Starting phenix.real_space_refine
on Wed Mar  4 11:08:32 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/6i5u_4420/03_2026/6i5u_4420.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/6i5u_4420/03_2026/6i5u_4420.map

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

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

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/6i5u_4420/03_2026/6i5u_4420.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/6i5u_4420/03_2026/6i5u_4420.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/6i5u_4420/03_2026/6i5u_4420.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/6i5u_4420/03_2026/6i5u_4420.cif"
  }
  resolution = 3.9
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.007
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 4
    Type Number    sf(0)   Gaussians
     S      78      5.16       5
     C    8550      2.51       5
     N    2286      2.21       5
     O    2442      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 12 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 13356
  Number of models: 1
  Model: ""
    Number of chains: 1
    Chain: "F"
      Number of atoms: 2226
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 289, 2226
          Classifications: {'peptide': 289}
          Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 274}
          Chain breaks: 1
  Restraints were copied for chains:
    E, D, C, B, A
  Residues with excluded nonbonded symmetry interactions: 510
    residue:
      pdb=" N   ARG F  37 " occ=0.97
      ... (9 atoms not shown)
      pdb=" NH2 ARG F  37 " occ=0.93
    residue:
      pdb=" N   ALA F  38 " occ=0.97
      ... (3 atoms not shown)
      pdb=" CB  ALA F  38 " occ=0.97
    residue:
      pdb=" N   VAL F  41 " occ=0.97
      ... (5 atoms not shown)
      pdb=" CG2 VAL F  41 " occ=0.93
    residue:
      pdb=" N   GLN F  42 " occ=0.97
      ... (7 atoms not shown)
      pdb=" NE2 GLN F  42 " occ=0.95
    residue:
      pdb=" N   ALA F  43 " occ=0.97
      ... (3 atoms not shown)
      pdb=" CB  ALA F  43 " occ=0.97
    residue:
      pdb=" N   VAL F  46 " occ=0.97
      ... (5 atoms not shown)
      pdb=" CG2 VAL F  46 " occ=0.94
    residue:
      pdb=" N   ALA F  52 " occ=0.96
      ... (3 atoms not shown)
      pdb=" CB  ALA F  52 " occ=0.93
    residue:
      pdb=" N   LYS F  56 " occ=0.97
      ... (7 atoms not shown)
      pdb=" NZ  LYS F  56 " occ=0.94
    residue:
      pdb=" N   ALA F  57 " occ=0.97
      ... (3 atoms not shown)
      pdb=" CB  ALA F  57 " occ=0.97
    residue:
      pdb=" N   LEU F  60 " occ=0.97
      ... (6 atoms not shown)
      pdb=" CD2 LEU F  60 " occ=0.80
    residue:
      pdb=" N   GLU F  63 " occ=0.97
      ... (7 atoms not shown)
      pdb=" OE2 GLU F  63 " occ=0.80
    residue:
      pdb=" N   ALA F  64 " occ=0.97
      ... (3 atoms not shown)
      pdb=" CB  ALA F  64 " occ=0.97
    ... (remaining 498 not shown)
  Time building chain proxies: 1.67, per 1000 atoms: 0.13
  Number of scatterers: 13356
  At special positions: 0
  Unit cell: (117.3, 132.6, 130.9, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     S      78     16.00
     O    2442      8.00
     N    2286      7.00
     C    8550      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 0.98
  Conformation dependent library (CDL) restraints added in 719.5 milliseconds
  

  3420 Ramachandran restraints generated.
    1710 Oldfield, 0 Emsley, 1710 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  3156

  Finding SS restraints...
    Secondary structure from input PDB file:
      36 helices and 21 sheets defined
      22.8% alpha, 16.1% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.54
  Creating SS restraints...
    Processing helix  chain 'F' and resid 54 through 66
    Processing helix  chain 'F' and resid 96 through 108
      removed outlier: 4.371A  pdb=" N   ARG F 100 " --> pdb=" O   THR F  96 " (cutoff:3.500A)
      removed outlier: 4.019A  pdb=" N   ASP F 101 " --> pdb=" O   ALA F  97 " (cutoff:3.500A)
      removed outlier: 5.520A  pdb=" N   ASP F 102 " --> pdb=" O   LYS F  98 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 115 through 127
      removed outlier: 3.511A  pdb=" N   GLU F 119 " --> pdb=" O   GLY F 115 " (cutoff:3.500A)
      removed outlier: 3.864A  pdb=" N   ARG F 120 " --> pdb=" O   PRO F 116 " (cutoff:3.500A)
      removed outlier: 3.929A  pdb=" N   LEU F 121 " --> pdb=" O   GLU F 117 " (cutoff:3.500A)
      removed outlier: 3.632A  pdb=" N   LYS F 127 " --> pdb=" O   LEU F 123 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 202 through 210
      removed outlier: 3.854A  pdb=" N   ARG F 206 " --> pdb=" O   MET F 202 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 211 through 213
      No H-bonds generated for 'chain 'F' and resid 211 through 213'
    Processing helix  chain 'F' and resid 225 through 239
      removed outlier: 4.437A  pdb=" N   LEU F 229 " --> pdb=" O   ARG F 225 " (cutoff:3.500A)
      removed outlier: 3.678A  pdb=" N   ALA F 230 " --> pdb=" O   GLU F 226 " (cutoff:3.500A)
      removed outlier: 3.904A  pdb=" N   HIS F 234 " --> pdb=" O   ALA F 230 " (cutoff:3.500A)
      removed outlier: 3.907A  pdb=" N   ILE F 235 " --> pdb=" O   SER F 231 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 54 through 66
    Processing helix  chain 'E' and resid 96 through 108
      removed outlier: 4.371A  pdb=" N   ARG E 100 " --> pdb=" O   THR E  96 " (cutoff:3.500A)
      removed outlier: 4.019A  pdb=" N   ASP E 101 " --> pdb=" O   ALA E  97 " (cutoff:3.500A)
      removed outlier: 5.520A  pdb=" N   ASP E 102 " --> pdb=" O   LYS E  98 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 115 through 127
      removed outlier: 3.511A  pdb=" N   GLU E 119 " --> pdb=" O   GLY E 115 " (cutoff:3.500A)
      removed outlier: 3.864A  pdb=" N   ARG E 120 " --> pdb=" O   PRO E 116 " (cutoff:3.500A)
      removed outlier: 3.929A  pdb=" N   LEU E 121 " --> pdb=" O   GLU E 117 " (cutoff:3.500A)
      removed outlier: 3.633A  pdb=" N   LYS E 127 " --> pdb=" O   LEU E 123 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 202 through 210
      removed outlier: 3.855A  pdb=" N   ARG E 206 " --> pdb=" O   MET E 202 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 211 through 213
      No H-bonds generated for 'chain 'E' and resid 211 through 213'
    Processing helix  chain 'E' and resid 225 through 239
      removed outlier: 4.437A  pdb=" N   LEU E 229 " --> pdb=" O   ARG E 225 " (cutoff:3.500A)
      removed outlier: 3.679A  pdb=" N   ALA E 230 " --> pdb=" O   GLU E 226 " (cutoff:3.500A)
      removed outlier: 3.905A  pdb=" N   HIS E 234 " --> pdb=" O   ALA E 230 " (cutoff:3.500A)
      removed outlier: 3.907A  pdb=" N   ILE E 235 " --> pdb=" O   SER E 231 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 54 through 66
    Processing helix  chain 'D' and resid 96 through 108
      removed outlier: 4.371A  pdb=" N   ARG D 100 " --> pdb=" O   THR D  96 " (cutoff:3.500A)
      removed outlier: 4.020A  pdb=" N   ASP D 101 " --> pdb=" O   ALA D  97 " (cutoff:3.500A)
      removed outlier: 5.520A  pdb=" N   ASP D 102 " --> pdb=" O   LYS D  98 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 115 through 127
      removed outlier: 3.511A  pdb=" N   GLU D 119 " --> pdb=" O   GLY D 115 " (cutoff:3.500A)
      removed outlier: 3.864A  pdb=" N   ARG D 120 " --> pdb=" O   PRO D 116 " (cutoff:3.500A)
      removed outlier: 3.928A  pdb=" N   LEU D 121 " --> pdb=" O   GLU D 117 " (cutoff:3.500A)
      removed outlier: 3.632A  pdb=" N   LYS D 127 " --> pdb=" O   LEU D 123 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 202 through 210
      removed outlier: 3.854A  pdb=" N   ARG D 206 " --> pdb=" O   MET D 202 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 211 through 213
      No H-bonds generated for 'chain 'D' and resid 211 through 213'
    Processing helix  chain 'D' and resid 225 through 239
      removed outlier: 4.438A  pdb=" N   LEU D 229 " --> pdb=" O   ARG D 225 " (cutoff:3.500A)
      removed outlier: 3.679A  pdb=" N   ALA D 230 " --> pdb=" O   GLU D 226 " (cutoff:3.500A)
      removed outlier: 3.906A  pdb=" N   HIS D 234 " --> pdb=" O   ALA D 230 " (cutoff:3.500A)
      removed outlier: 3.907A  pdb=" N   ILE D 235 " --> pdb=" O   SER D 231 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 54 through 66
    Processing helix  chain 'C' and resid 96 through 108
      removed outlier: 4.372A  pdb=" N   ARG C 100 " --> pdb=" O   THR C  96 " (cutoff:3.500A)
      removed outlier: 4.020A  pdb=" N   ASP C 101 " --> pdb=" O   ALA C  97 " (cutoff:3.500A)
      removed outlier: 5.519A  pdb=" N   ASP C 102 " --> pdb=" O   LYS C  98 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 115 through 127
      removed outlier: 3.511A  pdb=" N   GLU C 119 " --> pdb=" O   GLY C 115 " (cutoff:3.500A)
      removed outlier: 3.863A  pdb=" N   ARG C 120 " --> pdb=" O   PRO C 116 " (cutoff:3.500A)
      removed outlier: 3.929A  pdb=" N   LEU C 121 " --> pdb=" O   GLU C 117 " (cutoff:3.500A)
      removed outlier: 3.632A  pdb=" N   LYS C 127 " --> pdb=" O   LEU C 123 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 202 through 210
      removed outlier: 3.854A  pdb=" N   ARG C 206 " --> pdb=" O   MET C 202 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 211 through 213
      No H-bonds generated for 'chain 'C' and resid 211 through 213'
    Processing helix  chain 'C' and resid 225 through 239
      removed outlier: 4.438A  pdb=" N   LEU C 229 " --> pdb=" O   ARG C 225 " (cutoff:3.500A)
      removed outlier: 3.679A  pdb=" N   ALA C 230 " --> pdb=" O   GLU C 226 " (cutoff:3.500A)
      removed outlier: 3.905A  pdb=" N   HIS C 234 " --> pdb=" O   ALA C 230 " (cutoff:3.500A)
      removed outlier: 3.907A  pdb=" N   ILE C 235 " --> pdb=" O   SER C 231 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 54 through 66
    Processing helix  chain 'B' and resid 96 through 108
      removed outlier: 4.372A  pdb=" N   ARG B 100 " --> pdb=" O   THR B  96 " (cutoff:3.500A)
      removed outlier: 4.020A  pdb=" N   ASP B 101 " --> pdb=" O   ALA B  97 " (cutoff:3.500A)
      removed outlier: 5.520A  pdb=" N   ASP B 102 " --> pdb=" O   LYS B  98 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 115 through 127
      removed outlier: 3.511A  pdb=" N   GLU B 119 " --> pdb=" O   GLY B 115 " (cutoff:3.500A)
      removed outlier: 3.864A  pdb=" N   ARG B 120 " --> pdb=" O   PRO B 116 " (cutoff:3.500A)
      removed outlier: 3.929A  pdb=" N   LEU B 121 " --> pdb=" O   GLU B 117 " (cutoff:3.500A)
      removed outlier: 3.631A  pdb=" N   LYS B 127 " --> pdb=" O   LEU B 123 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 202 through 210
      removed outlier: 3.854A  pdb=" N   ARG B 206 " --> pdb=" O   MET B 202 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 211 through 213
      No H-bonds generated for 'chain 'B' and resid 211 through 213'
    Processing helix  chain 'B' and resid 225 through 239
      removed outlier: 4.437A  pdb=" N   LEU B 229 " --> pdb=" O   ARG B 225 " (cutoff:3.500A)
      removed outlier: 3.680A  pdb=" N   ALA B 230 " --> pdb=" O   GLU B 226 " (cutoff:3.500A)
      removed outlier: 3.905A  pdb=" N   HIS B 234 " --> pdb=" O   ALA B 230 " (cutoff:3.500A)
      removed outlier: 3.907A  pdb=" N   ILE B 235 " --> pdb=" O   SER B 231 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 54 through 66
    Processing helix  chain 'A' and resid 96 through 108
      removed outlier: 4.371A  pdb=" N   ARG A 100 " --> pdb=" O   THR A  96 " (cutoff:3.500A)
      removed outlier: 4.019A  pdb=" N   ASP A 101 " --> pdb=" O   ALA A  97 " (cutoff:3.500A)
      removed outlier: 5.519A  pdb=" N   ASP A 102 " --> pdb=" O   LYS A  98 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 115 through 127
      removed outlier: 3.510A  pdb=" N   GLU A 119 " --> pdb=" O   GLY A 115 " (cutoff:3.500A)
      removed outlier: 3.864A  pdb=" N   ARG A 120 " --> pdb=" O   PRO A 116 " (cutoff:3.500A)
      removed outlier: 3.928A  pdb=" N   LEU A 121 " --> pdb=" O   GLU A 117 " (cutoff:3.500A)
      removed outlier: 3.632A  pdb=" N   LYS A 127 " --> pdb=" O   LEU A 123 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 202 through 210
      removed outlier: 3.854A  pdb=" N   ARG A 206 " --> pdb=" O   MET A 202 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 211 through 213
      No H-bonds generated for 'chain 'A' and resid 211 through 213'
    Processing helix  chain 'A' and resid 225 through 239
      removed outlier: 4.437A  pdb=" N   LEU A 229 " --> pdb=" O   ARG A 225 " (cutoff:3.500A)
      removed outlier: 3.678A  pdb=" N   ALA A 230 " --> pdb=" O   GLU A 226 " (cutoff:3.500A)
      removed outlier: 3.905A  pdb=" N   HIS A 234 " --> pdb=" O   ALA A 230 " (cutoff:3.500A)
      removed outlier: 3.907A  pdb=" N   ILE A 235 " --> pdb=" O   SER A 231 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'F' and resid 157 through 160
      removed outlier: 4.320A  pdb=" N   GLY F 159 " --> pdb=" O   PHE F 150 " (cutoff:3.500A)
      removed outlier: 3.519A  pdb=" N   PHE F 150 " --> pdb=" O   GLY F 159 " (cutoff:3.500A)
      removed outlier: 3.708A  pdb=" N   LEU F  71 " --> pdb=" O   ARG F  37 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'F' and resid 138 through 139
    Processing sheet with id=AA3, first strand: chain 'F' and resid 186 through 187
      removed outlier: 6.568A  pdb=" N   TYR F 217 " --> pdb=" O   LEU F 244 " (cutoff:3.500A)
      removed outlier: 8.036A  pdb=" N   ALA F 246 " --> pdb=" O   TYR F 217 " (cutoff:3.500A)
      removed outlier: 6.903A  pdb=" N   ALA F 219 " --> pdb=" O   ALA F 246 " (cutoff:3.500A)
      removed outlier: 7.005A  pdb=" N   ILE F 283 " --> pdb=" O   LEU F 291 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'E' and resid 330 through 334
      removed outlier: 3.531A  pdb=" N   SER E 331 " --> pdb=" O   ASN F 333 " (cutoff:3.500A)
      removed outlier: 3.511A  pdb=" N   SER F 331 " --> pdb=" O   ASN E 333 " (cutoff:3.500A)
      removed outlier: 8.866A  pdb=" N   SER D 343 " --> pdb=" O   PHE F 330 " (cutoff:3.500A)
      removed outlier: 6.808A  pdb=" N   LEU F 332 " --> pdb=" O   SER D 343 " (cutoff:3.500A)
      removed outlier: 7.707A  pdb=" N   LYS D 345 " --> pdb=" O   LEU F 332 " (cutoff:3.500A)
      removed outlier: 6.250A  pdb=" N   ILE F 334 " --> pdb=" O   LYS D 345 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'E' and resid 157 through 160
      removed outlier: 4.320A  pdb=" N   GLY E 159 " --> pdb=" O   PHE E 150 " (cutoff:3.500A)
      removed outlier: 3.519A  pdb=" N   PHE E 150 " --> pdb=" O   GLY E 159 " (cutoff:3.500A)
      removed outlier: 3.708A  pdb=" N   LEU E  71 " --> pdb=" O   ARG E  37 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'E' and resid 138 through 139
    Processing sheet with id=AA7, first strand: chain 'E' and resid 186 through 187
      removed outlier: 6.568A  pdb=" N   TYR E 217 " --> pdb=" O   LEU E 244 " (cutoff:3.500A)
      removed outlier: 8.036A  pdb=" N   ALA E 246 " --> pdb=" O   TYR E 217 " (cutoff:3.500A)
      removed outlier: 6.903A  pdb=" N   ALA E 219 " --> pdb=" O   ALA E 246 " (cutoff:3.500A)
      removed outlier: 7.004A  pdb=" N   ILE E 283 " --> pdb=" O   LEU E 291 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'E' and resid 342 through 345
      removed outlier: 3.531A  pdb=" N   SER C 331 " --> pdb=" O   ASN D 333 " (cutoff:3.500A)
      removed outlier: 3.519A  pdb=" N   SER D 331 " --> pdb=" O   ASN C 333 " (cutoff:3.500A)
      removed outlier: 8.854A  pdb=" N   SER B 343 " --> pdb=" O   PHE D 330 " (cutoff:3.500A)
      removed outlier: 6.814A  pdb=" N   LEU D 332 " --> pdb=" O   SER B 343 " (cutoff:3.500A)
      removed outlier: 7.712A  pdb=" N   LYS B 345 " --> pdb=" O   LEU D 332 " (cutoff:3.500A)
      removed outlier: 6.273A  pdb=" N   ILE D 334 " --> pdb=" O   LYS B 345 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'D' and resid 157 through 160
      removed outlier: 4.320A  pdb=" N   GLY D 159 " --> pdb=" O   PHE D 150 " (cutoff:3.500A)
      removed outlier: 3.519A  pdb=" N   PHE D 150 " --> pdb=" O   GLY D 159 " (cutoff:3.500A)
      removed outlier: 3.708A  pdb=" N   LEU D  71 " --> pdb=" O   ARG D  37 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'D' and resid 138 through 139
    Processing sheet with id=AB2, first strand: chain 'D' and resid 186 through 187
      removed outlier: 6.567A  pdb=" N   TYR D 217 " --> pdb=" O   LEU D 244 " (cutoff:3.500A)
      removed outlier: 8.037A  pdb=" N   ALA D 246 " --> pdb=" O   TYR D 217 " (cutoff:3.500A)
      removed outlier: 6.904A  pdb=" N   ALA D 219 " --> pdb=" O   ALA D 246 " (cutoff:3.500A)
      removed outlier: 7.005A  pdb=" N   ILE D 283 " --> pdb=" O   LEU D 291 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'C' and resid 157 through 160
      removed outlier: 4.319A  pdb=" N   GLY C 159 " --> pdb=" O   PHE C 150 " (cutoff:3.500A)
      removed outlier: 3.519A  pdb=" N   PHE C 150 " --> pdb=" O   GLY C 159 " (cutoff:3.500A)
      removed outlier: 3.709A  pdb=" N   LEU C  71 " --> pdb=" O   ARG C  37 " (cutoff:3.500A)
    Processing sheet with id=AB4, first strand: chain 'C' and resid 138 through 139
    Processing sheet with id=AB5, first strand: chain 'C' and resid 186 through 187
      removed outlier: 6.568A  pdb=" N   TYR C 217 " --> pdb=" O   LEU C 244 " (cutoff:3.500A)
      removed outlier: 8.036A  pdb=" N   ALA C 246 " --> pdb=" O   TYR C 217 " (cutoff:3.500A)
      removed outlier: 6.903A  pdb=" N   ALA C 219 " --> pdb=" O   ALA C 246 " (cutoff:3.500A)
      removed outlier: 7.005A  pdb=" N   ILE C 283 " --> pdb=" O   LEU C 291 " (cutoff:3.500A)
    Processing sheet with id=AB6, first strand: chain 'C' and resid 342 through 345
      removed outlier: 3.547A  pdb=" N   SER A 331 " --> pdb=" O   ASN B 333 " (cutoff:3.500A)
      removed outlier: 3.549A  pdb=" N   SER B 331 " --> pdb=" O   ASN A 333 " (cutoff:3.500A)
    Processing sheet with id=AB7, first strand: chain 'B' and resid 157 through 160
      removed outlier: 4.319A  pdb=" N   GLY B 159 " --> pdb=" O   PHE B 150 " (cutoff:3.500A)
      removed outlier: 3.518A  pdb=" N   PHE B 150 " --> pdb=" O   GLY B 159 " (cutoff:3.500A)
      removed outlier: 3.709A  pdb=" N   LEU B  71 " --> pdb=" O   ARG B  37 " (cutoff:3.500A)
    Processing sheet with id=AB8, first strand: chain 'B' and resid 138 through 139
    Processing sheet with id=AB9, first strand: chain 'B' and resid 186 through 187
      removed outlier: 6.568A  pdb=" N   TYR B 217 " --> pdb=" O   LEU B 244 " (cutoff:3.500A)
      removed outlier: 8.036A  pdb=" N   ALA B 246 " --> pdb=" O   TYR B 217 " (cutoff:3.500A)
      removed outlier: 6.903A  pdb=" N   ALA B 219 " --> pdb=" O   ALA B 246 " (cutoff:3.500A)
      removed outlier: 7.005A  pdb=" N   ILE B 283 " --> pdb=" O   LEU B 291 " (cutoff:3.500A)
    Processing sheet with id=AC1, first strand: chain 'A' and resid 157 through 160
      removed outlier: 4.319A  pdb=" N   GLY A 159 " --> pdb=" O   PHE A 150 " (cutoff:3.500A)
      removed outlier: 3.518A  pdb=" N   PHE A 150 " --> pdb=" O   GLY A 159 " (cutoff:3.500A)
      removed outlier: 3.709A  pdb=" N   LEU A  71 " --> pdb=" O   ARG A  37 " (cutoff:3.500A)
    Processing sheet with id=AC2, first strand: chain 'A' and resid 138 through 139
    Processing sheet with id=AC3, first strand: chain 'A' and resid 186 through 187
      removed outlier: 6.569A  pdb=" N   TYR A 217 " --> pdb=" O   LEU A 244 " (cutoff:3.500A)
      removed outlier: 8.036A  pdb=" N   ALA A 246 " --> pdb=" O   TYR A 217 " (cutoff:3.500A)
      removed outlier: 6.903A  pdb=" N   ALA A 219 " --> pdb=" O   ALA A 246 " (cutoff:3.500A)
      removed outlier: 7.005A  pdb=" N   ILE A 283 " --> pdb=" O   LEU A 291 " (cutoff:3.500A)

