Starting phenix.real_space_refine
on Mon Jun  9 12:14:04 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9itm_60871/06_2025/9itm_60871.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9itm_60871/06_2025/9itm_60871.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.16
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/9itm_60871/06_2025/9itm_60871.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9itm_60871/06_2025/9itm_60871.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9itm_60871/06_2025/9itm_60871.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9itm_60871/06_2025/9itm_60871.cif"
  }
  resolution = 3.16
  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=  -0.001 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      36      5.16       5
     C    7167      2.51       5
     N    1706      2.21       5
     O    1783      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 9 residue(s): 0.04s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib"
  Total number of atoms: 10692
  Number of models: 1
  Model: ""
    Number of chains: 16
    Chain: "H"
      Number of atoms: 506
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 72, 506
          Classifications: {'peptide': 72}
          Incomplete info: {'truncation_to_alanine': 2}
          Link IDs: {'PTRANS': 2, 'TRANS': 69}
          Unresolved non-hydrogen bonds: 7
          Unresolved non-hydrogen angles: 8
          Unresolved non-hydrogen dihedrals: 6
          Planarities with less than four sites: {'GLU:plan': 1}
          Unresolved non-hydrogen planarities: 4
    Chain: "I"
      Number of atoms: 513
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 72, 513
          Classifications: {'peptide': 72}
          Link IDs: {'PTRANS': 2, 'TRANS': 69}
    Chain: "J"
      Number of atoms: 513
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 72, 513
          Classifications: {'peptide': 72}
          Link IDs: {'PTRANS': 2, 'TRANS': 69}
    Chain: "K"
      Number of atoms: 513
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 72, 513
          Classifications: {'peptide': 72}
          Link IDs: {'PTRANS': 2, 'TRANS': 69}
    Chain: "L"
      Number of atoms: 513
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 72, 513
          Classifications: {'peptide': 72}
          Link IDs: {'PTRANS': 2, 'TRANS': 69}
    Chain: "M"
      Number of atoms: 513
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 72, 513
          Classifications: {'peptide': 72}
          Link IDs: {'PTRANS': 2, 'TRANS': 69}
    Chain: "N"
      Number of atoms: 513
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 72, 513
          Classifications: {'peptide': 72}
          Link IDs: {'PTRANS': 2, 'TRANS': 69}
    Chain: "O"
      Number of atoms: 513
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 72, 513
          Classifications: {'peptide': 72}
          Link IDs: {'PTRANS': 2, 'TRANS': 69}
    Chain: "P"
      Number of atoms: 513
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 72, 513
          Classifications: {'peptide': 72}
          Link IDs: {'PTRANS': 2, 'TRANS': 69}
    Chain: "Q"
      Number of atoms: 513
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 72, 513
          Classifications: {'peptide': 72}
          Link IDs: {'PTRANS': 2, 'TRANS': 69}
    Chain: "T"
      Number of atoms: 2064
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 266, 2064
          Classifications: {'peptide': 266}
          Incomplete info: {'truncation_to_alanine': 2}
          Link IDs: {'PTRANS': 15, 'TRANS': 250}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 8
          Unresolved non-hydrogen angles: 10
          Unresolved non-hydrogen dihedrals: 6
          Planarities with less than four sites: {'GLU:plan': 2}
          Unresolved non-hydrogen planarities: 8
    Chain: "U"
      Number of atoms: 396
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 48, 396
          Classifications: {'peptide': 48}
          Link IDs: {'PTRANS': 2, 'TRANS': 45}
    Chain: "V"
      Number of atoms: 335
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 40, 335
          Classifications: {'peptide': 40}
          Link IDs: {'PTRANS': 2, 'TRANS': 37}
    Chain: "X"
      Number of atoms: 348
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 42, 348
          Classifications: {'peptide': 42}
          Link IDs: {'PTRANS': 2, 'TRANS': 39}
    Chain: "Y"
      Number of atoms: 388
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 47, 388
          Classifications: {'peptide': 47}
          Link IDs: {'PTRANS': 2, 'TRANS': 44}
    Chain: "Z"
      Number of atoms: 2038
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 261, 2038
          Classifications: {'peptide': 261}
          Link IDs: {'PTRANS': 14, 'TRANS': 246}
          Chain breaks: 1
  Time building chain proxies: 7.60, per 1000 atoms: 0.71
  Number of scatterers: 10692
  At special positions: 0
  Unit cell: (86.49, 127.41, 82.77, 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      36     16.00
     O    1783      8.00
     N    1706      7.00
     C    7167      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=2, symmetry=0
    Simple disulfide: pdb=" SG  CYS T 135 " - pdb=" SG  CYS T 173 " distance=2.86
    Simple disulfide: pdb=" SG  CYS Z 135 " - pdb=" SG  CYS Z 173 " distance=2.70

  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: 3.09
  Conformation dependent library (CDL) restraints added in 1.6 seconds
  

  2776 Ramachandran restraints generated.
    1388 Oldfield, 0 Emsley, 1388 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2520

  Finding SS restraints...
    Secondary structure from input PDB file:
      52 helices and 3 sheets defined
      84.5% alpha, 0.7% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.98
  Creating SS restraints...
    Processing helix  chain 'H' and resid 4 through 38
      Proline residue:  H  20  - end of helix
    Processing helix  chain 'H' and resid 41 through 72
      removed outlier: 3.882A  pdb=" N   ALA H  58 " --> pdb=" O   ALA H  54 " (cutoff:3.500A)
      removed outlier: 3.575A  pdb=" N   ALA H  60 " --> pdb=" O   THR H  56 " (cutoff:3.500A)
    Processing helix  chain 'I' and resid 3 through 38
      Proline residue:  I  20  - end of helix
    Processing helix  chain 'I' and resid 41 through 71
      removed outlier: 3.914A  pdb=" N   ALA I  58 " --> pdb=" O   ALA I  54 " (cutoff:3.500A)
      removed outlier: 3.592A  pdb=" N   ALA I  60 " --> pdb=" O   THR I  56 " (cutoff:3.500A)
    Processing helix  chain 'J' and resid 3 through 38
      Proline residue:  J  20  - end of helix
    Processing helix  chain 'J' and resid 41 through 72
      removed outlier: 3.815A  pdb=" N   ALA J  58 " --> pdb=" O   ALA J  54 " (cutoff:3.500A)
    Processing helix  chain 'K' and resid 3 through 16
      removed outlier: 3.604A  pdb=" N   GLY K  16 " --> pdb=" O   ALA K  12 " (cutoff:3.500A)
    Processing helix  chain 'K' and resid 17 through 38
      removed outlier: 3.736A  pdb=" N   GLY K  21 " --> pdb=" O   ALA K  17 " (cutoff:3.500A)
      removed outlier: 4.099A  pdb=" N   VAL K  22 " --> pdb=" O   ILE K  18 " (cutoff:3.500A)
    Processing helix  chain 'K' and resid 41 through 72
      removed outlier: 3.674A  pdb=" N   ALA K  58 " --> pdb=" O   ALA K  54 " (cutoff:3.500A)
      removed outlier: 3.556A  pdb=" N   ALA K  67 " --> pdb=" O   GLY K  63 " (cutoff:3.500A)
      removed outlier: 3.512A  pdb=" N   LEU K  69 " --> pdb=" O   VAL K  65 " (cutoff:3.500A)
    Processing helix  chain 'L' and resid 3 through 17
    Processing helix  chain 'L' and resid 18 through 37
      removed outlier: 3.537A  pdb=" N   ARG L  37 " --> pdb=" O   GLN L  33 " (cutoff:3.500A)
    Processing helix  chain 'L' and resid 38 through 40
      No H-bonds generated for 'chain 'L' and resid 38 through 40'
    Processing helix  chain 'L' and resid 41 through 72
      removed outlier: 3.696A  pdb=" N   ALA L  58 " --> pdb=" O   ALA L  54 " (cutoff:3.500A)
    Processing helix  chain 'M' and resid 3 through 38
      Proline residue:  M  20  - end of helix
    Processing helix  chain 'M' and resid 41 through 72
      removed outlier: 4.683A  pdb=" N   THR M  47 " --> pdb=" O   ASN M  43 " (cutoff:3.500A)
      removed outlier: 4.440A  pdb=" N   TYR M  48 " --> pdb=" O   ARG M  44 " (cutoff:3.500A)
      removed outlier: 3.590A  pdb=" N   GLU M  57 " --> pdb=" O   ILE M  53 " (cutoff:3.500A)
      removed outlier: 3.863A  pdb=" N   ALA M  58 " --> pdb=" O   ALA M  54 " (cutoff:3.500A)
    Processing helix  chain 'N' and resid 3 through 38
      removed outlier: 3.988A  pdb=" N   GLY N  19 " --> pdb=" O   LEU N  15 " (cutoff:3.500A)
      Proline residue:  N  20  - end of helix
    Processing helix  chain 'N' and resid 41 through 72
      removed outlier: 3.590A  pdb=" N   ALA N  60 " --> pdb=" O   THR N  56 " (cutoff:3.500A)
    Processing helix  chain 'O' and resid 5 through 38
      Proline residue:  O  20  - end of helix
    Processing helix  chain 'O' and resid 41 through 72
      removed outlier: 4.724A  pdb=" N   LEU O  59 " --> pdb=" O   PHE O  55 " (cutoff:3.500A)
      removed outlier: 3.673A  pdb=" N   ALA O  60 " --> pdb=" O   THR O  56 " (cutoff:3.500A)
      removed outlier: 3.543A  pdb=" N   PHE O  72 " --> pdb=" O   PHE O  68 " (cutoff:3.500A)
    Processing helix  chain 'P' and resid 3 through 38
      removed outlier: 3.891A  pdb=" N   VAL P   7 " --> pdb=" O   GLY P   3 " (cutoff:3.500A)
      Proline residue:  P  20  - end of helix
    Processing helix  chain 'P' and resid 41 through 71
      removed outlier: 4.153A  pdb=" N   THR P  47 " --> pdb=" O   ASN P  43 " (cutoff:3.500A)
      removed outlier: 4.327A  pdb=" N   TYR P  48 " --> pdb=" O   ARG P  44 " (cutoff:3.500A)
      removed outlier: 3.705A  pdb=" N   ALA P  58 " --> pdb=" O   ALA P  54 " (cutoff:3.500A)
    Processing helix  chain 'Q' and resid 3 through 38
      removed outlier: 3.674A  pdb=" N   VAL Q   7 " --> pdb=" O   GLY Q   3 " (cutoff:3.500A)
      Proline residue:  Q  20  - end of helix
    Processing helix  chain 'Q' and resid 41 through 72
      removed outlier: 3.932A  pdb=" N   THR Q  47 " --> pdb=" O   ASN Q  43 " (cutoff:3.500A)
      removed outlier: 4.117A  pdb=" N   LEU Q  59 " --> pdb=" O   PHE Q  55 " (cutoff:3.500A)
      removed outlier: 3.963A  pdb=" N   ALA Q  60 " --> pdb=" O   THR Q  56 " (cutoff:3.500A)
    Processing helix  chain 'T' and resid 19 through 23
      removed outlier: 3.953A  pdb=" N   ARG T  22 " --> pdb=" O   ILE T  19 " (cutoff:3.500A)
      removed outlier: 3.640A  pdb=" N   PHE T  23 " --> pdb=" O   ALA T  20 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'T' and resid 19 through 23'
    Processing helix  chain 'T' and resid 50 through 71
      removed outlier: 5.197A  pdb=" N   ILE T  56 " --> pdb=" O   PHE T  52 " (cutoff:3.500A)
    Processing helix  chain 'T' and resid 79 through 97
    Processing helix  chain 'T' and resid 106 through 125
      removed outlier: 3.521A  pdb=" N   VAL T 110 " --> pdb=" O   ALA T 106 " (cutoff:3.500A)
      removed outlier: 4.219A  pdb=" N   PHE T 114 " --> pdb=" O   VAL T 110 " (cutoff:3.500A)
      removed outlier: 4.173A  pdb=" N   PHE T 119 " --> pdb=" O   LEU T 115 " (cutoff:3.500A)
      removed outlier: 3.555A  pdb=" N   GLY T 124 " --> pdb=" O   GLY T 120 " (cutoff:3.500A)
      removed outlier: 3.976A  pdb=" N   LEU T 125 " --> pdb=" O   ASN T 121 " (cutoff:3.500A)
    Processing helix  chain 'T' and resid 171 through 178
      removed outlier: 3.928A  pdb=" N   ALA T 175 " --> pdb=" O   THR T 172 " (cutoff:3.500A)
      removed outlier: 5.481A  pdb=" N   GLN T 176 " --> pdb=" O   CYS T 173 " (cutoff:3.500A)
      removed outlier: 3.803A  pdb=" N   LYS T 178 " --> pdb=" O   ALA T 175 " (cutoff:3.500A)
    Processing helix  chain 'T' and resid 186 through 190
    Processing helix  chain 'T' and resid 192 through 212
      removed outlier: 4.269A  pdb=" N   ALA T 212 " --> pdb=" O   TRP T 208 " (cutoff:3.500A)
    Processing helix  chain 'T' and resid 216 through 221
    Processing helix  chain 'T' and resid 227 through 268
      removed outlier: 3.536A  pdb=" N   VAL T 231 " --> pdb=" O   ILE T 227 " (cutoff:3.500A)
      Proline residue:  T 243  - end of helix
    Processing helix  chain 'T' and resid 272 through 304
      removed outlier: 4.579A  pdb=" N   PHE T 276 " --> pdb=" O   LEU T 272 " (cutoff:3.500A)
      removed outlier: 3.700A  pdb=" N   ALA T 292 " --> pdb=" O   ALA T 288 " (cutoff:3.500A)
    Processing helix  chain 'U' and resid 9 through 29
    Processing helix  chain 'U' and resid 30 through 48
    Processing helix  chain 'V' and resid 7 through 26
    Processing helix  chain 'V' and resid 30 through 43
    Processing helix  chain 'X' and resid 7 through 29
    Processing helix  chain 'X' and resid 29 through 43
    Processing helix  chain 'Y' and resid 7 through 29
    Processing helix  chain 'Y' and resid 30 through 47
      removed outlier: 3.608A  pdb=" N   SER Y  47 " --> pdb=" O   ARG Y  43 " (cutoff:3.500A)
    Processing helix  chain 'Z' and resid 17 through 24
      removed outlier: 3.846A  pdb=" N   ALA Z  20 " --> pdb=" O   ILE Z  17 " (cutoff:3.500A)
      removed outlier: 5.012A  pdb=" N   ARG Z  22 " --> pdb=" O   ILE Z  19 " (cutoff:3.500A)
    Processing helix  chain 'Z' and resid 50 through 71
      removed outlier: 3.898A  pdb=" N   VAL Z  54 " --> pdb=" O   ASN Z  50 " (cutoff:3.500A)
    Processing helix  chain 'Z' and resid 79 through 99
    Processing helix  chain 'Z' and resid 102 through 125
      Proline residue:  Z 108  - end of helix
      removed outlier: 4.108A  pdb=" N   LEU Z 125 " --> pdb=" O   ASN Z 121 " (cutoff:3.500A)
    Processing helix  chain 'Z' and resid 172 through 176
    Processing helix  chain 'Z' and resid 186 through 189
    Processing helix  chain 'Z' and resid 190 through 214
      removed outlier: 3.565A  pdb=" N   THR Z 194 " --> pdb=" O   ASP Z 190 " (cutoff:3.500A)
    Processing helix  chain 'Z' and resid 215 through 220
      removed outlier: 3.724A  pdb=" N   LYS Z 219 " --> pdb=" O   PRO Z 215 " (cutoff:3.500A)
    Processing helix  chain 'Z' and resid 221 through 225
      removed outlier: 3.798A  pdb=" N   ASN Z 225 " --> pdb=" O   PHE Z 222 " (cutoff:3.500A)
    Processing helix  chain 'Z' and resid 229 through 268
      removed outlier: 3.998A  pdb=" N   ILE Z 233 " --> pdb=" O   SER Z 229 " (cutoff:3.500A)
      Proline residue:  Z 243  - end of helix
      removed outlier: 3.777A  pdb=" N   LEU Z 250 " --> pdb=" O   LEU Z 246 " (cutoff:3.500A)
    Processing helix  chain 'Z' and resid 273 through 304
      removed outlier: 3.926A  pdb=" N   PHE Z 285 " --> pdb=" O   VAL Z 281 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'T' and resid 132 through 133
    Processing sheet with id=AA2, first strand: chain 'Y' and resid 4 through 5
    Processing sheet with id=AA3, first strand: chain 'Z' and resid 39 through 41
      removed outlier: 7.236A  pdb=" N   ILE Z  48 " --> pdb=" O   PHE Z  40 " (cutoff:3.500A)

