Starting phenix.real_space_refine
on Thu Aug  6 04:16:58 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8fyd_29565/08_2026/8fyd_29565.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8fyd_29565/08_2026/8fyd_29565.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.9
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/8fyd_29565/08_2026/8fyd_29565.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8fyd_29565/08_2026/8fyd_29565.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/8fyd_29565/08_2026/8fyd_29565.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8fyd_29565/08_2026/8fyd_29565.map"
  }
  resolution = 3.9
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=  -0.001 sd=   0.018
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     154      5.49       5
     S      32      5.16       5
     C    8107      2.51       5
     N    2481      2.21       5
     O    2838      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 4 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib"
  Total number of atoms: 13612
  Number of models: 1
  Model: ""
    Number of chains: 10
    Chain: "J"
      Number of atoms: 1005
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 49, 1005
          Classifications: {'DNA': 49}
          Modifications used: {'5*END': 1}
          Link IDs: {'rna3p': 48}
    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: 2163
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 278, 2163
          Classifications: {'peptide': 278}
          Link IDs: {'PTRANS': 10, 'TRANS': 267}
    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: "E"
      Number of atoms: 2261
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 288, 2261
          Classifications: {'peptide': 288}
          Link IDs: {'PTRANS': 10, 'TRANS': 277}
          Chain breaks: 1
    Chain: "F"
      Number of atoms: 2188
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 281, 2188
          Classifications: {'peptide': 281}
          Link IDs: {'PTRANS': 10, 'TRANS': 270}
    Chain: "G"
      Number of atoms: 1330
      Number of conformers: 2
      Conformer: "A"
        Number of residues, atoms: 64, 1308
          Classifications: {'DNA': 64}
          Modifications used: {'5*END': 1}
          Link IDs: {'rna3p': 63}
      Conformer: "B"
        Number of residues, atoms: 64, 1308
          Classifications: {'DNA': 64}
          Modifications used: {'5*END': 1}
          Link IDs: {'rna3p': 63}
          bond proxies already assigned to first conformer: 1440
    Chain: "H"
      Number of atoms: 613
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 30, 613
          Classifications: {'DNA': 30}
          Modifications used: {'5*END': 1}
          Link IDs: {'rna3p': 29}
    Chain: "I"
      Number of atoms: 265
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 13, 265
          Classifications: {'DNA': 13}
          Link IDs: {'rna3p': 12}
  Residues with excluded nonbonded symmetry interactions: 1
    residue:
      pdb=" P  A DG G  29 " occ=0.61
      ... (42 atoms not shown)
      pdb=" C4 B DG G  29 " occ=0.39
  Time building chain proxies: 3.24, per 1000 atoms: 0.24
  Number of scatterers: 13612
  At special positions: 0
  Unit cell: (115.96, 95.89, 154.985, 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      32     16.00
     P     154     15.00
     O    2838      8.00
     N    2481      7.00
     C    8107      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 1.13
  Conformation dependent library (CDL) restraints added in 533.7 milliseconds
  

  2622 Ramachandran restraints generated.
    1311 Oldfield, 0 Emsley, 1311 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2446

  Finding SS restraints...
    Secondary structure from input PDB file:
      56 helices and 7 sheets defined
      52.8% alpha, 12.8% beta
      61 base pairs and 119 stacking pairs defined.
    Time for finding SS restraints: 1.37
  Creating SS restraints...
    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 51
    Processing helix  chain 'B' and resid 51 through 55
    Processing helix  chain 'B' and resid 68 through 76
      removed outlier: 3.629A  pdb=" N   ASP B  76 " --> pdb=" O   GLU B  72 " (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
      removed outlier: 4.253A  pdb=" N   ASN B 114 " --> pdb=" O   GLU B 110 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 114 through 130
      removed outlier: 3.519A  pdb=" N   TYR B 126 " --> pdb=" O   ALA B 122 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 139 through 162
      removed outlier: 3.730A  pdb=" N   ARG B 152 " --> pdb=" O   GLY B 148 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 180 through 205
      removed outlier: 4.271A  pdb=" N   LEU B 196 " --> pdb=" O   ALA B 192 " (cutoff:3.500A)
      removed outlier: 3.515A  pdb=" N   VAL B 201 " --> pdb=" O   VAL B 197 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 219 through 231
      removed outlier: 3.879A  pdb=" N   LEU B 228 " --> pdb=" O   ASP B 224 " (cutoff:3.500A)
      removed outlier: 4.252A  pdb=" N   TYR B 229 " --> pdb=" O   VAL B 225 " (cutoff:3.500A)
      removed outlier: 4.649A  pdb=" N   ALA B 231 " --> pdb=" O   ASP B 227 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 233 through 244
    Processing helix  chain 'B' and resid 251 through 263
      removed outlier: 3.793A  pdb=" N   ALA B 262 " --> pdb=" O   ARG B 258 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 266 through 280
      removed outlier: 3.536A  pdb=" N   LYS B 270 " --> pdb=" O   GLY B 266 " (cutoff:3.500A)
      removed outlier: 3.721A  pdb=" N   ARG B 271 " --> pdb=" O   LYS B 267 " (cutoff:3.500A)
      removed outlier: 3.635A  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
    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: 3.930A  pdb=" N   ARG C  21 " --> pdb=" O   VAL C  18 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 51 through 53
      No H-bonds generated for 'chain 'C' and resid 51 through 53'
    Processing helix  chain 'C' and resid 68 through 77
      removed outlier: 3.551A  pdb=" N   THR C  77 " --> pdb=" O   LEU C  73 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 102 through 114
      removed outlier: 3.670A  pdb=" N   ASN C 114 " --> pdb=" O   GLU C 110 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 114 through 130
      removed outlier: 3.808A  pdb=" N   ARG C 129 " --> pdb=" O   MET C 125 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 139 through 163
      removed outlier: 3.553A  pdb=" N   ARG C 144 " --> pdb=" O   MET C 140 " (cutoff:3.500A)
      removed outlier: 4.082A  pdb=" N   SER C 145 " --> pdb=" O   GLN C 141 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 180 through 204
      removed outlier: 3.829A  pdb=" N   GLN C 184 " --> pdb=" O   ASP C 180 " (cutoff:3.500A)
      removed outlier: 3.678A  pdb=" N   ALA C 192 " --> pdb=" O   ALA C 188 " (cutoff:3.500A)
      removed outlier: 3.823A  pdb=" N   LEU C 193 " --> pdb=" O   ALA C 189 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 219 through 231
      removed outlier: 3.519A  pdb=" N   TYR C 223 " --> pdb=" O   ARG C 219 " (cutoff:3.500A)
      removed outlier: 3.754A  pdb=" N   TYR C 229 " --> pdb=" O   VAL C 225 " (cutoff:3.500A)
      removed outlier: 4.577A  pdb=" N   ALA C 231 " --> pdb=" O   ASP C 227 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 233 through 245
      removed outlier: 3.949A  pdb=" N   ILE C 237 " --> pdb=" O   ILE C 233 " (cutoff:3.500A)
      removed outlier: 3.636A  pdb=" N   ALA C 242 " --> pdb=" O   ALA C 238 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 250 through 266
      removed outlier: 3.518A  pdb=" N   ASP C 261 " --> pdb=" O   LEU C 257 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 267 through 278
    Processing helix  chain 'D' and resid 12 through 19
      removed outlier: 3.537A  pdb=" N   ARG D  16 " --> pdb=" O   PRO D  12 " (cutoff:3.500A)
      removed outlier: 3.518A  pdb=" N   GLY D  17 " --> pdb=" O   GLN D  13 " (cutoff:3.500A)
    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: 3.551A  pdb=" N   ARG D  40 " --> pdb=" O   ASN D  36 " (cutoff:3.500A)
      removed outlier: 3.836A  pdb=" N   GLU D  49 " --> pdb=" O   ARG D  45 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 68 through 77
      removed outlier: 3.556A  pdb=" N   LEU E  73 " --> pdb=" O   ARG E  69 " (cutoff:3.500A)
      removed outlier: 3.891A  pdb=" N   ASP E  76 " --> pdb=" O   GLU E  72 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 97 through 101
      removed outlier: 3.611A  pdb=" N   ARG E 100 " --> pdb=" O   ALA E  97 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 102 through 114
      removed outlier: 4.354A  pdb=" N   ASN E 114 " --> pdb=" O   GLU E 110 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 114 through 129
    Processing helix  chain 'E' and resid 139 through 162
      removed outlier: 3.549A  pdb=" N   HIS E 146 " --> pdb=" O   GLN E 142 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 180 through 205
      removed outlier: 3.518A  pdb=" N   ALA E 192 " --> pdb=" O   ALA E 188 " (cutoff:3.500A)
      removed outlier: 3.584A  pdb=" N   LEU E 193 " --> pdb=" O   ALA E 189 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 219 through 231
      removed outlier: 3.525A  pdb=" N   ASP E 227 " --> pdb=" O   TYR E 223 " (cutoff:3.500A)
      removed outlier: 4.434A  pdb=" N   LEU E 228 " --> pdb=" O   ASP E 224 " (cutoff:3.500A)
      removed outlier: 4.521A  pdb=" N   TYR E 229 " --> pdb=" O   VAL E 225 " (cutoff:3.500A)
      removed outlier: 4.822A  pdb=" N   ALA E 231 " --> pdb=" O   ASP E 227 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 233 through 245
    Processing helix  chain 'E' and resid 251 through 265
      removed outlier: 3.912A  pdb=" N   ALA E 262 " --> pdb=" O   ARG E 258 " (cutoff:3.500A)
      removed outlier: 4.010A  pdb=" N   ASP E 265 " --> pdb=" O   ASP E 261 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 266 through 280
      removed outlier: 3.550A  pdb=" N   LYS E 274 " --> pdb=" O   LYS E 270 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 298 through 303
    Processing helix  chain 'E' and resid 304 through 306
      No H-bonds generated for 'chain 'E' and resid 304 through 306'
    Processing helix  chain 'F' and resid 11 through 15
    Processing helix  chain 'F' and resid 17 through 21
      removed outlier: 4.018A  pdb=" N   ARG F  21 " --> pdb=" O   VAL F  18 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 51 through 55
    Processing helix  chain 'F' and resid 67 through 78
      removed outlier: 3.938A  pdb=" N   VAL F  71 " --> pdb=" O   SER F  67 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 102 through 114
      removed outlier: 3.747A  pdb=" N   ASN F 114 " --> pdb=" O   GLU F 110 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 114 through 130
      removed outlier: 4.169A  pdb=" N   TYR F 126 " --> pdb=" O   ALA F 122 " (cutoff:3.500A)
      removed outlier: 3.912A  pdb=" N   GLN F 127 " --> pdb=" O   ARG F 123 " (cutoff:3.500A)
      removed outlier: 3.580A  pdb=" N   MET F 128 " --> pdb=" O   ARG F 124 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 139 through 163
      removed outlier: 3.586A  pdb=" N   ARG F 152 " --> pdb=" O   GLY F 148 " (cutoff:3.500A)
      removed outlier: 3.510A  pdb=" N   TYR F 155 " --> pdb=" O   VAL F 151 " (cutoff:3.500A)
      removed outlier: 3.778A  pdb=" N   LYS F 160 " --> pdb=" O   ARG F 156 " (cutoff:3.500A)
      removed outlier: 3.752A  pdb=" N   ASN F 163 " --> pdb=" O   SER F 159 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 180 through 205
      removed outlier: 3.885A  pdb=" N   GLN F 184 " --> pdb=" O   ASP F 180 " (cutoff:3.500A)
      removed outlier: 3.529A  pdb=" N   ALA F 185 " --> pdb=" O   PRO F 181 " (cutoff:3.500A)
      removed outlier: 3.707A  pdb=" N   LEU F 193 " --> pdb=" O   ALA F 189 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 219 through 229
      removed outlier: 3.588A  pdb=" N   ASP F 227 " --> pdb=" O   TYR F 223 " (cutoff:3.500A)
      removed outlier: 3.867A  pdb=" N   TYR F 229 " --> pdb=" O   VAL F 225 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 233 through 244
      removed outlier: 3.517A  pdb=" N   ILE F 237 " --> pdb=" O   ILE F 233 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 250 through 267
      removed outlier: 3.893A  pdb=" N   LEU F 254 " --> pdb=" O   ASP F 250 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 267 through 280
      removed outlier: 3.679A  pdb=" N   VAL F 273 " --> pdb=" O   LEU F 269 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 24 through 27
      removed outlier: 5.910A  pdb=" N   GLU A  25 " --> pdb=" O   VAL A  32 " (cutoff:3.500A)
      removed outlier: 7.698A  pdb=" N   VAL A  32 " --> pdb=" O   GLU A  25 " (cutoff:3.500A)
      removed outlier: 4.013A  pdb=" N   ALA A  27 " --> pdb=" O   VAL A  30 " (cutoff:3.500A)
      removed outlier: 3.654A  pdb=" N   ALA A  56 " --> pdb=" O   GLU A  73 " (cutoff:3.500A)
      removed outlier: 3.508A  pdb=" N   LEU A  71 " --> pdb=" O   MET A  58 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 78 through 81
      removed outlier: 6.608A  pdb=" N   ARG E  34 " --> pdb=" O   SER E  67 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'B' and resid 91 through 94
      removed outlier: 5.979A  pdb=" N   LEU B  58 " --> pdb=" O   VAL B  82 " (cutoff:3.500A)
      removed outlier: 6.351A  pdb=" N   VAL B  84 " --> pdb=" O   LEU B  58 " (cutoff:3.500A)
      removed outlier: 5.648A  pdb=" N   LEU B  60 " --> pdb=" O   VAL B  84 " (cutoff:3.500A)
      removed outlier: 7.757A  pdb=" N   VAL B  57 " --> pdb=" O   ARG B  21 " (cutoff:3.500A)
      removed outlier: 5.820A  pdb=" N   THR B  23 " --> pdb=" O   VAL B  57 " (cutoff:3.500A)
      removed outlier: 6.406A  pdb=" N   LEU B  59 " --> pdb=" O   THR B  23 " (cutoff:3.500A)
      removed outlier: 6.836A  pdb=" N   ILE B  25 " --> pdb=" O   LEU B  59 " (cutoff:3.500A)
      removed outlier: 6.713A  pdb=" N   ALA B  22 " --> pdb=" O   GLU B 291 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'B' and resid 309 through 310
      removed outlier: 3.840A  pdb=" N   LYS B  31 " --> pdb=" O   ALA B  42 " (cutoff:3.500A)
      removed outlier: 3.686A  pdb=" N   ASP B  65 " --> pdb=" O   ALA B  30 " (cutoff:3.500A)
      removed outlier: 3.603A  pdb=" N   ILE B  32 " --> pdb=" O   ASP B  65 " (cutoff:3.500A)
      removed outlier: 3.665A  pdb=" N   SER B  67 " --> pdb=" O   ILE B  32 " (cutoff:3.500A)
      removed outlier: 6.536A  pdb=" N   ARG B  34 " --> pdb=" O   SER B  67 " (cutoff:3.500A)
      removed outlier: 6.644A  pdb=" N   ARG C  34 " --> pdb=" O   SER C  67 " (cutoff:3.500A)
      removed outlier: 4.031A  pdb=" N   ARG C  49 " --> pdb=" O   ILE D  88 " (cutoff:3.500A)
      removed outlier: 5.230A  pdb=" N   ILE D  88 " --> pdb=" O   ARG C  49 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'C' and resid 22 through 27
      removed outlier: 6.353A  pdb=" N   THR C  23 " --> pdb=" O   VAL C  57 " (cutoff:3.500A)
      removed outlier: 7.536A  pdb=" N   LEU C  59 " --> pdb=" O   THR C  23 " (cutoff:3.500A)
      removed outlier: 6.475A  pdb=" N   ILE C  25 " --> pdb=" O   LEU C  59 " (cutoff:3.500A)
      removed outlier: 3.538A  pdb=" N   ALA C  80 " --> pdb=" O   GLY C  56 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'D' and resid 24 through 27
      removed outlier: 6.211A  pdb=" N   GLU D  25 " --> pdb=" O   VAL D  32 " (cutoff:3.500A)
      removed outlier: 7.639A  pdb=" N   VAL D  32 " --> pdb=" O   GLU D  25 " (cutoff:3.500A)
      removed outlier: 4.145A  pdb=" N   ALA D  27 " --> pdb=" O   VAL D  30 " (cutoff:3.500A)
      removed outlier: 7.258A  pdb=" N   MET D   3 " --> pdb=" O   ALA D  61 " (cutoff:3.500A)
      removed outlier: 3.704A  pdb=" N   ALA D  61 " --> pdb=" O   MET D   3 " (cutoff:3.500A)
      removed outlier: 4.082A  pdb=" N   ALA D  56 " --> pdb=" O   GLU D  73 " (cutoff:3.500A)
      removed outlier: 3.714A  pdb=" N   GLU D  73 " --> pdb=" O   ALA D  56 " (cutoff:3.500A)
      removed outlier: 3.651A  pdb=" N   PHE D  60 " --> pdb=" O   ASP D  69 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'E' and resid 289 through 293
      removed outlier: 6.571A  pdb=" N   ALA E  22 " --> pdb=" O   GLU E 291 " (cutoff:3.500A)
      removed outlier: 7.245A  pdb=" N   LEU E 293 " --> pdb=" O   ALA E  22 " (cutoff:3.500A)
      removed outlier: 6.445A  pdb=" N   PHE E  24 " --> pdb=" O   LEU E 293 " (cutoff:3.500A)
      removed outlier: 8.405A  pdb=" N   VAL E  57 " --> pdb=" O   ARG E  21 " (cutoff:3.500A)
      removed outlier: 6.591A  pdb=" N   THR E  23 " --> pdb=" O   VAL E  57 " (cutoff:3.500A)
      removed outlier: 7.046A  pdb=" N   LEU E  59 " --> pdb=" O   THR E  23 " (cutoff:3.500A)
      removed outlier: 6.574A  pdb=" N   ILE E  25 " --> pdb=" O   LEU E  59 " (cutoff:3.500A)
      removed outlier: 5.735A  pdb=" N   LEU E  58 " --> pdb=" O   VAL E  82 " (cutoff:3.500A)
      removed outlier: 6.396A  pdb=" N   VAL E  84 " --> pdb=" O   LEU E  58 " (cutoff:3.500A)
      removed outlier: 5.731A  pdb=" N   LEU E  60 " --> pdb=" O   VAL E  84 " (cutoff:3.500A)
      removed outlier: 6.072A  pdb=" N   LEU E  81 " --> pdb=" O   GLY E  95 " (cutoff:3.500A)
      removed outlier: 5.374A  pdb=" N   VAL F  89 " --> pdb=" O   GLY F  85 " (cutoff:3.500A)
      removed outlier: 6.182A  pdb=" N   GLY F  85 " --> pdb=" O   VAL F  89 " (cutoff:3.500A)
      removed outlier: 6.666A  pdb=" N   LEU F  58 " --> pdb=" O   VAL F  82 " (cutoff:3.500A)
      removed outlier: 7.581A  pdb=" N   VAL F  84 " --> pdb=" O   LEU F  58 " (cutoff:3.500A)
      removed outlier: 5.646A  pdb=" N   LEU F  60 " --> pdb=" O   VAL F  84 " (cutoff:3.500A)
      removed outlier: 3.609A  pdb=" N   ILE F  25 " --> pdb=" O   VAL F  57 " (cutoff:3.500A)

