Starting phenix.real_space_refine
on Tue Mar  3 16:49:18 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/6vcc_21148/03_2026/6vcc_21148.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/6vcc_21148/03_2026/6vcc_21148.map

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

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

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/6vcc_21148/03_2026/6vcc_21148.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/6vcc_21148/03_2026/6vcc_21148.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/6vcc_21148/03_2026/6vcc_21148.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/6vcc_21148/03_2026/6vcc_21148.map"
  }
  resolution = 3.6
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=  -0.000 sd=   0.011
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      24      5.16       5
     C    4896      2.51       5
     N    1236      2.21       5
     O    1416      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 21 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 7572
  Number of models: 1
  Model: ""
    Number of chains: 12
    Chain: "A"
      Number of atoms: 631
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 78, 631
          Classifications: {'peptide': 78}
          Link IDs: {'PTRANS': 5, 'TRANS': 72}
    Chain: "B"
      Number of atoms: 631
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 78, 631
          Classifications: {'peptide': 78}
          Link IDs: {'PTRANS': 5, 'TRANS': 72}
    Chain: "C"
      Number of atoms: 631
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 78, 631
          Classifications: {'peptide': 78}
          Link IDs: {'PTRANS': 5, 'TRANS': 72}
    Chain: "D"
      Number of atoms: 631
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 78, 631
          Classifications: {'peptide': 78}
          Link IDs: {'PTRANS': 5, 'TRANS': 72}
    Chain: "E"
      Number of atoms: 631
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 78, 631
          Classifications: {'peptide': 78}
          Link IDs: {'PTRANS': 5, 'TRANS': 72}
    Chain: "F"
      Number of atoms: 631
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 78, 631
          Classifications: {'peptide': 78}
          Link IDs: {'PTRANS': 5, 'TRANS': 72}
    Chain: "G"
      Number of atoms: 631
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 78, 631
          Classifications: {'peptide': 78}
          Link IDs: {'PTRANS': 5, 'TRANS': 72}
    Chain: "H"
      Number of atoms: 631
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 78, 631
          Classifications: {'peptide': 78}
          Link IDs: {'PTRANS': 5, 'TRANS': 72}
    Chain: "I"
      Number of atoms: 631
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 78, 631
          Classifications: {'peptide': 78}
          Link IDs: {'PTRANS': 5, 'TRANS': 72}
    Chain: "J"
      Number of atoms: 631
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 78, 631
          Classifications: {'peptide': 78}
          Link IDs: {'PTRANS': 5, 'TRANS': 72}
    Chain: "K"
      Number of atoms: 631
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 78, 631
          Classifications: {'peptide': 78}
          Link IDs: {'PTRANS': 5, 'TRANS': 72}
    Chain: "L"
      Number of atoms: 631
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 78, 631
          Classifications: {'peptide': 78}
          Link IDs: {'PTRANS': 5, 'TRANS': 72}
  Time building chain proxies: 1.77, per 1000 atoms: 0.23
  Number of scatterers: 7572
  At special positions: 0
  Unit cell: (90, 92, 132, 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      24     16.00
     O    1416      8.00
     N    1236      7.00
     C    4896      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 0.73
  Conformation dependent library (CDL) restraints added in 240.5 milliseconds
  

  1824 Ramachandran restraints generated.
    912 Oldfield, 0 Emsley, 912 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1776

  Finding SS restraints...
    Secondary structure from input PDB file:
      21 helices and 8 sheets defined
      15.7% alpha, 26.4% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.17
  Creating SS restraints...
    Processing helix  chain 'A' and resid 39 through 46
      removed outlier: 3.620A  pdb=" N   PHE A  43 " --> pdb=" O   THR A  39 " (cutoff:3.500A)
      removed outlier: 4.148A  pdb=" N   VAL A  46 " --> pdb=" O   ASP A  42 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 80 through 84
      removed outlier: 3.655A  pdb=" N   GLY A  83 " --> pdb=" O   CYS A  80 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 39 through 46
      removed outlier: 3.636A  pdb=" N   PHE B  43 " --> pdb=" O   THR B  39 " (cutoff:3.500A)
      removed outlier: 3.865A  pdb=" N   VAL B  46 " --> pdb=" O   ASP B  42 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 80 through 84
      removed outlier: 3.765A  pdb=" N   GLY B  83 " --> pdb=" O   CYS B  80 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 39 through 46
      removed outlier: 3.750A  pdb=" N   PHE C  43 " --> pdb=" O   THR C  39 " (cutoff:3.500A)
      removed outlier: 3.893A  pdb=" N   VAL C  46 " --> pdb=" O   ASP C  42 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 80 through 84
      removed outlier: 3.609A  pdb=" N   GLY C  83 " --> pdb=" O   CYS C  80 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 39 through 46
      removed outlier: 3.663A  pdb=" N   PHE D  43 " --> pdb=" O   THR D  39 " (cutoff:3.500A)
      removed outlier: 3.819A  pdb=" N   VAL D  46 " --> pdb=" O   ASP D  42 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 39 through 46
      removed outlier: 3.757A  pdb=" N   PHE E  43 " --> pdb=" O   THR E  39 " (cutoff:3.500A)
      removed outlier: 3.901A  pdb=" N   VAL E  46 " --> pdb=" O   ASP E  42 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 39 through 46
      removed outlier: 3.587A  pdb=" N   PHE F  43 " --> pdb=" O   THR F  39 " (cutoff:3.500A)
      removed outlier: 4.102A  pdb=" N   VAL F  46 " --> pdb=" O   ASP F  42 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 80 through 84
      removed outlier: 3.598A  pdb=" N   GLY F  83 " --> pdb=" O   CYS F  80 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 39 through 48
      removed outlier: 3.867A  pdb=" N   VAL G  46 " --> pdb=" O   ASP G  42 " (cutoff:3.500A)
      removed outlier: 3.815A  pdb=" N   LEU G  47 " --> pdb=" O   PHE G  43 " (cutoff:3.500A)
      removed outlier: 3.789A  pdb=" N   GLN G  48 " --> pdb=" O   LYS G  44 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 80 through 84
      removed outlier: 3.800A  pdb=" N   GLY G  83 " --> pdb=" O   CYS G  80 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 39 through 48
      removed outlier: 3.946A  pdb=" N   VAL H  46 " --> pdb=" O   ASP H  42 " (cutoff:3.500A)
      removed outlier: 3.974A  pdb=" N   LEU H  47 " --> pdb=" O   PHE H  43 " (cutoff:3.500A)
      removed outlier: 3.887A  pdb=" N   GLN H  48 " --> pdb=" O   LYS H  44 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 80 through 84
      removed outlier: 3.529A  pdb=" N   GLY H  83 " --> pdb=" O   CYS H  80 " (cutoff:3.500A)
    Processing helix  chain 'I' and resid 39 through 45
    Processing helix  chain 'I' and resid 80 through 84
      removed outlier: 3.575A  pdb=" N   GLY I  83 " --> pdb=" O   CYS I  80 " (cutoff:3.500A)
    Processing helix  chain 'J' and resid 39 through 48
      removed outlier: 3.921A  pdb=" N   VAL J  46 " --> pdb=" O   ASP J  42 " (cutoff:3.500A)
      removed outlier: 3.960A  pdb=" N   LEU J  47 " --> pdb=" O   PHE J  43 " (cutoff:3.500A)
      removed outlier: 3.859A  pdb=" N   GLN J  48 " --> pdb=" O   LYS J  44 " (cutoff:3.500A)
    Processing helix  chain 'J' and resid 80 through 84
      removed outlier: 3.527A  pdb=" N   GLY J  83 " --> pdb=" O   CYS J  80 " (cutoff:3.500A)
    Processing helix  chain 'K' and resid 39 through 45
    Processing helix  chain 'K' and resid 80 through 84
      removed outlier: 3.559A  pdb=" N   GLY K  83 " --> pdb=" O   CYS K  80 " (cutoff:3.500A)
    Processing helix  chain 'L' and resid 39 through 48
      removed outlier: 3.895A  pdb=" N   VAL L  46 " --> pdb=" O   ASP L  42 " (cutoff:3.500A)
      removed outlier: 3.778A  pdb=" N   LEU L  47 " --> pdb=" O   PHE L  43 " (cutoff:3.500A)
      removed outlier: 3.784A  pdb=" N   GLN L  48 " --> pdb=" O   LYS L  44 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 65 through 70
      removed outlier: 5.164A  pdb=" N   VAL A  86 " --> pdb=" O   LYS A  58 " (cutoff:3.500A)
      removed outlier: 7.796A  pdb=" N   SER A  87 " --> pdb=" O   LYS A  15 " (cutoff:3.500A)
      removed outlier: 6.677A  pdb=" N   ILE A  17 " --> pdb=" O   SER A  87 " (cutoff:3.500A)
      removed outlier: 7.974A  pdb=" N   LEU A  89 " --> pdb=" O   ILE A  17 " (cutoff:3.500A)
      removed outlier: 6.916A  pdb=" N   LEU A  28 " --> pdb=" O   GLU B  70 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'B' and resid 14 through 18
      removed outlier: 6.963A  pdb=" N   LEU B  28 " --> pdb=" O   GLU C  70 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'C' and resid 14 through 16
      removed outlier: 6.940A  pdb=" N   LEU C  28 " --> pdb=" O   GLU D  70 " (cutoff:3.500A)
      removed outlier: 5.259A  pdb=" N   VAL D  86 " --> pdb=" O   LYS D  58 " (cutoff:3.500A)
      removed outlier: 7.889A  pdb=" N   SER D  87 " --> pdb=" O   LYS D  15 " (cutoff:3.500A)
      removed outlier: 6.589A  pdb=" N   ILE D  17 " --> pdb=" O   SER D  87 " (cutoff:3.500A)
      removed outlier: 3.654A  pdb=" N   TYR D  18 " --> pdb=" O   TYR D  27 " (cutoff:3.500A)
      removed outlier: 6.879A  pdb=" N   LEU D  28 " --> pdb=" O   GLU E  70 " (cutoff:3.500A)
      removed outlier: 5.085A  pdb=" N   VAL E  86 " --> pdb=" O   LYS E  58 " (cutoff:3.500A)
      removed outlier: 7.766A  pdb=" N   SER E  87 " --> pdb=" O   LYS E  15 " (cutoff:3.500A)
      removed outlier: 6.747A  pdb=" N   ILE E  17 " --> pdb=" O   SER E  87 " (cutoff:3.500A)
      removed outlier: 3.539A  pdb=" N   TYR E  18 " --> pdb=" O   TYR E  27 " (cutoff:3.500A)
      removed outlier: 6.929A  pdb=" N   LEU E  28 " --> pdb=" O   GLU F  70 " (cutoff:3.500A)
      removed outlier: 5.190A  pdb=" N   VAL F  86 " --> pdb=" O   LYS F  58 " (cutoff:3.500A)
      removed outlier: 8.010A  pdb=" N   SER F  87 " --> pdb=" O   LYS F  15 " (cutoff:3.500A)
      removed outlier: 6.874A  pdb=" N   ILE F  17 " --> pdb=" O   SER F  87 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'G' and resid 14 through 18
      removed outlier: 3.543A  pdb=" N   THR G  14 " --> pdb=" O   ILE G  31 " (cutoff:3.500A)
      removed outlier: 3.515A  pdb=" N   VAL G  29 " --> pdb=" O   VAL G  16 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'G' and resid 87 through 89
      removed outlier: 4.586A  pdb=" N   LYS H  30 " --> pdb=" O   GLU G  70 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'H' and resid 17 through 18
      removed outlier: 6.794A  pdb=" N   ILE H  17 " --> pdb=" O   SER H  87 " (cutoff:3.500A)
      removed outlier: 7.999A  pdb=" N   LEU H  89 " --> pdb=" O   ILE H  17 " (cutoff:3.500A)
      removed outlier: 5.111A  pdb=" N   VAL H  86 " --> pdb=" O   LYS H  58 " (cutoff:3.500A)
      removed outlier: 4.667A  pdb=" N   LYS I  30 " --> pdb=" O   GLU H  70 " (cutoff:3.500A)
      removed outlier: 3.506A  pdb=" N   TYR I  18 " --> pdb=" O   TYR I  27 " (cutoff:3.500A)
      removed outlier: 3.650A  pdb=" N   THR I  14 " --> pdb=" O   ILE I  31 " (cutoff:3.500A)
      removed outlier: 7.525A  pdb=" N   SER I  87 " --> pdb=" O   LYS I  15 " (cutoff:3.500A)
      removed outlier: 6.786A  pdb=" N   ILE I  17 " --> pdb=" O   SER I  87 " (cutoff:3.500A)
      removed outlier: 8.003A  pdb=" N   LEU I  89 " --> pdb=" O   ILE I  17 " (cutoff:3.500A)
      removed outlier: 5.263A  pdb=" N   VAL I  86 " --> pdb=" O   LYS I  58 " (cutoff:3.500A)
      removed outlier: 4.681A  pdb=" N   LYS J  30 " --> pdb=" O   GLU I  70 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'J' and resid 17 through 18
      removed outlier: 6.863A  pdb=" N   ILE J  17 " --> pdb=" O   SER J  87 " (cutoff:3.500A)
      removed outlier: 8.037A  pdb=" N   LEU J  89 " --> pdb=" O   ILE J  17 " (cutoff:3.500A)
      removed outlier: 5.223A  pdb=" N   VAL J  86 " --> pdb=" O   LYS J  58 " (cutoff:3.500A)
      removed outlier: 4.808A  pdb=" N   LYS K  30 " --> pdb=" O   GLU J  70 " (cutoff:3.500A)
      removed outlier: 3.584A  pdb=" N   TYR K  18 " --> pdb=" O   TYR K  27 " (cutoff:3.500A)
      removed outlier: 3.621A  pdb=" N   THR K  14 " --> pdb=" O   ILE K  31 " (cutoff:3.500A)
      removed outlier: 7.658A  pdb=" N   SER K  87 " --> pdb=" O   LYS K  15 " (cutoff:3.500A)
      removed outlier: 6.691A  pdb=" N   ILE K  17 " --> pdb=" O   SER K  87 " (cutoff:3.500A)
      removed outlier: 7.864A  pdb=" N   LEU K  89 " --> pdb=" O   ILE K  17 " (cutoff:3.500A)
      removed outlier: 5.146A  pdb=" N   VAL K  86 " --> pdb=" O   LYS K  58 " (cutoff:3.500A)
      removed outlier: 4.651A  pdb=" N   LYS L  30 " --> pdb=" O   GLU K  70 " (cutoff:3.500A)
      removed outlier: 3.548A  pdb=" N   THR L  14 " --> pdb=" O   ILE L  31 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'L' and resid 17 through 18
      removed outlier: 6.658A  pdb=" N   ILE L  17 " --> pdb=" O   SER L  87 " (cutoff:3.500A)
      removed outlier: 7.816A  pdb=" N   LEU L  89 " --> pdb=" O   ILE L  17 " (cutoff:3.500A)
      removed outlier: 5.156A  pdb=" N   VAL L  86 " --> pdb=" O   LYS L  58 " (cutoff:3.500A)

