Starting phenix.real_space_refine
on Fri Aug 22 17:53:31 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8w5i_37293/08_2025/8w5i_37293.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8w5i_37293/08_2025/8w5i_37293.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.6
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/8w5i_37293/08_2025/8w5i_37293.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8w5i_37293/08_2025/8w5i_37293.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/8w5i_37293/08_2025/8w5i_37293.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8w5i_37293/08_2025/8w5i_37293.map"
  }
  resolution = 3.6
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.005 sd=   0.096
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 4
    Type Number    sf(0)   Gaussians
     S      17      5.16       5
     C    4158      2.51       5
     N    1161      2.21       5
     O    1328      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model
  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 6664
  Number of models: 1
  Model: ""
    Number of chains: 7
    Chain: "H"
      Number of atoms: 926
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 116, 926
          Classifications: {'peptide': 116}
          Link IDs: {'PTRANS': 4, 'TRANS': 111}
    Chain: "L"
      Number of atoms: 773
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 104, 773
          Classifications: {'peptide': 104}
          Link IDs: {'PTRANS': 5, 'TRANS': 98}
    Chain: "A"
      Number of atoms: 993
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 132, 993
          Classifications: {'peptide': 132}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 8, 'TRANS': 123}
    Chain: "B"
      Number of atoms: 993
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 132, 993
          Classifications: {'peptide': 132}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 8, 'TRANS': 123}
    Chain: "C"
      Number of atoms: 993
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 132, 993
          Classifications: {'peptide': 132}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 8, 'TRANS': 123}
    Chain: "D"
      Number of atoms: 993
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 132, 993
          Classifications: {'peptide': 132}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 8, 'TRANS': 123}
    Chain: "E"
      Number of atoms: 993
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 132, 993
          Classifications: {'peptide': 132}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 8, 'TRANS': 123}
  Time building chain proxies: 1.97, per 1000 atoms: 0.30
  Number of scatterers: 6664
  At special positions: 0
  Unit cell: (127.84, 116.96, 112.88, 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      17     16.00
     O    1328      8.00
     N    1161      7.00
     C    4158      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=3, symmetry=0
    Simple disulfide: pdb=" SG  CYS H  25 " - pdb=" SG  CYS H  99 " distance=2.04
    Simple disulfide: pdb=" SG  CYS B  80 " - pdb=" SG  CYS C  74 " distance=2.02
    Simple disulfide: pdb=" SG  CYS C  80 " - pdb=" SG  CYS D  74 " distance=2.03

  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=1, symmetry=0
  Number of additional bonds: simple=1, symmetry=0
  Coordination:
  Other bonds:
  Time building additional restraints: 0.47
  Conformation dependent library (CDL) restraints added in 420.6 milliseconds
  
  Enol-peptide restraints added in 476.8 nanoseconds
  

  1732 Ramachandran restraints generated.
    866 Oldfield, 0 Emsley, 866 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1650

  Finding SS restraints...
    Secondary structure from input PDB file:
      10 helices and 21 sheets defined
      15.3% alpha, 28.1% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.27
  Creating SS restraints...
    Processing helix  chain 'A' and resid 101 through 116
      removed outlier: 3.816A  pdb=" N   ARG A 105 " --> pdb=" O   THR A 101 " (cutoff:3.500A)
      removed outlier: 3.669A  pdb=" N   ARG A 109 " --> pdb=" O   ARG A 105 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 118 through 128
      removed outlier: 3.718A  pdb=" N   GLN A 127 " --> pdb=" O   ASP A 123 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 101 through 116
      removed outlier: 3.816A  pdb=" N   ARG B 105 " --> pdb=" O   THR B 101 " (cutoff:3.500A)
      removed outlier: 3.670A  pdb=" N   ARG B 109 " --> pdb=" O   ARG B 105 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 118 through 128
      removed outlier: 3.716A  pdb=" N   GLN B 127 " --> pdb=" O   ASP B 123 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 101 through 116
      removed outlier: 3.816A  pdb=" N   ARG C 105 " --> pdb=" O   THR C 101 " (cutoff:3.500A)
      removed outlier: 3.670A  pdb=" N   ARG C 109 " --> pdb=" O   ARG C 105 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 118 through 128
      removed outlier: 3.716A  pdb=" N   GLN C 127 " --> pdb=" O   ASP C 123 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 101 through 116
      removed outlier: 3.816A  pdb=" N   ARG D 105 " --> pdb=" O   THR D 101 " (cutoff:3.500A)
      removed outlier: 3.669A  pdb=" N   ARG D 109 " --> pdb=" O   ARG D 105 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 118 through 128
      removed outlier: 3.717A  pdb=" N   GLN D 127 " --> pdb=" O   ASP D 123 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 101 through 116
      removed outlier: 3.816A  pdb=" N   ARG E 105 " --> pdb=" O   THR E 101 " (cutoff:3.500A)
      removed outlier: 3.670A  pdb=" N   ARG E 109 " --> pdb=" O   ARG E 105 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 118 through 128
      removed outlier: 3.718A  pdb=" N   GLN E 127 " --> pdb=" O   ASP E 123 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'H' and resid 6 through 8
      removed outlier: 3.518A  pdb=" N   GLN H   8 " --> pdb=" O   LYS H  26 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'H' and resid 22 through 24
      removed outlier: 3.512A  pdb=" N   THR H  81 " --> pdb=" O   GLU H  76 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'H' and resid 60 through 63
      removed outlier: 4.250A  pdb=" N   ASN H  60 " --> pdb=" O   TYR H  55 " (cutoff:3.500A)
      removed outlier: 6.793A  pdb=" N   TRP H  39 " --> pdb=" O   ILE H  51 " (cutoff:3.500A)
      removed outlier: 4.705A  pdb=" N   ARG H  53 " --> pdb=" O   ILE H  37 " (cutoff:3.500A)
      removed outlier: 6.298A  pdb=" N   ILE H  37 " --> pdb=" O   ARG H  53 " (cutoff:3.500A)
      removed outlier: 3.556A  pdb=" N   ASP H 102 " --> pdb=" O   TYR H  36 " (cutoff:3.500A)
      removed outlier: 3.639A  pdb=" N   ALA H 100 " --> pdb=" O   ASN H  38 " (cutoff:3.500A)
      removed outlier: 3.653A  pdb=" N   TYR H 111 " --> pdb=" O   ARG H 101 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'H' and resid 60 through 63
      removed outlier: 4.250A  pdb=" N   ASN H  60 " --> pdb=" O   TYR H  55 " (cutoff:3.500A)
      removed outlier: 6.793A  pdb=" N   TRP H  39 " --> pdb=" O   ILE H  51 " (cutoff:3.500A)
      removed outlier: 4.705A  pdb=" N   ARG H  53 " --> pdb=" O   ILE H  37 " (cutoff:3.500A)
      removed outlier: 6.298A  pdb=" N   ILE H  37 " --> pdb=" O   ARG H  53 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'L' and resid 21 through 27
      removed outlier: 3.684A  pdb=" N   SER L  76 " --> pdb=" O   SER L  69 " (cutoff:3.500A)
      removed outlier: 3.526A  pdb=" N   SER L  67 " --> pdb=" O   THR L  78 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'L' and resid 57 through 58
      removed outlier: 3.839A  pdb=" N   ASN L  57 " --> pdb=" O   TYR L  53 " (cutoff:3.500A)
      removed outlier: 3.846A  pdb=" N   TYR L  53 " --> pdb=" O   ASN L  57 " (cutoff:3.500A)
      removed outlier: 6.479A  pdb=" N   TRP L  39 " --> pdb=" O   TRP L  51 " (cutoff:3.500A)
      removed outlier: 5.549A  pdb=" N   TYR L  53 " --> pdb=" O   LEU L  37 " (cutoff:3.500A)
      removed outlier: 7.230A  pdb=" N   LEU L  37 " --> pdb=" O   TYR L  53 " (cutoff:3.500A)
      removed outlier: 3.686A  pdb=" N   GLN L  93 " --> pdb=" O   HIS L  38 " (cutoff:3.500A)
      removed outlier: 3.671A  pdb=" N   GLN L  94 " --> pdb=" O   THR L 101 " (cutoff:3.500A)
      removed outlier: 3.913A  pdb=" N   THR L 101 " --> pdb=" O   GLN L  94 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'A' and resid 7 through 11
      removed outlier: 5.253A  pdb=" N   GLY A   9 " --> pdb=" O   LEU A  19 " (cutoff:3.500A)
      removed outlier: 6.946A  pdb=" N   LEU A  19 " --> pdb=" O   GLY A   9 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'A' and resid 22 through 26
      removed outlier: 3.509A  pdb=" N   ARG A  24 " --> pdb=" O   SER A  34 " (cutoff:3.500A)
      removed outlier: 5.309A  pdb=" N   SER A  34 " --> pdb=" O   ARG A  24 " (cutoff:3.500A)
      removed outlier: 3.635A  pdb=" N   VAL A  50 " --> pdb=" O   ALA A  33 " (cutoff:3.500A)
      removed outlier: 3.623A  pdb=" N   ARG A  47 " --> pdb=" O   GLN A  69 " (cutoff:3.500A)
      removed outlier: 3.501A  pdb=" N   GLN A  65 " --> pdb=" O   SER A  51 " (cutoff:3.500A)
      removed outlier: 3.872A  pdb=" N   ARG A  86 " --> pdb=" O   THR A  72 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'A' and resid 22 through 26
      removed outlier: 3.509A  pdb=" N   ARG A  24 " --> pdb=" O   SER A  34 " (cutoff:3.500A)
      removed outlier: 5.309A  pdb=" N   SER A  34 " --> pdb=" O   ARG A  24 " (cutoff:3.500A)
      removed outlier: 3.635A  pdb=" N   VAL A  50 " --> pdb=" O   ALA A  33 " (cutoff:3.500A)
      removed outlier: 3.623A  pdb=" N   ARG A  47 " --> pdb=" O   GLN A  69 " (cutoff:3.500A)
      removed outlier: 3.501A  pdb=" N   GLN A  65 " --> pdb=" O   SER A  51 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'B' and resid 7 through 11
      removed outlier: 5.254A  pdb=" N   GLY B   9 " --> pdb=" O   LEU B  19 " (cutoff:3.500A)
      removed outlier: 6.946A  pdb=" N   LEU B  19 " --> pdb=" O   GLY B   9 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'B' and resid 22 through 26
      removed outlier: 3.508A  pdb=" N   ARG B  24 " --> pdb=" O   SER B  34 " (cutoff:3.500A)
      removed outlier: 5.308A  pdb=" N   SER B  34 " --> pdb=" O   ARG B  24 " (cutoff:3.500A)
      removed outlier: 3.634A  pdb=" N   VAL B  50 " --> pdb=" O   ALA B  33 " (cutoff:3.500A)
      removed outlier: 3.623A  pdb=" N   ARG B  47 " --> pdb=" O   GLN B  69 " (cutoff:3.500A)
      removed outlier: 3.502A  pdb=" N   GLN B  65 " --> pdb=" O   SER B  51 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'B' and resid 72 through 74
      removed outlier: 4.355A  pdb=" N   ARG B  86 " --> pdb=" O   THR B  72 " (cutoff:3.500A)
      removed outlier: 6.635A  pdb=" N   CYS B  74 " --> pdb=" O   VAL B  84 " (cutoff:3.500A)
      removed outlier: 5.561A  pdb=" N   VAL B  84 " --> pdb=" O   CYS B  74 " (cutoff:3.500A)
    Processing sheet with id=AB4, first strand: chain 'C' and resid 7 through 11
      removed outlier: 5.253A  pdb=" N   GLY C   9 " --> pdb=" O   LEU C  19 " (cutoff:3.500A)
      removed outlier: 6.946A  pdb=" N   LEU C  19 " --> pdb=" O   GLY C   9 " (cutoff:3.500A)
    Processing sheet with id=AB5, first strand: chain 'C' and resid 22 through 26
      removed outlier: 3.508A  pdb=" N   ARG C  24 " --> pdb=" O   SER C  34 " (cutoff:3.500A)
      removed outlier: 5.308A  pdb=" N   SER C  34 " --> pdb=" O   ARG C  24 " (cutoff:3.500A)
      removed outlier: 3.635A  pdb=" N   VAL C  50 " --> pdb=" O   ALA C  33 " (cutoff:3.500A)
      removed outlier: 3.623A  pdb=" N   ARG C  47 " --> pdb=" O   GLN C  69 " (cutoff:3.500A)
      removed outlier: 3.502A  pdb=" N   GLN C  65 " --> pdb=" O   SER C  51 " (cutoff:3.500A)
      removed outlier: 3.806A  pdb=" N   ILE C  68 " --> pdb=" O   ALA C  90 " (cutoff:3.500A)
    Processing sheet with id=AB6, first strand: chain 'C' and resid 72 through 74
      removed outlier: 7.326A  pdb=" N   THR C  72 " --> pdb=" O   THR C  85 " (cutoff:3.500A)
      removed outlier: 4.091A  pdb=" N   THR C  85 " --> pdb=" O   THR C  72 " (cutoff:3.500A)
      removed outlier: 3.621A  pdb=" N   CYS C  74 " --> pdb=" O   SER C  83 " (cutoff:3.500A)
      removed outlier: 3.596A  pdb=" N   SER C  83 " --> pdb=" O   CYS C  74 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AB6
    Processing sheet with id=AB7, first strand: chain 'D' and resid 7 through 11
      removed outlier: 5.253A  pdb=" N   GLY D   9 " --> pdb=" O   LEU D  19 " (cutoff:3.500A)
      removed outlier: 6.945A  pdb=" N   LEU D  19 " --> pdb=" O   GLY D   9 " (cutoff:3.500A)
    Processing sheet with id=AB8, first strand: chain 'D' and resid 22 through 26
      removed outlier: 3.509A  pdb=" N   ARG D  24 " --> pdb=" O   SER D  34 " (cutoff:3.500A)
      removed outlier: 5.307A  pdb=" N   SER D  34 " --> pdb=" O   ARG D  24 " (cutoff:3.500A)
      removed outlier: 3.634A  pdb=" N   VAL D  50 " --> pdb=" O   ALA D  33 " (cutoff:3.500A)
      removed outlier: 3.623A  pdb=" N   ARG D  47 " --> pdb=" O   GLN D  69 " (cutoff:3.500A)
      removed outlier: 3.500A  pdb=" N   GLN D  65 " --> pdb=" O   SER D  51 " (cutoff:3.500A)
      removed outlier: 3.806A  pdb=" N   ILE D  68 " --> pdb=" O   ALA D  90 " (cutoff:3.500A)
    Processing sheet with id=AB9, first strand: chain 'D' and resid 72 through 74
      removed outlier: 6.982A  pdb=" N   THR D  72 " --> pdb=" O   THR D  85 " (cutoff:3.500A)
      removed outlier: 3.613A  pdb=" N   SER D  83 " --> pdb=" O   CYS D  74 " (cutoff:3.500A)
    Processing sheet with id=AC1, first strand: chain 'E' and resid 7 through 11
      removed outlier: 5.253A  pdb=" N   GLY E   9 " --> pdb=" O   LEU E  19 " (cutoff:3.500A)
      removed outlier: 6.946A  pdb=" N   LEU E  19 " --> pdb=" O   GLY E   9 " (cutoff:3.500A)
    Processing sheet with id=AC2, first strand: chain 'E' and resid 22 through 26
      removed outlier: 3.509A  pdb=" N   ARG E  24 " --> pdb=" O   SER E  34 " (cutoff:3.500A)
      removed outlier: 5.308A  pdb=" N   SER E  34 " --> pdb=" O   ARG E  24 " (cutoff:3.500A)
      removed outlier: 3.634A  pdb=" N   VAL E  50 " --> pdb=" O   ALA E  33 " (cutoff:3.500A)
      removed outlier: 3.623A  pdb=" N   ARG E  47 " --> pdb=" O   GLN E  69 " (cutoff:3.500A)
      removed outlier: 3.501A  pdb=" N   GLN E  65 " --> pdb=" O   SER E  51 " (cutoff:3.500A)
      removed outlier: 3.806A  pdb=" N   ILE E  68 " --> pdb=" O   ALA E  90 " (cutoff:3.500A)
    Processing sheet with id=AC3, first strand: chain 'E' and resid 72 through 74
      removed outlier: 6.956A  pdb=" N   THR E  72 " --> pdb=" O   THR E  85 " (cutoff:3.500A)

