Starting phenix.real_space_refine
on Wed Feb 12 04:40:27 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/6vcc_21148/02_2025/6vcc_21148.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/6vcc_21148/02_2025/6vcc_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 {
    real_map_files = "/net/cci-nas-00/data/ceres_data/6vcc_21148/02_2025/6vcc_21148.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/6vcc_21148/02_2025/6vcc_21148.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/6vcc_21148/02_2025/6vcc_21148.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/6vcc_21148/02_2025/6vcc_21148.cif"
  }
  resolution = 3.6
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=  -0.000 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): 0.03s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/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: 5.07, per 1000 atoms: 0.67
  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: 1.74
  Conformation dependent library (CDL) restraints added in 1.1 seconds
  

  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: 0.96
  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: 2.21

  Time building geometry restraints manager: 2.06 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: 0.01
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:             0.140
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.250
  Check model and map are aligned:         0.060
  Set scattering table:                    0.060
  Process input model:                     21.000
  Find NCS groups from input model:        0.300
  Set up NCS constraints:                  0.050
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:2.870
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   24.730
-------------------------------------------------------------------------------
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= 0.236
  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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -4.54 (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
 TRP   0.007   0.001   TRP C  88 
 HIS   0.004   0.002   HIS J  19 
 PHE   0.008   0.001   PHE E  64 
 TYR   0.015   0.002   TYR D  18 
 ARG   0.023   0.000   ARG H  77 

*********************** 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  : 0.848 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   54 LYS cc_start: 0.7152 (mtpp) cc_final: 0.6888 (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: 0.6172 (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: 0.6724 (mtmm)
REVERT: F   66 VAL cc_start: 0.8090 (m) cc_final: 0.7838 (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: 0.5993 (mmp80)
REVERT: K   69 GLU cc_start: 0.6371 (pt0) cc_final: 0.5993 (pt0)
REVERT: K   74 ASP cc_start: 0.6733 (m-30) cc_final: 0.6384 (p0)
REVERT: L   34 PRO cc_start: 0.6822 (Cg_endo) cc_final: 0.6132 (Cg_exo)
  outliers start: 0
  outliers final: 0
  residues processed: 228
  average time/residue: 0.2561
  time to fit residues: 73.2365
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  : 0.877 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 84
   random chunks:
   chunk 70 optimal weight:    7.9990
   chunk 63 optimal weight:    3.9990
   chunk 35 optimal weight:   10.0000
   chunk 21 optimal weight:   10.0000
   chunk 42 optimal weight:   10.0000
   chunk 34 optimal weight:    0.9980
   chunk 65 optimal weight:    0.0980
   chunk 25 optimal weight:    3.9990
   chunk 40 optimal weight:    9.9990
   chunk 49 optimal weight:    6.9990
   chunk 76 optimal weight:    3.9990
   overall best weight:    2.6186

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

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

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4404 r_free = 0.4404 target = 0.221395 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.4076 r_free = 0.4076 target = 0.187608 restraints weight = 7465.502|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.4088 r_free = 0.4088 target = 0.190407 restraints weight = 6113.240|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.4110 r_free = 0.4110 target = 0.192865 restraints weight = 5350.466|
|-----------------------------------------------------------------------------|
r_work (final): 0.3898
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7014
moved from start:          0.3064

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.060   7752  Z= 0.264
  Angle     :  0.617   8.878  10500  Z= 0.300
  Chirality :  0.050   0.148   1152
  Planarity :  0.005   0.049   1356
  Dihedral  :  4.208  12.759   1008
  Min Nonbonded Distance : 2.350

Molprobity Statistics.
  All-atom Clashscore : 8.89
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.40 %
    Favored  : 96.60 %
  Rotamer:
    Outliers :  3.69 %
    Allowed  : 13.93 %
    Favored  : 82.38 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -3.85 (0.25), residues: 912
  helix: -1.60 (0.38), residues: 72
  sheet: -2.97 (0.24), residues: 360
  loop : -2.29 (0.27), residues: 480

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.002   TRP A  88 
 HIS   0.005   0.002   HIS F  19 
 PHE   0.016   0.002   PHE E  43 
 TYR   0.016   0.002   TYR A  27 
 ARG   0.004   0.001   ARG L  84 