    513 hydrogen bonds defined for protein.
    1467 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      157 hydrogen bonds
      314 hydrogen bond angles
      0 basepair planarities
      61 basepair parallelities
      120 stacking parallelities
  Total time for adding SS restraints: 1.79

  Time building geometry restraints manager: 1.55 seconds

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

  Histogram of bond lengths:
        1.22 -     1.34: 3797
        1.34 -     1.46: 3112
        1.46 -     1.57: 6912
        1.57 -     1.69: 308
        1.69 -     1.81: 62
  Bond restraints: 14191
  Sorted by residual:
  bond pdb=" C3'  DG J  26 "
       pdb=" C2'  DG J  26 "
    ideal  model  delta    sigma   weight residual
    1.516  1.544 -0.028 8.00e-03 1.56e+04 1.21e+01
  bond pdb=" C3'  DA H   1 "
       pdb=" C2'  DA H   1 "
    ideal  model  delta    sigma   weight residual
    1.516  1.543 -0.027 8.00e-03 1.56e+04 1.17e+01
  bond pdb=" C3'  DC H  10 "
       pdb=" C2'  DC H  10 "
    ideal  model  delta    sigma   weight residual
    1.516  1.542 -0.026 8.00e-03 1.56e+04 1.03e+01
  bond pdb=" C3'  DG G  60 "
       pdb=" C2'  DG G  60 "
    ideal  model  delta    sigma   weight residual
    1.516  1.541 -0.025 8.00e-03 1.56e+04 1.01e+01
  bond pdb=" C3'  DG G   8 "
       pdb=" C2'  DG G   8 "
    ideal  model  delta    sigma   weight residual
    1.516  1.541 -0.025 8.00e-03 1.56e+04 9.67e+00
  ... (remaining 14186 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.43: 18856
        1.43 -     2.86: 900
        2.86 -     4.29: 90
        4.29 -     5.72: 23
        5.72 -     7.15: 5
  Bond angle restraints: 19874
  Sorted by residual:
  angle pdb=" N3   DT G   5 "
        pdb=" C4   DT G   5 "
        pdb=" O4   DT G   5 "
      ideal   model   delta    sigma   weight residual
     119.90  122.62   -2.72 6.00e-01 2.78e+00 2.05e+01
  angle pdb=" N3   DT G  32 "
        pdb=" C4   DT G  32 "
        pdb=" O4   DT G  32 "
      ideal   model   delta    sigma   weight residual
     119.90  122.62   -2.72 6.00e-01 2.78e+00 2.05e+01
  angle pdb=" N3   DT G   4 "
        pdb=" C4   DT G   4 "
        pdb=" O4   DT G   4 "
      ideal   model   delta    sigma   weight residual
     119.90  122.60   -2.70 6.00e-01 2.78e+00 2.02e+01
  angle pdb=" N3   DT J   7 "
        pdb=" C4   DT J   7 "
        pdb=" O4   DT J   7 "
      ideal   model   delta    sigma   weight residual
     119.90  122.58   -2.68 6.00e-01 2.78e+00 2.00e+01
  angle pdb=" N3   DT G  17 "
        pdb=" C4   DT G  17 "
        pdb=" O4   DT G  17 "
      ideal   model   delta    sigma   weight residual
     119.90  122.52   -2.62 6.00e-01 2.78e+00 1.90e+01
  ... (remaining 19869 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    35.88: 7393
       35.88 -    71.75: 673
       71.75 -   107.63: 19
      107.63 -   143.50: 3
      143.50 -   179.38: 4
  Dihedral angle restraints: 8092
    sinusoidal: 4276
      harmonic: 3816
  Sorted by residual:
  dihedral pdb=" C4'  DA J  32 "
           pdb=" C3'  DA J  32 "
           pdb=" O3'  DA J  32 "
           pdb=" P    DA J  33 "
      ideal   model   delta sinusoidal    sigma   weight residual
    -140.00   39.38 -179.38     1      3.50e+01 8.16e-04 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
    -140.00   38.42 -178.42     1      3.50e+01 8.16e-04 1.57e+01
  dihedral pdb=" C4'  DG G  38 "
           pdb=" C3'  DG G  38 "
           pdb=" O3'  DG G  38 "
           pdb=" P    DC G  39 "
      ideal   model   delta sinusoidal    sigma   weight residual
    -140.00   34.60 -174.60     1      3.50e+01 8.16e-04 1.56e+01
  ... (remaining 8089 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.034: 1385
       0.034 -    0.068: 584
       0.068 -    0.101: 190
       0.101 -    0.135: 60
       0.135 -    0.169: 14
  Chirality restraints: 2233
  Sorted by residual:
  chirality pdb=" P    DC J  21 "
            pdb=" OP1  DC J  21 "
            pdb=" OP2  DC J  21 "
            pdb=" O5'  DC J  21 "
    both_signs  ideal   model   delta    sigma   weight residual
      True       2.34   -2.50   -0.17 2.00e-01 2.50e+01 7.14e-01
  chirality pdb=" C3'  DC J  21 "
            pdb=" C4'  DC J  21 "
            pdb=" O3'  DC J  21 "
            pdb=" C2'  DC J  21 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.73   -2.57   -0.16 2.00e-01 2.50e+01 6.80e-01
  chirality pdb=" C3'  DG J  34 "
            pdb=" C4'  DG J  34 "
            pdb=" O3'  DG J  34 "
            pdb=" C2'  DG J  34 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.73   -2.57   -0.16 2.00e-01 2.50e+01 6.43e-01
  ... (remaining 2230 not shown)

