Starting phenix.real_space_refine
on Thu Jul 31 12:25:03 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8fyd_29565/07_2025/8fyd_29565.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8fyd_29565/07_2025/8fyd_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 {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8fyd_29565/07_2025/8fyd_29565.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8fyd_29565/07_2025/8fyd_29565.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8fyd_29565/07_2025/8fyd_29565.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8fyd_29565/07_2025/8fyd_29565.cif"
  }
  resolution = 3.9
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=  -0.001 sd=   0.018
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): 0.03s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/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: 8.64, per 1000 atoms: 0.63
  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: 3.03
  Conformation dependent library (CDL) restraints added in 1.4 seconds
  

  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: 4.96
  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: 4.50

  Time building geometry restraints manager: 3.68 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:             0.560
  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:          0.500
  Check model and map are aligned:         0.090
  Set scattering table:                    0.120
  Process input model:                     35.290
  Find NCS groups from input model:        0.550
  Set up NCS constraints:                  0.050
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:2.730
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   39.900
-------------------------------------------------------------------------------
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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.04 (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
 TRP   0.028   0.002   TRP C 166 
 HIS   0.008   0.001   HIS C 190 
 PHE   0.014   0.001   PHE A  35 
 TYR   0.021   0.001   TYR B  91 
 ARG   0.007   0.000   ARG F  90 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.22576 (  670)
  hydrogen bonds       : angle       7.03387 ( 1781)
  covalent geometry    : bond        0.00315 (14191)
  covalent geometry    : angle       0.58218 (19874)

*********************** 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  : 1.263 
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: 0.8004 (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: 0.6574 (t0)
  outliers start: 0
  outliers final: 0
  residues processed: 268
  average time/residue: 0.2439
  time to fit residues: 95.0204
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  : 1.304 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 144
   random chunks:
   chunk 121 optimal weight:    5.9990
   chunk 109 optimal weight:    2.9990
   chunk 60 optimal weight:    0.7980
   chunk 37 optimal weight:    0.6980
   chunk 73 optimal weight:    0.9980
   chunk 58 optimal weight:    8.9990
   chunk 112 optimal weight:    1.9990
   chunk 43 optimal weight:    0.0670
   chunk 68 optimal weight:    0.9990
   chunk 84 optimal weight:    0.9990
   chunk 130 optimal weight:    9.9990
   overall best weight:    0.7120

-------------------------------------------------------------------------------
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
** 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 = 0.4160 r_free = 0.4160 target = 0.130105 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 54)----------------|
| r_work = 0.3463 r_free = 0.3463 target = 0.089015 restraints weight = 51787.332|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 43)----------------|
| r_work = 0.3522 r_free = 0.3522 target = 0.092184 restraints weight = 23694.704|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 43)----------------|
| r_work = 0.3560 r_free = 0.3560 target = 0.094234 restraints weight = 15119.505|
|-----------------------------------------------------------------------------|
r_work (final): 0.3521
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3519
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3519 r_free = 0.3519    target_work(ls_wunit_k1) = 0.092         |
| occupancies: max = 1.00  min = 0.39   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3518 r_free = 0.3518    target_work(ls_wunit_k1) = 0.092         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3518
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7855
moved from start:          0.1539

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= 0.163
  Angle     :  0.632   8.128  19874  Z= 0.347
  Chirality :  0.041   0.171   2233
  Planarity :  0.005   0.050   2009
  Dihedral  : 25.334 175.821   3174
  Min Nonbonded Distance : 2.448

Molprobity Statistics.
  All-atom Clashscore : 13.84
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.36 %
    Favored  : 96.64 %
  Rotamer:
    Outliers :  1.67 %
    Allowed  : 12.03 %
    Favored  : 86.31 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.10 (0.23), residues: 1311
  helix:  0.97 (0.20), residues: 626
  sheet: -0.35 (0.38), residues: 181
  loop : -0.83 (0.28), residues: 504

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.001   TRP C 166 
 HIS   0.006   0.001   HIS F 146 
 PHE   0.015   0.002   PHE A  35 
 TYR   0.032   0.002   TYR E 194 
 ARG   0.007   0.001   ARG B 156 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05210 (  670)
  hydrogen bonds       : angle       4.58724 ( 1781)
  covalent geometry    : bond        0.00361 (14191)
  covalent geometry    : angle       0.63188 (19874)

*********************** 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
  257 residues out of total 1081 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 239
  time to evaluate  : 1.312 
Fit side-chains
REVERT: A   23 MET cc_start: 0.8516 (mmt) cc_final: 0.7871 (mmt)
REVERT: A   32 VAL cc_start: 0.9207 (p) cc_final: 0.8473 (p)
REVERT: B   91 TYR cc_start: 0.7900 (t80) cc_final: 0.7319 (t80)
REVERT: B   94 SER cc_start: 0.8461 (p) cc_final: 0.8191 (p)
REVERT: B  272 MET cc_start: 0.8526 (mpp) cc_final: 0.8187 (mpp)
REVERT: C   54 MET cc_start: 0.9427 (mmt) cc_final: 0.9006 (mmt)
REVERT: C   67 SER cc_start: 0.8908 (OUTLIER) cc_final: 0.8275 (p)
REVERT: C  157 GLU cc_start: 0.9157 (pp20) cc_final: 0.8905 (pp20)
REVERT: C  183 ASN cc_start: 0.9103 (m110) cc_final: 0.8748 (m110)
REVERT: D   58 MET cc_start: 0.7663 (ppp) cc_final: 0.7099 (ppp)
REVERT: D   71 LEU cc_start: 0.8963 (mp) cc_final: 0.8733 (mp)
REVERT: E  194 TYR cc_start: 0.8557 (m-80) cc_final: 0.7982 (m-80)
REVERT: F  114 ASN cc_start: 0.7912 (t0) cc_final: 0.7662 (t0)
REVERT: F  119 LEU cc_start: 0.8879 (mm) cc_final: 0.8662 (mm)
REVERT: F  155 TYR cc_start: 0.7882 (m-80) cc_final: 0.7561 (m-80)
REVERT: F  190 HIS cc_start: 0.8219 (m170) cc_final: 0.7773 (m90)
REVERT: F  265 ASP cc_start: 0.7316 (m-30) cc_final: 0.6810 (t0)
  outliers start: 18
  outliers final: 9
  residues processed: 248
  average time/residue: 0.2342
  time to fit residues: 86.2995
Evaluate side-chains
  211 residues out of total 1081 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 201
  time to evaluate  : 1.301 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   59 CYS
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   59 CYS
Chi-restraints excluded: chain E residue   48 VAL
Chi-restraints excluded: chain E residue   66 ILE
Chi-restraints excluded: chain F residue  130 PHE
Chi-restraints excluded: chain F residue  174 ASP
Chi-restraints excluded: chain F residue  279 LEU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 144
   random chunks:
   chunk 0 optimal weight:   20.0000
   chunk 114 optimal weight:    0.6980
   chunk 48 optimal weight:    6.9990
   chunk 76 optimal weight:    3.9990
   chunk 45 optimal weight:    1.9990
   chunk 27 optimal weight:    5.9990
   chunk 128 optimal weight:    0.5980
   chunk 71 optimal weight:    1.9990
   chunk 103 optimal weight:    2.9990
   chunk 118 optimal weight:    8.9990
   chunk 57 optimal weight:   10.0000
   overall best weight:    1.6586

