Starting phenix.real_space_refine
on Thu Jul 31 05:17:36 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/6i5u_4420/07_2025/6i5u_4420.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/6i5u_4420/07_2025/6i5u_4420.map

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

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

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/6i5u_4420/07_2025/6i5u_4420.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/6i5u_4420/07_2025/6i5u_4420.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/6i5u_4420/07_2025/6i5u_4420.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/6i5u_4420/07_2025/6i5u_4420.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=   0.000 sd=   0.007
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 4
    Type Number    sf(0)   Gaussians
     S      78      5.16       5
     C    8550      2.51       5
     N    2286      2.21       5
     O    2442      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 12 residue(s): 0.04s

  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: 5.40, per 1000 atoms: 0.40
  Number of scatterers: 13356
  At special positions: 0
  Unit cell: (117.3, 132.6, 130.9, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     S      78     16.00
     O    2442      8.00
     N    2286      7.00
     C    8550      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 3.19
  Conformation dependent library (CDL) restraints added in 1.9 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:
      36 helices and 21 sheets defined
      22.8% alpha, 16.1% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 1.81
  Creating SS restraints...
    Processing helix  chain 'F' and resid 54 through 66
    Processing helix  chain 'F' and resid 96 through 108
      removed outlier: 4.371A  pdb=" N   ARG F 100 " --> pdb=" O   THR F  96 " (cutoff:3.500A)
      removed outlier: 4.019A  pdb=" N   ASP F 101 " --> pdb=" O   ALA F  97 " (cutoff:3.500A)
      removed outlier: 5.520A  pdb=" N   ASP F 102 " --> pdb=" O   LYS F  98 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 115 through 127
      removed outlier: 3.511A  pdb=" N   GLU F 119 " --> pdb=" O   GLY F 115 " (cutoff:3.500A)
      removed outlier: 3.864A  pdb=" N   ARG F 120 " --> pdb=" O   PRO F 116 " (cutoff:3.500A)
      removed outlier: 3.929A  pdb=" N   LEU F 121 " --> pdb=" O   GLU F 117 " (cutoff:3.500A)
      removed outlier: 3.632A  pdb=" N   LYS F 127 " --> pdb=" O   LEU F 123 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 202 through 210
      removed outlier: 3.854A  pdb=" N   ARG F 206 " --> pdb=" O   MET F 202 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 211 through 213
      No H-bonds generated for 'chain 'F' and resid 211 through 213'
    Processing helix  chain 'F' and resid 225 through 239
      removed outlier: 4.437A  pdb=" N   LEU F 229 " --> pdb=" O   ARG F 225 " (cutoff:3.500A)
      removed outlier: 3.678A  pdb=" N   ALA F 230 " --> pdb=" O   GLU F 226 " (cutoff:3.500A)
      removed outlier: 3.904A  pdb=" N   HIS F 234 " --> pdb=" O   ALA F 230 " (cutoff:3.500A)
      removed outlier: 3.907A  pdb=" N   ILE F 235 " --> pdb=" O   SER F 231 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 54 through 66
    Processing helix  chain 'E' and resid 96 through 108
      removed outlier: 4.371A  pdb=" N   ARG E 100 " --> pdb=" O   THR E  96 " (cutoff:3.500A)
      removed outlier: 4.019A  pdb=" N   ASP E 101 " --> pdb=" O   ALA E  97 " (cutoff:3.500A)
      removed outlier: 5.520A  pdb=" N   ASP E 102 " --> pdb=" O   LYS E  98 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 115 through 127
      removed outlier: 3.511A  pdb=" N   GLU E 119 " --> pdb=" O   GLY E 115 " (cutoff:3.500A)
      removed outlier: 3.864A  pdb=" N   ARG E 120 " --> pdb=" O   PRO E 116 " (cutoff:3.500A)
      removed outlier: 3.929A  pdb=" N   LEU E 121 " --> pdb=" O   GLU E 117 " (cutoff:3.500A)
      removed outlier: 3.633A  pdb=" N   LYS E 127 " --> pdb=" O   LEU E 123 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 202 through 210
      removed outlier: 3.855A  pdb=" N   ARG E 206 " --> pdb=" O   MET E 202 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 211 through 213
      No H-bonds generated for 'chain 'E' and resid 211 through 213'
    Processing helix  chain 'E' and resid 225 through 239
      removed outlier: 4.437A  pdb=" N   LEU E 229 " --> pdb=" O   ARG E 225 " (cutoff:3.500A)
      removed outlier: 3.679A  pdb=" N   ALA E 230 " --> pdb=" O   GLU E 226 " (cutoff:3.500A)
      removed outlier: 3.905A  pdb=" N   HIS E 234 " --> pdb=" O   ALA E 230 " (cutoff:3.500A)
      removed outlier: 3.907A  pdb=" N   ILE E 235 " --> pdb=" O   SER E 231 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 54 through 66
    Processing helix  chain 'D' and resid 96 through 108
      removed outlier: 4.371A  pdb=" N   ARG D 100 " --> pdb=" O   THR D  96 " (cutoff:3.500A)
      removed outlier: 4.020A  pdb=" N   ASP D 101 " --> pdb=" O   ALA D  97 " (cutoff:3.500A)
      removed outlier: 5.520A  pdb=" N   ASP D 102 " --> pdb=" O   LYS D  98 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 115 through 127
      removed outlier: 3.511A  pdb=" N   GLU D 119 " --> pdb=" O   GLY D 115 " (cutoff:3.500A)
      removed outlier: 3.864A  pdb=" N   ARG D 120 " --> pdb=" O   PRO D 116 " (cutoff:3.500A)
      removed outlier: 3.928A  pdb=" N   LEU D 121 " --> pdb=" O   GLU D 117 " (cutoff:3.500A)
      removed outlier: 3.632A  pdb=" N   LYS D 127 " --> pdb=" O   LEU D 123 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 202 through 210
      removed outlier: 3.854A  pdb=" N   ARG D 206 " --> pdb=" O   MET D 202 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 211 through 213
      No H-bonds generated for 'chain 'D' and resid 211 through 213'
    Processing helix  chain 'D' and resid 225 through 239
      removed outlier: 4.438A  pdb=" N   LEU D 229 " --> pdb=" O   ARG D 225 " (cutoff:3.500A)
      removed outlier: 3.679A  pdb=" N   ALA D 230 " --> pdb=" O   GLU D 226 " (cutoff:3.500A)
      removed outlier: 3.906A  pdb=" N   HIS D 234 " --> pdb=" O   ALA D 230 " (cutoff:3.500A)
      removed outlier: 3.907A  pdb=" N   ILE D 235 " --> pdb=" O   SER D 231 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 54 through 66
    Processing helix  chain 'C' and resid 96 through 108
      removed outlier: 4.372A  pdb=" N   ARG C 100 " --> pdb=" O   THR C  96 " (cutoff:3.500A)
      removed outlier: 4.020A  pdb=" N   ASP C 101 " --> pdb=" O   ALA C  97 " (cutoff:3.500A)
      removed outlier: 5.519A  pdb=" N   ASP C 102 " --> pdb=" O   LYS C  98 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 115 through 127
      removed outlier: 3.511A  pdb=" N   GLU C 119 " --> pdb=" O   GLY C 115 " (cutoff:3.500A)
      removed outlier: 3.863A  pdb=" N   ARG C 120 " --> pdb=" O   PRO C 116 " (cutoff:3.500A)
      removed outlier: 3.929A  pdb=" N   LEU C 121 " --> pdb=" O   GLU C 117 " (cutoff:3.500A)
      removed outlier: 3.632A  pdb=" N   LYS C 127 " --> pdb=" O   LEU C 123 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 202 through 210
      removed outlier: 3.854A  pdb=" N   ARG C 206 " --> pdb=" O   MET C 202 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 211 through 213
      No H-bonds generated for 'chain 'C' and resid 211 through 213'
    Processing helix  chain 'C' and resid 225 through 239
      removed outlier: 4.438A  pdb=" N   LEU C 229 " --> pdb=" O   ARG C 225 " (cutoff:3.500A)
      removed outlier: 3.679A  pdb=" N   ALA C 230 " --> pdb=" O   GLU C 226 " (cutoff:3.500A)
      removed outlier: 3.905A  pdb=" N   HIS C 234 " --> pdb=" O   ALA C 230 " (cutoff:3.500A)
      removed outlier: 3.907A  pdb=" N   ILE C 235 " --> pdb=" O   SER C 231 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 54 through 66
    Processing helix  chain 'B' and resid 96 through 108
      removed outlier: 4.372A  pdb=" N   ARG B 100 " --> pdb=" O   THR B  96 " (cutoff:3.500A)
      removed outlier: 4.020A  pdb=" N   ASP B 101 " --> pdb=" O   ALA B  97 " (cutoff:3.500A)
      removed outlier: 5.520A  pdb=" N   ASP B 102 " --> pdb=" O   LYS B  98 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 115 through 127
      removed outlier: 3.511A  pdb=" N   GLU B 119 " --> pdb=" O   GLY B 115 " (cutoff:3.500A)
      removed outlier: 3.864A  pdb=" N   ARG B 120 " --> pdb=" O   PRO B 116 " (cutoff:3.500A)
      removed outlier: 3.929A  pdb=" N   LEU B 121 " --> pdb=" O   GLU B 117 " (cutoff:3.500A)
      removed outlier: 3.631A  pdb=" N   LYS B 127 " --> pdb=" O   LEU B 123 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 202 through 210
      removed outlier: 3.854A  pdb=" N   ARG B 206 " --> pdb=" O   MET B 202 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 211 through 213
      No H-bonds generated for 'chain 'B' and resid 211 through 213'
    Processing helix  chain 'B' and resid 225 through 239
      removed outlier: 4.437A  pdb=" N   LEU B 229 " --> pdb=" O   ARG B 225 " (cutoff:3.500A)
      removed outlier: 3.680A  pdb=" N   ALA B 230 " --> pdb=" O   GLU B 226 " (cutoff:3.500A)
      removed outlier: 3.905A  pdb=" N   HIS B 234 " --> pdb=" O   ALA B 230 " (cutoff:3.500A)
      removed outlier: 3.907A  pdb=" N   ILE B 235 " --> pdb=" O   SER B 231 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 54 through 66
    Processing helix  chain 'A' and resid 96 through 108
      removed outlier: 4.371A  pdb=" N   ARG A 100 " --> pdb=" O   THR A  96 " (cutoff:3.500A)
      removed outlier: 4.019A  pdb=" N   ASP A 101 " --> pdb=" O   ALA A  97 " (cutoff:3.500A)
      removed outlier: 5.519A  pdb=" N   ASP A 102 " --> pdb=" O   LYS A  98 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 115 through 127
      removed outlier: 3.510A  pdb=" N   GLU A 119 " --> pdb=" O   GLY A 115 " (cutoff:3.500A)
      removed outlier: 3.864A  pdb=" N   ARG A 120 " --> pdb=" O   PRO A 116 " (cutoff:3.500A)
      removed outlier: 3.928A  pdb=" N   LEU A 121 " --> pdb=" O   GLU A 117 " (cutoff:3.500A)
      removed outlier: 3.632A  pdb=" N   LYS A 127 " --> pdb=" O   LEU A 123 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 202 through 210
      removed outlier: 3.854A  pdb=" N   ARG A 206 " --> pdb=" O   MET A 202 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 211 through 213
      No H-bonds generated for 'chain 'A' and resid 211 through 213'
    Processing helix  chain 'A' and resid 225 through 239
      removed outlier: 4.437A  pdb=" N   LEU A 229 " --> pdb=" O   ARG A 225 " (cutoff:3.500A)
      removed outlier: 3.678A  pdb=" N   ALA A 230 " --> pdb=" O   GLU A 226 " (cutoff:3.500A)
      removed outlier: 3.905A  pdb=" N   HIS A 234 " --> pdb=" O   ALA A 230 " (cutoff:3.500A)
      removed outlier: 3.907A  pdb=" N   ILE A 235 " --> pdb=" O   SER A 231 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'F' and resid 157 through 160
      removed outlier: 4.320A  pdb=" N   GLY F 159 " --> pdb=" O   PHE F 150 " (cutoff:3.500A)
      removed outlier: 3.519A  pdb=" N   PHE F 150 " --> pdb=" O   GLY F 159 " (cutoff:3.500A)
      removed outlier: 3.708A  pdb=" N   LEU F  71 " --> pdb=" O   ARG F  37 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'F' and resid 138 through 139
    Processing sheet with id=AA3, first strand: chain 'F' and resid 186 through 187
      removed outlier: 6.568A  pdb=" N   TYR F 217 " --> pdb=" O   LEU F 244 " (cutoff:3.500A)
      removed outlier: 8.036A  pdb=" N   ALA F 246 " --> pdb=" O   TYR F 217 " (cutoff:3.500A)
      removed outlier: 6.903A  pdb=" N   ALA F 219 " --> pdb=" O   ALA F 246 " (cutoff:3.500A)
      removed outlier: 7.005A  pdb=" N   ILE F 283 " --> pdb=" O   LEU F 291 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'E' and resid 330 through 334
      removed outlier: 3.531A  pdb=" N   SER E 331 " --> pdb=" O   ASN F 333 " (cutoff:3.500A)
      removed outlier: 3.511A  pdb=" N   SER F 331 " --> pdb=" O   ASN E 333 " (cutoff:3.500A)
      removed outlier: 8.866A  pdb=" N   SER D 343 " --> pdb=" O   PHE F 330 " (cutoff:3.500A)
      removed outlier: 6.808A  pdb=" N   LEU F 332 " --> pdb=" O   SER D 343 " (cutoff:3.500A)
      removed outlier: 7.707A  pdb=" N   LYS D 345 " --> pdb=" O   LEU F 332 " (cutoff:3.500A)
      removed outlier: 6.250A  pdb=" N   ILE F 334 " --> pdb=" O   LYS D 345 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'E' and resid 157 through 160
      removed outlier: 4.320A  pdb=" N   GLY E 159 " --> pdb=" O   PHE E 150 " (cutoff:3.500A)
      removed outlier: 3.519A  pdb=" N   PHE E 150 " --> pdb=" O   GLY E 159 " (cutoff:3.500A)
      removed outlier: 3.708A  pdb=" N   LEU E  71 " --> pdb=" O   ARG E  37 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'E' and resid 138 through 139
    Processing sheet with id=AA7, first strand: chain 'E' and resid 186 through 187
      removed outlier: 6.568A  pdb=" N   TYR E 217 " --> pdb=" O   LEU E 244 " (cutoff:3.500A)
      removed outlier: 8.036A  pdb=" N   ALA E 246 " --> pdb=" O   TYR E 217 " (cutoff:3.500A)
      removed outlier: 6.903A  pdb=" N   ALA E 219 " --> pdb=" O   ALA E 246 " (cutoff:3.500A)
      removed outlier: 7.004A  pdb=" N   ILE E 283 " --> pdb=" O   LEU E 291 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'E' and resid 342 through 345
      removed outlier: 3.531A  pdb=" N   SER C 331 " --> pdb=" O   ASN D 333 " (cutoff:3.500A)
      removed outlier: 3.519A  pdb=" N   SER D 331 " --> pdb=" O   ASN C 333 " (cutoff:3.500A)
      removed outlier: 8.854A  pdb=" N   SER B 343 " --> pdb=" O   PHE D 330 " (cutoff:3.500A)
      removed outlier: 6.814A  pdb=" N   LEU D 332 " --> pdb=" O   SER B 343 " (cutoff:3.500A)
      removed outlier: 7.712A  pdb=" N   LYS B 345 " --> pdb=" O   LEU D 332 " (cutoff:3.500A)
      removed outlier: 6.273A  pdb=" N   ILE D 334 " --> pdb=" O   LYS B 345 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'D' and resid 157 through 160
      removed outlier: 4.320A  pdb=" N   GLY D 159 " --> pdb=" O   PHE D 150 " (cutoff:3.500A)
      removed outlier: 3.519A  pdb=" N   PHE D 150 " --> pdb=" O   GLY D 159 " (cutoff:3.500A)
      removed outlier: 3.708A  pdb=" N   LEU D  71 " --> pdb=" O   ARG D  37 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'D' and resid 138 through 139
    Processing sheet with id=AB2, first strand: chain 'D' and resid 186 through 187
      removed outlier: 6.567A  pdb=" N   TYR D 217 " --> pdb=" O   LEU D 244 " (cutoff:3.500A)
      removed outlier: 8.037A  pdb=" N   ALA D 246 " --> pdb=" O   TYR D 217 " (cutoff:3.500A)
      removed outlier: 6.904A  pdb=" N   ALA D 219 " --> pdb=" O   ALA D 246 " (cutoff:3.500A)
      removed outlier: 7.005A  pdb=" N   ILE D 283 " --> pdb=" O   LEU D 291 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'C' and resid 157 through 160
      removed outlier: 4.319A  pdb=" N   GLY C 159 " --> pdb=" O   PHE C 150 " (cutoff:3.500A)
      removed outlier: 3.519A  pdb=" N   PHE C 150 " --> pdb=" O   GLY C 159 " (cutoff:3.500A)
      removed outlier: 3.709A  pdb=" N   LEU C  71 " --> pdb=" O   ARG C  37 " (cutoff:3.500A)
    Processing sheet with id=AB4, first strand: chain 'C' and resid 138 through 139
    Processing sheet with id=AB5, first strand: chain 'C' and resid 186 through 187
      removed outlier: 6.568A  pdb=" N   TYR C 217 " --> pdb=" O   LEU C 244 " (cutoff:3.500A)
      removed outlier: 8.036A  pdb=" N   ALA C 246 " --> pdb=" O   TYR C 217 " (cutoff:3.500A)
      removed outlier: 6.903A  pdb=" N   ALA C 219 " --> pdb=" O   ALA C 246 " (cutoff:3.500A)
      removed outlier: 7.005A  pdb=" N   ILE C 283 " --> pdb=" O   LEU C 291 " (cutoff:3.500A)
    Processing sheet with id=AB6, first strand: chain 'C' and resid 342 through 345
      removed outlier: 3.547A  pdb=" N   SER A 331 " --> pdb=" O   ASN B 333 " (cutoff:3.500A)
      removed outlier: 3.549A  pdb=" N   SER B 331 " --> pdb=" O   ASN A 333 " (cutoff:3.500A)
    Processing sheet with id=AB7, first strand: chain 'B' and resid 157 through 160
      removed outlier: 4.319A  pdb=" N   GLY B 159 " --> pdb=" O   PHE B 150 " (cutoff:3.500A)
      removed outlier: 3.518A  pdb=" N   PHE B 150 " --> pdb=" O   GLY B 159 " (cutoff:3.500A)
      removed outlier: 3.709A  pdb=" N   LEU B  71 " --> pdb=" O   ARG B  37 " (cutoff:3.500A)
    Processing sheet with id=AB8, first strand: chain 'B' and resid 138 through 139
    Processing sheet with id=AB9, first strand: chain 'B' and resid 186 through 187
      removed outlier: 6.568A  pdb=" N   TYR B 217 " --> pdb=" O   LEU B 244 " (cutoff:3.500A)
      removed outlier: 8.036A  pdb=" N   ALA B 246 " --> pdb=" O   TYR B 217 " (cutoff:3.500A)
      removed outlier: 6.903A  pdb=" N   ALA B 219 " --> pdb=" O   ALA B 246 " (cutoff:3.500A)
      removed outlier: 7.005A  pdb=" N   ILE B 283 " --> pdb=" O   LEU B 291 " (cutoff:3.500A)
    Processing sheet with id=AC1, first strand: chain 'A' and resid 157 through 160
      removed outlier: 4.319A  pdb=" N   GLY A 159 " --> pdb=" O   PHE A 150 " (cutoff:3.500A)
      removed outlier: 3.518A  pdb=" N   PHE A 150 " --> pdb=" O   GLY A 159 " (cutoff:3.500A)
      removed outlier: 3.709A  pdb=" N   LEU A  71 " --> pdb=" O   ARG A  37 " (cutoff:3.500A)
    Processing sheet with id=AC2, first strand: chain 'A' and resid 138 through 139
    Processing sheet with id=AC3, first strand: chain 'A' and resid 186 through 187
      removed outlier: 6.569A  pdb=" N   TYR A 217 " --> pdb=" O   LEU A 244 " (cutoff:3.500A)
      removed outlier: 8.036A  pdb=" N   ALA A 246 " --> pdb=" O   TYR A 217 " (cutoff:3.500A)
      removed outlier: 6.903A  pdb=" N   ALA A 219 " --> pdb=" O   ALA A 246 " (cutoff:3.500A)
      removed outlier: 7.005A  pdb=" N   ILE A 283 " --> pdb=" O   LEU A 291 " (cutoff:3.500A)