  Planarity restraints: 2009
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C1'  DG J   8 "    0.028 2.00e-02 2.50e+03   1.17e-02 4.11e+00
        pdb=" N9   DG J   8 "   -0.026 2.00e-02 2.50e+03
        pdb=" C8   DG J   8 "   -0.005 2.00e-02 2.50e+03
        pdb=" N7   DG J   8 "   -0.002 2.00e-02 2.50e+03
        pdb=" C5   DG J   8 "    0.000 2.00e-02 2.50e+03
        pdb=" C6   DG J   8 "    0.005 2.00e-02 2.50e+03
        pdb=" O6   DG J   8 "    0.009 2.00e-02 2.50e+03
        pdb=" N1   DG J   8 "   -0.002 2.00e-02 2.50e+03
        pdb=" C2   DG J   8 "   -0.000 2.00e-02 2.50e+03
        pdb=" N2   DG J   8 "   -0.001 2.00e-02 2.50e+03
        pdb=" N3   DG J   8 "   -0.005 2.00e-02 2.50e+03
        pdb=" C4   DG J   8 "   -0.002 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C1'  DA J  37 "    0.024 2.00e-02 2.50e+03   1.12e-02 3.48e+00
        pdb=" N9   DA J  37 "   -0.026 2.00e-02 2.50e+03
        pdb=" C8   DA J  37 "   -0.001 2.00e-02 2.50e+03
        pdb=" N7   DA J  37 "    0.002 2.00e-02 2.50e+03
        pdb=" C5   DA J  37 "    0.002 2.00e-02 2.50e+03
        pdb=" C6   DA J  37 "    0.007 2.00e-02 2.50e+03
        pdb=" N6   DA J  37 "    0.001 2.00e-02 2.50e+03
        pdb=" N1   DA J  37 "    0.003 2.00e-02 2.50e+03
        pdb=" C2   DA J  37 "   -0.001 2.00e-02 2.50e+03
        pdb=" N3   DA J  37 "   -0.005 2.00e-02 2.50e+03
        pdb=" C4   DA J  37 "   -0.007 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   MET A   1 "   -0.029 5.00e-02 4.00e+02   4.45e-02 3.16e+00
        pdb=" N   PRO A   2 "    0.077 5.00e-02 4.00e+02
        pdb=" CA  PRO A   2 "   -0.023 5.00e-02 4.00e+02
        pdb=" CD  PRO A   2 "   -0.025 5.00e-02 4.00e+02
  ... (remaining 2006 not shown)

  Histogram of nonbonded interaction distances:
        2.20 -     2.74: 1115
        2.74 -     3.28: 14284
        3.28 -     3.82: 25857
        3.82 -     4.36: 29081
        4.36 -     4.90: 45125
  Nonbonded interactions: 115462
  Sorted by model distance:
  nonbonded pdb=" OH  TYR B  91 "
            pdb=" OG  SER B  94 "
     model   vdw
     2.196 3.040
  nonbonded pdb=" O   ASN F  33 "
            pdb=" OG1 THR F  40 "
     model   vdw
     2.235 3.040
  nonbonded pdb=" NE2 GLN E 277 "
            pdb=" O   ILE E 288 "
     model   vdw
     2.247 3.120
  nonbonded pdb=" OG  SER B 159 "
            pdb=" O   VAL B 164 "
     model   vdw
     2.256 3.040
  nonbonded pdb=" NH2 ARG A  46 "
            pdb=" OG  SER C  10 "
     model   vdw
     2.259 3.120
  ... (remaining 115457 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' and (resid 20 through 129 or resid 134 through 279))
  selection = (chain 'C' and (resid 20 through 129 or resid 134 through 279))
  selection = (chain 'E' and resid 20 through 279)
  selection = (chain 'F' and (resid 20 through 129 or resid 134 through 279))
}

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=0.39 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             0.930
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.200
  Check model and map are aligned:         0.030
  Set scattering table:                    0.040
  Process input model:                     13.720
  Find NCS groups from input model:        0.150
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.010
  Load rotamer database and sin/cos tables:0.980
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   16.090
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7877
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   0.036  14191  Z= 0.364
  Angle     :  0.663   7.149  19874  Z= 0.504
  Chirality :  0.044   0.169   2233
  Planarity :  0.004   0.044   2009
  Dihedral  : 22.389 179.381   5646
  Min Nonbonded Distance : 2.196

Molprobity Statistics.
  All-atom Clashscore : 15.08
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.43 %
    Favored  : 96.57 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.28 %
    Favored  : 99.72 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.04 (0.23), residues: 1311
  helix:  0.80 (0.21), residues: 597
  sheet: -0.24 (0.37), residues: 191
  loop : -0.83 (0.27), residues: 523

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG F  90 
 TYR   0.021   0.001   TYR B  91 
 PHE   0.014   0.001   PHE A  35 
 TRP   0.028   0.002   TRP C 166 
 HIS   0.008   0.001   HIS C 190 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00429 /  0.36 (14191)
  covalent geometry    : angle       0.66291 /  0.50 (19874)
  hydrogen bonds       : bond        0.22576 / 24.90 (  670)
  hydrogen bonds       : angle       7.03387 /  9.24 ( 1781)

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

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

  2622 Ramachandran restraints generated.
    1311 Oldfield, 0 Emsley, 1311 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2622 Ramachandran restraints generated.
    1311 Oldfield, 0 Emsley, 1311 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  268 residues out of total 1081 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 268
  time to evaluate  : 0.409 
Fit side-chains
REVERT: A   34 ASN cc_start: 0.7529 (m-40) cc_final: 0.6416 (m110)
REVERT: B   32 ILE cc_start: 0.8858 (pt) cc_final: 0.8608 (pt)
REVERT: B   54 MET cc_start: 0.8246 (mtp) cc_final: 0.8005 (mtp)
REVERT: B   91 TYR cc_start: 0.7625 (t80) cc_final: 0.7311 (t80)
REVERT: B  128 MET cc_start: 0.9255 (mpp) cc_final: 0.9030 (mpp)
REVERT: C  157 GLU cc_start: 0.9159 (pp20) cc_final: 0.8920 (pp20)
REVERT: C  183 ASN cc_start: 0.8867 (m110) cc_final: 0.8427 (m110)
REVERT: D   60 PHE cc_start: 0.8180 (p90) cc_final: 0.7938 (p90)
REVERT: F  116 ARG cc_start: 0.8270 (tmm-80) cc_final: 0.8037 (tmm-80)
REVERT: F  239 PHE cc_start: 0.8719 (t80) cc_final: 0.8296 (t80)
REVERT: F  265 ASP cc_start: 0.6901 (m-30) cc_final: 0.6573 (t0)
  outliers start: 0
  outliers final: 0
  residues processed: 268
  average time/residue: 0.1017
  time to fit residues: 40.5280
Evaluate side-chains
  205 residues out of total 1081 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 205
  time to evaluate  : 0.263 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 144
   random chunks:
   chunk 98 optimal weight:    4.9990
   chunk 107 optimal weight:    5.9990
   chunk 10 optimal weight:    5.9990
   chunk 66 optimal weight:    3.9990
   chunk 130 optimal weight:    9.9990
   chunk 124 optimal weight:    9.9990
   chunk 103 optimal weight:    2.9990
   chunk 77 optimal weight:    0.7980
   chunk 122 optimal weight:    7.9990
   chunk 91 optimal weight:   10.0000
   chunk 55 optimal weight:    0.2980
   overall best weight:    2.6186

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
B 146 HIS
C 190 HIS
** E  87 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
E 108 GLN
F  87 GLN
F 114 ASN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4122 r_free = 0.4122 target = 0.127443 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3419 r_free = 0.3419 target = 0.087062 restraints weight = 36939.325|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3466 r_free = 0.3466 target = 0.089460 restraints weight = 21180.203|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3494 r_free = 0.3494 target = 0.090993 restraints weight = 15292.609|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 32)----------------|
| r_work = 0.3508 r_free = 0.3508 target = 0.091755 restraints weight = 12685.065|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 43)----------------|
| r_work = 0.3520 r_free = 0.3520 target = 0.092408 restraints weight = 11508.663|
|-----------------------------------------------------------------------------|
r_work (final): 0.3490
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3490
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3490 r_free = 0.3490    target_work(ls_wunit_k1) = 0.090         |
| occupancies: max = 1.00  min = 0.39   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3490 r_free = 0.3490    target_work(ls_wunit_k1) = 0.090         |
| occupancies: max = 1.00  min = 0.49   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 4 (4 function evaluations)
r_final: 0.3490
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7917
moved from start:          0.1390

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.066  14191  Z= 0.222
  Angle     :  0.716  10.148  19874  Z= 0.398
  Chirality :  0.046   0.259   2233
  Planarity :  0.005   0.068   2009
  Dihedral  : 25.532 177.406   3174
  Min Nonbonded Distance : 2.319

Molprobity Statistics.
  All-atom Clashscore : 16.54
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.89 %
    Favored  : 96.11 %
  Rotamer:
    Outliers :  1.94 %
    Allowed  : 12.49 %
    Favored  : 85.57 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.16 (0.22), residues: 1311
  helix:  0.74 (0.20), residues: 627
  sheet: -0.50 (0.37), residues: 181
  loop : -0.95 (0.27), residues: 503

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG B 156 
 TYR   0.029   0.002   TYR E 194 
 PHE   0.015   0.002   PHE F 176 
 TRP   0.013   0.002   TRP C 166 
 HIS   0.007   0.001   HIS C 146 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00463 /  0.22 (14191)
  covalent geometry    : angle       0.71558 /  0.40 (19874)
  hydrogen bonds       : bond        0.06556 /  7.25 (  670)
  hydrogen bonds       : angle       4.98758 /  6.64 ( 1781)

