1459 Oldfield, 0 Emsley, 1459 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  265 residues out of total 1210 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 265
  time to evaluate  : 1.396 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: K  142 ARG cc_start: 0.6236 (mtt180) cc_final: 0.4306 (mtm180)
REVERT: K  192 GLU cc_start: 0.7479 (pt0) cc_final: 0.7180 (mt-10)
REVERT: K  220 LEU cc_start: 0.6503 (tt) cc_final: 0.6235 (tt)
REVERT: K  271 ARG cc_start: 0.8449 (mtt180) cc_final: 0.7853 (mmp-170)
REVERT: D   38 ARG cc_start: 0.8624 (tmm-80) cc_final: 0.8351 (tmm-80)
REVERT: D   41 GLU cc_start: 0.8407 (mp0) cc_final: 0.8059 (mp0)
REVERT: D   69 ASP cc_start: 0.8386 (t70) cc_final: 0.8179 (t70)
REVERT: A   77 ARG cc_start: 0.8424 (mtt90) cc_final: 0.8204 (mtt-85)
REVERT: B   60 LEU cc_start: 0.7443 (mt) cc_final: 0.6792 (mt)
REVERT: B  134 ASP cc_start: 0.9222 (m-30) cc_final: 0.8543 (t0)
REVERT: B  163 ASN cc_start: 0.9020 (m-40) cc_final: 0.8807 (m-40)
REVERT: B  217 HIS cc_start: 0.9096 (t-90) cc_final: 0.8822 (t70)
REVERT: C  162 TYR cc_start: 0.7943 (m-10) cc_final: 0.7563 (m-10)
REVERT: C  190 HIS cc_start: 0.8024 (m90) cc_final: 0.7811 (m90)
REVERT: C  277 GLN cc_start: 0.8309 (tp-100) cc_final: 0.8061 (tp-100)
REVERT: E   91 TYR cc_start: 0.8754 (t80) cc_final: 0.8483 (t80)
REVERT: E  171 TYR cc_start: 0.8052 (p90) cc_final: 0.7373 (p90)
REVERT: E  272 MET cc_start: 0.8996 (mpp) cc_final: 0.8755 (mpp)
REVERT: F   15 LEU cc_start: 0.9266 (mt) cc_final: 0.9004 (mt)
REVERT: F   19 GLU cc_start: 0.7927 (mm-30) cc_final: 0.7495 (tp30)
REVERT: F  128 MET cc_start: 0.7691 (pmm) cc_final: 0.7490 (pmm)
  outliers start: 0
  outliers final: 0
  residues processed: 265
  average time/residue: 0.2578
  time to fit residues: 99.4501
Evaluate side-chains
  211 residues out of total 1210 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 211
  time to evaluate  : 1.308 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 159
   random chunks:
   chunk 94 optimal weight:    4.9990
   chunk 22 optimal weight:    4.9990
   chunk 58 optimal weight:    4.9990
   chunk 109 optimal weight:    8.9990
   chunk 98 optimal weight:    6.9990
   chunk 101 optimal weight:    5.9990
   chunk 41 optimal weight:    9.9990
   chunk 147 optimal weight:   10.0000
   chunk 30 optimal weight:    0.9980
   chunk 29 optimal weight:    4.9990
   chunk 105 optimal weight:    0.9990
   overall best weight:    3.3988

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

Flipped N/Q/H residues before XYZ refinement:
** K 212 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 190 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 142 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 146 HIS
C 183 ASN
** C 217 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
C 253 GLN
** E  29 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
F 184 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3950 r_free = 0.3950 target = 0.097464 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3415 r_free = 0.3415 target = 0.073909 restraints weight = 100555.302|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.3480 r_free = 0.3480 target = 0.076180 restraints weight = 53259.972|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 42)----------------|
| r_work = 0.3517 r_free = 0.3517 target = 0.077771 restraints weight = 35726.548|
|-----------------------------------------------------------------------------|
r_work (final): 0.3490
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3490
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3490 r_free = 0.3490    target_work(ls_wunit_k1) = 0.076         |
| occupancies: max = 1.00  min = 0.31   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3490 r_free = 0.3490    target_work(ls_wunit_k1) = 0.076         |
| occupancies: max = 1.00  min = 0.31   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3490
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7622
moved from start:          0.3877

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.039  15146  Z= 0.226
  Angle     :  0.693   9.135  21110  Z= 0.379
  Chirality :  0.044   0.198   2379
  Planarity :  0.005   0.057   2203
  Dihedral  : 24.774 176.539   3215
  Min Nonbonded Distance : 2.054

Molprobity Statistics.
  All-atom Clashscore : 21.47
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.39 %
    Favored  : 95.61 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.50 %
    Favored  : 99.50 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.13 (0.21), residues: 1459
  helix:  0.21 (0.19), residues: 678
  sheet: -1.68 (0.32), residues: 216
  loop : -1.43 (0.24), residues: 565

