Starting phenix.real_space_refine
on Sun Apr 27 15:46:59 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9fkp_50524/04_2025/9fkp_50524.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9fkp_50524/04_2025/9fkp_50524.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.72
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/9fkp_50524/04_2025/9fkp_50524.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9fkp_50524/04_2025/9fkp_50524.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9fkp_50524/04_2025/9fkp_50524.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9fkp_50524/04_2025/9fkp_50524.cif"
  }
  resolution = 3.72
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=  -0.000 sd=   0.006
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      59      5.16       5
     C    3859      2.51       5
     N    1037      2.21       5
     O    1137      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 7 residue(s): 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/chem_data/mon_lib"
  Total number of atoms: 6092
  Number of models: 1
  Model: ""
    Number of chains: 5
    Chain: "A"
      Number of atoms: 896
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 112, 896
          Classifications: {'peptide': 112}
          Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 102}
    Chain: "B"
      Number of atoms: 897
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 112, 897
          Classifications: {'peptide': 112}
          Modifications used: {'COO': 1}
          Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 102}
    Chain: "D"
      Number of atoms: 852
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 107, 852
          Classifications: {'peptide': 107}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 6, 'TRANS': 100}
    Chain: "E"
      Number of atoms: 868
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 109, 868
          Classifications: {'peptide': 109}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 6, 'TRANS': 102}
    Chain: "C"
      Number of atoms: 2579
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 329, 2579
          Classifications: {'peptide': 329}
          Link IDs: {'PCIS': 1, 'PTRANS': 18, 'TRANS': 309}
  Time building chain proxies: 4.95, per 1000 atoms: 0.81
  Number of scatterers: 6092
  At special positions: 0
  Unit cell: (89.28, 74.88, 143.28, 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      59     16.00
     O    1137      8.00
     N    1037      7.00
     C    3859      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=23, symmetry=0
    Simple disulfide: pdb=" SG  CYS A   7 " - pdb=" SG  CYS A  16 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A  15 " - pdb=" SG  CYS A  78 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A  44 " - pdb=" SG  CYS A 109 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A  48 " - pdb=" SG  CYS A 111 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A  77 " - pdb=" SG  CYS B  77 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B   7 " - pdb=" SG  CYS B  16 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B  15 " - pdb=" SG  CYS B  78 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B  44 " - pdb=" SG  CYS B 109 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B  48 " - pdb=" SG  CYS B 111 " distance=2.03
    Simple disulfide: pdb=" SG  CYS D  51 " - pdb=" SG  CYS D  84 " distance=2.03
    Simple disulfide: pdb=" SG  CYS D  54 " - pdb=" SG  CYS D  71 " distance=2.03
    Simple disulfide: pdb=" SG  CYS D  61 " - pdb=" SG  CYS D  67 " distance=2.03
    Simple disulfide: pdb=" SG  CYS D  77 " - pdb=" SG  CYS D 101 " distance=2.03
    Simple disulfide: pdb=" SG  CYS D 121 " - pdb=" SG  CYS D 136 " distance=2.03
    Simple disulfide: pdb=" SG  CYS D 138 " - pdb=" SG  CYS D 143 " distance=2.03
    Simple disulfide: pdb=" SG  CYS E  51 " - pdb=" SG  CYS E  84 " distance=2.03
    Simple disulfide: pdb=" SG  CYS E  54 " - pdb=" SG  CYS E  71 " distance=2.03
    Simple disulfide: pdb=" SG  CYS E  61 " - pdb=" SG  CYS E  67 " distance=2.03
    Simple disulfide: pdb=" SG  CYS E  77 " - pdb=" SG  CYS E 101 " distance=2.03
    Simple disulfide: pdb=" SG  CYS E 121 " - pdb=" SG  CYS E 136 " distance=2.03
    Simple disulfide: pdb=" SG  CYS E 138 " - pdb=" SG  CYS E 143 " distance=2.03
    Simple disulfide: pdb=" SG  CYS C  31 " - pdb=" SG  CYS C 225 " distance=2.03
    Simple disulfide: pdb=" SG  CYS C  55 " - pdb=" SG  CYS C 201 " distance=2.03

