Starting phenix.real_space_refine
on Tue Nov 18 08:53:33 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/6bze_7314/11_2025/6bze_7314.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/6bze_7314/11_2025/6bze_7314.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=4.0
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/6bze_7314/11_2025/6bze_7314.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/6bze_7314/11_2025/6bze_7314.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/6bze_7314/11_2025/6bze_7314.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/6bze_7314/11_2025/6bze_7314.map"
  }
  resolution = 4.0
  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
-------------------------------------------------------------------------------
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=   0.006 sd=   0.020
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
  Anisotropic ADP refinement not supported. Converting 7072 atoms to isotropic.
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      16      5.16       5
     C    4408      2.51       5
     N    1296      2.21       5
     O    1352      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 24 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5881/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 7072
  Number of models: 1
  Model: ""
    Number of chains: 8
    Chain: "A"
      Number of atoms: 884
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 106, 884
          Classifications: {'peptide': 106}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 1, 'TRANS': 104}
    Chain: "B"
      Number of atoms: 884
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 106, 884
          Classifications: {'peptide': 106}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 1, 'TRANS': 104}
    Chain: "C"
      Number of atoms: 884
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 106, 884
          Classifications: {'peptide': 106}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 1, 'TRANS': 104}
    Chain: "D"
      Number of atoms: 884
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 106, 884
          Classifications: {'peptide': 106}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 1, 'TRANS': 104}
    Chain: "E"
      Number of atoms: 884
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 106, 884
          Classifications: {'peptide': 106}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 1, 'TRANS': 104}
    Chain: "F"
      Number of atoms: 884
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 106, 884
          Classifications: {'peptide': 106}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 1, 'TRANS': 104}
    Chain: "G"
      Number of atoms: 884
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 106, 884
          Classifications: {'peptide': 106}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 1, 'TRANS': 104}
    Chain: "H"
      Number of atoms: 884
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 106, 884
          Classifications: {'peptide': 106}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 1, 'TRANS': 104}
  Time building chain proxies: 2.07, per 1000 atoms: 0.29
  Number of scatterers: 7072
  At special positions: 0
  Unit cell: (105.7, 105.7, 87.58, 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      16     16.00
     O    1352      8.00
     N    1296      7.00
     C    4408      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 0.71
  Conformation dependent library (CDL) restraints added in 494.2 milliseconds
  

  1664 Ramachandran restraints generated.
    832 Oldfield, 0 Emsley, 832 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1664

  Finding SS restraints...
    Secondary structure from input PDB file:
      56 helices and 0 sheets defined
      74.2% alpha, 0.0% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.19
  Creating SS restraints...
    Processing helix  chain 'A' and resid 12 through 25
      removed outlier: 3.778A  pdb=" N   VAL A  16 " --> pdb=" O   ASP A  12 " (cutoff:3.500A)
      removed outlier: 4.496A  pdb=" N   LYS A  18 " --> pdb=" O   THR A  14 " (cutoff:3.500A)
      removed outlier: 3.527A  pdb=" N   ASP A  19 " --> pdb=" O   GLU A  15 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 33 through 38
    Processing helix  chain 'A' and resid 38 through 44
      removed outlier: 4.213A  pdb=" N   ARG A  42 " --> pdb=" O   PHE A  38 " (cutoff:3.500A)
      removed outlier: 3.577A  pdb=" N   LYS A  44 " --> pdb=" O   HIS A  40 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 49 through 58
      removed outlier: 3.834A  pdb=" N   GLU A  53 " --> pdb=" O   ARG A  49 " (cutoff:3.500A)
      removed outlier: 3.619A  pdb=" N   ARG A  58 " --> pdb=" O   GLU A  54 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 62 through 73
      removed outlier: 3.709A  pdb=" N   LEU A  72 " --> pdb=" O   LEU A  68 " (cutoff:3.500A)
      removed outlier: 3.664A  pdb=" N   GLN A  73 " --> pdb=" O   LEU A  69 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 79 through 87
      removed outlier: 3.521A  pdb=" N   VAL A  83 " --> pdb=" O   LEU A  79 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 95 through 115
      removed outlier: 3.568A  pdb=" N   LEU A 114 " --> pdb=" O   LYS A 110 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 12 through 25
      removed outlier: 3.691A  pdb=" N   VAL B  16 " --> pdb=" O   ASP B  12 " (cutoff:3.500A)
      removed outlier: 4.119A  pdb=" N   LYS B  18 " --> pdb=" O   THR B  14 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 33 through 38
    Processing helix  chain 'B' and resid 38 through 44
      removed outlier: 4.184A  pdb=" N   ARG B  42 " --> pdb=" O   PHE B  38 " (cutoff:3.500A)
      removed outlier: 3.542A  pdb=" N   LYS B  44 " --> pdb=" O   HIS B  40 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 49 through 58
      removed outlier: 3.922A  pdb=" N   GLU B  53 " --> pdb=" O   ARG B  49 " (cutoff:3.500A)
      removed outlier: 3.882A  pdb=" N   ARG B  58 " --> pdb=" O   GLU B  54 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 62 through 73
      removed outlier: 3.927A  pdb=" N   LEU B  72 " --> pdb=" O   LEU B  68 " (cutoff:3.500A)
      removed outlier: 3.967A  pdb=" N   GLN B  73 " --> pdb=" O   LEU B  69 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 79 through 87
    Processing helix  chain 'B' and resid 95 through 115
      removed outlier: 3.808A  pdb=" N   LEU B 114 " --> pdb=" O   LYS B 110 " (cutoff:3.500A)
      removed outlier: 3.678A  pdb=" N   LYS B 115 " --> pdb=" O   LEU B 111 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 12 through 25
      removed outlier: 3.634A  pdb=" N   VAL C  16 " --> pdb=" O   ASP C  12 " (cutoff:3.500A)
      removed outlier: 4.220A  pdb=" N   LYS C  18 " --> pdb=" O   THR C  14 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 33 through 38
    Processing helix  chain 'C' and resid 38 through 44
      removed outlier: 4.216A  pdb=" N   ARG C  42 " --> pdb=" O   PHE C  38 " (cutoff:3.500A)
      removed outlier: 3.586A  pdb=" N   LYS C  44 " --> pdb=" O   HIS C  40 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 49 through 58
      removed outlier: 3.844A  pdb=" N   GLU C  53 " --> pdb=" O   ARG C  49 " (cutoff:3.500A)
      removed outlier: 3.890A  pdb=" N   ARG C  58 " --> pdb=" O   GLU C  54 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 62 through 73
      removed outlier: 3.891A  pdb=" N   LEU C  72 " --> pdb=" O   LEU C  68 " (cutoff:3.500A)
      removed outlier: 3.795A  pdb=" N   GLN C  73 " --> pdb=" O   LEU C  69 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 79 through 87
      removed outlier: 3.502A  pdb=" N   VAL C  83 " --> pdb=" O   LEU C  79 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 95 through 115
      removed outlier: 3.649A  pdb=" N   LEU C 114 " --> pdb=" O   LYS C 110 " (cutoff:3.500A)
      removed outlier: 3.548A  pdb=" N   LYS C 115 " --> pdb=" O   LEU C 111 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 12 through 25
      removed outlier: 3.810A  pdb=" N   VAL D  16 " --> pdb=" O   ASP D  12 " (cutoff:3.500A)
      removed outlier: 4.066A  pdb=" N   LYS D  18 " --> pdb=" O   THR D  14 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 33 through 38
    Processing helix  chain 'D' and resid 38 through 44
      removed outlier: 4.478A  pdb=" N   ARG D  42 " --> pdb=" O   PHE D  38 " (cutoff:3.500A)
      removed outlier: 3.505A  pdb=" N   LYS D  44 " --> pdb=" O   HIS D  40 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 49 through 58
      removed outlier: 3.530A  pdb=" N   GLU D  53 " --> pdb=" O   ARG D  49 " (cutoff:3.500A)
      removed outlier: 3.908A  pdb=" N   ARG D  58 " --> pdb=" O   GLU D  54 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 62 through 75
      removed outlier: 4.003A  pdb=" N   LEU D  72 " --> pdb=" O   LEU D  68 " (cutoff:3.500A)
      removed outlier: 3.762A  pdb=" N   GLN D  73 " --> pdb=" O   LEU D  69 " (cutoff:3.500A)
      removed outlier: 4.205A  pdb=" N   GLU D  74 " --> pdb=" O   ASP D  70 " (cutoff:3.500A)
      removed outlier: 3.916A  pdb=" N   ASN D  75 " --> pdb=" O   TYR D  71 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 79 through 87
    Processing helix  chain 'D' and resid 95 through 115
      removed outlier: 3.684A  pdb=" N   LEU D 114 " --> pdb=" O   LYS D 110 " (cutoff:3.500A)
      removed outlier: 3.608A  pdb=" N   LYS D 115 " --> pdb=" O   LEU D 111 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 12 through 25
      removed outlier: 3.736A  pdb=" N   VAL E  16 " --> pdb=" O   ASP E  12 " (cutoff:3.500A)
      removed outlier: 4.194A  pdb=" N   LYS E  18 " --> pdb=" O   THR E  14 " (cutoff:3.500A)
      removed outlier: 3.547A  pdb=" N   ASP E  19 " --> pdb=" O   GLU E  15 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 33 through 38
    Processing helix  chain 'E' and resid 38 through 44
      removed outlier: 4.343A  pdb=" N   ARG E  42 " --> pdb=" O   PHE E  38 " (cutoff:3.500A)
      removed outlier: 3.741A  pdb=" N   LYS E  44 " --> pdb=" O   HIS E  40 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 49 through 58
      removed outlier: 3.862A  pdb=" N   GLU E  53 " --> pdb=" O   ARG E  49 " (cutoff:3.500A)
      removed outlier: 3.818A  pdb=" N   ARG E  58 " --> pdb=" O   GLU E  54 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 62 through 72
      removed outlier: 4.102A  pdb=" N   LEU E  72 " --> pdb=" O   LEU E  68 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 79 through 87
    Processing helix  chain 'E' and resid 95 through 115
      removed outlier: 3.658A  pdb=" N   LEU E 114 " --> pdb=" O   LYS E 110 " (cutoff:3.500A)
      removed outlier: 3.648A  pdb=" N   LYS E 115 " --> pdb=" O   LEU E 111 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 12 through 25
      removed outlier: 3.650A  pdb=" N   VAL F  16 " --> pdb=" O   ASP F  12 " (cutoff:3.500A)
      removed outlier: 4.306A  pdb=" N   LYS F  18 " --> pdb=" O   THR F  14 " (cutoff:3.500A)
      removed outlier: 3.649A  pdb=" N   ASP F  19 " --> pdb=" O   GLU F  15 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 33 through 38
    Processing helix  chain 'F' and resid 38 through 44
      removed outlier: 4.390A  pdb=" N   ARG F  42 " --> pdb=" O   PHE F  38 " (cutoff:3.500A)
      removed outlier: 3.656A  pdb=" N   LYS F  44 " --> pdb=" O   HIS F  40 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 49 through 58
      removed outlier: 3.881A  pdb=" N   GLU F  53 " --> pdb=" O   ARG F  49 " (cutoff:3.500A)
      removed outlier: 3.745A  pdb=" N   ARG F  58 " --> pdb=" O   GLU F  54 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 62 through 72
      removed outlier: 4.089A  pdb=" N   LEU F  72 " --> pdb=" O   LEU F  68 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 79 through 87
    Processing helix  chain 'F' and resid 95 through 115
      removed outlier: 3.702A  pdb=" N   LEU F 114 " --> pdb=" O   LYS F 110 " (cutoff:3.500A)
      removed outlier: 3.571A  pdb=" N   LYS F 115 " --> pdb=" O   LEU F 111 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 12 through 25
      removed outlier: 3.914A  pdb=" N   VAL G  16 " --> pdb=" O   ASP G  12 " (cutoff:3.500A)
      removed outlier: 4.542A  pdb=" N   LYS G  18 " --> pdb=" O   THR G  14 " (cutoff:3.500A)
      removed outlier: 3.610A  pdb=" N   ASP G  19 " --> pdb=" O   GLU G  15 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 33 through 38
    Processing helix  chain 'G' and resid 38 through 44
      removed outlier: 4.369A  pdb=" N   ARG G  42 " --> pdb=" O   PHE G  38 " (cutoff:3.500A)
      removed outlier: 3.577A  pdb=" N   LYS G  44 " --> pdb=" O   HIS G  40 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 49 through 58
      removed outlier: 3.820A  pdb=" N   GLU G  53 " --> pdb=" O   ARG G  49 " (cutoff:3.500A)
      removed outlier: 3.622A  pdb=" N   ARG G  58 " --> pdb=" O   GLU G  54 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 62 through 72
      removed outlier: 4.103A  pdb=" N   LEU G  72 " --> pdb=" O   LEU G  68 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 79 through 87
    Processing helix  chain 'G' and resid 95 through 115
      removed outlier: 3.580A  pdb=" N   LEU G 114 " --> pdb=" O   LYS G 110 " (cutoff:3.500A)
      removed outlier: 3.576A  pdb=" N   LYS G 115 " --> pdb=" O   LEU G 111 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 12 through 25
      removed outlier: 3.699A  pdb=" N   VAL H  16 " --> pdb=" O   ASP H  12 " (cutoff:3.500A)
      removed outlier: 4.206A  pdb=" N   LYS H  18 " --> pdb=" O   THR H  14 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 32 through 36
    Processing helix  chain 'H' and resid 38 through 44
      removed outlier: 4.412A  pdb=" N   ARG H  42 " --> pdb=" O   PHE H  38 " (cutoff:3.500A)
      removed outlier: 3.616A  pdb=" N   LYS H  44 " --> pdb=" O   HIS H  40 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 49 through 58
      removed outlier: 3.790A  pdb=" N   GLU H  53 " --> pdb=" O   ARG H  49 " (cutoff:3.500A)
      removed outlier: 3.659A  pdb=" N   ARG H  58 " --> pdb=" O   GLU H  54 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 62 through 72
      removed outlier: 3.856A  pdb=" N   LEU H  72 " --> pdb=" O   LEU H  68 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 79 through 87
    Processing helix  chain 'H' and resid 95 through 115
      removed outlier: 3.778A  pdb=" N   LEU H 114 " --> pdb=" O   LYS H 110 " (cutoff:3.500A)
      removed outlier: 3.515A  pdb=" N   LYS H 115 " --> pdb=" O   LEU H 111 " (cutoff:3.500A)

    323 hydrogen bonds defined for protein.
    963 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: 0.87

