Starting phenix.real_space_refine
on Wed Aug  5 12:45:55 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/30od_57888/08_2026/30od_57888.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/30od_57888/08_2026/30od_57888.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.75
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/30od_57888/08_2026/30od_57888.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/30od_57888/08_2026/30od_57888.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/30od_57888/08_2026/30od_57888.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/30od_57888/08_2026/30od_57888.cif"
  }
  resolution = 3.75
  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=   0.005 sd=   0.038
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 5
    Type Number    sf(0)   Gaussians
     P      12      5.49       5
     S      78      5.16       5
     C    6102      2.51       5
     N    1650      2.21       5
     O    1878      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 16 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib"
  Total number of atoms: 9720
  Number of models: 1
  Model: ""
    Number of chains: 8
    Chain: "A"
      Number of atoms: 1608
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 206, 1608
          Classifications: {'peptide': 206}
          Link IDs: {'PCIS': 1, 'PTRANS': 12, 'TRANS': 192}
          Chain breaks: 1
    Chain: "B"
      Number of atoms: 1608
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 206, 1608
          Classifications: {'peptide': 206}
          Link IDs: {'PCIS': 1, 'PTRANS': 12, 'TRANS': 192}
          Chain breaks: 1
    Chain: "C"
      Number of atoms: 1608
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 206, 1608
          Classifications: {'peptide': 206}
          Link IDs: {'PCIS': 1, 'PTRANS': 12, 'TRANS': 192}
          Chain breaks: 1
    Chain: "D"
      Number of atoms: 1608
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 206, 1608
          Classifications: {'peptide': 206}
          Link IDs: {'PCIS': 1, 'PTRANS': 12, 'TRANS': 192}
          Chain breaks: 1
    Chain: "E"
      Number of atoms: 1608
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 206, 1608
          Classifications: {'peptide': 206}
          Link IDs: {'PCIS': 1, 'PTRANS': 12, 'TRANS': 192}
          Chain breaks: 1
    Chain: "F"
      Number of atoms: 1608
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 206, 1608
          Classifications: {'peptide': 206}
          Link IDs: {'PCIS': 1, 'PTRANS': 12, 'TRANS': 192}
          Chain breaks: 1
    Chain: "C"
      Number of atoms: 36
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 36
          Unusual residues: {'IHP': 1}
          Classifications: {'undetermined': 1}
    Chain: "F"
      Number of atoms: 36
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 36
          Unusual residues: {'IHP': 1}
          Classifications: {'undetermined': 1}
  Residues with excluded nonbonded symmetry interactions: 1238
    residue:
      pdb=" N   MET A   1 " occ=0.40
      ... (6 atoms not shown)
      pdb=" CE  MET A   1 " occ=0.40
    residue:
      pdb=" N   PRO A   2 " occ=0.44
      ... (5 atoms not shown)
      pdb=" CD  PRO A   2 " occ=0.44
    residue:
      pdb=" N   ILE A   3 " occ=0.52
      ... (6 atoms not shown)
      pdb=" CD1 ILE A   3 " occ=0.52
    residue:
      pdb=" N   VAL A   4 " occ=0.41
      ... (5 atoms not shown)
      pdb=" CG2 VAL A   4 " occ=0.41
    residue:
      pdb=" N   GLN A   5 " occ=0.37
      ... (7 atoms not shown)
      pdb=" NE2 GLN A   5 " occ=0.37
    residue:
      pdb=" N   ASN A   6 " occ=0.25
      ... (6 atoms not shown)
      pdb=" ND2 ASN A   6 " occ=0.25
    residue:
      pdb=" N   LEU A   7 " occ=0.28
      ... (6 atoms not shown)
      pdb=" CD2 LEU A   7 " occ=0.28
    residue:
      pdb=" N   GLN A   8 " occ=0.34
      ... (7 atoms not shown)
      pdb=" NE2 GLN A   8 " occ=0.34
    residue:
      pdb=" N   GLY A   9 " occ=0.40
      ... (2 atoms not shown)
      pdb=" O   GLY A   9 " occ=0.40
    residue:
      pdb=" N   GLN A  10 " occ=0.47
      ... (7 atoms not shown)
      pdb=" NE2 GLN A  10 " occ=0.47
    residue:
      pdb=" N   MET A  11 " occ=0.56
      ... (6 atoms not shown)
      pdb=" CE  MET A  11 " occ=0.56
    residue:
      pdb=" N   VAL A  12 " occ=0.27
      ... (5 atoms not shown)
      pdb=" CG2 VAL A  12 " occ=0.27
    ... (remaining 1226 not shown)
  Time building chain proxies: 2.19, per 1000 atoms: 0.23
  Number of scatterers: 9720
  At special positions: 0
  Unit cell: (113.3, 119.9, 78.1, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S      78     16.00
     P      12     15.00
     O    1878      8.00
     N    1650      7.00
     C    6102      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=2, symmetry=0
  Number of additional bonds: simple=2, symmetry=0
  Coordination:
  Other bonds:
  Time building additional restraints: 0.81
  Conformation dependent library (CDL) restraints added in 323.7 milliseconds
  

  2424 Ramachandran restraints generated.
    1212 Oldfield, 0 Emsley, 1212 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2304