    203 hydrogen bonds defined for protein.
    489 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 0.79

  Time building geometry restraints manager: 0.96 seconds

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

  Histogram of bond lengths:
        1.23 -     1.34: 2431
        1.34 -     1.46: 1687
        1.46 -     1.58: 3598
        1.58 -     1.69: 0
        1.69 -     1.81: 36
  Bond restraints: 7752
  Sorted by residual:
  bond pdb=" N   LYS L  54 "
       pdb=" CA  LYS L  54 "
    ideal  model  delta    sigma   weight residual
    1.459  1.484 -0.024 1.23e-02 6.61e+03 3.96e+00
  bond pdb=" N   GLN F  48 "
       pdb=" CA  GLN F  48 "
    ideal  model  delta    sigma   weight residual
    1.460  1.482 -0.022 1.54e-02 4.22e+03 2.06e+00
  bond pdb=" C   VAL A  33 "
       pdb=" N   PRO A  34 "
    ideal  model  delta    sigma   weight residual
    1.326  1.345 -0.019 1.44e-02 4.82e+03 1.73e+00
  bond pdb=" C   VAL B  33 "
       pdb=" N   PRO B  34 "
    ideal  model  delta    sigma   weight residual
    1.326  1.344 -0.018 1.44e-02 4.82e+03 1.51e+00
  bond pdb=" CA  GLN F  48 "
       pdb=" CB  GLN F  48 "
    ideal  model  delta    sigma   weight residual
    1.527  1.546 -0.019 1.70e-02 3.46e+03 1.24e+00
  ... (remaining 7747 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.27: 9856
        1.27 -     2.53: 526
        2.53 -     3.80: 91
        3.80 -     5.06: 23
        5.06 -     6.33: 4
  Bond angle restraints: 10500
  Sorted by residual:
  angle pdb=" C   LEU F  47 "
        pdb=" N   GLN F  48 "
        pdb=" CA  GLN F  48 "
      ideal   model   delta    sigma   weight residual
     122.46  127.44   -4.98 1.41e+00 5.03e-01 1.25e+01
  angle pdb=" CA  GLN F  48 "
        pdb=" CB  GLN F  48 "
        pdb=" CG  GLN F  48 "
      ideal   model   delta    sigma   weight residual
     114.10  120.26   -6.16 2.00e+00 2.50e-01 9.50e+00
  angle pdb=" N   VAL B  16 "
        pdb=" CA  VAL B  16 "
        pdb=" C   VAL B  16 "
      ideal   model   delta    sigma   weight residual
     106.55  110.06   -3.51 1.45e+00 4.76e-01 5.86e+00
  angle pdb=" C   LEU H  89 "
        pdb=" N   VAL H  90 "
        pdb=" CA  VAL H  90 "
      ideal   model   delta    sigma   weight residual
     121.70  125.73   -4.03 1.80e+00 3.09e-01 5.01e+00
  angle pdb=" C   LEU J  89 "
        pdb=" N   VAL J  90 "
        pdb=" CA  VAL J  90 "
      ideal   model   delta    sigma   weight residual
     121.70  125.70   -4.00 1.80e+00 3.09e-01 4.94e+00
  ... (remaining 10495 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.65: 4277
       17.65 -    35.30: 347
       35.30 -    52.95: 47
       52.95 -    70.60: 4
       70.60 -    88.24: 5
  Dihedral angle restraints: 4680
    sinusoidal: 1944
      harmonic: 2736
  Sorted by residual:
  dihedral pdb=" CB  GLU H  24 "
           pdb=" CG  GLU H  24 "
           pdb=" CD  GLU H  24 "
           pdb=" OE1 GLU H  24 "
      ideal   model   delta sinusoidal    sigma   weight residual
       0.00   88.24  -88.24     1      3.00e+01 1.11e-03 1.03e+01
  dihedral pdb=" CB  GLU I  24 "
           pdb=" CG  GLU I  24 "
           pdb=" CD  GLU I  24 "
           pdb=" OE1 GLU I  24 "
      ideal   model   delta sinusoidal    sigma   weight residual
       0.00   88.11  -88.11     1      3.00e+01 1.11e-03 1.03e+01
  dihedral pdb=" CA  ASP D  61 "
           pdb=" CB  ASP D  61 "
           pdb=" CG  ASP D  61 "
           pdb=" OD1 ASP D  61 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -30.00  -80.47   50.47     1      2.00e+01 2.50e-03 8.72e+00
  ... (remaining 4677 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.039: 684
       0.039 -    0.078: 292
       0.078 -    0.118: 135
       0.118 -    0.157: 31
       0.157 -    0.196: 10
  Chirality restraints: 1152
  Sorted by residual:
  chirality pdb=" CB  ILE F  38 "
            pdb=" CA  ILE F  38 "
            pdb=" CG1 ILE F  38 "
            pdb=" CG2 ILE F  38 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.45    0.20 2.00e-01 2.50e+01 9.58e-01
  chirality pdb=" CB  ILE A  38 "
            pdb=" CA  ILE A  38 "
            pdb=" CG1 ILE A  38 "
            pdb=" CG2 ILE A  38 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.45    0.19 2.00e-01 2.50e+01 9.26e-01
  chirality pdb=" CB  ILE E  38 "
            pdb=" CA  ILE E  38 "
            pdb=" CG1 ILE E  38 "
            pdb=" CG2 ILE E  38 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.45    0.19 2.00e-01 2.50e+01 9.23e-01
  ... (remaining 1149 not shown)