    921 hydrogen bonds defined for protein.
    2724 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: 3.41

  Time building geometry restraints manager: 3.59 seconds

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

  Histogram of bond lengths:
        1.22 -     1.34: 3313
        1.34 -     1.46: 1617
        1.46 -     1.58: 5905
        1.58 -     1.69: 0
        1.69 -     1.81: 68
  Bond restraints: 10903
  Sorted by residual:
  bond pdb=" N   ILE O  70 "
       pdb=" CA  ILE O  70 "
    ideal  model  delta    sigma   weight residual
    1.455  1.495 -0.040 1.06e-02 8.90e+03 1.41e+01
  bond pdb=" N   ILE M  70 "
       pdb=" CA  ILE M  70 "
    ideal  model  delta    sigma   weight residual
    1.460  1.495 -0.035 1.19e-02 7.06e+03 8.60e+00
  bond pdb=" N   ILE Q  70 "
       pdb=" CA  ILE Q  70 "
    ideal  model  delta    sigma   weight residual
    1.460  1.495 -0.035 1.19e-02 7.06e+03 8.46e+00
  bond pdb=" N   ILE K  70 "
       pdb=" CA  ILE K  70 "
    ideal  model  delta    sigma   weight residual
    1.460  1.495 -0.034 1.19e-02 7.06e+03 8.40e+00
  bond pdb=" N   ILE N  70 "
       pdb=" CA  ILE N  70 "
    ideal  model  delta    sigma   weight residual
    1.461  1.496 -0.035 1.22e-02 6.72e+03 8.21e+00
  ... (remaining 10898 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.99: 14553
        1.99 -     3.99: 241
        3.99 -     5.98: 27
        5.98 -     7.98: 1
        7.98 -     9.97: 1
  Bond angle restraints: 14823
  Sorted by residual:
  angle pdb=" C   THR T 172 "
        pdb=" N   CYS T 173 "
        pdb=" CA  CYS T 173 "
      ideal   model   delta    sigma   weight residual
     122.62  112.65    9.97 1.78e+00 3.16e-01 3.14e+01
  angle pdb=" N   ILE O  70 "
        pdb=" CA  ILE O  70 "
        pdb=" C   ILE O  70 "
      ideal   model   delta    sigma   weight residual
     112.12  108.50    3.62 8.40e-01 1.42e+00 1.86e+01
  angle pdb=" N   ILE P  70 "
        pdb=" CA  ILE P  70 "
        pdb=" C   ILE P  70 "
      ideal   model   delta    sigma   weight residual
     113.42  108.55    4.87 1.17e+00 7.31e-01 1.74e+01
  angle pdb=" C   CYS T 173 "
        pdb=" CA  CYS T 173 "
        pdb=" CB  CYS T 173 "
      ideal   model   delta    sigma   weight residual
     111.40  116.64   -5.24 1.29e+00 6.01e-01 1.65e+01
  angle pdb=" N   ILE L  70 "
        pdb=" CA  ILE L  70 "
        pdb=" C   ILE L  70 "
      ideal   model   delta    sigma   weight residual
     111.67  108.19    3.48 9.50e-01 1.11e+00 1.34e+01
  ... (remaining 14818 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.77: 5386
       17.77 -    35.53: 706
       35.53 -    53.30: 141
       53.30 -    71.07: 16
       71.07 -    88.83: 15
  Dihedral angle restraints: 6264
    sinusoidal: 2310
      harmonic: 3954
  Sorted by residual:
  dihedral pdb=" CB  CYS T 135 "
           pdb=" SG  CYS T 135 "
           pdb=" SG  CYS T 173 "
           pdb=" CB  CYS T 173 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00  173.86  -80.86     1      1.00e+01 1.00e-02 8.07e+01
  dihedral pdb=" CA  CYS T 173 "
           pdb=" C   CYS T 173 "
           pdb=" N   ALA T 174 "
           pdb=" CA  ALA T 174 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  156.52   23.48     0      5.00e+00 4.00e-02 2.20e+01
  dihedral pdb=" CA  PHE T  52 "
           pdb=" C   PHE T  52 "
           pdb=" N   VAL T  53 "
           pdb=" CA  VAL T  53 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  157.05   22.95     0      5.00e+00 4.00e-02 2.11e+01
  ... (remaining 6261 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.043: 1330
       0.043 -    0.086: 381
       0.086 -    0.129: 88
       0.129 -    0.172: 11
       0.172 -    0.215: 11
  Chirality restraints: 1821
  Sorted by residual:
  chirality pdb=" CA  ILE K  70 "
            pdb=" N   ILE K  70 "
            pdb=" C   ILE K  70 "
            pdb=" CB  ILE K  70 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.65   -0.22 2.00e-01 2.50e+01 1.16e+00
  chirality pdb=" CA  ILE L  70 "
            pdb=" N   ILE L  70 "
            pdb=" C   ILE L  70 "
            pdb=" CB  ILE L  70 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.65   -0.21 2.00e-01 2.50e+01 1.12e+00
  chirality pdb=" CA  CYS Z 135 "
            pdb=" N   CYS Z 135 "
            pdb=" C   CYS Z 135 "
            pdb=" CB  CYS Z 135 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.71   -0.20 2.00e-01 2.50e+01 9.84e-01
  ... (remaining 1818 not shown)

  Planarity restraints: 1852
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   GLY Q  19 "    0.048 5.00e-02 4.00e+02   7.34e-02 8.62e+00
        pdb=" N   PRO Q  20 "   -0.127 5.00e-02 4.00e+02
        pdb=" CA  PRO Q  20 "    0.038 5.00e-02 4.00e+02
        pdb=" CD  PRO Q  20 "    0.040 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   GLY M  19 "   -0.044 5.00e-02 4.00e+02   6.66e-02 7.09e+00
        pdb=" N   PRO M  20 "    0.115 5.00e-02 4.00e+02
        pdb=" CA  PRO M  20 "   -0.035 5.00e-02 4.00e+02
        pdb=" CD  PRO M  20 "   -0.037 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   GLY H  19 "    0.043 5.00e-02 4.00e+02   6.52e-02 6.79e+00
        pdb=" N   PRO H  20 "   -0.113 5.00e-02 4.00e+02
        pdb=" CA  PRO H  20 "    0.034 5.00e-02 4.00e+02
        pdb=" CD  PRO H  20 "    0.036 5.00e-02 4.00e+02
  ... (remaining 1849 not shown)