    211 hydrogen bonds defined for protein.
    549 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: 0.89

  Time building geometry restraints manager: 0.61 seconds

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

  Histogram of bond lengths:
        1.10 -     1.24: 972
        1.24 -     1.38: 1636
        1.38 -     1.52: 3207
        1.52 -     1.66: 944
        1.66 -     1.80: 20
  Bond restraints: 6779
  Sorted by residual:
  bond pdb=" C   ILE H  54 "
       pdb=" O   ILE H  54 "
    ideal  model  delta    sigma   weight residual
    1.235  1.097  0.138 9.90e-03 1.02e+04 1.94e+02
  bond pdb=" C   PRO B  71 "
       pdb=" N   THR B  72 "
    ideal  model  delta    sigma   weight residual
    1.331  1.497 -0.166 1.44e-02 4.82e+03 1.32e+02
  bond pdb=" C   ALA A  88 "
       pdb=" O   ALA A  88 "
    ideal  model  delta    sigma   weight residual
    1.236  1.132  0.104 1.14e-02 7.69e+03 8.28e+01
  bond pdb=" C   ALA H  52 "
       pdb=" O   ALA H  52 "
    ideal  model  delta    sigma   weight residual
    1.234  1.122  0.111 1.25e-02 6.40e+03 7.90e+01
  bond pdb=" CA  THR H  33 "
       pdb=" C   THR H  33 "
    ideal  model  delta    sigma   weight residual
    1.528  1.441  0.087 1.04e-02 9.25e+03 7.00e+01
  ... (remaining 6774 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     5.15: 9102
        5.15 -    10.29: 114
       10.29 -    15.44: 9
       15.44 -    20.59: 7
       20.59 -    25.73: 2
  Bond angle restraints: 9234
  Sorted by residual:
  angle pdb=" C   ASP C  81 "
        pdb=" N   PRO C  82 "
        pdb=" CA  PRO C  82 "
      ideal   model   delta    sigma   weight residual
     119.89  137.42  -17.53 1.02e+00 9.61e-01 2.96e+02
  angle pdb=" C   ASP E  81 "
        pdb=" N   PRO E  82 "
        pdb=" CA  PRO E  82 "
      ideal   model   delta    sigma   weight residual
     119.84  139.55  -19.71 1.25e+00 6.40e-01 2.49e+02
  angle pdb=" N   VAL H 104 "
        pdb=" CA  VAL H 104 "
        pdb=" C   VAL H 104 "
      ideal   model   delta    sigma   weight residual
     109.34  131.97  -22.63 2.08e+00 2.31e-01 1.18e+02
  angle pdb=" N   TYR B  89 "
        pdb=" CA  TYR B  89 "
        pdb=" C   TYR B  89 "
      ideal   model   delta    sigma   weight residual
     109.60  125.14  -15.54 1.53e+00 4.27e-01 1.03e+02
  angle pdb=" C   ASP A  81 "
        pdb=" N   PRO A  82 "
        pdb=" CA  PRO A  82 "
      ideal   model   delta    sigma   weight residual
     119.89  129.04   -9.15 1.02e+00 9.61e-01 8.05e+01
  ... (remaining 9229 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    16.52: 3978
       16.52 -    33.04: 119
       33.04 -    49.56: 31
       49.56 -    66.08: 10
       66.08 -    82.60: 6
  Dihedral angle restraints: 4144
    sinusoidal: 1581
      harmonic: 2563
  Sorted by residual:
  dihedral pdb=" N   TYR L  98 "
           pdb=" C   TYR L  98 "
           pdb=" CA  TYR L  98 "
           pdb=" CB  TYR L  98 "
      ideal   model   delta  harmonic     sigma   weight residual
     122.80  144.70  -21.90     0      2.50e+00 1.60e-01 7.67e+01
  dihedral pdb=" C   TYR L  98 "
           pdb=" N   TYR L  98 "
           pdb=" CA  TYR L  98 "
           pdb=" CB  TYR L  98 "
      ideal   model   delta  harmonic     sigma   weight residual
    -122.60 -142.02   19.42     0      2.50e+00 1.60e-01 6.04e+01
  dihedral pdb=" CB  CYS H  25 "
           pdb=" SG  CYS H  25 "
           pdb=" SG  CYS H  99 "
           pdb=" CB  CYS H  99 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00  146.69  -53.69     1      1.00e+01 1.00e-02 3.91e+01
  ... (remaining 4141 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.229: 1056
       0.229 -    0.457: 22
       0.457 -    0.686: 3
       0.686 -    0.915: 0
       0.915 -    1.144: 1
  Chirality restraints: 1082
  Sorted by residual:
  chirality pdb=" CA  TYR L  98 "
            pdb=" N   TYR L  98 "
            pdb=" C   TYR L  98 "
            pdb=" CB  TYR L  98 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    1.37    1.14 2.00e-01 2.50e+01 3.27e+01
  chirality pdb=" CA  VAL H 104 "
            pdb=" N   VAL H 104 "
            pdb=" C   VAL H 104 "
            pdb=" CB  VAL H 104 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    1.77    0.67 2.00e-01 2.50e+01 1.12e+01
  chirality pdb=" CA  TYR H 105 "
            pdb=" N   TYR H 105 "
            pdb=" C   TYR H 105 "
            pdb=" CB  TYR H 105 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    1.93    0.58 2.00e-01 2.50e+01 8.44e+00
  ... (remaining 1079 not shown)

  Planarity restraints: 1208
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ASP H 102 "    0.028 2.00e-02 2.50e+03   5.61e-02 3.15e+01
        pdb=" C   ASP H 102 "   -0.097 2.00e-02 2.50e+03
        pdb=" O   ASP H 102 "    0.037 2.00e-02 2.50e+03
        pdb=" N   ASP H 103 "    0.032 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  PHE H 107 "    0.056 2.00e-02 2.50e+03   3.47e-02 2.11e+01
        pdb=" CG  PHE H 107 "   -0.059 2.00e-02 2.50e+03
        pdb=" CD1 PHE H 107 "   -0.022 2.00e-02 2.50e+03
        pdb=" CD2 PHE H 107 "   -0.018 2.00e-02 2.50e+03
        pdb=" CE1 PHE H 107 "    0.008 2.00e-02 2.50e+03
        pdb=" CE2 PHE H 107 "    0.004 2.00e-02 2.50e+03
        pdb=" CZ  PHE H 107 "    0.031 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TYR H 105 "    0.047 2.00e-02 2.50e+03   3.00e-02 1.80e+01
        pdb=" CG  TYR H 105 "   -0.069 2.00e-02 2.50e+03
        pdb=" CD1 TYR H 105 "   -0.007 2.00e-02 2.50e+03
        pdb=" CD2 TYR H 105 "    0.002 2.00e-02 2.50e+03
        pdb=" CE1 TYR H 105 "    0.011 2.00e-02 2.50e+03
        pdb=" CE2 TYR H 105 "    0.002 2.00e-02 2.50e+03
        pdb=" CZ  TYR H 105 "    0.006 2.00e-02 2.50e+03
        pdb=" OH  TYR H 105 "    0.008 2.00e-02 2.50e+03
  ... (remaining 1205 not shown)

  Histogram of nonbonded interaction distances:
        2.04 -     2.61: 101
        2.61 -     3.18: 5549
        3.18 -     3.76: 8801
        3.76 -     4.33: 10986
        4.33 -     4.90: 18971
  Nonbonded interactions: 44408
  Sorted by model distance:
  nonbonded pdb=" O   VAL H 104 "
            pdb=" CG1 VAL H 104 "
     model   vdw
     2.039 3.460
  nonbonded pdb=" N   ASP C  81 "
            pdb=" OD1 ASP C  81 "
     model   vdw
     2.154 3.120
  nonbonded pdb=" N   GLN L  94 "
            pdb=" OE1 GLN L  94 "
     model   vdw
     2.170 3.120
  nonbonded pdb=" O   THR C  72 "
            pdb=" OG1 THR C  72 "
     model   vdw
     2.237 3.040
  nonbonded pdb=" OD1 ASP H  34 "
            pdb=" OG1 THR B  75 "
     model   vdw
     2.238 3.040
  ... (remaining 44403 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'
}

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:             0.430
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.130
  Check model and map are aligned:         0.020
  Set scattering table:                    0.030
  Process input model:                     8.130
  Find NCS groups from input model:        0.090
  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:1.340
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   10.190
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8100
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      :  0.015   0.212   6783  Z= 0.973
  Angle     :  1.551  38.496   9240  Z= 0.921
  Chirality :  0.093   1.144   1082
  Planarity :  0.008   0.065   1208
  Dihedral  : 10.131  82.596   2485
  Min Nonbonded Distance : 2.039

Molprobity Statistics.
  All-atom Clashscore : 11.19
  Ramachandran Plot:
    Outliers :  0.46 %
    Allowed  :  7.16 %
    Favored  : 92.38 %
  Rotamer:
    Outliers :  1.91 %
    Allowed  :  6.82 %
    Favored  : 91.27 %
  Cbeta Deviations :  1.09 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -4.13 (0.23), residues: 866
  helix: -2.00 (0.43), residues: 120
  sheet: -2.50 (0.24), residues: 341
  loop : -3.13 (0.23), residues: 405

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG L  27 
 TYR   0.069   0.004   TYR H 105 
 PHE   0.059   0.004   PHE H 107 
 TRP   0.013   0.003   TRP H 112 
 HIS   0.003   0.002   HIS L  38 

Details of bonding type rmsd
  covalent geometry    : bond        0.01521 ( 6779)
  covalent geometry    : angle       1.47712 ( 9234)
  SS BOND              : bond        0.00718 (    3)
  SS BOND              : angle      18.57499 (    6)
  hydrogen bonds       : bond        0.25847 (  196)
  hydrogen bonds       : angle       9.41836 (  549)
  Misc. bond           : bond        0.21234 (    1)

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

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

  1732 Ramachandran restraints generated.
    866 Oldfield, 0 Emsley, 866 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1732 Ramachandran restraints generated.
    866 Oldfield, 0 Emsley, 866 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  300 residues out of total 733 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 286
  time to evaluate  : 0.286 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: H   35 TYR cc_start: 0.9273 (m-80) cc_final: 0.8819 (m-80)
REVERT: H   46 GLN cc_start: 0.8616 (mp10) cc_final: 0.8307 (mp10)
REVERT: H   54 ILE cc_start: 0.9249 (OUTLIER) cc_final: 0.9007 (pp)
REVERT: H   89 LEU cc_start: 0.9037 (mm) cc_final: 0.8709 (mm)
REVERT: H  102 ASP cc_start: 0.9079 (p0) cc_final: 0.8762 (p0)
REVERT: H  111 TYR cc_start: 0.9029 (m-10) cc_final: 0.8671 (m-80)
REVERT: L   13 ILE cc_start: 0.9022 (pt) cc_final: 0.8820 (mm)
REVERT: L  101 THR cc_start: 0.8828 (p) cc_final: 0.8581 (p)
REVERT: A    2 LYS cc_start: 0.8343 (tttp) cc_final: 0.7210 (mmtt)
REVERT: A   24 ARG cc_start: 0.8788 (mtp180) cc_final: 0.8438 (mtp-110)
REVERT: A   47 ARG cc_start: 0.8541 (ptp-170) cc_final: 0.8292 (ptp-110)
REVERT: A   63 LYS cc_start: 0.8571 (tttt) cc_final: 0.8222 (ttmm)
REVERT: A   67 LYS cc_start: 0.8758 (mttt) cc_final: 0.8455 (mttp)
REVERT: A   69 GLN cc_start: 0.8432 (pt0) cc_final: 0.8139 (pt0)
REVERT: A  103 GLU cc_start: 0.8090 (mp0) cc_final: 0.7886 (mp0)
REVERT: A  127 GLN cc_start: 0.8952 (mm110) cc_final: 0.8675 (mm-40)
REVERT: B    2 LYS cc_start: 0.9157 (tttp) cc_final: 0.8593 (tppt)
REVERT: B   27 ASN cc_start: 0.8403 (t0) cc_final: 0.7720 (t0)
REVERT: B   47 ARG cc_start: 0.8537 (ptp-170) cc_final: 0.7978 (ptp90)
REVERT: B   69 GLN cc_start: 0.8285 (pt0) cc_final: 0.8039 (pt0)
REVERT: B   77 ASN cc_start: 0.9575 (t0) cc_final: 0.9087 (t0)
REVERT: B  102 ASP cc_start: 0.8158 (p0) cc_final: 0.7822 (t70)
REVERT: C    2 LYS cc_start: 0.8645 (tttp) cc_final: 0.8436 (mmtt)
REVERT: C   11 ILE cc_start: 0.9150 (mt) cc_final: 0.8887 (tp)
REVERT: C   41 VAL cc_start: 0.8778 (t) cc_final: 0.8528 (m)
REVERT: C   47 ARG cc_start: 0.8812 (ptp-170) cc_final: 0.8551 (mtm-85)
REVERT: C  102 ASP cc_start: 0.8464 (p0) cc_final: 0.8073 (t70)
REVERT: D   41 VAL cc_start: 0.8672 (t) cc_final: 0.8416 (t)
REVERT: D   47 ARG cc_start: 0.8752 (ptp-170) cc_final: 0.8060 (ptp-110)
REVERT: D   57 ARG cc_start: 0.7660 (ptt180) cc_final: 0.7456 (ttp80)
REVERT: D   61 ASN cc_start: 0.8727 (m110) cc_final: 0.8520 (m-40)
REVERT: D   63 LYS cc_start: 0.8389 (tttt) cc_final: 0.7947 (ttpp)
REVERT: D   86 ARG cc_start: 0.8138 (ptt-90) cc_final: 0.6868 (mtp180)
REVERT: D  122 ILE cc_start: 0.8710 (pp) cc_final: 0.8070 (mm)
REVERT: D  123 ASP cc_start: 0.7774 (t0) cc_final: 0.7081 (t0)
REVERT: D  127 GLN cc_start: 0.9202 (mm110) cc_final: 0.8469 (mm110)
REVERT: E    2 LYS cc_start: 0.8704 (tttp) cc_final: 0.7699 (mmtt)
REVERT: E   11 ILE cc_start: 0.8630 (mt) cc_final: 0.8371 (mt)
REVERT: E   14 ASP cc_start: 0.8586 (p0) cc_final: 0.8287 (p0)
REVERT: E   63 LYS cc_start: 0.8482 (tttt) cc_final: 0.8083 (ttmm)
REVERT: E   87 GLN cc_start: 0.9051 (OUTLIER) cc_final: 0.8379 (mm110)
REVERT: E  127 GLN cc_start: 0.9011 (mm110) cc_final: 0.8745 (mm-40)
REVERT: E  129 ASN cc_start: 0.8737 (m-40) cc_final: 0.8436 (t0)
  outliers start: 14
  outliers final: 5
  residues processed: 298
  average time/residue: 0.1171
  time to fit residues: 42.7518
Evaluate side-chains
  225 residues out of total 733 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 218
  time to evaluate  : 0.261 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain H residue   54 ILE
Chi-restraints excluded: chain H residue  108 TYR
Chi-restraints excluded: chain B residue   80 CYS
Chi-restraints excluded: chain C residue   81 ASP
Chi-restraints excluded: chain E residue   82 PRO
Chi-restraints excluded: chain E residue   85 THR
Chi-restraints excluded: chain E residue   87 GLN
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 86
   random chunks:
   chunk 49 optimal weight:    1.9990
   chunk 53 optimal weight:    4.9990
   chunk 5 optimal weight:    1.9990
   chunk 33 optimal weight:    4.9990
   chunk 65 optimal weight:    9.9990
   chunk 62 optimal weight:    3.9990
   chunk 51 optimal weight:    6.9990
   chunk 38 optimal weight:    1.9990
   chunk 61 optimal weight:    0.9980
   chunk 45 optimal weight:    3.9990
   chunk 74 optimal weight:    5.9990
   overall best weight:    2.1988