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 1.35
  Conformation dependent library (CDL) restraints added in 800.7 milliseconds
  

  1518 Ramachandran restraints generated.
    759 Oldfield, 0 Emsley, 759 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1476

  Finding SS restraints...
    Secondary structure from input PDB file:
      10 helices and 16 sheets defined
      12.1% alpha, 35.1% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.81
  Creating SS restraints...
    Processing helix  chain 'A' and resid 3 through 10
      removed outlier: 3.712A  pdb=" N   CYS A   7 " --> pdb=" O   ASP A   3 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 56 through 69
    Processing helix  chain 'B' and resid 3 through 10
      removed outlier: 3.559A  pdb=" N   SER B  10 " --> pdb=" O   TYR B   6 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 56 through 69
      removed outlier: 3.502A  pdb=" N   LYS B  60 " --> pdb=" O   THR B  56 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 142 through 144
      No H-bonds generated for 'chain 'E' and resid 142 through 144'
    Processing helix  chain 'C' and resid 58 through 62
      removed outlier: 3.867A  pdb=" N   SER C  62 " --> pdb=" O   GLY C  59 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 143 through 150
      removed outlier: 3.910A  pdb=" N   SER C 147 " --> pdb=" O   VAL C 143 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 160 through 173
    Processing helix  chain 'C' and resid 305 through 311
    Processing helix  chain 'C' and resid 325 through 336
    Processing sheet with id=AA1, first strand: chain 'A' and resid 16 through 18
    Processing sheet with id=AA2, first strand: chain 'A' and resid 21 through 23
    Processing sheet with id=AA3, first strand: chain 'A' and resid 77 through 80
    Processing sheet with id=AA4, first strand: chain 'A' and resid 95 through 106
      removed outlier: 6.868A  pdb=" N   LYS A  97 " --> pdb=" O   VAL A  92 " (cutoff:3.500A)
      removed outlier: 6.452A  pdb=" N   VAL A  92 " --> pdb=" O   LYS A  97 " (cutoff:3.500A)
      removed outlier: 7.208A  pdb=" N   GLU A  99 " --> pdb=" O   TYR A  90 " (cutoff:3.500A)
      removed outlier: 7.380A  pdb=" N   TYR A  90 " --> pdb=" O   GLU A  99 " (cutoff:3.500A)
      removed outlier: 6.741A  pdb=" N   LEU A 101 " --> pdb=" O   ILE A  88 " (cutoff:3.500A)
      removed outlier: 7.363A  pdb=" N   ILE A  88 " --> pdb=" O   LEU A 101 " (cutoff:3.500A)
      removed outlier: 7.348A  pdb=" N   ASN A 103 " --> pdb=" O   LEU A  86 " (cutoff:3.500A)
      removed outlier: 6.749A  pdb=" N   LEU A  86 " --> pdb=" O   ASN A 103 " (cutoff:3.500A)
      removed outlier: 10.190A  pdb=" N   ILE D  76 " --> pdb=" O   VAL A  89 " (cutoff:3.500A)
      removed outlier: 7.185A  pdb=" N   TYR A  91 " --> pdb=" O   ILE D  76 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'B' and resid 16 through 18
    Processing sheet with id=AA6, first strand: chain 'B' and resid 21 through 23
    Processing sheet with id=AA7, first strand: chain 'B' and resid 77 through 92
      removed outlier: 6.730A  pdb=" N   SER B 108 " --> pdb=" O   GLN B  81 " (cutoff:3.500A)