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

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

  2622 Ramachandran restraints generated.
    1311 Oldfield, 0 Emsley, 1311 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2622 Ramachandran restraints generated.
    1311 Oldfield, 0 Emsley, 1311 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  240 residues out of total 1081 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 219
  time to evaluate  : 0.293 
Fit side-chains
REVERT: A   23 MET cc_start: 0.8776 (mmt) cc_final: 0.7733 (mmt)
REVERT: B   91 TYR cc_start: 0.7908 (t80) cc_final: 0.7567 (t80)
REVERT: B  272 MET cc_start: 0.8628 (mpp) cc_final: 0.8339 (mpp)
REVERT: C   54 MET cc_start: 0.9459 (mmt) cc_final: 0.9028 (mmt)
REVERT: C  127 GLN cc_start: 0.8068 (pp30) cc_final: 0.7648 (pp30)
REVERT: C  128 MET cc_start: 0.8598 (mmm) cc_final: 0.8119 (mmm)
REVERT: C  157 GLU cc_start: 0.9168 (pp20) cc_final: 0.8908 (pp20)
REVERT: C  183 ASN cc_start: 0.9090 (m110) cc_final: 0.8720 (m-40)
REVERT: D   58 MET cc_start: 0.7789 (ppp) cc_final: 0.7286 (ppp)
REVERT: D   60 PHE cc_start: 0.8574 (p90) cc_final: 0.8264 (p90)
REVERT: E  194 TYR cc_start: 0.8595 (m-80) cc_final: 0.8167 (m-80)
REVERT: E  305 TYR cc_start: 0.8209 (m-10) cc_final: 0.7973 (m-10)
REVERT: F  114 ASN cc_start: 0.7987 (t0) cc_final: 0.7744 (t0)
REVERT: F  171 TYR cc_start: 0.4121 (t80) cc_final: 0.3910 (t80)
REVERT: F  190 HIS cc_start: 0.8238 (m170) cc_final: 0.7660 (m90)
REVERT: F  265 ASP cc_start: 0.7355 (m-30) cc_final: 0.6859 (t0)
  outliers start: 21
  outliers final: 16
  residues processed: 228
  average time/residue: 0.0951
  time to fit residues: 32.6754
Evaluate side-chains
  204 residues out of total 1081 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 188
  time to evaluate  : 0.314 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   11 VAL
Chi-restraints excluded: chain A residue   19 LEU
Chi-restraints excluded: chain A residue   59 CYS
Chi-restraints excluded: chain B residue   59 LEU
Chi-restraints excluded: chain B residue  193 LEU
Chi-restraints excluded: chain C residue   12 SER
Chi-restraints excluded: chain C residue   57 VAL
Chi-restraints excluded: chain C residue   72 GLU
Chi-restraints excluded: chain D residue   15 LEU
Chi-restraints excluded: chain D residue   37 SER
Chi-restraints excluded: chain D residue   59 CYS
Chi-restraints excluded: chain E residue   48 VAL
Chi-restraints excluded: chain E residue   66 ILE
Chi-restraints excluded: chain E residue  180 ASP
Chi-restraints excluded: chain F residue  130 PHE
Chi-restraints excluded: chain F residue  174 ASP
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 144
   random chunks:
   chunk 55 optimal weight:    0.0470
   chunk 63 optimal weight:    9.9990
   chunk 49 optimal weight:    0.0970
   chunk 44 optimal weight:    0.8980
   chunk 53 optimal weight:    0.9990
   chunk 20 optimal weight:    3.9990
   chunk 60 optimal weight:    0.7980
   chunk 40 optimal weight:   10.0000
   chunk 119 optimal weight:   20.0000
   chunk 29 optimal weight:    2.9990
   chunk 137 optimal weight:   40.0000
   overall best weight:    0.5678

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
B 127 GLN
B 146 HIS
** C 146 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
C 190 HIS
** E  87 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E 127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
F  87 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4149 r_free = 0.4149 target = 0.129477 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3443 r_free = 0.3443 target = 0.088124 restraints weight = 52221.501|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 43)----------------|
| r_work = 0.3502 r_free = 0.3502 target = 0.091296 restraints weight = 23874.898|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3540 r_free = 0.3540 target = 0.093371 restraints weight = 15200.072|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 42)----------------|
| r_work = 0.3564 r_free = 0.3564 target = 0.094625 restraints weight = 11659.337|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 32)----------------|
| r_work = 0.3574 r_free = 0.3574 target = 0.095237 restraints weight = 10070.345|
|-----------------------------------------------------------------------------|
r_work (final): 0.3544
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3544
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3544 r_free = 0.3544    target_work(ls_wunit_k1) = 0.093         |
| occupancies: max = 1.00  min = 0.49   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3544 r_free = 0.3544    target_work(ls_wunit_k1) = 0.093         |
| occupancies: max = 1.00  min = 0.47   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 3 (3 function evaluations)
r_final: 0.3544
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7839
moved from start:          0.1654

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032  14191  Z= 0.153
  Angle     :  0.656   8.664  19874  Z= 0.367
  Chirality :  0.045   0.279   2233
  Planarity :  0.005   0.048   2009
  Dihedral  : 25.489 177.564   3174
  Min Nonbonded Distance : 2.323

Molprobity Statistics.
  All-atom Clashscore : 15.27
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.43 %
    Favored  : 96.57 %
  Rotamer:
    Outliers :  1.48 %
    Allowed  : 15.73 %
    Favored  : 82.79 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.10 (0.23), residues: 1311
  helix:  0.80 (0.20), residues: 627
  sheet: -0.40 (0.38), residues: 181
  loop : -0.94 (0.27), residues: 503

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG A  77 
 TYR   0.024   0.002   TYR E 194 
 PHE   0.017   0.001   PHE F 239 
 TRP   0.009   0.001   TRP C 166 
 HIS   0.008   0.001   HIS B 146 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00288 /  0.15 (14191)
  covalent geometry    : angle       0.65567 /  0.37 (19874)
  hydrogen bonds       : bond        0.05524 /  6.15 (  670)
  hydrogen bonds       : angle       4.59969 /  6.12 ( 1781)

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

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

  2622 Ramachandran restraints generated.
    1311 Oldfield, 0 Emsley, 1311 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2622 Ramachandran restraints generated.
    1311 Oldfield, 0 Emsley, 1311 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  246 residues out of total 1081 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 230
  time to evaluate  : 0.306 
Fit side-chains
   revert: symmetry clash
REVERT: A   23 MET cc_start: 0.8627 (mmt) cc_final: 0.7998 (mmt)
REVERT: A   35 PHE cc_start: 0.8604 (m-10) cc_final: 0.8068 (m-10)
REVERT: B   91 TYR cc_start: 0.7950 (t80) cc_final: 0.7294 (t80)
REVERT: B   94 SER cc_start: 0.8466 (p) cc_final: 0.8138 (p)
REVERT: C   54 MET cc_start: 0.9454 (mmt) cc_final: 0.9012 (mmt)
REVERT: C   67 SER cc_start: 0.8985 (t) cc_final: 0.8312 (p)
REVERT: C  157 GLU cc_start: 0.9171 (pp20) cc_final: 0.8902 (pp20)
REVERT: C  183 ASN cc_start: 0.9099 (m110) cc_final: 0.8723 (m110)
REVERT: D   58 MET cc_start: 0.7788 (ppp) cc_final: 0.6998 (ppp)
REVERT: D   60 PHE cc_start: 0.8536 (p90) cc_final: 0.8211 (p90)
REVERT: D   71 LEU cc_start: 0.8952 (mp) cc_final: 0.8547 (mp)
REVERT: E  194 TYR cc_start: 0.8640 (m-80) cc_final: 0.8233 (m-80)
REVERT: F  125 MET cc_start: 0.9274 (mmp) cc_final: 0.8950 (mmp)
REVERT: F  155 TYR cc_start: 0.7867 (m-80) cc_final: 0.7616 (m-80)
REVERT: F  190 HIS cc_start: 0.8215 (m170) cc_final: 0.7855 (m90)
REVERT: F  265 ASP cc_start: 0.7387 (m-30) cc_final: 0.6888 (t0)
  outliers start: 16
  outliers final: 10
  residues processed: 242
  average time/residue: 0.0962
  time to fit residues: 35.6875
Evaluate side-chains
  208 residues out of total 1081 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 198
  time to evaluate  : 0.539 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   59 CYS
Chi-restraints excluded: chain C residue   12 SER
Chi-restraints excluded: chain C residue   39 VAL
Chi-restraints excluded: chain C residue  273 VAL
Chi-restraints excluded: chain D residue    5 VAL
Chi-restraints excluded: chain D residue   15 LEU
Chi-restraints excluded: chain E residue   48 VAL
Chi-restraints excluded: chain E residue   66 ILE
Chi-restraints excluded: chain E residue  299 LYS
Chi-restraints excluded: chain F residue  174 ASP
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 144
   random chunks:
   chunk 84 optimal weight:    2.9990
   chunk 115 optimal weight:    2.9990
   chunk 107 optimal weight:    0.7980
   chunk 26 optimal weight:    0.9980
   chunk 47 optimal weight:    0.7980
   chunk 29 optimal weight:    0.8980
   chunk 27 optimal weight:    6.9990
   chunk 6 optimal weight:    0.9980
   chunk 128 optimal weight:    0.3980
   chunk 10 optimal weight:    5.9990
   chunk 92 optimal weight:    5.9990
   overall best weight:    0.7780

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** C 146 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
C 190 HIS
** E  87 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
E 127 GLN
F  87 GLN
F 114 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4156 r_free = 0.4156 target = 0.130052 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3456 r_free = 0.3456 target = 0.088939 restraints weight = 41771.218|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3509 r_free = 0.3509 target = 0.091784 restraints weight = 21333.544|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 41)----------------|
| r_work = 0.3544 r_free = 0.3544 target = 0.093606 restraints weight = 14467.955|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 36)----------------|
| r_work = 0.3563 r_free = 0.3563 target = 0.094693 restraints weight = 11588.022|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 24)----------------|
| r_work = 0.3572 r_free = 0.3572 target = 0.095231 restraints weight = 10246.161|
|-----------------------------------------------------------------------------|
r_work (final): 0.3539
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3537
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3537 r_free = 0.3537    target_work(ls_wunit_k1) = 0.093         |
| occupancies: max = 1.00  min = 0.47   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3537 r_free = 0.3537    target_work(ls_wunit_k1) = 0.093         |
| occupancies: max = 1.00  min = 0.46   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 3 (3 function evaluations)
r_final: 0.3537
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7846
moved from start:          0.1934

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034  14191  Z= 0.147
  Angle     :  0.647   8.516  19874  Z= 0.358
  Chirality :  0.045   0.274   2233
  Planarity :  0.004   0.051   2009
  Dihedral  : 25.465 177.750   3174
  Min Nonbonded Distance : 2.318

Molprobity Statistics.
  All-atom Clashscore : 14.19
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.66 %
    Favored  : 96.34 %
  Rotamer:
    Outliers :  2.31 %
    Allowed  : 18.04 %
    Favored  : 79.65 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.10 (0.23), residues: 1311
  helix:  0.82 (0.20), residues: 624
  sheet: -0.40 (0.39), residues: 181
  loop : -0.98 (0.27), residues: 506

