Starting phenix.real_space_refine
on Wed Mar  4 15:10:28 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8fyc_29564/03_2026/8fyc_29564.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8fyc_29564/03_2026/8fyc_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_29564/03_2026/8fyc_29564.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8fyc_29564/03_2026/8fyc_29564.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8fyc_29564/03_2026/8fyc_29564.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8fyc_29564/03_2026/8fyc_29564.cif"
  }
  resolution = 4.1
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/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: 3.47, per 1000 atoms: 0.24
  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: 1.33
  Conformation dependent library (CDL) restraints added in 570.9 milliseconds
  

  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: 1.88
  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: 2.70

  Time building geometry restraints manager: 1.70 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:             1.270
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.240
  Check model and map are aligned:         0.040
  Set scattering table:                    0.040
  Process input model:                     15.760
  Find NCS groups from input model:        0.150
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.010
  Load rotamer database and sin/cos tables:1.410
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   18.950
-------------------------------------------------------------------------------
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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  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
 ARG   0.006   0.000   ARG F 116 
 TYR   0.012   0.001   TYR F  91 
 PHE   0.019   0.001   PHE K 224 
 TRP   0.017   0.002   TRP A  44 
 HIS   0.005   0.001   HIS E  29 

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

*********************** 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  : 0.458 
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: 0.8507 (tt)
REVERT: B   86 GLU cc_start: 0.8038 (tp30) cc_final: 0.7832 (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: 0.7452 (m-70)
  outliers start: 3
  outliers final: 0
  residues processed: 301
  average time/residue: 0.1343
  time to fit residues: 57.6703
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  : 0.487 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 159
   random chunks:
   chunk 98 optimal weight:    9.9990
   chunk 107 optimal weight:    9.9990
   chunk 10 optimal weight:    2.9990
   chunk 66 optimal weight:    1.9990
   chunk 130 optimal weight:    9.9990
   chunk 124 optimal weight:    4.9990
   chunk 103 optimal weight:    9.9990
   chunk 77 optimal weight:    0.9990
   chunk 122 optimal weight:    0.9990
   chunk 91 optimal weight:    6.9990
   chunk 149 optimal weight:    5.9990
   overall best weight:    2.3990

-------------------------------------------------------------------------------
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 ** both conformations clash, **PLEASE CHECK MANUALLY**
K 222 GLN
K 287 ASN
** D  48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** 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: 9

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3979 r_free = 0.3979 target = 0.099182 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3474 r_free = 0.3474 target = 0.076583 restraints weight = 76888.590|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 41)----------------|
| r_work = 0.3535 r_free = 0.3535 target = 0.078707 restraints weight = 44076.222|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3567 r_free = 0.3567 target = 0.080029 restraints weight = 30696.185|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 39)----------------|
| r_work = 0.3590 r_free = 0.3590 target = 0.081001 restraints weight = 24529.763|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 25)----------------|
| r_work = 0.3603 r_free = 0.3603 target = 0.081538 restraints weight = 21178.976|
|-----------------------------------------------------------------------------|
r_work (final): 0.3581
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3581
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3581 r_free = 0.3581    target_work(ls_wunit_k1) = 0.081         |
| occupancies: max = 1.00  min = 0.26   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3580 r_free = 0.3580    target_work(ls_wunit_k1) = 0.081         |
| occupancies: max = 1.00  min = 0.31   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3580
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7511
moved from start:          0.1877

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.045  15146  Z= 0.201
  Angle     :  0.648   6.862  21110  Z= 0.365
  Chirality :  0.042   0.156   2379
  Planarity :  0.004   0.048   2203
  Dihedral  : 23.997 179.474   3215
  Min Nonbonded Distance : 2.179

Molprobity Statistics.
  All-atom Clashscore : 17.11
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.43 %
    Favored  : 96.57 %
  Rotamer:
    Outliers :  0.08 %
    Allowed  :  6.69 %
    Favored  : 93.22 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.72 (0.21), residues: 1459
  helix:  0.46 (0.19), residues: 665
  sheet: -1.26 (0.33), residues: 216
  loop : -1.17 (0.24), residues: 578

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG C 129 
 TYR   0.018   0.002   TYR B 194 
 PHE   0.019   0.002   PHE K 202 
 TRP   0.014   0.002   TRP D  44 
 HIS   0.006   0.001   HIS E  29 

Details of bonding type rmsd
  covalent geometry    : bond        0.00433 (15146)
  covalent geometry    : angle       0.64812 (21110)
  hydrogen bonds       : bond        0.07068 (  672)
  hydrogen bonds       : angle       5.32752 ( 1831)

*********************** 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  : 0.471 
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: 0.8006 (mtt180) cc_final: 0.7634 (mmt180)
REVERT: D   69 ASP cc_start: 0.8429 (t70) cc_final: 0.8189 (t70)
REVERT: B   83 TRP cc_start: 0.9044 (m100) cc_final: 0.8792 (m100)
REVERT: B  134 ASP cc_start: 0.9075 (m-30) cc_final: 0.8561 (t0)
REVERT: B  141 GLN cc_start: 0.9397 (tm-30) cc_final: 0.9099 (tm-30)
REVERT: B  217 HIS cc_start: 0.9216 (t-90) cc_final: 0.8844 (t70)
REVERT: C   81 LEU cc_start: 0.8789 (mm) cc_final: 0.8583 (mm)
REVERT: C  282 ILE cc_start: 0.9107 (mm) cc_final: 0.8747 (mm)
REVERT: E   83 TRP cc_start: 0.8407 (m-90) cc_final: 0.7599 (m-90)
REVERT: E  272 MET cc_start: 0.9158 (mpp) cc_final: 0.8864 (mpp)
REVERT: F   15 LEU cc_start: 0.9281 (mt) cc_final: 0.9041 (mt)
REVERT: F   19 GLU cc_start: 0.8429 (mm-30) cc_final: 0.7935 (mm-30)
REVERT: F  190 HIS cc_start: 0.7595 (m170) cc_final: 0.7254 (m-70)
  outliers start: 1
  outliers final: 1
  residues processed: 274
  average time/residue: 0.1267
  time to fit residues: 51.0334
Evaluate side-chains
  208 residues out of total 1210 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 207
  time to evaluate  : 0.466 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 159
   random chunks:
   chunk 55 optimal weight:    2.9990
   chunk 158 optimal weight:   10.0000
   chunk 143 optimal weight:    8.9990
   chunk 37 optimal weight:    4.9990
   chunk 45 optimal weight:    3.9990
   chunk 24 optimal weight:    7.9990
   chunk 124 optimal weight:    0.9990
   chunk 132 optimal weight:    4.9990
   chunk 87 optimal weight:    0.6980
   chunk 105 optimal weight:    6.9990
   chunk 155 optimal weight:    5.9990
   overall best weight:    2.7388

