Starting phenix.real_space_refine
on Wed Mar  4 12:00:13 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8fyd_29565/03_2026/8fyd_29565.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8fyd_29565/03_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_29565/03_2026/8fyd_29565.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8fyd_29565/03_2026/8fyd_29565.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/8fyd_29565/03_2026/8fyd_29565.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8fyd_29565/03_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-dev-5986/lib/python3.9/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: 3.26, 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: 1.10
  Conformation dependent library (CDL) restraints added in 504.5 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: 1.87
  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: 2.43

  Time building geometry restraints manager: 1.51 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=" O3'  DC J  21 "
       pdb=" P    DT J  22 "
    ideal  model  delta    sigma   weight residual
    1.607  1.638 -0.031 1.50e-02 4.44e+03 4.38e+00
  bond pdb=" O3'  DG J  20 "
       pdb=" P    DC J  21 "
    ideal  model  delta    sigma   weight residual
    1.607  1.638 -0.031 1.50e-02 4.44e+03 4.32e+00
  bond pdb=" O3'  DT G  30 "
       pdb=" P    DC G  31 "
    ideal  model  delta    sigma   weight residual
    1.607  1.629 -0.022 1.50e-02 4.44e+03 2.19e+00
  bond pdb=" O3'  DA J  32 "
       pdb=" P    DA J  33 "
    ideal  model  delta    sigma   weight residual
    1.607  1.626 -0.019 1.50e-02 4.44e+03 1.64e+00
  bond pdb=" C3'  DG G   8 "
       pdb=" O3'  DG G   8 "
    ideal  model  delta    sigma   weight residual
    1.422  1.460 -0.038 3.00e-02 1.11e+03 1.59e+00
  ... (remaining 14186 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.43: 19221
        1.43 -     2.86: 543
        2.86 -     4.29: 85
        4.29 -     5.72: 20
        5.72 -     7.15: 5
  Bond angle restraints: 19874
  Sorted by residual:
  angle pdb=" CA  GLN F  87 "
        pdb=" CB  GLN F  87 "
        pdb=" CG  GLN F  87 "
      ideal   model   delta    sigma   weight residual
     114.10  119.91   -5.81 2.00e+00 2.50e-01 8.45e+00
  angle pdb=" C   GLU C 232 "
        pdb=" N   ILE C 233 "
        pdb=" CA  ILE C 233 "
      ideal   model   delta    sigma   weight residual
     122.97  120.14    2.83 9.80e-01 1.04e+00 8.35e+00
  angle pdb=" CA  MET F 125 "
        pdb=" CB  MET F 125 "
        pdb=" CG  MET F 125 "
      ideal   model   delta    sigma   weight residual
     114.10  119.79   -5.69 2.00e+00 2.50e-01 8.09e+00
  angle pdb=" O3'  DA J  37 "
        pdb=" C3'  DA J  37 "
        pdb=" C2'  DA J  37 "
      ideal   model   delta    sigma   weight residual
     111.50  107.47    4.03 1.50e+00 4.44e-01 7.20e+00
  angle pdb=" C3'  DT G  30 "
        pdb=" C2'  DT G  30 "
        pdb=" C1'  DT G  30 "
      ideal   model   delta    sigma   weight residual
     101.60  105.61   -4.01 1.50e+00 4.44e-01 7.14e+00
  ... (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 -    0.039: 1695
       0.039 -    0.078: 407
       0.078 -    0.116: 104
       0.116 -    0.155: 25
       0.155 -    0.194: 2
  Chirality restraints: 2233
  Sorted by residual:
  chirality pdb=" C1'  DC J  21 "
            pdb=" O4'  DC J  21 "
            pdb=" C2'  DC J  21 "
            pdb=" N1   DC J  21 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.47    2.28    0.19 2.00e-01 2.50e+01 9.41e-01
  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       2.35   -2.50   -0.16 2.00e-01 2.50e+01 6.30e-01
  chirality pdb=" CA  VAL B 303 "
            pdb=" N   VAL B 303 "
            pdb=" C   VAL B 303 "
            pdb=" CB  VAL B 303 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.29    0.15 2.00e-01 2.50e+01 5.94e-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:             1.000
  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:          0.190
  Check model and map are aligned:         0.020
  Set scattering table:                    0.030
  Process input model:                     14.660
  Find NCS groups from input model:        0.210
  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:             0.000
  Load rotamer database and sin/cos tables:1.410
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   17.550
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7871
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      :  0.003   0.038  14191  Z= 0.145
  Angle     :  0.582   7.149  19874  Z= 0.326
  Chirality :  0.038   0.194   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
  covalent geometry    : bond        0.00315 (14191)
  covalent geometry    : angle       0.58218 (19874)
  hydrogen bonds       : bond        0.22576 (  670)
  hydrogen bonds       : angle       7.03387 ( 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  : 0.435 
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: 0.1124
  time to fit residues: 44.3665
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  : 0.264 
-------------------------------------------------------------------------------
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:    8.9990
   chunk 55 optimal weight:    0.2980
   overall best weight:    2.6186

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

Flipped N/Q/H residues before XYZ refinement:
B 127 GLN
B 146 HIS
** B 198 HIS ** 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 108 GLN
F  87 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4114 r_free = 0.4114 target = 0.126925 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 53)----------------|
| r_work = 0.3402 r_free = 0.3402 target = 0.086056 restraints weight = 37027.927|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 49)----------------|
| r_work = 0.3450 r_free = 0.3450 target = 0.088545 restraints weight = 20899.199|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 42)----------------|
| r_work = 0.3479 r_free = 0.3479 target = 0.090120 restraints weight = 14994.968|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 53)----------------|
| r_work = 0.3497 r_free = 0.3497 target = 0.091064 restraints weight = 12401.004|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3504 r_free = 0.3504 target = 0.091487 restraints weight = 11161.689|
|-----------------------------------------------------------------------------|
r_work (final): 0.3476
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3474
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3474 r_free = 0.3474    target_work(ls_wunit_k1) = 0.089         |
| occupancies: max = 1.00  min = 0.39   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3474 r_free = 0.3474    target_work(ls_wunit_k1) = 0.089         |
| occupancies: max = 1.00  min = 0.47   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3474
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7926
moved from start:          0.1630

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.053  14191  Z= 0.230
  Angle     :  0.668   8.941  19874  Z= 0.367
  Chirality :  0.042   0.161   2233
  Planarity :  0.005   0.046   2009
  Dihedral  : 25.426 178.715   3174
  Min Nonbonded Distance : 2.442

Molprobity Statistics.
  All-atom Clashscore : 16.50
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.36 %
    Favored  : 96.64 %
  Rotamer:
    Outliers :  2.04 %
    Allowed  : 11.84 %
    Favored  : 86.12 %
  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: -0.03 (0.23), residues: 1311
  helix:  0.90 (0.20), residues: 626
  sheet: -0.52 (0.37), residues: 181
  loop : -0.92 (0.27), residues: 504

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG B 156 
 TYR   0.034   0.002   TYR E 194 
 PHE   0.018   0.002   PHE A  35 
 TRP   0.018   0.002   TRP C 166 
 HIS   0.006   0.001   HIS C 190 