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

Flipped N/Q/H residues before XYZ refinement:
H  42 GLN
L   4 GLN
C  10 ASN
D  65 GLN
E  69 GLN
E  87 GLN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3297 r_free = 0.3297 target = 0.102722 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3007 r_free = 0.3007 target = 0.082163 restraints weight = 13033.504|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 23)----------------|
| r_work = 0.3052 r_free = 0.3052 target = 0.085150 restraints weight = 6406.082|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3081 r_free = 0.3081 target = 0.087119 restraints weight = 4144.934|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 27)----------------|
| r_work = 0.3099 r_free = 0.3099 target = 0.088414 restraints weight = 3165.929|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 32)----------------|
| r_work = 0.3113 r_free = 0.3113 target = 0.089324 restraints weight = 2656.985|
|-----------------------------------------------------------------------------|
r_work (final): 0.3118
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8211
moved from start:          0.2909

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.025   6783  Z= 0.150
  Angle     :  0.667   8.654   9240  Z= 0.355
  Chirality :  0.047   0.167   1082
  Planarity :  0.004   0.042   1208
  Dihedral  :  7.153  58.535    974
  Min Nonbonded Distance : 2.534

Molprobity Statistics.
  All-atom Clashscore : 5.26
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.43 %
    Favored  : 94.57 %
  Rotamer:
    Outliers :  3.96 %
    Allowed  : 14.60 %
    Favored  : 81.45 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.12 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -3.27 (0.25), residues: 866
  helix: -0.40 (0.48), residues: 120
  sheet: -1.98 (0.25), residues: 339
  loop : -2.87 (0.24), residues: 407

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG D  24 
 TYR   0.023   0.002   TYR H 105 
 PHE   0.008   0.001   PHE H 109 
 TRP   0.017   0.002   TRP H 112 
 HIS   0.001   0.001   HIS L  38 

Details of bonding type rmsd
  covalent geometry    : bond        0.00332 ( 6779)
  covalent geometry    : angle       0.66667 ( 9234)
  SS BOND              : bond        0.00311 (    3)
  SS BOND              : angle       0.83257 (    6)
  hydrogen bonds       : bond        0.04471 (  196)
  hydrogen bonds       : angle       5.98828 (  549)
  Misc. bond           : bond        0.00038 (    1)

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

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

  1732 Ramachandran restraints generated.
    866 Oldfield, 0 Emsley, 866 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1732 Ramachandran restraints generated.
    866 Oldfield, 0 Emsley, 866 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  274 residues out of total 733 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 245
  time to evaluate  : 0.293 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: H   35 TYR cc_start: 0.9305 (m-80) cc_final: 0.8901 (m-80)
REVERT: H   46 GLN cc_start: 0.8930 (mp10) cc_final: 0.8730 (mp10)
REVERT: H   89 LEU cc_start: 0.9094 (mm) cc_final: 0.8856 (mm)
REVERT: H  104 VAL cc_start: 0.9027 (t) cc_final: 0.8401 (p)
REVERT: H  107 PHE cc_start: 0.8197 (m-80) cc_final: 0.7916 (m-80)
REVERT: L   13 ILE cc_start: 0.8892 (pt) cc_final: 0.8637 (mm)
REVERT: L   53 TYR cc_start: 0.9107 (p90) cc_final: 0.8836 (p90)
REVERT: L   85 GLU cc_start: 0.6099 (mp0) cc_final: 0.5467 (mp0)
REVERT: L   95 TYR cc_start: 0.9522 (t80) cc_final: 0.8835 (t80)
REVERT: A    2 LYS cc_start: 0.8368 (tttp) cc_final: 0.7341 (mmtt)
REVERT: A   63 LYS cc_start: 0.8734 (tttt) cc_final: 0.8470 (ttmm)
REVERT: A  103 GLU cc_start: 0.7722 (mp0) cc_final: 0.7499 (mp0)
REVERT: B    2 LYS cc_start: 0.9113 (tttp) cc_final: 0.8672 (tppt)
REVERT: B   14 ASP cc_start: 0.9091 (p0) cc_final: 0.8767 (p0)
REVERT: B   27 ASN cc_start: 0.8740 (t0) cc_final: 0.8022 (t0)
REVERT: B   77 ASN cc_start: 0.9384 (t0) cc_final: 0.8852 (t0)
REVERT: B   79 SER cc_start: 0.9564 (t) cc_final: 0.9046 (p)
REVERT: B  102 ASP cc_start: 0.8068 (p0) cc_final: 0.7642 (t70)
REVERT: C  102 ASP cc_start: 0.8485 (p0) cc_final: 0.8213 (t70)
REVERT: D   47 ARG cc_start: 0.8314 (ptp-170) cc_final: 0.8100 (ptp-110)
REVERT: D   61 ASN cc_start: 0.8656 (m110) cc_final: 0.8175 (m-40)
REVERT: D   63 LYS cc_start: 0.8479 (tttt) cc_final: 0.8187 (ttpp)
REVERT: D   81 ASP cc_start: 0.8585 (m-30) cc_final: 0.8284 (t0)
REVERT: D   86 ARG cc_start: 0.8689 (ptt-90) cc_final: 0.6853 (ttt180)
REVERT: D   98 GLN cc_start: 0.8756 (tt0) cc_final: 0.8087 (tm-30)
REVERT: D  122 ILE cc_start: 0.8759 (pp) cc_final: 0.8423 (mm)
REVERT: D  123 ASP cc_start: 0.7971 (t0) cc_final: 0.7324 (t0)
REVERT: D  127 GLN cc_start: 0.9004 (mm110) cc_final: 0.8461 (mm110)
REVERT: E    2 LYS cc_start: 0.8579 (tttp) cc_final: 0.7827 (mmtt)
REVERT: E   61 ASN cc_start: 0.8685 (m110) cc_final: 0.8425 (m-40)
REVERT: E   63 LYS cc_start: 0.8628 (tttt) cc_final: 0.8207 (ttmm)
REVERT: E   81 ASP cc_start: 0.8704 (m-30) cc_final: 0.8309 (m-30)
REVERT: E   83 SER cc_start: 0.8518 (m) cc_final: 0.8168 (t)
REVERT: E   87 GLN cc_start: 0.9063 (mm-40) cc_final: 0.8129 (mm-40)
REVERT: E  104 GLU cc_start: 0.7771 (mp0) cc_final: 0.7430 (mp0)
REVERT: E  129 ASN cc_start: 0.8888 (m-40) cc_final: 0.8518 (t0)
  outliers start: 29
  outliers final: 18
  residues processed: 257
  average time/residue: 0.1163
  time to fit residues: 36.7356
Evaluate side-chains
  238 residues out of total 733 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 220
  time to evaluate  : 0.268 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain H residue    5 VAL
Chi-restraints excluded: chain H residue   21 VAL
Chi-restraints excluded: chain H residue   54 ILE
Chi-restraints excluded: chain H residue   68 LYS
Chi-restraints excluded: chain H residue   93 ASP
Chi-restraints excluded: chain H residue  108 TYR
Chi-restraints excluded: chain L residue   26 CYS
Chi-restraints excluded: chain L residue   57 ASN
Chi-restraints excluded: chain A residue  111 GLU
Chi-restraints excluded: chain A residue  115 LEU
Chi-restraints excluded: chain B residue  111 GLU
Chi-restraints excluded: chain B residue  118 SER
Chi-restraints excluded: chain C residue  111 GLU
Chi-restraints excluded: chain D residue  111 GLU
Chi-restraints excluded: chain D residue  115 LEU
Chi-restraints excluded: chain E residue   80 CYS
Chi-restraints excluded: chain E residue   85 THR
Chi-restraints excluded: chain E residue  111 GLU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 86
   random chunks:
   chunk 0 optimal weight:   10.0000
   chunk 5 optimal weight:    2.9990
   chunk 54 optimal weight:   10.0000
   chunk 55 optimal weight:    0.0000
   chunk 70 optimal weight:    0.8980
   chunk 1 optimal weight:   10.0000
   chunk 21 optimal weight:   10.0000
   chunk 13 optimal weight:   10.0000
   chunk 46 optimal weight:    6.9990
   chunk 53 optimal weight:    4.9990
   chunk 29 optimal weight:    4.9990
   overall best weight:    2.7790

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

Flipped N/Q/H residues before XYZ refinement:
A  22 ASN
C  10 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3259 r_free = 0.3259 target = 0.100367 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.2973 r_free = 0.2973 target = 0.080284 restraints weight = 12947.683|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3015 r_free = 0.3015 target = 0.083094 restraints weight = 6623.958|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3044 r_free = 0.3044 target = 0.085015 restraints weight = 4396.000|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 24)----------------|
| r_work = 0.3062 r_free = 0.3062 target = 0.086281 restraints weight = 3382.624|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3074 r_free = 0.3074 target = 0.087092 restraints weight = 2854.589|
|-----------------------------------------------------------------------------|
r_work (final): 0.3075
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8220
moved from start:          0.3619

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.030   6783  Z= 0.168
  Angle     :  0.653  11.529   9240  Z= 0.341
  Chirality :  0.047   0.162   1082
  Planarity :  0.004   0.039   1208
  Dihedral  :  6.234  58.375    965
  Min Nonbonded Distance : 2.509

Molprobity Statistics.
  All-atom Clashscore : 3.83
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.31 %
    Favored  : 94.69 %
  Rotamer:
    Outliers :  7.09 %
    Allowed  : 14.87 %
    Favored  : 78.04 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -2.71 (0.26), residues: 866
  helix:  0.47 (0.49), residues: 120
  sheet: -1.67 (0.26), residues: 344
  loop : -2.61 (0.25), residues: 402

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG A  24 
 TYR   0.023   0.002   TYR H 105 
 PHE   0.012   0.001   PHE L  66 
 TRP   0.015   0.002   TRP H 112 
 HIS   0.002   0.001   HIS L  38 

Details of bonding type rmsd
  covalent geometry    : bond        0.00383 ( 6779)
  covalent geometry    : angle       0.65301 ( 9234)
  SS BOND              : bond        0.00281 (    3)
  SS BOND              : angle       1.03468 (    6)
  hydrogen bonds       : bond        0.04425 (  196)
  hydrogen bonds       : angle       5.55663 (  549)
  Misc. bond           : bond        0.00037 (    1)

