Starting phenix.real_space_refine
on Thu Jul 31 05:28:59 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/6i5t_4418/07_2025/6i5t_4418.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/6i5t_4418/07_2025/6i5t_4418.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/6i5t_4418/07_2025/6i5t_4418.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/6i5t_4418/07_2025/6i5t_4418.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/6i5t_4418/07_2025/6i5t_4418.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/6i5t_4418/07_2025/6i5t_4418.cif"
  }
  resolution = 3.9
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.001 sd=   0.006
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 18 residue(s): 0.04s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib"
  Total number of atoms: 13356
  Number of models: 1
  Model: ""
    Number of chains: 1
    Chain: "A"
      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:
    C, B, E, D, F
  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: 5.58, per 1000 atoms: 0.42
  Number of scatterers: 13356
  At special positions: 0
  Unit cell: (118.15, 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: 3.02
  Conformation dependent library (CDL) restraints added in 1.7 seconds
  

  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:
      42 helices and 21 sheets defined
      24.6% alpha, 15.1% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 1.84
  Creating SS restraints...
    Processing helix  chain 'F' and resid 53 through 66
      removed outlier: 3.801A  pdb=" N   ALA F  57 " --> pdb=" O   THR F  53 " (cutoff:3.500A)
      removed outlier: 3.596A  pdb=" N   GLU F  58 " --> pdb=" O   LEU F  54 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 96 through 108
      removed outlier: 4.333A  pdb=" N   ARG F 100 " --> pdb=" O   THR F  96 " (cutoff:3.500A)
      removed outlier: 3.944A  pdb=" N   ASP F 101 " --> pdb=" O   ALA F  97 " (cutoff:3.500A)
      removed outlier: 5.597A  pdb=" N   ASP F 102 " --> pdb=" O   LYS F  98 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 115 through 127
      removed outlier: 3.547A  pdb=" N   GLU F 119 " --> pdb=" O   GLY F 115 " (cutoff:3.500A)
      removed outlier: 4.148A  pdb=" N   ARG F 120 " --> pdb=" O   PRO F 116 " (cutoff:3.500A)
      removed outlier: 4.139A  pdb=" N   LEU F 121 " --> pdb=" O   GLU F 117 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 169 through 173
    Processing helix  chain 'F' and resid 202 through 210
      removed outlier: 3.915A  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 226 through 239
      removed outlier: 4.432A  pdb=" N   ALA F 230 " --> pdb=" O   GLU F 226 " (cutoff:3.500A)
      removed outlier: 3.988A  pdb=" N   HIS F 234 " --> pdb=" O   ALA F 230 " (cutoff:3.500A)
      removed outlier: 4.118A  pdb=" N   ILE F 235 " --> pdb=" O   SER F 231 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 53 through 66
      removed outlier: 3.801A  pdb=" N   ALA E  57 " --> pdb=" O   THR E  53 " (cutoff:3.500A)
      removed outlier: 3.596A  pdb=" N   GLU E  58 " --> pdb=" O   LEU E  54 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 96 through 108
      removed outlier: 4.333A  pdb=" N   ARG E 100 " --> pdb=" O   THR E  96 " (cutoff:3.500A)
      removed outlier: 3.945A  pdb=" N   ASP E 101 " --> pdb=" O   ALA E  97 " (cutoff:3.500A)
      removed outlier: 5.598A  pdb=" N   ASP E 102 " --> pdb=" O   LYS E  98 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 115 through 127
      removed outlier: 3.547A  pdb=" N   GLU E 119 " --> pdb=" O   GLY E 115 " (cutoff:3.500A)
      removed outlier: 4.149A  pdb=" N   ARG E 120 " --> pdb=" O   PRO E 116 " (cutoff:3.500A)
      removed outlier: 4.139A  pdb=" N   LEU E 121 " --> pdb=" O   GLU E 117 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 169 through 173
    Processing helix  chain 'E' and resid 202 through 210
      removed outlier: 3.915A  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 226 through 239
      removed outlier: 4.433A  pdb=" N   ALA E 230 " --> pdb=" O   GLU E 226 " (cutoff:3.500A)
      removed outlier: 3.989A  pdb=" N   HIS E 234 " --> pdb=" O   ALA E 230 " (cutoff:3.500A)
      removed outlier: 4.118A  pdb=" N   ILE E 235 " --> pdb=" O   SER E 231 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 53 through 66
      removed outlier: 3.800A  pdb=" N   ALA D  57 " --> pdb=" O   THR D  53 " (cutoff:3.500A)
      removed outlier: 3.597A  pdb=" N   GLU D  58 " --> pdb=" O   LEU D  54 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 96 through 108
      removed outlier: 4.333A  pdb=" N   ARG D 100 " --> pdb=" O   THR D  96 " (cutoff:3.500A)
      removed outlier: 3.943A  pdb=" N   ASP D 101 " --> pdb=" O   ALA D  97 " (cutoff:3.500A)
      removed outlier: 5.597A  pdb=" N   ASP D 102 " --> pdb=" O   LYS D  98 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 115 through 127
      removed outlier: 3.547A  pdb=" N   GLU D 119 " --> pdb=" O   GLY D 115 " (cutoff:3.500A)
      removed outlier: 4.149A  pdb=" N   ARG D 120 " --> pdb=" O   PRO D 116 " (cutoff:3.500A)
      removed outlier: 4.140A  pdb=" N   LEU D 121 " --> pdb=" O   GLU D 117 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 169 through 173
    Processing helix  chain 'D' and resid 202 through 210
      removed outlier: 3.915A  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 226 through 239
      removed outlier: 4.433A  pdb=" N   ALA D 230 " --> pdb=" O   GLU D 226 " (cutoff:3.500A)
      removed outlier: 3.988A  pdb=" N   HIS D 234 " --> pdb=" O   ALA D 230 " (cutoff:3.500A)
      removed outlier: 4.119A  pdb=" N   ILE D 235 " --> pdb=" O   SER D 231 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 53 through 66
      removed outlier: 3.801A  pdb=" N   ALA C  57 " --> pdb=" O   THR C  53 " (cutoff:3.500A)
      removed outlier: 3.596A  pdb=" N   GLU C  58 " --> pdb=" O   LEU C  54 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 96 through 108
      removed outlier: 4.333A  pdb=" N   ARG C 100 " --> pdb=" O   THR C  96 " (cutoff:3.500A)
      removed outlier: 3.943A  pdb=" N   ASP C 101 " --> pdb=" O   ALA C  97 " (cutoff:3.500A)
      removed outlier: 5.597A  pdb=" N   ASP C 102 " --> pdb=" O   LYS C  98 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 115 through 127
      removed outlier: 3.547A  pdb=" N   GLU C 119 " --> pdb=" O   GLY C 115 " (cutoff:3.500A)
      removed outlier: 4.149A  pdb=" N   ARG C 120 " --> pdb=" O   PRO C 116 " (cutoff:3.500A)
      removed outlier: 4.139A  pdb=" N   LEU C 121 " --> pdb=" O   GLU C 117 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 169 through 173
    Processing helix  chain 'C' and resid 202 through 210
      removed outlier: 3.915A  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 226 through 239
      removed outlier: 4.433A  pdb=" N   ALA C 230 " --> pdb=" O   GLU C 226 " (cutoff:3.500A)
      removed outlier: 3.989A  pdb=" N   HIS C 234 " --> pdb=" O   ALA C 230 " (cutoff:3.500A)
      removed outlier: 4.119A  pdb=" N   ILE C 235 " --> pdb=" O   SER C 231 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 53 through 66
      removed outlier: 3.800A  pdb=" N   ALA B  57 " --> pdb=" O   THR B  53 " (cutoff:3.500A)
      removed outlier: 3.596A  pdb=" N   GLU B  58 " --> pdb=" O   LEU B  54 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 96 through 108
      removed outlier: 4.334A  pdb=" N   ARG B 100 " --> pdb=" O   THR B  96 " (cutoff:3.500A)
      removed outlier: 3.944A  pdb=" N   ASP B 101 " --> pdb=" O   ALA B  97 " (cutoff:3.500A)
      removed outlier: 5.598A  pdb=" N   ASP B 102 " --> pdb=" O   LYS B  98 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 115 through 127
      removed outlier: 3.546A  pdb=" N   GLU B 119 " --> pdb=" O   GLY B 115 " (cutoff:3.500A)
      removed outlier: 4.149A  pdb=" N   ARG B 120 " --> pdb=" O   PRO B 116 " (cutoff:3.500A)
      removed outlier: 4.139A  pdb=" N   LEU B 121 " --> pdb=" O   GLU B 117 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 169 through 173
    Processing helix  chain 'B' and resid 202 through 210
      removed outlier: 3.915A  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 226 through 239
      removed outlier: 4.433A  pdb=" N   ALA B 230 " --> pdb=" O   GLU B 226 " (cutoff:3.500A)
      removed outlier: 3.989A  pdb=" N   HIS B 234 " --> pdb=" O   ALA B 230 " (cutoff:3.500A)
      removed outlier: 4.118A  pdb=" N   ILE B 235 " --> pdb=" O   SER B 231 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 53 through 66
      removed outlier: 3.801A  pdb=" N   ALA A  57 " --> pdb=" O   THR A  53 " (cutoff:3.500A)
      removed outlier: 3.596A  pdb=" N   GLU A  58 " --> pdb=" O   LEU A  54 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 96 through 108
      removed outlier: 4.333A  pdb=" N   ARG A 100 " --> pdb=" O   THR A  96 " (cutoff:3.500A)
      removed outlier: 3.944A  pdb=" N   ASP A 101 " --> pdb=" O   ALA A  97 " (cutoff:3.500A)
      removed outlier: 5.597A  pdb=" N   ASP A 102 " --> pdb=" O   LYS A  98 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 115 through 127
      removed outlier: 3.547A  pdb=" N   GLU A 119 " --> pdb=" O   GLY A 115 " (cutoff:3.500A)
      removed outlier: 4.148A  pdb=" N   ARG A 120 " --> pdb=" O   PRO A 116 " (cutoff:3.500A)
      removed outlier: 4.139A  pdb=" N   LEU A 121 " --> pdb=" O   GLU A 117 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 169 through 173
    Processing helix  chain 'A' and resid 202 through 210
      removed outlier: 3.915A  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 226 through 239
      removed outlier: 4.433A  pdb=" N   ALA A 230 " --> pdb=" O   GLU A 226 " (cutoff:3.500A)
      removed outlier: 3.989A  pdb=" N   HIS A 234 " --> pdb=" O   ALA A 230 " (cutoff:3.500A)
      removed outlier: 4.118A  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: 7.243A  pdb=" N   PHE F 150 " --> pdb=" O   LEU F 158 " (cutoff:3.500A)
      removed outlier: 6.439A  pdb=" N   VAL F  72 " --> pdb=" O   VAL F 133 " (cutoff:3.500A)
      removed outlier: 3.843A  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: 6.523A  pdb=" N   TYR F 217 " --> pdb=" O   LEU F 244 " (cutoff:3.500A)
      removed outlier: 8.131A  pdb=" N   ALA F 246 " --> pdb=" O   TYR F 217 " (cutoff:3.500A)
      removed outlier: 7.055A  pdb=" N   ALA F 219 " --> pdb=" O   ALA F 246 " (cutoff:3.500A)
      removed outlier: 7.233A  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: 3.544A  pdb=" N   SER E 331 " --> pdb=" O   ASN F 333 " (cutoff:3.500A)
      removed outlier: 3.528A  pdb=" N   SER F 331 " --> pdb=" O   ASN E 333 " (cutoff:3.500A)
      removed outlier: 8.800A  pdb=" N   SER D 343 " --> pdb=" O   PHE F 330 " (cutoff:3.500A)
      removed outlier: 6.884A  pdb=" N   LEU F 332 " --> pdb=" O   SER D 343 " (cutoff:3.500A)
      removed outlier: 7.885A  pdb=" N   LYS D 345 " --> pdb=" O   LEU F 332 " (cutoff:3.500A)
      removed outlier: 6.287A  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: 7.242A  pdb=" N   PHE E 150 " --> pdb=" O   LEU E 158 " (cutoff:3.500A)
      removed outlier: 6.439A  pdb=" N   VAL E  72 " --> pdb=" O   VAL E 133 " (cutoff:3.500A)
      removed outlier: 3.844A  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: 6.523A  pdb=" N   TYR E 217 " --> pdb=" O   LEU E 244 " (cutoff:3.500A)
      removed outlier: 8.130A  pdb=" N   ALA E 246 " --> pdb=" O   TYR E 217 " (cutoff:3.500A)
      removed outlier: 7.055A  pdb=" N   ALA E 219 " --> pdb=" O   ALA E 246 " (cutoff:3.500A)
      removed outlier: 7.234A  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: 3.537A  pdb=" N   SER C 331 " --> pdb=" O   ASN D 333 " (cutoff:3.500A)
      removed outlier: 3.532A  pdb=" N   SER D 331 " --> pdb=" O   ASN C 333 " (cutoff:3.500A)
      removed outlier: 8.782A  pdb=" N   SER B 343 " --> pdb=" O   PHE D 330 " (cutoff:3.500A)
      removed outlier: 6.869A  pdb=" N   LEU D 332 " --> pdb=" O   SER B 343 " (cutoff:3.500A)
      removed outlier: 7.870A  pdb=" N   LYS B 345 " --> pdb=" O   LEU D 332 " (cutoff:3.500A)
      removed outlier: 6.275A  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: 7.243A  pdb=" N   PHE D 150 " --> pdb=" O   LEU D 158 " (cutoff:3.500A)
      removed outlier: 6.439A  pdb=" N   VAL D  72 " --> pdb=" O   VAL D 133 " (cutoff:3.500A)
      removed outlier: 3.845A  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: 6.522A  pdb=" N   TYR D 217 " --> pdb=" O   LEU D 244 " (cutoff:3.500A)
      removed outlier: 8.131A  pdb=" N   ALA D 246 " --> pdb=" O   TYR D 217 " (cutoff:3.500A)
      removed outlier: 7.055A  pdb=" N   ALA D 219 " --> pdb=" O   ALA D 246 " (cutoff:3.500A)
      removed outlier: 7.234A  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: 7.243A  pdb=" N   PHE C 150 " --> pdb=" O   LEU C 158 " (cutoff:3.500A)
      removed outlier: 6.439A  pdb=" N   VAL C  72 " --> pdb=" O   VAL C 133 " (cutoff:3.500A)
      removed outlier: 3.845A  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: 6.523A  pdb=" N   TYR C 217 " --> pdb=" O   LEU C 244 " (cutoff:3.500A)
      removed outlier: 8.130A  pdb=" N   ALA C 246 " --> pdb=" O   TYR C 217 " (cutoff:3.500A)
      removed outlier: 7.055A  pdb=" N   ALA C 219 " --> pdb=" O   ALA C 246 " (cutoff:3.500A)
      removed outlier: 7.233A  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: 3.557A  pdb=" N   SER A 331 " --> pdb=" O   ASN B 333 " (cutoff:3.500A)
      removed outlier: 3.534A  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: 7.242A  pdb=" N   PHE B 150 " --> pdb=" O   LEU B 158 " (cutoff:3.500A)
      removed outlier: 6.439A  pdb=" N   VAL B  72 " --> pdb=" O   VAL B 133 " (cutoff:3.500A)
      removed outlier: 3.844A  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: 6.523A  pdb=" N   TYR B 217 " --> pdb=" O   LEU B 244 " (cutoff:3.500A)
      removed outlier: 8.131A  pdb=" N   ALA B 246 " --> pdb=" O   TYR B 217 " (cutoff:3.500A)
      removed outlier: 7.055A  pdb=" N   ALA B 219 " --> pdb=" O   ALA B 246 " (cutoff:3.500A)
      removed outlier: 7.233A  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: 7.243A  pdb=" N   PHE A 150 " --> pdb=" O   LEU A 158 " (cutoff:3.500A)
      removed outlier: 6.439A  pdb=" N   VAL A  72 " --> pdb=" O   VAL A 133 " (cutoff:3.500A)
      removed outlier: 3.845A  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: 6.523A  pdb=" N   TYR A 217 " --> pdb=" O   LEU A 244 " (cutoff:3.500A)
      removed outlier: 8.131A  pdb=" N   ALA A 246 " --> pdb=" O   TYR A 217 " (cutoff:3.500A)
      removed outlier: 7.054A  pdb=" N   ALA A 219 " --> pdb=" O   ALA A 246 " (cutoff:3.500A)
      removed outlier: 7.234A  pdb=" N   ILE A 283 " --> pdb=" O   LEU A 291 " (cutoff:3.500A)