    348 hydrogen bonds defined for protein.
    972 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: 1.94

  Time building geometry restraints manager: 1.40 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: 4311
        1.34 -     1.46: 2757
        1.46 -     1.58: 6474
        1.58 -     1.69: 0
        1.69 -     1.81: 114
  Bond restraints: 13656
  Sorted by residual:
  bond pdb=" CA  HIS C 323 "
       pdb=" C   HIS C 323 "
    ideal  model  delta    sigma   weight residual
    1.523  1.551 -0.028 1.34e-02 5.57e+03 4.37e+00
  bond pdb=" CA  HIS D 323 "
       pdb=" C   HIS D 323 "
    ideal  model  delta    sigma   weight residual
    1.523  1.551 -0.028 1.34e-02 5.57e+03 4.29e+00
  bond pdb=" CA  HIS E 323 "
       pdb=" C   HIS E 323 "
    ideal  model  delta    sigma   weight residual
    1.523  1.551 -0.027 1.34e-02 5.57e+03 4.20e+00
  bond pdb=" CA  HIS A 323 "
       pdb=" C   HIS A 323 "
    ideal  model  delta    sigma   weight residual
    1.523  1.551 -0.027 1.34e-02 5.57e+03 4.18e+00
  bond pdb=" CA  HIS B 323 "
       pdb=" C   HIS B 323 "
    ideal  model  delta    sigma   weight residual
    1.523  1.550 -0.027 1.34e-02 5.57e+03 4.15e+00
  ... (remaining 13651 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.49: 17878
        2.49 -     4.98: 482
        4.98 -     7.47: 86
        7.47 -     9.97: 27
        9.97 -    12.46: 13
  Bond angle restraints: 18486
  Sorted by residual:
  angle pdb=" C   VAL A 320 "
        pdb=" N   VAL A 321 "
        pdb=" CA  VAL A 321 "
      ideal   model   delta    sigma   weight residual
     121.97  130.87   -8.90 1.80e+00 3.09e-01 2.45e+01
  angle pdb=" C   VAL C 320 "
        pdb=" N   VAL C 321 "
        pdb=" CA  VAL C 321 "
      ideal   model   delta    sigma   weight residual
     121.97  130.87   -8.90 1.80e+00 3.09e-01 2.44e+01
  angle pdb=" C   VAL F 320 "
        pdb=" N   VAL F 321 "
        pdb=" CA  VAL F 321 "
      ideal   model   delta    sigma   weight residual
     121.97  130.86   -8.89 1.80e+00 3.09e-01 2.44e+01
  angle pdb=" C   VAL B 320 "
        pdb=" N   VAL B 321 "
        pdb=" CA  VAL B 321 "
      ideal   model   delta    sigma   weight residual
     121.97  130.85   -8.88 1.80e+00 3.09e-01 2.43e+01
  angle pdb=" C   VAL E 320 "
        pdb=" N   VAL E 321 "
        pdb=" CA  VAL E 321 "
      ideal   model   delta    sigma   weight residual
     121.97  130.79   -8.82 1.80e+00 3.09e-01 2.40e+01
  ... (remaining 18481 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    14.50: 7576
       14.50 -    28.99: 428
       28.99 -    43.48: 90
       43.48 -    57.98: 6
       57.98 -    72.47: 6
  Dihedral angle restraints: 8106
    sinusoidal: 3162
      harmonic: 4944
  Sorted by residual:
  dihedral pdb=" CA  GLY A 322 "
           pdb=" C   GLY A 322 "
           pdb=" N   HIS A 323 "
           pdb=" CA  HIS A 323 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -107.53  -72.47     0      5.00e+00 4.00e-02 2.10e+02
  dihedral pdb=" CA  GLY C 322 "
           pdb=" C   GLY C 322 "
           pdb=" N   HIS C 323 "
           pdb=" CA  HIS C 323 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -107.53  -72.47     0      5.00e+00 4.00e-02 2.10e+02
  dihedral pdb=" CA  GLY B 322 "
           pdb=" C   GLY B 322 "
           pdb=" N   HIS B 323 "
           pdb=" CA  HIS B 323 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -107.53  -72.47     0      5.00e+00 4.00e-02 2.10e+02
  ... (remaining 8103 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.061: 1530
       0.061 -    0.122: 457
       0.122 -    0.182: 29
       0.182 -    0.243: 24
       0.243 -    0.304: 18
  Chirality restraints: 2058
  Sorted by residual:
  chirality pdb=" CB  VAL B 320 "
            pdb=" CA  VAL B 320 "
            pdb=" CG1 VAL B 320 "
            pdb=" CG2 VAL B 320 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -2.33   -0.30 2.00e-01 2.50e+01 2.31e+00
  chirality pdb=" CB  VAL F 320 "
            pdb=" CA  VAL F 320 "
            pdb=" CG1 VAL F 320 "
            pdb=" CG2 VAL F 320 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -2.33   -0.30 2.00e-01 2.50e+01 2.30e+00
  chirality pdb=" CB  VAL C 320 "
            pdb=" CA  VAL C 320 "
            pdb=" CG1 VAL C 320 "
            pdb=" CG2 VAL C 320 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -2.33   -0.30 2.00e-01 2.50e+01 2.29e+00
  ... (remaining 2055 not shown)