      removed outlier: 7.021A  pdb=" N   LEU B  83 " --> pdb=" O   VAL B 106 " (cutoff:3.500A)
      removed outlier: 6.516A  pdb=" N   VAL B 106 " --> pdb=" O   LEU B  83 " (cutoff:3.500A)
      removed outlier: 6.410A  pdb=" N   MET B 104 " --> pdb=" O   PRO B  85 " (cutoff:3.500A)
      removed outlier: 8.595A  pdb=" N   SER B 102 " --> pdb=" O   PRO B  87 " (cutoff:3.500A)
      removed outlier: 9.752A  pdb=" N   VAL B  89 " --> pdb=" O   GLN B 100 " (cutoff:3.500A)
      removed outlier: 9.692A  pdb=" N   GLN B 100 " --> pdb=" O   VAL B  89 " (cutoff:3.500A)
      removed outlier: 9.586A  pdb=" N   TYR B  91 " --> pdb=" O   VAL B  98 " (cutoff:3.500A)
      removed outlier: 9.342A  pdb=" N   VAL B  98 " --> pdb=" O   TYR B  91 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'D' and resid 66 through 67
      removed outlier: 3.788A  pdb=" N   CYS D  67 " --> pdb=" O   ILE D 147 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'D' and resid 97 through 102
    Processing sheet with id=AB1, first strand: chain 'E' and resid 50 through 52
    Processing sheet with id=AB2, first strand: chain 'E' and resid 57 through 58
      removed outlier: 4.490A  pdb=" N   PHE E 133 " --> pdb=" O   LYS E 126 " (cutoff:3.500A)
      removed outlier: 4.208A  pdb=" N   SER E 137 " --> pdb=" O   ILE E 122 " (cutoff:3.500A)
      removed outlier: 4.298A  pdb=" N   ILE E 122 " --> pdb=" O   SER E 137 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'E' and resid 67 through 68
    Processing sheet with id=AB4, first strand: chain 'C' and resid 34 through 35
      removed outlier: 3.740A  pdb=" N   LEU C  34 " --> pdb=" O   GLY C 224 " (cutoff:3.500A)
      removed outlier: 6.339A  pdb=" N   VAL C 236 " --> pdb=" O   SER C 343 " (cutoff:3.500A)
      removed outlier: 7.896A  pdb=" N   THR C 345 " --> pdb=" O   VAL C 236 " (cutoff:3.500A)
      removed outlier: 6.048A  pdb=" N   ILE C 238 " --> pdb=" O   THR C 345 " (cutoff:3.500A)
      removed outlier: 7.563A  pdb=" N   THR C 347 " --> pdb=" O   ILE C 238 " (cutoff:3.500A)
      removed outlier: 6.424A  pdb=" N   GLU C 240 " --> pdb=" O   THR C 347 " (cutoff:3.500A)
      removed outlier: 7.058A  pdb=" N   VAL C 349 " --> pdb=" O   GLU C 240 " (cutoff:3.500A)
      removed outlier: 7.868A  pdb=" N   GLN C 242 " --> pdb=" O   VAL C 349 " (cutoff:3.500A)
      removed outlier: 3.506A  pdb=" N   LEU C 274 " --> pdb=" O   HIS C 237 " (cutoff:3.500A)
      removed outlier: 5.954A  pdb=" N   LEU C 267 " --> pdb=" O   MET C 291 " (cutoff:3.500A)
      removed outlier: 7.878A  pdb=" N   LYS C 293 " --> pdb=" O   LEU C 267 " (cutoff:3.500A)
    Processing sheet with id=AB5, first strand: chain 'C' and resid 34 through 35
      removed outlier: 3.740A  pdb=" N   LEU C  34 " --> pdb=" O   GLY C 224 " (cutoff:3.500A)
      removed outlier: 6.339A  pdb=" N   VAL C 236 " --> pdb=" O   SER C 343 " (cutoff:3.500A)
      removed outlier: 7.896A  pdb=" N   THR C 345 " --> pdb=" O   VAL C 236 " (cutoff:3.500A)
      removed outlier: 6.048A  pdb=" N   ILE C 238 " --> pdb=" O   THR C 345 " (cutoff:3.500A)
      removed outlier: 7.563A  pdb=" N   THR C 347 " --> pdb=" O   ILE C 238 " (cutoff:3.500A)