Details of bonding type rmsd
  covalent geometry    : bond        0.00517 (14191)
  covalent geometry    : angle       0.66834 (19874)
  hydrogen bonds       : bond        0.05547 (  670)
  hydrogen bonds       : angle       4.73318 ( 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
  246 residues out of total 1081 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 224
  time to evaluate  : 0.432 
Fit side-chains
   revert: symmetry clash
REVERT: B   91 TYR cc_start: 0.7939 (t80) cc_final: 0.7366 (t80)
REVERT: B   94 SER cc_start: 0.8511 (p) cc_final: 0.8205 (p)
REVERT: B  218 ASP cc_start: 0.7162 (p0) cc_final: 0.6943 (p0)
REVERT: B  272 MET cc_start: 0.8555 (mpp) cc_final: 0.8249 (mpp)
REVERT: C   17 ARG cc_start: 0.8066 (tpp80) cc_final: 0.7805 (tpp80)
REVERT: C   54 MET cc_start: 0.9439 (mmt) cc_final: 0.8982 (mmt)
REVERT: C   67 SER cc_start: 0.9047 (OUTLIER) cc_final: 0.8418 (p)
REVERT: C  157 GLU cc_start: 0.9182 (pp20) cc_final: 0.8907 (pp20)
REVERT: C  183 ASN cc_start: 0.9130 (m110) cc_final: 0.8791 (m-40)
REVERT: D   58 MET cc_start: 0.7795 (ppp) cc_final: 0.7242 (ppp)
REVERT: D   60 PHE cc_start: 0.8669 (p90) cc_final: 0.8190 (p90)
REVERT: D   71 LEU cc_start: 0.9007 (mp) cc_final: 0.8721 (mp)
REVERT: E  305 TYR cc_start: 0.8242 (m-10) cc_final: 0.7988 (m-10)
REVERT: F  114 ASN cc_start: 0.7891 (t0) cc_final: 0.7620 (t0)
REVERT: F  265 ASP cc_start: 0.7387 (m-30) cc_final: 0.6884 (t0)
  outliers start: 22
  outliers final: 13
  residues processed: 235
  average time/residue: 0.1004
  time to fit residues: 35.3184
Evaluate side-chains
  204 residues out of total 1081 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 190
  time to evaluate  : 0.270 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   11 VAL
Chi-restraints excluded: chain A residue   59 CYS
Chi-restraints excluded: chain C residue   39 VAL
Chi-restraints excluded: chain C residue   57 VAL
Chi-restraints excluded: chain C residue   67 SER
Chi-restraints excluded: chain C residue   72 GLU
Chi-restraints excluded: chain D residue    5 VAL
Chi-restraints excluded: chain D residue   15 LEU
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:    9.9990
   chunk 63 optimal weight:    9.9990
   chunk 49 optimal weight:    6.9990
   chunk 44 optimal weight:    1.9990
   chunk 53 optimal weight:    4.9990
   chunk 20 optimal weight:    0.9980
   chunk 60 optimal weight:    3.9990
   chunk 40 optimal weight:    5.9990
   chunk 119 optimal weight:    0.1980
   chunk 29 optimal weight:    6.9990
   chunk 137 optimal weight:   10.0000
   overall best weight:    2.4386

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

Flipped N/Q/H residues before XYZ refinement:
A  34 ASN
B 146 HIS
C 146 HIS
C 190 HIS
** C 217 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**
F 114 ASN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4104 r_free = 0.4104 target = 0.126329 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 55)----------------|
| r_work = 0.3370 r_free = 0.3370 target = 0.084593 restraints weight = 52945.864|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 52)----------------|
| r_work = 0.3429 r_free = 0.3429 target = 0.087614 restraints weight = 24704.795|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 42)----------------|
| r_work = 0.3466 r_free = 0.3466 target = 0.089552 restraints weight = 15990.480|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 44)----------------|
| r_work = 0.3489 r_free = 0.3489 target = 0.090775 restraints weight = 12461.387|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 38)----------------|
| r_work = 0.3502 r_free = 0.3502 target = 0.091463 restraints weight = 10774.635|
|-----------------------------------------------------------------------------|
r_work (final): 0.3467
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3467
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3467 r_free = 0.3467    target_work(ls_wunit_k1) = 0.089         |
| occupancies: max = 1.00  min = 0.47   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3467 r_free = 0.3467    target_work(ls_wunit_k1) = 0.089         |
| occupancies: max = 1.00  min = 0.43   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3467
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7924
moved from start:          0.1998

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.047  14191  Z= 0.213
  Angle     :  0.649   8.966  19874  Z= 0.354
  Chirality :  0.042   0.189   2233
  Planarity :  0.005   0.044   2009
  Dihedral  : 25.395 179.086   3174
  Min Nonbonded Distance : 2.447

Molprobity Statistics.
  All-atom Clashscore : 16.12
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.89 %
    Favored  : 96.11 %
  Rotamer:
    Outliers :  2.50 %
    Allowed  : 15.54 %
    Favored  : 81.96 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z 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: -0.13 (0.23), residues: 1311
  helix:  0.83 (0.20), residues: 628
  sheet: -0.62 (0.37), residues: 186
  loop : -0.97 (0.27), residues: 497

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B 124 
 TYR   0.025   0.002   TYR E 194 
 PHE   0.016   0.002   PHE F 239 
 TRP   0.015   0.001   TRP C 166 
 HIS   0.015   0.002   HIS C 146 

Details of bonding type rmsd
  covalent geometry    : bond        0.00479 (14191)
  covalent geometry    : angle       0.64868 (19874)
  hydrogen bonds       : bond        0.04855 (  670)
  hydrogen bonds       : angle       4.45368 ( 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
  236 residues out of total 1081 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 209
  time to evaluate  : 0.417 
Fit side-chains
   revert: symmetry clash
REVERT: A    3 MET cc_start: 0.8415 (OUTLIER) cc_final: 0.8198 (ttt)
REVERT: A   41 GLU cc_start: 0.8573 (tm-30) cc_final: 0.8359 (tm-30)
REVERT: B   91 TYR cc_start: 0.7947 (t80) cc_final: 0.7098 (t80)
REVERT: B   94 SER cc_start: 0.8520 (p) cc_final: 0.8075 (p)
REVERT: B  272 MET cc_start: 0.8529 (mpp) cc_final: 0.8305 (mpp)
REVERT: C   54 MET cc_start: 0.9447 (mmt) cc_final: 0.9080 (mmt)
REVERT: C   67 SER cc_start: 0.9012 (OUTLIER) cc_final: 0.8412 (p)
REVERT: C  157 GLU cc_start: 0.9197 (pp20) cc_final: 0.8903 (pp20)
REVERT: C  183 ASN cc_start: 0.9112 (m110) cc_final: 0.8835 (m110)
REVERT: C  184 GLN cc_start: 0.8952 (pm20) cc_final: 0.8695 (pm20)
REVERT: D   60 PHE cc_start: 0.8683 (p90) cc_final: 0.7926 (p90)
REVERT: E  305 TYR cc_start: 0.8500 (m-10) cc_final: 0.8206 (m-10)
REVERT: F  176 PHE cc_start: 0.7818 (t80) cc_final: 0.7433 (t80)
REVERT: F  190 HIS cc_start: 0.8148 (m170) cc_final: 0.7827 (m90)
REVERT: F  265 ASP cc_start: 0.7466 (m-30) cc_final: 0.7000 (t0)
  outliers start: 27
  outliers final: 21
  residues processed: 225
  average time/residue: 0.0938
  time to fit residues: 32.1958
Evaluate side-chains
  214 residues out of total 1081 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 191
  time to evaluate  : 0.435 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    3 MET
Chi-restraints excluded: chain A residue   11 VAL
Chi-restraints excluded: chain A residue   19 LEU
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 B residue  280 LEU
Chi-restraints excluded: chain C residue   47 VAL
Chi-restraints excluded: chain C residue   48 VAL
Chi-restraints excluded: chain C residue   57 VAL
Chi-restraints excluded: chain C residue   67 SER
Chi-restraints excluded: chain C residue   72 GLU
Chi-restraints excluded: chain C residue  273 VAL
Chi-restraints excluded: chain C residue  278 THR
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   59 CYS
Chi-restraints excluded: chain E residue   35 VAL
Chi-restraints excluded: chain E residue   48 VAL
Chi-restraints excluded: chain E residue   66 ILE
Chi-restraints excluded: chain F residue  276 LEU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 144
   random chunks:
   chunk 84 optimal weight:    0.8980
   chunk 115 optimal weight:    5.9990
   chunk 107 optimal weight:    0.9980
   chunk 26 optimal weight:    1.9990
   chunk 47 optimal weight:    0.8980
   chunk 29 optimal weight:    7.9990
   chunk 27 optimal weight:    0.0070
   chunk 6 optimal weight:    0.8980
   chunk 128 optimal weight:    7.9990
   chunk 10 optimal weight:    4.9990
   chunk 92 optimal weight:    5.9990
   overall best weight:    0.7398