  Planarity restraints: 2370
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  PHE E  47 "   -0.011 2.00e-02 2.50e+03   2.29e-02 5.24e+00
        pdb=" C   PHE E  47 "    0.040 2.00e-02 2.50e+03
        pdb=" O   PHE E  47 "   -0.015 2.00e-02 2.50e+03
        pdb=" N   TYR E  48 "   -0.013 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  PHE A  47 "    0.011 2.00e-02 2.50e+03   2.28e-02 5.19e+00
        pdb=" C   PHE A  47 "   -0.039 2.00e-02 2.50e+03
        pdb=" O   PHE A  47 "    0.015 2.00e-02 2.50e+03
        pdb=" N   TYR A  48 "    0.013 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  PHE C  47 "    0.011 2.00e-02 2.50e+03   2.28e-02 5.18e+00
        pdb=" C   PHE C  47 "   -0.039 2.00e-02 2.50e+03
        pdb=" O   PHE C  47 "    0.015 2.00e-02 2.50e+03
        pdb=" N   TYR C  48 "    0.013 2.00e-02 2.50e+03
  ... (remaining 2367 not shown)

  Histogram of nonbonded interaction distances:
        2.35 -     2.86: 4512
        2.86 -     3.37: 11075
        3.37 -     3.88: 20030
        3.88 -     4.39: 22434
        4.39 -     4.90: 39873
  Nonbonded interactions: 97924
  Sorted by model distance:
  nonbonded pdb=" OE1 GLU F  89 "
            pdb=" OG1 THR F  96 "
     model   vdw
     2.350 3.040
  nonbonded pdb=" OE1 GLU E  89 "
            pdb=" OG1 THR E  96 "
     model   vdw
     2.350 3.040
  nonbonded pdb=" OE1 GLU D  89 "
            pdb=" OG1 THR D  96 "
     model   vdw
     2.350 3.040
  nonbonded pdb=" OE1 GLU C  89 "
            pdb=" OG1 THR C  96 "
     model   vdw
     2.350 3.040
  nonbonded pdb=" OE1 GLU B  89 "
            pdb=" OG1 THR B  96 "
     model   vdw
     2.350 3.040
  ... (remaining 97919 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: 0.04
Found NCS groups:
ncs_group {
  reference = chain 'F'
  selection = chain 'E'
  selection = chain 'D'
  selection = chain 'C'
  selection = chain 'B'
  selection = chain 'A'
}

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=0.50 max=1.00 mean=0.97
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:             1.580
  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:          0.280
  Check model and map are aligned:         0.020
  Set scattering table:                    0.040
  Process input model:                     12.280
  Find NCS groups from input model:        0.120
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.350
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   15.700
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8251
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.053  13656  Z= 0.250
  Angle     :  1.059  12.457  18486  Z= 0.570
  Chirality :  0.063   0.304   2058
  Planarity :  0.008   0.054   2370
  Dihedral  :  9.934  72.475   4950
  Min Nonbonded Distance : 2.350

Molprobity Statistics.
  All-atom Clashscore : 4.04
  Ramachandran Plot:
    Outliers :  0.70 %
    Allowed  : 13.68 %
    Favored  : 85.61 %
  Rotamer:
    Outliers :  0.43 %
    Allowed  :  5.15 %
    Favored  : 94.42 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 7.14 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 1.10 %

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: -5.63 (0.14), residues: 1710
  helix: -3.77 (0.15), residues: 402
  sheet: -3.64 (0.23), residues: 324
  loop : -3.89 (0.14), residues: 984

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG A 339 
 TYR   0.029   0.003   TYR E 324 
 PHE   0.011   0.002   PHE D 316 
 TRP   0.019   0.002   TRP A 198 
 HIS   0.007   0.003   HIS C 234 

Details of bonding type rmsd
  covalent geometry    : bond        0.00547 (13656)
  covalent geometry    : angle       1.05920 (18486)
  hydrogen bonds       : bond        0.24475 (  348)
  hydrogen bonds       : angle       7.88255 (  972)

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

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

  3420 Ramachandran restraints generated.
    1710 Oldfield, 0 Emsley, 1710 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3420 Ramachandran restraints generated.
    1710 Oldfield, 0 Emsley, 1710 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  479 residues out of total 1398 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 473
  time to evaluate  : 0.502 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: F  310 ASP cc_start: 0.8184 (t0) cc_final: 0.7903 (t0)
REVERT: F  317 ASP cc_start: 0.8328 (m-30) cc_final: 0.8103 (m-30)
REVERT: F  339 ARG cc_start: 0.7139 (mtt-85) cc_final: 0.6655 (ttp-170)
REVERT: E  285 SER cc_start: 0.9097 (t) cc_final: 0.8613 (p)
REVERT: E  295 ASN cc_start: 0.7828 (t0) cc_final: 0.7595 (t0)
REVERT: E  310 ASP cc_start: 0.7858 (t0) cc_final: 0.6989 (t0)
REVERT: E  335 ARG cc_start: 0.8503 (mtm-85) cc_final: 0.8133 (mtt-85)
REVERT: D  215 GLU cc_start: 0.7877 (pm20) cc_final: 0.7528 (pm20)
REVERT: D  310 ASP cc_start: 0.8262 (t0) cc_final: 0.7756 (t0)
REVERT: C   54 LEU cc_start: 0.8674 (tp) cc_final: 0.8460 (tp)
REVERT: C  285 SER cc_start: 0.9198 (t) cc_final: 0.8742 (p)
REVERT: C  295 ASN cc_start: 0.7868 (t0) cc_final: 0.7642 (t0)
REVERT: C  310 ASP cc_start: 0.8116 (t0) cc_final: 0.7165 (t0)
REVERT: C  335 ARG cc_start: 0.8557 (mtm-85) cc_final: 0.8319 (mtt-85)
REVERT: B  138 GLU cc_start: 0.8411 (pt0) cc_final: 0.8159 (pt0)
REVERT: B  310 ASP cc_start: 0.8236 (t0) cc_final: 0.7802 (t0)
REVERT: B  315 LYS cc_start: 0.9111 (mtpp) cc_final: 0.8859 (mtmt)
REVERT: A  295 ASN cc_start: 0.7863 (t0) cc_final: 0.7597 (t0)
REVERT: A  310 ASP cc_start: 0.8126 (t0) cc_final: 0.7343 (t0)
REVERT: A  335 ARG cc_start: 0.8295 (mtm-85) cc_final: 0.8089 (mtt-85)
REVERT: A  343 SER cc_start: 0.9027 (m) cc_final: 0.8691 (p)
  outliers start: 6
  outliers final: 1
  residues processed: 479
  average time/residue: 0.1641
  time to fit residues: 104.0867
Evaluate side-chains
  242 residues out of total 1398 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 241
  time to evaluate  : 0.484 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  184 VAL
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 168
   random chunks:
   chunk 98 optimal weight:   10.0000
   chunk 107 optimal weight:    0.5980
   chunk 10 optimal weight:    8.9990
   chunk 66 optimal weight:   10.0000
   chunk 130 optimal weight:    0.9980
   chunk 124 optimal weight:    0.1980
   chunk 103 optimal weight:    0.9980
   chunk 77 optimal weight:    8.9990
   chunk 122 optimal weight:    9.9990
   chunk 91 optimal weight:    8.9990
   chunk 149 optimal weight:    1.9990
   overall best weight:    0.9582

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

Flipped N/Q/H residues before XYZ refinement:
F 200 ASN
F 248 GLN
E 200 ASN
E 323 HIS
D  42 GLN
D 200 ASN
D 248 GLN
C 200 ASN
B  42 GLN
B 200 ASN
B 248 GLN
B 323 HIS
B 337 HIS
A 200 ASN
A 323 HIS

Total number of N/Q/H flips: 15

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3473 r_free = 0.3473 target = 0.134165 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.3211 r_free = 0.3211 target = 0.113170 restraints weight = 20237.210|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3243 r_free = 0.3243 target = 0.115676 restraints weight = 13996.411|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3266 r_free = 0.3266 target = 0.117423 restraints weight = 10835.156|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.3278 r_free = 0.3278 target = 0.118399 restraints weight = 9005.698|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 42)----------------|
| r_work = 0.3290 r_free = 0.3290 target = 0.119313 restraints weight = 8039.957|
|-----------------------------------------------------------------------------|
r_work (final): 0.3285
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3285
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3285 r_free = 0.3285    target_work(ls_wunit_k1) = 0.119         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2999 r_free = 0.2999    target_work(ls_wunit_k1) = 0.098         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       72 |
|-----------------------------------------------------------------------------|
r_final: 0.2999
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8455
moved from start:          0.2751

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.027  13656  Z= 0.115
  Angle     :  0.707  11.254  18486  Z= 0.355
  Chirality :  0.045   0.167   2058
  Planarity :  0.006   0.041   2370
  Dihedral  :  6.069  53.916   1903
  Min Nonbonded Distance : 2.468

Molprobity Statistics.
  All-atom Clashscore : 6.00
  Ramachandran Plot:
    Outliers :  0.88 %
    Allowed  : 10.88 %
    Favored  : 88.25 %
  Rotamer:
    Outliers :  1.72 %
    Allowed  : 13.81 %
    Favored  : 84.48 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 7.14 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.37 %

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: -4.36 (0.16), residues: 1710
  helix: -2.11 (0.22), residues: 408
  sheet: -2.35 (0.26), residues: 342
  loop : -3.61 (0.15), residues: 960

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG B 139 
 TYR   0.020   0.001   TYR C 296 
 PHE   0.008   0.001   PHE C 316 
 TRP   0.006   0.001   TRP C 198 
 HIS   0.013   0.002   HIS E 323 

Details of bonding type rmsd
  covalent geometry    : bond        0.00256 (13656)
  covalent geometry    : angle       0.70729 (18486)
  hydrogen bonds       : bond        0.04133 (  348)
  hydrogen bonds       : angle       5.40235 (  972)

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

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

  3420 Ramachandran restraints generated.
    1710 Oldfield, 0 Emsley, 1710 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3420 Ramachandran restraints generated.
    1710 Oldfield, 0 Emsley, 1710 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  291 residues out of total 1398 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 267
  time to evaluate  : 0.457 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: F  169 LEU cc_start: 0.9108 (OUTLIER) cc_final: 0.8898 (tm)
REVERT: F  317 ASP cc_start: 0.8256 (m-30) cc_final: 0.8011 (m-30)
REVERT: F  336 GLU cc_start: 0.6895 (tt0) cc_final: 0.6420 (mt-10)
REVERT: F  339 ARG cc_start: 0.7194 (mtt-85) cc_final: 0.6838 (ttp-170)
REVERT: E  295 ASN cc_start: 0.8201 (t0) cc_final: 0.7624 (p0)
REVERT: E  297 ARG cc_start: 0.7549 (mpp-170) cc_final: 0.6996 (ppt170)
REVERT: E  310 ASP cc_start: 0.8529 (t0) cc_final: 0.7811 (t0)
REVERT: C  295 ASN cc_start: 0.8038 (t0) cc_final: 0.7428 (p0)
REVERT: C  297 ARG cc_start: 0.7540 (mmt180) cc_final: 0.6746 (ppt170)
REVERT: C  310 ASP cc_start: 0.8681 (t0) cc_final: 0.7608 (t0)
REVERT: A  182 ILE cc_start: 0.8367 (mt) cc_final: 0.8083 (mt)
REVERT: A  295 ASN cc_start: 0.8091 (t0) cc_final: 0.7080 (p0)
REVERT: A  310 ASP cc_start: 0.8534 (t0) cc_final: 0.7936 (t70)
REVERT: A  343 SER cc_start: 0.8983 (m) cc_final: 0.8682 (p)
  outliers start: 24
  outliers final: 13
  residues processed: 288
  average time/residue: 0.1250
  time to fit residues: 50.9857
Evaluate side-chains
  221 residues out of total 1398 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 207
  time to evaluate  : 0.387 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain F residue  147 THR
Chi-restraints excluded: chain F residue  169 LEU
Chi-restraints excluded: chain F residue  184 VAL
Chi-restraints excluded: chain E residue  147 THR
Chi-restraints excluded: chain E residue  227 THR
Chi-restraints excluded: chain D residue  184 VAL
Chi-restraints excluded: chain D residue  241 CYS
Chi-restraints excluded: chain C residue  227 THR
Chi-restraints excluded: chain B residue  169 LEU
Chi-restraints excluded: chain B residue  184 VAL
Chi-restraints excluded: chain A residue   90 LEU
Chi-restraints excluded: chain A residue  147 THR
Chi-restraints excluded: chain A residue  184 VAL
Chi-restraints excluded: chain A residue  227 THR
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 168
   random chunks:
   chunk 26 optimal weight:    4.9990
   chunk 115 optimal weight:   50.0000
   chunk 139 optimal weight:    3.9990
   chunk 43 optimal weight:    0.9980
   chunk 154 optimal weight:    9.9990
   chunk 136 optimal weight:    5.9990
   chunk 37 optimal weight:    4.9990
   chunk 41 optimal weight:    0.9980
   chunk 89 optimal weight:    0.4980
   chunk 86 optimal weight:   20.0000
   chunk 6 optimal weight:    3.9990
   overall best weight:    2.0984