    348 hydrogen bonds defined for protein.
    972 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 3.77

  Time building geometry restraints manager: 3.82 seconds

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.

  Histogram of bond lengths:
        1.22 -     1.34: 4311
        1.34 -     1.46: 2757
        1.46 -     1.58: 6474
        1.58 -     1.69: 0
        1.69 -     1.81: 114
  Bond restraints: 13656
  Sorted by residual:
  bond pdb=" CA  HIS C 323 "
       pdb=" C   HIS C 323 "
    ideal  model  delta    sigma   weight residual
    1.523  1.551 -0.028 1.34e-02 5.57e+03 4.37e+00
  bond pdb=" CA  HIS D 323 "
       pdb=" C   HIS D 323 "
    ideal  model  delta    sigma   weight residual
    1.523  1.551 -0.028 1.34e-02 5.57e+03 4.29e+00
  bond pdb=" CA  HIS E 323 "
       pdb=" C   HIS E 323 "
    ideal  model  delta    sigma   weight residual
    1.523  1.551 -0.027 1.34e-02 5.57e+03 4.20e+00
  bond pdb=" CA  HIS A 323 "
       pdb=" C   HIS A 323 "
    ideal  model  delta    sigma   weight residual
    1.523  1.551 -0.027 1.34e-02 5.57e+03 4.18e+00
  bond pdb=" CA  HIS B 323 "
       pdb=" C   HIS B 323 "
    ideal  model  delta    sigma   weight residual
    1.523  1.550 -0.027 1.34e-02 5.57e+03 4.15e+00
  ... (remaining 13651 not shown)

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

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

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

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

  Histogram of nonbonded interaction distances:
        2.35 -     2.86: 4512
        2.86 -     3.37: 11075
        3.37 -     3.88: 20030
        3.88 -     4.39: 22434
        4.39 -     4.90: 39873
  Nonbonded interactions: 97924
  Sorted by model distance:
  nonbonded pdb=" OE1 GLU F  89 "
            pdb=" OG1 THR F  96 "
     model   vdw
     2.350 3.040
  nonbonded pdb=" OE1 GLU E  89 "
            pdb=" OG1 THR E  96 "
     model   vdw
     2.350 3.040
  nonbonded pdb=" OE1 GLU D  89 "
            pdb=" OG1 THR D  96 "
     model   vdw
     2.350 3.040
  nonbonded pdb=" OE1 GLU C  89 "
            pdb=" OG1 THR C  96 "
     model   vdw
     2.350 3.040
  nonbonded pdb=" OE1 GLU B  89 "
            pdb=" OG1 THR B  96 "
     model   vdw
     2.350 3.040
  ... (remaining 97919 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.10
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:                  0.010
  Normalize map: mean=0, sd=1:             1.420
  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:          0.570
  Check model and map are aligned:         0.040
  Set scattering table:                    0.150
  Process input model:                     29.360
  Find NCS groups from input model:        0.270
  Set up NCS constraints:                  0.040
  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:2.960
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   34.840
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8251
moved from start:          0.0000

