Starting phenix.real_space_refine
on Sat May 10 17:04:17 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8w5i_37293/05_2025/8w5i_37293.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8w5i_37293/05_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 {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8w5i_37293/05_2025/8w5i_37293.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8w5i_37293/05_2025/8w5i_37293.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8w5i_37293/05_2025/8w5i_37293.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8w5i_37293/05_2025/8w5i_37293.cif"
  }
  resolution = 3.6
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.005 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-filer2/raid1/xp/phenix/phenix-dev-5687/modules/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: 4.55, per 1000 atoms: 0.68
  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: 1.75
  Conformation dependent library (CDL) restraints added in 1.0 seconds
  

  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: 0.94
  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: 1.65

  Time building geometry restraints manager: 2.05 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:             0.440
  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:             0.000
  Extract box with map and model:          0.300
  Check model and map are aligned:         0.060
  Set scattering table:                    0.070
  Process input model:                     19.720
  Find NCS groups from input model:        0.190
  Set up NCS constraints:                  0.030
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:2.570
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   23.380
-------------------------------------------------------------------------------
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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -4.13 (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
 TRP   0.013   0.003   TRP H 112 
 HIS   0.003   0.002   HIS L  38 
 PHE   0.059   0.004   PHE H 107 
 TYR   0.069   0.004   TYR H 105 
 ARG   0.005   0.001   ARG L  27 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.25847 (  196)
  hydrogen bonds       : angle       9.41836 (  549)
  SS BOND              : bond        0.00718 (    3)
  SS BOND              : angle      18.57499 (    6)
  covalent geometry    : bond        0.01521 ( 6779)
  covalent geometry    : angle       1.47712 ( 9234)
  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  : 0.862 
Fit side-chains
   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: 0.8308 (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: 0.8761 (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: 0.7719 (t0)
REVERT: B   47 ARG cc_start: 0.8537 (ptp-170) cc_final: 0.7977 (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: 0.8886 (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: 0.8417 (t)
REVERT: D   47 ARG cc_start: 0.8752 (ptp-170) cc_final: 0.8061 (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: 0.8470 (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: 0.8376 (mt)
REVERT: E   14 ASP cc_start: 0.8586 (p0) cc_final: 0.8260 (p0)
REVERT: E   17 GLN cc_start: 0.8364 (mt0) cc_final: 0.8163 (mp10)
REVERT: E   63 LYS cc_start: 0.8482 (tttt) cc_final: 0.8084 (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: 0.2472
  time to fit residues: 90.4967
Evaluate side-chains
  222 residues out of total 733 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 215
  time to evaluate  : 0.746 
-------------------------------------------------------------------------------
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 72 optimal weight:    0.5980
   chunk 65 optimal weight:    9.9990
   chunk 36 optimal weight:    0.9990
   chunk 22 optimal weight:    8.9990
   chunk 43 optimal weight:    3.9990
   chunk 34 optimal weight:    9.9990
   chunk 67 optimal weight:    8.9990
   chunk 26 optimal weight:    0.0030
   chunk 40 optimal weight:    5.9990
   chunk 50 optimal weight:    1.9990
   chunk 78 optimal weight:    2.9990
   overall best weight:    1.3196

-------------------------------------------------------------------------------
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 = 0.3317 r_free = 0.3317 target = 0.104048 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3030 r_free = 0.3030 target = 0.083539 restraints weight = 12778.749|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3075 r_free = 0.3075 target = 0.086538 restraints weight = 6312.653|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3104 r_free = 0.3104 target = 0.088557 restraints weight = 4119.151|
|-----------------------------------------------------------------------------|
r_work (final): 0.3104
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8197
moved from start:          0.2854

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= 0.123
  Angle     :  0.653   8.871   9240  Z= 0.347
  Chirality :  0.046   0.162   1082
  Planarity :  0.004   0.041   1208
  Dihedral  :  7.045  56.302    974
  Min Nonbonded Distance : 2.542

Molprobity Statistics.
  All-atom Clashscore : 5.11
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.08 %
    Favored  : 94.92 %
  Rotamer:
    Outliers :  3.96 %
    Allowed  : 14.32 %
    Favored  : 81.72 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -3.24 (0.25), residues: 866
  helix: -0.43 (0.48), residues: 120
  sheet: -1.92 (0.25), residues: 339
  loop : -2.87 (0.24), residues: 407

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.002   TRP H 112 
 HIS   0.001   0.001   HIS L  38 
 PHE   0.008   0.001   PHE H 109 
 TYR   0.022   0.001   TYR H  30 
 ARG   0.006   0.000   ARG D  24 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04325 (  196)
  hydrogen bonds       : angle       5.96904 (  549)
  SS BOND              : bond        0.00259 (    3)
  SS BOND              : angle       1.06443 (    6)
  covalent geometry    : bond        0.00264 ( 6779)
  covalent geometry    : angle       0.65275 ( 9234)
  Misc. bond           : bond        0.00049 (    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  : 0.772 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: H   35 TYR cc_start: 0.9317 (m-80) cc_final: 0.8923 (m-80)
REVERT: H   89 LEU cc_start: 0.9121 (mm) cc_final: 0.8907 (mm)
REVERT: H  104 VAL cc_start: 0.9033 (t) cc_final: 0.8434 (t)
REVERT: H  107 PHE cc_start: 0.8192 (m-80) cc_final: 0.7920 (m-80)
REVERT: L   13 ILE cc_start: 0.8876 (pt) cc_final: 0.8614 (mm)
REVERT: L   53 TYR cc_start: 0.9083 (p90) cc_final: 0.8796 (p90)
REVERT: L   95 TYR cc_start: 0.9478 (t80) cc_final: 0.8989 (t80)
REVERT: A    2 LYS cc_start: 0.8316 (tttp) cc_final: 0.7317 (mmtt)
REVERT: A   63 LYS cc_start: 0.8670 (tttt) cc_final: 0.8425 (ttmm)
REVERT: A  103 GLU cc_start: 0.7803 (mp0) cc_final: 0.7531 (mp0)
REVERT: B    2 LYS cc_start: 0.9124 (tttp) cc_final: 0.8653 (tppt)
REVERT: B   14 ASP cc_start: 0.9079 (p0) cc_final: 0.8754 (p0)
REVERT: B   27 ASN cc_start: 0.8651 (t0) cc_final: 0.7940 (t0)
REVERT: B   77 ASN cc_start: 0.9404 (t0) cc_final: 0.8943 (t0)
REVERT: B   79 SER cc_start: 0.9562 (t) cc_final: 0.8994 (p)
REVERT: B  102 ASP cc_start: 0.8099 (p0) cc_final: 0.7749 (t70)
REVERT: C  102 ASP cc_start: 0.8549 (p0) cc_final: 0.8233 (t70)
REVERT: D   47 ARG cc_start: 0.8298 (ptp-170) cc_final: 0.8074 (ptp-110)
REVERT: D   61 ASN cc_start: 0.8621 (m110) cc_final: 0.8099 (m-40)
REVERT: D   81 ASP cc_start: 0.8609 (m-30) cc_final: 0.8253 (t0)
REVERT: D   86 ARG cc_start: 0.8617 (ptt-90) cc_final: 0.6832 (ttt180)
REVERT: D   98 GLN cc_start: 0.8763 (tt0) cc_final: 0.8057 (tm-30)
REVERT: D  122 ILE cc_start: 0.8651 (pp) cc_final: 0.8281 (mm)
REVERT: D  123 ASP cc_start: 0.7953 (t0) cc_final: 0.7286 (t0)
REVERT: D  127 GLN cc_start: 0.8961 (mm110) cc_final: 0.8459 (mm110)
REVERT: E    2 LYS cc_start: 0.8577 (tttp) cc_final: 0.7830 (mmtt)
REVERT: E   63 LYS cc_start: 0.8546 (tttt) cc_final: 0.8107 (ttmm)
REVERT: E   81 ASP cc_start: 0.8740 (m-30) cc_final: 0.8343 (m-30)
REVERT: E   83 SER cc_start: 0.8393 (m) cc_final: 0.8055 (t)
REVERT: E  104 GLU cc_start: 0.7735 (mp0) cc_final: 0.7398 (mp0)
  outliers start: 29
  outliers final: 16
  residues processed: 256
  average time/residue: 0.2465
  time to fit residues: 78.6619
Evaluate side-chains
  230 residues out of total 733 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 214
  time to evaluate  : 0.712 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain H residue    5 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   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 46 optimal weight:    7.9990
   chunk 19 optimal weight:    9.9990
   chunk 44 optimal weight:    0.0970
   chunk 1 optimal weight:    0.8980
   chunk 31 optimal weight:    8.9990
   chunk 15 optimal weight:   10.0000
   chunk 34 optimal weight:    7.9990
   chunk 5 optimal weight:    0.9980
   chunk 57 optimal weight:    7.9990
   chunk 59 optimal weight:    1.9990
   chunk 69 optimal weight:    8.9990
   overall best weight:    2.3982