  Finding SS restraints...
    Secondary structure from input PDB file:
      79 helices and 6 sheets defined
      73.0% alpha, 1.9% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.27
  Creating SS restraints...
    Processing helix  chain 'A' and resid 17 through 31
      removed outlier: 3.631A  pdb=" N   LEU A  21 " --> pdb=" O   SER A  17 " (cutoff:3.500A)
      removed outlier: 3.875A  pdb=" N   ALA A  23 " --> pdb=" O   ARG A  19 " (cutoff:3.500A)
      removed outlier: 3.606A  pdb=" N   LYS A  26 " --> pdb=" O   ASN A  22 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 36 through 44
      removed outlier: 4.168A  pdb=" N   MET A  40 " --> pdb=" O   GLU A  36 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 49 through 59
      removed outlier: 3.692A  pdb=" N   THR A  55 " --> pdb=" O   GLN A  51 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 63 through 83
      removed outlier: 4.176A  pdb=" N   MET A  69 " --> pdb=" O   ALA A  65 " (cutoff:3.500A)
      removed outlier: 4.251A  pdb=" N   LEU A  70 " --> pdb=" O   ALA A  66 " (cutoff:3.500A)
      removed outlier: 4.280A  pdb=" N   LYS A  71 " --> pdb=" O   MET A  67 " (cutoff:3.500A)
      removed outlier: 3.846A  pdb=" N   ARG A  83 " --> pdb=" O   ALA A  79 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 103 through 107
    Processing helix  chain 'A' and resid 111 through 121
    Processing helix  chain 'A' and resid 126 through 131
      removed outlier: 3.756A  pdb=" N   TYR A 131 " --> pdb=" O   VAL A 127 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 131 through 145
      removed outlier: 3.515A  pdb=" N   LYS A 141 " --> pdb=" O   LEU A 137 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 150 through 154
    Processing helix  chain 'A' and resid 161 through 176
      removed outlier: 3.779A  pdb=" N   VAL A 166 " --> pdb=" O   PHE A 162 " (cutoff:3.500A)
      removed outlier: 4.324A  pdb=" N   ASP A 167 " --> pdb=" O   ARG A 163 " (cutoff:3.500A)
      removed outlier: 3.675A  pdb=" N   ARG A 168 " --> pdb=" O   ASP A 164 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 179 through 194
      removed outlier: 3.551A  pdb=" N   THR A 189 " --> pdb=" O   TRP A 185 " (cutoff:3.500A)
      removed outlier: 4.810A  pdb=" N   LEU A 191 " --> pdb=" O   THR A 187 " (cutoff:3.500A)
      removed outlier: 5.560A  pdb=" N   VAL A 192 " --> pdb=" O   GLU A 188 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 196 through 205
      removed outlier: 3.948A  pdb=" N   THR A 201 " --> pdb=" O   PRO A 197 " (cutoff:3.500A)
      removed outlier: 4.751A  pdb=" N   ILE A 202 " --> pdb=" O   ASP A 198 " (cutoff:3.500A)
      removed outlier: 3.785A  pdb=" N   ALA A 205 " --> pdb=" O   THR A 201 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 211 through 219
      removed outlier: 3.503A  pdb=" N   MET A 215 " --> pdb=" O   THR A 211 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 17 through 31
      removed outlier: 3.604A  pdb=" N   LEU B  21 " --> pdb=" O   SER B  17 " (cutoff:3.500A)
      removed outlier: 3.531A  pdb=" N   ALA B  23 " --> pdb=" O   ARG B  19 " (cutoff:3.500A)
      removed outlier: 3.835A  pdb=" N   LYS B  26 " --> pdb=" O   ASN B  22 " (cutoff:3.500A)
      removed outlier: 3.761A  pdb=" N   GLU B  29 " --> pdb=" O   VAL B  25 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 36 through 43
      removed outlier: 4.133A  pdb=" N   MET B  40 " --> pdb=" O   GLU B  36 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 49 through 60
      removed outlier: 3.638A  pdb=" N   THR B  59 " --> pdb=" O   THR B  55 " (cutoff:3.500A)
      removed outlier: 4.264A  pdb=" N   VAL B  60 " --> pdb=" O   MET B  56 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 63 through 84
      removed outlier: 3.589A  pdb=" N   MET B  67 " --> pdb=" O   HIS B  63 " (cutoff:3.500A)
      removed outlier: 4.108A  pdb=" N   MET B  69 " --> pdb=" O   ALA B  65 " (cutoff:3.500A)
      removed outlier: 3.894A  pdb=" N   LEU B  70 " --> pdb=" O   ALA B  66 " (cutoff:3.500A)
      removed outlier: 3.931A  pdb=" N   LYS B  71 " --> pdb=" O   MET B  67 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 103 through 107
    Processing helix  chain 'B' and resid 111 through 121
    Processing helix  chain 'B' and resid 126 through 145
      removed outlier: 3.640A  pdb=" N   LYS B 132 " --> pdb=" O   GLY B 128 " (cutoff:3.500A)
      removed outlier: 3.611A  pdb=" N   TRP B 134 " --> pdb=" O   ILE B 130 " (cutoff:3.500A)
      removed outlier: 3.836A  pdb=" N   MET B 145 " --> pdb=" O   LYS B 141 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 150 through 154
    Processing helix  chain 'B' and resid 161 through 176
      removed outlier: 3.935A  pdb=" N   ASP B 167 " --> pdb=" O   ARG B 163 " (cutoff:3.500A)
      removed outlier: 3.577A  pdb=" N   ARG B 168 " --> pdb=" O   ASP B 164 " (cutoff:3.500A)
      removed outlier: 3.566A  pdb=" N   ALA B 175 " --> pdb=" O   LYS B 171 " (cutoff:3.500A)
      removed outlier: 3.657A  pdb=" N   GLU B 176 " --> pdb=" O   THR B 172 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 179 through 189
      removed outlier: 3.765A  pdb=" N   TRP B 185 " --> pdb=" O   GLU B 181 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 189 through 194
    Processing helix  chain 'B' and resid 196 through 207
      removed outlier: 4.220A  pdb=" N   THR B 201 " --> pdb=" O   PRO B 197 " (cutoff:3.500A)
      removed outlier: 5.031A  pdb=" N   ILE B 202 " --> pdb=" O   ASP B 198 " (cutoff:3.500A)
      removed outlier: 3.816A  pdb=" N   LEU B 206 " --> pdb=" O   ILE B 202 " (cutoff:3.500A)
      removed outlier: 4.092A  pdb=" N   GLY B 207 " --> pdb=" O   LEU B 203 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 211 through 219
      removed outlier: 3.736A  pdb=" N   CYS B 219 " --> pdb=" O   MET B 215 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 17 through 31
      removed outlier: 3.519A  pdb=" N   ALA C  23 " --> pdb=" O   ARG C  19 " (cutoff:3.500A)
      removed outlier: 3.563A  pdb=" N   GLU C  29 " --> pdb=" O   VAL C  25 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 36 through 44
      removed outlier: 4.154A  pdb=" N   MET C  40 " --> pdb=" O   GLU C  36 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 49 through 60
      removed outlier: 4.200A  pdb=" N   VAL C  60 " --> pdb=" O   MET C  56 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 63 through 84
      removed outlier: 3.941A  pdb=" N   MET C  69 " --> pdb=" O   ALA C  65 " (cutoff:3.500A)
      removed outlier: 3.909A  pdb=" N   LEU C  70 " --> pdb=" O   ALA C  66 " (cutoff:3.500A)
      removed outlier: 3.817A  pdb=" N   LYS C  71 " --> pdb=" O   MET C  67 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 102 through 107
      removed outlier: 3.625A  pdb=" N   ILE C 105 " --> pdb=" O   GLY C 102 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 111 through 121
      removed outlier: 3.560A  pdb=" N   GLN C 115 " --> pdb=" O   THR C 111 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 126 through 146
      removed outlier: 3.733A  pdb=" N   LYS C 132 " --> pdb=" O   GLY C 128 " (cutoff:3.500A)
      removed outlier: 3.514A  pdb=" N   TRP C 134 " --> pdb=" O   ILE C 130 " (cutoff:3.500A)
      removed outlier: 3.630A  pdb=" N   MET C 145 " --> pdb=" O   LYS C 141 " (cutoff:3.500A)
      removed outlier: 3.920A  pdb=" N   TYR C 146 " --> pdb=" O   ILE C 142 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 150 through 154
    Processing helix  chain 'C' and resid 161 through 176
      removed outlier: 3.736A  pdb=" N   VAL C 166 " --> pdb=" O   PHE C 162 " (cutoff:3.500A)
      removed outlier: 4.561A  pdb=" N   ASP C 167 " --> pdb=" O   ARG C 163 " (cutoff:3.500A)
      removed outlier: 3.745A  pdb=" N   ARG C 168 " --> pdb=" O   ASP C 164 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 179 through 189
      removed outlier: 3.712A  pdb=" N   TRP C 185 " --> pdb=" O   GLU C 181 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 189 through 194
    Processing helix  chain 'C' and resid 196 through 204
      removed outlier: 3.712A  pdb=" N   THR C 201 " --> pdb=" O   PRO C 197 " (cutoff:3.500A)
      removed outlier: 4.670A  pdb=" N   ILE C 202 " --> pdb=" O   ASP C 198 " (cutoff:3.500A)
      removed outlier: 3.611A  pdb=" N   LYS C 204 " --> pdb=" O   LYS C 200 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 205 through 207
      No H-bonds generated for 'chain 'C' and resid 205 through 207'
    Processing helix  chain 'C' and resid 211 through 219
      removed outlier: 3.512A  pdb=" N   ALA C 218 " --> pdb=" O   GLU C 214 " (cutoff:3.500A)
      removed outlier: 3.795A  pdb=" N   CYS C 219 " --> pdb=" O   MET C 215 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 19 through 31
      removed outlier: 3.773A  pdb=" N   VAL D  25 " --> pdb=" O   LEU D  21 " (cutoff:3.500A)
      removed outlier: 3.663A  pdb=" N   LYS D  26 " --> pdb=" O   ASN D  22 " (cutoff:3.500A)
      removed outlier: 3.644A  pdb=" N   GLU D  29 " --> pdb=" O   VAL D  25 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 36 through 44
      removed outlier: 4.234A  pdb=" N   MET D  40 " --> pdb=" O   GLU D  36 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 49 through 60
      removed outlier: 4.240A  pdb=" N   VAL D  60 " --> pdb=" O   MET D  56 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 63 through 82
      removed outlier: 4.017A  pdb=" N   MET D  69 " --> pdb=" O   ALA D  65 " (cutoff:3.500A)
      removed outlier: 4.230A  pdb=" N   LEU D  70 " --> pdb=" O   ALA D  66 " (cutoff:3.500A)
      removed outlier: 4.209A  pdb=" N   LYS D  71 " --> pdb=" O   MET D  67 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 103 through 107
    Processing helix  chain 'D' and resid 111 through 120
    Processing helix  chain 'D' and resid 126 through 131
    Processing helix  chain 'D' and resid 131 through 145
      removed outlier: 3.551A  pdb=" N   LYS D 141 " --> pdb=" O   LEU D 137 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 150 through 154
    Processing helix  chain 'D' and resid 161 through 176
      removed outlier: 3.737A  pdb=" N   ASP D 167 " --> pdb=" O   ARG D 163 " (cutoff:3.500A)
      removed outlier: 3.713A  pdb=" N   ARG D 168 " --> pdb=" O   ASP D 164 " (cutoff:3.500A)
      removed outlier: 3.632A  pdb=" N   GLU D 176 " --> pdb=" O   THR D 172 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 179 through 194
      removed outlier: 3.734A  pdb=" N   THR D 187 " --> pdb=" O   LYS D 183 " (cutoff:3.500A)
      removed outlier: 4.375A  pdb=" N   GLU D 188 " --> pdb=" O   ASN D 184 " (cutoff:3.500A)
      removed outlier: 3.590A  pdb=" N   THR D 189 " --> pdb=" O   TRP D 185 " (cutoff:3.500A)
      removed outlier: 3.712A  pdb=" N   LEU D 191 " --> pdb=" O   THR D 187 " (cutoff:3.500A)
      removed outlier: 4.691A  pdb=" N   VAL D 192 " --> pdb=" O   GLU D 188 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 196 through 198
      No H-bonds generated for 'chain 'D' and resid 196 through 198'
    Processing helix  chain 'D' and resid 199 through 205
    Processing helix  chain 'D' and resid 211 through 219
      removed outlier: 3.671A  pdb=" N   MET D 215 " --> pdb=" O   THR D 211 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 17 through 32
      removed outlier: 3.666A  pdb=" N   ALA E  23 " --> pdb=" O   ARG E  19 " (cutoff:3.500A)
      removed outlier: 4.089A  pdb=" N   VAL E  25 " --> pdb=" O   LEU E  21 " (cutoff:3.500A)
      removed outlier: 3.955A  pdb=" N   LYS E  26 " --> pdb=" O   ASN E  22 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 38 through 43
    Processing helix  chain 'E' and resid 49 through 58
    Processing helix  chain 'E' and resid 63 through 82
      removed outlier: 4.061A  pdb=" N   MET E  69 " --> pdb=" O   ALA E  65 " (cutoff:3.500A)
      removed outlier: 3.954A  pdb=" N   LEU E  70 " --> pdb=" O   ALA E  66 " (cutoff:3.500A)
      removed outlier: 3.909A  pdb=" N   LYS E  71 " --> pdb=" O   MET E  67 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 83 through 84
      No H-bonds generated for 'chain 'E' and resid 83 through 84'
    Processing helix  chain 'E' and resid 102 through 107
      removed outlier: 4.020A  pdb=" N   ILE E 105 " --> pdb=" O   GLY E 102 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 111 through 121
    Processing helix  chain 'E' and resid 126 through 146
      removed outlier: 3.830A  pdb=" N   LYS E 132 " --> pdb=" O   GLY E 128 " (cutoff:3.500A)
      removed outlier: 3.609A  pdb=" N   TRP E 134 " --> pdb=" O   ILE E 130 " (cutoff:3.500A)
      removed outlier: 3.613A  pdb=" N   LYS E 141 " --> pdb=" O   LEU E 137 " (cutoff:3.500A)
      removed outlier: 3.962A  pdb=" N   TYR E 146 " --> pdb=" O   ILE E 142 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 150 through 154
    Processing helix  chain 'E' and resid 161 through 176
      removed outlier: 3.703A  pdb=" N   ARG E 168 " --> pdb=" O   ASP E 164 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 179 through 194
      removed outlier: 4.510A  pdb=" N   LEU E 191 " --> pdb=" O   THR E 187 " (cutoff:3.500A)
      removed outlier: 5.115A  pdb=" N   VAL E 192 " --> pdb=" O   GLU E 188 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 196 through 205
      removed outlier: 3.855A  pdb=" N   THR E 201 " --> pdb=" O   PRO E 197 " (cutoff:3.500A)
      removed outlier: 4.794A  pdb=" N   ILE E 202 " --> pdb=" O   ASP E 198 " (cutoff:3.500A)
      removed outlier: 3.716A  pdb=" N   ALA E 205 " --> pdb=" O   THR E 201 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 211 through 219
    Processing helix  chain 'F' and resid 17 through 32
      removed outlier: 3.520A  pdb=" N   LEU F  21 " --> pdb=" O   SER F  17 " (cutoff:3.500A)
      removed outlier: 3.673A  pdb=" N   ALA F  23 " --> pdb=" O   ARG F  19 " (cutoff:3.500A)
      removed outlier: 3.657A  pdb=" N   LYS F  26 " --> pdb=" O   ASN F  22 " (cutoff:3.500A)
      removed outlier: 3.661A  pdb=" N   GLU F  29 " --> pdb=" O   VAL F  25 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 36 through 45
      removed outlier: 4.200A  pdb=" N   MET F  40 " --> pdb=" O   GLU F  36 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 49 through 59
      removed outlier: 3.624A  pdb=" N   THR F  55 " --> pdb=" O   GLN F  51 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 63 through 84
      removed outlier: 3.916A  pdb=" N   ASN F  75 " --> pdb=" O   LYS F  71 " (cutoff:3.500A)
      removed outlier: 3.657A  pdb=" N   GLU F  76 " --> pdb=" O   GLU F  72 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 103 through 107
    Processing helix  chain 'F' and resid 111 through 120
    Processing helix  chain 'F' and resid 126 through 145
      removed outlier: 3.656A  pdb=" N   LYS F 132 " --> pdb=" O   GLY F 128 " (cutoff:3.500A)
      removed outlier: 3.690A  pdb=" N   LYS F 141 " --> pdb=" O   LEU F 137 " (cutoff:3.500A)
      removed outlier: 3.529A  pdb=" N   ILE F 142 " --> pdb=" O   GLY F 138 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 150 through 154
    Processing helix  chain 'F' and resid 161 through 176
      removed outlier: 3.538A  pdb=" N   ASP F 167 " --> pdb=" O   ARG F 163 " (cutoff:3.500A)
      removed outlier: 3.743A  pdb=" N   ARG F 168 " --> pdb=" O   ASP F 164 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 179 through 194
      removed outlier: 4.009A  pdb=" N   THR F 187 " --> pdb=" O   LYS F 183 " (cutoff:3.500A)
      removed outlier: 4.113A  pdb=" N   GLU F 188 " --> pdb=" O   ASN F 184 " (cutoff:3.500A)
      removed outlier: 3.844A  pdb=" N   THR F 189 " --> pdb=" O   TRP F 185 " (cutoff:3.500A)
      removed outlier: 4.494A  pdb=" N   LEU F 191 " --> pdb=" O   THR F 187 " (cutoff:3.500A)
      removed outlier: 5.296A  pdb=" N   VAL F 192 " --> pdb=" O   GLU F 188 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 196 through 207
      removed outlier: 3.533A  pdb=" N   LYS F 200 " --> pdb=" O   ASN F 196 " (cutoff:3.500A)
      removed outlier: 4.466A  pdb=" N   THR F 201 " --> pdb=" O   PRO F 197 " (cutoff:3.500A)
      removed outlier: 5.237A  pdb=" N   ILE F 202 " --> pdb=" O   ASP F 198 " (cutoff:3.500A)
      removed outlier: 3.765A  pdb=" N   LEU F 206 " --> pdb=" O   ILE F 202 " (cutoff:3.500A)
      removed outlier: 4.131A  pdb=" N   GLY F 207 " --> pdb=" O   LEU F 203 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 211 through 219
      removed outlier: 3.519A  pdb=" N   MET F 215 " --> pdb=" O   THR F 211 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 3 through 5
    Processing sheet with id=AA2, first strand: chain 'B' and resid 3 through 5
    Processing sheet with id=AA3, first strand: chain 'C' and resid 3 through 5
    Processing sheet with id=AA4, first strand: chain 'D' and resid 3 through 5
    Processing sheet with id=AA5, first strand: chain 'E' and resid 3 through 5
    Processing sheet with id=AA6, first strand: chain 'F' and resid 3 through 5

