Starting phenix.real_space_refine
on Fri May 16 13:08:04 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8fyc_29564/05_2025/8fyc_29564.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8fyc_29564/05_2025/8fyc_29564.map

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

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

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8fyc_29564/05_2025/8fyc_29564.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8fyc_29564/05_2025/8fyc_29564.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8fyc_29564/05_2025/8fyc_29564.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8fyc_29564/05_2025/8fyc_29564.cif"
  }
  resolution = 4.1
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=  -0.001 sd=   0.017
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 5
    Type Number    sf(0)   Gaussians
     P     143      5.49       5
     S      34      5.16       5
     C    8774      2.51       5
     N    2623      2.21       5
     O    3001      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

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

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib"
  Total number of atoms: 14575
  Number of models: 1
  Model: ""
    Number of chains: 11
    Chain: "K"
      Number of atoms: 1314
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 164, 1314
          Classifications: {'peptide': 164}
          Link IDs: {'PTRANS': 3, 'TRANS': 160}
    Chain: "J"
      Number of atoms: 881
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 43, 881
          Classifications: {'DNA': 43}
          Modifications used: {'5*END': 1}
          Link IDs: {'rna3p': 42}
    Chain: "D"
      Number of atoms: 746
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 93, 746
          Classifications: {'peptide': 93}
          Link IDs: {'PTRANS': 4, 'TRANS': 88}
    Chain: "A"
      Number of atoms: 746
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 93, 746
          Classifications: {'peptide': 93}
          Link IDs: {'PTRANS': 4, 'TRANS': 88}
    Chain: "B"
      Number of atoms: 2295
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 292, 2295
          Classifications: {'peptide': 292}
          Link IDs: {'PTRANS': 11, 'TRANS': 280}
    Chain: "C"
      Number of atoms: 2423
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 310, 2423
          Classifications: {'peptide': 310}
          Link IDs: {'PTRANS': 13, 'TRANS': 296}
    Chain: "E"
      Number of atoms: 2295
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 292, 2295
          Classifications: {'peptide': 292}
          Link IDs: {'PTRANS': 11, 'TRANS': 280}
    Chain: "F"
      Number of atoms: 1770
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 231, 1770
          Classifications: {'peptide': 231}
          Link IDs: {'PTRANS': 6, 'TRANS': 224}
          Chain breaks: 1
    Chain: "G"
      Number of atoms: 1187
      Number of conformers: 2
      Conformer: "A"
        Number of residues, atoms: 57, 1165
          Classifications: {'DNA': 57}
          Modifications used: {'5*END': 1}
          Link IDs: {'rna3p': 56}
      Conformer: "B"
        Number of residues, atoms: 57, 1165
          Classifications: {'DNA': 57}
          Modifications used: {'5*END': 1}
          Link IDs: {'rna3p': 56}
          bond proxies already assigned to first conformer: 1279
    Chain: "H"
      Number of atoms: 632
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 31, 632
          Classifications: {'DNA': 31}
          Modifications used: {'5*END': 1}
          Link IDs: {'rna3p': 30}
    Chain: "I"
      Number of atoms: 286
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 14, 286
          Classifications: {'DNA': 14}
          Link IDs: {'rna3p': 13}
  Residues with excluded nonbonded symmetry interactions: 1
    residue:
      pdb=" P  A DG G  29 " occ=0.74
      ... (42 atoms not shown)
      pdb=" C4 B DG G  29 " occ=0.26
  Time building chain proxies: 8.74, per 1000 atoms: 0.60
  Number of scatterers: 14575
  At special positions: 0
  Unit cell: (107.04, 95.89, 157.215, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S      34     16.00
     P     143     15.00
     O    3001      8.00
     N    2623      7.00
     C    8774      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 3.69
  Conformation dependent library (CDL) restraints added in 1.6 seconds
  