-------------------------------------------------------------------------------
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
D  37 GLN
E  10 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3278 r_free = 0.3278 target = 0.101499 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.2992 r_free = 0.2992 target = 0.081286 restraints weight = 12928.381|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3036 r_free = 0.3036 target = 0.084210 restraints weight = 6373.973|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3063 r_free = 0.3063 target = 0.086136 restraints weight = 4161.442|
|-----------------------------------------------------------------------------|
r_work (final): 0.3061
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8252
moved from start:          0.3588

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   6783  Z= 0.153
  Angle     :  0.648  11.291   9240  Z= 0.338
  Chirality :  0.047   0.163   1082
  Planarity :  0.004   0.037   1208
  Dihedral  :  6.094  55.793    965
  Min Nonbonded Distance : 2.516

Molprobity Statistics.
  All-atom Clashscore : 4.06
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.66 %
    Favored  : 94.34 %
  Rotamer:
    Outliers :  5.59 %
    Allowed  : 16.78 %
    Favored  : 77.63 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.70 (0.26), residues: 866
  helix:  0.50 (0.49), residues: 120
  sheet: -1.67 (0.25), residues: 353
  loop : -2.61 (0.26), residues: 393

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP H 112 
 HIS   0.002   0.001   HIS L  38 
 PHE   0.009   0.001   PHE H  67 
 TYR   0.022   0.001   TYR H 105 
 ARG   0.004   0.001   ARG D  57 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04196 (  196)
  hydrogen bonds       : angle       5.51177 (  549)
  SS BOND              : bond        0.00290 (    3)
  SS BOND              : angle       1.03378 (    6)
  covalent geometry    : bond        0.00345 ( 6779)
  covalent geometry    : angle       0.64786 ( 9234)
  Misc. bond           : bond        0.00036 (    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
  271 residues out of total 733 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 41
    poor density    : 230
  time to evaluate  : 0.839 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: H   35 TYR cc_start: 0.9182 (m-80) cc_final: 0.8933 (m-80)
REVERT: H   70 LYS cc_start: 0.9080 (tppp) cc_final: 0.8427 (tppt)
REVERT: H   89 LEU cc_start: 0.9150 (mm) cc_final: 0.8870 (mm)
REVERT: H  107 PHE cc_start: 0.8191 (m-80) cc_final: 0.7874 (m-80)
REVERT: H  110 ASP cc_start: 0.8088 (t0) cc_final: 0.7335 (t0)
REVERT: H  111 TYR cc_start: 0.8644 (m-10) cc_final: 0.8114 (m-80)
REVERT: L   13 ILE cc_start: 0.8849 (pt) cc_final: 0.8557 (mm)
REVERT: L   21 LYS cc_start: 0.9258 (ttmm) cc_final: 0.9014 (ttmm)
REVERT: L   53 TYR cc_start: 0.9044 (p90) cc_final: 0.8736 (p90)
REVERT: L   95 TYR cc_start: 0.9490 (t80) cc_final: 0.8426 (t80)
REVERT: A    2 LYS cc_start: 0.8586 (tttp) cc_final: 0.7553 (mmtt)
REVERT: A   60 LYS cc_start: 0.8565 (ttpp) cc_final: 0.8114 (pttm)
REVERT: A   63 LYS cc_start: 0.8755 (tttt) cc_final: 0.8506 (ttmm)
REVERT: A   81 ASP cc_start: 0.8629 (p0) cc_final: 0.8382 (p0)
REVERT: A  103 GLU cc_start: 0.7816 (mp0) cc_final: 0.7608 (mp0)
REVERT: B    2 LYS cc_start: 0.9260 (tttp) cc_final: 0.8163 (mmtt)
REVERT: B   14 ASP cc_start: 0.9181 (OUTLIER) cc_final: 0.8778 (p0)
REVERT: B   27 ASN cc_start: 0.8509 (t0) cc_final: 0.7776 (t0)
REVERT: B   77 ASN cc_start: 0.9405 (t0) cc_final: 0.8479 (t0)
REVERT: B   81 ASP cc_start: 0.8966 (t0) cc_final: 0.8025 (p0)
REVERT: B   98 GLN cc_start: 0.8598 (tm-30) cc_final: 0.8125 (tm-30)
REVERT: B  102 ASP cc_start: 0.8165 (p0) cc_final: 0.7631 (t70)
REVERT: B  132 TYR cc_start: 0.7632 (t80) cc_final: 0.7404 (t80)
REVERT: C   14 ASP cc_start: 0.8957 (p0) cc_final: 0.8562 (p0)
REVERT: C   16 LYS cc_start: 0.8303 (mtmm) cc_final: 0.8072 (ptpp)
REVERT: C   81 ASP cc_start: 0.8974 (m-30) cc_final: 0.8757 (m-30)
REVERT: C  102 ASP cc_start: 0.8554 (p0) cc_final: 0.8190 (t70)
REVERT: C  123 ASP cc_start: 0.8319 (t0) cc_final: 0.8051 (t0)
REVERT: D    2 LYS cc_start: 0.8589 (tttp) cc_final: 0.6351 (mmtt)
REVERT: D   47 ARG cc_start: 0.8524 (ptp-170) cc_final: 0.8254 (ptp-110)
REVERT: D   61 ASN cc_start: 0.8671 (m110) cc_final: 0.8352 (m-40)
REVERT: D   63 LYS cc_start: 0.8561 (tttt) cc_final: 0.8281 (ttpp)
REVERT: D   98 GLN cc_start: 0.8780 (tt0) cc_final: 0.8094 (tm-30)
REVERT: D  122 ILE cc_start: 0.8797 (pp) cc_final: 0.8499 (mm)
REVERT: D  123 ASP cc_start: 0.8022 (t0) cc_final: 0.7413 (t0)
REVERT: D  127 GLN cc_start: 0.9065 (mm110) cc_final: 0.8533 (mm110)
REVERT: E    2 LYS cc_start: 0.8549 (tttp) cc_final: 0.7935 (mmtt)
REVERT: E   17 GLN cc_start: 0.7855 (mp10) cc_final: 0.7515 (mp10)
REVERT: E   61 ASN cc_start: 0.8511 (m110) cc_final: 0.8242 (m-40)
REVERT: E   63 LYS cc_start: 0.8676 (tttt) cc_final: 0.8212 (ttmm)
REVERT: E   81 ASP cc_start: 0.8716 (m-30) cc_final: 0.8439 (m-30)
REVERT: E   83 SER cc_start: 0.8676 (m) cc_final: 0.8206 (t)
REVERT: E  104 GLU cc_start: 0.7759 (mp0) cc_final: 0.7316 (mp0)
  outliers start: 41
  outliers final: 23
  residues processed: 251
  average time/residue: 0.2292
  time to fit residues: 70.7508
Evaluate side-chains
  242 residues out of total 733 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 218
  time to evaluate  : 0.730 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain H residue   14 LEU
Chi-restraints excluded: chain H residue   31 THR
Chi-restraints excluded: chain H residue   37 ILE
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   57 ASN
Chi-restraints excluded: chain A residue   41 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   69 GLN
Chi-restraints excluded: chain B residue  111 GLU
Chi-restraints excluded: chain B residue  118 SER
Chi-restraints excluded: chain D residue   41 VAL
Chi-restraints excluded: chain D residue   51 SER
Chi-restraints excluded: chain D residue  115 LEU
Chi-restraints excluded: chain E residue   46 LYS
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 72 optimal weight:    9.9990
   chunk 13 optimal weight:   20.0000
   chunk 78 optimal weight:    7.9990
   chunk 70 optimal weight:    7.9990
   chunk 31 optimal weight:    6.9990
   chunk 16 optimal weight:    7.9990
   chunk 42 optimal weight:    0.9980
   chunk 17 optimal weight:    6.9990
   chunk 14 optimal weight:    6.9990
   chunk 68 optimal weight:    1.9990
   chunk 51 optimal weight:    8.9990
   overall best weight:    4.7988