  Time building geometry restraints manager: 0.93 seconds

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

  Histogram of bond lengths:
        1.14 -     1.28: 1247
        1.28 -     1.41: 1457
        1.41 -     1.54: 4361
        1.54 -     1.68: 47
        1.68 -     1.81: 16
  Bond restraints: 7128
  Sorted by residual:
  bond pdb=" C   GLU B  74 "
       pdb=" O   GLU B  74 "
    ideal  model  delta    sigma   weight residual
    1.235  1.145  0.091 1.26e-02 6.30e+03 5.18e+01
  bond pdb=" C   GLU D  74 "
       pdb=" O   GLU D  74 "
    ideal  model  delta    sigma   weight residual
    1.235  1.151  0.084 1.26e-02 6.30e+03 4.49e+01
  bond pdb=" C   GLU A  74 "
       pdb=" O   GLU A  74 "
    ideal  model  delta    sigma   weight residual
    1.235  1.161  0.074 1.26e-02 6.30e+03 3.46e+01
  bond pdb=" C   GLU C  74 "
       pdb=" O   GLU C  74 "
    ideal  model  delta    sigma   weight residual
    1.235  1.164  0.071 1.26e-02 6.30e+03 3.19e+01
  bond pdb=" ND1 HIS G  40 "
       pdb=" CE1 HIS G  40 "
    ideal  model  delta    sigma   weight residual
    1.321  1.359 -0.038 1.00e-02 1.00e+04 1.46e+01
  ... (remaining 7123 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.07: 8406
        2.07 -     4.15: 966
        4.15 -     6.22: 110
        6.22 -     8.30: 24
        8.30 -    10.37: 14
  Bond angle restraints: 9520
  Sorted by residual:
  angle pdb=" N   THR F 100 "
        pdb=" CA  THR F 100 "
        pdb=" C   THR F 100 "
      ideal   model   delta    sigma   weight residual
     111.36  101.89    9.47 1.09e+00 8.42e-01 7.55e+01
  angle pdb=" N   THR H 100 "
        pdb=" CA  THR H 100 "
        pdb=" C   THR H 100 "
      ideal   model   delta    sigma   weight residual
     111.82  101.98    9.84 1.16e+00 7.43e-01 7.20e+01
  angle pdb=" N   THR G 100 "
        pdb=" CA  THR G 100 "
        pdb=" C   THR G 100 "
      ideal   model   delta    sigma   weight residual
     111.36  102.22    9.14 1.09e+00 8.42e-01 7.03e+01
  angle pdb=" N   THR A 100 "
        pdb=" CA  THR A 100 "
        pdb=" C   THR A 100 "
      ideal   model   delta    sigma   weight residual
     111.36  102.30    9.06 1.09e+00 8.42e-01 6.91e+01
  angle pdb=" N   THR C 100 "
        pdb=" CA  THR C 100 "
        pdb=" C   THR C 100 "
      ideal   model   delta    sigma   weight residual
     111.36  102.68    8.68 1.09e+00 8.42e-01 6.35e+01
  ... (remaining 9515 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.56: 3971
       17.56 -    35.13: 430
       35.13 -    52.69: 124
       52.69 -    70.25: 42
       70.25 -    87.81: 17
  Dihedral angle restraints: 4584
    sinusoidal: 2064
      harmonic: 2520
  Sorted by residual:
  dihedral pdb=" CA  SER A  56 "
           pdb=" C   SER A  56 "
           pdb=" N   CYS A  57 "
           pdb=" CA  CYS A  57 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -162.05  -17.95     0      5.00e+00 4.00e-02 1.29e+01
  dihedral pdb=" C   PHE B  38 "
           pdb=" N   PHE B  38 "
           pdb=" CA  PHE B  38 "
           pdb=" CB  PHE B  38 "
      ideal   model   delta  harmonic     sigma   weight residual
    -122.60 -131.30    8.70     0      2.50e+00 1.60e-01 1.21e+01
  dihedral pdb=" CG  ARG D  49 "
           pdb=" CD  ARG D  49 "
           pdb=" NE  ARG D  49 "
           pdb=" CZ  ARG D  49 "
      ideal   model   delta sinusoidal    sigma   weight residual
      90.00   41.95   48.05     2      1.50e+01 4.44e-03 1.18e+01
  ... (remaining 4581 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.079: 756
       0.079 -    0.157: 286
       0.157 -    0.236: 54
       0.236 -    0.315: 5
       0.315 -    0.394: 3
  Chirality restraints: 1104
  Sorted by residual:
  chirality pdb=" CA  PHE B  38 "
            pdb=" N   PHE B  38 "
            pdb=" C   PHE B  38 "
            pdb=" CB  PHE B  38 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.12    0.39 2.00e-01 2.50e+01 3.87e+00
  chirality pdb=" CA  PHE D  38 "
            pdb=" N   PHE D  38 "
            pdb=" C   PHE D  38 "
            pdb=" CB  PHE D  38 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.18    0.33 2.00e-01 2.50e+01 2.78e+00
  chirality pdb=" CA  PHE A  38 "
            pdb=" N   PHE A  38 "
            pdb=" C   PHE A  38 "
            pdb=" CB  PHE A  38 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.19    0.33 2.00e-01 2.50e+01 2.65e+00
  ... (remaining 1101 not shown)

  Planarity restraints: 1216
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  PHE F  94 "    0.036 2.00e-02 2.50e+03   2.58e-02 1.17e+01
        pdb=" CG  PHE F  94 "   -0.055 2.00e-02 2.50e+03
        pdb=" CD1 PHE F  94 "   -0.003 2.00e-02 2.50e+03
        pdb=" CD2 PHE F  94 "    0.002 2.00e-02 2.50e+03
        pdb=" CE1 PHE F  94 "    0.004 2.00e-02 2.50e+03
        pdb=" CE2 PHE F  94 "   -0.000 2.00e-02 2.50e+03
        pdb=" CZ  PHE F  94 "    0.016 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  GLN B  92 "    0.016 2.00e-02 2.50e+03   3.33e-02 1.11e+01
        pdb=" C   GLN B  92 "   -0.058 2.00e-02 2.50e+03
        pdb=" O   GLN B  92 "    0.022 2.00e-02 2.50e+03
        pdb=" N   ASN B  93 "    0.019 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  HIS F  37 "    0.015 2.00e-02 2.50e+03   3.08e-02 9.49e+00
        pdb=" C   HIS F  37 "   -0.053 2.00e-02 2.50e+03
        pdb=" O   HIS F  37 "    0.020 2.00e-02 2.50e+03
        pdb=" N   PHE F  38 "    0.018 2.00e-02 2.50e+03
  ... (remaining 1213 not shown)

  Histogram of nonbonded interaction distances:
        1.65 -     2.30: 87
        2.30 -     2.95: 4208
        2.95 -     3.60: 11653
        3.60 -     4.25: 17484
        4.25 -     4.90: 26284
  Nonbonded interactions: 59716
  Sorted by model distance:
  nonbonded pdb=" OG  SER D  48 "
            pdb=" NE2 HIS H  37 "
     model   vdw
     1.648 3.120
  nonbonded pdb=" OD2 ASP A  70 "
            pdb=" NH2 ARG D  49 "
     model   vdw
     1.789 3.120
  nonbonded pdb=" OG  SER A  48 "
            pdb=" NE2 HIS E  37 "
     model   vdw
     1.793 3.120
  nonbonded pdb=" O   ARG F  49 "
            pdb=" NH1 ARG F  49 "
     model   vdw
     1.879 3.120
  nonbonded pdb=" O   ARG C  49 "
            pdb=" NH1 ARG C  49 "
     model   vdw
     1.883 3.120
  ... (remaining 59711 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: 0.00
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'B'
  selection = chain 'C'
  selection = chain 'D'
  selection = chain 'E'
  selection = chain 'F'
  selection = chain 'G'
  selection = chain 'H'
}

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=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             0.040
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.040
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.110
  Check model and map are aligned:         0.020
  Set scattering table:                    0.020
  Process input model:                     8.750
  Find NCS groups from input model:        0.100
  Set up NCS constraints:                  0.010
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.300
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   10.390
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.4815
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      :  0.009   0.091   7128  Z= 0.561
  Angle     :  1.421  10.371   9520  Z= 1.027
  Chirality :  0.082   0.394   1104
  Planarity :  0.005   0.033   1216
  Dihedral  : 17.335  87.814   2920
  Min Nonbonded Distance : 1.648

Molprobity Statistics.
  All-atom Clashscore : 79.95
  Ramachandran Plot:
    Outliers :  0.36 %
    Allowed  : 13.22 %
    Favored  : 86.42 %
  Rotamer:
    Outliers :  9.00 %
    Allowed  : 19.62 %
    Favored  : 71.38 %
  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 are not related in a simple way.
  whole: -5.34 (0.22), residues: 832
  helix: -4.12 (0.14), residues: 528
  sheet:  None (None), residues: 0
  loop : -1.99 (0.32), residues: 304

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG G  36 
 TYR   0.006   0.001   TYR H  71 
 PHE   0.055   0.006   PHE F  94 
 HIS   0.009   0.001   HIS H  37 

Details of bonding type rmsd
  covalent geometry    : bond        0.00859 ( 7128)
  covalent geometry    : angle       1.42118 ( 9520)
  hydrogen bonds       : bond        0.42477 (  323)
  hydrogen bonds       : angle       9.43892 (  963)

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

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

  1664 Ramachandran restraints generated.
    832 Oldfield, 0 Emsley, 832 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1664 Ramachandran restraints generated.
    832 Oldfield, 0 Emsley, 832 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  498 residues out of total 800 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 72
    poor density    : 426
  time to evaluate  : 0.311 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   11 GLU cc_start: 0.8128 (mm-30) cc_final: 0.7730 (tm-30)
REVERT: A   24 LEU cc_start: 0.7077 (tp) cc_final: 0.6803 (tt)
REVERT: A   28 LEU cc_start: 0.4443 (tp) cc_final: 0.3609 (tp)
REVERT: A   56 SER cc_start: 0.7951 (t) cc_final: 0.7659 (m)
REVERT: A   70 ASP cc_start: 0.7043 (t70) cc_final: 0.6809 (t70)
REVERT: A   84 GLU cc_start: 0.7343 (tp30) cc_final: 0.7140 (pp20)
REVERT: B   11 GLU cc_start: 0.9299 (mm-30) cc_final: 0.8899 (tm-30)
REVERT: B   12 ASP cc_start: 0.8451 (m-30) cc_final: 0.7930 (p0)
REVERT: B   23 ASN cc_start: 0.6061 (m110) cc_final: 0.5853 (m-40)
REVERT: B   37 HIS cc_start: 0.3331 (OUTLIER) cc_final: 0.2945 (m-70)
REVERT: B   55 ILE cc_start: 0.7265 (mt) cc_final: 0.6801 (tt)
REVERT: B   70 ASP cc_start: 0.7059 (t70) cc_final: 0.6615 (t0)
REVERT: B   74 GLU cc_start: 0.8355 (mt-10) cc_final: 0.7985 (mt-10)
REVERT: B   84 GLU cc_start: 0.8286 (tp30) cc_final: 0.7993 (tp30)
REVERT: B  107 ARG cc_start: 0.8124 (tpp-160) cc_final: 0.7899 (tpp80)
REVERT: B  113 HIS cc_start: 0.8341 (t-170) cc_final: 0.8029 (t70)
REVERT: C   11 GLU cc_start: 0.8050 (mm-30) cc_final: 0.7569 (tm-30)
REVERT: C   12 ASP cc_start: 0.8377 (m-30) cc_final: 0.7728 (p0)
REVERT: C   16 VAL cc_start: 0.6605 (OUTLIER) cc_final: 0.6368 (p)
REVERT: C   30 GLU cc_start: 0.4359 (mm-30) cc_final: 0.3486 (mt-10)
REVERT: C   74 GLU cc_start: 0.7860 (mt-10) cc_final: 0.7279 (tm-30)
REVERT: D   30 GLU cc_start: 0.5060 (mm-30) cc_final: 0.4691 (mm-30)
REVERT: D   35 GLU cc_start: 0.0530 (pt0) cc_final: 0.0008 (pt0)
REVERT: D   56 SER cc_start: 0.7292 (t) cc_final: 0.7076 (t)
REVERT: D   70 ASP cc_start: 0.7040 (t70) cc_final: 0.6497 (t0)
REVERT: D   73 GLN cc_start: 0.6688 (mt0) cc_final: 0.5887 (mt0)
REVERT: D   80 ASP cc_start: 0.7408 (m-30) cc_final: 0.7097 (m-30)
REVERT: D   95 LEU cc_start: 0.8740 (tp) cc_final: 0.8530 (tp)
REVERT: E   11 GLU cc_start: 0.8842 (mm-30) cc_final: 0.8392 (tm-30)
REVERT: E   16 VAL cc_start: 0.5912 (OUTLIER) cc_final: 0.5409 (p)
REVERT: E   32 ILE cc_start: 0.4377 (mm) cc_final: 0.2916 (mm)
REVERT: E   48 SER cc_start: 0.4230 (t) cc_final: 0.3264 (p)
REVERT: E   49 ARG cc_start: 0.6146 (tpt90) cc_final: 0.5866 (tpt90)
REVERT: E   80 ASP cc_start: 0.7311 (m-30) cc_final: 0.6580 (m-30)
REVERT: E   84 GLU cc_start: 0.7833 (tp30) cc_final: 0.7532 (tm-30)
REVERT: F   18 LYS cc_start: 0.7595 (mtmp) cc_final: 0.7233 (mtpp)
REVERT: F   25 ARG cc_start: 0.5008 (OUTLIER) cc_final: 0.4584 (tmt170)
REVERT: F   62 ARG cc_start: 0.7242 (mmt90) cc_final: 0.6865 (mmm-85)
REVERT: F   69 LEU cc_start: 0.7620 (mp) cc_final: 0.7391 (mp)
REVERT: F  104 LEU cc_start: 0.9153 (mt) cc_final: 0.8878 (mt)
REVERT: G   16 VAL cc_start: 0.3522 (OUTLIER) cc_final: 0.3117 (p)
REVERT: G   32 ILE cc_start: 0.2041 (mm) cc_final: 0.1800 (mm)
REVERT: G   55 ILE cc_start: 0.6531 (mt) cc_final: 0.5707 (mt)
REVERT: H   26 VAL cc_start: 0.8649 (t) cc_final: 0.8411 (p)
REVERT: H   63 LYS cc_start: 0.6063 (mmtt) cc_final: 0.5595 (mtmm)
REVERT: H   95 LEU cc_start: 0.8964 (tp) cc_final: 0.8651 (pt)
REVERT: H   96 ILE cc_start: 0.6795 (mm) cc_final: 0.6428 (mm)
  outliers start: 72
  outliers final: 18
  residues processed: 470
  average time/residue: 0.1343
  time to fit residues: 76.4928
Evaluate side-chains
  313 residues out of total 800 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 290
  time to evaluate  : 0.314 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   18 LYS
Chi-restraints excluded: chain A residue   37 HIS
Chi-restraints excluded: chain A residue   40 HIS
Chi-restraints excluded: chain B residue   37 HIS
Chi-restraints excluded: chain B residue   87 ARG
Chi-restraints excluded: chain C residue   16 VAL
Chi-restraints excluded: chain C residue   37 HIS
Chi-restraints excluded: chain C residue   87 ARG
Chi-restraints excluded: chain D residue   16 VAL
Chi-restraints excluded: chain D residue   49 ARG
Chi-restraints excluded: chain E residue   16 VAL
Chi-restraints excluded: chain E residue   37 HIS
Chi-restraints excluded: chain E residue   87 ARG
Chi-restraints excluded: chain F residue   16 VAL
Chi-restraints excluded: chain F residue   25 ARG
Chi-restraints excluded: chain F residue   27 TYR
Chi-restraints excluded: chain G residue   16 VAL
Chi-restraints excluded: chain G residue   22 GLU
Chi-restraints excluded: chain G residue   37 HIS
Chi-restraints excluded: chain H residue   16 VAL
Chi-restraints excluded: chain H residue   37 HIS
Chi-restraints excluded: chain H residue   40 HIS
Chi-restraints excluded: chain H residue   49 ARG
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 80
   random chunks:
   chunk 49 optimal weight:    8.9990
   chunk 53 optimal weight:    9.9990
   chunk 5 optimal weight:    6.9990
   chunk 33 optimal weight:    9.9990
   chunk 65 optimal weight:    7.9990
   chunk 62 optimal weight:   10.0000
   chunk 51 optimal weight:    0.5980
   chunk 38 optimal weight:    5.9990
   chunk 61 optimal weight:    1.9990
   chunk 45 optimal weight:    7.9990
   chunk 74 optimal weight:    4.9990
   overall best weight:    4.1188