-------------------------------------------------------------------------------
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
K 237 HIS
** D  48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 183 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 190 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 198 HIS
** C 142 GLN ** 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 = 0.3967 r_free = 0.3967 target = 0.098282 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3465 r_free = 0.3465 target = 0.075883 restraints weight = 71458.939|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3522 r_free = 0.3522 target = 0.077904 restraints weight = 42366.645|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3556 r_free = 0.3556 target = 0.079288 restraints weight = 30083.730|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 41)----------------|
| r_work = 0.3577 r_free = 0.3577 target = 0.080157 restraints weight = 23984.441|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.3589 r_free = 0.3589 target = 0.080641 restraints weight = 20855.187|
|-----------------------------------------------------------------------------|
r_work (final): 0.3564
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3565
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3565 r_free = 0.3565    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 = 0.3565 r_free = 0.3565    target_work(ls_wunit_k1) = 0.080         |
| occupancies: max = 1.00  min = 0.22   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3565
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7522
moved from start:          0.2453

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.044  15146  Z= 0.199
  Angle     :  0.628   6.693  21110  Z= 0.349
  Chirality :  0.042   0.156   2379
  Planarity :  0.004   0.049   2203
  Dihedral  : 24.194 177.302   3215
  Min Nonbonded Distance : 2.101

Molprobity Statistics.
  All-atom Clashscore : 17.61
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.56 %
    Favored  : 96.44 %
  Rotamer:
    Outliers :  0.08 %
    Allowed  :  4.88 %
    Favored  : 95.04 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.79 (0.21), residues: 1459
  helix:  0.43 (0.19), residues: 673
  sheet: -1.38 (0.33), residues: 217
  loop : -1.23 (0.24), residues: 569

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.001   ARG C 150 
 TYR   0.020   0.002   TYR K 231 
 PHE   0.018   0.002   PHE K 202 
 TRP   0.012   0.002   TRP D  44 
 HIS   0.007   0.001   HIS E  29 

Details of bonding type rmsd
  covalent geometry    : bond        0.00434 (15146)
  covalent geometry    : angle       0.62839 (21110)
  hydrogen bonds       : bond        0.06394 (  672)
  hydrogen bonds       : angle       4.96710 ( 1831)

*********************** 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
  270 residues out of total 1210 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 269
  time to evaluate  : 0.476 
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: 0.8127 (mtt180) cc_final: 0.7717 (mmt180)
REVERT: D   38 ARG cc_start: 0.8535 (tmm-80) cc_final: 0.8194 (tmm-80)
REVERT: D   41 GLU cc_start: 0.8481 (mp0) cc_final: 0.7937 (mp0)
REVERT: D   69 ASP cc_start: 0.8535 (t70) cc_final: 0.8304 (t70)
REVERT: A    3 MET cc_start: 0.7639 (mmm) cc_final: 0.7419 (tpt)
REVERT: A   58 MET cc_start: 0.7926 (mtm) cc_final: 0.7638 (mtp)
REVERT: B   83 TRP cc_start: 0.9102 (m100) cc_final: 0.8833 (m100)
REVERT: B  134 ASP cc_start: 0.9109 (m-30) cc_final: 0.8532 (t0)
REVERT: B  137 LYS cc_start: 0.9582 (mppt) cc_final: 0.9344 (mmtm)
REVERT: B  141 GLN cc_start: 0.9434 (tm-30) cc_final: 0.9141 (tm-30)
REVERT: B  210 LEU cc_start: 0.8973 (mm) cc_final: 0.8740 (mm)
REVERT: B  217 HIS cc_start: 0.9272 (t-90) cc_final: 0.8866 (t70)
REVERT: E   69 ARG cc_start: 0.7548 (tpm170) cc_final: 0.7255 (tpm170)
REVERT: F   15 LEU cc_start: 0.9248 (mt) cc_final: 0.9012 (mt)
REVERT: F   19 GLU cc_start: 0.8437 (mm-30) cc_final: 0.8177 (mm-30)
REVERT: F  190 HIS cc_start: 0.7717 (m170) cc_final: 0.7382 (m-70)
  outliers start: 1
  outliers final: 1
  residues processed: 270
  average time/residue: 0.1234
  time to fit residues: 49.2714
Evaluate side-chains
  210 residues out of total 1210 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 209
  time to evaluate  : 0.450 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 159
   random chunks:
   chunk 107 optimal weight:    9.9990
   chunk 70 optimal weight:    9.9990
   chunk 75 optimal weight:    1.9990
   chunk 38 optimal weight:    0.9990
   chunk 36 optimal weight:    9.9990
   chunk 96 optimal weight:    2.9990
   chunk 24 optimal weight:    6.9990
   chunk 141 optimal weight:    0.8980
   chunk 55 optimal weight:    0.9990
   chunk 149 optimal weight:    6.9990
   chunk 0 optimal weight:   30.0000
   overall best weight:    1.5788

-------------------------------------------------------------------------------
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  48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 183 ASN
** B 190 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 142 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
F 184 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3996 r_free = 0.3996 target = 0.099886 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3507 r_free = 0.3507 target = 0.077789 restraints weight = 65149.203|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 42)----------------|
| r_work = 0.3563 r_free = 0.3563 target = 0.079802 restraints weight = 39658.329|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3591 r_free = 0.3591 target = 0.080978 restraints weight = 28586.756|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 34)----------------|
| r_work = 0.3613 r_free = 0.3613 target = 0.081918 restraints weight = 23308.510|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 55)----------------|
| r_work = 0.3625 r_free = 0.3625 target = 0.082453 restraints weight = 20277.360|
|-----------------------------------------------------------------------------|
r_work (final): 0.3606
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3606
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3606 r_free = 0.3606    target_work(ls_wunit_k1) = 0.082         |
| occupancies: max = 1.00  min = 0.22   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3606 r_free = 0.3606    target_work(ls_wunit_k1) = 0.082         |
| occupancies: max = 1.00  min = 0.25   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3606
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7482
moved from start:          0.2775

