Starting phenix.real_space_refine
on Wed Mar  4 08:56:30 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/6r69_4733/03_2026/6r69_4733.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/6r69_4733/03_2026/6r69_4733.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.65
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/6r69_4733/03_2026/6r69_4733.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/6r69_4733/03_2026/6r69_4733.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/6r69_4733/03_2026/6r69_4733.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/6r69_4733/03_2026/6r69_4733.cif"
  }
  resolution = 3.65
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=  -0.000 sd=   0.002
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: 4
    Type Number    sf(0)   Gaussians
     S      99      5.16       5
     C    8390      2.51       5
     N    1934      2.21       5
     O    2118      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 38 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 12541
  Number of models: 1
  Model: ""
    Number of chains: 10
    Chain: "A"
      Number of atoms: 1575
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 203, 1575
          Classifications: {'peptide': 203}
          Link IDs: {'PTRANS': 15, 'TRANS': 187}
    Chain: "B"
      Number of atoms: 1575
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 203, 1575
          Classifications: {'peptide': 203}
          Link IDs: {'PTRANS': 15, 'TRANS': 187}
    Chain: "C"
      Number of atoms: 1575
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 203, 1575
          Classifications: {'peptide': 203}
          Link IDs: {'PTRANS': 15, 'TRANS': 187}
    Chain: "D"
      Number of atoms: 1575
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 203, 1575
          Classifications: {'peptide': 203}
          Link IDs: {'PTRANS': 15, 'TRANS': 187}
    Chain: "E"
      Number of atoms: 1575
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 203, 1575
          Classifications: {'peptide': 203}
          Link IDs: {'PTRANS': 15, 'TRANS': 187}
    Chain: "F"
      Number of atoms: 1986
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 258, 1986
          Classifications: {'peptide': 258}
          Link IDs: {'CIS': 1, 'PTRANS': 16, 'TRANS': 240}
    Chain: "G"
      Number of atoms: 670
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 89, 670
          Classifications: {'peptide': 89}
          Link IDs: {'PTRANS': 5, 'TRANS': 83}
    Chain: "H"
      Number of atoms: 670
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 89, 670
          Classifications: {'peptide': 89}
          Link IDs: {'PTRANS': 5, 'TRANS': 83}
    Chain: "I"
      Number of atoms: 670
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 89, 670
          Classifications: {'peptide': 89}
          Link IDs: {'PTRANS': 5, 'TRANS': 83}
    Chain: "J"
      Number of atoms: 670
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 89, 670
          Classifications: {'peptide': 89}
          Link IDs: {'PTRANS': 5, 'TRANS': 83}
  Time building chain proxies: 2.77, per 1000 atoms: 0.22
  Number of scatterers: 12541
  At special positions: 0
  Unit cell: (105.4, 101.15, 130.9, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     S      99     16.00
     O    2118      8.00
     N    1934      7.00
     C    8390      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: 0.98
  Conformation dependent library (CDL) restraints added in 503.8 milliseconds
  

  3218 Ramachandran restraints generated.
    1609 Oldfield, 0 Emsley, 1609 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  3094

