Starting phenix.real_space_refine
on Sun Aug 24 02:59:32 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8ud2_42144/08_2025/8ud2_42144.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8ud2_42144/08_2025/8ud2_42144.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.33
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/8ud2_42144/08_2025/8ud2_42144.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8ud2_42144/08_2025/8ud2_42144.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/8ud2_42144/08_2025/8ud2_42144.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8ud2_42144/08_2025/8ud2_42144.map"
  }
  resolution = 2.33
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.062
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      60      5.16       5
     C   10620      2.51       5
     N    2688      2.21       5
     O    3162      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 54 residue(s): 0.02s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 16530
  Number of models: 1
  Model: ""
    Number of chains: 1
    Chain: "A"
      Number of atoms: 2755
      Number of conformers: 2
      Conformer: "A"
        Number of residues, atoms: 346, 2731
          Classifications: {'peptide': 346}
          Link IDs: {'PTRANS': 14, 'TRANS': 331}
      Conformer: "B"
        Number of residues, atoms: 346, 2731
          Classifications: {'peptide': 346}
          Link IDs: {'PTRANS': 14, 'TRANS': 331}
          bond proxies already assigned to first conformer: 2762
  Restraints were copied for chains:
    B, C, D, E, F
  Residues with excluded nonbonded symmetry interactions: 18
    residue:
      pdb=" N  AILE A  27 " occ=0.52
      ... (14 atoms not shown)
      pdb=" CD1BILE A  27 " occ=0.48
    residue:
      pdb=" N  AASN A  28 " occ=0.52
      ... (14 atoms not shown)
      pdb=" ND2BASN A  28 " occ=0.48
    residue:
      pdb=" N  AASN A  29 " occ=0.52
      ... (14 atoms not shown)
      pdb=" ND2BASN A  29 " occ=0.48
    residue:
      pdb=" N  AILE B  27 " occ=0.52
      ... (14 atoms not shown)
      pdb=" CD1BILE B  27 " occ=0.48
    residue:
      pdb=" N  AASN B  28 " occ=0.52
      ... (14 atoms not shown)
      pdb=" ND2BASN B  28 " occ=0.48
    residue:
      pdb=" N  AASN B  29 " occ=0.52
      ... (14 atoms not shown)
      pdb=" ND2BASN B  29 " occ=0.48
    residue:
      pdb=" N  AILE C  27 " occ=0.52
      ... (14 atoms not shown)
      pdb=" CD1BILE C  27 " occ=0.48
    residue:
      pdb=" N  AASN C  28 " occ=0.52
      ... (14 atoms not shown)
      pdb=" ND2BASN C  28 " occ=0.48
    residue:
      pdb=" N  AASN C  29 " occ=0.52
      ... (14 atoms not shown)
      pdb=" ND2BASN C  29 " occ=0.48
    residue:
      pdb=" N  AILE D  27 " occ=0.52
      ... (14 atoms not shown)
      pdb=" CD1BILE D  27 " occ=0.48
    residue:
      pdb=" N  AASN D  28 " occ=0.52
      ... (14 atoms not shown)
      pdb=" ND2BASN D  28 " occ=0.48
    residue:
      pdb=" N  AASN D  29 " occ=0.52
      ... (14 atoms not shown)
      pdb=" ND2BASN D  29 " occ=0.48
    ... (remaining 6 not shown)
  Time building chain proxies: 2.90, per 1000 atoms: 0.18
  Number of scatterers: 16530
  At special positions: 0
  Unit cell: (115, 107.64, 122.36, 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      60     16.00
     O    3162      8.00
     N    2688      7.00
     C   10620      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: 1.04
  Conformation dependent library (CDL) restraints added in 1.4 seconds
  
  Enol-peptide restraints added in 1.2 microseconds
  

  4188 Ramachandran restraints generated.
    2094 Oldfield, 0 Emsley, 2094 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  3924