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

Flipped N/Q/H residues before XYZ refinement:
** 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 = 0.4145 r_free = 0.4145 target = 0.129153 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 53)----------------|
| r_work = 0.3444 r_free = 0.3444 target = 0.088517 restraints weight = 41611.776|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3498 r_free = 0.3498 target = 0.091334 restraints weight = 21323.638|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 56)----------------|
| r_work = 0.3532 r_free = 0.3532 target = 0.093126 restraints weight = 14472.856|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 32)----------------|
| r_work = 0.3552 r_free = 0.3552 target = 0.094201 restraints weight = 11588.478|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 41)----------------|
| r_work = 0.3564 r_free = 0.3564 target = 0.094838 restraints weight = 10240.285|
|-----------------------------------------------------------------------------|
r_work (final): 0.3532
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3531
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3531 r_free = 0.3531    target_work(ls_wunit_k1) = 0.093         |
| occupancies: max = 1.00  min = 0.43   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3531 r_free = 0.3531    target_work(ls_wunit_k1) = 0.093         |
| occupancies: max = 1.00  min = 0.43   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3531
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7847
moved from start:          0.2227

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039  14191  Z= 0.146
  Angle     :  0.618   7.700  19874  Z= 0.335
  Chirality :  0.041   0.191   2233
  Planarity :  0.004   0.049   2009
  Dihedral  : 25.275 178.742   3174
  Min Nonbonded Distance : 2.452

Molprobity Statistics.
  All-atom Clashscore : 13.23
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.51 %
    Favored  : 96.49 %
  Rotamer:
    Outliers :  2.41 %
    Allowed  : 17.76 %
    Favored  : 79.83 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z 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: -0.03 (0.23), residues: 1311
  helix:  0.90 (0.20), residues: 628
  sheet: -0.60 (0.37), residues: 186
  loop : -0.88 (0.28), residues: 497

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG D  40 
 TYR   0.021   0.002   TYR E 194 
 PHE   0.016   0.002   PHE F 239 
 TRP   0.011   0.001   TRP D  44 
 HIS   0.011   0.001   HIS B 146 

Details of bonding type rmsd
  covalent geometry    : bond        0.00326 (14191)
  covalent geometry    : angle       0.61773 (19874)
  hydrogen bonds       : bond        0.04053 (  670)
  hydrogen bonds       : angle       4.13962 ( 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
  264 residues out of total 1081 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 238
  time to evaluate  : 0.374 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   23 MET cc_start: 0.8901 (mmt) cc_final: 0.7676 (mmt)
REVERT: A   35 PHE cc_start: 0.8808 (m-80) cc_final: 0.8405 (m-10)
REVERT: B   91 TYR cc_start: 0.7906 (t80) cc_final: 0.7031 (t80)
REVERT: B   94 SER cc_start: 0.8675 (p) cc_final: 0.8144 (p)
REVERT: C   54 MET cc_start: 0.9415 (mmt) cc_final: 0.9065 (mmt)
REVERT: C   67 SER cc_start: 0.8749 (OUTLIER) cc_final: 0.8156 (p)
REVERT: C  157 GLU cc_start: 0.9186 (pp20) cc_final: 0.8879 (pp20)
REVERT: C  183 ASN cc_start: 0.9055 (m110) cc_final: 0.8799 (m110)
REVERT: C  184 GLN cc_start: 0.8921 (pm20) cc_final: 0.8676 (pm20)
REVERT: D   18 ASP cc_start: 0.8497 (t0) cc_final: 0.8261 (t70)
REVERT: D   60 PHE cc_start: 0.8468 (p90) cc_final: 0.8030 (p90)
REVERT: E  107 LYS cc_start: 0.8878 (mmtt) cc_final: 0.8599 (mmtm)
REVERT: E  194 TYR cc_start: 0.8632 (m-80) cc_final: 0.8164 (m-80)
REVERT: F  119 LEU cc_start: 0.8879 (mm) cc_final: 0.8643 (mm)
REVERT: F  265 ASP cc_start: 0.7366 (m-30) cc_final: 0.6891 (t0)
  outliers start: 26
  outliers final: 18
  residues processed: 253
  average time/residue: 0.1006
  time to fit residues: 39.2985
Evaluate side-chains
  221 residues out of total 1081 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 202
  time to evaluate  : 0.412 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   43 LEU
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 C residue   67 SER
Chi-restraints excluded: chain C residue  235 VAL
Chi-restraints excluded: chain C residue  278 THR
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 D residue   59 CYS
Chi-restraints excluded: chain E residue   35 VAL
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   39 VAL
Chi-restraints excluded: chain F residue  130 PHE
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 144
   random chunks:
   chunk 46 optimal weight:    6.9990
   chunk 51 optimal weight:   10.0000
   chunk 73 optimal weight:    0.3980
   chunk 41 optimal weight:    0.8980
   chunk 108 optimal weight:    1.9990
   chunk 141 optimal weight:    5.9990
   chunk 96 optimal weight:    1.9990
   chunk 72 optimal weight:    0.9990
   chunk 125 optimal weight:    0.9980
   chunk 85 optimal weight:    0.7980
   chunk 67 optimal weight:    0.7980
   overall best weight:    0.7780

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

Flipped N/Q/H residues before XYZ refinement:
A  34 ASN
C 190 HIS
D  10 ASN
** 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: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4152 r_free = 0.4152 target = 0.129622 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.3445 r_free = 0.3445 target = 0.088574 restraints weight = 41391.498|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 46)----------------|
| r_work = 0.3498 r_free = 0.3498 target = 0.091312 restraints weight = 21860.638|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3531 r_free = 0.3531 target = 0.093074 restraints weight = 15083.792|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 36)----------------|
| r_work = 0.3550 r_free = 0.3550 target = 0.094144 restraints weight = 12161.783|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 44)----------------|
| r_work = 0.3562 r_free = 0.3562 target = 0.094772 restraints weight = 10774.101|
|-----------------------------------------------------------------------------|
r_work (final): 0.3529
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3526
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3526 r_free = 0.3526    target_work(ls_wunit_k1) = 0.092         |
| occupancies: max = 1.00  min = 0.43   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3526 r_free = 0.3526    target_work(ls_wunit_k1) = 0.092         |
| occupancies: max = 1.00  min = 0.45   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3526
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7846
moved from start:          0.2423