  Finding SS restraints...
    Secondary structure from input PDB file:
      73 helices and 0 sheets defined
      81.8% alpha, 0.0% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.25
  Creating SS restraints...
    Processing helix  chain 'A' and resid 43 through 61
      removed outlier: 3.714A  pdb=" N   PHE A  47 " --> pdb=" O   GLN A  43 " (cutoff:3.500A)
      removed outlier: 3.943A  pdb=" N   SER A  50 " --> pdb=" O   VAL A  46 " (cutoff:3.500A)
      removed outlier: 3.801A  pdb=" N   LEU A  51 " --> pdb=" O   PHE A  47 " (cutoff:3.500A)
      removed outlier: 4.467A  pdb=" N   THR A  52 " --> pdb=" O   ILE A  48 " (cutoff:3.500A)
      removed outlier: 3.654A  pdb=" N   LEU A  54 " --> pdb=" O   SER A  50 " (cutoff:3.500A)
      Proline residue:  A  55  - end of helix
    Processing helix  chain 'A' and resid 66 through 77
    Processing helix  chain 'A' and resid 87 through 101
      removed outlier: 3.637A  pdb=" N   THR A  97 " --> pdb=" O   ALA A  93 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 101 through 112
    Processing helix  chain 'A' and resid 112 through 119
      removed outlier: 3.957A  pdb=" N   GLU A 118 " --> pdb=" O   GLN A 114 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 124 through 140
      Proline residue:  A 133  - end of helix
      removed outlier: 3.556A  pdb=" N   ARG A 140 " --> pdb=" O   ALA A 136 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 143 through 154
      removed outlier: 3.806A  pdb=" N   LEU A 147 " --> pdb=" O   ARG A 143 " (cutoff:3.500A)
      removed outlier: 3.543A  pdb=" N   ALA A 154 " --> pdb=" O   PHE A 150 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 166 through 208
      Proline residue:  A 172  - end of helix
      removed outlier: 3.874A  pdb=" N   GLN A 184 " --> pdb=" O   LYS A 180 " (cutoff:3.500A)
      removed outlier: 3.711A  pdb=" N   THR A 188 " --> pdb=" O   GLN A 184 " (cutoff:3.500A)
      removed outlier: 4.125A  pdb=" N   ILE A 191 " --> pdb=" O   PHE A 187 " (cutoff:3.500A)
      Proline residue:  A 192  - end of helix
      removed outlier: 3.525A  pdb=" N   LEU A 207 " --> pdb=" O   VAL A 203 " (cutoff:3.500A)
      removed outlier: 3.588A  pdb=" N   GLY A 208 " --> pdb=" O   LEU A 204 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 214 through 228
      removed outlier: 3.767A  pdb=" N   LEU A 219 " --> pdb=" O   ALA A 215 " (cutoff:3.500A)
      Proline residue:  A 220  - end of helix
      removed outlier: 4.348A  pdb=" N   PHE A 226 " --> pdb=" O   LYS A 222 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 230 through 245
      removed outlier: 3.628A  pdb=" N   LEU A 234 " --> pdb=" O   ASP A 230 " (cutoff:3.500A)
      removed outlier: 3.884A  pdb=" N   PHE A 243 " --> pdb=" O   LEU A 239 " (cutoff:3.500A)
      removed outlier: 4.351A  pdb=" N   TYR A 244 " --> pdb=" O   ALA A 240 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 44 through 63
      Proline residue:  B  55  - end of helix
      removed outlier: 3.964A  pdb=" N   LEU B  59 " --> pdb=" O   PRO B  55 " (cutoff:3.500A)
      removed outlier: 3.694A  pdb=" N   THR B  62 " --> pdb=" O   LEU B  58 " (cutoff:3.500A)
      removed outlier: 3.770A  pdb=" N   SER B  63 " --> pdb=" O   LEU B  59 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 66 through 77
      removed outlier: 3.765A  pdb=" N   ALA B  77 " --> pdb=" O   LEU B  73 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 87 through 119
      removed outlier: 3.598A  pdb=" N   GLY B  91 " --> pdb=" O   GLN B  87 " (cutoff:3.500A)
      Proline residue:  B 103  - end of helix
      removed outlier: 4.825A  pdb=" N   GLN B 114 " --> pdb=" O   VAL B 110 " (cutoff:3.500A)
      Proline residue:  B 115  - end of helix
      removed outlier: 3.811A  pdb=" N   GLU B 118 " --> pdb=" O   GLN B 114 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 125 through 142
      Proline residue:  B 133  - end of helix
      removed outlier: 3.688A  pdb=" N   GLN B 141 " --> pdb=" O   PHE B 137 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 143 through 153
      removed outlier: 3.803A  pdb=" N   LEU B 147 " --> pdb=" O   ARG B 143 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 161 through 165
    Processing helix  chain 'B' and resid 166 through 205
      Proline residue:  B 172  - end of helix
      removed outlier: 4.127A  pdb=" N   ILE B 191 " --> pdb=" O   PHE B 187 " (cutoff:3.500A)
      Proline residue:  B 192  - end of helix
    Processing helix  chain 'B' and resid 217 through 229
      removed outlier: 4.061A  pdb=" N   PHE B 221 " --> pdb=" O   ILE B 217 " (cutoff:3.500A)
      removed outlier: 3.598A  pdb=" N   LEU B 223 " --> pdb=" O   LEU B 219 " (cutoff:3.500A)
      removed outlier: 4.297A  pdb=" N   PHE B 226 " --> pdb=" O   LYS B 222 " (cutoff:3.500A)
      removed outlier: 3.642A  pdb=" N   VAL B 229 " --> pdb=" O   LEU B 225 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 230 through 245
      removed outlier: 3.620A  pdb=" N   LEU B 234 " --> pdb=" O   ASP B 230 " (cutoff:3.500A)
      removed outlier: 4.057A  pdb=" N   VAL B 236 " --> pdb=" O   TRP B 232 " (cutoff:3.500A)
      removed outlier: 3.896A  pdb=" N   PHE B 243 " --> pdb=" O   LEU B 239 " (cutoff:3.500A)
      removed outlier: 4.320A  pdb=" N   TYR B 244 " --> pdb=" O   ALA B 240 " (cutoff:3.500A)
      removed outlier: 4.076A  pdb=" N   SER B 245 " --> pdb=" O   GLN B 241 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 44 through 62
      removed outlier: 3.743A  pdb=" N   ILE C  48 " --> pdb=" O   THR C  44 " (cutoff:3.500A)
      Proline residue:  C  55  - end of helix
      removed outlier: 3.755A  pdb=" N   THR C  62 " --> pdb=" O   LEU C  58 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 64 through 75
      removed outlier: 3.879A  pdb=" N   ILE C  68 " --> pdb=" O   PHE C  64 " (cutoff:3.500A)
      removed outlier: 3.748A  pdb=" N   ILE C  69 " --> pdb=" O   THR C  65 " (cutoff:3.500A)
      removed outlier: 3.656A  pdb=" N   VAL C  70 " --> pdb=" O   ARG C  66 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 88 through 101
    Processing helix  chain 'C' and resid 101 through 117
      removed outlier: 4.766A  pdb=" N   GLN C 114 " --> pdb=" O   VAL C 110 " (cutoff:3.500A)
      Proline residue:  C 115  - end of helix
    Processing helix  chain 'C' and resid 123 through 140
      removed outlier: 4.063A  pdb=" N   LEU C 127 " --> pdb=" O   MET C 123 " (cutoff:3.500A)
      removed outlier: 4.027A  pdb=" N   GLY C 130 " --> pdb=" O   ALA C 126 " (cutoff:3.500A)
      removed outlier: 3.604A  pdb=" N   GLN C 132 " --> pdb=" O   ASP C 128 " (cutoff:3.500A)
      Proline residue:  C 133  - end of helix
      removed outlier: 3.555A  pdb=" N   ALA C 136 " --> pdb=" O   GLN C 132 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 143 through 154
      removed outlier: 3.956A  pdb=" N   LEU C 147 " --> pdb=" O   ARG C 143 " (cutoff:3.500A)
      removed outlier: 3.848A  pdb=" N   ALA C 154 " --> pdb=" O   PHE C 150 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 166 through 190
      removed outlier: 3.665A  pdb=" N   LEU C 170 " --> pdb=" O   PRO C 166 " (cutoff:3.500A)
      removed outlier: 3.529A  pdb=" N   LEU C 171 " --> pdb=" O   MET C 167 " (cutoff:3.500A)
      Proline residue:  C 172  - end of helix
      removed outlier: 3.609A  pdb=" N   PHE C 190 " --> pdb=" O   GLY C 186 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 190 through 208
    Processing helix  chain 'C' and resid 213 through 216
    Processing helix  chain 'C' and resid 217 through 228
      removed outlier: 4.269A  pdb=" N   PHE C 221 " --> pdb=" O   ILE C 217 " (cutoff:3.500A)
      removed outlier: 3.802A  pdb=" N   PHE C 226 " --> pdb=" O   LYS C 222 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 230 through 245
      removed outlier: 3.614A  pdb=" N   LEU C 234 " --> pdb=" O   ASP C 230 " (cutoff:3.500A)
      removed outlier: 3.691A  pdb=" N   LEU C 235 " --> pdb=" O   GLY C 231 " (cutoff:3.500A)
      removed outlier: 3.577A  pdb=" N   VAL C 236 " --> pdb=" O   TRP C 232 " (cutoff:3.500A)
      removed outlier: 4.275A  pdb=" N   PHE C 243 " --> pdb=" O   LEU C 239 " (cutoff:3.500A)
      removed outlier: 4.549A  pdb=" N   TYR C 244 " --> pdb=" O   ALA C 240 " (cutoff:3.500A)
      removed outlier: 3.951A  pdb=" N   SER C 245 " --> pdb=" O   GLN C 241 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 44 through 62
      removed outlier: 3.675A  pdb=" N   ILE D  48 " --> pdb=" O   THR D  44 " (cutoff:3.500A)
      removed outlier: 3.634A  pdb=" N   THR D  52 " --> pdb=" O   ILE D  48 " (cutoff:3.500A)
      removed outlier: 4.225A  pdb=" N   PHE D  53 " --> pdb=" O   THR D  49 " (cutoff:3.500A)
      Proline residue:  D  55  - end of helix
      removed outlier: 3.994A  pdb=" N   THR D  62 " --> pdb=" O   LEU D  58 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 64 through 75
    Processing helix  chain 'D' and resid 87 through 112
      Proline residue:  D 103  - end of helix
    Processing helix  chain 'D' and resid 114 through 118
    Processing helix  chain 'D' and resid 127 through 140
      Proline residue:  D 133  - end of helix
    Processing helix  chain 'D' and resid 143 through 153
      removed outlier: 3.637A  pdb=" N   LEU D 147 " --> pdb=" O   ARG D 143 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 166 through 190
      removed outlier: 3.701A  pdb=" N   LEU D 171 " --> pdb=" O   MET D 167 " (cutoff:3.500A)
      Proline residue:  D 172  - end of helix
    Processing helix  chain 'D' and resid 190 through 208
    Processing helix  chain 'D' and resid 213 through 228
      removed outlier: 3.543A  pdb=" N   ILE D 217 " --> pdb=" O   PRO D 213 " (cutoff:3.500A)
      removed outlier: 4.679A  pdb=" N   LEU D 219 " --> pdb=" O   ALA D 215 " (cutoff:3.500A)
      Proline residue:  D 220  - end of helix
    Processing helix  chain 'D' and resid 232 through 245
      removed outlier: 3.522A  pdb=" N   VAL D 236 " --> pdb=" O   TRP D 232 " (cutoff:3.500A)
      removed outlier: 3.904A  pdb=" N   ALA D 240 " --> pdb=" O   VAL D 236 " (cutoff:3.500A)
      removed outlier: 4.318A  pdb=" N   PHE D 243 " --> pdb=" O   LEU D 239 " (cutoff:3.500A)
      removed outlier: 4.170A  pdb=" N   TYR D 244 " --> pdb=" O   ALA D 240 " (cutoff:3.500A)
      removed outlier: 3.724A  pdb=" N   SER D 245 " --> pdb=" O   GLN D 241 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 44 through 63
      removed outlier: 4.414A  pdb=" N   ILE E  48 " --> pdb=" O   THR E  44 " (cutoff:3.500A)
      Proline residue:  E  55  - end of helix
      removed outlier: 3.847A  pdb=" N   THR E  62 " --> pdb=" O   LEU E  58 " (cutoff:3.500A)
      removed outlier: 3.540A  pdb=" N   SER E  63 " --> pdb=" O   LEU E  59 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 66 through 77
      removed outlier: 3.809A  pdb=" N   VAL E  70 " --> pdb=" O   ARG E  66 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 87 through 117
      removed outlier: 4.234A  pdb=" N   ALA E  93 " --> pdb=" O   LEU E  89 " (cutoff:3.500A)
      removed outlier: 3.868A  pdb=" N   THR E  97 " --> pdb=" O   ALA E  93 " (cutoff:3.500A)
      Proline residue:  E 103  - end of helix
      removed outlier: 4.593A  pdb=" N   GLN E 114 " --> pdb=" O   VAL E 110 " (cutoff:3.500A)
      Proline residue:  E 115  - end of helix
    Processing helix  chain 'E' and resid 124 through 140
      Proline residue:  E 133  - end of helix
    Processing helix  chain 'E' and resid 143 through 155
      removed outlier: 3.949A  pdb=" N   LEU E 147 " --> pdb=" O   ARG E 143 " (cutoff:3.500A)
      removed outlier: 3.762A  pdb=" N   ALA E 148 " --> pdb=" O   GLU E 144 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 166 through 208
      removed outlier: 3.509A  pdb=" N   LEU E 170 " --> pdb=" O   PRO E 166 " (cutoff:3.500A)
      removed outlier: 3.865A  pdb=" N   LEU E 171 " --> pdb=" O   MET E 167 " (cutoff:3.500A)
      Proline residue:  E 172  - end of helix
      removed outlier: 3.730A  pdb=" N   ILE E 191 " --> pdb=" O   PHE E 187 " (cutoff:3.500A)
      Proline residue:  E 192  - end of helix
      removed outlier: 3.589A  pdb=" N   LEU E 207 " --> pdb=" O   VAL E 203 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 217 through 228
      removed outlier: 4.564A  pdb=" N   PHE E 221 " --> pdb=" O   ILE E 217 " (cutoff:3.500A)
      removed outlier: 3.809A  pdb=" N   LYS E 222 " --> pdb=" O   ALA E 218 " (cutoff:3.500A)
      removed outlier: 3.932A  pdb=" N   LEU E 223 " --> pdb=" O   LEU E 219 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 230 through 245
      removed outlier: 3.861A  pdb=" N   LEU E 234 " --> pdb=" O   ASP E 230 " (cutoff:3.500A)
      removed outlier: 4.186A  pdb=" N   PHE E 243 " --> pdb=" O   LEU E 239 " (cutoff:3.500A)
      removed outlier: 4.520A  pdb=" N   TYR E 244 " --> pdb=" O   ALA E 240 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 6 through 14
      removed outlier: 4.248A  pdb=" N   LEU F  10 " --> pdb=" O   SER F   6 " (cutoff:3.500A)
      removed outlier: 3.698A  pdb=" N   TYR F  11 " --> pdb=" O   GLU F   7 " (cutoff:3.500A)
      removed outlier: 4.027A  pdb=" N   TRP F  12 " --> pdb=" O   GLN F   8 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 16 through 29
    Processing helix  chain 'F' and resid 44 through 55
      removed outlier: 3.834A  pdb=" N   ILE F  48 " --> pdb=" O   LEU F  44 " (cutoff:3.500A)
      removed outlier: 3.628A  pdb=" N   VAL F  53 " --> pdb=" O   MET F  49 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 70 through 89
      removed outlier: 3.662A  pdb=" N   MET F  75 " --> pdb=" O   LEU F  71 " (cutoff:3.500A)
      removed outlier: 4.037A  pdb=" N   GLN F  76 " --> pdb=" O   TRP F  72 " (cutoff:3.500A)
      removed outlier: 3.846A  pdb=" N   GLN F  77 " --> pdb=" O   LEU F  73 " (cutoff:3.500A)
      removed outlier: 3.840A  pdb=" N   ILE F  78 " --> pdb=" O   ALA F  74 " (cutoff:3.500A)
      removed outlier: 3.752A  pdb=" N   LEU F  79 " --> pdb=" O   MET F  75 " (cutoff:3.500A)
      removed outlier: 3.959A  pdb=" N   THR F  87 " --> pdb=" O   ALA F  83 " (cutoff:3.500A)
      removed outlier: 3.533A  pdb=" N   GLN F  89 " --> pdb=" O   GLY F  85 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 89 through 104
      removed outlier: 4.063A  pdb=" N   VAL F  95 " --> pdb=" O   ALA F  91 " (cutoff:3.500A)
      removed outlier: 3.502A  pdb=" N   PHE F 101 " --> pdb=" O   THR F  97 " (cutoff:3.500A)
      removed outlier: 3.833A  pdb=" N   ILE F 102 " --> pdb=" O   ALA F  98 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 125 through 141
      removed outlier: 3.808A  pdb=" N   MET F 131 " --> pdb=" O   ARG F 127 " (cutoff:3.500A)
      removed outlier: 3.984A  pdb=" N   PHE F 137 " --> pdb=" O   ALA F 133 " (cutoff:3.500A)
      removed outlier: 3.810A  pdb=" N   LEU F 138 " --> pdb=" O   MET F 134 " (cutoff:3.500A)
      removed outlier: 3.622A  pdb=" N   PHE F 140 " --> pdb=" O   LEU F 136 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 143 through 157
      removed outlier: 3.535A  pdb=" N   HIS F 155 " --> pdb=" O   VAL F 151 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 168 through 176
      removed outlier: 4.297A  pdb=" N   GLY F 176 " --> pdb=" O   LEU F 172 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 177 through 206
      removed outlier: 4.097A  pdb=" N   LEU F 181 " --> pdb=" O   GLY F 177 " (cutoff:3.500A)
      removed outlier: 3.625A  pdb=" N   ALA F 187 " --> pdb=" O   GLY F 183 " (cutoff:3.500A)
      Proline residue:  F 189  - end of helix
      removed outlier: 3.658A  pdb=" N   GLY F 202 " --> pdb=" O   ASN F 198 " (cutoff:3.500A)
      removed outlier: 3.808A  pdb=" N   LEU F 204 " --> pdb=" O   ALA F 200 " (cutoff:3.500A)
      removed outlier: 3.745A  pdb=" N   ASN F 205 " --> pdb=" O   LEU F 201 " (cutoff:3.500A)
      removed outlier: 3.748A  pdb=" N   ARG F 206 " --> pdb=" O   GLY F 202 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 208 through 212
      removed outlier: 3.641A  pdb=" N   LEU F 211 " --> pdb=" O   ALA F 208 " (cutoff:3.500A)
      removed outlier: 4.275A  pdb=" N   SER F 212 " --> pdb=" O   PRO F 209 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'F' and resid 208 through 212'
    Processing helix  chain 'F' and resid 216 through 232
      removed outlier: 4.197A  pdb=" N   THR F 223 " --> pdb=" O   PRO F 219 " (cutoff:3.500A)
      removed outlier: 3.552A  pdb=" N   MET F 229 " --> pdb=" O   GLY F 225 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 235 through 261
      removed outlier: 3.573A  pdb=" N   PHE F 239 " --> pdb=" O   LEU F 235 " (cutoff:3.500A)
      removed outlier: 4.059A  pdb=" N   GLU F 241 " --> pdb=" O   ALA F 237 " (cutoff:3.500A)
      removed outlier: 3.865A  pdb=" N   HIS F 242 " --> pdb=" O   PRO F 238 " (cutoff:3.500A)
      removed outlier: 3.941A  pdb=" N   ILE F 247 " --> pdb=" O   LEU F 243 " (cutoff:3.500A)
      Proline residue:  F 259  - end of helix
    Processing helix  chain 'G' and resid 2 through 40
      removed outlier: 3.585A  pdb=" N   MET G   7 " --> pdb=" O   PRO G   3 " (cutoff:3.500A)
      removed outlier: 3.519A  pdb=" N   GLY G  10 " --> pdb=" O   VAL G   6 " (cutoff:3.500A)
      Proline residue:  G  23  - end of helix
    Processing helix  chain 'G' and resid 50 through 66
      removed outlier: 3.782A  pdb=" N   VAL G  58 " --> pdb=" O   LYS G  54 " (cutoff:3.500A)
      removed outlier: 3.830A  pdb=" N   ILE G  63 " --> pdb=" O   PHE G  59 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 66 through 89
      removed outlier: 3.997A  pdb=" N   LEU G  73 " --> pdb=" O   MET G  69 " (cutoff:3.500A)
      Proline residue:  G  85  - end of helix
      removed outlier: 3.693A  pdb=" N   ILE G  88 " --> pdb=" O   LEU G  84 " (cutoff:3.500A)
      removed outlier: 3.884A  pdb=" N   GLY G  89 " --> pdb=" O   PRO G  85 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 2 through 40
      Proline residue:  H  23  - end of helix
      removed outlier: 3.705A  pdb=" N   LEU H  38 " --> pdb=" O   ILE H  34 " (cutoff:3.500A)
      removed outlier: 3.927A  pdb=" N   ALA H  40 " --> pdb=" O   SER H  36 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 50 through 66
      removed outlier: 3.631A  pdb=" N   VAL H  58 " --> pdb=" O   LYS H  54 " (cutoff:3.500A)
      removed outlier: 3.582A  pdb=" N   ILE H  63 " --> pdb=" O   PHE H  59 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 66 through 84
      removed outlier: 4.083A  pdb=" N   LEU H  73 " --> pdb=" O   MET H  69 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 85 through 87
      No H-bonds generated for 'chain 'H' and resid 85 through 87'
    Processing helix  chain 'I' and resid 2 through 39
      Proline residue:  I  23  - end of helix
    Processing helix  chain 'I' and resid 50 through 66
      removed outlier: 3.531A  pdb=" N   VAL I  58 " --> pdb=" O   LYS I  54 " (cutoff:3.500A)
      removed outlier: 3.619A  pdb=" N   ILE I  63 " --> pdb=" O   PHE I  59 " (cutoff:3.500A)
    Processing helix  chain 'I' and resid 66 through 88
      Proline residue:  I  85  - end of helix
      removed outlier: 4.104A  pdb=" N   ILE I  88 " --> pdb=" O   LEU I  84 " (cutoff:3.500A)
    Processing helix  chain 'J' and resid 4 through 38
      removed outlier: 4.157A  pdb=" N   GLY J  10 " --> pdb=" O   VAL J   6 " (cutoff:3.500A)
      removed outlier: 3.596A  pdb=" N   LYS J  15 " --> pdb=" O   THR J  11 " (cutoff:3.500A)
      Proline residue:  J  23  - end of helix
      removed outlier: 3.701A  pdb=" N   LEU J  38 " --> pdb=" O   ILE J  34 " (cutoff:3.500A)
    Processing helix  chain 'J' and resid 50 through 66
      removed outlier: 4.011A  pdb=" N   LYS J  54 " --> pdb=" O   SER J  50 " (cutoff:3.500A)
      removed outlier: 3.800A  pdb=" N   ILE J  63 " --> pdb=" O   PHE J  59 " (cutoff:3.500A)
    Processing helix  chain 'J' and resid 66 through 88
      removed outlier: 3.815A  pdb=" N   LEU J  73 " --> pdb=" O   MET J  69 " (cutoff:3.500A)
      removed outlier: 3.508A  pdb=" N   ARG J  78 " --> pdb=" O   LEU J  74 " (cutoff:3.500A)
      Proline residue:  J  85  - end of helix
      removed outlier: 3.619A  pdb=" N   ILE J  88 " --> pdb=" O   LEU J  84 " (cutoff:3.500A)