    484 hydrogen bonds defined for protein.
    1404 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: 1.23

  Time building geometry restraints manager: 1.01 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: 3200
        1.34 -     1.46: 1636
        1.46 -     1.58: 4920
        1.58 -     1.69: 12
        1.69 -     1.81: 144
  Bond restraints: 9912
  Sorted by residual:
  bond pdb=" N   MET A   1 "
       pdb=" CA  MET A   1 "
    ideal  model  delta    sigma   weight residual
    1.458  1.489 -0.031 1.90e-02 2.77e+03 2.62e+00
  bond pdb=" N   MET D   1 "
       pdb=" CA  MET D   1 "
    ideal  model  delta    sigma   weight residual
    1.458  1.488 -0.030 1.90e-02 2.77e+03 2.49e+00
  bond pdb=" N   MET E   1 "
       pdb=" CA  MET E   1 "
    ideal  model  delta    sigma   weight residual
    1.458  1.487 -0.029 1.90e-02 2.77e+03 2.41e+00
  bond pdb=" N   MET B   1 "
       pdb=" CA  MET B   1 "
    ideal  model  delta    sigma   weight residual
    1.458  1.484 -0.026 1.90e-02 2.77e+03 1.89e+00
  bond pdb=" N   MET F   1 "
       pdb=" CA  MET F   1 "
    ideal  model  delta    sigma   weight residual
    1.458  1.483 -0.025 1.90e-02 2.77e+03 1.73e+00
  ... (remaining 9907 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.90: 13234
        1.90 -     3.81: 206
        3.81 -     5.71: 30
        5.71 -     7.62: 2
        7.62 -     9.52: 4
  Bond angle restraints: 13476
  Sorted by residual:
  angle pdb=" C   ALA B  32 "
        pdb=" CA  ALA B  32 "
        pdb=" CB  ALA B  32 "
      ideal   model   delta    sigma   weight residual
     115.79  111.01    4.78 1.19e+00 7.06e-01 1.61e+01
  angle pdb=" C1  IHP F 301 "
        pdb=" C6  IHP F 301 "
        pdb=" C5  IHP F 301 "
      ideal   model   delta    sigma   weight residual
     108.26  117.78   -9.52 3.00e+00 1.11e-01 1.01e+01
  angle pdb=" C4  IHP F 301 "
        pdb=" C5  IHP F 301 "
        pdb=" C6  IHP F 301 "
      ideal   model   delta    sigma   weight residual
     109.60  118.53   -8.93 3.00e+00 1.11e-01 8.85e+00
  angle pdb=" C2  IHP F 301 "
        pdb=" C1  IHP F 301 "
        pdb=" C6  IHP F 301 "
      ideal   model   delta    sigma   weight residual
     110.87  119.56   -8.69 3.00e+00 1.11e-01 8.40e+00
  angle pdb=" CB  LYS F 204 "
        pdb=" CG  LYS F 204 "
        pdb=" CD  LYS F 204 "
      ideal   model   delta    sigma   weight residual
     111.30  117.38   -6.08 2.30e+00 1.89e-01 7.00e+00
  ... (remaining 13471 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    23.65: 5512
       23.65 -    47.30: 470
       47.30 -    70.95: 67
       70.95 -    94.60: 35
       94.60 -   118.25: 12
  Dihedral angle restraints: 6096
    sinusoidal: 2544
      harmonic: 3552
  Sorted by residual:
  dihedral pdb=" C2  IHP F 301 "
           pdb=" C3  IHP F 301 "
           pdb=" C4  IHP F 301 "
           pdb=" C5  IHP F 301 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -61.64   56.61 -118.25     1      3.00e+01 1.11e-03 1.57e+01
  dihedral pdb=" C5  IHP F 301 "
           pdb=" C3  IHP F 301 "
           pdb=" C4  IHP F 301 "
           pdb=" O13 IHP F 301 "
      ideal   model   delta sinusoidal    sigma   weight residual
     186.74   70.61  116.13     1      3.00e+01 1.11e-03 1.54e+01
  dihedral pdb=" C4  IHP F 301 "
           pdb=" C2  IHP F 301 "
           pdb=" C3  IHP F 301 "
           pdb=" O12 IHP F 301 "
      ideal   model   delta sinusoidal    sigma   weight residual
      60.90  176.74 -115.84     1      3.00e+01 1.11e-03 1.53e+01
  ... (remaining 6093 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.044: 1222
       0.044 -    0.087: 220
       0.087 -    0.131: 76
       0.131 -    0.175: 5
       0.175 -    0.218: 1
  Chirality restraints: 1524
  Sorted by residual:
  chirality pdb=" C6  IHP F 301 "
            pdb=" C1  IHP F 301 "
            pdb=" C5  IHP F 301 "
            pdb=" O16 IHP F 301 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.50   -2.28   -0.22 2.00e-01 2.50e+01 1.19e+00
  chirality pdb=" CA  ILE E 125 "
            pdb=" N   ILE E 125 "
            pdb=" C   ILE E 125 "
            pdb=" CB  ILE E 125 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.58   -0.15 2.00e-01 2.50e+01 5.62e-01
  chirality pdb=" CA  ILE F 125 "
            pdb=" N   ILE F 125 "
            pdb=" C   ILE F 125 "
            pdb=" CB  ILE F 125 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.58   -0.14 2.00e-01 2.50e+01 5.21e-01
  ... (remaining 1521 not shown)

  Planarity restraints: 1728
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   SER D  17 "    0.024 5.00e-02 4.00e+02   3.65e-02 2.14e+00
        pdb=" N   PRO D  18 "   -0.063 5.00e-02 4.00e+02
        pdb=" CA  PRO D  18 "    0.019 5.00e-02 4.00e+02
        pdb=" CD  PRO D  18 "    0.020 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   THR B  49 "    0.019 5.00e-02 4.00e+02   2.95e-02 1.39e+00
        pdb=" N   PRO B  50 "   -0.051 5.00e-02 4.00e+02
        pdb=" CA  PRO B  50 "    0.015 5.00e-02 4.00e+02
        pdb=" CD  PRO B  50 "    0.017 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   THR E  49 "   -0.017 5.00e-02 4.00e+02   2.61e-02 1.09e+00
        pdb=" N   PRO E  50 "    0.045 5.00e-02 4.00e+02
        pdb=" CA  PRO E  50 "   -0.013 5.00e-02 4.00e+02
        pdb=" CD  PRO E  50 "   -0.015 5.00e-02 4.00e+02
  ... (remaining 1725 not shown)

  Histogram of nonbonded interaction distances:
        2.34 -     2.85: 3354
        2.85 -     3.36: 10113
        3.36 -     3.87: 14346
        3.87 -     4.39: 16766
        4.39 -     4.90: 27479
  Nonbonded interactions: 72058
  Sorted by model distance:
  nonbonded pdb=" O   ASP C 164 "
            pdb=" OD1 ASP C 164 "
     model   vdw
     2.336 3.040
  nonbonded pdb=" O   ASP A 164 "
            pdb=" OD1 ASP A 164 "
     model   vdw
     2.353 3.040
  nonbonded pdb=" OE1 GLN F  14 "
            pdb=" O   ALA F  15 "
     model   vdw
     2.362 3.040
  nonbonded pdb=" O34 IHP F 301 "
            pdb=" O36 IHP F 301 "
     model   vdw
     2.367 3.040
  nonbonded pdb=" O   LYS B  71 "
            pdb=" OD1 ASN B  75 "
     model   vdw
     2.457 3.040
  ... (remaining 72053 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: 0.01
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'B'
  selection = (chain 'C' and resid 1 through 223)
  selection = chain 'D'
  selection = chain 'E'
  selection = (chain 'F' and resid 1 through 223)
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=0.23 max=0.77 mean=0.49
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             1.120
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.160
  Check model and map are aligned:         0.000
  Set scattering table:                    0.020
  Process input model:                     8.850
  Find NCS groups from input model:        0.170
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:0.970
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   11.320
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7835
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   9914  Z= 0.119
  Angle     :  0.606   9.523  13476  Z= 0.308
  Chirality :  0.039   0.218   1524
  Planarity :  0.003   0.037   1728
  Dihedral  : 18.888 118.249   3792
  Min Nonbonded Distance : 2.336

Molprobity Statistics.
  All-atom Clashscore : 3.09
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.39 %
    Favored  : 97.61 %
  Rotamer:
    Outliers :  1.61 %
    Allowed  : 17.14 %
    Favored  : 81.25 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 7.69 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.39 (0.26), residues: 1212
  helix: -0.32 (0.21), residues: 666
  sheet:  None (None), residues: 0
  loop :  1.36 (0.30), residues: 546

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG C  19 
 TYR   0.005   0.001   TYR A 170 
 PHE   0.009   0.001   PHE F 162 
 TRP   0.006   0.001   TRP F 118 
 HIS   0.004   0.001   HIS F  13 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00258 /  0.12 ( 9912)
  covalent geometry    : angle       0.60569 /  0.31 (13476)
  hydrogen bonds       : bond        0.18379 / 13.40 (  484)
  hydrogen bonds       : angle       6.04125 /  4.48 ( 1404)
  Misc. bond           : bond        0.00128 /  0.07 (    2)