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

  Finding SS restraints...
    Secondary structure from input PDB file:
      62 helices and 9 sheets defined
      50.2% alpha, 13.7% beta
      44 base pairs and 103 stacking pairs defined.
    Time for finding SS restraints: 6.07
  Creating SS restraints...
    Processing helix  chain 'K' and resid 171 through 178
    Processing helix  chain 'K' and resid 181 through 189
    Processing helix  chain 'K' and resid 191 through 203
    Processing helix  chain 'K' and resid 212 through 228
      removed outlier: 3.929A  pdb=" N   ASP K 216 " --> pdb=" O   HIS K 212 " (cutoff:3.500A)
    Processing helix  chain 'K' and resid 238 through 246
      removed outlier: 3.922A  pdb=" N   ILE K 242 " --> pdb=" O   ASP K 238 " (cutoff:3.500A)
      removed outlier: 3.939A  pdb=" N   GLU K 246 " --> pdb=" O   ILE K 242 " (cutoff:3.500A)
    Processing helix  chain 'K' and resid 254 through 262
    Processing helix  chain 'K' and resid 271 through 287
    Processing helix  chain 'D' and resid 12 through 19
    Processing helix  chain 'D' and resid 20 through 22
      No H-bonds generated for 'chain 'D' and resid 20 through 22'
    Processing helix  chain 'D' and resid 36 through 51
      removed outlier: 4.057A  pdb=" N   GLU D  41 " --> pdb=" O   SER D  37 " (cutoff:3.500A)
      removed outlier: 4.030A  pdb=" N   TYR D  42 " --> pdb=" O   ARG D  38 " (cutoff:3.500A)
      removed outlier: 3.521A  pdb=" N   MET D  51 " --> pdb=" O   VAL D  47 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 12 through 19
    Processing helix  chain 'A' and resid 20 through 22
      No H-bonds generated for 'chain 'A' and resid 20 through 22'
    Processing helix  chain 'A' and resid 36 through 49
      removed outlier: 3.577A  pdb=" N   GLU A  49 " --> pdb=" O   ARG A  45 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 68 through 77
      removed outlier: 3.755A  pdb=" N   THR B  77 " --> pdb=" O   LEU B  73 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 86 through 89
    Processing helix  chain 'B' and resid 97 through 101
    Processing helix  chain 'B' and resid 102 through 114
    Processing helix  chain 'B' and resid 114 through 129
      removed outlier: 3.532A  pdb=" N   ARG B 120 " --> pdb=" O   ARG B 116 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 140 through 163
      removed outlier: 3.533A  pdb=" N   ARG B 144 " --> pdb=" O   MET B 140 " (cutoff:3.500A)
      removed outlier: 4.205A  pdb=" N   SER B 145 " --> pdb=" O   GLN B 141 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 180 through 205
      removed outlier: 3.938A  pdb=" N   LEU B 196 " --> pdb=" O   ALA B 192 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 219 through 227
    Processing helix  chain 'B' and resid 228 through 230
      No H-bonds generated for 'chain 'B' and resid 228 through 230'
    Processing helix  chain 'B' and resid 233 through 245
    Processing helix  chain 'B' and resid 250 through 265
      removed outlier: 4.337A  pdb=" N   ASP B 265 " --> pdb=" O   ASP B 261 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 266 through 280
      removed outlier: 4.380A  pdb=" N   GLN B 277 " --> pdb=" O   VAL B 273 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 283 through 287
    Processing helix  chain 'B' and resid 298 through 303
      removed outlier: 3.642A  pdb=" N   VAL B 303 " --> pdb=" O   LYS B 299 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 304 through 306
      No H-bonds generated for 'chain 'B' and resid 304 through 306'
    Processing helix  chain 'C' and resid 17 through 21
      removed outlier: 3.883A  pdb=" N   ARG C  21 " --> pdb=" O   VAL C  18 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 51 through 55
    Processing helix  chain 'C' and resid 68 through 77
      removed outlier: 3.897A  pdb=" N   THR C  77 " --> pdb=" O   LEU C  73 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 102 through 114
      removed outlier: 3.910A  pdb=" N   ASN C 114 " --> pdb=" O   GLU C 110 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 114 through 130
      removed outlier: 3.572A  pdb=" N   ARG C 129 " --> pdb=" O   MET C 125 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 139 through 141
      No H-bonds generated for 'chain 'C' and resid 139 through 141'
    Processing helix  chain 'C' and resid 142 through 163
    Processing helix  chain 'C' and resid 180 through 205
      removed outlier: 3.693A  pdb=" N   GLN C 184 " --> pdb=" O   ASP C 180 " (cutoff:3.500A)
      removed outlier: 3.528A  pdb=" N   ALA C 192 " --> pdb=" O   ALA C 188 " (cutoff:3.500A)
      removed outlier: 3.710A  pdb=" N   LEU C 193 " --> pdb=" O   ALA C 189 " (cutoff:3.500A)
      removed outlier: 3.684A  pdb=" N   LEU C 196 " --> pdb=" O   ALA C 192 " (cutoff:3.500A)
      removed outlier: 3.636A  pdb=" N   ALA C 202 " --> pdb=" O   HIS C 198 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 219 through 231
      removed outlier: 3.748A  pdb=" N   TYR C 223 " --> pdb=" O   ARG C 219 " (cutoff:3.500A)
      removed outlier: 4.078A  pdb=" N   LEU C 228 " --> pdb=" O   ASP C 224 " (cutoff:3.500A)
      removed outlier: 4.411A  pdb=" N   TYR C 229 " --> pdb=" O   VAL C 225 " (cutoff:3.500A)
      removed outlier: 4.416A  pdb=" N   ALA C 231 " --> pdb=" O   ASP C 227 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 233 through 245
    Processing helix  chain 'C' and resid 250 through 266
      removed outlier: 3.722A  pdb=" N   ARG C 260 " --> pdb=" O   ARG C 256 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 267 through 281
    Processing helix  chain 'E' and resid 68 through 77
      removed outlier: 4.483A  pdb=" N   LEU E  73 " --> pdb=" O   ARG E  69 " (cutoff:3.500A)
      removed outlier: 3.872A  pdb=" N   LEU E  74 " --> pdb=" O   ALA E  70 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 97 through 101
      removed outlier: 3.799A  pdb=" N   ARG E 100 " --> pdb=" O   ALA E  97 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 102 through 114
      removed outlier: 3.954A  pdb=" N   LYS E 107 " --> pdb=" O   ARG E 103 " (cutoff:3.500A)
      removed outlier: 3.862A  pdb=" N   VAL E 112 " --> pdb=" O   GLN E 108 " (cutoff:3.500A)
      removed outlier: 3.627A  pdb=" N   THR E 113 " --> pdb=" O   ALA E 109 " (cutoff:3.500A)
      removed outlier: 3.793A  pdb=" N   ASN E 114 " --> pdb=" O   GLU E 110 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 114 through 130
    Processing helix  chain 'E' and resid 139 through 162
      removed outlier: 3.761A  pdb=" N   LYS E 160 " --> pdb=" O   ARG E 156 " (cutoff:3.500A)
      removed outlier: 3.574A  pdb=" N   LYS E 161 " --> pdb=" O   GLU E 157 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 180 through 205
      removed outlier: 4.077A  pdb=" N   GLN E 184 " --> pdb=" O   ASP E 180 " (cutoff:3.500A)
      removed outlier: 4.017A  pdb=" N   LEU E 196 " --> pdb=" O   ALA E 192 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 219 through 224
    Processing helix  chain 'E' and resid 226 through 231
      removed outlier: 4.625A  pdb=" N   ALA E 231 " --> pdb=" O   ASP E 227 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 233 through 244
    Processing helix  chain 'E' and resid 250 through 265
      removed outlier: 4.199A  pdb=" N   ASP E 265 " --> pdb=" O   ASP E 261 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 266 through 280
    Processing helix  chain 'E' and resid 298 through 303
    Processing helix  chain 'F' and resid 51 through 53
      No H-bonds generated for 'chain 'F' and resid 51 through 53'
    Processing helix  chain 'F' and resid 68 through 78
      removed outlier: 3.560A  pdb=" N   THR F  77 " --> pdb=" O   LEU F  73 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 102 through 114
      removed outlier: 3.704A  pdb=" N   ASN F 114 " --> pdb=" O   GLU F 110 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 114 through 130
      removed outlier: 3.753A  pdb=" N   GLN F 127 " --> pdb=" O   ARG F 123 " (cutoff:3.500A)
      removed outlier: 4.331A  pdb=" N   MET F 128 " --> pdb=" O   ARG F 124 " (cutoff:3.500A)
      removed outlier: 3.751A  pdb=" N   ARG F 129 " --> pdb=" O   MET F 125 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 183 through 204
    Processing helix  chain 'F' and resid 219 through 226
    Processing helix  chain 'F' and resid 226 through 231
      removed outlier: 4.306A  pdb=" N   ALA F 231 " --> pdb=" O   ASP F 227 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 233 through 244
    Processing helix  chain 'F' and resid 250 through 267
      removed outlier: 3.534A  pdb=" N   ARG F 256 " --> pdb=" O   GLY F 252 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 267 through 280
      removed outlier: 4.024A  pdb=" N   VAL F 273 " --> pdb=" O   LEU F 269 " (cutoff:3.500A)
      removed outlier: 3.753A  pdb=" N   LYS F 274 " --> pdb=" O   LYS F 270 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'K' and resid 161 through 164
      removed outlier: 3.655A  pdb=" N   PHE K 161 " --> pdb=" O   ALA K 150 " (cutoff:3.500A)
      removed outlier: 3.548A  pdb=" N   GLU K 147 " --> pdb=" O   GLU K 134 " (cutoff:3.500A)
      removed outlier: 3.556A  pdb=" N   GLU K 134 " --> pdb=" O   GLU K 147 " (cutoff:3.500A)
      removed outlier: 3.891A  pdb=" N   TYR K 128 " --> pdb=" O   CYS K 153 " (cutoff:3.500A)
      removed outlier: 5.512A  pdb=" N   VAL K 129 " --> pdb=" O   VAL K 209 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'D' and resid 24 through 25
      removed outlier: 4.485A  pdb=" N   ALA D  56 " --> pdb=" O   GLU D  73 " (cutoff:3.500A)
      removed outlier: 3.821A  pdb=" N   GLU D  73 " --> pdb=" O   ALA D  56 " (cutoff:3.500A)
      removed outlier: 3.811A  pdb=" N   PHE D  60 " --> pdb=" O   ASP D  69 " (cutoff:3.500A)
      removed outlier: 3.588A  pdb=" N   ASP D  69 " --> pdb=" O   PHE D  60 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'D' and resid 78 through 81
      removed outlier: 5.591A  pdb=" N   ILE D  88 " --> pdb=" O   ARG C  49 " (cutoff:3.500A)
      removed outlier: 4.515A  pdb=" N   ARG C  49 " --> pdb=" O   ILE D  88 " (cutoff:3.500A)
      removed outlier: 3.618A  pdb=" N   SER C  67 " --> pdb=" O   ILE C  32 " (cutoff:3.500A)
      removed outlier: 6.890A  pdb=" N   ARG C  34 " --> pdb=" O   SER C  67 " (cutoff:3.500A)
      removed outlier: 6.253A  pdb=" N   ALA B  30 " --> pdb=" O   ASP B  65 " (cutoff:3.500A)
      removed outlier: 7.964A  pdb=" N   SER B  67 " --> pdb=" O   ALA B  30 " (cutoff:3.500A)
      removed outlier: 7.215A  pdb=" N   ILE B  32 " --> pdb=" O   SER B  67 " (cutoff:3.500A)
      removed outlier: 3.888A  pdb=" N   GLY B  46 " --> pdb=" O   GLU B  43 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 24 through 27
      removed outlier: 5.679A  pdb=" N   GLU A  25 " --> pdb=" O   VAL A  32 " (cutoff:3.500A)
      removed outlier: 7.295A  pdb=" N   VAL A  32 " --> pdb=" O   GLU A  25 " (cutoff:3.500A)
      removed outlier: 3.762A  pdb=" N   ALA A  27 " --> pdb=" O   VAL A  30 " (cutoff:3.500A)
      removed outlier: 3.608A  pdb=" N   ALA A  56 " --> pdb=" O   GLU A  73 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'A' and resid 78 through 82
      removed outlier: 6.773A  pdb=" N   ARG F  34 " --> pdb=" O   SER F  67 " (cutoff:3.500A)
      removed outlier: 8.208A  pdb=" N   ILE E  32 " --> pdb=" O   SER E  67 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'B' and resid 289 through 291
      removed outlier: 7.773A  pdb=" N   VAL B  57 " --> pdb=" O   ARG B  21 " (cutoff:3.500A)
      removed outlier: 5.576A  pdb=" N   THR B  23 " --> pdb=" O   VAL B  57 " (cutoff:3.500A)
      removed outlier: 6.603A  pdb=" N   LEU B  59 " --> pdb=" O   THR B  23 " (cutoff:3.500A)
      removed outlier: 6.596A  pdb=" N   ILE B  25 " --> pdb=" O   LEU B  59 " (cutoff:3.500A)
      removed outlier: 3.621A  pdb=" N   VAL B  82 " --> pdb=" O   LEU B  58 " (cutoff:3.500A)
      removed outlier: 5.731A  pdb=" N   LEU B  81 " --> pdb=" O   GLY B  95 " (cutoff:3.500A)
      removed outlier: 3.836A  pdb=" N   GLY C  88 " --> pdb=" O   GLY C  85 " (cutoff:3.500A)
      removed outlier: 3.536A  pdb=" N   GLY C  85 " --> pdb=" O   GLY C  88 " (cutoff:3.500A)
      removed outlier: 7.106A  pdb=" N   TRP C  83 " --> pdb=" O   ARG C  90 " (cutoff:3.500A)
      removed outlier: 4.915A  pdb=" N   TYR C  92 " --> pdb=" O   LEU C  81 " (cutoff:3.500A)
      removed outlier: 6.835A  pdb=" N   LEU C  81 " --> pdb=" O   TYR C  92 " (cutoff:3.500A)
      removed outlier: 6.326A  pdb=" N   LEU C  58 " --> pdb=" O   VAL C  82 " (cutoff:3.500A)
      removed outlier: 7.335A  pdb=" N   VAL C  84 " --> pdb=" O   LEU C  58 " (cutoff:3.500A)
      removed outlier: 5.369A  pdb=" N   LEU C  60 " --> pdb=" O   VAL C  84 " (cutoff:3.500A)
      removed outlier: 6.195A  pdb=" N   ILE C  25 " --> pdb=" O   LEU C  59 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'B' and resid 214 through 215
    Processing sheet with id=AA8, first strand: chain 'E' and resid 289 through 292
      removed outlier: 6.293A  pdb=" N   ALA E  22 " --> pdb=" O   GLU E 291 " (cutoff:3.500A)
      removed outlier: 7.785A  pdb=" N   VAL E  57 " --> pdb=" O   ARG E  21 " (cutoff:3.500A)
      removed outlier: 5.745A  pdb=" N   THR E  23 " --> pdb=" O   VAL E  57 " (cutoff:3.500A)
      removed outlier: 6.708A  pdb=" N   LEU E  59 " --> pdb=" O   THR E  23 " (cutoff:3.500A)
      removed outlier: 6.086A  pdb=" N   ILE E  25 " --> pdb=" O   LEU E  59 " (cutoff:3.500A)
      removed outlier: 6.196A  pdb=" N   LEU E  58 " --> pdb=" O   VAL E  82 " (cutoff:3.500A)
      removed outlier: 6.978A  pdb=" N   VAL E  84 " --> pdb=" O   LEU E  58 " (cutoff:3.500A)
      removed outlier: 5.563A  pdb=" N   LEU E  60 " --> pdb=" O   VAL E  84 " (cutoff:3.500A)
      removed outlier: 5.918A  pdb=" N   LEU E  81 " --> pdb=" O   GLY E  95 " (cutoff:3.500A)
      removed outlier: 3.770A  pdb=" N   TYR F  91 " --> pdb=" O   TRP F  83 " (cutoff:3.500A)
      removed outlier: 3.515A  pdb=" N   LEU F  81 " --> pdb=" O   ALA F  93 " (cutoff:3.500A)
      removed outlier: 3.618A  pdb=" N   VAL F  82 " --> pdb=" O   LEU F  58 " (cutoff:3.500A)
      removed outlier: 6.455A  pdb=" N   THR F  23 " --> pdb=" O   VAL F  57 " (cutoff:3.500A)
      removed outlier: 7.345A  pdb=" N   LEU F  59 " --> pdb=" O   THR F  23 " (cutoff:3.500A)
      removed outlier: 6.064A  pdb=" N   ILE F  25 " --> pdb=" O   LEU F  59 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'E' and resid 47 through 48