    354 hydrogen bonds defined for protein.
    936 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: 3.77

  Time building geometry restraints manager: 3.61 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: 4295
        1.34 -     1.46: 2618
        1.46 -     1.57: 6629
        1.57 -     1.69: 0
        1.69 -     1.81: 114
  Bond restraints: 13656
  Sorted by residual:
  bond pdb=" CA  HIS E 323 "
       pdb=" C   HIS E 323 "
    ideal  model  delta    sigma   weight residual
    1.523  1.550 -0.027 1.34e-02 5.57e+03 3.93e+00
  bond pdb=" CA  HIS B 323 "
       pdb=" C   HIS B 323 "
    ideal  model  delta    sigma   weight residual
    1.523  1.549 -0.026 1.34e-02 5.57e+03 3.70e+00
  bond pdb=" CA  HIS C 323 "
       pdb=" C   HIS C 323 "
    ideal  model  delta    sigma   weight residual
    1.523  1.549 -0.026 1.34e-02 5.57e+03 3.68e+00
  bond pdb=" CA  HIS A 323 "
       pdb=" C   HIS A 323 "
    ideal  model  delta    sigma   weight residual
    1.523  1.549 -0.025 1.34e-02 5.57e+03 3.58e+00
  bond pdb=" CA  HIS F 323 "
       pdb=" C   HIS F 323 "
    ideal  model  delta    sigma   weight residual
    1.523  1.548 -0.025 1.34e-02 5.57e+03 3.56e+00
  ... (remaining 13651 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     3.40: 18241
        3.40 -     6.81: 191
        6.81 -    10.21: 34
       10.21 -    13.61: 14
       13.61 -    17.01: 6
  Bond angle restraints: 18486
  Sorted by residual:
  angle pdb=" C   VAL E 320 "
        pdb=" N   VAL E 321 "
        pdb=" CA  VAL E 321 "
      ideal   model   delta    sigma   weight residual
     121.97  130.89   -8.92 1.80e+00 3.09e-01 2.46e+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  130.86   -8.89 1.80e+00 3.09e-01 2.44e+01
  angle pdb=" C   VAL A 320 "
        pdb=" N   VAL A 321 "
        pdb=" CA  VAL A 321 "
      ideal   model   delta    sigma   weight residual
     121.97  130.86   -8.89 1.80e+00 3.09e-01 2.44e+01
  angle pdb=" C   VAL D 320 "
        pdb=" N   VAL D 321 "
        pdb=" CA  VAL D 321 "
      ideal   model   delta    sigma   weight residual
     121.97  130.84   -8.87 1.80e+00 3.09e-01 2.43e+01
  angle pdb=" N   VAL D 321 "
        pdb=" CA  VAL D 321 "
        pdb=" C   VAL D 321 "
      ideal   model   delta    sigma   weight residual
     109.34  119.58  -10.24 2.08e+00 2.31e-01 2.42e+01
  ... (remaining 18481 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    14.53: 7564
       14.53 -    29.05: 434
       29.05 -    43.58: 96
       43.58 -    58.10: 6
       58.10 -    72.63: 6
  Dihedral angle restraints: 8106
    sinusoidal: 3162
      harmonic: 4944
  Sorted by residual:
  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 -107.37  -72.63     0      5.00e+00 4.00e-02 2.11e+02
  dihedral pdb=" CA  GLY F 322 "
           pdb=" C   GLY F 322 "
           pdb=" N   HIS F 323 "
           pdb=" CA  HIS F 323 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -107.40  -72.60     0      5.00e+00 4.00e-02 2.11e+02
  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 -107.41  -72.59     0      5.00e+00 4.00e-02 2.11e+02
  ... (remaining 8103 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.066: 1591
       0.066 -    0.132: 408
       0.132 -    0.198: 29
       0.198 -    0.265: 18
       0.265 -    0.331: 12
  Chirality restraints: 2058
  Sorted by residual:
  chirality pdb=" CB  VAL E 320 "
            pdb=" CA  VAL E 320 "
            pdb=" CG1 VAL E 320 "
            pdb=" CG2 VAL E 320 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -2.30   -0.33 2.00e-01 2.50e+01 2.73e+00
  chirality pdb=" CB  VAL A 320 "
            pdb=" CA  VAL A 320 "
            pdb=" CG1 VAL A 320 "
            pdb=" CG2 VAL A 320 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -2.30   -0.33 2.00e-01 2.50e+01 2.72e+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   -2.30   -0.33 2.00e-01 2.50e+01 2.70e+00
  ... (remaining 2055 not shown)

  Planarity restraints: 2370
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   THR F 187 "   -0.035 5.00e-02 4.00e+02   5.31e-02 4.51e+00
        pdb=" N   PRO F 188 "    0.092 5.00e-02 4.00e+02
        pdb=" CA  PRO F 188 "   -0.027 5.00e-02 4.00e+02
        pdb=" CD  PRO F 188 "   -0.030 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   THR A 187 "    0.035 5.00e-02 4.00e+02   5.31e-02 4.50e+00
        pdb=" N   PRO A 188 "   -0.092 5.00e-02 4.00e+02
        pdb=" CA  PRO A 188 "    0.027 5.00e-02 4.00e+02
        pdb=" CD  PRO A 188 "    0.030 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   THR C 187 "    0.035 5.00e-02 4.00e+02   5.29e-02 4.48e+00
        pdb=" N   PRO C 188 "   -0.092 5.00e-02 4.00e+02
        pdb=" CA  PRO C 188 "    0.027 5.00e-02 4.00e+02
        pdb=" CD  PRO C 188 "    0.029 5.00e-02 4.00e+02
  ... (remaining 2367 not shown)

  Histogram of nonbonded interaction distances:
        2.36 -     2.87: 4687
        2.87 -     3.38: 11187
        3.38 -     3.88: 19763
        3.88 -     4.39: 22052
        4.39 -     4.90: 39536
  Nonbonded interactions: 97225
  Sorted by model distance:
  nonbonded pdb=" OE1 GLU A  89 "
            pdb=" OG1 THR A  96 "
     model   vdw
     2.362 3.040
  nonbonded pdb=" OE1 GLU E  89 "
            pdb=" OG1 THR E  96 "
     model   vdw
     2.362 3.040
  nonbonded pdb=" OE1 GLU F  89 "
            pdb=" OG1 THR F  96 "
     model   vdw
     2.362 3.040
  nonbonded pdb=" OE1 GLU D  89 "
            pdb=" OG1 THR D  96 "
     model   vdw
     2.362 3.040
  nonbonded pdb=" OE1 GLU C  89 "
            pdb=" OG1 THR C  96 "
     model   vdw
     2.363 3.040
  ... (remaining 97220 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: 0.11
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'C'
  selection = chain 'B'
  selection = chain 'E'
  selection = chain 'D'
  selection = chain 'F'
}

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:             1.230
  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:          0.600
  Check model and map are aligned:         0.040
  Set scattering table:                    0.130
  Process input model:                     29.280
  Find NCS groups from input model:        0.270
  Set up NCS constraints:                  0.030
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.010
  Load rotamer database and sin/cos tables:2.700
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   34.300
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8301
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      :  0.006   0.045  13656  Z= 0.273
  Angle     :  1.110  17.014  18486  Z= 0.584
  Chirality :  0.064   0.331   2058
  Planarity :  0.008   0.053   2370
  Dihedral  : 10.098  72.626   4950
  Min Nonbonded Distance : 2.362

Molprobity Statistics.
  All-atom Clashscore : 4.19
  Ramachandran Plot:
    Outliers :  0.70 %
    Allowed  : 15.09 %
    Favored  : 84.21 %
  Rotamer:
    Outliers :  0.43 %
    Allowed  :  6.01 %
    Favored  : 93.56 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 7.14 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.73 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -5.80 (0.13), residues: 1710
  helix: -3.89 (0.13), residues: 438
  sheet: -4.21 (0.25), residues: 216
  loop : -3.96 (0.13), residues: 1056