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

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

  1732 Ramachandran restraints generated.
    866 Oldfield, 0 Emsley, 866 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1732 Ramachandran restraints generated.
    866 Oldfield, 0 Emsley, 866 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  282 residues out of total 733 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 52
    poor density    : 230
  time to evaluate  : 0.272 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: H   35 TYR cc_start: 0.9174 (m-80) cc_final: 0.8890 (m-80)
REVERT: H   46 GLN cc_start: 0.8926 (mp10) cc_final: 0.8674 (mp10)
REVERT: H   70 LYS cc_start: 0.9092 (tppp) cc_final: 0.8435 (tppt)
REVERT: H   89 LEU cc_start: 0.9144 (mm) cc_final: 0.8891 (mm)
REVERT: H  110 ASP cc_start: 0.8166 (t0) cc_final: 0.7495 (t0)
REVERT: H  111 TYR cc_start: 0.8570 (m-10) cc_final: 0.8087 (m-80)
REVERT: L   13 ILE cc_start: 0.8852 (pt) cc_final: 0.8565 (mm)
REVERT: L   53 TYR cc_start: 0.9036 (p90) cc_final: 0.8697 (p90)
REVERT: L   85 GLU cc_start: 0.6163 (mp0) cc_final: 0.5504 (mp0)
REVERT: L   95 TYR cc_start: 0.9488 (t80) cc_final: 0.8734 (t80)
REVERT: A    2 LYS cc_start: 0.8612 (tttp) cc_final: 0.7520 (mmtt)
REVERT: A   60 LYS cc_start: 0.8604 (ttpp) cc_final: 0.8155 (pttm)
REVERT: A   63 LYS cc_start: 0.8830 (tttt) cc_final: 0.8580 (ttmm)
REVERT: A   81 ASP cc_start: 0.8605 (p0) cc_final: 0.8354 (p0)
REVERT: A  103 GLU cc_start: 0.7808 (mp0) cc_final: 0.7603 (mp0)
REVERT: B    2 LYS cc_start: 0.9233 (tttp) cc_final: 0.8099 (mmtt)
REVERT: B   14 ASP cc_start: 0.9147 (OUTLIER) cc_final: 0.8816 (p0)
REVERT: B   27 ASN cc_start: 0.8556 (t0) cc_final: 0.7912 (t0)
REVERT: B   77 ASN cc_start: 0.9375 (t0) cc_final: 0.8401 (t0)
REVERT: B   81 ASP cc_start: 0.8911 (t0) cc_final: 0.8074 (p0)
REVERT: B   98 GLN cc_start: 0.8707 (tm-30) cc_final: 0.8213 (tm-30)
REVERT: B  102 ASP cc_start: 0.8142 (p0) cc_final: 0.7536 (t70)
REVERT: C   14 ASP cc_start: 0.8916 (p0) cc_final: 0.8516 (p0)
REVERT: C   16 LYS cc_start: 0.8375 (mtmm) cc_final: 0.8135 (ptpp)
REVERT: C   47 ARG cc_start: 0.8401 (mtm-85) cc_final: 0.8194 (mtm-85)
REVERT: C   81 ASP cc_start: 0.8927 (m-30) cc_final: 0.8697 (m-30)
REVERT: C   89 TYR cc_start: 0.9095 (m-80) cc_final: 0.8888 (m-80)
REVERT: C  102 ASP cc_start: 0.8545 (p0) cc_final: 0.8177 (t70)
REVERT: C  123 ASP cc_start: 0.8301 (t0) cc_final: 0.8053 (t0)
REVERT: D    2 LYS cc_start: 0.8621 (tttp) cc_final: 0.6322 (mmtt)
REVERT: D   47 ARG cc_start: 0.8399 (ptp-170) cc_final: 0.8198 (ptp-110)
REVERT: D   57 ARG cc_start: 0.8004 (ttp80) cc_final: 0.7763 (ttp80)
REVERT: D   61 ASN cc_start: 0.8664 (m110) cc_final: 0.8367 (m-40)
REVERT: D   63 LYS cc_start: 0.8534 (tttt) cc_final: 0.8311 (ttpp)
REVERT: D   98 GLN cc_start: 0.8803 (tt0) cc_final: 0.8108 (tm-30)
REVERT: D  122 ILE cc_start: 0.8782 (pp) cc_final: 0.8498 (mm)
REVERT: D  123 ASP cc_start: 0.8051 (t0) cc_final: 0.7579 (t0)
REVERT: D  127 GLN cc_start: 0.9058 (mm110) cc_final: 0.8521 (mm110)
REVERT: E    2 LYS cc_start: 0.8484 (tttp) cc_final: 0.7897 (mmtt)
REVERT: E   34 SER cc_start: 0.8621 (m) cc_final: 0.8366 (t)
REVERT: E   61 ASN cc_start: 0.8605 (m110) cc_final: 0.7464 (p0)
REVERT: E   63 LYS cc_start: 0.8727 (tttt) cc_final: 0.8273 (ttmm)
REVERT: E   81 ASP cc_start: 0.8715 (m-30) cc_final: 0.8409 (m-30)
REVERT: E   83 SER cc_start: 0.8658 (m) cc_final: 0.8185 (t)
REVERT: E  104 GLU cc_start: 0.7765 (mp0) cc_final: 0.7286 (mp0)
  outliers start: 52
  outliers final: 32
  residues processed: 254
  average time/residue: 0.1100
  time to fit residues: 34.7897
Evaluate side-chains
  250 residues out of total 733 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 217
  time to evaluate  : 0.263 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain H residue   14 LEU
Chi-restraints excluded: chain H residue   26 LYS
Chi-restraints excluded: chain H residue   31 THR
Chi-restraints excluded: chain H residue   37 ILE
Chi-restraints excluded: chain H residue   42 GLN
Chi-restraints excluded: chain H residue   68 LYS
Chi-restraints excluded: chain H residue   78 SER
Chi-restraints excluded: chain H residue  108 TYR
Chi-restraints excluded: chain L residue   26 CYS
Chi-restraints excluded: chain L residue   57 ASN
Chi-restraints excluded: chain L residue   62 VAL
Chi-restraints excluded: chain A residue   50 VAL
Chi-restraints excluded: chain A residue   69 GLN
Chi-restraints excluded: chain A residue  111 GLU
Chi-restraints excluded: chain A residue  115 LEU
Chi-restraints excluded: chain A residue  121 LEU
Chi-restraints excluded: chain B residue   14 ASP
Chi-restraints excluded: chain B residue   36 SER
Chi-restraints excluded: chain B residue   50 VAL
Chi-restraints excluded: chain B residue   69 GLN
Chi-restraints excluded: chain B residue  111 GLU
Chi-restraints excluded: chain B residue  118 SER
Chi-restraints excluded: chain C residue   50 VAL
Chi-restraints excluded: chain D residue   41 VAL
Chi-restraints excluded: chain D residue   50 VAL
Chi-restraints excluded: chain D residue   72 THR
Chi-restraints excluded: chain D residue  115 LEU
Chi-restraints excluded: chain D residue  121 LEU
Chi-restraints excluded: chain E residue   46 LYS
Chi-restraints excluded: chain E residue   50 VAL
Chi-restraints excluded: chain E residue   51 SER
Chi-restraints excluded: chain E residue   74 CYS
Chi-restraints excluded: chain E residue  111 GLU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 86
   random chunks:
   chunk 78 optimal weight:    0.9990
   chunk 17 optimal weight:    7.9990
   chunk 49 optimal weight:    4.9990
   chunk 65 optimal weight:    3.9990
   chunk 8 optimal weight:    9.9990
   chunk 75 optimal weight:    9.9990
   chunk 7 optimal weight:    9.9990
   chunk 47 optimal weight:    8.9990
   chunk 60 optimal weight:    6.9990
   chunk 37 optimal weight:    9.9990
   chunk 28 optimal weight:    9.9990
   overall best weight:    4.9990

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

Flipped N/Q/H residues before XYZ refinement:
A  10 ASN
C  10 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3215 r_free = 0.3215 target = 0.097531 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.2919 r_free = 0.2919 target = 0.077150 restraints weight = 13172.120|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.2963 r_free = 0.2963 target = 0.079946 restraints weight = 6557.110|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.2991 r_free = 0.2991 target = 0.081860 restraints weight = 4315.595|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 26)----------------|
| r_work = 0.3009 r_free = 0.3009 target = 0.083095 restraints weight = 3318.594|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.3022 r_free = 0.3022 target = 0.083935 restraints weight = 2812.931|
|-----------------------------------------------------------------------------|
r_work (final): 0.3022
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8314
moved from start:          0.4058

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.040   6783  Z= 0.279
  Angle     :  0.737   7.823   9240  Z= 0.389
  Chirality :  0.051   0.178   1082
  Planarity :  0.004   0.041   1208
  Dihedral  :  6.200  61.924    962
  Min Nonbonded Distance : 2.545

Molprobity Statistics.
  All-atom Clashscore : 5.26
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.39 %
    Favored  : 92.61 %
  Rotamer:
    Outliers :  6.82 %
    Allowed  : 16.78 %
    Favored  : 76.40 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -2.67 (0.26), residues: 866
  helix:  0.76 (0.50), residues: 120
  sheet: -1.71 (0.26), residues: 355
  loop : -2.60 (0.26), residues: 391

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG A  24 
 TYR   0.033   0.002   TYR H 105 
 PHE   0.013   0.002   PHE L  66 
 TRP   0.016   0.002   TRP H 112 
 HIS   0.003   0.002   HIS L  38 

Details of bonding type rmsd
  covalent geometry    : bond        0.00643 ( 6779)
  covalent geometry    : angle       0.73657 ( 9234)
  SS BOND              : bond        0.00282 (    3)
  SS BOND              : angle       1.07789 (    6)
  hydrogen bonds       : bond        0.05175 (  196)
  hydrogen bonds       : angle       5.63165 (  549)
  Misc. bond           : bond        0.00055 (    1)

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

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

  1732 Ramachandran restraints generated.
    866 Oldfield, 0 Emsley, 866 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1732 Ramachandran restraints generated.
    866 Oldfield, 0 Emsley, 866 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  273 residues out of total 733 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 50
    poor density    : 223
  time to evaluate  : 0.304 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: H   35 TYR cc_start: 0.9232 (m-80) cc_final: 0.8938 (m-80)
REVERT: H   70 LYS cc_start: 0.9169 (tppp) cc_final: 0.8544 (tppt)
REVERT: H   89 LEU cc_start: 0.9240 (mm) cc_final: 0.8951 (mm)
REVERT: H  103 ASP cc_start: 0.8813 (t0) cc_final: 0.8444 (t0)
REVERT: H  110 ASP cc_start: 0.8195 (t0) cc_final: 0.7500 (t0)
REVERT: H  111 TYR cc_start: 0.8610 (m-10) cc_final: 0.8087 (m-80)
REVERT: L   13 ILE cc_start: 0.8889 (pt) cc_final: 0.8665 (mm)
REVERT: L   53 TYR cc_start: 0.9032 (p90) cc_final: 0.8713 (p90)
REVERT: L   85 GLU cc_start: 0.5704 (mp0) cc_final: 0.5162 (mp0)
REVERT: A    2 LYS cc_start: 0.8568 (tttp) cc_final: 0.6271 (mmtt)
REVERT: A   60 LYS cc_start: 0.8641 (ttpp) cc_final: 0.8426 (pttm)
REVERT: A   63 LYS cc_start: 0.8980 (tttt) cc_final: 0.8723 (ttmm)
REVERT: A   81 ASP cc_start: 0.8609 (p0) cc_final: 0.8302 (p0)
REVERT: B    2 LYS cc_start: 0.9134 (tttp) cc_final: 0.8054 (mmtt)
REVERT: B   14 ASP cc_start: 0.9158 (p0) cc_final: 0.8955 (p0)
REVERT: B   27 ASN cc_start: 0.8747 (t0) cc_final: 0.8102 (t0)
REVERT: B   63 LYS cc_start: 0.8631 (tttt) cc_final: 0.8303 (ttmt)
REVERT: B   77 ASN cc_start: 0.9361 (t0) cc_final: 0.8396 (t0)
REVERT: B   81 ASP cc_start: 0.8828 (t0) cc_final: 0.8278 (p0)
REVERT: B   98 GLN cc_start: 0.8669 (tm-30) cc_final: 0.8294 (tm-30)
REVERT: B  102 ASP cc_start: 0.8315 (p0) cc_final: 0.7637 (t70)
REVERT: C   47 ARG cc_start: 0.8513 (mtm-85) cc_final: 0.7819 (mtp85)
REVERT: C   89 TYR cc_start: 0.9112 (m-80) cc_final: 0.8899 (m-80)
REVERT: C  102 ASP cc_start: 0.8639 (p0) cc_final: 0.8239 (t70)
REVERT: C  123 ASP cc_start: 0.8361 (t0) cc_final: 0.8066 (t0)
REVERT: D    2 LYS cc_start: 0.8089 (tttp) cc_final: 0.7767 (mmtt)
REVERT: D   24 ARG cc_start: 0.9196 (ttm110) cc_final: 0.8858 (mmm-85)
REVERT: D   61 ASN cc_start: 0.8749 (m110) cc_final: 0.8299 (m-40)
REVERT: D   63 LYS cc_start: 0.8638 (tttt) cc_final: 0.8436 (ttpp)
REVERT: D   98 GLN cc_start: 0.8846 (tt0) cc_final: 0.8168 (tm-30)
REVERT: D  102 ASP cc_start: 0.8148 (p0) cc_final: 0.7659 (p0)
REVERT: D  123 ASP cc_start: 0.8130 (t0) cc_final: 0.7751 (t0)
REVERT: D  127 GLN cc_start: 0.9052 (mm110) cc_final: 0.8433 (mm110)
REVERT: E    2 LYS cc_start: 0.8380 (tttp) cc_final: 0.7867 (mmtt)
REVERT: E   16 LYS cc_start: 0.8961 (mmmt) cc_final: 0.8726 (mmmt)
REVERT: E   61 ASN cc_start: 0.8734 (m110) cc_final: 0.7844 (p0)
REVERT: E   63 LYS cc_start: 0.8730 (tttt) cc_final: 0.8431 (ttmm)
REVERT: E   83 SER cc_start: 0.8668 (m) cc_final: 0.8174 (t)
REVERT: E  102 ASP cc_start: 0.8791 (p0) cc_final: 0.8433 (p0)
REVERT: E  104 GLU cc_start: 0.8159 (mp0) cc_final: 0.7832 (mp0)
REVERT: E  129 ASN cc_start: 0.9156 (m-40) cc_final: 0.8615 (t0)
  outliers start: 50
  outliers final: 41
  residues processed: 250
  average time/residue: 0.1138
  time to fit residues: 35.1480
Evaluate side-chains
  251 residues out of total 733 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 41
    poor density    : 210
  time to evaluate  : 0.297 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain H residue   14 LEU
Chi-restraints excluded: chain H residue   26 LYS
Chi-restraints excluded: chain H residue   31 THR
Chi-restraints excluded: chain H residue   42 GLN
Chi-restraints excluded: chain H residue   68 LYS
Chi-restraints excluded: chain H residue   78 SER
Chi-restraints excluded: chain H residue  108 TYR
Chi-restraints excluded: chain L residue   25 THR
Chi-restraints excluded: chain L residue   26 CYS
Chi-restraints excluded: chain L residue   57 ASN
Chi-restraints excluded: chain L residue   62 VAL
Chi-restraints excluded: chain L residue   71 SER
Chi-restraints excluded: chain L residue  107 LYS
Chi-restraints excluded: chain A residue   50 VAL
Chi-restraints excluded: chain A residue   69 GLN
Chi-restraints excluded: chain A residue  111 GLU
Chi-restraints excluded: chain A residue  115 LEU
Chi-restraints excluded: chain A residue  121 LEU
Chi-restraints excluded: chain B residue   36 SER
Chi-restraints excluded: chain B residue   50 VAL
Chi-restraints excluded: chain B residue   68 ILE
Chi-restraints excluded: chain B residue   69 GLN
Chi-restraints excluded: chain B residue  111 GLU
Chi-restraints excluded: chain B residue  118 SER
Chi-restraints excluded: chain B residue  128 LEU
Chi-restraints excluded: chain C residue   37 GLN
Chi-restraints excluded: chain C residue   50 VAL
Chi-restraints excluded: chain C residue  111 GLU
Chi-restraints excluded: chain D residue   41 VAL
Chi-restraints excluded: chain D residue   50 VAL
Chi-restraints excluded: chain D residue   72 THR
Chi-restraints excluded: chain D residue   93 THR
Chi-restraints excluded: chain D residue  115 LEU
Chi-restraints excluded: chain D residue  121 LEU
Chi-restraints excluded: chain E residue   46 LYS
Chi-restraints excluded: chain E residue   50 VAL
Chi-restraints excluded: chain E residue   51 SER
Chi-restraints excluded: chain E residue   74 CYS
Chi-restraints excluded: chain E residue   98 GLN
Chi-restraints excluded: chain E residue  111 GLU
Chi-restraints excluded: chain E residue  121 LEU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 86
   random chunks:
   chunk 2 optimal weight:    8.9990
   chunk 71 optimal weight:    7.9990
   chunk 32 optimal weight:    6.9990
   chunk 75 optimal weight:    8.9990
   chunk 42 optimal weight:    3.9990
   chunk 64 optimal weight:    5.9990
   chunk 41 optimal weight:    0.9990
   chunk 43 optimal weight:    1.9990
   chunk 11 optimal weight:    8.9990
   chunk 79 optimal weight:    2.9990
   chunk 16 optimal weight:    6.9990
   overall best weight:    3.1990