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038  14191  Z= 0.147
  Angle     :  0.627   8.623  19874  Z= 0.339
  Chirality :  0.041   0.218   2233
  Planarity :  0.004   0.050   2009
  Dihedral  : 25.198 179.621   3174
  Min Nonbonded Distance : 2.452

Molprobity Statistics.
  All-atom Clashscore : 13.57
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.04 %
    Favored  : 95.96 %
  Rotamer:
    Outliers :  2.41 %
    Allowed  : 21.09 %
    Favored  : 76.50 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.03 (0.23), residues: 1311
  helix:  0.89 (0.20), residues: 632
  sheet: -0.52 (0.37), residues: 186
  loop : -0.92 (0.28), residues: 493

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG D  46 
 TYR   0.025   0.001   TYR F 171 
 PHE   0.015   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
  covalent geometry    : bond        0.00329 (14191)
  covalent geometry    : angle       0.62717 (19874)
  hydrogen bonds       : bond        0.03915 (  670)
  hydrogen bonds       : angle       4.04311 ( 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
  254 residues out of total 1081 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 228
  time to evaluate  : 0.438 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A    1 MET cc_start: 0.7573 (tmm) cc_final: 0.7310 (tmm)
REVERT: A   23 MET cc_start: 0.8844 (mmt) cc_final: 0.7752 (mmt)
REVERT: A   35 PHE cc_start: 0.8769 (m-10) cc_final: 0.8373 (m-10)
REVERT: B   91 TYR cc_start: 0.7977 (t80) cc_final: 0.7110 (t80)
REVERT: B   94 SER cc_start: 0.8626 (p) cc_final: 0.8069 (p)
REVERT: C   54 MET cc_start: 0.9344 (mmt) cc_final: 0.9024 (mmt)
REVERT: C   67 SER cc_start: 0.8794 (OUTLIER) cc_final: 0.8238 (p)
REVERT: C  100 ARG cc_start: 0.8629 (tpp-160) cc_final: 0.7923 (mmp-170)
REVERT: C  128 MET cc_start: 0.8552 (mmm) cc_final: 0.8122 (mmm)
REVERT: C  157 GLU cc_start: 0.9207 (pp20) cc_final: 0.8914 (pp20)
REVERT: C  183 ASN cc_start: 0.9071 (m110) cc_final: 0.8797 (m110)
REVERT: C  184 GLN cc_start: 0.8917 (pm20) cc_final: 0.8684 (pm20)
REVERT: C  249 GLN cc_start: 0.7540 (tp40) cc_final: 0.7314 (tp40)
REVERT: D   18 ASP cc_start: 0.8485 (t0) cc_final: 0.8244 (t70)
REVERT: D   60 PHE cc_start: 0.8569 (p90) cc_final: 0.8063 (p90)
REVERT: E  194 TYR cc_start: 0.8640 (m-80) cc_final: 0.8161 (m-80)
REVERT: E  218 ASP cc_start: 0.8516 (p0) cc_final: 0.8283 (p0)
REVERT: F   19 GLU cc_start: 0.8608 (mp0) cc_final: 0.8368 (mp0)
REVERT: F   54 MET cc_start: 0.9142 (mpp) cc_final: 0.8931 (mtm)
REVERT: F  119 LEU cc_start: 0.8905 (mm) cc_final: 0.8660 (mm)
REVERT: F  265 ASP cc_start: 0.7340 (m-30) cc_final: 0.6935 (t0)
  outliers start: 26
  outliers final: 18
  residues processed: 241
  average time/residue: 0.0997
  time to fit residues: 36.8458
Evaluate side-chains
  230 residues out of total 1081 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 211
  time to evaluate  : 0.387 
-------------------------------------------------------------------------------
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   66 LEU
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   67 SER
Chi-restraints excluded: chain C residue  235 VAL
Chi-restraints excluded: chain C residue  278 THR
Chi-restraints excluded: chain D residue    5 VAL
Chi-restraints excluded: chain D residue    7 THR
Chi-restraints excluded: chain D residue   11 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
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 144
   random chunks:
   chunk 57 optimal weight:    4.9990
   chunk 64 optimal weight:    1.9990
   chunk 62 optimal weight:    0.0060
   chunk 95 optimal weight:    2.9990
   chunk 49 optimal weight:    8.9990
   chunk 8 optimal weight:    0.8980
   chunk 39 optimal weight:    8.9990
   chunk 83 optimal weight:    0.9980
   chunk 47 optimal weight:    3.9990
   chunk 131 optimal weight:    6.9990
   chunk 14 optimal weight:    0.2980
   overall best weight:    0.8398

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

Flipped N/Q/H residues before XYZ refinement:
C 190 HIS
** E  87 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E 127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** F  87 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
F 183 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4157 r_free = 0.4157 target = 0.129955 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 53)----------------|
| r_work = 0.3459 r_free = 0.3459 target = 0.089370 restraints weight = 36923.261|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 43)----------------|
| r_work = 0.3509 r_free = 0.3509 target = 0.091944 restraints weight = 20509.636|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 48)----------------|
| r_work = 0.3539 r_free = 0.3539 target = 0.093577 restraints weight = 14539.806|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 42)----------------|
| r_work = 0.3557 r_free = 0.3557 target = 0.094571 restraints weight = 11925.881|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.3564 r_free = 0.3564 target = 0.094989 restraints weight = 10658.012|
|-----------------------------------------------------------------------------|
r_work (final): 0.3532
-------------------------------------------------------------------------------
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 = 0.45   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3532 r_free = 0.3532    target_work(ls_wunit_k1) = 0.093         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3532
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7847
moved from start:          0.2602

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039  14191  Z= 0.147
  Angle     :  0.629   9.389  19874  Z= 0.341
  Chirality :  0.041   0.214   2233
  Planarity :  0.004   0.049   2009
  Dihedral  : 25.135 179.272   3174
  Min Nonbonded Distance : 2.453

Molprobity Statistics.
  All-atom Clashscore : 13.69
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.66 %
    Favored  : 96.34 %
  Rotamer:
    Outliers :  2.96 %
    Allowed  : 21.83 %
    Favored  : 75.21 %
  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:  0.01 (0.23), residues: 1311
  helix:  0.92 (0.20), residues: 632
  sheet: -0.53 (0.37), residues: 186
  loop : -0.89 (0.28), residues: 493

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG C 256 
 TYR   0.022   0.001   TYR B 223 
 PHE   0.027   0.002   PHE F  24 
 TRP   0.010   0.001   TRP E  83 
 HIS   0.009   0.001   HIS B 146 