    568 hydrogen bonds defined for protein.
    1635 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      104 hydrogen bonds
      196 hydrogen bond angles
      0 basepair planarities
      44 basepair parallelities
      103 stacking parallelities
  Total time for adding SS restraints: 4.89

  Time building geometry restraints manager: 4.28 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:                         0.010
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             0.670
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.020
  Extract box with map and model:          0.540
  Check model and map are aligned:         0.090
  Set scattering table:                    0.130
  Process input model:                     38.450
  Find NCS groups from input model:        0.380
  Set up NCS constraints:                  0.070
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.010
  Load rotamer database and sin/cos tables:2.930
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   43.300
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7526
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.077  15146  Z= 0.252
  Angle     :  0.684   8.108  21110  Z= 0.429
  Chirality :  0.046   0.331   2379
  Planarity :  0.004   0.051   2203
  Dihedral  : 20.674 178.623   5982
  Min Nonbonded Distance : 2.196

Molprobity Statistics.
  All-atom Clashscore : 18.87
  Ramachandran Plot:
    Outliers :  0.07 %
    Allowed  :  3.22 %
    Favored  : 96.71 %
  Rotamer:
    Outliers :  0.25 %
    Allowed  :  1.16 %
    Favored  : 98.60 %
  Cbeta Deviations :  0.15 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.60 (0.21), residues: 1459
  helix:  0.48 (0.21), residues: 624
  sheet: -0.95 (0.34), residues: 211
  loop : -1.00 (0.23), residues: 624

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

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

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

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

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

  2918 Ramachandran restraints generated.
    1459 Oldfield, 0 Emsley, 1459 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  304 residues out of total 1210 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 301
  time to evaluate  : 1.274 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: K  271 ARG cc_start: 0.7809 (mtt180) cc_final: 0.7533 (mmt180)
REVERT: D   69 ASP cc_start: 0.8191 (t70) cc_final: 0.7957 (t70)
REVERT: A   49 GLU cc_start: 0.8822 (mm-30) cc_final: 0.8269 (mt-10)
REVERT: B   81 LEU cc_start: 0.8752 (tt) cc_final: 0.8506 (tt)
REVERT: B   86 GLU cc_start: 0.8038 (tp30) cc_final: 0.7831 (tp30)
REVERT: B  141 GLN cc_start: 0.9381 (tm-30) cc_final: 0.8875 (tm-30)
REVERT: B  163 ASN cc_start: 0.8846 (m-40) cc_final: 0.8543 (m-40)
REVERT: B  217 HIS cc_start: 0.9200 (t-90) cc_final: 0.8844 (t70)
REVERT: C  156 ARG cc_start: 0.9251 (mtt180) cc_final: 0.8567 (tpp80)
REVERT: C  197 VAL cc_start: 0.8996 (t) cc_final: 0.8762 (p)
REVERT: C  253 GLN cc_start: 0.7502 (tm-30) cc_final: 0.7148 (tp40)
REVERT: C  282 ILE cc_start: 0.9182 (mm) cc_final: 0.8981 (mm)
REVERT: C  295 LEU cc_start: 0.9372 (mm) cc_final: 0.9144 (mm)
REVERT: E   69 ARG cc_start: 0.7745 (tpm170) cc_final: 0.7099 (tpm170)
REVERT: E  272 MET cc_start: 0.9143 (mpp) cc_final: 0.8934 (mpp)
REVERT: F  114 ASN cc_start: 0.9107 (m110) cc_final: 0.8903 (t0)
REVERT: F  125 MET cc_start: 0.8866 (ttt) cc_final: 0.8263 (tmm)
REVERT: F  190 HIS cc_start: 0.7674 (m170) cc_final: 0.7453 (m-70)
  outliers start: 3
  outliers final: 0
  residues processed: 301
  average time/residue: 0.2885
  time to fit residues: 122.6175
Evaluate side-chains
  223 residues out of total 1210 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 223
  time to evaluate  : 1.477 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 159
   random chunks:
   chunk 134 optimal weight:   10.0000
   chunk 120 optimal weight:    0.0050
   chunk 66 optimal weight:    1.9990
   chunk 41 optimal weight:    9.9990
   chunk 81 optimal weight:    3.9990
   chunk 64 optimal weight:    8.9990
   chunk 124 optimal weight:   10.0000
   chunk 48 optimal weight:    5.9990
   chunk 75 optimal weight:    6.9990
   chunk 92 optimal weight:    8.9990
   chunk 144 optimal weight:    0.7980
   overall best weight:    2.5600

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

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

Total number of N/Q/H flips: 8

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3974 r_free = 0.3974 target = 0.098872 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3479 r_free = 0.3479 target = 0.076660 restraints weight = 72097.598|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3538 r_free = 0.3538 target = 0.078714 restraints weight = 42903.380|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3568 r_free = 0.3568 target = 0.079947 restraints weight = 30304.823|
|-----------------------------------------------------------------------------|
r_work (final): 0.3541
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3541
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3541 r_free = 0.3541    target_work(ls_wunit_k1) = 0.079         |
| occupancies: max = 1.00  min = 0.26   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3540 r_free = 0.3540    target_work(ls_wunit_k1) = 0.079         |
| occupancies: max = 1.00  min = 0.27   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3540
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7547
moved from start:          0.1842

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

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

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

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

Details of bonding type rmsd
  hydrogen bonds       : bond        0.07178 (  672)
  hydrogen bonds       : angle       5.36542 ( 1831)
  covalent geometry    : bond        0.00444 (15146)
  covalent geometry    : angle       0.65103 (21110)