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

Flipped N/Q/H residues before XYZ refinement:
B 146 HIS
C 146 HIS
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 114 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4137 r_free = 0.4137 target = 0.128732 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3441 r_free = 0.3441 target = 0.088206 restraints weight = 37165.180|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 52)----------------|
| r_work = 0.3490 r_free = 0.3490 target = 0.090793 restraints weight = 20632.314|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.3519 r_free = 0.3519 target = 0.092410 restraints weight = 14611.953|
|-----------------------------------------------------------------------------|
r_work (final): 0.3485
-------------------------------------------------------------------------------
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 = 0.50   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 = 0.46   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3483
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7903
moved from start:          0.1888

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.043  14191  Z= 0.177
  Angle     :  0.615   7.082  19874  Z= 0.337
  Chirality :  0.041   0.183   2233
  Planarity :  0.004   0.048   2009
  Dihedral  : 25.291 178.498   3174
  Min Nonbonded Distance : 2.449

Molprobity Statistics.
  All-atom Clashscore : 14.81
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.74 %
    Favored  : 96.26 %
  Rotamer:
    Outliers :  2.22 %
    Allowed  : 15.36 %
    Favored  : 82.42 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.07 (0.23), residues: 1311
  helix:  0.95 (0.21), residues: 628
  sheet: -0.37 (0.38), residues: 181
  loop : -0.86 (0.28), residues: 502

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP C 166 
 HIS   0.008   0.001   HIS C 146 
 PHE   0.015   0.002   PHE F 239 
 TYR   0.025   0.002   TYR E 194 
 ARG   0.004   0.000   ARG D  40 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04580 (  670)
  hydrogen bonds       : angle       4.34808 ( 1781)
  covalent geometry    : bond        0.00399 (14191)
  covalent geometry    : angle       0.61500 (19874)

*********************** 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
  242 residues out of total 1081 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 218
  time to evaluate  : 1.176 
Fit side-chains
   revert: symmetry clash
REVERT: A   23 MET cc_start: 0.8747 (mmt) cc_final: 0.7992 (mmt)
REVERT: A   32 VAL cc_start: 0.9227 (p) cc_final: 0.8378 (p)
REVERT: A   35 PHE cc_start: 0.8710 (m-10) cc_final: 0.8169 (m-10)
REVERT: B   91 TYR cc_start: 0.7943 (t80) cc_final: 0.7316 (t80)
REVERT: B   94 SER cc_start: 0.8486 (p) cc_final: 0.8133 (p)
REVERT: C   54 MET cc_start: 0.9394 (mmt) cc_final: 0.8984 (mmt)
REVERT: C   67 SER cc_start: 0.8904 (OUTLIER) cc_final: 0.8298 (p)
REVERT: C  157 GLU cc_start: 0.9189 (pp20) cc_final: 0.8922 (pp20)
REVERT: C  183 ASN cc_start: 0.9116 (m110) cc_final: 0.8838 (m110)
REVERT: C  184 GLN cc_start: 0.8948 (pm20) cc_final: 0.8689 (pm20)
REVERT: D   58 MET cc_start: 0.7810 (ppp) cc_final: 0.7418 (ppp)
REVERT: D   71 LEU cc_start: 0.8954 (mp) cc_final: 0.8702 (mp)
REVERT: E   49 ARG cc_start: 0.8853 (ttt90) cc_final: 0.8531 (tpp80)
REVERT: E  107 LYS cc_start: 0.8877 (mmtt) cc_final: 0.8554 (mmtm)
REVERT: E  194 TYR cc_start: 0.8665 (m-80) cc_final: 0.8188 (m-80)
REVERT: E  305 TYR cc_start: 0.8393 (m-10) cc_final: 0.8084 (m-10)
REVERT: F  119 LEU cc_start: 0.8916 (mm) cc_final: 0.8692 (mm)
REVERT: F  265 ASP cc_start: 0.7470 (m-30) cc_final: 0.6954 (t0)
  outliers start: 24
  outliers final: 16
  residues processed: 230
  average time/residue: 0.2384
  time to fit residues: 81.7614
Evaluate side-chains
  213 residues out of total 1081 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 196
  time to evaluate  : 1.332 
-------------------------------------------------------------------------------
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 B residue  193 LEU
Chi-restraints excluded: chain C residue   39 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 D residue    5 VAL
Chi-restraints excluded: chain D residue    7 THR
Chi-restraints excluded: chain D residue   15 LEU
Chi-restraints excluded: chain E residue   48 VAL
Chi-restraints excluded: chain E residue   66 ILE
Chi-restraints excluded: chain F residue   71 VAL
Chi-restraints excluded: chain F residue  174 ASP
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 144
   random chunks:
   chunk 118 optimal weight:    0.9990
   chunk 139 optimal weight:   10.0000
   chunk 19 optimal weight:    6.9990
   chunk 50 optimal weight:    4.9990
   chunk 134 optimal weight:    5.9990
   chunk 77 optimal weight:    0.9990
   chunk 129 optimal weight:    0.9990
   chunk 35 optimal weight:    5.9990
   chunk 88 optimal weight:    2.9990
   chunk 125 optimal weight:    6.9990
   chunk 140 optimal weight:    5.9990
   overall best weight:    2.1990

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

Flipped N/Q/H residues before XYZ refinement:
C 146 HIS
C 190 HIS
** E  87 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** F  87 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** F 114 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
F 183 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4116 r_free = 0.4116 target = 0.127278 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3407 r_free = 0.3407 target = 0.086522 restraints weight = 41416.324|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 49)----------------|
| r_work = 0.3460 r_free = 0.3460 target = 0.089253 restraints weight = 21500.198|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 50)----------------|
| r_work = 0.3492 r_free = 0.3492 target = 0.090979 restraints weight = 14665.850|
|-----------------------------------------------------------------------------|
r_work (final): 0.3450
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3452
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3452 r_free = 0.3452    target_work(ls_wunit_k1) = 0.088         |
| occupancies: max = 1.00  min = 0.46   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3452 r_free = 0.3452    target_work(ls_wunit_k1) = 0.088         |
| occupancies: max = 1.00  min = 0.44   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3452
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7930
moved from start:          0.2158