Details of bonding type rmsd
  covalent geometry    : bond        0.00328 (14191)
  covalent geometry    : angle       0.62907 (19874)
  hydrogen bonds       : bond        0.03779 (  670)
  hydrogen bonds       : angle       3.98755 ( 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
  265 residues out of total 1081 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 233
  time to evaluate  : 0.350 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A    1 MET cc_start: 0.7441 (tmm) cc_final: 0.7128 (tmm)
REVERT: A   23 MET cc_start: 0.8876 (mmt) cc_final: 0.7736 (mmt)
REVERT: A   35 PHE cc_start: 0.8766 (m-10) cc_final: 0.8487 (m-10)
REVERT: A   42 TYR cc_start: 0.8299 (m-10) cc_final: 0.7969 (m-10)
REVERT: A   55 GLU cc_start: 0.7557 (mm-30) cc_final: 0.7345 (tp30)
REVERT: B   91 TYR cc_start: 0.7952 (t80) cc_final: 0.7001 (t80)
REVERT: B   94 SER cc_start: 0.8627 (p) cc_final: 0.8034 (p)
REVERT: C   54 MET cc_start: 0.9288 (mmt) cc_final: 0.9025 (mmt)
REVERT: C   67 SER cc_start: 0.8837 (OUTLIER) cc_final: 0.8297 (p)
REVERT: C  100 ARG cc_start: 0.8965 (tpp-160) cc_final: 0.8660 (tpp-160)
REVERT: C  157 GLU cc_start: 0.9226 (pp20) cc_final: 0.8922 (pp20)
REVERT: C  184 GLN cc_start: 0.8918 (pm20) cc_final: 0.8717 (pm20)
REVERT: C  249 GLN cc_start: 0.7501 (tp40) cc_final: 0.7292 (tp40)
REVERT: D   18 ASP cc_start: 0.8456 (t0) cc_final: 0.8232 (t70)
REVERT: D   60 PHE cc_start: 0.8564 (p90) cc_final: 0.8152 (p90)
REVERT: E  107 LYS cc_start: 0.8857 (mmtt) cc_final: 0.8602 (mmtm)
REVERT: E  194 TYR cc_start: 0.8610 (m-80) cc_final: 0.8200 (m-80)
REVERT: F  119 LEU cc_start: 0.8901 (mm) cc_final: 0.8657 (mm)
REVERT: F  222 ILE cc_start: 0.9378 (mm) cc_final: 0.8984 (tp)
REVERT: F  265 ASP cc_start: 0.7389 (m-30) cc_final: 0.6954 (t0)
  outliers start: 32
  outliers final: 24
  residues processed: 254
  average time/residue: 0.1064
  time to fit residues: 40.3705
Evaluate side-chains
  235 residues out of total 1081 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 210
  time to evaluate  : 0.469 
-------------------------------------------------------------------------------
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   66 LEU
Chi-restraints excluded: chain A residue   79 VAL
Chi-restraints excluded: chain B residue   32 ILE
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   47 VAL
Chi-restraints excluded: chain C residue   48 VAL
Chi-restraints excluded: chain C residue   67 SER
Chi-restraints excluded: chain C residue  139 THR
Chi-restraints excluded: chain C residue  160 LYS
Chi-restraints excluded: chain C residue  235 VAL
Chi-restraints excluded: chain C residue  273 VAL
Chi-restraints excluded: chain D residue    5 VAL
Chi-restraints excluded: chain D residue    7 THR
Chi-restraints excluded: chain D residue   11 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  193 LEU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 144
   random chunks:
   chunk 82 optimal weight:    2.9990
   chunk 78 optimal weight:    0.3980
   chunk 5 optimal weight:    1.9990
   chunk 117 optimal weight:    0.4980
   chunk 63 optimal weight:    9.9990
   chunk 105 optimal weight:    0.9980
   chunk 12 optimal weight:    0.0670
   chunk 54 optimal weight:    2.9990
   chunk 48 optimal weight:    6.9990
   chunk 121 optimal weight:   20.0000
   chunk 36 optimal weight:    3.9990
   overall best weight:    0.7920

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

Flipped N/Q/H residues before XYZ refinement:
** 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**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4151 r_free = 0.4151 target = 0.129799 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3443 r_free = 0.3443 target = 0.088721 restraints weight = 40925.149|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 50)----------------|
| r_work = 0.3496 r_free = 0.3496 target = 0.091466 restraints weight = 21429.480|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 47)----------------|
| r_work = 0.3529 r_free = 0.3529 target = 0.093233 restraints weight = 14713.107|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 37)----------------|
| r_work = 0.3549 r_free = 0.3549 target = 0.094308 restraints weight = 11822.015|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 44)----------------|
| r_work = 0.3561 r_free = 0.3561 target = 0.094933 restraints weight = 10427.104|
|-----------------------------------------------------------------------------|
r_work (final): 0.3530
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3530
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3530 r_free = 0.3530    target_work(ls_wunit_k1) = 0.093         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3530 r_free = 0.3530    target_work(ls_wunit_k1) = 0.093         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3530
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7832
moved from start:          0.2773

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.043  14191  Z= 0.149
  Angle     :  0.652  13.871  19874  Z= 0.350
  Chirality :  0.041   0.239   2233
  Planarity :  0.004   0.048   2009
  Dihedral  : 25.088 179.135   3174
  Min Nonbonded Distance : 2.453

Molprobity Statistics.
  All-atom Clashscore : 14.34
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.12 %
    Favored  : 95.88 %
  Rotamer:
    Outliers :  3.24 %
    Allowed  : 22.94 %
    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:  0.11 (0.23), residues: 1311
  helix:  1.00 (0.21), residues: 627
  sheet: -0.40 (0.36), residues: 201
  loop : -0.85 (0.29), residues: 483

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.000   ARG C 169 
 TYR   0.021   0.001   TYR B 223 
 PHE   0.037   0.002   PHE F  24 
 TRP   0.008   0.001   TRP A  22 
 HIS   0.007   0.001   HIS B 146 

Details of bonding type rmsd
  covalent geometry    : bond        0.00336 (14191)
  covalent geometry    : angle       0.65218 (19874)
  hydrogen bonds       : bond        0.03713 (  670)
  hydrogen bonds       : angle       3.96025 ( 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
  261 residues out of total 1081 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 226
  time to evaluate  : 0.372 
Fit side-chains
   revert: symmetry clash
REVERT: A   23 MET cc_start: 0.8856 (mmt) cc_final: 0.7865 (mmt)
REVERT: A   35 PHE cc_start: 0.8718 (m-10) cc_final: 0.8492 (m-10)
REVERT: B   91 TYR cc_start: 0.7933 (t80) cc_final: 0.6879 (t80)
REVERT: B   94 SER cc_start: 0.8627 (p) cc_final: 0.8021 (p)
REVERT: B  157 GLU cc_start: 0.8776 (tm-30) cc_final: 0.8420 (pp20)
REVERT: C   54 MET cc_start: 0.9273 (mmt) cc_final: 0.8993 (mmt)
REVERT: C   67 SER cc_start: 0.8879 (OUTLIER) cc_final: 0.8318 (p)
REVERT: C  100 ARG cc_start: 0.8995 (tpp-160) cc_final: 0.8561 (mmp-170)
REVERT: C  157 GLU cc_start: 0.9219 (pp20) cc_final: 0.8915 (pp20)
REVERT: C  184 GLN cc_start: 0.8878 (pm20) cc_final: 0.8568 (pm20)
REVERT: D   18 ASP cc_start: 0.8429 (t0) cc_final: 0.8205 (t70)
REVERT: E  194 TYR cc_start: 0.8626 (m-80) cc_final: 0.8208 (m-80)
REVERT: E  218 ASP cc_start: 0.8504 (p0) cc_final: 0.8279 (p0)
REVERT: F   19 GLU cc_start: 0.8578 (mp0) cc_final: 0.8029 (mm-30)
REVERT: F  119 LEU cc_start: 0.8888 (mm) cc_final: 0.8640 (mm)
REVERT: F  222 ILE cc_start: 0.9399 (mm) cc_final: 0.9068 (tp)
REVERT: F  249 GLN cc_start: 0.7390 (pp30) cc_final: 0.7175 (pp30)
REVERT: F  265 ASP cc_start: 0.7408 (m-30) cc_final: 0.6946 (t0)
  outliers start: 35
  outliers final: 24
  residues processed: 250
  average time/residue: 0.0991
  time to fit residues: 37.8788
Evaluate side-chains
  234 residues out of total 1081 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 209
  time to evaluate  : 0.351 
-------------------------------------------------------------------------------
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   66 LEU
Chi-restraints excluded: chain A residue   79 VAL
Chi-restraints excluded: chain B residue   32 ILE
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   47 VAL
Chi-restraints excluded: chain C residue   48 VAL
Chi-restraints excluded: chain C residue   67 SER
Chi-restraints excluded: chain C residue  139 THR
Chi-restraints excluded: chain C residue  235 VAL
Chi-restraints excluded: chain C residue  273 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   71 VAL
Chi-restraints excluded: chain F residue  193 LEU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 144
   random chunks:
   chunk 67 optimal weight:    4.9990
   chunk 102 optimal weight:    2.9990
   chunk 109 optimal weight:    4.9990
   chunk 126 optimal weight:    6.9990
   chunk 54 optimal weight:    0.9980
   chunk 46 optimal weight:    4.9990
   chunk 133 optimal weight:    0.5980
   chunk 43 optimal weight:    5.9990
   chunk 134 optimal weight:    5.9990
   chunk 108 optimal weight:    0.8980
   chunk 121 optimal weight:   20.0000
   overall best weight:    2.0984