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

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

  2424 Ramachandran restraints generated.
    1212 Oldfield, 0 Emsley, 1212 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2424 Ramachandran restraints generated.
    1212 Oldfield, 0 Emsley, 1212 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  211 residues out of total 1056 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 194
  time to evaluate  : 0.375 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   16 ILE cc_start: 0.7164 (tp) cc_final: 0.6765 (tt)
REVERT: A  139 LEU cc_start: 0.8810 (OUTLIER) cc_final: 0.8400 (mt)
REVERT: B   52 ASP cc_start: 0.8230 (m-30) cc_final: 0.7871 (m-30)
REVERT: C   31 LYS cc_start: 0.8236 (mmtt) cc_final: 0.7929 (mmtp)
REVERT: C  139 LEU cc_start: 0.8817 (OUTLIER) cc_final: 0.8441 (mm)
REVERT: C  153 ASP cc_start: 0.7618 (t0) cc_final: 0.6948 (t0)
REVERT: C  186 MET cc_start: 0.7845 (mtt) cc_final: 0.7307 (mpp)
REVERT: E    1 MET cc_start: 0.3098 (ttt) cc_final: 0.2759 (ttt)
REVERT: E  112 LEU cc_start: 0.8456 (pt) cc_final: 0.8240 (pp)
  outliers start: 17
  outliers final: 13
  residues processed: 206
  average time/residue: 0.0979
  time to fit residues: 27.2983
Evaluate side-chains
  185 residues out of total 1056 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 170
  time to evaluate  : 0.282 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  139 LEU
Chi-restraints excluded: chain A residue  143 VAL
Chi-restraints excluded: chain B residue  152 LEU
Chi-restraints excluded: chain C residue  139 LEU
Chi-restraints excluded: chain C residue  143 VAL
Chi-restraints excluded: chain D residue  139 LEU
Chi-restraints excluded: chain D residue  143 VAL
Chi-restraints excluded: chain E residue   57 LEU
Chi-restraints excluded: chain E residue  139 LEU
Chi-restraints excluded: chain E residue  143 VAL
Chi-restraints excluded: chain F residue   52 ASP
Chi-restraints excluded: chain F residue  139 LEU
Chi-restraints excluded: chain F residue  143 VAL
Chi-restraints excluded: chain F residue  152 LEU
Chi-restraints excluded: chain F residue  166 VAL
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 120
   random chunks:
   chunk 108 optimal weight:    4.9990
   chunk 49 optimal weight:    0.5980
   chunk 97 optimal weight:    4.9990
   chunk 113 optimal weight:    0.2980
   chunk 53 optimal weight:    6.9990
   chunk 5 optimal weight:    3.9990
   chunk 33 optimal weight:    6.9990
   chunk 65 optimal weight:    1.9990
   chunk 62 optimal weight:    1.9990
   chunk 51 optimal weight:    2.9990
   chunk 117 optimal weight:    0.5980
   overall best weight:    1.0984

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
F  22 ASN
F 180 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3946 r_free = 0.3946 target = 0.171131 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 66)----------------|
| r_work = 0.3627 r_free = 0.3627 target = 0.142349 restraints weight = 13393.759|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3604 r_free = 0.3604 target = 0.140340 restraints weight = 18734.973|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3615 r_free = 0.3615 target = 0.141807 restraints weight = 16407.345|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.3607 r_free = 0.3607 target = 0.141103 restraints weight = 13691.258|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.3607 r_free = 0.3607 target = 0.141097 restraints weight = 12985.506|
|-----------------------------------------------------------------------------|
r_work (final): 0.3600
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3600
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3600 r_free = 0.3600    target_work(ls_wunit_k1) = 0.140         |
| occupancies: max = 0.77  min = 0.23   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3528 r_free = 0.3528    target_work(ls_wunit_k1) = 0.135         |
| occupancies: max = 0.83  min = 0.15   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 24 (30 function evaluations)
r_final: 0.3528
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7846
moved from start:          0.1230

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.047   9914  Z= 0.147
  Angle     :  0.626  10.655  13476  Z= 0.308
  Chirality :  0.042   0.265   1524
  Planarity :  0.004   0.038   1728
  Dihedral  : 16.850 122.858   1404
  Min Nonbonded Distance : 2.546

Molprobity Statistics.
  All-atom Clashscore : 1.65
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.38 %
    Favored  : 96.62 %
  Rotamer:
    Outliers :  2.94 %
    Allowed  : 15.25 %
    Favored  : 81.82 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 7.69 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.26 (0.25), residues: 1212
  helix: -0.45 (0.19), residues: 744
  sheet: -1.19 (0.64), residues: 66
  loop :  1.06 (0.34), residues: 402

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG E  83 
 TYR   0.008   0.001   TYR E 165 
 PHE   0.010   0.001   PHE B 162 
 TRP   0.009   0.001   TRP D 185 
 HIS   0.002   0.001   HIS A  63 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00337 /  0.15 ( 9912)
  covalent geometry    : angle       0.62567 /  0.31 (13476)
  hydrogen bonds       : bond        0.05471 /  3.69 (  484)
  hydrogen bonds       : angle       4.60544 /  3.43 ( 1404)
  Misc. bond           : bond        0.00099 /  0.05 (    2)

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

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

  2424 Ramachandran restraints generated.
    1212 Oldfield, 0 Emsley, 1212 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2424 Ramachandran restraints generated.
    1212 Oldfield, 0 Emsley, 1212 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  223 residues out of total 1056 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 192
  time to evaluate  : 0.317 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  130 ILE cc_start: 0.8836 (pt) cc_final: 0.8623 (mm)
REVERT: B   52 ASP cc_start: 0.7812 (m-30) cc_final: 0.7511 (m-30)
REVERT: B  144 ARG cc_start: 0.7850 (tpt90) cc_final: 0.7520 (tpt170)
REVERT: C  153 ASP cc_start: 0.7251 (t0) cc_final: 0.6523 (t0)
REVERT: E  186 MET cc_start: 0.7961 (mtt) cc_final: 0.7182 (mtt)
REVERT: F  110 SER cc_start: 0.8287 (t) cc_final: 0.8073 (m)
  outliers start: 31
  outliers final: 21
  residues processed: 216
  average time/residue: 0.0882
  time to fit residues: 26.5581
Evaluate side-chains
  191 residues out of total 1056 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 170
  time to evaluate  : 0.251 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   55 THR
Chi-restraints excluded: chain A residue  127 VAL
Chi-restraints excluded: chain A residue  139 LEU
Chi-restraints excluded: chain A residue  143 VAL
Chi-restraints excluded: chain B residue   16 ILE
Chi-restraints excluded: chain B residue  149 THR
Chi-restraints excluded: chain B residue  172 THR
Chi-restraints excluded: chain C residue  139 LEU
Chi-restraints excluded: chain C residue  143 VAL
Chi-restraints excluded: chain C residue  149 THR
Chi-restraints excluded: chain D residue  139 LEU
Chi-restraints excluded: chain D residue  143 VAL
Chi-restraints excluded: chain E residue   57 LEU
Chi-restraints excluded: chain E residue  139 LEU
Chi-restraints excluded: chain E residue  143 VAL
Chi-restraints excluded: chain E residue  149 THR
Chi-restraints excluded: chain F residue   27 VAL
Chi-restraints excluded: chain F residue  127 VAL
Chi-restraints excluded: chain F residue  139 LEU
Chi-restraints excluded: chain F residue  142 ILE
Chi-restraints excluded: chain F residue  143 VAL
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 120
   random chunks:
   chunk 47 optimal weight:    1.9990
   chunk 110 optimal weight:    7.9990
   chunk 10 optimal weight:    0.8980
   chunk 67 optimal weight:    2.9990
   chunk 31 optimal weight:    2.9990
   chunk 84 optimal weight:    2.9990
   chunk 100 optimal weight:    3.9990
   chunk 116 optimal weight:    3.9990
   chunk 86 optimal weight:    0.0050
   chunk 35 optimal weight:    0.9990
   chunk 99 optimal weight:    5.9990
   overall best weight:    1.3800

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A  75 ASN
F   5 GLN
F  22 ASN
F 177 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3828 r_free = 0.3828 target = 0.160275 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 92)----------------|
| r_work = 0.3521 r_free = 0.3521 target = 0.134422 restraints weight = 13408.952|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3519 r_free = 0.3519 target = 0.134143 restraints weight = 12963.446|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3518 r_free = 0.3518 target = 0.134120 restraints weight = 12787.655|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 24)----------------|
| r_work = 0.3519 r_free = 0.3519 target = 0.134142 restraints weight = 12448.035|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.3519 r_free = 0.3519 target = 0.134146 restraints weight = 12372.813|
|-----------------------------------------------------------------------------|
r_work (final): 0.3512
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3512
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3512 r_free = 0.3512    target_work(ls_wunit_k1) = 0.132         |
| occupancies: max = 0.83  min = 0.15   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3477 r_free = 0.3477    target_work(ls_wunit_k1) = 0.130         |
| occupancies: max = 0.92  min = 0.07   number of occupancies < 0.1:        8 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 15 (23 function evaluations)
r_final: 0.3477
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7900
moved from start:          0.1605

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.050   9914  Z= 0.157
  Angle     :  0.620  10.504  13476  Z= 0.304
  Chirality :  0.042   0.216   1524
  Planarity :  0.004   0.053   1728
  Dihedral  : 16.637 123.157   1397
  Min Nonbonded Distance : 2.453

Molprobity Statistics.
  All-atom Clashscore : 1.86
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.80 %
    Favored  : 96.20 %
  Rotamer:
    Outliers :  3.60 %
    Allowed  : 17.33 %
    Favored  : 79.07 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 7.69 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.18 (0.25), residues: 1212
  helix: -0.41 (0.19), residues: 744
  sheet: -0.96 (0.64), residues: 66
  loop :  1.10 (0.35), residues: 402

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG E  83 
 TYR   0.008   0.001   TYR A 165 
 PHE   0.009   0.002   PHE B 162 
 TRP   0.016   0.001   TRP C 185 
 HIS   0.006   0.001   HIS E  13 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00379 /  0.16 ( 9912)
  covalent geometry    : angle       0.61975 /  0.30 (13476)
  hydrogen bonds       : bond        0.05099 /  3.42 (  484)
  hydrogen bonds       : angle       4.44107 /  3.30 ( 1404)
  Misc. bond           : bond        0.00078 /  0.04 (    2)

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

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

  2424 Ramachandran restraints generated.
    1212 Oldfield, 0 Emsley, 1212 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2424 Ramachandran restraints generated.
    1212 Oldfield, 0 Emsley, 1212 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  229 residues out of total 1056 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 38
    poor density    : 191
  time to evaluate  : 0.373 
Fit side-chains
   revert: symmetry clash
REVERT: B   52 ASP cc_start: 0.7727 (m-30) cc_final: 0.7489 (m-30)
REVERT: B  144 ARG cc_start: 0.7807 (tpt90) cc_final: 0.7441 (tpt170)
REVERT: C  153 ASP cc_start: 0.7155 (t0) cc_final: 0.6471 (t0)
REVERT: C  186 MET cc_start: 0.7665 (mtt) cc_final: 0.7037 (mtp)
REVERT: D    1 MET cc_start: 0.1402 (ttt) cc_final: 0.1119 (ttt)
REVERT: E    1 MET cc_start: 0.3606 (ttt) cc_final: 0.3070 (ttt)
REVERT: E   17 SER cc_start: 0.8802 (p) cc_final: 0.8375 (m)
REVERT: E  153 ASP cc_start: 0.7142 (t70) cc_final: 0.6598 (t0)
REVERT: E  186 MET cc_start: 0.7778 (mtt) cc_final: 0.7033 (mtt)
  outliers start: 38
  outliers final: 28
  residues processed: 219
  average time/residue: 0.0898
  time to fit residues: 27.4852
Evaluate side-chains
  196 residues out of total 1056 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 168
  time to evaluate  : 0.334 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   55 THR
Chi-restraints excluded: chain A residue  139 LEU
Chi-restraints excluded: chain A residue  143 VAL
Chi-restraints excluded: chain A residue  149 THR
Chi-restraints excluded: chain B residue   16 ILE
Chi-restraints excluded: chain B residue  149 THR
Chi-restraints excluded: chain B residue  152 LEU
Chi-restraints excluded: chain B residue  172 THR
Chi-restraints excluded: chain B residue  198 ASP
Chi-restraints excluded: chain C residue   16 ILE
Chi-restraints excluded: chain C residue   27 VAL
Chi-restraints excluded: chain C residue  139 LEU
Chi-restraints excluded: chain C residue  143 VAL
Chi-restraints excluded: chain C residue  149 THR
Chi-restraints excluded: chain D residue  139 LEU
Chi-restraints excluded: chain D residue  143 VAL
Chi-restraints excluded: chain E residue   57 LEU
Chi-restraints excluded: chain E residue  139 LEU
Chi-restraints excluded: chain E residue  143 VAL
Chi-restraints excluded: chain E residue  149 THR
Chi-restraints excluded: chain E residue  180 GLN
Chi-restraints excluded: chain F residue   27 VAL
Chi-restraints excluded: chain F residue   52 ASP
Chi-restraints excluded: chain F residue  127 VAL
Chi-restraints excluded: chain F residue  139 LEU
Chi-restraints excluded: chain F residue  142 ILE
Chi-restraints excluded: chain F residue  143 VAL
Chi-restraints excluded: chain F residue  172 THR
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 120
   random chunks:
   chunk 40 optimal weight:    9.9990
   chunk 43 optimal weight:    0.0270
   chunk 63 optimal weight:    2.9990
   chunk 101 optimal weight:    2.9990
   chunk 32 optimal weight:    0.8980
   chunk 24 optimal weight:    2.9990
   chunk 100 optimal weight:    2.9990
   chunk 73 optimal weight:    5.9990
   chunk 28 optimal weight:    9.9990
   chunk 87 optimal weight:    1.9990
   chunk 117 optimal weight:    6.9990
   overall best weight:    1.7844