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= 0.198
  Angle     :  0.629   8.498  19874  Z= 0.344
  Chirality :  0.041   0.190   2233
  Planarity :  0.004   0.048   2009
  Dihedral  : 25.290 179.807   3174
  Min Nonbonded Distance : 2.449

Molprobity Statistics.
  All-atom Clashscore : 15.58
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.27 %
    Favored  : 95.73 %
  Rotamer:
    Outliers :  2.13 %
    Allowed  : 18.32 %
    Favored  : 79.56 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.05 (0.23), residues: 1311
  helix:  0.96 (0.20), residues: 628
  sheet: -0.44 (0.39), residues: 181
  loop : -0.88 (0.28), residues: 502

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP C 166 
 HIS   0.011   0.001   HIS B 146 
 PHE   0.016   0.002   PHE F 239 
 TYR   0.021   0.002   TYR E 194 
 ARG   0.004   0.000   ARG C  17 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04433 (  670)
  hydrogen bonds       : angle       4.25620 ( 1781)
  covalent geometry    : bond        0.00448 (14191)
  covalent geometry    : angle       0.62918 (19874)

*********************** 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
  239 residues out of total 1081 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 216
  time to evaluate  : 1.935 
Fit side-chains
   revert: symmetry clash
REVERT: A   23 MET cc_start: 0.8936 (mmt) cc_final: 0.7816 (mmt)
REVERT: A   32 VAL cc_start: 0.9246 (p) cc_final: 0.8228 (p)
REVERT: B   91 TYR cc_start: 0.7947 (t80) cc_final: 0.7156 (t80)
REVERT: B   94 SER cc_start: 0.8709 (p) cc_final: 0.8225 (p)
REVERT: C   54 MET cc_start: 0.9378 (mmt) cc_final: 0.9060 (mmt)
REVERT: C   67 SER cc_start: 0.8921 (OUTLIER) cc_final: 0.8339 (p)
REVERT: C  100 ARG cc_start: 0.8749 (tpp-160) cc_final: 0.8431 (mmp-170)
REVERT: C  157 GLU cc_start: 0.9212 (pp20) cc_final: 0.8911 (pp20)
REVERT: C  183 ASN cc_start: 0.9095 (m110) cc_final: 0.8790 (m110)
REVERT: C  184 GLN cc_start: 0.8927 (pm20) cc_final: 0.8652 (pm20)
REVERT: D   58 MET cc_start: 0.8153 (ppp) cc_final: 0.7675 (ppp)
REVERT: D   60 PHE cc_start: 0.8493 (p90) cc_final: 0.8182 (p90)
REVERT: D   71 LEU cc_start: 0.8948 (mp) cc_final: 0.8708 (mp)
REVERT: E   49 ARG cc_start: 0.8890 (ttt90) cc_final: 0.8653 (tpp80)
REVERT: F   19 GLU cc_start: 0.8552 (mp0) cc_final: 0.8291 (mp0)
REVERT: F  119 LEU cc_start: 0.8926 (mm) cc_final: 0.8669 (mm)
REVERT: F  265 ASP cc_start: 0.7470 (m-30) cc_final: 0.6971 (t0)
  outliers start: 23
  outliers final: 17
  residues processed: 229
  average time/residue: 0.2296
  time to fit residues: 79.3951
Evaluate side-chains
  212 residues out of total 1081 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 194
  time to evaluate  : 1.245 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   11 VAL
Chi-restraints excluded: chain A residue   43 LEU
Chi-restraints excluded: chain A residue   59 CYS
Chi-restraints excluded: chain A residue   79 VAL
Chi-restraints excluded: chain B residue  193 LEU
Chi-restraints excluded: chain C residue   12 SER
Chi-restraints excluded: chain C residue   39 VAL
Chi-restraints excluded: chain C residue   48 VAL
Chi-restraints excluded: chain C residue   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 D residue    5 VAL
Chi-restraints excluded: chain D residue    7 THR
Chi-restraints excluded: chain D residue   15 LEU
Chi-restraints excluded: chain E residue   48 VAL
Chi-restraints excluded: chain E residue   66 ILE
Chi-restraints excluded: chain F residue   71 VAL
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 144
   random chunks:
   chunk 21 optimal weight:    7.9990
   chunk 24 optimal weight:    3.9990
   chunk 79 optimal weight:    7.9990
   chunk 40 optimal weight:    6.9990
   chunk 115 optimal weight:    2.9990
   chunk 19 optimal weight:    5.9990
   chunk 78 optimal weight:    0.9990
   chunk 124 optimal weight:    0.5980
   chunk 4 optimal weight:    3.9990
   chunk 18 optimal weight:    2.9990
   chunk 143 optimal weight:   10.0000
   overall best weight:    2.3188

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

Flipped N/Q/H residues before XYZ refinement:
B 184 GLN
C 146 HIS
C 190 HIS
** 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: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4109 r_free = 0.4109 target = 0.126738 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3393 r_free = 0.3393 target = 0.085820 restraints weight = 41149.196|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.3446 r_free = 0.3446 target = 0.088445 restraints weight = 21582.040|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 49)----------------|
| r_work = 0.3478 r_free = 0.3478 target = 0.090158 restraints weight = 14850.721|
|-----------------------------------------------------------------------------|
r_work (final): 0.3435
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3434
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3434 r_free = 0.3434    target_work(ls_wunit_k1) = 0.087         |
| occupancies: max = 1.00  min = 0.44   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3434 r_free = 0.3434    target_work(ls_wunit_k1) = 0.087         |
| occupancies: max = 1.00  min = 0.46   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3434
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7951
moved from start:          0.2380

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.045  14191  Z= 0.204
  Angle     :  0.642   8.816  19874  Z= 0.351
  Chirality :  0.042   0.231   2233
  Planarity :  0.004   0.046   2009
  Dihedral  : 25.285 179.817   3174
  Min Nonbonded Distance : 2.449

Molprobity Statistics.
  All-atom Clashscore : 15.31
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.27 %
    Favored  : 95.73 %
  Rotamer:
    Outliers :  3.24 %
    Allowed  : 19.06 %
    Favored  : 77.71 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.01 (0.23), residues: 1311
  helix:  0.98 (0.20), residues: 628
  sheet: -0.57 (0.38), residues: 191
  loop : -0.99 (0.28), residues: 492

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP C 166 
 HIS   0.008   0.001   HIS B 146 
 PHE   0.013   0.002   PHE F 239 
 TYR   0.018   0.002   TYR E 194 
 ARG   0.004   0.000   ARG E  21 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04353 (  670)
  hydrogen bonds       : angle       4.20723 ( 1781)
  covalent geometry    : bond        0.00461 (14191)
  covalent geometry    : angle       0.64198 (19874)