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

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

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

  2918 Ramachandran restraints generated.
    1459 Oldfield, 0 Emsley, 1459 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  274 residues out of total 1210 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 273
  time to evaluate  : 1.343 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: K  271 ARG cc_start: 0.7973 (mtt180) cc_final: 0.7583 (mmt180)
REVERT: D   69 ASP cc_start: 0.8407 (t70) cc_final: 0.8175 (t70)
REVERT: B  125 MET cc_start: 0.8655 (mpp) cc_final: 0.8415 (mpp)
REVERT: B  134 ASP cc_start: 0.9111 (m-30) cc_final: 0.8590 (t0)
REVERT: B  141 GLN cc_start: 0.9387 (tm-30) cc_final: 0.9104 (tm-30)
REVERT: B  217 HIS cc_start: 0.9190 (t-90) cc_final: 0.8834 (t70)
REVERT: C   81 LEU cc_start: 0.8826 (mm) cc_final: 0.8614 (mm)
REVERT: C  156 ARG cc_start: 0.8892 (mtt180) cc_final: 0.8672 (tpp80)
REVERT: C  282 ILE cc_start: 0.9114 (mm) cc_final: 0.8763 (mm)
REVERT: E   83 TRP cc_start: 0.8405 (m-90) cc_final: 0.7657 (m-90)
REVERT: E  272 MET cc_start: 0.9146 (mpp) cc_final: 0.8864 (mpp)
REVERT: F   15 LEU cc_start: 0.9285 (mt) cc_final: 0.9048 (mt)
REVERT: F   19 GLU cc_start: 0.8427 (mm-30) cc_final: 0.7939 (mm-30)
  outliers start: 1
  outliers final: 1
  residues processed: 274
  average time/residue: 0.2607
  time to fit residues: 104.2256
Evaluate side-chains
  207 residues out of total 1210 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 206
  time to evaluate  : 1.301 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 159
   random chunks:
   chunk 68 optimal weight:    0.9980
   chunk 114 optimal weight:    4.9990
   chunk 94 optimal weight:    0.9990
   chunk 66 optimal weight:    7.9990
   chunk 131 optimal weight:    0.8980
   chunk 112 optimal weight:    6.9990
   chunk 26 optimal weight:    0.4980
   chunk 13 optimal weight:   10.0000
   chunk 11 optimal weight:    0.0970
   chunk 72 optimal weight:    2.9990
   chunk 142 optimal weight:    7.9990
   overall best weight:    0.6980

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

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

Total number of N/Q/H flips: 8

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4031 r_free = 0.4031 target = 0.102122 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3539 r_free = 0.3539 target = 0.079520 restraints weight = 71379.033|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 42)----------------|
| r_work = 0.3602 r_free = 0.3602 target = 0.081735 restraints weight = 41018.916|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 41)----------------|
| r_work = 0.3636 r_free = 0.3636 target = 0.083197 restraints weight = 28646.601|
|-----------------------------------------------------------------------------|
r_work (final): 0.3615
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3615
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3615 r_free = 0.3615    target_work(ls_wunit_k1) = 0.082         |
| occupancies: max = 1.00  min = 0.27   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3615 r_free = 0.3615    target_work(ls_wunit_k1) = 0.082         |
| occupancies: max = 1.00  min = 0.26   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3615
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7453
moved from start:          0.2542

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.045  15146  Z= 0.146
  Angle     :  0.607   6.603  21110  Z= 0.334
  Chirality :  0.041   0.172   2379
  Planarity :  0.004   0.049   2203
  Dihedral  : 24.122 179.493   3215
  Min Nonbonded Distance : 2.177

Molprobity Statistics.
  All-atom Clashscore : 14.18
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.88 %
    Favored  : 97.12 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  5.54 %
    Favored  : 94.46 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.66 (0.21), residues: 1459
  helix:  0.55 (0.19), residues: 677
  sheet: -1.21 (0.33), residues: 218
  loop : -1.22 (0.24), residues: 564

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.037   0.002   TRP B  83 
 HIS   0.007   0.001   HIS F 217 
 PHE   0.018   0.002   PHE K 202 
 TYR   0.020   0.001   TYR F  91 
 ARG   0.015   0.001   ARG A  77 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05811 (  672)
  hydrogen bonds       : angle       4.75733 ( 1831)
  covalent geometry    : bond        0.00316 (15146)
  covalent geometry    : angle       0.60706 (21110)

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

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

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

  2918 Ramachandran restraints generated.
    1459 Oldfield, 0 Emsley, 1459 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  283 residues out of total 1210 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 283
  time to evaluate  : 1.271 
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: 0.8094 (mtt180) cc_final: 0.7706 (mmt180)
REVERT: D   21 ARG cc_start: 0.8502 (ttm110) cc_final: 0.8284 (ttm110)
REVERT: D   38 ARG cc_start: 0.8488 (tmm-80) cc_final: 0.8125 (tmm-80)
REVERT: D   41 GLU cc_start: 0.8533 (mp0) cc_final: 0.8031 (mp0)
REVERT: D   69 ASP cc_start: 0.8456 (t70) cc_final: 0.8106 (t70)
REVERT: A   20 THR cc_start: 0.9066 (p) cc_final: 0.8797 (t)
REVERT: B  134 ASP cc_start: 0.9109 (m-30) cc_final: 0.8530 (t0)
REVERT: B  163 ASN cc_start: 0.9024 (m-40) cc_final: 0.8755 (m-40)
REVERT: B  210 LEU cc_start: 0.8882 (mm) cc_final: 0.8641 (mm)
REVERT: B  217 HIS cc_start: 0.9263 (t-90) cc_final: 0.8874 (t70)
REVERT: C  282 ILE cc_start: 0.9090 (mm) cc_final: 0.8824 (mm)
REVERT: F   15 LEU cc_start: 0.9193 (mt) cc_final: 0.8946 (mt)
  outliers start: 0
  outliers final: 0
  residues processed: 283
  average time/residue: 0.2526
  time to fit residues: 104.2250
Evaluate side-chains
  211 residues out of total 1210 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 211
  time to evaluate  : 1.301 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 159
   random chunks:
   chunk 100 optimal weight:   20.0000
   chunk 1 optimal weight:    7.9990
   chunk 21 optimal weight:    7.9990
   chunk 35 optimal weight:    9.9990
   chunk 42 optimal weight:   10.0000
   chunk 111 optimal weight:   10.0000
   chunk 5 optimal weight:    6.9990
   chunk 26 optimal weight:    0.5980
   chunk 53 optimal weight:    6.9990
   chunk 153 optimal weight:   10.0000
   chunk 89 optimal weight:   10.0000
   overall best weight:    6.1188

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

Flipped N/Q/H residues before XYZ refinement:
K 222 GLN
** A  34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 190 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 142 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 146 HIS
C 183 ASN
** C 184 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 217 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
C 253 GLN
F  33 ASN
** F 184 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3909 r_free = 0.3909 target = 0.094891 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3394 r_free = 0.3394 target = 0.072761 restraints weight = 74328.998|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3450 r_free = 0.3450 target = 0.074576 restraints weight = 44840.063|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3482 r_free = 0.3482 target = 0.075843 restraints weight = 32088.396|
|-----------------------------------------------------------------------------|
r_work (final): 0.3454
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3454
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3454 r_free = 0.3454    target_work(ls_wunit_k1) = 0.075         |
| occupancies: max = 1.00  min = 0.26   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3454 r_free = 0.3454    target_work(ls_wunit_k1) = 0.075         |
| occupancies: max = 1.00  min = 0.18   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3454
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7651
moved from start:          0.2951

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.008   0.062  15146  Z= 0.349
  Angle     :  0.763  10.639  21110  Z= 0.418
  Chirality :  0.046   0.176   2379
  Planarity :  0.006   0.057   2203
  Dihedral  : 24.463 173.360   3215
  Min Nonbonded Distance : 2.016

Molprobity Statistics.
  All-atom Clashscore : 24.44
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.52 %
    Favored  : 95.48 %
  Rotamer:
    Outliers :  0.08 %
    Allowed  :  6.28 %
    Favored  : 93.64 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.21 (0.21), residues: 1459
  helix:  0.03 (0.19), residues: 673
  sheet: -1.53 (0.32), residues: 217
  loop : -1.38 (0.24), residues: 569

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.021   0.003   TRP B  83 
 HIS   0.007   0.002   HIS E  29 
 PHE   0.023   0.002   PHE K 224 
 TYR   0.035   0.003   TYR B 194 
 ARG   0.009   0.001   ARG D  77 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.07680 (  672)
  hydrogen bonds       : angle       5.20533 ( 1831)
  covalent geometry    : bond        0.00752 (15146)
  covalent geometry    : angle       0.76268 (21110)