*********************** 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
  231 residues out of total 840 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 200
  time to evaluate  : 0.967 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   58 LYS cc_start: 0.8094 (tttt) cc_final: 0.7782 (tttp)
REVERT: D   54 LYS cc_start: 0.7507 (mtpp) cc_final: 0.7215 (mtpt)
REVERT: D   70 GLU cc_start: 0.5477 (tt0) cc_final: 0.5130 (tt0)
REVERT: H   27 TYR cc_start: 0.8404 (m-80) cc_final: 0.8175 (m-80)
REVERT: H   54 LYS cc_start: 0.8184 (mmtt) cc_final: 0.7801 (mmtm)
REVERT: J   48 GLN cc_start: 0.7137 (mp10) cc_final: 0.6925 (mm-40)
  outliers start: 31
  outliers final: 18
  residues processed: 218
  average time/residue: 0.2487
  time to fit residues: 68.5342
Evaluate side-chains
  199 residues out of total 840 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 181
  time to evaluate  : 0.849 
-------------------------------------------------------------------------------
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 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 H residue   89 LEU
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 L residue   85 VAL
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 84
   random chunks:
   chunk 4 optimal weight:   10.0000
   chunk 47 optimal weight:    5.9990
   chunk 28 optimal weight:   10.0000
   chunk 72 optimal weight:    6.9990
   chunk 6 optimal weight:   20.0000
   chunk 11 optimal weight:    2.9990
   chunk 48 optimal weight:   20.0000
   chunk 14 optimal weight:   10.0000
   chunk 64 optimal weight:    0.9980
   chunk 44 optimal weight:    6.9990
   chunk 54 optimal weight:    2.9990
   overall best weight:    3.9988

-------------------------------------------------------------------------------
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 = 0.4300 r_free = 0.4300 target = 0.210762 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3960 r_free = 0.3960 target = 0.176534 restraints weight = 7576.193|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.4002 r_free = 0.4002 target = 0.180898 restraints weight = 5660.916|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.4034 r_free = 0.4034 target = 0.184119 restraints weight = 4609.172|
|-----------------------------------------------------------------------------|
r_work (final): 0.4036
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7125
moved from start:          0.4396

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.043   7752  Z= 0.348
  Angle     :  0.650   9.397  10500  Z= 0.316
  Chirality :  0.051   0.193   1152
  Planarity :  0.005   0.049   1356
  Dihedral  :  4.724  15.165   1008
  Min Nonbonded Distance : 2.508

Molprobity Statistics.
  All-atom Clashscore : 10.02
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.82 %
    Favored  : 95.18 %
  Rotamer:
    Outliers :  3.81 %
    Allowed  : 17.50 %
    Favored  : 78.69 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -3.46 (0.26), residues: 912
  helix: -0.15 (0.54), residues: 84
  sheet: -2.80 (0.25), residues: 360
  loop : -2.21 (0.27), residues: 468

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP I  88 
 HIS   0.005   0.003   HIS A  19 
 PHE   0.017   0.002   PHE I  64 
 TYR   0.016   0.002   TYR G  55 
 ARG   0.004   0.001   ARG C  77 

*********************** 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
  230 residues out of total 840 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 198
  time to evaluate  : 0.842 
Fit side-chains
   revert: symmetry clash
REVERT: B   58 LYS cc_start: 0.8107 (tttt) cc_final: 0.7805 (tttp)
REVERT: D   54 LYS cc_start: 0.7626 (mtpp) cc_final: 0.7252 (mtpt)
REVERT: D   70 GLU cc_start: 0.5533 (tt0) cc_final: 0.5187 (tt0)
REVERT: H   54 LYS cc_start: 0.8251 (mmtt) cc_final: 0.7930 (mmtm)
REVERT: J   17 ILE cc_start: 0.8819 (OUTLIER) cc_final: 0.8487 (mt)
REVERT: J   60 MET cc_start: 0.8430 (tpp) cc_final: 0.8209 (tpp)
REVERT: K   39 THR cc_start: 0.7625 (OUTLIER) cc_final: 0.7105 (m)
REVERT: K   54 LYS cc_start: 0.8268 (mmmt) cc_final: 0.8005 (mmmt)
REVERT: K   74 ASP cc_start: 0.6483 (t0) cc_final: 0.6241 (p0)
  outliers start: 32
  outliers final: 22
  residues processed: 216
  average time/residue: 0.2436
  time to fit residues: 66.7103
Evaluate side-chains
  211 residues out of total 840 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 187
  time to evaluate  : 0.864 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   16 VAL
Chi-restraints excluded: chain A residue   67 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 D residue   90 VAL
Chi-restraints excluded: chain E residue   14 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   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   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 16 optimal weight:    1.9990
   chunk 69 optimal weight:   10.0000
   chunk 61 optimal weight:    0.5980
   chunk 79 optimal weight:   10.0000
   chunk 42 optimal weight:   10.0000
   chunk 14 optimal weight:    8.9990
   chunk 12 optimal weight:    1.9990
   chunk 37 optimal weight:   30.0000
   chunk 46 optimal weight:   10.0000
   chunk 83 optimal weight:    8.9990
   chunk 52 optimal weight:    6.9990
   overall best weight:    4.1188