  Histogram of nonbonded interaction distances:
        2.24 -     2.77: 2295
        2.77 -     3.30: 11530
        3.30 -     3.84: 18620
        3.84 -     4.37: 20861
        4.37 -     4.90: 36088
  Nonbonded interactions: 89394
  Sorted by model distance:
  nonbonded pdb=" OH  TYR L  48 "
            pdb=" OE2 GLU M  42 "
     model   vdw
     2.239 3.040
  nonbonded pdb=" O   PRO Z 108 "
            pdb=" OG1 THR Z 112 "
     model   vdw
     2.249 3.040
  nonbonded pdb=" O   PHE T  86 "
            pdb=" OG  SER T  90 "
     model   vdw
     2.279 3.040
  nonbonded pdb=" O   ASN T  99 "
            pdb=" OH  TYR T 296 "
     model   vdw
     2.294 3.040
  nonbonded pdb=" OE1 GLU T  85 "
            pdb=" NH2 ARG X  40 "
     model   vdw
     2.304 3.120
  ... (remaining 89389 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.00
Found NCS groups:
ncs_group {
  reference = chain 'H'
  selection = (chain 'I' and ((resid 1 through 2 and (name N or name CA or name C or name O or \ 
 name CB )) or resid 3 through 72))
  selection = (chain 'J' and ((resid 1 through 2 and (name N or name CA or name C or name O or \ 
 name CB )) or resid 3 through 72))
  selection = (chain 'K' and ((resid 1 through 2 and (name N or name CA or name C or name O or \ 
 name CB )) or resid 3 through 72))
  selection = (chain 'L' and ((resid 1 through 2 and (name N or name CA or name C or name O or \ 
 name CB )) or resid 3 through 72))
  selection = (chain 'M' and ((resid 1 through 2 and (name N or name CA or name C or name O or \ 
 name CB )) or resid 3 through 72))
  selection = (chain 'N' and ((resid 1 through 2 and (name N or name CA or name C or name O or \ 
 name CB )) or resid 3 through 72))
  selection = (chain 'O' and ((resid 1 through 2 and (name N or name CA or name C or name O or \ 
 name CB )) or resid 3 through 72))
  selection = (chain 'P' and ((resid 1 through 2 and (name N or name CA or name C or name O or \ 
 name CB )) or resid 3 through 72))
  selection = (chain 'Q' and ((resid 1 through 2 and (name N or name CA or name C or name O or \ 
 name CB )) or resid 3 through 72))
}
ncs_group {
  reference = (chain 'T' and (resid 19 through 136 or resid 169 through 304))
  selection = (chain 'Z' and resid 19 through 304)
}
ncs_group {
  reference = (chain 'U' and resid 3 through 44)
  selection = chain 'X'
  selection = (chain 'Y' and resid 3 through 44)
}

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 individual isotropic
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:             5.140
  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:             0.010
  Extract box with map and model:          0.430
  Check model and map are aligned:         0.070
  Set scattering table:                    0.100
  Process input model:                     28.930
  Find NCS groups from input model:        0.510
  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:3.180
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   38.420
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7979
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      :  0.011   0.824  10905  Z= 0.554
  Angle     :  0.646  30.404  14827  Z= 0.395
  Chirality :  0.043   0.215   1821
  Planarity :  0.006   0.073   1852
  Dihedral  : 16.324  88.834   3738
  Min Nonbonded Distance : 2.239

Molprobity Statistics.
  All-atom Clashscore : 11.88
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.32 %
    Favored  : 95.68 %
  Rotamer:
    Outliers :  0.28 %
    Allowed  : 29.68 %
    Favored  : 70.05 %
  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:  0.18 (0.22), residues: 1388
  helix:  0.53 (0.15), residues: 1112
  sheet:  None (None), residues: 0
  loop : -1.20 (0.39), residues: 276

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.029   0.002   TRP T 208 
 HIS   0.001   0.000   HIS Z  31 
 PHE   0.008   0.001   PHE T 276 
 TYR   0.011   0.001   TYR Z 296 
 ARG   0.002   0.000   ARG M  44 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.15155 (  921)
  hydrogen bonds       : angle       6.69737 ( 2724)
  SS BOND              : bond        0.74898 (    2)
  SS BOND              : angle      15.64313 (    4)
  covalent geometry    : bond        0.00395 (10903)
  covalent geometry    : angle       0.59260 (14823)

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

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

  2776 Ramachandran restraints generated.
    1388 Oldfield, 0 Emsley, 1388 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2776 Ramachandran restraints generated.
    1388 Oldfield, 0 Emsley, 1388 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  318 residues out of total 1089 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 315
  time to evaluate  : 1.023 
Fit side-chains
   revert: symmetry clash
REVERT: J   24 ILE cc_start: 0.9394 (mm) cc_final: 0.9187 (mt)
REVERT: O    1 MET cc_start: 0.7541 (tpp) cc_final: 0.7293 (tpp)
REVERT: O   38 ASN cc_start: 0.8270 (t0) cc_final: 0.7915 (t0)
REVERT: O   41 ILE cc_start: 0.9071 (tp) cc_final: 0.8730 (tp)
REVERT: P   41 ILE cc_start: 0.9022 (tp) cc_final: 0.8677 (tt)
REVERT: Q   41 ILE cc_start: 0.9388 (tp) cc_final: 0.9012 (tp)
REVERT: T   37 GLU cc_start: 0.6779 (tm-30) cc_final: 0.6464 (pm20)
REVERT: T   96 ARG cc_start: 0.9046 (ttm-80) cc_final: 0.8833 (ttm110)
REVERT: T  180 LEU cc_start: 0.8008 (tt) cc_final: 0.7798 (tt)
REVERT: T  255 PHE cc_start: 0.8990 (t80) cc_final: 0.8565 (t80)
REVERT: T  264 MET cc_start: 0.9046 (mmt) cc_final: 0.8812 (mmt)
REVERT: T  280 GLU cc_start: 0.8866 (tm-30) cc_final: 0.8653 (tm-30)
REVERT: V   24 ILE cc_start: 0.8568 (tt) cc_final: 0.8253 (mm)
REVERT: V   28 LEU cc_start: 0.8827 (tt) cc_final: 0.8592 (tt)
REVERT: Z  179 LYS cc_start: 0.7327 (tptp) cc_final: 0.7102 (ttpt)
REVERT: Z  236 PHE cc_start: 0.8802 (t80) cc_final: 0.8305 (t80)
  outliers start: 3
  outliers final: 2
  residues processed: 318
  average time/residue: 0.2615
  time to fit residues: 115.4590
Evaluate side-chains
  267 residues out of total 1089 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 265
  time to evaluate  : 1.099 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain T residue  283 VAL
Chi-restraints excluded: chain Z residue  169 ILE
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 138
   random chunks:
   chunk 116 optimal weight:    1.9990
   chunk 104 optimal weight:    5.9990
   chunk 58 optimal weight:    0.5980
   chunk 35 optimal weight:    0.7980
   chunk 70 optimal weight:    6.9990
   chunk 55 optimal weight:    0.9980
   chunk 108 optimal weight:    2.9990
   chunk 41 optimal weight:    0.7980
   chunk 65 optimal weight:    0.5980
   chunk 80 optimal weight:    3.9990
   chunk 125 optimal weight:    1.9990
   overall best weight:    0.7580

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3841 r_free = 0.3841 target = 0.121500 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3333 r_free = 0.3333 target = 0.087767 restraints weight = 18746.935|
|-----------------------------------------------------------------------------|
r_work (start): 0.3383 rms_B_bonded: 2.51
r_work: 0.3259 rms_B_bonded: 3.38 restraints_weight: 0.5000
r_work (final): 0.3259
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8016
moved from start:          0.1328

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.045  10905  Z= 0.175
  Angle     :  0.581   9.399  14827  Z= 0.312
  Chirality :  0.042   0.169   1821
  Planarity :  0.006   0.073   1852
  Dihedral  :  3.907  29.270   1491
  Min Nonbonded Distance : 2.547

Molprobity Statistics.
  All-atom Clashscore : 11.65
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.53 %
    Favored  : 96.47 %
  Rotamer:
    Outliers :  3.96 %
    Allowed  : 29.49 %
    Favored  : 66.54 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.33 (0.22), residues: 1388
  helix:  1.37 (0.15), residues: 1132
  sheet:  None (None), residues: 0
  loop : -1.19 (0.41), residues: 256

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.002   TRP T 208 
 HIS   0.002   0.001   HIS T 136 
 PHE   0.023   0.001   PHE T 230 
 TYR   0.019   0.002   TYR V  30 
 ARG   0.005   0.000   ARG Z 249 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.06317 (  921)
  hydrogen bonds       : angle       4.50986 ( 2724)
  SS BOND              : bond        0.00569 (    2)
  SS BOND              : angle       1.44251 (    4)
  covalent geometry    : bond        0.00378 (10903)
  covalent geometry    : angle       0.58045 (14823)

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

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

  2776 Ramachandran restraints generated.
    1388 Oldfield, 0 Emsley, 1388 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2776 Ramachandran restraints generated.
    1388 Oldfield, 0 Emsley, 1388 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  329 residues out of total 1089 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 43
    poor density    : 286
  time to evaluate  : 1.119 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: K   57 GLU cc_start: 0.8727 (tp30) cc_final: 0.8515 (tp30)
REVERT: K   70 ILE cc_start: 0.9404 (mm) cc_final: 0.9164 (mt)
REVERT: O    1 MET cc_start: 0.7587 (tpp) cc_final: 0.7355 (tpp)
REVERT: O   38 ASN cc_start: 0.8251 (t0) cc_final: 0.7638 (t0)
REVERT: O   41 ILE cc_start: 0.9135 (tp) cc_final: 0.8736 (tp)
REVERT: P   41 ILE cc_start: 0.9088 (tp) cc_final: 0.8805 (tp)
REVERT: Q   41 ILE cc_start: 0.9318 (tp) cc_final: 0.9045 (tp)
REVERT: T   25 LEU cc_start: 0.7541 (OUTLIER) cc_final: 0.7207 (pp)
REVERT: T  255 PHE cc_start: 0.8974 (t80) cc_final: 0.8538 (t80)
REVERT: T  280 GLU cc_start: 0.8780 (tm-30) cc_final: 0.8567 (tm-30)
REVERT: U   31 ARG cc_start: 0.8633 (tpp-160) cc_final: 0.8381 (tpp80)
REVERT: V   24 ILE cc_start: 0.8604 (tt) cc_final: 0.8290 (mm)
REVERT: Z   26 TYR cc_start: 0.7751 (t80) cc_final: 0.7411 (t80)
REVERT: Z  179 LYS cc_start: 0.7395 (tptp) cc_final: 0.7139 (ttpt)
REVERT: Z  236 PHE cc_start: 0.8820 (t80) cc_final: 0.8298 (t80)
REVERT: Z  258 GLU cc_start: 0.8263 (tm-30) cc_final: 0.7919 (tm-30)
  outliers start: 43
  outliers final: 22
  residues processed: 308
  average time/residue: 0.2957
  time to fit residues: 130.3856
Evaluate side-chains
  295 residues out of total 1089 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 272
  time to evaluate  : 2.371 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain H residue   41 ILE
Chi-restraints excluded: chain H residue   45 VAL
Chi-restraints excluded: chain H residue   49 MET
Chi-restraints excluded: chain I residue   18 ILE
Chi-restraints excluded: chain J residue   41 ILE
Chi-restraints excluded: chain K residue   45 VAL
Chi-restraints excluded: chain M residue   45 VAL
Chi-restraints excluded: chain M residue   66 ILE
Chi-restraints excluded: chain N residue   13 VAL
Chi-restraints excluded: chain T residue   25 LEU
Chi-restraints excluded: chain T residue   32 VAL
Chi-restraints excluded: chain T residue  200 ILE
Chi-restraints excluded: chain T residue  206 GLU
Chi-restraints excluded: chain T residue  208 TRP
Chi-restraints excluded: chain T residue  289 LEU
Chi-restraints excluded: chain V residue   11 PHE
Chi-restraints excluded: chain V residue   16 ILE
Chi-restraints excluded: chain X residue   37 LEU
Chi-restraints excluded: chain Y residue    4 LEU
Chi-restraints excluded: chain Y residue    6 ILE
Chi-restraints excluded: chain Z residue  169 ILE
Chi-restraints excluded: chain Z residue  205 ILE
Chi-restraints excluded: chain Z residue  290 ILE
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 138
   random chunks:
   chunk 77 optimal weight:    0.8980
   chunk 57 optimal weight:    1.9990
   chunk 27 optimal weight:    0.6980
   chunk 39 optimal weight:    1.9990
   chunk 106 optimal weight:    0.9990
   chunk 10 optimal weight:    0.7980
   chunk 53 optimal weight:    1.9990
   chunk 2 optimal weight:    0.6980
   chunk 131 optimal weight:    6.9990
   chunk 7 optimal weight:    0.0970
   chunk 117 optimal weight:    0.9990
   overall best weight:    0.6378