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

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

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

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

Details of bonding type rmsd
  hydrogen bonds       : bond        0.24475 (  348)
  hydrogen bonds       : angle       7.88255 (  972)
  covalent geometry    : bond        0.00547 (13656)
  covalent geometry    : angle       1.05920 (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
  479 residues out of total 1398 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 473
  time to evaluate  : 1.558 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: F  310 ASP cc_start: 0.8184 (t0) cc_final: 0.7903 (t0)
REVERT: F  317 ASP cc_start: 0.8328 (m-30) cc_final: 0.8103 (m-30)
REVERT: F  339 ARG cc_start: 0.7139 (mtt-85) cc_final: 0.6655 (ttp-170)
REVERT: E  285 SER cc_start: 0.9097 (t) cc_final: 0.8613 (p)
REVERT: E  295 ASN cc_start: 0.7828 (t0) cc_final: 0.7595 (t0)
REVERT: E  310 ASP cc_start: 0.7858 (t0) cc_final: 0.6989 (t0)
REVERT: E  335 ARG cc_start: 0.8503 (mtm-85) cc_final: 0.8133 (mtt-85)
REVERT: D  215 GLU cc_start: 0.7877 (pm20) cc_final: 0.7528 (pm20)
REVERT: D  310 ASP cc_start: 0.8262 (t0) cc_final: 0.7756 (t0)
REVERT: C   54 LEU cc_start: 0.8674 (tp) cc_final: 0.8460 (tp)
REVERT: C  285 SER cc_start: 0.9198 (t) cc_final: 0.8742 (p)
REVERT: C  295 ASN cc_start: 0.7868 (t0) cc_final: 0.7642 (t0)
REVERT: C  310 ASP cc_start: 0.8116 (t0) cc_final: 0.7165 (t0)
REVERT: C  335 ARG cc_start: 0.8557 (mtm-85) cc_final: 0.8319 (mtt-85)
REVERT: B  138 GLU cc_start: 0.8411 (pt0) cc_final: 0.8159 (pt0)
REVERT: B  310 ASP cc_start: 0.8236 (t0) cc_final: 0.7802 (t0)
REVERT: B  315 LYS cc_start: 0.9111 (mtpp) cc_final: 0.8859 (mtmt)
REVERT: A  295 ASN cc_start: 0.7863 (t0) cc_final: 0.7597 (t0)
REVERT: A  310 ASP cc_start: 0.8126 (t0) cc_final: 0.7343 (t0)
REVERT: A  335 ARG cc_start: 0.8295 (mtm-85) cc_final: 0.8089 (mtt-85)
REVERT: A  343 SER cc_start: 0.9027 (m) cc_final: 0.8691 (p)
  outliers start: 6
  outliers final: 1
  residues processed: 479
  average time/residue: 0.3428
  time to fit residues: 216.5904
Evaluate side-chains
  242 residues out of total 1398 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 241
  time to evaluate  : 2.364 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  184 VAL
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 168
   random chunks:
   chunk 141 optimal weight:   20.0000
   chunk 127 optimal weight:    7.9990
   chunk 70 optimal weight:    5.9990
   chunk 43 optimal weight:    8.9990
   chunk 85 optimal weight:   20.0000
   chunk 68 optimal weight:   10.0000
   chunk 131 optimal weight:    6.9990
   chunk 50 optimal weight:    5.9990
   chunk 80 optimal weight:    0.9980
   chunk 98 optimal weight:   10.0000
   chunk 152 optimal weight:   10.0000
   overall best weight:    5.5988

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

Flipped N/Q/H residues before XYZ refinement:
F  42 GLN
F 200 ASN
F 248 GLN
E 200 ASN
D  42 GLN
D 200 ASN
D 248 GLN
C 161 HIS
C 200 ASN
B  42 GLN
B 200 ASN
B 337 HIS
A 200 ASN

Total number of N/Q/H flips: 13

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3370 r_free = 0.3370 target = 0.125369 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3080 r_free = 0.3080 target = 0.103414 restraints weight = 20566.225|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3115 r_free = 0.3115 target = 0.105869 restraints weight = 14248.407|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3135 r_free = 0.3135 target = 0.107406 restraints weight = 11117.891|
|-----------------------------------------------------------------------------|
r_work (final): 0.3116
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3116
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3116 r_free = 0.3116    target_work(ls_wunit_k1) = 0.106         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2844 r_free = 0.2844    target_work(ls_wunit_k1) = 0.088         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       49 |
|-----------------------------------------------------------------------------|
r_final: 0.2844
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8656
moved from start:          0.3021

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.034  13656  Z= 0.232
  Angle     :  0.805  10.808  18486  Z= 0.414
  Chirality :  0.050   0.208   2058
  Planarity :  0.006   0.042   2370
  Dihedral  :  6.682  56.059   1903
  Min Nonbonded Distance : 2.449

Molprobity Statistics.
  All-atom Clashscore : 6.30
  Ramachandran Plot:
    Outliers :  1.05 %
    Allowed  : 14.85 %
    Favored  : 84.09 %
  Rotamer:
    Outliers :  3.29 %
    Allowed  : 13.88 %
    Favored  : 82.83 %
  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: -4.73 (0.16), residues: 1710
  helix: -2.59 (0.20), residues: 438
  sheet: -2.32 (0.27), residues: 342
  loop : -3.89 (0.15), residues: 930

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP F 198 
 HIS   0.008   0.003   HIS E 323 
 PHE   0.014   0.002   PHE D 316 
 TYR   0.021   0.002   TYR C 296 
 ARG   0.004   0.001   ARG B 139 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05357 (  348)
  hydrogen bonds       : angle       5.61828 (  972)
  covalent geometry    : bond        0.00557 (13656)
  covalent geometry    : angle       0.80543 (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
  288 residues out of total 1398 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 46
    poor density    : 242
  time to evaluate  : 1.477 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: F  317 ASP cc_start: 0.8352 (m-30) cc_final: 0.8083 (m-30)
REVERT: F  339 ARG cc_start: 0.7435 (mtt-85) cc_final: 0.6728 (ttp-170)
REVERT: E   47 PHE cc_start: 0.7653 (t80) cc_final: 0.7343 (t80)
REVERT: E  140 GLU cc_start: 0.7678 (tt0) cc_final: 0.7418 (mt-10)
REVERT: E  221 THR cc_start: 0.9191 (t) cc_final: 0.8927 (m)
REVERT: E  295 ASN cc_start: 0.8381 (t0) cc_final: 0.8105 (t0)
REVERT: E  297 ARG cc_start: 0.7772 (mpp-170) cc_final: 0.7270 (ptt90)
REVERT: E  310 ASP cc_start: 0.8659 (t0) cc_final: 0.7825 (t0)
REVERT: E  335 ARG cc_start: 0.8639 (mtm-85) cc_final: 0.8333 (mtt-85)
REVERT: D  215 GLU cc_start: 0.9299 (pm20) cc_final: 0.9056 (pm20)
REVERT: D  283 ILE cc_start: 0.9330 (OUTLIER) cc_final: 0.9029 (mt)
REVERT: D  328 GLU cc_start: 0.8575 (mp0) cc_final: 0.8333 (mp0)
REVERT: C  295 ASN cc_start: 0.8360 (t0) cc_final: 0.7968 (t0)
REVERT: C  297 ARG cc_start: 0.7710 (mmt180) cc_final: 0.6726 (ppt170)
REVERT: C  310 ASP cc_start: 0.8798 (t0) cc_final: 0.7577 (t0)
REVERT: B  283 ILE cc_start: 0.9364 (OUTLIER) cc_final: 0.9158 (mt)
REVERT: A  140 GLU cc_start: 0.7692 (tt0) cc_final: 0.7473 (mt-10)
REVERT: A  295 ASN cc_start: 0.8303 (t0) cc_final: 0.7770 (t0)
REVERT: A  310 ASP cc_start: 0.8684 (t0) cc_final: 0.7768 (t0)
REVERT: A  339 ARG cc_start: 0.4339 (ttt180) cc_final: 0.3925 (ttt180)
REVERT: A  343 SER cc_start: 0.9031 (m) cc_final: 0.8541 (p)
  outliers start: 46
  outliers final: 23
  residues processed: 278
  average time/residue: 0.2831
  time to fit residues: 110.5604
Evaluate side-chains
  196 residues out of total 1398 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 171
  time to evaluate  : 1.556 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain F residue  147 THR
Chi-restraints excluded: chain F residue  148 VAL
Chi-restraints excluded: chain F residue  184 VAL
Chi-restraints excluded: chain E residue   96 THR
Chi-restraints excluded: chain E residue  148 VAL
Chi-restraints excluded: chain E residue  227 THR
Chi-restraints excluded: chain D residue  148 VAL
Chi-restraints excluded: chain D residue  184 VAL
Chi-restraints excluded: chain D residue  241 CYS
Chi-restraints excluded: chain D residue  283 ILE
Chi-restraints excluded: chain C residue   96 THR
Chi-restraints excluded: chain C residue  147 THR
Chi-restraints excluded: chain C residue  148 VAL
Chi-restraints excluded: chain C residue  227 THR
Chi-restraints excluded: chain B residue  148 VAL
Chi-restraints excluded: chain B residue  169 LEU
Chi-restraints excluded: chain B residue  184 VAL
Chi-restraints excluded: chain B residue  227 THR
Chi-restraints excluded: chain B residue  283 ILE
Chi-restraints excluded: chain A residue   54 LEU
Chi-restraints excluded: chain A residue   90 LEU
Chi-restraints excluded: chain A residue   96 THR
Chi-restraints excluded: chain A residue  148 VAL
Chi-restraints excluded: chain A residue  184 VAL
Chi-restraints excluded: chain A residue  227 THR
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 168
   random chunks:
   chunk 112 optimal weight:   10.0000
   chunk 53 optimal weight:    8.9990
   chunk 2 optimal weight:    8.9990
   chunk 87 optimal weight:   10.0000
   chunk 119 optimal weight:    9.9990
   chunk 138 optimal weight:    8.9990
   chunk 86 optimal weight:    6.9990
   chunk 1 optimal weight:    9.9990
   chunk 54 optimal weight:    0.0870
   chunk 97 optimal weight:    0.6980
   chunk 98 optimal weight:    5.9990
   overall best weight:    4.5564

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

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

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3077 r_free = 0.3077 target = 0.103668 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.2785 r_free = 0.2785 target = 0.083957 restraints weight = 22929.130|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.2815 r_free = 0.2815 target = 0.085911 restraints weight = 15521.962|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.2836 r_free = 0.2836 target = 0.087220 restraints weight = 12077.743|
|-----------------------------------------------------------------------------|
r_work (final): 0.2833
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2832
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2832 r_free = 0.2832    target_work(ls_wunit_k1) = 0.087         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       49 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2789 r_free = 0.2789    target_work(ls_wunit_k1) = 0.084         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:      173 |
|-----------------------------------------------------------------------------|
r_final: 0.2789
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8669
moved from start:          0.3552

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= 0.194
  Angle     :  0.750  10.474  18486  Z= 0.381
  Chirality :  0.048   0.165   2058
  Planarity :  0.006   0.041   2370
  Dihedral  :  6.449  55.286   1903
  Min Nonbonded Distance : 2.493

Molprobity Statistics.
  All-atom Clashscore : 5.73
  Ramachandran Plot:
    Outliers :  1.05 %
    Allowed  : 14.15 %
    Favored  : 84.80 %
  Rotamer:
    Outliers :  4.43 %
    Allowed  : 14.38 %
    Favored  : 81.19 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 7.14 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.37 %

Rama-Z (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: -4.42 (0.17), residues: 1710
  helix: -2.10 (0.22), residues: 438
  sheet: -2.11 (0.27), residues: 342
  loop : -3.84 (0.15), residues: 930