  Finding SS restraints...
    Secondary structure from input PDB file:
      60 helices and 48 sheets defined
      26.6% alpha, 25.5% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.65
  Creating SS restraints...
    Processing helix  chain 'A' and resid 1 through 13
    Processing helix  chain 'A' and resid 50 through 60
    Processing helix  chain 'A' and resid 68 through 75
    Processing helix  chain 'A' and resid 113 through 117
    Processing helix  chain 'A' and resid 129 through 136
    Processing helix  chain 'A' and resid 207 through 216
    Processing helix  chain 'A' and resid 217 through 225
    Processing helix  chain 'A' and resid 231 through 236
    Processing helix  chain 'A' and resid 250 through 261
      removed outlier: 3.594A  pdb=" N   GLU A 260 " --> pdb=" O   LYS A 256 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 298 through 308
    Processing helix  chain 'B' and resid 2 through 13
    Processing helix  chain 'B' and resid 50 through 60
    Processing helix  chain 'B' and resid 68 through 75
    Processing helix  chain 'B' and resid 113 through 117
    Processing helix  chain 'B' and resid 129 through 136
    Processing helix  chain 'B' and resid 207 through 216
    Processing helix  chain 'B' and resid 217 through 225
    Processing helix  chain 'B' and resid 231 through 236
    Processing helix  chain 'B' and resid 250 through 261
      removed outlier: 3.594A  pdb=" N   GLU B 260 " --> pdb=" O   LYS B 256 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 298 through 308
    Processing helix  chain 'C' and resid 2 through 13
    Processing helix  chain 'C' and resid 50 through 60
    Processing helix  chain 'C' and resid 68 through 75
    Processing helix  chain 'C' and resid 113 through 117
    Processing helix  chain 'C' and resid 129 through 136
    Processing helix  chain 'C' and resid 207 through 216
    Processing helix  chain 'C' and resid 217 through 225
    Processing helix  chain 'C' and resid 231 through 236
    Processing helix  chain 'C' and resid 250 through 261
      removed outlier: 3.594A  pdb=" N   GLU C 260 " --> pdb=" O   LYS C 256 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 298 through 308
    Processing helix  chain 'D' and resid 2 through 13
    Processing helix  chain 'D' and resid 50 through 60
    Processing helix  chain 'D' and resid 68 through 75
    Processing helix  chain 'D' and resid 113 through 117
    Processing helix  chain 'D' and resid 129 through 136
    Processing helix  chain 'D' and resid 207 through 216
    Processing helix  chain 'D' and resid 217 through 225
    Processing helix  chain 'D' and resid 231 through 236
    Processing helix  chain 'D' and resid 250 through 261
      removed outlier: 3.593A  pdb=" N   GLU D 260 " --> pdb=" O   LYS D 256 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 298 through 308
    Processing helix  chain 'E' and resid 2 through 13
    Processing helix  chain 'E' and resid 50 through 60
    Processing helix  chain 'E' and resid 68 through 75
    Processing helix  chain 'E' and resid 113 through 117
    Processing helix  chain 'E' and resid 129 through 136
    Processing helix  chain 'E' and resid 207 through 216
    Processing helix  chain 'E' and resid 217 through 225
    Processing helix  chain 'E' and resid 231 through 236
    Processing helix  chain 'E' and resid 250 through 261
      removed outlier: 3.593A  pdb=" N   GLU E 260 " --> pdb=" O   LYS E 256 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 298 through 308
    Processing helix  chain 'F' and resid 2 through 13
    Processing helix  chain 'F' and resid 50 through 60
    Processing helix  chain 'F' and resid 68 through 75
    Processing helix  chain 'F' and resid 113 through 117
    Processing helix  chain 'F' and resid 129 through 136
    Processing helix  chain 'F' and resid 207 through 216
    Processing helix  chain 'F' and resid 217 through 225
    Processing helix  chain 'F' and resid 231 through 236
    Processing helix  chain 'F' and resid 250 through 261
      removed outlier: 3.594A  pdb=" N   GLU F 260 " --> pdb=" O   LYS F 256 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 298 through 308
    Processing sheet with id=AA1, first strand: chain 'A' and resid 24 through 27
      removed outlier: 6.647A  pdb=" N   VAL A  31 " --> pdb=" O   LEU A  42 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 79 through 80
      removed outlier: 7.158A  pdb=" N   ILE A  79 " --> pdb=" O   PHE A 122 " (cutoff:3.500A)
      removed outlier: 8.725A  pdb=" N   ASP A 124 " --> pdb=" O   ILE A  79 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 79 through 80
      removed outlier: 7.158A  pdb=" N   ILE A  79 " --> pdb=" O   PHE A 122 " (cutoff:3.500A)
      removed outlier: 8.725A  pdb=" N   ASP A 124 " --> pdb=" O   ILE A  79 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 86 through 87
    Processing sheet with id=AA5, first strand: chain 'A' and resid 98 through 99
      removed outlier: 7.949A  pdb=" N   THR A  98 " --> pdb=" O   ILE A 107 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA5
    Processing sheet with id=AA6, first strand: chain 'A' and resid 160 through 162
    Processing sheet with id=AA7, first strand: chain 'A' and resid 264 through 266
      removed outlier: 4.908A  pdb=" N   ILE A 280 " --> pdb=" O   CYS A 290 " (cutoff:3.500A)
      removed outlier: 5.074A  pdb=" N   CYS A 290 " --> pdb=" O   ILE A 280 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'A' and resid 315 through 322
      removed outlier: 7.446A  pdb=" N   SER A 328 " --> pdb=" O   PRO A 343 " (cutoff:3.500A)
      removed outlier: 6.468A  pdb=" N   MET A 330 " --> pdb=" O   PHE A 341 " (cutoff:3.500A)
      removed outlier: 3.951A  pdb=" N   PHE A 341 " --> pdb=" O   MET A 330 " (cutoff:3.500A)
      removed outlier: 6.543A  pdb=" N   TRP A 332 " --> pdb=" O   GLU A 339 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'B' and resid 24 through 27
      removed outlier: 6.647A  pdb=" N   VAL B  31 " --> pdb=" O   LEU B  42 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'B' and resid 79 through 80
      removed outlier: 7.158A  pdb=" N   ILE B  79 " --> pdb=" O   PHE B 122 " (cutoff:3.500A)
      removed outlier: 8.725A  pdb=" N   ASP B 124 " --> pdb=" O   ILE B  79 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'B' and resid 79 through 80
      removed outlier: 7.158A  pdb=" N   ILE B  79 " --> pdb=" O   PHE B 122 " (cutoff:3.500A)
      removed outlier: 8.725A  pdb=" N   ASP B 124 " --> pdb=" O   ILE B  79 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'B' and resid 86 through 87
    Processing sheet with id=AB4, first strand: chain 'B' and resid 98 through 99
      removed outlier: 7.949A  pdb=" N   THR B  98 " --> pdb=" O   ILE B 107 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AB4
    Processing sheet with id=AB5, first strand: chain 'B' and resid 160 through 162
    Processing sheet with id=AB6, first strand: chain 'B' and resid 264 through 266
      removed outlier: 4.909A  pdb=" N   ILE B 280 " --> pdb=" O   CYS B 290 " (cutoff:3.500A)
      removed outlier: 5.074A  pdb=" N   CYS B 290 " --> pdb=" O   ILE B 280 " (cutoff:3.500A)
    Processing sheet with id=AB7, first strand: chain 'B' and resid 315 through 322
      removed outlier: 7.447A  pdb=" N   SER B 328 " --> pdb=" O   PRO B 343 " (cutoff:3.500A)
      removed outlier: 6.467A  pdb=" N   MET B 330 " --> pdb=" O   PHE B 341 " (cutoff:3.500A)
      removed outlier: 3.951A  pdb=" N   PHE B 341 " --> pdb=" O   MET B 330 " (cutoff:3.500A)
      removed outlier: 6.543A  pdb=" N   TRP B 332 " --> pdb=" O   GLU B 339 " (cutoff:3.500A)
    Processing sheet with id=AB8, first strand: chain 'C' and resid 24 through 27
      removed outlier: 6.647A  pdb=" N   VAL C  31 " --> pdb=" O   LEU C  42 " (cutoff:3.500A)
    Processing sheet with id=AB9, first strand: chain 'C' and resid 79 through 80
      removed outlier: 7.158A  pdb=" N   ILE C  79 " --> pdb=" O   PHE C 122 " (cutoff:3.500A)
      removed outlier: 8.725A  pdb=" N   ASP C 124 " --> pdb=" O   ILE C  79 " (cutoff:3.500A)
    Processing sheet with id=AC1, first strand: chain 'C' and resid 79 through 80
      removed outlier: 7.158A  pdb=" N   ILE C  79 " --> pdb=" O   PHE C 122 " (cutoff:3.500A)
      removed outlier: 8.725A  pdb=" N   ASP C 124 " --> pdb=" O   ILE C  79 " (cutoff:3.500A)
      removed outlier: 4.805A  pdb=" N   LYS C 180 " --> pdb=" O   GLN C 187 " (cutoff:3.500A)
    Processing sheet with id=AC2, first strand: chain 'C' and resid 86 through 87
    Processing sheet with id=AC3, first strand: chain 'C' and resid 98 through 99
      removed outlier: 7.950A  pdb=" N   THR C  98 " --> pdb=" O   ILE C 107 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AC3
    Processing sheet with id=AC4, first strand: chain 'C' and resid 160 through 162
    Processing sheet with id=AC5, first strand: chain 'C' and resid 264 through 266
      removed outlier: 4.909A  pdb=" N   ILE C 280 " --> pdb=" O   CYS C 290 " (cutoff:3.500A)
      removed outlier: 5.073A  pdb=" N   CYS C 290 " --> pdb=" O   ILE C 280 " (cutoff:3.500A)
    Processing sheet with id=AC6, first strand: chain 'C' and resid 315 through 322
      removed outlier: 7.447A  pdb=" N   SER C 328 " --> pdb=" O   PRO C 343 " (cutoff:3.500A)
      removed outlier: 6.467A  pdb=" N   MET C 330 " --> pdb=" O   PHE C 341 " (cutoff:3.500A)
      removed outlier: 3.951A  pdb=" N   PHE C 341 " --> pdb=" O   MET C 330 " (cutoff:3.500A)
      removed outlier: 6.544A  pdb=" N   TRP C 332 " --> pdb=" O   GLU C 339 " (cutoff:3.500A)
    Processing sheet with id=AC7, first strand: chain 'D' and resid 24 through 27
      removed outlier: 6.647A  pdb=" N   VAL D  31 " --> pdb=" O   LEU D  42 " (cutoff:3.500A)
    Processing sheet with id=AC8, first strand: chain 'D' and resid 79 through 80
      removed outlier: 7.158A  pdb=" N   ILE D  79 " --> pdb=" O   PHE D 122 " (cutoff:3.500A)
      removed outlier: 8.726A  pdb=" N   ASP D 124 " --> pdb=" O   ILE D  79 " (cutoff:3.500A)
    Processing sheet with id=AC9, first strand: chain 'D' and resid 79 through 80
      removed outlier: 7.158A  pdb=" N   ILE D  79 " --> pdb=" O   PHE D 122 " (cutoff:3.500A)
      removed outlier: 8.726A  pdb=" N   ASP D 124 " --> pdb=" O   ILE D  79 " (cutoff:3.500A)
    Processing sheet with id=AD1, first strand: chain 'D' and resid 86 through 87
    Processing sheet with id=AD2, first strand: chain 'D' and resid 98 through 99
      removed outlier: 7.949A  pdb=" N   THR D  98 " --> pdb=" O   ILE D 107 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AD2
    Processing sheet with id=AD3, first strand: chain 'D' and resid 160 through 162
    Processing sheet with id=AD4, first strand: chain 'D' and resid 264 through 266
      removed outlier: 4.908A  pdb=" N   ILE D 280 " --> pdb=" O   CYS D 290 " (cutoff:3.500A)
      removed outlier: 5.075A  pdb=" N   CYS D 290 " --> pdb=" O   ILE D 280 " (cutoff:3.500A)
    Processing sheet with id=AD5, first strand: chain 'D' and resid 315 through 322
      removed outlier: 7.446A  pdb=" N   SER D 328 " --> pdb=" O   PRO D 343 " (cutoff:3.500A)
      removed outlier: 6.467A  pdb=" N   MET D 330 " --> pdb=" O   PHE D 341 " (cutoff:3.500A)
      removed outlier: 3.951A  pdb=" N   PHE D 341 " --> pdb=" O   MET D 330 " (cutoff:3.500A)
      removed outlier: 6.544A  pdb=" N   TRP D 332 " --> pdb=" O   GLU D 339 " (cutoff:3.500A)
    Processing sheet with id=AD6, first strand: chain 'E' and resid 24 through 27
      removed outlier: 6.647A  pdb=" N   VAL E  31 " --> pdb=" O   LEU E  42 " (cutoff:3.500A)
    Processing sheet with id=AD7, first strand: chain 'E' and resid 79 through 80
      removed outlier: 7.158A  pdb=" N   ILE E  79 " --> pdb=" O   PHE E 122 " (cutoff:3.500A)
      removed outlier: 8.726A  pdb=" N   ASP E 124 " --> pdb=" O   ILE E  79 " (cutoff:3.500A)
    Processing sheet with id=AD8, first strand: chain 'E' and resid 79 through 80
      removed outlier: 7.158A  pdb=" N   ILE E  79 " --> pdb=" O   PHE E 122 " (cutoff:3.500A)
      removed outlier: 8.726A  pdb=" N   ASP E 124 " --> pdb=" O   ILE E  79 " (cutoff:3.500A)
    Processing sheet with id=AD9, first strand: chain 'E' and resid 86 through 87
    Processing sheet with id=AE1, first strand: chain 'E' and resid 98 through 99
      removed outlier: 7.950A  pdb=" N   THR E  98 " --> pdb=" O   ILE E 107 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AE1
    Processing sheet with id=AE2, first strand: chain 'E' and resid 160 through 162
    Processing sheet with id=AE3, first strand: chain 'E' and resid 264 through 266
      removed outlier: 4.909A  pdb=" N   ILE E 280 " --> pdb=" O   CYS E 290 " (cutoff:3.500A)
      removed outlier: 5.074A  pdb=" N   CYS E 290 " --> pdb=" O   ILE E 280 " (cutoff:3.500A)
    Processing sheet with id=AE4, first strand: chain 'E' and resid 315 through 322
      removed outlier: 7.446A  pdb=" N   SER E 328 " --> pdb=" O   PRO E 343 " (cutoff:3.500A)
      removed outlier: 6.466A  pdb=" N   MET E 330 " --> pdb=" O   PHE E 341 " (cutoff:3.500A)
      removed outlier: 3.951A  pdb=" N   PHE E 341 " --> pdb=" O   MET E 330 " (cutoff:3.500A)
      removed outlier: 6.543A  pdb=" N   TRP E 332 " --> pdb=" O   GLU E 339 " (cutoff:3.500A)
    Processing sheet with id=AE5, first strand: chain 'F' and resid 24 through 27
      removed outlier: 6.647A  pdb=" N   VAL F  31 " --> pdb=" O   LEU F  42 " (cutoff:3.500A)
    Processing sheet with id=AE6, first strand: chain 'F' and resid 79 through 80
      removed outlier: 7.158A  pdb=" N   ILE F  79 " --> pdb=" O   PHE F 122 " (cutoff:3.500A)
      removed outlier: 8.725A  pdb=" N   ASP F 124 " --> pdb=" O   ILE F  79 " (cutoff:3.500A)
    Processing sheet with id=AE7, first strand: chain 'F' and resid 79 through 80
      removed outlier: 7.158A  pdb=" N   ILE F  79 " --> pdb=" O   PHE F 122 " (cutoff:3.500A)
      removed outlier: 8.725A  pdb=" N   ASP F 124 " --> pdb=" O   ILE F  79 " (cutoff:3.500A)
      removed outlier: 4.805A  pdb=" N   LYS F 180 " --> pdb=" O   GLN F 187 " (cutoff:3.500A)
    Processing sheet with id=AE8, first strand: chain 'F' and resid 86 through 87
    Processing sheet with id=AE9, first strand: chain 'F' and resid 98 through 99
      removed outlier: 7.950A  pdb=" N   THR F  98 " --> pdb=" O   ILE F 107 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AE9
    Processing sheet with id=AF1, first strand: chain 'F' and resid 160 through 162
    Processing sheet with id=AF2, first strand: chain 'F' and resid 264 through 266
      removed outlier: 4.909A  pdb=" N   ILE F 280 " --> pdb=" O   CYS F 290 " (cutoff:3.500A)
      removed outlier: 5.074A  pdb=" N   CYS F 290 " --> pdb=" O   ILE F 280 " (cutoff:3.500A)
    Processing sheet with id=AF3, first strand: chain 'F' and resid 315 through 322
      removed outlier: 7.446A  pdb=" N   SER F 328 " --> pdb=" O   PRO F 343 " (cutoff:3.500A)
      removed outlier: 6.467A  pdb=" N   MET F 330 " --> pdb=" O   PHE F 341 " (cutoff:3.500A)
      removed outlier: 3.951A  pdb=" N   PHE F 341 " --> pdb=" O   MET F 330 " (cutoff:3.500A)
      removed outlier: 6.544A  pdb=" N   TRP F 332 " --> pdb=" O   GLU F 339 " (cutoff:3.500A)

    663 hydrogen bonds defined for protein.
    1683 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: 2.95