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

Flipped N/Q/H residues before XYZ refinement:
** 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 = 0.4276 r_free = 0.4276 target = 0.207738 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3929 r_free = 0.3929 target = 0.173593 restraints weight = 7588.305|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 42)----------------|
| r_work = 0.3972 r_free = 0.3972 target = 0.177754 restraints weight = 5826.830|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 42)----------------|
| r_work = 0.4003 r_free = 0.4003 target = 0.180739 restraints weight = 4820.613|
|-----------------------------------------------------------------------------|
r_work (final): 0.4011
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7203
moved from start:          0.5043

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.046   7752  Z= 0.359
  Angle     :  0.648   9.697  10500  Z= 0.313
  Chirality :  0.052   0.214   1152
  Planarity :  0.005   0.050   1356
  Dihedral  :  4.708  16.834   1008
  Min Nonbonded Distance : 2.524

Molprobity Statistics.
  All-atom Clashscore : 10.62
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.28 %
    Favored  : 95.72 %
  Rotamer:
    Outliers :  4.29 %
    Allowed  : 17.86 %
    Favored  : 77.86 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -3.18 (0.27), residues: 912
  helix:  0.49 (0.61), residues: 84
  sheet: -2.70 (0.25), residues: 360
  loop : -2.03 (0.28), residues: 468

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP I  88 
 HIS   0.005   0.002   HIS F  19 
 PHE   0.020   0.002   PHE L  64 
 TYR   0.013   0.002   TYR B  27 
 ARG   0.006   0.001   ARG K  49 

*********************** 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
  227 residues out of total 840 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 191
  time to evaluate  : 0.841 
Fit side-chains
   revert: symmetry clash
REVERT: D   15 LYS cc_start: 0.8131 (mttt) cc_final: 0.7681 (mttt)
REVERT: E   54 LYS cc_start: 0.7661 (mmmt) cc_final: 0.6686 (mptt)
REVERT: F   27 TYR cc_start: 0.7180 (m-80) cc_final: 0.6131 (m-80)
REVERT: F   60 MET cc_start: 0.7643 (tpp) cc_final: 0.6424 (tmm)
REVERT: J   17 ILE cc_start: 0.8793 (OUTLIER) cc_final: 0.8568 (mt)
REVERT: J   60 MET cc_start: 0.8337 (tpp) cc_final: 0.8006 (tpp)
REVERT: K   39 THR cc_start: 0.7688 (OUTLIER) cc_final: 0.7244 (m)
  outliers start: 36
  outliers final: 26
  residues processed: 210
  average time/residue: 0.2519
  time to fit residues: 67.1029
Evaluate side-chains
  214 residues out of total 840 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 186
  time to evaluate  : 0.921 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   16 VAL
Chi-restraints excluded: chain A residue   67 VAL
Chi-restraints excluded: chain C residue   17 ILE
Chi-restraints excluded: chain C residue   25 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   46 VAL
Chi-restraints excluded: chain E residue   17 ILE
Chi-restraints excluded: chain E residue   25 THR
Chi-restraints excluded: chain E residue   90 VAL
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 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 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=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 84
   random chunks:
   chunk 36 optimal weight:    4.9990
   chunk 29 optimal weight:    2.9990
   chunk 33 optimal weight:    6.9990
   chunk 27 optimal weight:    5.9990
   chunk 75 optimal weight:    1.9990
   chunk 28 optimal weight:    5.9990
   chunk 57 optimal weight:    2.9990
   chunk 42 optimal weight:   10.0000
   chunk 59 optimal weight:    5.9990
   chunk 53 optimal weight:    0.9980
   chunk 3 optimal weight:    6.9990
   overall best weight:    2.7988

-------------------------------------------------------------------------------
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**
** J  62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
J  82 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4298 r_free = 0.4298 target = 0.209563 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 54)----------------|
| r_work = 0.3978 r_free = 0.3978 target = 0.178430 restraints weight = 7439.488|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.4016 r_free = 0.4016 target = 0.182207 restraints weight = 5860.003|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 45)----------------|
| r_work = 0.4044 r_free = 0.4044 target = 0.184887 restraints weight = 4890.709|
|-----------------------------------------------------------------------------|
r_work (final): 0.4046
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7154
moved from start:          0.5280

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.037   7752  Z= 0.262
  Angle     :  0.593   9.200  10500  Z= 0.288
  Chirality :  0.050   0.172   1152
  Planarity :  0.005   0.048   1356
  Dihedral  :  4.504  15.084   1008
  Min Nonbonded Distance : 2.541