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.022   0.003   TRP D 198 
 HIS   0.007   0.002   HIS F 234 
 PHE   0.011   0.002   PHE C 316 
 TYR   0.030   0.003   TYR B 324 
 ARG   0.005   0.001   ARG A 206 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.25207 (  354)
  hydrogen bonds       : angle       8.11915 (  936)
  covalent geometry    : bond        0.00608 (13656)
  covalent geometry    : angle       1.10978 (18486)

*********************** 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
  442 residues out of total 1398 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 436
  time to evaluate  : 1.520 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: F  138 GLU cc_start: 0.8759 (pt0) cc_final: 0.8275 (pt0)
REVERT: F  162 ARG cc_start: 0.8582 (mtt180) cc_final: 0.8348 (mtt180)
REVERT: F  221 THR cc_start: 0.9351 (t) cc_final: 0.8951 (m)
REVERT: E  134 MET cc_start: 0.7090 (tpp) cc_final: 0.6817 (tpp)
REVERT: D   89 GLU cc_start: 0.7569 (mt-10) cc_final: 0.7266 (tt0)
REVERT: D  138 GLU cc_start: 0.8764 (pt0) cc_final: 0.8254 (pt0)
REVERT: D  221 THR cc_start: 0.9432 (t) cc_final: 0.9027 (m)
REVERT: C  285 SER cc_start: 0.8506 (t) cc_final: 0.7628 (p)
REVERT: B  138 GLU cc_start: 0.8746 (pt0) cc_final: 0.8078 (pt0)
REVERT: B  221 THR cc_start: 0.9407 (t) cc_final: 0.8950 (m)
REVERT: B  285 SER cc_start: 0.9045 (t) cc_final: 0.8192 (p)
REVERT: B  315 LYS cc_start: 0.8751 (mtpp) cc_final: 0.8183 (tttt)
REVERT: A  134 MET cc_start: 0.7057 (tpp) cc_final: 0.6848 (tpp)
REVERT: A  167 THR cc_start: 0.8400 (p) cc_final: 0.8195 (m)
  outliers start: 6
  outliers final: 1
  residues processed: 436
  average time/residue: 0.3022
  time to fit residues: 178.4468
Evaluate side-chains
  196 residues out of total 1398 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 195
  time to evaluate  : 1.407 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain F residue   61 LEU
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 168
   random chunks:
   chunk 141 optimal weight:    7.9990
   chunk 127 optimal weight:    9.9990
   chunk 70 optimal weight:    6.9990
   chunk 43 optimal weight:    6.9990
   chunk 85 optimal weight:    7.9990
   chunk 68 optimal weight:   10.0000
   chunk 131 optimal weight:    5.9990
   chunk 50 optimal weight:    0.6980
   chunk 80 optimal weight:   20.0000
   chunk 98 optimal weight:    0.1980
   chunk 152 optimal weight:    0.9980
   overall best weight:    2.9784

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

Flipped N/Q/H residues before XYZ refinement:
F  70 GLN
F 154 GLN
F 200 ASN
F 295 ASN
E 154 GLN
E 200 ASN
E 337 HIS
D 200 ASN
D 295 ASN
C 200 ASN
** C 337 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 154 GLN
B 200 ASN
B 295 ASN
A 200 ASN
** A 337 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 14

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3482 r_free = 0.3482 target = 0.131986 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3215 r_free = 0.3215 target = 0.111536 restraints weight = 20927.139|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3251 r_free = 0.3251 target = 0.114225 restraints weight = 13568.582|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3275 r_free = 0.3275 target = 0.115999 restraints weight = 10131.640|
|-----------------------------------------------------------------------------|
r_work (final): 0.3262
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3182
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3182 r_free = 0.3182    target_work(ls_wunit_k1) = 0.109         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2910 r_free = 0.2910    target_work(ls_wunit_k1) = 0.090         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       51 |
|-----------------------------------------------------------------------------|
r_final: 0.2910
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8583
moved from start:          0.2696

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.030  13656  Z= 0.156
  Angle     :  0.758  11.370  18486  Z= 0.383
  Chirality :  0.048   0.159   2058
  Planarity :  0.006   0.042   2370
  Dihedral  :  6.537  53.847   1904
  Min Nonbonded Distance : 2.299

Molprobity Statistics.
  All-atom Clashscore : 5.81
  Ramachandran Plot:
    Outliers :  0.88 %
    Allowed  : 12.46 %
    Favored  : 86.67 %
  Rotamer:
    Outliers :  3.51 %
    Allowed  : 11.16 %
    Favored  : 85.34 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 7.14 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.37 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -4.64 (0.16), residues: 1710
  helix: -2.31 (0.22), residues: 402
  sheet: -2.92 (0.26), residues: 312
  loop : -3.63 (0.15), residues: 996

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.001   TRP B 198 
 HIS   0.011   0.002   HIS A 323 
 PHE   0.009   0.001   PHE F 316 
 TYR   0.019   0.001   TYR D 128 
 ARG   0.005   0.000   ARG B 201 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04291 (  354)
  hydrogen bonds       : angle       5.64483 (  936)
  covalent geometry    : bond        0.00361 (13656)
  covalent geometry    : angle       0.75801 (18486)

*********************** 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
  264 residues out of total 1398 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 49
    poor density    : 215
  time to evaluate  : 1.722 
Fit side-chains
   revert: symmetry clash
REVERT: F  127 LYS cc_start: 0.7531 (pttt) cc_final: 0.6285 (mtpp)
REVERT: F  129 LYS cc_start: 0.7343 (mmtt) cc_final: 0.6980 (mmtm)
REVERT: F  169 LEU cc_start: 0.8602 (OUTLIER) cc_final: 0.8182 (tm)
REVERT: F  221 THR cc_start: 0.9289 (t) cc_final: 0.8923 (m)
REVERT: E  154 GLN cc_start: 0.7529 (mp-120) cc_final: 0.7327 (mp10)
REVERT: D   67 ASN cc_start: 0.8531 (p0) cc_final: 0.8028 (t0)
REVERT: D   89 GLU cc_start: 0.7908 (mt-10) cc_final: 0.7708 (tt0)
REVERT: D  127 LYS cc_start: 0.7565 (pttt) cc_final: 0.6600 (mtpp)
REVERT: D  138 GLU cc_start: 0.9486 (pt0) cc_final: 0.9239 (pt0)
REVERT: D  169 LEU cc_start: 0.8900 (OUTLIER) cc_final: 0.8463 (tm)
REVERT: D  221 THR cc_start: 0.9270 (t) cc_final: 0.8933 (m)
REVERT: D  227 THR cc_start: 0.8669 (OUTLIER) cc_final: 0.8403 (m)
REVERT: C  310 ASP cc_start: 0.8570 (t0) cc_final: 0.8269 (t0)
REVERT: B  127 LYS cc_start: 0.7570 (pttt) cc_final: 0.6361 (mtpp)
REVERT: B  221 THR cc_start: 0.9213 (t) cc_final: 0.8932 (m)
REVERT: B  227 THR cc_start: 0.8691 (OUTLIER) cc_final: 0.8397 (m)
REVERT: B  315 LYS cc_start: 0.8901 (mtpp) cc_final: 0.8521 (pttt)
  outliers start: 49
  outliers final: 23
  residues processed: 254
  average time/residue: 0.2564
  time to fit residues: 96.8346
Evaluate side-chains
  210 residues out of total 1398 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 183
  time to evaluate  : 1.473 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain F residue   66 GLU
Chi-restraints excluded: chain F residue  169 LEU
Chi-restraints excluded: chain F residue  181 THR
Chi-restraints excluded: chain F residue  227 THR
Chi-restraints excluded: chain F residue  241 CYS
Chi-restraints excluded: chain F residue  308 LEU
Chi-restraints excluded: chain E residue   55 ASP
Chi-restraints excluded: chain E residue  289 ILE
Chi-restraints excluded: chain D residue   66 GLU
Chi-restraints excluded: chain D residue  148 VAL
Chi-restraints excluded: chain D residue  169 LEU
Chi-restraints excluded: chain D residue  227 THR
Chi-restraints excluded: chain D residue  241 CYS
Chi-restraints excluded: chain D residue  282 SER
Chi-restraints excluded: chain C residue   55 ASP
Chi-restraints excluded: chain C residue   61 LEU
Chi-restraints excluded: chain C residue  227 THR
Chi-restraints excluded: chain C residue  289 ILE
Chi-restraints excluded: chain B residue   50 THR
Chi-restraints excluded: chain B residue   66 GLU
Chi-restraints excluded: chain B residue  169 LEU
Chi-restraints excluded: chain B residue  227 THR
Chi-restraints excluded: chain B residue  241 CYS
Chi-restraints excluded: chain B residue  282 SER
Chi-restraints excluded: chain B residue  308 LEU
Chi-restraints excluded: chain A residue   55 ASP
Chi-restraints excluded: chain A residue  289 ILE
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 168
   random chunks:
   chunk 112 optimal weight:   20.0000
   chunk 53 optimal weight:    9.9990
   chunk 2 optimal weight:    5.9990
   chunk 87 optimal weight:   50.0000
   chunk 119 optimal weight:    0.0010
   chunk 138 optimal weight:    0.4980
   chunk 86 optimal weight:    7.9990
   chunk 1 optimal weight:    5.9990
   chunk 54 optimal weight:    0.8980
   chunk 97 optimal weight:    9.9990
   chunk 98 optimal weight:    5.9990
   overall best weight:    2.6790

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

Flipped N/Q/H residues before XYZ refinement:
F 295 ASN
D 295 ASN
C 295 ASN
B 295 ASN
** A  42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3120 r_free = 0.3120 target = 0.105457 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.2824 r_free = 0.2824 target = 0.085470 restraints weight = 23761.823|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 41)----------------|
| r_work = 0.2860 r_free = 0.2860 target = 0.087794 restraints weight = 14869.636|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.2885 r_free = 0.2885 target = 0.089384 restraints weight = 11012.445|
|-----------------------------------------------------------------------------|
r_work (final): 0.2864
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2864
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2864 r_free = 0.2864    target_work(ls_wunit_k1) = 0.088         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       51 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2823 r_free = 0.2823    target_work(ls_wunit_k1) = 0.085         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:      225 |
|-----------------------------------------------------------------------------|
r_final: 0.2823
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8599
moved from start:          0.3192

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033  13656  Z= 0.138
  Angle     :  0.722  11.589  18486  Z= 0.360
  Chirality :  0.047   0.165   2058
  Planarity :  0.006   0.037   2370
  Dihedral  :  6.078  53.937   1902
  Min Nonbonded Distance : 2.286

Molprobity Statistics.
  All-atom Clashscore : 6.27
  Ramachandran Plot:
    Outliers :  0.88 %
    Allowed  : 11.87 %
    Favored  : 87.25 %
  Rotamer:
    Outliers :  4.58 %
    Allowed  : 11.37 %
    Favored  : 84.05 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 7.14 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.37 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -4.05 (0.17), residues: 1710
  helix: -1.65 (0.25), residues: 402
  sheet: -2.18 (0.29), residues: 312
  loop : -3.48 (0.15), residues: 996

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP B 198 
 HIS   0.007   0.002   HIS C 323 
 PHE   0.009   0.001   PHE F 157 
 TYR   0.016   0.001   TYR D 128 
 ARG   0.006   0.000   ARG C 201 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03459 (  354)
  hydrogen bonds       : angle       5.23440 (  936)
  covalent geometry    : bond        0.00324 (13656)
  covalent geometry    : angle       0.72153 (18486)