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

Flipped N/Q/H residues before XYZ refinement:
A  10 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3237 r_free = 0.3237 target = 0.098798 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.2943 r_free = 0.2943 target = 0.078458 restraints weight = 13030.006|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.2988 r_free = 0.2988 target = 0.081324 restraints weight = 6413.479|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.3017 r_free = 0.3017 target = 0.083286 restraints weight = 4183.631|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3035 r_free = 0.3035 target = 0.084521 restraints weight = 3191.719|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 32)----------------|
| r_work = 0.3048 r_free = 0.3048 target = 0.085387 restraints weight = 2698.890|
|-----------------------------------------------------------------------------|
r_work (final): 0.3053
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8274
moved from start:          0.4270

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.029   6783  Z= 0.184
  Angle     :  0.653   8.543   9240  Z= 0.344
  Chirality :  0.047   0.162   1082
  Planarity :  0.004   0.041   1208
  Dihedral  :  5.868  59.054    962
  Min Nonbonded Distance : 2.558

Molprobity Statistics.
  All-atom Clashscore : 4.28
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.54 %
    Favored  : 94.46 %
  Rotamer:
    Outliers :  6.28 %
    Allowed  : 17.87 %
    Favored  : 75.85 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -2.44 (0.27), residues: 866
  helix:  1.01 (0.50), residues: 120
  sheet: -1.58 (0.26), residues: 359
  loop : -2.47 (0.26), residues: 387

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A  24 
 TYR   0.021   0.001   TYR H  30 
 PHE   0.014   0.001   PHE L  66 
 TRP   0.013   0.002   TRP H  50 
 HIS   0.002   0.002   HIS L  38 

Details of bonding type rmsd
  covalent geometry    : bond        0.00424 ( 6779)
  covalent geometry    : angle       0.65254 ( 9234)
  SS BOND              : bond        0.00247 (    3)
  SS BOND              : angle       1.11485 (    6)
  hydrogen bonds       : bond        0.04258 (  196)
  hydrogen bonds       : angle       5.41206 (  549)
  Misc. bond           : bond        0.00026 (    1)

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

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

  1732 Ramachandran restraints generated.
    866 Oldfield, 0 Emsley, 866 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1732 Ramachandran restraints generated.
    866 Oldfield, 0 Emsley, 866 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  265 residues out of total 733 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 46
    poor density    : 219
  time to evaluate  : 0.287 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: H   35 TYR cc_start: 0.9172 (m-80) cc_final: 0.8910 (m-80)
REVERT: H   70 LYS cc_start: 0.9165 (tppp) cc_final: 0.8544 (tppt)
REVERT: H   76 GLU cc_start: 0.7894 (tm-30) cc_final: 0.7634 (tm-30)
REVERT: H   89 LEU cc_start: 0.9224 (mm) cc_final: 0.8925 (mm)
REVERT: H  110 ASP cc_start: 0.8167 (t0) cc_final: 0.7557 (t0)
REVERT: H  111 TYR cc_start: 0.8526 (m-10) cc_final: 0.7964 (m-80)
REVERT: L   13 ILE cc_start: 0.8987 (pt) cc_final: 0.8781 (mm)
REVERT: L   53 TYR cc_start: 0.8956 (p90) cc_final: 0.8617 (p90)
REVERT: L   85 GLU cc_start: 0.5456 (mp0) cc_final: 0.4955 (mp0)
REVERT: L   95 TYR cc_start: 0.9412 (t80) cc_final: 0.8742 (t80)
REVERT: A    2 LYS cc_start: 0.8078 (tttp) cc_final: 0.6761 (mmtt)
REVERT: A   63 LYS cc_start: 0.8962 (tttt) cc_final: 0.8679 (ttmm)
REVERT: A  127 GLN cc_start: 0.8877 (mm-40) cc_final: 0.8454 (mp10)
REVERT: B    2 LYS cc_start: 0.9137 (tttp) cc_final: 0.8056 (mmtt)
REVERT: B   14 ASP cc_start: 0.9184 (OUTLIER) cc_final: 0.8871 (p0)
REVERT: B   27 ASN cc_start: 0.8727 (t0) cc_final: 0.8082 (t0)
REVERT: B   77 ASN cc_start: 0.9280 (t0) cc_final: 0.8794 (t0)
REVERT: B   98 GLN cc_start: 0.8660 (tm-30) cc_final: 0.8398 (tm-30)
REVERT: B  102 ASP cc_start: 0.8144 (p0) cc_final: 0.7489 (t70)
REVERT: C   47 ARG cc_start: 0.8494 (mtm-85) cc_final: 0.7896 (mtp85)
REVERT: C  102 ASP cc_start: 0.8563 (p0) cc_final: 0.8139 (t70)
REVERT: C  123 ASP cc_start: 0.8351 (t0) cc_final: 0.8051 (t0)
REVERT: D    2 LYS cc_start: 0.8761 (tttp) cc_final: 0.7924 (mmtt)
REVERT: D   24 ARG cc_start: 0.9068 (ttm110) cc_final: 0.8770 (mmm-85)
REVERT: D   47 ARG cc_start: 0.8528 (ptp90) cc_final: 0.8246 (ptp-110)
REVERT: D   61 ASN cc_start: 0.8634 (m110) cc_final: 0.8205 (m-40)
REVERT: D   98 GLN cc_start: 0.8813 (tt0) cc_final: 0.8169 (tm-30)
REVERT: D  127 GLN cc_start: 0.8993 (mm110) cc_final: 0.8375 (mm110)
REVERT: E    2 LYS cc_start: 0.8389 (tttp) cc_final: 0.7890 (mmtt)
REVERT: E   61 ASN cc_start: 0.8625 (m110) cc_final: 0.7809 (p0)
REVERT: E   63 LYS cc_start: 0.8680 (tttt) cc_final: 0.8341 (ttmm)
REVERT: E   83 SER cc_start: 0.8654 (m) cc_final: 0.8157 (t)
REVERT: E  102 ASP cc_start: 0.8719 (p0) cc_final: 0.8322 (p0)
REVERT: E  129 ASN cc_start: 0.9075 (m-40) cc_final: 0.8690 (t0)
  outliers start: 46
  outliers final: 40
  residues processed: 243
  average time/residue: 0.1124
  time to fit residues: 33.7906
Evaluate side-chains
  254 residues out of total 733 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 41
    poor density    : 213
  time to evaluate  : 0.267 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain H residue   14 LEU
Chi-restraints excluded: chain H residue   26 LYS
Chi-restraints excluded: chain H residue   31 THR
Chi-restraints excluded: chain H residue   42 GLN
Chi-restraints excluded: chain H residue   68 LYS
Chi-restraints excluded: chain H residue  108 TYR
Chi-restraints excluded: chain L residue   25 THR
Chi-restraints excluded: chain L residue   26 CYS
Chi-restraints excluded: chain L residue   57 ASN
Chi-restraints excluded: chain L residue  101 THR
Chi-restraints excluded: chain L residue  107 LYS
Chi-restraints excluded: chain A residue   44 LEU
Chi-restraints excluded: chain A residue   50 VAL
Chi-restraints excluded: chain A residue   69 GLN
Chi-restraints excluded: chain A residue   75 THR
Chi-restraints excluded: chain A residue  111 GLU
Chi-restraints excluded: chain A residue  115 LEU
Chi-restraints excluded: chain A residue  121 LEU
Chi-restraints excluded: chain A residue  128 LEU
Chi-restraints excluded: chain B residue   14 ASP
Chi-restraints excluded: chain B residue   36 SER
Chi-restraints excluded: chain B residue   50 VAL
Chi-restraints excluded: chain B residue   68 ILE
Chi-restraints excluded: chain B residue   69 GLN
Chi-restraints excluded: chain B residue  111 GLU
Chi-restraints excluded: chain B residue  118 SER
Chi-restraints excluded: chain C residue   36 SER
Chi-restraints excluded: chain C residue   50 VAL
Chi-restraints excluded: chain C residue  111 GLU
Chi-restraints excluded: chain D residue   41 VAL
Chi-restraints excluded: chain D residue   46 LYS
Chi-restraints excluded: chain D residue   50 VAL
Chi-restraints excluded: chain D residue  115 LEU
Chi-restraints excluded: chain D residue  121 LEU
Chi-restraints excluded: chain E residue   46 LYS
Chi-restraints excluded: chain E residue   50 VAL
Chi-restraints excluded: chain E residue   51 SER
Chi-restraints excluded: chain E residue   74 CYS
Chi-restraints excluded: chain E residue   98 GLN
Chi-restraints excluded: chain E residue  111 GLU
Chi-restraints excluded: chain E residue  121 LEU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 86
   random chunks:
   chunk 63 optimal weight:    9.9990
   chunk 30 optimal weight:    5.9990
   chunk 14 optimal weight:   10.0000
   chunk 12 optimal weight:    0.0470
   chunk 17 optimal weight:    5.9990
   chunk 35 optimal weight:    0.0470
   chunk 66 optimal weight:    1.9990
   chunk 2 optimal weight:    9.9990
   chunk 21 optimal weight:    3.9990
   chunk 33 optimal weight:    0.5980
   chunk 19 optimal weight:    5.9990
   overall best weight:    1.3380

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

Flipped N/Q/H residues before XYZ refinement:
H   9 GLN
L   4 GLN
A  10 ASN
** D  65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
E  22 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3280 r_free = 0.3280 target = 0.101515 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.2993 r_free = 0.2993 target = 0.081330 restraints weight = 12989.070|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3036 r_free = 0.3036 target = 0.084167 restraints weight = 6547.171|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3065 r_free = 0.3065 target = 0.086159 restraints weight = 4320.687|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.3084 r_free = 0.3084 target = 0.087462 restraints weight = 3314.928|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.3095 r_free = 0.3095 target = 0.088267 restraints weight = 2787.146|
|-----------------------------------------------------------------------------|
r_work (final): 0.3095
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8196
moved from start:          0.4461

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.027   6783  Z= 0.109
  Angle     :  0.596   7.298   9240  Z= 0.311
  Chirality :  0.045   0.150   1082
  Planarity :  0.003   0.039   1208
  Dihedral  :  5.261  52.385    962
  Min Nonbonded Distance : 2.541

Molprobity Statistics.
  All-atom Clashscore : 4.06
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.73 %
    Favored  : 95.27 %
  Rotamer:
    Outliers :  5.46 %
    Allowed  : 18.01 %
    Favored  : 76.53 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -2.08 (0.27), residues: 866
  helix:  1.35 (0.49), residues: 120
  sheet: -1.28 (0.26), residues: 357
  loop : -2.35 (0.27), residues: 389

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG A  24 
 TYR   0.019   0.001   TYR H  30 
 PHE   0.010   0.001   PHE L  66 
 TRP   0.011   0.001   TRP H  50 
 HIS   0.002   0.001   HIS L  38 

Details of bonding type rmsd
  covalent geometry    : bond        0.00246 ( 6779)
  covalent geometry    : angle       0.59527 ( 9234)
  SS BOND              : bond        0.00256 (    3)
  SS BOND              : angle       1.21584 (    6)
  hydrogen bonds       : bond        0.03244 (  196)
  hydrogen bonds       : angle       5.16215 (  549)
  Misc. bond           : bond        0.00007 (    1)