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP F 198 
 HIS   0.011   0.002   HIS B 323 
 PHE   0.013   0.002   PHE D 316 
 TYR   0.018   0.002   TYR C 296 
 ARG   0.004   0.000   ARG C 335 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04705 (  348)
  hydrogen bonds       : angle       5.44347 (  972)
  covalent geometry    : bond        0.00469 (13656)
  covalent geometry    : angle       0.74973 (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
  251 residues out of total 1398 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 62
    poor density    : 189
  time to evaluate  : 1.374 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: F  317 ASP cc_start: 0.8367 (m-30) cc_final: 0.8052 (m-30)
REVERT: F  339 ARG cc_start: 0.7427 (mtt-85) cc_final: 0.6472 (ttp-170)
REVERT: F  342 VAL cc_start: 0.9592 (t) cc_final: 0.9366 (p)
REVERT: E   47 PHE cc_start: 0.7640 (t80) cc_final: 0.7376 (t80)
REVERT: E  140 GLU cc_start: 0.7484 (tt0) cc_final: 0.7179 (mt-10)
REVERT: E  283 ILE cc_start: 0.9490 (OUTLIER) cc_final: 0.9284 (mt)
REVERT: E  295 ASN cc_start: 0.8448 (t0) cc_final: 0.7989 (t0)
REVERT: E  297 ARG cc_start: 0.7811 (mpp-170) cc_final: 0.7077 (ppt170)
REVERT: E  335 ARG cc_start: 0.8608 (mtm-85) cc_final: 0.8369 (mtt-85)
REVERT: D  169 LEU cc_start: 0.9479 (OUTLIER) cc_final: 0.9174 (tm)
REVERT: D  215 GLU cc_start: 0.9184 (pm20) cc_final: 0.8906 (pm20)
REVERT: D  283 ILE cc_start: 0.9232 (OUTLIER) cc_final: 0.8950 (mt)
REVERT: D  336 GLU cc_start: 0.6894 (OUTLIER) cc_final: 0.6530 (mt-10)
REVERT: C  287 LEU cc_start: 0.9183 (OUTLIER) cc_final: 0.8858 (mt)
REVERT: C  295 ASN cc_start: 0.8448 (t0) cc_final: 0.7867 (t0)
REVERT: B  283 ILE cc_start: 0.9393 (OUTLIER) cc_final: 0.9137 (mt)
REVERT: B  336 GLU cc_start: 0.7029 (OUTLIER) cc_final: 0.6667 (mt-10)
REVERT: A  287 LEU cc_start: 0.9158 (OUTLIER) cc_final: 0.8844 (mt)
REVERT: A  295 ASN cc_start: 0.8332 (t0) cc_final: 0.8092 (t0)
REVERT: A  297 ARG cc_start: 0.7677 (mpp-170) cc_final: 0.6820 (ppt170)
REVERT: A  339 ARG cc_start: 0.4269 (ttt180) cc_final: 0.2654 (ttt-90)
REVERT: A  343 SER cc_start: 0.8914 (m) cc_final: 0.8474 (p)
  outliers start: 62
  outliers final: 30
  residues processed: 237
  average time/residue: 0.2723
  time to fit residues: 91.3774
Evaluate side-chains
  199 residues out of total 1398 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 38
    poor density    : 161
  time to evaluate  : 1.528 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain F residue   86 SER
Chi-restraints excluded: chain F residue  147 THR
Chi-restraints excluded: chain F residue  184 VAL
Chi-restraints excluded: chain F residue  197 CYS
Chi-restraints excluded: chain E residue  148 VAL
Chi-restraints excluded: chain E residue  227 THR
Chi-restraints excluded: chain E residue  283 ILE
Chi-restraints excluded: chain D residue  148 VAL
Chi-restraints excluded: chain D residue  169 LEU
Chi-restraints excluded: chain D residue  184 VAL
Chi-restraints excluded: chain D residue  197 CYS
Chi-restraints excluded: chain D residue  241 CYS
Chi-restraints excluded: chain D residue  283 ILE
Chi-restraints excluded: chain D residue  324 TYR
Chi-restraints excluded: chain D residue  336 GLU
Chi-restraints excluded: chain C residue  147 THR
Chi-restraints excluded: chain C residue  148 VAL
Chi-restraints excluded: chain C residue  182 ILE
Chi-restraints excluded: chain C residue  227 THR
Chi-restraints excluded: chain C residue  241 CYS
Chi-restraints excluded: chain C residue  287 LEU
Chi-restraints excluded: chain B residue   86 SER
Chi-restraints excluded: chain B residue  148 VAL
Chi-restraints excluded: chain B residue  184 VAL
Chi-restraints excluded: chain B residue  197 CYS
Chi-restraints excluded: chain B residue  215 GLU
Chi-restraints excluded: chain B residue  227 THR
Chi-restraints excluded: chain B residue  283 ILE
Chi-restraints excluded: chain B residue  336 GLU
Chi-restraints excluded: chain A residue   54 LEU
Chi-restraints excluded: chain A residue   90 LEU
Chi-restraints excluded: chain A residue   96 THR
Chi-restraints excluded: chain A residue  148 VAL
Chi-restraints excluded: chain A residue  181 THR
Chi-restraints excluded: chain A residue  184 VAL
Chi-restraints excluded: chain A residue  227 THR
Chi-restraints excluded: chain A residue  241 CYS
Chi-restraints excluded: chain A residue  287 LEU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 168
   random chunks:
   chunk 44 optimal weight:    7.9990
   chunk 49 optimal weight:    6.9990
   chunk 66 optimal weight:    6.9990
   chunk 104 optimal weight:    4.9990
   chunk 82 optimal weight:    0.0170
   chunk 24 optimal weight:    6.9990
   chunk 70 optimal weight:   10.0000
   chunk 30 optimal weight:    5.9990
   chunk 153 optimal weight:    1.9990
   chunk 122 optimal weight:    9.9990
   chunk 11 optimal weight:    6.9990
   overall best weight:    4.0026

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

Flipped N/Q/H residues before XYZ refinement:
E 107 HIS
D  42 GLN
B 248 GLN
A 107 HIS

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3110 r_free = 0.3110 target = 0.106322 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.2827 r_free = 0.2827 target = 0.087080 restraints weight = 22420.861|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.2860 r_free = 0.2860 target = 0.089172 restraints weight = 14429.524|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.2882 r_free = 0.2882 target = 0.090606 restraints weight = 10874.335|
|-----------------------------------------------------------------------------|
r_work (final): 0.2863
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2814
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2814 r_free = 0.2814    target_work(ls_wunit_k1) = 0.087         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:      173 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2806 r_free = 0.2806    target_work(ls_wunit_k1) = 0.086         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:      210 |
|-----------------------------------------------------------------------------|
r_final: 0.2806
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8662
moved from start:          0.3862

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.039  13656  Z= 0.175
  Angle     :  0.722  10.656  18486  Z= 0.368
  Chirality :  0.047   0.174   2058
  Planarity :  0.005   0.037   2370
  Dihedral  :  6.284  56.071   1903
  Min Nonbonded Distance : 2.505

Molprobity Statistics.
  All-atom Clashscore : 5.48
  Ramachandran Plot:
    Outliers :  1.05 %
    Allowed  : 14.15 %
    Favored  : 84.80 %
  Rotamer:
    Outliers :  5.01 %
    Allowed  : 14.59 %
    Favored  : 80.40 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 7.14 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.37 %

Rama-Z (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: -4.03 (0.18), residues: 1710
  helix: -1.55 (0.24), residues: 414
  sheet: -1.93 (0.28), residues: 354
  loop : -3.66 (0.16), residues: 942

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP F 198 
 HIS   0.013   0.002   HIS B 323 
 PHE   0.011   0.001   PHE B 330 
 TYR   0.016   0.001   TYR F  48 
 ARG   0.003   0.000   ARG D 139 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04346 (  348)
  hydrogen bonds       : angle       5.26732 (  972)
  covalent geometry    : bond        0.00421 (13656)
  covalent geometry    : angle       0.72167 (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
  249 residues out of total 1398 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 70
    poor density    : 179
  time to evaluate  : 1.381 
Fit side-chains
   revert: symmetry clash
REVERT: F  317 ASP cc_start: 0.8401 (m-30) cc_final: 0.8044 (m-30)
REVERT: F  324 TYR cc_start: 0.8475 (OUTLIER) cc_final: 0.8004 (t80)
REVERT: F  339 ARG cc_start: 0.7416 (mtt-85) cc_final: 0.6407 (ttp-170)
REVERT: F  342 VAL cc_start: 0.9607 (t) cc_final: 0.9400 (p)
REVERT: E   94 SER cc_start: 0.8080 (m) cc_final: 0.7673 (p)
REVERT: E  123 LEU cc_start: 0.8135 (mm) cc_final: 0.7729 (pp)
REVERT: E  283 ILE cc_start: 0.9482 (OUTLIER) cc_final: 0.9273 (mt)
REVERT: E  295 ASN cc_start: 0.8501 (t0) cc_final: 0.8028 (t0)
REVERT: E  297 ARG cc_start: 0.7837 (mpp-170) cc_final: 0.7115 (ppt170)
REVERT: E  305 ASP cc_start: 0.8177 (p0) cc_final: 0.7942 (p0)
REVERT: E  310 ASP cc_start: 0.8897 (t0) cc_final: 0.8031 (t0)
REVERT: E  335 ARG cc_start: 0.8629 (mtm-85) cc_final: 0.8376 (mtt-85)
REVERT: D  169 LEU cc_start: 0.9474 (OUTLIER) cc_final: 0.9192 (tm)
REVERT: D  283 ILE cc_start: 0.9205 (OUTLIER) cc_final: 0.8932 (mt)
REVERT: C  295 ASN cc_start: 0.8482 (t0) cc_final: 0.7889 (t0)
REVERT: C  310 ASP cc_start: 0.8948 (t0) cc_final: 0.7914 (t0)
REVERT: B  336 GLU cc_start: 0.6967 (OUTLIER) cc_final: 0.6704 (mt-10)
REVERT: A  287 LEU cc_start: 0.9112 (OUTLIER) cc_final: 0.8792 (mt)
REVERT: A  295 ASN cc_start: 0.8440 (t0) cc_final: 0.8108 (t0)
REVERT: A  297 ARG cc_start: 0.7656 (mpp-170) cc_final: 0.6847 (ppt170)
REVERT: A  339 ARG cc_start: 0.3788 (ttt180) cc_final: 0.2660 (ttt180)
REVERT: A  343 SER cc_start: 0.8851 (m) cc_final: 0.8469 (p)
  outliers start: 70
  outliers final: 39
  residues processed: 234
  average time/residue: 0.2608
  time to fit residues: 88.2631
Evaluate side-chains
  198 residues out of total 1398 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 45
    poor density    : 153
  time to evaluate  : 1.497 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain F residue   86 SER
Chi-restraints excluded: chain F residue  147 THR
Chi-restraints excluded: chain F residue  148 VAL
Chi-restraints excluded: chain F residue  169 LEU
Chi-restraints excluded: chain F residue  184 VAL
Chi-restraints excluded: chain F residue  197 CYS
Chi-restraints excluded: chain F residue  241 CYS
Chi-restraints excluded: chain F residue  324 TYR
Chi-restraints excluded: chain E residue  148 VAL
Chi-restraints excluded: chain E residue  227 THR
Chi-restraints excluded: chain E residue  283 ILE
Chi-restraints excluded: chain E residue  324 TYR
Chi-restraints excluded: chain D residue  148 VAL
Chi-restraints excluded: chain D residue  169 LEU
Chi-restraints excluded: chain D residue  181 THR
Chi-restraints excluded: chain D residue  184 VAL
Chi-restraints excluded: chain D residue  241 CYS
Chi-restraints excluded: chain D residue  283 ILE
Chi-restraints excluded: chain D residue  324 TYR
Chi-restraints excluded: chain C residue   96 THR
Chi-restraints excluded: chain C residue  147 THR
Chi-restraints excluded: chain C residue  148 VAL
Chi-restraints excluded: chain C residue  182 ILE
Chi-restraints excluded: chain C residue  227 THR
Chi-restraints excluded: chain C residue  241 CYS
Chi-restraints excluded: chain C residue  333 ASN
Chi-restraints excluded: chain B residue   61 LEU
Chi-restraints excluded: chain B residue   86 SER
Chi-restraints excluded: chain B residue  148 VAL
Chi-restraints excluded: chain B residue  169 LEU
Chi-restraints excluded: chain B residue  184 VAL
Chi-restraints excluded: chain B residue  197 CYS
Chi-restraints excluded: chain B residue  215 GLU
Chi-restraints excluded: chain B residue  227 THR
Chi-restraints excluded: chain B residue  324 TYR
Chi-restraints excluded: chain B residue  336 GLU
Chi-restraints excluded: chain A residue   54 LEU
Chi-restraints excluded: chain A residue   90 LEU
Chi-restraints excluded: chain A residue  147 THR
Chi-restraints excluded: chain A residue  148 VAL
Chi-restraints excluded: chain A residue  169 LEU
Chi-restraints excluded: chain A residue  184 VAL
Chi-restraints excluded: chain A residue  227 THR
Chi-restraints excluded: chain A residue  241 CYS
Chi-restraints excluded: chain A residue  287 LEU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 168
   random chunks:
   chunk 8 optimal weight:    6.9990
   chunk 148 optimal weight:    1.9990
   chunk 47 optimal weight:    9.9990
   chunk 160 optimal weight:    6.9990
   chunk 164 optimal weight:    8.9990
   chunk 16 optimal weight:    6.9990
   chunk 81 optimal weight:    0.0470
   chunk 143 optimal weight:    0.8980
   chunk 35 optimal weight:   20.0000
   chunk 118 optimal weight:    8.9990
   chunk 122 optimal weight:    9.9990
   overall best weight:    3.3884