*********************** 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
  280 residues out of total 1398 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 64
    poor density    : 216
  time to evaluate  : 1.399 
Fit side-chains
REVERT: F  127 LYS cc_start: 0.7555 (pttt) cc_final: 0.6577 (mtpp)
REVERT: F  169 LEU cc_start: 0.8664 (OUTLIER) cc_final: 0.8213 (tm)
REVERT: F  221 THR cc_start: 0.9341 (t) cc_final: 0.8891 (m)
REVERT: F  227 THR cc_start: 0.8494 (OUTLIER) cc_final: 0.8082 (m)
REVERT: D  127 LYS cc_start: 0.7619 (pttt) cc_final: 0.6813 (mtpp)
REVERT: D  169 LEU cc_start: 0.8852 (OUTLIER) cc_final: 0.8451 (tm)
REVERT: D  221 THR cc_start: 0.9275 (t) cc_final: 0.8979 (m)
REVERT: C  310 ASP cc_start: 0.9051 (t0) cc_final: 0.8719 (t0)
REVERT: B  127 LYS cc_start: 0.7882 (pttt) cc_final: 0.6686 (mtpp)
REVERT: B  199 GLU cc_start: 0.9369 (mt-10) cc_final: 0.8980 (mt-10)
REVERT: B  221 THR cc_start: 0.9165 (t) cc_final: 0.8891 (m)
REVERT: B  315 LYS cc_start: 0.8833 (mtpp) cc_final: 0.8201 (pttt)
  outliers start: 64
  outliers final: 31
  residues processed: 266
  average time/residue: 0.2102
  time to fit residues: 86.1255
Evaluate side-chains
  205 residues out of total 1398 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 171
  time to evaluate  : 1.511 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain F residue   50 THR
Chi-restraints excluded: chain F residue  169 LEU
Chi-restraints excluded: chain F residue  181 THR
Chi-restraints excluded: chain F residue  227 THR
Chi-restraints excluded: chain F residue  241 CYS
Chi-restraints excluded: chain F residue  301 LEU
Chi-restraints excluded: chain F residue  308 LEU
Chi-restraints excluded: chain E residue   55 ASP
Chi-restraints excluded: chain E residue  113 VAL
Chi-restraints excluded: chain E residue  289 ILE
Chi-restraints excluded: chain D residue   50 THR
Chi-restraints excluded: chain D residue  148 VAL
Chi-restraints excluded: chain D residue  169 LEU
Chi-restraints excluded: chain D residue  241 CYS
Chi-restraints excluded: chain D residue  282 SER
Chi-restraints excluded: chain D residue  283 ILE
Chi-restraints excluded: chain C residue   50 THR
Chi-restraints excluded: chain C residue   55 ASP
Chi-restraints excluded: chain C residue   61 LEU
Chi-restraints excluded: chain C residue  113 VAL
Chi-restraints excluded: chain C residue  119 GLU
Chi-restraints excluded: chain C residue  227 THR
Chi-restraints excluded: chain C residue  277 CYS
Chi-restraints excluded: chain C residue  283 ILE
Chi-restraints excluded: chain C residue  289 ILE
Chi-restraints excluded: chain B residue   41 VAL
Chi-restraints excluded: chain B residue   50 THR
Chi-restraints excluded: chain B residue  147 THR
Chi-restraints excluded: chain B residue  241 CYS
Chi-restraints excluded: chain B residue  282 SER
Chi-restraints excluded: chain B residue  283 ILE
Chi-restraints excluded: chain A residue   55 ASP
Chi-restraints excluded: chain A residue  113 VAL
Chi-restraints excluded: chain A residue  289 ILE
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 168
   random chunks:
   chunk 44 optimal weight:   10.0000
   chunk 49 optimal weight:    1.9990
   chunk 66 optimal weight:   20.0000
   chunk 104 optimal weight:    7.9990
   chunk 82 optimal weight:    0.6980
   chunk 24 optimal weight:    7.9990
   chunk 70 optimal weight:    9.9990
   chunk 30 optimal weight:   10.0000
   chunk 153 optimal weight:    0.9990
   chunk 122 optimal weight:   10.0000
   chunk 11 optimal weight:    0.2980
   overall best weight:    2.3986

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

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

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3080 r_free = 0.3080 target = 0.102423 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.2794 r_free = 0.2794 target = 0.083416 restraints weight = 23785.542|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.2830 r_free = 0.2830 target = 0.085704 restraints weight = 14637.834|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 43)----------------|
| r_work = 0.2854 r_free = 0.2854 target = 0.087224 restraints weight = 10730.095|
|-----------------------------------------------------------------------------|
r_work (final): 0.2845
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2861
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2861 r_free = 0.2861    target_work(ls_wunit_k1) = 0.087         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:      225 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2852 r_free = 0.2852    target_work(ls_wunit_k1) = 0.087         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:      245 |
|-----------------------------------------------------------------------------|
r_final: 0.2852
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8592
moved from start:          0.3480

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028  13656  Z= 0.131
  Angle     :  0.710  11.411  18486  Z= 0.353
  Chirality :  0.047   0.172   2058
  Planarity :  0.005   0.036   2370
  Dihedral  :  5.881  55.785   1902
  Min Nonbonded Distance : 2.270

Molprobity Statistics.
  All-atom Clashscore : 5.94
  Ramachandran Plot:
    Outliers :  0.76 %
    Allowed  : 11.75 %
    Favored  : 87.49 %
  Rotamer:
    Outliers :  5.36 %
    Allowed  : 12.59 %
    Favored  : 82.05 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 7.14 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.37 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -3.74 (0.18), residues: 1710
  helix: -1.31 (0.26), residues: 402
  sheet: -1.91 (0.29), residues: 342
  loop : -3.37 (0.15), residues: 966

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP B 198 
 HIS   0.008   0.002   HIS A 323 
 PHE   0.008   0.001   PHE C 185 
 TYR   0.015   0.001   TYR D 128 
 ARG   0.004   0.000   ARG D 162 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03094 (  354)
  hydrogen bonds       : angle       5.04329 (  936)
  covalent geometry    : bond        0.00307 (13656)
  covalent geometry    : angle       0.71003 (18486)

*********************** 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
  264 residues out of total 1398 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 75
    poor density    : 189
  time to evaluate  : 1.465 
Fit side-chains
REVERT: F  127 LYS cc_start: 0.7408 (pttt) cc_final: 0.6554 (mtpt)
REVERT: F  169 LEU cc_start: 0.8643 (OUTLIER) cc_final: 0.8161 (tm)
REVERT: F  217 TYR cc_start: 0.9092 (t80) cc_final: 0.8863 (t80)
REVERT: F  221 THR cc_start: 0.9363 (t) cc_final: 0.8909 (m)
REVERT: F  227 THR cc_start: 0.8391 (OUTLIER) cc_final: 0.7989 (m)
REVERT: F  287 LEU cc_start: 0.9102 (OUTLIER) cc_final: 0.8855 (mt)
REVERT: E  232 MET cc_start: 0.8918 (mmm) cc_final: 0.7688 (mmm)
REVERT: D   89 GLU cc_start: 0.8282 (mt-10) cc_final: 0.7659 (tt0)
REVERT: D  127 LYS cc_start: 0.7611 (pttt) cc_final: 0.6864 (mtpp)
REVERT: D  169 LEU cc_start: 0.8837 (OUTLIER) cc_final: 0.8401 (tm)
REVERT: D  324 TYR cc_start: 0.8329 (OUTLIER) cc_final: 0.7286 (t80)
REVERT: C  134 MET cc_start: 0.7687 (mmm) cc_final: 0.7477 (tpt)
REVERT: C  310 ASP cc_start: 0.9047 (t0) cc_final: 0.8814 (t0)
REVERT: B  127 LYS cc_start: 0.7785 (pttt) cc_final: 0.6685 (mtpp)
REVERT: B  129 LYS cc_start: 0.7576 (mmtt) cc_final: 0.6842 (mmtm)
REVERT: B  199 GLU cc_start: 0.9342 (mt-10) cc_final: 0.9043 (mt-10)
REVERT: B  221 THR cc_start: 0.9112 (t) cc_final: 0.8881 (m)
REVERT: B  324 TYR cc_start: 0.8240 (OUTLIER) cc_final: 0.7681 (t80)
  outliers start: 75
  outliers final: 41
  residues processed: 251
  average time/residue: 0.3090
  time to fit residues: 119.1565
Evaluate side-chains
  220 residues out of total 1398 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 47
    poor density    : 173
  time to evaluate  : 2.245 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain F residue   41 VAL
Chi-restraints excluded: chain F residue   50 THR
Chi-restraints excluded: chain F residue   66 GLU
Chi-restraints excluded: chain F residue  169 LEU
Chi-restraints excluded: chain F residue  181 THR
Chi-restraints excluded: chain F residue  227 THR
Chi-restraints excluded: chain F residue  241 CYS
Chi-restraints excluded: chain F residue  287 LEU
Chi-restraints excluded: chain F residue  301 LEU
Chi-restraints excluded: chain F residue  308 LEU
Chi-restraints excluded: chain F residue  324 TYR
Chi-restraints excluded: chain E residue   55 ASP
Chi-restraints excluded: chain E residue  113 VAL
Chi-restraints excluded: chain E residue  169 LEU
Chi-restraints excluded: chain E residue  283 ILE
Chi-restraints excluded: chain E residue  289 ILE
Chi-restraints excluded: chain D residue   41 VAL
Chi-restraints excluded: chain D residue   50 THR
Chi-restraints excluded: chain D residue   66 GLU
Chi-restraints excluded: chain D residue  169 LEU
Chi-restraints excluded: chain D residue  241 CYS
Chi-restraints excluded: chain D residue  282 SER
Chi-restraints excluded: chain D residue  301 LEU
Chi-restraints excluded: chain D residue  324 TYR
Chi-restraints excluded: chain C residue   50 THR
Chi-restraints excluded: chain C residue   55 ASP
Chi-restraints excluded: chain C residue   61 LEU
Chi-restraints excluded: chain C residue  113 VAL
Chi-restraints excluded: chain C residue  227 THR
Chi-restraints excluded: chain C residue  277 CYS
Chi-restraints excluded: chain C residue  283 ILE
Chi-restraints excluded: chain C residue  289 ILE
Chi-restraints excluded: chain C residue  324 TYR
Chi-restraints excluded: chain B residue   41 VAL
Chi-restraints excluded: chain B residue   50 THR
Chi-restraints excluded: chain B residue   66 GLU
Chi-restraints excluded: chain B residue  147 THR
Chi-restraints excluded: chain B residue  184 VAL
Chi-restraints excluded: chain B residue  241 CYS
Chi-restraints excluded: chain B residue  282 SER
Chi-restraints excluded: chain B residue  283 ILE
Chi-restraints excluded: chain B residue  308 LEU
Chi-restraints excluded: chain B residue  324 TYR
Chi-restraints excluded: chain A residue   55 ASP
Chi-restraints excluded: chain A residue   61 LEU
Chi-restraints excluded: chain A residue  113 VAL
Chi-restraints excluded: chain A residue  289 ILE
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 168
   random chunks:
   chunk 8 optimal weight:    7.9990
   chunk 148 optimal weight:    9.9990
   chunk 47 optimal weight:    3.9990
   chunk 160 optimal weight:   10.0000
   chunk 164 optimal weight:    5.9990
   chunk 16 optimal weight:    1.9990
   chunk 81 optimal weight:   20.0000
   chunk 143 optimal weight:   20.0000
   chunk 35 optimal weight:    4.9990
   chunk 118 optimal weight:    7.9990
   chunk 122 optimal weight:    9.9990
   overall best weight:    4.9990

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

Flipped N/Q/H residues before XYZ refinement:
F 295 ASN
E 295 ASN
D 295 ASN
C 295 ASN
B 295 ASN
A 295 ASN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3002 r_free = 0.3002 target = 0.097119 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.2733 r_free = 0.2733 target = 0.079735 restraints weight = 23872.132|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.2766 r_free = 0.2766 target = 0.081721 restraints weight = 15059.805|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.2786 r_free = 0.2786 target = 0.083002 restraints weight = 11233.171|
|-----------------------------------------------------------------------------|
r_work (final): 0.2787
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2801
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2801 r_free = 0.2801    target_work(ls_wunit_k1) = 0.084         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:      245 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2790 r_free = 0.2790    target_work(ls_wunit_k1) = 0.083         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:      246 |
|-----------------------------------------------------------------------------|
r_final: 0.2790
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8670
moved from start:          0.3697

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.033  13656  Z= 0.207
  Angle     :  0.789  12.043  18486  Z= 0.396
  Chirality :  0.050   0.200   2058
  Planarity :  0.005   0.036   2370
  Dihedral  :  6.314  57.779   1902
  Min Nonbonded Distance : 2.217

Molprobity Statistics.
  All-atom Clashscore : 6.36
  Ramachandran Plot:
    Outliers :  0.82 %
    Allowed  : 13.51 %
    Favored  : 85.67 %
  Rotamer:
    Outliers :  5.79 %
    Allowed  : 13.95 %
    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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -3.77 (0.18), residues: 1710
  helix: -1.63 (0.24), residues: 432
  sheet: -1.82 (0.29), residues: 342
  loop : -3.32 (0.16), residues: 936