Molprobity Statistics.
  All-atom Clashscore : 9.42
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.39 %
    Favored  : 95.61 %
  Rotamer:
    Outliers :  4.52 %
    Allowed  : 19.17 %
    Favored  : 76.31 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.86 (0.27), residues: 912
  helix:  0.65 (0.61), residues: 84
  sheet: -2.34 (0.26), residues: 348
  loop : -1.97 (0.28), residues: 480

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP I  88 
 HIS   0.003   0.002   HIS F  19 
 PHE   0.016   0.002   PHE I  64 
 TYR   0.013   0.002   TYR F  27 
 ARG   0.006   0.000   ARG K  49 

*********************** 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
  230 residues out of total 840 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 38
    poor density    : 192
  time to evaluate  : 0.915 
Fit side-chains
REVERT: D   15 LYS cc_start: 0.8086 (mttt) cc_final: 0.7647 (mttt)
REVERT: D   54 LYS cc_start: 0.7893 (mtpt) cc_final: 0.7507 (mtpt)
REVERT: E   69 GLU cc_start: 0.7624 (pt0) cc_final: 0.7371 (pt0)
REVERT: F   60 MET cc_start: 0.7702 (tpp) cc_final: 0.6444 (tmm)
REVERT: K   54 LYS cc_start: 0.8359 (mmmt) cc_final: 0.8083 (mmmt)
REVERT: L   20 LEU cc_start: 0.7765 (OUTLIER) cc_final: 0.7523 (mp)
  outliers start: 38
  outliers final: 29
  residues processed: 217
  average time/residue: 0.2346
  time to fit residues: 65.5497
Evaluate side-chains
  214 residues out of total 840 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 184
  time to evaluate  : 0.885 
-------------------------------------------------------------------------------
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 C residue   39 THR
Chi-restraints excluded: chain D residue   16 VAL
Chi-restraints excluded: chain D residue   25 THR
Chi-restraints excluded: chain D residue   82 ASN
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   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   13 GLU
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   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=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 84
   random chunks:
   chunk 17 optimal weight:   10.0000
   chunk 39 optimal weight:    4.9990
   chunk 23 optimal weight:    9.9990
   chunk 76 optimal weight:    0.9990
   chunk 3 optimal weight:    6.9990
   chunk 32 optimal weight:    0.8980
   chunk 44 optimal weight:    0.0010
   chunk 73 optimal weight:    3.9990
   chunk 41 optimal weight:   20.0000
   chunk 42 optimal weight:   10.0000
   chunk 0 optimal weight:   10.0000
   overall best weight:    2.1792

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

Flipped N/Q/H residues before XYZ refinement:
B  62 GLN
** E  19 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
G  48 GLN
** J  62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4335 r_free = 0.4335 target = 0.213215 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.4007 r_free = 0.4007 target = 0.180501 restraints weight = 7512.024|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 42)----------------|
| r_work = 0.4057 r_free = 0.4057 target = 0.185381 restraints weight = 5464.821|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.4082 r_free = 0.4082 target = 0.188231 restraints weight = 4346.967|
|-----------------------------------------------------------------------------|
r_work (final): 0.3841
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7103
moved from start:          0.5464

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   7752  Z= 0.221
  Angle     :  0.578   9.606  10500  Z= 0.280
  Chirality :  0.050   0.243   1152
  Planarity :  0.004   0.048   1356
  Dihedral  :  4.319  16.186   1008
  Min Nonbonded Distance : 2.491

Molprobity Statistics.
  All-atom Clashscore : 9.22
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.62 %
    Favored  : 96.38 %
  Rotamer:
    Outliers :  4.52 %
    Allowed  : 20.60 %
    Favored  : 74.88 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.64 (0.28), residues: 912
  helix:  0.92 (0.60), residues: 84
  sheet: -2.04 (0.25), residues: 384
  loop : -1.92 (0.31), residues: 444

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP I  88 
 HIS   0.003   0.001   HIS F  19 
 PHE   0.021   0.002   PHE J  64 
 TYR   0.011   0.001   TYR B  27 
 ARG   0.007   0.000   ARG K  49 