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

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

  1732 Ramachandran restraints generated.
    866 Oldfield, 0 Emsley, 866 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1732 Ramachandran restraints generated.
    866 Oldfield, 0 Emsley, 866 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  275 residues out of total 733 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 40
    poor density    : 235
  time to evaluate  : 0.278 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: H   22 LYS cc_start: 0.9262 (tptt) cc_final: 0.8938 (tptt)
REVERT: H   70 LYS cc_start: 0.9154 (tppp) cc_final: 0.8578 (tppt)
REVERT: H   76 GLU cc_start: 0.7797 (tm-30) cc_final: 0.7263 (tm-30)
REVERT: H   89 LEU cc_start: 0.9213 (mm) cc_final: 0.8951 (mm)
REVERT: H  110 ASP cc_start: 0.8160 (t0) cc_final: 0.7724 (t0)
REVERT: H  111 TYR cc_start: 0.8503 (m-10) cc_final: 0.7937 (m-80)
REVERT: L   13 ILE cc_start: 0.9000 (pt) cc_final: 0.8728 (mm)
REVERT: L   53 TYR cc_start: 0.8865 (p90) cc_final: 0.8603 (p90)
REVERT: L   85 GLU cc_start: 0.5506 (mp0) cc_final: 0.4822 (mp0)
REVERT: L   95 TYR cc_start: 0.9440 (t80) cc_final: 0.9013 (t80)
REVERT: A    2 LYS cc_start: 0.8004 (tttp) cc_final: 0.6609 (mmtt)
REVERT: A   60 LYS cc_start: 0.8488 (ttpp) cc_final: 0.8003 (pttm)
REVERT: A   63 LYS cc_start: 0.8887 (tttt) cc_final: 0.8608 (ttmm)
REVERT: A  127 GLN cc_start: 0.8863 (mm-40) cc_final: 0.8416 (mp10)
REVERT: B    2 LYS cc_start: 0.9144 (tttp) cc_final: 0.8074 (mmtt)
REVERT: B   14 ASP cc_start: 0.9149 (OUTLIER) cc_final: 0.8856 (p0)
REVERT: B   27 ASN cc_start: 0.8612 (t0) cc_final: 0.7952 (t0)
REVERT: B   77 ASN cc_start: 0.9307 (t0) cc_final: 0.8835 (t0)
REVERT: B   98 GLN cc_start: 0.8602 (tm-30) cc_final: 0.8370 (tm-30)
REVERT: B  102 ASP cc_start: 0.8079 (p0) cc_final: 0.7430 (t70)
REVERT: C   47 ARG cc_start: 0.8489 (mtm-85) cc_final: 0.7865 (mtp85)
REVERT: C   89 TYR cc_start: 0.9078 (m-80) cc_final: 0.8827 (m-80)
REVERT: C  123 ASP cc_start: 0.8565 (t0) cc_final: 0.8208 (t0)
REVERT: D    2 LYS cc_start: 0.8647 (tttp) cc_final: 0.7789 (mmtt)
REVERT: D   13 LYS cc_start: 0.2230 (mttt) cc_final: 0.0990 (mttt)
REVERT: D   24 ARG cc_start: 0.9004 (ttm110) cc_final: 0.8551 (mtt180)
REVERT: D   47 ARG cc_start: 0.8462 (ptp90) cc_final: 0.8053 (ptp-110)
REVERT: D   61 ASN cc_start: 0.8609 (m110) cc_final: 0.8163 (m-40)
REVERT: D   95 SER cc_start: 0.8876 (t) cc_final: 0.8655 (t)
REVERT: D   98 GLN cc_start: 0.8825 (tt0) cc_final: 0.8185 (tm-30)
REVERT: D  127 GLN cc_start: 0.8865 (mm110) cc_final: 0.8279 (mm110)
REVERT: E    2 LYS cc_start: 0.8474 (tttp) cc_final: 0.7905 (mmtt)
REVERT: E   34 SER cc_start: 0.8623 (m) cc_final: 0.8320 (t)
REVERT: E   61 ASN cc_start: 0.8558 (m110) cc_final: 0.7653 (p0)
REVERT: E   63 LYS cc_start: 0.8646 (tttt) cc_final: 0.8286 (ttmm)
REVERT: E   83 SER cc_start: 0.8640 (m) cc_final: 0.8163 (t)
REVERT: E  129 ASN cc_start: 0.8991 (m-40) cc_final: 0.8711 (t0)
  outliers start: 40
  outliers final: 32
  residues processed: 252
  average time/residue: 0.1075
  time to fit residues: 33.2523
Evaluate side-chains
  258 residues out of total 733 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 225
  time to evaluate  : 0.276 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain H residue    9 GLN
Chi-restraints excluded: chain H residue   14 LEU
Chi-restraints excluded: chain H residue   26 LYS
Chi-restraints excluded: chain H residue   31 THR
Chi-restraints excluded: chain H residue   42 GLN
Chi-restraints excluded: chain H residue   68 LYS
Chi-restraints excluded: chain H residue  103 ASP
Chi-restraints excluded: chain H residue  108 TYR
Chi-restraints excluded: chain L residue   26 CYS
Chi-restraints excluded: chain L residue   36 TYR
Chi-restraints excluded: chain L residue   57 ASN
Chi-restraints excluded: chain L residue  101 THR
Chi-restraints excluded: chain A residue   14 ASP
Chi-restraints excluded: chain A residue   75 THR
Chi-restraints excluded: chain A residue  111 GLU
Chi-restraints excluded: chain B residue   14 ASP
Chi-restraints excluded: chain B residue   36 SER
Chi-restraints excluded: chain B residue   68 ILE
Chi-restraints excluded: chain B residue   69 GLN
Chi-restraints excluded: chain B residue  111 GLU
Chi-restraints excluded: chain B residue  118 SER
Chi-restraints excluded: chain B residue  128 LEU
Chi-restraints excluded: chain C residue   50 VAL
Chi-restraints excluded: chain C residue  111 GLU
Chi-restraints excluded: chain C residue  116 LEU
Chi-restraints excluded: chain D residue   41 VAL
Chi-restraints excluded: chain D residue   46 LYS
Chi-restraints excluded: chain D residue   72 THR
Chi-restraints excluded: chain D residue  115 LEU
Chi-restraints excluded: chain E residue   74 CYS
Chi-restraints excluded: chain E residue   98 GLN
Chi-restraints excluded: chain E residue  111 GLU
Chi-restraints excluded: chain E residue  121 LEU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 86
   random chunks:
   chunk 82 optimal weight:    0.0010
   chunk 21 optimal weight:    6.9990
   chunk 56 optimal weight:    1.9990
   chunk 69 optimal weight:    6.9990
   chunk 8 optimal weight:   10.0000
   chunk 27 optimal weight:    0.5980
   chunk 6 optimal weight:    6.9990
   chunk 59 optimal weight:    6.9990
   chunk 33 optimal weight:    0.9990
   chunk 52 optimal weight:    5.9990
   chunk 14 optimal weight:    6.9990
   overall best weight:    1.9192

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

Flipped N/Q/H residues before XYZ refinement:
A  10 ASN
** D  65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
E  70 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3370 r_free = 0.3370 target = 0.104846 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3099 r_free = 0.3099 target = 0.085909 restraints weight = 12879.483|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3144 r_free = 0.3144 target = 0.088844 restraints weight = 6286.652|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3171 r_free = 0.3171 target = 0.090756 restraints weight = 4114.559|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 37)----------------|
| r_work = 0.3189 r_free = 0.3189 target = 0.092004 restraints weight = 3171.558|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 31)----------------|
| r_work = 0.3200 r_free = 0.3200 target = 0.092783 restraints weight = 2684.123|
|-----------------------------------------------------------------------------|
r_work (final): 0.3195
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8320
moved from start:          0.4590

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028   6783  Z= 0.132
  Angle     :  0.624   8.802   9240  Z= 0.323
  Chirality :  0.045   0.152   1082
  Planarity :  0.004   0.037   1208
  Dihedral  :  5.046  49.060    962
  Min Nonbonded Distance : 2.559

Molprobity Statistics.
  All-atom Clashscore : 4.36
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.97 %
    Favored  : 95.03 %
  Rotamer:
    Outliers :  6.41 %
    Allowed  : 18.55 %
    Favored  : 75.03 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.94 (0.27), residues: 866
  helix:  1.49 (0.49), residues: 120
  sheet: -1.21 (0.26), residues: 364
  loop : -2.25 (0.27), residues: 382

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A  24 
 TYR   0.028   0.001   TYR H 105 
 PHE   0.012   0.001   PHE L  66 
 TRP   0.010   0.001   TRP H  50 
 HIS   0.002   0.001   HIS L  38 

Details of bonding type rmsd
  covalent geometry    : bond        0.00303 ( 6779)
  covalent geometry    : angle       0.62229 ( 9234)
  SS BOND              : bond        0.00255 (    3)
  SS BOND              : angle       1.69235 (    6)
  hydrogen bonds       : bond        0.03420 (  196)
  hydrogen bonds       : angle       5.09767 (  549)
  Misc. bond           : bond        0.00013 (    1)

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

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

  1732 Ramachandran restraints generated.
    866 Oldfield, 0 Emsley, 866 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1732 Ramachandran restraints generated.
    866 Oldfield, 0 Emsley, 866 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  276 residues out of total 733 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 47
    poor density    : 229
  time to evaluate  : 0.274 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: H   22 LYS cc_start: 0.9190 (tptt) cc_final: 0.8844 (tptt)
REVERT: H   70 LYS cc_start: 0.9244 (tppp) cc_final: 0.8717 (tppt)
REVERT: H   76 GLU cc_start: 0.7953 (tm-30) cc_final: 0.7565 (tm-30)
REVERT: H  110 ASP cc_start: 0.8079 (t0) cc_final: 0.7696 (t0)
REVERT: H  111 TYR cc_start: 0.8575 (m-10) cc_final: 0.8095 (m-80)
REVERT: L   85 GLU cc_start: 0.5340 (mp0) cc_final: 0.4736 (mp0)
REVERT: L   95 TYR cc_start: 0.9369 (t80) cc_final: 0.9122 (t80)
REVERT: A    2 LYS cc_start: 0.7963 (tttp) cc_final: 0.6695 (mmtt)
REVERT: A   60 LYS cc_start: 0.8527 (ttpp) cc_final: 0.8129 (pttt)
REVERT: A  127 GLN cc_start: 0.9056 (mm-40) cc_final: 0.8679 (mp10)
REVERT: B    2 LYS cc_start: 0.9088 (tttp) cc_final: 0.8174 (mmtt)
REVERT: B   14 ASP cc_start: 0.8985 (OUTLIER) cc_final: 0.8748 (p0)
REVERT: B   27 ASN cc_start: 0.8802 (t0) cc_final: 0.8200 (t0)
REVERT: B   77 ASN cc_start: 0.9099 (t0) cc_final: 0.8630 (t0)
REVERT: B  102 ASP cc_start: 0.8087 (p0) cc_final: 0.7315 (t70)
REVERT: C   47 ARG cc_start: 0.8572 (mtm-85) cc_final: 0.8108 (mtp85)
REVERT: C  123 ASP cc_start: 0.8382 (t0) cc_final: 0.8125 (t0)
REVERT: D    2 LYS cc_start: 0.8580 (tttp) cc_final: 0.7810 (mmtt)
REVERT: D    4 GLU cc_start: 0.8255 (mm-30) cc_final: 0.8050 (mm-30)
REVERT: D   13 LYS cc_start: 0.2485 (mttt) cc_final: 0.1153 (mttt)
REVERT: D   47 ARG cc_start: 0.8496 (ptp90) cc_final: 0.8034 (ptp-110)
REVERT: D   61 ASN cc_start: 0.8518 (m110) cc_final: 0.8129 (m-40)
REVERT: D   98 GLN cc_start: 0.8602 (tt0) cc_final: 0.8199 (tm-30)
REVERT: D  127 GLN cc_start: 0.8965 (mm110) cc_final: 0.8384 (mm110)
REVERT: E    2 LYS cc_start: 0.8415 (tttp) cc_final: 0.7978 (mmtt)
REVERT: E    4 GLU cc_start: 0.8031 (mm-30) cc_final: 0.7753 (mm-30)
REVERT: E   34 SER cc_start: 0.8742 (m) cc_final: 0.8469 (t)
REVERT: E   61 ASN cc_start: 0.8491 (m110) cc_final: 0.7848 (p0)
REVERT: E   63 LYS cc_start: 0.8705 (tttt) cc_final: 0.8440 (ttmm)
REVERT: E   83 SER cc_start: 0.8985 (m) cc_final: 0.8488 (t)
  outliers start: 47
  outliers final: 41
  residues processed: 252
  average time/residue: 0.1133
  time to fit residues: 35.3383
Evaluate side-chains
  264 residues out of total 733 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 42
    poor density    : 222
  time to evaluate  : 0.286 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain H residue   14 LEU
Chi-restraints excluded: chain H residue   26 LYS
Chi-restraints excluded: chain H residue   31 THR
Chi-restraints excluded: chain H residue   68 LYS
Chi-restraints excluded: chain H residue  108 TYR
Chi-restraints excluded: chain L residue   26 CYS
Chi-restraints excluded: chain L residue   36 TYR
Chi-restraints excluded: chain L residue   57 ASN
Chi-restraints excluded: chain L residue   71 SER
Chi-restraints excluded: chain L residue  101 THR
Chi-restraints excluded: chain L residue  107 LYS
Chi-restraints excluded: chain A residue   14 ASP
Chi-restraints excluded: chain A residue   50 VAL
Chi-restraints excluded: chain A residue   75 THR
Chi-restraints excluded: chain A residue  111 GLU
Chi-restraints excluded: chain A residue  115 LEU
Chi-restraints excluded: chain A residue  121 LEU
Chi-restraints excluded: chain A residue  128 LEU
Chi-restraints excluded: chain B residue   14 ASP
Chi-restraints excluded: chain B residue   36 SER
Chi-restraints excluded: chain B residue   68 ILE
Chi-restraints excluded: chain B residue   69 GLN
Chi-restraints excluded: chain B residue  111 GLU
Chi-restraints excluded: chain B residue  118 SER
Chi-restraints excluded: chain B residue  128 LEU
Chi-restraints excluded: chain C residue   36 SER
Chi-restraints excluded: chain C residue   50 VAL
Chi-restraints excluded: chain C residue  111 GLU
Chi-restraints excluded: chain C residue  116 LEU
Chi-restraints excluded: chain D residue   41 VAL
Chi-restraints excluded: chain D residue   46 LYS
Chi-restraints excluded: chain D residue   50 VAL
Chi-restraints excluded: chain D residue   51 SER
Chi-restraints excluded: chain D residue   69 GLN
Chi-restraints excluded: chain D residue   72 THR
Chi-restraints excluded: chain D residue  115 LEU
Chi-restraints excluded: chain E residue   50 VAL
Chi-restraints excluded: chain E residue   51 SER
Chi-restraints excluded: chain E residue   74 CYS
Chi-restraints excluded: chain E residue   98 GLN
Chi-restraints excluded: chain E residue  111 GLU
Chi-restraints excluded: chain E residue  121 LEU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 86
   random chunks:
   chunk 70 optimal weight:    6.9990
   chunk 44 optimal weight:    0.7980
   chunk 59 optimal weight:    0.1980
   chunk 11 optimal weight:    9.9990
   chunk 35 optimal weight:    5.9990
   chunk 58 optimal weight:   10.0000
   chunk 38 optimal weight:    8.9990
   chunk 72 optimal weight:    0.0770
   chunk 77 optimal weight:    7.9990
   chunk 85 optimal weight:    7.9990
   chunk 73 optimal weight:    8.9990
   overall best weight:    2.8142

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

Flipped N/Q/H residues before XYZ refinement:
A  10 ASN
** D  65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
D  70 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3259 r_free = 0.3259 target = 0.100086 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.2975 r_free = 0.2975 target = 0.080165 restraints weight = 12946.338|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3018 r_free = 0.3018 target = 0.082993 restraints weight = 6551.348|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3047 r_free = 0.3047 target = 0.084910 restraints weight = 4319.360|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3063 r_free = 0.3063 target = 0.086111 restraints weight = 3325.521|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 24)----------------|
| r_work = 0.3076 r_free = 0.3076 target = 0.086960 restraints weight = 2823.695|
|-----------------------------------------------------------------------------|
r_work (final): 0.3077
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8230
moved from start:          0.4677

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.031   6783  Z= 0.171
  Angle     :  0.662   8.214   9240  Z= 0.346
  Chirality :  0.047   0.153   1082
  Planarity :  0.004   0.042   1208
  Dihedral  :  5.092  49.091    962
  Min Nonbonded Distance : 2.539