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

Flipped N/Q/H residues before XYZ refinement:
F  42 GLN
D  42 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3055 r_free = 0.3055 target = 0.102737 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.2777 r_free = 0.2777 target = 0.084195 restraints weight = 23027.178|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.2810 r_free = 0.2810 target = 0.086301 restraints weight = 14440.587|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.2832 r_free = 0.2832 target = 0.087727 restraints weight = 10736.467|
|-----------------------------------------------------------------------------|
r_work (final): 0.2823
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2823
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2823 r_free = 0.2823    target_work(ls_wunit_k1) = 0.087         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:      210 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2819 r_free = 0.2819    target_work(ls_wunit_k1) = 0.087         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:      243 |
|-----------------------------------------------------------------------------|
r_final: 0.2819
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8633
moved from start:          0.4068

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.033  13656  Z= 0.156
  Angle     :  0.704  10.567  18486  Z= 0.356
  Chirality :  0.046   0.215   2058
  Planarity :  0.005   0.038   2370
  Dihedral  :  6.173  59.765   1903
  Min Nonbonded Distance : 2.498

Molprobity Statistics.
  All-atom Clashscore : 5.22
  Ramachandran Plot:
    Outliers :  1.05 %
    Allowed  : 13.63 %
    Favored  : 85.32 %
  Rotamer:
    Outliers :  4.22 %
    Allowed  : 15.31 %
    Favored  : 80.47 %
  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: -1.33 (0.25), residues: 408
  sheet: -1.69 (0.28), residues: 354
  loop : -3.54 (0.16), residues: 948

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP D 228 
 HIS   0.012   0.002   HIS B 323 
 PHE   0.014   0.001   PHE F 330 
 TYR   0.015   0.001   TYR C 296 
 ARG   0.003   0.000   ARG B 139 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03944 (  348)
  hydrogen bonds       : angle       5.11348 (  972)
  covalent geometry    : bond        0.00374 (13656)
  covalent geometry    : angle       0.70383 (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
  233 residues out of total 1398 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 59
    poor density    : 174
  time to evaluate  : 1.553 
Fit side-chains
   revert: symmetry clash
REVERT: F  317 ASP cc_start: 0.8349 (m-30) cc_final: 0.7992 (m-30)
REVERT: F  324 TYR cc_start: 0.8402 (OUTLIER) cc_final: 0.8035 (t80)
REVERT: F  342 VAL cc_start: 0.9605 (t) cc_final: 0.9374 (p)
REVERT: E   94 SER cc_start: 0.8073 (m) cc_final: 0.7683 (p)
REVERT: E  283 ILE cc_start: 0.9503 (OUTLIER) cc_final: 0.9274 (mt)
REVERT: E  295 ASN cc_start: 0.8464 (t0) cc_final: 0.7762 (t0)
REVERT: D  169 LEU cc_start: 0.9473 (OUTLIER) cc_final: 0.9161 (tm)
REVERT: D  324 TYR cc_start: 0.8416 (OUTLIER) cc_final: 0.7961 (t80)
REVERT: D  336 GLU cc_start: 0.7065 (OUTLIER) cc_final: 0.6698 (mt-10)
REVERT: C   94 SER cc_start: 0.7926 (m) cc_final: 0.7556 (p)
REVERT: C  287 LEU cc_start: 0.9181 (OUTLIER) cc_final: 0.8895 (mt)
REVERT: C  295 ASN cc_start: 0.8445 (t0) cc_final: 0.7809 (t0)
REVERT: C  324 TYR cc_start: 0.8968 (OUTLIER) cc_final: 0.7546 (t80)
REVERT: B  324 TYR cc_start: 0.8506 (OUTLIER) cc_final: 0.8248 (t80)
REVERT: B  336 GLU cc_start: 0.7080 (OUTLIER) cc_final: 0.6852 (mt-10)
REVERT: A   87 THR cc_start: 0.9157 (p) cc_final: 0.8898 (t)
REVERT: A   94 SER cc_start: 0.7674 (m) cc_final: 0.7120 (p)
REVERT: A  215 GLU cc_start: 0.9052 (pt0) cc_final: 0.8776 (pt0)
REVERT: A  287 LEU cc_start: 0.9100 (OUTLIER) cc_final: 0.8786 (mt)
REVERT: A  295 ASN cc_start: 0.8411 (t0) cc_final: 0.7599 (p0)
REVERT: A  297 ARG cc_start: 0.7790 (mpp-170) cc_final: 0.6922 (ppt170)
REVERT: A  339 ARG cc_start: 0.3355 (ttt180) cc_final: 0.2951 (ttt180)
REVERT: A  343 SER cc_start: 0.8848 (m) cc_final: 0.8494 (p)
  outliers start: 59
  outliers final: 37
  residues processed: 221
  average time/residue: 0.3078
  time to fit residues: 99.1946
Evaluate side-chains
  203 residues out of total 1398 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 47
    poor density    : 156
  time to evaluate  : 1.456 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain F residue   86 SER
Chi-restraints excluded: chain F residue   89 GLU
Chi-restraints excluded: chain F residue  148 VAL
Chi-restraints excluded: chain F residue  169 LEU
Chi-restraints excluded: chain F residue  181 THR
Chi-restraints excluded: chain F residue  184 VAL
Chi-restraints excluded: chain F residue  197 CYS
Chi-restraints excluded: chain F residue  324 TYR
Chi-restraints excluded: chain E residue  227 THR
Chi-restraints excluded: chain E residue  283 ILE
Chi-restraints excluded: chain E residue  324 TYR
Chi-restraints excluded: chain E residue  333 ASN
Chi-restraints excluded: chain E residue  340 LYS
Chi-restraints excluded: chain D residue  148 VAL
Chi-restraints excluded: chain D residue  169 LEU
Chi-restraints excluded: chain D residue  181 THR
Chi-restraints excluded: chain D residue  184 VAL
Chi-restraints excluded: chain D residue  241 CYS
Chi-restraints excluded: chain D residue  324 TYR
Chi-restraints excluded: chain D residue  336 GLU
Chi-restraints excluded: chain C residue   96 THR
Chi-restraints excluded: chain C residue  147 THR
Chi-restraints excluded: chain C residue  148 VAL
Chi-restraints excluded: chain C residue  182 ILE
Chi-restraints excluded: chain C residue  227 THR
Chi-restraints excluded: chain C residue  241 CYS
Chi-restraints excluded: chain C residue  287 LEU
Chi-restraints excluded: chain C residue  324 TYR
Chi-restraints excluded: chain C residue  333 ASN
Chi-restraints excluded: chain B residue   50 THR
Chi-restraints excluded: chain B residue   61 LEU
Chi-restraints excluded: chain B residue   86 SER
Chi-restraints excluded: chain B residue  148 VAL
Chi-restraints excluded: chain B residue  184 VAL
Chi-restraints excluded: chain B residue  215 GLU
Chi-restraints excluded: chain B residue  324 TYR
Chi-restraints excluded: chain B residue  336 GLU
Chi-restraints excluded: chain A residue   54 LEU
Chi-restraints excluded: chain A residue   61 LEU
Chi-restraints excluded: chain A residue   90 LEU
Chi-restraints excluded: chain A residue  147 THR
Chi-restraints excluded: chain A residue  148 VAL
Chi-restraints excluded: chain A residue  169 LEU
Chi-restraints excluded: chain A residue  227 THR
Chi-restraints excluded: chain A residue  241 CYS
Chi-restraints excluded: chain A residue  287 LEU
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:    0.7980
   chunk 29 optimal weight:   20.0000
   chunk 102 optimal weight:    9.9990
   chunk 46 optimal weight:    3.9990
   chunk 16 optimal weight:    8.9990
   chunk 34 optimal weight:    8.9990
   chunk 51 optimal weight:    6.9990
   chunk 43 optimal weight:    8.9990
   chunk 115 optimal weight:   40.0000
   chunk 150 optimal weight:   10.0000
   chunk 52 optimal weight:   10.0000
   overall best weight:    5.9588

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

Flipped N/Q/H residues before XYZ refinement:
F  42 GLN
F 248 GLN
D 248 GLN
B 248 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3035 r_free = 0.3035 target = 0.101139 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.2752 r_free = 0.2752 target = 0.082560 restraints weight = 23280.647|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.2785 r_free = 0.2785 target = 0.084583 restraints weight = 14818.658|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 22)----------------|
| r_work = 0.2806 r_free = 0.2806 target = 0.085906 restraints weight = 11114.036|
|-----------------------------------------------------------------------------|
r_work (final): 0.2783
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2783
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2783 r_free = 0.2783    target_work(ls_wunit_k1) = 0.084         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:      243 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2777 r_free = 0.2777    target_work(ls_wunit_k1) = 0.084         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:      252 |
|-----------------------------------------------------------------------------|
r_final: 0.2777
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8701
moved from start:          0.4276

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.042  13656  Z= 0.239
  Angle     :  0.786  11.264  18486  Z= 0.401
  Chirality :  0.049   0.216   2058
  Planarity :  0.005   0.038   2370
  Dihedral  :  6.402  57.651   1902
  Min Nonbonded Distance : 2.509

Molprobity Statistics.
  All-atom Clashscore : 6.25
  Ramachandran Plot:
    Outliers :  0.88 %
    Allowed  : 15.44 %
    Favored  : 83.68 %
  Rotamer:
    Outliers :  5.22 %
    Allowed  : 14.59 %
    Favored  : 80.19 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 7.14 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.37 %

Rama-Z (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: -3.92 (0.18), residues: 1710
  helix: -1.76 (0.23), residues: 444
  sheet: -1.70 (0.27), residues: 390
  loop : -3.61 (0.17), residues: 876