  Time building geometry restraints manager: 1.34 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: 5346
        1.34 -     1.46: 2447
        1.46 -     1.57: 8989
        1.57 -     1.69: 0
        1.69 -     1.81: 90
  Bond restraints: 16872
  Sorted by residual:
  bond pdb=" N   LEU F 345 "
       pdb=" CA  LEU F 345 "
    ideal  model  delta    sigma   weight residual
    1.457  1.472 -0.014 1.29e-02 6.01e+03 1.21e+00
  bond pdb=" N   LEU C 345 "
       pdb=" CA  LEU C 345 "
    ideal  model  delta    sigma   weight residual
    1.457  1.472 -0.014 1.29e-02 6.01e+03 1.20e+00
  bond pdb=" N   LEU B 345 "
       pdb=" CA  LEU B 345 "
    ideal  model  delta    sigma   weight residual
    1.457  1.471 -0.014 1.29e-02 6.01e+03 1.16e+00
  bond pdb=" N   LEU D 345 "
       pdb=" CA  LEU D 345 "
    ideal  model  delta    sigma   weight residual
    1.457  1.471 -0.014 1.29e-02 6.01e+03 1.15e+00
  bond pdb=" N   LEU A 345 "
       pdb=" CA  LEU A 345 "
    ideal  model  delta    sigma   weight residual
    1.457  1.471 -0.014 1.29e-02 6.01e+03 1.13e+00
  ... (remaining 16867 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.06: 21753
        1.06 -     2.12: 941
        2.12 -     3.18: 159
        3.18 -     4.25: 31
        4.25 -     5.31: 18
  Bond angle restraints: 22902
  Sorted by residual:
  angle pdb=" C   GLN E 188 "
        pdb=" N   LEU E 189 "
        pdb=" CA  LEU E 189 "
      ideal   model   delta    sigma   weight residual
     120.67  116.80    3.87 1.34e+00 5.57e-01 8.33e+00
  angle pdb=" C   GLN D 188 "
        pdb=" N   LEU D 189 "
        pdb=" CA  LEU D 189 "
      ideal   model   delta    sigma   weight residual
     120.67  116.81    3.86 1.34e+00 5.57e-01 8.30e+00
  angle pdb=" C   GLN B 188 "
        pdb=" N   LEU B 189 "
        pdb=" CA  LEU B 189 "
      ideal   model   delta    sigma   weight residual
     120.67  116.81    3.86 1.34e+00 5.57e-01 8.28e+00
  angle pdb=" C   GLN C 188 "
        pdb=" N   LEU C 189 "
        pdb=" CA  LEU C 189 "
      ideal   model   delta    sigma   weight residual
     120.67  116.85    3.82 1.34e+00 5.57e-01 8.13e+00
  angle pdb=" C   GLN A 188 "
        pdb=" N   LEU A 189 "
        pdb=" CA  LEU A 189 "
      ideal   model   delta    sigma   weight residual
     120.67  116.87    3.80 1.34e+00 5.57e-01 8.05e+00
  ... (remaining 22897 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.82: 8918
       17.82 -    35.64: 868
       35.64 -    53.46: 198
       53.46 -    71.28: 84
       71.28 -    89.11: 36
  Dihedral angle restraints: 10104
    sinusoidal: 4020
      harmonic: 6084
  Sorted by residual:
  dihedral pdb=" CA  THR B 192 "
           pdb=" C   THR B 192 "
           pdb=" N   TYR B 193 "
           pdb=" CA  TYR B 193 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  161.55   18.45     0      5.00e+00 4.00e-02 1.36e+01
  dihedral pdb=" CA  THR D 192 "
           pdb=" C   THR D 192 "
           pdb=" N   TYR D 193 "
           pdb=" CA  TYR D 193 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  161.55   18.45     0      5.00e+00 4.00e-02 1.36e+01
  dihedral pdb=" CA  THR C 192 "
           pdb=" C   THR C 192 "
           pdb=" N   TYR C 193 "
           pdb=" CA  TYR C 193 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  161.56   18.44     0      5.00e+00 4.00e-02 1.36e+01
  ... (remaining 10101 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.027: 1359
       0.027 -    0.053: 729
       0.053 -    0.079: 268
       0.079 -    0.106: 195
       0.106 -    0.132: 83
  Chirality restraints: 2634
  Sorted by residual:
  chirality pdb=" CA  ILE B 168 "
            pdb=" N   ILE B 168 "
            pdb=" C   ILE B 168 "
            pdb=" CB  ILE B 168 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.57   -0.13 2.00e-01 2.50e+01 4.39e-01
  chirality pdb=" CA  ILE E 168 "
            pdb=" N   ILE E 168 "
            pdb=" C   ILE E 168 "
            pdb=" CB  ILE E 168 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.57   -0.13 2.00e-01 2.50e+01 4.39e-01
  chirality pdb=" CA  VAL B 313 "
            pdb=" N   VAL B 313 "
            pdb=" C   VAL B 313 "
            pdb=" CB  VAL B 313 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.57   -0.13 2.00e-01 2.50e+01 4.25e-01
  ... (remaining 2631 not shown)

  Planarity restraints: 2952
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   LYS E 110 "   -0.023 5.00e-02 4.00e+02   3.44e-02 1.89e+00
        pdb=" N   PRO E 111 "    0.059 5.00e-02 4.00e+02
        pdb=" CA  PRO E 111 "   -0.018 5.00e-02 4.00e+02
        pdb=" CD  PRO E 111 "   -0.019 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   LYS C 110 "    0.023 5.00e-02 4.00e+02   3.44e-02 1.89e+00
        pdb=" N   PRO C 111 "   -0.059 5.00e-02 4.00e+02
        pdb=" CA  PRO C 111 "    0.018 5.00e-02 4.00e+02
        pdb=" CD  PRO C 111 "    0.019 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   LYS F 110 "    0.023 5.00e-02 4.00e+02   3.43e-02 1.89e+00
        pdb=" N   PRO F 111 "   -0.059 5.00e-02 4.00e+02
        pdb=" CA  PRO F 111 "    0.018 5.00e-02 4.00e+02
        pdb=" CD  PRO F 111 "    0.019 5.00e-02 4.00e+02
  ... (remaining 2949 not shown)

  Histogram of nonbonded interaction distances:
        2.29 -     2.81: 4744
        2.81 -     3.34: 14847
        3.34 -     3.86: 30023
        3.86 -     4.38: 35609
        4.38 -     4.90: 58582
  Nonbonded interactions: 143805
  Sorted by model distance:
  nonbonded pdb=" O   ALA C 117 "
            pdb=" ND2 ASN C 139 "
     model   vdw
     2.293 3.120
  nonbonded pdb=" O   ALA F 117 "
            pdb=" ND2 ASN F 139 "
     model   vdw
     2.293 3.120
  nonbonded pdb=" O   ALA A 117 "
            pdb=" ND2 ASN A 139 "
     model   vdw
     2.293 3.120
  nonbonded pdb=" O   ALA E 117 "
            pdb=" ND2 ASN E 139 "
     model   vdw
     2.293 3.120
  nonbonded pdb=" O   ALA D 117 "
            pdb=" ND2 ASN D 139 "
     model   vdw
     2.293 3.120
  ... (remaining 143800 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: 0.05
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'B'
  selection = chain 'C'
  selection = chain 'D'
  selection = chain 'E'
  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=0.48 max=1.00 mean=0.99
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             5.860
  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:          0.200
  Check model and map are aligned:         0.060
  Set scattering table:                    0.050
  Process input model:                     15.740
  Find NCS groups from input model:        0.150
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:6.630
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   28.720
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8095
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.019  16872  Z= 0.138
  Angle     :  0.532   5.308  22902  Z= 0.324
  Chirality :  0.045   0.132   2634
  Planarity :  0.003   0.034   2952
  Dihedral  : 16.449  89.106   6180
  Min Nonbonded Distance : 2.293

Molprobity Statistics.
  All-atom Clashscore : 6.23
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.50 %
    Favored  : 98.50 %
  Rotamer:
    Outliers :  1.08 %
    Allowed  : 17.74 %
    Favored  : 81.18 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.47 (0.19), residues: 2094
  helix:  0.69 (0.23), residues: 528
  sheet:  0.50 (0.29), residues: 312
  loop :  0.21 (0.18), residues: 1254

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG B 135 
 TYR   0.006   0.001   TYR C 324 
 PHE   0.009   0.001   PHE C 221 
 TRP   0.006   0.001   TRP F  58 
 HIS   0.004   0.001   HIS C  95 

Details of bonding type rmsd
  covalent geometry    : bond        0.00264 (16872)
  covalent geometry    : angle       0.53202 (22902)
  hydrogen bonds       : bond        0.15356 (  609)
  hydrogen bonds       : angle       7.84473 ( 1683)

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

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

  4188 Ramachandran restraints generated.
    2094 Oldfield, 0 Emsley, 2094 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4188 Ramachandran restraints generated.
    2094 Oldfield, 0 Emsley, 2094 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  270 residues out of total 1824 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 250
  time to evaluate  : 0.641 
Fit side-chains
REVERT: B  149 LYS cc_start: 0.8133 (mmmm) cc_final: 0.7706 (mppt)
REVERT: B  239 ASP cc_start: 0.7288 (t0) cc_final: 0.7026 (t0)
REVERT: B  284 GLN cc_start: 0.6881 (tm-30) cc_final: 0.6658 (tm130)
REVERT: C   19 GLN cc_start: 0.8207 (mm-40) cc_final: 0.7991 (mp10)
REVERT: C  149 LYS cc_start: 0.8040 (mmmm) cc_final: 0.7546 (ptmm)
REVERT: C  330 MET cc_start: 0.7205 (mmt) cc_final: 0.7000 (mmt)
REVERT: D   19 GLN cc_start: 0.8211 (mm-40) cc_final: 0.7994 (mp10)
REVERT: D  149 LYS cc_start: 0.8048 (mmmm) cc_final: 0.7517 (ptmm)
REVERT: D  330 MET cc_start: 0.7184 (mmt) cc_final: 0.6981 (mmt)
REVERT: E  149 LYS cc_start: 0.8139 (mmmm) cc_final: 0.7713 (mppt)
  outliers start: 20
  outliers final: 9
  residues processed: 268
  average time/residue: 0.5056
  time to fit residues: 153.2612
Evaluate side-chains
  228 residues out of total 1824 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 219
  time to evaluate  : 0.652 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  340 THR
Chi-restraints excluded: chain B residue  300 ASP
Chi-restraints excluded: chain B residue  340 THR
Chi-restraints excluded: chain C residue  300 ASP
Chi-restraints excluded: chain C residue  340 THR
Chi-restraints excluded: chain D residue  340 THR
Chi-restraints excluded: chain E residue  340 THR
Chi-restraints excluded: chain F residue  300 ASP
Chi-restraints excluded: chain F residue  340 THR
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 204
   random chunks:
   chunk 98 optimal weight:    0.7980
   chunk 194 optimal weight:    6.9990
   chunk 107 optimal weight:    2.9990
   chunk 10 optimal weight:    2.9990
   chunk 66 optimal weight:    1.9990
   chunk 130 optimal weight:    0.6980
   chunk 124 optimal weight:    3.9990
   chunk 103 optimal weight:    0.7980
   chunk 200 optimal weight:    1.9990
   chunk 77 optimal weight:    0.9980
   chunk 122 optimal weight:    0.5980
   overall best weight:    0.7780

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

Flipped N/Q/H residues before XYZ refinement:
B  19 GLN
C 152 GLN
D 152 GLN
E  19 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3856 r_free = 0.3856 target = 0.170895 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 26)----------------|
| r_work = 0.3373 r_free = 0.3373 target = 0.127559 restraints weight = 89596.317|
|-----------------------------------------------------------------------------|
r_work (start): 0.3281 rms_B_bonded: 4.95
r_work: 0.2959 rms_B_bonded: 3.37 restraints_weight: 0.5000
r_work (final): 0.2959
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2936
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2936 r_free = 0.2936    target_work(ls_wunit_k1) = 0.095         |
| occupancies: max = 1.00  min = 0.48   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2936 r_free = 0.2936    target_work(ls_wunit_k1) = 0.095         |
| occupancies: max = 1.00  min = 0.48   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2936
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8257
moved from start:          0.1003