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

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

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3221 r_free = 0.3221 target = 0.097785 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.2932 r_free = 0.2932 target = 0.077834 restraints weight = 13323.233|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.2975 r_free = 0.2975 target = 0.080613 restraints weight = 6758.479|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3002 r_free = 0.3002 target = 0.082459 restraints weight = 4469.837|
|-----------------------------------------------------------------------------|
r_work (final): 0.3004
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8307
moved from start:          0.4022

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.036   6783  Z= 0.272
  Angle     :  0.730   7.664   9240  Z= 0.386
  Chirality :  0.050   0.178   1082
  Planarity :  0.004   0.040   1208
  Dihedral  :  6.098  60.173    962
  Min Nonbonded Distance : 2.481

Molprobity Statistics.
  All-atom Clashscore : 4.81
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.04 %
    Favored  : 92.96 %
  Rotamer:
    Outliers :  6.68 %
    Allowed  : 17.60 %
    Favored  : 75.72 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.61 (0.26), residues: 866
  helix:  0.81 (0.49), residues: 120
  sheet: -1.70 (0.26), residues: 365
  loop : -2.55 (0.26), residues: 381

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.002   TRP H 112 
 HIS   0.001   0.001   HIS L  38 
 PHE   0.008   0.002   PHE H  98 
 TYR   0.034   0.002   TYR H 105 
 ARG   0.006   0.001   ARG C  47 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05036 (  196)
  hydrogen bonds       : angle       5.61362 (  549)
  SS BOND              : bond        0.00294 (    3)
  SS BOND              : angle       1.07180 (    6)
  covalent geometry    : bond        0.00627 ( 6779)
  covalent geometry    : angle       0.72991 ( 9234)
  Misc. bond           : bond        0.00052 (    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
  269 residues out of total 733 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 49
    poor density    : 220
  time to evaluate  : 0.815 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: H   35 TYR cc_start: 0.9235 (m-80) cc_final: 0.8954 (m-80)
REVERT: H   46 GLN cc_start: 0.9022 (mp10) cc_final: 0.8773 (mp10)
REVERT: H   70 LYS cc_start: 0.9105 (tppp) cc_final: 0.8458 (tppt)
REVERT: H   89 LEU cc_start: 0.9245 (mm) cc_final: 0.8954 (mm)
REVERT: H   93 ASP cc_start: 0.8722 (OUTLIER) cc_final: 0.8428 (p0)
REVERT: H  103 ASP cc_start: 0.8812 (t0) cc_final: 0.8452 (t0)
REVERT: H  110 ASP cc_start: 0.8214 (t0) cc_final: 0.7438 (t0)
REVERT: H  111 TYR cc_start: 0.8641 (m-10) cc_final: 0.7763 (m-10)
REVERT: L   13 ILE cc_start: 0.8859 (pt) cc_final: 0.8644 (mm)
REVERT: L   53 TYR cc_start: 0.9023 (p90) cc_final: 0.8735 (p90)
REVERT: L   83 GLU cc_start: 0.7966 (pm20) cc_final: 0.7765 (pm20)
REVERT: A    2 LYS cc_start: 0.8574 (tttp) cc_final: 0.7565 (mmtt)
REVERT: A   60 LYS cc_start: 0.8637 (ttpp) cc_final: 0.8403 (pttm)
REVERT: A   63 LYS cc_start: 0.8982 (tttt) cc_final: 0.8684 (ttmm)
REVERT: A   81 ASP cc_start: 0.8635 (p0) cc_final: 0.8321 (p0)
REVERT: B    2 LYS cc_start: 0.9184 (tttp) cc_final: 0.8085 (mmtt)
REVERT: B   14 ASP cc_start: 0.9131 (p0) cc_final: 0.8903 (p0)
REVERT: B   27 ASN cc_start: 0.8637 (t0) cc_final: 0.7972 (t0)
REVERT: B   63 LYS cc_start: 0.8652 (tttt) cc_final: 0.8321 (ttmt)
REVERT: B   77 ASN cc_start: 0.9387 (t0) cc_final: 0.8298 (t0)
REVERT: B   81 ASP cc_start: 0.8918 (t0) cc_final: 0.8259 (p0)
REVERT: B   98 GLN cc_start: 0.8683 (tm-30) cc_final: 0.8363 (tm-30)
REVERT: B  102 ASP cc_start: 0.8503 (p0) cc_final: 0.7667 (t70)
REVERT: C   47 ARG cc_start: 0.8485 (mtm-85) cc_final: 0.7984 (mtp85)
REVERT: C   81 ASP cc_start: 0.9062 (m-30) cc_final: 0.8826 (m-30)
REVERT: C   89 TYR cc_start: 0.9102 (m-80) cc_final: 0.8896 (m-80)
REVERT: C  102 ASP cc_start: 0.8694 (p0) cc_final: 0.8267 (t70)
REVERT: C  123 ASP cc_start: 0.8373 (t0) cc_final: 0.8051 (t0)
REVERT: D    2 LYS cc_start: 0.8085 (tttp) cc_final: 0.7783 (mmtt)
REVERT: D   24 ARG cc_start: 0.8961 (ttm-80) cc_final: 0.8751 (mmm-85)
REVERT: D   47 ARG cc_start: 0.8452 (ptp-170) cc_final: 0.8201 (ptp-110)
REVERT: D   57 ARG cc_start: 0.8014 (ttp80) cc_final: 0.7797 (ptt180)
REVERT: D   61 ASN cc_start: 0.8740 (m110) cc_final: 0.8274 (m-40)
REVERT: D   98 GLN cc_start: 0.8901 (tt0) cc_final: 0.8003 (tm-30)
REVERT: D  123 ASP cc_start: 0.8120 (t0) cc_final: 0.7721 (t0)
REVERT: D  127 GLN cc_start: 0.9057 (mm110) cc_final: 0.8520 (mm110)
REVERT: E    2 LYS cc_start: 0.8459 (tttp) cc_final: 0.7870 (mmtt)
REVERT: E   10 ASN cc_start: 0.8600 (m110) cc_final: 0.8192 (t0)
REVERT: E   61 ASN cc_start: 0.8626 (m110) cc_final: 0.7638 (p0)
REVERT: E   63 LYS cc_start: 0.8742 (tttt) cc_final: 0.8360 (ttmm)
REVERT: E   83 SER cc_start: 0.8574 (m) cc_final: 0.8085 (t)
REVERT: E  102 ASP cc_start: 0.8819 (p0) cc_final: 0.8437 (p0)
REVERT: E  104 GLU cc_start: 0.8165 (mp0) cc_final: 0.7861 (mp0)
REVERT: E  129 ASN cc_start: 0.9125 (m-40) cc_final: 0.8444 (t0)
  outliers start: 49
  outliers final: 38
  residues processed: 247
  average time/residue: 0.2285
  time to fit residues: 69.8715
Evaluate side-chains
  248 residues out of total 733 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 39
    poor density    : 209
  time to evaluate  : 0.700 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain H residue   14 LEU
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   93 ASP
Chi-restraints excluded: chain H residue  108 TYR
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 A residue   41 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   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  116 LEU
Chi-restraints excluded: chain B residue  118 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   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 58 optimal weight:   10.0000
   chunk 14 optimal weight:    8.9990
   chunk 65 optimal weight:    3.9990
   chunk 11 optimal weight:   10.0000
   chunk 35 optimal weight:    3.9990
   chunk 17 optimal weight:    8.9990
   chunk 83 optimal weight:    5.9990
   chunk 46 optimal weight:    0.8980
   chunk 8 optimal weight:   10.0000
   chunk 23 optimal weight:    5.9990
   chunk 10 optimal weight:    1.9990
   overall best weight:    3.3788