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

Flipped N/Q/H residues before XYZ refinement:
** C 184 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E  87 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
F 108 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4109 r_free = 0.4109 target = 0.127027 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 55)----------------|
| r_work = 0.3386 r_free = 0.3386 target = 0.085920 restraints weight = 37252.722|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 52)----------------|
| r_work = 0.3433 r_free = 0.3433 target = 0.088309 restraints weight = 21124.562|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 45)----------------|
| r_work = 0.3463 r_free = 0.3463 target = 0.089861 restraints weight = 15189.277|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 43)----------------|
| r_work = 0.3481 r_free = 0.3481 target = 0.090802 restraints weight = 12527.978|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 44)----------------|
| r_work = 0.3491 r_free = 0.3491 target = 0.091347 restraints weight = 11225.893|
|-----------------------------------------------------------------------------|
r_work (final): 0.3469
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3469
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3469 r_free = 0.3469    target_work(ls_wunit_k1) = 0.089         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3469 r_free = 0.3469    target_work(ls_wunit_k1) = 0.089         |
| occupancies: max = 1.00  min = 0.48   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3469
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7912
moved from start:          0.2844

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.046  14191  Z= 0.197
  Angle     :  0.703  12.736  19874  Z= 0.372
  Chirality :  0.042   0.241   2233
  Planarity :  0.005   0.048   2009
  Dihedral  : 25.109 179.502   3174
  Min Nonbonded Distance : 2.452

Molprobity Statistics.
  All-atom Clashscore : 15.77
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.35 %
    Favored  : 95.65 %
  Rotamer:
    Outliers :  3.33 %
    Allowed  : 23.50 %
    Favored  : 73.17 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.01 (0.23), residues: 1311
  helix:  0.90 (0.21), residues: 626
  sheet: -0.44 (0.37), residues: 195
  loop : -0.92 (0.28), residues: 490

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.000   ARG F 129 
 TYR   0.020   0.002   TYR B 223 
 PHE   0.036   0.002   PHE F  24 
 TRP   0.011   0.002   TRP D  44 
 HIS   0.008   0.001   HIS F 146 

Details of bonding type rmsd
  covalent geometry    : bond        0.00448 (14191)
  covalent geometry    : angle       0.70334 (19874)
  hydrogen bonds       : bond        0.04117 (  670)
  hydrogen bonds       : angle       4.16807 ( 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
  248 residues out of total 1081 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 212
  time to evaluate  : 0.350 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A    1 MET cc_start: 0.7537 (tmm) cc_final: 0.7283 (tmm)
REVERT: A   23 MET cc_start: 0.8979 (mmt) cc_final: 0.7850 (mmt)
REVERT: A   35 PHE cc_start: 0.8814 (m-10) cc_final: 0.8570 (m-10)
REVERT: A   42 TYR cc_start: 0.8329 (m-10) cc_final: 0.8054 (m-10)
REVERT: B   91 TYR cc_start: 0.7934 (t80) cc_final: 0.6973 (t80)
REVERT: B   94 SER cc_start: 0.8654 (p) cc_final: 0.8012 (p)
REVERT: B  153 ARG cc_start: 0.9246 (mtt90) cc_final: 0.8534 (mmm160)
REVERT: B  157 GLU cc_start: 0.8746 (tm-30) cc_final: 0.8392 (pp20)
REVERT: C   54 MET cc_start: 0.9298 (mmt) cc_final: 0.9014 (mmt)
REVERT: C   67 SER cc_start: 0.9070 (OUTLIER) cc_final: 0.8529 (p)
REVERT: C  100 ARG cc_start: 0.8978 (tpp-160) cc_final: 0.8548 (mmp-170)
REVERT: C  157 GLU cc_start: 0.9243 (pp20) cc_final: 0.8933 (pp20)
REVERT: C  184 GLN cc_start: 0.8953 (pm20) cc_final: 0.8650 (pm20)
REVERT: D   18 ASP cc_start: 0.8477 (t0) cc_final: 0.8267 (t70)
REVERT: E   49 ARG cc_start: 0.8880 (tpp80) cc_final: 0.8520 (tpp80)
REVERT: E  194 TYR cc_start: 0.8598 (m-80) cc_final: 0.8141 (m-80)
REVERT: F  119 LEU cc_start: 0.8802 (mm) cc_final: 0.8520 (mm)
REVERT: F  265 ASP cc_start: 0.7400 (m-30) cc_final: 0.6964 (t0)
  outliers start: 36
  outliers final: 25
  residues processed: 233
  average time/residue: 0.0959
  time to fit residues: 34.2774
Evaluate side-chains
  225 residues out of total 1081 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 199
  time to evaluate  : 0.299 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   11 VAL
Chi-restraints excluded: chain A residue   59 CYS
Chi-restraints excluded: chain A residue   66 LEU
Chi-restraints excluded: chain A residue   79 VAL
Chi-restraints excluded: chain B residue   32 ILE
Chi-restraints excluded: chain B residue  193 LEU
Chi-restraints excluded: chain B residue  251 ILE
Chi-restraints excluded: chain C residue   12 SER
Chi-restraints excluded: chain C residue   39 VAL
Chi-restraints excluded: chain C residue   47 VAL
Chi-restraints excluded: chain C residue   48 VAL
Chi-restraints excluded: chain C residue   57 VAL
Chi-restraints excluded: chain C residue   67 SER
Chi-restraints excluded: chain C residue  141 GLN
Chi-restraints excluded: chain C residue  235 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 E residue   39 VAL
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  182 ILE
Chi-restraints excluded: chain F residue  193 LEU
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:    7.9990
   chunk 28 optimal weight:    4.9990
   chunk 129 optimal weight:    0.0010
   chunk 83 optimal weight:    0.0370
   chunk 40 optimal weight:    9.9990
   chunk 125 optimal weight:    4.9990
   chunk 80 optimal weight:    5.9990
   chunk 31 optimal weight:    1.9990
   chunk 139 optimal weight:    7.9990
   chunk 126 optimal weight:    0.1980
   chunk 57 optimal weight:    9.9990
   overall best weight:    1.4468