      removed outlier: 6.424A  pdb=" N   GLU C 240 " --> pdb=" O   THR C 347 " (cutoff:3.500A)
      removed outlier: 7.058A  pdb=" N   VAL C 349 " --> pdb=" O   GLU C 240 " (cutoff:3.500A)
      removed outlier: 7.868A  pdb=" N   GLN C 242 " --> pdb=" O   VAL C 349 " (cutoff:3.500A)
      removed outlier: 3.506A  pdb=" N   LEU C 274 " --> pdb=" O   HIS C 237 " (cutoff:3.500A)
      removed outlier: 6.931A  pdb=" N   GLN C 313 " --> pdb=" O   VAL C 290 " (cutoff:3.500A)
      removed outlier: 6.528A  pdb=" N   GLY C 292 " --> pdb=" O   GLN C 313 " (cutoff:3.500A)
    Processing sheet with id=AB6, first strand: chain 'C' and resid 138 through 141
      removed outlier: 6.927A  pdb=" N   VAL C  87 " --> pdb=" O   LYS C 117 " (cutoff:3.500A)
      removed outlier: 7.196A  pdb=" N   ARG C 119 " --> pdb=" O   VAL C  87 " (cutoff:3.500A)
      removed outlier: 5.808A  pdb=" N   LEU C  89 " --> pdb=" O   ARG C 119 " (cutoff:3.500A)
      removed outlier: 8.906A  pdb=" N   ILE C 187 " --> pdb=" O   GLU C  86 " (cutoff:3.500A)
      removed outlier: 7.360A  pdb=" N   ALA C  88 " --> pdb=" O   ILE C 187 " (cutoff:3.500A)
      removed outlier: 8.339A  pdb=" N   ILE C 189 " --> pdb=" O   ALA C  88 " (cutoff:3.500A)
      removed outlier: 5.977A  pdb=" N   HIS C  90 " --> pdb=" O   ILE C 189 " (cutoff:3.500A)
      removed outlier: 6.444A  pdb=" N   VAL C 191 " --> pdb=" O   HIS C  90 " (cutoff:3.500A)
      removed outlier: 6.023A  pdb=" N   ARG C  92 " --> pdb=" O   VAL C 191 " (cutoff:3.500A)
      removed outlier: 8.157A  pdb=" N   PHE C 353 " --> pdb=" O   ASP C 253 " (cutoff:3.500A)
      removed outlier: 6.083A  pdb=" N   ILE C 255 " --> pdb=" O   PHE C 353 " (cutoff:3.500A)
      removed outlier: 7.373A  pdb=" N   LEU C 355 " --> pdb=" O   ILE C 255 " (cutoff:3.500A)
      removed outlier: 6.001A  pdb=" N   ASP C 257 " --> pdb=" O   LEU C 355 " (cutoff:3.500A)
      removed outlier: 7.577A  pdb=" N   LEU C 357 " --> pdb=" O   ASP C 257 " (cutoff:3.500A)
      removed outlier: 7.455A  pdb=" N   ARG C 259 " --> pdb=" O   LEU C 357 " (cutoff:3.500A)
      removed outlier: 6.129A  pdb=" N   VAL C 252 " --> pdb=" O   ASN C 282 " (cutoff:3.500A)
      removed outlier: 6.933A  pdb=" N   VAL C 284 " --> pdb=" O   VAL C 252 " (cutoff:3.500A)
      removed outlier: 5.829A  pdb=" N   VAL C 254 " --> pdb=" O   VAL C 284 " (cutoff:3.500A)
      removed outlier: 7.159A  pdb=" N   LYS C 286 " --> pdb=" O   VAL C 254 " (cutoff:3.500A)
      removed outlier: 6.170A  pdb=" N   VAL C 256 " --> pdb=" O   LYS C 286 " (cutoff:3.500A)
      removed outlier: 8.098A  pdb=" N   SER C 303 " --> pdb=" O   VAL C 281 " (cutoff:3.500A)
      removed outlier: 6.118A  pdb=" N   TRP C 283 " --> pdb=" O   SER C 303 " (cutoff:3.500A)
    Processing sheet with id=AB7, first strand: chain 'C' and resid 53 through 56
      removed outlier: 5.821A  pdb=" N   GLU C  66 " --> pdb=" O   VAL C 105 " (cutoff:3.500A)
      removed outlier: 6.924A  pdb=" N   ILE C 107 " --> pdb=" O   GLU C  66 " (cutoff:3.500A)
      removed outlier: 6.427A  pdb=" N   HIS C  68 " --> pdb=" O   ILE C 107 " (cutoff:3.500A)
      removed outlier: 3.587A  pdb=" N   ILE C 130 " --> pdb=" O   LEU C 104 " (cutoff:3.500A)