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037  15146  Z= 0.159
  Angle     :  0.609   9.216  21110  Z= 0.334
  Chirality :  0.042   0.156   2379
  Planarity :  0.004   0.056   2203
  Dihedral  : 24.290 179.336   3215
  Min Nonbonded Distance : 2.137

Molprobity Statistics.
  All-atom Clashscore : 15.86
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.02 %
    Favored  : 96.98 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  4.38 %
    Favored  : 95.62 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.69 (0.21), residues: 1459
  helix:  0.54 (0.19), residues: 673
  sheet: -1.24 (0.33), residues: 212
  loop : -1.24 (0.24), residues: 574

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG B 144 
 TYR   0.015   0.001   TYR C 162 
 PHE   0.021   0.002   PHE B  24 
 TRP   0.012   0.001   TRP E  83 
 HIS   0.006   0.001   HIS E  29 

Details of bonding type rmsd
  covalent geometry    : bond        0.00349 (15146)
  covalent geometry    : angle       0.60926 (21110)
  hydrogen bonds       : bond        0.05555 (  672)
  hydrogen bonds       : angle       4.60874 ( 1831)

*********************** 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
  278 residues out of total 1210 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 278
  time to evaluate  : 0.479 
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: symmetry clash
REVERT: K  271 ARG cc_start: 0.8113 (mtt180) cc_final: 0.7678 (mmt180)
REVERT: D   19 LEU cc_start: 0.8883 (mp) cc_final: 0.8668 (mp)
REVERT: D   38 ARG cc_start: 0.8568 (tmm-80) cc_final: 0.8324 (tmm-80)
REVERT: D   41 GLU cc_start: 0.8571 (mp0) cc_final: 0.8163 (mp0)
REVERT: D   69 ASP cc_start: 0.8423 (t70) cc_final: 0.8182 (t70)
REVERT: B   84 VAL cc_start: 0.8189 (m) cc_final: 0.7148 (m)
REVERT: B  134 ASP cc_start: 0.9036 (m-30) cc_final: 0.8552 (t0)
REVERT: B  163 ASN cc_start: 0.8990 (m-40) cc_final: 0.8748 (m-40)
REVERT: B  194 TYR cc_start: 0.7696 (m-10) cc_final: 0.7494 (m-80)
REVERT: B  206 LEU cc_start: 0.8835 (mt) cc_final: 0.8293 (mt)
REVERT: B  217 HIS cc_start: 0.9128 (t-90) cc_final: 0.8818 (t70)
REVERT: C   23 THR cc_start: 0.9368 (p) cc_final: 0.9164 (t)
REVERT: C   72 GLU cc_start: 0.8371 (tt0) cc_final: 0.7880 (tp30)
REVERT: C  282 ILE cc_start: 0.9141 (mm) cc_final: 0.8825 (mm)
REVERT: E   90 ARG cc_start: 0.7635 (ttm110) cc_final: 0.7233 (mtm110)
REVERT: F   15 LEU cc_start: 0.9191 (mt) cc_final: 0.8984 (mt)
REVERT: F   19 GLU cc_start: 0.8449 (mm-30) cc_final: 0.7998 (mm-30)
REVERT: F   92 TYR cc_start: 0.8419 (m-80) cc_final: 0.8172 (m-10)
  outliers start: 0
  outliers final: 0
  residues processed: 278
  average time/residue: 0.1222
  time to fit residues: 50.0966
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  : 0.505 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 159
   random chunks:
   chunk 143 optimal weight:    8.9990
   chunk 147 optimal weight:    6.9990
   chunk 58 optimal weight:    9.9990
   chunk 66 optimal weight:   10.0000
   chunk 18 optimal weight:   10.0000
   chunk 52 optimal weight:    0.9990
   chunk 57 optimal weight:   10.0000
   chunk 53 optimal weight:    5.9990
   chunk 60 optimal weight:    1.9990
   chunk 71 optimal weight:    6.9990
   chunk 88 optimal weight:   10.0000
   overall best weight:    4.5990

-------------------------------------------------------------------------------
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**
** B 190 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
C 183 ASN
** F 184 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3935 r_free = 0.3935 target = 0.095960 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3393 r_free = 0.3393 target = 0.072613 restraints weight = 98331.681|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3456 r_free = 0.3456 target = 0.074813 restraints weight = 52538.611|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3495 r_free = 0.3495 target = 0.076362 restraints weight = 35215.729|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3518 r_free = 0.3518 target = 0.077266 restraints weight = 27168.934|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 35)----------------|
| r_work = 0.3536 r_free = 0.3536 target = 0.077973 restraints weight = 23270.352|
|-----------------------------------------------------------------------------|
r_work (final): 0.3512
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3511
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3511 r_free = 0.3511    target_work(ls_wunit_k1) = 0.077         |
| occupancies: max = 1.00  min = 0.25   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3511 r_free = 0.3511    target_work(ls_wunit_k1) = 0.077         |
| occupancies: max = 1.00  min = 0.22   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3511
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7595
moved from start:          0.3097

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.068  15146  Z= 0.275
  Angle     :  0.693   7.041  21110  Z= 0.381
  Chirality :  0.044   0.164   2379
  Planarity :  0.005   0.055   2203
  Dihedral  : 24.524 174.774   3215
  Min Nonbonded Distance : 2.035

Molprobity Statistics.
  All-atom Clashscore : 21.15
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.18 %
    Favored  : 95.82 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  4.05 %
    Favored  : 95.95 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.06 (0.21), residues: 1459
  helix:  0.20 (0.19), residues: 674
  sheet: -1.46 (0.32), residues: 220
  loop : -1.37 (0.24), residues: 565

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG C 153 
 TYR   0.033   0.002   TYR E 229 
 PHE   0.025   0.002   PHE K 224 
 TRP   0.011   0.002   TRP C  83 
 HIS   0.007   0.001   HIS C  68 

Details of bonding type rmsd
  covalent geometry    : bond        0.00602 (15146)
  covalent geometry    : angle       0.69305 (21110)
  hydrogen bonds       : bond        0.06822 (  672)
  hydrogen bonds       : angle       4.92014 ( 1831)