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

Flipped N/Q/H residues before XYZ refinement:
A  92 GLN
A  97 GLN
B  92 GLN
B  97 GLN
C  92 GLN
C  97 GLN
D  37 HIS
** D  92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
D  97 GLN
** E  37 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** E  92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
E  97 GLN
E 113 HIS
F  23 ASN
** F  37 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** F  92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
F  97 GLN
F 113 HIS
G  23 ASN
** G  37 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** G  92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
G  97 GLN
G 113 HIS
** H  37 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** H  92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
H  97 GLN

Total number of N/Q/H flips: 17

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4067 r_free = 0.4067 target = 0.138361 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 25)----------------|
| r_work = 0.3864 r_free = 0.3864 target = 0.124288 restraints weight = 21701.048|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3903 r_free = 0.3903 target = 0.126994 restraints weight = 14668.654|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 21)----------------|
| r_work = 0.3931 r_free = 0.3931 target = 0.128945 restraints weight = 10705.191|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 33)----------------|
| r_work = 0.3952 r_free = 0.3952 target = 0.130416 restraints weight = 8236.801|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.3967 r_free = 0.3967 target = 0.131452 restraints weight = 6556.412|
|-----------------------------------------------------------------------------|
r_work (final): 0.3963
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7039
moved from start:          0.6800

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.060   7128  Z= 0.214
  Angle     :  0.975   9.411   9520  Z= 0.518
  Chirality :  0.053   0.297   1104
  Planarity :  0.006   0.067   1216
  Dihedral  :  9.237  79.786    999
  Min Nonbonded Distance : 2.499

Molprobity Statistics.
  All-atom Clashscore : 24.74
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.73 %
    Favored  : 93.27 %
  Rotamer:
    Outliers :  7.75 %
    Allowed  : 26.00 %
    Favored  : 66.25 %
  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 are not related in a simple way.
  whole: -3.54 (0.26), residues: 832
  helix: -2.04 (0.19), residues: 576
  sheet:  None (None), residues: 0
  loop : -2.67 (0.38), residues: 256

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.013   0.001   ARG E  42 
 TYR   0.016   0.002   TYR B  71 
 PHE   0.017   0.003   PHE D  38 
 HIS   0.012   0.002   HIS F  37 

Details of bonding type rmsd
  covalent geometry    : bond        0.00440 ( 7128)
  covalent geometry    : angle       0.97512 ( 9520)
  hydrogen bonds       : bond        0.07575 (  323)
  hydrogen bonds       : angle       6.55783 (  963)

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

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

  1664 Ramachandran restraints generated.
    832 Oldfield, 0 Emsley, 832 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1664 Ramachandran restraints generated.
    832 Oldfield, 0 Emsley, 832 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  456 residues out of total 800 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 62
    poor density    : 394
  time to evaluate  : 0.327 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   17 LYS cc_start: 0.9197 (mmmm) cc_final: 0.8943 (mmtp)
REVERT: A   24 LEU cc_start: 0.8579 (tp) cc_final: 0.8203 (tt)
REVERT: A   53 GLU cc_start: 0.7898 (mt-10) cc_final: 0.7670 (mt-10)
REVERT: A  101 ASP cc_start: 0.7113 (OUTLIER) cc_final: 0.6370 (t0)
REVERT: B  101 ASP cc_start: 0.7369 (OUTLIER) cc_final: 0.6965 (t0)
REVERT: C   16 VAL cc_start: 0.8694 (OUTLIER) cc_final: 0.8474 (p)
REVERT: C   18 LYS cc_start: 0.7540 (mmtt) cc_final: 0.7001 (mmtt)
REVERT: C   19 ASP cc_start: 0.8225 (m-30) cc_final: 0.8024 (m-30)
REVERT: C   39 ASP cc_start: 0.8005 (m-30) cc_final: 0.7727 (m-30)
REVERT: C   51 ASP cc_start: 0.6614 (m-30) cc_final: 0.6033 (m-30)
REVERT: C   67 LYS cc_start: 0.9128 (mmmt) cc_final: 0.8856 (mttt)
REVERT: C   70 ASP cc_start: 0.7511 (t70) cc_final: 0.6158 (t0)
REVERT: C  105 LYS cc_start: 0.8764 (mmmt) cc_final: 0.8107 (mppt)
REVERT: D   28 LEU cc_start: 0.8521 (tp) cc_final: 0.8297 (tp)
REVERT: D   56 SER cc_start: 0.8183 (t) cc_final: 0.7973 (p)
REVERT: D   64 ARG cc_start: 0.7348 (ptp-170) cc_final: 0.7004 (ptt-90)
REVERT: D   73 GLN cc_start: 0.8381 (mt0) cc_final: 0.8068 (mt0)
REVERT: D   74 GLU cc_start: 0.7565 (mt-10) cc_final: 0.7094 (mt-10)
REVERT: D   80 ASP cc_start: 0.8762 (m-30) cc_final: 0.8362 (m-30)
REVERT: D   95 LEU cc_start: 0.6496 (tp) cc_final: 0.6041 (tp)
REVERT: E   16 VAL cc_start: 0.9232 (OUTLIER) cc_final: 0.9020 (p)
REVERT: E   22 GLU cc_start: 0.8663 (mm-30) cc_final: 0.8219 (mm-30)
REVERT: E   23 ASN cc_start: 0.8922 (m-40) cc_final: 0.8687 (m-40)
REVERT: E   62 ARG cc_start: 0.8246 (mmt90) cc_final: 0.7666 (mmm-85)
REVERT: F   16 VAL cc_start: 0.7821 (OUTLIER) cc_final: 0.7426 (p)
REVERT: F   25 ARG cc_start: 0.7554 (OUTLIER) cc_final: 0.5868 (ttt-90)
REVERT: F   39 ASP cc_start: 0.7567 (m-30) cc_final: 0.7159 (m-30)
REVERT: F   58 ARG cc_start: 0.6221 (mpt180) cc_final: 0.5935 (mtt90)
REVERT: F   79 LEU cc_start: 0.7989 (mt) cc_final: 0.7162 (mm)
REVERT: F   90 LYS cc_start: 0.7312 (ttmt) cc_final: 0.6914 (ttmt)
REVERT: G   17 LYS cc_start: 0.8415 (mttp) cc_final: 0.8056 (mttm)
REVERT: G   73 GLN cc_start: 0.8320 (mt0) cc_final: 0.7831 (mt0)
REVERT: G   90 LYS cc_start: 0.6990 (ptpt) cc_final: 0.6382 (pttm)
REVERT: G  105 LYS cc_start: 0.8209 (mmmt) cc_final: 0.8000 (mmmt)
REVERT: G  113 HIS cc_start: 0.8327 (t70) cc_final: 0.8039 (t70)
REVERT: H   15 GLU cc_start: 0.8194 (mp0) cc_final: 0.7951 (mp0)
REVERT: H   63 LYS cc_start: 0.7853 (mmtt) cc_final: 0.7512 (mtmm)
REVERT: H  105 LYS cc_start: 0.8647 (mmmt) cc_final: 0.8136 (mmmt)
  outliers start: 62
  outliers final: 29
  residues processed: 421
  average time/residue: 0.1382
  time to fit residues: 70.2156
Evaluate side-chains
  309 residues out of total 800 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 274
  time to evaluate  : 0.357 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   37 HIS
Chi-restraints excluded: chain A residue   40 HIS
Chi-restraints excluded: chain A residue   69 LEU
Chi-restraints excluded: chain A residue   80 ASP
Chi-restraints excluded: chain A residue  101 ASP
Chi-restraints excluded: chain B residue   37 HIS
Chi-restraints excluded: chain B residue   75 ASN
Chi-restraints excluded: chain B residue  101 ASP
Chi-restraints excluded: chain B residue  106 LEU
Chi-restraints excluded: chain C residue   16 VAL
Chi-restraints excluded: chain C residue   37 HIS
Chi-restraints excluded: chain C residue   80 ASP
Chi-restraints excluded: chain C residue   87 ARG
Chi-restraints excluded: chain C residue   91 THR
Chi-restraints excluded: chain D residue   37 HIS
Chi-restraints excluded: chain D residue   40 HIS
Chi-restraints excluded: chain E residue   16 VAL
Chi-restraints excluded: chain E residue   37 HIS
Chi-restraints excluded: chain E residue   87 ARG
Chi-restraints excluded: chain F residue   16 VAL
Chi-restraints excluded: chain F residue   25 ARG
Chi-restraints excluded: chain F residue   80 ASP
Chi-restraints excluded: chain G residue   26 VAL
Chi-restraints excluded: chain G residue   29 CYS
Chi-restraints excluded: chain G residue   35 GLU
Chi-restraints excluded: chain G residue   41 LEU
Chi-restraints excluded: chain G residue   80 ASP
Chi-restraints excluded: chain H residue   16 VAL
Chi-restraints excluded: chain H residue   29 CYS
Chi-restraints excluded: chain H residue   35 GLU
Chi-restraints excluded: chain H residue   37 HIS
Chi-restraints excluded: chain H residue   40 HIS
Chi-restraints excluded: chain H residue   77 LYS
Chi-restraints excluded: chain H residue   80 ASP
Chi-restraints excluded: chain H residue  111 LEU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 80
   random chunks:
   chunk 48 optimal weight:   20.0000
   chunk 8 optimal weight:    6.9990
   chunk 13 optimal weight:   20.0000
   chunk 77 optimal weight:    4.9990
   chunk 70 optimal weight:   40.0000
   chunk 79 optimal weight:    6.9990
   chunk 5 optimal weight:    9.9990
   chunk 46 optimal weight:    0.3980
   chunk 19 optimal weight:    6.9990
   chunk 21 optimal weight:    7.9990
   chunk 45 optimal weight:    5.9990
   overall best weight:    5.0788

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

Flipped N/Q/H residues before XYZ refinement:
B  40 HIS
C 108 ASN
C 113 HIS
D  23 ASN
E  40 HIS
** E  92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
F  23 ASN
** F  37 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** F  92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
G  92 GLN
** H  37 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 7

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4024 r_free = 0.4024 target = 0.134960 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3801 r_free = 0.3801 target = 0.120199 restraints weight = 21310.689|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3843 r_free = 0.3843 target = 0.123046 restraints weight = 13965.685|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3871 r_free = 0.3871 target = 0.125015 restraints weight = 9984.571|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 39)----------------|
| r_work = 0.3894 r_free = 0.3894 target = 0.126526 restraints weight = 7612.967|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.3909 r_free = 0.3909 target = 0.127587 restraints weight = 6065.483|
|-----------------------------------------------------------------------------|
r_work (final): 0.3907
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7157
moved from start:          0.8848

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.039   7128  Z= 0.192
  Angle     :  0.901  13.020   9520  Z= 0.467
  Chirality :  0.051   0.317   1104
  Planarity :  0.006   0.051   1216
  Dihedral  :  8.372  60.880    974
  Min Nonbonded Distance : 2.495

Molprobity Statistics.
  All-atom Clashscore : 26.26
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.29 %
    Favored  : 91.71 %
  Rotamer:
    Outliers :  7.62 %
    Allowed  : 28.50 %
    Favored  : 63.88 %
  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 are not related in a simple way.
  whole: -2.33 (0.28), residues: 832
  helix: -0.98 (0.21), residues: 576
  sheet:  None (None), residues: 0
  loop : -2.64 (0.37), residues: 256

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG A  42 
 TYR   0.008   0.001   TYR H  27 
 PHE   0.028   0.003   PHE H  94 
 HIS   0.017   0.001   HIS D  37 

Details of bonding type rmsd
  covalent geometry    : bond        0.00408 ( 7128)
  covalent geometry    : angle       0.90074 ( 9520)
  hydrogen bonds       : bond        0.05320 (  323)
  hydrogen bonds       : angle       5.88418 (  963)