    788 hydrogen bonds defined for protein.
    2349 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 1.89

  Time building geometry restraints manager: 1.30 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: 3717
        1.34 -     1.46: 1593
        1.46 -     1.57: 7313
        1.57 -     1.69: 0
        1.69 -     1.81: 197
  Bond restraints: 12820
  Sorted by residual:
  bond pdb=" N   PHE F 140 "
       pdb=" CA  PHE F 140 "
    ideal  model  delta    sigma   weight residual
    1.468  1.451  0.018 1.24e-02 6.50e+03 2.00e+00
  bond pdb=" CG1 ILE B  68 "
       pdb=" CD1 ILE B  68 "
    ideal  model  delta    sigma   weight residual
    1.513  1.461  0.052 3.90e-02 6.57e+02 1.76e+00
  bond pdb=" C   GLU I  46 "
       pdb=" O   GLU I  46 "
    ideal  model  delta    sigma   weight residual
    1.234  1.245 -0.011 8.30e-03 1.45e+04 1.72e+00
  bond pdb=" N   GLU J  46 "
       pdb=" CA  GLU J  46 "
    ideal  model  delta    sigma   weight residual
    1.468  1.452  0.016 1.24e-02 6.50e+03 1.71e+00
  bond pdb=" CB  TRP C 232 "
       pdb=" CG  TRP C 232 "
    ideal  model  delta    sigma   weight residual
    1.498  1.458  0.040 3.10e-02 1.04e+03 1.64e+00
  ... (remaining 12815 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.93: 17198
        2.93 -     5.85: 258
        5.85 -     8.78: 18
        8.78 -    11.70: 1
       11.70 -    14.63: 1
  Bond angle restraints: 17476
  Sorted by residual:
  angle pdb=" C   THR J  42 "
        pdb=" N   GLN J  43 "
        pdb=" CA  GLN J  43 "
      ideal   model   delta    sigma   weight residual
     120.38  126.95   -6.57 1.46e+00 4.69e-01 2.02e+01
  angle pdb=" CA  LEU F 150 "
        pdb=" CB  LEU F 150 "
        pdb=" CG  LEU F 150 "
      ideal   model   delta    sigma   weight residual
     116.30  101.67   14.63 3.50e+00 8.16e-02 1.75e+01
  angle pdb=" C   ILE F 159 "
        pdb=" N   GLY F 160 "
        pdb=" CA  GLY F 160 "
      ideal   model   delta    sigma   weight residual
     121.41  113.52    7.89 1.96e+00 2.60e-01 1.62e+01
  angle pdb=" N   PHE B  64 "
        pdb=" CA  PHE B  64 "
        pdb=" CB  PHE B  64 "
      ideal   model   delta    sigma   weight residual
     114.27  107.74    6.53 1.64e+00 3.72e-01 1.58e+01
  angle pdb=" N   PHE D  64 "
        pdb=" CA  PHE D  64 "
        pdb=" CB  PHE D  64 "
      ideal   model   delta    sigma   weight residual
     114.17  110.02    4.15 1.14e+00 7.69e-01 1.33e+01
  ... (remaining 17471 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.38: 6847
       17.38 -    34.75: 745
       34.75 -    52.13: 114
       52.13 -    69.50: 16
       69.50 -    86.88: 9
  Dihedral angle restraints: 7731
    sinusoidal: 2988
      harmonic: 4743
  Sorted by residual:
  dihedral pdb=" CA  ALA I  41 "
           pdb=" C   ALA I  41 "
           pdb=" N   THR I  42 "
           pdb=" CA  THR I  42 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -140.71  -39.29     0      5.00e+00 4.00e-02 6.17e+01
  dihedral pdb=" CA  ALA G  41 "
           pdb=" C   ALA G  41 "
           pdb=" N   THR G  42 "
           pdb=" CA  THR G  42 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -141.80  -38.20     0      5.00e+00 4.00e-02 5.84e+01
  dihedral pdb=" CA  LEU F 211 "
           pdb=" C   LEU F 211 "
           pdb=" N   SER F 212 "
           pdb=" CA  SER F 212 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  142.14   37.86     0      5.00e+00 4.00e-02 5.73e+01
  ... (remaining 7728 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.035: 1309
       0.035 -    0.070: 610
       0.070 -    0.105: 222
       0.105 -    0.140: 39
       0.140 -    0.175: 9
  Chirality restraints: 2189
  Sorted by residual:
  chirality pdb=" CA  PRO G  67 "
            pdb=" N   PRO G  67 "
            pdb=" C   PRO G  67 "
            pdb=" CB  PRO G  67 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.72    2.54    0.18 2.00e-01 2.50e+01 7.66e-01
  chirality pdb=" CG  LEU D 223 "
            pdb=" CB  LEU D 223 "
            pdb=" CD1 LEU D 223 "
            pdb=" CD2 LEU D 223 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.59   -2.76    0.17 2.00e-01 2.50e+01 7.12e-01
  chirality pdb=" CA  PRO E  81 "
            pdb=" N   PRO E  81 "
            pdb=" C   PRO E  81 "
            pdb=" CB  PRO E  81 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.72    2.55    0.17 2.00e-01 2.50e+01 7.00e-01
  ... (remaining 2186 not shown)

  Planarity restraints: 2130
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   PRO C  84 "    0.051 5.00e-02 4.00e+02   7.82e-02 9.79e+00
        pdb=" N   PRO C  85 "   -0.135 5.00e-02 4.00e+02
        pdb=" CA  PRO C  85 "    0.041 5.00e-02 4.00e+02
        pdb=" CD  PRO C  85 "    0.043 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   PRO D 213 "    0.047 5.00e-02 4.00e+02   7.13e-02 8.13e+00
        pdb=" N   PRO D 214 "   -0.123 5.00e-02 4.00e+02
        pdb=" CA  PRO D 214 "    0.037 5.00e-02 4.00e+02
        pdb=" CD  PRO D 214 "    0.039 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   PRO D  84 "    0.046 5.00e-02 4.00e+02   7.04e-02 7.93e+00
        pdb=" N   PRO D  85 "   -0.122 5.00e-02 4.00e+02
        pdb=" CA  PRO D  85 "    0.037 5.00e-02 4.00e+02
        pdb=" CD  PRO D  85 "    0.039 5.00e-02 4.00e+02
  ... (remaining 2127 not shown)

  Histogram of nonbonded interaction distances:
        2.19 -     2.73: 1146
        2.73 -     3.27: 13976
        3.27 -     3.82: 19782
        3.82 -     4.36: 23427
        4.36 -     4.90: 39753
  Nonbonded interactions: 98084
  Sorted by model distance:
  nonbonded pdb=" OE1 GLU G  46 "
            pdb=" OG  SER H  50 "
     model   vdw
     2.191 3.040
  nonbonded pdb=" O   ALA D 131 "
            pdb=" N   ARG D 135 "
     model   vdw
     2.195 3.120
  nonbonded pdb=" OG1 THR D  65 "
            pdb=" OE1 GLU D 178 "
     model   vdw
     2.199 3.040
  nonbonded pdb=" O   ALA F  83 "
            pdb=" OG1 THR F  87 "
     model   vdw
     2.201 3.040
  nonbonded pdb=" O   MET C 138 "
            pdb=" OG1 THR C 142 "
     model   vdw
     2.203 3.040
  ... (remaining 98079 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 'B'
  selection = chain 'C'
  selection = chain 'D'
  selection = chain 'E'
}
ncs_group {
  reference = chain 'G'
  selection = chain 'H'
  selection = chain 'I'
  selection = chain 'J'
}

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=1.00 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:             2.200
  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:             0.000
  Extract box with map and model:          0.170
  Check model and map are aligned:         0.040
  Set scattering table:                    0.030
  Process input model:                     11.370
  Find NCS groups from input model:        0.160
  Set up NCS constraints:                  0.030
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.360
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   15.360
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7844
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      :  0.005   0.052  12820  Z= 0.232
  Angle     :  0.896  14.628  17476  Z= 0.506
  Chirality :  0.045   0.175   2189
  Planarity :  0.007   0.078   2130
  Dihedral  : 14.420  86.876   4637
  Min Nonbonded Distance : 2.191

Molprobity Statistics.
  All-atom Clashscore : 13.18
  Ramachandran Plot:
    Outliers :  0.37 %
    Allowed  :  9.82 %
    Favored  : 89.81 %
  Rotamer:
    Outliers :  0.15 %
    Allowed  :  5.38 %
    Favored  : 94.48 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.07 %
    Twisted Proline : 0.00 %
    Twisted General : 0.33 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -3.99 (0.18), residues: 1609
  helix: -1.98 (0.12), residues: 1203
  sheet:  None (None), residues: 0
  loop : -4.27 (0.27), residues: 406

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG B  66 
 TYR   0.013   0.001   TYR A 113 
 PHE   0.030   0.002   PHE B  64 
 TRP   0.015   0.002   TRP G  68 
 HIS   0.003   0.001   HIS F  14 

Details of bonding type rmsd
  covalent geometry    : bond        0.00539 (12820)
  covalent geometry    : angle       0.89633 (17476)
  hydrogen bonds       : bond        0.17116 (  788)
  hydrogen bonds       : angle       6.84625 ( 2349)