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP F 198 
 HIS   0.005   0.001   HIS C 323 
 PHE   0.016   0.002   PHE C 330 
 TYR   0.014   0.002   TYR D 128 
 ARG   0.004   0.000   ARG E 171 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03834 (  354)
  hydrogen bonds       : angle       5.32922 (  936)
  covalent geometry    : bond        0.00495 (13656)
  covalent geometry    : angle       0.78907 (18486)

*********************** 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
  259 residues out of total 1398 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 81
    poor density    : 178
  time to evaluate  : 1.430 
Fit side-chains
REVERT: F  127 LYS cc_start: 0.7399 (pttt) cc_final: 0.6691 (mtpt)
REVERT: F  169 LEU cc_start: 0.8692 (OUTLIER) cc_final: 0.8345 (tm)
REVERT: F  227 THR cc_start: 0.8550 (OUTLIER) cc_final: 0.8193 (m)
REVERT: E  144 LEU cc_start: 0.9291 (OUTLIER) cc_final: 0.9074 (mt)
REVERT: E  324 TYR cc_start: 0.7828 (OUTLIER) cc_final: 0.6539 (t80)
REVERT: D   89 GLU cc_start: 0.8344 (mt-10) cc_final: 0.7745 (tt0)
REVERT: D  127 LYS cc_start: 0.7516 (pttt) cc_final: 0.7075 (mtpp)
REVERT: D  169 LEU cc_start: 0.8939 (OUTLIER) cc_final: 0.8546 (tm)
REVERT: D  199 GLU cc_start: 0.9434 (mt-10) cc_final: 0.9219 (mt-10)
REVERT: B  127 LYS cc_start: 0.8034 (pttt) cc_final: 0.7022 (mtpp)
REVERT: B  324 TYR cc_start: 0.8336 (OUTLIER) cc_final: 0.7677 (t80)
REVERT: A  324 TYR cc_start: 0.7683 (OUTLIER) cc_final: 0.6642 (t80)
  outliers start: 81
  outliers final: 52
  residues processed: 246
  average time/residue: 0.2142
  time to fit residues: 81.9219
Evaluate side-chains
  219 residues out of total 1398 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 59
    poor density    : 160
  time to evaluate  : 1.688 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain F residue   41 VAL
Chi-restraints excluded: chain F residue   50 THR
Chi-restraints excluded: chain F residue   66 GLU
Chi-restraints excluded: chain F residue  169 LEU
Chi-restraints excluded: chain F residue  181 THR
Chi-restraints excluded: chain F residue  227 THR
Chi-restraints excluded: chain F residue  241 CYS
Chi-restraints excluded: chain F residue  287 LEU
Chi-restraints excluded: chain F residue  301 LEU
Chi-restraints excluded: chain F residue  308 LEU
Chi-restraints excluded: chain F residue  324 TYR
Chi-restraints excluded: chain E residue  113 VAL
Chi-restraints excluded: chain E residue  144 LEU
Chi-restraints excluded: chain E residue  169 LEU
Chi-restraints excluded: chain E residue  181 THR
Chi-restraints excluded: chain E residue  283 ILE
Chi-restraints excluded: chain E residue  289 ILE
Chi-restraints excluded: chain E residue  324 TYR
Chi-restraints excluded: chain D residue   41 VAL
Chi-restraints excluded: chain D residue   50 THR
Chi-restraints excluded: chain D residue   66 GLU
Chi-restraints excluded: chain D residue  148 VAL
Chi-restraints excluded: chain D residue  169 LEU
Chi-restraints excluded: chain D residue  214 ILE
Chi-restraints excluded: chain D residue  227 THR
Chi-restraints excluded: chain D residue  241 CYS
Chi-restraints excluded: chain D residue  282 SER
Chi-restraints excluded: chain D residue  301 LEU
Chi-restraints excluded: chain D residue  324 TYR
Chi-restraints excluded: chain D residue  346 THR
Chi-restraints excluded: chain C residue   50 THR
Chi-restraints excluded: chain C residue   55 ASP
Chi-restraints excluded: chain C residue   90 LEU
Chi-restraints excluded: chain C residue  113 VAL
Chi-restraints excluded: chain C residue  119 GLU
Chi-restraints excluded: chain C residue  181 THR
Chi-restraints excluded: chain C residue  227 THR
Chi-restraints excluded: chain C residue  277 CYS
Chi-restraints excluded: chain C residue  283 ILE
Chi-restraints excluded: chain C residue  289 ILE
Chi-restraints excluded: chain C residue  324 TYR
Chi-restraints excluded: chain B residue   41 VAL
Chi-restraints excluded: chain B residue   50 THR
Chi-restraints excluded: chain B residue   66 GLU
Chi-restraints excluded: chain B residue  147 THR
Chi-restraints excluded: chain B residue  184 VAL
Chi-restraints excluded: chain B residue  227 THR
Chi-restraints excluded: chain B residue  241 CYS
Chi-restraints excluded: chain B residue  282 SER
Chi-restraints excluded: chain B residue  283 ILE
Chi-restraints excluded: chain B residue  301 LEU
Chi-restraints excluded: chain B residue  308 LEU
Chi-restraints excluded: chain B residue  324 TYR
Chi-restraints excluded: chain A residue   55 ASP
Chi-restraints excluded: chain A residue  113 VAL
Chi-restraints excluded: chain A residue  169 LEU
Chi-restraints excluded: chain A residue  181 THR
Chi-restraints excluded: chain A residue  289 ILE
Chi-restraints excluded: chain A residue  324 TYR
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 168
   random chunks:
   chunk 92 optimal weight:    8.9990
   chunk 29 optimal weight:   20.0000
   chunk 102 optimal weight:   10.0000
   chunk 46 optimal weight:    8.9990
   chunk 16 optimal weight:    0.5980
   chunk 34 optimal weight:    9.9990
   chunk 51 optimal weight:    8.9990
   chunk 43 optimal weight:    7.9990
   chunk 115 optimal weight:   50.0000
   chunk 150 optimal weight:    7.9990
   chunk 52 optimal weight:    8.9990
   overall best weight:    6.9188

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

Flipped N/Q/H residues before XYZ refinement:
F 295 ASN
F 337 HIS
E 295 ASN
D 295 ASN
C 295 ASN
B 295 ASN
A 295 ASN

Total number of N/Q/H flips: 7

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.2969 r_free = 0.2969 target = 0.094942 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.2709 r_free = 0.2709 target = 0.078321 restraints weight = 24232.691|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.2738 r_free = 0.2738 target = 0.080100 restraints weight = 15907.865|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.2758 r_free = 0.2758 target = 0.081307 restraints weight = 12127.025|
|-----------------------------------------------------------------------------|
r_work (final): 0.2751
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2753
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2753 r_free = 0.2753    target_work(ls_wunit_k1) = 0.081         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:      246 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2747 r_free = 0.2747    target_work(ls_wunit_k1) = 0.081         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:      257 |
|-----------------------------------------------------------------------------|
r_final: 0.2747
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8709
moved from start:          0.3911

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.045  13656  Z= 0.266
  Angle     :  0.842  11.398  18486  Z= 0.427
  Chirality :  0.053   0.190   2058
  Planarity :  0.006   0.039   2370
  Dihedral  :  6.606  58.249   1902
  Min Nonbonded Distance : 2.217

Molprobity Statistics.
  All-atom Clashscore : 7.24
  Ramachandran Plot:
    Outliers :  0.76 %
    Allowed  : 14.27 %
    Favored  : 84.97 %
  Rotamer:
    Outliers :  6.15 %
    Allowed  : 15.31 %
    Favored  : 78.54 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 7.14 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.37 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -3.91 (0.18), residues: 1710
  helix: -1.77 (0.23), residues: 432
  sheet: -1.75 (0.29), residues: 330
  loop : -3.46 (0.17), residues: 948

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP D 198 
 HIS   0.006   0.002   HIS F 323 
 PHE   0.014   0.002   PHE D 318 
 TYR   0.014   0.002   TYR D 128 
 ARG   0.004   0.000   ARG E 171 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04275 (  354)
  hydrogen bonds       : angle       5.58531 (  936)
  covalent geometry    : bond        0.00641 (13656)
  covalent geometry    : angle       0.84192 (18486)

*********************** 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
  239 residues out of total 1398 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 86
    poor density    : 153
  time to evaluate  : 1.487 
Fit side-chains
REVERT: F  127 LYS cc_start: 0.7478 (pttt) cc_final: 0.6991 (mtpp)
REVERT: F  227 THR cc_start: 0.8616 (OUTLIER) cc_final: 0.8281 (m)
REVERT: F  324 TYR cc_start: 0.8438 (OUTLIER) cc_final: 0.7775 (t80)
REVERT: E  134 MET cc_start: 0.7300 (tpp) cc_final: 0.7081 (tpp)
REVERT: E  232 MET cc_start: 0.9016 (mmm) cc_final: 0.7805 (mmm)
REVERT: E  324 TYR cc_start: 0.7892 (OUTLIER) cc_final: 0.6507 (t80)
REVERT: D   89 GLU cc_start: 0.8345 (mt-10) cc_final: 0.7766 (tt0)
REVERT: D  127 LYS cc_start: 0.7167 (pttt) cc_final: 0.6966 (mtpp)
REVERT: D  169 LEU cc_start: 0.8977 (OUTLIER) cc_final: 0.8623 (tm)
REVERT: D  199 GLU cc_start: 0.9463 (mt-10) cc_final: 0.9228 (mt-10)
REVERT: B  127 LYS cc_start: 0.7910 (pttt) cc_final: 0.7210 (mtpp)
REVERT: B  199 GLU cc_start: 0.9418 (mt-10) cc_final: 0.9016 (mt-10)
REVERT: B  324 TYR cc_start: 0.8470 (OUTLIER) cc_final: 0.7893 (t80)
REVERT: A  119 GLU cc_start: 0.8981 (OUTLIER) cc_final: 0.8690 (mp0)
REVERT: A  324 TYR cc_start: 0.7849 (OUTLIER) cc_final: 0.6704 (t80)
  outliers start: 86
  outliers final: 61
  residues processed: 226
  average time/residue: 0.2329
  time to fit residues: 81.3104
Evaluate side-chains
  214 residues out of total 1398 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 68
    poor density    : 146
  time to evaluate  : 1.808 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain F residue   41 VAL
Chi-restraints excluded: chain F residue   50 THR
Chi-restraints excluded: chain F residue   66 GLU
Chi-restraints excluded: chain F residue  169 LEU
Chi-restraints excluded: chain F residue  181 THR
Chi-restraints excluded: chain F residue  221 THR
Chi-restraints excluded: chain F residue  227 THR
Chi-restraints excluded: chain F residue  241 CYS
Chi-restraints excluded: chain F residue  301 LEU
Chi-restraints excluded: chain F residue  308 LEU
Chi-restraints excluded: chain F residue  324 TYR
Chi-restraints excluded: chain E residue  113 VAL
Chi-restraints excluded: chain E residue  136 VAL
Chi-restraints excluded: chain E residue  169 LEU
Chi-restraints excluded: chain E residue  181 THR
Chi-restraints excluded: chain E residue  283 ILE
Chi-restraints excluded: chain E residue  289 ILE
Chi-restraints excluded: chain E residue  324 TYR
Chi-restraints excluded: chain D residue   41 VAL
Chi-restraints excluded: chain D residue   50 THR
Chi-restraints excluded: chain D residue   66 GLU
Chi-restraints excluded: chain D residue  148 VAL
Chi-restraints excluded: chain D residue  169 LEU
Chi-restraints excluded: chain D residue  214 ILE
Chi-restraints excluded: chain D residue  227 THR
Chi-restraints excluded: chain D residue  241 CYS
Chi-restraints excluded: chain D residue  282 SER
Chi-restraints excluded: chain D residue  301 LEU
Chi-restraints excluded: chain D residue  308 LEU
Chi-restraints excluded: chain D residue  324 TYR
Chi-restraints excluded: chain D residue  346 THR
Chi-restraints excluded: chain C residue   50 THR
Chi-restraints excluded: chain C residue   55 ASP
Chi-restraints excluded: chain C residue   61 LEU
Chi-restraints excluded: chain C residue   90 LEU
Chi-restraints excluded: chain C residue  113 VAL
Chi-restraints excluded: chain C residue  119 GLU
Chi-restraints excluded: chain C residue  136 VAL
Chi-restraints excluded: chain C residue  147 THR
Chi-restraints excluded: chain C residue  181 THR
Chi-restraints excluded: chain C residue  227 THR
Chi-restraints excluded: chain C residue  277 CYS
Chi-restraints excluded: chain C residue  283 ILE
Chi-restraints excluded: chain C residue  289 ILE
Chi-restraints excluded: chain C residue  301 LEU
Chi-restraints excluded: chain C residue  324 TYR
Chi-restraints excluded: chain B residue   41 VAL
Chi-restraints excluded: chain B residue   50 THR
Chi-restraints excluded: chain B residue   66 GLU
Chi-restraints excluded: chain B residue  147 THR
Chi-restraints excluded: chain B residue  184 VAL
Chi-restraints excluded: chain B residue  227 THR
Chi-restraints excluded: chain B residue  241 CYS
Chi-restraints excluded: chain B residue  282 SER
Chi-restraints excluded: chain B residue  283 ILE
Chi-restraints excluded: chain B residue  287 LEU
Chi-restraints excluded: chain B residue  301 LEU
Chi-restraints excluded: chain B residue  308 LEU
Chi-restraints excluded: chain B residue  324 TYR
Chi-restraints excluded: chain A residue   55 ASP
Chi-restraints excluded: chain A residue  113 VAL
Chi-restraints excluded: chain A residue  119 GLU
Chi-restraints excluded: chain A residue  133 VAL
Chi-restraints excluded: chain A residue  136 VAL
Chi-restraints excluded: chain A residue  169 LEU
Chi-restraints excluded: chain A residue  181 THR
Chi-restraints excluded: chain A residue  289 ILE
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 16 optimal weight:    0.6980
   chunk 150 optimal weight:   10.0000
   chunk 50 optimal weight:    6.9990
   chunk 93 optimal weight:   10.0000
   chunk 18 optimal weight:    8.9990
   chunk 27 optimal weight:    5.9990
   chunk 21 optimal weight:    2.9990
   chunk 92 optimal weight:    6.9990
   chunk 163 optimal weight:    4.9990
   chunk 29 optimal weight:   20.0000
   chunk 76 optimal weight:    5.9990
   overall best weight:    4.1388