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

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

  1664 Ramachandran restraints generated.
    832 Oldfield, 0 Emsley, 832 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1664 Ramachandran restraints generated.
    832 Oldfield, 0 Emsley, 832 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  397 residues out of total 800 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 61
    poor density    : 336
  time to evaluate  : 0.318 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   17 LYS cc_start: 0.9058 (mmmm) cc_final: 0.8793 (mmtp)
REVERT: A   37 HIS cc_start: 0.6126 (OUTLIER) cc_final: 0.5630 (m-70)
REVERT: A   73 GLN cc_start: 0.8291 (mt0) cc_final: 0.7811 (mt0)
REVERT: A   79 LEU cc_start: 0.8226 (mm) cc_final: 0.7926 (mm)
REVERT: A   94 PHE cc_start: 0.0815 (OUTLIER) cc_final: 0.0606 (m-80)
REVERT: A  101 ASP cc_start: 0.7216 (OUTLIER) cc_final: 0.6887 (t0)
REVERT: A  105 LYS cc_start: 0.8790 (mmmt) cc_final: 0.8463 (mmmt)
REVERT: B   51 ASP cc_start: 0.5449 (m-30) cc_final: 0.5245 (m-30)
REVERT: B   67 LYS cc_start: 0.8388 (mttt) cc_final: 0.8108 (mtmt)
REVERT: B   73 GLN cc_start: 0.8196 (mt0) cc_final: 0.7876 (mt0)
REVERT: B   75 ASN cc_start: 0.7177 (OUTLIER) cc_final: 0.6580 (m-40)
REVERT: C   16 VAL cc_start: 0.8670 (OUTLIER) cc_final: 0.8409 (p)
REVERT: C   27 TYR cc_start: 0.7504 (m-10) cc_final: 0.7303 (m-10)
REVERT: C   35 GLU cc_start: 0.6920 (pt0) cc_final: 0.6386 (mt-10)
REVERT: C   40 HIS cc_start: 0.8943 (OUTLIER) cc_final: 0.7720 (m-70)
REVERT: C  105 LYS cc_start: 0.8494 (mmmt) cc_final: 0.7949 (mppt)
REVERT: D   18 LYS cc_start: 0.8394 (mtpp) cc_final: 0.8062 (mtpp)
REVERT: D   22 GLU cc_start: 0.8425 (mm-30) cc_final: 0.8093 (mm-30)
REVERT: D   56 SER cc_start: 0.8233 (t) cc_final: 0.8018 (p)
REVERT: D   62 ARG cc_start: 0.6920 (OUTLIER) cc_final: 0.6319 (mmt90)
REVERT: E   58 ARG cc_start: 0.6327 (OUTLIER) cc_final: 0.4930 (ttt180)
REVERT: E   62 ARG cc_start: 0.7974 (mmt90) cc_final: 0.7649 (mmm-85)
REVERT: E   79 LEU cc_start: 0.8651 (mt) cc_final: 0.8442 (tt)
REVERT: E   90 LYS cc_start: 0.6698 (ttmt) cc_final: 0.6373 (ttmt)
REVERT: F   37 HIS cc_start: 0.6717 (t70) cc_final: 0.6013 (t-170)
REVERT: F   49 ARG cc_start: 0.6400 (tpt90) cc_final: 0.5833 (tpt90)
REVERT: F   53 GLU cc_start: 0.8240 (mt-10) cc_final: 0.7905 (mt-10)
REVERT: F   70 ASP cc_start: 0.7422 (t0) cc_final: 0.7154 (t0)
REVERT: F   87 ARG cc_start: 0.7289 (OUTLIER) cc_final: 0.6814 (mpt180)
REVERT: F   90 LYS cc_start: 0.7710 (ttmt) cc_final: 0.7482 (ttmt)
REVERT: F  104 LEU cc_start: 0.8872 (mp) cc_final: 0.7252 (mm)
REVERT: G   15 GLU cc_start: 0.8029 (mp0) cc_final: 0.7739 (pm20)
REVERT: G   40 HIS cc_start: 0.8909 (m170) cc_final: 0.8569 (m170)
REVERT: G   53 GLU cc_start: 0.8166 (mt-10) cc_final: 0.7512 (tm-30)
REVERT: G   64 ARG cc_start: 0.6259 (ptp90) cc_final: 0.6053 (ptp90)
REVERT: G   73 GLN cc_start: 0.8348 (mt0) cc_final: 0.8116 (mt0)
REVERT: G  105 LYS cc_start: 0.8545 (mmmt) cc_final: 0.8141 (tptp)
  outliers start: 61
  outliers final: 27
  residues processed: 365
  average time/residue: 0.1354
  time to fit residues: 59.8806
Evaluate side-chains
  299 residues out of total 800 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 263
  time to evaluate  : 0.306 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   37 HIS
Chi-restraints excluded: chain A residue   40 HIS
Chi-restraints excluded: chain A residue   80 ASP
Chi-restraints excluded: chain A residue   94 PHE
Chi-restraints excluded: chain A residue  101 ASP
Chi-restraints excluded: chain A residue  106 LEU
Chi-restraints excluded: chain B residue   24 LEU
Chi-restraints excluded: chain B residue   75 ASN
Chi-restraints excluded: chain B residue  106 LEU
Chi-restraints excluded: chain C residue   16 VAL
Chi-restraints excluded: chain C residue   37 HIS
Chi-restraints excluded: chain C residue   40 HIS
Chi-restraints excluded: chain C residue   80 ASP
Chi-restraints excluded: chain C residue   87 ARG
Chi-restraints excluded: chain C residue   91 THR
Chi-restraints excluded: chain C residue  114 LEU
Chi-restraints excluded: chain D residue   62 ARG
Chi-restraints excluded: chain E residue   58 ARG
Chi-restraints excluded: chain E residue   82 LEU
Chi-restraints excluded: chain E residue   87 ARG
Chi-restraints excluded: chain F residue   13 LEU
Chi-restraints excluded: chain F residue   16 VAL
Chi-restraints excluded: chain F residue   26 VAL
Chi-restraints excluded: chain F residue   27 TYR
Chi-restraints excluded: chain F residue   59 THR
Chi-restraints excluded: chain F residue   80 ASP
Chi-restraints excluded: chain F residue   87 ARG
Chi-restraints excluded: chain G residue   24 LEU
Chi-restraints excluded: chain G residue   29 CYS
Chi-restraints excluded: chain G residue   41 LEU
Chi-restraints excluded: chain G residue   80 ASP
Chi-restraints excluded: chain H residue   16 VAL
Chi-restraints excluded: chain H residue   29 CYS
Chi-restraints excluded: chain H residue   40 HIS
Chi-restraints excluded: chain H residue   75 ASN
Chi-restraints excluded: chain H residue   80 ASP
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 80
   random chunks:
   chunk 2 optimal weight:   10.0000
   chunk 0 optimal weight:   30.0000
   chunk 60 optimal weight:   30.0000
   chunk 20 optimal weight:   30.0000
   chunk 31 optimal weight:    9.9990
   chunk 68 optimal weight:   30.0000
   chunk 30 optimal weight:    5.9990
   chunk 57 optimal weight:    7.9990
   chunk 77 optimal weight:    1.9990
   chunk 50 optimal weight:   40.0000
   chunk 16 optimal weight:    9.9990
   overall best weight:    7.1990

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

Flipped N/Q/H residues before XYZ refinement:
B  40 HIS
D  37 HIS
D  40 HIS
** D  92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E  92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
F  23 ASN
** F  37 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
F 113 HIS
G 113 HIS
** H  37 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3954 r_free = 0.3954 target = 0.130883 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3745 r_free = 0.3745 target = 0.116855 restraints weight = 21834.729|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3785 r_free = 0.3785 target = 0.119615 restraints weight = 14034.031|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3814 r_free = 0.3814 target = 0.121592 restraints weight = 9936.397|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.3834 r_free = 0.3834 target = 0.122957 restraints weight = 7494.760|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3849 r_free = 0.3849 target = 0.124006 restraints weight = 5966.206|
|-----------------------------------------------------------------------------|
r_work (final): 0.3845
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7298
moved from start:          0.9883

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.051   7128  Z= 0.215
  Angle     :  0.878  10.868   9520  Z= 0.462
  Chirality :  0.050   0.233   1104
  Planarity :  0.005   0.044   1216
  Dihedral  :  8.042  61.093    963
  Min Nonbonded Distance : 2.472

Molprobity Statistics.
  All-atom Clashscore : 27.92
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.01 %
    Favored  : 90.99 %
  Rotamer:
    Outliers :  9.12 %
    Allowed  : 31.12 %
    Favored  : 59.75 %
  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 are not related in a simple way.
  whole: -2.01 (0.29), residues: 832
  helix: -0.70 (0.22), residues: 576
  sheet:  None (None), residues: 0
  loop : -2.61 (0.37), residues: 256

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.001   ARG E  88 
 TYR   0.012   0.002   TYR B  27 
 PHE   0.021   0.003   PHE H  94 
 HIS   0.012   0.001   HIS E  37 

Details of bonding type rmsd
  covalent geometry    : bond        0.00469 ( 7128)
  covalent geometry    : angle       0.87847 ( 9520)
  hydrogen bonds       : bond        0.04641 (  323)
  hydrogen bonds       : angle       5.55740 (  963)

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

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

  1664 Ramachandran restraints generated.
    832 Oldfield, 0 Emsley, 832 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1664 Ramachandran restraints generated.
    832 Oldfield, 0 Emsley, 832 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  380 residues out of total 800 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 73
    poor density    : 307
  time to evaluate  : 0.252 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   17 LYS cc_start: 0.9255 (mmmm) cc_final: 0.8951 (mmtp)
REVERT: A   32 ILE cc_start: 0.7999 (mm) cc_final: 0.7529 (mm)
REVERT: A   39 ASP cc_start: 0.8594 (m-30) cc_final: 0.8004 (m-30)
REVERT: A   53 GLU cc_start: 0.8004 (mt-10) cc_final: 0.7677 (mp0)
REVERT: A   63 LYS cc_start: 0.8351 (mmtt) cc_final: 0.8104 (mtmt)
REVERT: A  105 LYS cc_start: 0.8839 (mmmt) cc_final: 0.8587 (mmmt)
REVERT: B   17 LYS cc_start: 0.9242 (mmmm) cc_final: 0.8514 (tmtt)
REVERT: B   42 ARG cc_start: 0.6351 (mmt180) cc_final: 0.6084 (mmt180)
REVERT: B   50 GLU cc_start: 0.7853 (mp0) cc_final: 0.7563 (mp0)
REVERT: B   70 ASP cc_start: 0.8128 (t0) cc_final: 0.7276 (t0)
REVERT: B   73 GLN cc_start: 0.8207 (mt0) cc_final: 0.7864 (mt0)
REVERT: B   75 ASN cc_start: 0.7838 (OUTLIER) cc_final: 0.7392 (m-40)
REVERT: C   35 GLU cc_start: 0.7149 (pt0) cc_final: 0.6642 (pt0)
REVERT: C   40 HIS cc_start: 0.9237 (OUTLIER) cc_final: 0.7959 (m-70)
REVERT: C   49 ARG cc_start: 0.8057 (tpt90) cc_final: 0.7822 (tpt90)
REVERT: C   53 GLU cc_start: 0.8275 (mt-10) cc_final: 0.7901 (pt0)
REVERT: C   63 LYS cc_start: 0.8791 (mmtt) cc_final: 0.8146 (mtmt)
REVERT: C   64 ARG cc_start: 0.8262 (OUTLIER) cc_final: 0.7937 (ptp-170)
REVERT: C   71 TYR cc_start: 0.8801 (m-80) cc_final: 0.8532 (m-10)
REVERT: C   74 GLU cc_start: 0.8179 (mp0) cc_final: 0.7878 (mp0)
REVERT: D   18 LYS cc_start: 0.8606 (mtpp) cc_final: 0.8298 (mtpp)
REVERT: D   22 GLU cc_start: 0.8470 (mm-30) cc_final: 0.8264 (mm-30)
REVERT: D   51 ASP cc_start: 0.6144 (m-30) cc_final: 0.5934 (m-30)
REVERT: D   52 THR cc_start: 0.8597 (p) cc_final: 0.8056 (p)
REVERT: D   56 SER cc_start: 0.8382 (t) cc_final: 0.8071 (p)
REVERT: D   62 ARG cc_start: 0.7044 (OUTLIER) cc_final: 0.6403 (mmt90)
REVERT: D   74 GLU cc_start: 0.8003 (mp0) cc_final: 0.7783 (mt-10)
REVERT: D  105 LYS cc_start: 0.8509 (mmmt) cc_final: 0.8128 (mmmt)
REVERT: E   18 LYS cc_start: 0.8798 (mtpp) cc_final: 0.8506 (tttm)
REVERT: E   58 ARG cc_start: 0.6771 (OUTLIER) cc_final: 0.4879 (ttt180)
REVERT: E   62 ARG cc_start: 0.8249 (mmt90) cc_final: 0.7468 (mmt90)
REVERT: E   90 LYS cc_start: 0.7093 (ttmt) cc_final: 0.6715 (ttmt)
REVERT: F   25 ARG cc_start: 0.8190 (OUTLIER) cc_final: 0.6365 (tmt170)
REVERT: F   37 HIS cc_start: 0.6913 (t70) cc_final: 0.5925 (t-170)
REVERT: F   42 ARG cc_start: 0.7887 (tmt-80) cc_final: 0.7645 (tpt90)
REVERT: F   53 GLU cc_start: 0.8431 (mt-10) cc_final: 0.7999 (mt-10)
REVERT: F   63 LYS cc_start: 0.8422 (mmtt) cc_final: 0.8053 (mtpt)
REVERT: F   90 LYS cc_start: 0.7975 (ttmt) cc_final: 0.7496 (ttmt)
REVERT: G   15 GLU cc_start: 0.8625 (mp0) cc_final: 0.8232 (pm20)
REVERT: G   23 ASN cc_start: 0.8259 (m110) cc_final: 0.7350 (m110)
REVERT: G   40 HIS cc_start: 0.8874 (m170) cc_final: 0.8505 (m170)
REVERT: G   53 GLU cc_start: 0.8145 (mt-10) cc_final: 0.7736 (tm-30)
REVERT: G   64 ARG cc_start: 0.6690 (ptp90) cc_final: 0.6313 (ptp90)
REVERT: G   70 ASP cc_start: 0.8498 (t70) cc_final: 0.8170 (t0)
REVERT: G  105 LYS cc_start: 0.8717 (mmmt) cc_final: 0.8504 (tptp)
REVERT: G  107 ARG cc_start: 0.7952 (tmm-80) cc_final: 0.7112 (tmm-80)
REVERT: H   18 LYS cc_start: 0.8424 (mtmm) cc_final: 0.8116 (mtmm)
REVERT: H   82 LEU cc_start: 0.8853 (OUTLIER) cc_final: 0.8350 (mm)
REVERT: H  104 LEU cc_start: 0.9071 (mm) cc_final: 0.8802 (tt)
  outliers start: 73
  outliers final: 41
  residues processed: 348
  average time/residue: 0.1406
  time to fit residues: 58.9016
Evaluate side-chains
  322 residues out of total 800 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 48
    poor density    : 274
  time to evaluate  : 0.299 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   27 TYR
Chi-restraints excluded: chain A residue   37 HIS
Chi-restraints excluded: chain A residue   40 HIS
Chi-restraints excluded: chain A residue   55 ILE
Chi-restraints excluded: chain A residue   80 ASP
Chi-restraints excluded: chain A residue  101 ASP
Chi-restraints excluded: chain A residue  106 LEU
Chi-restraints excluded: chain B residue   21 LEU
Chi-restraints excluded: chain B residue   40 HIS
Chi-restraints excluded: chain B residue   56 SER
Chi-restraints excluded: chain B residue   75 ASN
Chi-restraints excluded: chain C residue   37 HIS
Chi-restraints excluded: chain C residue   40 HIS
Chi-restraints excluded: chain C residue   64 ARG
Chi-restraints excluded: chain C residue   79 LEU
Chi-restraints excluded: chain C residue   91 THR
Chi-restraints excluded: chain D residue   13 LEU
Chi-restraints excluded: chain D residue   26 VAL
Chi-restraints excluded: chain D residue   41 LEU
Chi-restraints excluded: chain D residue   59 THR
Chi-restraints excluded: chain D residue   62 ARG
Chi-restraints excluded: chain D residue   80 ASP
Chi-restraints excluded: chain E residue   41 LEU
Chi-restraints excluded: chain E residue   58 ARG
Chi-restraints excluded: chain E residue   87 ARG
Chi-restraints excluded: chain F residue   13 LEU
Chi-restraints excluded: chain F residue   16 VAL
Chi-restraints excluded: chain F residue   25 ARG
Chi-restraints excluded: chain F residue   26 VAL
Chi-restraints excluded: chain F residue   27 TYR
Chi-restraints excluded: chain F residue   59 THR
Chi-restraints excluded: chain F residue   80 ASP
Chi-restraints excluded: chain F residue  113 HIS
Chi-restraints excluded: chain G residue   16 VAL
Chi-restraints excluded: chain G residue   24 LEU
Chi-restraints excluded: chain G residue   26 VAL
Chi-restraints excluded: chain G residue   33 ILE
Chi-restraints excluded: chain G residue   59 THR
Chi-restraints excluded: chain G residue   80 ASP
Chi-restraints excluded: chain G residue   82 LEU
Chi-restraints excluded: chain G residue   98 LYS
Chi-restraints excluded: chain G residue  113 HIS
Chi-restraints excluded: chain H residue   16 VAL
Chi-restraints excluded: chain H residue   29 CYS
Chi-restraints excluded: chain H residue   40 HIS
Chi-restraints excluded: chain H residue   75 ASN
Chi-restraints excluded: chain H residue   80 ASP
Chi-restraints excluded: chain H residue   82 LEU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 80
   random chunks:
   chunk 78 optimal weight:    1.9990
   chunk 11 optimal weight:   10.0000
   chunk 46 optimal weight:    6.9990
   chunk 73 optimal weight:   20.0000
   chunk 72 optimal weight:   10.0000
   chunk 42 optimal weight:    0.9990
   chunk 17 optimal weight:   20.0000
   chunk 66 optimal weight:    9.9990
   chunk 32 optimal weight:    5.9990
   chunk 26 optimal weight:    5.9990
   chunk 43 optimal weight:    8.9990
   overall best weight:    4.3990