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG C  21 
 TYR   0.020   0.002   TYR E 194 
 PHE   0.028   0.002   PHE F 239 
 TRP   0.008   0.001   TRP C 166 
 HIS   0.012   0.001   HIS B 146 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00281 /  0.15 (14191)
  covalent geometry    : angle       0.64666 /  0.36 (19874)
  hydrogen bonds       : bond        0.04936 /  5.53 (  670)
  hydrogen bonds       : angle       4.34749 /  5.74 ( 1781)

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

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

  2622 Ramachandran restraints generated.
    1311 Oldfield, 0 Emsley, 1311 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2622 Ramachandran restraints generated.
    1311 Oldfield, 0 Emsley, 1311 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  238 residues out of total 1081 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 213
  time to evaluate  : 0.371 
Fit side-chains
   revert: symmetry clash
REVERT: A   23 MET cc_start: 0.8786 (mmt) cc_final: 0.8138 (mmt)
REVERT: A   35 PHE cc_start: 0.8543 (m-10) cc_final: 0.8040 (m-10)
REVERT: B   91 TYR cc_start: 0.7947 (t80) cc_final: 0.7235 (t80)
REVERT: B   94 SER cc_start: 0.8409 (p) cc_final: 0.8040 (p)
REVERT: B  163 ASN cc_start: 0.8829 (p0) cc_final: 0.8615 (p0)
REVERT: C   54 MET cc_start: 0.9412 (mmt) cc_final: 0.9037 (mmt)
REVERT: C   67 SER cc_start: 0.8885 (t) cc_final: 0.8248 (p)
REVERT: C  128 MET cc_start: 0.8621 (mmm) cc_final: 0.8236 (mmm)
REVERT: C  157 GLU cc_start: 0.9177 (pp20) cc_final: 0.8891 (pp20)
REVERT: C  183 ASN cc_start: 0.9076 (m110) cc_final: 0.8741 (m110)
REVERT: D   60 PHE cc_start: 0.8549 (p90) cc_final: 0.8137 (p90)
REVERT: E  107 LYS cc_start: 0.8826 (mmtt) cc_final: 0.8530 (mmtm)
REVERT: F  119 LEU cc_start: 0.8859 (mm) cc_final: 0.8646 (mm)
REVERT: F  155 TYR cc_start: 0.7867 (m-80) cc_final: 0.7631 (m-10)
REVERT: F  190 HIS cc_start: 0.8137 (m170) cc_final: 0.7868 (m90)
REVERT: F  265 ASP cc_start: 0.7360 (m-30) cc_final: 0.6876 (t0)
  outliers start: 25
  outliers final: 16
  residues processed: 230
  average time/residue: 0.0909
  time to fit residues: 32.1906
Evaluate side-chains
  221 residues out of total 1081 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 205
  time to evaluate  : 0.388 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   43 LEU
Chi-restraints excluded: chain A residue   59 CYS
Chi-restraints excluded: chain A residue   79 VAL
Chi-restraints excluded: chain B residue  193 LEU
Chi-restraints excluded: chain C residue   12 SER
Chi-restraints excluded: chain C residue   39 VAL
Chi-restraints excluded: chain D residue    5 VAL
Chi-restraints excluded: chain D residue    7 THR
Chi-restraints excluded: chain D residue   15 LEU
Chi-restraints excluded: chain E residue   48 VAL
Chi-restraints excluded: chain E residue   66 ILE
Chi-restraints excluded: chain E residue  299 LYS
Chi-restraints excluded: chain F residue   65 ASP
Chi-restraints excluded: chain F residue   71 VAL
Chi-restraints excluded: chain F residue  130 PHE
Chi-restraints excluded: chain F residue  174 ASP
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 144
   random chunks:
   chunk 46 optimal weight:    2.9990
   chunk 51 optimal weight:    5.9990
   chunk 73 optimal weight:    0.7980
   chunk 41 optimal weight:    4.9990
   chunk 108 optimal weight:    0.8980
   chunk 141 optimal weight:   20.0000
   chunk 96 optimal weight:    6.9990
   chunk 72 optimal weight:    0.6980
   chunk 125 optimal weight:    0.7980
   chunk 85 optimal weight:    7.9990
   chunk 67 optimal weight:    5.9990
   overall best weight:    1.2382

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
C 190 HIS
** E  87 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
F  87 GLN
F 183 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4144 r_free = 0.4144 target = 0.129330 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3451 r_free = 0.3451 target = 0.088724 restraints weight = 41028.189|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 43)----------------|
| r_work = 0.3505 r_free = 0.3505 target = 0.091533 restraints weight = 20993.230|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 48)----------------|
| r_work = 0.3538 r_free = 0.3538 target = 0.093334 restraints weight = 14206.990|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 42)----------------|
| r_work = 0.3557 r_free = 0.3557 target = 0.094409 restraints weight = 11335.994|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 24)----------------|
| r_work = 0.3566 r_free = 0.3566 target = 0.094935 restraints weight = 10005.471|
|-----------------------------------------------------------------------------|
r_work (final): 0.3533
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3533
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3533 r_free = 0.3533    target_work(ls_wunit_k1) = 0.093         |
| occupancies: max = 1.00  min = 0.46   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3533 r_free = 0.3533    target_work(ls_wunit_k1) = 0.093         |
| occupancies: max = 1.00  min = 0.46   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 3 (3 function evaluations)
r_final: 0.3533
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7855
moved from start:          0.2098

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035  14191  Z= 0.153
  Angle     :  0.647   8.756  19874  Z= 0.357
  Chirality :  0.045   0.273   2233
  Planarity :  0.004   0.049   2009
  Dihedral  : 25.453 177.744   3174
  Min Nonbonded Distance : 2.319

Molprobity Statistics.
  All-atom Clashscore : 14.58
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.59 %
    Favored  : 96.41 %
  Rotamer:
    Outliers :  2.31 %
    Allowed  : 19.61 %
    Favored  : 78.08 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.08 (0.23), residues: 1311
  helix:  0.83 (0.20), residues: 628
  sheet: -0.38 (0.39), residues: 181
  loop : -0.98 (0.27), residues: 502

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG C  17 
 TYR   0.016   0.002   TYR E 194 
 PHE   0.035   0.002   PHE F 239 
 TRP   0.008   0.001   TRP C 166 
 HIS   0.010   0.001   HIS B 146 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00303 /  0.15 (14191)
  covalent geometry    : angle       0.64727 /  0.36 (19874)
  hydrogen bonds       : bond        0.04694 /  5.27 (  670)
  hydrogen bonds       : angle       4.27614 /  5.65 ( 1781)

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

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

  2622 Ramachandran restraints generated.
    1311 Oldfield, 0 Emsley, 1311 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2622 Ramachandran restraints generated.
    1311 Oldfield, 0 Emsley, 1311 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  239 residues out of total 1081 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 214
  time to evaluate  : 0.445 
Fit side-chains
   revert: symmetry clash
REVERT: A   23 MET cc_start: 0.8756 (mmt) cc_final: 0.8071 (mmt)
REVERT: A   35 PHE cc_start: 0.8564 (m-10) cc_final: 0.8104 (m-10)
REVERT: B   91 TYR cc_start: 0.7958 (t80) cc_final: 0.7284 (t80)
REVERT: B   94 SER cc_start: 0.8424 (p) cc_final: 0.8047 (p)
REVERT: B  125 MET cc_start: 0.9085 (mtt) cc_final: 0.8617 (tmm)
REVERT: C   54 MET cc_start: 0.9391 (mmt) cc_final: 0.9058 (mmt)
REVERT: C   67 SER cc_start: 0.8894 (t) cc_final: 0.8321 (p)
REVERT: C  157 GLU cc_start: 0.9182 (pp20) cc_final: 0.8895 (pp20)
REVERT: C  183 ASN cc_start: 0.9055 (m110) cc_final: 0.8783 (m-40)
REVERT: C  184 GLN cc_start: 0.8928 (pm20) cc_final: 0.8644 (pm20)
REVERT: D   60 PHE cc_start: 0.8441 (p90) cc_final: 0.8110 (p90)
REVERT: E  107 LYS cc_start: 0.8833 (mmtt) cc_final: 0.8492 (mmtm)
REVERT: F   54 MET cc_start: 0.9114 (mpp) cc_final: 0.8836 (mtm)
REVERT: F  119 LEU cc_start: 0.8849 (mm) cc_final: 0.8621 (mm)
REVERT: F  155 TYR cc_start: 0.7826 (m-80) cc_final: 0.7602 (m-80)
REVERT: F  190 HIS cc_start: 0.8034 (m170) cc_final: 0.7833 (m90)
REVERT: F  265 ASP cc_start: 0.7376 (m-30) cc_final: 0.6884 (t0)
  outliers start: 25
  outliers final: 19
  residues processed: 228
  average time/residue: 0.0905
  time to fit residues: 32.2876
Evaluate side-chains
  216 residues out of total 1081 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 197
  time to evaluate  : 0.429 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   11 VAL
Chi-restraints excluded: chain A residue   43 LEU
Chi-restraints excluded: chain A residue   59 CYS
Chi-restraints excluded: chain A residue   79 VAL
Chi-restraints excluded: chain B residue  193 LEU
Chi-restraints excluded: chain C residue   12 SER
Chi-restraints excluded: chain C residue   39 VAL
Chi-restraints excluded: chain C residue   48 VAL
Chi-restraints excluded: chain C residue  160 LYS
Chi-restraints excluded: chain D residue    5 VAL
Chi-restraints excluded: chain D residue    7 THR
Chi-restraints excluded: chain D residue   15 LEU
Chi-restraints excluded: chain E residue   48 VAL
Chi-restraints excluded: chain E residue   66 ILE
Chi-restraints excluded: chain F residue   39 VAL
Chi-restraints excluded: chain F residue   71 VAL
Chi-restraints excluded: chain F residue  130 PHE
Chi-restraints excluded: chain F residue  174 ASP
Chi-restraints excluded: chain F residue  272 MET
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 144
   random chunks:
   chunk 57 optimal weight:    5.9990
   chunk 64 optimal weight:    4.9990
   chunk 62 optimal weight:    0.1980
   chunk 95 optimal weight:    2.9990
   chunk 49 optimal weight:    0.9980
   chunk 8 optimal weight:    0.9990
   chunk 39 optimal weight:    2.9990
   chunk 83 optimal weight:    0.2980
   chunk 47 optimal weight:    0.8980
   chunk 131 optimal weight:    4.9990
   chunk 14 optimal weight:    6.9990
   overall best weight:    0.6782

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
C 190 HIS
** E  87 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
F  87 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4161 r_free = 0.4161 target = 0.130414 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3483 r_free = 0.3483 target = 0.090349 restraints weight = 36566.960|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 44)----------------|
| r_work = 0.3534 r_free = 0.3534 target = 0.093020 restraints weight = 19591.855|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 44)----------------|
| r_work = 0.3565 r_free = 0.3565 target = 0.094736 restraints weight = 13626.495|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 41)----------------|
| r_work = 0.3584 r_free = 0.3584 target = 0.095779 restraints weight = 11033.598|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 42)----------------|
| r_work = 0.3595 r_free = 0.3595 target = 0.096379 restraints weight = 9780.627|
|-----------------------------------------------------------------------------|
r_work (final): 0.3559
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3558
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3558 r_free = 0.3558    target_work(ls_wunit_k1) = 0.094         |
| occupancies: max = 1.00  min = 0.46   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3558 r_free = 0.3558    target_work(ls_wunit_k1) = 0.094         |
| occupancies: max = 1.00  min = 0.46   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 3 (3 function evaluations)
r_final: 0.3558
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7816
moved from start:          0.2267