*********************** 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
  250 residues out of total 1210 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 250
  time to evaluate  : 0.437 
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: 0.8288 (mtt180) cc_final: 0.7824 (mmt180)
REVERT: D   19 LEU cc_start: 0.9203 (mp) cc_final: 0.9003 (mp)
REVERT: D   38 ARG cc_start: 0.8654 (tmm-80) cc_final: 0.8142 (tmm-80)
REVERT: D   41 GLU cc_start: 0.8547 (mp0) cc_final: 0.7760 (mp0)
REVERT: D   63 ARG cc_start: 0.8307 (mmt180) cc_final: 0.7627 (mmm160)
REVERT: D   69 ASP cc_start: 0.8584 (t70) cc_final: 0.8096 (t70)
REVERT: A   20 THR cc_start: 0.9162 (p) cc_final: 0.8923 (t)
REVERT: B   86 GLU cc_start: 0.8187 (tp30) cc_final: 0.7878 (tp30)
REVERT: B  163 ASN cc_start: 0.9078 (m-40) cc_final: 0.8862 (m-40)
REVERT: B  217 HIS cc_start: 0.9204 (t-90) cc_final: 0.8855 (t70)
REVERT: C   72 GLU cc_start: 0.8655 (tt0) cc_final: 0.8129 (tp30)
REVERT: C  295 LEU cc_start: 0.9269 (mm) cc_final: 0.8996 (mt)
REVERT: E  128 MET cc_start: 0.8921 (tpp) cc_final: 0.8699 (tpp)
REVERT: E  272 MET cc_start: 0.8879 (mpp) cc_final: 0.8614 (mpp)
REVERT: F   15 LEU cc_start: 0.9325 (mt) cc_final: 0.9098 (mt)
REVERT: F   92 TYR cc_start: 0.8601 (m-80) cc_final: 0.8367 (m-10)
REVERT: F  128 MET cc_start: 0.7405 (pmm) cc_final: 0.7128 (pmm)
  outliers start: 0
  outliers final: 0
  residues processed: 250
  average time/residue: 0.1260
  time to fit residues: 45.8685
Evaluate side-chains
  206 residues out of total 1210 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 206
  time to evaluate  : 0.470 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 159
   random chunks:
   chunk 141 optimal weight:    7.9990
   chunk 52 optimal weight:    2.9990
   chunk 35 optimal weight:    3.9990
   chunk 92 optimal weight:    9.9990
   chunk 64 optimal weight:    0.9980
   chunk 121 optimal weight:    6.9990
   chunk 115 optimal weight:    0.7980
   chunk 42 optimal weight:    9.9990
   chunk 143 optimal weight:    5.9990
   chunk 57 optimal weight:    6.9990
   chunk 97 optimal weight:   10.0000
   overall best weight:    2.9586

-------------------------------------------------------------------------------
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  48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 190 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
C 183 ASN
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 = 0.3954 r_free = 0.3954 target = 0.097408 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3419 r_free = 0.3419 target = 0.073661 restraints weight = 102953.024|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 45)----------------|
| r_work = 0.3484 r_free = 0.3484 target = 0.076023 restraints weight = 53654.633|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3523 r_free = 0.3523 target = 0.077657 restraints weight = 35380.847|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 43)----------------|
| r_work = 0.3546 r_free = 0.3546 target = 0.078667 restraints weight = 27210.681|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 47)----------------|
| r_work = 0.3560 r_free = 0.3560 target = 0.079350 restraints weight = 23138.943|
|-----------------------------------------------------------------------------|
r_work (final): 0.3540
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3540
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3540 r_free = 0.3540    target_work(ls_wunit_k1) = 0.079         |
| occupancies: max = 1.00  min = 0.22   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 = 0.23   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3540
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7571
moved from start:          0.3277

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.038  15146  Z= 0.201
  Angle     :  0.638   6.870  21110  Z= 0.350
  Chirality :  0.042   0.171   2379
  Planarity :  0.005   0.156   2203
  Dihedral  : 24.631 178.692   3215
  Min Nonbonded Distance : 2.090

Molprobity Statistics.
  All-atom Clashscore : 17.94
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.63 %
    Favored  : 96.37 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  3.06 %
    Favored  : 96.94 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.99 (0.21), residues: 1459
  helix:  0.29 (0.19), residues: 675
  sheet: -1.39 (0.33), residues: 209
  loop : -1.40 (0.24), residues: 575

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG F  96 
 TYR   0.034   0.002   TYR E 229 
 PHE   0.025   0.002   PHE K 224 
 TRP   0.031   0.002   TRP B  83 
 HIS   0.008   0.001   HIS E  29 

Details of bonding type rmsd
  covalent geometry    : bond        0.00442 (15146)
  covalent geometry    : angle       0.63793 (21110)
  hydrogen bonds       : bond        0.05734 (  672)
  hydrogen bonds       : angle       4.67074 ( 1831)

*********************** 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
  259 residues out of total 1210 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 259
  time to evaluate  : 0.495 
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: 0.6264 (mtt180) cc_final: 0.4252 (mtm180)
REVERT: K  151 ILE cc_start: 0.4695 (tp) cc_final: 0.4431 (tp)
REVERT: K  219 PHE cc_start: 0.4002 (t80) cc_final: 0.3696 (t80)
REVERT: K  271 ARG cc_start: 0.8391 (mtt180) cc_final: 0.7877 (mmt180)
REVERT: D   19 LEU cc_start: 0.9143 (mp) cc_final: 0.8930 (mp)
REVERT: D   26 ILE cc_start: 0.8702 (mt) cc_final: 0.8486 (mt)
REVERT: D   38 ARG cc_start: 0.8619 (tmm-80) cc_final: 0.8127 (tmm-80)
REVERT: D   41 GLU cc_start: 0.8510 (mp0) cc_final: 0.7707 (mp0)
REVERT: D   63 ARG cc_start: 0.8245 (mmt180) cc_final: 0.7529 (mmm160)
REVERT: D   69 ASP cc_start: 0.8464 (t70) cc_final: 0.8196 (t70)
REVERT: A   20 THR cc_start: 0.9149 (p) cc_final: 0.8868 (t)
REVERT: B   83 TRP cc_start: 0.8737 (m100) cc_final: 0.8531 (m100)
REVERT: B   84 VAL cc_start: 0.8116 (m) cc_final: 0.6956 (m)
REVERT: B  134 ASP cc_start: 0.9046 (m-30) cc_final: 0.8522 (t0)
REVERT: B  163 ASN cc_start: 0.8988 (m-40) cc_final: 0.8759 (m-40)
REVERT: B  217 HIS cc_start: 0.9164 (t-90) cc_final: 0.8876 (t70)
REVERT: F   15 LEU cc_start: 0.9334 (mt) cc_final: 0.9131 (mt)
REVERT: F   54 MET cc_start: 0.8394 (mmm) cc_final: 0.8190 (mmt)
REVERT: F   92 TYR cc_start: 0.8569 (m-80) cc_final: 0.8339 (m-10)
REVERT: F  128 MET cc_start: 0.7466 (pmm) cc_final: 0.7254 (pmm)
  outliers start: 0
  outliers final: 0
  residues processed: 259
  average time/residue: 0.1216
  time to fit residues: 45.8514
Evaluate side-chains
  209 residues out of total 1210 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 209
  time to evaluate  : 0.397 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 159
   random chunks:
   chunk 113 optimal weight:    8.9990
   chunk 153 optimal weight:    8.9990
   chunk 31 optimal weight:    4.9990
   chunk 39 optimal weight:    8.9990
   chunk 86 optimal weight:    6.9990
   chunk 82 optimal weight:    3.9990
   chunk 14 optimal weight:    0.0020
   chunk 84 optimal weight:    8.9990
   chunk 150 optimal weight:    7.9990
   chunk 114 optimal weight:    0.9990
   chunk 2 optimal weight:    0.6980
   overall best weight:    2.1394