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

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

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

  2918 Ramachandran restraints generated.
    1459 Oldfield, 0 Emsley, 1459 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  251 residues out of total 1210 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 250
  time to evaluate  : 1.502 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: K  158 GLU cc_start: 0.6689 (mp0) cc_final: 0.6482 (mp0)
REVERT: K  271 ARG cc_start: 0.8099 (mtt180) cc_final: 0.7668 (mmt180)
REVERT: D   38 ARG cc_start: 0.8675 (tmm-80) cc_final: 0.8085 (tmm-80)
REVERT: D   41 GLU cc_start: 0.8569 (mp0) cc_final: 0.7803 (mp0)
REVERT: D   63 ARG cc_start: 0.8351 (mmt180) cc_final: 0.7672 (mmm160)
REVERT: D   69 ASP cc_start: 0.8664 (t70) cc_final: 0.8126 (t70)
REVERT: A   20 THR cc_start: 0.9092 (p) cc_final: 0.8890 (t)
REVERT: B  125 MET cc_start: 0.8690 (mpp) cc_final: 0.8456 (mpp)
REVERT: B  217 HIS cc_start: 0.9253 (t-90) cc_final: 0.8878 (t70)
REVERT: C   28 GLU cc_start: 0.7650 (tm-30) cc_final: 0.7298 (tm-30)
REVERT: C   72 GLU cc_start: 0.8626 (tt0) cc_final: 0.8277 (tp30)
REVERT: C  184 GLN cc_start: 0.9154 (pm20) cc_final: 0.8799 (pm20)
REVERT: C  282 ILE cc_start: 0.9201 (mm) cc_final: 0.8828 (mm)
REVERT: E   69 ARG cc_start: 0.7646 (tpm170) cc_final: 0.7308 (tpm170)
REVERT: E  128 MET cc_start: 0.8980 (tpp) cc_final: 0.8768 (tpp)
REVERT: E  272 MET cc_start: 0.8929 (mpp) cc_final: 0.8611 (mpp)
REVERT: F   15 LEU cc_start: 0.9357 (mt) cc_final: 0.9124 (mt)
REVERT: F  198 HIS cc_start: 0.8484 (t70) cc_final: 0.8211 (t-90)
  outliers start: 1
  outliers final: 0
  residues processed: 251
  average time/residue: 0.2736
  time to fit residues: 99.9935
Evaluate side-chains
  194 residues out of total 1210 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 194
  time to evaluate  : 1.376 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 159
   random chunks:
   chunk 152 optimal weight:    6.9990
   chunk 22 optimal weight:    0.7980
   chunk 73 optimal weight:    8.9990
   chunk 21 optimal weight:    1.9990
   chunk 100 optimal weight:   10.0000
   chunk 52 optimal weight:    7.9990
   chunk 153 optimal weight:    8.9990
   chunk 2 optimal weight:    8.9990
   chunk 128 optimal weight:    1.9990
   chunk 4 optimal weight:   20.0000
   chunk 32 optimal weight:    1.9990
   overall best weight:    2.7588

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

Flipped N/Q/H residues before XYZ refinement:
** K 212 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 190 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 142 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 146 HIS
** C 217 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
F  33 ASN
** F 184 GLN ** 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 = 0.3971 r_free = 0.3971 target = 0.098476 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3446 r_free = 0.3446 target = 0.075410 restraints weight = 91276.863|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3509 r_free = 0.3509 target = 0.077667 restraints weight = 49382.911|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 42)----------------|
| r_work = 0.3546 r_free = 0.3546 target = 0.079218 restraints weight = 33239.527|
|-----------------------------------------------------------------------------|
r_work (final): 0.3517
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3517
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3517 r_free = 0.3517    target_work(ls_wunit_k1) = 0.078         |
| occupancies: max = 1.00  min = 0.18   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3517 r_free = 0.3517    target_work(ls_wunit_k1) = 0.078         |
| occupancies: max = 1.00  min = 0.27   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3517
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7584
moved from start:          0.3126

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= 0.196
  Angle     :  0.650   7.529  21110  Z= 0.356
  Chirality :  0.043   0.176   2379
  Planarity :  0.004   0.055   2203
  Dihedral  : 24.564 179.250   3215
  Min Nonbonded Distance : 2.095

Molprobity Statistics.
  All-atom Clashscore : 19.40
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.63 %
    Favored  : 96.37 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  3.47 %
    Favored  : 96.53 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.05 (0.21), residues: 1459
  helix:  0.22 (0.19), residues: 673
  sheet: -1.45 (0.32), residues: 218
  loop : -1.38 (0.24), residues: 568

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.046   0.003   TRP B  83 
 HIS   0.008   0.001   HIS E  29 
 PHE   0.022   0.002   PHE K 224 
 TYR   0.035   0.002   TYR E 229 
 ARG   0.012   0.001   ARG D  77 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05795 (  672)
  hydrogen bonds       : angle       4.83096 ( 1831)
  covalent geometry    : bond        0.00434 (15146)
  covalent geometry    : angle       0.65028 (21110)

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

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

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

  2918 Ramachandran restraints generated.
    1459 Oldfield, 0 Emsley, 1459 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  256 residues out of total 1210 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 256
  time to evaluate  : 1.295 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: K  142 ARG cc_start: 0.6221 (mtt180) cc_final: 0.4359 (mtm180)
REVERT: K  220 LEU cc_start: 0.6419 (tt) cc_final: 0.6199 (tt)
REVERT: K  227 TYR cc_start: 0.7520 (m-80) cc_final: 0.7309 (m-10)
REVERT: K  271 ARG cc_start: 0.8280 (mtt180) cc_final: 0.7823 (mmt180)
REVERT: D   38 ARG cc_start: 0.8631 (tmm-80) cc_final: 0.8113 (tmm-80)
REVERT: D   41 GLU cc_start: 0.8536 (mp0) cc_final: 0.7732 (mp0)
REVERT: D   69 ASP cc_start: 0.8495 (t70) cc_final: 0.8224 (t70)
REVERT: B   84 VAL cc_start: 0.8226 (m) cc_final: 0.7176 (m)
REVERT: B  125 MET cc_start: 0.8605 (mpp) cc_final: 0.8386 (mpp)
REVERT: B  134 ASP cc_start: 0.9102 (m-30) cc_final: 0.8355 (t0)
REVERT: B  163 ASN cc_start: 0.9024 (m-40) cc_final: 0.8797 (m-40)
REVERT: B  217 HIS cc_start: 0.9210 (t-90) cc_final: 0.8867 (t70)
REVERT: C   72 GLU cc_start: 0.8446 (tt0) cc_final: 0.8057 (tp30)
REVERT: C  184 GLN cc_start: 0.9206 (pm20) cc_final: 0.8960 (pm20)
REVERT: C  282 ILE cc_start: 0.9146 (mm) cc_final: 0.8820 (mm)
REVERT: E  239 PHE cc_start: 0.8663 (m-80) cc_final: 0.8441 (m-80)
REVERT: F   15 LEU cc_start: 0.9299 (mt) cc_final: 0.9078 (mt)
REVERT: F  128 MET cc_start: 0.7539 (pmm) cc_final: 0.7309 (pmm)
  outliers start: 0
  outliers final: 0
  residues processed: 256
  average time/residue: 0.2651
  time to fit residues: 98.3334
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  : 1.342 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 159
   random chunks:
   chunk 87 optimal weight:    5.9990
   chunk 126 optimal weight:    7.9990
   chunk 11 optimal weight:    6.9990
   chunk 43 optimal weight:    7.9990
   chunk 89 optimal weight:    3.9990
   chunk 48 optimal weight:    1.9990
   chunk 151 optimal weight:    6.9990
   chunk 82 optimal weight:   10.0000
   chunk 155 optimal weight:    5.9990
   chunk 60 optimal weight:   20.0000
   chunk 0 optimal weight:   30.0000
   overall best weight:    4.9990

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

Flipped N/Q/H residues before XYZ refinement:
** K 212 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 190 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 142 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 146 HIS
** C 184 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 217 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
C 253 GLN
** C 308 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** 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 = 0.3908 r_free = 0.3908 target = 0.095263 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3385 r_free = 0.3385 target = 0.072301 restraints weight = 100009.945|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 45)----------------|
| r_work = 0.3444 r_free = 0.3444 target = 0.074458 restraints weight = 54342.953|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.3479 r_free = 0.3479 target = 0.075932 restraints weight = 36475.600|
|-----------------------------------------------------------------------------|
r_work (final): 0.3451
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3452
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3452 r_free = 0.3452    target_work(ls_wunit_k1) = 0.075         |
| occupancies: max = 1.00  min = 0.27   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3452 r_free = 0.3452    target_work(ls_wunit_k1) = 0.075         |
| occupancies: max = 1.00  min = 0.27   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3452
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7678
moved from start:          0.3443

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.051  15146  Z= 0.297
  Angle     :  0.724   7.512  21110  Z= 0.397
  Chirality :  0.046   0.206   2379
  Planarity :  0.007   0.159   2203
  Dihedral  : 24.807 174.683   3215
  Min Nonbonded Distance : 2.022