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3829 r_free = 0.3829 target = 0.122266 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3305 r_free = 0.3305 target = 0.088708 restraints weight = 18885.565|
|-----------------------------------------------------------------------------|
r_work (start): 0.3283 rms_B_bonded: 2.54
r_work: 0.3163 rms_B_bonded: 3.47 restraints_weight: 0.5000
r_work (final): 0.3163
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7906
moved from start:          0.1657

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.060  10905  Z= 0.159
  Angle     :  0.566  10.000  14827  Z= 0.297
  Chirality :  0.041   0.168   1821
  Planarity :  0.005   0.072   1852
  Dihedral  :  3.826  30.861   1490
  Min Nonbonded Distance : 2.547

Molprobity Statistics.
  All-atom Clashscore : 11.38
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.89 %
    Favored  : 96.11 %
  Rotamer:
    Outliers :  4.88 %
    Allowed  : 28.76 %
    Favored  : 66.36 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.56 (0.22), residues: 1388
  helix:  1.53 (0.15), residues: 1132
  sheet:  None (None), residues: 0
  loop : -1.13 (0.42), residues: 256

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.019   0.002   TRP T 208 
 HIS   0.001   0.001   HIS Z  31 
 PHE   0.024   0.001   PHE T  24 
 TYR   0.014   0.002   TYR Q  48 
 ARG   0.006   0.000   ARG M  44 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05724 (  921)
  hydrogen bonds       : angle       4.21777 ( 2724)
  SS BOND              : bond        0.00304 (    2)
  SS BOND              : angle       1.34214 (    4)
  covalent geometry    : bond        0.00338 (10903)
  covalent geometry    : angle       0.56571 (14823)

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

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

  2776 Ramachandran restraints generated.
    1388 Oldfield, 0 Emsley, 1388 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2776 Ramachandran restraints generated.
    1388 Oldfield, 0 Emsley, 1388 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  348 residues out of total 1089 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 53
    poor density    : 295
  time to evaluate  : 1.218 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: K   70 ILE cc_start: 0.9338 (mm) cc_final: 0.9137 (mt)
REVERT: M   41 ILE cc_start: 0.9182 (OUTLIER) cc_final: 0.8888 (tp)
REVERT: O    1 MET cc_start: 0.7602 (tpp) cc_final: 0.7239 (tpp)
REVERT: O   38 ASN cc_start: 0.8213 (t0) cc_final: 0.7957 (t0)
REVERT: O   41 ILE cc_start: 0.9103 (tp) cc_final: 0.8826 (tp)
REVERT: P   41 ILE cc_start: 0.9008 (tp) cc_final: 0.8741 (tp)
REVERT: P   48 TYR cc_start: 0.9092 (m-80) cc_final: 0.8880 (m-80)
REVERT: Q   41 ILE cc_start: 0.9275 (tp) cc_final: 0.8977 (tp)
REVERT: T   25 LEU cc_start: 0.7483 (OUTLIER) cc_final: 0.7137 (pp)
REVERT: T  180 LEU cc_start: 0.8476 (tt) cc_final: 0.8061 (mp)
REVERT: T  255 PHE cc_start: 0.8942 (t80) cc_final: 0.8554 (t80)
REVERT: T  280 GLU cc_start: 0.8800 (tm-30) cc_final: 0.8582 (tm-30)
REVERT: U   31 ARG cc_start: 0.8606 (tpp-160) cc_final: 0.8356 (tpp80)
REVERT: V   24 ILE cc_start: 0.8574 (tt) cc_final: 0.8253 (mm)
REVERT: Z   26 TYR cc_start: 0.7722 (t80) cc_final: 0.7313 (t80)
REVERT: Z   85 GLU cc_start: 0.8857 (tt0) cc_final: 0.8514 (tt0)
REVERT: Z  179 LYS cc_start: 0.7399 (tptp) cc_final: 0.7144 (ttpt)
REVERT: Z  236 PHE cc_start: 0.8786 (t80) cc_final: 0.8301 (t80)
REVERT: Z  258 GLU cc_start: 0.8249 (tm-30) cc_final: 0.7890 (tm-30)
REVERT: Z  296 TYR cc_start: 0.8175 (t80) cc_final: 0.7315 (t80)
  outliers start: 53
  outliers final: 37
  residues processed: 321
  average time/residue: 0.2938
  time to fit residues: 131.2533
Evaluate side-chains
  315 residues out of total 1089 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 39
    poor density    : 276
  time to evaluate  : 1.195 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain H residue   49 MET
Chi-restraints excluded: chain H residue   66 ILE
Chi-restraints excluded: chain J residue   41 ILE
Chi-restraints excluded: chain J residue   46 VAL
Chi-restraints excluded: chain J residue   49 MET
Chi-restraints excluded: chain J residue   65 VAL
Chi-restraints excluded: chain K residue   45 VAL
Chi-restraints excluded: chain M residue   41 ILE
Chi-restraints excluded: chain M residue   45 VAL
Chi-restraints excluded: chain M residue   66 ILE
Chi-restraints excluded: chain N residue   13 VAL
Chi-restraints excluded: chain N residue   32 VAL
Chi-restraints excluded: chain O residue   32 VAL
Chi-restraints excluded: chain O residue   53 ILE
Chi-restraints excluded: chain P residue   49 MET
Chi-restraints excluded: chain Q residue   44 ARG
Chi-restraints excluded: chain Q residue   45 VAL
Chi-restraints excluded: chain T residue   25 LEU
Chi-restraints excluded: chain T residue   53 VAL
Chi-restraints excluded: chain T residue   65 LEU
Chi-restraints excluded: chain T residue   89 GLU
Chi-restraints excluded: chain T residue  110 VAL
Chi-restraints excluded: chain T residue  200 ILE
Chi-restraints excluded: chain T residue  206 GLU
Chi-restraints excluded: chain T residue  208 TRP
Chi-restraints excluded: chain T residue  260 LEU
Chi-restraints excluded: chain T residue  286 ILE
Chi-restraints excluded: chain T residue  289 LEU
Chi-restraints excluded: chain V residue   11 PHE
Chi-restraints excluded: chain V residue   16 ILE
Chi-restraints excluded: chain X residue   25 LEU
Chi-restraints excluded: chain X residue   37 LEU
Chi-restraints excluded: chain Y residue    4 LEU
Chi-restraints excluded: chain Y residue    6 ILE
Chi-restraints excluded: chain Z residue   15 LEU
Chi-restraints excluded: chain Z residue  136 HIS
Chi-restraints excluded: chain Z residue  169 ILE
Chi-restraints excluded: chain Z residue  205 ILE
Chi-restraints excluded: chain Z residue  290 ILE
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 138
   random chunks:
   chunk 37 optimal weight:    0.6980
   chunk 137 optimal weight:    1.9990
   chunk 13 optimal weight:    0.9990
   chunk 6 optimal weight:    2.9990
   chunk 87 optimal weight:    0.0980
   chunk 105 optimal weight:    3.9990
   chunk 41 optimal weight:    0.7980
   chunk 12 optimal weight:    0.8980
   chunk 111 optimal weight:    4.9990
   chunk 5 optimal weight:    1.9990
   chunk 29 optimal weight:    0.9990
   overall best weight:    0.6982

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3828 r_free = 0.3828 target = 0.122269 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3296 r_free = 0.3296 target = 0.088267 restraints weight = 18695.063|
|-----------------------------------------------------------------------------|
r_work (start): 0.3276 rms_B_bonded: 2.53
r_work: 0.3155 rms_B_bonded: 3.47 restraints_weight: 0.5000
r_work (final): 0.3155
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7923
moved from start:          0.1815

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037  10905  Z= 0.159
  Angle     :  0.564  10.661  14827  Z= 0.294
  Chirality :  0.041   0.169   1821
  Planarity :  0.005   0.072   1852
  Dihedral  :  3.816  31.877   1490
  Min Nonbonded Distance : 2.524

Molprobity Statistics.
  All-atom Clashscore : 11.65
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.67 %
    Favored  : 96.33 %
  Rotamer:
    Outliers :  5.90 %
    Allowed  : 28.48 %
    Favored  : 65.62 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.60 (0.22), residues: 1388
  helix:  1.55 (0.15), residues: 1134
  sheet:  None (None), residues: 0
  loop : -1.05 (0.42), residues: 254

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.021   0.002   TRP T 208 
 HIS   0.001   0.000   HIS Z  31 
 PHE   0.025   0.001   PHE T 230 
 TYR   0.014   0.002   TYR N  48 
 ARG   0.007   0.000   ARG Z  78 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05547 (  921)
  hydrogen bonds       : angle       4.10634 ( 2724)
  SS BOND              : bond        0.00263 (    2)
  SS BOND              : angle       1.20276 (    4)
  covalent geometry    : bond        0.00344 (10903)
  covalent geometry    : angle       0.56350 (14823)

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

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

  2776 Ramachandran restraints generated.
    1388 Oldfield, 0 Emsley, 1388 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2776 Ramachandran restraints generated.
    1388 Oldfield, 0 Emsley, 1388 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  348 residues out of total 1089 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 64
    poor density    : 284
  time to evaluate  : 1.161 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: M   41 ILE cc_start: 0.9192 (OUTLIER) cc_final: 0.8910 (tp)
REVERT: O    1 MET cc_start: 0.7535 (tpp) cc_final: 0.7070 (tmm)
REVERT: O   41 ILE cc_start: 0.9134 (tp) cc_final: 0.8859 (tp)
REVERT: P   41 ILE cc_start: 0.9029 (tp) cc_final: 0.8817 (tp)
REVERT: P   57 GLU cc_start: 0.8985 (mm-30) cc_final: 0.8720 (mm-30)
REVERT: Q   41 ILE cc_start: 0.9280 (tp) cc_final: 0.8968 (tp)
REVERT: T   25 LEU cc_start: 0.7432 (OUTLIER) cc_final: 0.7052 (pp)
REVERT: T  239 GLU cc_start: 0.9235 (tp30) cc_final: 0.8833 (tp30)
REVERT: T  255 PHE cc_start: 0.8956 (t80) cc_final: 0.8541 (t80)
REVERT: T  280 GLU cc_start: 0.8805 (tm-30) cc_final: 0.8590 (tm-30)
REVERT: V   24 ILE cc_start: 0.8588 (tt) cc_final: 0.8271 (mm)
REVERT: Z   85 GLU cc_start: 0.8877 (OUTLIER) cc_final: 0.8529 (tt0)
REVERT: Z  179 LYS cc_start: 0.7364 (tptp) cc_final: 0.7052 (ttpt)
REVERT: Z  236 PHE cc_start: 0.8794 (t80) cc_final: 0.8310 (t80)
REVERT: Z  258 GLU cc_start: 0.8250 (tm-30) cc_final: 0.7873 (tm-30)
  outliers start: 64
  outliers final: 43
  residues processed: 318
  average time/residue: 0.2447
  time to fit residues: 110.3825
Evaluate side-chains
  312 residues out of total 1089 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 46
    poor density    : 266
  time to evaluate  : 1.296 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain H residue   45 VAL
Chi-restraints excluded: chain H residue   49 MET
Chi-restraints excluded: chain H residue   66 ILE
Chi-restraints excluded: chain I residue   18 ILE
Chi-restraints excluded: chain I residue   46 VAL
Chi-restraints excluded: chain I residue   64 LEU
Chi-restraints excluded: chain J residue   46 VAL
Chi-restraints excluded: chain J residue   49 MET
Chi-restraints excluded: chain J residue   65 VAL
Chi-restraints excluded: chain K residue   29 SER
Chi-restraints excluded: chain K residue   45 VAL
Chi-restraints excluded: chain K residue   68 PHE
Chi-restraints excluded: chain L residue   49 MET
Chi-restraints excluded: chain M residue   41 ILE
Chi-restraints excluded: chain M residue   45 VAL
Chi-restraints excluded: chain M residue   66 ILE
Chi-restraints excluded: chain N residue   13 VAL
Chi-restraints excluded: chain N residue   18 ILE
Chi-restraints excluded: chain N residue   32 VAL
Chi-restraints excluded: chain O residue   32 VAL
Chi-restraints excluded: chain Q residue   44 ARG
Chi-restraints excluded: chain Q residue   45 VAL
Chi-restraints excluded: chain T residue   25 LEU
Chi-restraints excluded: chain T residue   32 VAL
Chi-restraints excluded: chain T residue   53 VAL
Chi-restraints excluded: chain T residue   65 LEU
Chi-restraints excluded: chain T residue   89 GLU
Chi-restraints excluded: chain T residue  110 VAL
Chi-restraints excluded: chain T residue  200 ILE
Chi-restraints excluded: chain T residue  206 GLU
Chi-restraints excluded: chain T residue  208 TRP
Chi-restraints excluded: chain T residue  260 LEU
Chi-restraints excluded: chain T residue  289 LEU
Chi-restraints excluded: chain V residue   11 PHE
Chi-restraints excluded: chain V residue   16 ILE
Chi-restraints excluded: chain X residue   25 LEU
Chi-restraints excluded: chain X residue   37 LEU
Chi-restraints excluded: chain Y residue    4 LEU
Chi-restraints excluded: chain Y residue    6 ILE
Chi-restraints excluded: chain Y residue   25 LEU
Chi-restraints excluded: chain Z residue   15 LEU
Chi-restraints excluded: chain Z residue   85 GLU
Chi-restraints excluded: chain Z residue  136 HIS
Chi-restraints excluded: chain Z residue  169 ILE
Chi-restraints excluded: chain Z residue  205 ILE
Chi-restraints excluded: chain Z residue  290 ILE
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 138
   random chunks:
   chunk 17 optimal weight:    0.9980
   chunk 62 optimal weight:    0.7980
   chunk 84 optimal weight:    0.9990
   chunk 97 optimal weight:    0.5980
   chunk 59 optimal weight:    0.6980
   chunk 128 optimal weight:    0.4980
   chunk 106 optimal weight:    1.9990
   chunk 104 optimal weight:    2.9990
   chunk 85 optimal weight:    0.5980
   chunk 29 optimal weight:    1.9990
   chunk 7 optimal weight:    0.6980
   overall best weight:    0.6180