Molprobity Statistics.
  All-atom Clashscore : 3.98
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.43 %
    Favored  : 94.57 %
  Rotamer:
    Outliers :  6.41 %
    Allowed  : 18.69 %
    Favored  : 74.90 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.94 (0.27), residues: 866
  helix:  1.57 (0.49), residues: 120
  sheet: -1.19 (0.27), residues: 365
  loop : -2.31 (0.27), residues: 381

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG H 101 
 TYR   0.030   0.002   TYR H  35 
 PHE   0.012   0.001   PHE L  66 
 TRP   0.011   0.001   TRP H  50 
 HIS   0.002   0.002   HIS L  38 

Details of bonding type rmsd
  covalent geometry    : bond        0.00397 ( 6779)
  covalent geometry    : angle       0.66137 ( 9234)
  SS BOND              : bond        0.00294 (    3)
  SS BOND              : angle       0.87708 (    6)
  hydrogen bonds       : bond        0.03859 (  196)
  hydrogen bonds       : angle       5.13235 (  549)
  Misc. bond           : bond        0.00024 (    1)

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

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

  1732 Ramachandran restraints generated.
    866 Oldfield, 0 Emsley, 866 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1732 Ramachandran restraints generated.
    866 Oldfield, 0 Emsley, 866 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  271 residues out of total 733 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 47
    poor density    : 224
  time to evaluate  : 0.288 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: H   22 LYS cc_start: 0.9251 (tptt) cc_final: 0.8918 (tptt)
REVERT: H   70 LYS cc_start: 0.9209 (tppp) cc_final: 0.8645 (tppt)
REVERT: H   76 GLU cc_start: 0.7874 (tm-30) cc_final: 0.7297 (tm-30)
REVERT: H  110 ASP cc_start: 0.8106 (t0) cc_final: 0.7558 (t0)
REVERT: H  111 TYR cc_start: 0.8626 (m-10) cc_final: 0.8143 (m-80)
REVERT: L   53 TYR cc_start: 0.8878 (p90) cc_final: 0.8578 (p90)
REVERT: L   85 GLU cc_start: 0.5105 (mp0) cc_final: 0.4547 (mp0)
REVERT: L   95 TYR cc_start: 0.9426 (t80) cc_final: 0.9152 (t80)
REVERT: A    2 LYS cc_start: 0.8169 (tttp) cc_final: 0.7154 (mmtt)
REVERT: A   60 LYS cc_start: 0.8618 (ttpp) cc_final: 0.8193 (pttt)
REVERT: A  127 GLN cc_start: 0.9155 (mm-40) cc_final: 0.8593 (mp10)
REVERT: B    2 LYS cc_start: 0.9180 (tttp) cc_final: 0.8232 (mmtt)
REVERT: B   14 ASP cc_start: 0.9031 (OUTLIER) cc_final: 0.8735 (p0)
REVERT: B   27 ASN cc_start: 0.8618 (t0) cc_final: 0.7975 (t0)
REVERT: B   77 ASN cc_start: 0.9261 (t0) cc_final: 0.8759 (t0)
REVERT: B  102 ASP cc_start: 0.8333 (p0) cc_final: 0.7330 (t70)
REVERT: C    2 LYS cc_start: 0.4459 (mmmt) cc_final: 0.4207 (mmmt)
REVERT: C   47 ARG cc_start: 0.8565 (mtm-85) cc_final: 0.7938 (mtp85)
REVERT: C  123 ASP cc_start: 0.8410 (t0) cc_final: 0.8052 (t0)
REVERT: D    2 LYS cc_start: 0.8679 (tttp) cc_final: 0.7776 (mmtt)
REVERT: D   13 LYS cc_start: 0.2167 (mttt) cc_final: 0.0776 (ttmt)
REVERT: D   24 ARG cc_start: 0.9080 (ttm-80) cc_final: 0.8689 (mmm-85)
REVERT: D   47 ARG cc_start: 0.8478 (ptp90) cc_final: 0.8017 (ptp-110)
REVERT: D   61 ASN cc_start: 0.8621 (m110) cc_final: 0.8169 (m-40)
REVERT: D   98 GLN cc_start: 0.8797 (tt0) cc_final: 0.8164 (tm-30)
REVERT: D  127 GLN cc_start: 0.8880 (mm110) cc_final: 0.8294 (mm110)
REVERT: E    2 LYS cc_start: 0.8425 (tttp) cc_final: 0.7864 (mmtt)
REVERT: E    4 GLU cc_start: 0.8133 (mm-30) cc_final: 0.7838 (mm-30)
REVERT: E   13 LYS cc_start: 0.3329 (mttp) cc_final: 0.2503 (mttt)
REVERT: E   61 ASN cc_start: 0.8615 (m110) cc_final: 0.7744 (p0)
REVERT: E   63 LYS cc_start: 0.8728 (tttt) cc_final: 0.8373 (ttmm)
REVERT: E   83 SER cc_start: 0.8646 (m) cc_final: 0.8152 (t)
REVERT: E  102 ASP cc_start: 0.8726 (p0) cc_final: 0.8307 (p0)
  outliers start: 47
  outliers final: 44
  residues processed: 247
  average time/residue: 0.1183
  time to fit residues: 36.0403
Evaluate side-chains
  263 residues out of total 733 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 45
    poor density    : 218
  time to evaluate  : 0.266 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain H residue   14 LEU
Chi-restraints excluded: chain H residue   26 LYS
Chi-restraints excluded: chain H residue   31 THR
Chi-restraints excluded: chain H residue   42 GLN
Chi-restraints excluded: chain H residue   68 LYS
Chi-restraints excluded: chain H residue  103 ASP
Chi-restraints excluded: chain H residue  108 TYR
Chi-restraints excluded: chain L residue   26 CYS
Chi-restraints excluded: chain L residue   57 ASN
Chi-restraints excluded: chain L residue   71 SER
Chi-restraints excluded: chain L residue  101 THR
Chi-restraints excluded: chain L residue  107 LYS
Chi-restraints excluded: chain A residue   14 ASP
Chi-restraints excluded: chain A residue   50 VAL
Chi-restraints excluded: chain A residue   75 THR
Chi-restraints excluded: chain A residue  111 GLU
Chi-restraints excluded: chain A residue  115 LEU
Chi-restraints excluded: chain A residue  121 LEU
Chi-restraints excluded: chain A residue  128 LEU
Chi-restraints excluded: chain B residue   14 ASP
Chi-restraints excluded: chain B residue   36 SER
Chi-restraints excluded: chain B residue   50 VAL
Chi-restraints excluded: chain B residue   68 ILE
Chi-restraints excluded: chain B residue   69 GLN
Chi-restraints excluded: chain B residue   80 CYS
Chi-restraints excluded: chain B residue  111 GLU
Chi-restraints excluded: chain B residue  118 SER
Chi-restraints excluded: chain B residue  128 LEU
Chi-restraints excluded: chain C residue   36 SER
Chi-restraints excluded: chain C residue   50 VAL
Chi-restraints excluded: chain C residue  111 GLU
Chi-restraints excluded: chain D residue   41 VAL
Chi-restraints excluded: chain D residue   46 LYS
Chi-restraints excluded: chain D residue   50 VAL
Chi-restraints excluded: chain D residue   51 SER
Chi-restraints excluded: chain D residue   72 THR
Chi-restraints excluded: chain D residue  115 LEU
Chi-restraints excluded: chain D residue  121 LEU
Chi-restraints excluded: chain E residue   50 VAL
Chi-restraints excluded: chain E residue   51 SER
Chi-restraints excluded: chain E residue   74 CYS
Chi-restraints excluded: chain E residue   85 THR
Chi-restraints excluded: chain E residue   98 GLN
Chi-restraints excluded: chain E residue  111 GLU
Chi-restraints excluded: chain E residue  121 LEU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 86
   random chunks:
   chunk 30 optimal weight:    5.9990
   chunk 79 optimal weight:    1.9990
   chunk 42 optimal weight:    2.9990
   chunk 80 optimal weight:    9.9990
   chunk 0 optimal weight:   10.0000
   chunk 73 optimal weight:    8.9990
   chunk 58 optimal weight:    9.9990
   chunk 5 optimal weight:    0.9980
   chunk 13 optimal weight:    3.9990
   chunk 84 optimal weight:    0.9980
   chunk 26 optimal weight:    4.9990
   overall best weight:    2.1986

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

Flipped N/Q/H residues before XYZ refinement:
A  10 ASN
** D  65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
E  70 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3269 r_free = 0.3269 target = 0.100714 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.2981 r_free = 0.2981 target = 0.080564 restraints weight = 12930.637|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 41)----------------|
| r_work = 0.3026 r_free = 0.3026 target = 0.083464 restraints weight = 6361.762|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3055 r_free = 0.3055 target = 0.085453 restraints weight = 4140.199|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 36)----------------|
| r_work = 0.3075 r_free = 0.3075 target = 0.086762 restraints weight = 3158.166|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 21)----------------|
| r_work = 0.3086 r_free = 0.3086 target = 0.087593 restraints weight = 2648.004|
|-----------------------------------------------------------------------------|
r_work (final): 0.3089
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8244
moved from start:          0.4773

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   6783  Z= 0.147
  Angle     :  0.655   8.796   9240  Z= 0.340
  Chirality :  0.046   0.152   1082
  Planarity :  0.004   0.039   1208
  Dihedral  :  4.858  47.503    962
  Min Nonbonded Distance : 2.551

Molprobity Statistics.
  All-atom Clashscore : 4.58
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.85 %
    Favored  : 95.15 %
  Rotamer:
    Outliers :  6.41 %
    Allowed  : 18.96 %
    Favored  : 74.62 %
  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 aren not related in a simple way.
  whole: -1.88 (0.27), residues: 866
  helix:  1.59 (0.48), residues: 120
  sheet: -1.10 (0.27), residues: 365
  loop : -2.32 (0.27), residues: 381

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG H 101 
 TYR   0.025   0.001   TYR H  35 
 PHE   0.013   0.001   PHE L  66 
 TRP   0.011   0.001   TRP H  50 
 HIS   0.002   0.001   HIS L  38 

Details of bonding type rmsd
  covalent geometry    : bond        0.00344 ( 6779)
  covalent geometry    : angle       0.65507 ( 9234)
  SS BOND              : bond        0.00284 (    3)
  SS BOND              : angle       0.83249 (    6)
  hydrogen bonds       : bond        0.03552 (  196)
  hydrogen bonds       : angle       5.05387 (  549)
  Misc. bond           : bond        0.00011 (    1)

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

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

  1732 Ramachandran restraints generated.
    866 Oldfield, 0 Emsley, 866 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1732 Ramachandran restraints generated.
    866 Oldfield, 0 Emsley, 866 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  273 residues out of total 733 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 47
    poor density    : 226
  time to evaluate  : 0.290 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: H   22 LYS cc_start: 0.9233 (tptt) cc_final: 0.8873 (tptt)
REVERT: H   70 LYS cc_start: 0.9194 (tppp) cc_final: 0.8643 (tppt)
REVERT: H   76 GLU cc_start: 0.7858 (tm-30) cc_final: 0.7371 (tm-30)
REVERT: H   77 LYS cc_start: 0.9238 (tppp) cc_final: 0.8994 (tppt)
REVERT: H  110 ASP cc_start: 0.8131 (t0) cc_final: 0.7590 (t0)
REVERT: H  111 TYR cc_start: 0.8586 (m-10) cc_final: 0.8069 (m-80)
REVERT: L   53 TYR cc_start: 0.8863 (p90) cc_final: 0.8543 (p90)
REVERT: L   85 GLU cc_start: 0.5099 (mp0) cc_final: 0.4578 (mp0)
REVERT: L   95 TYR cc_start: 0.9394 (t80) cc_final: 0.9127 (t80)
REVERT: A    2 LYS cc_start: 0.8191 (tttp) cc_final: 0.7531 (mmtt)
REVERT: A   60 LYS cc_start: 0.8639 (ttpp) cc_final: 0.8248 (pttt)
REVERT: A  127 GLN cc_start: 0.9183 (mm-40) cc_final: 0.8675 (mp10)
REVERT: B    2 LYS cc_start: 0.9161 (tttp) cc_final: 0.8297 (mmtt)
REVERT: B   14 ASP cc_start: 0.9011 (OUTLIER) cc_final: 0.8746 (p0)
REVERT: B   27 ASN cc_start: 0.8657 (t0) cc_final: 0.8000 (t0)
REVERT: B   77 ASN cc_start: 0.9239 (t0) cc_final: 0.8757 (t0)
REVERT: B  102 ASP cc_start: 0.8333 (p0) cc_final: 0.7885 (p0)
REVERT: C    2 LYS cc_start: 0.4780 (mmmt) cc_final: 0.4481 (mmmt)
REVERT: C   47 ARG cc_start: 0.8575 (mtm-85) cc_final: 0.7896 (mtp85)
REVERT: C  123 ASP cc_start: 0.8422 (t0) cc_final: 0.8100 (t0)
REVERT: D    2 LYS cc_start: 0.8762 (tttp) cc_final: 0.7782 (mmtt)
REVERT: D   13 LYS cc_start: 0.2188 (mttt) cc_final: 0.0774 (ttmt)
REVERT: D   24 ARG cc_start: 0.9076 (ttm-80) cc_final: 0.8670 (mmm-85)
REVERT: D   47 ARG cc_start: 0.8511 (ptp90) cc_final: 0.8134 (ptp-110)
REVERT: D   61 ASN cc_start: 0.8592 (m110) cc_final: 0.8150 (m-40)
REVERT: D   98 GLN cc_start: 0.8756 (tt0) cc_final: 0.8168 (tm-30)
REVERT: D  127 GLN cc_start: 0.8925 (mm110) cc_final: 0.8314 (mm110)
REVERT: E    2 LYS cc_start: 0.8513 (tttp) cc_final: 0.7907 (mmtt)
REVERT: E    4 GLU cc_start: 0.8089 (mm-30) cc_final: 0.7786 (mm-30)
REVERT: E   13 LYS cc_start: 0.3220 (mttp) cc_final: 0.2166 (ttmt)
REVERT: E   61 ASN cc_start: 0.8579 (m110) cc_final: 0.7764 (p0)
REVERT: E   63 LYS cc_start: 0.8730 (tttt) cc_final: 0.8396 (ttmm)
REVERT: E   83 SER cc_start: 0.8724 (m) cc_final: 0.8239 (t)
REVERT: E  102 ASP cc_start: 0.8662 (p0) cc_final: 0.8281 (p0)
  outliers start: 47
  outliers final: 45
  residues processed: 249
  average time/residue: 0.1129
  time to fit residues: 34.8476
Evaluate side-chains
  267 residues out of total 733 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 46
    poor density    : 221
  time to evaluate  : 0.238 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain H residue   14 LEU
Chi-restraints excluded: chain H residue   26 LYS
Chi-restraints excluded: chain H residue   31 THR
Chi-restraints excluded: chain H residue   42 GLN
Chi-restraints excluded: chain H residue   68 LYS
Chi-restraints excluded: chain H residue  103 ASP
Chi-restraints excluded: chain H residue  108 TYR
Chi-restraints excluded: chain L residue   25 THR
Chi-restraints excluded: chain L residue   26 CYS
Chi-restraints excluded: chain L residue   36 TYR
Chi-restraints excluded: chain L residue   57 ASN
Chi-restraints excluded: chain L residue   71 SER
Chi-restraints excluded: chain L residue  101 THR
Chi-restraints excluded: chain L residue  107 LYS
Chi-restraints excluded: chain A residue   14 ASP
Chi-restraints excluded: chain A residue   50 VAL
Chi-restraints excluded: chain A residue   75 THR
Chi-restraints excluded: chain A residue  111 GLU
Chi-restraints excluded: chain A residue  115 LEU
Chi-restraints excluded: chain A residue  121 LEU
Chi-restraints excluded: chain B residue   14 ASP
Chi-restraints excluded: chain B residue   36 SER
Chi-restraints excluded: chain B residue   50 VAL
Chi-restraints excluded: chain B residue   68 ILE
Chi-restraints excluded: chain B residue   69 GLN
Chi-restraints excluded: chain B residue   80 CYS
Chi-restraints excluded: chain B residue  111 GLU
Chi-restraints excluded: chain B residue  118 SER
Chi-restraints excluded: chain B residue  128 LEU
Chi-restraints excluded: chain C residue   50 VAL
Chi-restraints excluded: chain C residue  111 GLU
Chi-restraints excluded: chain D residue   41 VAL
Chi-restraints excluded: chain D residue   46 LYS
Chi-restraints excluded: chain D residue   50 VAL
Chi-restraints excluded: chain D residue   51 SER
Chi-restraints excluded: chain D residue   69 GLN
Chi-restraints excluded: chain D residue   72 THR
Chi-restraints excluded: chain D residue  115 LEU
Chi-restraints excluded: chain E residue   50 VAL
Chi-restraints excluded: chain E residue   51 SER
Chi-restraints excluded: chain E residue   70 ASN
Chi-restraints excluded: chain E residue   74 CYS
Chi-restraints excluded: chain E residue   85 THR
Chi-restraints excluded: chain E residue   98 GLN
Chi-restraints excluded: chain E residue  111 GLU
Chi-restraints excluded: chain E residue  121 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 86
   random chunks:
   chunk 31 optimal weight:    4.9990
   chunk 58 optimal weight:    0.0970
   chunk 22 optimal weight:    2.9990
   chunk 5 optimal weight:    0.9980
   chunk 34 optimal weight:    0.9990
   chunk 79 optimal weight:    7.9990
   chunk 59 optimal weight:    0.0970
   chunk 36 optimal weight:   10.0000
   chunk 32 optimal weight:    4.9990
   chunk 38 optimal weight:    5.9990
   chunk 17 optimal weight:    2.9990
   overall best weight:    1.0380