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

Flipped N/Q/H residues before XYZ refinement:
B  40 HIS
** E  92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
F  23 ASN
F 113 HIS
** H  37 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3982 r_free = 0.3982 target = 0.132495 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3771 r_free = 0.3771 target = 0.118635 restraints weight = 21885.381|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3810 r_free = 0.3810 target = 0.121301 restraints weight = 14401.271|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3837 r_free = 0.3837 target = 0.123175 restraints weight = 10392.838|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 37)----------------|
| r_work = 0.3858 r_free = 0.3858 target = 0.124602 restraints weight = 7986.830|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3873 r_free = 0.3873 target = 0.125608 restraints weight = 6371.925|
|-----------------------------------------------------------------------------|
r_work (final): 0.3862
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7244
moved from start:          1.0352

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.036   7128  Z= 0.162
  Angle     :  0.827  11.623   9520  Z= 0.430
  Chirality :  0.049   0.314   1104
  Planarity :  0.005   0.061   1216
  Dihedral  :  7.703  63.792    958
  Min Nonbonded Distance : 2.471

Molprobity Statistics.
  All-atom Clashscore : 24.18
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.65 %
    Favored  : 91.35 %
  Rotamer:
    Outliers :  9.12 %
    Allowed  : 31.12 %
    Favored  : 59.75 %
  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 are not related in a simple way.
  whole: -2.20 (0.29), residues: 832
  helix: -0.72 (0.22), residues: 592
  sheet:  None (None), residues: 0
  loop : -3.17 (0.35), residues: 240

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG E  88 
 TYR   0.012   0.001   TYR B  27 
 PHE   0.014   0.002   PHE E  94 
 HIS   0.024   0.002   HIS G 113 

Details of bonding type rmsd
  covalent geometry    : bond        0.00355 ( 7128)
  covalent geometry    : angle       0.82707 ( 9520)
  hydrogen bonds       : bond        0.04056 (  323)
  hydrogen bonds       : angle       5.32400 (  963)

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

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

  1664 Ramachandran restraints generated.
    832 Oldfield, 0 Emsley, 832 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1664 Ramachandran restraints generated.
    832 Oldfield, 0 Emsley, 832 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  374 residues out of total 800 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 73
    poor density    : 301
  time to evaluate  : 0.311 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   17 LYS cc_start: 0.9096 (mmmm) cc_final: 0.8854 (mmtp)
REVERT: A   32 ILE cc_start: 0.7812 (mm) cc_final: 0.7339 (mm)
REVERT: A   37 HIS cc_start: 0.5964 (OUTLIER) cc_final: 0.5347 (t70)
REVERT: A   39 ASP cc_start: 0.8528 (m-30) cc_final: 0.7853 (m-30)
REVERT: A   53 GLU cc_start: 0.7984 (mt-10) cc_final: 0.7702 (mp0)
REVERT: A  101 ASP cc_start: 0.7715 (OUTLIER) cc_final: 0.7421 (t0)
REVERT: A  105 LYS cc_start: 0.8689 (mmmt) cc_final: 0.8378 (mmmt)
REVERT: B   17 LYS cc_start: 0.8822 (mmmm) cc_final: 0.7787 (tptp)
REVERT: B   50 GLU cc_start: 0.7938 (mp0) cc_final: 0.7656 (mp0)
REVERT: B   51 ASP cc_start: 0.5346 (m-30) cc_final: 0.4626 (m-30)
REVERT: B   70 ASP cc_start: 0.7779 (t0) cc_final: 0.7123 (t0)
REVERT: B   75 ASN cc_start: 0.7710 (OUTLIER) cc_final: 0.7115 (m-40)
REVERT: C   27 TYR cc_start: 0.7230 (m-10) cc_final: 0.6902 (m-10)
REVERT: C   35 GLU cc_start: 0.7133 (pt0) cc_final: 0.6383 (pt0)
REVERT: C   39 ASP cc_start: 0.8734 (m-30) cc_final: 0.8499 (m-30)
REVERT: C   40 HIS cc_start: 0.9132 (OUTLIER) cc_final: 0.7835 (m-70)
REVERT: C   53 GLU cc_start: 0.8074 (mt-10) cc_final: 0.7738 (pt0)
REVERT: C   63 LYS cc_start: 0.8653 (mmtt) cc_final: 0.8141 (mtmt)
REVERT: C   64 ARG cc_start: 0.8199 (OUTLIER) cc_final: 0.7937 (ptp-170)
REVERT: D   18 LYS cc_start: 0.8651 (mtpp) cc_final: 0.8404 (mtpp)
REVERT: D   19 ASP cc_start: 0.8328 (m-30) cc_final: 0.7999 (m-30)
REVERT: D   22 GLU cc_start: 0.8408 (mm-30) cc_final: 0.8182 (mm-30)
REVERT: D   25 ARG cc_start: 0.8799 (mmm-85) cc_final: 0.8302 (mmm-85)
REVERT: D   35 GLU cc_start: 0.6221 (pt0) cc_final: 0.6009 (pt0)
REVERT: D   62 ARG cc_start: 0.6764 (OUTLIER) cc_final: 0.6162 (mmt90)
REVERT: E   18 LYS cc_start: 0.8869 (mtpp) cc_final: 0.8564 (tttm)
REVERT: E   42 ARG cc_start: 0.8480 (OUTLIER) cc_final: 0.8013 (tmt-80)
REVERT: E   51 ASP cc_start: 0.7700 (p0) cc_final: 0.7493 (p0)
REVERT: E   53 GLU cc_start: 0.7998 (mt-10) cc_final: 0.7534 (mt-10)
REVERT: E   58 ARG cc_start: 0.6605 (OUTLIER) cc_final: 0.4943 (ttt180)
REVERT: E   90 LYS cc_start: 0.7403 (ttmt) cc_final: 0.7050 (ttmt)
REVERT: F   25 ARG cc_start: 0.8175 (OUTLIER) cc_final: 0.6425 (tmt170)
REVERT: F   37 HIS cc_start: 0.6752 (t70) cc_final: 0.6499 (t70)
REVERT: F   49 ARG cc_start: 0.6704 (tpt90) cc_final: 0.6436 (tpt-90)
REVERT: F   53 GLU cc_start: 0.8251 (mt-10) cc_final: 0.8015 (mt-10)
REVERT: F   87 ARG cc_start: 0.7464 (OUTLIER) cc_final: 0.7194 (mpt180)
REVERT: G   15 GLU cc_start: 0.8603 (mp0) cc_final: 0.8321 (pm20)
REVERT: G   23 ASN cc_start: 0.8126 (m110) cc_final: 0.7786 (m110)
REVERT: G   53 GLU cc_start: 0.8391 (mt-10) cc_final: 0.7920 (tm-30)
REVERT: G   70 ASP cc_start: 0.7975 (t70) cc_final: 0.7716 (t70)
REVERT: G   73 GLN cc_start: 0.8711 (mt0) cc_final: 0.8409 (mt0)
REVERT: H   70 ASP cc_start: 0.7844 (t70) cc_final: 0.6608 (t70)
REVERT: H   73 GLN cc_start: 0.8561 (mt0) cc_final: 0.8212 (mt0)
REVERT: H  104 LEU cc_start: 0.9092 (OUTLIER) cc_final: 0.8454 (tt)
REVERT: H  107 ARG cc_start: 0.8149 (ttp80) cc_final: 0.7702 (ttp80)
  outliers start: 73
  outliers final: 42
  residues processed: 339
  average time/residue: 0.1389
  time to fit residues: 56.6780
Evaluate side-chains
  324 residues out of total 800 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 53
    poor density    : 271
  time to evaluate  : 0.303 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   27 TYR
Chi-restraints excluded: chain A residue   37 HIS
Chi-restraints excluded: chain A residue   40 HIS
Chi-restraints excluded: chain A residue   48 SER
Chi-restraints excluded: chain A residue   55 ILE
Chi-restraints excluded: chain A residue   80 ASP
Chi-restraints excluded: chain A residue  101 ASP
Chi-restraints excluded: chain A residue  106 LEU
Chi-restraints excluded: chain B residue   21 LEU
Chi-restraints excluded: chain B residue   40 HIS
Chi-restraints excluded: chain B residue   75 ASN
Chi-restraints excluded: chain C residue   24 LEU
Chi-restraints excluded: chain C residue   37 HIS
Chi-restraints excluded: chain C residue   40 HIS
Chi-restraints excluded: chain C residue   64 ARG
Chi-restraints excluded: chain C residue   79 LEU
Chi-restraints excluded: chain D residue   13 LEU
Chi-restraints excluded: chain D residue   26 VAL
Chi-restraints excluded: chain D residue   37 HIS
Chi-restraints excluded: chain D residue   41 LEU
Chi-restraints excluded: chain D residue   46 ILE
Chi-restraints excluded: chain D residue   62 ARG
Chi-restraints excluded: chain D residue   80 ASP
Chi-restraints excluded: chain E residue   16 VAL
Chi-restraints excluded: chain E residue   32 ILE
Chi-restraints excluded: chain E residue   41 LEU
Chi-restraints excluded: chain E residue   42 ARG
Chi-restraints excluded: chain E residue   58 ARG
Chi-restraints excluded: chain E residue   82 LEU
Chi-restraints excluded: chain F residue   13 LEU
Chi-restraints excluded: chain F residue   16 VAL
Chi-restraints excluded: chain F residue   25 ARG
Chi-restraints excluded: chain F residue   26 VAL
Chi-restraints excluded: chain F residue   27 TYR
Chi-restraints excluded: chain F residue   59 THR
Chi-restraints excluded: chain F residue   80 ASP
Chi-restraints excluded: chain F residue   87 ARG
Chi-restraints excluded: chain F residue  113 HIS
Chi-restraints excluded: chain G residue   16 VAL
Chi-restraints excluded: chain G residue   24 LEU
Chi-restraints excluded: chain G residue   26 VAL
Chi-restraints excluded: chain G residue   33 ILE
Chi-restraints excluded: chain G residue   41 LEU
Chi-restraints excluded: chain G residue   59 THR
Chi-restraints excluded: chain G residue   80 ASP
Chi-restraints excluded: chain G residue   82 LEU
Chi-restraints excluded: chain G residue   98 LYS
Chi-restraints excluded: chain H residue   16 VAL
Chi-restraints excluded: chain H residue   29 CYS
Chi-restraints excluded: chain H residue   75 ASN
Chi-restraints excluded: chain H residue   80 ASP
Chi-restraints excluded: chain H residue   98 LYS
Chi-restraints excluded: chain H residue  104 LEU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 80
   random chunks:
   chunk 79 optimal weight:    9.9990
   chunk 43 optimal weight:   20.0000
   chunk 41 optimal weight:    7.9990
   chunk 53 optimal weight:    9.9990
   chunk 37 optimal weight:    5.9990
   chunk 14 optimal weight:    0.1980
   chunk 77 optimal weight:    3.9990
   chunk 32 optimal weight:    9.9990
   chunk 18 optimal weight:    1.9990
   chunk 76 optimal weight:    5.9990
   chunk 26 optimal weight:    0.9980
   overall best weight:    2.6386

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

Flipped N/Q/H residues before XYZ refinement:
B  40 HIS
D  37 HIS
E  73 GLN
F  23 ASN
** F  92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
F 113 HIS
** G  73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** H  23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** H  37 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4011 r_free = 0.4011 target = 0.134826 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3802 r_free = 0.3802 target = 0.120973 restraints weight = 21705.622|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3842 r_free = 0.3842 target = 0.123744 restraints weight = 14091.285|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3872 r_free = 0.3872 target = 0.125775 restraints weight = 10046.171|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 24)----------------|
| r_work = 0.3892 r_free = 0.3892 target = 0.127184 restraints weight = 7583.982|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.3907 r_free = 0.3907 target = 0.128228 restraints weight = 6022.099|
|-----------------------------------------------------------------------------|
r_work (final): 0.3905
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7217
moved from start:          1.0851

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   7128  Z= 0.145
  Angle     :  0.801  10.666   9520  Z= 0.418
  Chirality :  0.048   0.331   1104
  Planarity :  0.004   0.037   1216
  Dihedral  :  7.154  58.830    952
  Min Nonbonded Distance : 2.466

Molprobity Statistics.
  All-atom Clashscore : 20.87
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.53 %
    Favored  : 91.47 %
  Rotamer:
    Outliers :  7.38 %
    Allowed  : 32.50 %
    Favored  : 60.12 %
  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 are not related in a simple way.
  whole: -1.92 (0.29), residues: 832
  helix: -0.59 (0.22), residues: 576
  sheet:  None (None), residues: 0
  loop : -2.70 (0.35), residues: 256

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG A  87 
 TYR   0.008   0.001   TYR B  27 
 PHE   0.018   0.002   PHE H  94 
 HIS   0.021   0.001   HIS F 113 

Details of bonding type rmsd
  covalent geometry    : bond        0.00311 ( 7128)
  covalent geometry    : angle       0.80109 ( 9520)
  hydrogen bonds       : bond        0.03609 (  323)
  hydrogen bonds       : angle       5.06063 (  963)