-------------------------------------------------------------------------------
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  48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 190 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
C 183 ASN
F 184 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3975 r_free = 0.3975 target = 0.098283 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3464 r_free = 0.3464 target = 0.075726 restraints weight = 70640.280|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3522 r_free = 0.3522 target = 0.077732 restraints weight = 41910.332|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3556 r_free = 0.3556 target = 0.079119 restraints weight = 29797.401|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 43)----------------|
| r_work = 0.3576 r_free = 0.3576 target = 0.079985 restraints weight = 23814.318|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.3588 r_free = 0.3588 target = 0.080478 restraints weight = 20764.388|
|-----------------------------------------------------------------------------|
r_work (final): 0.3569
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3570
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3570 r_free = 0.3570    target_work(ls_wunit_k1) = 0.080         |
| occupancies: max = 1.00  min = 0.23   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3570 r_free = 0.3570    target_work(ls_wunit_k1) = 0.080         |
| occupancies: max = 1.00  min = 0.29   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3570
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7535
moved from start:          0.3430

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.041  15146  Z= 0.179
  Angle     :  0.645   9.133  21110  Z= 0.353
  Chirality :  0.042   0.180   2379
  Planarity :  0.005   0.118   2203
  Dihedral  : 24.637 178.397   3215
  Min Nonbonded Distance : 2.101

Molprobity Statistics.
  All-atom Clashscore : 17.76
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.63 %
    Favored  : 96.37 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.73 %
    Favored  : 97.27 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.97 (0.21), residues: 1459
  helix:  0.33 (0.19), residues: 678
  sheet: -1.45 (0.32), residues: 210
  loop : -1.40 (0.24), residues: 571

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.001   ARG K 241 
 TYR   0.032   0.002   TYR E 229 
 PHE   0.024   0.002   PHE K 224 
 TRP   0.013   0.002   TRP B  83 
 HIS   0.007   0.001   HIS E  29 

Details of bonding type rmsd
  covalent geometry    : bond        0.00395 (15146)
  covalent geometry    : angle       0.64527 (21110)
  hydrogen bonds       : bond        0.05575 (  672)
  hydrogen bonds       : angle       4.59596 ( 1831)

*********************** 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
  265 residues out of total 1210 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 265
  time to evaluate  : 0.516 
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: 0.6154 (mtt180) cc_final: 0.4212 (mtm180)
REVERT: K  188 GLU cc_start: 0.5436 (mm-30) cc_final: 0.5224 (tp30)
REVERT: K  219 PHE cc_start: 0.3787 (t80) cc_final: 0.3534 (t80)
REVERT: K  220 LEU cc_start: 0.6520 (tt) cc_final: 0.6297 (tt)
REVERT: K  271 ARG cc_start: 0.8420 (mtt180) cc_final: 0.7888 (mmt180)
REVERT: D   19 LEU cc_start: 0.9036 (mp) cc_final: 0.8808 (mp)
REVERT: D   69 ASP cc_start: 0.8507 (t70) cc_final: 0.8257 (t70)
REVERT: A   20 THR cc_start: 0.9137 (p) cc_final: 0.8845 (t)
REVERT: B   60 LEU cc_start: 0.7434 (mt) cc_final: 0.7033 (mt)
REVERT: B   81 LEU cc_start: 0.8835 (tt) cc_final: 0.8417 (tt)
REVERT: B   84 VAL cc_start: 0.8112 (m) cc_final: 0.6886 (m)
REVERT: B  134 ASP cc_start: 0.9009 (m-30) cc_final: 0.8439 (t0)
REVERT: B  217 HIS cc_start: 0.9132 (t-90) cc_final: 0.8802 (t70)
REVERT: C  190 HIS cc_start: 0.8062 (m90) cc_final: 0.7833 (m170)
REVERT: C  277 GLN cc_start: 0.8440 (tp-100) cc_final: 0.8188 (tp-100)
REVERT: F   15 LEU cc_start: 0.9295 (mt) cc_final: 0.9080 (mt)
REVERT: F   19 GLU cc_start: 0.8312 (mm-30) cc_final: 0.8089 (mm-30)
REVERT: F   54 MET cc_start: 0.8341 (mmm) cc_final: 0.7866 (mmt)
REVERT: F   92 TYR cc_start: 0.8594 (m-80) cc_final: 0.8355 (m-10)
REVERT: F  128 MET cc_start: 0.7543 (pmm) cc_final: 0.7301 (pmm)
  outliers start: 0
  outliers final: 0
  residues processed: 265
  average time/residue: 0.1253
  time to fit residues: 48.7026
Evaluate side-chains
  208 residues out of total 1210 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 208
  time to evaluate  : 0.373 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 159
   random chunks:
   chunk 52 optimal weight:    6.9990
   chunk 25 optimal weight:   10.0000
   chunk 155 optimal weight:    6.9990
   chunk 156 optimal weight:    6.9990
   chunk 150 optimal weight:    7.9990
   chunk 147 optimal weight:    1.9990
   chunk 95 optimal weight:   10.0000
   chunk 66 optimal weight:    8.9990
   chunk 90 optimal weight:    2.9990
   chunk 22 optimal weight:    5.9990
   chunk 51 optimal weight:    5.9990
   overall best weight:    4.7990