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037  14191  Z= 0.140
  Angle     :  0.648   9.249  19874  Z= 0.356
  Chirality :  0.044   0.277   2233
  Planarity :  0.004   0.050   2009
  Dihedral  : 25.416 177.518   3174
  Min Nonbonded Distance : 2.318

Molprobity Statistics.
  All-atom Clashscore : 14.69
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.51 %
    Favored  : 96.49 %
  Rotamer:
    Outliers :  1.85 %
    Allowed  : 21.37 %
    Favored  : 76.78 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.05 (0.23), residues: 1311
  helix:  0.89 (0.20), residues: 626
  sheet: -0.47 (0.39), residues: 186
  loop : -0.95 (0.27), residues: 499

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG C  17 
 TYR   0.017   0.001   TYR B 223 
 PHE   0.014   0.001   PHE F 239 
 TRP   0.008   0.001   TRP A  22 
 HIS   0.010   0.001   HIS B 146 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00269 /  0.14 (14191)
  covalent geometry    : angle       0.64752 /  0.36 (19874)
  hydrogen bonds       : bond        0.04388 /  4.97 (  670)
  hydrogen bonds       : angle       4.13167 /  5.44 ( 1781)

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

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

  2622 Ramachandran restraints generated.
    1311 Oldfield, 0 Emsley, 1311 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2622 Ramachandran restraints generated.
    1311 Oldfield, 0 Emsley, 1311 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  254 residues out of total 1081 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 234
  time to evaluate  : 0.362 
Fit side-chains
REVERT: A   23 MET cc_start: 0.8717 (mmt) cc_final: 0.7985 (mmt)
REVERT: A   35 PHE cc_start: 0.8591 (m-10) cc_final: 0.8290 (m-10)
REVERT: A   46 ARG cc_start: 0.8788 (OUTLIER) cc_final: 0.8250 (ttm-80)
REVERT: B   91 TYR cc_start: 0.7919 (t80) cc_final: 0.6944 (t80)
REVERT: B   94 SER cc_start: 0.8642 (p) cc_final: 0.8300 (m)
REVERT: B  125 MET cc_start: 0.9087 (mtt) cc_final: 0.8647 (tmm)
REVERT: B  272 MET cc_start: 0.8569 (mpp) cc_final: 0.8320 (mpp)
REVERT: C   54 MET cc_start: 0.9362 (mmt) cc_final: 0.9028 (mmt)
REVERT: C   67 SER cc_start: 0.8746 (t) cc_final: 0.8159 (p)
REVERT: C  128 MET cc_start: 0.8629 (mmm) cc_final: 0.8158 (mmm)
REVERT: C  157 GLU cc_start: 0.9195 (pp20) cc_final: 0.8901 (pp20)
REVERT: C  184 GLN cc_start: 0.8923 (pm20) cc_final: 0.8722 (pm20)
REVERT: D   18 ASP cc_start: 0.8469 (t0) cc_final: 0.8215 (t70)
REVERT: D   60 PHE cc_start: 0.8498 (p90) cc_final: 0.8069 (p90)
REVERT: E  107 LYS cc_start: 0.8813 (mmtt) cc_final: 0.8493 (mmtm)
REVERT: F  119 LEU cc_start: 0.8866 (mm) cc_final: 0.8626 (mm)
REVERT: F  155 TYR cc_start: 0.7786 (m-80) cc_final: 0.7570 (m-80)
REVERT: F  265 ASP cc_start: 0.7345 (m-30) cc_final: 0.6915 (t0)
  outliers start: 20
  outliers final: 14
  residues processed: 244
  average time/residue: 0.0989
  time to fit residues: 37.0924
Evaluate side-chains
  226 residues out of total 1081 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 211
  time to evaluate  : 0.299 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   43 LEU
Chi-restraints excluded: chain A residue   46 ARG
Chi-restraints excluded: chain A residue   59 CYS
Chi-restraints excluded: chain B residue  193 LEU
Chi-restraints excluded: chain C residue   12 SER
Chi-restraints excluded: chain C residue   39 VAL
Chi-restraints excluded: chain D residue    5 VAL
Chi-restraints excluded: chain D residue    7 THR
Chi-restraints excluded: chain D residue   15 LEU
Chi-restraints excluded: chain D residue   58 MET
Chi-restraints excluded: chain E residue   48 VAL
Chi-restraints excluded: chain E residue   66 ILE
Chi-restraints excluded: chain F residue   39 VAL
Chi-restraints excluded: chain F residue  174 ASP
Chi-restraints excluded: chain F residue  272 MET
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 144
   random chunks:
   chunk 82 optimal weight:    3.9990
   chunk 78 optimal weight:    0.9990
   chunk 5 optimal weight:    1.9990
   chunk 117 optimal weight:    3.9990
   chunk 63 optimal weight:    0.0170
   chunk 105 optimal weight:    7.9990
   chunk 12 optimal weight:    0.9980
   chunk 54 optimal weight:    2.9990
   chunk 48 optimal weight:    5.9990
   chunk 121 optimal weight:    7.9990
   chunk 36 optimal weight:    0.8980
   overall best weight:    0.9822

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
C 146 HIS
C 183 ASN
** C 184 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 190 HIS
** E  87 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E 127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
F  87 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4160 r_free = 0.4160 target = 0.130226 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 54)----------------|
| r_work = 0.3460 r_free = 0.3460 target = 0.089167 restraints weight = 41091.689|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3512 r_free = 0.3512 target = 0.091886 restraints weight = 21695.862|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 47)----------------|
| r_work = 0.3544 r_free = 0.3544 target = 0.093635 restraints weight = 14976.824|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 35)----------------|
| r_work = 0.3563 r_free = 0.3563 target = 0.094695 restraints weight = 12106.114|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 41)----------------|
| r_work = 0.3574 r_free = 0.3574 target = 0.095318 restraints weight = 10732.117|
|-----------------------------------------------------------------------------|
r_work (final): 0.3540
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3540
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3540 r_free = 0.3540    target_work(ls_wunit_k1) = 0.093         |
| occupancies: max = 1.00  min = 0.46   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3540 r_free = 0.3540    target_work(ls_wunit_k1) = 0.093         |
| occupancies: max = 1.00  min = 0.48   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 3 (3 function evaluations)
r_final: 0.3540
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7841
moved from start:          0.2379

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.066  14191  Z= 0.150
  Angle     :  0.685  13.411  19874  Z= 0.372
  Chirality :  0.046   0.300   2233
  Planarity :  0.004   0.049   2009
  Dihedral  : 25.410 177.500   3174
  Min Nonbonded Distance : 2.319

Molprobity Statistics.
  All-atom Clashscore : 14.77
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.51 %
    Favored  : 96.49 %
  Rotamer:
    Outliers :  2.41 %
    Allowed  : 22.94 %
    Favored  : 74.65 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.05 (0.23), residues: 1311
  helix:  0.86 (0.20), residues: 628
  sheet: -0.44 (0.38), residues: 186
  loop : -0.94 (0.27), residues: 497

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG C 100 
 TYR   0.018   0.001   TYR F 229 
 PHE   0.028   0.001   PHE F  24 
 TRP   0.007   0.001   TRP A  22 
 HIS   0.010   0.001   HIS B 146 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00300 /  0.15 (14191)
  covalent geometry    : angle       0.68491 /  0.37 (19874)
  hydrogen bonds       : bond        0.04378 /  4.95 (  670)
  hydrogen bonds       : angle       4.17213 /  5.47 ( 1781)

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

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

  2622 Ramachandran restraints generated.
    1311 Oldfield, 0 Emsley, 1311 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2622 Ramachandran restraints generated.
    1311 Oldfield, 0 Emsley, 1311 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  247 residues out of total 1081 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 221
  time to evaluate  : 0.286 
Fit side-chains
REVERT: A    1 MET cc_start: 0.7344 (tmm) cc_final: 0.7081 (tmm)
REVERT: A   35 PHE cc_start: 0.8633 (m-10) cc_final: 0.8338 (m-10)
REVERT: A   46 ARG cc_start: 0.8801 (OUTLIER) cc_final: 0.8263 (ttm-80)
REVERT: B   91 TYR cc_start: 0.7917 (t80) cc_final: 0.7014 (t80)
REVERT: B   94 SER cc_start: 0.8626 (p) cc_final: 0.8136 (p)
REVERT: B  125 MET cc_start: 0.9130 (mtt) cc_final: 0.8654 (tmm)
REVERT: B  272 MET cc_start: 0.8575 (OUTLIER) cc_final: 0.8297 (mpp)
REVERT: C   54 MET cc_start: 0.9349 (mmt) cc_final: 0.9023 (mmt)
REVERT: C   67 SER cc_start: 0.8745 (t) cc_final: 0.8174 (p)
REVERT: C  100 ARG cc_start: 0.8998 (tpp-160) cc_final: 0.8756 (tpp-160)
REVERT: C  128 MET cc_start: 0.8580 (mmm) cc_final: 0.8092 (mmm)
REVERT: C  157 GLU cc_start: 0.9211 (pp20) cc_final: 0.8918 (pp20)
REVERT: C  184 GLN cc_start: 0.8996 (pm20) cc_final: 0.8716 (pm20)
REVERT: C  190 HIS cc_start: 0.8617 (m90) cc_final: 0.8358 (m170)
REVERT: D   18 ASP cc_start: 0.8449 (t0) cc_final: 0.8212 (t70)
REVERT: D   60 PHE cc_start: 0.8485 (p90) cc_final: 0.8118 (p90)
REVERT: D   73 GLU cc_start: 0.6813 (pm20) cc_final: 0.6529 (pm20)
REVERT: F   19 GLU cc_start: 0.8710 (mp0) cc_final: 0.8474 (mp0)
REVERT: F  119 LEU cc_start: 0.8874 (mm) cc_final: 0.8632 (mm)
REVERT: F  128 MET cc_start: 0.8016 (pmm) cc_final: 0.7717 (pmm)
REVERT: F  155 TYR cc_start: 0.7893 (m-80) cc_final: 0.7556 (m-80)
REVERT: F  265 ASP cc_start: 0.7383 (m-30) cc_final: 0.6942 (t0)
  outliers start: 26
  outliers final: 21
  residues processed: 233
  average time/residue: 0.1022
  time to fit residues: 36.4778
Evaluate side-chains
  228 residues out of total 1081 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 205
  time to evaluate  : 0.427 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   11 VAL
Chi-restraints excluded: chain A residue   43 LEU
Chi-restraints excluded: chain A residue   46 ARG
Chi-restraints excluded: chain A residue   59 CYS
Chi-restraints excluded: chain A residue   79 VAL
Chi-restraints excluded: chain B residue  193 LEU
Chi-restraints excluded: chain B residue  272 MET
Chi-restraints excluded: chain C residue   39 VAL
Chi-restraints excluded: chain C residue   48 VAL
Chi-restraints excluded: chain C residue  160 LYS
Chi-restraints excluded: chain D residue    5 VAL
Chi-restraints excluded: chain D residue    7 THR
Chi-restraints excluded: chain D residue   15 LEU
Chi-restraints excluded: chain D residue   50 THR
Chi-restraints excluded: chain D residue   58 MET
Chi-restraints excluded: chain E residue   48 VAL
Chi-restraints excluded: chain E residue   66 ILE
Chi-restraints excluded: chain F residue   39 VAL
Chi-restraints excluded: chain F residue  130 PHE
Chi-restraints excluded: chain F residue  174 ASP
Chi-restraints excluded: chain F residue  182 ILE
Chi-restraints excluded: chain F residue  193 LEU
Chi-restraints excluded: chain F residue  272 MET
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 144
   random chunks:
   chunk 67 optimal weight:    2.9990
   chunk 102 optimal weight:    2.9990
   chunk 109 optimal weight:    0.2980
   chunk 126 optimal weight:    0.9990
   chunk 54 optimal weight:    0.9990
   chunk 46 optimal weight:    3.9990
   chunk 133 optimal weight:    1.9990
   chunk 43 optimal weight:    7.9990
   chunk 134 optimal weight:   10.0000
   chunk 108 optimal weight:    3.9990
   chunk 121 optimal weight:    9.9990
   overall best weight:    1.4588