*********************** 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
  241 residues out of total 1081 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 206
  time to evaluate  : 1.246 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   32 VAL cc_start: 0.9292 (p) cc_final: 0.9072 (p)
REVERT: A   35 PHE cc_start: 0.8866 (m-10) cc_final: 0.8492 (m-10)
REVERT: B   91 TYR cc_start: 0.8002 (t80) cc_final: 0.7095 (t80)
REVERT: B   94 SER cc_start: 0.8692 (p) cc_final: 0.8139 (p)
REVERT: C   54 MET cc_start: 0.9363 (mmt) cc_final: 0.9028 (mmt)
REVERT: C   67 SER cc_start: 0.8932 (OUTLIER) cc_final: 0.8336 (p)
REVERT: C  100 ARG cc_start: 0.8795 (tpp-160) cc_final: 0.8410 (mmp-170)
REVERT: C  157 GLU cc_start: 0.9234 (pp20) cc_final: 0.8938 (pp20)
REVERT: C  183 ASN cc_start: 0.9057 (m110) cc_final: 0.8770 (m110)
REVERT: C  184 GLN cc_start: 0.8962 (pm20) cc_final: 0.8712 (pm20)
REVERT: D   18 ASP cc_start: 0.8567 (t0) cc_final: 0.8330 (t70)
REVERT: D   58 MET cc_start: 0.8165 (ppp) cc_final: 0.7637 (ppp)
REVERT: D   60 PHE cc_start: 0.8534 (p90) cc_final: 0.8156 (p90)
REVERT: D   71 LEU cc_start: 0.8965 (mp) cc_final: 0.8711 (mp)
REVERT: E   49 ARG cc_start: 0.8884 (ttt90) cc_final: 0.8574 (tpp80)
REVERT: F   19 GLU cc_start: 0.8509 (mp0) cc_final: 0.8283 (mp0)
REVERT: F  119 LEU cc_start: 0.8913 (mm) cc_final: 0.8640 (mm)
  outliers start: 35
  outliers final: 24
  residues processed: 224
  average time/residue: 0.2316
  time to fit residues: 77.6109
Evaluate side-chains
  220 residues out of total 1081 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 195
  time to evaluate  : 1.213 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   11 VAL
Chi-restraints excluded: chain A residue   43 LEU
Chi-restraints excluded: chain A residue   59 CYS
Chi-restraints excluded: chain A residue   79 VAL
Chi-restraints excluded: chain B residue  193 LEU
Chi-restraints excluded: chain C residue   12 SER
Chi-restraints excluded: chain C residue   39 VAL
Chi-restraints excluded: chain C residue   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  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   11 VAL
Chi-restraints excluded: chain D residue   15 LEU
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 E residue   81 LEU
Chi-restraints excluded: chain E residue  299 LYS
Chi-restraints excluded: chain F residue   39 VAL
Chi-restraints excluded: chain F residue   71 VAL
Chi-restraints excluded: chain F residue  182 ILE
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 144
   random chunks:
   chunk 106 optimal weight:    0.0570
   chunk 133 optimal weight:    0.7980
   chunk 65 optimal weight:    0.6980
   chunk 90 optimal weight:   10.0000
   chunk 105 optimal weight:    5.9990
   chunk 102 optimal weight:    2.9990
   chunk 11 optimal weight:    5.9990
   chunk 97 optimal weight:    0.9990
   chunk 51 optimal weight:    9.9990
   chunk 82 optimal weight:    2.9990
   chunk 19 optimal weight:    5.9990
   overall best weight:    1.1102

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

Flipped N/Q/H residues before XYZ refinement:
** B 198 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
C 146 HIS
** C 190 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** E  87 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E 127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** F  87 GLN ** 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 = 0.4139 r_free = 0.4139 target = 0.128871 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3436 r_free = 0.3436 target = 0.087965 restraints weight = 41835.020|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 47)----------------|
| r_work = 0.3489 r_free = 0.3489 target = 0.090762 restraints weight = 21517.686|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.3522 r_free = 0.3522 target = 0.092533 restraints weight = 14592.328|
|-----------------------------------------------------------------------------|
r_work (final): 0.3483
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3481
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3481 r_free = 0.3481    target_work(ls_wunit_k1) = 0.090         |
| occupancies: max = 1.00  min = 0.46   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3481 r_free = 0.3481    target_work(ls_wunit_k1) = 0.090         |
| occupancies: max = 1.00  min = 0.47   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3481
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7903
moved from start:          0.2542

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.043  14191  Z= 0.155
  Angle     :  0.633   9.364  19874  Z= 0.344
  Chirality :  0.041   0.169   2233
  Planarity :  0.004   0.045   2009
  Dihedral  : 25.213 179.118   3174
  Min Nonbonded Distance : 2.452

Molprobity Statistics.
  All-atom Clashscore : 13.77
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.89 %
    Favored  : 96.11 %
  Rotamer:
    Outliers :  2.22 %
    Allowed  : 21.28 %
    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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.00 (0.23), residues: 1311
  helix:  0.97 (0.20), residues: 632
  sheet: -0.58 (0.37), residues: 186
  loop : -0.95 (0.28), residues: 493

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP A  22 
 HIS   0.013   0.001   HIS C 146 
 PHE   0.022   0.002   PHE F 239 
 TYR   0.017   0.001   TYR E 194 
 ARG   0.005   0.000   ARG C 144 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03931 (  670)
  hydrogen bonds       : angle       4.07517 ( 1781)
  covalent geometry    : bond        0.00351 (14191)
  covalent geometry    : angle       0.63312 (19874)