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

Flipped N/Q/H residues before XYZ refinement:
** C 184 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E  87 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E 127 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 = 0.4129 r_free = 0.4129 target = 0.128233 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3385 r_free = 0.3385 target = 0.085648 restraints weight = 52677.299|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 46)----------------|
| r_work = 0.3443 r_free = 0.3443 target = 0.088663 restraints weight = 25067.811|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 41)----------------|
| r_work = 0.3479 r_free = 0.3479 target = 0.090575 restraints weight = 16329.457|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 48)----------------|
| r_work = 0.3502 r_free = 0.3502 target = 0.091767 restraints weight = 12781.752|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 39)----------------|
| r_work = 0.3515 r_free = 0.3515 target = 0.092463 restraints weight = 11062.614|
|-----------------------------------------------------------------------------|
r_work (final): 0.3482
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3483
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3483 r_free = 0.3483    target_work(ls_wunit_k1) = 0.090         |
| occupancies: max = 1.00  min = 0.48   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3483 r_free = 0.3483    target_work(ls_wunit_k1) = 0.090         |
| occupancies: max = 1.00  min = 0.49   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3483
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7885
moved from start:          0.2939

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.044  14191  Z= 0.171
  Angle     :  0.705  11.581  19874  Z= 0.373
  Chirality :  0.043   0.254   2233
  Planarity :  0.004   0.048   2009
  Dihedral  : 25.103 178.778   3174
  Min Nonbonded Distance : 2.454

Molprobity Statistics.
  All-atom Clashscore : 15.42
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.81 %
    Favored  : 96.19 %
  Rotamer:
    Outliers :  2.04 %
    Allowed  : 25.16 %
    Favored  : 72.80 %
  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: -0.03 (0.23), residues: 1311
  helix:  0.90 (0.21), residues: 629
  sheet: -0.46 (0.38), residues: 190
  loop : -0.96 (0.28), residues: 492

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG C 256 
 TYR   0.026   0.001   TYR B 223 
 PHE   0.036   0.002   PHE F  24 
 TRP   0.009   0.001   TRP C 166 
 HIS   0.009   0.001   HIS F 146 

Details of bonding type rmsd
  covalent geometry    : bond        0.00391 (14191)
  covalent geometry    : angle       0.70484 (19874)
  hydrogen bonds       : bond        0.03872 (  670)
  hydrogen bonds       : angle       4.15526 ( 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
  241 residues out of total 1081 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 219
  time to evaluate  : 0.463 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A    1 MET cc_start: 0.7509 (tmm) cc_final: 0.7245 (tmm)
REVERT: A   23 MET cc_start: 0.8951 (mmt) cc_final: 0.7858 (mmt)
REVERT: A   35 PHE cc_start: 0.8805 (m-10) cc_final: 0.8578 (m-10)
REVERT: A   42 TYR cc_start: 0.8368 (m-10) cc_final: 0.8063 (m-10)
REVERT: B   91 TYR cc_start: 0.7968 (t80) cc_final: 0.6941 (t80)
REVERT: B   94 SER cc_start: 0.8685 (p) cc_final: 0.8040 (p)
REVERT: B  153 ARG cc_start: 0.9246 (mtt90) cc_final: 0.8516 (mmm160)
REVERT: B  157 GLU cc_start: 0.8813 (tm-30) cc_final: 0.8390 (pp20)
REVERT: C   54 MET cc_start: 0.9329 (mmt) cc_final: 0.9045 (mmt)
REVERT: C   67 SER cc_start: 0.8965 (t) cc_final: 0.8427 (p)
REVERT: C  100 ARG cc_start: 0.9001 (tpp-160) cc_final: 0.8561 (mmp-170)
REVERT: C  128 MET cc_start: 0.8680 (mmm) cc_final: 0.8203 (mmt)
REVERT: C  143 LEU cc_start: 0.8188 (mt) cc_final: 0.7633 (mt)
REVERT: C  147 GLU cc_start: 0.8745 (mt-10) cc_final: 0.8252 (mp0)
REVERT: C  157 GLU cc_start: 0.9252 (pp20) cc_final: 0.8956 (pp20)
REVERT: C  184 GLN cc_start: 0.8912 (pm20) cc_final: 0.8603 (pm20)
REVERT: D   18 ASP cc_start: 0.8492 (t0) cc_final: 0.8279 (t70)
REVERT: E   49 ARG cc_start: 0.8876 (tpp80) cc_final: 0.8493 (tpp80)
REVERT: E  107 LYS cc_start: 0.8809 (mmtt) cc_final: 0.8588 (mmtm)
REVERT: E  194 TYR cc_start: 0.8643 (m-80) cc_final: 0.8171 (m-80)
REVERT: E  218 ASP cc_start: 0.8521 (p0) cc_final: 0.8300 (p0)
REVERT: F  119 LEU cc_start: 0.8847 (mm) cc_final: 0.8582 (mm)
REVERT: F  128 MET cc_start: 0.8207 (pmm) cc_final: 0.7949 (pmm)
REVERT: F  222 ILE cc_start: 0.9401 (mm) cc_final: 0.9064 (tp)
REVERT: F  265 ASP cc_start: 0.7435 (m-30) cc_final: 0.6994 (t0)
  outliers start: 22
  outliers final: 22
  residues processed: 234
  average time/residue: 0.0990
  time to fit residues: 35.4467
Evaluate side-chains
  233 residues out of total 1081 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 211
  time to evaluate  : 0.421 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   11 VAL
Chi-restraints excluded: chain A residue   59 CYS
Chi-restraints excluded: chain A residue   66 LEU
Chi-restraints excluded: chain A residue   79 VAL
Chi-restraints excluded: chain B residue   32 ILE
Chi-restraints excluded: chain B residue  193 LEU
Chi-restraints excluded: chain B residue  251 ILE
Chi-restraints excluded: chain C residue   12 SER
Chi-restraints excluded: chain C residue   39 VAL
Chi-restraints excluded: chain C residue   47 VAL
Chi-restraints excluded: chain C residue   48 VAL
Chi-restraints excluded: chain C residue  141 GLN
Chi-restraints excluded: chain C residue  235 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 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  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:    4.9990
   chunk 70 optimal weight:    0.5980
   chunk 6 optimal weight:    0.4980
   chunk 77 optimal weight:    0.0370
   chunk 45 optimal weight:    2.9990
   chunk 94 optimal weight:    5.9990
   chunk 44 optimal weight:    1.9990
   chunk 100 optimal weight:    0.9990
   chunk 87 optimal weight:    0.8980
   chunk 129 optimal weight:    0.9980
   chunk 28 optimal weight:    6.9990
   overall best weight:    0.6058

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

Flipped N/Q/H residues before XYZ refinement:
A  34 ASN
C 163 ASN
** C 184 GLN ** 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 ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4152 r_free = 0.4152 target = 0.129909 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3431 r_free = 0.3431 target = 0.088063 restraints weight = 52041.659|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 46)----------------|
| r_work = 0.3489 r_free = 0.3489 target = 0.091117 restraints weight = 24493.507|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 45)----------------|
| r_work = 0.3526 r_free = 0.3526 target = 0.093088 restraints weight = 15823.471|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 37)----------------|
| r_work = 0.3549 r_free = 0.3549 target = 0.094300 restraints weight = 12229.823|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 43)----------------|
| r_work = 0.3562 r_free = 0.3562 target = 0.095033 restraints weight = 10569.685|
|-----------------------------------------------------------------------------|
r_work (final): 0.3536
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3535
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3535 r_free = 0.3535    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 = 0.3535 r_free = 0.3535    target_work(ls_wunit_k1) = 0.093         |
| occupancies: max = 1.00  min = 0.49   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3535
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7818
moved from start:          0.3080