-------------------------------------------------------------------------------
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**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3239 r_free = 0.3239 target = 0.098833 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.2950 r_free = 0.2950 target = 0.078908 restraints weight = 12964.962|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.2994 r_free = 0.2994 target = 0.081709 restraints weight = 6588.391|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3022 r_free = 0.3022 target = 0.083597 restraints weight = 4365.780|
|-----------------------------------------------------------------------------|
r_work (final): 0.3023
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8285
moved from start:          0.4267

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= 0.193
  Angle     :  0.656   7.895   9240  Z= 0.346
  Chirality :  0.048   0.164   1082
  Planarity :  0.004   0.041   1208
  Dihedral  :  5.805  58.621    962
  Min Nonbonded Distance : 2.485

Molprobity Statistics.
  All-atom Clashscore : 4.73
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.58 %
    Favored  : 93.42 %
  Rotamer:
    Outliers :  6.68 %
    Allowed  : 18.01 %
    Favored  : 75.31 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.38 (0.27), residues: 866
  helix:  1.00 (0.49), residues: 120
  sheet: -1.51 (0.26), residues: 361
  loop : -2.46 (0.26), residues: 385

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.002   TRP H  50 
 HIS   0.001   0.001   HIS L  38 
 PHE   0.006   0.001   PHE H  98 
 TYR   0.021   0.002   TYR H  30 
 ARG   0.005   0.001   ARG A  24 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04291 (  196)
  hydrogen bonds       : angle       5.40288 (  549)
  SS BOND              : bond        0.00238 (    3)
  SS BOND              : angle       1.17168 (    6)
  covalent geometry    : bond        0.00446 ( 6779)
  covalent geometry    : angle       0.65566 ( 9234)
  Misc. bond           : bond        0.00032 (    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: 49
    poor density    : 216
  time to evaluate  : 0.820 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: H   35 TYR cc_start: 0.9183 (m-80) cc_final: 0.8913 (m-80)
REVERT: H   70 LYS cc_start: 0.9181 (tppp) cc_final: 0.8541 (tppt)
REVERT: H   76 GLU cc_start: 0.7825 (tm-30) cc_final: 0.7456 (tm-30)
REVERT: H   89 LEU cc_start: 0.9233 (mm) cc_final: 0.8942 (mm)
REVERT: H  110 ASP cc_start: 0.8160 (t0) cc_final: 0.7561 (t0)
REVERT: H  111 TYR cc_start: 0.8533 (m-10) cc_final: 0.8045 (m-80)
REVERT: L   13 ILE cc_start: 0.8979 (pt) cc_final: 0.8769 (mm)
REVERT: L   53 TYR cc_start: 0.8961 (p90) cc_final: 0.8619 (p90)
REVERT: L   95 TYR cc_start: 0.9408 (t80) cc_final: 0.8720 (t80)
REVERT: A    2 LYS cc_start: 0.8589 (tttp) cc_final: 0.7649 (mmtt)
REVERT: A   60 LYS cc_start: 0.8520 (ttpp) cc_final: 0.8319 (pttm)
REVERT: A   63 LYS cc_start: 0.8962 (tttt) cc_final: 0.8673 (ttmm)
REVERT: A  127 GLN cc_start: 0.8860 (mm-40) cc_final: 0.8441 (mp10)
REVERT: B    2 LYS cc_start: 0.9171 (tttp) cc_final: 0.8053 (mmtt)
REVERT: B   27 ASN cc_start: 0.8645 (t0) cc_final: 0.7960 (t0)
REVERT: B   77 ASN cc_start: 0.9315 (t0) cc_final: 0.8206 (t0)
REVERT: B   81 ASP cc_start: 0.8914 (t0) cc_final: 0.8276 (p0)
REVERT: B   98 GLN cc_start: 0.8655 (tm-30) cc_final: 0.8394 (tm-30)
REVERT: B  102 ASP cc_start: 0.8356 (p0) cc_final: 0.7511 (t70)
REVERT: C   14 ASP cc_start: 0.8888 (p0) cc_final: 0.8505 (p0)
REVERT: C   47 ARG cc_start: 0.8550 (mtm-85) cc_final: 0.8066 (mtp85)
REVERT: C  102 ASP cc_start: 0.8604 (p0) cc_final: 0.8180 (t70)
REVERT: C  123 ASP cc_start: 0.8360 (t0) cc_final: 0.8057 (t0)
REVERT: D    2 LYS cc_start: 0.8737 (tttp) cc_final: 0.7922 (mmtt)
REVERT: D   47 ARG cc_start: 0.8440 (ptp-170) cc_final: 0.8176 (ptp-110)
REVERT: D   60 LYS cc_start: 0.8369 (ptpp) cc_final: 0.8152 (ptpp)
REVERT: D   61 ASN cc_start: 0.8636 (m110) cc_final: 0.8188 (m-40)
REVERT: D   98 GLN cc_start: 0.8851 (tt0) cc_final: 0.8165 (tm-30)
REVERT: D  127 GLN cc_start: 0.8994 (mm110) cc_final: 0.8402 (mm110)
REVERT: E    2 LYS cc_start: 0.8451 (tttp) cc_final: 0.7894 (mmtt)
REVERT: E   10 ASN cc_start: 0.8648 (m110) cc_final: 0.8246 (t0)
REVERT: E   61 ASN cc_start: 0.8546 (m110) cc_final: 0.7698 (p0)
REVERT: E   63 LYS cc_start: 0.8679 (tttt) cc_final: 0.8335 (ttmm)
REVERT: E   83 SER cc_start: 0.8598 (m) cc_final: 0.8116 (t)
REVERT: E  102 ASP cc_start: 0.8789 (p0) cc_final: 0.8385 (p0)
REVERT: E  129 ASN cc_start: 0.9131 (m-40) cc_final: 0.8500 (t0)
  outliers start: 49
  outliers final: 39
  residues processed: 242
  average time/residue: 0.2239
  time to fit residues: 67.0847
Evaluate side-chains
  249 residues out of total 733 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 39
    poor density    : 210
  time to evaluate  : 0.821 
-------------------------------------------------------------------------------
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   57 ASN
Chi-restraints excluded: chain L residue   71 SER
Chi-restraints excluded: chain L residue  107 LYS
Chi-restraints excluded: chain A residue   41 VAL
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 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   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   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 1 optimal weight:    6.9990
   chunk 10 optimal weight:    3.9990
   chunk 29 optimal weight:    0.6980
   chunk 12 optimal weight:    6.9990
   chunk 72 optimal weight:    0.6980
   chunk 81 optimal weight:    1.9990
   chunk 57 optimal weight:    8.9990
   chunk 33 optimal weight:    0.6980
   chunk 60 optimal weight:    0.0470
   chunk 15 optimal weight:    5.9990
   chunk 61 optimal weight:    0.8980
   overall best weight:    0.6078

-------------------------------------------------------------------------------
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
E  22 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3399 r_free = 0.3399 target = 0.106991 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3134 r_free = 0.3134 target = 0.088003 restraints weight = 12738.197|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3176 r_free = 0.3176 target = 0.090966 restraints weight = 6162.847|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3205 r_free = 0.3205 target = 0.092966 restraints weight = 4015.215|
|-----------------------------------------------------------------------------|
r_work (final): 0.3205
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8291
moved from start:          0.4539

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.034   6783  Z= 0.104
  Angle     :  0.582   6.436   9240  Z= 0.301
  Chirality :  0.044   0.143   1082
  Planarity :  0.004   0.038   1208
  Dihedral  :  4.904  47.762    962
  Min Nonbonded Distance : 2.500