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

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

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.2989 r_free = 0.2989 target = 0.096335 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.2738 r_free = 0.2738 target = 0.080209 restraints weight = 23958.879|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.2767 r_free = 0.2767 target = 0.081990 restraints weight = 15671.197|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.2787 r_free = 0.2787 target = 0.083195 restraints weight = 11860.949|
|-----------------------------------------------------------------------------|
r_work (final): 0.2790
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2792
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2792 r_free = 0.2792    target_work(ls_wunit_k1) = 0.083         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:      257 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2789 r_free = 0.2789    target_work(ls_wunit_k1) = 0.083         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:      267 |
|-----------------------------------------------------------------------------|
r_final: 0.2789
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8666
moved from start:          0.3986

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.034  13656  Z= 0.179
  Angle     :  0.767  11.929  18486  Z= 0.383
  Chirality :  0.049   0.170   2058
  Planarity :  0.005   0.037   2370
  Dihedral  :  6.272  57.264   1902
  Min Nonbonded Distance : 2.461

Molprobity Statistics.
  All-atom Clashscore : 6.56
  Ramachandran Plot:
    Outliers :  0.94 %
    Allowed  : 12.75 %
    Favored  : 86.32 %
  Rotamer:
    Outliers :  4.72 %
    Allowed  : 16.88 %
    Favored  : 78.40 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 7.14 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.37 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -3.78 (0.18), residues: 1710
  helix: -1.61 (0.24), residues: 432
  sheet: -1.82 (0.28), residues: 342
  loop : -3.35 (0.17), residues: 936

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP B 228 
 HIS   0.006   0.001   HIS F 323 
 PHE   0.011   0.001   PHE C 330 
 TYR   0.014   0.001   TYR D 128 
 ARG   0.003   0.000   ARG E 171 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03505 (  354)
  hydrogen bonds       : angle       5.32507 (  936)
  covalent geometry    : bond        0.00430 (13656)
  covalent geometry    : angle       0.76674 (18486)

*********************** 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
  234 residues out of total 1398 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 66
    poor density    : 168
  time to evaluate  : 1.514 
Fit side-chains
REVERT: F  127 LYS cc_start: 0.7337 (pttt) cc_final: 0.6899 (mtpp)
REVERT: F  169 LEU cc_start: 0.8712 (OUTLIER) cc_final: 0.8359 (tm)
REVERT: F  227 THR cc_start: 0.8533 (OUTLIER) cc_final: 0.8155 (m)
REVERT: F  324 TYR cc_start: 0.8396 (OUTLIER) cc_final: 0.7885 (t80)
REVERT: E  232 MET cc_start: 0.8974 (mmm) cc_final: 0.7725 (mmm)
REVERT: E  324 TYR cc_start: 0.7791 (OUTLIER) cc_final: 0.6540 (t80)
REVERT: D   89 GLU cc_start: 0.8309 (mt-10) cc_final: 0.7745 (tt0)
REVERT: D  129 LYS cc_start: 0.7866 (mmtt) cc_final: 0.7625 (mmtm)
REVERT: D  169 LEU cc_start: 0.8973 (OUTLIER) cc_final: 0.8539 (tm)
REVERT: D  199 GLU cc_start: 0.9395 (mt-10) cc_final: 0.9149 (mt-10)
REVERT: D  324 TYR cc_start: 0.8539 (OUTLIER) cc_final: 0.7530 (t80)
REVERT: C  324 TYR cc_start: 0.7984 (OUTLIER) cc_final: 0.6419 (t80)
REVERT: B  127 LYS cc_start: 0.7788 (pttt) cc_final: 0.7429 (mtpp)
REVERT: B  129 LYS cc_start: 0.7490 (mmtt) cc_final: 0.7151 (mmtp)
REVERT: B  199 GLU cc_start: 0.9392 (mt-10) cc_final: 0.8963 (mt-10)
REVERT: B  324 TYR cc_start: 0.8393 (OUTLIER) cc_final: 0.7880 (t80)
REVERT: A  324 TYR cc_start: 0.7780 (OUTLIER) cc_final: 0.6703 (t80)
  outliers start: 66
  outliers final: 48
  residues processed: 221
  average time/residue: 0.2080
  time to fit residues: 71.2562
Evaluate side-chains
  222 residues out of total 1398 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 57
    poor density    : 165
  time to evaluate  : 1.394 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain F residue   41 VAL
Chi-restraints excluded: chain F residue   50 THR
Chi-restraints excluded: chain F residue   66 GLU
Chi-restraints excluded: chain F residue  169 LEU
Chi-restraints excluded: chain F residue  181 THR
Chi-restraints excluded: chain F residue  227 THR
Chi-restraints excluded: chain F residue  241 CYS
Chi-restraints excluded: chain F residue  287 LEU
Chi-restraints excluded: chain F residue  301 LEU
Chi-restraints excluded: chain F residue  308 LEU
Chi-restraints excluded: chain F residue  324 TYR
Chi-restraints excluded: chain E residue  113 VAL
Chi-restraints excluded: chain E residue  169 LEU
Chi-restraints excluded: chain E residue  181 THR
Chi-restraints excluded: chain E residue  283 ILE
Chi-restraints excluded: chain E residue  289 ILE
Chi-restraints excluded: chain E residue  324 TYR
Chi-restraints excluded: chain D residue   41 VAL
Chi-restraints excluded: chain D residue   50 THR
Chi-restraints excluded: chain D residue   66 GLU
Chi-restraints excluded: chain D residue  169 LEU
Chi-restraints excluded: chain D residue  241 CYS
Chi-restraints excluded: chain D residue  282 SER
Chi-restraints excluded: chain D residue  287 LEU
Chi-restraints excluded: chain D residue  301 LEU
Chi-restraints excluded: chain D residue  308 LEU
Chi-restraints excluded: chain D residue  324 TYR
Chi-restraints excluded: chain D residue  346 THR
Chi-restraints excluded: chain C residue   50 THR
Chi-restraints excluded: chain C residue   55 ASP
Chi-restraints excluded: chain C residue   90 LEU
Chi-restraints excluded: chain C residue  113 VAL
Chi-restraints excluded: chain C residue  119 GLU
Chi-restraints excluded: chain C residue  181 THR
Chi-restraints excluded: chain C residue  227 THR
Chi-restraints excluded: chain C residue  277 CYS
Chi-restraints excluded: chain C residue  283 ILE
Chi-restraints excluded: chain C residue  301 LEU
Chi-restraints excluded: chain C residue  324 TYR
Chi-restraints excluded: chain B residue   41 VAL
Chi-restraints excluded: chain B residue   50 THR
Chi-restraints excluded: chain B residue   66 GLU
Chi-restraints excluded: chain B residue  147 THR
Chi-restraints excluded: chain B residue  184 VAL
Chi-restraints excluded: chain B residue  241 CYS
Chi-restraints excluded: chain B residue  282 SER
Chi-restraints excluded: chain B residue  283 ILE
Chi-restraints excluded: chain B residue  287 LEU
Chi-restraints excluded: chain B residue  301 LEU
Chi-restraints excluded: chain B residue  308 LEU
Chi-restraints excluded: chain B residue  324 TYR
Chi-restraints excluded: chain A residue   55 ASP
Chi-restraints excluded: chain A residue  113 VAL
Chi-restraints excluded: chain A residue  169 LEU
Chi-restraints excluded: chain A residue  181 THR
Chi-restraints excluded: chain A residue  289 ILE
Chi-restraints excluded: chain A residue  324 TYR
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 168
   random chunks:
   chunk 83 optimal weight:    0.9980
   chunk 15 optimal weight:    7.9990
   chunk 98 optimal weight:    2.9990
   chunk 26 optimal weight:    4.9990
   chunk 166 optimal weight:    0.8980
   chunk 167 optimal weight:    6.9990
   chunk 57 optimal weight:   20.0000
   chunk 27 optimal weight:    3.9990
   chunk 33 optimal weight:   10.0000
   chunk 58 optimal weight:    5.9990
   chunk 140 optimal weight:   20.0000
   overall best weight:    2.7786

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

Flipped N/Q/H residues before XYZ refinement:
F 295 ASN
D 295 ASN
C 337 HIS
B 295 ASN
A 337 HIS

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3033 r_free = 0.3033 target = 0.099491 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.2785 r_free = 0.2785 target = 0.083198 restraints weight = 23629.531|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.2814 r_free = 0.2814 target = 0.085045 restraints weight = 15336.438|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.2834 r_free = 0.2834 target = 0.086292 restraints weight = 11577.463|
|-----------------------------------------------------------------------------|
r_work (final): 0.2821
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2822
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2822 r_free = 0.2822    target_work(ls_wunit_k1) = 0.085         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:      267 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2819 r_free = 0.2819    target_work(ls_wunit_k1) = 0.085         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:      281 |
|-----------------------------------------------------------------------------|
r_final: 0.2819
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8623
moved from start:          0.4095

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035  13656  Z= 0.144
  Angle     :  0.738  12.132  18486  Z= 0.365
  Chirality :  0.047   0.165   2058
  Planarity :  0.005   0.033   2370
  Dihedral  :  5.949  56.359   1902
  Min Nonbonded Distance : 2.458

Molprobity Statistics.
  All-atom Clashscore : 6.37
  Ramachandran Plot:
    Outliers :  0.70 %
    Allowed  : 11.87 %
    Favored  : 87.43 %
  Rotamer:
    Outliers :  4.51 %
    Allowed  : 16.95 %
    Favored  : 78.54 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 7.14 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.37 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -3.60 (0.19), residues: 1710
  helix: -1.43 (0.25), residues: 432
  sheet: -1.63 (0.29), residues: 342
  loop : -3.30 (0.17), residues: 936

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP B 198 
 HIS   0.007   0.001   HIS E 323 
 PHE   0.010   0.001   PHE C 330 
 TYR   0.014   0.001   TYR E 296 
 ARG   0.003   0.000   ARG C 201 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03101 (  354)
  hydrogen bonds       : angle       5.08090 (  936)
  covalent geometry    : bond        0.00343 (13656)
  covalent geometry    : angle       0.73800 (18486)