*********************** 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
  231 residues out of total 840 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 38
    poor density    : 193
  time to evaluate  : 0.952 
Fit side-chains
   revert: symmetry clash
REVERT: D   15 LYS cc_start: 0.8128 (mttt) cc_final: 0.7649 (mttt)
REVERT: D   54 LYS cc_start: 0.7859 (mtpt) cc_final: 0.7309 (mtpt)
REVERT: D   70 GLU cc_start: 0.5993 (tt0) cc_final: 0.5562 (mt-10)
REVERT: E   69 GLU cc_start: 0.7634 (pt0) cc_final: 0.7305 (pt0)
REVERT: F   60 MET cc_start: 0.7771 (tpp) cc_final: 0.6458 (tmm)
REVERT: J   60 MET cc_start: 0.8354 (tpp) cc_final: 0.8136 (tpp)
REVERT: K   54 LYS cc_start: 0.8322 (mmmt) cc_final: 0.8109 (mmmt)
REVERT: L   20 LEU cc_start: 0.7740 (OUTLIER) cc_final: 0.7474 (mp)
  outliers start: 38
  outliers final: 32
  residues processed: 214
  average time/residue: 0.2465
  time to fit residues: 67.3934
Evaluate side-chains
  221 residues out of total 840 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 188
  time to evaluate  : 0.853 
-------------------------------------------------------------------------------
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   62 GLN
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 D residue   16 VAL
Chi-restraints excluded: chain D residue   66 VAL
Chi-restraints excluded: chain D residue   82 ASN
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   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   13 GLU
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   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 20 optimal weight:    1.9990
   chunk 68 optimal weight:    3.9990
   chunk 8 optimal weight:    7.9990
   chunk 62 optimal weight:   10.0000
   chunk 21 optimal weight:   10.0000
   chunk 57 optimal weight:    1.9990
   chunk 60 optimal weight:    3.9990
   chunk 47 optimal weight:    5.9990
   chunk 76 optimal weight:    2.9990
   chunk 52 optimal weight:    9.9990
   chunk 53 optimal weight:    4.9990
   overall best weight:    2.9990

-------------------------------------------------------------------------------
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 = 0.4114 r_free = 0.4114 target = 0.189755 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3740 r_free = 0.3740 target = 0.153172 restraints weight = 7573.221|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 49)----------------|
| r_work = 0.3782 r_free = 0.3782 target = 0.157123 restraints weight = 5702.330|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3811 r_free = 0.3811 target = 0.159850 restraints weight = 4661.396|
|-----------------------------------------------------------------------------|
r_work (final): 0.3718
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7140
moved from start:          0.5660

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.038   7752  Z= 0.274
  Angle     :  0.606  10.202  10500  Z= 0.292
  Chirality :  0.050   0.175   1152
  Planarity :  0.004   0.052   1356
  Dihedral  :  4.372  13.530   1008
  Min Nonbonded Distance : 2.463

Molprobity Statistics.
  All-atom Clashscore : 9.16
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.82 %
    Favored  : 95.18 %
  Rotamer:
    Outliers :  5.71 %
    Allowed  : 19.17 %
    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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.56 (0.28), residues: 912
  helix:  1.18 (0.62), residues: 84
  sheet: -1.97 (0.26), residues: 372
  loop : -1.95 (0.30), residues: 456

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP I  88 
 HIS   0.004   0.002   HIS F  19 
 PHE   0.014   0.002   PHE J  64 
 TYR   0.012   0.002   TYR A  27 
 ARG   0.005   0.000   ARG K  49 

*********************** 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
  239 residues out of total 840 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 48
    poor density    : 191
  time to evaluate  : 0.881 
Fit side-chains
   revert: symmetry clash
REVERT: D   15 LYS cc_start: 0.8168 (mttt) cc_final: 0.7651 (mttt)
REVERT: D   54 LYS cc_start: 0.7909 (mtpt) cc_final: 0.7477 (mtpt)
REVERT: D   70 GLU cc_start: 0.6050 (tt0) cc_final: 0.5666 (mt-10)
REVERT: E   69 GLU cc_start: 0.7697 (pt0) cc_final: 0.7303 (pt0)
REVERT: F   60 MET cc_start: 0.7832 (tpp) cc_final: 0.6518 (tmm)
REVERT: G   79 PRO cc_start: 0.7471 (Cg_endo) cc_final: 0.6970 (Cg_exo)
REVERT: H   47 LEU cc_start: 0.7804 (OUTLIER) cc_final: 0.7515 (mp)
REVERT: J   24 GLU cc_start: 0.5753 (mm-30) cc_final: 0.4899 (mm-30)
REVERT: L   20 LEU cc_start: 0.7845 (OUTLIER) cc_final: 0.7565 (mp)
  outliers start: 48
  outliers final: 39
  residues processed: 218
  average time/residue: 0.2553
  time to fit residues: 73.0357
Evaluate side-chains
  231 residues out of total 840 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 41
    poor density    : 190
  time to evaluate  : 0.890 
-------------------------------------------------------------------------------
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   38 ILE
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 D residue   16 VAL
Chi-restraints excluded: chain D residue   20 LEU
Chi-restraints excluded: chain D residue   25 THR
Chi-restraints excluded: chain D residue   46 VAL
Chi-restraints excluded: chain D residue   66 VAL
Chi-restraints excluded: chain D residue   82 ASN
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   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   47 LEU
Chi-restraints excluded: chain H residue   89 LEU
Chi-restraints excluded: chain I residue   13 GLU
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 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   33 VAL
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 17 optimal weight:    6.9990
   chunk 76 optimal weight:   10.0000
   chunk 5 optimal weight:   10.0000
   chunk 9 optimal weight:    8.9990
   chunk 49 optimal weight:    0.8980
   chunk 31 optimal weight:   10.0000
   chunk 65 optimal weight:   10.0000
   chunk 64 optimal weight:    2.9990
   chunk 60 optimal weight:    2.9990
   chunk 4 optimal weight:    4.9990
   chunk 44 optimal weight:    0.0970
   overall best weight:    2.3984