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3833 r_free = 0.3833 target = 0.122510 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3310 r_free = 0.3310 target = 0.088929 restraints weight = 18639.714|
|-----------------------------------------------------------------------------|
r_work (start): 0.3286 rms_B_bonded: 2.52
r_work: 0.3164 rms_B_bonded: 3.47 restraints_weight: 0.5000
r_work (final): 0.3164
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7911
moved from start:          0.1947

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.066  10905  Z= 0.154
  Angle     :  0.572  11.023  14827  Z= 0.296
  Chirality :  0.041   0.167   1821
  Planarity :  0.005   0.072   1852
  Dihedral  :  3.808  33.132   1490
  Min Nonbonded Distance : 2.541

Molprobity Statistics.
  All-atom Clashscore : 11.56
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.75 %
    Favored  : 96.25 %
  Rotamer:
    Outliers :  5.35 %
    Allowed  : 29.31 %
    Favored  : 65.35 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.66 (0.22), residues: 1388
  helix:  1.60 (0.15), residues: 1133
  sheet:  None (None), residues: 0
  loop : -1.06 (0.42), residues: 255

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.022   0.002   TRP T 208 
 HIS   0.001   0.000   HIS T 136 
 PHE   0.026   0.001   PHE T  24 
 TYR   0.014   0.002   TYR Q  48 
 ARG   0.005   0.000   ARG M  44 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05414 (  921)
  hydrogen bonds       : angle       4.04528 ( 2724)
  SS BOND              : bond        0.00268 (    2)
  SS BOND              : angle       1.14710 (    4)
  covalent geometry    : bond        0.00334 (10903)
  covalent geometry    : angle       0.57149 (14823)

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

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

  2776 Ramachandran restraints generated.
    1388 Oldfield, 0 Emsley, 1388 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2776 Ramachandran restraints generated.
    1388 Oldfield, 0 Emsley, 1388 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  341 residues out of total 1089 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 58
    poor density    : 283
  time to evaluate  : 1.156 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: J    2 GLU cc_start: 0.8500 (mp0) cc_final: 0.8001 (pm20)
REVERT: K   66 ILE cc_start: 0.9207 (tt) cc_final: 0.8996 (tt)
REVERT: M   41 ILE cc_start: 0.9191 (OUTLIER) cc_final: 0.8906 (tp)
REVERT: Q   41 ILE cc_start: 0.9263 (tp) cc_final: 0.8954 (tp)
REVERT: T   25 LEU cc_start: 0.7471 (OUTLIER) cc_final: 0.7066 (pp)
REVERT: T  239 GLU cc_start: 0.9240 (tp30) cc_final: 0.8857 (tp30)
REVERT: T  255 PHE cc_start: 0.8954 (t80) cc_final: 0.8542 (t80)
REVERT: T  280 GLU cc_start: 0.8824 (tm-30) cc_final: 0.8600 (tm-30)
REVERT: V   24 ILE cc_start: 0.8577 (tt) cc_final: 0.8258 (mm)
REVERT: Z  179 LYS cc_start: 0.7323 (tptp) cc_final: 0.7026 (ttpt)
REVERT: Z  236 PHE cc_start: 0.8796 (t80) cc_final: 0.8323 (t80)
REVERT: Z  258 GLU cc_start: 0.8263 (tm-30) cc_final: 0.7873 (tm-30)
  outliers start: 58
  outliers final: 47
  residues processed: 312
  average time/residue: 0.2404
  time to fit residues: 104.4454
Evaluate side-chains
  317 residues out of total 1089 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 49
    poor density    : 268
  time to evaluate  : 1.043 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain H residue   45 VAL
Chi-restraints excluded: chain H residue   49 MET
Chi-restraints excluded: chain H residue   66 ILE
Chi-restraints excluded: chain I residue   18 ILE
Chi-restraints excluded: chain I residue   46 VAL
Chi-restraints excluded: chain I residue   64 LEU
Chi-restraints excluded: chain J residue   46 VAL
Chi-restraints excluded: chain J residue   49 MET
Chi-restraints excluded: chain J residue   65 VAL
Chi-restraints excluded: chain K residue   68 PHE
Chi-restraints excluded: chain L residue   49 MET
Chi-restraints excluded: chain M residue   41 ILE
Chi-restraints excluded: chain M residue   45 VAL
Chi-restraints excluded: chain M residue   66 ILE
Chi-restraints excluded: chain N residue   13 VAL
Chi-restraints excluded: chain N residue   18 ILE
Chi-restraints excluded: chain N residue   32 VAL
Chi-restraints excluded: chain N residue   59 LEU
Chi-restraints excluded: chain O residue   32 VAL
Chi-restraints excluded: chain Q residue   44 ARG
Chi-restraints excluded: chain Q residue   45 VAL
Chi-restraints excluded: chain T residue   25 LEU
Chi-restraints excluded: chain T residue   32 VAL
Chi-restraints excluded: chain T residue   53 VAL
Chi-restraints excluded: chain T residue   65 LEU
Chi-restraints excluded: chain T residue   89 GLU
Chi-restraints excluded: chain T residue  110 VAL
Chi-restraints excluded: chain T residue  172 THR
Chi-restraints excluded: chain T residue  200 ILE
Chi-restraints excluded: chain T residue  206 GLU
Chi-restraints excluded: chain T residue  208 TRP
Chi-restraints excluded: chain T residue  258 GLU
Chi-restraints excluded: chain T residue  260 LEU
Chi-restraints excluded: chain T residue  286 ILE
Chi-restraints excluded: chain T residue  289 LEU
Chi-restraints excluded: chain V residue   11 PHE
Chi-restraints excluded: chain V residue   16 ILE
Chi-restraints excluded: chain X residue   25 LEU
Chi-restraints excluded: chain X residue   37 LEU
Chi-restraints excluded: chain Y residue    4 LEU
Chi-restraints excluded: chain Y residue    6 ILE
Chi-restraints excluded: chain Z residue   15 LEU
Chi-restraints excluded: chain Z residue   85 GLU
Chi-restraints excluded: chain Z residue  136 HIS
Chi-restraints excluded: chain Z residue  169 ILE
Chi-restraints excluded: chain Z residue  171 ASP
Chi-restraints excluded: chain Z residue  205 ILE
Chi-restraints excluded: chain Z residue  283 VAL
Chi-restraints excluded: chain Z residue  290 ILE
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 138
   random chunks:
   chunk 2 optimal weight:    0.5980
   chunk 39 optimal weight:    0.0870
   chunk 13 optimal weight:    0.7980
   chunk 91 optimal weight:    2.9990
   chunk 46 optimal weight:    0.9990
   chunk 66 optimal weight:    2.9990
   chunk 110 optimal weight:    0.8980
   chunk 69 optimal weight:    0.5980
   chunk 22 optimal weight:    2.9990
   chunk 31 optimal weight:    0.7980
   chunk 63 optimal weight:    0.5980
   overall best weight:    0.5358

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3841 r_free = 0.3841 target = 0.123147 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3321 r_free = 0.3321 target = 0.089598 restraints weight = 18754.235|
|-----------------------------------------------------------------------------|
r_work (start): 0.3298 rms_B_bonded: 2.51
r_work: 0.3179 rms_B_bonded: 3.47 restraints_weight: 0.5000
r_work (final): 0.3179
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7899
moved from start:          0.2091

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.088  10905  Z= 0.150
  Angle     :  0.578  10.843  14827  Z= 0.298
  Chirality :  0.041   0.180   1821
  Planarity :  0.005   0.072   1852
  Dihedral  :  3.862  33.751   1490
  Min Nonbonded Distance : 2.539

Molprobity Statistics.
  All-atom Clashscore : 11.84
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.60 %
    Favored  : 96.40 %
  Rotamer:
    Outliers :  5.90 %
    Allowed  : 29.40 %
    Favored  : 64.70 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.71 (0.22), residues: 1388
  helix:  1.63 (0.15), residues: 1134
  sheet:  None (None), residues: 0
  loop : -1.06 (0.42), residues: 254

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.023   0.002   TRP T 208 
 HIS   0.001   0.000   HIS T 136 
 PHE   0.024   0.001   PHE T 230 
 TYR   0.013   0.002   TYR Z 207 
 ARG   0.005   0.000   ARG M  44 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05285 (  921)
  hydrogen bonds       : angle       3.98613 ( 2724)
  SS BOND              : bond        0.00991 (    2)
  SS BOND              : angle       2.71016 (    4)
  covalent geometry    : bond        0.00322 (10903)
  covalent geometry    : angle       0.57617 (14823)