*********************** 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
  252 residues out of total 1081 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 228
  time to evaluate  : 1.207 
Fit side-chains
   revert: symmetry clash
REVERT: A    1 MET cc_start: 0.7560 (tmm) cc_final: 0.7315 (tmm)
REVERT: A   35 PHE cc_start: 0.8754 (m-10) cc_final: 0.8387 (m-10)
REVERT: B   91 TYR cc_start: 0.7987 (t80) cc_final: 0.6903 (t80)
REVERT: B   94 SER cc_start: 0.8668 (p) cc_final: 0.8078 (p)
REVERT: B  128 MET cc_start: 0.8768 (pmm) cc_final: 0.8562 (pmm)
REVERT: C   54 MET cc_start: 0.9298 (mmt) cc_final: 0.8993 (mmt)
REVERT: C   67 SER cc_start: 0.8812 (t) cc_final: 0.8212 (p)
REVERT: C  100 ARG cc_start: 0.8843 (tpp-160) cc_final: 0.8438 (mmp-170)
REVERT: C  128 MET cc_start: 0.8668 (mmm) cc_final: 0.8226 (mmm)
REVERT: C  157 GLU cc_start: 0.9231 (pp20) cc_final: 0.8935 (pp20)
REVERT: C  183 ASN cc_start: 0.8996 (m110) cc_final: 0.8733 (m110)
REVERT: C  184 GLN cc_start: 0.8976 (pm20) cc_final: 0.8711 (pm20)
REVERT: D   18 ASP cc_start: 0.8485 (t0) cc_final: 0.8241 (t70)
REVERT: D   23 MET cc_start: 0.8116 (mpp) cc_final: 0.7682 (mpp)
REVERT: D   58 MET cc_start: 0.8112 (ppp) cc_final: 0.7524 (ppp)
REVERT: D   60 PHE cc_start: 0.8543 (p90) cc_final: 0.8105 (p90)
REVERT: D   71 LEU cc_start: 0.8915 (mp) cc_final: 0.8685 (mp)
REVERT: E  107 LYS cc_start: 0.8872 (mmtt) cc_final: 0.8612 (mmtm)
REVERT: E  194 TYR cc_start: 0.8601 (m-80) cc_final: 0.8175 (m-80)
REVERT: F  119 LEU cc_start: 0.8888 (mm) cc_final: 0.8618 (mm)
REVERT: F  265 ASP cc_start: 0.7464 (m-30) cc_final: 0.6996 (t0)
  outliers start: 24
  outliers final: 19
  residues processed: 246
  average time/residue: 0.2228
  time to fit residues: 82.7895
Evaluate side-chains
  225 residues out of total 1081 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 206
  time to evaluate  : 1.145 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   11 VAL
Chi-restraints excluded: chain A residue   43 LEU
Chi-restraints excluded: chain A residue   59 CYS
Chi-restraints excluded: chain A residue   79 VAL
Chi-restraints excluded: chain B residue  193 LEU
Chi-restraints excluded: chain C residue   12 SER
Chi-restraints excluded: chain C residue   39 VAL
Chi-restraints excluded: chain C residue   47 VAL
Chi-restraints excluded: chain C residue   48 VAL
Chi-restraints excluded: chain C residue   57 VAL
Chi-restraints excluded: chain C residue  235 VAL
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 E residue   48 VAL
Chi-restraints excluded: chain E residue   66 ILE
Chi-restraints excluded: chain F residue   39 VAL
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 144
   random chunks:
   chunk 47 optimal weight:    2.9990
   chunk 19 optimal weight:    3.9990
   chunk 131 optimal weight:    6.9990
   chunk 43 optimal weight:    3.9990
   chunk 100 optimal weight:    6.9990
   chunk 97 optimal weight:    3.9990
   chunk 48 optimal weight:    0.9990
   chunk 67 optimal weight:    0.9980
   chunk 42 optimal weight:    5.9990
   chunk 117 optimal weight:    0.9990
   chunk 112 optimal weight:    1.9990
   overall best weight:    1.5988

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

Flipped N/Q/H residues before XYZ refinement:
B 184 GLN
C 146 HIS
** C 184 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 190 HIS
** E  87 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E 127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** F  87 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** F 146 HIS ** 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 = 0.4123 r_free = 0.4123 target = 0.127721 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3379 r_free = 0.3379 target = 0.085215 restraints weight = 52841.436|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 47)----------------|
| r_work = 0.3438 r_free = 0.3438 target = 0.088259 restraints weight = 25118.838|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 42)----------------|
| r_work = 0.3475 r_free = 0.3475 target = 0.090181 restraints weight = 16361.170|
|-----------------------------------------------------------------------------|
r_work (final): 0.3438
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3439
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3439 r_free = 0.3439    target_work(ls_wunit_k1) = 0.088         |
| occupancies: max = 1.00  min = 0.47   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3439 r_free = 0.3439    target_work(ls_wunit_k1) = 0.088         |
| occupancies: max = 1.00  min = 0.49   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3439
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7945
moved from start:          0.2636

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= 0.176
  Angle     :  0.651   8.978  19874  Z= 0.354
  Chirality :  0.041   0.208   2233
  Planarity :  0.004   0.046   2009
  Dihedral  : 25.175 179.591   3174
  Min Nonbonded Distance : 2.452

Molprobity Statistics.
  All-atom Clashscore : 15.08
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.20 %
    Favored  : 95.80 %
  Rotamer:
    Outliers :  2.87 %
    Allowed  : 22.94 %
    Favored  : 74.19 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.02 (0.23), residues: 1311
  helix:  0.90 (0.21), residues: 634
  sheet: -0.51 (0.36), residues: 201
  loop : -0.94 (0.29), residues: 476

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP A  22 
 HIS   0.015   0.002   HIS C 146 
 PHE   0.035   0.002   PHE B 239 
 TYR   0.022   0.002   TYR F 171 
 ARG   0.004   0.000   ARG D  46 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04044 (  670)
  hydrogen bonds       : angle       4.11426 ( 1781)
  covalent geometry    : bond        0.00401 (14191)
  covalent geometry    : angle       0.65103 (19874)

*********************** 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
  245 residues out of total 1081 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 214
  time to evaluate  : 1.207 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A    1 MET cc_start: 0.7550 (tmm) cc_final: 0.7297 (tmm)
REVERT: A   23 MET cc_start: 0.8535 (mmt) cc_final: 0.7356 (mmp)
REVERT: B   91 TYR cc_start: 0.7993 (t80) cc_final: 0.7017 (t80)
REVERT: B   94 SER cc_start: 0.8699 (p) cc_final: 0.8077 (p)
REVERT: B  153 ARG cc_start: 0.9276 (mtt90) cc_final: 0.8674 (mmm160)
REVERT: C   54 MET cc_start: 0.9196 (mmt) cc_final: 0.8976 (mmt)
REVERT: C   67 SER cc_start: 0.8879 (OUTLIER) cc_final: 0.8304 (p)
REVERT: C  100 ARG cc_start: 0.8793 (tpp-160) cc_final: 0.8193 (mmp-170)
REVERT: C  128 MET cc_start: 0.8650 (mmm) cc_final: 0.8255 (mmm)
REVERT: C  157 GLU cc_start: 0.9256 (pp20) cc_final: 0.8947 (pp20)
REVERT: C  184 GLN cc_start: 0.8984 (pm20) cc_final: 0.8766 (pm20)
REVERT: D   18 ASP cc_start: 0.8538 (t0) cc_final: 0.8290 (t70)
REVERT: D   23 MET cc_start: 0.8330 (mpp) cc_final: 0.7941 (mpp)
REVERT: D   58 MET cc_start: 0.8227 (ppp) cc_final: 0.7652 (ppp)
REVERT: D   60 PHE cc_start: 0.8616 (p90) cc_final: 0.8187 (p90)
REVERT: D   71 LEU cc_start: 0.8939 (mp) cc_final: 0.8684 (mp)
REVERT: E  194 TYR cc_start: 0.8555 (m-80) cc_final: 0.8043 (m-80)
REVERT: F   19 GLU cc_start: 0.8632 (mp0) cc_final: 0.8106 (mm-30)
REVERT: F  119 LEU cc_start: 0.8893 (mm) cc_final: 0.8626 (mm)
  outliers start: 31
  outliers final: 22
  residues processed: 236
  average time/residue: 0.2322
  time to fit residues: 81.8938
Evaluate side-chains
  218 residues out of total 1081 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 195
  time to evaluate  : 1.236 
-------------------------------------------------------------------------------
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   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   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 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 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  272 MET
Chi-restraints excluded: chain F residue  276 LEU
Chi-restraints excluded: chain F residue  279 LEU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 144
   random chunks:
   chunk 53 optimal weight:   10.0000
   chunk 113 optimal weight:    3.9990
   chunk 41 optimal weight:    0.0040
   chunk 84 optimal weight:    0.9990
   chunk 120 optimal weight:    5.9990
   chunk 111 optimal weight:    6.9990
   chunk 83 optimal weight:    0.0980
   chunk 70 optimal weight:    0.8980
   chunk 44 optimal weight:    2.9990
   chunk 98 optimal weight:    0.2980
   chunk 54 optimal weight:    0.9990
   overall best weight:    0.4594