  Planarity restraints: 1356
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   VAL C  33 "    0.030 5.00e-02 4.00e+02   4.60e-02 3.39e+00
        pdb=" N   PRO C  34 "   -0.080 5.00e-02 4.00e+02
        pdb=" CA  PRO C  34 "    0.024 5.00e-02 4.00e+02
        pdb=" CD  PRO C  34 "    0.026 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   VAL H  33 "   -0.030 5.00e-02 4.00e+02   4.50e-02 3.25e+00
        pdb=" N   PRO H  34 "    0.078 5.00e-02 4.00e+02
        pdb=" CA  PRO H  34 "   -0.023 5.00e-02 4.00e+02
        pdb=" CD  PRO H  34 "   -0.025 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CD  ARG H  77 "    0.108 9.50e-02 1.11e+02   5.00e-02 3.19e+00
        pdb=" NE  ARG H  77 "    0.001 2.00e-02 2.50e+03
        pdb=" CZ  ARG H  77 "   -0.024 2.00e-02 2.50e+03
        pdb=" NH1 ARG H  77 "    0.006 2.00e-02 2.50e+03
        pdb=" NH2 ARG H  77 "    0.012 2.00e-02 2.50e+03
  ... (remaining 1353 not shown)

  Histogram of nonbonded interaction distances:
        2.25 -     2.78: 1573
        2.78 -     3.31: 6085
        3.31 -     3.84: 12354
        3.84 -     4.37: 13207
        4.37 -     4.90: 24311
  Nonbonded interactions: 57530
  Sorted by model distance:
  nonbonded pdb=" ND2 ASN D  82 "
            pdb=" OD1 ASP I  63 "
     model   vdw
     2.253 3.120
  nonbonded pdb=" OD1 ASP E  63 "
            pdb=" ND2 ASN J  82 "
     model   vdw
     2.273 3.120
  nonbonded pdb=" OD1 ASP D  63 "
            pdb=" ND2 ASN I  82 "
     model   vdw
     2.425 3.120
  nonbonded pdb=" ND2 ASN E  82 "
            pdb=" OD1 ASP J  63 "
     model   vdw
     2.433 3.120
  nonbonded pdb=" OD1 ASP B  63 "
            pdb=" ND2 ASN G  82 "
     model   vdw
     2.442 3.120
  ... (remaining 57525 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.00
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'B'
  selection = chain 'C'
  selection = chain 'D'
  selection = chain 'E'
  selection = chain 'F'
  selection = chain 'G'
  selection = chain 'H'
  selection = chain 'I'
  selection = chain 'J'
  selection = chain 'K'
  selection = chain 'L'
}

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:             0.220
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.010
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.140
  Check model and map are aligned:         0.030
  Set scattering table:                    0.020
  Process input model:                     7.830
  Find NCS groups from input model:        0.100
  Set up NCS constraints:                  0.010
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.250
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:    9.610
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6621
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      :  0.004   0.036   7752  Z= 0.169
  Angle     :  0.664   6.330  10500  Z= 0.376
  Chirality :  0.054   0.196   1152
  Planarity :  0.006   0.050   1356
  Dihedral  : 12.504  88.244   2904
  Min Nonbonded Distance : 2.253

Molprobity Statistics.
  All-atom Clashscore : 4.58
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.62 %
    Favored  : 96.38 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  9.17 %
    Favored  : 90.83 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -4.54 (0.24), residues: 912
  helix: -3.99 (0.12), residues: 72
  sheet: -3.22 (0.23), residues: 360
  loop : -2.61 (0.27), residues: 480

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.023   0.000   ARG H  77 
 TYR   0.015   0.002   TYR D  18 
 PHE   0.008   0.001   PHE E  64 
 TRP   0.007   0.001   TRP C  88 
 HIS   0.004   0.002   HIS J  19 

Details of bonding type rmsd
  covalent geometry    : bond        0.00360 ( 7752)
  covalent geometry    : angle       0.66413 (10500)
  hydrogen bonds       : bond        0.27340 (  203)
  hydrogen bonds       : angle      10.65453 (  489)

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

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

  1824 Ramachandran restraints generated.
    912 Oldfield, 0 Emsley, 912 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1824 Ramachandran restraints generated.
    912 Oldfield, 0 Emsley, 912 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  228 residues out of total 840 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 228
  time to evaluate  : 0.267 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   54 LYS cc_start: 0.7152 (mtpp) cc_final: 0.6887 (mmtt)
REVERT: B   70 GLU cc_start: 0.7086 (tt0) cc_final: 0.6733 (tt0)
REVERT: C   23 GLU cc_start: 0.6398 (mt-10) cc_final: 0.6171 (mt-10)
REVERT: D   15 LYS cc_start: 0.7854 (mttt) cc_final: 0.7217 (mmtt)
REVERT: D   23 GLU cc_start: 0.6388 (mt-10) cc_final: 0.6174 (mt-10)
REVERT: D   54 LYS cc_start: 0.7453 (mtpp) cc_final: 0.7117 (mtpt)
REVERT: D   55 TYR cc_start: 0.7498 (m-80) cc_final: 0.7077 (m-80)
REVERT: E   54 LYS cc_start: 0.7143 (mtpp) cc_final: 0.6725 (mtmm)
REVERT: F   66 VAL cc_start: 0.8090 (m) cc_final: 0.7837 (m)
REVERT: H   20 LEU cc_start: 0.8541 (mp) cc_final: 0.8293 (mt)
REVERT: H   54 LYS cc_start: 0.7945 (mmtt) cc_final: 0.7695 (mmtm)
REVERT: I   72 SER cc_start: 0.7102 (m) cc_final: 0.6847 (p)
REVERT: J   60 MET cc_start: 0.8315 (tpp) cc_final: 0.8097 (tpp)
REVERT: K   49 ARG cc_start: 0.6228 (mmm160) cc_final: 0.5992 (mmp80)
REVERT: K   69 GLU cc_start: 0.6371 (pt0) cc_final: 0.5998 (pt0)
REVERT: K   74 ASP cc_start: 0.6733 (m-30) cc_final: 0.6382 (p0)
REVERT: L   34 PRO cc_start: 0.6822 (Cg_endo) cc_final: 0.6462 (Cg_exo)
  outliers start: 0
  outliers final: 0
  residues processed: 228
  average time/residue: 0.1106
  time to fit residues: 32.0562
Evaluate side-chains
  184 residues out of total 840 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 184
  time to evaluate  : 0.289 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 84
   random chunks:
   chunk 49 optimal weight:    6.9990
   chunk 53 optimal weight:    8.9990
   chunk 5 optimal weight:   10.0000
   chunk 33 optimal weight:    6.9990
   chunk 65 optimal weight:    9.9990
   chunk 62 optimal weight:    9.9990
   chunk 51 optimal weight:    0.4980
   chunk 38 optimal weight:    4.9990
   chunk 61 optimal weight:    0.9990
   chunk 45 optimal weight:    7.9990
   chunk 74 optimal weight:    2.9990
   overall best weight:    3.2988

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

Flipped N/Q/H residues before XYZ refinement:
** E  19 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
G  62 GLN
G  82 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4378 r_free = 0.4378 target = 0.218557 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.4057 r_free = 0.4057 target = 0.185455 restraints weight = 7541.638|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.4050 r_free = 0.4050 target = 0.185959 restraints weight = 6256.550|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.4071 r_free = 0.4071 target = 0.188406 restraints weight = 5654.352|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.4106 r_free = 0.4106 target = 0.192180 restraints weight = 4773.018|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.4109 r_free = 0.4109 target = 0.192513 restraints weight = 3957.525|
|-----------------------------------------------------------------------------|
r_work (final): 0.3903
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7021
moved from start:          0.3306

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.049   7752  Z= 0.215
  Angle     :  0.646   9.329  10500  Z= 0.316
  Chirality :  0.051   0.173   1152
  Planarity :  0.005   0.051   1356
  Dihedral  :  4.399  13.013   1008
  Min Nonbonded Distance : 2.499

Molprobity Statistics.
  All-atom Clashscore : 9.09
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.29 %
    Favored  : 96.71 %
  Rotamer:
    Outliers :  3.81 %
    Allowed  : 14.40 %
    Favored  : 81.79 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -3.94 (0.25), residues: 912
  helix: -1.50 (0.39), residues: 72
  sheet: -3.05 (0.24), residues: 360
  loop : -2.35 (0.26), residues: 480

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG L  84 
 TYR   0.017   0.002   TYR B  27 
 PHE   0.016   0.002   PHE G  57 
 TRP   0.007   0.002   TRP A  88 
 HIS   0.006   0.003   HIS F  19 

Details of bonding type rmsd
  covalent geometry    : bond        0.00486 ( 7752)
  covalent geometry    : angle       0.64624 (10500)
  hydrogen bonds       : bond        0.03818 (  203)
  hydrogen bonds       : angle       7.08985 (  489)