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

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

  3218 Ramachandran restraints generated.
    1609 Oldfield, 0 Emsley, 1609 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3218 Ramachandran restraints generated.
    1609 Oldfield, 0 Emsley, 1609 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  388 residues out of total 1376 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 386
  time to evaluate  : 0.458 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  224 MET cc_start: 0.7711 (ptm) cc_final: 0.7419 (ptt)
REVERT: B   47 PHE cc_start: 0.7840 (t80) cc_final: 0.7616 (t80)
REVERT: C   60 MET cc_start: 0.8002 (mmp) cc_final: 0.7786 (mmt)
  outliers start: 2
  outliers final: 0
  residues processed: 387
  average time/residue: 0.1110
  time to fit residues: 60.9234
Evaluate side-chains
  250 residues out of total 1376 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 250
  time to evaluate  : 0.398 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 157
   random chunks:
   chunk 98 optimal weight:    1.9990
   chunk 107 optimal weight:    1.9990
   chunk 10 optimal weight:    0.9980
   chunk 66 optimal weight:    5.9990
   chunk 130 optimal weight:   10.0000
   chunk 124 optimal weight:    6.9990
   chunk 103 optimal weight:    8.9990
   chunk 77 optimal weight:    1.9990
   chunk 122 optimal weight:    6.9990
   chunk 91 optimal weight:    0.0570
   chunk 149 optimal weight:    2.9990
   overall best weight:    1.4104

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

Flipped N/Q/H residues before XYZ refinement:
A 233 GLN
B 241 GLN
C  76 ASN
C 184 GLN
C 241 GLN
D  87 GLN
E  76 ASN
E 155 ASN
F 105 GLN
F 121 ASN
F 143 HIS
F 165 ASN
** I  39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
I  45 ASN
J  39 GLN

Total number of N/Q/H flips: 14

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3562 r_free = 0.3562 target = 0.075097 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3234 r_free = 0.3234 target = 0.059622 restraints weight = 47732.257|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3280 r_free = 0.3280 target = 0.061580 restraints weight = 26750.832|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3309 r_free = 0.3309 target = 0.062882 restraints weight = 18211.000|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 32)----------------|
| r_work = 0.3328 r_free = 0.3328 target = 0.063736 restraints weight = 14100.900|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3337 r_free = 0.3337 target = 0.064238 restraints weight = 11905.517|
|-----------------------------------------------------------------------------|
r_work (final): 0.3327
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8370
moved from start:          0.2749

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.042  12820  Z= 0.170
  Angle     :  0.815  11.178  17476  Z= 0.400
  Chirality :  0.045   0.176   2189
  Planarity :  0.007   0.076   2130
  Dihedral  :  6.160  42.825   1695
  Min Nonbonded Distance : 2.337

Molprobity Statistics.
  All-atom Clashscore : 12.80
  Ramachandran Plot:
    Outliers :  0.12 %
    Allowed  :  8.27 %
    Favored  : 91.61 %
  Rotamer:
    Outliers :  1.96 %
    Allowed  : 15.12 %
    Favored  : 82.92 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.07 %
    Twisted Proline : 0.00 %
    Twisted General : 0.27 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.88 (0.21), residues: 1609
  helix: -0.50 (0.14), residues: 1243
  sheet:  None (None), residues: 0
  loop : -3.59 (0.30), residues: 366

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG E 152 
 TYR   0.016   0.002   TYR E 174 
 PHE   0.039   0.002   PHE B  64 
 TRP   0.012   0.002   TRP C 232 
 HIS   0.006   0.001   HIS F  14 

Details of bonding type rmsd
  covalent geometry    : bond        0.00380 (12820)
  covalent geometry    : angle       0.81471 (17476)
  hydrogen bonds       : bond        0.04799 (  788)
  hydrogen bonds       : angle       4.77508 ( 2349)

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

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

  3218 Ramachandran restraints generated.
    1609 Oldfield, 0 Emsley, 1609 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3218 Ramachandran restraints generated.
    1609 Oldfield, 0 Emsley, 1609 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  316 residues out of total 1376 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 289
  time to evaluate  : 0.449 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   62 THR cc_start: 0.7620 (OUTLIER) cc_final: 0.7139 (t)
REVERT: A   87 GLN cc_start: 0.7367 (mm-40) cc_final: 0.6990 (mm-40)
REVERT: A  129 LYS cc_start: 0.8995 (OUTLIER) cc_final: 0.8421 (tttm)
REVERT: A  180 LYS cc_start: 0.8345 (mttp) cc_final: 0.8133 (mttp)
REVERT: B  129 LYS cc_start: 0.8933 (mmtm) cc_final: 0.8704 (mmtm)
REVERT: B  174 TYR cc_start: 0.8403 (t80) cc_final: 0.7752 (t80)
REVERT: B  178 GLU cc_start: 0.8251 (mt-10) cc_final: 0.7713 (mt-10)
REVERT: C  123 MET cc_start: 0.7586 (tmm) cc_final: 0.7266 (tmm)
REVERT: D   60 MET cc_start: 0.8604 (mmm) cc_final: 0.8331 (mmm)
REVERT: D   73 LEU cc_start: 0.9212 (mp) cc_final: 0.8917 (mp)
REVERT: D   76 ASN cc_start: 0.8758 (m-40) cc_final: 0.8544 (m110)
REVERT: D  101 MET cc_start: 0.9042 (tpp) cc_final: 0.8773 (tpp)
REVERT: D  123 MET cc_start: 0.8299 (mpp) cc_final: 0.6893 (ptm)
REVERT: D  210 MET cc_start: 0.7793 (tpt) cc_final: 0.7565 (tpt)
REVERT: E  123 MET cc_start: 0.8306 (mtp) cc_final: 0.7908 (mtp)
REVERT: E  160 GLN cc_start: 0.8681 (pm20) cc_final: 0.8046 (pp30)
REVERT: F  210 GLN cc_start: 0.8071 (OUTLIER) cc_final: 0.7557 (pt0)
REVERT: F  229 MET cc_start: 0.9055 (tpp) cc_final: 0.8824 (tpp)
REVERT: I   45 ASN cc_start: 0.6741 (OUTLIER) cc_final: 0.5828 (t0)
REVERT: J    7 MET cc_start: 0.8913 (tpp) cc_final: 0.8472 (tpp)
REVERT: J   14 MET cc_start: 0.7409 (mmt) cc_final: 0.6809 (ttm)
  outliers start: 27
  outliers final: 6
  residues processed: 301
  average time/residue: 0.1072
  time to fit residues: 46.5149
Evaluate side-chains
  249 residues out of total 1376 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 239
  time to evaluate  : 0.459 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   62 THR
Chi-restraints excluded: chain A residue   66 ARG
Chi-restraints excluded: chain A residue  129 LYS
Chi-restraints excluded: chain C residue   76 ASN
Chi-restraints excluded: chain F residue   95 VAL
Chi-restraints excluded: chain F residue  210 GLN
Chi-restraints excluded: chain G residue    9 MET
Chi-restraints excluded: chain I residue   45 ASN
Chi-restraints excluded: chain J residue   52 ILE
Chi-restraints excluded: chain J residue   84 LEU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 157
   random chunks:
   chunk 16 optimal weight:    0.9990
   chunk 130 optimal weight:    0.4980
   chunk 19 optimal weight:    3.9990
   chunk 78 optimal weight:    0.9980
   chunk 9 optimal weight:    0.9990
   chunk 99 optimal weight:    7.9990
   chunk 7 optimal weight:    7.9990
   chunk 147 optimal weight:    0.9990
   chunk 101 optimal weight:    7.9990
   chunk 105 optimal weight:    0.0670
   chunk 25 optimal weight:    7.9990
   overall best weight:    0.7122

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

Flipped N/Q/H residues before XYZ refinement:
C  76 ASN
** E 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** I  39 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 = 0.3599 r_free = 0.3599 target = 0.077076 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3296 r_free = 0.3296 target = 0.061791 restraints weight = 47949.047|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3340 r_free = 0.3340 target = 0.063806 restraints weight = 26461.121|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.3369 r_free = 0.3369 target = 0.065145 restraints weight = 17745.109|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3382 r_free = 0.3382 target = 0.065927 restraints weight = 13634.524|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.3394 r_free = 0.3394 target = 0.066534 restraints weight = 11610.521|
|-----------------------------------------------------------------------------|
r_work (final): 0.3377
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8329
moved from start:          0.3466

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.105  12820  Z= 0.156
  Angle     :  0.797  12.499  17476  Z= 0.383
  Chirality :  0.045   0.335   2189
  Planarity :  0.006   0.068   2130
  Dihedral  :  5.858  42.969   1695
  Min Nonbonded Distance : 2.487

Molprobity Statistics.
  All-atom Clashscore : 11.79
  Ramachandran Plot:
    Outliers :  0.12 %
    Allowed  :  7.33 %
    Favored  : 92.54 %
  Rotamer:
    Outliers :  2.47 %
    Allowed  : 16.86 %
    Favored  : 80.67 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.07 %
    Twisted Proline : 0.00 %
    Twisted General : 0.33 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.17 (0.21), residues: 1609
  helix:  0.09 (0.15), residues: 1238
  sheet:  None (None), residues: 0
  loop : -3.61 (0.29), residues: 371

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG E 152 
 TYR   0.022   0.002   TYR I  76 
 PHE   0.034   0.001   PHE B  64 
 TRP   0.014   0.001   TRP D 232 
 HIS   0.006   0.001   HIS F 143 

Details of bonding type rmsd
  covalent geometry    : bond        0.00339 (12820)
  covalent geometry    : angle       0.79699 (17476)
  hydrogen bonds       : bond        0.03949 (  788)
  hydrogen bonds       : angle       4.30646 ( 2349)

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

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

  3218 Ramachandran restraints generated.
    1609 Oldfield, 0 Emsley, 1609 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3218 Ramachandran restraints generated.
    1609 Oldfield, 0 Emsley, 1609 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  316 residues out of total 1376 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 282
  time to evaluate  : 0.457 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   62 THR cc_start: 0.7683 (OUTLIER) cc_final: 0.7274 (t)
REVERT: A   66 ARG cc_start: 0.8534 (OUTLIER) cc_final: 0.7403 (ptp-170)
REVERT: A   87 GLN cc_start: 0.7271 (mm-40) cc_final: 0.6895 (mm-40)
REVERT: A  128 ASP cc_start: 0.8718 (m-30) cc_final: 0.8454 (m-30)
REVERT: B  129 LYS cc_start: 0.8983 (mmtm) cc_final: 0.8694 (mmtm)
REVERT: B  152 ARG cc_start: 0.9079 (tmm-80) cc_final: 0.8766 (tmm-80)
REVERT: B  174 TYR cc_start: 0.8317 (t80) cc_final: 0.7872 (t80)
REVERT: B  178 GLU cc_start: 0.8301 (mt-10) cc_final: 0.7637 (mt-10)
REVERT: B  205 MET cc_start: 0.8195 (ttp) cc_final: 0.7785 (mtm)
REVERT: B  211 MET cc_start: 0.8574 (mmm) cc_final: 0.7593 (mmm)
REVERT: C   95 PHE cc_start: 0.9032 (m-10) cc_final: 0.8743 (m-80)
REVERT: C  123 MET cc_start: 0.7481 (tmm) cc_final: 0.7153 (tmm)
REVERT: C  205 MET cc_start: 0.8973 (mmm) cc_final: 0.8630 (tpp)
REVERT: C  210 MET cc_start: 0.8421 (ptp) cc_final: 0.7975 (pmm)
REVERT: D   73 LEU cc_start: 0.9274 (mp) cc_final: 0.9066 (mp)
REVERT: D  129 LYS cc_start: 0.8677 (mptt) cc_final: 0.8350 (pttt)
REVERT: E  123 MET cc_start: 0.8222 (mtp) cc_final: 0.7897 (mtp)
REVERT: E  160 GLN cc_start: 0.8748 (pm20) cc_final: 0.8088 (pp30)
REVERT: F   52 LEU cc_start: 0.8716 (OUTLIER) cc_final: 0.8437 (mm)
REVERT: F  210 GLN cc_start: 0.7948 (OUTLIER) cc_final: 0.7721 (pt0)
REVERT: H    1 MET cc_start: 0.6671 (mmt) cc_final: 0.6108 (mmm)
REVERT: I   45 ASN cc_start: 0.7188 (p0) cc_final: 0.6162 (t0)
REVERT: J    7 MET cc_start: 0.8824 (tpp) cc_final: 0.8254 (tpp)
REVERT: J   11 THR cc_start: 0.9271 (p) cc_final: 0.9062 (p)
REVERT: J   14 MET cc_start: 0.7140 (mmt) cc_final: 0.6750 (ttm)
REVERT: J   26 LEU cc_start: 0.9459 (OUTLIER) cc_final: 0.9230 (mm)
  outliers start: 34
  outliers final: 8
  residues processed: 308
  average time/residue: 0.0991
  time to fit residues: 45.3616
Evaluate side-chains
  259 residues out of total 1376 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 246
  time to evaluate  : 0.370 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   62 THR
Chi-restraints excluded: chain A residue   66 ARG
Chi-restraints excluded: chain A residue  233 GLN
Chi-restraints excluded: chain C residue   76 ASN
Chi-restraints excluded: chain D residue   90 LEU
Chi-restraints excluded: chain E residue  200 ILE
Chi-restraints excluded: chain E residue  210 MET
Chi-restraints excluded: chain E residue  235 LEU
Chi-restraints excluded: chain F residue   52 LEU
Chi-restraints excluded: chain F residue   95 VAL
Chi-restraints excluded: chain F residue  210 GLN
Chi-restraints excluded: chain F residue  250 LEU
Chi-restraints excluded: chain J residue   26 LEU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 157
   random chunks:
   chunk 43 optimal weight:    6.9990
   chunk 109 optimal weight:    0.1980
   chunk 59 optimal weight:    4.9990
   chunk 102 optimal weight:    5.9990
   chunk 89 optimal weight:    0.9980
   chunk 71 optimal weight:    1.9990
   chunk 104 optimal weight:    0.8980
   chunk 143 optimal weight:    0.3980
   chunk 96 optimal weight:    2.9990
   chunk 147 optimal weight:    0.6980
   chunk 150 optimal weight:    0.0870
   overall best weight:    0.4558