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

Flipped N/Q/H residues before XYZ refinement:
E 107 HIS
D  42 GLN
C 323 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3150 r_free = 0.3150 target = 0.109003 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.2878 r_free = 0.2878 target = 0.090064 restraints weight = 22671.573|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.2908 r_free = 0.2908 target = 0.092037 restraints weight = 15408.306|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.2926 r_free = 0.2926 target = 0.093253 restraints weight = 12002.850|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.2941 r_free = 0.2941 target = 0.094271 restraints weight = 10220.689|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 32)----------------|
| r_work = 0.2949 r_free = 0.2949 target = 0.094841 restraints weight = 9123.075|
|-----------------------------------------------------------------------------|
r_work (final): 0.2954
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2945
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2945 r_free = 0.2945    target_work(ls_wunit_k1) = 0.094         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       72 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2902 r_free = 0.2902    target_work(ls_wunit_k1) = 0.092         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:      204 |
|-----------------------------------------------------------------------------|
r_final: 0.2902
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8518
moved from start:          0.3206

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.050  13656  Z= 0.126
  Angle     :  0.695  10.881  18486  Z= 0.347
  Chirality :  0.045   0.173   2058
  Planarity :  0.005   0.038   2370
  Dihedral  :  5.849  54.506   1903
  Min Nonbonded Distance : 2.481

Molprobity Statistics.
  All-atom Clashscore : 5.25
  Ramachandran Plot:
    Outliers :  1.05 %
    Allowed  : 11.87 %
    Favored  : 87.08 %
  Rotamer:
    Outliers :  2.93 %
    Allowed  : 14.88 %
    Favored  : 82.19 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 7.14 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.37 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -3.85 (0.17), residues: 1710
  helix: -1.33 (0.25), residues: 408
  sheet: -2.02 (0.27), residues: 354
  loop : -3.49 (0.15), residues: 948

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.000   ARG E 335 
 TYR   0.017   0.001   TYR C 296 
 PHE   0.008   0.001   PHE E 242 
 TRP   0.012   0.001   TRP F 198 
 HIS   0.010   0.002   HIS E 107 

Details of bonding type rmsd
  covalent geometry    : bond        0.00299 (13656)
  covalent geometry    : angle       0.69474 (18486)
  hydrogen bonds       : bond        0.03764 (  348)
  hydrogen bonds       : angle       4.96839 (  972)

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

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

  3420 Ramachandran restraints generated.
    1710 Oldfield, 0 Emsley, 1710 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3420 Ramachandran restraints generated.
    1710 Oldfield, 0 Emsley, 1710 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  259 residues out of total 1398 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 41
    poor density    : 218
  time to evaluate  : 0.497 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: F   46 VAL cc_start: 0.8812 (p) cc_final: 0.8596 (p)
REVERT: F  317 ASP cc_start: 0.8206 (m-30) cc_final: 0.7925 (m-30)
REVERT: F  339 ARG cc_start: 0.7328 (mtt-85) cc_final: 0.6752 (ttp-170)
REVERT: E   94 SER cc_start: 0.7887 (m) cc_final: 0.7413 (p)
REVERT: E  186 ASP cc_start: 0.8277 (p0) cc_final: 0.7916 (p0)
REVERT: E  295 ASN cc_start: 0.8214 (t0) cc_final: 0.7895 (p0)
REVERT: E  297 ARG cc_start: 0.7618 (mpp-170) cc_final: 0.7057 (ppt170)
REVERT: E  305 ASP cc_start: 0.8052 (p0) cc_final: 0.7837 (p0)
REVERT: C  295 ASN cc_start: 0.8111 (t0) cc_final: 0.7634 (p0)
REVERT: C  297 ARG cc_start: 0.7541 (mmt180) cc_final: 0.6754 (ppt170)
REVERT: C  310 ASP cc_start: 0.8929 (t0) cc_final: 0.8007 (t0)
REVERT: A  182 ILE cc_start: 0.8740 (mt) cc_final: 0.8523 (mt)
REVERT: A  295 ASN cc_start: 0.8236 (t0) cc_final: 0.7242 (p0)
REVERT: A  310 ASP cc_start: 0.8806 (t0) cc_final: 0.8114 (t70)
REVERT: A  339 ARG cc_start: 0.4046 (ttt180) cc_final: 0.3537 (ttt180)
REVERT: A  343 SER cc_start: 0.9014 (m) cc_final: 0.8704 (p)
  outliers start: 41
  outliers final: 23
  residues processed: 254
  average time/residue: 0.1177
  time to fit residues: 43.3783
Evaluate side-chains
  219 residues out of total 1398 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 196
  time to evaluate  : 0.491 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain F residue   86 SER
Chi-restraints excluded: chain F residue  147 THR
Chi-restraints excluded: chain F residue  184 VAL
Chi-restraints excluded: chain F residue  241 CYS
Chi-restraints excluded: chain E residue  227 THR
Chi-restraints excluded: chain D residue   50 THR
Chi-restraints excluded: chain D residue  184 VAL
Chi-restraints excluded: chain D residue  241 CYS
Chi-restraints excluded: chain D residue  324 TYR
Chi-restraints excluded: chain C residue   61 LEU
Chi-restraints excluded: chain C residue  227 THR
Chi-restraints excluded: chain C residue  333 ASN
Chi-restraints excluded: chain B residue   61 LEU
Chi-restraints excluded: chain B residue  169 LEU
Chi-restraints excluded: chain B residue  184 VAL
Chi-restraints excluded: chain B residue  215 GLU
Chi-restraints excluded: chain B residue  227 THR
Chi-restraints excluded: chain B residue  241 CYS
Chi-restraints excluded: chain A residue   61 LEU
Chi-restraints excluded: chain A residue   90 LEU
Chi-restraints excluded: chain A residue   96 THR
Chi-restraints excluded: chain A residue  184 VAL
Chi-restraints excluded: chain A residue  227 THR
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 168
   random chunks:
   chunk 165 optimal weight:    2.9990
   chunk 39 optimal weight:    8.9990
   chunk 27 optimal weight:    6.9990
   chunk 159 optimal weight:   20.0000
   chunk 42 optimal weight:    9.9990
   chunk 116 optimal weight:    2.9990
   chunk 80 optimal weight:    5.9990
   chunk 31 optimal weight:   10.0000
   chunk 72 optimal weight:    6.9990
   chunk 105 optimal weight:    5.9990
   chunk 121 optimal weight:    3.9990
   overall best weight:    4.3990

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

Flipped N/Q/H residues before XYZ refinement:
C 107 HIS
B 248 GLN
A 107 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3110 r_free = 0.3110 target = 0.106454 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.2830 r_free = 0.2830 target = 0.087461 restraints weight = 22781.523|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 41)----------------|
| r_work = 0.2864 r_free = 0.2864 target = 0.089580 restraints weight = 14575.576|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.2886 r_free = 0.2886 target = 0.091018 restraints weight = 10958.382|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 41)----------------|
| r_work = 0.2900 r_free = 0.2900 target = 0.091961 restraints weight = 9095.044|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 36)----------------|
| r_work = 0.2910 r_free = 0.2910 target = 0.092595 restraints weight = 8047.707|
|-----------------------------------------------------------------------------|
r_work (final): 0.2858
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2854
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2854 r_free = 0.2854    target_work(ls_wunit_k1) = 0.089         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:      204 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2843 r_free = 0.2843    target_work(ls_wunit_k1) = 0.088         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:      230 |
|-----------------------------------------------------------------------------|
r_final: 0.2843
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8603
moved from start:          0.3603

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.031  13656  Z= 0.188
  Angle     :  0.735  10.876  18486  Z= 0.374
  Chirality :  0.048   0.206   2058
  Planarity :  0.005   0.036   2370
  Dihedral  :  6.156  56.037   1903
  Min Nonbonded Distance : 2.402

Molprobity Statistics.
  All-atom Clashscore : 5.63
  Ramachandran Plot:
    Outliers :  1.05 %
    Allowed  : 14.21 %
    Favored  : 84.74 %
  Rotamer:
    Outliers :  3.58 %
    Allowed  : 15.31 %
    Favored  : 81.12 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 7.14 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.37 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -3.73 (0.18), residues: 1710
  helix: -1.18 (0.25), residues: 408
  sheet: -1.96 (0.27), residues: 354
  loop : -3.43 (0.16), residues: 948

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG D 171 
 TYR   0.018   0.001   TYR E 296 
 PHE   0.014   0.002   PHE D 330 
 TRP   0.014   0.002   TRP B 198 
 HIS   0.011   0.002   HIS F 323 

Details of bonding type rmsd
  covalent geometry    : bond        0.00453 (13656)
  covalent geometry    : angle       0.73505 (18486)
  hydrogen bonds       : bond        0.04419 (  348)
  hydrogen bonds       : angle       5.12188 (  972)

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

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

  3420 Ramachandran restraints generated.
    1710 Oldfield, 0 Emsley, 1710 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3420 Ramachandran restraints generated.
    1710 Oldfield, 0 Emsley, 1710 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  261 residues out of total 1398 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 50
    poor density    : 211
  time to evaluate  : 0.504 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: F  317 ASP cc_start: 0.8397 (m-30) cc_final: 0.8038 (m-30)
REVERT: F  324 TYR cc_start: 0.8434 (OUTLIER) cc_final: 0.7914 (t80)
REVERT: F  339 ARG cc_start: 0.7415 (mtt-85) cc_final: 0.6541 (ttp-170)
REVERT: E   94 SER cc_start: 0.7808 (m) cc_final: 0.7361 (p)
REVERT: E  123 LEU cc_start: 0.8202 (mm) cc_final: 0.7559 (pp)
REVERT: E  215 GLU cc_start: 0.9013 (pt0) cc_final: 0.8685 (pt0)
REVERT: E  295 ASN cc_start: 0.8394 (t0) cc_final: 0.7657 (p0)
REVERT: E  297 ARG cc_start: 0.7741 (mpp-170) cc_final: 0.7270 (ppt170)
REVERT: E  305 ASP cc_start: 0.8115 (p0) cc_final: 0.7897 (p0)
REVERT: E  310 ASP cc_start: 0.8895 (t0) cc_final: 0.8145 (t0)
REVERT: D  283 ILE cc_start: 0.9186 (OUTLIER) cc_final: 0.8894 (mt)
REVERT: D  336 GLU cc_start: 0.6892 (OUTLIER) cc_final: 0.6513 (mt-10)
REVERT: C  287 LEU cc_start: 0.9150 (OUTLIER) cc_final: 0.8830 (mt)
REVERT: C  295 ASN cc_start: 0.8361 (t0) cc_final: 0.7491 (p0)
REVERT: C  297 ARG cc_start: 0.7591 (mmt180) cc_final: 0.6655 (ppt170)
REVERT: C  310 ASP cc_start: 0.8962 (t0) cc_final: 0.8074 (t0)
REVERT: A   87 THR cc_start: 0.9156 (p) cc_final: 0.8900 (t)
REVERT: A  287 LEU cc_start: 0.9020 (OUTLIER) cc_final: 0.8740 (mt)
REVERT: A  295 ASN cc_start: 0.8451 (t0) cc_final: 0.7598 (p0)
REVERT: A  297 ARG cc_start: 0.7564 (mpp-170) cc_final: 0.6722 (ppt170)
REVERT: A  310 ASP cc_start: 0.8869 (t0) cc_final: 0.7905 (t0)
REVERT: A  339 ARG cc_start: 0.4057 (ttt180) cc_final: 0.3419 (ttt180)
REVERT: A  343 SER cc_start: 0.8937 (m) cc_final: 0.8526 (p)
  outliers start: 50
  outliers final: 24
  residues processed: 249
  average time/residue: 0.1164
  time to fit residues: 41.6277
Evaluate side-chains
  196 residues out of total 1398 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 167
  time to evaluate  : 0.482 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain F residue   86 SER
Chi-restraints excluded: chain F residue  184 VAL
Chi-restraints excluded: chain F residue  241 CYS
Chi-restraints excluded: chain F residue  324 TYR
Chi-restraints excluded: chain E residue  227 THR
Chi-restraints excluded: chain E residue  324 TYR
Chi-restraints excluded: chain D residue   50 THR
Chi-restraints excluded: chain D residue   61 LEU
Chi-restraints excluded: chain D residue  181 THR
Chi-restraints excluded: chain D residue  184 VAL
Chi-restraints excluded: chain D residue  215 GLU
Chi-restraints excluded: chain D residue  241 CYS
Chi-restraints excluded: chain D residue  283 ILE
Chi-restraints excluded: chain D residue  324 TYR
Chi-restraints excluded: chain D residue  336 GLU
Chi-restraints excluded: chain C residue   61 LEU
Chi-restraints excluded: chain C residue  147 THR
Chi-restraints excluded: chain C residue  227 THR
Chi-restraints excluded: chain C residue  287 LEU
Chi-restraints excluded: chain B residue   61 LEU
Chi-restraints excluded: chain B residue  184 VAL
Chi-restraints excluded: chain B residue  215 GLU
Chi-restraints excluded: chain B residue  241 CYS
Chi-restraints excluded: chain B residue  324 TYR
Chi-restraints excluded: chain A residue   61 LEU
Chi-restraints excluded: chain A residue  148 VAL
Chi-restraints excluded: chain A residue  184 VAL
Chi-restraints excluded: chain A residue  227 THR
Chi-restraints excluded: chain A residue  287 LEU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 168
   random chunks:
   chunk 108 optimal weight:    9.9990
   chunk 127 optimal weight:    9.9990
   chunk 38 optimal weight:    5.9990
   chunk 78 optimal weight:    5.9990
   chunk 132 optimal weight:    2.9990
   chunk 109 optimal weight:   10.0000
   chunk 66 optimal weight:    1.9990
   chunk 72 optimal weight:    8.9990
   chunk 12 optimal weight:    0.3980
   chunk 166 optimal weight:    7.9990
   chunk 63 optimal weight:    9.9990
   overall best weight:    3.4788