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

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

  1824 Ramachandran restraints generated.
    912 Oldfield, 0 Emsley, 912 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1824 Ramachandran restraints generated.
    912 Oldfield, 0 Emsley, 912 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  234 residues out of total 840 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 202
  time to evaluate  : 0.275 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   58 LYS cc_start: 0.8087 (tttt) cc_final: 0.7764 (tttp)
REVERT: D   54 LYS cc_start: 0.7575 (mtpp) cc_final: 0.7216 (mtpt)
REVERT: D   70 GLU cc_start: 0.5529 (tt0) cc_final: 0.5112 (tt0)
  outliers start: 32
  outliers final: 19
  residues processed: 221
  average time/residue: 0.1079
  time to fit residues: 30.3174
Evaluate side-chains
  204 residues out of total 840 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 185
  time to evaluate  : 0.309 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   16 VAL
Chi-restraints excluded: chain C residue   17 ILE
Chi-restraints excluded: chain C residue   25 THR
Chi-restraints excluded: chain C residue   39 THR
Chi-restraints excluded: chain C residue   90 VAL
Chi-restraints excluded: chain D residue   16 VAL
Chi-restraints excluded: chain D residue   25 THR
Chi-restraints excluded: chain E residue   17 ILE
Chi-restraints excluded: chain F residue   17 ILE
Chi-restraints excluded: chain G residue   17 ILE
Chi-restraints excluded: chain G residue   38 ILE
Chi-restraints excluded: chain G residue   90 VAL
Chi-restraints excluded: chain H residue   17 ILE
Chi-restraints excluded: chain I residue   17 ILE
Chi-restraints excluded: chain I residue   33 VAL
Chi-restraints excluded: chain J residue   17 ILE
Chi-restraints excluded: chain K residue   17 ILE
Chi-restraints excluded: chain K residue   39 THR
Chi-restraints excluded: chain L residue   85 VAL
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 84
   random chunks:
   chunk 75 optimal weight:    2.9990
   chunk 36 optimal weight:    6.9990
   chunk 66 optimal weight:    7.9990
   chunk 69 optimal weight:   10.0000
   chunk 60 optimal weight:    0.8980
   chunk 46 optimal weight:    9.9990
   chunk 12 optimal weight:    3.9990
   chunk 0 optimal weight:   10.0000
   chunk 43 optimal weight:   10.0000
   chunk 44 optimal weight:   10.0000
   chunk 58 optimal weight:    7.9990
   overall best weight:    4.5788

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

Flipped N/Q/H residues before XYZ refinement:
** E  19 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4303 r_free = 0.4303 target = 0.209839 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3936 r_free = 0.3936 target = 0.174855 restraints weight = 7425.000|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3958 r_free = 0.3958 target = 0.179015 restraints weight = 6037.273|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.3997 r_free = 0.3997 target = 0.182150 restraints weight = 4894.759|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.4009 r_free = 0.4009 target = 0.183378 restraints weight = 4166.947|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 31)----------------|
| r_work = 0.4028 r_free = 0.4028 target = 0.185375 restraints weight = 3766.047|
|-----------------------------------------------------------------------------|
r_work (final): 0.3814
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7118
moved from start:          0.4637

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.047   7752  Z= 0.262
  Angle     :  0.678   9.759  10500  Z= 0.328
  Chirality :  0.053   0.202   1152
  Planarity :  0.005   0.053   1356
  Dihedral  :  4.873  16.152   1008
  Min Nonbonded Distance : 2.529

Molprobity Statistics.
  All-atom Clashscore : 11.08
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.93 %
    Favored  : 95.07 %
  Rotamer:
    Outliers :  4.17 %
    Allowed  : 18.10 %
    Favored  : 77.74 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -3.50 (0.26), residues: 912
  helix: -0.14 (0.55), residues: 84
  sheet: -2.85 (0.24), residues: 360
  loop : -2.21 (0.27), residues: 468

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.001   ARG L  84 
 TYR   0.015   0.002   TYR G  55 
 PHE   0.017   0.002   PHE G  57 
 TRP   0.011   0.002   TRP I  88 
 HIS   0.006   0.003   HIS A  19 

Details of bonding type rmsd
  covalent geometry    : bond        0.00618 ( 7752)
  covalent geometry    : angle       0.67798 (10500)
  hydrogen bonds       : bond        0.04002 (  203)
  hydrogen bonds       : angle       7.20089 (  489)

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

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

  1824 Ramachandran restraints generated.
    912 Oldfield, 0 Emsley, 912 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1824 Ramachandran restraints generated.
    912 Oldfield, 0 Emsley, 912 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  235 residues out of total 840 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 200
  time to evaluate  : 0.294 
Fit side-chains
   revert: symmetry clash
REVERT: B   58 LYS cc_start: 0.8145 (tttt) cc_final: 0.7832 (tttp)
REVERT: C   23 GLU cc_start: 0.6683 (mt-10) cc_final: 0.6467 (mt-10)
REVERT: D   15 LYS cc_start: 0.8381 (mttt) cc_final: 0.7811 (ptmt)
REVERT: D   54 LYS cc_start: 0.7706 (mtpp) cc_final: 0.7325 (mtpt)
REVERT: F   64 PHE cc_start: 0.8151 (m-80) cc_final: 0.7921 (m-80)
REVERT: K   54 LYS cc_start: 0.8285 (mmmt) cc_final: 0.8057 (mmmt)
REVERT: L   47 LEU cc_start: 0.8452 (mp) cc_final: 0.8218 (tp)
  outliers start: 35
  outliers final: 27
  residues processed: 221
  average time/residue: 0.1093
  time to fit residues: 30.5519
Evaluate side-chains
  219 residues out of total 840 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 192
  time to evaluate  : 0.228 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   16 VAL
Chi-restraints excluded: chain A residue   67 VAL
Chi-restraints excluded: chain B residue   82 ASN
Chi-restraints excluded: chain C residue   17 ILE
Chi-restraints excluded: chain C residue   25 THR
Chi-restraints excluded: chain C residue   39 THR
Chi-restraints excluded: chain C residue   90 VAL
Chi-restraints excluded: chain D residue   16 VAL
Chi-restraints excluded: chain D residue   25 THR
Chi-restraints excluded: chain D residue   90 VAL
Chi-restraints excluded: chain E residue   17 ILE
Chi-restraints excluded: chain F residue   17 ILE
Chi-restraints excluded: chain F residue   29 VAL
Chi-restraints excluded: chain G residue   17 ILE
Chi-restraints excluded: chain G residue   38 ILE
Chi-restraints excluded: chain G residue   90 VAL
Chi-restraints excluded: chain H residue   17 ILE
Chi-restraints excluded: chain I residue   17 ILE
Chi-restraints excluded: chain I residue   33 VAL
Chi-restraints excluded: chain I residue   39 THR
Chi-restraints excluded: chain I residue   74 ASP
Chi-restraints excluded: chain J residue   17 ILE
Chi-restraints excluded: chain J residue   25 THR
Chi-restraints excluded: chain K residue   16 VAL
Chi-restraints excluded: chain K residue   17 ILE
Chi-restraints excluded: chain K residue   39 THR
Chi-restraints excluded: chain L residue   85 VAL
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 84
   random chunks:
   chunk 29 optimal weight:    0.2980
   chunk 59 optimal weight:    0.2980
   chunk 19 optimal weight:    5.9990
   chunk 5 optimal weight:   10.0000
   chunk 28 optimal weight:    3.9990
   chunk 30 optimal weight:   30.0000
   chunk 53 optimal weight:    1.9990
   chunk 71 optimal weight:    0.0070
   chunk 27 optimal weight:    5.9990
   chunk 8 optimal weight:    3.9990
   chunk 1 optimal weight:    4.9990
   overall best weight:    1.3202

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

Flipped N/Q/H residues before XYZ refinement:
E  19 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4330 r_free = 0.4330 target = 0.213648 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.4000 r_free = 0.4000 target = 0.180632 restraints weight = 7526.645|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 41)----------------|
| r_work = 0.4047 r_free = 0.4047 target = 0.185340 restraints weight = 5582.523|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.4077 r_free = 0.4077 target = 0.188487 restraints weight = 4483.899|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 36)----------------|
| r_work = 0.4102 r_free = 0.4102 target = 0.190929 restraints weight = 3794.553|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 25)----------------|
| r_work = 0.4112 r_free = 0.4112 target = 0.192001 restraints weight = 3317.607|
|-----------------------------------------------------------------------------|
r_work (final): 0.3936
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7012
moved from start:          0.4788

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.027   7752  Z= 0.115
  Angle     :  0.556   8.570  10500  Z= 0.269
  Chirality :  0.049   0.165   1152
  Planarity :  0.004   0.042   1356
  Dihedral  :  4.218  15.121   1008
  Min Nonbonded Distance : 2.554

Molprobity Statistics.
  All-atom Clashscore : 9.69
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.52 %
    Favored  : 97.48 %
  Rotamer:
    Outliers :  2.98 %
    Allowed  : 19.52 %
    Favored  : 77.50 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.98 (0.27), residues: 912
  helix:  0.46 (0.59), residues: 84
  sheet: -2.38 (0.25), residues: 348
  loop : -2.06 (0.28), residues: 480

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG K  49 
 TYR   0.012   0.001   TYR B  27 
 PHE   0.020   0.001   PHE L  64 
 TRP   0.011   0.001   TRP A  88 
 HIS   0.003   0.001   HIS D  19 

Details of bonding type rmsd
  covalent geometry    : bond        0.00264 ( 7752)
  covalent geometry    : angle       0.55602 (10500)
  hydrogen bonds       : bond        0.02839 (  203)
  hydrogen bonds       : angle       6.57295 (  489)