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A  22 ASN
B 220 GLN
C  14 GLN
E  75 ASN
F  22 ASN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3769 r_free = 0.3769 target = 0.154630 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 77)----------------|
| r_work = 0.3503 r_free = 0.3503 target = 0.131801 restraints weight = 13524.834|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 22)----------------|
| r_work = 0.3503 r_free = 0.3503 target = 0.131807 restraints weight = 12542.483|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 22)----------------|
| r_work = 0.3503 r_free = 0.3503 target = 0.131807 restraints weight = 12426.677|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 22)----------------|
| r_work = 0.3503 r_free = 0.3503 target = 0.131807 restraints weight = 12414.248|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 22)----------------|
| r_work = 0.3503 r_free = 0.3503 target = 0.131807 restraints weight = 12414.248|
|-----------------------------------------------------------------------------|
r_work (final): 0.3498
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3498
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3498 r_free = 0.3498    target_work(ls_wunit_k1) = 0.131         |
| occupancies: max = 0.92  min = 0.07   number of occupancies < 0.1:        8 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3457 r_free = 0.3457    target_work(ls_wunit_k1) = 0.129         |
| occupancies: max = 1.00  min = 0.04   number of occupancies < 0.1:       94 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 26 (36 function evaluations)
r_final: 0.3457
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7903
moved from start:          0.1908

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.053   9914  Z= 0.182
  Angle     :  0.656  10.264  13476  Z= 0.321
  Chirality :  0.044   0.181   1524
  Planarity :  0.005   0.054   1728
  Dihedral  : 16.530 123.274   1397
  Min Nonbonded Distance : 2.441

Molprobity Statistics.
  All-atom Clashscore : 3.76
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.13 %
    Favored  : 95.87 %
  Rotamer:
    Outliers :  4.64 %
    Allowed  : 18.56 %
    Favored  : 76.80 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 7.69 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.15 (0.25), residues: 1212
  helix: -0.43 (0.19), residues: 744
  sheet: -0.84 (0.63), residues: 66
  loop :  1.19 (0.35), residues: 402

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 155 
 TYR   0.009   0.001   TYR A 165 
 PHE   0.013   0.002   PHE B 162 
 TRP   0.014   0.001   TRP D 185 
 HIS   0.004   0.001   HIS A  63 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00451 /  0.18 ( 9912)
  covalent geometry    : angle       0.65636 /  0.32 (13476)
  hydrogen bonds       : bond        0.05245 /  3.49 (  484)
  hydrogen bonds       : angle       4.45130 /  3.31 ( 1404)
  Misc. bond           : bond        0.00062 /  0.03 (    2)

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

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

  2424 Ramachandran restraints generated.
    1212 Oldfield, 0 Emsley, 1212 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2424 Ramachandran restraints generated.
    1212 Oldfield, 0 Emsley, 1212 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  226 residues out of total 1056 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 49
    poor density    : 177
  time to evaluate  : 0.375 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   67 MET cc_start: 0.8363 (OUTLIER) cc_final: 0.8143 (mtt)
REVERT: C  153 ASP cc_start: 0.7248 (t0) cc_final: 0.6642 (t0)
REVERT: C  186 MET cc_start: 0.7605 (mtt) cc_final: 0.7182 (mtp)
REVERT: E    1 MET cc_start: 0.2745 (ttt) cc_final: 0.2488 (ttt)
REVERT: E   17 SER cc_start: 0.8760 (p) cc_final: 0.8499 (m)
REVERT: E  153 ASP cc_start: 0.7153 (t70) cc_final: 0.6630 (t0)
REVERT: E  186 MET cc_start: 0.7698 (mtt) cc_final: 0.6991 (mtt)
  outliers start: 49
  outliers final: 36
  residues processed: 212
  average time/residue: 0.0792
  time to fit residues: 24.1160
Evaluate side-chains
  198 residues out of total 1056 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 37
    poor density    : 161
  time to evaluate  : 0.254 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   55 THR
Chi-restraints excluded: chain A residue   67 MET
Chi-restraints excluded: chain A residue  127 VAL
Chi-restraints excluded: chain A residue  139 LEU
Chi-restraints excluded: chain A residue  143 VAL
Chi-restraints excluded: chain A residue  149 THR
Chi-restraints excluded: chain B residue   16 ILE
Chi-restraints excluded: chain B residue   17 SER
Chi-restraints excluded: chain B residue   20 THR
Chi-restraints excluded: chain B residue  149 THR
Chi-restraints excluded: chain B residue  152 LEU
Chi-restraints excluded: chain B residue  172 THR
Chi-restraints excluded: chain B residue  198 ASP
Chi-restraints excluded: chain C residue   16 ILE
Chi-restraints excluded: chain C residue   27 VAL
Chi-restraints excluded: chain C residue  139 LEU
Chi-restraints excluded: chain C residue  143 VAL
Chi-restraints excluded: chain C residue  149 THR
Chi-restraints excluded: chain D residue   17 SER
Chi-restraints excluded: chain D residue   27 VAL
Chi-restraints excluded: chain D residue  139 LEU
Chi-restraints excluded: chain D residue  143 VAL
Chi-restraints excluded: chain D residue  203 LEU
Chi-restraints excluded: chain E residue   27 VAL
Chi-restraints excluded: chain E residue  139 LEU
Chi-restraints excluded: chain E residue  143 VAL
Chi-restraints excluded: chain E residue  149 THR
Chi-restraints excluded: chain E residue  180 GLN
Chi-restraints excluded: chain F residue   21 LEU
Chi-restraints excluded: chain F residue   27 VAL
Chi-restraints excluded: chain F residue   52 ASP
Chi-restraints excluded: chain F residue  127 VAL
Chi-restraints excluded: chain F residue  139 LEU
Chi-restraints excluded: chain F residue  142 ILE
Chi-restraints excluded: chain F residue  143 VAL
Chi-restraints excluded: chain F residue  172 THR
Chi-restraints excluded: chain F residue  187 THR
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 120
   random chunks:
   chunk 48 optimal weight:    9.9990
   chunk 12 optimal weight:    3.9990
   chunk 70 optimal weight:    7.9990
   chunk 27 optimal weight:    0.7980
   chunk 74 optimal weight:    2.9990
   chunk 81 optimal weight:    1.9990
   chunk 0 optimal weight:   10.0000
   chunk 116 optimal weight:    6.9990
   chunk 83 optimal weight:    3.9990
   chunk 3 optimal weight:    0.0570
   chunk 68 optimal weight:    7.9990
   overall best weight:    1.9704

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 220 GLN
C  14 GLN
C 220 GLN
F   5 GLN
F  22 ASN
F 177 GLN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3668 r_free = 0.3668 target = 0.146436 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 68)----------------|
| r_work = 0.3521 r_free = 0.3521 target = 0.133687 restraints weight = 13639.387|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3516 r_free = 0.3516 target = 0.133372 restraints weight = 17654.940|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.3511 r_free = 0.3511 target = 0.133077 restraints weight = 13471.959|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 32)----------------|
| r_work = 0.3508 r_free = 0.3508 target = 0.132810 restraints weight = 13139.624|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 31)----------------|
| r_work = 0.3511 r_free = 0.3511 target = 0.133116 restraints weight = 10730.901|
|-----------------------------------------------------------------------------|
r_work (final): 0.3506
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3507
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3507 r_free = 0.3507    target_work(ls_wunit_k1) = 0.133         |
| occupancies: max = 1.00  min = 0.04   number of occupancies < 0.1:       94 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3475 r_free = 0.3475    target_work(ls_wunit_k1) = 0.131         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:      130 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 14 (17 function evaluations)
r_final: 0.3475
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7836
moved from start:          0.2059

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.057   9914  Z= 0.196
  Angle     :  0.680   9.892  13476  Z= 0.331
  Chirality :  0.044   0.178   1524
  Planarity :  0.005   0.056   1728
  Dihedral  : 16.397 123.133   1395
  Min Nonbonded Distance : 2.496

Molprobity Statistics.
  All-atom Clashscore : 3.15
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.46 %
    Favored  : 95.54 %
  Rotamer:
    Outliers :  5.11 %
    Allowed  : 18.75 %
    Favored  : 76.14 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 7.69 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.18 (0.25), residues: 1212
  helix: -0.44 (0.19), residues: 744
  sheet: -0.87 (0.62), residues: 66
  loop :  1.14 (0.35), residues: 402

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B 163 
 TYR   0.009   0.001   TYR D 165 
 PHE   0.017   0.002   PHE B 162 
 TRP   0.014   0.001   TRP D 185 
 HIS   0.005   0.001   HIS F  13 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00491 /  0.20 ( 9912)
  covalent geometry    : angle       0.67975 /  0.33 (13476)
  hydrogen bonds       : bond        0.05383 /  3.56 (  484)
  hydrogen bonds       : angle       4.49570 /  3.34 ( 1404)
  Misc. bond           : bond        0.00063 /  0.03 (    2)