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031  16872  Z= 0.147
  Angle     :  0.537   9.395  22902  Z= 0.286
  Chirality :  0.047   0.135   2634
  Planarity :  0.003   0.032   2952
  Dihedral  :  5.322  53.921   2226
  Min Nonbonded Distance : 2.598

Molprobity Statistics.
  All-atom Clashscore : 4.66
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.36 %
    Favored  : 98.64 %
  Rotamer:
    Outliers :  1.29 %
    Allowed  : 18.82 %
    Favored  : 79.89 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.36 (0.18), residues: 2094
  helix:  0.57 (0.23), residues: 540
  sheet:  0.47 (0.26), residues: 354
  loop :  0.12 (0.18), residues: 1200

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG E 138 
 TYR   0.009   0.001   TYR A 225 
 PHE   0.021   0.002   PHE D 221 
 TRP   0.013   0.002   TRP D  58 
 HIS   0.002   0.001   HIS D  95 

Details of bonding type rmsd
  covalent geometry    : bond        0.00326 (16872)
  covalent geometry    : angle       0.53738 (22902)
  hydrogen bonds       : bond        0.04172 (  609)
  hydrogen bonds       : angle       5.94575 ( 1683)

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

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

  4188 Ramachandran restraints generated.
    2094 Oldfield, 0 Emsley, 2094 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4188 Ramachandran restraints generated.
    2094 Oldfield, 0 Emsley, 2094 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  277 residues out of total 1824 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 253
  time to evaluate  : 0.526 
Fit side-chains
REVERT: A  259 LYS cc_start: 0.6834 (tttt) cc_final: 0.6506 (mttp)
REVERT: B  149 LYS cc_start: 0.8396 (mmmm) cc_final: 0.8025 (mppt)
REVERT: C  152 GLN cc_start: 0.8236 (tp40) cc_final: 0.7884 (mp10)
REVERT: C  202 GLU cc_start: 0.7034 (OUTLIER) cc_final: 0.6584 (tt0)
REVERT: C  259 LYS cc_start: 0.6933 (tttt) cc_final: 0.6587 (mttp)
REVERT: C  330 MET cc_start: 0.7931 (mmt) cc_final: 0.7245 (mmm)
REVERT: D  202 GLU cc_start: 0.7047 (OUTLIER) cc_final: 0.6584 (tt0)
REVERT: D  259 LYS cc_start: 0.6984 (tttt) cc_final: 0.6656 (mttp)
REVERT: D  330 MET cc_start: 0.7942 (mmt) cc_final: 0.7263 (mmm)
REVERT: E  149 LYS cc_start: 0.8409 (mmmm) cc_final: 0.8038 (mppt)
REVERT: E  259 LYS cc_start: 0.6862 (tttt) cc_final: 0.6538 (mttp)
REVERT: F  259 LYS cc_start: 0.6856 (tttt) cc_final: 0.6505 (mttp)
  outliers start: 24
  outliers final: 12
  residues processed: 264
  average time/residue: 0.5697
  time to fit residues: 168.6947
Evaluate side-chains
  247 residues out of total 1824 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 233
  time to evaluate  : 0.665 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  114 THR
Chi-restraints excluded: chain A residue  261 SER
Chi-restraints excluded: chain A residue  340 THR
Chi-restraints excluded: chain B residue  340 THR
Chi-restraints excluded: chain C residue  202 GLU
Chi-restraints excluded: chain C residue  306 ILE
Chi-restraints excluded: chain C residue  340 THR
Chi-restraints excluded: chain D residue  202 GLU
Chi-restraints excluded: chain D residue  306 ILE
Chi-restraints excluded: chain D residue  340 THR
Chi-restraints excluded: chain E residue  340 THR
Chi-restraints excluded: chain F residue  114 THR
Chi-restraints excluded: chain F residue  261 SER
Chi-restraints excluded: chain F residue  340 THR
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 204
   random chunks:
   chunk 169 optimal weight:   10.0000
   chunk 48 optimal weight:    1.9990
   chunk 72 optimal weight:    1.9990
   chunk 181 optimal weight:    1.9990
   chunk 184 optimal weight:    4.9990
   chunk 178 optimal weight:    1.9990
   chunk 142 optimal weight:    0.0170
   chunk 12 optimal weight:    0.8980
   chunk 99 optimal weight:    4.9990
   chunk 141 optimal weight:    0.6980
   chunk 166 optimal weight:    5.9990
   overall best weight:    1.1222

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

Flipped N/Q/H residues before XYZ refinement:
A  19 GLN
B  19 GLN
C  19 GLN
C 277 ASN
D  19 GLN
D 152 GLN
D 277 ASN
E  19 GLN
F  19 GLN

Total number of N/Q/H flips: 9

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3835 r_free = 0.3835 target = 0.169031 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 26)----------------|
| r_work = 0.3351 r_free = 0.3351 target = 0.125839 restraints weight = 91835.179|
|-----------------------------------------------------------------------------|
r_work (start): 0.3282 rms_B_bonded: 4.91
r_work: 0.2960 rms_B_bonded: 3.34 restraints_weight: 0.5000
r_work (final): 0.2960
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2936
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2936 r_free = 0.2936    target_work(ls_wunit_k1) = 0.095         |
| occupancies: max = 1.00  min = 0.48   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2936 r_free = 0.2936    target_work(ls_wunit_k1) = 0.095         |
| occupancies: max = 1.00  min = 0.48   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2936
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8280
moved from start:          0.1311

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.035  16872  Z= 0.182
  Angle     :  0.561  10.147  22902  Z= 0.300
  Chirality :  0.048   0.137   2634
  Planarity :  0.004   0.044   2952
  Dihedral  :  5.158  35.021   2220
  Min Nonbonded Distance : 2.592

Molprobity Statistics.
  All-atom Clashscore : 5.11
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.45 %
    Favored  : 98.55 %
  Rotamer:
    Outliers :  2.15 %
    Allowed  : 18.12 %
    Favored  : 79.73 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.28 (0.18), residues: 2094
  helix:  0.34 (0.22), residues: 552
  sheet:  0.33 (0.27), residues: 342
  loop :  0.20 (0.18), residues: 1200

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG E 138 
 TYR   0.010   0.001   TYR A 225 
 PHE   0.023   0.002   PHE D 221 
 TRP   0.014   0.002   TRP C  58 
 HIS   0.004   0.001   HIS A  95 

Details of bonding type rmsd
  covalent geometry    : bond        0.00410 (16872)
  covalent geometry    : angle       0.56143 (22902)
  hydrogen bonds       : bond        0.04295 (  609)
  hydrogen bonds       : angle       5.79103 ( 1683)

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

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

  4188 Ramachandran restraints generated.
    2094 Oldfield, 0 Emsley, 2094 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4188 Ramachandran restraints generated.
    2094 Oldfield, 0 Emsley, 2094 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  297 residues out of total 1824 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 40
    poor density    : 257
  time to evaluate  : 0.579 
Fit side-chains
REVERT: A  259 LYS cc_start: 0.6919 (tttt) cc_final: 0.6619 (mttp)
REVERT: B  149 LYS cc_start: 0.8409 (mmmm) cc_final: 0.8033 (mppt)
REVERT: B  340 THR cc_start: 0.7346 (OUTLIER) cc_final: 0.6962 (p)
REVERT: C  202 GLU cc_start: 0.7045 (OUTLIER) cc_final: 0.6656 (tt0)
REVERT: C  233 GLU cc_start: 0.6772 (mp0) cc_final: 0.6534 (pm20)
REVERT: C  259 LYS cc_start: 0.7138 (tttt) cc_final: 0.6649 (mttp)
REVERT: C  330 MET cc_start: 0.8044 (mmt) cc_final: 0.7482 (mmm)
REVERT: D  202 GLU cc_start: 0.7048 (OUTLIER) cc_final: 0.6663 (tt0)
REVERT: D  259 LYS cc_start: 0.7155 (tttt) cc_final: 0.6690 (mttp)
REVERT: D  330 MET cc_start: 0.8040 (mmt) cc_final: 0.7501 (mmm)
REVERT: E  149 LYS cc_start: 0.8410 (mmmm) cc_final: 0.8041 (mppt)
REVERT: E  259 LYS cc_start: 0.7033 (tttt) cc_final: 0.6609 (mttp)
REVERT: E  340 THR cc_start: 0.7365 (OUTLIER) cc_final: 0.6987 (p)
REVERT: F  259 LYS cc_start: 0.6927 (tttt) cc_final: 0.6629 (mttp)
  outliers start: 40
  outliers final: 21
  residues processed: 282
  average time/residue: 0.5823
  time to fit residues: 183.4300
Evaluate side-chains
  271 residues out of total 1824 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 246
  time to evaluate  : 0.551 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  114 THR
Chi-restraints excluded: chain A residue  147 SER
Chi-restraints excluded: chain A residue  261 SER
Chi-restraints excluded: chain B residue  147 SER
Chi-restraints excluded: chain B residue  202 GLU
Chi-restraints excluded: chain B residue  232 PHE
Chi-restraints excluded: chain B residue  340 THR
Chi-restraints excluded: chain C residue  147 SER
Chi-restraints excluded: chain C residue  149 LYS
Chi-restraints excluded: chain C residue  202 GLU
Chi-restraints excluded: chain C residue  232 PHE
Chi-restraints excluded: chain C residue  306 ILE
Chi-restraints excluded: chain C residue  340 THR
Chi-restraints excluded: chain D residue  147 SER
Chi-restraints excluded: chain D residue  149 LYS
Chi-restraints excluded: chain D residue  202 GLU
Chi-restraints excluded: chain D residue  232 PHE
Chi-restraints excluded: chain D residue  306 ILE
Chi-restraints excluded: chain D residue  340 THR
Chi-restraints excluded: chain E residue  147 SER
Chi-restraints excluded: chain E residue  232 PHE
Chi-restraints excluded: chain E residue  340 THR
Chi-restraints excluded: chain F residue  114 THR
Chi-restraints excluded: chain F residue  147 SER
Chi-restraints excluded: chain F residue  261 SER
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 204
   random chunks:
   chunk 168 optimal weight:    5.9990
   chunk 174 optimal weight:    1.9990
   chunk 33 optimal weight:    0.0040
   chunk 177 optimal weight:    0.0980
   chunk 98 optimal weight:    6.9990
   chunk 102 optimal weight:    2.9990
   chunk 89 optimal weight:    5.9990
   chunk 140 optimal weight:    2.9990
   chunk 151 optimal weight:    3.9990
   chunk 126 optimal weight:    0.6980
   chunk 121 optimal weight:    0.9980
   overall best weight:    0.7594

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

Flipped N/Q/H residues before XYZ refinement:
A  19 GLN
B  19 GLN
B 277 ASN
C  19 GLN
C 152 GLN
C 277 ASN
D  19 GLN
D 152 GLN
D 277 ASN
E  19 GLN
E 277 ASN
F  19 GLN