Molprobity Statistics.
  All-atom Clashscore : 23.37
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.80 %
    Favored  : 95.20 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  4.46 %
    Favored  : 95.54 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.39 (0.21), residues: 1459
  helix: -0.04 (0.19), residues: 676
  sheet: -1.67 (0.33), residues: 215
  loop : -1.58 (0.24), residues: 568

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.023   0.002   TRP B  83 
 HIS   0.010   0.001   HIS E  29 
 PHE   0.030   0.002   PHE K 224 
 TYR   0.037   0.002   TYR E 229 
 ARG   0.011   0.001   ARG E  34 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.07199 (  672)
  hydrogen bonds       : angle       5.09084 ( 1831)
  covalent geometry    : bond        0.00645 (15146)
  covalent geometry    : angle       0.72422 (21110)

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

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

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

  2918 Ramachandran restraints generated.
    1459 Oldfield, 0 Emsley, 1459 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  247 residues out of total 1210 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 247
  time to evaluate  : 1.293 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: K  142 ARG cc_start: 0.6125 (mtt180) cc_final: 0.4203 (mtm180)
REVERT: K  192 GLU cc_start: 0.7643 (pt0) cc_final: 0.7339 (mt-10)
REVERT: K  271 ARG cc_start: 0.8407 (mtt180) cc_final: 0.7930 (mmt180)
REVERT: D   41 GLU cc_start: 0.8519 (mp0) cc_final: 0.7740 (mp0)
REVERT: D   63 ARG cc_start: 0.8314 (mmt180) cc_final: 0.7603 (mmm160)
REVERT: D   69 ASP cc_start: 0.8682 (t70) cc_final: 0.8159 (t70)
REVERT: A   20 THR cc_start: 0.9132 (p) cc_final: 0.8917 (t)
REVERT: A   77 ARG cc_start: 0.8168 (mtt-85) cc_final: 0.7952 (mtt180)
REVERT: B  163 ASN cc_start: 0.9056 (m-40) cc_final: 0.8848 (m-40)
REVERT: B  217 HIS cc_start: 0.9206 (t-90) cc_final: 0.8892 (t70)
REVERT: C   72 GLU cc_start: 0.8652 (tt0) cc_final: 0.8080 (tp30)
REVERT: C  184 GLN cc_start: 0.9197 (pm20) cc_final: 0.8925 (pm20)
REVERT: C  282 ILE cc_start: 0.9175 (mm) cc_final: 0.8871 (mm)
REVERT: E  239 PHE cc_start: 0.8756 (m-80) cc_final: 0.8384 (m-80)
REVERT: F   15 LEU cc_start: 0.9373 (mt) cc_final: 0.9171 (mt)
REVERT: F  128 MET cc_start: 0.7769 (pmm) cc_final: 0.7566 (pmm)
REVERT: F  198 HIS cc_start: 0.8348 (t-90) cc_final: 0.7919 (t-90)
  outliers start: 0
  outliers final: 0
  residues processed: 247
  average time/residue: 0.2652
  time to fit residues: 94.7632
Evaluate side-chains
  203 residues out of total 1210 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 203
  time to evaluate  : 1.297 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 159
   random chunks:
   chunk 96 optimal weight:    5.9990
   chunk 95 optimal weight:    6.9990
   chunk 108 optimal weight:    6.9990
   chunk 79 optimal weight:    6.9990
   chunk 17 optimal weight:    8.9990
   chunk 86 optimal weight:    0.9990
   chunk 152 optimal weight:    8.9990
   chunk 12 optimal weight:   10.0000
   chunk 78 optimal weight:    1.9990
   chunk 66 optimal weight:    8.9990
   chunk 32 optimal weight:    0.8980
   overall best weight:    3.3788

-------------------------------------------------------------------------------
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
** A  34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 142 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 146 HIS
** C 217 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
F  33 ASN
F 184 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3941 r_free = 0.3941 target = 0.096779 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3434 r_free = 0.3434 target = 0.074527 restraints weight = 74207.674|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 44)----------------|
| r_work = 0.3491 r_free = 0.3491 target = 0.076380 restraints weight = 44202.452|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3520 r_free = 0.3520 target = 0.077576 restraints weight = 31539.263|
|-----------------------------------------------------------------------------|
r_work (final): 0.3496
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3496
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3496 r_free = 0.3496    target_work(ls_wunit_k1) = 0.077         |
| occupancies: max = 1.00  min = 0.27   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3496 r_free = 0.3496    target_work(ls_wunit_k1) = 0.077         |
| occupancies: max = 1.00  min = 0.27   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3496
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7625
moved from start:          0.3552

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.040  15146  Z= 0.221
  Angle     :  0.671   6.887  21110  Z= 0.368
  Chirality :  0.044   0.192   2379
  Planarity :  0.005   0.122   2203
  Dihedral  : 24.869 178.540   3215
  Min Nonbonded Distance : 2.078

Molprobity Statistics.
  All-atom Clashscore : 21.04
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.25 %
    Favored  : 95.75 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.23 %
    Favored  : 97.77 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.26 (0.21), residues: 1459
  helix:  0.11 (0.19), residues: 675
  sheet: -1.65 (0.33), residues: 217
  loop : -1.54 (0.24), residues: 567

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.027   0.002   TRP B  83 
 HIS   0.009   0.001   HIS E  29 
 PHE   0.027   0.002   PHE K 224 
 TYR   0.028   0.002   TYR E 229 
 ARG   0.013   0.001   ARG K 241 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05988 (  672)
  hydrogen bonds       : angle       4.91331 ( 1831)
  covalent geometry    : bond        0.00487 (15146)
  covalent geometry    : angle       0.67079 (21110)

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

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

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

  2918 Ramachandran restraints generated.
    1459 Oldfield, 0 Emsley, 1459 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  261 residues out of total 1210 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 261
  time to evaluate  : 1.490 
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: symmetry clash
REVERT: K  142 ARG cc_start: 0.6223 (mtt180) cc_final: 0.4319 (mtm180)
REVERT: K  192 GLU cc_start: 0.7521 (pt0) cc_final: 0.7177 (mt-10)
REVERT: K  271 ARG cc_start: 0.8408 (mtt180) cc_final: 0.7861 (mmt180)
REVERT: D   41 GLU cc_start: 0.8419 (mp0) cc_final: 0.8204 (mp0)
REVERT: D   63 ARG cc_start: 0.8291 (mmt180) cc_final: 0.7589 (mmm160)
REVERT: D   69 ASP cc_start: 0.8497 (t70) cc_final: 0.8197 (t70)
REVERT: A   20 THR cc_start: 0.9068 (p) cc_final: 0.8858 (t)
REVERT: B   84 VAL cc_start: 0.8232 (m) cc_final: 0.7269 (m)
REVERT: B  134 ASP cc_start: 0.9016 (m-30) cc_final: 0.8432 (t0)
REVERT: B  163 ASN cc_start: 0.8979 (m-40) cc_final: 0.8776 (m-40)
REVERT: B  217 HIS cc_start: 0.9144 (t-90) cc_final: 0.8864 (t70)
REVERT: C   72 GLU cc_start: 0.8508 (tt0) cc_final: 0.8043 (tp30)
REVERT: C  282 ILE cc_start: 0.9160 (mm) cc_final: 0.8874 (mm)
REVERT: E   73 LEU cc_start: 0.9568 (mt) cc_final: 0.9338 (mt)
REVERT: E  128 MET cc_start: 0.8835 (tpp) cc_final: 0.8602 (tpp)
REVERT: E  239 PHE cc_start: 0.8736 (m-80) cc_final: 0.8345 (m-80)
REVERT: E  272 MET cc_start: 0.9013 (mpp) cc_final: 0.8805 (mpp)
REVERT: E  300 GLU cc_start: 0.8571 (mp0) cc_final: 0.8323 (pm20)
REVERT: F   17 ARG cc_start: 0.8406 (mtm-85) cc_final: 0.7883 (ptp-170)
REVERT: F  198 HIS cc_start: 0.8263 (t-90) cc_final: 0.7918 (t-90)
  outliers start: 0
  outliers final: 0
  residues processed: 261
  average time/residue: 0.2981
  time to fit residues: 109.9678
Evaluate side-chains
  211 residues out of total 1210 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 211
  time to evaluate  : 1.481 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 159
   random chunks:
   chunk 75 optimal weight:    7.9990
   chunk 65 optimal weight:   10.0000
   chunk 124 optimal weight:    8.9990
   chunk 20 optimal weight:    5.9990
   chunk 71 optimal weight:    0.1980
   chunk 6 optimal weight:    6.9990
   chunk 2 optimal weight:    0.9980
   chunk 123 optimal weight:    0.9990
   chunk 125 optimal weight:    2.9990
   chunk 43 optimal weight:    0.9980
   chunk 154 optimal weight:    8.9990
   overall best weight:    1.2384