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

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

  2424 Ramachandran restraints generated.
    1212 Oldfield, 0 Emsley, 1212 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2424 Ramachandran restraints generated.
    1212 Oldfield, 0 Emsley, 1212 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  225 residues out of total 1056 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 54
    poor density    : 171
  time to evaluate  : 0.254 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  145 MET cc_start: 0.6643 (ttm) cc_final: 0.6390 (ttp)
REVERT: C   80 GLU cc_start: 0.6842 (OUTLIER) cc_final: 0.6523 (mp0)
REVERT: C  153 ASP cc_start: 0.7336 (t0) cc_final: 0.6797 (t0)
REVERT: C  186 MET cc_start: 0.7473 (mtt) cc_final: 0.7183 (mtt)
REVERT: E    1 MET cc_start: 0.2997 (ttt) cc_final: 0.2516 (ttt)
REVERT: E   17 SER cc_start: 0.8798 (p) cc_final: 0.8486 (m)
REVERT: E   52 ASP cc_start: 0.7848 (m-30) cc_final: 0.7625 (m-30)
REVERT: E  153 ASP cc_start: 0.7246 (t70) cc_final: 0.6749 (t0)
REVERT: E  186 MET cc_start: 0.7718 (mtt) cc_final: 0.7046 (mtt)
  outliers start: 54
  outliers final: 37
  residues processed: 210
  average time/residue: 0.0781
  time to fit residues: 23.6884
Evaluate side-chains
  199 residues out of total 1056 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 38
    poor density    : 161
  time to evaluate  : 0.343 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   17 SER
Chi-restraints excluded: chain A residue   55 THR
Chi-restraints excluded: chain A residue  127 VAL
Chi-restraints excluded: chain A residue  139 LEU
Chi-restraints excluded: chain A residue  143 VAL
Chi-restraints excluded: chain A residue  149 THR
Chi-restraints excluded: chain B residue   17 SER
Chi-restraints excluded: chain B residue   20 THR
Chi-restraints excluded: chain B residue  149 THR
Chi-restraints excluded: chain B residue  152 LEU
Chi-restraints excluded: chain B residue  172 THR
Chi-restraints excluded: chain B residue  198 ASP
Chi-restraints excluded: chain C residue   27 VAL
Chi-restraints excluded: chain C residue   52 ASP
Chi-restraints excluded: chain C residue   80 GLU
Chi-restraints excluded: chain C residue  139 LEU
Chi-restraints excluded: chain C residue  143 VAL
Chi-restraints excluded: chain C residue  149 THR
Chi-restraints excluded: chain D residue   17 SER
Chi-restraints excluded: chain D residue  139 LEU
Chi-restraints excluded: chain D residue  143 VAL
Chi-restraints excluded: chain D residue  185 TRP
Chi-restraints excluded: chain E residue   27 VAL
Chi-restraints excluded: chain E residue  139 LEU
Chi-restraints excluded: chain E residue  143 VAL
Chi-restraints excluded: chain E residue  149 THR
Chi-restraints excluded: chain E residue  180 GLN
Chi-restraints excluded: chain F residue   20 THR
Chi-restraints excluded: chain F residue   21 LEU
Chi-restraints excluded: chain F residue   27 VAL
Chi-restraints excluded: chain F residue   52 ASP
Chi-restraints excluded: chain F residue  127 VAL
Chi-restraints excluded: chain F residue  139 LEU
Chi-restraints excluded: chain F residue  142 ILE
Chi-restraints excluded: chain F residue  143 VAL
Chi-restraints excluded: chain F residue  152 LEU
Chi-restraints excluded: chain F residue  172 THR
Chi-restraints excluded: chain F residue  187 THR
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 120
   random chunks:
   chunk 118 optimal weight:    6.9990
   chunk 1 optimal weight:    0.0980
   chunk 85 optimal weight:    0.7980
   chunk 49 optimal weight:   10.0000
   chunk 45 optimal weight:    0.8980
   chunk 110 optimal weight:    6.9990
   chunk 100 optimal weight:    0.7980
   chunk 3 optimal weight:    0.6980
   chunk 75 optimal weight:    2.9990
   chunk 68 optimal weight:    0.0030
   chunk 57 optimal weight:    2.9990
   overall best weight:    0.4790

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 220 GLN
C  14 GLN
E 115 GLN
** F   5 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
F  22 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3663 r_free = 0.3663 target = 0.144682 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 109)---------------|
| r_work = 0.3547 r_free = 0.3547 target = 0.134981 restraints weight = 13782.653|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3556 r_free = 0.3556 target = 0.135911 restraints weight = 10065.499|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3558 r_free = 0.3558 target = 0.136109 restraints weight = 8032.565|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 39)----------------|
| r_work = 0.3566 r_free = 0.3566 target = 0.136765 restraints weight = 7561.210|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 34)----------------|
| r_work = 0.3567 r_free = 0.3567 target = 0.136842 restraints weight = 6928.924|
|-----------------------------------------------------------------------------|
r_work (final): 0.3564
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3564
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3564 r_free = 0.3564    target_work(ls_wunit_k1) = 0.136         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:      130 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3524 r_free = 0.3524    target_work(ls_wunit_k1) = 0.132         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:      126 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 18 (23 function evaluations)
r_final: 0.3524
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7626
moved from start:          0.2377

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   9914  Z= 0.124
  Angle     :  0.627   9.223  13476  Z= 0.306
  Chirality :  0.041   0.173   1524
  Planarity :  0.004   0.053   1728
  Dihedral  : 15.901 120.654   1395
  Min Nonbonded Distance : 2.481

Molprobity Statistics.
  All-atom Clashscore : 2.27
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.97 %
    Favored  : 97.03 %
  Rotamer:
    Outliers :  2.65 %
    Allowed  : 21.02 %
    Favored  : 76.33 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 7.69 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.07 (0.25), residues: 1212
  helix: -0.37 (0.19), residues: 786
  sheet: -0.81 (0.64), residues: 66
  loop :  1.81 (0.37), residues: 360

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG C  19 
 TYR   0.008   0.001   TYR F 170 
 PHE   0.006   0.001   PHE B 162 
 TRP   0.013   0.001   TRP D 185 
 HIS   0.003   0.001   HIS F  13 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00274 /  0.12 ( 9912)
  covalent geometry    : angle       0.62723 /  0.31 (13476)
  hydrogen bonds       : bond        0.04010 /  2.62 (  484)
  hydrogen bonds       : angle       4.09474 /  3.06 ( 1404)
  Misc. bond           : bond        0.00095 /  0.05 (    2)

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

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

  2424 Ramachandran restraints generated.
    1212 Oldfield, 0 Emsley, 1212 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2424 Ramachandran restraints generated.
    1212 Oldfield, 0 Emsley, 1212 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  205 residues out of total 1056 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 177
  time to evaluate  : 0.404 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  139 LEU cc_start: 0.8962 (OUTLIER) cc_final: 0.8695 (mm)
REVERT: B   31 LYS cc_start: 0.8347 (mptt) cc_final: 0.8028 (mttt)
REVERT: B  145 MET cc_start: 0.6915 (ttm) cc_final: 0.6651 (ttp)
REVERT: C   80 GLU cc_start: 0.6450 (OUTLIER) cc_final: 0.6098 (mp0)
REVERT: C  153 ASP cc_start: 0.7315 (t0) cc_final: 0.6730 (t0)
REVERT: C  186 MET cc_start: 0.7006 (mtt) cc_final: 0.6804 (mtp)
REVERT: D    1 MET cc_start: 0.0920 (ttt) cc_final: 0.0583 (ttt)
REVERT: E   17 SER cc_start: 0.8661 (p) cc_final: 0.8343 (m)
REVERT: E  144 ARG cc_start: 0.7156 (tpt90) cc_final: 0.6843 (tpt170)
REVERT: E  153 ASP cc_start: 0.7164 (t70) cc_final: 0.6695 (t0)
REVERT: E  186 MET cc_start: 0.7350 (mtt) cc_final: 0.7094 (mtt)
  outliers start: 28
  outliers final: 19
  residues processed: 197
  average time/residue: 0.0869
  time to fit residues: 24.5983
Evaluate side-chains
  186 residues out of total 1056 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 165
  time to evaluate  : 0.362 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   17 SER
Chi-restraints excluded: chain A residue   55 THR
Chi-restraints excluded: chain A residue  139 LEU
Chi-restraints excluded: chain A residue  149 THR
Chi-restraints excluded: chain B residue   17 SER
Chi-restraints excluded: chain B residue  152 LEU
Chi-restraints excluded: chain B residue  198 ASP
Chi-restraints excluded: chain C residue   16 ILE
Chi-restraints excluded: chain C residue   52 ASP
Chi-restraints excluded: chain C residue   80 GLU
Chi-restraints excluded: chain C residue  139 LEU
Chi-restraints excluded: chain C residue  143 VAL
Chi-restraints excluded: chain D residue  139 LEU
Chi-restraints excluded: chain D residue  143 VAL
Chi-restraints excluded: chain E residue   60 VAL
Chi-restraints excluded: chain E residue  139 LEU
Chi-restraints excluded: chain F residue   52 ASP
Chi-restraints excluded: chain F residue   57 LEU
Chi-restraints excluded: chain F residue  139 LEU
Chi-restraints excluded: chain F residue  142 ILE
Chi-restraints excluded: chain F residue  143 VAL
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 120
   random chunks:
   chunk 42 optimal weight:    1.9990
   chunk 4 optimal weight:    2.9990
   chunk 81 optimal weight:    0.5980
   chunk 72 optimal weight:    3.9990
   chunk 69 optimal weight:    2.9990
   chunk 5 optimal weight:    0.7980
   chunk 40 optimal weight:   10.0000
   chunk 34 optimal weight:    0.4980
   chunk 46 optimal weight:    3.9990
   chunk 113 optimal weight:    3.9990
   chunk 91 optimal weight:    2.9990
   overall best weight:    1.3784

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 177 GLN
B  22 ASN
C  14 GLN
F  22 ASN
F 177 GLN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3532 r_free = 0.3532 target = 0.132030 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.3496 r_free = 0.3496 target = 0.129093 restraints weight = 14425.778|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3494 r_free = 0.3494 target = 0.129074 restraints weight = 13361.569|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3498 r_free = 0.3498 target = 0.129341 restraints weight = 8854.851|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 44)----------------|
| r_work = 0.3502 r_free = 0.3502 target = 0.129742 restraints weight = 6297.466|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3502 r_free = 0.3502 target = 0.129764 restraints weight = 5148.295|
|-----------------------------------------------------------------------------|
r_work (final): 0.3466
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3466
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3466 r_free = 0.3466    target_work(ls_wunit_k1) = 0.127         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:      126 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3456 r_free = 0.3456    target_work(ls_wunit_k1) = 0.126         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:      143 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 12 (18 function evaluations)
r_final: 0.3456
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7651
moved from start:          0.2440

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.047   9914  Z= 0.160
  Angle     :  0.675   8.889  13476  Z= 0.326
  Chirality :  0.043   0.168   1524
  Planarity :  0.004   0.054   1728
  Dihedral  : 15.836 120.780   1393
  Min Nonbonded Distance : 2.467

Molprobity Statistics.
  All-atom Clashscore : 2.59
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.55 %
    Favored  : 96.45 %
  Rotamer:
    Outliers :  3.88 %
    Allowed  : 20.64 %
    Favored  : 75.47 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 7.69 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.01 (0.25), residues: 1212
  helix: -0.40 (0.19), residues: 786
  sheet: -0.82 (0.64), residues: 66
  loop :  1.74 (0.37), residues: 360

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG F 133 
 TYR   0.007   0.001   TYR E 165 
 PHE   0.011   0.002   PHE B 162 
 TRP   0.029   0.001   TRP F 185 
 HIS   0.004   0.001   HIS F  13 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00395 /  0.16 ( 9912)
  covalent geometry    : angle       0.67457 /  0.33 (13476)
  hydrogen bonds       : bond        0.04666 /  3.06 (  484)
  hydrogen bonds       : angle       4.22099 /  3.15 ( 1404)
  Misc. bond           : bond        0.00070 /  0.04 (    2)