Total number of N/Q/H flips: 12

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3851 r_free = 0.3851 target = 0.170665 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 26)----------------|
| r_work = 0.3376 r_free = 0.3376 target = 0.127743 restraints weight = 89191.281|
|-----------------------------------------------------------------------------|
r_work (start): 0.3308 rms_B_bonded: 4.84
r_work: 0.2982 rms_B_bonded: 3.45 restraints_weight: 0.5000
r_work (final): 0.2982
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2927
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2927 r_free = 0.2927    target_work(ls_wunit_k1) = 0.094         |
| occupancies: max = 1.00  min = 0.48   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2927 r_free = 0.2927    target_work(ls_wunit_k1) = 0.094         |
| occupancies: max = 1.00  min = 0.48   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2927
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8266
moved from start:          0.1409

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.024  16872  Z= 0.138
  Angle     :  0.529  12.046  22902  Z= 0.278
  Chirality :  0.046   0.135   2634
  Planarity :  0.003   0.045   2952
  Dihedral  :  4.757  20.205   2218
  Min Nonbonded Distance : 2.602

Molprobity Statistics.
  All-atom Clashscore : 4.66
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.31 %
    Favored  : 98.69 %
  Rotamer:
    Outliers :  1.18 %
    Allowed  : 19.46 %
    Favored  : 79.35 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.38 (0.18), residues: 2094
  helix:  0.52 (0.23), residues: 552
  sheet:  0.44 (0.26), residues: 342
  loop :  0.19 (0.18), residues: 1200

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG E 138 
 TYR   0.008   0.001   TYR E 225 
 PHE   0.026   0.002   PHE D 221 
 TRP   0.010   0.001   TRP C  58 
 HIS   0.003   0.001   HIS F  95 

Details of bonding type rmsd
  covalent geometry    : bond        0.00307 (16872)
  covalent geometry    : angle       0.52889 (22902)
  hydrogen bonds       : bond        0.03678 (  609)
  hydrogen bonds       : angle       5.51239 ( 1683)

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

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

  4188 Ramachandran restraints generated.
    2094 Oldfield, 0 Emsley, 2094 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4188 Ramachandran restraints generated.
    2094 Oldfield, 0 Emsley, 2094 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  268 residues out of total 1824 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 246
  time to evaluate  : 0.685 
Fit side-chains
REVERT: A  259 LYS cc_start: 0.6992 (tttt) cc_final: 0.6588 (mttp)
REVERT: B  149 LYS cc_start: 0.8395 (mmmm) cc_final: 0.8019 (mppt)
REVERT: B  259 LYS cc_start: 0.7072 (tttt) cc_final: 0.6622 (mttp)
REVERT: C  149 LYS cc_start: 0.8374 (OUTLIER) cc_final: 0.7929 (tptt)
REVERT: C  202 GLU cc_start: 0.6988 (OUTLIER) cc_final: 0.6627 (tt0)
REVERT: C  233 GLU cc_start: 0.6755 (mp0) cc_final: 0.6522 (pm20)
REVERT: C  259 LYS cc_start: 0.7147 (tttt) cc_final: 0.6641 (mttp)
REVERT: C  330 MET cc_start: 0.8024 (mmt) cc_final: 0.7488 (mmm)
REVERT: D  202 GLU cc_start: 0.7019 (OUTLIER) cc_final: 0.6642 (tt0)
REVERT: D  233 GLU cc_start: 0.6718 (mp0) cc_final: 0.6454 (pm20)
REVERT: D  259 LYS cc_start: 0.7147 (tttt) cc_final: 0.6664 (mttp)
REVERT: D  330 MET cc_start: 0.8032 (mmt) cc_final: 0.7500 (mmm)
REVERT: E  149 LYS cc_start: 0.8389 (mmmm) cc_final: 0.8015 (mppt)
REVERT: E  259 LYS cc_start: 0.7091 (tttt) cc_final: 0.6639 (mttp)
REVERT: F  259 LYS cc_start: 0.6974 (tttt) cc_final: 0.6619 (mttp)
  outliers start: 22
  outliers final: 12
  residues processed: 255
  average time/residue: 0.6191
  time to fit residues: 176.5994
Evaluate side-chains
  249 residues out of total 1824 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 234
  time to evaluate  : 0.643 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  147 SER
Chi-restraints excluded: chain A residue  261 SER
Chi-restraints excluded: chain B residue  147 SER
Chi-restraints excluded: chain B residue  232 PHE
Chi-restraints excluded: chain C residue  147 SER
Chi-restraints excluded: chain C residue  149 LYS
Chi-restraints excluded: chain C residue  202 GLU
Chi-restraints excluded: chain C residue  232 PHE
Chi-restraints excluded: chain D residue  147 SER
Chi-restraints excluded: chain D residue  149 LYS
Chi-restraints excluded: chain D residue  202 GLU
Chi-restraints excluded: chain D residue  232 PHE
Chi-restraints excluded: chain E residue  202 GLU
Chi-restraints excluded: chain E residue  232 PHE
Chi-restraints excluded: chain F residue  147 SER
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 204
   random chunks:
   chunk 189 optimal weight:    0.8980
   chunk 29 optimal weight:    2.9990
   chunk 1 optimal weight:    0.8980
   chunk 203 optimal weight:    0.5980
   chunk 175 optimal weight:    2.9990
   chunk 139 optimal weight:    0.8980
   chunk 132 optimal weight:    0.8980
   chunk 95 optimal weight:    0.8980
   chunk 21 optimal weight:    6.9990
   chunk 62 optimal weight:    0.9990
   chunk 87 optimal weight:    0.9980
   overall best weight:    0.8380

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

Flipped N/Q/H residues before XYZ refinement:
A  19 GLN
B  19 GLN
C  19 GLN
C 152 GLN
C 277 ASN
D  19 GLN
D 152 GLN
D 277 ASN
E  19 GLN
F  19 GLN

Total number of N/Q/H flips: 10

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3844 r_free = 0.3844 target = 0.169987 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 26)----------------|
| r_work = 0.3368 r_free = 0.3368 target = 0.127167 restraints weight = 84336.129|
|-----------------------------------------------------------------------------|
r_work (start): 0.3300 rms_B_bonded: 4.83
r_work: 0.2973 rms_B_bonded: 3.44 restraints_weight: 0.5000
r_work (final): 0.2973
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2948
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2948 r_free = 0.2948    target_work(ls_wunit_k1) = 0.096         |
| occupancies: max = 1.00  min = 0.48   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2948 r_free = 0.2948    target_work(ls_wunit_k1) = 0.096         |
| occupancies: max = 1.00  min = 0.48   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2948
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8275
moved from start:          0.1448

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028  16872  Z= 0.148
  Angle     :  0.533  11.229  22902  Z= 0.282
  Chirality :  0.047   0.136   2634
  Planarity :  0.003   0.046   2952
  Dihedral  :  4.755  16.667   2214
  Min Nonbonded Distance : 2.600

Molprobity Statistics.
  All-atom Clashscore : 4.87
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.65 %
    Favored  : 98.35 %
  Rotamer:
    Outliers :  1.56 %
    Allowed  : 18.92 %
    Favored  : 79.52 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.35 (0.18), residues: 2094
  helix:  0.51 (0.23), residues: 552
  sheet:  0.44 (0.26), residues: 342
  loop :  0.16 (0.18), residues: 1200

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG E 138 
 TYR   0.009   0.001   TYR F 225 
 PHE   0.028   0.002   PHE C 221 
 TRP   0.011   0.001   TRP C  58 
 HIS   0.004   0.001   HIS A  95 

Details of bonding type rmsd
  covalent geometry    : bond        0.00331 (16872)
  covalent geometry    : angle       0.53347 (22902)
  hydrogen bonds       : bond        0.03760 (  609)
  hydrogen bonds       : angle       5.50048 ( 1683)

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

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

  4188 Ramachandran restraints generated.
    2094 Oldfield, 0 Emsley, 2094 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4188 Ramachandran restraints generated.
    2094 Oldfield, 0 Emsley, 2094 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  273 residues out of total 1824 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 244
  time to evaluate  : 0.696 
Fit side-chains
REVERT: A  259 LYS cc_start: 0.7015 (tttt) cc_final: 0.6583 (mttp)
REVERT: B  149 LYS cc_start: 0.8398 (mmmm) cc_final: 0.8028 (mppt)
REVERT: B  259 LYS cc_start: 0.7011 (tttt) cc_final: 0.6641 (ttpp)
REVERT: C  202 GLU cc_start: 0.7004 (OUTLIER) cc_final: 0.6637 (tt0)
REVERT: C  233 GLU cc_start: 0.6763 (mp0) cc_final: 0.6528 (pm20)
REVERT: C  330 MET cc_start: 0.7972 (mmt) cc_final: 0.7388 (mmm)
REVERT: D  202 GLU cc_start: 0.7027 (OUTLIER) cc_final: 0.6646 (tt0)
REVERT: D  220 GLU cc_start: 0.6773 (mt-10) cc_final: 0.6461 (pt0)
REVERT: D  233 GLU cc_start: 0.6733 (mp0) cc_final: 0.6478 (pm20)
REVERT: D  330 MET cc_start: 0.7981 (mmt) cc_final: 0.7402 (mmm)
REVERT: E   68 GLU cc_start: 0.7670 (OUTLIER) cc_final: 0.7341 (mp0)
REVERT: E  149 LYS cc_start: 0.8408 (mmmm) cc_final: 0.8033 (mppt)
REVERT: E  259 LYS cc_start: 0.7029 (tttt) cc_final: 0.6652 (ttpp)
REVERT: F  259 LYS cc_start: 0.7059 (tttt) cc_final: 0.6606 (mttp)
  outliers start: 29
  outliers final: 18
  residues processed: 256
  average time/residue: 0.6400
  time to fit residues: 182.7936
Evaluate side-chains
  254 residues out of total 1824 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 233
  time to evaluate  : 0.706 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  114 THR
Chi-restraints excluded: chain A residue  147 SER
Chi-restraints excluded: chain A residue  261 SER
Chi-restraints excluded: chain B residue  147 SER
Chi-restraints excluded: chain B residue  232 PHE
Chi-restraints excluded: chain C residue  147 SER
Chi-restraints excluded: chain C residue  149 LYS
Chi-restraints excluded: chain C residue  202 GLU
Chi-restraints excluded: chain C residue  232 PHE
Chi-restraints excluded: chain C residue  306 ILE
Chi-restraints excluded: chain D residue  147 SER
Chi-restraints excluded: chain D residue  149 LYS
Chi-restraints excluded: chain D residue  202 GLU
Chi-restraints excluded: chain D residue  232 PHE
Chi-restraints excluded: chain D residue  306 ILE
Chi-restraints excluded: chain E residue   68 GLU
Chi-restraints excluded: chain E residue  147 SER
Chi-restraints excluded: chain E residue  202 GLU
Chi-restraints excluded: chain E residue  232 PHE
Chi-restraints excluded: chain F residue  114 THR
Chi-restraints excluded: chain F residue  147 SER
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 204
   random chunks:
   chunk 171 optimal weight:    0.0670
   chunk 131 optimal weight:    3.9990
   chunk 2 optimal weight:    0.6980
   chunk 106 optimal weight:    2.9990
   chunk 8 optimal weight:    1.9990
   chunk 20 optimal weight:    1.9990
   chunk 83 optimal weight:    3.9990
   chunk 112 optimal weight:    4.9990
   chunk 22 optimal weight:    3.9990
   chunk 64 optimal weight:    0.7980
   chunk 149 optimal weight:    2.9990
   overall best weight:    1.1122