*********************** 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
  242 residues out of total 1398 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 63
    poor density    : 179
  time to evaluate  : 1.432 
Fit side-chains
REVERT: F  127 LYS cc_start: 0.7388 (pttt) cc_final: 0.6911 (mtpp)
REVERT: F  169 LEU cc_start: 0.8672 (OUTLIER) cc_final: 0.8291 (tm)
REVERT: F  324 TYR cc_start: 0.8283 (OUTLIER) cc_final: 0.7896 (t80)
REVERT: E  134 MET cc_start: 0.7259 (tpp) cc_final: 0.7044 (tpp)
REVERT: E  232 MET cc_start: 0.8926 (mmm) cc_final: 0.7715 (mmm)
REVERT: E  324 TYR cc_start: 0.7710 (OUTLIER) cc_final: 0.6574 (t80)
REVERT: D   89 GLU cc_start: 0.8301 (mt-10) cc_final: 0.7732 (tt0)
REVERT: D  169 LEU cc_start: 0.8958 (OUTLIER) cc_final: 0.8488 (tm)
REVERT: D  199 GLU cc_start: 0.9348 (mt-10) cc_final: 0.9101 (mt-10)
REVERT: D  324 TYR cc_start: 0.8386 (OUTLIER) cc_final: 0.7705 (t80)
REVERT: C  134 MET cc_start: 0.8126 (mmm) cc_final: 0.7734 (tpp)
REVERT: C  324 TYR cc_start: 0.7811 (OUTLIER) cc_final: 0.6419 (t80)
REVERT: B  127 LYS cc_start: 0.7992 (pttt) cc_final: 0.7414 (mtpp)
REVERT: B  129 LYS cc_start: 0.7501 (mmtt) cc_final: 0.7142 (mmtp)
REVERT: B  199 GLU cc_start: 0.9406 (mt-10) cc_final: 0.8999 (mt-10)
REVERT: B  324 TYR cc_start: 0.8240 (OUTLIER) cc_final: 0.7799 (t80)
REVERT: A  242 PHE cc_start: 0.8829 (m-80) cc_final: 0.8565 (m-80)
REVERT: A  324 TYR cc_start: 0.7577 (OUTLIER) cc_final: 0.6705 (t80)
  outliers start: 63
  outliers final: 46
  residues processed: 229
  average time/residue: 0.2232
  time to fit residues: 79.1412
Evaluate side-chains
  216 residues out of total 1398 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 54
    poor density    : 162
  time to evaluate  : 1.480 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain F residue   41 VAL
Chi-restraints excluded: chain F residue   50 THR
Chi-restraints excluded: chain F residue   66 GLU
Chi-restraints excluded: chain F residue  169 LEU
Chi-restraints excluded: chain F residue  181 THR
Chi-restraints excluded: chain F residue  227 THR
Chi-restraints excluded: chain F residue  241 CYS
Chi-restraints excluded: chain F residue  287 LEU
Chi-restraints excluded: chain F residue  301 LEU
Chi-restraints excluded: chain F residue  308 LEU
Chi-restraints excluded: chain F residue  324 TYR
Chi-restraints excluded: chain E residue  113 VAL
Chi-restraints excluded: chain E residue  169 LEU
Chi-restraints excluded: chain E residue  181 THR
Chi-restraints excluded: chain E residue  283 ILE
Chi-restraints excluded: chain E residue  289 ILE
Chi-restraints excluded: chain E residue  324 TYR
Chi-restraints excluded: chain D residue   41 VAL
Chi-restraints excluded: chain D residue   50 THR
Chi-restraints excluded: chain D residue   66 GLU
Chi-restraints excluded: chain D residue  136 VAL
Chi-restraints excluded: chain D residue  148 VAL
Chi-restraints excluded: chain D residue  169 LEU
Chi-restraints excluded: chain D residue  241 CYS
Chi-restraints excluded: chain D residue  282 SER
Chi-restraints excluded: chain D residue  287 LEU
Chi-restraints excluded: chain D residue  301 LEU
Chi-restraints excluded: chain D residue  308 LEU
Chi-restraints excluded: chain D residue  324 TYR
Chi-restraints excluded: chain C residue   50 THR
Chi-restraints excluded: chain C residue   90 LEU
Chi-restraints excluded: chain C residue  113 VAL
Chi-restraints excluded: chain C residue  119 GLU
Chi-restraints excluded: chain C residue  147 THR
Chi-restraints excluded: chain C residue  181 THR
Chi-restraints excluded: chain C residue  227 THR
Chi-restraints excluded: chain C residue  277 CYS
Chi-restraints excluded: chain C residue  283 ILE
Chi-restraints excluded: chain C residue  301 LEU
Chi-restraints excluded: chain C residue  324 TYR
Chi-restraints excluded: chain B residue   41 VAL
Chi-restraints excluded: chain B residue   50 THR
Chi-restraints excluded: chain B residue   66 GLU
Chi-restraints excluded: chain B residue  184 VAL
Chi-restraints excluded: chain B residue  241 CYS
Chi-restraints excluded: chain B residue  282 SER
Chi-restraints excluded: chain B residue  283 ILE
Chi-restraints excluded: chain B residue  308 LEU
Chi-restraints excluded: chain B residue  324 TYR
Chi-restraints excluded: chain A residue  113 VAL
Chi-restraints excluded: chain A residue  169 LEU
Chi-restraints excluded: chain A residue  181 THR
Chi-restraints excluded: chain A residue  289 ILE
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 21 optimal weight:    5.9990
   chunk 127 optimal weight:    7.9990
   chunk 14 optimal weight:    4.9990
   chunk 18 optimal weight:    6.9990
   chunk 110 optimal weight:    1.9990
   chunk 57 optimal weight:   20.0000
   chunk 44 optimal weight:    2.9990
   chunk 143 optimal weight:    9.9990
   chunk 9 optimal weight:   10.0000
   chunk 26 optimal weight:    6.9990
   chunk 139 optimal weight:   10.0000
   overall best weight:    4.5990

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

Flipped N/Q/H residues before XYZ refinement:
F 295 ASN
D 295 ASN
B 295 ASN
A 337 HIS

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.2989 r_free = 0.2989 target = 0.096383 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.2731 r_free = 0.2731 target = 0.079806 restraints weight = 23783.150|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.2762 r_free = 0.2762 target = 0.081744 restraints weight = 14944.517|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.2784 r_free = 0.2784 target = 0.083080 restraints weight = 11076.152|
|-----------------------------------------------------------------------------|
r_work (final): 0.2778
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2778
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2778 r_free = 0.2778    target_work(ls_wunit_k1) = 0.083         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:      281 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2776 r_free = 0.2776    target_work(ls_wunit_k1) = 0.083         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:      292 |
|-----------------------------------------------------------------------------|
r_final: 0.2776
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8663
moved from start:          0.4130

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.036  13656  Z= 0.195
  Angle     :  0.792  12.206  18486  Z= 0.394
  Chirality :  0.049   0.202   2058
  Planarity :  0.005   0.033   2370
  Dihedral  :  6.208  57.383   1902
  Min Nonbonded Distance : 2.391

Molprobity Statistics.
  All-atom Clashscore : 6.72
  Ramachandran Plot:
    Outliers :  0.94 %
    Allowed  : 13.51 %
    Favored  : 85.56 %
  Rotamer:
    Outliers :  4.72 %
    Allowed  : 17.60 %
    Favored  : 77.68 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 7.14 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.37 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -3.65 (0.18), residues: 1710
  helix: -1.49 (0.24), residues: 432
  sheet: -1.65 (0.28), residues: 342
  loop : -3.32 (0.17), residues: 936

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP A 228 
 HIS   0.005   0.001   HIS F 323 
 PHE   0.011   0.001   PHE A 103 
 TYR   0.012   0.001   TYR B 128 
 ARG   0.005   0.000   ARG B 171 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03641 (  354)
  hydrogen bonds       : angle       5.24526 (  936)
  covalent geometry    : bond        0.00470 (13656)
  covalent geometry    : angle       0.79220 (18486)

*********************** 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
  232 residues out of total 1398 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 66
    poor density    : 166
  time to evaluate  : 2.003 
Fit side-chains
REVERT: F  127 LYS cc_start: 0.7424 (pttt) cc_final: 0.7107 (mtpp)
REVERT: F  169 LEU cc_start: 0.8703 (OUTLIER) cc_final: 0.8324 (tm)
REVERT: F  324 TYR cc_start: 0.8380 (OUTLIER) cc_final: 0.7848 (t80)
REVERT: E  232 MET cc_start: 0.9003 (mmm) cc_final: 0.7822 (mmm)
REVERT: E  324 TYR cc_start: 0.7779 (OUTLIER) cc_final: 0.6566 (t80)
REVERT: D   89 GLU cc_start: 0.8365 (mt-10) cc_final: 0.7763 (tt0)
REVERT: D  120 ARG cc_start: 0.8630 (OUTLIER) cc_final: 0.7751 (ttt180)
REVERT: D  129 LYS cc_start: 0.7989 (mmtt) cc_final: 0.7630 (mmtm)
REVERT: D  169 LEU cc_start: 0.8961 (OUTLIER) cc_final: 0.8547 (tm)
REVERT: D  199 GLU cc_start: 0.9389 (mt-10) cc_final: 0.9052 (mt-10)
REVERT: D  324 TYR cc_start: 0.8474 (OUTLIER) cc_final: 0.7552 (t80)
REVERT: C  134 MET cc_start: 0.8074 (mmm) cc_final: 0.7723 (tpt)
REVERT: B  127 LYS cc_start: 0.8130 (pttt) cc_final: 0.7545 (mtpp)
REVERT: B  199 GLU cc_start: 0.9436 (mt-10) cc_final: 0.9073 (mt-10)
REVERT: B  324 TYR cc_start: 0.8307 (OUTLIER) cc_final: 0.7865 (t80)
REVERT: A  119 GLU cc_start: 0.8929 (OUTLIER) cc_final: 0.8666 (mp0)
REVERT: A  324 TYR cc_start: 0.7603 (OUTLIER) cc_final: 0.6652 (t80)
  outliers start: 66
  outliers final: 49
  residues processed: 220
  average time/residue: 0.3107
  time to fit residues: 108.7604
Evaluate side-chains
  215 residues out of total 1398 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 58
    poor density    : 157
  time to evaluate  : 1.218 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain F residue   41 VAL
Chi-restraints excluded: chain F residue   50 THR
Chi-restraints excluded: chain F residue   66 GLU
Chi-restraints excluded: chain F residue  169 LEU
Chi-restraints excluded: chain F residue  181 THR
Chi-restraints excluded: chain F residue  227 THR
Chi-restraints excluded: chain F residue  241 CYS
Chi-restraints excluded: chain F residue  285 SER
Chi-restraints excluded: chain F residue  301 LEU
Chi-restraints excluded: chain F residue  308 LEU
Chi-restraints excluded: chain F residue  324 TYR
Chi-restraints excluded: chain E residue  113 VAL
Chi-restraints excluded: chain E residue  169 LEU
Chi-restraints excluded: chain E residue  181 THR
Chi-restraints excluded: chain E residue  283 ILE
Chi-restraints excluded: chain E residue  289 ILE
Chi-restraints excluded: chain E residue  324 TYR
Chi-restraints excluded: chain D residue   41 VAL
Chi-restraints excluded: chain D residue   50 THR
Chi-restraints excluded: chain D residue   66 GLU
Chi-restraints excluded: chain D residue  120 ARG
Chi-restraints excluded: chain D residue  136 VAL
Chi-restraints excluded: chain D residue  148 VAL
Chi-restraints excluded: chain D residue  169 LEU
Chi-restraints excluded: chain D residue  241 CYS
Chi-restraints excluded: chain D residue  282 SER
Chi-restraints excluded: chain D residue  301 LEU
Chi-restraints excluded: chain D residue  308 LEU
Chi-restraints excluded: chain D residue  324 TYR
Chi-restraints excluded: chain C residue   50 THR
Chi-restraints excluded: chain C residue   90 LEU
Chi-restraints excluded: chain C residue  113 VAL
Chi-restraints excluded: chain C residue  119 GLU
Chi-restraints excluded: chain C residue  147 THR
Chi-restraints excluded: chain C residue  181 THR
Chi-restraints excluded: chain C residue  227 THR
Chi-restraints excluded: chain C residue  277 CYS
Chi-restraints excluded: chain C residue  283 ILE
Chi-restraints excluded: chain C residue  301 LEU
Chi-restraints excluded: chain C residue  324 TYR
Chi-restraints excluded: chain B residue   41 VAL
Chi-restraints excluded: chain B residue   50 THR
Chi-restraints excluded: chain B residue   66 GLU
Chi-restraints excluded: chain B residue  147 THR
Chi-restraints excluded: chain B residue  184 VAL
Chi-restraints excluded: chain B residue  241 CYS
Chi-restraints excluded: chain B residue  282 SER
Chi-restraints excluded: chain B residue  283 ILE
Chi-restraints excluded: chain B residue  301 LEU
Chi-restraints excluded: chain B residue  308 LEU
Chi-restraints excluded: chain B residue  324 TYR
Chi-restraints excluded: chain A residue  113 VAL
Chi-restraints excluded: chain A residue  119 GLU
Chi-restraints excluded: chain A residue  169 LEU
Chi-restraints excluded: chain A residue  181 THR
Chi-restraints excluded: chain A residue  289 ILE
Chi-restraints excluded: chain A residue  324 TYR
Chi-restraints excluded: chain A residue  329 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 168
   random chunks:
   chunk 26 optimal weight:    0.8980
   chunk 133 optimal weight:    5.9990
   chunk 139 optimal weight:    5.9990
   chunk 21 optimal weight:    7.9990
   chunk 146 optimal weight:    9.9990
   chunk 131 optimal weight:    8.9990
   chunk 1 optimal weight:   20.0000
   chunk 31 optimal weight:    8.9990
   chunk 3 optimal weight:   20.0000
   chunk 110 optimal weight:    6.9990
   chunk 83 optimal weight:    6.9990
   overall best weight:    5.3788