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP F 198 
 HIS   0.010   0.002   HIS B 323 
 PHE   0.014   0.002   PHE F 330 
 TYR   0.014   0.002   TYR C 296 
 ARG   0.008   0.001   ARG E 335 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04838 (  348)
  hydrogen bonds       : angle       5.35122 (  972)
  covalent geometry    : bond        0.00578 (13656)
  covalent geometry    : angle       0.78555 (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
  242 residues out of total 1398 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 73
    poor density    : 169
  time to evaluate  : 1.480 
Fit side-chains
REVERT: F  317 ASP cc_start: 0.8391 (m-30) cc_final: 0.8053 (m-30)
REVERT: F  324 TYR cc_start: 0.8572 (OUTLIER) cc_final: 0.8055 (t80)
REVERT: F  336 GLU cc_start: 0.7450 (OUTLIER) cc_final: 0.7121 (mt-10)
REVERT: F  342 VAL cc_start: 0.9612 (t) cc_final: 0.9405 (p)
REVERT: E   47 PHE cc_start: 0.7853 (t80) cc_final: 0.7533 (t80)
REVERT: E  295 ASN cc_start: 0.8490 (t0) cc_final: 0.7770 (t0)
REVERT: D  169 LEU cc_start: 0.9461 (OUTLIER) cc_final: 0.9162 (tm)
REVERT: D  336 GLU cc_start: 0.7210 (OUTLIER) cc_final: 0.6849 (mt-10)
REVERT: C   94 SER cc_start: 0.8267 (m) cc_final: 0.8029 (p)
REVERT: C  287 LEU cc_start: 0.9186 (OUTLIER) cc_final: 0.8869 (mt)
REVERT: C  295 ASN cc_start: 0.8511 (t0) cc_final: 0.7844 (t0)
REVERT: C  324 TYR cc_start: 0.9091 (OUTLIER) cc_final: 0.7683 (t80)
REVERT: B  117 GLU cc_start: 0.7439 (mp0) cc_final: 0.7080 (mm-30)
REVERT: B  336 GLU cc_start: 0.7286 (OUTLIER) cc_final: 0.7086 (mt-10)
REVERT: A   87 THR cc_start: 0.9204 (p) cc_final: 0.8967 (t)
REVERT: A   94 SER cc_start: 0.7933 (m) cc_final: 0.7416 (p)
REVERT: A  215 GLU cc_start: 0.9102 (pt0) cc_final: 0.8850 (pt0)
REVERT: A  287 LEU cc_start: 0.9161 (OUTLIER) cc_final: 0.8842 (mt)
REVERT: A  295 ASN cc_start: 0.8438 (t0) cc_final: 0.8141 (t0)
REVERT: A  297 ARG cc_start: 0.7872 (mpp-170) cc_final: 0.7053 (ppt170)
REVERT: A  339 ARG cc_start: 0.3364 (ttt180) cc_final: 0.2907 (ttt180)
REVERT: A  343 SER cc_start: 0.8880 (m) cc_final: 0.8457 (p)
  outliers start: 73
  outliers final: 46
  residues processed: 222
  average time/residue: 0.2754
  time to fit residues: 89.3016
Evaluate side-chains
  213 residues out of total 1398 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 54
    poor density    : 159
  time to evaluate  : 1.599 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain F residue   86 SER
Chi-restraints excluded: chain F residue  148 VAL
Chi-restraints excluded: chain F residue  169 LEU
Chi-restraints excluded: chain F residue  184 VAL
Chi-restraints excluded: chain F residue  197 CYS
Chi-restraints excluded: chain F residue  324 TYR
Chi-restraints excluded: chain F residue  336 GLU
Chi-restraints excluded: chain E residue  148 VAL
Chi-restraints excluded: chain E residue  182 ILE
Chi-restraints excluded: chain E residue  227 THR
Chi-restraints excluded: chain E residue  238 GLU
Chi-restraints excluded: chain E residue  283 ILE
Chi-restraints excluded: chain E residue  324 TYR
Chi-restraints excluded: chain E residue  333 ASN
Chi-restraints excluded: chain E residue  340 LYS
Chi-restraints excluded: chain D residue  148 VAL
Chi-restraints excluded: chain D residue  169 LEU
Chi-restraints excluded: chain D residue  181 THR
Chi-restraints excluded: chain D residue  184 VAL
Chi-restraints excluded: chain D residue  197 CYS
Chi-restraints excluded: chain D residue  215 GLU
Chi-restraints excluded: chain D residue  241 CYS
Chi-restraints excluded: chain D residue  283 ILE
Chi-restraints excluded: chain D residue  324 TYR
Chi-restraints excluded: chain D residue  336 GLU
Chi-restraints excluded: chain C residue   54 LEU
Chi-restraints excluded: chain C residue   96 THR
Chi-restraints excluded: chain C residue  147 THR
Chi-restraints excluded: chain C residue  148 VAL
Chi-restraints excluded: chain C residue  182 ILE
Chi-restraints excluded: chain C residue  227 THR
Chi-restraints excluded: chain C residue  241 CYS
Chi-restraints excluded: chain C residue  287 LEU
Chi-restraints excluded: chain C residue  321 VAL
Chi-restraints excluded: chain C residue  324 TYR
Chi-restraints excluded: chain C residue  333 ASN
Chi-restraints excluded: chain B residue   50 THR
Chi-restraints excluded: chain B residue   61 LEU
Chi-restraints excluded: chain B residue   86 SER
Chi-restraints excluded: chain B residue  148 VAL
Chi-restraints excluded: chain B residue  184 VAL
Chi-restraints excluded: chain B residue  197 CYS
Chi-restraints excluded: chain B residue  215 GLU
Chi-restraints excluded: chain B residue  227 THR
Chi-restraints excluded: chain B residue  324 TYR
Chi-restraints excluded: chain B residue  336 GLU
Chi-restraints excluded: chain A residue   54 LEU
Chi-restraints excluded: chain A residue  147 THR
Chi-restraints excluded: chain A residue  148 VAL
Chi-restraints excluded: chain A residue  169 LEU
Chi-restraints excluded: chain A residue  181 THR
Chi-restraints excluded: chain A residue  227 THR
Chi-restraints excluded: chain A residue  241 CYS
Chi-restraints excluded: chain A residue  287 LEU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 168
   random chunks:
   chunk 16 optimal weight:    0.2980
   chunk 150 optimal weight:    7.9990
   chunk 50 optimal weight:    6.9990
   chunk 93 optimal weight:    7.9990
   chunk 18 optimal weight:    6.9990
   chunk 27 optimal weight:    7.9990
   chunk 21 optimal weight:    8.9990
   chunk 92 optimal weight:    7.9990
   chunk 163 optimal weight:    8.9990
   chunk 29 optimal weight:   20.0000
   chunk 76 optimal weight:    5.9990
   overall best weight:    5.6588

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

Flipped N/Q/H residues before XYZ refinement:
F  42 GLN
D  42 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3033 r_free = 0.3033 target = 0.101083 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.2755 r_free = 0.2755 target = 0.082784 restraints weight = 23260.667|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.2788 r_free = 0.2788 target = 0.084812 restraints weight = 14755.934|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.2808 r_free = 0.2808 target = 0.086081 restraints weight = 11038.870|
|-----------------------------------------------------------------------------|
r_work (final): 0.2772
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2773
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2773 r_free = 0.2773    target_work(ls_wunit_k1) = 0.084         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:      252 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2770 r_free = 0.2770    target_work(ls_wunit_k1) = 0.084         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:      276 |
|-----------------------------------------------------------------------------|
r_final: 0.2770
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8696
moved from start:          0.4415

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.046  13656  Z= 0.227
  Angle     :  0.772  10.786  18486  Z= 0.394
  Chirality :  0.049   0.217   2058
  Planarity :  0.005   0.037   2370
  Dihedral  :  6.375  57.275   1902
  Min Nonbonded Distance : 2.494

Molprobity Statistics.
  All-atom Clashscore : 6.45
  Ramachandran Plot:
    Outliers :  0.88 %
    Allowed  : 15.09 %
    Favored  : 84.04 %
  Rotamer:
    Outliers :  4.36 %
    Allowed  : 16.17 %
    Favored  : 79.47 %
  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: -1.44 (0.24), residues: 414
  sheet: -1.61 (0.27), residues: 384
  loop : -3.55 (0.16), residues: 912

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP F 198 
 HIS   0.011   0.002   HIS B 323 
 PHE   0.013   0.002   PHE D 316 
 TYR   0.014   0.001   TYR C 296 
 ARG   0.007   0.000   ARG E 335 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04628 (  348)
  hydrogen bonds       : angle       5.33025 (  972)
  covalent geometry    : bond        0.00549 (13656)
  covalent geometry    : angle       0.77226 (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
  223 residues out of total 1398 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 61
    poor density    : 162
  time to evaluate  : 1.598 
Fit side-chains
   revert: symmetry clash
REVERT: F  317 ASP cc_start: 0.8394 (m-30) cc_final: 0.8021 (m-30)
REVERT: F  324 TYR cc_start: 0.8519 (OUTLIER) cc_final: 0.8091 (t80)
REVERT: F  336 GLU cc_start: 0.7528 (OUTLIER) cc_final: 0.7176 (mt-10)
REVERT: E  295 ASN cc_start: 0.8476 (t0) cc_final: 0.7710 (t0)
REVERT: D  169 LEU cc_start: 0.9467 (OUTLIER) cc_final: 0.9146 (tm)
REVERT: D  336 GLU cc_start: 0.7188 (OUTLIER) cc_final: 0.6849 (mt-10)
REVERT: C  287 LEU cc_start: 0.9133 (OUTLIER) cc_final: 0.8800 (mt)
REVERT: C  295 ASN cc_start: 0.8503 (t0) cc_final: 0.7829 (t0)
REVERT: C  324 TYR cc_start: 0.9082 (OUTLIER) cc_final: 0.7653 (t80)
REVERT: B  324 TYR cc_start: 0.8658 (OUTLIER) cc_final: 0.8179 (t80)
REVERT: A   94 SER cc_start: 0.7906 (m) cc_final: 0.7473 (p)
REVERT: A  295 ASN cc_start: 0.8401 (t0) cc_final: 0.8091 (t0)
REVERT: A  297 ARG cc_start: 0.7874 (mpp-170) cc_final: 0.7074 (ppt170)
REVERT: A  339 ARG cc_start: 0.3496 (ttt180) cc_final: 0.2991 (ttt180)
REVERT: A  343 SER cc_start: 0.8869 (m) cc_final: 0.8465 (p)
  outliers start: 61
  outliers final: 44
  residues processed: 208
  average time/residue: 0.2619
  time to fit residues: 80.4651
Evaluate side-chains
  205 residues out of total 1398 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 51
    poor density    : 154
  time to evaluate  : 1.889 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain F residue   61 LEU
Chi-restraints excluded: chain F residue   86 SER
Chi-restraints excluded: chain F residue  148 VAL
Chi-restraints excluded: chain F residue  169 LEU
Chi-restraints excluded: chain F residue  184 VAL
Chi-restraints excluded: chain F residue  197 CYS
Chi-restraints excluded: chain F residue  324 TYR
Chi-restraints excluded: chain F residue  336 GLU
Chi-restraints excluded: chain E residue  148 VAL
Chi-restraints excluded: chain E residue  182 ILE
Chi-restraints excluded: chain E residue  227 THR
Chi-restraints excluded: chain E residue  238 GLU
Chi-restraints excluded: chain E residue  283 ILE
Chi-restraints excluded: chain E residue  324 TYR
Chi-restraints excluded: chain E residue  340 LYS
Chi-restraints excluded: chain D residue  148 VAL
Chi-restraints excluded: chain D residue  169 LEU
Chi-restraints excluded: chain D residue  181 THR
Chi-restraints excluded: chain D residue  184 VAL
Chi-restraints excluded: chain D residue  197 CYS
Chi-restraints excluded: chain D residue  215 GLU
Chi-restraints excluded: chain D residue  241 CYS
Chi-restraints excluded: chain D residue  283 ILE
Chi-restraints excluded: chain D residue  324 TYR
Chi-restraints excluded: chain D residue  336 GLU
Chi-restraints excluded: chain C residue   54 LEU
Chi-restraints excluded: chain C residue  147 THR
Chi-restraints excluded: chain C residue  148 VAL
Chi-restraints excluded: chain C residue  182 ILE
Chi-restraints excluded: chain C residue  227 THR
Chi-restraints excluded: chain C residue  241 CYS
Chi-restraints excluded: chain C residue  287 LEU
Chi-restraints excluded: chain C residue  321 VAL
Chi-restraints excluded: chain C residue  324 TYR
Chi-restraints excluded: chain C residue  333 ASN
Chi-restraints excluded: chain B residue   50 THR
Chi-restraints excluded: chain B residue   61 LEU
Chi-restraints excluded: chain B residue   86 SER
Chi-restraints excluded: chain B residue  148 VAL
Chi-restraints excluded: chain B residue  184 VAL
Chi-restraints excluded: chain B residue  197 CYS
Chi-restraints excluded: chain B residue  215 GLU
Chi-restraints excluded: chain B residue  227 THR
Chi-restraints excluded: chain B residue  324 TYR
Chi-restraints excluded: chain A residue   54 LEU
Chi-restraints excluded: chain A residue  147 THR
Chi-restraints excluded: chain A residue  148 VAL
Chi-restraints excluded: chain A residue  169 LEU
Chi-restraints excluded: chain A residue  181 THR
Chi-restraints excluded: chain A residue  227 THR
Chi-restraints excluded: chain A residue  241 CYS
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 168
   random chunks:
   chunk 83 optimal weight:    6.9990
   chunk 15 optimal weight:    5.9990
   chunk 98 optimal weight:    5.9990
   chunk 26 optimal weight:    0.0270
   chunk 166 optimal weight:    7.9990
   chunk 167 optimal weight:    6.9990
   chunk 57 optimal weight:    9.9990
   chunk 27 optimal weight:    7.9990
   chunk 33 optimal weight:    8.9990
   chunk 58 optimal weight:    5.9990
   chunk 140 optimal weight:   20.0000
   overall best weight:    5.0046