-------------------------------------------------------------------------------
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
** D  48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 190 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
C 183 ASN
** C 184 GLN ** 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 = 0.3917 r_free = 0.3917 target = 0.095529 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3392 r_free = 0.3392 target = 0.073076 restraints weight = 77830.291|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 42)----------------|
| r_work = 0.3450 r_free = 0.3450 target = 0.074892 restraints weight = 46143.501|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3481 r_free = 0.3481 target = 0.076156 restraints weight = 32672.189|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 51)----------------|
| r_work = 0.3501 r_free = 0.3501 target = 0.077023 restraints weight = 26448.484|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 24)----------------|
| r_work = 0.3513 r_free = 0.3513 target = 0.077446 restraints weight = 23124.626|
|-----------------------------------------------------------------------------|
r_work (final): 0.3489
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3491
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3491 r_free = 0.3491    target_work(ls_wunit_k1) = 0.077         |
| occupancies: max = 1.00  min = 0.29   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3491 r_free = 0.3491    target_work(ls_wunit_k1) = 0.077         |
| occupancies: max = 1.00  min = 0.20   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3491
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7636
moved from start:          0.3679

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.063  15146  Z= 0.287
  Angle     :  0.725   7.496  21110  Z= 0.397
  Chirality :  0.045   0.172   2379
  Planarity :  0.006   0.115   2203
  Dihedral  : 24.829 174.798   3215
  Min Nonbonded Distance : 2.021

Molprobity Statistics.
  All-atom Clashscore : 23.37
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.00 %
    Favored  : 95.00 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.49 %
    Favored  : 98.51 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.33 (0.21), residues: 1459
  helix:  0.02 (0.19), residues: 679
  sheet: -1.74 (0.32), residues: 214
  loop : -1.51 (0.24), residues: 566

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.014   0.001   ARG K 241 
 TYR   0.034   0.002   TYR E 229 
 PHE   0.033   0.002   PHE K 224 
 TRP   0.030   0.002   TRP B  83 
 HIS   0.011   0.001   HIS E  29 

Details of bonding type rmsd
  covalent geometry    : bond        0.00627 (15146)
  covalent geometry    : angle       0.72504 (21110)
  hydrogen bonds       : bond        0.06848 (  672)
  hydrogen bonds       : angle       4.94365 ( 1831)

*********************** 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
  248 residues out of total 1210 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 248
  time to evaluate  : 0.520 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: K  142 ARG cc_start: 0.6178 (mtt180) cc_final: 0.4137 (mtm180)
REVERT: K  148 ILE cc_start: 0.9339 (mt) cc_final: 0.9128 (mt)
REVERT: K  188 GLU cc_start: 0.5472 (mm-30) cc_final: 0.5266 (tp30)
REVERT: K  219 PHE cc_start: 0.4038 (t80) cc_final: 0.3808 (t80)
REVERT: K  271 ARG cc_start: 0.8394 (mtt180) cc_final: 0.7867 (mmp-170)
REVERT: D   38 ARG cc_start: 0.8621 (tmm-80) cc_final: 0.8416 (tmm-80)
REVERT: D   41 GLU cc_start: 0.8461 (mp0) cc_final: 0.8120 (mp0)
REVERT: D   63 ARG cc_start: 0.8323 (mmt180) cc_final: 0.7601 (mmm160)
REVERT: D   69 ASP cc_start: 0.8434 (t70) cc_final: 0.7980 (t70)
REVERT: A   20 THR cc_start: 0.9106 (p) cc_final: 0.8828 (t)
REVERT: B   83 TRP cc_start: 0.9001 (m100) cc_final: 0.8791 (m100)
REVERT: B   84 VAL cc_start: 0.8151 (m) cc_final: 0.7018 (m)
REVERT: B  217 HIS cc_start: 0.9250 (t-90) cc_final: 0.8998 (t70)
REVERT: C  277 GLN cc_start: 0.8475 (tp-100) cc_final: 0.8201 (tp-100)
REVERT: E  128 MET cc_start: 0.8914 (tpp) cc_final: 0.8677 (tpp)
REVERT: E  272 MET cc_start: 0.8897 (mpp) cc_final: 0.8671 (mpp)
REVERT: F   15 LEU cc_start: 0.9369 (mt) cc_final: 0.9140 (mt)
REVERT: F   19 GLU cc_start: 0.8497 (mm-30) cc_final: 0.8206 (mm-30)
REVERT: F   54 MET cc_start: 0.8271 (mmm) cc_final: 0.8043 (mmm)
REVERT: F  128 MET cc_start: 0.7625 (pmm) cc_final: 0.7362 (pmm)
REVERT: F  198 HIS cc_start: 0.8317 (t-90) cc_final: 0.7914 (t-90)
  outliers start: 0
  outliers final: 0
  residues processed: 248
  average time/residue: 0.1273
  time to fit residues: 46.3834
Evaluate side-chains
  204 residues out of total 1210 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 204
  time to evaluate  : 0.474 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 159
   random chunks:
   chunk 152 optimal weight:    8.9990
   chunk 56 optimal weight:    0.8980
   chunk 146 optimal weight:    0.0770
   chunk 59 optimal weight:    5.9990
   chunk 34 optimal weight:    1.9990
   chunk 119 optimal weight:    0.0470
   chunk 20 optimal weight:    0.9990
   chunk 127 optimal weight:    7.9990
   chunk 23 optimal weight:    1.9990
   chunk 128 optimal weight:    2.9990
   chunk 14 optimal weight:    0.0070
   overall best weight:    0.4056