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

Flipped N/Q/H residues before XYZ refinement:
B 295 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3058 r_free = 0.3058 target = 0.102993 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.2793 r_free = 0.2793 target = 0.085245 restraints weight = 23229.318|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.2824 r_free = 0.2824 target = 0.087174 restraints weight = 15194.153|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.2843 r_free = 0.2843 target = 0.088464 restraints weight = 11563.279|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 36)----------------|
| r_work = 0.2857 r_free = 0.2857 target = 0.089359 restraints weight = 9671.787|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.2866 r_free = 0.2866 target = 0.089941 restraints weight = 8576.740|
|-----------------------------------------------------------------------------|
r_work (final): 0.2865
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2866
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2866 r_free = 0.2866    target_work(ls_wunit_k1) = 0.090         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:      230 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2861 r_free = 0.2861    target_work(ls_wunit_k1) = 0.090         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:      251 |
|-----------------------------------------------------------------------------|
r_final: 0.2861
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8601
moved from start:          0.3900

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.028  13656  Z= 0.160
  Angle     :  0.713  10.582  18486  Z= 0.361
  Chirality :  0.047   0.199   2058
  Planarity :  0.005   0.035   2370
  Dihedral  :  6.054  55.821   1903
  Min Nonbonded Distance : 2.253

Molprobity Statistics.
  All-atom Clashscore : 5.53
  Ramachandran Plot:
    Outliers :  0.99 %
    Allowed  : 12.51 %
    Favored  : 86.49 %
  Rotamer:
    Outliers :  4.43 %
    Allowed  : 14.81 %
    Favored  : 80.76 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 7.14 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.37 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -3.58 (0.18), residues: 1710
  helix: -1.07 (0.25), residues: 408
  sheet: -1.82 (0.27), residues: 354
  loop : -3.34 (0.16), residues: 948

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG E 335 
 TYR   0.015   0.001   TYR E 296 
 PHE   0.012   0.001   PHE D 330 
 TRP   0.009   0.001   TRP B 198 
 HIS   0.013   0.002   HIS F 323 

Details of bonding type rmsd
  covalent geometry    : bond        0.00385 (13656)
  covalent geometry    : angle       0.71335 (18486)
  hydrogen bonds       : bond        0.03927 (  348)
  hydrogen bonds       : angle       4.96612 (  972)

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

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

  3420 Ramachandran restraints generated.
    1710 Oldfield, 0 Emsley, 1710 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3420 Ramachandran restraints generated.
    1710 Oldfield, 0 Emsley, 1710 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  234 residues out of total 1398 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 62
    poor density    : 172
  time to evaluate  : 0.415 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: F  317 ASP cc_start: 0.8404 (m-30) cc_final: 0.8073 (m-30)
REVERT: F  324 TYR cc_start: 0.8425 (OUTLIER) cc_final: 0.7996 (t80)
REVERT: F  336 GLU cc_start: 0.7305 (tt0) cc_final: 0.6898 (mt-10)
REVERT: F  339 ARG cc_start: 0.7409 (mtt-85) cc_final: 0.6442 (ttp-170)
REVERT: E   94 SER cc_start: 0.7901 (m) cc_final: 0.7499 (p)
REVERT: E  123 LEU cc_start: 0.8428 (mm) cc_final: 0.7916 (pp)
REVERT: E  295 ASN cc_start: 0.8391 (t0) cc_final: 0.7522 (p0)
REVERT: E  297 ARG cc_start: 0.7724 (mpp-170) cc_final: 0.7334 (ppt170)
REVERT: D  117 GLU cc_start: 0.7369 (mp0) cc_final: 0.7102 (mm-30)
REVERT: D  283 ILE cc_start: 0.9167 (OUTLIER) cc_final: 0.8933 (mt)
REVERT: D  324 TYR cc_start: 0.8337 (OUTLIER) cc_final: 0.7923 (t80)
REVERT: D  336 GLU cc_start: 0.6923 (OUTLIER) cc_final: 0.6522 (mt-10)
REVERT: C  295 ASN cc_start: 0.8384 (t0) cc_final: 0.7489 (p0)
REVERT: C  297 ARG cc_start: 0.7562 (mmt180) cc_final: 0.6674 (ppt170)
REVERT: C  324 TYR cc_start: 0.8906 (OUTLIER) cc_final: 0.7596 (t80)
REVERT: B  117 GLU cc_start: 0.6980 (mp0) cc_final: 0.6698 (mm-30)
REVERT: B  336 GLU cc_start: 0.6920 (OUTLIER) cc_final: 0.6585 (mt-10)
REVERT: A   87 THR cc_start: 0.9139 (p) cc_final: 0.8908 (t)
REVERT: A  215 GLU cc_start: 0.8973 (pt0) cc_final: 0.8668 (pt0)
REVERT: A  287 LEU cc_start: 0.8986 (OUTLIER) cc_final: 0.8747 (mt)
REVERT: A  295 ASN cc_start: 0.8469 (t0) cc_final: 0.7453 (p0)
REVERT: A  297 ARG cc_start: 0.7656 (mpp-170) cc_final: 0.6788 (ppt170)
REVERT: A  339 ARG cc_start: 0.4134 (ttt180) cc_final: 0.2927 (ttt180)
REVERT: A  343 SER cc_start: 0.8871 (m) cc_final: 0.8532 (p)
  outliers start: 62
  outliers final: 33
  residues processed: 221
  average time/residue: 0.1185
  time to fit residues: 37.8255
Evaluate side-chains
  200 residues out of total 1398 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 40
    poor density    : 160
  time to evaluate  : 0.483 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain F residue   86 SER
Chi-restraints excluded: chain F residue  181 THR
Chi-restraints excluded: chain F residue  184 VAL
Chi-restraints excluded: chain F residue  241 CYS
Chi-restraints excluded: chain F residue  324 TYR
Chi-restraints excluded: chain E residue  147 THR
Chi-restraints excluded: chain E residue  148 VAL
Chi-restraints excluded: chain E residue  227 THR
Chi-restraints excluded: chain E residue  324 TYR
Chi-restraints excluded: chain D residue   50 THR
Chi-restraints excluded: chain D residue   61 LEU
Chi-restraints excluded: chain D residue  184 VAL
Chi-restraints excluded: chain D residue  215 GLU
Chi-restraints excluded: chain D residue  241 CYS
Chi-restraints excluded: chain D residue  283 ILE
Chi-restraints excluded: chain D residue  324 TYR
Chi-restraints excluded: chain D residue  336 GLU
Chi-restraints excluded: chain C residue   61 LEU
Chi-restraints excluded: chain C residue  147 THR
Chi-restraints excluded: chain C residue  182 ILE
Chi-restraints excluded: chain C residue  227 THR
Chi-restraints excluded: chain C residue  324 TYR
Chi-restraints excluded: chain C residue  333 ASN
Chi-restraints excluded: chain B residue   50 THR
Chi-restraints excluded: chain B residue   61 LEU
Chi-restraints excluded: chain B residue   86 SER
Chi-restraints excluded: chain B residue  169 LEU
Chi-restraints excluded: chain B residue  184 VAL
Chi-restraints excluded: chain B residue  215 GLU
Chi-restraints excluded: chain B residue  241 CYS
Chi-restraints excluded: chain B residue  324 TYR
Chi-restraints excluded: chain B residue  336 GLU
Chi-restraints excluded: chain A residue   61 LEU
Chi-restraints excluded: chain A residue  147 THR
Chi-restraints excluded: chain A residue  148 VAL
Chi-restraints excluded: chain A residue  169 LEU
Chi-restraints excluded: chain A residue  181 THR
Chi-restraints excluded: chain A residue  184 VAL
Chi-restraints excluded: chain A residue  227 THR
Chi-restraints excluded: chain A residue  287 LEU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 168
   random chunks:
   chunk 41 optimal weight:    5.9990
   chunk 2 optimal weight:    2.9990
   chunk 121 optimal weight:   10.0000
   chunk 120 optimal weight:    8.9990
   chunk 85 optimal weight:    7.9990
   chunk 153 optimal weight:    4.9990
   chunk 99 optimal weight:    0.6980
   chunk 57 optimal weight:   20.0000
   chunk 38 optimal weight:    9.9990
   chunk 26 optimal weight:    0.8980
   chunk 104 optimal weight:    9.9990
   overall best weight:    3.1186

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

Flipped N/Q/H residues before XYZ refinement:
F 295 ASN
B  42 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3058 r_free = 0.3058 target = 0.102856 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.2801 r_free = 0.2801 target = 0.085688 restraints weight = 22980.746|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.2829 r_free = 0.2829 target = 0.087508 restraints weight = 15461.188|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 41)----------------|
| r_work = 0.2849 r_free = 0.2849 target = 0.088720 restraints weight = 11955.822|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 24)----------------|
| r_work = 0.2860 r_free = 0.2860 target = 0.089467 restraints weight = 10109.529|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 31)----------------|
| r_work = 0.2868 r_free = 0.2868 target = 0.090015 restraints weight = 9073.888|
|-----------------------------------------------------------------------------|
r_work (final): 0.2881
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2874
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2874 r_free = 0.2874    target_work(ls_wunit_k1) = 0.090         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:      251 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2869 r_free = 0.2869    target_work(ls_wunit_k1) = 0.090         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:      279 |
|-----------------------------------------------------------------------------|
r_final: 0.2869
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8591
moved from start:          0.4120

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.025  13656  Z= 0.150
  Angle     :  0.710  10.637  18486  Z= 0.357
  Chirality :  0.046   0.178   2058
  Planarity :  0.005   0.036   2370
  Dihedral  :  5.974  55.961   1903
  Min Nonbonded Distance : 2.486

Molprobity Statistics.
  All-atom Clashscore : 5.54
  Ramachandran Plot:
    Outliers :  0.94 %
    Allowed  : 12.63 %
    Favored  : 86.43 %
  Rotamer:
    Outliers :  4.29 %
    Allowed  : 14.59 %
    Favored  : 81.12 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 7.14 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.37 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -3.41 (0.18), residues: 1710
  helix: -0.94 (0.26), residues: 408
  sheet: -1.66 (0.28), residues: 354
  loop : -3.25 (0.16), residues: 948

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG E 335 
 TYR   0.015   0.001   TYR E 296 
 PHE   0.010   0.001   PHE A 330 
 TRP   0.011   0.001   TRP B 198 
 HIS   0.013   0.002   HIS F 323 

Details of bonding type rmsd
  covalent geometry    : bond        0.00359 (13656)
  covalent geometry    : angle       0.70956 (18486)
  hydrogen bonds       : bond        0.03773 (  348)
  hydrogen bonds       : angle       4.84073 (  972)