    176 hydrogen bonds defined for protein.
    462 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 1.88

  Time building geometry restraints manager: 1.65 seconds

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

  Histogram of bond lengths:
        1.23 -     1.35: 1979
        1.35 -     1.46: 1392
        1.46 -     1.58: 2801
        1.58 -     1.70: 0
        1.70 -     1.82: 72
  Bond restraints: 6244
  Sorted by residual:
  bond pdb=" N   CYS A   7 "
       pdb=" CA  CYS A   7 "
    ideal  model  delta    sigma   weight residual
    1.456  1.492 -0.036 1.33e-02 5.65e+03 7.33e+00
  bond pdb=" N   THR C 317 "
       pdb=" CA  THR C 317 "
    ideal  model  delta    sigma   weight residual
    1.456  1.483 -0.028 1.22e-02 6.72e+03 5.16e+00
  bond pdb=" N   GLU C 193 "
       pdb=" CA  GLU C 193 "
    ideal  model  delta    sigma   weight residual
    1.459  1.487 -0.028 1.23e-02 6.61e+03 5.14e+00
  bond pdb=" N   GLU C 240 "
       pdb=" CA  GLU C 240 "
    ideal  model  delta    sigma   weight residual
    1.456  1.483 -0.027 1.21e-02 6.83e+03 4.84e+00
  bond pdb=" N   ALA A   1 "
       pdb=" CA  ALA A   1 "
    ideal  model  delta    sigma   weight residual
    1.458  1.490 -0.032 1.90e-02 2.77e+03 2.89e+00
  ... (remaining 6239 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     0.81: 7814
        0.81 -     1.61: 533
        1.61 -     2.42: 63
        2.42 -     3.22: 39
        3.22 -     4.03: 21
  Bond angle restraints: 8470
  Sorted by residual:
  angle pdb=" CA  THR C 317 "
        pdb=" C   THR C 317 "
        pdb=" O   THR C 317 "
      ideal   model   delta    sigma   weight residual
     121.16  118.36    2.80 1.12e+00 7.97e-01 6.27e+00
  angle pdb=" CA  CYS A  16 "
        pdb=" C   CYS A  16 "
        pdb=" O   CYS A  16 "
      ideal   model   delta    sigma   weight residual
     121.32  118.54    2.78 1.18e+00 7.18e-01 5.55e+00
  angle pdb=" CA  GLU C 193 "
        pdb=" C   GLU C 193 "
        pdb=" O   GLU C 193 "
      ideal   model   delta    sigma   weight residual
     120.58  118.31    2.27 1.07e+00 8.73e-01 4.49e+00
  angle pdb=" C   CYS A  15 "
        pdb=" N   CYS A  16 "
        pdb=" CA  CYS A  16 "
      ideal   model   delta    sigma   weight residual
     122.39  119.07    3.32 1.64e+00 3.72e-01 4.09e+00
  angle pdb=" CA  THR C 317 "
        pdb=" CB  THR C 317 "
        pdb=" CG2 THR C 317 "
      ideal   model   delta    sigma   weight residual
     110.50  113.89   -3.39 1.70e+00 3.46e-01 3.97e+00
  ... (remaining 8465 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    14.93: 3695
       14.93 -    29.86: 142
       29.86 -    44.79: 24
       44.79 -    59.72: 7
       59.72 -    74.65: 1
  Dihedral angle restraints: 3869
    sinusoidal: 1604
      harmonic: 2265
  Sorted by residual:
  dihedral pdb=" N   CYS A  16 "
           pdb=" CA  CYS A  16 "
           pdb=" CB  CYS A  16 "
           pdb=" SG  CYS A  16 "
      ideal   model   delta sinusoidal    sigma   weight residual
      60.00  119.15  -59.15     3      1.50e+01 4.44e-03 9.48e+00
  dihedral pdb=" CB  LYS A  37 "
           pdb=" CG  LYS A  37 "
           pdb=" CD  LYS A  37 "
           pdb=" CE  LYS A  37 "
      ideal   model   delta sinusoidal    sigma   weight residual
    -180.00 -122.71  -57.29     3      1.50e+01 4.44e-03 9.43e+00
  dihedral pdb=" N   CYS B   7 "
           pdb=" CA  CYS B   7 "
           pdb=" CB  CYS B   7 "
           pdb=" SG  CYS B   7 "
      ideal   model   delta sinusoidal    sigma   weight residual
    -180.00 -124.73  -55.27     3      1.50e+01 4.44e-03 9.34e+00
  ... (remaining 3866 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.030: 563
       0.030 -    0.060: 235
       0.060 -    0.089: 40
       0.089 -    0.119: 82
       0.119 -    0.149: 12
  Chirality restraints: 932
  Sorted by residual:
  chirality pdb=" CA  THR C 317 "
            pdb=" N   THR C 317 "
            pdb=" C   THR C 317 "
            pdb=" CB  THR C 317 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.53    2.67   -0.15 2.00e-01 2.50e+01 5.53e-01
  chirality pdb=" CA  ILE E  76 "
            pdb=" N   ILE E  76 "
            pdb=" C   ILE E  76 "
            pdb=" CB  ILE E  76 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.57   -0.14 2.00e-01 2.50e+01 4.76e-01
  chirality pdb=" CA  ILE B 105 "
            pdb=" N   ILE B 105 "
            pdb=" C   ILE B 105 "
            pdb=" CB  ILE B 105 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.57   -0.13 2.00e-01 2.50e+01 4.45e-01
  ... (remaining 929 not shown)