Molprobity Statistics.
  All-atom Clashscore : 3.98
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.35 %
    Favored  : 96.65 %
  Rotamer:
    Outliers :  5.73 %
    Allowed  : 17.74 %
    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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.98 (0.27), residues: 866
  helix:  1.39 (0.49), residues: 120
  sheet: -1.22 (0.27), residues: 353
  loop : -2.25 (0.27), residues: 393

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP H  50 
 HIS   0.001   0.001   HIS L  38 
 PHE   0.007   0.001   PHE B  96 
 TYR   0.017   0.001   TYR H  30 
 ARG   0.006   0.000   ARG A  24 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02728 (  196)
  hydrogen bonds       : angle       5.04202 (  549)
  SS BOND              : bond        0.00311 (    3)
  SS BOND              : angle       1.39116 (    6)
  covalent geometry    : bond        0.00227 ( 6779)
  covalent geometry    : angle       0.58074 ( 9234)
  Misc. bond           : bond        0.00005 (    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
  282 residues out of total 733 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 42
    poor density    : 240
  time to evaluate  : 0.774 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: H   70 LYS cc_start: 0.9231 (tppp) cc_final: 0.8701 (tppt)
REVERT: H   76 GLU cc_start: 0.7875 (tm-30) cc_final: 0.7577 (tm-30)
REVERT: H   85 ARG cc_start: 0.8579 (ttm110) cc_final: 0.8261 (ttm110)
REVERT: H  103 ASP cc_start: 0.8822 (OUTLIER) cc_final: 0.8578 (m-30)
REVERT: H  110 ASP cc_start: 0.7992 (t0) cc_final: 0.7613 (t0)
REVERT: H  111 TYR cc_start: 0.8471 (m-10) cc_final: 0.7973 (m-80)
REVERT: L   13 ILE cc_start: 0.8994 (pt) cc_final: 0.8726 (mm)
REVERT: L   95 TYR cc_start: 0.9362 (t80) cc_final: 0.9136 (t80)
REVERT: A    2 LYS cc_start: 0.8582 (tttp) cc_final: 0.7773 (mmtt)
REVERT: A  127 GLN cc_start: 0.9002 (mm-40) cc_final: 0.8608 (mp10)
REVERT: B    2 LYS cc_start: 0.9106 (tttp) cc_final: 0.8118 (mmtt)
REVERT: B   27 ASN cc_start: 0.8736 (t0) cc_final: 0.8110 (t0)
REVERT: B   77 ASN cc_start: 0.9100 (t0) cc_final: 0.8671 (t0)
REVERT: B  102 ASP cc_start: 0.8132 (p0) cc_final: 0.7679 (p0)
REVERT: B  103 GLU cc_start: 0.7987 (mm-30) cc_final: 0.7737 (mm-30)
REVERT: C    2 LYS cc_start: 0.5929 (mmtt) cc_final: 0.5680 (mmmt)
REVERT: C   47 ARG cc_start: 0.8548 (mtm-85) cc_final: 0.8060 (mtp85)
REVERT: C   89 TYR cc_start: 0.9026 (m-80) cc_final: 0.8770 (m-80)
REVERT: C  123 ASP cc_start: 0.8489 (t0) cc_final: 0.8152 (t0)
REVERT: D    2 LYS cc_start: 0.8582 (tttp) cc_final: 0.7742 (mmtt)
REVERT: D    4 GLU cc_start: 0.8289 (mm-30) cc_final: 0.8082 (mm-30)
REVERT: D   13 LYS cc_start: 0.2079 (mttt) cc_final: 0.0701 (ttmt)
REVERT: D   61 ASN cc_start: 0.8468 (m110) cc_final: 0.8062 (m-40)
REVERT: D   98 GLN cc_start: 0.8604 (tt0) cc_final: 0.8143 (tm-30)
REVERT: D  127 GLN cc_start: 0.9036 (mm110) cc_final: 0.8442 (mm110)
REVERT: E    2 LYS cc_start: 0.8540 (tttp) cc_final: 0.7977 (mmtt)
REVERT: E   17 GLN cc_start: 0.8200 (mp10) cc_final: 0.7949 (mp10)
REVERT: E   34 SER cc_start: 0.8694 (m) cc_final: 0.8451 (t)
REVERT: E   46 LYS cc_start: 0.8819 (OUTLIER) cc_final: 0.8598 (mttp)
REVERT: E   61 ASN cc_start: 0.8328 (m110) cc_final: 0.7566 (p0)
REVERT: E   63 LYS cc_start: 0.8609 (tttt) cc_final: 0.8328 (ttmm)
REVERT: E   83 SER cc_start: 0.8979 (m) cc_final: 0.8510 (t)
REVERT: E  129 ASN cc_start: 0.9089 (m-40) cc_final: 0.8578 (t0)
  outliers start: 42
  outliers final: 31
  residues processed: 260
  average time/residue: 0.2632
  time to fit residues: 83.8542
Evaluate side-chains
  260 residues out of total 733 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 227
  time to evaluate  : 0.824 
-------------------------------------------------------------------------------
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   68 LYS
Chi-restraints excluded: chain H residue  103 ASP
Chi-restraints excluded: chain H residue  108 TYR
Chi-restraints excluded: chain L residue   36 TYR
Chi-restraints excluded: chain L residue   57 ASN
Chi-restraints excluded: chain A residue   13 LYS
Chi-restraints excluded: chain A residue   14 ASP
Chi-restraints excluded: chain A residue   41 VAL
Chi-restraints excluded: chain A residue  111 GLU
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   50 VAL
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  115 LEU
Chi-restraints excluded: chain D residue  128 LEU
Chi-restraints excluded: chain E residue   46 LYS
Chi-restraints excluded: chain E residue   50 VAL
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:    6.9990
   chunk 44 optimal weight:    0.9990
   chunk 39 optimal weight:    3.9990
   chunk 60 optimal weight:   10.0000
   chunk 66 optimal weight:    8.9990
   chunk 78 optimal weight:    4.9990
   chunk 58 optimal weight:   10.0000
   chunk 32 optimal weight:    8.9990
   chunk 4 optimal weight:    0.9980
   chunk 35 optimal weight:    0.9990
   chunk 8 optimal weight:    8.9990
   overall best weight:    2.3988

-------------------------------------------------------------------------------
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
A  22 ASN
E  10 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3375 r_free = 0.3375 target = 0.105631 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3104 r_free = 0.3104 target = 0.086613 restraints weight = 13021.926|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3148 r_free = 0.3148 target = 0.089541 restraints weight = 6255.623|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3175 r_free = 0.3175 target = 0.091484 restraints weight = 4054.166|
|-----------------------------------------------------------------------------|
r_work (final): 0.3159
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8335
moved from start:          0.4662

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.026   6783  Z= 0.154
  Angle     :  0.650   9.187   9240  Z= 0.337
  Chirality :  0.046   0.155   1082
  Planarity :  0.004   0.037   1208
  Dihedral  :  4.884  45.881    962
  Min Nonbonded Distance : 2.464

Molprobity Statistics.
  All-atom Clashscore : 4.06
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.77 %
    Favored  : 94.23 %
  Rotamer:
    Outliers :  5.59 %
    Allowed  : 19.78 %
    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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.90 (0.27), residues: 866
  helix:  1.61 (0.49), residues: 120
  sheet: -1.13 (0.26), residues: 360
  loop : -2.31 (0.27), residues: 386