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

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

  3420 Ramachandran restraints generated.
    1710 Oldfield, 0 Emsley, 1710 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3420 Ramachandran restraints generated.
    1710 Oldfield, 0 Emsley, 1710 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  245 residues out of total 1398 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 60
    poor density    : 185
  time to evaluate  : 0.489 
Fit side-chains
   revert: symmetry clash
REVERT: F  201 ARG cc_start: 0.8555 (OUTLIER) cc_final: 0.7808 (mtt-85)
REVERT: F  317 ASP cc_start: 0.8343 (m-30) cc_final: 0.7962 (m-30)
REVERT: F  324 TYR cc_start: 0.8418 (OUTLIER) cc_final: 0.8104 (t80)
REVERT: F  336 GLU cc_start: 0.7279 (tt0) cc_final: 0.6891 (mt-10)
REVERT: F  339 ARG cc_start: 0.7359 (mtt-85) cc_final: 0.6389 (ttp-170)
REVERT: E   94 SER cc_start: 0.7911 (m) cc_final: 0.7534 (p)
REVERT: E  123 LEU cc_start: 0.8601 (OUTLIER) cc_final: 0.8007 (pp)
REVERT: E  295 ASN cc_start: 0.8404 (t0) cc_final: 0.7533 (p0)
REVERT: E  297 ARG cc_start: 0.7700 (mpp-170) cc_final: 0.7391 (ppt170)
REVERT: E  305 ASP cc_start: 0.8050 (p0) cc_final: 0.7817 (p0)
REVERT: E  310 ASP cc_start: 0.8862 (t0) cc_final: 0.8009 (t0)
REVERT: D  283 ILE cc_start: 0.9166 (OUTLIER) cc_final: 0.8933 (mt)
REVERT: D  324 TYR cc_start: 0.8321 (OUTLIER) cc_final: 0.8018 (t80)
REVERT: D  336 GLU cc_start: 0.6966 (OUTLIER) cc_final: 0.6578 (mt-10)
REVERT: C  287 LEU cc_start: 0.9092 (OUTLIER) cc_final: 0.8747 (mt)
REVERT: C  295 ASN cc_start: 0.8380 (t0) cc_final: 0.7476 (p0)
REVERT: C  297 ARG cc_start: 0.7602 (mmt180) cc_final: 0.6693 (ppt170)
REVERT: C  310 ASP cc_start: 0.8951 (t0) cc_final: 0.8070 (t0)
REVERT: C  324 TYR cc_start: 0.8923 (OUTLIER) cc_final: 0.7736 (t80)
REVERT: B  117 GLU cc_start: 0.6992 (mp0) cc_final: 0.6725 (mm-30)
REVERT: B  138 GLU cc_start: 0.9020 (pt0) cc_final: 0.8682 (pt0)
REVERT: B  324 TYR cc_start: 0.8435 (OUTLIER) cc_final: 0.8158 (t80)
REVERT: B  336 GLU cc_start: 0.6933 (OUTLIER) cc_final: 0.6718 (mt-10)
REVERT: A   87 THR cc_start: 0.9149 (p) cc_final: 0.8921 (t)
REVERT: A   94 SER cc_start: 0.7773 (m) cc_final: 0.7164 (p)
REVERT: A  215 GLU cc_start: 0.8948 (pt0) cc_final: 0.8683 (pt0)
REVERT: A  283 ILE cc_start: 0.9471 (OUTLIER) cc_final: 0.9252 (mt)
REVERT: A  287 LEU cc_start: 0.8948 (OUTLIER) cc_final: 0.8699 (mt)
REVERT: A  295 ASN cc_start: 0.8453 (t0) cc_final: 0.7724 (p0)
REVERT: A  297 ARG cc_start: 0.7788 (mpp-170) cc_final: 0.6937 (ppt170)
REVERT: A  339 ARG cc_start: 0.4158 (ttt180) cc_final: 0.2927 (ttt180)
REVERT: A  343 SER cc_start: 0.8845 (m) cc_final: 0.8544 (p)
  outliers start: 60
  outliers final: 34
  residues processed: 232
  average time/residue: 0.1254
  time to fit residues: 41.4284
Evaluate side-chains
  213 residues out of total 1398 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 46
    poor density    : 167
  time to evaluate  : 0.447 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain F residue   86 SER
Chi-restraints excluded: chain F residue  181 THR
Chi-restraints excluded: chain F residue  184 VAL
Chi-restraints excluded: chain F residue  201 ARG
Chi-restraints excluded: chain F residue  241 CYS
Chi-restraints excluded: chain F residue  324 TYR
Chi-restraints excluded: chain E residue  123 LEU
Chi-restraints excluded: chain E residue  147 THR
Chi-restraints excluded: chain E residue  148 VAL
Chi-restraints excluded: chain E residue  227 THR
Chi-restraints excluded: chain E residue  333 ASN
Chi-restraints excluded: chain E residue  340 LYS
Chi-restraints excluded: chain D residue   50 THR
Chi-restraints excluded: chain D residue   61 LEU
Chi-restraints excluded: chain D residue  184 VAL
Chi-restraints excluded: chain D residue  215 GLU
Chi-restraints excluded: chain D residue  241 CYS
Chi-restraints excluded: chain D residue  283 ILE
Chi-restraints excluded: chain D residue  324 TYR
Chi-restraints excluded: chain D residue  336 GLU
Chi-restraints excluded: chain C residue   61 LEU
Chi-restraints excluded: chain C residue  124 MET
Chi-restraints excluded: chain C residue  147 THR
Chi-restraints excluded: chain C residue  148 VAL
Chi-restraints excluded: chain C residue  182 ILE
Chi-restraints excluded: chain C residue  184 VAL
Chi-restraints excluded: chain C residue  227 THR
Chi-restraints excluded: chain C residue  287 LEU
Chi-restraints excluded: chain C residue  324 TYR
Chi-restraints excluded: chain C residue  333 ASN
Chi-restraints excluded: chain B residue   50 THR
Chi-restraints excluded: chain B residue   61 LEU
Chi-restraints excluded: chain B residue  184 VAL
Chi-restraints excluded: chain B residue  215 GLU
Chi-restraints excluded: chain B residue  241 CYS
Chi-restraints excluded: chain B residue  324 TYR
Chi-restraints excluded: chain B residue  336 GLU
Chi-restraints excluded: chain A residue   61 LEU
Chi-restraints excluded: chain A residue  147 THR
Chi-restraints excluded: chain A residue  148 VAL
Chi-restraints excluded: chain A residue  169 LEU
Chi-restraints excluded: chain A residue  227 THR
Chi-restraints excluded: chain A residue  241 CYS
Chi-restraints excluded: chain A residue  283 ILE
Chi-restraints excluded: chain A residue  287 LEU
Chi-restraints excluded: chain A residue  324 TYR
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 168
   random chunks:
   chunk 150 optimal weight:    9.9990
   chunk 63 optimal weight:   10.0000
   chunk 91 optimal weight:    4.9990
   chunk 109 optimal weight:    3.9990
   chunk 5 optimal weight:    8.9990
   chunk 110 optimal weight:    0.5980
   chunk 52 optimal weight:   10.0000
   chunk 142 optimal weight:    7.9990
   chunk 149 optimal weight:    9.9990
   chunk 38 optimal weight:    8.9990
   chunk 77 optimal weight:   10.0000
   overall best weight:    5.3188

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

Flipped N/Q/H residues before XYZ refinement:
F 248 GLN
D 248 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3045 r_free = 0.3045 target = 0.102164 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.2775 r_free = 0.2775 target = 0.084209 restraints weight = 23113.112|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.2805 r_free = 0.2805 target = 0.086133 restraints weight = 15511.593|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.2826 r_free = 0.2826 target = 0.087445 restraints weight = 11928.590|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 32)----------------|
| r_work = 0.2839 r_free = 0.2839 target = 0.088297 restraints weight = 10020.901|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 25)----------------|
| r_work = 0.2847 r_free = 0.2847 target = 0.088860 restraints weight = 8936.937|
|-----------------------------------------------------------------------------|
r_work (final): 0.2844
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2843
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2843 r_free = 0.2843    target_work(ls_wunit_k1) = 0.088         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:      279 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2820 r_free = 0.2820    target_work(ls_wunit_k1) = 0.087         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:      332 |
|-----------------------------------------------------------------------------|
r_final: 0.2820
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8652
moved from start:          0.4280

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.040  13656  Z= 0.217
  Angle     :  0.772  10.645  18486  Z= 0.391
  Chirality :  0.048   0.211   2058
  Planarity :  0.005   0.039   2370
  Dihedral  :  6.223  57.514   1902
  Min Nonbonded Distance : 2.493

Molprobity Statistics.
  All-atom Clashscore : 6.51
  Ramachandran Plot:
    Outliers :  0.94 %
    Allowed  : 14.09 %
    Favored  : 84.97 %
  Rotamer:
    Outliers :  4.22 %
    Allowed  : 15.52 %
    Favored  : 80.26 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 7.14 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.37 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -3.44 (0.18), residues: 1710
  helix: -1.05 (0.25), residues: 408
  sheet: -1.67 (0.26), residues: 384
  loop : -3.27 (0.17), residues: 918

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG C 171 
 TYR   0.014   0.001   TYR E 296 
 PHE   0.013   0.002   PHE F 316 
 TRP   0.011   0.001   TRP B 198 
 HIS   0.012   0.002   HIS F 323 

Details of bonding type rmsd
  covalent geometry    : bond        0.00527 (13656)
  covalent geometry    : angle       0.77174 (18486)
  hydrogen bonds       : bond        0.04549 (  348)
  hydrogen bonds       : angle       5.13425 (  972)

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

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

  3420 Ramachandran restraints generated.
    1710 Oldfield, 0 Emsley, 1710 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3420 Ramachandran restraints generated.
    1710 Oldfield, 0 Emsley, 1710 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  239 residues out of total 1398 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 59
    poor density    : 180
  time to evaluate  : 0.491 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: F  201 ARG cc_start: 0.8598 (OUTLIER) cc_final: 0.7855 (mtt-85)
REVERT: F  317 ASP cc_start: 0.8377 (m-30) cc_final: 0.8041 (m-30)
REVERT: F  324 TYR cc_start: 0.8558 (OUTLIER) cc_final: 0.8164 (t80)
REVERT: F  336 GLU cc_start: 0.7427 (tt0) cc_final: 0.7041 (mt-10)
REVERT: E   47 PHE cc_start: 0.7738 (t80) cc_final: 0.7402 (t80)
REVERT: E   94 SER cc_start: 0.8135 (m) cc_final: 0.7830 (p)
REVERT: E  295 ASN cc_start: 0.8461 (t0) cc_final: 0.7487 (p0)
REVERT: E  297 ARG cc_start: 0.7742 (mpp-170) cc_final: 0.7424 (ppt170)
REVERT: E  310 ASP cc_start: 0.8904 (t0) cc_final: 0.8012 (t0)
REVERT: D   42 GLN cc_start: 0.9340 (tt0) cc_final: 0.8974 (tt0)
REVERT: D  117 GLU cc_start: 0.7336 (mp0) cc_final: 0.7029 (mm-30)
REVERT: D  283 ILE cc_start: 0.9207 (OUTLIER) cc_final: 0.8880 (mt)
REVERT: D  324 TYR cc_start: 0.8520 (OUTLIER) cc_final: 0.8079 (t80)
REVERT: D  336 GLU cc_start: 0.7052 (OUTLIER) cc_final: 0.6683 (mt-10)
REVERT: C  287 LEU cc_start: 0.9125 (OUTLIER) cc_final: 0.8788 (mt)
REVERT: C  295 ASN cc_start: 0.8464 (t0) cc_final: 0.7341 (p0)
REVERT: B  336 GLU cc_start: 0.7058 (OUTLIER) cc_final: 0.6848 (mt-10)
REVERT: A   87 THR cc_start: 0.9197 (p) cc_final: 0.8986 (t)
REVERT: A   94 SER cc_start: 0.7940 (m) cc_final: 0.7370 (p)
REVERT: A  215 GLU cc_start: 0.8915 (pt0) cc_final: 0.8665 (pt0)
REVERT: A  287 LEU cc_start: 0.9070 (OUTLIER) cc_final: 0.8693 (mt)
REVERT: A  295 ASN cc_start: 0.8463 (t0) cc_final: 0.7664 (p0)
REVERT: A  297 ARG cc_start: 0.7843 (mpp-170) cc_final: 0.7067 (ppt170)
REVERT: A  310 ASP cc_start: 0.8905 (t0) cc_final: 0.7905 (t0)
REVERT: A  339 ARG cc_start: 0.3646 (ttt180) cc_final: 0.3215 (ttt180)
REVERT: A  343 SER cc_start: 0.8874 (m) cc_final: 0.8502 (p)
  outliers start: 59
  outliers final: 34
  residues processed: 220
  average time/residue: 0.1231
  time to fit residues: 39.2035
Evaluate side-chains
  202 residues out of total 1398 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 42
    poor density    : 160
  time to evaluate  : 0.527 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain F residue   86 SER
Chi-restraints excluded: chain F residue  184 VAL
Chi-restraints excluded: chain F residue  201 ARG
Chi-restraints excluded: chain F residue  324 TYR
Chi-restraints excluded: chain E residue  148 VAL
Chi-restraints excluded: chain E residue  227 THR
Chi-restraints excluded: chain E residue  289 ILE
Chi-restraints excluded: chain E residue  324 TYR
Chi-restraints excluded: chain E residue  333 ASN
Chi-restraints excluded: chain D residue   50 THR
Chi-restraints excluded: chain D residue   61 LEU
Chi-restraints excluded: chain D residue  184 VAL
Chi-restraints excluded: chain D residue  215 GLU
Chi-restraints excluded: chain D residue  241 CYS
Chi-restraints excluded: chain D residue  283 ILE
Chi-restraints excluded: chain D residue  324 TYR
Chi-restraints excluded: chain D residue  336 GLU
Chi-restraints excluded: chain C residue   96 THR
Chi-restraints excluded: chain C residue  124 MET
Chi-restraints excluded: chain C residue  147 THR
Chi-restraints excluded: chain C residue  148 VAL
Chi-restraints excluded: chain C residue  182 ILE
Chi-restraints excluded: chain C residue  227 THR
Chi-restraints excluded: chain C residue  241 CYS
Chi-restraints excluded: chain C residue  287 LEU
Chi-restraints excluded: chain C residue  333 ASN
Chi-restraints excluded: chain B residue   50 THR
Chi-restraints excluded: chain B residue   61 LEU
Chi-restraints excluded: chain B residue   86 SER
Chi-restraints excluded: chain B residue  184 VAL
Chi-restraints excluded: chain B residue  215 GLU
Chi-restraints excluded: chain B residue  241 CYS
Chi-restraints excluded: chain B residue  324 TYR
Chi-restraints excluded: chain B residue  336 GLU
Chi-restraints excluded: chain A residue   61 LEU
Chi-restraints excluded: chain A residue  124 MET
Chi-restraints excluded: chain A residue  148 VAL
Chi-restraints excluded: chain A residue  169 LEU
Chi-restraints excluded: chain A residue  181 THR
Chi-restraints excluded: chain A residue  227 THR
Chi-restraints excluded: chain A residue  241 CYS
Chi-restraints excluded: chain A residue  287 LEU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 168
   random chunks:
   chunk 74 optimal weight:    4.9990
   chunk 149 optimal weight:    5.9990
   chunk 122 optimal weight:    9.9990
   chunk 58 optimal weight:   20.0000
   chunk 97 optimal weight:    3.9990
   chunk 19 optimal weight:    3.9990
   chunk 144 optimal weight:    0.5980
   chunk 66 optimal weight:    4.9990
   chunk 8 optimal weight:    0.0980
   chunk 56 optimal weight:   10.0000
   chunk 119 optimal weight:    7.9990
   overall best weight:    2.7386