-------------------------------------------------------------------------------
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 = 0.4109 r_free = 0.4109 target = 0.189696 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3751 r_free = 0.3751 target = 0.154520 restraints weight = 7561.617|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3784 r_free = 0.3784 target = 0.157763 restraints weight = 5847.712|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3811 r_free = 0.3811 target = 0.160415 restraints weight = 4893.862|
|-----------------------------------------------------------------------------|
r_work (final): 0.3756
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7139
moved from start:          0.5767

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= 0.236
  Angle     :  0.597  10.122  10500  Z= 0.288
  Chirality :  0.050   0.159   1152
  Planarity :  0.004   0.051   1356
  Dihedral  :  4.271  13.421   1008
  Min Nonbonded Distance : 2.490

Molprobity Statistics.
  All-atom Clashscore : 8.96
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.62 %
    Favored  : 96.38 %
  Rotamer:
    Outliers :  5.12 %
    Allowed  : 20.12 %
    Favored  : 74.76 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.37 (0.29), residues: 912
  helix:  1.28 (0.62), residues: 84
  sheet: -1.84 (0.26), residues: 384
  loop : -1.81 (0.31), residues: 444

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP I  88 
 HIS   0.003   0.001   HIS F  19 
 PHE   0.014   0.002   PHE J  64 
 TYR   0.011   0.001   TYR B  27 
 ARG   0.005   0.000   ARG K  49 

*********************** 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
  237 residues out of total 840 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 43
    poor density    : 194
  time to evaluate  : 0.906 
Fit side-chains
   revert: symmetry clash
REVERT: D   15 LYS cc_start: 0.8089 (mttt) cc_final: 0.7595 (mttt)
REVERT: D   54 LYS cc_start: 0.7940 (mtpt) cc_final: 0.7541 (mtpt)
REVERT: D   70 GLU cc_start: 0.6142 (tt0) cc_final: 0.5764 (mt-10)
REVERT: E   69 GLU cc_start: 0.7669 (pt0) cc_final: 0.7299 (pt0)
REVERT: F   60 MET cc_start: 0.7820 (tpp) cc_final: 0.6525 (tmm)
REVERT: G   79 PRO cc_start: 0.7473 (Cg_endo) cc_final: 0.6967 (Cg_exo)
REVERT: H   47 LEU cc_start: 0.7719 (OUTLIER) cc_final: 0.7420 (mp)
REVERT: J   24 GLU cc_start: 0.5778 (mm-30) cc_final: 0.4937 (mm-30)
REVERT: J   61 ASP cc_start: 0.7650 (t70) cc_final: 0.7364 (t70)
REVERT: K   54 LYS cc_start: 0.8286 (mmmt) cc_final: 0.8017 (mmmt)
REVERT: L   20 LEU cc_start: 0.7741 (OUTLIER) cc_final: 0.7467 (mp)
  outliers start: 43
  outliers final: 39
  residues processed: 216
  average time/residue: 0.2317
  time to fit residues: 63.9200
Evaluate side-chains
  230 residues out of total 840 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 41
    poor density    : 189
  time to evaluate  : 0.878 
-------------------------------------------------------------------------------
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   38 ILE
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   39 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 D residue   46 VAL
Chi-restraints excluded: chain D residue   66 VAL
Chi-restraints excluded: chain D residue   82 ASN
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   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   47 LEU
Chi-restraints excluded: chain H residue   89 LEU
Chi-restraints excluded: chain I residue   13 GLU
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 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   33 VAL
Chi-restraints excluded: chain L residue   85 VAL
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 84
   random chunks:
   chunk 15 optimal weight:    1.9990
   chunk 82 optimal weight:    4.9990
   chunk 34 optimal weight:    9.9990
   chunk 48 optimal weight:    4.9990
   chunk 4 optimal weight:    7.9990
   chunk 25 optimal weight:    4.9990
   chunk 54 optimal weight:    0.8980
   chunk 66 optimal weight:    0.0060
   chunk 64 optimal weight:    2.9990
   chunk 2 optimal weight:    5.9990
   chunk 70 optimal weight:    0.4980
   overall best weight:    1.2800