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP H  50 
 HIS   0.002   0.001   HIS L  38 
 PHE   0.011   0.001   PHE C  96 
 TYR   0.025   0.002   TYR H 105 
 ARG   0.005   0.000   ARG A  24 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03615 (  196)
  hydrogen bonds       : angle       5.03390 (  549)
  SS BOND              : bond        0.00504 (    3)
  SS BOND              : angle       0.89836 (    6)
  covalent geometry    : bond        0.00354 ( 6779)
  covalent geometry    : angle       0.65031 ( 9234)
  Misc. bond           : bond        0.00021 (    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
  268 residues out of total 733 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 41
    poor density    : 227
  time to evaluate  : 0.818 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: H   70 LYS cc_start: 0.9199 (tppp) cc_final: 0.8672 (tppt)
REVERT: H   76 GLU cc_start: 0.7907 (tm-30) cc_final: 0.7546 (tm-30)
REVERT: H  110 ASP cc_start: 0.8091 (t0) cc_final: 0.7534 (t0)
REVERT: H  111 TYR cc_start: 0.8645 (m-10) cc_final: 0.8142 (m-80)
REVERT: L   95 TYR cc_start: 0.9415 (t80) cc_final: 0.9212 (t80)
REVERT: A    2 LYS cc_start: 0.8709 (tttp) cc_final: 0.7826 (mmtt)
REVERT: A  127 GLN cc_start: 0.9007 (mm-40) cc_final: 0.8549 (mp10)
REVERT: B    2 LYS cc_start: 0.9169 (tttp) cc_final: 0.7980 (mmtt)
REVERT: B   27 ASN cc_start: 0.8726 (t0) cc_final: 0.8096 (t0)
REVERT: B   41 VAL cc_start: 0.9132 (t) cc_final: 0.8833 (m)
REVERT: B   77 ASN cc_start: 0.9192 (t0) cc_final: 0.8750 (t0)
REVERT: B  102 ASP cc_start: 0.8337 (p0) cc_final: 0.7921 (p0)
REVERT: C   47 ARG cc_start: 0.8610 (mtm-85) cc_final: 0.8092 (mtp85)
REVERT: C  123 ASP cc_start: 0.8433 (t0) cc_final: 0.8146 (t0)
REVERT: D    2 LYS cc_start: 0.8592 (tttp) cc_final: 0.7704 (mmtt)
REVERT: D    4 GLU cc_start: 0.8215 (mm-30) cc_final: 0.7998 (mm-30)
REVERT: D   13 LYS cc_start: 0.2420 (mttt) cc_final: 0.1019 (ttmt)
REVERT: D   98 GLN cc_start: 0.8626 (tt0) cc_final: 0.8142 (tm-30)
REVERT: D  127 GLN cc_start: 0.9046 (mm110) cc_final: 0.8447 (mm110)
REVERT: E    2 LYS cc_start: 0.8425 (tttp) cc_final: 0.7988 (mmtt)
REVERT: E   13 LYS cc_start: 0.3075 (mttp) cc_final: 0.2289 (mttt)
REVERT: E   34 SER cc_start: 0.8696 (m) cc_final: 0.8440 (t)
REVERT: E   61 ASN cc_start: 0.8449 (m110) cc_final: 0.7675 (p0)
REVERT: E   63 LYS cc_start: 0.8690 (tttt) cc_final: 0.8398 (ttmm)
REVERT: E   83 SER cc_start: 0.8899 (m) cc_final: 0.8407 (t)
REVERT: E  129 ASN cc_start: 0.9029 (m-40) cc_final: 0.8614 (t0)
  outliers start: 41
  outliers final: 39
  residues processed: 251
  average time/residue: 0.2337
  time to fit residues: 72.3767
Evaluate side-chains
  259 residues out of total 733 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 39
    poor density    : 220
  time to evaluate  : 0.769 
-------------------------------------------------------------------------------
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   68 LYS
Chi-restraints excluded: chain H residue  108 TYR
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 L residue  107 LYS
Chi-restraints excluded: chain A residue   41 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  128 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   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  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   69 GLN
Chi-restraints excluded: chain D residue  115 LEU
Chi-restraints excluded: chain D residue  121 LEU
Chi-restraints excluded: chain D residue  128 LEU
Chi-restraints excluded: chain E residue   41 VAL
Chi-restraints excluded: chain E residue   46 LYS
Chi-restraints excluded: chain E residue   50 VAL
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 71 optimal weight:   10.0000
   chunk 63 optimal weight:   10.0000
   chunk 31 optimal weight:    7.9990
   chunk 12 optimal weight:    4.9990
   chunk 66 optimal weight:    7.9990
   chunk 59 optimal weight:    0.9990
   chunk 44 optimal weight:   10.0000
   chunk 42 optimal weight:    0.9990
   chunk 20 optimal weight:    3.9990
   chunk 24 optimal weight:   10.0000
   chunk 41 optimal weight:    0.8980
   overall best weight:    2.3788

-------------------------------------------------------------------------------
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

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3367 r_free = 0.3367 target = 0.105271 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3090 r_free = 0.3090 target = 0.085997 restraints weight = 13168.824|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3134 r_free = 0.3134 target = 0.088946 restraints weight = 6253.234|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3163 r_free = 0.3163 target = 0.090917 restraints weight = 4035.018|
|-----------------------------------------------------------------------------|
r_work (final): 0.3153
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8327
moved from start:          0.4719

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.027   6783  Z= 0.153
  Angle     :  0.656   8.353   9240  Z= 0.342
  Chirality :  0.046   0.156   1082
  Planarity :  0.004   0.036   1208
  Dihedral  :  4.839  45.114    962
  Min Nonbonded Distance : 2.463

Molprobity Statistics.
  All-atom Clashscore : 4.81
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.97 %
    Favored  : 95.03 %
  Rotamer:
    Outliers :  5.59 %
    Allowed  : 21.15 %
    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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.88 (0.27), residues: 866
  helix:  1.63 (0.49), residues: 120
  sheet: -1.14 (0.26), residues: 364
  loop : -2.28 (0.27), residues: 382

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP H  50 
 HIS   0.002   0.001   HIS L  38 
 PHE   0.008   0.001   PHE C  96 
 TYR   0.039   0.002   TYR L  53 
 ARG   0.006   0.001   ARG H 101 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03619 (  196)
  hydrogen bonds       : angle       5.05245 (  549)
  SS BOND              : bond        0.00289 (    3)
  SS BOND              : angle       0.74505 (    6)
  covalent geometry    : bond        0.00354 ( 6779)
  covalent geometry    : angle       0.65592 ( 9234)
  Misc. bond           : bond        0.00022 (    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
  264 residues out of total 733 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 41
    poor density    : 223
  time to evaluate  : 0.805 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: H   70 LYS cc_start: 0.9189 (tppp) cc_final: 0.8648 (tppt)
REVERT: H   76 GLU cc_start: 0.7948 (tm-30) cc_final: 0.7506 (tm-30)
REVERT: H  110 ASP cc_start: 0.8087 (t0) cc_final: 0.7542 (t0)
REVERT: H  111 TYR cc_start: 0.8648 (m-10) cc_final: 0.8157 (m-80)
REVERT: L   95 TYR cc_start: 0.9393 (t80) cc_final: 0.9182 (t80)
REVERT: A    2 LYS cc_start: 0.8712 (tttp) cc_final: 0.7875 (mmtt)
REVERT: A  127 GLN cc_start: 0.9088 (mm-40) cc_final: 0.8632 (mp10)
REVERT: B    2 LYS cc_start: 0.8937 (tttp) cc_final: 0.8126 (mmtt)
REVERT: B   27 ASN cc_start: 0.8730 (t0) cc_final: 0.8091 (t0)
REVERT: B   41 VAL cc_start: 0.9129 (t) cc_final: 0.8833 (m)
REVERT: B   77 ASN cc_start: 0.9204 (t0) cc_final: 0.8772 (t0)
REVERT: B  102 ASP cc_start: 0.8359 (p0) cc_final: 0.7933 (p0)
REVERT: C   47 ARG cc_start: 0.8611 (mtm-85) cc_final: 0.8096 (mtp85)
REVERT: C  123 ASP cc_start: 0.8384 (t0) cc_final: 0.8045 (t0)
REVERT: D    2 LYS cc_start: 0.8614 (tttp) cc_final: 0.7694 (mmtt)
REVERT: D   13 LYS cc_start: 0.2422 (mttt) cc_final: 0.1010 (ttmt)
REVERT: D   61 ASN cc_start: 0.8481 (m-40) cc_final: 0.8261 (m-40)
REVERT: D   98 GLN cc_start: 0.8653 (tt0) cc_final: 0.8154 (tm-30)
REVERT: D  127 GLN cc_start: 0.9062 (mm110) cc_final: 0.8423 (mm110)
REVERT: E    2 LYS cc_start: 0.8367 (tttp) cc_final: 0.7934 (mmtt)
REVERT: E   13 LYS cc_start: 0.3109 (mttp) cc_final: 0.2041 (ttmt)
REVERT: E   61 ASN cc_start: 0.8468 (m110) cc_final: 0.7710 (p0)
REVERT: E   63 LYS cc_start: 0.8742 (tttt) cc_final: 0.8444 (ttmm)
REVERT: E   83 SER cc_start: 0.8859 (m) cc_final: 0.8362 (t)
REVERT: E  129 ASN cc_start: 0.9072 (m-40) cc_final: 0.8620 (t0)
  outliers start: 41
  outliers final: 38
  residues processed: 248
  average time/residue: 0.2375
  time to fit residues: 72.2789
Evaluate side-chains
  252 residues out of total 733 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 38
    poor density    : 214
  time to evaluate  : 0.776 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain H residue    7 LEU
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   68 LYS
Chi-restraints excluded: chain H residue  108 TYR
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   41 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  128 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   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  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  115 LEU
Chi-restraints excluded: chain D residue  128 LEU
Chi-restraints excluded: chain E residue   41 VAL
Chi-restraints excluded: chain E residue   50 VAL
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=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 86
   random chunks:
   chunk 81 optimal weight:    6.9990
   chunk 48 optimal weight:    3.9990
   chunk 82 optimal weight:    0.9990
   chunk 34 optimal weight:    0.7980
   chunk 28 optimal weight:    9.9990
   chunk 43 optimal weight:    3.9990
   chunk 29 optimal weight:    5.9990
   chunk 53 optimal weight:    3.9990
   chunk 22 optimal weight:    4.9990
   chunk 4 optimal weight:    0.9990
   chunk 39 optimal weight:    6.9990
   overall best weight:    2.1588