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

Flipped N/Q/H residues before XYZ refinement:
C 146 HIS
** C 184 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 190 HIS
** E  87 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** F 146 HIS ** 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 = 0.4158 r_free = 0.4158 target = 0.130320 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.3456 r_free = 0.3456 target = 0.089359 restraints weight = 37615.878|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3505 r_free = 0.3505 target = 0.091967 restraints weight = 20507.726|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 41)----------------|
| r_work = 0.3536 r_free = 0.3536 target = 0.093692 restraints weight = 14441.708|
|-----------------------------------------------------------------------------|
r_work (final): 0.3501
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3500
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3500 r_free = 0.3500    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 = 0.3500 r_free = 0.3500    target_work(ls_wunit_k1) = 0.091         |
| occupancies: max = 1.00  min = 0.49   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3500
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7873
moved from start:          0.2818

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     :  0.666  13.985  19874  Z= 0.357
  Chirality :  0.042   0.224   2233
  Planarity :  0.004   0.048   2009
  Dihedral  : 25.107 178.877   3174
  Min Nonbonded Distance : 2.454

Molprobity Statistics.
  All-atom Clashscore : 14.23
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.51 %
    Favored  : 96.49 %
  Rotamer:
    Outliers :  2.13 %
    Allowed  : 23.40 %
    Favored  : 74.47 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.03 (0.23), residues: 1311
  helix:  0.92 (0.21), residues: 632
  sheet: -0.64 (0.36), residues: 197
  loop : -0.91 (0.28), residues: 482

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP A  22 
 HIS   0.015   0.001   HIS C 146 
 PHE   0.030   0.002   PHE B 239 
 TYR   0.015   0.001   TYR B 223 
 ARG   0.002   0.000   ARG B 150 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03761 (  670)
  hydrogen bonds       : angle       4.06494 ( 1781)
  covalent geometry    : bond        0.00329 (14191)
  covalent geometry    : angle       0.66629 (19874)

*********************** 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
  260 residues out of total 1081 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 237
  time to evaluate  : 1.265 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A    1 MET cc_start: 0.7429 (tmm) cc_final: 0.7204 (tmm)
REVERT: A   23 MET cc_start: 0.8265 (mmt) cc_final: 0.7246 (mmt)
REVERT: B   91 TYR cc_start: 0.7956 (t80) cc_final: 0.6946 (t80)
REVERT: B   94 SER cc_start: 0.8653 (p) cc_final: 0.8027 (p)
REVERT: B  157 GLU cc_start: 0.8923 (tm-30) cc_final: 0.8449 (pp20)
REVERT: C   54 MET cc_start: 0.9249 (mmt) cc_final: 0.8999 (mmt)
REVERT: C   67 SER cc_start: 0.8654 (t) cc_final: 0.8111 (p)
REVERT: C  100 ARG cc_start: 0.8860 (tpp-160) cc_final: 0.8241 (mmp-170)
REVERT: C  128 MET cc_start: 0.8574 (mmm) cc_final: 0.8137 (mmm)
REVERT: C  157 GLU cc_start: 0.9250 (pp20) cc_final: 0.8946 (pp20)
REVERT: C  184 GLN cc_start: 0.8859 (pm20) cc_final: 0.8532 (pm20)
REVERT: D   23 MET cc_start: 0.8000 (mpp) cc_final: 0.7691 (mpp)
REVERT: D   58 MET cc_start: 0.8074 (ppp) cc_final: 0.7473 (ppp)
REVERT: D   60 PHE cc_start: 0.8582 (p90) cc_final: 0.8156 (p90)
REVERT: D   71 LEU cc_start: 0.8926 (mp) cc_final: 0.8697 (mp)
REVERT: E   49 ARG cc_start: 0.8874 (ttt90) cc_final: 0.8578 (tpp80)
REVERT: E  107 LYS cc_start: 0.8830 (mmtt) cc_final: 0.8597 (mmtm)
REVERT: E  194 TYR cc_start: 0.8598 (m-80) cc_final: 0.8174 (m-80)
REVERT: E  218 ASP cc_start: 0.8494 (p0) cc_final: 0.8266 (p0)
REVERT: F  119 LEU cc_start: 0.8856 (mm) cc_final: 0.8584 (mm)
REVERT: F  260 ARG cc_start: 0.7673 (ttm-80) cc_final: 0.7059 (ttm-80)
REVERT: F  265 ASP cc_start: 0.7438 (m-30) cc_final: 0.6969 (t0)
  outliers start: 23
  outliers final: 17
  residues processed: 252
  average time/residue: 0.2585
  time to fit residues: 98.6785
Evaluate side-chains
  227 residues out of total 1081 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 210
  time to evaluate  : 1.178 
-------------------------------------------------------------------------------
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   79 VAL
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  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 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  272 MET
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 144
   random chunks:
   chunk 75 optimal weight:    0.6980
   chunk 57 optimal weight:    2.9990
   chunk 80 optimal weight:    7.9990
   chunk 91 optimal weight:    0.9990
   chunk 41 optimal weight:    0.0980
   chunk 16 optimal weight:    0.9980
   chunk 14 optimal weight:    8.9990
   chunk 109 optimal weight:    4.9990
   chunk 87 optimal weight:    0.7980
   chunk 55 optimal weight:    7.9990
   chunk 113 optimal weight:    0.9990
   overall best weight:    0.7182