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.047  14191  Z= 0.152
  Angle     :  0.700  11.316  19874  Z= 0.372
  Chirality :  0.042   0.255   2233
  Planarity :  0.004   0.049   2009
  Dihedral  : 25.029 178.461   3174
  Min Nonbonded Distance : 2.222

Molprobity Statistics.
  All-atom Clashscore : 14.46
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.51 %
    Favored  : 96.49 %
  Rotamer:
    Outliers :  2.13 %
    Allowed  : 25.53 %
    Favored  : 72.34 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z 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:  0.03 (0.23), residues: 1311
  helix:  0.92 (0.21), residues: 626
  sheet: -0.30 (0.38), residues: 190
  loop : -0.92 (0.28), residues: 495

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG C 256 
 TYR   0.033   0.001   TYR B 223 
 PHE   0.036   0.002   PHE F  24 
 TRP   0.010   0.001   TRP A  22 
 HIS   0.011   0.001   HIS F 146 

Details of bonding type rmsd
  covalent geometry    : bond        0.00340 (14191)
  covalent geometry    : angle       0.70035 (19874)
  hydrogen bonds       : bond        0.03716 (  670)
  hydrogen bonds       : angle       4.11829 ( 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
  252 residues out of total 1081 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 229
  time to evaluate  : 0.383 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   35 PHE cc_start: 0.8699 (m-10) cc_final: 0.8433 (m-10)
REVERT: A   42 TYR cc_start: 0.8317 (m-10) cc_final: 0.8026 (m-10)
REVERT: B   91 TYR cc_start: 0.7938 (t80) cc_final: 0.6853 (t80)
REVERT: B   94 SER cc_start: 0.8659 (p) cc_final: 0.7998 (p)
REVERT: B  153 ARG cc_start: 0.9244 (mtt90) cc_final: 0.8500 (mmm160)
REVERT: B  157 GLU cc_start: 0.8786 (tm-30) cc_final: 0.8394 (pp20)
REVERT: C   54 MET cc_start: 0.9310 (mmt) cc_final: 0.9089 (mmt)
REVERT: C   67 SER cc_start: 0.8857 (t) cc_final: 0.8288 (p)
REVERT: C  100 ARG cc_start: 0.9031 (tpp-160) cc_final: 0.8581 (mmp-170)
REVERT: C  128 MET cc_start: 0.8614 (mmm) cc_final: 0.8157 (mmt)
REVERT: C  147 GLU cc_start: 0.8675 (mt-10) cc_final: 0.8217 (mp0)
REVERT: C  157 GLU cc_start: 0.9247 (pp20) cc_final: 0.8960 (pp20)
REVERT: C  184 GLN cc_start: 0.8903 (pm20) cc_final: 0.8604 (pm20)
REVERT: E   49 ARG cc_start: 0.8886 (tpp80) cc_final: 0.8510 (tpp80)
REVERT: E  107 LYS cc_start: 0.8833 (mmtt) cc_final: 0.8593 (mmtm)
REVERT: E  194 TYR cc_start: 0.8623 (m-80) cc_final: 0.8174 (m-80)
REVERT: E  218 ASP cc_start: 0.8487 (p0) cc_final: 0.8260 (p0)
REVERT: E  269 LEU cc_start: 0.9075 (mp) cc_final: 0.8795 (tt)
REVERT: F  119 LEU cc_start: 0.8814 (mm) cc_final: 0.8552 (mm)
REVERT: F  128 MET cc_start: 0.7984 (pmm) cc_final: 0.7648 (pmm)
REVERT: F  222 ILE cc_start: 0.9425 (mm) cc_final: 0.9071 (tp)
REVERT: F  265 ASP cc_start: 0.7425 (m-30) cc_final: 0.6957 (t0)
  outliers start: 23
  outliers final: 22
  residues processed: 243
  average time/residue: 0.1027
  time to fit residues: 37.7833
Evaluate side-chains
  237 residues out of total 1081 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 215
  time to evaluate  : 0.371 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   11 VAL
Chi-restraints excluded: chain A residue   59 CYS
Chi-restraints excluded: chain A residue   66 LEU
Chi-restraints excluded: chain A residue   79 VAL
Chi-restraints excluded: chain B residue   32 ILE
Chi-restraints excluded: chain B residue  251 ILE
Chi-restraints excluded: chain C residue   12 SER
Chi-restraints excluded: chain C residue   39 VAL
Chi-restraints excluded: chain C residue   47 VAL
Chi-restraints excluded: chain C residue   48 VAL
Chi-restraints excluded: chain C residue  141 GLN
Chi-restraints excluded: chain C residue  163 ASN
Chi-restraints excluded: chain C residue  235 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 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  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:    6.9990
   chunk 97 optimal weight:    0.5980
   chunk 40 optimal weight:    2.9990
   chunk 64 optimal weight:    3.9990
   chunk 107 optimal weight:   10.0000
   chunk 79 optimal weight:    8.9990
   chunk 65 optimal weight:    2.9990
   chunk 36 optimal weight:    6.9990
   chunk 125 optimal weight:    0.8980
   chunk 54 optimal weight:    1.9990
   chunk 67 optimal weight:    2.9990
   overall best weight:    1.8986

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

Flipped N/Q/H residues before XYZ refinement:
C 163 ASN
** C 184 GLN ** 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 ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4133 r_free = 0.4133 target = 0.128477 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 58)----------------|
| r_work = 0.3417 r_free = 0.3417 target = 0.087357 restraints weight = 37394.327|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 48)----------------|
| r_work = 0.3465 r_free = 0.3465 target = 0.089875 restraints weight = 20718.753|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3495 r_free = 0.3495 target = 0.091482 restraints weight = 14650.572|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 44)----------------|
| r_work = 0.3514 r_free = 0.3514 target = 0.092458 restraints weight = 11967.558|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 31)----------------|
| r_work = 0.3523 r_free = 0.3523 target = 0.092924 restraints weight = 10672.448|
|-----------------------------------------------------------------------------|
r_work (final): 0.3497
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3498
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3498 r_free = 0.3498    target_work(ls_wunit_k1) = 0.091         |
| occupancies: max = 1.00  min = 0.49   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3498 r_free = 0.3498    target_work(ls_wunit_k1) = 0.091         |
| occupancies: max = 1.00  min = 0.49   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3498
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7875
moved from start:          0.3106

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.049  14191  Z= 0.191
  Angle     :  0.721  10.590  19874  Z= 0.385
  Chirality :  0.043   0.240   2233
  Planarity :  0.004   0.049   2009
  Dihedral  : 25.022 178.945   3174
  Min Nonbonded Distance : 2.301

Molprobity Statistics.
  All-atom Clashscore : 15.46
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.04 %
    Favored  : 95.96 %
  Rotamer:
    Outliers :  2.41 %
    Allowed  : 25.99 %
    Favored  : 71.60 %
  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:  0.01 (0.23), residues: 1311
  helix:  0.93 (0.21), residues: 623
  sheet: -0.45 (0.37), residues: 200
  loop : -0.91 (0.29), residues: 488

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG C 256 
 TYR   0.032   0.002   TYR B 223 
 PHE   0.034   0.002   PHE F  24 
 TRP   0.008   0.001   TRP D  22 
 HIS   0.006   0.001   HIS B 146 

Details of bonding type rmsd
  covalent geometry    : bond        0.00436 (14191)
  covalent geometry    : angle       0.72142 (19874)
  hydrogen bonds       : bond        0.03993 (  670)
  hydrogen bonds       : angle       4.14384 ( 1781)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2749.46 seconds
wall clock time: 47 minutes 50.69 seconds (2870.69 seconds total)