-------------------------------------------------------------------------------
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  70 ASN
E  10 ASN
E  70 ASN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3275 r_free = 0.3275 target = 0.101181 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.2987 r_free = 0.2987 target = 0.080971 restraints weight = 12924.112|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3031 r_free = 0.3031 target = 0.083911 restraints weight = 6355.479|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 45)----------------|
| r_work = 0.3061 r_free = 0.3061 target = 0.085909 restraints weight = 4122.503|
|-----------------------------------------------------------------------------|
r_work (final): 0.3062
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8242
moved from start:          0.4818

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= 0.148
  Angle     :  0.670   8.864   9240  Z= 0.349
  Chirality :  0.047   0.155   1082
  Planarity :  0.004   0.037   1208
  Dihedral  :  4.687  43.562    962
  Min Nonbonded Distance : 2.458

Molprobity Statistics.
  All-atom Clashscore : 5.33
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.43 %
    Favored  : 94.57 %
  Rotamer:
    Outliers :  5.73 %
    Allowed  : 20.87 %
    Favored  : 73.40 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.83 (0.27), residues: 866
  helix:  1.70 (0.48), residues: 120
  sheet: -1.07 (0.26), residues: 365
  loop : -2.30 (0.27), residues: 381

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP H  50 
 HIS   0.001   0.001   HIS L  38 
 PHE   0.008   0.001   PHE H  98 
 TYR   0.025   0.001   TYR H  35 
 ARG   0.004   0.000   ARG H  85 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03566 (  196)
  hydrogen bonds       : angle       5.01785 (  549)
  SS BOND              : bond        0.00270 (    3)
  SS BOND              : angle       0.63131 (    6)
  covalent geometry    : bond        0.00344 ( 6779)
  covalent geometry    : angle       0.67033 ( 9234)
  Misc. bond           : bond        0.00016 (    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
  269 residues out of total 733 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 42
    poor density    : 227
  time to evaluate  : 0.815 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: H   43 ARG cc_start: 0.7907 (ttm170) cc_final: 0.7707 (ttm170)
REVERT: H   70 LYS cc_start: 0.9134 (tppp) cc_final: 0.8578 (tppt)
REVERT: H   76 GLU cc_start: 0.7898 (tm-30) cc_final: 0.7372 (tm-30)
REVERT: H  110 ASP cc_start: 0.8122 (t0) cc_final: 0.7488 (t0)
REVERT: H  111 TYR cc_start: 0.8633 (m-10) cc_final: 0.8118 (m-80)
REVERT: L   95 TYR cc_start: 0.9419 (t80) cc_final: 0.9218 (t80)
REVERT: A    2 LYS cc_start: 0.8719 (tttp) cc_final: 0.7842 (mmtt)
REVERT: A  127 GLN cc_start: 0.9064 (mm-40) cc_final: 0.8586 (mp10)
REVERT: B    2 LYS cc_start: 0.8925 (tttp) cc_final: 0.8140 (mmtt)
REVERT: B   27 ASN cc_start: 0.8586 (t0) cc_final: 0.7910 (t0)
REVERT: B   41 VAL cc_start: 0.9030 (t) cc_final: 0.8743 (m)
REVERT: B   77 ASN cc_start: 0.9325 (t0) cc_final: 0.8853 (t0)
REVERT: B  102 ASP cc_start: 0.8471 (p0) cc_final: 0.8035 (p0)
REVERT: C   47 ARG cc_start: 0.8578 (mtm-85) cc_final: 0.7980 (mtp85)
REVERT: C  123 ASP cc_start: 0.8443 (t0) cc_final: 0.8107 (t0)
REVERT: D    2 LYS cc_start: 0.8703 (tttp) cc_final: 0.7831 (mmtt)
REVERT: D   13 LYS cc_start: 0.2346 (mttt) cc_final: 0.0936 (ttmt)
REVERT: D   61 ASN cc_start: 0.8500 (m-40) cc_final: 0.8241 (m-40)
REVERT: D   98 GLN cc_start: 0.8784 (tt0) cc_final: 0.8152 (tm-30)
REVERT: D  127 GLN cc_start: 0.8995 (mm110) cc_final: 0.8416 (mm110)
REVERT: E    2 LYS cc_start: 0.8290 (tttp) cc_final: 0.7882 (mmtt)
REVERT: E   13 LYS cc_start: 0.3110 (mttp) cc_final: 0.2108 (ttmt)
REVERT: E   34 SER cc_start: 0.8591 (m) cc_final: 0.8350 (t)
REVERT: E   61 ASN cc_start: 0.8487 (m110) cc_final: 0.7589 (p0)
REVERT: E   63 LYS cc_start: 0.8748 (tttt) cc_final: 0.8386 (ttmm)
REVERT: E  129 ASN cc_start: 0.9035 (m-40) cc_final: 0.8601 (t0)
  outliers start: 42
  outliers final: 41
  residues processed: 253
  average time/residue: 0.2265
  time to fit residues: 70.6691
Evaluate side-chains
  262 residues out of total 733 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 41
    poor density    : 221
  time to evaluate  : 0.717 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain H residue    7 LEU
Chi-restraints excluded: chain H residue    9 GLN
Chi-restraints excluded: chain H residue   14 LEU
Chi-restraints excluded: chain H residue   31 THR
Chi-restraints excluded: chain H residue   37 ILE
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   36 TYR
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   41 VAL
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  128 LEU
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  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  115 LEU
Chi-restraints excluded: chain D residue  128 LEU
Chi-restraints excluded: chain E residue   41 VAL
Chi-restraints excluded: chain E residue   50 VAL
Chi-restraints excluded: chain E residue   70 ASN
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=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 86
   random chunks:
   chunk 34 optimal weight:    2.9990
   chunk 14 optimal weight:    7.9990
   chunk 83 optimal weight:    3.9990
   chunk 62 optimal weight:   10.0000
   chunk 45 optimal weight:    0.7980
   chunk 38 optimal weight:    8.9990
   chunk 21 optimal weight:    4.9990
   chunk 26 optimal weight:    0.5980
   chunk 53 optimal weight:    4.9990
   chunk 55 optimal weight:    5.9990
   chunk 4 optimal weight:    0.9990
   overall best weight:    1.8786