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

Flipped N/Q/H residues before XYZ refinement:
F 248 GLN
D 248 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3065 r_free = 0.3065 target = 0.103587 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.2813 r_free = 0.2813 target = 0.086527 restraints weight = 22963.573|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.2839 r_free = 0.2839 target = 0.088310 restraints weight = 15467.514|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 41)----------------|
| r_work = 0.2859 r_free = 0.2859 target = 0.089594 restraints weight = 11968.898|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.2870 r_free = 0.2870 target = 0.090332 restraints weight = 10111.949|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.2879 r_free = 0.2879 target = 0.090911 restraints weight = 9072.474|
|-----------------------------------------------------------------------------|
r_work (final): 0.2896
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2879
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2879 r_free = 0.2879    target_work(ls_wunit_k1) = 0.091         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:      332 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2876 r_free = 0.2876    target_work(ls_wunit_k1) = 0.091         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:      355 |
|-----------------------------------------------------------------------------|
r_final: 0.2876
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8590
moved from start:          0.4379

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031  13656  Z= 0.141
  Angle     :  0.706  10.598  18486  Z= 0.355
  Chirality :  0.046   0.194   2058
  Planarity :  0.005   0.039   2370
  Dihedral  :  5.835  55.774   1902
  Min Nonbonded Distance : 2.466

Molprobity Statistics.
  All-atom Clashscore : 5.94
  Ramachandran Plot:
    Outliers :  0.94 %
    Allowed  : 11.58 %
    Favored  : 87.49 %
  Rotamer:
    Outliers :  3.43 %
    Allowed  : 15.81 %
    Favored  : 80.76 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 7.14 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.37 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -3.29 (0.18), residues: 1710
  helix: -0.86 (0.26), residues: 408
  sheet: -1.55 (0.28), residues: 354
  loop : -3.18 (0.16), residues: 948

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG E 335 
 TYR   0.013   0.001   TYR E 296 
 PHE   0.009   0.001   PHE F 316 
 TRP   0.010   0.001   TRP B 198 
 HIS   0.013   0.002   HIS F 323 

Details of bonding type rmsd
  covalent geometry    : bond        0.00338 (13656)
  covalent geometry    : angle       0.70628 (18486)
  hydrogen bonds       : bond        0.03589 (  348)
  hydrogen bonds       : angle       4.84280 (  972)

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

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

  3420 Ramachandran restraints generated.
    1710 Oldfield, 0 Emsley, 1710 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3420 Ramachandran restraints generated.
    1710 Oldfield, 0 Emsley, 1710 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  221 residues out of total 1398 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 48
    poor density    : 173
  time to evaluate  : 0.487 
Fit side-chains
   revert: symmetry clash
REVERT: F  201 ARG cc_start: 0.8450 (OUTLIER) cc_final: 0.7727 (mtt-85)
REVERT: F  317 ASP cc_start: 0.8372 (m-30) cc_final: 0.8093 (m-30)
REVERT: F  324 TYR cc_start: 0.8356 (OUTLIER) cc_final: 0.8065 (t80)
REVERT: F  336 GLU cc_start: 0.7327 (tt0) cc_final: 0.6997 (mt-10)
REVERT: E   94 SER cc_start: 0.8022 (m) cc_final: 0.7740 (p)
REVERT: E  295 ASN cc_start: 0.8447 (t0) cc_final: 0.7481 (p0)
REVERT: E  297 ARG cc_start: 0.7690 (mpp-170) cc_final: 0.7433 (ppt170)
REVERT: E  324 TYR cc_start: 0.8872 (OUTLIER) cc_final: 0.7748 (t80)
REVERT: D   42 GLN cc_start: 0.9303 (tt0) cc_final: 0.8914 (tt0)
REVERT: D  117 GLU cc_start: 0.7388 (mp0) cc_final: 0.7111 (mm-30)
REVERT: D  283 ILE cc_start: 0.9201 (OUTLIER) cc_final: 0.8949 (mt)
REVERT: D  324 TYR cc_start: 0.8265 (OUTLIER) cc_final: 0.7951 (t80)
REVERT: C  123 LEU cc_start: 0.8876 (mm) cc_final: 0.8291 (pp)
REVERT: C  287 LEU cc_start: 0.9043 (OUTLIER) cc_final: 0.8672 (mt)
REVERT: C  295 ASN cc_start: 0.8449 (t0) cc_final: 0.7971 (t0)
REVERT: C  324 TYR cc_start: 0.8929 (OUTLIER) cc_final: 0.7678 (t80)
REVERT: B  117 GLU cc_start: 0.7397 (mp0) cc_final: 0.7012 (mm-30)
REVERT: B  324 TYR cc_start: 0.8453 (OUTLIER) cc_final: 0.8205 (t80)
REVERT: A   87 THR cc_start: 0.9149 (p) cc_final: 0.8906 (t)
REVERT: A   94 SER cc_start: 0.7837 (m) cc_final: 0.7301 (p)
REVERT: A  215 GLU cc_start: 0.8814 (pt0) cc_final: 0.8541 (pt0)
REVERT: A  287 LEU cc_start: 0.9003 (OUTLIER) cc_final: 0.8694 (mt)
REVERT: A  295 ASN cc_start: 0.8407 (t0) cc_final: 0.7645 (p0)
REVERT: A  297 ARG cc_start: 0.7832 (mpp-170) cc_final: 0.7096 (ppt170)
REVERT: A  339 ARG cc_start: 0.3644 (ttt180) cc_final: 0.2911 (ttt180)
REVERT: A  343 SER cc_start: 0.8830 (m) cc_final: 0.8534 (p)
  outliers start: 48
  outliers final: 26
  residues processed: 208
  average time/residue: 0.1217
  time to fit residues: 36.7001
Evaluate side-chains
  204 residues out of total 1398 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 169
  time to evaluate  : 0.474 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain F residue  147 THR
Chi-restraints excluded: chain F residue  184 VAL
Chi-restraints excluded: chain F residue  201 ARG
Chi-restraints excluded: chain F residue  241 CYS
Chi-restraints excluded: chain F residue  324 TYR
Chi-restraints excluded: chain E residue  148 VAL
Chi-restraints excluded: chain E residue  227 THR
Chi-restraints excluded: chain E residue  324 TYR
Chi-restraints excluded: chain D residue   50 THR
Chi-restraints excluded: chain D residue   61 LEU
Chi-restraints excluded: chain D residue  184 VAL
Chi-restraints excluded: chain D residue  215 GLU
Chi-restraints excluded: chain D residue  241 CYS
Chi-restraints excluded: chain D residue  283 ILE
Chi-restraints excluded: chain D residue  324 TYR
Chi-restraints excluded: chain C residue  124 MET
Chi-restraints excluded: chain C residue  147 THR
Chi-restraints excluded: chain C residue  148 VAL
Chi-restraints excluded: chain C residue  182 ILE
Chi-restraints excluded: chain C residue  227 THR
Chi-restraints excluded: chain C residue  241 CYS
Chi-restraints excluded: chain C residue  287 LEU
Chi-restraints excluded: chain C residue  324 TYR
Chi-restraints excluded: chain C residue  333 ASN
Chi-restraints excluded: chain B residue   61 LEU
Chi-restraints excluded: chain B residue   86 SER
Chi-restraints excluded: chain B residue  184 VAL
Chi-restraints excluded: chain B residue  215 GLU
Chi-restraints excluded: chain B residue  241 CYS
Chi-restraints excluded: chain B residue  324 TYR
Chi-restraints excluded: chain A residue   61 LEU
Chi-restraints excluded: chain A residue  169 LEU
Chi-restraints excluded: chain A residue  241 CYS
Chi-restraints excluded: chain A residue  287 LEU
Chi-restraints excluded: chain A residue  324 TYR
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 168
   random chunks:
   chunk 148 optimal weight:    7.9990
   chunk 75 optimal weight:    7.9990
   chunk 150 optimal weight:    8.9990
   chunk 57 optimal weight:   10.0000
   chunk 10 optimal weight:    7.9990
   chunk 125 optimal weight:    0.6980
   chunk 113 optimal weight:    7.9990
   chunk 52 optimal weight:    6.9990
   chunk 88 optimal weight:    6.9990
   chunk 46 optimal weight:    5.9990
   chunk 99 optimal weight:    4.9990
   overall best weight:    5.1388

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

Flipped N/Q/H residues before XYZ refinement:
F 248 GLN
D 248 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3017 r_free = 0.3017 target = 0.100180 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.2759 r_free = 0.2759 target = 0.083116 restraints weight = 23494.738|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.2787 r_free = 0.2787 target = 0.084918 restraints weight = 15744.268|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.2806 r_free = 0.2806 target = 0.086159 restraints weight = 12128.124|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 39)----------------|
| r_work = 0.2819 r_free = 0.2819 target = 0.086981 restraints weight = 10199.746|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 22)----------------|
| r_work = 0.2827 r_free = 0.2827 target = 0.087463 restraints weight = 9105.649|
|-----------------------------------------------------------------------------|
r_work (final): 0.2832
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2837
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2837 r_free = 0.2837    target_work(ls_wunit_k1) = 0.088         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:      355 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2835 r_free = 0.2835    target_work(ls_wunit_k1) = 0.088         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:      362 |
|-----------------------------------------------------------------------------|
r_final: 0.2835
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8650
moved from start:          0.4449

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.043  13656  Z= 0.212
  Angle     :  0.773  10.728  18486  Z= 0.392
  Chirality :  0.048   0.226   2058
  Planarity :  0.005   0.040   2370
  Dihedral  :  6.202  57.965   1902
  Min Nonbonded Distance : 2.436

Molprobity Statistics.
  All-atom Clashscore : 6.52
  Ramachandran Plot:
    Outliers :  0.99 %
    Allowed  : 14.44 %
    Favored  : 84.56 %
  Rotamer:
    Outliers :  2.72 %
    Allowed  : 16.88 %
    Favored  : 80.40 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 7.14 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.37 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -3.35 (0.18), residues: 1710
  helix: -0.97 (0.26), residues: 408
  sheet: -1.55 (0.26), residues: 384
  loop : -3.24 (0.17), residues: 918

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG C 171 
 TYR   0.013   0.001   TYR E 296 
 PHE   0.013   0.002   PHE F 316 
 TRP   0.011   0.001   TRP B 198 
 HIS   0.011   0.002   HIS F 323 

Details of bonding type rmsd
  covalent geometry    : bond        0.00514 (13656)
  covalent geometry    : angle       0.77292 (18486)
  hydrogen bonds       : bond        0.04490 (  348)
  hydrogen bonds       : angle       5.09966 (  972)