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

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

  2776 Ramachandran restraints generated.
    1388 Oldfield, 0 Emsley, 1388 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2776 Ramachandran restraints generated.
    1388 Oldfield, 0 Emsley, 1388 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  347 residues out of total 1089 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 64
    poor density    : 283
  time to evaluate  : 1.192 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: K   66 ILE cc_start: 0.9228 (tt) cc_final: 0.9018 (tt)
REVERT: M   41 ILE cc_start: 0.9199 (OUTLIER) cc_final: 0.8925 (tp)
REVERT: O    1 MET cc_start: 0.7583 (tpp) cc_final: 0.7201 (tpp)
REVERT: P   57 GLU cc_start: 0.8950 (mm-30) cc_final: 0.8705 (mm-30)
REVERT: Q   41 ILE cc_start: 0.9240 (tp) cc_final: 0.8949 (tp)
REVERT: T   25 LEU cc_start: 0.7445 (OUTLIER) cc_final: 0.7043 (pp)
REVERT: T   92 TYR cc_start: 0.8671 (t80) cc_final: 0.8116 (t80)
REVERT: T  239 GLU cc_start: 0.9226 (tp30) cc_final: 0.8846 (tp30)
REVERT: T  255 PHE cc_start: 0.8943 (t80) cc_final: 0.8535 (t80)
REVERT: T  280 GLU cc_start: 0.8811 (tm-30) cc_final: 0.8521 (tm-30)
REVERT: V   24 ILE cc_start: 0.8556 (tt) cc_final: 0.8235 (mm)
REVERT: Z  179 LYS cc_start: 0.7339 (tptp) cc_final: 0.7028 (ttpt)
REVERT: Z  236 PHE cc_start: 0.8789 (t80) cc_final: 0.8314 (t80)
REVERT: Z  258 GLU cc_start: 0.8219 (OUTLIER) cc_final: 0.7814 (tm-30)
REVERT: Z  296 TYR cc_start: 0.8182 (t80) cc_final: 0.7458 (t80)
  outliers start: 64
  outliers final: 51
  residues processed: 316
  average time/residue: 0.2242
  time to fit residues: 100.7390
Evaluate side-chains
  329 residues out of total 1089 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 54
    poor density    : 275
  time to evaluate  : 1.152 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain H residue   45 VAL
Chi-restraints excluded: chain H residue   49 MET
Chi-restraints excluded: chain H residue   66 ILE
Chi-restraints excluded: chain I residue   18 ILE
Chi-restraints excluded: chain I residue   46 VAL
Chi-restraints excluded: chain I residue   64 LEU
Chi-restraints excluded: chain J residue   46 VAL
Chi-restraints excluded: chain J residue   49 MET
Chi-restraints excluded: chain J residue   65 VAL
Chi-restraints excluded: chain K residue   13 VAL
Chi-restraints excluded: chain K residue   68 PHE
Chi-restraints excluded: chain L residue   49 MET
Chi-restraints excluded: chain M residue   41 ILE
Chi-restraints excluded: chain M residue   45 VAL
Chi-restraints excluded: chain M residue   66 ILE
Chi-restraints excluded: chain N residue   13 VAL
Chi-restraints excluded: chain N residue   18 ILE
Chi-restraints excluded: chain N residue   32 VAL
Chi-restraints excluded: chain N residue   59 LEU
Chi-restraints excluded: chain O residue   32 VAL
Chi-restraints excluded: chain O residue   56 THR
Chi-restraints excluded: chain P residue   64 LEU
Chi-restraints excluded: chain Q residue   44 ARG
Chi-restraints excluded: chain Q residue   45 VAL
Chi-restraints excluded: chain T residue   25 LEU
Chi-restraints excluded: chain T residue   32 VAL
Chi-restraints excluded: chain T residue   37 GLU
Chi-restraints excluded: chain T residue   53 VAL
Chi-restraints excluded: chain T residue   65 LEU
Chi-restraints excluded: chain T residue   89 GLU
Chi-restraints excluded: chain T residue  110 VAL
Chi-restraints excluded: chain T residue  136 HIS
Chi-restraints excluded: chain T residue  200 ILE
Chi-restraints excluded: chain T residue  206 GLU
Chi-restraints excluded: chain T residue  208 TRP
Chi-restraints excluded: chain T residue  258 GLU
Chi-restraints excluded: chain T residue  260 LEU
Chi-restraints excluded: chain T residue  286 ILE
Chi-restraints excluded: chain T residue  289 LEU
Chi-restraints excluded: chain V residue   11 PHE
Chi-restraints excluded: chain V residue   16 ILE
Chi-restraints excluded: chain X residue   25 LEU
Chi-restraints excluded: chain X residue   37 LEU
Chi-restraints excluded: chain Y residue    4 LEU
Chi-restraints excluded: chain Y residue    6 ILE
Chi-restraints excluded: chain Z residue   15 LEU
Chi-restraints excluded: chain Z residue   85 GLU
Chi-restraints excluded: chain Z residue  136 HIS
Chi-restraints excluded: chain Z residue  169 ILE
Chi-restraints excluded: chain Z residue  171 ASP
Chi-restraints excluded: chain Z residue  205 ILE
Chi-restraints excluded: chain Z residue  258 GLU
Chi-restraints excluded: chain Z residue  283 VAL
Chi-restraints excluded: chain Z residue  290 ILE
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 138
   random chunks:
   chunk 48 optimal weight:    1.9990
   chunk 39 optimal weight:    1.9990
   chunk 134 optimal weight:    3.9990
   chunk 27 optimal weight:    0.9980
   chunk 49 optimal weight:    2.9990
   chunk 104 optimal weight:    4.9990
   chunk 38 optimal weight:    0.7980
   chunk 125 optimal weight:    0.0040
   chunk 21 optimal weight:    1.9990
   chunk 56 optimal weight:    0.4980
   chunk 110 optimal weight:    0.9990
   overall best weight:    0.6594

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3837 r_free = 0.3837 target = 0.122847 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3320 r_free = 0.3320 target = 0.089426 restraints weight = 19095.067|
|-----------------------------------------------------------------------------|
r_work (start): 0.3291 rms_B_bonded: 2.56
r_work: 0.3169 rms_B_bonded: 3.52 restraints_weight: 0.5000
r_work (final): 0.3169
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7911
moved from start:          0.2205

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.081  10905  Z= 0.157
  Angle     :  0.590  12.231  14827  Z= 0.303
  Chirality :  0.041   0.178   1821
  Planarity :  0.005   0.072   1852
  Dihedral  :  3.856  34.242   1490
  Min Nonbonded Distance : 2.532

Molprobity Statistics.
  All-atom Clashscore : 12.15
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.11 %
    Favored  : 95.89 %
  Rotamer:
    Outliers :  5.44 %
    Allowed  : 30.23 %
    Favored  : 64.33 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.75 (0.22), residues: 1388
  helix:  1.66 (0.15), residues: 1133
  sheet:  None (None), residues: 0
  loop : -1.01 (0.43), residues: 255

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.023   0.002   TRP T 208 
 HIS   0.001   0.000   HIS Z 170 
 PHE   0.028   0.001   PHE T  24 
 TYR   0.017   0.002   TYR Q  48 
 ARG   0.005   0.000   ARG M  44 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05288 (  921)
  hydrogen bonds       : angle       3.97900 ( 2724)
  SS BOND              : bond        0.00791 (    2)
  SS BOND              : angle       2.33880 (    4)
  covalent geometry    : bond        0.00344 (10903)
  covalent geometry    : angle       0.58867 (14823)

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

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

  2776 Ramachandran restraints generated.
    1388 Oldfield, 0 Emsley, 1388 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2776 Ramachandran restraints generated.
    1388 Oldfield, 0 Emsley, 1388 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  338 residues out of total 1089 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 59
    poor density    : 279
  time to evaluate  : 1.215 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: K   66 ILE cc_start: 0.9233 (tt) cc_final: 0.9030 (tt)
REVERT: M   40 GLU cc_start: 0.8034 (tm-30) cc_final: 0.7727 (tm-30)
REVERT: M   41 ILE cc_start: 0.9198 (OUTLIER) cc_final: 0.8878 (tp)
REVERT: Q   41 ILE cc_start: 0.9251 (tp) cc_final: 0.8953 (tp)
REVERT: T   25 LEU cc_start: 0.7445 (OUTLIER) cc_final: 0.7018 (pp)
REVERT: T   92 TYR cc_start: 0.8683 (t80) cc_final: 0.8149 (t80)
REVERT: T  239 GLU cc_start: 0.9226 (tp30) cc_final: 0.8818 (tp30)
REVERT: T  255 PHE cc_start: 0.8955 (t80) cc_final: 0.8542 (t80)
REVERT: T  280 GLU cc_start: 0.8824 (tm-30) cc_final: 0.8556 (tm-30)
REVERT: V   24 ILE cc_start: 0.8516 (tt) cc_final: 0.8190 (mm)
REVERT: Z  179 LYS cc_start: 0.7411 (tptp) cc_final: 0.6985 (ttpt)
REVERT: Z  236 PHE cc_start: 0.8738 (t80) cc_final: 0.8272 (t80)
REVERT: Z  239 GLU cc_start: 0.9134 (mm-30) cc_final: 0.8835 (mm-30)
REVERT: Z  242 LYS cc_start: 0.8788 (mttt) cc_final: 0.8547 (mtmt)
REVERT: Z  258 GLU cc_start: 0.8184 (OUTLIER) cc_final: 0.7782 (tm-30)
  outliers start: 59
  outliers final: 48
  residues processed: 312
  average time/residue: 0.2152
  time to fit residues: 94.8282
Evaluate side-chains
  316 residues out of total 1089 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 51
    poor density    : 265
  time to evaluate  : 1.065 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain H residue   45 VAL
Chi-restraints excluded: chain H residue   49 MET
Chi-restraints excluded: chain H residue   66 ILE
Chi-restraints excluded: chain I residue   18 ILE
Chi-restraints excluded: chain I residue   46 VAL
Chi-restraints excluded: chain I residue   64 LEU
Chi-restraints excluded: chain J residue   46 VAL
Chi-restraints excluded: chain J residue   65 VAL
Chi-restraints excluded: chain K residue   13 VAL
Chi-restraints excluded: chain K residue   29 SER
Chi-restraints excluded: chain K residue   68 PHE
Chi-restraints excluded: chain L residue   49 MET
Chi-restraints excluded: chain M residue   41 ILE
Chi-restraints excluded: chain M residue   45 VAL
Chi-restraints excluded: chain M residue   66 ILE
Chi-restraints excluded: chain N residue   13 VAL
Chi-restraints excluded: chain N residue   18 ILE
Chi-restraints excluded: chain N residue   32 VAL
Chi-restraints excluded: chain N residue   59 LEU
Chi-restraints excluded: chain O residue   32 VAL
Chi-restraints excluded: chain O residue   56 THR
Chi-restraints excluded: chain Q residue   44 ARG
Chi-restraints excluded: chain Q residue   45 VAL
Chi-restraints excluded: chain T residue   25 LEU
Chi-restraints excluded: chain T residue   32 VAL
Chi-restraints excluded: chain T residue   53 VAL
Chi-restraints excluded: chain T residue   65 LEU
Chi-restraints excluded: chain T residue   89 GLU
Chi-restraints excluded: chain T residue  110 VAL
Chi-restraints excluded: chain T residue  200 ILE
Chi-restraints excluded: chain T residue  206 GLU
Chi-restraints excluded: chain T residue  208 TRP
Chi-restraints excluded: chain T residue  258 GLU
Chi-restraints excluded: chain T residue  260 LEU
Chi-restraints excluded: chain T residue  286 ILE
Chi-restraints excluded: chain T residue  289 LEU
Chi-restraints excluded: chain V residue   11 PHE
Chi-restraints excluded: chain V residue   16 ILE
Chi-restraints excluded: chain X residue   25 LEU
Chi-restraints excluded: chain X residue   37 LEU
Chi-restraints excluded: chain Y residue    4 LEU
Chi-restraints excluded: chain Y residue    6 ILE
Chi-restraints excluded: chain Y residue   25 LEU
Chi-restraints excluded: chain Z residue   15 LEU
Chi-restraints excluded: chain Z residue   85 GLU
Chi-restraints excluded: chain Z residue  136 HIS
Chi-restraints excluded: chain Z residue  169 ILE
Chi-restraints excluded: chain Z residue  171 ASP
Chi-restraints excluded: chain Z residue  205 ILE
Chi-restraints excluded: chain Z residue  258 GLU
Chi-restraints excluded: chain Z residue  286 ILE
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 138
   random chunks:
   chunk 61 optimal weight:    0.5980
   chunk 3 optimal weight:    0.9990
   chunk 70 optimal weight:    0.5980
   chunk 74 optimal weight:    0.9980
   chunk 65 optimal weight:    0.9990
   chunk 102 optimal weight:    0.7980
   chunk 20 optimal weight:    1.9990
   chunk 87 optimal weight:    0.0370
   chunk 54 optimal weight:    0.9990
   chunk 35 optimal weight:    0.9980
   chunk 29 optimal weight:    1.9990
   overall best weight:    0.6058

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3841 r_free = 0.3841 target = 0.122958 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3321 r_free = 0.3321 target = 0.089483 restraints weight = 18679.915|
|-----------------------------------------------------------------------------|
r_work (start): 0.3300 rms_B_bonded: 2.53
r_work: 0.3181 rms_B_bonded: 3.47 restraints_weight: 0.5000
r_work (final): 0.3181
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7894
moved from start:          0.2274

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.065  10905  Z= 0.155
  Angle     :  0.598  11.923  14827  Z= 0.306
  Chirality :  0.041   0.167   1821
  Planarity :  0.005   0.072   1852
  Dihedral  :  3.874  34.246   1490
  Min Nonbonded Distance : 2.501