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

Flipped N/Q/H residues before XYZ refinement:
A  19 GLN
A 277 ASN
B  19 GLN
C  19 GLN
C 152 GLN
C 277 ASN
D  19 GLN
D 152 GLN
D 277 ASN
E  19 GLN
F  19 GLN
F 277 ASN

Total number of N/Q/H flips: 12

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3838 r_free = 0.3838 target = 0.169247 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 26)----------------|
| r_work = 0.3356 r_free = 0.3356 target = 0.126179 restraints weight = 88425.923|
|-----------------------------------------------------------------------------|
r_work (start): 0.3285 rms_B_bonded: 4.77
r_work: 0.2968 rms_B_bonded: 3.38 restraints_weight: 0.5000
r_work (final): 0.2968
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2940
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2940 r_free = 0.2940    target_work(ls_wunit_k1) = 0.095         |
| occupancies: max = 1.00  min = 0.48   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2940 r_free = 0.2940    target_work(ls_wunit_k1) = 0.095         |
| occupancies: max = 1.00  min = 0.47   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2940
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8293
moved from start:          0.1497

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.035  16872  Z= 0.178
  Angle     :  0.560  11.171  22902  Z= 0.297
  Chirality :  0.047   0.137   2634
  Planarity :  0.004   0.047   2952
  Dihedral  :  4.919  17.556   2214
  Min Nonbonded Distance : 2.595

Molprobity Statistics.
  All-atom Clashscore : 5.45
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.65 %
    Favored  : 98.35 %
  Rotamer:
    Outliers :  1.40 %
    Allowed  : 19.41 %
    Favored  : 79.19 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.27 (0.18), residues: 2094
  helix:  0.40 (0.23), residues: 552
  sheet:  0.43 (0.26), residues: 342
  loop :  0.12 (0.18), residues: 1200

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG B 138 
 TYR   0.009   0.001   TYR F 225 
 PHE   0.029   0.002   PHE D 221 
 TRP   0.012   0.002   TRP C  58 
 HIS   0.004   0.001   HIS A  95 

Details of bonding type rmsd
  covalent geometry    : bond        0.00400 (16872)
  covalent geometry    : angle       0.55976 (22902)
  hydrogen bonds       : bond        0.04041 (  609)
  hydrogen bonds       : angle       5.61607 ( 1683)

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

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

  4188 Ramachandran restraints generated.
    2094 Oldfield, 0 Emsley, 2094 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4188 Ramachandran restraints generated.
    2094 Oldfield, 0 Emsley, 2094 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  269 residues out of total 1824 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 243
  time to evaluate  : 0.691 
Fit side-chains
REVERT: A  193 TYR cc_start: 0.8885 (m-80) cc_final: 0.8643 (m-80)
REVERT: A  259 LYS cc_start: 0.6972 (tttt) cc_final: 0.6535 (mttp)
REVERT: B  149 LYS cc_start: 0.8417 (mmmm) cc_final: 0.8050 (mppt)
REVERT: C  202 GLU cc_start: 0.7040 (OUTLIER) cc_final: 0.6676 (tt0)
REVERT: C  220 GLU cc_start: 0.6855 (mt-10) cc_final: 0.6566 (pt0)
REVERT: C  233 GLU cc_start: 0.6788 (mp0) cc_final: 0.6537 (pm20)
REVERT: C  330 MET cc_start: 0.7976 (mmt) cc_final: 0.7654 (mmm)
REVERT: D  202 GLU cc_start: 0.7062 (OUTLIER) cc_final: 0.6686 (tt0)
REVERT: D  233 GLU cc_start: 0.6817 (mp0) cc_final: 0.6557 (pm20)
REVERT: D  330 MET cc_start: 0.7968 (mmt) cc_final: 0.7641 (mmm)
REVERT: E   68 GLU cc_start: 0.7764 (OUTLIER) cc_final: 0.7444 (mp0)
REVERT: E  149 LYS cc_start: 0.8428 (mmmm) cc_final: 0.8060 (mppt)
REVERT: F  193 TYR cc_start: 0.8887 (m-80) cc_final: 0.8643 (m-80)
REVERT: F  257 ARG cc_start: 0.7796 (tpt170) cc_final: 0.7416 (tpt170)
REVERT: F  259 LYS cc_start: 0.7029 (tttt) cc_final: 0.6572 (mttp)
  outliers start: 26
  outliers final: 20
  residues processed: 254
  average time/residue: 0.6322
  time to fit residues: 178.9697
Evaluate side-chains
  254 residues out of total 1824 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 231
  time to evaluate  : 0.784 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  114 THR
Chi-restraints excluded: chain A residue  147 SER
Chi-restraints excluded: chain A residue  261 SER
Chi-restraints excluded: chain B residue  147 SER
Chi-restraints excluded: chain B residue  232 PHE
Chi-restraints excluded: chain C residue   12 LYS
Chi-restraints excluded: chain C residue  147 SER
Chi-restraints excluded: chain C residue  149 LYS
Chi-restraints excluded: chain C residue  202 GLU
Chi-restraints excluded: chain C residue  232 PHE
Chi-restraints excluded: chain C residue  306 ILE
Chi-restraints excluded: chain D residue   12 LYS
Chi-restraints excluded: chain D residue  147 SER
Chi-restraints excluded: chain D residue  149 LYS
Chi-restraints excluded: chain D residue  202 GLU
Chi-restraints excluded: chain D residue  232 PHE
Chi-restraints excluded: chain D residue  306 ILE
Chi-restraints excluded: chain E residue   68 GLU
Chi-restraints excluded: chain E residue  147 SER
Chi-restraints excluded: chain E residue  202 GLU
Chi-restraints excluded: chain E residue  232 PHE
Chi-restraints excluded: chain F residue  114 THR
Chi-restraints excluded: chain F residue  147 SER
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 204
   random chunks:
   chunk 161 optimal weight:    0.6980
   chunk 94 optimal weight:    0.9980
   chunk 189 optimal weight:    0.8980
   chunk 152 optimal weight:    1.9990
   chunk 20 optimal weight:    0.9980
   chunk 78 optimal weight:    1.9990
   chunk 74 optimal weight:    0.1980
   chunk 39 optimal weight:    0.5980
   chunk 52 optimal weight:    1.9990
   chunk 198 optimal weight:    0.5980
   chunk 38 optimal weight:    1.9990
   overall best weight:    0.5980

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

Flipped N/Q/H residues before XYZ refinement:
A  19 GLN
B  19 GLN
C  19 GLN
C 152 GLN
C 277 ASN
D  19 GLN
D 152 GLN
D 277 ASN
E  19 GLN
F  19 GLN

Total number of N/Q/H flips: 10

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3854 r_free = 0.3854 target = 0.170903 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 26)----------------|
| r_work = 0.3379 r_free = 0.3379 target = 0.128034 restraints weight = 91133.198|
|-----------------------------------------------------------------------------|
r_work (start): 0.3292 rms_B_bonded: 4.78
r_work: 0.2976 rms_B_bonded: 3.36 restraints_weight: 0.5000
r_work (final): 0.2976
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2978
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2978 r_free = 0.2978    target_work(ls_wunit_k1) = 0.097         |
| occupancies: max = 1.00  min = 0.47   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2978 r_free = 0.2978    target_work(ls_wunit_k1) = 0.097         |
| occupancies: max = 1.00  min = 0.47   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2978
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8250
moved from start:          0.1524

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.026  16872  Z= 0.123
  Angle     :  0.514  11.163  22902  Z= 0.271
  Chirality :  0.046   0.135   2634
  Planarity :  0.003   0.046   2952
  Dihedral  :  4.633  15.862   2214
  Min Nonbonded Distance : 2.604

Molprobity Statistics.
  All-atom Clashscore : 4.81
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.26 %
    Favored  : 98.74 %
  Rotamer:
    Outliers :  1.34 %
    Allowed  : 19.52 %
    Favored  : 79.14 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.42 (0.18), residues: 2094
  helix:  0.60 (0.23), residues: 552
  sheet:  0.49 (0.26), residues: 342
  loop :  0.18 (0.18), residues: 1200

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG E 138 
 TYR   0.008   0.001   TYR A 225 
 PHE   0.030   0.002   PHE D 221 
 TRP   0.009   0.001   TRP D  58 
 HIS   0.003   0.001   HIS F  95 

Details of bonding type rmsd
  covalent geometry    : bond        0.00270 (16872)
  covalent geometry    : angle       0.51400 (22902)
  hydrogen bonds       : bond        0.03438 (  609)
  hydrogen bonds       : angle       5.36620 ( 1683)

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

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

  4188 Ramachandran restraints generated.
    2094 Oldfield, 0 Emsley, 2094 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4188 Ramachandran restraints generated.
    2094 Oldfield, 0 Emsley, 2094 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  259 residues out of total 1824 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 234
  time to evaluate  : 0.707 
Fit side-chains
REVERT: B  149 LYS cc_start: 0.8362 (mmmm) cc_final: 0.8006 (mppt)
REVERT: B  202 GLU cc_start: 0.7010 (OUTLIER) cc_final: 0.6580 (tt0)
REVERT: C  149 LYS cc_start: 0.8352 (OUTLIER) cc_final: 0.7923 (tptt)
REVERT: C  202 GLU cc_start: 0.6941 (OUTLIER) cc_final: 0.6599 (tt0)
REVERT: C  220 GLU cc_start: 0.6793 (mt-10) cc_final: 0.6490 (pt0)
REVERT: C  233 GLU cc_start: 0.6733 (mp0) cc_final: 0.6492 (pm20)
REVERT: C  330 MET cc_start: 0.7934 (mmt) cc_final: 0.7647 (mmm)
REVERT: D  149 LYS cc_start: 0.8338 (OUTLIER) cc_final: 0.7908 (tptt)
REVERT: D  202 GLU cc_start: 0.6969 (OUTLIER) cc_final: 0.6614 (tt0)
REVERT: D  220 GLU cc_start: 0.6795 (mt-10) cc_final: 0.6425 (pt0)
REVERT: D  233 GLU cc_start: 0.6703 (mp0) cc_final: 0.6458 (pm20)
REVERT: D  330 MET cc_start: 0.7945 (mmt) cc_final: 0.7656 (mmm)
REVERT: E  149 LYS cc_start: 0.8381 (mmmm) cc_final: 0.8018 (mppt)
REVERT: F  257 ARG cc_start: 0.7740 (tpt170) cc_final: 0.7474 (tpt170)
REVERT: F  259 LYS cc_start: 0.7028 (tttt) cc_final: 0.6619 (mttp)
REVERT: F  330 MET cc_start: 0.8001 (mmt) cc_final: 0.7242 (mmm)
  outliers start: 25
  outliers final: 13
  residues processed: 245
  average time/residue: 0.6227
  time to fit residues: 170.7025
Evaluate side-chains
  247 residues out of total 1824 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 229
  time to evaluate  : 0.685 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  114 THR
Chi-restraints excluded: chain A residue  147 SER
Chi-restraints excluded: chain B residue  202 GLU
Chi-restraints excluded: chain B residue  232 PHE
Chi-restraints excluded: chain C residue   12 LYS
Chi-restraints excluded: chain C residue  147 SER
Chi-restraints excluded: chain C residue  149 LYS
Chi-restraints excluded: chain C residue  202 GLU
Chi-restraints excluded: chain C residue  232 PHE
Chi-restraints excluded: chain D residue   12 LYS
Chi-restraints excluded: chain D residue  147 SER
Chi-restraints excluded: chain D residue  149 LYS
Chi-restraints excluded: chain D residue  202 GLU
Chi-restraints excluded: chain D residue  232 PHE
Chi-restraints excluded: chain E residue  147 SER
Chi-restraints excluded: chain E residue  232 PHE
Chi-restraints excluded: chain F residue  114 THR
Chi-restraints excluded: chain F residue  147 SER
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 204
   random chunks:
   chunk 16 optimal weight:    2.9990
   chunk 110 optimal weight:    1.9990
   chunk 123 optimal weight:    6.9990
   chunk 162 optimal weight:    0.7980
   chunk 112 optimal weight:    0.9990
   chunk 152 optimal weight:    0.9990
   chunk 5 optimal weight:    0.5980
   chunk 24 optimal weight:    6.9990
   chunk 194 optimal weight:    4.9990
   chunk 144 optimal weight:    0.0970
   chunk 173 optimal weight:    3.9990
   overall best weight:    0.6982