-------------------------------------------------------------------------------
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**
J  82 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4146 r_free = 0.4146 target = 0.192903 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3776 r_free = 0.3776 target = 0.156448 restraints weight = 7656.465|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3815 r_free = 0.3815 target = 0.160304 restraints weight = 5659.296|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.3850 r_free = 0.3850 target = 0.163533 restraints weight = 4576.037|
|-----------------------------------------------------------------------------|
r_work (final): 0.3744
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7065
moved from start:          0.5782

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   7752  Z= 0.166
  Angle     :  0.569   9.505  10500  Z= 0.273
  Chirality :  0.049   0.142   1152
  Planarity :  0.004   0.051   1356
  Dihedral  :  4.004  12.773   1008
  Min Nonbonded Distance : 2.412

Molprobity Statistics.
  All-atom Clashscore : 8.43
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.63 %
    Favored  : 97.37 %
  Rotamer:
    Outliers :  4.52 %
    Allowed  : 21.43 %
    Favored  : 74.05 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.16 (0.29), residues: 912
  helix:  1.55 (0.62), residues: 84
  sheet: -1.72 (0.26), residues: 384
  loop : -1.67 (0.32), residues: 444

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP A  88 
 HIS   0.002   0.001   HIS I  19 
 PHE   0.014   0.001   PHE J  64 
 TYR   0.011   0.001   TYR L  55 
 ARG   0.008   0.000   ARG D  37 