Molprobity Statistics.
  All-atom Clashscore : 12.34
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.03 %
    Favored  : 95.97 %
  Rotamer:
    Outliers :  5.81 %
    Allowed  : 29.68 %
    Favored  : 64.52 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.80 (0.23), residues: 1388
  helix:  1.69 (0.15), residues: 1132
  sheet:  None (None), residues: 0
  loop : -0.95 (0.43), residues: 256

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.023   0.002   TRP T 208 
 HIS   0.001   0.000   HIS T 136 
 PHE   0.021   0.001   PHE X  11 
 TYR   0.012   0.002   TYR Z 296 
 ARG   0.009   0.000   ARG Z  78 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05249 (  921)
  hydrogen bonds       : angle       3.96150 ( 2724)
  SS BOND              : bond        0.00809 (    2)
  SS BOND              : angle       1.62203 (    4)
  covalent geometry    : bond        0.00338 (10903)
  covalent geometry    : angle       0.59722 (14823)

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

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

  2776 Ramachandran restraints generated.
    1388 Oldfield, 0 Emsley, 1388 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2776 Ramachandran restraints generated.
    1388 Oldfield, 0 Emsley, 1388 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  341 residues out of total 1089 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 63
    poor density    : 278
  time to evaluate  : 1.129 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: K   66 ILE cc_start: 0.9227 (tt) cc_final: 0.9027 (tt)
REVERT: M   40 GLU cc_start: 0.8056 (tm-30) cc_final: 0.7748 (tm-30)
REVERT: M   41 ILE cc_start: 0.9194 (OUTLIER) cc_final: 0.8853 (tp)
REVERT: O    1 MET cc_start: 0.7449 (tpp) cc_final: 0.7180 (tpt)
REVERT: Q   41 ILE cc_start: 0.9247 (tp) cc_final: 0.8965 (tp)
REVERT: T   25 LEU cc_start: 0.7398 (OUTLIER) cc_final: 0.6970 (pp)
REVERT: T   92 TYR cc_start: 0.8680 (t80) cc_final: 0.8155 (t80)
REVERT: T  239 GLU cc_start: 0.9223 (tp30) cc_final: 0.8814 (tp30)
REVERT: T  255 PHE cc_start: 0.8944 (t80) cc_final: 0.8533 (t80)
REVERT: T  280 GLU cc_start: 0.8825 (tm-30) cc_final: 0.8555 (tm-30)
REVERT: V   24 ILE cc_start: 0.8502 (tt) cc_final: 0.7982 (pt)
REVERT: Z  179 LYS cc_start: 0.7422 (tptp) cc_final: 0.6977 (ttpt)
REVERT: Z  236 PHE cc_start: 0.8710 (t80) cc_final: 0.8250 (t80)
REVERT: Z  239 GLU cc_start: 0.9128 (mm-30) cc_final: 0.8804 (mm-30)
REVERT: Z  242 LYS cc_start: 0.8740 (mttt) cc_final: 0.8480 (mtmt)
REVERT: Z  258 GLU cc_start: 0.8162 (OUTLIER) cc_final: 0.7789 (tm-30)
  outliers start: 63
  outliers final: 52
  residues processed: 315
  average time/residue: 0.2186
  time to fit residues: 97.2621
Evaluate side-chains
  327 residues out of total 1089 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 55
    poor density    : 272
  time to evaluate  : 1.050 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain H residue   29 SER
Chi-restraints excluded: chain H residue   45 VAL
Chi-restraints excluded: chain H residue   49 MET
Chi-restraints excluded: chain H residue   66 ILE
Chi-restraints excluded: chain I residue   18 ILE
Chi-restraints excluded: chain I residue   46 VAL
Chi-restraints excluded: chain I residue   64 LEU
Chi-restraints excluded: chain I residue   66 ILE
Chi-restraints excluded: chain J residue   46 VAL
Chi-restraints excluded: chain J residue   65 VAL
Chi-restraints excluded: chain K residue   13 VAL
Chi-restraints excluded: chain K residue   29 SER
Chi-restraints excluded: chain K residue   68 PHE
Chi-restraints excluded: chain L residue   13 VAL
Chi-restraints excluded: chain L residue   49 MET
Chi-restraints excluded: chain M residue   41 ILE
Chi-restraints excluded: chain M residue   45 VAL
Chi-restraints excluded: chain M residue   66 ILE
Chi-restraints excluded: chain N residue   13 VAL
Chi-restraints excluded: chain N residue   18 ILE
Chi-restraints excluded: chain N residue   32 VAL
Chi-restraints excluded: chain N residue   59 LEU
Chi-restraints excluded: chain N residue   68 PHE
Chi-restraints excluded: chain O residue   32 VAL
Chi-restraints excluded: chain O residue   56 THR
Chi-restraints excluded: chain Q residue   44 ARG
Chi-restraints excluded: chain Q residue   45 VAL
Chi-restraints excluded: chain T residue   25 LEU
Chi-restraints excluded: chain T residue   32 VAL
Chi-restraints excluded: chain T residue   53 VAL
Chi-restraints excluded: chain T residue   65 LEU
Chi-restraints excluded: chain T residue   89 GLU
Chi-restraints excluded: chain T residue  110 VAL
Chi-restraints excluded: chain T residue  136 HIS
Chi-restraints excluded: chain T residue  200 ILE
Chi-restraints excluded: chain T residue  206 GLU
Chi-restraints excluded: chain T residue  208 TRP
Chi-restraints excluded: chain T residue  258 GLU
Chi-restraints excluded: chain T residue  260 LEU
Chi-restraints excluded: chain T residue  286 ILE
Chi-restraints excluded: chain T residue  289 LEU
Chi-restraints excluded: chain V residue   11 PHE
Chi-restraints excluded: chain V residue   16 ILE
Chi-restraints excluded: chain X residue   25 LEU
Chi-restraints excluded: chain X residue   37 LEU
Chi-restraints excluded: chain Y residue    4 LEU
Chi-restraints excluded: chain Y residue    6 ILE
Chi-restraints excluded: chain Y residue   25 LEU
Chi-restraints excluded: chain Z residue   15 LEU
Chi-restraints excluded: chain Z residue  136 HIS
Chi-restraints excluded: chain Z residue  169 ILE
Chi-restraints excluded: chain Z residue  171 ASP
Chi-restraints excluded: chain Z residue  205 ILE
Chi-restraints excluded: chain Z residue  258 GLU
Chi-restraints excluded: chain Z residue  283 VAL
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 138
   random chunks:
   chunk 6 optimal weight:    1.9990
   chunk 94 optimal weight:    0.9990
   chunk 24 optimal weight:    2.9990
   chunk 88 optimal weight:    5.9990
   chunk 66 optimal weight:    0.5980
   chunk 44 optimal weight:    0.5980
   chunk 90 optimal weight:    2.9990
   chunk 53 optimal weight:    0.8980
   chunk 45 optimal weight:    0.9980
   chunk 98 optimal weight:    0.9990
   chunk 86 optimal weight:    0.7980
   overall best weight:    0.7780

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3828 r_free = 0.3828 target = 0.122094 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3307 r_free = 0.3307 target = 0.088631 restraints weight = 19009.307|
|-----------------------------------------------------------------------------|
r_work (start): 0.3286 rms_B_bonded: 2.54
r_work: 0.3164 rms_B_bonded: 3.49 restraints_weight: 0.5000
r_work (final): 0.3164
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7913
moved from start:          0.2306

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.094  10905  Z= 0.168
  Angle     :  0.625  16.874  14827  Z= 0.315
  Chirality :  0.042   0.169   1821
  Planarity :  0.005   0.072   1852
  Dihedral  :  3.883  34.274   1490
  Min Nonbonded Distance : 2.496

Molprobity Statistics.
  All-atom Clashscore : 12.52
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.18 %
    Favored  : 95.82 %
  Rotamer:
    Outliers :  5.71 %
    Allowed  : 30.05 %
    Favored  : 64.24 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.78 (0.22), residues: 1388
  helix:  1.66 (0.15), residues: 1133
  sheet:  None (None), residues: 0
  loop : -0.91 (0.43), residues: 255

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.024   0.002   TRP T 208 
 HIS   0.001   0.000   HIS Z 170 
 PHE   0.029   0.001   PHE T  24 
 TYR   0.017   0.002   TYR Q  48 
 ARG   0.008   0.000   ARG Z  78 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05356 (  921)
  hydrogen bonds       : angle       3.98298 ( 2724)
  SS BOND              : bond        0.00704 (    2)
  SS BOND              : angle       1.61762 (    4)
  covalent geometry    : bond        0.00378 (10903)
  covalent geometry    : angle       0.62414 (14823)

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

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

  2776 Ramachandran restraints generated.
    1388 Oldfield, 0 Emsley, 1388 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2776 Ramachandran restraints generated.
    1388 Oldfield, 0 Emsley, 1388 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  338 residues out of total 1089 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 62
    poor density    : 276
  time to evaluate  : 1.132 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: K    1 MET cc_start: 0.7277 (mmt) cc_final: 0.6810 (mmt)
REVERT: K   66 ILE cc_start: 0.9236 (tt) cc_final: 0.9030 (tt)
REVERT: M   40 GLU cc_start: 0.8070 (tm-30) cc_final: 0.7770 (tm-30)
REVERT: M   41 ILE cc_start: 0.9188 (OUTLIER) cc_final: 0.8864 (tp)
REVERT: O    1 MET cc_start: 0.7536 (tpp) cc_final: 0.6879 (mmm)
REVERT: Q   41 ILE cc_start: 0.9257 (tp) cc_final: 0.8980 (tp)
REVERT: T   25 LEU cc_start: 0.7417 (OUTLIER) cc_final: 0.6986 (pp)
REVERT: T   92 TYR cc_start: 0.8693 (t80) cc_final: 0.8160 (t80)
REVERT: T  239 GLU cc_start: 0.9226 (tp30) cc_final: 0.8838 (tp30)
REVERT: T  255 PHE cc_start: 0.8951 (t80) cc_final: 0.8536 (t80)
REVERT: T  280 GLU cc_start: 0.8838 (tm-30) cc_final: 0.8564 (tm-30)
REVERT: V   24 ILE cc_start: 0.8456 (tt) cc_final: 0.7929 (pt)
REVERT: Z  179 LYS cc_start: 0.7423 (tptp) cc_final: 0.6975 (ttpt)
REVERT: Z  236 PHE cc_start: 0.8677 (t80) cc_final: 0.8204 (t80)
REVERT: Z  239 GLU cc_start: 0.9131 (mm-30) cc_final: 0.8827 (mm-30)
REVERT: Z  242 LYS cc_start: 0.8709 (mttt) cc_final: 0.8497 (mtmt)
REVERT: Z  258 GLU cc_start: 0.8212 (OUTLIER) cc_final: 0.7816 (tm-30)
  outliers start: 62
  outliers final: 54
  residues processed: 311
  average time/residue: 0.2182
  time to fit residues: 96.1817
Evaluate side-chains
  325 residues out of total 1089 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 57
    poor density    : 268
  time to evaluate  : 1.095 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain H residue   29 SER
Chi-restraints excluded: chain H residue   45 VAL
Chi-restraints excluded: chain H residue   49 MET
Chi-restraints excluded: chain H residue   66 ILE
Chi-restraints excluded: chain I residue   18 ILE
Chi-restraints excluded: chain I residue   46 VAL
Chi-restraints excluded: chain I residue   64 LEU
Chi-restraints excluded: chain I residue   66 ILE
Chi-restraints excluded: chain J residue   46 VAL
Chi-restraints excluded: chain J residue   65 VAL
Chi-restraints excluded: chain K residue   13 VAL
Chi-restraints excluded: chain K residue   29 SER
Chi-restraints excluded: chain K residue   68 PHE
Chi-restraints excluded: chain L residue   13 VAL
Chi-restraints excluded: chain L residue   49 MET
Chi-restraints excluded: chain M residue   41 ILE
Chi-restraints excluded: chain M residue   45 VAL
Chi-restraints excluded: chain M residue   66 ILE
Chi-restraints excluded: chain N residue   13 VAL
Chi-restraints excluded: chain N residue   18 ILE
Chi-restraints excluded: chain N residue   32 VAL
Chi-restraints excluded: chain N residue   59 LEU
Chi-restraints excluded: chain O residue   32 VAL
Chi-restraints excluded: chain O residue   56 THR
Chi-restraints excluded: chain P residue   69 LEU
Chi-restraints excluded: chain Q residue   44 ARG
Chi-restraints excluded: chain Q residue   45 VAL
Chi-restraints excluded: chain T residue   25 LEU
Chi-restraints excluded: chain T residue   32 VAL
Chi-restraints excluded: chain T residue   37 GLU
Chi-restraints excluded: chain T residue   53 VAL
Chi-restraints excluded: chain T residue   65 LEU
Chi-restraints excluded: chain T residue   89 GLU
Chi-restraints excluded: chain T residue  110 VAL
Chi-restraints excluded: chain T residue  136 HIS
Chi-restraints excluded: chain T residue  200 ILE
Chi-restraints excluded: chain T residue  206 GLU
Chi-restraints excluded: chain T residue  208 TRP
Chi-restraints excluded: chain T residue  258 GLU
Chi-restraints excluded: chain T residue  260 LEU
Chi-restraints excluded: chain T residue  283 VAL
Chi-restraints excluded: chain T residue  286 ILE
Chi-restraints excluded: chain T residue  289 LEU
Chi-restraints excluded: chain V residue   11 PHE
Chi-restraints excluded: chain V residue   16 ILE
Chi-restraints excluded: chain X residue   25 LEU
Chi-restraints excluded: chain X residue   37 LEU
Chi-restraints excluded: chain Y residue    4 LEU
Chi-restraints excluded: chain Y residue    6 ILE
Chi-restraints excluded: chain Y residue   25 LEU
Chi-restraints excluded: chain Z residue   15 LEU
Chi-restraints excluded: chain Z residue   85 GLU
Chi-restraints excluded: chain Z residue  169 ILE
Chi-restraints excluded: chain Z residue  171 ASP
Chi-restraints excluded: chain Z residue  205 ILE
Chi-restraints excluded: chain Z residue  258 GLU
Chi-restraints excluded: chain Z residue  283 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 138
   random chunks:
   chunk 15 optimal weight:    0.9980
   chunk 6 optimal weight:    2.9990
   chunk 1 optimal weight:    0.7980
   chunk 116 optimal weight:    0.5980
   chunk 37 optimal weight:    0.8980
   chunk 135 optimal weight:    0.8980
   chunk 82 optimal weight:   20.0000
   chunk 7 optimal weight:    1.9990
   chunk 31 optimal weight:    0.7980
   chunk 113 optimal weight:    0.0000
   chunk 40 optimal weight:    0.5980
   overall best weight:    0.5584