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

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

  1824 Ramachandran restraints generated.
    912 Oldfield, 0 Emsley, 912 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1824 Ramachandran restraints generated.
    912 Oldfield, 0 Emsley, 912 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  218 residues out of total 840 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 193
  time to evaluate  : 0.278 
Fit side-chains
   revert: symmetry clash
REVERT: B   58 LYS cc_start: 0.7945 (tttt) cc_final: 0.7591 (ttmt)
REVERT: C   23 GLU cc_start: 0.6529 (mt-10) cc_final: 0.6315 (mt-10)
REVERT: D   15 LYS cc_start: 0.8168 (mttt) cc_final: 0.7688 (mttt)
REVERT: D   46 VAL cc_start: 0.7783 (m) cc_final: 0.7182 (p)
REVERT: D   54 LYS cc_start: 0.7772 (mtpp) cc_final: 0.7450 (mtpt)
REVERT: E   54 LYS cc_start: 0.7691 (mmmt) cc_final: 0.6594 (mptt)
REVERT: F   27 TYR cc_start: 0.7207 (m-80) cc_final: 0.6016 (m-80)
REVERT: F   60 MET cc_start: 0.7670 (tpp) cc_final: 0.6504 (tmm)
REVERT: J   17 ILE cc_start: 0.8662 (OUTLIER) cc_final: 0.8409 (mt)
REVERT: J   61 ASP cc_start: 0.7311 (t70) cc_final: 0.7028 (t70)
REVERT: L   77 ARG cc_start: 0.7210 (tpp80) cc_final: 0.6813 (tpp80)
  outliers start: 25
  outliers final: 21
  residues processed: 210
  average time/residue: 0.1044
  time to fit residues: 28.0212
Evaluate side-chains
  205 residues out of total 840 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 183
  time to evaluate  : 0.280 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   16 VAL
Chi-restraints excluded: chain A residue   67 VAL
Chi-restraints excluded: chain A residue   90 VAL
Chi-restraints excluded: chain C residue   17 ILE
Chi-restraints excluded: chain C residue   25 THR
Chi-restraints excluded: chain D residue   16 VAL
Chi-restraints excluded: chain D residue   25 THR
Chi-restraints excluded: chain E residue   17 ILE
Chi-restraints excluded: chain G residue   17 ILE
Chi-restraints excluded: chain G residue   38 ILE
Chi-restraints excluded: chain G residue   89 LEU
Chi-restraints excluded: chain G residue   90 VAL
Chi-restraints excluded: chain H residue   17 ILE
Chi-restraints excluded: chain H residue   28 LEU
Chi-restraints excluded: chain H residue   66 VAL
Chi-restraints excluded: chain I residue   17 ILE
Chi-restraints excluded: chain I residue   33 VAL
Chi-restraints excluded: chain J residue   17 ILE
Chi-restraints excluded: chain J residue   39 THR
Chi-restraints excluded: chain K residue   16 VAL
Chi-restraints excluded: chain K residue   17 ILE
Chi-restraints excluded: chain L residue   85 VAL
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 84
   random chunks:
   chunk 47 optimal weight:    7.9990
   chunk 22 optimal weight:    7.9990
   chunk 79 optimal weight:    9.9990
   chunk 28 optimal weight:   10.0000
   chunk 58 optimal weight:    6.9990
   chunk 26 optimal weight:    9.9990
   chunk 80 optimal weight:    8.9990
   chunk 1 optimal weight:    4.9990
   chunk 21 optimal weight:    4.9990
   chunk 69 optimal weight:    5.9990
   chunk 25 optimal weight:    0.7980
   overall best weight:    4.7588

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

Flipped N/Q/H residues before XYZ refinement:
J  62 GLN
J  82 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4267 r_free = 0.4267 target = 0.206306 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3926 r_free = 0.3926 target = 0.173234 restraints weight = 7533.495|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 46)----------------|
| r_work = 0.3970 r_free = 0.3970 target = 0.177474 restraints weight = 5716.375|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.4002 r_free = 0.4002 target = 0.180512 restraints weight = 4680.837|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 41)----------------|
| r_work = 0.4024 r_free = 0.4024 target = 0.182667 restraints weight = 3994.032|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.4034 r_free = 0.4034 target = 0.183812 restraints weight = 3542.650|
|-----------------------------------------------------------------------------|
r_work (final): 0.4044
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7170
moved from start:          0.5351

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.051   7752  Z= 0.267
  Angle     :  0.669   9.971  10500  Z= 0.323
  Chirality :  0.052   0.145   1152
  Planarity :  0.005   0.053   1356
  Dihedral  :  4.802  15.965   1008
  Min Nonbonded Distance : 2.524

Molprobity Statistics.
  All-atom Clashscore : 10.62
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.69 %
    Favored  : 93.31 %
  Rotamer:
    Outliers :  4.76 %
    Allowed  : 18.81 %
    Favored  : 76.43 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.93 (0.27), residues: 912
  helix:  0.75 (0.64), residues: 84
  sheet: -2.41 (0.26), residues: 348
  loop : -2.03 (0.28), residues: 480

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG K  49 
 TYR   0.015   0.002   TYR A  27 
 PHE   0.015   0.002   PHE I  64 
 TRP   0.009   0.001   TRP I  88 
 HIS   0.005   0.002   HIS F  19 

Details of bonding type rmsd
  covalent geometry    : bond        0.00631 ( 7752)
  covalent geometry    : angle       0.66896 (10500)
  hydrogen bonds       : bond        0.03467 (  203)
  hydrogen bonds       : angle       6.93198 (  489)

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

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

  1824 Ramachandran restraints generated.
    912 Oldfield, 0 Emsley, 912 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1824 Ramachandran restraints generated.
    912 Oldfield, 0 Emsley, 912 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  238 residues out of total 840 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 40
    poor density    : 198
  time to evaluate  : 0.313 
Fit side-chains
   revert: symmetry clash
REVERT: D   15 LYS cc_start: 0.8088 (mttt) cc_final: 0.7641 (mttt)
REVERT: F   60 MET cc_start: 0.7517 (tpp) cc_final: 0.6540 (tmm)
REVERT: K   54 LYS cc_start: 0.8233 (mmmt) cc_final: 0.8016 (mmmt)
REVERT: L   20 LEU cc_start: 0.7773 (OUTLIER) cc_final: 0.7540 (mp)
REVERT: L   77 ARG cc_start: 0.7182 (tpp80) cc_final: 0.6951 (tpp80)
  outliers start: 40
  outliers final: 30
  residues processed: 223
  average time/residue: 0.1028
  time to fit residues: 29.3945
Evaluate side-chains
  222 residues out of total 840 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 191
  time to evaluate  : 0.293 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   16 VAL
Chi-restraints excluded: chain A residue   67 VAL
Chi-restraints excluded: chain A residue   90 VAL
Chi-restraints excluded: chain C residue   17 ILE
Chi-restraints excluded: chain C residue   25 THR
Chi-restraints excluded: chain D residue   16 VAL
Chi-restraints excluded: chain D residue   20 LEU
Chi-restraints excluded: chain D residue   25 THR
Chi-restraints excluded: chain E residue   17 ILE
Chi-restraints excluded: chain E residue   25 THR
Chi-restraints excluded: chain F residue   17 ILE
Chi-restraints excluded: chain F residue   29 VAL
Chi-restraints excluded: chain F residue   90 VAL
Chi-restraints excluded: chain G residue   17 ILE
Chi-restraints excluded: chain G residue   38 ILE
Chi-restraints excluded: chain G residue   89 LEU
Chi-restraints excluded: chain G residue   90 VAL
Chi-restraints excluded: chain H residue   17 ILE
Chi-restraints excluded: chain H residue   28 LEU
Chi-restraints excluded: chain H residue   33 VAL
Chi-restraints excluded: chain I residue   17 ILE
Chi-restraints excluded: chain I residue   33 VAL
Chi-restraints excluded: chain I residue   90 VAL
Chi-restraints excluded: chain J residue   17 ILE
Chi-restraints excluded: chain J residue   39 THR
Chi-restraints excluded: chain J residue   62 GLN
Chi-restraints excluded: chain K residue   16 VAL
Chi-restraints excluded: chain K residue   17 ILE
Chi-restraints excluded: chain K residue   39 THR
Chi-restraints excluded: chain L residue   20 LEU
Chi-restraints excluded: chain L residue   85 VAL
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 84
   random chunks:
   chunk 1 optimal weight:    1.9990
   chunk 12 optimal weight:    7.9990
   chunk 47 optimal weight:    0.9980
   chunk 72 optimal weight:    6.9990
   chunk 51 optimal weight:    3.9990
   chunk 56 optimal weight:    1.9990
   chunk 22 optimal weight:    4.9990
   chunk 73 optimal weight:    6.9990
   chunk 26 optimal weight:    3.9990
   chunk 61 optimal weight:    1.9990
   chunk 3 optimal weight:    8.9990
   overall best weight:    2.1988

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

Flipped N/Q/H residues before XYZ refinement:
B  62 GLN
J  62 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4310 r_free = 0.4310 target = 0.211445 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 64)----------------|
| r_work = 0.3978 r_free = 0.3978 target = 0.178561 restraints weight = 7511.292|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 44)----------------|
| r_work = 0.4022 r_free = 0.4022 target = 0.182940 restraints weight = 5696.231|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.4054 r_free = 0.4054 target = 0.186098 restraints weight = 4641.457|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 31)----------------|
| r_work = 0.4071 r_free = 0.4071 target = 0.187958 restraints weight = 3950.498|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 41)----------------|
| r_work = 0.4093 r_free = 0.4093 target = 0.189874 restraints weight = 3522.829|
|-----------------------------------------------------------------------------|
r_work (final): 0.3923
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7073
moved from start:          0.5453

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.032   7752  Z= 0.150
  Angle     :  0.595   8.903  10500  Z= 0.286
  Chirality :  0.050   0.207   1152
  Planarity :  0.004   0.050   1356
  Dihedral  :  4.415  16.913   1008
  Min Nonbonded Distance : 2.492

Molprobity Statistics.
  All-atom Clashscore : 9.16
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.51 %
    Favored  : 96.49 %
  Rotamer:
    Outliers :  4.88 %
    Allowed  : 20.00 %
    Favored  : 75.12 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.67 (0.28), residues: 912
  helix:  0.82 (0.63), residues: 84
  sheet: -2.04 (0.25), residues: 384
  loop : -1.95 (0.30), residues: 444

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG K  49 
 TYR   0.012   0.002   TYR B  27 
 PHE   0.018   0.002   PHE L  81 
 TRP   0.010   0.001   TRP A  88 
 HIS   0.003   0.001   HIS F  19 