*********************** 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
  235 residues out of total 840 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 38
    poor density    : 197
  time to evaluate  : 0.864 
Fit side-chains
   revert: symmetry clash
REVERT: B   36 GLU cc_start: 0.5389 (OUTLIER) cc_final: 0.4867 (tt0)
REVERT: D   15 LYS cc_start: 0.8017 (mttt) cc_final: 0.7511 (mttt)
REVERT: D   46 VAL cc_start: 0.8200 (OUTLIER) cc_final: 0.7742 (p)
REVERT: D   54 LYS cc_start: 0.7925 (mtpt) cc_final: 0.7556 (mtpt)
REVERT: D   70 GLU cc_start: 0.6246 (tt0) cc_final: 0.5879 (mt-10)
REVERT: E   69 GLU cc_start: 0.7664 (pt0) cc_final: 0.7312 (pt0)
REVERT: F   60 MET cc_start: 0.7898 (tpp) cc_final: 0.6562 (tmm)
REVERT: G   54 LYS cc_start: 0.8300 (mmtt) cc_final: 0.8062 (mmtt)
REVERT: G   60 MET cc_start: 0.8000 (tpt) cc_final: 0.7750 (tpt)
REVERT: G   77 ARG cc_start: 0.6756 (ptm160) cc_final: 0.6443 (ptm160)
REVERT: G   79 PRO cc_start: 0.7454 (Cg_endo) cc_final: 0.6948 (Cg_exo)
REVERT: J   24 GLU cc_start: 0.5676 (mm-30) cc_final: 0.4787 (mm-30)
REVERT: J   61 ASP cc_start: 0.7684 (t70) cc_final: 0.7388 (t0)
REVERT: K   13 GLU cc_start: 0.5529 (OUTLIER) cc_final: 0.5179 (pm20)
REVERT: K   54 LYS cc_start: 0.8285 (mmmt) cc_final: 0.8009 (mmmt)
  outliers start: 38
  outliers final: 29
  residues processed: 218
  average time/residue: 0.2318
  time to fit residues: 64.9706
Evaluate side-chains
  217 residues out of total 840 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 185
  time to evaluate  : 0.778 
-------------------------------------------------------------------------------
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   36 GLU
Chi-restraints excluded: chain B residue   38 ILE
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 D residue   46 VAL
Chi-restraints excluded: chain D residue   66 VAL
Chi-restraints excluded: chain D residue   82 ASN
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   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   33 VAL
Chi-restraints excluded: chain I residue   13 GLU
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 K residue   13 GLU
Chi-restraints excluded: chain K residue   16 VAL
Chi-restraints excluded: chain K residue   17 ILE
Chi-restraints excluded: chain L residue   33 VAL
Chi-restraints excluded: chain L residue   85 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Traceback (most recent call last):
  File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in <module>
    run_program(real_space_refine.Program)
  File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/cctbx_project/iotbx/cli_parser.py", line 946, in run_program
    task.run()
  File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/phenix/phenix/programs/real_space_refine.py", line 210, in run
    log         = self.logger)
  File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__
    log                   = log)
  File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__
    self.caller(self.refine_xyz)
  File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller
    func()
  File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz
    self.minimization_no_ncs()
  File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 767, in minimization_no_ncs
    log                         = self.log)
  File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__
    gradients_method            = gradients_method)
  File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__
    rms_angles_limit = rms_angles_limit)
  File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine
    rms_angles_limit = rms_angles_limit)
  File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__
    weight     = weight)
  File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine
    states_collector                = self.states_accumulator)
  File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__
    exception_handling_params=lbfgs_exception_handling_params)
  File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run
    line_search)
  File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus
    f, g = target_evaluator.compute_functional_and_gradients()
  File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients
    compute_gradients=True)
  File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1525, in energies_sites
    flags=flags, sites_cart=sites_cart, site_labels=site_labels)
  File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1427, in pair_proxies
    check_bonded_distance_cutoff(sites_frac=sites_frac)
  File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1308, in check_bonded_distance_cutoff
    raise RuntimeError(msg)
RuntimeError: Bond distance > max_reasonable_bond_distance: 64.0522 > 50:
  distance: 83 - 89:  15.495
  distance: 89 - 90:  18.263
  distance: 90 - 91:  22.024
  distance: 90 - 93:   6.121
  distance: 91 - 92:  16.036
  distance: 91 - 95:   9.922
  distance: 93 - 94:  17.563
  distance: 95 - 96:  16.432
  distance: 96 - 97:  11.915
  distance: 96 - 99:  21.035
  distance: 97 - 98:   5.857
  distance: 97 - 103:  14.018
  distance: 99 - 100:  22.718
  distance: 100 - 101:   6.011
  distance: 100 - 102:  16.812
  distance: 103 - 104:  21.934
  distance: 104 - 105:  15.084
  distance: 104 - 107:  17.196
  distance: 105 - 106:  16.894
  distance: 105 - 111:  33.074
  distance: 107 - 108:  14.792
  distance: 108 - 109:  19.720
  distance: 108 - 110:  26.725
  distance: 111 - 112:  13.516
  distance: 112 - 113:  26.328
  distance: 112 - 115:  25.253
  distance: 113 - 114:  14.953
  distance: 113 - 119:  30.112
  distance: 115 - 116:  27.388
  distance: 116 - 117:  27.047
  distance: 116 - 118:  29.155
  distance: 119 - 120:  19.348
  distance: 120 - 121:   8.815
  distance: 120 - 123:   7.996
  distance: 121 - 122:  16.770
  distance: 121 - 124:  17.151
  distance: 124 - 125:  15.799
  distance: 125 - 126:  10.132
  distance: 125 - 128:  17.748
  distance: 126 - 127:  26.107
  distance: 126 - 135:  50.544
  distance: 128 - 129:  23.168
  distance: 129 - 130:   4.240
  distance: 130 - 131:  11.697
  distance: 131 - 132:   9.963
  distance: 132 - 133:   7.654
  distance: 132 - 134:  17.067
  distance: 135 - 136:  30.924
  distance: 136 - 137:  18.545
  distance: 136 - 139:  37.903
  distance: 137 - 138:  19.699
  distance: 137 - 143:  24.393
  distance: 139 - 140:  55.542
  distance: 140 - 141:  51.124
  distance: 140 - 142:  38.634
  distance: 143 - 144:  13.667
  distance: 143 - 149:  26.571
  distance: 144 - 145:  43.298
  distance: 144 - 147:   6.178
  distance: 145 - 146:  11.548
  distance: 145 - 150:  22.542
  distance: 147 - 148:  12.574
  distance: 148 - 149:  22.577
  distance: 150 - 151:  15.162
  distance: 151 - 152:  38.806
  distance: 151 - 154:  12.432
  distance: 152 - 153:  27.921
  distance: 152 - 156:  33.558
  distance: 154 - 155:  45.056
  distance: 156 - 157:   5.927
  distance: 157 - 158:   5.177
  distance: 157 - 160:  28.245
  distance: 158 - 159:  48.353
  distance: 158 - 167:  28.063
  distance: 159 - 178:  20.951
  distance: 160 - 161:  24.092
  distance: 161 - 162:  16.823
  distance: 161 - 163:  14.109
  distance: 162 - 164:  14.613
  distance: 163 - 165:  29.077
  distance: 164 - 166:  28.043
  distance: 165 - 166:  23.866