-------------------------------------------------------------------------------
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

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3283 r_free = 0.3283 target = 0.101735 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.2998 r_free = 0.2998 target = 0.081645 restraints weight = 13087.942|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3042 r_free = 0.3042 target = 0.084542 restraints weight = 6518.716|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3071 r_free = 0.3071 target = 0.086537 restraints weight = 4265.779|
|-----------------------------------------------------------------------------|
r_work (final): 0.3070
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8215
moved from start:          0.4866

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   6783  Z= 0.139
  Angle     :  0.679  10.078   9240  Z= 0.349
  Chirality :  0.046   0.152   1082
  Planarity :  0.004   0.036   1208
  Dihedral  :  4.576  41.858    962
  Min Nonbonded Distance : 2.543

Molprobity Statistics.
  All-atom Clashscore : 5.41
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.73 %
    Favored  : 95.27 %
  Rotamer:
    Outliers :  5.46 %
    Allowed  : 21.69 %
    Favored  : 72.85 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.79 (0.27), residues: 866
  helix:  1.76 (0.48), residues: 120
  sheet: -1.01 (0.26), residues: 365
  loop : -2.33 (0.27), residues: 381

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP H  50 
 HIS   0.001   0.001   HIS L  38 
 PHE   0.007   0.001   PHE H  98 
 TYR   0.036   0.002   TYR L  53 
 ARG   0.004   0.000   ARG H  85 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03512 (  196)
  hydrogen bonds       : angle       4.98866 (  549)
  SS BOND              : bond        0.00300 (    3)
  SS BOND              : angle       0.63130 (    6)
  covalent geometry    : bond        0.00322 ( 6779)
  covalent geometry    : angle       0.67884 ( 9234)
  Misc. bond           : bond        0.00012 (    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
  266 residues out of total 733 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 40
    poor density    : 226
  time to evaluate  : 0.717 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: H   70 LYS cc_start: 0.9101 (tppp) cc_final: 0.8556 (tppt)
REVERT: H   76 GLU cc_start: 0.7888 (tm-30) cc_final: 0.7329 (tm-30)
REVERT: H  110 ASP cc_start: 0.8131 (t0) cc_final: 0.7527 (t0)
REVERT: H  111 TYR cc_start: 0.8613 (m-10) cc_final: 0.8094 (m-80)
REVERT: A    2 LYS cc_start: 0.8714 (tttp) cc_final: 0.7759 (mmtt)
REVERT: A  127 GLN cc_start: 0.9074 (mm-40) cc_final: 0.8613 (mp10)
REVERT: B    2 LYS cc_start: 0.8914 (tttp) cc_final: 0.8143 (mmtt)
REVERT: B   27 ASN cc_start: 0.8552 (t0) cc_final: 0.7869 (t0)
REVERT: B   41 VAL cc_start: 0.8991 (t) cc_final: 0.8703 (m)
REVERT: B   77 ASN cc_start: 0.9331 (t0) cc_final: 0.8840 (t0)
REVERT: B  102 ASP cc_start: 0.8473 (p0) cc_final: 0.8035 (p0)
REVERT: C    2 LYS cc_start: 0.4192 (mmmt) cc_final: 0.3938 (mmmt)
REVERT: C   47 ARG cc_start: 0.8567 (mtm-85) cc_final: 0.7952 (mtp85)
REVERT: C  123 ASP cc_start: 0.8446 (t0) cc_final: 0.8122 (t0)
REVERT: D    2 LYS cc_start: 0.8691 (tttp) cc_final: 0.7822 (mmtt)
REVERT: D   13 LYS cc_start: 0.2084 (mttt) cc_final: 0.0721 (ttmt)
REVERT: D   61 ASN cc_start: 0.8564 (m-40) cc_final: 0.8311 (m-40)
REVERT: D   98 GLN cc_start: 0.8796 (tt0) cc_final: 0.8144 (tm-30)
REVERT: D  127 GLN cc_start: 0.8977 (mm110) cc_final: 0.8400 (mm110)
REVERT: E    2 LYS cc_start: 0.8367 (tttp) cc_final: 0.7921 (mmtt)
REVERT: E   10 ASN cc_start: 0.8766 (m110) cc_final: 0.8141 (t0)
REVERT: E   13 LYS cc_start: 0.3112 (mttp) cc_final: 0.2017 (ttmt)
REVERT: E   34 SER cc_start: 0.8575 (m) cc_final: 0.8327 (t)
REVERT: E   61 ASN cc_start: 0.8475 (m110) cc_final: 0.7556 (p0)
REVERT: E   63 LYS cc_start: 0.8738 (tttt) cc_final: 0.8368 (ttmm)
REVERT: E  129 ASN cc_start: 0.9042 (m-40) cc_final: 0.8635 (t0)
  outliers start: 40
  outliers final: 37
  residues processed: 249
  average time/residue: 0.2373
  time to fit residues: 72.5030
Evaluate side-chains
  258 residues out of total 733 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 37
    poor density    : 221
  time to evaluate  : 0.792 
-------------------------------------------------------------------------------
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   31 THR
Chi-restraints excluded: chain H residue   37 ILE
Chi-restraints excluded: chain H residue  103 ASP
Chi-restraints excluded: chain H residue  108 TYR
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 L residue  107 LYS
Chi-restraints excluded: chain A residue   41 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   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  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 D residue  128 LEU
Chi-restraints excluded: chain E residue   41 VAL
Chi-restraints excluded: chain E residue   50 VAL
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=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 86
   random chunks:
   chunk 57 optimal weight:    8.9990
   chunk 10 optimal weight:    4.9990
   chunk 78 optimal weight:    0.0670
   chunk 46 optimal weight:    9.9990
   chunk 41 optimal weight:   10.0000
   chunk 60 optimal weight:    0.9980
   chunk 33 optimal weight:    0.8980
   chunk 26 optimal weight:    0.0060
   chunk 79 optimal weight:    1.9990
   chunk 7 optimal weight:    0.3980
   chunk 80 optimal weight:    0.7980
   overall best weight:    0.4334

-------------------------------------------------------------------------------
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
E  70 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3328 r_free = 0.3328 target = 0.104859 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3045 r_free = 0.3045 target = 0.084619 restraints weight = 12832.119|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3089 r_free = 0.3089 target = 0.087615 restraints weight = 6264.352|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 45)----------------|
| r_work = 0.3119 r_free = 0.3119 target = 0.089671 restraints weight = 4051.881|
|-----------------------------------------------------------------------------|
r_work (final): 0.3116
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8168
moved from start:          0.5080

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   6783  Z= 0.119
  Angle     :  0.663  10.007   9240  Z= 0.337
  Chirality :  0.045   0.147   1082
  Planarity :  0.004   0.035   1208
  Dihedral  :  4.153  33.149    962
  Min Nonbonded Distance : 2.496

Molprobity Statistics.
  All-atom Clashscore : 5.18
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.16 %
    Favored  : 95.84 %
  Rotamer:
    Outliers :  4.77 %
    Allowed  : 22.24 %
    Favored  : 72.99 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.61 (0.27), residues: 866
  helix:  1.91 (0.47), residues: 120
  sheet: -0.78 (0.27), residues: 361
  loop : -2.34 (0.27), residues: 385

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP H 112 
 HIS   0.001   0.001   HIS L  38 
 PHE   0.007   0.001   PHE B  96 
 TYR   0.030   0.001   TYR L  95 
 ARG   0.004   0.000   ARG C  47 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02597 (  196)
  hydrogen bonds       : angle       4.82414 (  549)
  SS BOND              : bond        0.00246 (    3)
  SS BOND              : angle       0.64068 (    6)
  covalent geometry    : bond        0.00267 ( 6779)
  covalent geometry    : angle       0.66261 ( 9234)
  Misc. bond           : bond        0.00006 (    1)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2717.72 seconds
wall clock time: 48 minutes 9.69 seconds (2889.69 seconds total)