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

Flipped N/Q/H residues before XYZ refinement:
** C 146 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
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 = 0.4159 r_free = 0.4159 target = 0.130251 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3431 r_free = 0.3431 target = 0.088095 restraints weight = 53266.192|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 48)----------------|
| r_work = 0.3491 r_free = 0.3491 target = 0.091173 restraints weight = 25202.239|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 42)----------------|
| r_work = 0.3528 r_free = 0.3528 target = 0.093148 restraints weight = 16326.435|
|-----------------------------------------------------------------------------|
r_work (final): 0.3489
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3488
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3488 r_free = 0.3488    target_work(ls_wunit_k1) = 0.090         |
| occupancies: max = 1.00  min = 0.49   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3488 r_free = 0.3488    target_work(ls_wunit_k1) = 0.090         |
| occupancies: max = 1.00  min = 0.49   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3488
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7891
moved from start:          0.2956

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042  14191  Z= 0.154
  Angle     :  0.700  13.149  19874  Z= 0.371
  Chirality :  0.042   0.249   2233
  Planarity :  0.004   0.048   2009
  Dihedral  : 25.065 179.056   3174
  Min Nonbonded Distance : 2.309

Molprobity Statistics.
  All-atom Clashscore : 14.73
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.81 %
    Favored  : 96.19 %
  Rotamer:
    Outliers :  2.04 %
    Allowed  : 24.88 %
    Favored  : 73.08 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.07 (0.23), residues: 1311
  helix:  0.83 (0.21), residues: 630
  sheet: -0.44 (0.37), residues: 193
  loop : -0.94 (0.28), residues: 488

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP A  22 
 HIS   0.017   0.001   HIS C 146 
 PHE   0.022   0.002   PHE F 239 
 TYR   0.022   0.001   TYR B 223 
 ARG   0.004   0.000   ARG B 271 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03782 (  670)
  hydrogen bonds       : angle       4.10382 ( 1781)
  covalent geometry    : bond        0.00347 (14191)
  covalent geometry    : angle       0.69994 (19874)

*********************** 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
  252 residues out of total 1081 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 230
  time to evaluate  : 1.770 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A    1 MET cc_start: 0.7353 (tmm) cc_final: 0.7089 (tmm)
REVERT: A   23 MET cc_start: 0.8253 (mmt) cc_final: 0.7405 (mmt)
REVERT: B   91 TYR cc_start: 0.7953 (t80) cc_final: 0.6967 (t80)
REVERT: B   94 SER cc_start: 0.8652 (p) cc_final: 0.7994 (p)
REVERT: B  157 GLU cc_start: 0.8870 (tm-30) cc_final: 0.8382 (pp20)
REVERT: B  218 ASP cc_start: 0.7016 (p0) cc_final: 0.6558 (p0)
REVERT: C   67 SER cc_start: 0.8718 (t) cc_final: 0.8244 (p)
REVERT: C  100 ARG cc_start: 0.8850 (tpp-160) cc_final: 0.7806 (mmp-170)
REVERT: C  140 MET cc_start: 0.9503 (mmt) cc_final: 0.9224 (mmt)
REVERT: C  143 LEU cc_start: 0.8030 (mt) cc_final: 0.7789 (mt)
REVERT: C  157 GLU cc_start: 0.9260 (pp20) cc_final: 0.8960 (pp20)
REVERT: C  184 GLN cc_start: 0.8895 (pm20) cc_final: 0.8598 (pm20)
REVERT: D   23 MET cc_start: 0.8113 (mpp) cc_final: 0.7817 (mpp)
REVERT: D   26 ILE cc_start: 0.8626 (pt) cc_final: 0.8421 (pt)
REVERT: D   58 MET cc_start: 0.8178 (ppp) cc_final: 0.7609 (ppp)
REVERT: D   60 PHE cc_start: 0.8585 (p90) cc_final: 0.8165 (p90)
REVERT: D   71 LEU cc_start: 0.8890 (mp) cc_final: 0.8684 (mp)
REVERT: E   49 ARG cc_start: 0.8861 (ttt90) cc_final: 0.8573 (tpp80)
REVERT: E  107 LYS cc_start: 0.8883 (mmtt) cc_final: 0.8640 (mmtm)
REVERT: E  194 TYR cc_start: 0.8596 (m-80) cc_final: 0.8207 (m-80)
REVERT: E  218 ASP cc_start: 0.8492 (p0) cc_final: 0.8264 (p0)
REVERT: F  119 LEU cc_start: 0.8859 (mm) cc_final: 0.8543 (mm)
REVERT: F  154 LYS cc_start: 0.8845 (tptt) cc_final: 0.8645 (tptt)
REVERT: F  260 ARG cc_start: 0.7750 (ttm-80) cc_final: 0.7086 (ttm-80)
REVERT: F  265 ASP cc_start: 0.7531 (m-30) cc_final: 0.7013 (t0)
  outliers start: 22
  outliers final: 18
  residues processed: 243
  average time/residue: 0.2753
  time to fit residues: 100.1102
Evaluate side-chains
  238 residues out of total 1081 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 220
  time to evaluate  : 1.199 
-------------------------------------------------------------------------------
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   79 VAL
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  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 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
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 88 optimal weight:    0.8980
   chunk 41 optimal weight:    0.9980
   chunk 102 optimal weight:    0.9990
   chunk 79 optimal weight:   10.0000
   chunk 2 optimal weight:   20.0000
   chunk 140 optimal weight:    3.9990
   chunk 63 optimal weight:    7.9990
   chunk 61 optimal weight:    2.9990
   chunk 42 optimal weight:    7.9990
   chunk 83 optimal weight:    4.9990
   chunk 27 optimal weight:    0.9990
   overall best weight:    1.3786

-------------------------------------------------------------------------------
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 108 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4145 r_free = 0.4145 target = 0.129170 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3437 r_free = 0.3437 target = 0.088375 restraints weight = 37307.787|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 48)----------------|
| r_work = 0.3486 r_free = 0.3486 target = 0.090915 restraints weight = 20740.387|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 48)----------------|
| r_work = 0.3517 r_free = 0.3517 target = 0.092564 restraints weight = 14666.411|
|-----------------------------------------------------------------------------|
r_work (final): 0.3480
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3480
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3480 r_free = 0.3480    target_work(ls_wunit_k1) = 0.090         |
| occupancies: max = 1.00  min = 0.49   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3480 r_free = 0.3480    target_work(ls_wunit_k1) = 0.090         |
| occupancies: max = 1.00  min = 0.49   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3480
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7903
moved from start:          0.3035

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.041  14191  Z= 0.171
  Angle     :  0.715  16.989  19874  Z= 0.378
  Chirality :  0.043   0.240   2233
  Planarity :  0.004   0.050   2009
  Dihedral  : 25.047 179.104   3174
  Min Nonbonded Distance : 2.249