  Planarity restraints: 1093
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   GLU B  84 "    0.020 5.00e-02 4.00e+02   2.96e-02 1.41e+00
        pdb=" N   PRO B  85 "   -0.051 5.00e-02 4.00e+02
        pdb=" CA  PRO B  85 "    0.015 5.00e-02 4.00e+02
        pdb=" CD  PRO B  85 "    0.017 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ARG C  92 "   -0.019 5.00e-02 4.00e+02   2.92e-02 1.37e+00
        pdb=" N   PRO C  93 "    0.051 5.00e-02 4.00e+02
        pdb=" CA  PRO C  93 "   -0.015 5.00e-02 4.00e+02
        pdb=" CD  PRO C  93 "   -0.016 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   LYS A  95 "    0.019 5.00e-02 4.00e+02   2.92e-02 1.37e+00
        pdb=" N   PRO A  96 "   -0.051 5.00e-02 4.00e+02
        pdb=" CA  PRO A  96 "    0.015 5.00e-02 4.00e+02
        pdb=" CD  PRO A  96 "    0.016 5.00e-02 4.00e+02
  ... (remaining 1090 not shown)

  Histogram of nonbonded interaction distances:
        2.20 -     2.74: 528
        2.74 -     3.28: 6306
        3.28 -     3.82: 9994
        3.82 -     4.36: 12217
        4.36 -     4.90: 20681
  Nonbonded interactions: 49726
  Sorted by model distance:
  nonbonded pdb=" NZ  LYS E  52 "
            pdb=" OD2 ASP E 145 "
     model   vdw
     2.202 3.120
  nonbonded pdb=" O   HIS C  40 "
            pdb=" NE2 GLN C  43 "
     model   vdw
     2.220 3.120
  nonbonded pdb=" ND1 HIS C 237 "
            pdb=" OG  SER C 343 "
     model   vdw
     2.222 3.120
  nonbonded pdb=" ND2 ASN C  71 "
            pdb=" OD1 ASN C 161 "
     model   vdw
     2.223 3.120
  nonbonded pdb=" N   GLU E  93 "
            pdb=" OE1 GLU E  93 "
     model   vdw
     2.228 3.120
  ... (remaining 49721 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.00
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = (chain 'B' and (resid 1 through 111 or (resid 112 and (name N or name CA or name \ 
 C or name O or name CB or name OG ))))
}
ncs_group {
  reference = chain 'D'
  selection = (chain 'E' and resid 47 through 153)
}