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

Flipped N/Q/H residues before XYZ refinement:
** K 212 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 142 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 146 HIS
** C 217 HIS ** 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 = 0.3993 r_free = 0.3993 target = 0.099572 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3479 r_free = 0.3479 target = 0.076404 restraints weight = 81495.378|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.3539 r_free = 0.3539 target = 0.078550 restraints weight = 45797.531|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3575 r_free = 0.3575 target = 0.080082 restraints weight = 31407.609|
|-----------------------------------------------------------------------------|
r_work (final): 0.3555
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3555
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3555 r_free = 0.3555    target_work(ls_wunit_k1) = 0.079         |
| occupancies: max = 1.00  min = 0.27   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3555 r_free = 0.3555    target_work(ls_wunit_k1) = 0.079         |
| occupancies: max = 1.00  min = 0.28   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3555
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7556
moved from start:          0.3667

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040  15146  Z= 0.157
  Angle     :  0.641   7.020  21110  Z= 0.349
  Chirality :  0.042   0.185   2379
  Planarity :  0.005   0.100   2203
  Dihedral  : 24.778 179.771   3215
  Min Nonbonded Distance : 2.125

Molprobity Statistics.
  All-atom Clashscore : 17.11
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.63 %
    Favored  : 96.37 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.65 %
    Favored  : 98.35 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.01 (0.21), residues: 1459
  helix:  0.32 (0.19), residues: 678
  sheet: -1.52 (0.32), residues: 221
  loop : -1.42 (0.24), residues: 560

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.002   TRP A  22 
 HIS   0.007   0.001   HIS E  29 
 PHE   0.027   0.002   PHE K 224 
 TYR   0.023   0.002   TYR E 229 
 ARG   0.007   0.001   ARG K 241 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05301 (  672)
  hydrogen bonds       : angle       4.58530 ( 1831)
  covalent geometry    : bond        0.00345 (15146)
  covalent geometry    : angle       0.64134 (21110)

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

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

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

  2918 Ramachandran restraints generated.
    1459 Oldfield, 0 Emsley, 1459 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  262 residues out of total 1210 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 262
  time to evaluate  : 1.305 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: K  142 ARG cc_start: 0.6236 (mtt180) cc_final: 0.4306 (mtm180)
REVERT: K  192 GLU cc_start: 0.7336 (pt0) cc_final: 0.6998 (mt-10)
REVERT: K  220 LEU cc_start: 0.6404 (tt) cc_final: 0.6099 (tt)
REVERT: K  271 ARG cc_start: 0.8421 (mtt180) cc_final: 0.7912 (mmt180)
REVERT: D    4 THR cc_start: 0.7884 (t) cc_final: 0.7550 (t)
REVERT: D    9 LYS cc_start: 0.9032 (pttt) cc_final: 0.8801 (pttm)
REVERT: D   38 ARG cc_start: 0.8604 (tmm-80) cc_final: 0.8022 (tmm-80)
REVERT: D   41 GLU cc_start: 0.8417 (mp0) cc_final: 0.7596 (mp0)
REVERT: D   58 MET cc_start: 0.8196 (ttp) cc_final: 0.7623 (tpp)
REVERT: D   69 ASP cc_start: 0.8433 (t70) cc_final: 0.8175 (t70)
REVERT: B  163 ASN cc_start: 0.9056 (m-40) cc_final: 0.8855 (m-40)
REVERT: B  217 HIS cc_start: 0.9075 (t-90) cc_final: 0.8769 (t70)
REVERT: C   72 GLU cc_start: 0.8442 (tt0) cc_final: 0.7958 (tp30)
REVERT: C  282 ILE cc_start: 0.9146 (mm) cc_final: 0.8797 (mm)
REVERT: E  239 PHE cc_start: 0.8719 (m-80) cc_final: 0.8260 (m-80)
REVERT: E  272 MET cc_start: 0.8996 (mpp) cc_final: 0.8774 (mpp)
REVERT: E  300 GLU cc_start: 0.8619 (mp0) cc_final: 0.8366 (pm20)
REVERT: F   15 LEU cc_start: 0.9270 (mt) cc_final: 0.8988 (mt)
  outliers start: 0
  outliers final: 0
  residues processed: 262
  average time/residue: 0.2619
  time to fit residues: 99.2434
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  : 1.293 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 159
   random chunks:
   chunk 56 optimal weight:    1.9990
   chunk 84 optimal weight:    0.6980
   chunk 120 optimal weight:    0.0870
   chunk 112 optimal weight:    0.3980
   chunk 43 optimal weight:    5.9990
   chunk 42 optimal weight:    7.9990
   chunk 37 optimal weight:    3.9990
   chunk 58 optimal weight:    8.9990
   chunk 15 optimal weight:    0.8980
   chunk 55 optimal weight:    1.9990
   chunk 103 optimal weight:    1.9990
   overall best weight:    0.8160

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

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

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4018 r_free = 0.4018 target = 0.100810 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3519 r_free = 0.3519 target = 0.077999 restraints weight = 72199.959|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 47)----------------|
| r_work = 0.3578 r_free = 0.3578 target = 0.080176 restraints weight = 41841.427|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3611 r_free = 0.3611 target = 0.081632 restraints weight = 29010.382|
|-----------------------------------------------------------------------------|
r_work (final): 0.3592
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3592
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3592 r_free = 0.3592    target_work(ls_wunit_k1) = 0.081         |
| occupancies: max = 1.00  min = 0.28   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3592 r_free = 0.3592    target_work(ls_wunit_k1) = 0.081         |
| occupancies: max = 1.00  min = 0.34   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3592
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7509
moved from start:          0.3856

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.056  15146  Z= 0.152
  Angle     :  0.651   8.960  21110  Z= 0.351
  Chirality :  0.043   0.193   2379
  Planarity :  0.005   0.142   2203
  Dihedral  : 24.696 179.685   3215
  Min Nonbonded Distance : 2.122

Molprobity Statistics.
  All-atom Clashscore : 16.44
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.63 %
    Favored  : 96.37 %
  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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.96 (0.21), residues: 1459
  helix:  0.32 (0.19), residues: 684
  sheet: -1.49 (0.32), residues: 223
  loop : -1.36 (0.24), residues: 552

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.042   0.002   TRP B  83 
 HIS   0.006   0.001   HIS E  29 
 PHE   0.027   0.001   PHE K 224 
 TYR   0.032   0.002   TYR B 194 
 ARG   0.011   0.001   ARG K 152 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05244 (  672)
  hydrogen bonds       : angle       4.54276 ( 1831)
  covalent geometry    : bond        0.00340 (15146)
  covalent geometry    : angle       0.65062 (21110)

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

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

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

  2918 Ramachandran restraints generated.
    1459 Oldfield, 0 Emsley, 1459 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  275 residues out of total 1210 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 275
  time to evaluate  : 1.400 
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: 0.6195 (mtt180) cc_final: 0.4291 (mtm180)
REVERT: K  192 GLU cc_start: 0.7260 (pt0) cc_final: 0.6870 (mt-10)
REVERT: K  219 PHE cc_start: 0.3536 (t80) cc_final: 0.3232 (t80)
REVERT: K  220 LEU cc_start: 0.6472 (tt) cc_final: 0.6205 (tt)
REVERT: K  271 ARG cc_start: 0.8432 (mtt180) cc_final: 0.7893 (mmp-170)
REVERT: D    4 THR cc_start: 0.7892 (t) cc_final: 0.7661 (t)
REVERT: D    6 ILE cc_start: 0.8754 (mt) cc_final: 0.8480 (mt)
REVERT: D    9 LYS cc_start: 0.8992 (pttt) cc_final: 0.8699 (pttm)
REVERT: D   38 ARG cc_start: 0.8603 (tmm-80) cc_final: 0.7989 (tmm-80)
REVERT: D   41 GLU cc_start: 0.8466 (mp0) cc_final: 0.7635 (mp0)
REVERT: D   58 MET cc_start: 0.8176 (ttp) cc_final: 0.7558 (tpp)
REVERT: D   69 ASP cc_start: 0.8406 (t70) cc_final: 0.8143 (t70)
REVERT: A    1 MET cc_start: 0.7917 (tpp) cc_final: 0.7666 (mmm)
REVERT: A   20 THR cc_start: 0.9117 (p) cc_final: 0.8885 (t)
REVERT: A   49 GLU cc_start: 0.8821 (mm-30) cc_final: 0.8161 (mt-10)
REVERT: B  134 ASP cc_start: 0.9280 (m-30) cc_final: 0.8557 (t0)
REVERT: B  163 ASN cc_start: 0.9068 (m-40) cc_final: 0.8862 (m-40)
REVERT: B  217 HIS cc_start: 0.9024 (t-90) cc_final: 0.8697 (t70)
REVERT: C   72 GLU cc_start: 0.8584 (tt0) cc_final: 0.8007 (tp30)
REVERT: C   83 TRP cc_start: 0.8377 (m100) cc_final: 0.8037 (m100)
REVERT: C  277 GLN cc_start: 0.8339 (tp-100) cc_final: 0.8076 (tp-100)
REVERT: E   90 ARG cc_start: 0.7582 (ttm110) cc_final: 0.7377 (ttm170)
REVERT: E   91 TYR cc_start: 0.8690 (t80) cc_final: 0.8460 (t80)
REVERT: E  239 PHE cc_start: 0.8808 (m-80) cc_final: 0.8315 (m-80)
REVERT: E  272 MET cc_start: 0.8989 (mpp) cc_final: 0.8757 (mpp)
REVERT: E  300 GLU cc_start: 0.8670 (mp0) cc_final: 0.8358 (pm20)
REVERT: F   15 LEU cc_start: 0.9225 (mt) cc_final: 0.8951 (mt)
  outliers start: 0
  outliers final: 0
  residues processed: 275
  average time/residue: 0.2745
  time to fit residues: 108.5128
Evaluate side-chains
  219 residues out of total 1210 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 219
  time to evaluate  : 1.492 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 159
   random chunks:
   chunk 94 optimal weight:    1.9990
   chunk 22 optimal weight:    6.9990
   chunk 58 optimal weight:    4.9990
   chunk 109 optimal weight:    0.4980
   chunk 98 optimal weight:    5.9990
   chunk 101 optimal weight:    4.9990
   chunk 41 optimal weight:    9.9990
   chunk 147 optimal weight:    7.9990
   chunk 30 optimal weight:    0.9980
   chunk 29 optimal weight:    5.9990
   chunk 105 optimal weight:    3.9990
   overall best weight:    2.4986