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

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

  1664 Ramachandran restraints generated.
    832 Oldfield, 0 Emsley, 832 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1664 Ramachandran restraints generated.
    832 Oldfield, 0 Emsley, 832 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  370 residues out of total 800 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 59
    poor density    : 311
  time to evaluate  : 0.316 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   17 LYS cc_start: 0.9012 (mmmm) cc_final: 0.8713 (mmtp)
REVERT: A   30 GLU cc_start: 0.6539 (mt-10) cc_final: 0.5403 (tp30)
REVERT: A   37 HIS cc_start: 0.6115 (OUTLIER) cc_final: 0.5542 (t70)
REVERT: A   39 ASP cc_start: 0.8504 (m-30) cc_final: 0.7829 (m-30)
REVERT: A  101 ASP cc_start: 0.7613 (OUTLIER) cc_final: 0.7335 (t0)
REVERT: A  105 LYS cc_start: 0.8603 (mmmt) cc_final: 0.8312 (mmmt)
REVERT: A  106 LEU cc_start: 0.8212 (OUTLIER) cc_final: 0.7947 (tt)
REVERT: B   17 LYS cc_start: 0.8708 (mmmm) cc_final: 0.7634 (tptp)
REVERT: B   18 LYS cc_start: 0.9129 (mtmm) cc_final: 0.8839 (mtmm)
REVERT: B   50 GLU cc_start: 0.7997 (mp0) cc_final: 0.7244 (mp0)
REVERT: B   51 ASP cc_start: 0.5772 (m-30) cc_final: 0.5249 (m-30)
REVERT: B   53 GLU cc_start: 0.8266 (OUTLIER) cc_final: 0.7820 (pt0)
REVERT: B   75 ASN cc_start: 0.7220 (t0) cc_final: 0.6852 (t0)
REVERT: B   99 ILE cc_start: 0.7336 (OUTLIER) cc_final: 0.7091 (pt)
REVERT: C   18 LYS cc_start: 0.8666 (OUTLIER) cc_final: 0.8338 (mtmm)
REVERT: C   53 GLU cc_start: 0.8223 (mt-10) cc_final: 0.7819 (pt0)
REVERT: D   23 ASN cc_start: 0.9030 (m-40) cc_final: 0.8727 (m-40)
REVERT: D   27 TYR cc_start: 0.6726 (m-80) cc_final: 0.6409 (m-80)
REVERT: D   62 ARG cc_start: 0.6902 (OUTLIER) cc_final: 0.6247 (mmt90)
REVERT: E   18 LYS cc_start: 0.8881 (mtpp) cc_final: 0.8572 (tttp)
REVERT: E   37 HIS cc_start: 0.6889 (t-170) cc_final: 0.6597 (t-170)
REVERT: E   51 ASP cc_start: 0.8107 (p0) cc_final: 0.7841 (p0)
REVERT: E   53 GLU cc_start: 0.8020 (mt-10) cc_final: 0.7563 (mt-10)
REVERT: E   58 ARG cc_start: 0.6628 (OUTLIER) cc_final: 0.4751 (ttt180)
REVERT: E   90 LYS cc_start: 0.7157 (ttmt) cc_final: 0.6786 (ttmt)
REVERT: F   22 GLU cc_start: 0.7503 (mm-30) cc_final: 0.7113 (mm-30)
REVERT: F   49 ARG cc_start: 0.6595 (tpt90) cc_final: 0.6390 (tpt-90)
REVERT: F   79 LEU cc_start: 0.8478 (mm) cc_final: 0.8159 (mt)
REVERT: F   87 ARG cc_start: 0.7366 (mpt180) cc_final: 0.7019 (mpt180)
REVERT: F  107 ARG cc_start: 0.8147 (mmm160) cc_final: 0.7733 (mmm160)
REVERT: F  109 ILE cc_start: 0.9057 (mm) cc_final: 0.8764 (pt)
REVERT: G   17 LYS cc_start: 0.8776 (mttp) cc_final: 0.8473 (mttm)
REVERT: G   23 ASN cc_start: 0.8149 (m110) cc_final: 0.7227 (m110)
REVERT: G   53 GLU cc_start: 0.8383 (mt-10) cc_final: 0.7898 (tm-30)
REVERT: G   70 ASP cc_start: 0.7975 (t70) cc_final: 0.7748 (t0)
REVERT: G   83 VAL cc_start: 0.8273 (p) cc_final: 0.6275 (p)
REVERT: G   89 GLU cc_start: 0.7811 (tp30) cc_final: 0.7521 (tp30)
REVERT: G   90 LYS cc_start: 0.7331 (ptpt) cc_final: 0.6995 (ptpp)
REVERT: G   91 THR cc_start: 0.5200 (p) cc_final: 0.4912 (p)
REVERT: G  102 GLU cc_start: 0.8225 (pp20) cc_final: 0.7884 (pp20)
REVERT: H   70 ASP cc_start: 0.7825 (t70) cc_final: 0.6601 (t70)
REVERT: H   73 GLN cc_start: 0.8487 (mt0) cc_final: 0.8174 (mt0)
REVERT: H   82 LEU cc_start: 0.8628 (OUTLIER) cc_final: 0.8163 (mm)
REVERT: H  104 LEU cc_start: 0.8934 (OUTLIER) cc_final: 0.8545 (tp)
  outliers start: 59
  outliers final: 33
  residues processed: 337
  average time/residue: 0.1284
  time to fit residues: 53.2979
Evaluate side-chains
  331 residues out of total 800 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 43
    poor density    : 288
  time to evaluate  : 0.308 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   37 HIS
Chi-restraints excluded: chain A residue   40 HIS
Chi-restraints excluded: chain A residue   48 SER
Chi-restraints excluded: chain A residue   55 ILE
Chi-restraints excluded: chain A residue   80 ASP
Chi-restraints excluded: chain A residue  101 ASP
Chi-restraints excluded: chain A residue  106 LEU
Chi-restraints excluded: chain B residue   40 HIS
Chi-restraints excluded: chain B residue   53 GLU
Chi-restraints excluded: chain B residue   99 ILE
Chi-restraints excluded: chain C residue   18 LYS
Chi-restraints excluded: chain C residue   24 LEU
Chi-restraints excluded: chain C residue   37 HIS
Chi-restraints excluded: chain C residue   79 LEU
Chi-restraints excluded: chain D residue   13 LEU
Chi-restraints excluded: chain D residue   26 VAL
Chi-restraints excluded: chain D residue   37 HIS
Chi-restraints excluded: chain D residue   41 LEU
Chi-restraints excluded: chain D residue   46 ILE
Chi-restraints excluded: chain D residue   59 THR
Chi-restraints excluded: chain D residue   62 ARG
Chi-restraints excluded: chain E residue   16 VAL
Chi-restraints excluded: chain E residue   41 LEU
Chi-restraints excluded: chain E residue   58 ARG
Chi-restraints excluded: chain E residue   73 GLN
Chi-restraints excluded: chain E residue   82 LEU
Chi-restraints excluded: chain F residue   13 LEU
Chi-restraints excluded: chain F residue   16 VAL
Chi-restraints excluded: chain F residue   27 TYR
Chi-restraints excluded: chain F residue   41 LEU
Chi-restraints excluded: chain F residue   59 THR
Chi-restraints excluded: chain F residue   80 ASP
Chi-restraints excluded: chain G residue   24 LEU
Chi-restraints excluded: chain G residue   26 VAL
Chi-restraints excluded: chain G residue   59 THR
Chi-restraints excluded: chain G residue   80 ASP
Chi-restraints excluded: chain G residue   82 LEU
Chi-restraints excluded: chain H residue   16 VAL
Chi-restraints excluded: chain H residue   51 ASP
Chi-restraints excluded: chain H residue   75 ASN
Chi-restraints excluded: chain H residue   80 ASP
Chi-restraints excluded: chain H residue   82 LEU
Chi-restraints excluded: chain H residue  104 LEU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 80
   random chunks:
   chunk 63 optimal weight:    5.9990
   chunk 27 optimal weight:    4.9990
   chunk 66 optimal weight:    0.0980
   chunk 65 optimal weight:    7.9990
   chunk 25 optimal weight:    8.9990
   chunk 42 optimal weight:    0.9990
   chunk 52 optimal weight:    0.9980
   chunk 0 optimal weight:   30.0000
   chunk 1 optimal weight:   30.0000
   chunk 60 optimal weight:   20.0000
   chunk 47 optimal weight:    8.9990
   overall best weight:    2.6186

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

Flipped N/Q/H residues before XYZ refinement:
** B  40 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** E  92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
F  23 ASN
** F  37 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** F  92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** G  73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** H  23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** H  37 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4027 r_free = 0.4027 target = 0.135312 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3814 r_free = 0.3814 target = 0.121143 restraints weight = 21572.909|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3855 r_free = 0.3855 target = 0.123958 restraints weight = 14119.980|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3885 r_free = 0.3885 target = 0.125991 restraints weight = 10103.581|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.3905 r_free = 0.3905 target = 0.127397 restraints weight = 7649.739|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 36)----------------|
| r_work = 0.3923 r_free = 0.3923 target = 0.128527 restraints weight = 6083.668|
|-----------------------------------------------------------------------------|
r_work (final): 0.3913
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7189
moved from start:          1.1296

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   7128  Z= 0.151
  Angle     :  0.843  11.579   9520  Z= 0.436
  Chirality :  0.049   0.354   1104
  Planarity :  0.005   0.089   1216
  Dihedral  :  7.124  58.731    952
  Min Nonbonded Distance : 2.444

Molprobity Statistics.
  All-atom Clashscore : 21.35
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.89 %
    Favored  : 91.11 %
  Rotamer:
    Outliers :  6.75 %
    Allowed  : 33.88 %
    Favored  : 59.38 %
  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 are not related in a simple way.
  whole: -1.76 (0.29), residues: 832
  helix: -0.42 (0.23), residues: 568
  sheet:  None (None), residues: 0
  loop : -2.72 (0.35), residues: 264

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.014   0.001   ARG G 107 
 TYR   0.009   0.001   TYR B  27 
 PHE   0.012   0.002   PHE F  38 
 HIS   0.005   0.001   HIS E  37 

Details of bonding type rmsd
  covalent geometry    : bond        0.00328 ( 7128)
  covalent geometry    : angle       0.84275 ( 9520)
  hydrogen bonds       : bond        0.03516 (  323)
  hydrogen bonds       : angle       5.00297 (  963)

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

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

  1664 Ramachandran restraints generated.
    832 Oldfield, 0 Emsley, 832 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1664 Ramachandran restraints generated.
    832 Oldfield, 0 Emsley, 832 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  353 residues out of total 800 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 54
    poor density    : 299
  time to evaluate  : 0.328 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   17 LYS cc_start: 0.8971 (mmmm) cc_final: 0.8679 (mmtp)
REVERT: A   30 GLU cc_start: 0.6192 (mt-10) cc_final: 0.5413 (tp30)
REVERT: A   37 HIS cc_start: 0.6538 (OUTLIER) cc_final: 0.5930 (t70)
REVERT: A   39 ASP cc_start: 0.8411 (m-30) cc_final: 0.7793 (m-30)
REVERT: A   40 HIS cc_start: 0.8960 (OUTLIER) cc_final: 0.8403 (m170)
REVERT: A  105 LYS cc_start: 0.8545 (mmmt) cc_final: 0.8293 (mmmt)
REVERT: A  106 LEU cc_start: 0.8132 (OUTLIER) cc_final: 0.7828 (tp)
REVERT: B   17 LYS cc_start: 0.8587 (mmmm) cc_final: 0.7578 (tptp)
REVERT: B   18 LYS cc_start: 0.9165 (mtmm) cc_final: 0.8838 (mtmm)
REVERT: B   24 LEU cc_start: 0.8783 (mm) cc_final: 0.8537 (mm)
REVERT: B   50 GLU cc_start: 0.7925 (mp0) cc_final: 0.7207 (mp0)
REVERT: B   53 GLU cc_start: 0.8263 (OUTLIER) cc_final: 0.7835 (pt0)
REVERT: B   75 ASN cc_start: 0.7241 (t0) cc_final: 0.6927 (t0)
REVERT: C   18 LYS cc_start: 0.8760 (OUTLIER) cc_final: 0.8378 (mtmm)
REVERT: C   35 GLU cc_start: 0.7171 (pt0) cc_final: 0.6382 (pt0)
REVERT: C   53 GLU cc_start: 0.8230 (mt-10) cc_final: 0.7928 (pt0)
REVERT: C   64 ARG cc_start: 0.8358 (ptt180) cc_final: 0.7856 (ptp-170)
REVERT: C   82 LEU cc_start: 0.8855 (pp) cc_final: 0.8566 (pp)
REVERT: D   19 ASP cc_start: 0.8295 (m-30) cc_final: 0.7862 (m-30)
REVERT: D   23 ASN cc_start: 0.9020 (m-40) cc_final: 0.8675 (m-40)
REVERT: D   27 TYR cc_start: 0.6741 (m-80) cc_final: 0.6422 (m-80)
REVERT: D   50 GLU cc_start: 0.7941 (mp0) cc_final: 0.7656 (mp0)
REVERT: D   53 GLU cc_start: 0.7931 (tt0) cc_final: 0.7301 (pt0)
REVERT: D   62 ARG cc_start: 0.6854 (OUTLIER) cc_final: 0.6270 (mmt90)
REVERT: E   18 LYS cc_start: 0.8884 (mtpp) cc_final: 0.8631 (tttm)
REVERT: E   46 ILE cc_start: 0.7115 (pt) cc_final: 0.6877 (pt)
REVERT: E   53 GLU cc_start: 0.7992 (mt-10) cc_final: 0.7582 (mt-10)
REVERT: E   90 LYS cc_start: 0.7327 (ttmt) cc_final: 0.6965 (ttmt)
REVERT: F   79 LEU cc_start: 0.8333 (mm) cc_final: 0.8026 (mt)
REVERT: F   87 ARG cc_start: 0.7191 (mpt180) cc_final: 0.6950 (mpt180)
REVERT: F  109 ILE cc_start: 0.9089 (mm) cc_final: 0.8834 (pt)
REVERT: G   17 LYS cc_start: 0.8816 (mttp) cc_final: 0.8421 (mttm)
REVERT: G   67 LYS cc_start: 0.9058 (mptt) cc_final: 0.8846 (mptt)
REVERT: G   89 GLU cc_start: 0.7724 (tp30) cc_final: 0.7431 (tp30)
REVERT: G   90 LYS cc_start: 0.7282 (ptpt) cc_final: 0.6989 (ptpp)
REVERT: G   91 THR cc_start: 0.5401 (p) cc_final: 0.5049 (p)
REVERT: H   70 ASP cc_start: 0.7685 (t70) cc_final: 0.6429 (t70)
REVERT: H   73 GLN cc_start: 0.8408 (mt0) cc_final: 0.8134 (mt0)
REVERT: H   82 LEU cc_start: 0.8684 (OUTLIER) cc_final: 0.8251 (mm)
REVERT: H   98 LYS cc_start: 0.6179 (OUTLIER) cc_final: 0.5968 (tptp)
REVERT: H  104 LEU cc_start: 0.8873 (OUTLIER) cc_final: 0.8445 (tp)
  outliers start: 54
  outliers final: 34
  residues processed: 319
  average time/residue: 0.1265
  time to fit residues: 49.0969
Evaluate side-chains
  312 residues out of total 800 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 43
    poor density    : 269
  time to evaluate  : 0.328 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   37 HIS
Chi-restraints excluded: chain A residue   40 HIS
Chi-restraints excluded: chain A residue   48 SER
Chi-restraints excluded: chain A residue   55 ILE
Chi-restraints excluded: chain A residue  106 LEU
Chi-restraints excluded: chain B residue   40 HIS
Chi-restraints excluded: chain B residue   53 GLU
Chi-restraints excluded: chain B residue   70 ASP
Chi-restraints excluded: chain C residue   18 LYS
Chi-restraints excluded: chain C residue   21 LEU
Chi-restraints excluded: chain C residue   24 LEU
Chi-restraints excluded: chain C residue   37 HIS
Chi-restraints excluded: chain C residue   79 LEU
Chi-restraints excluded: chain D residue   13 LEU
Chi-restraints excluded: chain D residue   26 VAL
Chi-restraints excluded: chain D residue   41 LEU
Chi-restraints excluded: chain D residue   46 ILE
Chi-restraints excluded: chain D residue   59 THR
Chi-restraints excluded: chain D residue   62 ARG
Chi-restraints excluded: chain E residue   16 VAL
Chi-restraints excluded: chain E residue   41 LEU
Chi-restraints excluded: chain E residue   82 LEU
Chi-restraints excluded: chain F residue   13 LEU
Chi-restraints excluded: chain F residue   16 VAL
Chi-restraints excluded: chain F residue   27 TYR
Chi-restraints excluded: chain F residue   41 LEU
Chi-restraints excluded: chain F residue   59 THR
Chi-restraints excluded: chain F residue   80 ASP
Chi-restraints excluded: chain G residue   24 LEU
Chi-restraints excluded: chain G residue   33 ILE
Chi-restraints excluded: chain G residue   41 LEU
Chi-restraints excluded: chain G residue   59 THR
Chi-restraints excluded: chain G residue   80 ASP
Chi-restraints excluded: chain G residue   98 LYS
Chi-restraints excluded: chain G residue  109 ILE
Chi-restraints excluded: chain H residue   16 VAL
Chi-restraints excluded: chain H residue   51 ASP
Chi-restraints excluded: chain H residue   75 ASN
Chi-restraints excluded: chain H residue   80 ASP
Chi-restraints excluded: chain H residue   81 THR
Chi-restraints excluded: chain H residue   82 LEU
Chi-restraints excluded: chain H residue   98 LYS
Chi-restraints excluded: chain H residue  104 LEU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 80
   random chunks:
   chunk 13 optimal weight:   20.0000
   chunk 75 optimal weight:    8.9990
   chunk 24 optimal weight:   10.0000
   chunk 21 optimal weight:    5.9990
   chunk 62 optimal weight:    9.9990
   chunk 65 optimal weight:    5.9990
   chunk 17 optimal weight:    2.9990
   chunk 76 optimal weight:    7.9990
   chunk 72 optimal weight:   10.0000
   chunk 37 optimal weight:    0.4980
   chunk 47 optimal weight:    3.9990
   overall best weight:    3.8988