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=0.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             3.640
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.300
  Check model and map are aligned:         0.040
  Set scattering table:                    0.070
  Process input model:                     18.710
  Find NCS groups from input model:        0.140
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:2.760
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   25.680
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5775
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      :  0.002   0.036   6267  Z= 0.139
  Angle     :  0.497   4.031   8516  Z= 0.285
  Chirality :  0.045   0.149    932
  Planarity :  0.004   0.030   1093
  Dihedral  :  8.233  74.645   2324
  Min Nonbonded Distance : 2.202

Molprobity Statistics.
  All-atom Clashscore : 7.06
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.95 %
    Favored  : 96.05 %
  Rotamer:
    Outliers :  1.86 %
    Allowed  :  4.86 %
    Favored  : 93.28 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.12 %
    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: -0.16 (0.31), residues: 759
  helix:  1.01 (0.57), residues: 105
  sheet: -0.29 (0.33), residues: 272
  loop : -0.14 (0.32), residues: 382

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.004   0.001   TRP B  32 
 HIS   0.001   0.000   HIS C 169 
 PHE   0.005   0.001   PHE A  24 
 TYR   0.005   0.001   TYR A  65 
 ARG   0.002   0.000   ARG A  25 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.18240 (  161)
  hydrogen bonds       : angle       6.99608 (  462)
  SS BOND              : bond        0.00209 (   23)
  SS BOND              : angle       0.59843 (   46)
  covalent geometry    : bond        0.00238 ( 6244)
  covalent geometry    : angle       0.49641 ( 8470)

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

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

  1518 Ramachandran restraints generated.
    759 Oldfield, 0 Emsley, 759 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1518 Ramachandran restraints generated.
    759 Oldfield, 0 Emsley, 759 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  173 residues out of total 699 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 160
  time to evaluate  : 0.731 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: D  106 LEU cc_start: 0.6692 (mp) cc_final: 0.6457 (tt)
REVERT: D  123 MET cc_start: 0.3331 (mmt) cc_final: 0.2361 (mmt)
REVERT: E   68 MET cc_start: 0.6230 (ppp) cc_final: 0.5764 (ppp)
REVERT: E   78 GLU cc_start: 0.7759 (tp30) cc_final: 0.7408 (tp30)
REVERT: E  127 LYS cc_start: 0.5067 (OUTLIER) cc_final: 0.4638 (pptt)
REVERT: C  122 LYS cc_start: 0.9103 (mttt) cc_final: 0.8745 (tttt)
REVERT: C  188 TYR cc_start: 0.7735 (m-80) cc_final: 0.7431 (m-80)
REVERT: C  205 ASN cc_start: 0.8100 (m-40) cc_final: 0.7128 (t0)
REVERT: C  274 LEU cc_start: 0.6989 (mp) cc_final: 0.6766 (mm)
  outliers start: 13
  outliers final: 8
  residues processed: 169
  average time/residue: 0.2127
  time to fit residues: 45.5212
Evaluate side-chains
  111 residues out of total 699 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 102
  time to evaluate  : 0.737 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   37 LYS
Chi-restraints excluded: chain A residue   39 TYR
Chi-restraints excluded: chain B residue    7 CYS
Chi-restraints excluded: chain B residue   77 CYS
Chi-restraints excluded: chain B residue  111 CYS
Chi-restraints excluded: chain E residue   58 PHE
Chi-restraints excluded: chain E residue   74 THR
Chi-restraints excluded: chain E residue  127 LYS
Chi-restraints excluded: chain C residue  201 CYS
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 74
   random chunks:
   chunk 62 optimal weight:    2.9990
   chunk 56 optimal weight:    3.9990
   chunk 31 optimal weight:    6.9990
   chunk 19 optimal weight:    3.9990
   chunk 37 optimal weight:    0.9990
   chunk 29 optimal weight:    9.9990
   chunk 58 optimal weight:    0.2980
   chunk 22 optimal weight:    0.2980
   chunk 35 optimal weight:    0.4980
   chunk 43 optimal weight:    1.9990
   chunk 67 optimal weight:    1.9990
   overall best weight:    0.8184