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** A  24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 184 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
D  10 ASN
** E  87 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E 127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
F  87 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4151 r_free = 0.4151 target = 0.129619 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3453 r_free = 0.3453 target = 0.088829 restraints weight = 37509.846|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 42)----------------|
| r_work = 0.3502 r_free = 0.3502 target = 0.091385 restraints weight = 20796.047|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.3532 r_free = 0.3532 target = 0.093006 restraints weight = 14760.794|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 36)----------------|
| r_work = 0.3550 r_free = 0.3550 target = 0.093991 restraints weight = 12132.876|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 31)----------------|
| r_work = 0.3559 r_free = 0.3559 target = 0.094473 restraints weight = 10855.985|
|-----------------------------------------------------------------------------|
r_work (final): 0.3524
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3522
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3522 r_free = 0.3522    target_work(ls_wunit_k1) = 0.092         |
| occupancies: max = 1.00  min = 0.48   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3522 r_free = 0.3522    target_work(ls_wunit_k1) = 0.092         |
| occupancies: max = 1.00  min = 0.46   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 3 (3 function evaluations)
r_final: 0.3522
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7865
moved from start:          0.2469

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.044  14191  Z= 0.160
  Angle     :  0.683  11.134  19874  Z= 0.371
  Chirality :  0.045   0.271   2233
  Planarity :  0.004   0.049   2009
  Dihedral  : 25.408 177.582   3174
  Min Nonbonded Distance : 2.320

Molprobity Statistics.
  All-atom Clashscore : 15.23
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.97 %
    Favored  : 96.03 %
  Rotamer:
    Outliers :  2.59 %
    Allowed  : 23.50 %
    Favored  : 73.91 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.04 (0.23), residues: 1311
  helix:  0.89 (0.20), residues: 629
  sheet: -0.45 (0.39), residues: 186
  loop : -0.96 (0.27), residues: 496

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG B 169 
 TYR   0.015   0.001   TYR F 229 
 PHE   0.040   0.002   PHE F  24 
 TRP   0.008   0.001   TRP A  22 
 HIS   0.009   0.001   HIS B 146 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00327 /  0.16 (14191)
  covalent geometry    : angle       0.68330 /  0.37 (19874)
  hydrogen bonds       : bond        0.04369 /  4.97 (  670)
  hydrogen bonds       : angle       4.18211 /  5.47 ( 1781)

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

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

  2622 Ramachandran restraints generated.
    1311 Oldfield, 0 Emsley, 1311 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2622 Ramachandran restraints generated.
    1311 Oldfield, 0 Emsley, 1311 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  242 residues out of total 1081 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 214
  time to evaluate  : 0.496 
Fit side-chains
   revert: symmetry clash
REVERT: A   23 MET cc_start: 0.8750 (mmt) cc_final: 0.8292 (mmt)
REVERT: A   35 PHE cc_start: 0.8688 (m-10) cc_final: 0.8410 (m-10)
REVERT: A   46 ARG cc_start: 0.8820 (OUTLIER) cc_final: 0.8241 (ttm-80)
REVERT: B   91 TYR cc_start: 0.7922 (t80) cc_final: 0.7014 (t80)
REVERT: B   94 SER cc_start: 0.8651 (p) cc_final: 0.8147 (p)
REVERT: B  125 MET cc_start: 0.9121 (mtt) cc_final: 0.8693 (tmm)
REVERT: C   54 MET cc_start: 0.9337 (mmt) cc_final: 0.9014 (mmt)
REVERT: C   67 SER cc_start: 0.8841 (t) cc_final: 0.8284 (p)
REVERT: C  100 ARG cc_start: 0.8964 (tpp-160) cc_final: 0.8728 (tpp-160)
REVERT: C  157 GLU cc_start: 0.9225 (pp20) cc_final: 0.8931 (pp20)
REVERT: C  184 GLN cc_start: 0.8957 (pm20) cc_final: 0.8663 (pm20)
REVERT: D   18 ASP cc_start: 0.8471 (t0) cc_final: 0.8258 (t70)
REVERT: D   60 PHE cc_start: 0.8539 (p90) cc_final: 0.8084 (p90)
REVERT: E   49 ARG cc_start: 0.8834 (tpp80) cc_final: 0.8361 (tpp80)
REVERT: E  107 LYS cc_start: 0.8837 (mmtt) cc_final: 0.8608 (mmtm)
REVERT: F   19 GLU cc_start: 0.8642 (mp0) cc_final: 0.8379 (mp0)
REVERT: F  119 LEU cc_start: 0.8887 (mm) cc_final: 0.8640 (mm)
REVERT: F  128 MET cc_start: 0.8039 (pmm) cc_final: 0.7741 (pmm)
REVERT: F  265 ASP cc_start: 0.7408 (m-30) cc_final: 0.6974 (t0)
  outliers start: 28
  outliers final: 22
  residues processed: 229
  average time/residue: 0.0921
  time to fit residues: 32.8555
Evaluate side-chains
  230 residues out of total 1081 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 207
  time to evaluate  : 0.489 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   11 VAL
Chi-restraints excluded: chain A residue   43 LEU
Chi-restraints excluded: chain A residue   46 ARG
Chi-restraints excluded: chain A residue   59 CYS
Chi-restraints excluded: chain A residue   79 VAL
Chi-restraints excluded: chain B residue  193 LEU
Chi-restraints excluded: chain B residue  272 MET
Chi-restraints excluded: chain C residue   12 SER
Chi-restraints excluded: chain C residue   39 VAL
Chi-restraints excluded: chain C residue   48 VAL
Chi-restraints excluded: chain D residue    5 VAL
Chi-restraints excluded: chain D residue   15 LEU
Chi-restraints excluded: chain D residue   50 THR
Chi-restraints excluded: chain D residue   58 MET
Chi-restraints excluded: chain E residue   48 VAL
Chi-restraints excluded: chain E residue   66 ILE
Chi-restraints excluded: chain E residue   81 LEU
Chi-restraints excluded: chain F residue   39 VAL
Chi-restraints excluded: chain F residue   71 VAL
Chi-restraints excluded: chain F residue   87 GLN
Chi-restraints excluded: chain F residue  174 ASP
Chi-restraints excluded: chain F residue  182 ILE
Chi-restraints excluded: chain F residue  272 MET
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 144
   random chunks:
   chunk 131 optimal weight:    0.0270
   chunk 28 optimal weight:    5.9990
   chunk 129 optimal weight:    0.0020
   chunk 83 optimal weight:    0.8980
   chunk 40 optimal weight:    8.9990
   chunk 125 optimal weight:    1.9990
   chunk 80 optimal weight:   10.0000
   chunk 31 optimal weight:    0.9980
   chunk 139 optimal weight:   30.0000
   chunk 126 optimal weight:    1.9990
   chunk 57 optimal weight:    2.9990
   overall best weight:    0.7848

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** A  24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 184 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 190 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** E  87 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** F  87 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4160 r_free = 0.4160 target = 0.130424 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3446 r_free = 0.3446 target = 0.088528 restraints weight = 53002.623|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 42)----------------|
| r_work = 0.3505 r_free = 0.3505 target = 0.091577 restraints weight = 25302.394|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 45)----------------|
| r_work = 0.3542 r_free = 0.3542 target = 0.093578 restraints weight = 16516.006|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 48)----------------|
| r_work = 0.3564 r_free = 0.3564 target = 0.094819 restraints weight = 12890.986|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3575 r_free = 0.3575 target = 0.095418 restraints weight = 11196.824|
|-----------------------------------------------------------------------------|
r_work (final): 0.3547
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3540
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3540 r_free = 0.3540    target_work(ls_wunit_k1) = 0.093         |
| occupancies: max = 1.00  min = 0.46   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3540 r_free = 0.3540    target_work(ls_wunit_k1) = 0.093         |
| occupancies: max = 1.00  min = 0.48   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 3 (3 function evaluations)
r_final: 0.3540
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7859
moved from start:          0.2545

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.053  14191  Z= 0.146
  Angle     :  0.690  12.606  19874  Z= 0.372
  Chirality :  0.045   0.277   2233
  Planarity :  0.004   0.049   2009
  Dihedral  : 25.381 177.347   3174
  Min Nonbonded Distance : 2.319

Molprobity Statistics.
  All-atom Clashscore : 15.35
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.66 %
    Favored  : 96.34 %
  Rotamer:
    Outliers :  1.94 %
    Allowed  : 24.24 %
    Favored  : 73.82 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.07 (0.23), residues: 1311
  helix:  0.85 (0.20), residues: 629
  sheet: -0.48 (0.38), residues: 191
  loop : -0.95 (0.28), residues: 491

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B 169 
 TYR   0.018   0.001   TYR F 171 
 PHE   0.052   0.002   PHE B 239 
 TRP   0.009   0.001   TRP A  22 
 HIS   0.009   0.001   HIS F 146 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00291 /  0.15 (14191)
  covalent geometry    : angle       0.69005 /  0.37 (19874)
  hydrogen bonds       : bond        0.04206 /  4.80 (  670)
  hydrogen bonds       : angle       4.15284 /  5.45 ( 1781)