Details of bonding type rmsd
  covalent geometry    : bond        0.00352 ( 7752)
  covalent geometry    : angle       0.59478 (10500)
  hydrogen bonds       : bond        0.02966 (  203)
  hydrogen bonds       : angle       6.61840 (  489)

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

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

  1824 Ramachandran restraints generated.
    912 Oldfield, 0 Emsley, 912 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1824 Ramachandran restraints generated.
    912 Oldfield, 0 Emsley, 912 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  235 residues out of total 840 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 41
    poor density    : 194
  time to evaluate  : 0.298 
Fit side-chains
   revert: symmetry clash
REVERT: D   15 LYS cc_start: 0.8105 (mttt) cc_final: 0.7615 (mttt)
REVERT: E   69 GLU cc_start: 0.7618 (pt0) cc_final: 0.7315 (pt0)
REVERT: F   60 MET cc_start: 0.7589 (tpp) cc_final: 0.6701 (tmm)
REVERT: J   17 ILE cc_start: 0.8700 (OUTLIER) cc_final: 0.8461 (mt)
REVERT: J   61 ASP cc_start: 0.7117 (t70) cc_final: 0.6901 (t70)
REVERT: J   64 PHE cc_start: 0.8148 (m-80) cc_final: 0.7886 (m-80)
REVERT: K   54 LYS cc_start: 0.8199 (mmmt) cc_final: 0.7833 (mmmt)
REVERT: L   20 LEU cc_start: 0.7620 (OUTLIER) cc_final: 0.7351 (mp)
  outliers start: 41
  outliers final: 33
  residues processed: 218
  average time/residue: 0.1057
  time to fit residues: 29.4772
Evaluate side-chains
  226 residues out of total 840 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 191
  time to evaluate  : 0.242 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   16 VAL
Chi-restraints excluded: chain A residue   67 VAL
Chi-restraints excluded: chain A residue   90 VAL
Chi-restraints excluded: chain B residue   33 VAL
Chi-restraints excluded: chain B residue   62 GLN
Chi-restraints excluded: chain C residue   17 ILE
Chi-restraints excluded: chain C residue   25 THR
Chi-restraints excluded: chain C residue   38 ILE
Chi-restraints excluded: chain C residue   77 ARG
Chi-restraints excluded: chain D residue   16 VAL
Chi-restraints excluded: chain D residue   20 LEU
Chi-restraints excluded: chain D residue   25 THR
Chi-restraints excluded: chain E residue   15 LYS
Chi-restraints excluded: chain E residue   17 ILE
Chi-restraints excluded: chain E residue   25 THR
Chi-restraints excluded: chain F residue   17 ILE
Chi-restraints excluded: chain F residue   39 THR
Chi-restraints excluded: chain G residue   17 ILE
Chi-restraints excluded: chain G residue   38 ILE
Chi-restraints excluded: chain G residue   89 LEU
Chi-restraints excluded: chain G residue   90 VAL
Chi-restraints excluded: chain H residue   17 ILE
Chi-restraints excluded: chain H residue   28 LEU
Chi-restraints excluded: chain H residue   33 VAL
Chi-restraints excluded: chain I residue   17 ILE
Chi-restraints excluded: chain I residue   33 VAL
Chi-restraints excluded: chain I residue   39 THR
Chi-restraints excluded: chain I residue   90 VAL
Chi-restraints excluded: chain J residue   17 ILE
Chi-restraints excluded: chain J residue   39 THR
Chi-restraints excluded: chain K residue   16 VAL
Chi-restraints excluded: chain K residue   17 ILE
Chi-restraints excluded: chain K residue   39 THR
Chi-restraints excluded: chain L residue   20 LEU
Chi-restraints excluded: chain L residue   85 VAL
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 84
   random chunks:
   chunk 64 optimal weight:    3.9990
   chunk 37 optimal weight:   20.0000
   chunk 34 optimal weight:    9.9990
   chunk 61 optimal weight:    0.9980
   chunk 82 optimal weight:    1.9990
   chunk 56 optimal weight:    7.9990
   chunk 20 optimal weight:    0.0670
   chunk 48 optimal weight:   20.0000
   chunk 70 optimal weight:    5.9990
   chunk 66 optimal weight:   10.0000
   chunk 16 optimal weight:   10.0000
   overall best weight:    2.6124

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

Flipped N/Q/H residues before XYZ refinement:
G  48 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4302 r_free = 0.4302 target = 0.210355 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3966 r_free = 0.3966 target = 0.177434 restraints weight = 7496.035|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.4009 r_free = 0.4009 target = 0.181726 restraints weight = 5722.460|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.4042 r_free = 0.4042 target = 0.184884 restraints weight = 4687.101|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.4058 r_free = 0.4058 target = 0.186682 restraints weight = 3999.557|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 31)----------------|
| r_work = 0.4073 r_free = 0.4073 target = 0.188311 restraints weight = 3578.956|
|-----------------------------------------------------------------------------|
r_work (final): 0.4072
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7127
moved from start:          0.5628

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.036   7752  Z= 0.166
  Angle     :  0.599   9.925  10500  Z= 0.287
  Chirality :  0.050   0.139   1152
  Planarity :  0.005   0.052   1356
  Dihedral  :  4.397  15.797   1008
  Min Nonbonded Distance : 2.507

Molprobity Statistics.
  All-atom Clashscore : 9.36
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.04 %
    Favored  : 94.96 %
  Rotamer:
    Outliers :  5.36 %
    Allowed  : 20.36 %
    Favored  : 74.29 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.58 (0.28), residues: 912
  helix:  0.91 (0.63), residues: 84
  sheet: -1.94 (0.26), residues: 372
  loop : -1.95 (0.30), residues: 456

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG D  37 
 TYR   0.012   0.002   TYR B  27 
 PHE   0.015   0.002   PHE I  64 
 TRP   0.008   0.001   TRP I  88 
 HIS   0.004   0.002   HIS F  19 

Details of bonding type rmsd
  covalent geometry    : bond        0.00389 ( 7752)
  covalent geometry    : angle       0.59867 (10500)
  hydrogen bonds       : bond        0.02958 (  203)
  hydrogen bonds       : angle       6.59014 (  489)

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

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

  1824 Ramachandran restraints generated.
    912 Oldfield, 0 Emsley, 912 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1824 Ramachandran restraints generated.
    912 Oldfield, 0 Emsley, 912 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  240 residues out of total 840 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 45
    poor density    : 195
  time to evaluate  : 0.281 
Fit side-chains
   revert: symmetry clash
REVERT: D   15 LYS cc_start: 0.7966 (mttt) cc_final: 0.7557 (mttt)
REVERT: F   60 MET cc_start: 0.7466 (tpp) cc_final: 0.6556 (tmm)
REVERT: G   44 LYS cc_start: 0.7465 (ttpt) cc_final: 0.7227 (ttmt)
REVERT: G   79 PRO cc_start: 0.7580 (Cg_endo) cc_final: 0.7036 (Cg_exo)
REVERT: J   17 ILE cc_start: 0.8727 (OUTLIER) cc_final: 0.8494 (mt)
  outliers start: 45
  outliers final: 38
  residues processed: 216
  average time/residue: 0.1084
  time to fit residues: 29.7529
Evaluate side-chains
  232 residues out of total 840 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 39
    poor density    : 193
  time to evaluate  : 0.295 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   16 VAL
Chi-restraints excluded: chain A residue   67 VAL
Chi-restraints excluded: chain A residue   90 VAL
Chi-restraints excluded: chain B residue   33 VAL
Chi-restraints excluded: chain C residue   17 ILE
Chi-restraints excluded: chain C residue   25 THR
Chi-restraints excluded: chain C residue   38 ILE
Chi-restraints excluded: chain C residue   39 THR
Chi-restraints excluded: chain C residue   77 ARG
Chi-restraints excluded: chain D residue   16 VAL
Chi-restraints excluded: chain D residue   20 LEU
Chi-restraints excluded: chain D residue   25 THR
Chi-restraints excluded: chain E residue   15 LYS
Chi-restraints excluded: chain E residue   17 ILE
Chi-restraints excluded: chain E residue   25 THR
Chi-restraints excluded: chain F residue   17 ILE
Chi-restraints excluded: chain F residue   29 VAL
Chi-restraints excluded: chain F residue   39 THR
Chi-restraints excluded: chain F residue   90 VAL
Chi-restraints excluded: chain G residue   17 ILE
Chi-restraints excluded: chain G residue   38 ILE
Chi-restraints excluded: chain G residue   89 LEU
Chi-restraints excluded: chain G residue   90 VAL
Chi-restraints excluded: chain H residue   17 ILE
Chi-restraints excluded: chain H residue   28 LEU
Chi-restraints excluded: chain H residue   33 VAL
Chi-restraints excluded: chain H residue   89 LEU
Chi-restraints excluded: chain I residue   17 ILE
Chi-restraints excluded: chain I residue   20 LEU
Chi-restraints excluded: chain I residue   33 VAL
Chi-restraints excluded: chain I residue   39 THR
Chi-restraints excluded: chain I residue   70 GLU
Chi-restraints excluded: chain I residue   90 VAL
Chi-restraints excluded: chain J residue   17 ILE
Chi-restraints excluded: chain J residue   39 THR
Chi-restraints excluded: chain K residue   16 VAL
Chi-restraints excluded: chain K residue   17 ILE
Chi-restraints excluded: chain K residue   39 THR
Chi-restraints excluded: chain L residue   85 VAL
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 84
   random chunks:
   chunk 7 optimal weight:   10.0000
   chunk 0 optimal weight:   10.0000
   chunk 30 optimal weight:    9.9990
   chunk 36 optimal weight:    7.9990
   chunk 23 optimal weight:    8.9990
   chunk 40 optimal weight:    3.9990
   chunk 4 optimal weight:    5.9990
   chunk 59 optimal weight:    8.9990
   chunk 69 optimal weight:    0.0270
   chunk 45 optimal weight:    5.9990
   chunk 41 optimal weight:    3.9990
   overall best weight:    4.0046