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.032   0.002   TRP B  83 
 HIS   0.007   0.001   HIS E  29 
 PHE   0.030   0.002   PHE A  70 
 TYR   0.040   0.002   TYR B 194 
 ARG   0.011   0.001   ARG E  34 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05990 (  672)
  hydrogen bonds       : angle       4.82373 ( 1831)
  covalent geometry    : bond        0.00498 (15146)
  covalent geometry    : angle       0.69277 (21110)

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

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

  2918 Ramachandran restraints generated.
    1459 Oldfield, 0 Emsley, 1459 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2918 Ramachandran restraints generated.
    1459 Oldfield, 0 Emsley, 1459 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  243 residues out of total 1210 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 243
  time to evaluate  : 1.341 
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: K  142 ARG cc_start: 0.6209 (mtt180) cc_final: 0.4275 (mtm180)
REVERT: K  219 PHE cc_start: 0.3648 (t80) cc_final: 0.3403 (t80)
REVERT: K  220 LEU cc_start: 0.6409 (tt) cc_final: 0.6124 (tt)
REVERT: K  271 ARG cc_start: 0.8415 (mtt180) cc_final: 0.7909 (mmp-170)
REVERT: D   38 ARG cc_start: 0.8662 (tmm-80) cc_final: 0.8130 (tmm-80)
REVERT: D   41 GLU cc_start: 0.8476 (mp0) cc_final: 0.7744 (mp0)
REVERT: D   69 ASP cc_start: 0.8566 (t70) cc_final: 0.8131 (t70)
REVERT: D   70 PHE cc_start: 0.8234 (m-10) cc_final: 0.7918 (m-10)
REVERT: A   77 ARG cc_start: 0.8561 (mtt90) cc_final: 0.8308 (mtt90)
REVERT: B   86 GLU cc_start: 0.7937 (tp30) cc_final: 0.7722 (tp30)
REVERT: B  217 HIS cc_start: 0.9162 (t-90) cc_final: 0.8525 (t70)
REVERT: B  223 TYR cc_start: 0.7932 (m-80) cc_final: 0.7548 (m-80)
REVERT: E  272 MET cc_start: 0.8970 (mpp) cc_final: 0.8752 (mpp)
REVERT: F   15 LEU cc_start: 0.9300 (mt) cc_final: 0.9024 (mt)
REVERT: F  128 MET cc_start: 0.7710 (pmm) cc_final: 0.7484 (pmm)
  outliers start: 0
  outliers final: 0
  residues processed: 243
  average time/residue: 0.2678
  time to fit residues: 95.1263
Evaluate side-chains
  198 residues out of total 1210 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 198
  time to evaluate  : 1.506 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 159
   random chunks:
   chunk 98 optimal weight:    3.9990
   chunk 26 optimal weight:    0.8980
   chunk 117 optimal weight:    3.9990
   chunk 75 optimal weight:    6.9990
   chunk 36 optimal weight:   10.0000
   chunk 93 optimal weight:    0.8980
   chunk 53 optimal weight:    3.9990
   chunk 127 optimal weight:   10.0000
   chunk 128 optimal weight:    0.4980
   chunk 15 optimal weight:    1.9990
   chunk 13 optimal weight:    0.0770
   overall best weight:    0.8740

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

Flipped N/Q/H residues before XYZ refinement:
** K 212 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** D  34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 142 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 190 HIS
C 146 HIS
** C 217 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
F 184 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4016 r_free = 0.4016 target = 0.100472 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3495 r_free = 0.3495 target = 0.076988 restraints weight = 92715.748|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3557 r_free = 0.3557 target = 0.079356 restraints weight = 49241.915|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3596 r_free = 0.3596 target = 0.081014 restraints weight = 32726.877|
|-----------------------------------------------------------------------------|
r_work (final): 0.3574
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3574
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3574 r_free = 0.3574    target_work(ls_wunit_k1) = 0.080         |
| occupancies: max = 1.00  min = 0.31   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3574 r_free = 0.3574    target_work(ls_wunit_k1) = 0.080         |
| occupancies: max = 1.00  min = 0.33   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3574
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7530
moved from start:          0.4010

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041  15146  Z= 0.152
  Angle     :  0.664   9.382  21110  Z= 0.359
  Chirality :  0.043   0.214   2379
  Planarity :  0.004   0.058   2203
  Dihedral  : 24.714 178.284   3215
  Min Nonbonded Distance : 2.124

Molprobity Statistics.
  All-atom Clashscore : 16.86
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.43 %
    Favored  : 96.57 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.33 %
    Favored  : 99.67 %
  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: -0.96 (0.21), residues: 1459
  helix:  0.36 (0.19), residues: 683
  sheet: -1.59 (0.31), residues: 226
  loop : -1.35 (0.24), residues: 550

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.002   TRP E  83 
 HIS   0.007   0.001   HIS E  29 
 PHE   0.023   0.001   PHE K 224 
 TYR   0.033   0.002   TYR B 194 
 ARG   0.009   0.000   ARG E  34 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05229 (  672)
  hydrogen bonds       : angle       4.56257 ( 1831)
  covalent geometry    : bond        0.00337 (15146)
  covalent geometry    : angle       0.66376 (21110)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 6199.09 seconds
wall clock time: 110 minutes 42.89 seconds (6642.89 seconds total)