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

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

  2622 Ramachandran restraints generated.
    1311 Oldfield, 0 Emsley, 1311 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2622 Ramachandran restraints generated.
    1311 Oldfield, 0 Emsley, 1311 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  234 residues out of total 1081 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 213
  time to evaluate  : 0.449 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A    1 MET cc_start: 0.7267 (tmm) cc_final: 0.7008 (tmm)
REVERT: A   23 MET cc_start: 0.8630 (mmt) cc_final: 0.8228 (mmt)
REVERT: A   46 ARG cc_start: 0.8756 (OUTLIER) cc_final: 0.8216 (ttm-80)
REVERT: B   91 TYR cc_start: 0.7945 (t80) cc_final: 0.7000 (t80)
REVERT: B   94 SER cc_start: 0.8587 (p) cc_final: 0.8060 (p)
REVERT: B  125 MET cc_start: 0.9070 (mtt) cc_final: 0.8616 (tmm)
REVERT: C   54 MET cc_start: 0.9323 (mmt) cc_final: 0.9028 (mmt)
REVERT: C   67 SER cc_start: 0.8773 (t) cc_final: 0.8230 (p)
REVERT: C  100 ARG cc_start: 0.8890 (tpp-160) cc_final: 0.8673 (tpp-160)
REVERT: C  128 MET cc_start: 0.8666 (mmm) cc_final: 0.8218 (mmm)
REVERT: C  157 GLU cc_start: 0.9201 (pp20) cc_final: 0.8904 (pp20)
REVERT: C  184 GLN cc_start: 0.8924 (pm20) cc_final: 0.8636 (pm20)
REVERT: D   18 ASP cc_start: 0.8382 (t0) cc_final: 0.8167 (t70)
REVERT: D   60 PHE cc_start: 0.8460 (p90) cc_final: 0.8118 (p90)
REVERT: D   73 GLU cc_start: 0.6944 (pm20) cc_final: 0.6534 (pm20)
REVERT: E   49 ARG cc_start: 0.8825 (tpp80) cc_final: 0.8342 (tpp80)
REVERT: E  107 LYS cc_start: 0.8829 (mmtt) cc_final: 0.8584 (mmtm)
REVERT: F  119 LEU cc_start: 0.8842 (mm) cc_final: 0.8585 (mm)
REVERT: F  128 MET cc_start: 0.8047 (pmm) cc_final: 0.7668 (pmm)
REVERT: F  155 TYR cc_start: 0.7972 (m-80) cc_final: 0.7636 (m-80)
REVERT: F  265 ASP cc_start: 0.7280 (m-30) cc_final: 0.6878 (t0)
  outliers start: 21
  outliers final: 19
  residues processed: 224
  average time/residue: 0.0934
  time to fit residues: 32.0793
Evaluate side-chains
  223 residues out of total 1081 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 203
  time to evaluate  : 0.354 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   11 VAL
Chi-restraints excluded: chain A residue   43 LEU
Chi-restraints excluded: chain A residue   46 ARG
Chi-restraints excluded: chain A residue   59 CYS
Chi-restraints excluded: chain A residue   79 VAL
Chi-restraints excluded: chain B residue  193 LEU
Chi-restraints excluded: chain B residue  272 MET
Chi-restraints excluded: chain C residue   39 VAL
Chi-restraints excluded: chain C residue  160 LYS
Chi-restraints excluded: chain D residue    5 VAL
Chi-restraints excluded: chain D residue   15 LEU
Chi-restraints excluded: chain D residue   50 THR
Chi-restraints excluded: chain D residue   58 MET
Chi-restraints excluded: chain E residue   48 VAL
Chi-restraints excluded: chain E residue   66 ILE
Chi-restraints excluded: chain F residue   39 VAL
Chi-restraints excluded: chain F residue  174 ASP
Chi-restraints excluded: chain F residue  182 ILE
Chi-restraints excluded: chain F residue  193 LEU
Chi-restraints excluded: chain F residue  272 MET
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 144
   random chunks:
   chunk 54 optimal weight:    2.9990
   chunk 70 optimal weight:    0.6980
   chunk 6 optimal weight:    1.9990
   chunk 77 optimal weight:    1.9990
   chunk 45 optimal weight:    5.9990
   chunk 94 optimal weight:    7.9990
   chunk 44 optimal weight:    0.8980
   chunk 100 optimal weight:    0.7980
   chunk 87 optimal weight:    4.9990
   chunk 129 optimal weight:    4.9990
   chunk 28 optimal weight:    8.9990
   overall best weight:    1.2784

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** A  24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 184 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 190 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** E  87 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E 127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
F  87 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4153 r_free = 0.4153 target = 0.129892 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3437 r_free = 0.3437 target = 0.087943 restraints weight = 52993.949|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 44)----------------|
| r_work = 0.3495 r_free = 0.3495 target = 0.090980 restraints weight = 25332.928|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 45)----------------|
| r_work = 0.3532 r_free = 0.3532 target = 0.092969 restraints weight = 16540.359|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 48)----------------|
| r_work = 0.3554 r_free = 0.3554 target = 0.094206 restraints weight = 12859.144|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.3565 r_free = 0.3565 target = 0.094794 restraints weight = 11152.478|
|-----------------------------------------------------------------------------|
r_work (final): 0.3532
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3528
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3528 r_free = 0.3528    target_work(ls_wunit_k1) = 0.092         |
| occupancies: max = 1.00  min = 0.48   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3528 r_free = 0.3528    target_work(ls_wunit_k1) = 0.092         |
| occupancies: max = 1.00  min = 0.47   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 3 (3 function evaluations)
r_final: 0.3528
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7862
moved from start:          0.2642

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.048  14191  Z= 0.157
  Angle     :  0.703  11.550  19874  Z= 0.379
  Chirality :  0.045   0.272   2233
  Planarity :  0.004   0.048   2009
  Dihedral  : 25.369 177.355   3174
  Min Nonbonded Distance : 2.321

Molprobity Statistics.
  All-atom Clashscore : 15.54
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.04 %
    Favored  : 95.96 %
  Rotamer:
    Outliers :  2.22 %
    Allowed  : 24.51 %
    Favored  : 73.27 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.10 (0.23), residues: 1311
  helix:  0.83 (0.20), residues: 629
  sheet: -0.49 (0.38), residues: 186
  loop : -0.97 (0.27), residues: 496

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG C 256 
 TYR   0.015   0.002   TYR C 171 
 PHE   0.042   0.002   PHE F  24 
 TRP   0.011   0.001   TRP A  22 
 HIS   0.010   0.001   HIS F 146 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00323 /  0.16 (14191)
  covalent geometry    : angle       0.70256 /  0.38 (19874)
  hydrogen bonds       : bond        0.04222 /  4.82 (  670)
  hydrogen bonds       : angle       4.17361 /  5.45 ( 1781)

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

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

  2622 Ramachandran restraints generated.
    1311 Oldfield, 0 Emsley, 1311 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2622 Ramachandran restraints generated.
    1311 Oldfield, 0 Emsley, 1311 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  233 residues out of total 1081 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 209
  time to evaluate  : 0.442 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A    1 MET cc_start: 0.7205 (tmm) cc_final: 0.6959 (tmm)
REVERT: A   23 MET cc_start: 0.8802 (mmt) cc_final: 0.8357 (mmt)
REVERT: A   46 ARG cc_start: 0.8784 (OUTLIER) cc_final: 0.8161 (ttm-80)
REVERT: B   91 TYR cc_start: 0.7919 (t80) cc_final: 0.6958 (t80)
REVERT: B   94 SER cc_start: 0.8673 (p) cc_final: 0.8134 (p)
REVERT: B  125 MET cc_start: 0.9106 (mtt) cc_final: 0.8687 (tmm)
REVERT: C   67 SER cc_start: 0.8832 (t) cc_final: 0.8261 (p)
REVERT: C  100 ARG cc_start: 0.8954 (tpp-160) cc_final: 0.8697 (tpp-160)
REVERT: C  128 MET cc_start: 0.8643 (mmm) cc_final: 0.8067 (mmt)
REVERT: C  157 GLU cc_start: 0.9232 (pp20) cc_final: 0.8937 (pp20)
REVERT: C  184 GLN cc_start: 0.8969 (pm20) cc_final: 0.8662 (pm20)
REVERT: D   18 ASP cc_start: 0.8480 (t0) cc_final: 0.8239 (t70)
REVERT: D   60 PHE cc_start: 0.8585 (p90) cc_final: 0.8026 (p90)
REVERT: D   73 GLU cc_start: 0.6846 (pm20) cc_final: 0.6466 (pm20)
REVERT: E   49 ARG cc_start: 0.8843 (tpp80) cc_final: 0.8344 (tpp80)
REVERT: E  107 LYS cc_start: 0.8867 (mmtt) cc_final: 0.8614 (mmtm)
REVERT: F  119 LEU cc_start: 0.8878 (mm) cc_final: 0.8626 (mm)
REVERT: F  128 MET cc_start: 0.8083 (pmm) cc_final: 0.7687 (pmm)
REVERT: F  265 ASP cc_start: 0.7404 (m-30) cc_final: 0.6970 (t0)
  outliers start: 24
  outliers final: 19
  residues processed: 222
  average time/residue: 0.0917
  time to fit residues: 30.9943
Evaluate side-chains
  225 residues out of total 1081 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 205
  time to evaluate  : 0.278 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   11 VAL
Chi-restraints excluded: chain A residue   46 ARG
Chi-restraints excluded: chain A residue   59 CYS
Chi-restraints excluded: chain A residue   79 VAL
Chi-restraints excluded: chain B residue  193 LEU
Chi-restraints excluded: chain B residue  272 MET
Chi-restraints excluded: chain C residue   39 VAL
Chi-restraints excluded: chain C residue   48 VAL
Chi-restraints excluded: chain D residue    5 VAL
Chi-restraints excluded: chain D residue    7 THR
Chi-restraints excluded: chain D residue   15 LEU
Chi-restraints excluded: chain D residue   50 THR
Chi-restraints excluded: chain D residue   58 MET
Chi-restraints excluded: chain E residue   48 VAL
Chi-restraints excluded: chain E residue   66 ILE
Chi-restraints excluded: chain F residue   39 VAL
Chi-restraints excluded: chain F residue   87 GLN
Chi-restraints excluded: chain F residue  174 ASP
Chi-restraints excluded: chain F residue  193 LEU
Chi-restraints excluded: chain F residue  272 MET
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 144
   random chunks:
   chunk 119 optimal weight:    2.9990
   chunk 97 optimal weight:    0.5980
   chunk 40 optimal weight:    8.9990
   chunk 64 optimal weight:    0.6980
   chunk 107 optimal weight:    8.9990
   chunk 79 optimal weight:    0.9990
   chunk 65 optimal weight:    3.9990
   chunk 36 optimal weight:    4.9990
   chunk 125 optimal weight:    0.7980
   chunk 54 optimal weight:    0.5980
   chunk 67 optimal weight:    3.9990
   overall best weight:    0.7382

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** A  24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 184 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 190 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** E  87 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4151 r_free = 0.4151 target = 0.129831 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3463 r_free = 0.3463 target = 0.089294 restraints weight = 37578.145|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3511 r_free = 0.3511 target = 0.091831 restraints weight = 20836.418|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 44)----------------|
| r_work = 0.3541 r_free = 0.3541 target = 0.093466 restraints weight = 14800.825|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 52)----------------|
| r_work = 0.3558 r_free = 0.3558 target = 0.094437 restraints weight = 12134.469|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 24)----------------|
| r_work = 0.3566 r_free = 0.3566 target = 0.094903 restraints weight = 10858.085|
|-----------------------------------------------------------------------------|
r_work (final): 0.3533
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3532
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3532 r_free = 0.3532    target_work(ls_wunit_k1) = 0.092         |
| occupancies: max = 1.00  min = 0.47   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3532 r_free = 0.3532    target_work(ls_wunit_k1) = 0.092         |
| occupancies: max = 1.00  min = 0.47   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 3 (3 function evaluations)
r_final: 0.3532
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7858
moved from start:          0.2628

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.160  14191  Z= 0.197
  Angle     :  0.893  59.200  19874  Z= 0.513
  Chirality :  0.046   0.669   2233
  Planarity :  0.004   0.049   2009
  Dihedral  : 25.369 177.352   3174
  Min Nonbonded Distance : 2.259

Molprobity Statistics.
  All-atom Clashscore : 16.74
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.89 %
    Favored  : 96.11 %
  Rotamer:
    Outliers :  2.13 %
    Allowed  : 24.70 %
    Favored  : 73.17 %
  Cbeta Deviations :  0.08 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.10 (0.23), residues: 1311
  helix:  0.83 (0.20), residues: 629
  sheet: -0.49 (0.38), residues: 186
  loop : -0.97 (0.27), residues: 496

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG C 256 
 TYR   0.014   0.001   TYR C  26 
 PHE   0.038   0.002   PHE F  24 
 TRP   0.010   0.001   TRP A  22 
 HIS   0.010   0.001   HIS F 146 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00394 /  0.20 (14191)
  covalent geometry    : angle       0.89280 /  0.51 (19874)
  hydrogen bonds       : bond        0.04221 /  4.82 (  670)
  hydrogen bonds       : angle       4.17534 /  5.46 ( 1781)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2450.18 seconds
wall clock time: 42 minutes 46.98 seconds (2566.98 seconds total)