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

Flipped N/Q/H residues before XYZ refinement:
C  76 ASN
D  76 ASN
** E 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
F 121 ASN
** I  39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
I  45 ASN
J  83 ASN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3621 r_free = 0.3621 target = 0.078014 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3323 r_free = 0.3323 target = 0.062750 restraints weight = 47971.853|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3366 r_free = 0.3366 target = 0.064761 restraints weight = 26370.919|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3395 r_free = 0.3395 target = 0.066116 restraints weight = 17725.612|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.3409 r_free = 0.3409 target = 0.066924 restraints weight = 13581.067|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 34)----------------|
| r_work = 0.3424 r_free = 0.3424 target = 0.067518 restraints weight = 11510.483|
|-----------------------------------------------------------------------------|
r_work (final): 0.3405
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8305
moved from start:          0.3905

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.068  12820  Z= 0.140
  Angle     :  0.782  12.266  17476  Z= 0.373
  Chirality :  0.044   0.194   2189
  Planarity :  0.006   0.064   2130
  Dihedral  :  5.668  43.103   1695
  Min Nonbonded Distance : 2.469

Molprobity Statistics.
  All-atom Clashscore : 10.83
  Ramachandran Plot:
    Outliers :  0.06 %
    Allowed  :  7.46 %
    Favored  : 92.48 %
  Rotamer:
    Outliers :  2.47 %
    Allowed  : 18.90 %
    Favored  : 78.63 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.07 %
    Twisted Proline : 0.00 %
    Twisted General : 0.27 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.73 (0.21), residues: 1609
  helix:  0.41 (0.15), residues: 1240
  sheet:  None (None), residues: 0
  loop : -3.51 (0.28), residues: 369

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG C 152 
 TYR   0.024   0.002   TYR J  76 
 PHE   0.030   0.001   PHE B  64 
 TRP   0.009   0.001   TRP F  72 
 HIS   0.004   0.001   HIS F  14 

Details of bonding type rmsd
  covalent geometry    : bond        0.00299 (12820)
  covalent geometry    : angle       0.78220 (17476)
  hydrogen bonds       : bond        0.03636 (  788)
  hydrogen bonds       : angle       4.13645 ( 2349)

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

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

  3218 Ramachandran restraints generated.
    1609 Oldfield, 0 Emsley, 1609 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3218 Ramachandran restraints generated.
    1609 Oldfield, 0 Emsley, 1609 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  312 residues out of total 1376 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 278
  time to evaluate  : 0.440 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   62 THR cc_start: 0.7569 (OUTLIER) cc_final: 0.7219 (t)
REVERT: A   66 ARG cc_start: 0.8521 (OUTLIER) cc_final: 0.7510 (ptp-170)
REVERT: A   87 GLN cc_start: 0.7250 (mm-40) cc_final: 0.6885 (mm-40)
REVERT: A  180 LYS cc_start: 0.8409 (mttp) cc_final: 0.7890 (ptmm)
REVERT: B  129 LYS cc_start: 0.8886 (mmtm) cc_final: 0.8584 (mmtm)
REVERT: B  152 ARG cc_start: 0.9092 (tmm-80) cc_final: 0.8759 (tmm-80)
REVERT: B  174 TYR cc_start: 0.8293 (t80) cc_final: 0.7530 (t80)
REVERT: B  178 GLU cc_start: 0.8221 (mt-10) cc_final: 0.7122 (mt-10)
REVERT: B  205 MET cc_start: 0.8415 (OUTLIER) cc_final: 0.7918 (mtm)
REVERT: C   95 PHE cc_start: 0.9036 (m-10) cc_final: 0.8737 (m-80)
REVERT: C  123 MET cc_start: 0.7364 (tmm) cc_final: 0.6655 (tmm)
REVERT: C  194 LEU cc_start: 0.9420 (mt) cc_final: 0.9125 (tp)
REVERT: D  101 MET cc_start: 0.9023 (tpp) cc_final: 0.8584 (tpp)
REVERT: D  125 GLU cc_start: 0.8802 (tp30) cc_final: 0.8387 (tp30)
REVERT: D  210 MET cc_start: 0.8307 (tpp) cc_final: 0.8068 (tpp)
REVERT: D  211 MET cc_start: 0.8410 (tpp) cc_final: 0.8017 (mpp)
REVERT: E   66 ARG cc_start: 0.8181 (ttt180) cc_final: 0.7730 (ttm170)
REVERT: E  160 GLN cc_start: 0.8704 (pm20) cc_final: 0.7973 (pp30)
REVERT: E  209 MET cc_start: 0.8056 (mpp) cc_final: 0.7795 (mpp)
REVERT: F   52 LEU cc_start: 0.8704 (OUTLIER) cc_final: 0.8381 (mm)
REVERT: F  127 ARG cc_start: 0.7915 (mtp85) cc_final: 0.7643 (mtp180)
REVERT: F  229 MET cc_start: 0.9072 (tpp) cc_final: 0.8839 (tpp)
REVERT: I   45 ASN cc_start: 0.6850 (OUTLIER) cc_final: 0.5882 (t0)
REVERT: J    7 MET cc_start: 0.8790 (tpp) cc_final: 0.8276 (tpp)
REVERT: J   14 MET cc_start: 0.7103 (mmt) cc_final: 0.6847 (ttm)
REVERT: J   26 LEU cc_start: 0.9462 (OUTLIER) cc_final: 0.9219 (mm)
  outliers start: 34
  outliers final: 9
  residues processed: 301
  average time/residue: 0.1022
  time to fit residues: 45.1774
Evaluate side-chains
  260 residues out of total 1376 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 245
  time to evaluate  : 0.498 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   62 THR
Chi-restraints excluded: chain A residue   66 ARG
Chi-restraints excluded: chain A residue  233 GLN
Chi-restraints excluded: chain B residue  205 MET
Chi-restraints excluded: chain C residue   78 LEU
Chi-restraints excluded: chain E residue  219 LEU
Chi-restraints excluded: chain E residue  235 LEU
Chi-restraints excluded: chain F residue   52 LEU
Chi-restraints excluded: chain F residue   95 VAL
Chi-restraints excluded: chain F residue  106 MET
Chi-restraints excluded: chain F residue  250 LEU
Chi-restraints excluded: chain H residue   56 VAL
Chi-restraints excluded: chain I residue   45 ASN
Chi-restraints excluded: chain J residue   26 LEU
Chi-restraints excluded: chain J residue   52 ILE
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 157
   random chunks:
   chunk 12 optimal weight:    6.9990
   chunk 65 optimal weight:    0.9990
   chunk 60 optimal weight:    0.7980
   chunk 47 optimal weight:    0.9980
   chunk 3 optimal weight:    5.9990
   chunk 1 optimal weight:   10.0000
   chunk 152 optimal weight:    7.9990
   chunk 16 optimal weight:    5.9990
   chunk 56 optimal weight:    7.9990
   chunk 133 optimal weight:    0.7980
   chunk 89 optimal weight:    0.3980
   overall best weight:    0.7982

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

Flipped N/Q/H residues before XYZ refinement:
F 143 HIS
** I  39 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 = 0.3626 r_free = 0.3626 target = 0.078118 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3328 r_free = 0.3328 target = 0.062959 restraints weight = 48135.957|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3370 r_free = 0.3370 target = 0.064913 restraints weight = 26445.012|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3398 r_free = 0.3398 target = 0.066219 restraints weight = 17784.832|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 32)----------------|
| r_work = 0.3412 r_free = 0.3412 target = 0.067037 restraints weight = 13693.169|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 31)----------------|
| r_work = 0.3425 r_free = 0.3425 target = 0.067666 restraints weight = 11609.085|
|-----------------------------------------------------------------------------|
r_work (final): 0.3405
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8304
moved from start:          0.4232

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042  12820  Z= 0.141
  Angle     :  0.779  11.163  17476  Z= 0.371
  Chirality :  0.044   0.232   2189
  Planarity :  0.006   0.063   2130
  Dihedral  :  5.536  43.590   1695
  Min Nonbonded Distance : 2.430

Molprobity Statistics.
  All-atom Clashscore : 11.37
  Ramachandran Plot:
    Outliers :  0.06 %
    Allowed  :  7.46 %
    Favored  : 92.48 %
  Rotamer:
    Outliers :  2.54 %
    Allowed  : 19.84 %
    Favored  : 77.62 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.07 %
    Twisted Proline : 0.00 %
    Twisted General : 0.27 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.41 (0.22), residues: 1609
  helix:  0.60 (0.15), residues: 1241
  sheet:  None (None), residues: 0
  loop : -3.27 (0.30), residues: 368

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG F  96 
 TYR   0.021   0.002   TYR A 174 
 PHE   0.028   0.001   PHE B  64 
 TRP   0.010   0.001   TRP I  68 
 HIS   0.004   0.001   HIS F  14 

Details of bonding type rmsd
  covalent geometry    : bond        0.00307 (12820)
  covalent geometry    : angle       0.77859 (17476)
  hydrogen bonds       : bond        0.03567 (  788)
  hydrogen bonds       : angle       4.06266 ( 2349)