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

Flipped N/Q/H residues before XYZ refinement:
B  62 GLN
J  82 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4075 r_free = 0.4075 target = 0.186260 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3752 r_free = 0.3752 target = 0.153964 restraints weight = 7693.543|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3749 r_free = 0.3749 target = 0.153966 restraints weight = 6111.453|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3759 r_free = 0.3759 target = 0.155083 restraints weight = 5869.541|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.3772 r_free = 0.3772 target = 0.156354 restraints weight = 5083.933|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3778 r_free = 0.3778 target = 0.157025 restraints weight = 4655.993|
|-----------------------------------------------------------------------------|
r_work (final): 0.3784
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7177
moved from start:          0.5877

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.045   7752  Z= 0.230
  Angle     :  0.651  10.514  10500  Z= 0.314
  Chirality :  0.051   0.140   1152
  Planarity :  0.005   0.056   1356
  Dihedral  :  4.700  15.722   1008
  Min Nonbonded Distance : 2.433

Molprobity Statistics.
  All-atom Clashscore : 11.01
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.48 %
    Favored  : 94.52 %
  Rotamer:
    Outliers :  5.60 %
    Allowed  : 20.24 %
    Favored  : 74.17 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.60 (0.28), residues: 912
  helix:  0.92 (0.63), residues: 84
  sheet: -1.98 (0.26), residues: 372
  loop : -1.95 (0.29), residues: 456

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG D  37 
 TYR   0.013   0.002   TYR A  27 
 PHE   0.013   0.002   PHE I  64 
 TRP   0.009   0.001   TRP I  88 
 HIS   0.005   0.002   HIS F  19 

Details of bonding type rmsd
  covalent geometry    : bond        0.00546 ( 7752)
  covalent geometry    : angle       0.65063 (10500)
  hydrogen bonds       : bond        0.03200 (  203)
  hydrogen bonds       : angle       6.78283 (  489)

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

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

  1824 Ramachandran restraints generated.
    912 Oldfield, 0 Emsley, 912 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1824 Ramachandran restraints generated.
    912 Oldfield, 0 Emsley, 912 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  239 residues out of total 840 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 47
    poor density    : 192
  time to evaluate  : 0.285 
Fit side-chains
   revert: symmetry clash
REVERT: D   15 LYS cc_start: 0.8109 (mttt) cc_final: 0.7612 (mttt)
REVERT: F   60 MET cc_start: 0.7623 (tpp) cc_final: 0.6578 (tmm)
REVERT: G   44 LYS cc_start: 0.7570 (ttpt) cc_final: 0.7304 (ttmt)
REVERT: G   79 PRO cc_start: 0.7554 (Cg_endo) cc_final: 0.7003 (Cg_exo)
REVERT: J   17 ILE cc_start: 0.8819 (OUTLIER) cc_final: 0.8505 (mt)
REVERT: J   24 GLU cc_start: 0.5788 (mm-30) cc_final: 0.4992 (mm-30)
  outliers start: 47
  outliers final: 41
  residues processed: 218
  average time/residue: 0.1109
  time to fit residues: 30.6879
Evaluate side-chains
  231 residues out of total 840 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 42
    poor density    : 189
  time to evaluate  : 0.232 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   16 VAL
Chi-restraints excluded: chain A residue   67 VAL
Chi-restraints excluded: chain A residue   90 VAL
Chi-restraints excluded: chain B residue   33 VAL
Chi-restraints excluded: chain B residue   38 ILE
Chi-restraints excluded: chain B residue   62 GLN
Chi-restraints excluded: chain C residue   17 ILE
Chi-restraints excluded: chain C residue   25 THR
Chi-restraints excluded: chain C residue   38 ILE
Chi-restraints excluded: chain C residue   39 THR
Chi-restraints excluded: chain C residue   77 ARG
Chi-restraints excluded: chain D residue   16 VAL
Chi-restraints excluded: chain D residue   20 LEU
Chi-restraints excluded: chain D residue   25 THR
Chi-restraints excluded: chain E residue   15 LYS
Chi-restraints excluded: chain E residue   17 ILE
Chi-restraints excluded: chain E residue   25 THR
Chi-restraints excluded: chain F residue   17 ILE
Chi-restraints excluded: chain F residue   29 VAL
Chi-restraints excluded: chain F residue   39 THR
Chi-restraints excluded: chain F residue   90 VAL
Chi-restraints excluded: chain G residue   17 ILE
Chi-restraints excluded: chain G residue   89 LEU
Chi-restraints excluded: chain G residue   90 VAL
Chi-restraints excluded: chain H residue   17 ILE
Chi-restraints excluded: chain H residue   28 LEU
Chi-restraints excluded: chain H residue   33 VAL
Chi-restraints excluded: chain H residue   89 LEU
Chi-restraints excluded: chain I residue   17 ILE
Chi-restraints excluded: chain I residue   20 LEU
Chi-restraints excluded: chain I residue   33 VAL
Chi-restraints excluded: chain I residue   39 THR
Chi-restraints excluded: chain I residue   70 GLU
Chi-restraints excluded: chain I residue   90 VAL
Chi-restraints excluded: chain J residue   17 ILE
Chi-restraints excluded: chain J residue   39 THR
Chi-restraints excluded: chain K residue   16 VAL
Chi-restraints excluded: chain K residue   17 ILE
Chi-restraints excluded: chain K residue   39 THR
Chi-restraints excluded: chain K residue   46 VAL
Chi-restraints excluded: chain L residue   85 VAL
Chi-restraints excluded: chain L residue   89 LEU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 84
   random chunks:
   chunk 31 optimal weight:    1.9990
   chunk 78 optimal weight:    5.9990
   chunk 43 optimal weight:    2.9990
   chunk 17 optimal weight:    4.9990
   chunk 9 optimal weight:    5.9990
   chunk 10 optimal weight:    0.8980
   chunk 64 optimal weight:    2.9990
   chunk 50 optimal weight:    0.6980
   chunk 12 optimal weight:    8.9990
   chunk 57 optimal weight:    0.9980
   chunk 82 optimal weight:    6.9990
   overall best weight:    1.5184

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

Flipped N/Q/H residues before XYZ refinement:
J  82 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4105 r_free = 0.4105 target = 0.189380 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 54)----------------|
| r_work = 0.3762 r_free = 0.3762 target = 0.155171 restraints weight = 7532.375|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 44)----------------|
| r_work = 0.3795 r_free = 0.3795 target = 0.158429 restraints weight = 5971.922|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 23)----------------|
| r_work = 0.3817 r_free = 0.3817 target = 0.160559 restraints weight = 5021.739|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 39)----------------|
| r_work = 0.3839 r_free = 0.3839 target = 0.162624 restraints weight = 4428.718|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 32)----------------|
| r_work = 0.3850 r_free = 0.3850 target = 0.163760 restraints weight = 3983.220|
|-----------------------------------------------------------------------------|
r_work (final): 0.3775
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7055
moved from start:          0.5849

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   7752  Z= 0.127
  Angle     :  0.593   9.717  10500  Z= 0.285
  Chirality :  0.050   0.138   1152
  Planarity :  0.004   0.052   1356
  Dihedral  :  4.377  14.498   1008
  Min Nonbonded Distance : 2.484

Molprobity Statistics.
  All-atom Clashscore : 8.69
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.96 %
    Favored  : 97.04 %
  Rotamer:
    Outliers :  4.40 %
    Allowed  : 21.67 %
    Favored  : 73.93 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.30 (0.29), residues: 912
  helix:  1.08 (0.62), residues: 84
  sheet: -1.77 (0.26), residues: 384
  loop : -1.72 (0.31), residues: 444

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG D  37 
 TYR   0.011   0.001   TYR L  55 
 PHE   0.015   0.002   PHE I  64 
 TRP   0.010   0.001   TRP I  88 
 HIS   0.002   0.001   HIS E  19 

Details of bonding type rmsd
  covalent geometry    : bond        0.00295 ( 7752)
  covalent geometry    : angle       0.59298 (10500)
  hydrogen bonds       : bond        0.02828 (  203)
  hydrogen bonds       : angle       6.51532 (  489)

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

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

  1824 Ramachandran restraints generated.
    912 Oldfield, 0 Emsley, 912 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1824 Ramachandran restraints generated.
    912 Oldfield, 0 Emsley, 912 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  231 residues out of total 840 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 37
    poor density    : 194
  time to evaluate  : 0.299 
Fit side-chains
   revert: symmetry clash
REVERT: C   40 LEU cc_start: 0.7402 (OUTLIER) cc_final: 0.7088 (tp)
REVERT: D   15 LYS cc_start: 0.8064 (mttt) cc_final: 0.7563 (mttt)
REVERT: E   69 GLU cc_start: 0.7730 (pt0) cc_final: 0.7347 (pt0)
REVERT: F   60 MET cc_start: 0.7665 (tpp) cc_final: 0.6621 (tmm)
REVERT: G   44 LYS cc_start: 0.7478 (ttpt) cc_final: 0.7252 (ttmt)
REVERT: G   79 PRO cc_start: 0.7477 (Cg_endo) cc_final: 0.6968 (Cg_exo)
REVERT: J   17 ILE cc_start: 0.8708 (OUTLIER) cc_final: 0.8439 (mt)
REVERT: K   54 LYS cc_start: 0.8018 (mmmt) cc_final: 0.7658 (mmmt)
  outliers start: 37
  outliers final: 32
  residues processed: 215
  average time/residue: 0.1085
  time to fit residues: 30.0358
Evaluate side-chains
  225 residues out of total 840 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 191
  time to evaluate  : 0.269 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   16 VAL
Chi-restraints excluded: chain A residue   67 VAL
Chi-restraints excluded: chain A residue   90 VAL
Chi-restraints excluded: chain B residue   33 VAL
Chi-restraints excluded: chain B residue   54 LYS
Chi-restraints excluded: chain C residue   17 ILE
Chi-restraints excluded: chain C residue   25 THR
Chi-restraints excluded: chain C residue   38 ILE
Chi-restraints excluded: chain C residue   39 THR
Chi-restraints excluded: chain C residue   40 LEU
Chi-restraints excluded: chain D residue   16 VAL
Chi-restraints excluded: chain D residue   25 THR
Chi-restraints excluded: chain E residue   15 LYS
Chi-restraints excluded: chain E residue   17 ILE
Chi-restraints excluded: chain E residue   25 THR
Chi-restraints excluded: chain F residue   17 ILE
Chi-restraints excluded: chain F residue   90 VAL
Chi-restraints excluded: chain G residue   17 ILE
Chi-restraints excluded: chain G residue   89 LEU
Chi-restraints excluded: chain G residue   90 VAL
Chi-restraints excluded: chain H residue   17 ILE
Chi-restraints excluded: chain H residue   28 LEU
Chi-restraints excluded: chain H residue   33 VAL
Chi-restraints excluded: chain H residue   66 VAL
Chi-restraints excluded: chain H residue   89 LEU
Chi-restraints excluded: chain I residue   17 ILE
Chi-restraints excluded: chain I residue   20 LEU
Chi-restraints excluded: chain I residue   33 VAL
Chi-restraints excluded: chain I residue   39 THR
Chi-restraints excluded: chain J residue   17 ILE
Chi-restraints excluded: chain J residue   39 THR
Chi-restraints excluded: chain K residue   16 VAL
Chi-restraints excluded: chain K residue   17 ILE
Chi-restraints excluded: chain L residue   85 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 84
   random chunks:
   chunk 48 optimal weight:    0.0970
   chunk 11 optimal weight:    9.9990
   chunk 49 optimal weight:    0.9990
   chunk 65 optimal weight:    6.9990
   chunk 2 optimal weight:    3.9990
   chunk 54 optimal weight:    0.6980
   chunk 28 optimal weight:   10.0000
   chunk 56 optimal weight:   10.0000
   chunk 73 optimal weight:    5.9990
   chunk 42 optimal weight:   10.0000
   chunk 22 optimal weight:    6.9990
   overall best weight:    2.3584