-------------------------------------------------------------------------------
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  48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 190 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
C 183 ASN
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 = 0.4021 r_free = 0.4021 target = 0.101052 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3525 r_free = 0.3525 target = 0.078509 restraints weight = 69989.871|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3581 r_free = 0.3581 target = 0.080573 restraints weight = 41469.697|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3615 r_free = 0.3615 target = 0.082023 restraints weight = 29323.906|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 38)----------------|
| r_work = 0.3636 r_free = 0.3636 target = 0.082933 restraints weight = 23381.912|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 39)----------------|
| r_work = 0.3649 r_free = 0.3649 target = 0.083519 restraints weight = 20304.725|
|-----------------------------------------------------------------------------|
r_work (final): 0.3636
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3636
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3636 r_free = 0.3636    target_work(ls_wunit_k1) = 0.083         |
| occupancies: max = 1.00  min = 0.20   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3636 r_free = 0.3636    target_work(ls_wunit_k1) = 0.083         |
| occupancies: max = 1.00  min = 0.32   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3636
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7468
moved from start:          0.3794

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042  15146  Z= 0.151
  Angle     :  0.654   7.462  21110  Z= 0.353
  Chirality :  0.043   0.191   2379
  Planarity :  0.005   0.096   2203
  Dihedral  : 24.739 176.687   3215
  Min Nonbonded Distance : 2.133

Molprobity Statistics.
  All-atom Clashscore : 15.51
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.29 %
    Favored  : 96.71 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.83 %
    Favored  : 99.17 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.84 (0.21), residues: 1459
  helix:  0.40 (0.19), residues: 676
  sheet: -1.35 (0.32), residues: 222
  loop : -1.29 (0.24), residues: 561

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.001   ARG K 241 
 TYR   0.027   0.002   TYR E 229 
 PHE   0.024   0.001   PHE K 224 
 TRP   0.040   0.002   TRP B  83 
 HIS   0.007   0.001   HIS E  29 

Details of bonding type rmsd
  covalent geometry    : bond        0.00327 (15146)
  covalent geometry    : angle       0.65442 (21110)
  hydrogen bonds       : bond        0.05346 (  672)
  hydrogen bonds       : angle       4.45400 ( 1831)

*********************** 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
  267 residues out of total 1210 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 267
  time to evaluate  : 0.343 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: K  142 ARG cc_start: 0.5915 (mtt180) cc_final: 0.4127 (mtm180)
REVERT: K  148 ILE cc_start: 0.9309 (mt) cc_final: 0.9066 (mt)
REVERT: K  188 GLU cc_start: 0.5417 (mm-30) cc_final: 0.5210 (tp30)
REVERT: K  220 LEU cc_start: 0.6577 (tt) cc_final: 0.6313 (tt)
REVERT: K  271 ARG cc_start: 0.8434 (mtt180) cc_final: 0.7848 (mmp-170)
REVERT: D   41 GLU cc_start: 0.8329 (mp0) cc_final: 0.8039 (mp0)
REVERT: D   69 ASP cc_start: 0.8112 (t70) cc_final: 0.7730 (t70)
REVERT: B   84 VAL cc_start: 0.7886 (m) cc_final: 0.6497 (m)
REVERT: B  104 PHE cc_start: 0.9108 (m-80) cc_final: 0.8194 (m-80)
REVERT: B  134 ASP cc_start: 0.9107 (m-30) cc_final: 0.8480 (t0)
REVERT: B  163 ASN cc_start: 0.8955 (m-40) cc_final: 0.8751 (m-40)
REVERT: B  217 HIS cc_start: 0.8996 (t-90) cc_final: 0.8722 (t70)
REVERT: C   23 THR cc_start: 0.9384 (p) cc_final: 0.9134 (t)
REVERT: C   54 MET cc_start: 0.8838 (mmp) cc_final: 0.8636 (mmp)
REVERT: C  277 GLN cc_start: 0.8402 (tp-100) cc_final: 0.8107 (tp-100)
REVERT: E   73 LEU cc_start: 0.9594 (mt) cc_final: 0.9377 (mp)
REVERT: E   90 ARG cc_start: 0.7635 (ttm110) cc_final: 0.7081 (mtm110)
REVERT: E   91 TYR cc_start: 0.8773 (t80) cc_final: 0.8173 (t80)
REVERT: E  180 ASP cc_start: 0.7948 (p0) cc_final: 0.7717 (p0)
REVERT: F   19 GLU cc_start: 0.8425 (mm-30) cc_final: 0.8152 (mm-30)
REVERT: F   54 MET cc_start: 0.8198 (mmm) cc_final: 0.7732 (mmt)
REVERT: F  128 MET cc_start: 0.7666 (pmm) cc_final: 0.7415 (pmm)
  outliers start: 0
  outliers final: 0
  residues processed: 267
  average time/residue: 0.1299
  time to fit residues: 50.2051
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  : 0.448 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 159
   random chunks:
   chunk 59 optimal weight:   10.0000
   chunk 42 optimal weight:    5.9990
   chunk 83 optimal weight:    0.9980
   chunk 151 optimal weight:    6.9990
   chunk 12 optimal weight:   10.0000
   chunk 128 optimal weight:    3.9990
   chunk 37 optimal weight:    0.6980
   chunk 85 optimal weight:    1.9990
   chunk 6 optimal weight:    0.9990
   chunk 44 optimal weight:    0.9980
   chunk 117 optimal weight:   10.0000
   overall best weight:    1.1384

-------------------------------------------------------------------------------
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  48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 190 HIS
C 183 ASN
** C 184 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E  29 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 = 0.4012 r_free = 0.4012 target = 0.100452 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3481 r_free = 0.3481 target = 0.076468 restraints weight = 104435.233|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3548 r_free = 0.3548 target = 0.079037 restraints weight = 53236.772|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3587 r_free = 0.3587 target = 0.080747 restraints weight = 34498.759|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3611 r_free = 0.3611 target = 0.081774 restraints weight = 26353.505|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 25)----------------|
| r_work = 0.3620 r_free = 0.3620 target = 0.082171 restraints weight = 22388.771|
|-----------------------------------------------------------------------------|
r_work (final): 0.3601
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3601
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3601 r_free = 0.3601    target_work(ls_wunit_k1) = 0.081         |
| occupancies: max = 1.00  min = 0.32   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3601 r_free = 0.3601    target_work(ls_wunit_k1) = 0.081         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3601
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7510
moved from start:          0.3911

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= 0.157
  Angle     :  0.663   9.203  21110  Z= 0.358
  Chirality :  0.043   0.185   2379
  Planarity :  0.005   0.093   2203
  Dihedral  : 24.653 178.942   3215
  Min Nonbonded Distance : 2.105