Molprobity Statistics.
  All-atom Clashscore : 15.46
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.89 %
    Favored  : 96.11 %
  Rotamer:
    Outliers :  2.13 %
    Allowed  : 25.62 %
    Favored  : 72.25 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.07 (0.23), residues: 1311
  helix:  0.84 (0.21), residues: 627
  sheet: -0.57 (0.37), residues: 190
  loop : -0.86 (0.28), residues: 494

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP E 296 
 HIS   0.020   0.002   HIS C 146 
 PHE   0.023   0.002   PHE F 239 
 TYR   0.028   0.001   TYR B 223 
 ARG   0.004   0.000   ARG B 258 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03893 (  670)
  hydrogen bonds       : angle       4.18360 ( 1781)
  covalent geometry    : bond        0.00389 (14191)
  covalent geometry    : angle       0.71459 (19874)

********************** 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
  243 residues out of total 1081 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 220
  time to evaluate  : 1.370 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A    1 MET cc_start: 0.7396 (tmm) cc_final: 0.7127 (tmm)
REVERT: A    9 LYS cc_start: 0.8661 (ttpp) cc_final: 0.8024 (pttm)
REVERT: A   23 MET cc_start: 0.8314 (mmt) cc_final: 0.7441 (mmt)
REVERT: A   41 GLU cc_start: 0.8405 (OUTLIER) cc_final: 0.8149 (tm-30)
REVERT: B   91 TYR cc_start: 0.7976 (t80) cc_final: 0.6967 (t80)
REVERT: B   94 SER cc_start: 0.8683 (p) cc_final: 0.8043 (p)
REVERT: B  153 ARG cc_start: 0.9230 (mtt90) cc_final: 0.8510 (mmm160)
REVERT: B  157 GLU cc_start: 0.8913 (tm-30) cc_final: 0.8431 (pp20)
REVERT: B  218 ASP cc_start: 0.6940 (p0) cc_final: 0.6583 (p0)
REVERT: C   67 SER cc_start: 0.8809 (t) cc_final: 0.8307 (p)
REVERT: C  100 ARG cc_start: 0.8824 (tpp-160) cc_final: 0.7897 (mmp-170)
REVERT: C  140 MET cc_start: 0.9505 (mmt) cc_final: 0.9283 (mmt)
REVERT: C  143 LEU cc_start: 0.8175 (mt) cc_final: 0.7904 (mt)
REVERT: C  157 GLU cc_start: 0.9280 (pp20) cc_final: 0.9008 (pp20)
REVERT: C  184 GLN cc_start: 0.8927 (pm20) cc_final: 0.8616 (pm20)
REVERT: D   18 ASP cc_start: 0.8476 (t0) cc_final: 0.8244 (t70)
REVERT: D   23 MET cc_start: 0.8219 (mpp) cc_final: 0.7912 (mpp)
REVERT: D   58 MET cc_start: 0.8255 (ppp) cc_final: 0.7630 (ppp)
REVERT: D   60 PHE cc_start: 0.8628 (p90) cc_final: 0.8218 (p90)
REVERT: D   71 LEU cc_start: 0.8896 (mp) cc_final: 0.8631 (mp)
REVERT: E   49 ARG cc_start: 0.8828 (ttt90) cc_final: 0.8523 (tpp80)
REVERT: E  194 TYR cc_start: 0.8596 (m-80) cc_final: 0.8093 (m-80)
REVERT: E  269 LEU cc_start: 0.9093 (mp) cc_final: 0.8827 (tt)
REVERT: F   19 GLU cc_start: 0.8702 (mp0) cc_final: 0.8045 (mm-30)
REVERT: F  125 MET cc_start: 0.9296 (mmp) cc_final: 0.9094 (mmp)
REVERT: F  265 ASP cc_start: 0.7527 (m-30) cc_final: 0.7030 (t0)
  outliers start: 23
  outliers final: 19
  residues processed: 235
  average time/residue: 0.2708
  time to fit residues: 97.3378
Evaluate side-chains
  235 residues out of total 1081 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 215
  time to evaluate  : 1.331 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   11 VAL
Chi-restraints excluded: chain A residue   41 GLU
Chi-restraints excluded: chain A residue   59 CYS
Chi-restraints excluded: chain A residue   79 VAL
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  160 LYS
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    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 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
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 27 optimal weight:    0.8980
   chunk 125 optimal weight:    0.7980
   chunk 140 optimal weight:    4.9990
   chunk 51 optimal weight:    0.3980
   chunk 43 optimal weight:    4.9990
   chunk 118 optimal weight:   10.0000
   chunk 81 optimal weight:    3.9990
   chunk 53 optimal weight:   10.0000
   chunk 97 optimal weight:    3.9990
   chunk 126 optimal weight:    1.9990
   chunk 89 optimal weight:   10.0000
   overall best weight:    1.6184

-------------------------------------------------------------------------------
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**
** F 183 ASN ** 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 = 0.4141 r_free = 0.4141 target = 0.128975 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3434 r_free = 0.3434 target = 0.088186 restraints weight = 37262.700|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 53)----------------|
| r_work = 0.3483 r_free = 0.3483 target = 0.090710 restraints weight = 20667.368|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3513 r_free = 0.3513 target = 0.092326 restraints weight = 14614.835|
|-----------------------------------------------------------------------------|
r_work (final): 0.3477
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3477
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3477 r_free = 0.3477    target_work(ls_wunit_k1) = 0.090         |
| occupancies: max = 1.00  min = 0.49   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3477 r_free = 0.3477    target_work(ls_wunit_k1) = 0.090         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3477
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7907
moved from start:          0.3031

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.183  14191  Z= 0.206
  Angle     :  0.913  59.200  19874  Z= 0.523
  Chirality :  0.044   0.510   2233
  Planarity :  0.004   0.050   2009
  Dihedral  : 25.052 179.104   3174
  Min Nonbonded Distance : 2.155

Molprobity Statistics.
  All-atom Clashscore : 17.31
  Ramachandran Plot:
    Outliers :  0.08 %
    Allowed  :  3.81 %
    Favored  : 96.11 %
  Rotamer:
    Outliers :  1.94 %
    Allowed  : 25.99 %
    Favored  : 72.06 %
  Cbeta Deviations :  0.08 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.08 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.07 (0.23), residues: 1311
  helix:  0.83 (0.21), residues: 627
  sheet: -0.57 (0.37), residues: 190
  loop : -0.86 (0.28), residues: 494

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP E 296 
 HIS   0.017   0.001   HIS C 146 
 PHE   0.022   0.002   PHE F 239 
 TYR   0.018   0.001   TYR B 223 
 ARG   0.004   0.000   ARG B 258 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03916 (  670)
  hydrogen bonds       : angle       4.18110 ( 1781)
  covalent geometry    : bond        0.00462 (14191)
  covalent geometry    : angle       0.91339 (19874)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 6509.65 seconds
wall clock time: 117 minutes 16.85 seconds (7036.85 seconds total)