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

Flipped N/Q/H residues before XYZ refinement:
H   9 GLN
A  10 ASN
** D  65 GLN ** 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 = 0.3295 r_free = 0.3295 target = 0.102555 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3012 r_free = 0.3012 target = 0.082548 restraints weight = 12800.934|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3056 r_free = 0.3056 target = 0.085452 restraints weight = 6389.047|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3085 r_free = 0.3085 target = 0.087439 restraints weight = 4186.279|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 37)----------------|
| r_work = 0.3103 r_free = 0.3103 target = 0.088740 restraints weight = 3195.769|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.3115 r_free = 0.3115 target = 0.089568 restraints weight = 2685.792|
|-----------------------------------------------------------------------------|
r_work (final): 0.3117
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8170
moved from start:          0.4887

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   6783  Z= 0.119
  Angle     :  0.665  13.216   9240  Z= 0.338
  Chirality :  0.045   0.152   1082
  Planarity :  0.003   0.036   1208
  Dihedral  :  4.547  43.176    962
  Min Nonbonded Distance : 2.527

Molprobity Statistics.
  All-atom Clashscore : 4.66
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.50 %
    Favored  : 95.50 %
  Rotamer:
    Outliers :  5.73 %
    Allowed  : 20.19 %
    Favored  : 74.08 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.77 (0.27), residues: 866
  helix:  1.71 (0.48), residues: 120
  sheet: -1.01 (0.26), residues: 365
  loop : -2.28 (0.27), residues: 381

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG E  24 
 TYR   0.023   0.001   TYR H 105 
 PHE   0.009   0.001   PHE L  66 
 TRP   0.011   0.001   TRP H  50 
 HIS   0.001   0.001   HIS L  38 

Details of bonding type rmsd
  covalent geometry    : bond        0.00276 ( 6779)
  covalent geometry    : angle       0.66445 ( 9234)
  SS BOND              : bond        0.00266 (    3)
  SS BOND              : angle       0.76148 (    6)
  hydrogen bonds       : bond        0.03096 (  196)
  hydrogen bonds       : angle       4.93898 (  549)
  Misc. bond           : bond        0.00004 (    1)

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

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

  1732 Ramachandran restraints generated.
    866 Oldfield, 0 Emsley, 866 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1732 Ramachandran restraints generated.
    866 Oldfield, 0 Emsley, 866 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  275 residues out of total 733 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 42
    poor density    : 233
  time to evaluate  : 0.291 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: H   22 LYS cc_start: 0.9214 (tptt) cc_final: 0.8647 (tptt)
REVERT: H   70 LYS cc_start: 0.9167 (tppp) cc_final: 0.8647 (tppt)
REVERT: H   76 GLU cc_start: 0.7805 (tm-30) cc_final: 0.7307 (tm-30)
REVERT: H   77 LYS cc_start: 0.9222 (tppp) cc_final: 0.8984 (tppt)
REVERT: H   85 ARG cc_start: 0.8669 (ttm-80) cc_final: 0.8464 (mtp-110)
REVERT: H  110 ASP cc_start: 0.8062 (t0) cc_final: 0.7585 (t0)
REVERT: H  111 TYR cc_start: 0.8550 (m-10) cc_final: 0.7995 (m-80)
REVERT: L   14 MET cc_start: 0.7785 (mmm) cc_final: 0.7416 (mmp)
REVERT: L   83 GLU cc_start: 0.8190 (pm20) cc_final: 0.7725 (pm20)
REVERT: L   85 GLU cc_start: 0.5358 (mp0) cc_final: 0.4812 (mp0)
REVERT: L   95 TYR cc_start: 0.9396 (t80) cc_final: 0.9192 (t80)
REVERT: A    2 LYS cc_start: 0.8465 (tttp) cc_final: 0.6991 (mmtt)
REVERT: A   60 LYS cc_start: 0.8584 (ttpp) cc_final: 0.8234 (pttt)
REVERT: A  127 GLN cc_start: 0.9117 (mm-40) cc_final: 0.8655 (mp10)
REVERT: B    2 LYS cc_start: 0.9121 (tttp) cc_final: 0.8329 (mmtt)
REVERT: B   14 ASP cc_start: 0.9143 (OUTLIER) cc_final: 0.8938 (p0)
REVERT: B   27 ASN cc_start: 0.8544 (t0) cc_final: 0.7873 (t0)
REVERT: B   41 VAL cc_start: 0.8952 (t) cc_final: 0.8627 (m)
REVERT: B  102 ASP cc_start: 0.8317 (p0) cc_final: 0.7845 (p0)
REVERT: C   47 ARG cc_start: 0.8433 (mtm-85) cc_final: 0.7847 (mtp85)
REVERT: C  123 ASP cc_start: 0.8424 (t0) cc_final: 0.8112 (t0)
REVERT: D    2 LYS cc_start: 0.8741 (tttp) cc_final: 0.7811 (mmtt)
REVERT: D   13 LYS cc_start: 0.2082 (mttt) cc_final: 0.0704 (ttmt)
REVERT: D   24 ARG cc_start: 0.9043 (ttm-80) cc_final: 0.8633 (mmm-85)
REVERT: D   47 ARG cc_start: 0.8448 (ptp90) cc_final: 0.8088 (ptp-110)
REVERT: D   61 ASN cc_start: 0.8543 (m110) cc_final: 0.8086 (m-40)
REVERT: D   83 SER cc_start: 0.9064 (m) cc_final: 0.8766 (p)
REVERT: D   95 SER cc_start: 0.8873 (t) cc_final: 0.8652 (t)
REVERT: D   98 GLN cc_start: 0.8774 (tt0) cc_final: 0.8147 (tm-30)
REVERT: D  127 GLN cc_start: 0.8921 (mm110) cc_final: 0.8310 (mm110)
REVERT: E    2 LYS cc_start: 0.8513 (tttp) cc_final: 0.7834 (mmtt)
REVERT: E    4 GLU cc_start: 0.8137 (mm-30) cc_final: 0.7825 (mm-30)
REVERT: E   13 LYS cc_start: 0.3101 (mttp) cc_final: 0.2091 (ttmt)
REVERT: E   34 SER cc_start: 0.8540 (m) cc_final: 0.8299 (t)
REVERT: E   61 ASN cc_start: 0.8565 (m110) cc_final: 0.7659 (p0)
REVERT: E   63 LYS cc_start: 0.8716 (tttt) cc_final: 0.8343 (ttmm)
REVERT: E   83 SER cc_start: 0.8618 (m) cc_final: 0.8151 (t)
  outliers start: 42
  outliers final: 40
  residues processed: 253
  average time/residue: 0.1149
  time to fit residues: 35.9332
Evaluate side-chains
  266 residues out of total 733 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 41
    poor density    : 225
  time to evaluate  : 0.266 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain H residue    9 GLN
Chi-restraints excluded: chain H residue   14 LEU
Chi-restraints excluded: chain H residue   26 LYS
Chi-restraints excluded: chain H residue   31 THR
Chi-restraints excluded: chain H residue  103 ASP
Chi-restraints excluded: chain H residue  104 VAL
Chi-restraints excluded: chain H residue  108 TYR
Chi-restraints excluded: chain L residue   25 THR
Chi-restraints excluded: chain L residue   26 CYS
Chi-restraints excluded: chain L residue   36 TYR
Chi-restraints excluded: chain L residue   57 ASN
Chi-restraints excluded: chain L residue   71 SER
Chi-restraints excluded: chain L residue  101 THR
Chi-restraints excluded: chain L residue  107 LYS
Chi-restraints excluded: chain A residue   14 ASP
Chi-restraints excluded: chain A residue   50 VAL
Chi-restraints excluded: chain A residue   75 THR
Chi-restraints excluded: chain A residue  111 GLU
Chi-restraints excluded: chain A residue  115 LEU
Chi-restraints excluded: chain B residue   14 ASP
Chi-restraints excluded: chain B residue   50 VAL
Chi-restraints excluded: chain B residue   68 ILE
Chi-restraints excluded: chain B residue   69 GLN
Chi-restraints excluded: chain B residue   80 CYS
Chi-restraints excluded: chain B residue  111 GLU
Chi-restraints excluded: chain B residue  118 SER
Chi-restraints excluded: chain B residue  128 LEU
Chi-restraints excluded: chain C residue   50 VAL
Chi-restraints excluded: chain C residue  111 GLU
Chi-restraints excluded: chain D residue   41 VAL
Chi-restraints excluded: chain D residue   46 LYS
Chi-restraints excluded: chain D residue   51 SER
Chi-restraints excluded: chain D residue   69 GLN
Chi-restraints excluded: chain D residue   72 THR
Chi-restraints excluded: chain D residue  115 LEU
Chi-restraints excluded: chain E residue   50 VAL
Chi-restraints excluded: chain E residue   74 CYS
Chi-restraints excluded: chain E residue   85 THR
Chi-restraints excluded: chain E residue   98 GLN
Chi-restraints excluded: chain E residue  111 GLU
Chi-restraints excluded: chain E residue  121 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 86
   random chunks:
   chunk 69 optimal weight:   10.0000
   chunk 21 optimal weight:    6.9990
   chunk 72 optimal weight:    7.9990
   chunk 51 optimal weight:    5.9990
   chunk 33 optimal weight:    0.1980
   chunk 78 optimal weight:    2.9990
   chunk 26 optimal weight:    6.9990
   chunk 14 optimal weight:    4.9990
   chunk 66 optimal weight:    3.9990
   chunk 47 optimal weight:    3.9990
   chunk 74 optimal weight:    0.9990
   overall best weight:    2.4388

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

Flipped N/Q/H residues before XYZ refinement:
A  10 ASN
** D  65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
E  70 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3271 r_free = 0.3271 target = 0.100894 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.2981 r_free = 0.2981 target = 0.080657 restraints weight = 12915.100|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 24)----------------|
| r_work = 0.3026 r_free = 0.3026 target = 0.083613 restraints weight = 6298.993|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3056 r_free = 0.3056 target = 0.085600 restraints weight = 4078.582|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.3073 r_free = 0.3073 target = 0.086870 restraints weight = 3104.688|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 37)----------------|
| r_work = 0.3087 r_free = 0.3087 target = 0.087756 restraints weight = 2611.662|
|-----------------------------------------------------------------------------|
r_work (final): 0.3087
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8231
moved from start:          0.4893

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.033   6783  Z= 0.158
  Angle     :  0.700  12.597   9240  Z= 0.355
  Chirality :  0.046   0.151   1082
  Planarity :  0.004   0.036   1208
  Dihedral  :  4.529  43.055    962
  Min Nonbonded Distance : 2.515

Molprobity Statistics.
  All-atom Clashscore : 4.73
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.73 %
    Favored  : 95.27 %
  Rotamer:
    Outliers :  6.14 %
    Allowed  : 20.60 %
    Favored  : 73.26 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.71 (0.27), residues: 866
  helix:  1.77 (0.48), residues: 120
  sheet: -0.92 (0.27), residues: 363
  loop : -2.30 (0.27), residues: 383

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG E  24 
 TYR   0.024   0.001   TYR H 105 
 PHE   0.012   0.001   PHE L  66 
 TRP   0.010   0.002   TRP H  50 
 HIS   0.001   0.001   HIS L  38 

Details of bonding type rmsd
  covalent geometry    : bond        0.00373 ( 6779)
  covalent geometry    : angle       0.70005 ( 9234)
  SS BOND              : bond        0.00245 (    3)
  SS BOND              : angle       0.76077 (    6)
  hydrogen bonds       : bond        0.03565 (  196)
  hydrogen bonds       : angle       4.97576 (  549)
  Misc. bond           : bond        0.00016 (    1)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1479.02 seconds
wall clock time: 26 minutes 11.79 seconds (1571.79 seconds total)