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

Flipped N/Q/H residues before XYZ refinement:
B  62 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4075 r_free = 0.4075 target = 0.185997 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3728 r_free = 0.3728 target = 0.151734 restraints weight = 7697.636|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3759 r_free = 0.3759 target = 0.154787 restraints weight = 6093.452|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3785 r_free = 0.3785 target = 0.157232 restraints weight = 5152.326|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 45)----------------|
| r_work = 0.3804 r_free = 0.3804 target = 0.158972 restraints weight = 4528.485|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.3815 r_free = 0.3815 target = 0.160053 restraints weight = 4112.582|
|-----------------------------------------------------------------------------|
r_work (final): 0.3814
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7071
moved from start:          0.5937

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.034   7752  Z= 0.157
  Angle     :  0.609  10.680  10500  Z= 0.290
  Chirality :  0.050   0.139   1152
  Planarity :  0.004   0.056   1356
  Dihedral  :  4.334  14.539   1008
  Min Nonbonded Distance : 2.504

Molprobity Statistics.
  All-atom Clashscore : 9.62
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.17 %
    Favored  : 95.83 %
  Rotamer:
    Outliers :  4.29 %
    Allowed  : 22.02 %
    Favored  : 73.69 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.23 (0.29), residues: 912
  helix:  1.33 (0.64), residues: 84
  sheet: -1.77 (0.26), residues: 372
  loop : -1.69 (0.30), residues: 456

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.000   ARG D  37 
 TYR   0.012   0.002   TYR A  27 
 PHE   0.016   0.002   PHE I  64 
 TRP   0.009   0.001   TRP I  88 
 HIS   0.004   0.002   HIS L  19 

Details of bonding type rmsd
  covalent geometry    : bond        0.00371 ( 7752)
  covalent geometry    : angle       0.60945 (10500)
  hydrogen bonds       : bond        0.02900 (  203)
  hydrogen bonds       : angle       6.51668 (  489)

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

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

  1824 Ramachandran restraints generated.
    912 Oldfield, 0 Emsley, 912 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1824 Ramachandran restraints generated.
    912 Oldfield, 0 Emsley, 912 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  227 residues out of total 840 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 191
  time to evaluate  : 0.201 
Fit side-chains
   revert: symmetry clash
REVERT: C   37 ARG cc_start: 0.6905 (ppt170) cc_final: 0.6528 (ppt170)
REVERT: C   40 LEU cc_start: 0.7397 (OUTLIER) cc_final: 0.7104 (tp)
REVERT: D   15 LYS cc_start: 0.8055 (mttt) cc_final: 0.7576 (mttt)
REVERT: E   69 GLU cc_start: 0.7742 (pt0) cc_final: 0.7342 (pt0)
REVERT: F   60 MET cc_start: 0.7695 (tpp) cc_final: 0.6617 (tmm)
REVERT: G   79 PRO cc_start: 0.7476 (Cg_endo) cc_final: 0.6970 (Cg_exo)
REVERT: J   17 ILE cc_start: 0.8749 (OUTLIER) cc_final: 0.8378 (mt)
REVERT: J   24 GLU cc_start: 0.5915 (mm-30) cc_final: 0.5095 (mm-30)
REVERT: K   54 LYS cc_start: 0.8041 (mmmt) cc_final: 0.7671 (mmmt)
  outliers start: 36
  outliers final: 33
  residues processed: 212
  average time/residue: 0.1071
  time to fit residues: 29.1328
Evaluate side-chains
  222 residues out of total 840 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 187
  time to evaluate  : 0.286 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   16 VAL
Chi-restraints excluded: chain A residue   67 VAL
Chi-restraints excluded: chain A residue   90 VAL
Chi-restraints excluded: chain B residue   33 VAL
Chi-restraints excluded: chain B residue   38 ILE
Chi-restraints excluded: chain B residue   54 LYS
Chi-restraints excluded: chain B residue   62 GLN
Chi-restraints excluded: chain C residue   17 ILE
Chi-restraints excluded: chain C residue   25 THR
Chi-restraints excluded: chain C residue   38 ILE
Chi-restraints excluded: chain C residue   39 THR
Chi-restraints excluded: chain C residue   40 LEU
Chi-restraints excluded: chain D residue   16 VAL
Chi-restraints excluded: chain D residue   25 THR
Chi-restraints excluded: chain E residue   15 LYS
Chi-restraints excluded: chain E residue   17 ILE
Chi-restraints excluded: chain E residue   25 THR
Chi-restraints excluded: chain F residue   17 ILE
Chi-restraints excluded: chain F residue   90 VAL
Chi-restraints excluded: chain G residue   17 ILE
Chi-restraints excluded: chain G residue   89 LEU
Chi-restraints excluded: chain G residue   90 VAL
Chi-restraints excluded: chain H residue   17 ILE
Chi-restraints excluded: chain H residue   28 LEU
Chi-restraints excluded: chain H residue   33 VAL
Chi-restraints excluded: chain H residue   89 LEU
Chi-restraints excluded: chain I residue   17 ILE
Chi-restraints excluded: chain I residue   20 LEU
Chi-restraints excluded: chain I residue   33 VAL
Chi-restraints excluded: chain I residue   39 THR
Chi-restraints excluded: chain J residue   17 ILE
Chi-restraints excluded: chain J residue   39 THR
Chi-restraints excluded: chain K residue   16 VAL
Chi-restraints excluded: chain K residue   17 ILE
Chi-restraints excluded: chain L residue   85 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 84
   random chunks:
   chunk 37 optimal weight:    8.9990
   chunk 12 optimal weight:    0.4980
   chunk 35 optimal weight:   10.0000
   chunk 53 optimal weight:    4.9990
   chunk 74 optimal weight:    4.9990
   chunk 6 optimal weight:   10.0000
   chunk 1 optimal weight:    0.8980
   chunk 36 optimal weight:    5.9990
   chunk 71 optimal weight:    8.9990
   chunk 40 optimal weight:    1.9990
   chunk 2 optimal weight:    0.1980
   overall best weight:    1.7184

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

Flipped N/Q/H residues before XYZ refinement:
B  62 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4135 r_free = 0.4135 target = 0.191891 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3802 r_free = 0.3802 target = 0.158567 restraints weight = 7593.565|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 42)----------------|
| r_work = 0.3837 r_free = 0.3837 target = 0.161935 restraints weight = 5960.499|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3861 r_free = 0.3861 target = 0.164331 restraints weight = 4966.069|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 27)----------------|
| r_work = 0.3875 r_free = 0.3875 target = 0.165687 restraints weight = 4327.431|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 33)----------------|
| r_work = 0.3890 r_free = 0.3890 target = 0.167183 restraints weight = 3924.435|
|-----------------------------------------------------------------------------|
r_work (final): 0.3786
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7042
moved from start:          0.5943

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   7752  Z= 0.130
  Angle     :  0.597  10.607  10500  Z= 0.284
  Chirality :  0.049   0.148   1152
  Planarity :  0.004   0.054   1356
  Dihedral  :  4.209  13.881   1008
  Min Nonbonded Distance : 2.506

Molprobity Statistics.
  All-atom Clashscore : 9.09
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.96 %
    Favored  : 97.04 %
  Rotamer:
    Outliers :  4.17 %
    Allowed  : 22.02 %
    Favored  : 73.81 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.10 (0.29), residues: 912
  helix:  1.37 (0.63), residues: 84
  sheet: -1.69 (0.26), residues: 384
  loop : -1.57 (0.32), residues: 444

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.000   ARG D  37 
 TYR   0.011   0.001   TYR L  55 
 PHE   0.020   0.002   PHE I  64 
 TRP   0.008   0.001   TRP I  88 
 HIS   0.003   0.001   HIS L  19 

Details of bonding type rmsd
  covalent geometry    : bond        0.00304 ( 7752)
  covalent geometry    : angle       0.59706 (10500)
  hydrogen bonds       : bond        0.02793 (  203)
  hydrogen bonds       : angle       6.39511 (  489)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1338.91 seconds
wall clock time: 23 minutes 44.05 seconds (1424.05 seconds total)