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

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

  2424 Ramachandran restraints generated.
    1212 Oldfield, 0 Emsley, 1212 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2424 Ramachandran restraints generated.
    1212 Oldfield, 0 Emsley, 1212 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  204 residues out of total 1056 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 41
    poor density    : 163
  time to evaluate  : 0.383 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  145 MET cc_start: 0.6918 (ttm) cc_final: 0.6693 (ttp)
REVERT: C   80 GLU cc_start: 0.6284 (OUTLIER) cc_final: 0.5996 (mp0)
REVERT: C  153 ASP cc_start: 0.7130 (t0) cc_final: 0.6560 (t0)
REVERT: D  216 MET cc_start: 0.4799 (ttt) cc_final: 0.4520 (ttt)
REVERT: E  153 ASP cc_start: 0.6982 (t70) cc_final: 0.6525 (t0)
REVERT: E  186 MET cc_start: 0.7545 (mtt) cc_final: 0.7171 (mtt)
REVERT: F  120 THR cc_start: 0.7213 (OUTLIER) cc_final: 0.6937 (m)
  outliers start: 41
  outliers final: 31
  residues processed: 194
  average time/residue: 0.0802
  time to fit residues: 22.2450
Evaluate side-chains
  194 residues out of total 1056 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 161
  time to evaluate  : 0.246 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   17 SER
Chi-restraints excluded: chain A residue   27 VAL
Chi-restraints excluded: chain A residue   55 THR
Chi-restraints excluded: chain A residue  139 LEU
Chi-restraints excluded: chain A residue  143 VAL
Chi-restraints excluded: chain A residue  149 THR
Chi-restraints excluded: chain B residue   17 SER
Chi-restraints excluded: chain B residue   20 THR
Chi-restraints excluded: chain B residue  149 THR
Chi-restraints excluded: chain B residue  152 LEU
Chi-restraints excluded: chain B residue  198 ASP
Chi-restraints excluded: chain C residue   52 ASP
Chi-restraints excluded: chain C residue   80 GLU
Chi-restraints excluded: chain C residue  139 LEU
Chi-restraints excluded: chain C residue  143 VAL
Chi-restraints excluded: chain C residue  149 THR
Chi-restraints excluded: chain D residue   27 VAL
Chi-restraints excluded: chain D residue  139 LEU
Chi-restraints excluded: chain D residue  143 VAL
Chi-restraints excluded: chain E residue   57 LEU
Chi-restraints excluded: chain E residue   60 VAL
Chi-restraints excluded: chain E residue  139 LEU
Chi-restraints excluded: chain E residue  143 VAL
Chi-restraints excluded: chain E residue  149 THR
Chi-restraints excluded: chain F residue   21 LEU
Chi-restraints excluded: chain F residue   52 ASP
Chi-restraints excluded: chain F residue  120 THR
Chi-restraints excluded: chain F residue  139 LEU
Chi-restraints excluded: chain F residue  142 ILE
Chi-restraints excluded: chain F residue  143 VAL
Chi-restraints excluded: chain F residue  152 LEU
Chi-restraints excluded: chain F residue  172 THR
Chi-restraints excluded: chain F residue  187 THR
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 120
   random chunks:
   chunk 12 optimal weight:    1.9990
   chunk 75 optimal weight:    2.9990
   chunk 55 optimal weight:    0.9990
   chunk 38 optimal weight:    7.9990
   chunk 18 optimal weight:    3.9990
   chunk 64 optimal weight:    0.7980
   chunk 27 optimal weight:    2.9990
   chunk 108 optimal weight:    4.9990
   chunk 20 optimal weight:    0.9990
   chunk 13 optimal weight:    2.9990
   chunk 65 optimal weight:    0.7980
   overall best weight:    1.1186

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
B  22 ASN
C  14 GLN
F  22 ASN
F 220 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3530 r_free = 0.3530 target = 0.131637 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 59)----------------|
| r_work = 0.3506 r_free = 0.3506 target = 0.129804 restraints weight = 14411.735|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 52)----------------|
| r_work = 0.3513 r_free = 0.3513 target = 0.130383 restraints weight = 6961.700|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 45)----------------|
| r_work = 0.3519 r_free = 0.3519 target = 0.130826 restraints weight = 4298.951|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 45)----------------|
| r_work = 0.3523 r_free = 0.3523 target = 0.131090 restraints weight = 2703.093|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 22)----------------|
| r_work = 0.3523 r_free = 0.3523 target = 0.131090 restraints weight = 1857.682|
|-----------------------------------------------------------------------------|
r_work (final): 0.3513
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3513
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3513 r_free = 0.3513    target_work(ls_wunit_k1) = 0.130         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:      143 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3506 r_free = 0.3506    target_work(ls_wunit_k1) = 0.130         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:      191 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 11 (16 function evaluations)
r_final: 0.3506
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7610
moved from start:          0.2561

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.043   9914  Z= 0.144
  Angle     :  0.662   8.472  13476  Z= 0.320
  Chirality :  0.042   0.160   1524
  Planarity :  0.004   0.054   1728
  Dihedral  : 15.695 120.145   1393
  Min Nonbonded Distance : 2.459

Molprobity Statistics.
  All-atom Clashscore : 2.33
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.22 %
    Favored  : 96.78 %
  Rotamer:
    Outliers :  3.60 %
    Allowed  : 21.02 %
    Favored  : 75.38 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 7.69 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.11 (0.25), residues: 1212
  helix: -0.28 (0.19), residues: 780
  sheet: -0.70 (0.64), residues: 66
  loop :  1.58 (0.37), residues: 366

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B 163 
 TYR   0.007   0.001   TYR F 170 
 PHE   0.010   0.001   PHE B 162 
 TRP   0.026   0.001   TRP F 185 
 HIS   0.004   0.001   HIS F  13 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00351 /  0.14 ( 9912)
  covalent geometry    : angle       0.66202 /  0.32 (13476)
  hydrogen bonds       : bond        0.04360 /  2.88 (  484)
  hydrogen bonds       : angle       4.15322 /  3.09 ( 1404)
  Misc. bond           : bond        0.00080 /  0.04 (    2)

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

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

  2424 Ramachandran restraints generated.
    1212 Oldfield, 0 Emsley, 1212 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2424 Ramachandran restraints generated.
    1212 Oldfield, 0 Emsley, 1212 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  211 residues out of total 1056 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 38
    poor density    : 173
  time to evaluate  : 0.295 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: C   80 GLU cc_start: 0.6479 (OUTLIER) cc_final: 0.6154 (mp0)
REVERT: C  153 ASP cc_start: 0.7094 (t0) cc_final: 0.6491 (t0)
REVERT: E  153 ASP cc_start: 0.6981 (t70) cc_final: 0.6533 (t0)
REVERT: E  186 MET cc_start: 0.7399 (mtt) cc_final: 0.7171 (mtt)
REVERT: F  120 THR cc_start: 0.6988 (OUTLIER) cc_final: 0.6782 (m)
  outliers start: 38
  outliers final: 27
  residues processed: 203
  average time/residue: 0.0822
  time to fit residues: 24.0136
Evaluate side-chains
  194 residues out of total 1056 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 165
  time to evaluate  : 0.365 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   55 THR
Chi-restraints excluded: chain A residue  139 LEU
Chi-restraints excluded: chain A residue  143 VAL
Chi-restraints excluded: chain A residue  149 THR
Chi-restraints excluded: chain B residue   17 SER
Chi-restraints excluded: chain B residue  149 THR
Chi-restraints excluded: chain B residue  152 LEU
Chi-restraints excluded: chain B residue  198 ASP
Chi-restraints excluded: chain C residue   52 ASP
Chi-restraints excluded: chain C residue   80 GLU
Chi-restraints excluded: chain C residue  139 LEU
Chi-restraints excluded: chain C residue  143 VAL
Chi-restraints excluded: chain D residue   27 VAL
Chi-restraints excluded: chain D residue  139 LEU
Chi-restraints excluded: chain D residue  143 VAL
Chi-restraints excluded: chain E residue   57 LEU
Chi-restraints excluded: chain E residue   60 VAL
Chi-restraints excluded: chain E residue  139 LEU
Chi-restraints excluded: chain E residue  143 VAL
Chi-restraints excluded: chain E residue  149 THR
Chi-restraints excluded: chain F residue   20 THR
Chi-restraints excluded: chain F residue   21 LEU
Chi-restraints excluded: chain F residue   52 ASP
Chi-restraints excluded: chain F residue  120 THR
Chi-restraints excluded: chain F residue  139 LEU
Chi-restraints excluded: chain F residue  142 ILE
Chi-restraints excluded: chain F residue  143 VAL
Chi-restraints excluded: chain F residue  152 LEU
Chi-restraints excluded: chain F residue  172 THR
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 120
   random chunks:
   chunk 46 optimal weight:    2.9990
   chunk 42 optimal weight:    0.9990
   chunk 70 optimal weight:    0.5980
   chunk 86 optimal weight:    1.9990
   chunk 95 optimal weight:    0.7980
   chunk 9 optimal weight:    1.9990
   chunk 101 optimal weight:    0.9980
   chunk 66 optimal weight:    0.9980
   chunk 98 optimal weight:   10.0000
   chunk 92 optimal weight:    0.9990
   chunk 25 optimal weight:    0.9990
   overall best weight:    0.8782

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
C  14 GLN
C 194 ASN
F  22 ASN
F 177 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3520 r_free = 0.3520 target = 0.130931 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3507 r_free = 0.3507 target = 0.129877 restraints weight = 14457.459|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 49)----------------|
| r_work = 0.3512 r_free = 0.3512 target = 0.130295 restraints weight = 6341.772|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 44)----------------|
| r_work = 0.3515 r_free = 0.3515 target = 0.130564 restraints weight = 3387.471|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 43)----------------|
| r_work = 0.3517 r_free = 0.3517 target = 0.130731 restraints weight = 1891.209|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.3518 r_free = 0.3518 target = 0.130785 restraints weight = 1068.777|
|-----------------------------------------------------------------------------|
r_work (final): 0.3518
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3518
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3518 r_free = 0.3518    target_work(ls_wunit_k1) = 0.131         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:      191 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3515 r_free = 0.3515    target_work(ls_wunit_k1) = 0.131         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:      193 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 8 (16 function evaluations)
r_final: 0.3515
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7582
moved from start:          0.2662

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039   9914  Z= 0.138
  Angle     :  0.689   9.896  13476  Z= 0.331
  Chirality :  0.042   0.234   1524
  Planarity :  0.004   0.054   1728
  Dihedral  : 15.566 119.552   1393
  Min Nonbonded Distance : 2.457

Molprobity Statistics.
  All-atom Clashscore : 2.23
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.30 %
    Favored  : 96.70 %
  Rotamer:
    Outliers :  3.60 %
    Allowed  : 21.21 %
    Favored  : 75.19 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 7.69 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.12 (0.25), residues: 1212
  helix: -0.26 (0.19), residues: 780
  sheet: -0.69 (0.65), residues: 66
  loop :  1.57 (0.37), residues: 366

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG F 133 
 TYR   0.007   0.001   TYR F 170 
 PHE   0.008   0.001   PHE B 162 
 TRP   0.025   0.001   TRP F 185 
 HIS   0.004   0.001   HIS F  13 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00332 /  0.14 ( 9912)
  covalent geometry    : angle       0.68943 /  0.33 (13476)
  hydrogen bonds       : bond        0.04179 /  2.76 (  484)
  hydrogen bonds       : angle       4.10903 /  3.04 ( 1404)
  Misc. bond           : bond        0.00083 /  0.04 (    2)