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

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

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.2998 r_free = 0.2998 target = 0.098863 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.2734 r_free = 0.2734 target = 0.081681 restraints weight = 23610.023|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 41)----------------|
| r_work = 0.2763 r_free = 0.2763 target = 0.083452 restraints weight = 15675.786|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 41)----------------|
| r_work = 0.2782 r_free = 0.2782 target = 0.084649 restraints weight = 12061.523|
|-----------------------------------------------------------------------------|
r_work (final): 0.2780
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2780
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2780 r_free = 0.2780    target_work(ls_wunit_k1) = 0.084         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:      276 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2779 r_free = 0.2779    target_work(ls_wunit_k1) = 0.084         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:      286 |
|-----------------------------------------------------------------------------|
r_final: 0.2779
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8693
moved from start:          0.4507

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.042  13656  Z= 0.206
  Angle     :  0.760  10.706  18486  Z= 0.386
  Chirality :  0.048   0.211   2058
  Planarity :  0.005   0.044   2370
  Dihedral  :  6.300  57.890   1902
  Min Nonbonded Distance : 2.465

Molprobity Statistics.
  All-atom Clashscore : 6.60
  Ramachandran Plot:
    Outliers :  0.82 %
    Allowed  : 15.32 %
    Favored  : 83.86 %
  Rotamer:
    Outliers :  4.65 %
    Allowed  : 16.24 %
    Favored  : 79.11 %
  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: -3.85 (0.18), residues: 1710
  helix: -1.62 (0.23), residues: 444
  sheet: -1.66 (0.27), residues: 384
  loop : -3.60 (0.17), residues: 882

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP F 198 
 HIS   0.010   0.002   HIS B 323 
 PHE   0.012   0.002   PHE F 330 
 TYR   0.014   0.001   TYR C 296 
 ARG   0.010   0.000   ARG B  95 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04434 (  348)
  hydrogen bonds       : angle       5.24261 (  972)
  covalent geometry    : bond        0.00498 (13656)
  covalent geometry    : angle       0.76023 (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
  229 residues out of total 1398 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 65
    poor density    : 164
  time to evaluate  : 1.374 
Fit side-chains
REVERT: F   95 ARG cc_start: 0.6752 (OUTLIER) cc_final: 0.6266 (mtt-85)
REVERT: F  225 ARG cc_start: 0.6987 (mpt-90) cc_final: 0.6745 (mpt-90)
REVERT: F  324 TYR cc_start: 0.8543 (OUTLIER) cc_final: 0.8139 (t80)
REVERT: F  336 GLU cc_start: 0.7431 (OUTLIER) cc_final: 0.7079 (mt-10)
REVERT: E  295 ASN cc_start: 0.8436 (t0) cc_final: 0.8003 (t0)
REVERT: E  297 ARG cc_start: 0.7943 (mtm-85) cc_final: 0.7516 (ppt170)
REVERT: D   42 GLN cc_start: 0.9308 (tt0) cc_final: 0.9100 (tt0)
REVERT: D  169 LEU cc_start: 0.9488 (OUTLIER) cc_final: 0.9167 (tm)
REVERT: D  283 ILE cc_start: 0.9173 (OUTLIER) cc_final: 0.8823 (mt)
REVERT: D  336 GLU cc_start: 0.7101 (OUTLIER) cc_final: 0.6780 (mt-10)
REVERT: C  287 LEU cc_start: 0.9106 (OUTLIER) cc_final: 0.8768 (mt)
REVERT: C  295 ASN cc_start: 0.8533 (t0) cc_final: 0.7926 (t0)
REVERT: C  324 TYR cc_start: 0.9066 (OUTLIER) cc_final: 0.7676 (t80)
REVERT: B  117 GLU cc_start: 0.7292 (mp0) cc_final: 0.6894 (mm-30)
REVERT: B  324 TYR cc_start: 0.8652 (OUTLIER) cc_final: 0.8220 (t80)
REVERT: A   94 SER cc_start: 0.7881 (m) cc_final: 0.7474 (p)
REVERT: A  287 LEU cc_start: 0.9043 (mm) cc_final: 0.8807 (mt)
REVERT: A  295 ASN cc_start: 0.8373 (t0) cc_final: 0.8157 (t0)
REVERT: A  297 ARG cc_start: 0.7881 (mpp-170) cc_final: 0.7204 (ppt170)
REVERT: A  339 ARG cc_start: 0.3692 (ttt180) cc_final: 0.2627 (ttt-90)
REVERT: A  343 SER cc_start: 0.8859 (m) cc_final: 0.8470 (p)
  outliers start: 65
  outliers final: 48
  residues processed: 212
  average time/residue: 0.2439
  time to fit residues: 75.2268
Evaluate side-chains
  211 residues out of total 1398 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 57
    poor density    : 154
  time to evaluate  : 1.334 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain F residue   61 LEU
Chi-restraints excluded: chain F residue   86 SER
Chi-restraints excluded: chain F residue   89 GLU
Chi-restraints excluded: chain F residue   95 ARG
Chi-restraints excluded: chain F residue  148 VAL
Chi-restraints excluded: chain F residue  169 LEU
Chi-restraints excluded: chain F residue  197 CYS
Chi-restraints excluded: chain F residue  324 TYR
Chi-restraints excluded: chain F residue  336 GLU
Chi-restraints excluded: chain E residue   96 THR
Chi-restraints excluded: chain E residue  113 VAL
Chi-restraints excluded: chain E residue  148 VAL
Chi-restraints excluded: chain E residue  182 ILE
Chi-restraints excluded: chain E residue  227 THR
Chi-restraints excluded: chain E residue  238 GLU
Chi-restraints excluded: chain E residue  283 ILE
Chi-restraints excluded: chain E residue  324 TYR
Chi-restraints excluded: chain E residue  333 ASN
Chi-restraints excluded: chain E residue  340 LYS
Chi-restraints excluded: chain D residue  148 VAL
Chi-restraints excluded: chain D residue  169 LEU
Chi-restraints excluded: chain D residue  181 THR
Chi-restraints excluded: chain D residue  184 VAL
Chi-restraints excluded: chain D residue  215 GLU
Chi-restraints excluded: chain D residue  241 CYS
Chi-restraints excluded: chain D residue  283 ILE
Chi-restraints excluded: chain D residue  324 TYR
Chi-restraints excluded: chain D residue  336 GLU
Chi-restraints excluded: chain C residue   54 LEU
Chi-restraints excluded: chain C residue  136 VAL
Chi-restraints excluded: chain C residue  147 THR
Chi-restraints excluded: chain C residue  148 VAL
Chi-restraints excluded: chain C residue  182 ILE
Chi-restraints excluded: chain C residue  227 THR
Chi-restraints excluded: chain C residue  241 CYS
Chi-restraints excluded: chain C residue  287 LEU
Chi-restraints excluded: chain C residue  321 VAL
Chi-restraints excluded: chain C residue  324 TYR
Chi-restraints excluded: chain C residue  333 ASN
Chi-restraints excluded: chain B residue   50 THR
Chi-restraints excluded: chain B residue   61 LEU
Chi-restraints excluded: chain B residue   86 SER
Chi-restraints excluded: chain B residue  148 VAL
Chi-restraints excluded: chain B residue  184 VAL
Chi-restraints excluded: chain B residue  197 CYS
Chi-restraints excluded: chain B residue  215 GLU
Chi-restraints excluded: chain B residue  227 THR
Chi-restraints excluded: chain B residue  241 CYS
Chi-restraints excluded: chain B residue  324 TYR
Chi-restraints excluded: chain A residue   54 LEU
Chi-restraints excluded: chain A residue  136 VAL
Chi-restraints excluded: chain A residue  148 VAL
Chi-restraints excluded: chain A residue  169 LEU
Chi-restraints excluded: chain A residue  181 THR
Chi-restraints excluded: chain A residue  227 THR
Chi-restraints excluded: chain A residue  241 CYS
Chi-restraints excluded: chain A residue  324 TYR
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 168
   random chunks:
   chunk 21 optimal weight:    6.9990
   chunk 127 optimal weight:    1.9990
   chunk 14 optimal weight:    5.9990
   chunk 18 optimal weight:    5.9990
   chunk 110 optimal weight:    0.9990
   chunk 57 optimal weight:   10.0000
   chunk 44 optimal weight:    0.9990
   chunk 143 optimal weight:    0.6980
   chunk 9 optimal weight:    0.9990
   chunk 26 optimal weight:    2.9990
   chunk 139 optimal weight:    6.9990
   overall best weight:    1.1388

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

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

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3108 r_free = 0.3108 target = 0.106447 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.2846 r_free = 0.2846 target = 0.088485 restraints weight = 22596.569|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.2880 r_free = 0.2880 target = 0.090659 restraints weight = 14012.170|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.2902 r_free = 0.2902 target = 0.092107 restraints weight = 10295.756|
|-----------------------------------------------------------------------------|
r_work (final): 0.2902
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2878
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2878 r_free = 0.2878    target_work(ls_wunit_k1) = 0.091         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:      286 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2873 r_free = 0.2873    target_work(ls_wunit_k1) = 0.090         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:      297 |
|-----------------------------------------------------------------------------|
r_final: 0.2873
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8578
moved from start:          0.4598

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036  13656  Z= 0.113
  Angle     :  0.680  10.970  18486  Z= 0.342
  Chirality :  0.045   0.206   2058
  Planarity :  0.005   0.095   2370
  Dihedral  :  5.670  54.994   1902
  Min Nonbonded Distance : 2.448

Molprobity Statistics.
  All-atom Clashscore : 6.61
  Ramachandran Plot:
    Outliers :  0.88 %
    Allowed  : 11.40 %
    Favored  : 87.72 %
  Rotamer:
    Outliers :  2.93 %
    Allowed  : 18.31 %
    Favored  : 78.76 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 7.14 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.37 %

Rama-Z (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: -3.39 (0.19), residues: 1710
  helix: -0.91 (0.26), residues: 408
  sheet: -1.51 (0.28), residues: 354
  loop : -3.31 (0.17), residues: 948