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

Flipped N/Q/H residues before XYZ refinement:
** K 212 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 190 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 142 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 146 HIS
C 183 ASN
** 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 = 0.3984 r_free = 0.3984 target = 0.098912 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.3453 r_free = 0.3453 target = 0.075272 restraints weight = 97912.243|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 46)----------------|
| r_work = 0.3517 r_free = 0.3517 target = 0.077656 restraints weight = 52008.290|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 44)----------------|
| r_work = 0.3555 r_free = 0.3555 target = 0.079268 restraints weight = 34441.862|
|-----------------------------------------------------------------------------|
r_work (final): 0.3529
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3529
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3529 r_free = 0.3529    target_work(ls_wunit_k1) = 0.078         |
| occupancies: max = 1.00  min = 0.34   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3529 r_free = 0.3529    target_work(ls_wunit_k1) = 0.078         |
| occupancies: max = 1.00  min = 0.32   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3529
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7574
moved from start:          0.3926

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.043  15146  Z= 0.191
  Angle     :  0.671   9.193  21110  Z= 0.364
  Chirality :  0.043   0.181   2379
  Planarity :  0.005   0.133   2203
  Dihedral  : 24.678 177.847   3215
  Min Nonbonded Distance : 2.084

Molprobity Statistics.
  All-atom Clashscore : 18.87
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.91 %
    Favored  : 96.09 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.17 %
    Favored  : 99.83 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.99 (0.21), residues: 1459
  helix:  0.35 (0.19), residues: 679
  sheet: -1.57 (0.31), residues: 228
  loop : -1.40 (0.24), residues: 552

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.057   0.003   TRP B  83 
 HIS   0.007   0.001   HIS E  29 
 PHE   0.027   0.002   PHE K 224 
 TYR   0.026   0.002   TYR E 229 
 ARG   0.011   0.001   ARG K 241 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05573 (  672)
  hydrogen bonds       : angle       4.60524 ( 1831)
  covalent geometry    : bond        0.00426 (15146)
  covalent geometry    : angle       0.67061 (21110)

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

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

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

  2918 Ramachandran restraints generated.
    1459 Oldfield, 0 Emsley, 1459 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  258 residues out of total 1210 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 258
  time to evaluate  : 1.375 
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: 0.6231 (mtt180) cc_final: 0.4300 (mtm180)
REVERT: K  192 GLU cc_start: 0.7245 (pt0) cc_final: 0.6792 (mt-10)
REVERT: K  220 LEU cc_start: 0.6485 (tt) cc_final: 0.6189 (tt)
REVERT: K  271 ARG cc_start: 0.8427 (mtt180) cc_final: 0.7905 (mmp-170)
REVERT: D    6 ILE cc_start: 0.8738 (mt) cc_final: 0.8514 (mt)
REVERT: D   38 ARG cc_start: 0.8694 (tmm-80) cc_final: 0.8076 (tmm-80)
REVERT: D   41 GLU cc_start: 0.8482 (mp0) cc_final: 0.7708 (mp0)
REVERT: D   58 MET cc_start: 0.8198 (ttp) cc_final: 0.7594 (tpp)
REVERT: A    1 MET cc_start: 0.7935 (tpp) cc_final: 0.7708 (mmm)
REVERT: A   20 THR cc_start: 0.9162 (p) cc_final: 0.8940 (t)
REVERT: B   81 LEU cc_start: 0.8517 (tt) cc_final: 0.8263 (tt)
REVERT: B   86 GLU cc_start: 0.7800 (tp30) cc_final: 0.7481 (tp30)
REVERT: B  134 ASP cc_start: 0.9205 (m-30) cc_final: 0.8511 (t0)
REVERT: B  217 HIS cc_start: 0.9144 (t-90) cc_final: 0.8867 (t70)
REVERT: B  223 TYR cc_start: 0.8156 (m-80) cc_final: 0.7901 (m-80)
REVERT: C  190 HIS cc_start: 0.7956 (m90) cc_final: 0.7506 (m90)
REVERT: C  277 GLN cc_start: 0.8396 (tp-100) cc_final: 0.8095 (tp-100)
REVERT: E   90 ARG cc_start: 0.7584 (ttm110) cc_final: 0.7142 (mtm110)
REVERT: E   91 TYR cc_start: 0.8703 (t80) cc_final: 0.8346 (t80)
REVERT: E  239 PHE cc_start: 0.8791 (m-80) cc_final: 0.8324 (m-80)
REVERT: F   15 LEU cc_start: 0.9247 (mt) cc_final: 0.8982 (mt)
REVERT: F  274 LYS cc_start: 0.8593 (mmmt) cc_final: 0.8308 (mmmt)
  outliers start: 0
  outliers final: 0
  residues processed: 258
  average time/residue: 0.2607
  time to fit residues: 98.1461
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  : 1.316 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 159
   random chunks:
   chunk 98 optimal weight:    0.9990
   chunk 26 optimal weight:    1.9990
   chunk 117 optimal weight:    7.9990
   chunk 75 optimal weight:    0.9990
   chunk 36 optimal weight:    7.9990
   chunk 93 optimal weight:    9.9990
   chunk 53 optimal weight:    5.9990
   chunk 127 optimal weight:    0.5980
   chunk 128 optimal weight:    0.9990
   chunk 15 optimal weight:    0.8980
   chunk 13 optimal weight:    0.9990
   overall best weight:    0.8986

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

Flipped N/Q/H residues before XYZ refinement:
** K 212 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** D  34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A  34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 142 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 190 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 142 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 146 HIS
C 183 ASN
F 184 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4025 r_free = 0.4025 target = 0.101187 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3503 r_free = 0.3503 target = 0.077684 restraints weight = 92601.319|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3565 r_free = 0.3565 target = 0.080003 restraints weight = 49465.470|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3606 r_free = 0.3606 target = 0.081690 restraints weight = 32987.566|
|-----------------------------------------------------------------------------|
r_work (final): 0.3585
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3585
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3585 r_free = 0.3585    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 = 0.3585 r_free = 0.3585    target_work(ls_wunit_k1) = 0.081         |
| occupancies: max = 1.00  min = 0.33   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3585
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7506
moved from start:          0.4066

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041  15146  Z= 0.150
  Angle     :  0.662  12.977  21110  Z= 0.354
  Chirality :  0.043   0.259   2379
  Planarity :  0.005   0.123   2203
  Dihedral  : 24.639 179.168   3215
  Min Nonbonded Distance : 2.123

Molprobity Statistics.
  All-atom Clashscore : 15.97
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.70 %
    Favored  : 96.30 %
  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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.80 (0.21), residues: 1459
  helix:  0.49 (0.20), residues: 680
  sheet: -1.39 (0.32), residues: 222
  loop : -1.34 (0.24), residues: 557

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.002   TRP E  83 
 HIS   0.007   0.001   HIS E  29 
 PHE   0.024   0.001   PHE K 224 
 TYR   0.025   0.001   TYR C  91 
 ARG   0.009   0.001   ARG K 241 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05186 (  672)
  hydrogen bonds       : angle       4.47321 ( 1831)
  covalent geometry    : bond        0.00334 (15146)
  covalent geometry    : angle       0.66191 (21110)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 5510.88 seconds
wall clock time: 97 minutes 4.75 seconds (5824.75 seconds total)