Molprobity Statistics.
  All-atom Clashscore : 16.54
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.56 %
    Favored  : 96.44 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.41 %
    Favored  : 99.59 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.84 (0.21), residues: 1459
  helix:  0.39 (0.19), residues: 680
  sheet: -1.36 (0.33), residues: 216
  loop : -1.29 (0.24), residues: 563

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.001   ARG K 241 
 TYR   0.040   0.002   TYR B 194 
 PHE   0.032   0.002   PHE A  70 
 TRP   0.068   0.003   TRP B  83 
 HIS   0.005   0.001   HIS B  29 

Details of bonding type rmsd
  covalent geometry    : bond        0.00352 (15146)
  covalent geometry    : angle       0.66314 (21110)
  hydrogen bonds       : bond        0.05275 (  672)
  hydrogen bonds       : angle       4.57728 ( 1831)

********************** 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
  261 residues out of total 1210 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 261
  time to evaluate  : 0.510 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: K  142 ARG cc_start: 0.5985 (mtt180) cc_final: 0.4174 (mtm180)
REVERT: K  148 ILE cc_start: 0.9329 (mt) cc_final: 0.9084 (mt)
REVERT: K  188 GLU cc_start: 0.5382 (mm-30) cc_final: 0.5010 (tp30)
REVERT: K  220 LEU cc_start: 0.6528 (tt) cc_final: 0.6231 (tt)
REVERT: K  271 ARG cc_start: 0.8391 (mtt180) cc_final: 0.7837 (mmp-170)
REVERT: D   41 GLU cc_start: 0.8375 (mp0) cc_final: 0.8101 (mp0)
REVERT: D   69 ASP cc_start: 0.8231 (t70) cc_final: 0.7926 (t70)
REVERT: A   44 TRP cc_start: 0.8077 (t60) cc_final: 0.7844 (t60)
REVERT: B   84 VAL cc_start: 0.7908 (m) cc_final: 0.6828 (m)
REVERT: B  134 ASP cc_start: 0.9241 (m-30) cc_final: 0.8524 (t0)
REVERT: B  163 ASN cc_start: 0.9010 (m-40) cc_final: 0.8807 (m-40)
REVERT: B  217 HIS cc_start: 0.9142 (t-90) cc_final: 0.8831 (t70)
REVERT: C   23 THR cc_start: 0.9348 (p) cc_final: 0.9138 (t)
REVERT: C   60 LEU cc_start: 0.8958 (mt) cc_final: 0.8753 (mt)
REVERT: C  155 TYR cc_start: 0.8463 (m-10) cc_final: 0.8246 (m-10)
REVERT: C  277 GLN cc_start: 0.8463 (tp-100) cc_final: 0.8170 (tp-100)
REVERT: E   90 ARG cc_start: 0.7583 (ttm110) cc_final: 0.6986 (mtm110)
REVERT: E   91 TYR cc_start: 0.8734 (t80) cc_final: 0.8133 (t80)
REVERT: F   15 LEU cc_start: 0.9249 (mt) cc_final: 0.8983 (mt)
REVERT: F   19 GLU cc_start: 0.8469 (mm-30) cc_final: 0.8136 (mm-30)
REVERT: F   54 MET cc_start: 0.8177 (mmm) cc_final: 0.7633 (mmt)
REVERT: F  274 LYS cc_start: 0.8574 (mmmt) cc_final: 0.8271 (mmmt)
  outliers start: 0
  outliers final: 0
  residues processed: 261
  average time/residue: 0.1239
  time to fit residues: 47.8597
Evaluate side-chains
  212 residues out of total 1210 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 212
  time to evaluate  : 0.499 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 159
   random chunks:
   chunk 93 optimal weight:   10.0000
   chunk 104 optimal weight:    3.9990
   chunk 24 optimal weight:    1.9990
   chunk 49 optimal weight:    8.9990
   chunk 15 optimal weight:    3.9990
   chunk 76 optimal weight:    7.9990
   chunk 122 optimal weight:    0.7980
   chunk 155 optimal weight:    6.9990
   chunk 39 optimal weight:    9.9990
   chunk 115 optimal weight:    7.9990
   chunk 112 optimal weight:    0.0870
   overall best weight:    2.1764

-------------------------------------------------------------------------------
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  48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 190 HIS
C 183 ASN
** E  29 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
F 184 GLN
F 190 HIS

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3989 r_free = 0.3989 target = 0.099311 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3461 r_free = 0.3461 target = 0.075868 restraints weight = 97664.911|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 44)----------------|
| r_work = 0.3529 r_free = 0.3529 target = 0.078211 restraints weight = 51533.489|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3566 r_free = 0.3566 target = 0.079772 restraints weight = 33983.785|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.3587 r_free = 0.3587 target = 0.080659 restraints weight = 26422.328|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 59)----------------|
| r_work = 0.3602 r_free = 0.3602 target = 0.081367 restraints weight = 22870.006|
|-----------------------------------------------------------------------------|
r_work (final): 0.3586
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3586
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3586 r_free = 0.3586    target_work(ls_wunit_k1) = 0.081         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3586 r_free = 0.3586    target_work(ls_wunit_k1) = 0.081         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3586
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7531
moved from start:          0.3973

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.039  15146  Z= 0.178
  Angle     :  0.660   9.857  21110  Z= 0.358
  Chirality :  0.043   0.186   2379
  Planarity :  0.005   0.085   2203
  Dihedral  : 24.659 178.194   3215
  Min Nonbonded Distance : 2.084

Molprobity Statistics.
  All-atom Clashscore : 18.04
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.91 %
    Favored  : 96.09 %
  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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.87 (0.21), residues: 1459
  helix:  0.38 (0.19), residues: 678
  sheet: -1.50 (0.33), residues: 214
  loop : -1.26 (0.24), residues: 567

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.001   ARG K 241 
 TYR   0.030   0.002   TYR B 155 
 PHE   0.025   0.002   PHE K 224 
 TRP   0.022   0.002   TRP E  83 
 HIS   0.012   0.001   HIS F 190 

Details of bonding type rmsd
  covalent geometry    : bond        0.00396 (15146)
  covalent geometry    : angle       0.65961 (21110)
  hydrogen bonds       : bond        0.05441 (  672)
  hydrogen bonds       : angle       4.59511 ( 1831)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3013.77 seconds
wall clock time: 52 minutes 37.94 seconds (3157.94 seconds total)