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

Flipped N/Q/H residues before XYZ refinement:
** A  75 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B  40 HIS
D  37 HIS
** E  92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
F  23 ASN
** F  37 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** F  92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
F 113 HIS
** G  73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
H  23 ASN
** H  37 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4002 r_free = 0.4002 target = 0.133906 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3795 r_free = 0.3795 target = 0.120322 restraints weight = 21914.611|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3836 r_free = 0.3836 target = 0.123067 restraints weight = 14258.371|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 42)----------------|
| r_work = 0.3866 r_free = 0.3866 target = 0.125084 restraints weight = 10098.086|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.3886 r_free = 0.3886 target = 0.126466 restraints weight = 7585.705|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.3902 r_free = 0.3902 target = 0.127526 restraints weight = 5985.944|
|-----------------------------------------------------------------------------|
r_work (final): 0.3904
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7165
moved from start:          1.1637

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.038   7128  Z= 0.162
  Angle     :  0.869  12.679   9520  Z= 0.450
  Chirality :  0.049   0.301   1104
  Planarity :  0.004   0.041   1216
  Dihedral  :  7.156  58.979    952
  Min Nonbonded Distance : 2.448

Molprobity Statistics.
  All-atom Clashscore : 23.42
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.98 %
    Favored  : 90.02 %
  Rotamer:
    Outliers :  7.25 %
    Allowed  : 33.50 %
    Favored  : 59.25 %
  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 are not related in a simple way.
  whole: -1.44 (0.29), residues: 832
  helix:  0.00 (0.23), residues: 528
  sheet:  None (None), residues: 0
  loop : -2.68 (0.34), residues: 304

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.011   0.001   ARG A  87 
 TYR   0.012   0.001   TYR B  27 
 PHE   0.013   0.002   PHE F  94 
 HIS   0.009   0.001   HIS E  37 

Details of bonding type rmsd
  covalent geometry    : bond        0.00354 ( 7128)
  covalent geometry    : angle       0.86911 ( 9520)
  hydrogen bonds       : bond        0.03685 (  323)
  hydrogen bonds       : angle       4.99886 (  963)

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

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

  1664 Ramachandran restraints generated.
    832 Oldfield, 0 Emsley, 832 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1664 Ramachandran restraints generated.
    832 Oldfield, 0 Emsley, 832 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  341 residues out of total 800 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 58
    poor density    : 283
  time to evaluate  : 0.315 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   17 LYS cc_start: 0.8900 (mmmm) cc_final: 0.8673 (mmtp)
REVERT: A   30 GLU cc_start: 0.6237 (mt-10) cc_final: 0.5697 (tp30)
REVERT: A   37 HIS cc_start: 0.6447 (OUTLIER) cc_final: 0.5458 (t70)
REVERT: A  106 LEU cc_start: 0.8179 (OUTLIER) cc_final: 0.7900 (tp)
REVERT: B   17 LYS cc_start: 0.8476 (mmmm) cc_final: 0.7562 (tptp)
REVERT: B   18 LYS cc_start: 0.9093 (mtmm) cc_final: 0.8811 (mtmm)
REVERT: B   24 LEU cc_start: 0.8901 (mm) cc_final: 0.8641 (mm)
REVERT: B   53 GLU cc_start: 0.8224 (OUTLIER) cc_final: 0.7915 (pt0)
REVERT: B   75 ASN cc_start: 0.7042 (t0) cc_final: 0.6756 (t0)
REVERT: C   18 LYS cc_start: 0.8931 (OUTLIER) cc_final: 0.8667 (mtmm)
REVERT: D   19 ASP cc_start: 0.8187 (m-30) cc_final: 0.7816 (m-30)
REVERT: D   23 ASN cc_start: 0.8928 (m-40) cc_final: 0.8628 (m-40)
REVERT: D   53 GLU cc_start: 0.7847 (tt0) cc_final: 0.7380 (tt0)
REVERT: D   62 ARG cc_start: 0.6930 (OUTLIER) cc_final: 0.6253 (mmt90)
REVERT: E   18 LYS cc_start: 0.8908 (mtpp) cc_final: 0.8669 (tttp)
REVERT: E   53 GLU cc_start: 0.7919 (mt-10) cc_final: 0.7603 (mt-10)
REVERT: F   18 LYS cc_start: 0.9170 (mmmm) cc_final: 0.8910 (mmmm)
REVERT: F   25 ARG cc_start: 0.8140 (OUTLIER) cc_final: 0.6609 (ttt180)
REVERT: F   79 LEU cc_start: 0.8233 (mm) cc_final: 0.8029 (mt)
REVERT: F  109 ILE cc_start: 0.9015 (mm) cc_final: 0.8704 (pt)
REVERT: G   23 ASN cc_start: 0.8552 (OUTLIER) cc_final: 0.8350 (t0)
REVERT: G   70 ASP cc_start: 0.7786 (t70) cc_final: 0.7554 (t0)
REVERT: G   73 GLN cc_start: 0.8775 (mt0) cc_final: 0.8573 (mt0)
REVERT: G   89 GLU cc_start: 0.7630 (tp30) cc_final: 0.7397 (tp30)
REVERT: G   91 THR cc_start: 0.5399 (p) cc_final: 0.4940 (p)
REVERT: H   70 ASP cc_start: 0.7560 (t70) cc_final: 0.6261 (t70)
REVERT: H   82 LEU cc_start: 0.8582 (OUTLIER) cc_final: 0.8232 (mm)
REVERT: H   98 LYS cc_start: 0.5920 (OUTLIER) cc_final: 0.5720 (tptp)
REVERT: H  104 LEU cc_start: 0.8632 (mm) cc_final: 0.8291 (tp)
  outliers start: 58
  outliers final: 39
  residues processed: 307
  average time/residue: 0.1254
  time to fit residues: 47.3613
Evaluate side-chains
  308 residues out of total 800 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 48
    poor density    : 260
  time to evaluate  : 0.234 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   37 HIS
Chi-restraints excluded: chain A residue   40 HIS
Chi-restraints excluded: chain A residue   48 SER
Chi-restraints excluded: chain A residue   55 ILE
Chi-restraints excluded: chain A residue   80 ASP
Chi-restraints excluded: chain A residue  106 LEU
Chi-restraints excluded: chain B residue   40 HIS
Chi-restraints excluded: chain B residue   53 GLU
Chi-restraints excluded: chain B residue   70 ASP
Chi-restraints excluded: chain C residue   16 VAL
Chi-restraints excluded: chain C residue   18 LYS
Chi-restraints excluded: chain C residue   24 LEU
Chi-restraints excluded: chain C residue   37 HIS
Chi-restraints excluded: chain C residue   79 LEU
Chi-restraints excluded: chain D residue   13 LEU
Chi-restraints excluded: chain D residue   26 VAL
Chi-restraints excluded: chain D residue   37 HIS
Chi-restraints excluded: chain D residue   41 LEU
Chi-restraints excluded: chain D residue   46 ILE
Chi-restraints excluded: chain D residue   59 THR
Chi-restraints excluded: chain D residue   62 ARG
Chi-restraints excluded: chain E residue   82 LEU
Chi-restraints excluded: chain E residue  102 GLU
Chi-restraints excluded: chain F residue   13 LEU
Chi-restraints excluded: chain F residue   16 VAL
Chi-restraints excluded: chain F residue   25 ARG
Chi-restraints excluded: chain F residue   26 VAL
Chi-restraints excluded: chain F residue   27 TYR
Chi-restraints excluded: chain F residue   41 LEU
Chi-restraints excluded: chain F residue   59 THR
Chi-restraints excluded: chain F residue   80 ASP
Chi-restraints excluded: chain F residue  104 LEU
Chi-restraints excluded: chain F residue  113 HIS
Chi-restraints excluded: chain G residue   23 ASN
Chi-restraints excluded: chain G residue   24 LEU
Chi-restraints excluded: chain G residue   33 ILE
Chi-restraints excluded: chain G residue   59 THR
Chi-restraints excluded: chain G residue   80 ASP
Chi-restraints excluded: chain G residue   82 LEU
Chi-restraints excluded: chain G residue   98 LYS
Chi-restraints excluded: chain G residue  109 ILE
Chi-restraints excluded: chain H residue   16 VAL
Chi-restraints excluded: chain H residue   51 ASP
Chi-restraints excluded: chain H residue   75 ASN
Chi-restraints excluded: chain H residue   80 ASP
Chi-restraints excluded: chain H residue   81 THR
Chi-restraints excluded: chain H residue   82 LEU
Chi-restraints excluded: chain H residue   98 LYS
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 80
   random chunks:
   chunk 77 optimal weight:    9.9990
   chunk 31 optimal weight:    6.9990
   chunk 70 optimal weight:   40.0000
   chunk 29 optimal weight:    9.9990
   chunk 59 optimal weight:    9.9990
   chunk 73 optimal weight:    2.9990
   chunk 36 optimal weight:    7.9990
   chunk 27 optimal weight:    3.9990
   chunk 25 optimal weight:    8.9990
   chunk 74 optimal weight:   20.0000
   chunk 64 optimal weight:    7.9990
   overall best weight:    5.9990

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

Flipped N/Q/H residues before XYZ refinement:
** A  75 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E  92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
F  23 ASN
** F  37 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** F  92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
F 113 HIS
** G  73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** H  23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** H  37 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3972 r_free = 0.3972 target = 0.131857 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3761 r_free = 0.3761 target = 0.118024 restraints weight = 21166.157|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3802 r_free = 0.3802 target = 0.120801 restraints weight = 13722.186|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3833 r_free = 0.3833 target = 0.122781 restraints weight = 9717.267|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 33)----------------|
| r_work = 0.3855 r_free = 0.3855 target = 0.124264 restraints weight = 7313.318|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3871 r_free = 0.3871 target = 0.125313 restraints weight = 5727.033|
|-----------------------------------------------------------------------------|
r_work (final): 0.3872
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7230
moved from start:          1.1885

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.037   7128  Z= 0.188
  Angle     :  0.910  11.961   9520  Z= 0.474
  Chirality :  0.051   0.318   1104
  Planarity :  0.005   0.055   1216
  Dihedral  :  7.347  60.039    952
  Min Nonbonded Distance : 2.401

Molprobity Statistics.
  All-atom Clashscore : 26.19
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 10.82 %
    Favored  : 89.18 %
  Rotamer:
    Outliers :  6.62 %
    Allowed  : 34.75 %
    Favored  : 58.62 %
  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 are not related in a simple way.
  whole: -1.57 (0.29), residues: 832
  helix: -0.07 (0.23), residues: 528
  sheet:  None (None), residues: 0
  loop : -2.79 (0.34), residues: 304

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.012   0.001   ARG A  87 
 TYR   0.014   0.001   TYR B  27 
 PHE   0.032   0.003   PHE H  94 
 HIS   0.008   0.001   HIS E  37 

Details of bonding type rmsd
  covalent geometry    : bond        0.00415 ( 7128)
  covalent geometry    : angle       0.91009 ( 9520)
  hydrogen bonds       : bond        0.03906 (  323)
  hydrogen bonds       : angle       5.11905 (  963)