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

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

  3420 Ramachandran restraints generated.
    1710 Oldfield, 0 Emsley, 1710 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3420 Ramachandran restraints generated.
    1710 Oldfield, 0 Emsley, 1710 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  211 residues out of total 1398 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 38
    poor density    : 173
  time to evaluate  : 0.521 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: F  201 ARG cc_start: 0.8567 (OUTLIER) cc_final: 0.7844 (mtt-85)
REVERT: F  317 ASP cc_start: 0.8328 (m-30) cc_final: 0.7985 (m-30)
REVERT: F  324 TYR cc_start: 0.8586 (OUTLIER) cc_final: 0.8172 (t80)
REVERT: F  336 GLU cc_start: 0.7484 (tt0) cc_final: 0.7106 (mt-10)
REVERT: E   47 PHE cc_start: 0.7721 (t80) cc_final: 0.7392 (t80)
REVERT: E  295 ASN cc_start: 0.8464 (t0) cc_final: 0.7477 (p0)
REVERT: E  297 ARG cc_start: 0.7739 (mpp-170) cc_final: 0.7497 (ppt170)
REVERT: D   42 GLN cc_start: 0.9353 (tt0) cc_final: 0.8937 (tt0)
REVERT: D  283 ILE cc_start: 0.9216 (OUTLIER) cc_final: 0.8860 (mt)
REVERT: D  324 TYR cc_start: 0.8550 (OUTLIER) cc_final: 0.8110 (t80)
REVERT: C  123 LEU cc_start: 0.8940 (mm) cc_final: 0.8375 (pp)
REVERT: C  287 LEU cc_start: 0.9089 (OUTLIER) cc_final: 0.8725 (mt)
REVERT: C  295 ASN cc_start: 0.8493 (t0) cc_final: 0.7981 (t0)
REVERT: C  324 TYR cc_start: 0.9052 (OUTLIER) cc_final: 0.7655 (t80)
REVERT: B  117 GLU cc_start: 0.7479 (mp0) cc_final: 0.7104 (mm-30)
REVERT: B  324 TYR cc_start: 0.8648 (OUTLIER) cc_final: 0.8190 (t80)
REVERT: A   87 THR cc_start: 0.9204 (p) cc_final: 0.8996 (t)
REVERT: A   94 SER cc_start: 0.7911 (m) cc_final: 0.7454 (p)
REVERT: A  215 GLU cc_start: 0.8835 (pt0) cc_final: 0.8572 (pt0)
REVERT: A  287 LEU cc_start: 0.9069 (OUTLIER) cc_final: 0.8707 (mt)
REVERT: A  295 ASN cc_start: 0.8418 (t0) cc_final: 0.7679 (p0)
REVERT: A  297 ARG cc_start: 0.7870 (mpp-170) cc_final: 0.7202 (ppt170)
REVERT: A  310 ASP cc_start: 0.8914 (t0) cc_final: 0.7967 (t0)
REVERT: A  339 ARG cc_start: 0.3331 (ttt180) cc_final: 0.2897 (ttt180)
REVERT: A  343 SER cc_start: 0.8887 (m) cc_final: 0.8506 (p)
  outliers start: 38
  outliers final: 28
  residues processed: 199
  average time/residue: 0.1189
  time to fit residues: 34.5127
Evaluate side-chains
  200 residues out of total 1398 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 164
  time to evaluate  : 0.485 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain F residue   86 SER
Chi-restraints excluded: chain F residue  184 VAL
Chi-restraints excluded: chain F residue  201 ARG
Chi-restraints excluded: chain F residue  324 TYR
Chi-restraints excluded: chain E residue  148 VAL
Chi-restraints excluded: chain E residue  227 THR
Chi-restraints excluded: chain E residue  324 TYR
Chi-restraints excluded: chain E residue  333 ASN
Chi-restraints excluded: chain D residue   50 THR
Chi-restraints excluded: chain D residue   61 LEU
Chi-restraints excluded: chain D residue  184 VAL
Chi-restraints excluded: chain D residue  215 GLU
Chi-restraints excluded: chain D residue  241 CYS
Chi-restraints excluded: chain D residue  283 ILE
Chi-restraints excluded: chain D residue  324 TYR
Chi-restraints excluded: chain C residue  147 THR
Chi-restraints excluded: chain C residue  148 VAL
Chi-restraints excluded: chain C residue  182 ILE
Chi-restraints excluded: chain C residue  227 THR
Chi-restraints excluded: chain C residue  241 CYS
Chi-restraints excluded: chain C residue  287 LEU
Chi-restraints excluded: chain C residue  324 TYR
Chi-restraints excluded: chain C residue  333 ASN
Chi-restraints excluded: chain B residue   61 LEU
Chi-restraints excluded: chain B residue   86 SER
Chi-restraints excluded: chain B residue  184 VAL
Chi-restraints excluded: chain B residue  215 GLU
Chi-restraints excluded: chain B residue  241 CYS
Chi-restraints excluded: chain B residue  324 TYR
Chi-restraints excluded: chain A residue   61 LEU
Chi-restraints excluded: chain A residue  124 MET
Chi-restraints excluded: chain A residue  169 LEU
Chi-restraints excluded: chain A residue  227 THR
Chi-restraints excluded: chain A residue  241 CYS
Chi-restraints excluded: chain A residue  287 LEU
Chi-restraints excluded: chain A residue  324 TYR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 168
   random chunks:
   chunk 143 optimal weight:    0.7980
   chunk 87 optimal weight:    7.9990
   chunk 102 optimal weight:    8.9990
   chunk 61 optimal weight:    0.1980
   chunk 33 optimal weight:    1.9990
   chunk 103 optimal weight:   10.0000
   chunk 83 optimal weight:    6.9990
   chunk 90 optimal weight:    5.9990
   chunk 98 optimal weight:    9.9990
   chunk 30 optimal weight:    4.9990
   chunk 48 optimal weight:    4.9990
   overall best weight:    2.5986

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

Flipped N/Q/H residues before XYZ refinement:
F  67 ASN
F 248 GLN
D  67 ASN
D 248 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3067 r_free = 0.3067 target = 0.103581 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.2813 r_free = 0.2813 target = 0.086441 restraints weight = 23139.028|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.2843 r_free = 0.2843 target = 0.088351 restraints weight = 15180.102|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.2863 r_free = 0.2863 target = 0.089663 restraints weight = 11576.707|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.2874 r_free = 0.2874 target = 0.090436 restraints weight = 9665.562|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.2882 r_free = 0.2882 target = 0.090979 restraints weight = 8615.935|
|-----------------------------------------------------------------------------|
r_work (final): 0.2879
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2879
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2879 r_free = 0.2879    target_work(ls_wunit_k1) = 0.091         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:      362 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2877 r_free = 0.2877    target_work(ls_wunit_k1) = 0.091         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:      370 |
|-----------------------------------------------------------------------------|
r_final: 0.2877
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8585
moved from start:          0.4528

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034  13656  Z= 0.139
  Angle     :  0.712  10.652  18486  Z= 0.360
  Chirality :  0.046   0.200   2058
  Planarity :  0.005   0.040   2370
  Dihedral  :  5.804  55.647   1902
  Min Nonbonded Distance : 2.284

Molprobity Statistics.
  All-atom Clashscore : 6.07
  Ramachandran Plot:
    Outliers :  0.94 %
    Allowed  : 11.70 %
    Favored  : 87.37 %
  Rotamer:
    Outliers :  2.50 %
    Allowed  : 17.74 %
    Favored  : 79.76 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 7.14 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.37 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -3.19 (0.19), residues: 1710
  helix: -0.77 (0.26), residues: 408
  sheet: -1.44 (0.28), residues: 354
  loop : -3.14 (0.17), residues: 948

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG E 335 
 TYR   0.013   0.001   TYR E 296 
 PHE   0.009   0.001   PHE C 330 
 TRP   0.010   0.001   TRP B 198 
 HIS   0.013   0.002   HIS F 323 

Details of bonding type rmsd
  covalent geometry    : bond        0.00332 (13656)
  covalent geometry    : angle       0.71242 (18486)
  hydrogen bonds       : bond        0.03520 (  348)
  hydrogen bonds       : angle       4.81785 (  972)

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

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

  3420 Ramachandran restraints generated.
    1710 Oldfield, 0 Emsley, 1710 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3420 Ramachandran restraints generated.
    1710 Oldfield, 0 Emsley, 1710 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  210 residues out of total 1398 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 175
  time to evaluate  : 0.522 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: F  201 ARG cc_start: 0.8451 (OUTLIER) cc_final: 0.7717 (mtt-85)
REVERT: F  317 ASP cc_start: 0.8332 (m-30) cc_final: 0.7958 (m-30)
REVERT: F  324 TYR cc_start: 0.8354 (OUTLIER) cc_final: 0.8091 (t80)
REVERT: F  336 GLU cc_start: 0.7419 (tt0) cc_final: 0.7071 (mt-10)
REVERT: E   47 PHE cc_start: 0.7634 (t80) cc_final: 0.7356 (t80)
REVERT: E  295 ASN cc_start: 0.8370 (t0) cc_final: 0.7386 (p0)
REVERT: E  297 ARG cc_start: 0.7789 (mpp-170) cc_final: 0.7472 (ppt170)
REVERT: E  324 TYR cc_start: 0.8890 (OUTLIER) cc_final: 0.7772 (t80)
REVERT: D   42 GLN cc_start: 0.9294 (tt0) cc_final: 0.8888 (tt0)
REVERT: D  283 ILE cc_start: 0.9202 (OUTLIER) cc_final: 0.8944 (mt)
REVERT: D  324 TYR cc_start: 0.8270 (OUTLIER) cc_final: 0.7958 (t80)
REVERT: C  123 LEU cc_start: 0.8905 (mm) cc_final: 0.8316 (pp)
REVERT: C  287 LEU cc_start: 0.9041 (OUTLIER) cc_final: 0.8624 (mt)
REVERT: C  295 ASN cc_start: 0.8443 (t0) cc_final: 0.7325 (p0)
REVERT: C  310 ASP cc_start: 0.8963 (t0) cc_final: 0.8127 (t0)
REVERT: C  324 TYR cc_start: 0.8941 (OUTLIER) cc_final: 0.7678 (t80)
REVERT: B  117 GLU cc_start: 0.7481 (mp0) cc_final: 0.7118 (mm-30)
REVERT: B  297 ARG cc_start: 0.7672 (ptp90) cc_final: 0.7356 (mpp-170)
REVERT: B  324 TYR cc_start: 0.8435 (OUTLIER) cc_final: 0.8198 (t80)
REVERT: A   87 THR cc_start: 0.9156 (p) cc_final: 0.8901 (t)
REVERT: A   94 SER cc_start: 0.7685 (m) cc_final: 0.7256 (p)
REVERT: A  215 GLU cc_start: 0.8787 (pt0) cc_final: 0.8528 (pt0)
REVERT: A  295 ASN cc_start: 0.8336 (t0) cc_final: 0.7696 (p0)
REVERT: A  297 ARG cc_start: 0.7864 (mpp-170) cc_final: 0.7140 (ppt170)
REVERT: A  339 ARG cc_start: 0.3370 (ttt180) cc_final: 0.2755 (ttt180)
REVERT: A  343 SER cc_start: 0.8830 (m) cc_final: 0.8541 (p)
  outliers start: 35
  outliers final: 25
  residues processed: 199
  average time/residue: 0.1211
  time to fit residues: 34.9302
Evaluate side-chains
  200 residues out of total 1398 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 167
  time to evaluate  : 0.510 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain F residue   86 SER
Chi-restraints excluded: chain F residue  184 VAL
Chi-restraints excluded: chain F residue  201 ARG
Chi-restraints excluded: chain F residue  324 TYR
Chi-restraints excluded: chain E residue  148 VAL
Chi-restraints excluded: chain E residue  227 THR
Chi-restraints excluded: chain E residue  324 TYR
Chi-restraints excluded: chain E residue  340 LYS
Chi-restraints excluded: chain D residue   61 LEU
Chi-restraints excluded: chain D residue  184 VAL
Chi-restraints excluded: chain D residue  215 GLU
Chi-restraints excluded: chain D residue  241 CYS
Chi-restraints excluded: chain D residue  283 ILE
Chi-restraints excluded: chain D residue  324 TYR
Chi-restraints excluded: chain C residue  147 THR
Chi-restraints excluded: chain C residue  148 VAL
Chi-restraints excluded: chain C residue  182 ILE
Chi-restraints excluded: chain C residue  241 CYS
Chi-restraints excluded: chain C residue  287 LEU
Chi-restraints excluded: chain C residue  324 TYR
Chi-restraints excluded: chain C residue  333 ASN
Chi-restraints excluded: chain B residue   61 LEU
Chi-restraints excluded: chain B residue   86 SER
Chi-restraints excluded: chain B residue  184 VAL
Chi-restraints excluded: chain B residue  215 GLU
Chi-restraints excluded: chain B residue  241 CYS
Chi-restraints excluded: chain B residue  324 TYR
Chi-restraints excluded: chain A residue   61 LEU
Chi-restraints excluded: chain A residue  148 VAL
Chi-restraints excluded: chain A residue  169 LEU
Chi-restraints excluded: chain A residue  227 THR
Chi-restraints excluded: chain A residue  241 CYS
Chi-restraints excluded: chain A residue  324 TYR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 168
   random chunks:
   chunk 92 optimal weight:   20.0000
   chunk 85 optimal weight:   20.0000
   chunk 121 optimal weight:    5.9990
   chunk 133 optimal weight:    3.9990
   chunk 36 optimal weight:    0.2980
   chunk 113 optimal weight:   10.0000
   chunk 70 optimal weight:    0.5980
   chunk 148 optimal weight:    6.9990
   chunk 103 optimal weight:    4.9990
   chunk 33 optimal weight:   10.0000
   chunk 165 optimal weight:    6.9990
   overall best weight:    3.1786

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

Flipped N/Q/H residues before XYZ refinement:
F  67 ASN
F 248 GLN
D  67 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3064 r_free = 0.3064 target = 0.103378 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.2811 r_free = 0.2811 target = 0.086288 restraints weight = 22936.470|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.2839 r_free = 0.2839 target = 0.088094 restraints weight = 15506.879|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.2858 r_free = 0.2858 target = 0.089327 restraints weight = 12005.484|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 21)----------------|
| r_work = 0.2868 r_free = 0.2868 target = 0.090008 restraints weight = 10150.518|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 33)----------------|
| r_work = 0.2877 r_free = 0.2877 target = 0.090631 restraints weight = 9148.723|
|-----------------------------------------------------------------------------|
r_work (final): 0.2874
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2871
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2871 r_free = 0.2871    target_work(ls_wunit_k1) = 0.090         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:      370 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2870 r_free = 0.2870    target_work(ls_wunit_k1) = 0.090         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:      381 |
|-----------------------------------------------------------------------------|
r_final: 0.2870
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8603
moved from start:          0.4565

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.028  13656  Z= 0.153
  Angle     :  0.723  10.629  18486  Z= 0.364
  Chirality :  0.046   0.218   2058
  Planarity :  0.005   0.040   2370
  Dihedral  :  5.852  56.547   1902
  Min Nonbonded Distance : 2.430

Molprobity Statistics.
  All-atom Clashscore : 6.15
  Ramachandran Plot:
    Outliers :  0.99 %
    Allowed  : 13.39 %
    Favored  : 85.61 %
  Rotamer:
    Outliers :  2.79 %
    Allowed  : 17.88 %
    Favored  : 79.33 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 7.14 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.37 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -3.13 (0.19), residues: 1710
  helix: -0.71 (0.26), residues: 408
  sheet: -1.40 (0.28), residues: 354
  loop : -3.11 (0.17), residues: 948

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG E 335 
 TYR   0.013   0.001   TYR E 296 
 PHE   0.010   0.001   PHE F 330 
 TRP   0.011   0.001   TRP B 198 
 HIS   0.013   0.002   HIS F 323 

Details of bonding type rmsd
  covalent geometry    : bond        0.00367 (13656)
  covalent geometry    : angle       0.72264 (18486)
  hydrogen bonds       : bond        0.03734 (  348)
  hydrogen bonds       : angle       4.82240 (  972)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2158.99 seconds
wall clock time: 38 minutes 1.86 seconds (2281.86 seconds total)