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP E 198 
 HIS   0.013   0.002   HIS B 323 
 PHE   0.009   0.001   PHE F 330 
 TYR   0.014   0.001   TYR C 296 
 ARG   0.015   0.000   ARG D  95 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02999 (  348)
  hydrogen bonds       : angle       4.79000 (  972)
  covalent geometry    : bond        0.00260 (13656)
  covalent geometry    : angle       0.68032 (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
  224 residues out of total 1398 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 41
    poor density    : 183
  time to evaluate  : 1.522 
Fit side-chains
REVERT: E   47 PHE cc_start: 0.7668 (t80) cc_final: 0.7425 (t80)
REVERT: E  295 ASN cc_start: 0.8341 (t0) cc_final: 0.7427 (p0)
REVERT: E  297 ARG cc_start: 0.7902 (mtm-85) cc_final: 0.7582 (ppt170)
REVERT: D  169 LEU cc_start: 0.9376 (OUTLIER) cc_final: 0.9029 (tm)
REVERT: D  283 ILE cc_start: 0.9137 (OUTLIER) cc_final: 0.8868 (mt)
REVERT: D  324 TYR cc_start: 0.8184 (OUTLIER) cc_final: 0.7898 (t80)
REVERT: C  287 LEU cc_start: 0.9089 (OUTLIER) cc_final: 0.8751 (mt)
REVERT: C  295 ASN cc_start: 0.8412 (t0) cc_final: 0.7904 (t0)
REVERT: C  324 TYR cc_start: 0.8798 (OUTLIER) cc_final: 0.7709 (t80)
REVERT: B  117 GLU cc_start: 0.7323 (mp0) cc_final: 0.6982 (mm-30)
REVERT: B  324 TYR cc_start: 0.8421 (OUTLIER) cc_final: 0.8180 (t80)
REVERT: A   87 THR cc_start: 0.9055 (p) cc_final: 0.8775 (t)
REVERT: A   94 SER cc_start: 0.7594 (m) cc_final: 0.7229 (p)
REVERT: A  215 GLU cc_start: 0.8944 (pt0) cc_final: 0.8724 (pt0)
REVERT: A  295 ASN cc_start: 0.8238 (t0) cc_final: 0.7686 (p0)
REVERT: A  297 ARG cc_start: 0.7851 (mpp-170) cc_final: 0.7189 (ppt170)
REVERT: A  339 ARG cc_start: 0.3502 (ttt180) cc_final: 0.2591 (ttt-90)
REVERT: A  343 SER cc_start: 0.8826 (m) cc_final: 0.8580 (p)
  outliers start: 41
  outliers final: 23
  residues processed: 210
  average time/residue: 0.2516
  time to fit residues: 77.0181
Evaluate side-chains
  190 residues out of total 1398 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 161
  time to evaluate  : 1.427 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain F residue   89 GLU
Chi-restraints excluded: chain F residue  147 THR
Chi-restraints excluded: chain F residue  148 VAL
Chi-restraints excluded: chain F residue  169 LEU
Chi-restraints excluded: chain E residue  113 VAL
Chi-restraints excluded: chain E residue  182 ILE
Chi-restraints excluded: chain E residue  186 ASP
Chi-restraints excluded: chain E residue  238 GLU
Chi-restraints excluded: chain E residue  324 TYR
Chi-restraints excluded: chain E residue  333 ASN
Chi-restraints excluded: chain D residue  169 LEU
Chi-restraints excluded: chain D residue  184 VAL
Chi-restraints excluded: chain D residue  215 GLU
Chi-restraints excluded: chain D residue  241 CYS
Chi-restraints excluded: chain D residue  283 ILE
Chi-restraints excluded: chain D residue  324 TYR
Chi-restraints excluded: chain C residue  147 THR
Chi-restraints excluded: chain C residue  182 ILE
Chi-restraints excluded: chain C residue  241 CYS
Chi-restraints excluded: chain C residue  287 LEU
Chi-restraints excluded: chain C residue  324 TYR
Chi-restraints excluded: chain C residue  333 ASN
Chi-restraints excluded: chain B residue   61 LEU
Chi-restraints excluded: chain B residue  184 VAL
Chi-restraints excluded: chain B residue  215 GLU
Chi-restraints excluded: chain B residue  324 TYR
Chi-restraints excluded: chain A residue  169 LEU
Chi-restraints excluded: chain A residue  241 CYS
Chi-restraints excluded: chain A residue  324 TYR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 168
   random chunks:
   chunk 26 optimal weight:    0.0000
   chunk 133 optimal weight:    6.9990
   chunk 139 optimal weight:    2.9990
   chunk 21 optimal weight:    8.9990
   chunk 146 optimal weight:   10.0000
   chunk 131 optimal weight:    0.9980
   chunk 1 optimal weight:    7.9990
   chunk 31 optimal weight:   20.0000
   chunk 3 optimal weight:   40.0000
   chunk 110 optimal weight:    3.9990
   chunk 83 optimal weight:    3.9990
   overall best weight:    2.3990

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

Flipped N/Q/H residues before XYZ refinement:
F  42 GLN
C 323 HIS
B 248 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3178 r_free = 0.3178 target = 0.111217 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.2922 r_free = 0.2922 target = 0.093368 restraints weight = 22021.379|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.2955 r_free = 0.2955 target = 0.095535 restraints weight = 13868.192|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 41)----------------|
| r_work = 0.2978 r_free = 0.2978 target = 0.097026 restraints weight = 10267.113|
|-----------------------------------------------------------------------------|
r_work (final): 0.2859
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2869
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2869 r_free = 0.2869    target_work(ls_wunit_k1) = 0.090         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:      297 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2866 r_free = 0.2866    target_work(ls_wunit_k1) = 0.090         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:      317 |
|-----------------------------------------------------------------------------|
r_final: 0.2866
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8597
moved from start:          0.4655

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= 0.134
  Angle     :  0.702  10.961  18486  Z= 0.353
  Chirality :  0.045   0.197   2058
  Planarity :  0.005   0.055   2370
  Dihedral  :  5.702  55.871   1902
  Min Nonbonded Distance : 2.434

Molprobity Statistics.
  All-atom Clashscore : 5.98
  Ramachandran Plot:
    Outliers :  0.94 %
    Allowed  : 12.63 %
    Favored  : 86.43 %
  Rotamer:
    Outliers :  2.07 %
    Allowed  : 19.24 %
    Favored  : 78.68 %
  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: -3.40 (0.19), residues: 1710
  helix: -1.12 (0.25), residues: 438
  sheet: -1.43 (0.28), residues: 354
  loop : -3.31 (0.17), residues: 918

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP D 198 
 HIS   0.013   0.002   HIS C 323 
 PHE   0.011   0.001   PHE A  47 
 TYR   0.014   0.001   TYR C 296 
 ARG   0.010   0.000   ARG D  95 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03340 (  348)
  hydrogen bonds       : angle       4.71635 (  972)
  covalent geometry    : bond        0.00316 (13656)
  covalent geometry    : angle       0.70226 (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
  191 residues out of total 1398 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 162
  time to evaluate  : 1.851 
Fit side-chains
REVERT: E   47 PHE cc_start: 0.7772 (t80) cc_final: 0.7498 (t80)
REVERT: E  295 ASN cc_start: 0.8345 (t0) cc_final: 0.7569 (p0)
REVERT: E  297 ARG cc_start: 0.7846 (mtm-85) cc_final: 0.7620 (ppt170)
REVERT: D  169 LEU cc_start: 0.9406 (OUTLIER) cc_final: 0.9019 (tm)
REVERT: D  283 ILE cc_start: 0.9074 (OUTLIER) cc_final: 0.8841 (mt)
REVERT: D  324 TYR cc_start: 0.8380 (OUTLIER) cc_final: 0.8053 (t80)
REVERT: C  287 LEU cc_start: 0.9090 (OUTLIER) cc_final: 0.8779 (mt)
REVERT: C  295 ASN cc_start: 0.8381 (t0) cc_final: 0.7315 (p0)
REVERT: C  324 TYR cc_start: 0.8906 (OUTLIER) cc_final: 0.7886 (t80)
REVERT: B  117 GLU cc_start: 0.7321 (mp0) cc_final: 0.6964 (mm-30)
REVERT: A   87 THR cc_start: 0.9103 (p) cc_final: 0.8837 (t)
REVERT: A   94 SER cc_start: 0.7713 (m) cc_final: 0.7360 (p)
REVERT: A  295 ASN cc_start: 0.8212 (t0) cc_final: 0.7757 (p0)
REVERT: A  297 ARG cc_start: 0.7854 (mpp-170) cc_final: 0.7208 (ppt170)
REVERT: A  339 ARG cc_start: 0.3434 (ttt180) cc_final: 0.2276 (ttt-90)
REVERT: A  343 SER cc_start: 0.8847 (m) cc_final: 0.8567 (p)
  outliers start: 29
  outliers final: 19
  residues processed: 180
  average time/residue: 0.4091
  time to fit residues: 109.7832
Evaluate side-chains
  184 residues out of total 1398 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 160
  time to evaluate  : 1.776 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain F residue   89 GLU
Chi-restraints excluded: chain F residue  169 LEU
Chi-restraints excluded: chain E residue  113 VAL
Chi-restraints excluded: chain E residue  182 ILE
Chi-restraints excluded: chain E residue  238 GLU
Chi-restraints excluded: chain E residue  324 TYR
Chi-restraints excluded: chain E residue  333 ASN
Chi-restraints excluded: chain D residue  169 LEU
Chi-restraints excluded: chain D residue  184 VAL
Chi-restraints excluded: chain D residue  215 GLU
Chi-restraints excluded: chain D residue  241 CYS
Chi-restraints excluded: chain D residue  283 ILE
Chi-restraints excluded: chain D residue  324 TYR
Chi-restraints excluded: chain C residue  182 ILE
Chi-restraints excluded: chain C residue  287 LEU
Chi-restraints excluded: chain C residue  324 TYR
Chi-restraints excluded: chain C residue  333 ASN
Chi-restraints excluded: chain B residue   61 LEU
Chi-restraints excluded: chain B residue  184 VAL
Chi-restraints excluded: chain B residue  215 GLU
Chi-restraints excluded: chain B residue  241 CYS
Chi-restraints excluded: chain A residue  169 LEU
Chi-restraints excluded: chain A residue  241 CYS
Chi-restraints excluded: chain A residue  324 TYR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 168
   random chunks:
   chunk 118 optimal weight:    0.6980
   chunk 141 optimal weight:   20.0000
   chunk 116 optimal weight:    0.0980
   chunk 158 optimal weight:    9.9990
   chunk 144 optimal weight:    7.9990
   chunk 35 optimal weight:    3.9990
   chunk 27 optimal weight:    6.9990
   chunk 112 optimal weight:    5.9990
   chunk 39 optimal weight:    7.9990
   chunk 42 optimal weight:    9.9990
   chunk 50 optimal weight:    7.9990
   overall best weight:    3.5586

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

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

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3034 r_free = 0.3034 target = 0.101209 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.2779 r_free = 0.2779 target = 0.084138 restraints weight = 23044.657|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.2807 r_free = 0.2807 target = 0.085947 restraints weight = 15364.150|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.2826 r_free = 0.2826 target = 0.087191 restraints weight = 11789.509|
|-----------------------------------------------------------------------------|
r_work (final): 0.2835
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2838
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2838 r_free = 0.2838    target_work(ls_wunit_k1) = 0.088         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:      317 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2836 r_free = 0.2836    target_work(ls_wunit_k1) = 0.088         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:      323 |
|-----------------------------------------------------------------------------|
r_final: 0.2836
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8638
moved from start:          0.4652

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.031  13656  Z= 0.163
  Angle     :  0.728  10.764  18486  Z= 0.368
  Chirality :  0.046   0.184   2058
  Planarity :  0.005   0.060   2370
  Dihedral  :  5.895  56.276   1902
  Min Nonbonded Distance : 2.447

Molprobity Statistics.
  All-atom Clashscore : 5.90
  Ramachandran Plot:
    Outliers :  0.99 %
    Allowed  : 13.92 %
    Favored  : 85.09 %
  Rotamer:
    Outliers :  2.22 %
    Allowed  : 19.03 %
    Favored  : 78.76 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 7.14 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.37 %

Rama-Z (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: -3.41 (0.19), residues: 1710
  helix: -1.17 (0.25), residues: 438
  sheet: -1.44 (0.28), residues: 354
  loop : -3.29 (0.17), residues: 918

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP D 198 
 HIS   0.010   0.002   HIS B 323 
 PHE   0.012   0.001   PHE C 103 
 TYR   0.014   0.001   TYR C 296 
 ARG   0.010   0.000   ARG D  95 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03808 (  348)
  hydrogen bonds       : angle       4.85949 (  972)
  covalent geometry    : bond        0.00390 (13656)
  covalent geometry    : angle       0.72775 (18486)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 5820.95 seconds
wall clock time: 107 minutes 11.17 seconds (6431.17 seconds total)