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3836 r_free = 0.3836 target = 0.122877 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3319 r_free = 0.3319 target = 0.089447 restraints weight = 18839.217|
|-----------------------------------------------------------------------------|
r_work (start): 0.3296 rms_B_bonded: 2.53
r_work: 0.3175 rms_B_bonded: 3.49 restraints_weight: 0.5000
r_work (final): 0.3175
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7891
moved from start:          0.2408

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.099  10905  Z= 0.155
  Angle     :  0.629  17.043  14827  Z= 0.316
  Chirality :  0.042   0.183   1821
  Planarity :  0.005   0.072   1852
  Dihedral  :  3.875  34.174   1490
  Min Nonbonded Distance : 2.475

Molprobity Statistics.
  All-atom Clashscore : 12.79
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.03 %
    Favored  : 95.97 %
  Rotamer:
    Outliers :  5.35 %
    Allowed  : 30.51 %
    Favored  : 64.15 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.80 (0.22), residues: 1388
  helix:  1.68 (0.15), residues: 1132
  sheet:  None (None), residues: 0
  loop : -0.94 (0.43), residues: 256

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.024   0.002   TRP T 208 
 HIS   0.001   0.000   HIS Z 170 
 PHE   0.023   0.001   PHE X  11 
 TYR   0.013   0.002   TYR O  48 
 ARG   0.007   0.000   ARG Z  78 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05250 (  921)
  hydrogen bonds       : angle       3.94922 ( 2724)
  SS BOND              : bond        0.00712 (    2)
  SS BOND              : angle       1.34051 (    4)
  covalent geometry    : bond        0.00343 (10903)
  covalent geometry    : angle       0.62854 (14823)

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

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

  2776 Ramachandran restraints generated.
    1388 Oldfield, 0 Emsley, 1388 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2776 Ramachandran restraints generated.
    1388 Oldfield, 0 Emsley, 1388 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  336 residues out of total 1089 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 58
    poor density    : 278
  time to evaluate  : 1.091 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: K    1 MET cc_start: 0.7033 (mmt) cc_final: 0.6659 (mmt)
REVERT: M   40 GLU cc_start: 0.8052 (tm-30) cc_final: 0.7741 (tm-30)
REVERT: M   41 ILE cc_start: 0.9176 (OUTLIER) cc_final: 0.8805 (tp)
REVERT: N   35 ILE cc_start: 0.9266 (mm) cc_final: 0.9048 (mm)
REVERT: Q   41 ILE cc_start: 0.9229 (tp) cc_final: 0.8947 (tp)
REVERT: T   25 LEU cc_start: 0.7366 (OUTLIER) cc_final: 0.6933 (pp)
REVERT: T   92 TYR cc_start: 0.8682 (t80) cc_final: 0.8157 (t80)
REVERT: T  136 HIS cc_start: 0.5672 (OUTLIER) cc_final: 0.5396 (m-70)
REVERT: T  239 GLU cc_start: 0.9225 (tp30) cc_final: 0.8846 (tp30)
REVERT: T  255 PHE cc_start: 0.8933 (t80) cc_final: 0.8521 (t80)
REVERT: T  280 GLU cc_start: 0.8828 (tm-30) cc_final: 0.8572 (tm-30)
REVERT: V   24 ILE cc_start: 0.8380 (tt) cc_final: 0.7911 (pt)
REVERT: Z  179 LYS cc_start: 0.7439 (tptp) cc_final: 0.6992 (ttpt)
REVERT: Z  236 PHE cc_start: 0.8682 (t80) cc_final: 0.8212 (t80)
REVERT: Z  239 GLU cc_start: 0.9177 (mm-30) cc_final: 0.8882 (mm-30)
REVERT: Z  258 GLU cc_start: 0.8278 (tm-30) cc_final: 0.7890 (tm-30)
  outliers start: 58
  outliers final: 50
  residues processed: 311
  average time/residue: 0.2436
  time to fit residues: 109.5528
Evaluate side-chains
  326 residues out of total 1089 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 53
    poor density    : 273
  time to evaluate  : 1.090 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain H residue   29 SER
Chi-restraints excluded: chain H residue   45 VAL
Chi-restraints excluded: chain H residue   49 MET
Chi-restraints excluded: chain H residue   66 ILE
Chi-restraints excluded: chain I residue   18 ILE
Chi-restraints excluded: chain I residue   46 VAL
Chi-restraints excluded: chain I residue   64 LEU
Chi-restraints excluded: chain I residue   66 ILE
Chi-restraints excluded: chain J residue   46 VAL
Chi-restraints excluded: chain J residue   65 VAL
Chi-restraints excluded: chain K residue   13 VAL
Chi-restraints excluded: chain K residue   29 SER
Chi-restraints excluded: chain K residue   68 PHE
Chi-restraints excluded: chain L residue   49 MET
Chi-restraints excluded: chain M residue   41 ILE
Chi-restraints excluded: chain M residue   45 VAL
Chi-restraints excluded: chain M residue   66 ILE
Chi-restraints excluded: chain N residue   13 VAL
Chi-restraints excluded: chain N residue   18 ILE
Chi-restraints excluded: chain N residue   32 VAL
Chi-restraints excluded: chain N residue   59 LEU
Chi-restraints excluded: chain N residue   68 PHE
Chi-restraints excluded: chain O residue   32 VAL
Chi-restraints excluded: chain O residue   56 THR
Chi-restraints excluded: chain P residue   69 LEU
Chi-restraints excluded: chain Q residue   44 ARG
Chi-restraints excluded: chain Q residue   45 VAL
Chi-restraints excluded: chain Q residue   66 ILE
Chi-restraints excluded: chain T residue   25 LEU
Chi-restraints excluded: chain T residue   32 VAL
Chi-restraints excluded: chain T residue   65 LEU
Chi-restraints excluded: chain T residue   89 GLU
Chi-restraints excluded: chain T residue  110 VAL
Chi-restraints excluded: chain T residue  136 HIS
Chi-restraints excluded: chain T residue  200 ILE
Chi-restraints excluded: chain T residue  206 GLU
Chi-restraints excluded: chain T residue  208 TRP
Chi-restraints excluded: chain T residue  258 GLU
Chi-restraints excluded: chain T residue  260 LEU
Chi-restraints excluded: chain T residue  286 ILE
Chi-restraints excluded: chain T residue  289 LEU
Chi-restraints excluded: chain V residue   11 PHE
Chi-restraints excluded: chain V residue   16 ILE
Chi-restraints excluded: chain X residue   25 LEU
Chi-restraints excluded: chain X residue   37 LEU
Chi-restraints excluded: chain Y residue    4 LEU
Chi-restraints excluded: chain Y residue    6 ILE
Chi-restraints excluded: chain Y residue   25 LEU
Chi-restraints excluded: chain Z residue   15 LEU
Chi-restraints excluded: chain Z residue   85 GLU
Chi-restraints excluded: chain Z residue  169 ILE
Chi-restraints excluded: chain Z residue  171 ASP
Chi-restraints excluded: chain Z residue  205 ILE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 138
   random chunks:
   chunk 131 optimal weight:    1.9990
   chunk 122 optimal weight:    1.9990
   chunk 107 optimal weight:    0.9980
   chunk 29 optimal weight:    1.9990
   chunk 2 optimal weight:    0.5980
   chunk 21 optimal weight:    0.5980
   chunk 69 optimal weight:    0.9990
   chunk 94 optimal weight:    0.8980
   chunk 101 optimal weight:    0.9990
   chunk 43 optimal weight:    0.7980
   chunk 50 optimal weight:    1.9990
   overall best weight:    0.7780

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3832 r_free = 0.3832 target = 0.122232 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3308 r_free = 0.3308 target = 0.088652 restraints weight = 18696.552|
|-----------------------------------------------------------------------------|
r_work (start): 0.3287 rms_B_bonded: 2.54
r_work: 0.3167 rms_B_bonded: 3.47 restraints_weight: 0.5000
r_work (final): 0.3167
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7902
moved from start:          0.2406

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.103  10905  Z= 0.171
  Angle     :  0.639  16.617  14827  Z= 0.323
  Chirality :  0.042   0.212   1821
  Planarity :  0.005   0.072   1852
  Dihedral  :  3.888  33.880   1490
  Min Nonbonded Distance : 2.490

Molprobity Statistics.
  All-atom Clashscore : 12.61
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.32 %
    Favored  : 95.68 %
  Rotamer:
    Outliers :  5.16 %
    Allowed  : 30.78 %
    Favored  : 64.06 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.76 (0.22), residues: 1388
  helix:  1.67 (0.15), residues: 1129
  sheet:  None (None), residues: 0
  loop : -1.02 (0.42), residues: 259

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.024   0.002   TRP T 208 
 HIS   0.001   0.000   HIS Z 170 
 PHE   0.026   0.001   PHE T  24 
 TYR   0.018   0.002   TYR Q  48 
 ARG   0.008   0.000   ARG Z  78 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05339 (  921)
  hydrogen bonds       : angle       3.96525 ( 2724)
  SS BOND              : bond        0.00640 (    2)
  SS BOND              : angle       1.33856 (    4)
  covalent geometry    : bond        0.00391 (10903)
  covalent geometry    : angle       0.63914 (14823)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 5388.23 seconds
wall clock time: 94 minutes 49.53 seconds (5689.53 seconds total)