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

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

  1664 Ramachandran restraints generated.
    832 Oldfield, 0 Emsley, 832 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1664 Ramachandran restraints generated.
    832 Oldfield, 0 Emsley, 832 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  313 residues out of total 800 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 53
    poor density    : 260
  time to evaluate  : 0.321 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   17 LYS cc_start: 0.8819 (mmmm) cc_final: 0.8608 (mttt)
REVERT: A   30 GLU cc_start: 0.6019 (mt-10) cc_final: 0.5549 (tp30)
REVERT: A   37 HIS cc_start: 0.6654 (OUTLIER) cc_final: 0.5631 (t70)
REVERT: A  106 LEU cc_start: 0.8177 (OUTLIER) cc_final: 0.7938 (tp)
REVERT: B   17 LYS cc_start: 0.8520 (mmmm) cc_final: 0.7667 (tptp)
REVERT: B   18 LYS cc_start: 0.9127 (mtmm) cc_final: 0.8784 (mtmm)
REVERT: B   50 GLU cc_start: 0.7562 (mp0) cc_final: 0.7165 (mp0)
REVERT: B   70 ASP cc_start: 0.8674 (OUTLIER) cc_final: 0.6523 (t0)
REVERT: B   75 ASN cc_start: 0.6940 (t0) cc_final: 0.6657 (t0)
REVERT: D   19 ASP cc_start: 0.8204 (m-30) cc_final: 0.7865 (m-30)
REVERT: D   27 TYR cc_start: 0.6404 (m-80) cc_final: 0.6195 (m-80)
REVERT: D   53 GLU cc_start: 0.7956 (OUTLIER) cc_final: 0.7447 (tt0)
REVERT: E   18 LYS cc_start: 0.8924 (mtpp) cc_final: 0.8690 (tttm)
REVERT: F   25 ARG cc_start: 0.8207 (OUTLIER) cc_final: 0.6487 (tmt170)
REVERT: F   79 LEU cc_start: 0.8129 (mm) cc_final: 0.7872 (mt)
REVERT: F  104 LEU cc_start: 0.8094 (pp) cc_final: 0.7836 (pp)
REVERT: F  105 LYS cc_start: 0.8464 (mtpt) cc_final: 0.8022 (tttt)
REVERT: F  109 ILE cc_start: 0.9076 (mm) cc_final: 0.8774 (pt)
REVERT: G   89 GLU cc_start: 0.7494 (tp30) cc_final: 0.7269 (tp30)
REVERT: G   91 THR cc_start: 0.5748 (p) cc_final: 0.5267 (p)
REVERT: H   79 LEU cc_start: 0.8142 (tp) cc_final: 0.7875 (tp)
REVERT: H   82 LEU cc_start: 0.8675 (OUTLIER) cc_final: 0.8172 (mm)
REVERT: H  104 LEU cc_start: 0.8706 (mm) cc_final: 0.8261 (tp)
  outliers start: 53
  outliers final: 35
  residues processed: 284
  average time/residue: 0.1295
  time to fit residues: 44.8874
Evaluate side-chains
  285 residues out of total 800 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 41
    poor density    : 244
  time to evaluate  : 0.325 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   13 LEU
Chi-restraints excluded: chain A residue   37 HIS
Chi-restraints excluded: chain A residue   40 HIS
Chi-restraints excluded: chain A residue   48 SER
Chi-restraints excluded: chain A residue   55 ILE
Chi-restraints excluded: chain A residue   80 ASP
Chi-restraints excluded: chain A residue  106 LEU
Chi-restraints excluded: chain B residue   21 LEU
Chi-restraints excluded: chain B residue   70 ASP
Chi-restraints excluded: chain B residue   99 ILE
Chi-restraints excluded: chain C residue   16 VAL
Chi-restraints excluded: chain C residue   21 LEU
Chi-restraints excluded: chain C residue   24 LEU
Chi-restraints excluded: chain C residue   37 HIS
Chi-restraints excluded: chain C residue   61 SER
Chi-restraints excluded: chain C residue   79 LEU
Chi-restraints excluded: chain C residue   80 ASP
Chi-restraints excluded: chain D residue   26 VAL
Chi-restraints excluded: chain D residue   37 HIS
Chi-restraints excluded: chain D residue   46 ILE
Chi-restraints excluded: chain D residue   53 GLU
Chi-restraints excluded: chain D residue   62 ARG
Chi-restraints excluded: chain D residue   82 LEU
Chi-restraints excluded: chain E residue   82 LEU
Chi-restraints excluded: chain F residue   13 LEU
Chi-restraints excluded: chain F residue   16 VAL
Chi-restraints excluded: chain F residue   25 ARG
Chi-restraints excluded: chain F residue   26 VAL
Chi-restraints excluded: chain F residue   27 TYR
Chi-restraints excluded: chain F residue   41 LEU
Chi-restraints excluded: chain F residue   80 ASP
Chi-restraints excluded: chain F residue  113 HIS
Chi-restraints excluded: chain G residue   33 ILE
Chi-restraints excluded: chain G residue   59 THR
Chi-restraints excluded: chain G residue   80 ASP
Chi-restraints excluded: chain H residue   16 VAL
Chi-restraints excluded: chain H residue   51 ASP
Chi-restraints excluded: chain H residue   75 ASN
Chi-restraints excluded: chain H residue   80 ASP
Chi-restraints excluded: chain H residue   81 THR
Chi-restraints excluded: chain H residue   82 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 80
   random chunks:
   chunk 13 optimal weight:    9.9990
   chunk 4 optimal weight:   30.0000
   chunk 28 optimal weight:    7.9990
   chunk 30 optimal weight:   40.0000
   chunk 57 optimal weight:    0.6980
   chunk 14 optimal weight:    6.9990
   chunk 63 optimal weight:    6.9990
   chunk 61 optimal weight:    3.9990
   chunk 9 optimal weight:    0.5980
   chunk 6 optimal weight:    0.9980
   chunk 5 optimal weight:    8.9990
   overall best weight:    2.6584

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

Flipped N/Q/H residues before XYZ refinement:
** B  75 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
E  92 GLN
E  93 ASN
F  23 ASN
F  37 HIS
F 113 HIS
** H  37 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4022 r_free = 0.4022 target = 0.135287 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3810 r_free = 0.3810 target = 0.121181 restraints weight = 21050.296|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3851 r_free = 0.3851 target = 0.124007 restraints weight = 13696.719|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3881 r_free = 0.3881 target = 0.126039 restraints weight = 9781.830|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 33)----------------|
| r_work = 0.3904 r_free = 0.3904 target = 0.127561 restraints weight = 7417.662|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.3919 r_free = 0.3919 target = 0.128636 restraints weight = 5866.917|
|-----------------------------------------------------------------------------|
r_work (final): 0.3918
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7163
moved from start:          1.2180

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.043   7128  Z= 0.165
  Angle     :  0.963  18.750   9520  Z= 0.491
  Chirality :  0.052   0.312   1104
  Planarity :  0.005   0.061   1216
  Dihedral  :  7.277  58.612    952
  Min Nonbonded Distance : 2.377

Molprobity Statistics.
  All-atom Clashscore : 23.63
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 10.10 %
    Favored  : 89.90 %
  Rotamer:
    Outliers :  4.75 %
    Allowed  : 37.12 %
    Favored  : 58.12 %
  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 are not related in a simple way.
  whole: -1.55 (0.29), residues: 832
  helix: -0.10 (0.23), residues: 528
  sheet:  None (None), residues: 0
  loop : -2.70 (0.35), residues: 304

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.013   0.001   ARG D 107 
 TYR   0.011   0.001   TYR B  27 
 PHE   0.030   0.002   PHE H  94 
 HIS   0.007   0.001   HIS E  37 

Details of bonding type rmsd
  covalent geometry    : bond        0.00364 ( 7128)
  covalent geometry    : angle       0.96302 ( 9520)
  hydrogen bonds       : bond        0.03790 (  323)
  hydrogen bonds       : angle       5.02926 (  963)

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

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

  1664 Ramachandran restraints generated.
    832 Oldfield, 0 Emsley, 832 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1664 Ramachandran restraints generated.
    832 Oldfield, 0 Emsley, 832 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  314 residues out of total 800 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 38
    poor density    : 276
  time to evaluate  : 0.302 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   17 LYS cc_start: 0.8783 (mmmm) cc_final: 0.8567 (mttt)
REVERT: A   30 GLU cc_start: 0.5677 (mt-10) cc_final: 0.5259 (tp30)
REVERT: A   37 HIS cc_start: 0.6609 (OUTLIER) cc_final: 0.5518 (t70)
REVERT: A   39 ASP cc_start: 0.8162 (m-30) cc_final: 0.7387 (m-30)
REVERT: A  106 LEU cc_start: 0.8092 (OUTLIER) cc_final: 0.7862 (tt)
REVERT: B   17 LYS cc_start: 0.8409 (mmmm) cc_final: 0.7532 (tptp)
REVERT: B   70 ASP cc_start: 0.7894 (m-30) cc_final: 0.7668 (t70)
REVERT: B   75 ASN cc_start: 0.6511 (t0) cc_final: 0.6236 (t0)
REVERT: D   19 ASP cc_start: 0.8169 (m-30) cc_final: 0.7728 (m-30)
REVERT: D   23 ASN cc_start: 0.8811 (m-40) cc_final: 0.8521 (m-40)
REVERT: D   27 TYR cc_start: 0.6303 (m-80) cc_final: 0.6058 (m-80)
REVERT: D   50 GLU cc_start: 0.7650 (mp0) cc_final: 0.7346 (mp0)
REVERT: D   53 GLU cc_start: 0.7841 (tt0) cc_final: 0.7530 (pt0)
REVERT: E   90 LYS cc_start: 0.7521 (ttmt) cc_final: 0.7087 (ttmt)
REVERT: F   79 LEU cc_start: 0.8306 (mm) cc_final: 0.8063 (mt)
REVERT: F  105 LYS cc_start: 0.8361 (mtpt) cc_final: 0.8044 (tttt)
REVERT: F  107 ARG cc_start: 0.8708 (mmm160) cc_final: 0.8278 (mmm160)
REVERT: G   49 ARG cc_start: 0.6945 (tpt90) cc_final: 0.6732 (tpt90)
REVERT: G   89 GLU cc_start: 0.7649 (tp30) cc_final: 0.7336 (tp30)
REVERT: G   91 THR cc_start: 0.5257 (p) cc_final: 0.4875 (p)
REVERT: H   15 GLU cc_start: 0.8491 (pp20) cc_final: 0.8219 (mp0)
REVERT: H   82 LEU cc_start: 0.8615 (OUTLIER) cc_final: 0.8117 (mm)
REVERT: H  104 LEU cc_start: 0.8623 (mm) cc_final: 0.8255 (tp)
  outliers start: 38
  outliers final: 28
  residues processed: 293
  average time/residue: 0.1210
  time to fit residues: 43.8329
Evaluate side-chains
  292 residues out of total 800 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 261
  time to evaluate  : 0.289 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   37 HIS
Chi-restraints excluded: chain A residue   40 HIS
Chi-restraints excluded: chain A residue   48 SER
Chi-restraints excluded: chain A residue   55 ILE
Chi-restraints excluded: chain A residue  106 LEU
Chi-restraints excluded: chain C residue   16 VAL
Chi-restraints excluded: chain C residue   21 LEU
Chi-restraints excluded: chain C residue   24 LEU
Chi-restraints excluded: chain C residue   37 HIS
Chi-restraints excluded: chain C residue   79 LEU
Chi-restraints excluded: chain D residue   46 ILE
Chi-restraints excluded: chain D residue   62 ARG
Chi-restraints excluded: chain D residue   82 LEU
Chi-restraints excluded: chain E residue   82 LEU
Chi-restraints excluded: chain E residue   88 ARG
Chi-restraints excluded: chain E residue   93 ASN
Chi-restraints excluded: chain F residue   13 LEU
Chi-restraints excluded: chain F residue   16 VAL
Chi-restraints excluded: chain F residue   27 TYR
Chi-restraints excluded: chain F residue   41 LEU
Chi-restraints excluded: chain F residue   80 ASP
Chi-restraints excluded: chain F residue  113 HIS
Chi-restraints excluded: chain G residue   33 ILE
Chi-restraints excluded: chain G residue   80 ASP
Chi-restraints excluded: chain G residue   82 LEU
Chi-restraints excluded: chain H residue   16 VAL
Chi-restraints excluded: chain H residue   51 ASP
Chi-restraints excluded: chain H residue   75 ASN
Chi-restraints excluded: chain H residue   80 ASP
Chi-restraints excluded: chain H residue   81 THR
Chi-restraints excluded: chain H residue   82 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 80
   random chunks:
   chunk 19 optimal weight:    6.9990
   chunk 9 optimal weight:   10.0000
   chunk 36 optimal weight:    0.4980
   chunk 69 optimal weight:    7.9990
   chunk 70 optimal weight:   40.0000
   chunk 71 optimal weight:   30.0000
   chunk 47 optimal weight:    0.8980
   chunk 55 optimal weight:   20.0000
   chunk 77 optimal weight:    8.9990
   chunk 59 optimal weight:    8.9990
   chunk 73 optimal weight:    6.9990
   overall best weight:    4.6786

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

Flipped N/Q/H residues before XYZ refinement:
A 108 ASN
** B  75 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
E  93 ASN
F  23 ASN
F  37 HIS
** F 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
F 113 HIS
** H  37 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3994 r_free = 0.3994 target = 0.133010 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 23)----------------|
| r_work = 0.3792 r_free = 0.3792 target = 0.119570 restraints weight = 21120.672|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3833 r_free = 0.3833 target = 0.122343 restraints weight = 13775.968|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3863 r_free = 0.3863 target = 0.124355 restraints weight = 9775.916|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 44)----------------|
| r_work = 0.3884 r_free = 0.3884 target = 0.125801 restraints weight = 7347.228|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 31)----------------|
| r_work = 0.3899 r_free = 0.3899 target = 0.126829 restraints weight = 5770.583|
|-----------------------------------------------------------------------------|
r_work (final): 0.3893
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7214
moved from start:          1.2343

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.043   7128  Z= 0.174
  Angle     :  0.973  16.191   9520  Z= 0.495
  Chirality :  0.051   0.323   1104
  Planarity :  0.006   0.054   1216
  Dihedral  :  7.319  59.637    952
  Min Nonbonded Distance : 2.440

Molprobity Statistics.
  All-atom Clashscore : 25.57
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 10.82 %
    Favored  : 89.18 %
  Rotamer:
    Outliers :  4.62 %
    Allowed  : 37.12 %
    Favored  : 58.25 %
  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 are not related in a simple way.
  whole: -1.63 (0.30), residues: 832
  helix: -0.17 (0.23), residues: 528
  sheet:  None (None), residues: 0
  loop : -2.72 (0.35), residues: 304

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.013   0.001   ARG D 107 
 TYR   0.012   0.001   TYR B  27 
 PHE   0.020   0.002   PHE H  94 
 HIS   0.006   0.001   HIS E  37 

Details of bonding type rmsd
  covalent geometry    : bond        0.00392 ( 7128)
  covalent geometry    : angle       0.97266 ( 9520)
  hydrogen bonds       : bond        0.03753 (  323)
  hydrogen bonds       : angle       4.97861 (  963)

===============================================================================
Job complete
usr+sys time: 1449.82 seconds
wall clock time: 25 minutes 51.51 seconds (1551.51 seconds total)