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

Flipped N/Q/H residues before XYZ refinement:
B  19 GLN
C  19 GLN
C 152 GLN
C 277 ASN
D  19 GLN
D 152 GLN
D 277 ASN
E  19 GLN

Total number of N/Q/H flips: 8

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3851 r_free = 0.3851 target = 0.170643 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 26)----------------|
| r_work = 0.3376 r_free = 0.3376 target = 0.127747 restraints weight = 87586.126|
|-----------------------------------------------------------------------------|
r_work (start): 0.3306 rms_B_bonded: 4.82
r_work: 0.2990 rms_B_bonded: 3.43 restraints_weight: 0.5000
r_work (final): 0.2990
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2936
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2936 r_free = 0.2936    target_work(ls_wunit_k1) = 0.095         |
| occupancies: max = 1.00  min = 0.47   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2936 r_free = 0.2936    target_work(ls_wunit_k1) = 0.095         |
| occupancies: max = 1.00  min = 0.47   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2936
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8267
moved from start:          0.1538

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.026  16872  Z= 0.132
  Angle     :  0.518  11.057  22902  Z= 0.273
  Chirality :  0.046   0.135   2634
  Planarity :  0.003   0.046   2952
  Dihedral  :  4.657  16.114   2214
  Min Nonbonded Distance : 2.603

Molprobity Statistics.
  All-atom Clashscore : 4.84
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.36 %
    Favored  : 98.64 %
  Rotamer:
    Outliers :  1.08 %
    Allowed  : 19.78 %
    Favored  : 79.14 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.42 (0.18), residues: 2094
  helix:  0.65 (0.23), residues: 546
  sheet:  0.50 (0.26), residues: 342
  loop :  0.15 (0.18), residues: 1206

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG B 138 
 TYR   0.008   0.001   TYR F 225 
 PHE   0.032   0.002   PHE D 221 
 TRP   0.010   0.001   TRP C  58 
 HIS   0.003   0.001   HIS A  95 

Details of bonding type rmsd
  covalent geometry    : bond        0.00292 (16872)
  covalent geometry    : angle       0.51832 (22902)
  hydrogen bonds       : bond        0.03510 (  609)
  hydrogen bonds       : angle       5.36466 ( 1683)

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

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

  4188 Ramachandran restraints generated.
    2094 Oldfield, 0 Emsley, 2094 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4188 Ramachandran restraints generated.
    2094 Oldfield, 0 Emsley, 2094 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  256 residues out of total 1824 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 236
  time to evaluate  : 0.700 
Fit side-chains
REVERT: B  149 LYS cc_start: 0.8361 (mmmm) cc_final: 0.8012 (mppt)
REVERT: C  149 LYS cc_start: 0.8361 (OUTLIER) cc_final: 0.7931 (tptt)
REVERT: C  202 GLU cc_start: 0.6967 (OUTLIER) cc_final: 0.6599 (tt0)
REVERT: C  220 GLU cc_start: 0.6844 (mt-10) cc_final: 0.6526 (pt0)
REVERT: C  233 GLU cc_start: 0.6756 (mp0) cc_final: 0.6512 (pm20)
REVERT: C  330 MET cc_start: 0.7958 (mmt) cc_final: 0.7632 (mmm)
REVERT: D  149 LYS cc_start: 0.8343 (OUTLIER) cc_final: 0.7914 (tptt)
REVERT: D  202 GLU cc_start: 0.6995 (OUTLIER) cc_final: 0.6607 (tt0)
REVERT: D  220 GLU cc_start: 0.6829 (mt-10) cc_final: 0.6445 (pt0)
REVERT: D  233 GLU cc_start: 0.6709 (mp0) cc_final: 0.6466 (pm20)
REVERT: D  330 MET cc_start: 0.7954 (mmt) cc_final: 0.7629 (mmm)
REVERT: E  149 LYS cc_start: 0.8377 (mmmm) cc_final: 0.8024 (mppt)
REVERT: F  257 ARG cc_start: 0.7753 (tpt170) cc_final: 0.7310 (tpt170)
REVERT: F  259 LYS cc_start: 0.7015 (tttt) cc_final: 0.6588 (mttp)
REVERT: F  330 MET cc_start: 0.7999 (mmt) cc_final: 0.7255 (mmm)
  outliers start: 20
  outliers final: 14
  residues processed: 247
  average time/residue: 0.6424
  time to fit residues: 177.0038
Evaluate side-chains
  251 residues out of total 1824 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 233
  time to evaluate  : 0.797 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  114 THR
Chi-restraints excluded: chain A residue  147 SER
Chi-restraints excluded: chain B residue   47 THR
Chi-restraints excluded: chain B residue  232 PHE
Chi-restraints excluded: chain C residue   12 LYS
Chi-restraints excluded: chain C residue  147 SER
Chi-restraints excluded: chain C residue  149 LYS
Chi-restraints excluded: chain C residue  202 GLU
Chi-restraints excluded: chain C residue  232 PHE
Chi-restraints excluded: chain D residue   12 LYS
Chi-restraints excluded: chain D residue  147 SER
Chi-restraints excluded: chain D residue  149 LYS
Chi-restraints excluded: chain D residue  202 GLU
Chi-restraints excluded: chain D residue  232 PHE
Chi-restraints excluded: chain E residue  147 SER
Chi-restraints excluded: chain E residue  232 PHE
Chi-restraints excluded: chain F residue  114 THR
Chi-restraints excluded: chain F residue  147 SER
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 204
   random chunks:
   chunk 33 optimal weight:    8.9990
   chunk 118 optimal weight:    0.8980
   chunk 197 optimal weight:    0.9990
   chunk 176 optimal weight:    0.1980
   chunk 113 optimal weight:    1.9990
   chunk 83 optimal weight:    0.8980
   chunk 75 optimal weight:    0.9990
   chunk 76 optimal weight:    0.7980
   chunk 97 optimal weight:    4.9990
   chunk 37 optimal weight:    2.9990
   chunk 110 optimal weight:    0.5980
   overall best weight:    0.6780

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

Flipped N/Q/H residues before XYZ refinement:
A  19 GLN
B  19 GLN
C  19 GLN
C 152 GLN
C 277 ASN
D 152 GLN
D 277 ASN
E  19 GLN
F  19 GLN

Total number of N/Q/H flips: 9

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3854 r_free = 0.3854 target = 0.170808 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 26)----------------|
| r_work = 0.3378 r_free = 0.3378 target = 0.127930 restraints weight = 92147.834|
|-----------------------------------------------------------------------------|
r_work (start): 0.3307 rms_B_bonded: 4.86
r_work: 0.2991 rms_B_bonded: 3.40 restraints_weight: 0.5000
r_work (final): 0.2991
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2940
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2940 r_free = 0.2940    target_work(ls_wunit_k1) = 0.095         |
| occupancies: max = 1.00  min = 0.47   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2940 r_free = 0.2940    target_work(ls_wunit_k1) = 0.095         |
| occupancies: max = 1.00  min = 0.47   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2940
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8257
moved from start:          0.1557

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.027  16872  Z= 0.130
  Angle     :  0.515  10.979  22902  Z= 0.272
  Chirality :  0.046   0.135   2634
  Planarity :  0.003   0.046   2952
  Dihedral  :  4.630  15.991   2214
  Min Nonbonded Distance : 2.603

Molprobity Statistics.
  All-atom Clashscore : 4.81
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.36 %
    Favored  : 98.64 %
  Rotamer:
    Outliers :  1.18 %
    Allowed  : 19.89 %
    Favored  : 78.92 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.45 (0.18), residues: 2094
  helix:  0.67 (0.23), residues: 546
  sheet:  0.53 (0.26), residues: 342
  loop :  0.16 (0.18), residues: 1206

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG B 138 
 TYR   0.008   0.001   TYR F 225 
 PHE   0.033   0.002   PHE D 221 
 TRP   0.009   0.001   TRP D  58 
 HIS   0.003   0.001   HIS F  95 

Details of bonding type rmsd
  covalent geometry    : bond        0.00286 (16872)
  covalent geometry    : angle       0.51458 (22902)
  hydrogen bonds       : bond        0.03461 (  609)
  hydrogen bonds       : angle       5.33601 ( 1683)