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

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

  3218 Ramachandran restraints generated.
    1609 Oldfield, 0 Emsley, 1609 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3218 Ramachandran restraints generated.
    1609 Oldfield, 0 Emsley, 1609 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  289 residues out of total 1376 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 254
  time to evaluate  : 0.423 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   66 ARG cc_start: 0.8559 (OUTLIER) cc_final: 0.7384 (ptp-170)
REVERT: A   87 GLN cc_start: 0.7194 (mm-40) cc_final: 0.6855 (mm-40)
REVERT: A  180 LYS cc_start: 0.8299 (mttp) cc_final: 0.7978 (ptmm)
REVERT: B  138 MET cc_start: 0.9028 (OUTLIER) cc_final: 0.8809 (mmt)
REVERT: B  152 ARG cc_start: 0.9144 (tmm-80) cc_final: 0.8826 (tmm-80)
REVERT: C   95 PHE cc_start: 0.9050 (m-10) cc_final: 0.8764 (m-80)
REVERT: C  123 MET cc_start: 0.7332 (tmm) cc_final: 0.6669 (tmm)
REVERT: C  194 LEU cc_start: 0.9403 (mt) cc_final: 0.9123 (tp)
REVERT: C  210 MET cc_start: 0.8401 (pmm) cc_final: 0.7823 (pmm)
REVERT: D  101 MET cc_start: 0.9082 (tpp) cc_final: 0.8652 (tpp)
REVERT: D  209 MET cc_start: 0.7894 (mmp) cc_final: 0.7152 (mmt)
REVERT: D  210 MET cc_start: 0.8240 (tpp) cc_final: 0.8002 (tpp)
REVERT: E   66 ARG cc_start: 0.8091 (ttt180) cc_final: 0.7673 (ttm170)
REVERT: E  160 GLN cc_start: 0.8713 (pm20) cc_final: 0.8307 (pp30)
REVERT: F   52 LEU cc_start: 0.8715 (OUTLIER) cc_final: 0.8460 (mm)
REVERT: F  210 GLN cc_start: 0.8140 (OUTLIER) cc_final: 0.7861 (pt0)
REVERT: F  220 LEU cc_start: 0.8724 (OUTLIER) cc_final: 0.8517 (tt)
REVERT: F  258 MET cc_start: 0.7939 (tpp) cc_final: 0.7696 (ptt)
REVERT: J    7 MET cc_start: 0.8736 (tpp) cc_final: 0.8216 (tpp)
REVERT: J   14 MET cc_start: 0.7041 (mmt) cc_final: 0.6770 (ttm)
REVERT: J   26 LEU cc_start: 0.9467 (OUTLIER) cc_final: 0.9198 (mm)
REVERT: J   54 LYS cc_start: 0.9089 (mttt) cc_final: 0.8800 (mtmm)
  outliers start: 35
  outliers final: 11
  residues processed: 278
  average time/residue: 0.1013
  time to fit residues: 41.5976
Evaluate side-chains
  256 residues out of total 1376 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 239
  time to evaluate  : 0.525 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   66 ARG
Chi-restraints excluded: chain A residue  211 MET
Chi-restraints excluded: chain A residue  233 GLN
Chi-restraints excluded: chain B residue   80 THR
Chi-restraints excluded: chain B residue  138 MET
Chi-restraints excluded: chain C residue  219 LEU
Chi-restraints excluded: chain E residue  219 LEU
Chi-restraints excluded: chain E residue  235 LEU
Chi-restraints excluded: chain F residue   52 LEU
Chi-restraints excluded: chain F residue   95 VAL
Chi-restraints excluded: chain F residue  106 MET
Chi-restraints excluded: chain F residue  210 GLN
Chi-restraints excluded: chain F residue  220 LEU
Chi-restraints excluded: chain H residue   56 VAL
Chi-restraints excluded: chain I residue   25 LEU
Chi-restraints excluded: chain J residue   26 LEU
Chi-restraints excluded: chain J residue   52 ILE
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 157
   random chunks:
   chunk 125 optimal weight:    3.9990
   chunk 44 optimal weight:    7.9990
   chunk 113 optimal weight:    1.9990
   chunk 58 optimal weight:    6.9990
   chunk 149 optimal weight:    0.1980
   chunk 133 optimal weight:    0.9980
   chunk 29 optimal weight:    0.0980
   chunk 2 optimal weight:    0.4980
   chunk 142 optimal weight:    0.9980
   chunk 28 optimal weight:    9.9990
   chunk 85 optimal weight:    1.9990
   overall best weight:    0.5580

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

Flipped N/Q/H residues before XYZ refinement:
D  76 ASN
** I  39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
I  83 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3643 r_free = 0.3643 target = 0.078821 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3349 r_free = 0.3349 target = 0.063760 restraints weight = 47635.780|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3394 r_free = 0.3394 target = 0.065775 restraints weight = 26196.987|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3422 r_free = 0.3422 target = 0.067108 restraints weight = 17603.235|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.3436 r_free = 0.3436 target = 0.067902 restraints weight = 13539.037|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.3453 r_free = 0.3453 target = 0.068522 restraints weight = 11456.558|
|-----------------------------------------------------------------------------|
r_work (final): 0.3427
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8283
moved from start:          0.4534

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034  12820  Z= 0.137
  Angle     :  0.799  11.761  17476  Z= 0.378
  Chirality :  0.044   0.252   2189
  Planarity :  0.006   0.071   2130
  Dihedral  :  5.425  42.474   1695
  Min Nonbonded Distance : 2.322

Molprobity Statistics.
  All-atom Clashscore : 11.10
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.58 %
    Favored  : 92.42 %
  Rotamer:
    Outliers :  2.40 %
    Allowed  : 20.71 %
    Favored  : 76.89 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.07 %
    Twisted Proline : 0.00 %
    Twisted General : 0.27 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.20 (0.22), residues: 1609
  helix:  0.76 (0.15), residues: 1245
  sheet:  None (None), residues: 0
  loop : -3.25 (0.29), residues: 364

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG F  96 
 TYR   0.020   0.002   TYR E 174 
 PHE   0.026   0.001   PHE B  64 
 TRP   0.014   0.001   TRP B 232 
 HIS   0.006   0.001   HIS F  14 

Details of bonding type rmsd
  covalent geometry    : bond        0.00294 (12820)
  covalent geometry    : angle       0.79889 (17476)
  hydrogen bonds       : bond        0.03425 (  788)
  hydrogen bonds       : angle       4.00738 ( 2349)

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

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

  3218 Ramachandran restraints generated.
    1609 Oldfield, 0 Emsley, 1609 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3218 Ramachandran restraints generated.
    1609 Oldfield, 0 Emsley, 1609 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  298 residues out of total 1376 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 265
  time to evaluate  : 0.529 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   66 ARG cc_start: 0.8685 (OUTLIER) cc_final: 0.7578 (ptp-170)
REVERT: A   87 GLN cc_start: 0.7099 (mm-40) cc_final: 0.6739 (mm-40)
REVERT: A  180 LYS cc_start: 0.8216 (mttp) cc_final: 0.8014 (ptmm)
REVERT: A  209 MET cc_start: 0.8537 (mmt) cc_final: 0.8312 (mmt)
REVERT: B  138 MET cc_start: 0.8947 (OUTLIER) cc_final: 0.8706 (mmt)
REVERT: B  152 ARG cc_start: 0.9161 (tmm-80) cc_final: 0.8852 (tmm-80)
REVERT: B  205 MET cc_start: 0.8541 (mtm) cc_final: 0.8193 (mtm)
REVERT: C   95 PHE cc_start: 0.9068 (m-10) cc_final: 0.8719 (m-80)
REVERT: C  101 MET cc_start: 0.8586 (mpp) cc_final: 0.8266 (mpp)
REVERT: C  123 MET cc_start: 0.7333 (tmm) cc_final: 0.6765 (tmm)
REVERT: C  194 LEU cc_start: 0.9395 (mt) cc_final: 0.9111 (tp)
REVERT: C  210 MET cc_start: 0.7908 (pmm) cc_final: 0.7182 (pmm)
REVERT: D  101 MET cc_start: 0.9043 (tpp) cc_final: 0.8703 (tpp)
REVERT: D  123 MET cc_start: 0.7835 (mpp) cc_final: 0.6344 (ttt)
REVERT: D  129 LYS cc_start: 0.8905 (mptt) cc_final: 0.8509 (pttt)
REVERT: E  160 GLN cc_start: 0.8716 (pm20) cc_final: 0.8339 (pp30)
REVERT: E  205 MET cc_start: 0.8726 (tpt) cc_final: 0.8485 (tpt)
REVERT: F   52 LEU cc_start: 0.8684 (OUTLIER) cc_final: 0.8475 (mm)
REVERT: F  258 MET cc_start: 0.7976 (tpp) cc_final: 0.7712 (ptp)
REVERT: J    7 MET cc_start: 0.8685 (tpp) cc_final: 0.8131 (tpp)
REVERT: J   14 MET cc_start: 0.6972 (mmt) cc_final: 0.6650 (ttm)
REVERT: J   26 LEU cc_start: 0.9447 (OUTLIER) cc_final: 0.9210 (mm)
  outliers start: 33
  outliers final: 15
  residues processed: 287
  average time/residue: 0.0952
  time to fit residues: 41.0118
Evaluate side-chains
  260 residues out of total 1376 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 241
  time to evaluate  : 0.457 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   66 ARG
Chi-restraints excluded: chain A residue  211 MET
Chi-restraints excluded: chain B residue   62 THR
Chi-restraints excluded: chain B residue   80 THR
Chi-restraints excluded: chain B residue  138 MET
Chi-restraints excluded: chain B residue  225 LEU
Chi-restraints excluded: chain C residue  219 LEU
Chi-restraints excluded: chain E residue  219 LEU
Chi-restraints excluded: chain E residue  235 LEU
Chi-restraints excluded: chain F residue   52 LEU
Chi-restraints excluded: chain F residue   95 VAL
Chi-restraints excluded: chain F residue  106 MET
Chi-restraints excluded: chain F residue  143 HIS
Chi-restraints excluded: chain F residue  157 LEU
Chi-restraints excluded: chain H residue   29 LEU
Chi-restraints excluded: chain H residue   56 VAL
Chi-restraints excluded: chain I residue   25 LEU
Chi-restraints excluded: chain J residue   26 LEU
Chi-restraints excluded: chain J residue   52 ILE
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 157
   random chunks:
   chunk 113 optimal weight:    1.9990
   chunk 145 optimal weight:    5.9990
   chunk 67 optimal weight:    7.9990
   chunk 17 optimal weight:    6.9990
   chunk 36 optimal weight:    8.9990
   chunk 18 optimal weight:    0.9980
   chunk 86 optimal weight:    1.9990
   chunk 38 optimal weight:    0.4980
   chunk 59 optimal weight:    0.9990
   chunk 139 optimal weight:    0.9980
   chunk 20 optimal weight:   10.0000
   overall best weight:    1.0984

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

Flipped N/Q/H residues before XYZ refinement:
C  76 ASN
E 119 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3634 r_free = 0.3634 target = 0.078360 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3335 r_free = 0.3335 target = 0.063162 restraints weight = 47846.381|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3379 r_free = 0.3379 target = 0.065152 restraints weight = 26410.042|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3408 r_free = 0.3408 target = 0.066501 restraints weight = 17728.198|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 33)----------------|
| r_work = 0.3427 r_free = 0.3427 target = 0.067371 restraints weight = 13604.079|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.3436 r_free = 0.3436 target = 0.067893 restraints weight = 11406.595|
|-----------------------------------------------------------------------------|
r_work (final): 0.3417
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8300
moved from start:          0.4686

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.071  12820  Z= 0.145
  Angle     :  0.821  16.124  17476  Z= 0.387
  Chirality :  0.044   0.196   2189
  Planarity :  0.006   0.070   2130
  Dihedral  :  5.318  42.165   1695
  Min Nonbonded Distance : 2.497

Molprobity Statistics.
  All-atom Clashscore : 11.99
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.33 %
    Favored  : 92.67 %
  Rotamer:
    Outliers :  2.11 %
    Allowed  : 22.02 %
    Favored  : 75.87 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.07 %
    Twisted Proline : 0.00 %
    Twisted General : 0.27 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.06 (0.22), residues: 1609
  helix:  0.83 (0.15), residues: 1249
  sheet:  None (None), residues: 0
  loop : -3.14 (0.30), residues: 360

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG F  96 
 TYR   0.036   0.002   TYR A 174 
 PHE   0.025   0.001   PHE B  64 
 TRP   0.018   0.001   TRP B 232 
 HIS   0.008   0.001   HIS F  14 

Details of bonding type rmsd
  covalent geometry    : bond        0.00330 (12820)
  covalent geometry    : angle       0.82138 (17476)
  hydrogen bonds       : bond        0.03491 (  788)
  hydrogen bonds       : angle       4.01878 ( 2349)