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

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

  2424 Ramachandran restraints generated.
    1212 Oldfield, 0 Emsley, 1212 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2424 Ramachandran restraints generated.
    1212 Oldfield, 0 Emsley, 1212 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  205 residues out of total 1056 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 38
    poor density    : 167
  time to evaluate  : 0.444 
Fit side-chains
   revert: symmetry clash
REVERT: C   80 GLU cc_start: 0.6403 (OUTLIER) cc_final: 0.6093 (mp0)
REVERT: C  153 ASP cc_start: 0.7033 (t0) cc_final: 0.6381 (t0)
REVERT: C  186 MET cc_start: 0.6568 (mpp) cc_final: 0.6013 (mtm)
REVERT: D   52 ASP cc_start: 0.7432 (m-30) cc_final: 0.7208 (m-30)
REVERT: E  139 LEU cc_start: 0.8980 (OUTLIER) cc_final: 0.8517 (mt)
REVERT: E  153 ASP cc_start: 0.6933 (t70) cc_final: 0.6525 (t0)
REVERT: E  177 GLN cc_start: 0.8019 (tp40) cc_final: 0.7780 (tt0)
REVERT: F  120 THR cc_start: 0.7031 (OUTLIER) cc_final: 0.6761 (m)
  outliers start: 38
  outliers final: 30
  residues processed: 194
  average time/residue: 0.0783
  time to fit residues: 21.8749
Evaluate side-chains
  192 residues out of total 1056 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 159
  time to evaluate  : 0.266 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   20 THR
Chi-restraints excluded: chain A residue   55 THR
Chi-restraints excluded: chain A residue  139 LEU
Chi-restraints excluded: chain A residue  143 VAL
Chi-restraints excluded: chain A residue  149 THR
Chi-restraints excluded: chain B residue   17 SER
Chi-restraints excluded: chain B residue   20 THR
Chi-restraints excluded: chain B residue  149 THR
Chi-restraints excluded: chain B residue  152 LEU
Chi-restraints excluded: chain C residue   52 ASP
Chi-restraints excluded: chain C residue   80 GLU
Chi-restraints excluded: chain C residue  139 LEU
Chi-restraints excluded: chain C residue  143 VAL
Chi-restraints excluded: chain C residue  149 THR
Chi-restraints excluded: chain D residue   27 VAL
Chi-restraints excluded: chain D residue  139 LEU
Chi-restraints excluded: chain D residue  143 VAL
Chi-restraints excluded: chain E residue   57 LEU
Chi-restraints excluded: chain E residue   60 VAL
Chi-restraints excluded: chain E residue  139 LEU
Chi-restraints excluded: chain E residue  143 VAL
Chi-restraints excluded: chain E residue  149 THR
Chi-restraints excluded: chain E residue  198 ASP
Chi-restraints excluded: chain F residue   20 THR
Chi-restraints excluded: chain F residue   21 LEU
Chi-restraints excluded: chain F residue   52 ASP
Chi-restraints excluded: chain F residue   57 LEU
Chi-restraints excluded: chain F residue  120 THR
Chi-restraints excluded: chain F residue  127 VAL
Chi-restraints excluded: chain F residue  139 LEU
Chi-restraints excluded: chain F residue  142 ILE
Chi-restraints excluded: chain F residue  143 VAL
Chi-restraints excluded: chain F residue  152 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 120
   random chunks:
   chunk 118 optimal weight:    5.9990
   chunk 76 optimal weight:    0.9990
   chunk 88 optimal weight:    4.9990
   chunk 23 optimal weight:    0.7980
   chunk 92 optimal weight:    0.9990
   chunk 20 optimal weight:    7.9990
   chunk 31 optimal weight:    0.9980
   chunk 115 optimal weight:    2.9990
   chunk 107 optimal weight:    6.9990
   chunk 54 optimal weight:    0.9980
   chunk 90 optimal weight:   10.0000
   overall best weight:    0.9584

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
C  14 GLN
F  22 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3539 r_free = 0.3539 target = 0.132424 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3529 r_free = 0.3529 target = 0.131568 restraints weight = 14535.081|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3533 r_free = 0.3533 target = 0.131894 restraints weight = 6291.415|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.3535 r_free = 0.3535 target = 0.132136 restraints weight = 3106.801|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 49)----------------|
| r_work = 0.3537 r_free = 0.3537 target = 0.132276 restraints weight = 1682.500|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 32)----------------|
| r_work = 0.3538 r_free = 0.3538 target = 0.132338 restraints weight = 889.710|
|-----------------------------------------------------------------------------|
r_work (final): 0.3538
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3538
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3538 r_free = 0.3538    target_work(ls_wunit_k1) = 0.132         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:      193 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3535 r_free = 0.3535    target_work(ls_wunit_k1) = 0.132         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:      202 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 7 (15 function evaluations)
r_final: 0.3535
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7571
moved from start:          0.2759

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.041   9914  Z= 0.145
  Angle     :  0.712   9.474  13476  Z= 0.342
  Chirality :  0.043   0.217   1524
  Planarity :  0.004   0.055   1728
  Dihedral  : 15.478 119.251   1393
  Min Nonbonded Distance : 2.453

Molprobity Statistics.
  All-atom Clashscore : 2.43
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.05 %
    Favored  : 96.95 %
  Rotamer:
    Outliers :  3.41 %
    Allowed  : 21.78 %
    Favored  : 74.81 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 7.69 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.22 (0.26), residues: 1212
  helix: -0.20 (0.19), residues: 780
  sheet: -0.61 (0.66), residues: 66
  loop :  1.64 (0.37), residues: 366

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG E 163 
 TYR   0.007   0.001   TYR F 170 
 PHE   0.008   0.001   PHE B 162 
 TRP   0.031   0.001   TRP F 185 
 HIS   0.004   0.001   HIS F  13 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00351 /  0.15 ( 9912)
  covalent geometry    : angle       0.71232 /  0.34 (13476)
  hydrogen bonds       : bond        0.04164 /  2.75 (  484)
  hydrogen bonds       : angle       4.13177 /  3.05 ( 1404)
  Misc. bond           : bond        0.00080 /  0.04 (    2)

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

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

  2424 Ramachandran restraints generated.
    1212 Oldfield, 0 Emsley, 1212 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2424 Ramachandran restraints generated.
    1212 Oldfield, 0 Emsley, 1212 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  204 residues out of total 1056 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 168
  time to evaluate  : 0.360 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A    1 MET cc_start: 0.2764 (tpp) cc_final: 0.2405 (tpp)
REVERT: B    1 MET cc_start: 0.2625 (tpp) cc_final: 0.2395 (tpp)
REVERT: C   80 GLU cc_start: 0.6380 (OUTLIER) cc_final: 0.6059 (mp0)
REVERT: C  153 ASP cc_start: 0.7031 (t0) cc_final: 0.6397 (t0)
REVERT: D    1 MET cc_start: 0.1310 (ttt) cc_final: 0.1109 (ttt)
REVERT: D   52 ASP cc_start: 0.7587 (m-30) cc_final: 0.7321 (m-30)
REVERT: E  153 ASP cc_start: 0.6921 (t70) cc_final: 0.6421 (t0)
  outliers start: 36
  outliers final: 30
  residues processed: 194
  average time/residue: 0.0786
  time to fit residues: 22.0584
Evaluate side-chains
  195 residues out of total 1056 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 164
  time to evaluate  : 0.346 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   20 THR
Chi-restraints excluded: chain A residue   55 THR
Chi-restraints excluded: chain A residue  139 LEU
Chi-restraints excluded: chain A residue  143 VAL
Chi-restraints excluded: chain A residue  149 THR
Chi-restraints excluded: chain B residue   17 SER
Chi-restraints excluded: chain B residue   20 THR
Chi-restraints excluded: chain B residue  149 THR
Chi-restraints excluded: chain B residue  152 LEU
Chi-restraints excluded: chain C residue   80 GLU
Chi-restraints excluded: chain C residue  139 LEU
Chi-restraints excluded: chain C residue  143 VAL
Chi-restraints excluded: chain C residue  149 THR
Chi-restraints excluded: chain D residue   27 VAL
Chi-restraints excluded: chain D residue  139 LEU
Chi-restraints excluded: chain E residue   52 ASP
Chi-restraints excluded: chain E residue   57 LEU
Chi-restraints excluded: chain E residue   60 VAL
Chi-restraints excluded: chain E residue  139 LEU
Chi-restraints excluded: chain E residue  143 VAL
Chi-restraints excluded: chain E residue  149 THR
Chi-restraints excluded: chain E residue  198 ASP
Chi-restraints excluded: chain F residue   20 THR
Chi-restraints excluded: chain F residue   21 LEU
Chi-restraints excluded: chain F residue   52 ASP
Chi-restraints excluded: chain F residue   57 LEU
Chi-restraints excluded: chain F residue  127 VAL
Chi-restraints excluded: chain F residue  139 LEU
Chi-restraints excluded: chain F residue  142 ILE
Chi-restraints excluded: chain F residue  143 VAL
Chi-restraints excluded: chain F residue  152 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 120
   random chunks:
   chunk 114 optimal weight:    3.9990
   chunk 102 optimal weight:    3.9990
   chunk 46 optimal weight:    0.9990
   chunk 9 optimal weight:   10.0000
   chunk 67 optimal weight:    3.9990
   chunk 101 optimal weight:    0.7980
   chunk 34 optimal weight:    2.9990
   chunk 35 optimal weight:    0.6980
   chunk 52 optimal weight:    0.9990
   chunk 71 optimal weight:    0.9980
   chunk 87 optimal weight:    2.9990
   overall best weight:    0.8984

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
C  14 GLN
E 184 ASN
E 194 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3537 r_free = 0.3537 target = 0.132215 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3527 r_free = 0.3527 target = 0.131368 restraints weight = 14449.794|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 42)----------------|
| r_work = 0.3531 r_free = 0.3531 target = 0.131752 restraints weight = 6022.642|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 57)----------------|
| r_work = 0.3534 r_free = 0.3534 target = 0.131980 restraints weight = 2841.688|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 40)----------------|
| r_work = 0.3535 r_free = 0.3535 target = 0.132070 restraints weight = 1473.211|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 22)----------------|
| r_work = 0.3535 r_free = 0.3535 target = 0.132070 restraints weight = 777.969|
|-----------------------------------------------------------------------------|
r_work (final): 0.3535
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3535
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3535 r_free = 0.3535    target_work(ls_wunit_k1) = 0.132         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:      202 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3531 r_free = 0.3531    target_work(ls_wunit_k1) = 0.132         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:      227 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 9 (16 function evaluations)
r_final: 0.3531
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7573
moved from start:          0.2873

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039   9914  Z= 0.143
  Angle     :  0.707   9.154  13476  Z= 0.342
  Chirality :  0.043   0.227   1524
  Planarity :  0.004   0.054   1728
  Dihedral  : 15.375 118.859   1392
  Min Nonbonded Distance : 2.454

Molprobity Statistics.
  All-atom Clashscore : 2.28
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.22 %
    Favored  : 96.78 %
  Rotamer:
    Outliers :  2.94 %
    Allowed  : 22.25 %
    Favored  : 74.81 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 7.69 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.27 (0.26), residues: 1212
  helix: -0.23 (0.19), residues: 786
  sheet: -0.55 (0.67), residues: 66
  loop :  1.87 (0.37), residues: 360

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 163 
 TYR   0.008   0.001   TYR F 170 
 PHE   0.009   0.001   PHE B 162 
 TRP   0.030   0.001   TRP F 185 
 HIS   0.004   0.001   HIS F  13 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00344 /  0.14 ( 9912)
  covalent geometry    : angle       0.70677 /  0.34 (13476)
  hydrogen bonds       : bond        0.04043 /  2.68 (  484)
  hydrogen bonds       : angle       4.11738 /  3.03 ( 1404)
  Misc. bond           : bond        0.00082 /  0.04 (    2)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1415.35 seconds
wall clock time: 25 minutes 5.54 seconds (1505.54 seconds total)