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

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

  4188 Ramachandran restraints generated.
    2094 Oldfield, 0 Emsley, 2094 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4188 Ramachandran restraints generated.
    2094 Oldfield, 0 Emsley, 2094 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  262 residues out of total 1824 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 240
  time to evaluate  : 0.704 
Fit side-chains
REVERT: B  149 LYS cc_start: 0.8362 (mmmm) cc_final: 0.8013 (mppt)
REVERT: B  202 GLU cc_start: 0.7019 (OUTLIER) cc_final: 0.6608 (tt0)
REVERT: C  149 LYS cc_start: 0.8365 (OUTLIER) cc_final: 0.7925 (tptt)
REVERT: C  202 GLU cc_start: 0.6946 (OUTLIER) cc_final: 0.6577 (tt0)
REVERT: C  220 GLU cc_start: 0.6852 (mt-10) cc_final: 0.6531 (pt0)
REVERT: C  233 GLU cc_start: 0.6760 (mp0) cc_final: 0.6515 (pm20)
REVERT: C  330 MET cc_start: 0.7943 (mmt) cc_final: 0.7622 (mmm)
REVERT: D  149 LYS cc_start: 0.8348 (OUTLIER) cc_final: 0.7914 (tptt)
REVERT: D  202 GLU cc_start: 0.6997 (OUTLIER) cc_final: 0.6625 (tt0)
REVERT: D  220 GLU cc_start: 0.6854 (mt-10) cc_final: 0.6469 (pt0)
REVERT: D  233 GLU cc_start: 0.6720 (mp0) cc_final: 0.6474 (pm20)
REVERT: D  330 MET cc_start: 0.7957 (mmt) cc_final: 0.7635 (mmm)
REVERT: E  149 LYS cc_start: 0.8396 (mmmm) cc_final: 0.8034 (mppt)
REVERT: F  257 ARG cc_start: 0.7764 (tpt170) cc_final: 0.7319 (tpt170)
REVERT: F  330 MET cc_start: 0.7991 (mmt) cc_final: 0.7251 (mmm)
  outliers start: 22
  outliers final: 15
  residues processed: 251
  average time/residue: 0.6517
  time to fit residues: 181.9078
Evaluate side-chains
  252 residues out of total 1824 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 232
  time to evaluate  : 0.671 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  114 THR
Chi-restraints excluded: chain A residue  147 SER
Chi-restraints excluded: chain B residue   47 THR
Chi-restraints excluded: chain B residue  147 SER
Chi-restraints excluded: chain B residue  202 GLU
Chi-restraints excluded: chain B residue  232 PHE
Chi-restraints excluded: chain C residue   12 LYS
Chi-restraints excluded: chain C residue  147 SER
Chi-restraints excluded: chain C residue  149 LYS
Chi-restraints excluded: chain C residue  202 GLU
Chi-restraints excluded: chain C residue  232 PHE
Chi-restraints excluded: chain D residue   12 LYS
Chi-restraints excluded: chain D residue  147 SER
Chi-restraints excluded: chain D residue  149 LYS
Chi-restraints excluded: chain D residue  202 GLU
Chi-restraints excluded: chain D residue  232 PHE
Chi-restraints excluded: chain E residue  147 SER
Chi-restraints excluded: chain E residue  232 PHE
Chi-restraints excluded: chain F residue  114 THR
Chi-restraints excluded: chain F residue  147 SER
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 204
   random chunks:
   chunk 167 optimal weight:    6.9990
   chunk 13 optimal weight:    3.9990
   chunk 119 optimal weight:    4.9990
   chunk 54 optimal weight:    1.9990
   chunk 186 optimal weight:    0.6980
   chunk 189 optimal weight:    0.7980
   chunk 107 optimal weight:    0.8980
   chunk 33 optimal weight:    5.9990
   chunk 51 optimal weight:    3.9990
   chunk 31 optimal weight:    3.9990
   chunk 117 optimal weight:    1.9990
   overall best weight:    1.2784

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

Flipped N/Q/H residues before XYZ refinement:
A  19 GLN
B  19 GLN
C  19 GLN
C 152 GLN
C 277 ASN
D 152 GLN
D 277 ASN
E  19 GLN
F  19 GLN

Total number of N/Q/H flips: 9

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3837 r_free = 0.3837 target = 0.168977 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 26)----------------|
| r_work = 0.3352 r_free = 0.3352 target = 0.125815 restraints weight = 88646.770|
|-----------------------------------------------------------------------------|
r_work (start): 0.3280 rms_B_bonded: 4.94
r_work: 0.2963 rms_B_bonded: 3.43 restraints_weight: 0.5000
r_work (final): 0.2963
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2932
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2932 r_free = 0.2932    target_work(ls_wunit_k1) = 0.095         |
| occupancies: max = 1.00  min = 0.47   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2932 r_free = 0.2932    target_work(ls_wunit_k1) = 0.095         |
| occupancies: max = 1.00  min = 0.47   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2932
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8297
moved from start:          0.1578

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.039  16872  Z= 0.196
  Angle     :  0.572  10.717  22902  Z= 0.304
  Chirality :  0.048   0.149   2634
  Planarity :  0.004   0.048   2952
  Dihedral  :  4.965  17.917   2214
  Min Nonbonded Distance : 2.592

Molprobity Statistics.
  All-atom Clashscore : 5.72
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.65 %
    Favored  : 98.35 %
  Rotamer:
    Outliers :  1.18 %
    Allowed  : 20.11 %
    Favored  : 78.71 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.26 (0.18), residues: 2094
  helix:  0.36 (0.23), residues: 552
  sheet:  0.48 (0.26), residues: 342
  loop :  0.11 (0.18), residues: 1200

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG B 138 
 TYR   0.009   0.001   TYR F 225 
 PHE   0.033   0.002   PHE D 221 
 TRP   0.013   0.002   TRP D  58 
 HIS   0.004   0.001   HIS F  95 

Details of bonding type rmsd
  covalent geometry    : bond        0.00442 (16872)
  covalent geometry    : angle       0.57162 (22902)
  hydrogen bonds       : bond        0.04159 (  609)
  hydrogen bonds       : angle       5.61014 ( 1683)

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

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

  4188 Ramachandran restraints generated.
    2094 Oldfield, 0 Emsley, 2094 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4188 Ramachandran restraints generated.
    2094 Oldfield, 0 Emsley, 2094 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  261 residues out of total 1824 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 239
  time to evaluate  : 0.684 
Fit side-chains
REVERT: A  193 TYR cc_start: 0.8889 (m-80) cc_final: 0.8619 (m-80)
REVERT: A  257 ARG cc_start: 0.7720 (tpt170) cc_final: 0.7336 (tpt170)
REVERT: B  149 LYS cc_start: 0.8417 (mmmm) cc_final: 0.8042 (mppt)
REVERT: C  149 LYS cc_start: 0.8369 (OUTLIER) cc_final: 0.7933 (tptt)
REVERT: C  202 GLU cc_start: 0.7057 (OUTLIER) cc_final: 0.6689 (tt0)
REVERT: C  220 GLU cc_start: 0.6802 (mt-10) cc_final: 0.6430 (pt0)
REVERT: C  233 GLU cc_start: 0.6800 (mp0) cc_final: 0.6538 (pm20)
REVERT: C  330 MET cc_start: 0.7950 (mmt) cc_final: 0.7629 (mmm)
REVERT: D  149 LYS cc_start: 0.8366 (OUTLIER) cc_final: 0.7921 (tptt)
REVERT: D  202 GLU cc_start: 0.7083 (OUTLIER) cc_final: 0.6698 (tt0)
REVERT: D  233 GLU cc_start: 0.6826 (mp0) cc_final: 0.6557 (pm20)
REVERT: D  330 MET cc_start: 0.7945 (mmt) cc_final: 0.7619 (mmm)
REVERT: E  149 LYS cc_start: 0.8427 (mmmm) cc_final: 0.8067 (mppt)
REVERT: F  193 TYR cc_start: 0.8896 (m-80) cc_final: 0.8626 (m-80)
REVERT: F  257 ARG cc_start: 0.7731 (tpt170) cc_final: 0.7331 (tpt170)
REVERT: F  330 MET cc_start: 0.7974 (mmt) cc_final: 0.7236 (mmm)
  outliers start: 22
  outliers final: 15
  residues processed: 250
  average time/residue: 0.6342
  time to fit residues: 177.2538
Evaluate side-chains
  254 residues out of total 1824 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 235
  time to evaluate  : 0.795 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  114 THR
Chi-restraints excluded: chain A residue  147 SER
Chi-restraints excluded: chain B residue  147 SER
Chi-restraints excluded: chain B residue  232 PHE
Chi-restraints excluded: chain C residue   12 LYS
Chi-restraints excluded: chain C residue  147 SER
Chi-restraints excluded: chain C residue  149 LYS
Chi-restraints excluded: chain C residue  202 GLU
Chi-restraints excluded: chain C residue  232 PHE
Chi-restraints excluded: chain D residue   12 LYS
Chi-restraints excluded: chain D residue  147 SER
Chi-restraints excluded: chain D residue  149 LYS
Chi-restraints excluded: chain D residue  202 GLU
Chi-restraints excluded: chain D residue  232 PHE
Chi-restraints excluded: chain E residue   47 THR
Chi-restraints excluded: chain E residue  147 SER
Chi-restraints excluded: chain E residue  232 PHE
Chi-restraints excluded: chain F residue  114 THR
Chi-restraints excluded: chain F residue  147 SER
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 204
   random chunks:
   chunk 28 optimal weight:    1.9990
   chunk 133 optimal weight:    7.9990
   chunk 94 optimal weight:    0.9980
   chunk 42 optimal weight:    1.9990
   chunk 54 optimal weight:    0.8980
   chunk 151 optimal weight:    1.9990
   chunk 109 optimal weight:    0.3980
   chunk 161 optimal weight:    0.0970
   chunk 93 optimal weight:    0.6980
   chunk 116 optimal weight:    0.9980
   chunk 123 optimal weight:    5.9990
   overall best weight:    0.6178

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

Flipped N/Q/H residues before XYZ refinement:
A  19 GLN
B  19 GLN
C  19 GLN
C 152 GLN
D 152 GLN
D 277 ASN
E  19 GLN
F  19 GLN

Total number of N/Q/H flips: 8

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3856 r_free = 0.3856 target = 0.170868 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 26)----------------|
| r_work = 0.3378 r_free = 0.3378 target = 0.127915 restraints weight = 92961.572|
|-----------------------------------------------------------------------------|
r_work (start): 0.3305 rms_B_bonded: 4.84
r_work: 0.2988 rms_B_bonded: 3.48 restraints_weight: 0.5000
r_work (final): 0.2988
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2934
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2934 r_free = 0.2934    target_work(ls_wunit_k1) = 0.095         |
| occupancies: max = 1.00  min = 0.47   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2934 r_free = 0.2934    target_work(ls_wunit_k1) = 0.095         |
| occupancies: max = 1.00  min = 0.47   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2934
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8268
moved from start:          0.1585

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.027  16872  Z= 0.125
  Angle     :  0.518  11.913  22902  Z= 0.273
  Chirality :  0.046   0.134   2634
  Planarity :  0.003   0.045   2952
  Dihedral  :  4.659  16.002   2214
  Min Nonbonded Distance : 2.605

Molprobity Statistics.
  All-atom Clashscore : 4.90
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.16 %
    Favored  : 98.84 %
  Rotamer:
    Outliers :  1.18 %
    Allowed  : 20.11 %
    Favored  : 78.71 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.43 (0.18), residues: 2094
  helix:  0.62 (0.23), residues: 546
  sheet:  0.56 (0.26), residues: 342
  loop :  0.17 (0.18), residues: 1206

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG B 138 
 TYR   0.008   0.001   TYR F 225 
 PHE   0.033   0.002   PHE C 221 
 TRP   0.008   0.001   TRP D  58 
 HIS   0.003   0.001   HIS F  95 

Details of bonding type rmsd
  covalent geometry    : bond        0.00275 (16872)
  covalent geometry    : angle       0.51804 (22902)
  hydrogen bonds       : bond        0.03442 (  609)
  hydrogen bonds       : angle       5.36409 ( 1683)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 6650.36 seconds
wall clock time: 114 minutes 17.49 seconds (6857.49 seconds total)