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

Flipped N/Q/H residues before XYZ refinement:
F 295 ASN
D 295 ASN
B 295 ASN
A 337 HIS

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.2972 r_free = 0.2972 target = 0.095206 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.2711 r_free = 0.2711 target = 0.078598 restraints weight = 23962.551|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.2742 r_free = 0.2742 target = 0.080497 restraints weight = 15141.587|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.2763 r_free = 0.2763 target = 0.081774 restraints weight = 11265.404|
|-----------------------------------------------------------------------------|
r_work (final): 0.2765
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2767
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2767 r_free = 0.2767    target_work(ls_wunit_k1) = 0.082         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:      292 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2765 r_free = 0.2765    target_work(ls_wunit_k1) = 0.082         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:      289 |
|-----------------------------------------------------------------------------|
r_final: 0.2765
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8684
moved from start:          0.4209

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.037  13656  Z= 0.221
  Angle     :  0.821  11.972  18486  Z= 0.411
  Chirality :  0.050   0.210   2058
  Planarity :  0.005   0.035   2370
  Dihedral  :  6.358  57.552   1902
  Min Nonbonded Distance : 2.329

Molprobity Statistics.
  All-atom Clashscore : 7.52
  Ramachandran Plot:
    Outliers :  0.94 %
    Allowed  : 13.74 %
    Favored  : 85.32 %
  Rotamer:
    Outliers :  4.79 %
    Allowed  : 17.67 %
    Favored  : 77.54 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 7.14 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.37 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -3.76 (0.18), residues: 1710
  helix: -1.54 (0.24), residues: 432
  sheet: -1.85 (0.28), residues: 336
  loop : -3.35 (0.17), residues: 942

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP D 198 
 HIS   0.005   0.001   HIS F 323 
 PHE   0.011   0.002   PHE F 318 
 TYR   0.014   0.002   TYR E 106 
 ARG   0.006   0.000   ARG B 171 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03909 (  354)
  hydrogen bonds       : angle       5.40615 (  936)
  covalent geometry    : bond        0.00531 (13656)
  covalent geometry    : angle       0.82058 (18486)

********************** 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
  220 residues out of total 1398 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 67
    poor density    : 153
  time to evaluate  : 2.271 
Fit side-chains
REVERT: F  169 LEU cc_start: 0.8733 (OUTLIER) cc_final: 0.8385 (tm)
REVERT: F  227 THR cc_start: 0.8491 (OUTLIER) cc_final: 0.8151 (m)
REVERT: F  324 TYR cc_start: 0.8405 (OUTLIER) cc_final: 0.7846 (t80)
REVERT: E  232 MET cc_start: 0.8997 (mmm) cc_final: 0.7833 (mmm)
REVERT: E  324 TYR cc_start: 0.7842 (OUTLIER) cc_final: 0.6524 (t80)
REVERT: D   89 GLU cc_start: 0.8362 (mt-10) cc_final: 0.7764 (tt0)
REVERT: D  120 ARG cc_start: 0.8643 (OUTLIER) cc_final: 0.7786 (ttt180)
REVERT: D  169 LEU cc_start: 0.8990 (OUTLIER) cc_final: 0.8614 (tm)
REVERT: D  199 GLU cc_start: 0.9347 (mt-10) cc_final: 0.9065 (mt-10)
REVERT: D  324 TYR cc_start: 0.8528 (OUTLIER) cc_final: 0.7603 (t80)
REVERT: C  134 MET cc_start: 0.7985 (mmm) cc_final: 0.7647 (tpt)
REVERT: B  127 LYS cc_start: 0.8149 (pttt) cc_final: 0.7643 (mtpp)
REVERT: B  199 GLU cc_start: 0.9404 (mt-10) cc_final: 0.9106 (mt-10)
REVERT: B  324 TYR cc_start: 0.8382 (OUTLIER) cc_final: 0.7973 (t80)
REVERT: A  119 GLU cc_start: 0.8949 (OUTLIER) cc_final: 0.8629 (mp0)
REVERT: A  324 TYR cc_start: 0.7718 (OUTLIER) cc_final: 0.6763 (t80)
  outliers start: 67
  outliers final: 52
  residues processed: 208
  average time/residue: 0.3169
  time to fit residues: 102.9569
Evaluate side-chains
  208 residues out of total 1398 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 62
    poor density    : 146
  time to evaluate  : 1.476 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain F residue   41 VAL
Chi-restraints excluded: chain F residue   50 THR
Chi-restraints excluded: chain F residue   66 GLU
Chi-restraints excluded: chain F residue  169 LEU
Chi-restraints excluded: chain F residue  181 THR
Chi-restraints excluded: chain F residue  227 THR
Chi-restraints excluded: chain F residue  241 CYS
Chi-restraints excluded: chain F residue  301 LEU
Chi-restraints excluded: chain F residue  308 LEU
Chi-restraints excluded: chain F residue  324 TYR
Chi-restraints excluded: chain E residue  113 VAL
Chi-restraints excluded: chain E residue  169 LEU
Chi-restraints excluded: chain E residue  181 THR
Chi-restraints excluded: chain E residue  184 VAL
Chi-restraints excluded: chain E residue  283 ILE
Chi-restraints excluded: chain E residue  289 ILE
Chi-restraints excluded: chain E residue  324 TYR
Chi-restraints excluded: chain D residue   41 VAL
Chi-restraints excluded: chain D residue   50 THR
Chi-restraints excluded: chain D residue   66 GLU
Chi-restraints excluded: chain D residue  120 ARG
Chi-restraints excluded: chain D residue  136 VAL
Chi-restraints excluded: chain D residue  148 VAL
Chi-restraints excluded: chain D residue  169 LEU
Chi-restraints excluded: chain D residue  214 ILE
Chi-restraints excluded: chain D residue  227 THR
Chi-restraints excluded: chain D residue  241 CYS
Chi-restraints excluded: chain D residue  282 SER
Chi-restraints excluded: chain D residue  301 LEU
Chi-restraints excluded: chain D residue  308 LEU
Chi-restraints excluded: chain D residue  324 TYR
Chi-restraints excluded: chain D residue  346 THR
Chi-restraints excluded: chain C residue   50 THR
Chi-restraints excluded: chain C residue   90 LEU
Chi-restraints excluded: chain C residue  113 VAL
Chi-restraints excluded: chain C residue  119 GLU
Chi-restraints excluded: chain C residue  147 THR
Chi-restraints excluded: chain C residue  181 THR
Chi-restraints excluded: chain C residue  227 THR
Chi-restraints excluded: chain C residue  277 CYS
Chi-restraints excluded: chain C residue  283 ILE
Chi-restraints excluded: chain C residue  301 LEU
Chi-restraints excluded: chain C residue  308 LEU
Chi-restraints excluded: chain C residue  324 TYR
Chi-restraints excluded: chain B residue   41 VAL
Chi-restraints excluded: chain B residue   50 THR
Chi-restraints excluded: chain B residue   66 GLU
Chi-restraints excluded: chain B residue  147 THR
Chi-restraints excluded: chain B residue  184 VAL
Chi-restraints excluded: chain B residue  241 CYS
Chi-restraints excluded: chain B residue  282 SER
Chi-restraints excluded: chain B residue  283 ILE
Chi-restraints excluded: chain B residue  301 LEU
Chi-restraints excluded: chain B residue  308 LEU
Chi-restraints excluded: chain B residue  324 TYR
Chi-restraints excluded: chain A residue  113 VAL
Chi-restraints excluded: chain A residue  119 GLU
Chi-restraints excluded: chain A residue  169 LEU
Chi-restraints excluded: chain A residue  181 THR
Chi-restraints excluded: chain A residue  289 ILE
Chi-restraints excluded: chain A residue  324 TYR
Chi-restraints excluded: chain A residue  329 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 168
   random chunks:
   chunk 118 optimal weight:   10.0000
   chunk 141 optimal weight:   20.0000
   chunk 116 optimal weight:    9.9990
   chunk 158 optimal weight:    0.7980
   chunk 144 optimal weight:    3.9990
   chunk 35 optimal weight:    7.9990
   chunk 27 optimal weight:    4.9990
   chunk 112 optimal weight:    4.9990
   chunk 39 optimal weight:    0.5980
   chunk 42 optimal weight:    5.9990
   chunk 50 optimal weight:    0.9990
   overall best weight:    2.2786

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

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

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3173 r_free = 0.3173 target = 0.109044 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.2908 r_free = 0.2908 target = 0.091115 restraints weight = 22397.509|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 41)----------------|
| r_work = 0.2942 r_free = 0.2942 target = 0.093345 restraints weight = 14176.053|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 44)----------------|
| r_work = 0.2965 r_free = 0.2965 target = 0.094844 restraints weight = 10578.200|
|-----------------------------------------------------------------------------|
r_work (final): 0.2850
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2835
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2835 r_free = 0.2835    target_work(ls_wunit_k1) = 0.086         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:      289 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2829 r_free = 0.2829    target_work(ls_wunit_k1) = 0.086         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:      306 |
|-----------------------------------------------------------------------------|
r_final: 0.2829
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8621
moved from start:          0.4297

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040  13656  Z= 0.138
  Angle     :  0.745  12.065  18486  Z= 0.370
  Chirality :  0.047   0.177   2058
  Planarity :  0.005   0.033   2370
  Dihedral  :  5.912  55.926   1902
  Min Nonbonded Distance : 2.355

Molprobity Statistics.
  All-atom Clashscore : 6.54
  Ramachandran Plot:
    Outliers :  0.76 %
    Allowed  : 11.64 %
    Favored  : 87.60 %
  Rotamer:
    Outliers :  4.22 %
    Allowed  : 18.24 %
    Favored  : 77.54 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 7.14 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.37 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -3.47 (0.18), residues: 1710
  helix: -1.04 (0.26), residues: 402
  sheet: -1.66 (0.28), residues: 336
  loop : -3.26 (0.16), residues: 972

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP B 198 
 HIS   0.007   0.001   HIS E 323 
 PHE   0.010   0.001   PHE C 330 
 TYR   0.013   0.001   TYR B 128 
 ARG   0.004   0.000   ARG F 171 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03050 (  354)
  hydrogen bonds       : angle       5.07169 (  936)
  covalent geometry    : bond        0.00325 (13656)
  covalent geometry    : angle       0.74487 (18486)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 5430.59 seconds
wall clock time: 101 minutes 3.92 seconds (6063.92 seconds total)