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

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

  3218 Ramachandran restraints generated.
    1609 Oldfield, 0 Emsley, 1609 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3218 Ramachandran restraints generated.
    1609 Oldfield, 0 Emsley, 1609 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  284 residues out of total 1376 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 255
  time to evaluate  : 0.546 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   66 ARG cc_start: 0.8724 (OUTLIER) cc_final: 0.7644 (ptp-170)
REVERT: A   87 GLN cc_start: 0.7155 (mm-40) cc_final: 0.6802 (mm-40)
REVERT: A  209 MET cc_start: 0.8691 (mmt) cc_final: 0.8360 (mmt)
REVERT: B  138 MET cc_start: 0.9006 (OUTLIER) cc_final: 0.8735 (mmt)
REVERT: B  152 ARG cc_start: 0.9190 (tmm-80) cc_final: 0.8884 (tmm-80)
REVERT: B  205 MET cc_start: 0.8616 (mtm) cc_final: 0.8187 (mtm)
REVERT: C   95 PHE cc_start: 0.9039 (m-10) cc_final: 0.8773 (m-80)
REVERT: C  101 MET cc_start: 0.8653 (mpp) cc_final: 0.8021 (mpp)
REVERT: C  123 MET cc_start: 0.7337 (tmm) cc_final: 0.6737 (tmm)
REVERT: C  194 LEU cc_start: 0.9390 (mt) cc_final: 0.9115 (tp)
REVERT: C  210 MET cc_start: 0.7401 (pmm) cc_final: 0.6746 (pmm)
REVERT: C  211 MET cc_start: 0.6605 (OUTLIER) cc_final: 0.6368 (ttm)
REVERT: D  101 MET cc_start: 0.9035 (tpp) cc_final: 0.8694 (tpp)
REVERT: D  123 MET cc_start: 0.7856 (mpp) cc_final: 0.6376 (ttt)
REVERT: D  129 LYS cc_start: 0.8910 (mptt) cc_final: 0.8539 (pttt)
REVERT: E  160 GLN cc_start: 0.8733 (pm20) cc_final: 0.8352 (pp30)
REVERT: F  258 MET cc_start: 0.8025 (tpp) cc_final: 0.7816 (ptt)
REVERT: I    7 MET cc_start: 0.8348 (tpp) cc_final: 0.8135 (tpt)
REVERT: I   59 PHE cc_start: 0.8120 (t80) cc_final: 0.6706 (t80)
REVERT: J    7 MET cc_start: 0.8680 (tpp) cc_final: 0.8186 (tpp)
REVERT: J   14 MET cc_start: 0.6881 (mmt) cc_final: 0.6629 (ttm)
REVERT: J   26 LEU cc_start: 0.9470 (OUTLIER) cc_final: 0.9219 (mm)
  outliers start: 29
  outliers final: 15
  residues processed: 274
  average time/residue: 0.0956
  time to fit residues: 39.6651
Evaluate side-chains
  264 residues out of total 1376 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 245
  time to evaluate  : 0.393 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   66 ARG
Chi-restraints excluded: chain A residue  211 MET
Chi-restraints excluded: chain A residue  233 GLN
Chi-restraints excluded: chain B residue   80 THR
Chi-restraints excluded: chain B residue  138 MET
Chi-restraints excluded: chain B residue  225 LEU
Chi-restraints excluded: chain C residue   88 VAL
Chi-restraints excluded: chain C residue  211 MET
Chi-restraints excluded: chain C residue  219 LEU
Chi-restraints excluded: chain E residue  235 LEU
Chi-restraints excluded: chain F residue   95 VAL
Chi-restraints excluded: chain F residue  106 MET
Chi-restraints excluded: chain F residue  157 LEU
Chi-restraints excluded: chain H residue   29 LEU
Chi-restraints excluded: chain H residue   56 VAL
Chi-restraints excluded: chain I residue   25 LEU
Chi-restraints excluded: chain J residue   25 LEU
Chi-restraints excluded: chain J residue   26 LEU
Chi-restraints excluded: chain J residue   52 ILE
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 157
   random chunks:
   chunk 55 optimal weight:    0.9980
   chunk 150 optimal weight:    0.9990
   chunk 0 optimal weight:   20.0000
   chunk 21 optimal weight:    0.0040
   chunk 128 optimal weight:    0.9990
   chunk 99 optimal weight:    6.9990
   chunk 126 optimal weight:    8.9990
   chunk 142 optimal weight:    1.9990
   chunk 113 optimal weight:    3.9990
   chunk 137 optimal weight:    0.4980
   chunk 78 optimal weight:    7.9990
   overall best weight:    0.6996

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

Flipped N/Q/H residues before XYZ refinement:
** C 184 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
E 119 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3649 r_free = 0.3649 target = 0.078943 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3357 r_free = 0.3357 target = 0.063856 restraints weight = 47396.610|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3400 r_free = 0.3400 target = 0.065830 restraints weight = 26078.908|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3428 r_free = 0.3428 target = 0.067183 restraints weight = 17518.752|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.3442 r_free = 0.3442 target = 0.067981 restraints weight = 13418.560|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 34)----------------|
| r_work = 0.3458 r_free = 0.3458 target = 0.068576 restraints weight = 11364.469|
|-----------------------------------------------------------------------------|
r_work (final): 0.3437
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8280
moved from start:          0.4887

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.049  12820  Z= 0.142
  Angle     :  0.841  14.814  17476  Z= 0.394
  Chirality :  0.045   0.203   2189
  Planarity :  0.006   0.071   2130
  Dihedral  :  5.259  41.605   1695
  Min Nonbonded Distance : 2.449

Molprobity Statistics.
  All-atom Clashscore : 12.10
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.27 %
    Favored  : 92.73 %
  Rotamer:
    Outliers :  2.25 %
    Allowed  : 22.24 %
    Favored  : 75.51 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.07 %
    Twisted Proline : 0.00 %
    Twisted General : 0.27 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.03 (0.22), residues: 1609
  helix:  0.90 (0.15), residues: 1249
  sheet:  None (None), residues: 0
  loop : -3.12 (0.31), residues: 360

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG C 135 
 TYR   0.022   0.002   TYR C 174 
 PHE   0.024   0.001   PHE B  64 
 TRP   0.018   0.001   TRP B 232 
 HIS   0.007   0.001   HIS F  14 

Details of bonding type rmsd
  covalent geometry    : bond        0.00312 (12820)
  covalent geometry    : angle       0.84081 (17476)
  hydrogen bonds       : bond        0.03415 (  788)
  hydrogen bonds       : angle       4.03554 ( 2349)

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

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

  3218 Ramachandran restraints generated.
    1609 Oldfield, 0 Emsley, 1609 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3218 Ramachandran restraints generated.
    1609 Oldfield, 0 Emsley, 1609 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  298 residues out of total 1376 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 267
  time to evaluate  : 0.497 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   66 ARG cc_start: 0.8755 (OUTLIER) cc_final: 0.7675 (ptp-170)
REVERT: A   87 GLN cc_start: 0.7201 (mm-40) cc_final: 0.6887 (mm-40)
REVERT: A  180 LYS cc_start: 0.8249 (mmtt) cc_final: 0.8007 (mmtt)
REVERT: A  209 MET cc_start: 0.8717 (mmt) cc_final: 0.8339 (mmt)
REVERT: B  138 MET cc_start: 0.8995 (OUTLIER) cc_final: 0.8757 (mmt)
REVERT: B  152 ARG cc_start: 0.9183 (tmm-80) cc_final: 0.8882 (tmm-80)
REVERT: B  205 MET cc_start: 0.8571 (mtm) cc_final: 0.8174 (mtm)
REVERT: C   95 PHE cc_start: 0.9060 (m-10) cc_final: 0.8664 (m-80)
REVERT: C  101 MET cc_start: 0.8703 (mpp) cc_final: 0.8158 (mpp)
REVERT: C  123 MET cc_start: 0.7295 (tmm) cc_final: 0.6705 (tmm)
REVERT: C  194 LEU cc_start: 0.9383 (mt) cc_final: 0.9104 (tp)
REVERT: C  210 MET cc_start: 0.7210 (pmm) cc_final: 0.6440 (pmm)
REVERT: C  211 MET cc_start: 0.6654 (ttm) cc_final: 0.6369 (ttm)
REVERT: D  101 MET cc_start: 0.9011 (tpp) cc_final: 0.8721 (tpp)
REVERT: D  123 MET cc_start: 0.7857 (mpp) cc_final: 0.6402 (ttt)
REVERT: D  129 LYS cc_start: 0.8826 (mptt) cc_final: 0.8535 (pttt)
REVERT: E   80 THR cc_start: 0.8457 (t) cc_final: 0.8251 (t)
REVERT: E  160 GLN cc_start: 0.8754 (pm20) cc_final: 0.8347 (pp30)
REVERT: I   59 PHE cc_start: 0.8019 (t80) cc_final: 0.6530 (t80)
REVERT: J    7 MET cc_start: 0.8611 (tpp) cc_final: 0.8159 (tpp)
REVERT: J   14 MET cc_start: 0.6864 (mmt) cc_final: 0.6613 (ttm)
REVERT: J   26 LEU cc_start: 0.9474 (OUTLIER) cc_final: 0.9193 (mm)
  outliers start: 31
  outliers final: 18
  residues processed: 288
  average time/residue: 0.0959
  time to fit residues: 41.9846
Evaluate side-chains
  278 residues out of total 1376 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 257
  time to evaluate  : 0.492 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   62 THR
Chi-restraints excluded: chain A residue   66 ARG
Chi-restraints excluded: chain A residue  211 MET
Chi-restraints excluded: chain A residue  233 GLN
Chi-restraints excluded: chain B residue   62 THR
Chi-restraints excluded: chain B residue   80 THR
Chi-restraints excluded: chain B residue  138 MET
Chi-restraints excluded: chain B residue  225 LEU
Chi-restraints excluded: chain C residue  219 LEU
Chi-restraints excluded: chain E residue  219 LEU
Chi-restraints excluded: chain E residue  235 LEU
Chi-restraints excluded: chain F residue   95 VAL
Chi-restraints excluded: chain F residue  106 MET
Chi-restraints excluded: chain F residue  157 LEU
Chi-restraints excluded: chain F residue  211 LEU
Chi-restraints excluded: chain H residue   29 LEU
Chi-restraints excluded: chain H residue   56 VAL
Chi-restraints excluded: chain I residue   25 LEU
Chi-restraints excluded: chain J residue   25 LEU
Chi-restraints excluded: chain J residue   26 LEU
Chi-restraints excluded: chain J residue   52 ILE
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 157
   random chunks:
   chunk 95 optimal weight:    0.7980
   chunk 107 optimal weight:    0.4980
   chunk 131 optimal weight:    2.9990
   chunk 33 optimal weight:    0.9980
   chunk 78 optimal weight:    6.9990
   chunk 98 optimal weight:    2.9990
   chunk 32 optimal weight:    0.7980
   chunk 112 optimal weight:    0.9990
   chunk 21 optimal weight:    0.0980
   chunk 102 optimal weight:    2.9990
   chunk 26 optimal weight:    0.7980
   overall best weight:    0.5980

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

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

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3656 r_free = 0.3656 target = 0.079551 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3364 r_free = 0.3364 target = 0.064434 restraints weight = 47514.451|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3407 r_free = 0.3407 target = 0.066403 restraints weight = 26219.947|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3436 r_free = 0.3436 target = 0.067771 restraints weight = 17583.173|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 35)----------------|
| r_work = 0.3455 r_free = 0.3455 target = 0.068667 restraints weight = 13439.872|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3464 r_free = 0.3464 target = 0.069167 restraints weight = 11199.436|
|-----------------------------------------------------------------------------|
r_work (final): 0.3446
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8266
moved from start:          0.5077

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.048  12820  Z= 0.147
  Angle     :  0.859  14.538  17476  Z= 0.405
  Chirality :  0.046   0.296   2189
  Planarity :  0.006   0.071   2130
  Dihedral  :  5.232  41.554   1695
  Min Nonbonded Distance : 2.473

Molprobity Statistics.
  All-atom Clashscore : 12.18
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.46 %
    Favored  : 92.54 %
  Rotamer:
    Outliers :  1.74 %
    Allowed  : 22.67 %
    Favored  : 75.58 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.07 %
    Twisted Proline : 0.00 %
    Twisted General : 0.27 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.02 (0.22), residues: 1609
  helix:  0.86 (0.15), residues: 1258
  sheet:  None (None), residues: 0
  loop : -3.25 (0.31), residues: 351

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG F  96 
 TYR   0.030   0.002   TYR A 174 
 PHE   0.033   0.001   PHE B  64 
 TRP   0.016   0.001   TRP B 232 
 HIS   0.005   0.001   HIS F  14 

Details of bonding type rmsd
  covalent geometry    : bond        0.00323 (12820)
  covalent geometry    : angle       0.85944 (17476)
  hydrogen bonds       : bond        0.03435 (  788)
  hydrogen bonds       : angle       4.07701 ( 2349)

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

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

  3218 Ramachandran restraints generated.
    1609 Oldfield, 0 Emsley, 1609 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3218 Ramachandran restraints generated.
    1609 Oldfield, 0 Emsley, 1609 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  287 residues out of total 1376 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 263
  time to evaluate  : 0.387 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   66 ARG cc_start: 0.8758 (OUTLIER) cc_final: 0.7747 (ptp-170)
REVERT: A   87 GLN cc_start: 0.7192 (mm-40) cc_final: 0.6862 (mm-40)
REVERT: A  209 MET cc_start: 0.8701 (mmt) cc_final: 0.8280 (mmt)
REVERT: B  138 MET cc_start: 0.8986 (OUTLIER) cc_final: 0.8751 (mmt)
REVERT: B  205 MET cc_start: 0.8502 (mtm) cc_final: 0.8073 (mtm)
REVERT: C   95 PHE cc_start: 0.9009 (m-10) cc_final: 0.8775 (m-80)
REVERT: C  101 MET cc_start: 0.8707 (mpp) cc_final: 0.8188 (mpp)
REVERT: C  123 MET cc_start: 0.7309 (tmm) cc_final: 0.6794 (tmm)
REVERT: C  194 LEU cc_start: 0.9391 (mt) cc_final: 0.9033 (tp)
REVERT: C  210 MET cc_start: 0.7080 (pmm) cc_final: 0.6256 (pmm)
REVERT: C  211 MET cc_start: 0.6649 (ttm) cc_final: 0.6373 (ttm)
REVERT: D   94 LEU cc_start: 0.9241 (OUTLIER) cc_final: 0.9028 (mt)
REVERT: D  123 MET cc_start: 0.7843 (mpp) cc_final: 0.6501 (ttt)
REVERT: D  129 LYS cc_start: 0.8806 (mptt) cc_final: 0.8567 (pttt)
REVERT: F  105 GLN cc_start: 0.8704 (mt0) cc_final: 0.8454 (mt0)
REVERT: F  130 ASP cc_start: 0.8695 (t0) cc_final: 0.8441 (t0)
REVERT: I   59 PHE cc_start: 0.7899 (t80) cc_final: 0.6453 (t80)
REVERT: J    7 MET cc_start: 0.8662 (tpp) cc_final: 0.8198 (tpp)
REVERT: J   14 MET cc_start: 0.6888 (mmt) cc_final: 0.6645 (ttm)
REVERT: J   26 LEU cc_start: 0.9449 (OUTLIER) cc_final: 0.9201 (mm)
  outliers start: 24
  outliers final: 17
  residues processed: 278
  average time/residue: 0.0930
  time to fit residues: 39.5053
Evaluate side-chains
  268 residues out of total 1376 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 247
  time to evaluate  : 0.470 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   66 ARG
Chi-restraints excluded: chain A residue  211 MET
Chi-restraints excluded: chain A residue  233 GLN
Chi-restraints excluded: chain B residue   62 THR
Chi-restraints excluded: chain B residue   80 THR
Chi-restraints excluded: chain B residue  138 MET
Chi-restraints excluded: chain B residue  225 LEU
Chi-restraints excluded: chain C residue  219 LEU
Chi-restraints excluded: chain D residue   94 LEU
Chi-restraints excluded: chain E residue  235 LEU
Chi-restraints excluded: chain F residue   95 VAL
Chi-restraints excluded: chain F residue  106 MET
Chi-restraints excluded: chain F residue  211 LEU
Chi-restraints excluded: chain H residue   29 LEU
Chi-restraints excluded: chain H residue   44 ILE
Chi-restraints excluded: chain H residue   56 VAL
Chi-restraints excluded: chain I residue   25 LEU
Chi-restraints excluded: chain I residue   52 ILE
Chi-restraints excluded: chain J residue   25 LEU
Chi-restraints excluded: chain J residue   26 LEU
Chi-restraints excluded: chain J residue   52 ILE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 157
   random chunks:
   chunk 135 optimal weight:    0.9980
   chunk 42 optimal weight:    0.0370
   chunk 80 optimal weight:   10.0000
   chunk 88 optimal weight:    4.9990
   chunk 13 optimal weight:    2.9990
   chunk 126 optimal weight:    3.9990
   chunk 48 optimal weight:    1.9990
   chunk 105 optimal weight:    6.9990
   chunk 70 optimal weight:    0.9980
   chunk 21 optimal weight:    3.9990
   chunk 56 optimal weight:    0.9980
   overall best weight:    1.0060

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

Flipped N/Q/H residues before XYZ refinement:
D 233 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3653 r_free = 0.3653 target = 0.079342 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3364 r_free = 0.3364 target = 0.064320 restraints weight = 47860.677|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3405 r_free = 0.3405 target = 0.066264 restraints weight = 26350.450|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3433 r_free = 0.3433 target = 0.067574 restraints weight = 17679.343|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 39)----------------|
| r_work = 0.3452 r_free = 0.3452 target = 0.068447 restraints weight = 13615.294|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 33)----------------|
| r_work = 0.3460 r_free = 0.3460 target = 0.068949 restraints weight = 11435.722|
|-----------------------------------------------------------------------------|
r_work (final): 0.3440
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8278
moved from start:          0.5168

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.045  12820  Z= 0.147
  Angle     :  0.871  14.213  17476  Z= 0.407
  Chirality :  0.046   0.296   2189
  Planarity :  0.006   0.071   2130
  Dihedral  :  5.163  40.629   1695
  Min Nonbonded Distance : 2.456

Molprobity Statistics.
  All-atom Clashscore : 12.45
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.58 %
    Favored  : 92.42 %
  Rotamer:
    Outliers :  1.60 %
    Allowed  : 23.11 %
    Favored  : 75.29 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.07 %
    Twisted Proline : 0.00 %
    Twisted General : 0.20 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.13 (0.22), residues: 1609
  helix:  0.97 (0.15), residues: 1254
  sheet:  None (None), residues: 0
  loop : -3.12 (0.31), residues: 355

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.014   0.001   ARG F  96 
 TYR   0.023   0.001   TYR C 174 
 PHE   0.031   0.001   PHE B  64 
 TRP   0.010   0.001   TRP B 232 
 HIS   0.004   0.001   HIS F  14 

Details of bonding type rmsd
  covalent geometry    : bond        0.00334 (12820)
  covalent geometry    : angle       0.87060 (17476)
  hydrogen bonds       : bond        0.03447 (  788)
  hydrogen bonds       : angle       4.07006 ( 2349)

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

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

  3218 Ramachandran restraints generated.
    1609 Oldfield, 0 Emsley, 1609 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3218 Ramachandran restraints generated.
    1609 Oldfield, 0 Emsley, 1609 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  273 residues out of total 1376 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 251
  time to evaluate  : 0.489 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   66 ARG cc_start: 0.8800 (OUTLIER) cc_final: 0.7814 (ptp-170)
REVERT: A   87 GLN cc_start: 0.7209 (mm-40) cc_final: 0.6911 (mm-40)
REVERT: B  138 MET cc_start: 0.8951 (OUTLIER) cc_final: 0.8608 (mmt)
REVERT: C   95 PHE cc_start: 0.9034 (m-10) cc_final: 0.8678 (m-80)
REVERT: C  101 MET cc_start: 0.8718 (mpp) cc_final: 0.8182 (mpp)
REVERT: C  123 MET cc_start: 0.7297 (tmm) cc_final: 0.6793 (tmm)
REVERT: C  194 LEU cc_start: 0.9379 (mt) cc_final: 0.9029 (tp)
REVERT: C  210 MET cc_start: 0.7048 (pmm) cc_final: 0.6517 (pmm)
REVERT: D  123 MET cc_start: 0.7830 (mpp) cc_final: 0.6461 (ttt)
REVERT: D  129 LYS cc_start: 0.8781 (mptt) cc_final: 0.8570 (pttt)
REVERT: F  100 GLU cc_start: 0.8439 (tm-30) cc_final: 0.8173 (tm-30)
REVERT: F  105 GLN cc_start: 0.8689 (mt0) cc_final: 0.8466 (mt0)
REVERT: F  130 ASP cc_start: 0.8595 (t0) cc_final: 0.8390 (t0)
REVERT: I   59 PHE cc_start: 0.7807 (t80) cc_final: 0.7514 (t80)
REVERT: J    7 MET cc_start: 0.8647 (tpp) cc_final: 0.8215 (tpp)
REVERT: J   26 LEU cc_start: 0.9471 (OUTLIER) cc_final: 0.9194 (mm)
  outliers start: 22
  outliers final: 13
  residues processed: 265
  average time/residue: 0.0920
  time to fit residues: 37.4628
Evaluate side-chains
  254 residues out of total 1376 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 238
  time to evaluate  : 0.496 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   66 ARG
Chi-restraints excluded: chain A residue  211 MET
Chi-restraints excluded: chain A residue  233 GLN
Chi-restraints excluded: chain B residue   62 THR
Chi-restraints excluded: chain B residue   80 THR
Chi-restraints excluded: chain B residue  138 MET
Chi-restraints excluded: chain B residue  225 LEU
Chi-restraints excluded: chain C residue  219 LEU
Chi-restraints excluded: chain E residue  235 LEU
Chi-restraints excluded: chain F residue  211 LEU
Chi-restraints excluded: chain H residue   29 LEU
Chi-restraints excluded: chain H residue   56 VAL
Chi-restraints excluded: chain I residue   25 LEU
Chi-restraints excluded: chain J residue   25 LEU
Chi-restraints excluded: chain J residue   26 LEU
Chi-restraints excluded: chain J residue   52 ILE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 157
   random chunks:
   chunk 114 optimal weight:    6.9990
   chunk 117 optimal weight:    1.9990
   chunk 130 optimal weight:    0.7980
   chunk 151 optimal weight:    0.6980
   chunk 90 optimal weight:    2.9990
   chunk 72 optimal weight:    4.9990
   chunk 97 optimal weight:    0.0020
   chunk 137 optimal weight:    0.8980
   chunk 12 optimal weight:    3.9990
   chunk 145 optimal weight:    0.8980
   chunk 131 optimal weight:    2.9990
   overall best weight:    0.6588

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3659 r_free = 0.3659 target = 0.079662 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3357 r_free = 0.3357 target = 0.064621 restraints weight = 47608.921|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3400 r_free = 0.3400 target = 0.066584 restraints weight = 26811.485|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3429 r_free = 0.3429 target = 0.067943 restraints weight = 18212.020|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 35)----------------|
| r_work = 0.3448 r_free = 0.3448 target = 0.068802 restraints weight = 14092.633|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3456 r_free = 0.3456 target = 0.069302 restraints weight = 11879.295|
|-----------------------------------------------------------------------------|
r_work (final): 0.3446
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8254
moved from start:          0.5330

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.045  12820  Z= 0.146
  Angle     :  0.863  14.426  17476  Z= 0.406
  Chirality :  0.046   0.284   2189
  Planarity :  0.006   0.071   2130
  Dihedral  :  5.150  41.331   1695
  Min Nonbonded Distance : 2.432

Molprobity Statistics.
  All-atom Clashscore : 12.41
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.33 %
    Favored  : 92.67 %
  Rotamer:
    Outliers :  1.45 %
    Allowed  : 22.75 %
    Favored  : 75.80 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.07 %
    Twisted Proline : 0.00 %
    Twisted General : 0.20 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.15 (0.22), residues: 1609
  helix:  0.98 (0.15), residues: 1252
  sheet:  None (None), residues: 0
  loop : -3.09 (0.31), residues: 357

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG F  96 
 TYR   0.033   0.002   TYR A 174 
 PHE   0.030   0.001   PHE B  64 
 TRP   0.009   0.001   TRP I  68 
 HIS   0.004   0.001   HIS F  14 

Details of bonding type rmsd
  covalent geometry    : bond        0.00323 (12820)
  covalent geometry    : angle       0.86333 (17476)
  hydrogen bonds       : bond        0.03449 (  788)
  hydrogen bonds       : angle       4.08502 ( 2349)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1948.68 seconds
wall clock time: 34 minutes 27.69 seconds (2067.69 seconds total)