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

Flipped N/Q/H residues before XYZ refinement:
** A  57 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
E 102 HIS
** C  40 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 100 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
C 169 HIS
C 346 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4536 r_free = 0.4536 target = 0.136160 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.4133 r_free = 0.4133 target = 0.111350 restraints weight = 15507.507|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.4181 r_free = 0.4181 target = 0.114067 restraints weight = 10046.578|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.4215 r_free = 0.4215 target = 0.116015 restraints weight = 7326.907|
|-----------------------------------------------------------------------------|
r_work (final): 0.4216
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6084
moved from start:          0.2173

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.038   6267  Z= 0.154
  Angle     :  0.594   8.868   8516  Z= 0.304
  Chirality :  0.046   0.131    932
  Planarity :  0.004   0.041   1093
  Dihedral  :  5.812  49.416    834
  Min Nonbonded Distance : 2.494

Molprobity Statistics.
  All-atom Clashscore : 8.56
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.08 %
    Favored  : 95.92 %
  Rotamer:
    Outliers :  2.86 %
    Allowed  : 11.16 %
    Favored  : 85.98 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.12 %
    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: -0.34 (0.31), residues: 759
  helix:  0.39 (0.50), residues: 106
  sheet: -0.45 (0.33), residues: 259
  loop : -0.08 (0.31), residues: 394

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP C 283 
 HIS   0.003   0.001   HIS C 132 
 PHE   0.009   0.002   PHE A  43 
 TYR   0.010   0.001   TYR B  58 
 ARG   0.007   0.001   ARG C 259 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03614 (  161)
  hydrogen bonds       : angle       5.88709 (  462)
  SS BOND              : bond        0.00421 (   23)
  SS BOND              : angle       1.03330 (   46)
  covalent geometry    : bond        0.00352 ( 6244)
  covalent geometry    : angle       0.59024 ( 8470)

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

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

  1518 Ramachandran restraints generated.
    759 Oldfield, 0 Emsley, 759 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1518 Ramachandran restraints generated.
    759 Oldfield, 0 Emsley, 759 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  135 residues out of total 699 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 115
  time to evaluate  : 0.738 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: D  123 MET cc_start: 0.0702 (mmt) cc_final: 0.0046 (mmt)
REVERT: E   78 GLU cc_start: 0.7869 (tp30) cc_final: 0.7278 (pt0)
REVERT: E   81 GLN cc_start: 0.8459 (pp30) cc_final: 0.8234 (pp30)
REVERT: E  123 MET cc_start: 0.7679 (mmt) cc_final: 0.6979 (tpt)
  outliers start: 20
  outliers final: 18
  residues processed: 126
  average time/residue: 0.1590
  time to fit residues: 28.0202
Evaluate side-chains
  110 residues out of total 699 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 92
  time to evaluate  : 0.694 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   17 VAL
Chi-restraints excluded: chain A residue   39 TYR
Chi-restraints excluded: chain A residue  104 MET
Chi-restraints excluded: chain B residue    7 CYS
Chi-restraints excluded: chain B residue   17 VAL
Chi-restraints excluded: chain B residue   79 VAL
Chi-restraints excluded: chain B residue  111 CYS
Chi-restraints excluded: chain D residue   85 VAL
Chi-restraints excluded: chain D residue  121 CYS
Chi-restraints excluded: chain E residue   66 SER
Chi-restraints excluded: chain E residue   74 THR
Chi-restraints excluded: chain E residue  121 CYS
Chi-restraints excluded: chain C residue  201 CYS
Chi-restraints excluded: chain C residue  204 ASP
Chi-restraints excluded: chain C residue  258 LEU
Chi-restraints excluded: chain C residue  271 VAL
Chi-restraints excluded: chain C residue  291 MET
Chi-restraints excluded: chain C residue  355 LEU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 74
   random chunks:
   chunk 41 optimal weight:    1.9990
   chunk 9 optimal weight:    4.9990
   chunk 69 optimal weight:    2.9990
   chunk 68 optimal weight:    0.6980
   chunk 20 optimal weight:    1.9990
   chunk 23 optimal weight:   20.0000
   chunk 0 optimal weight:    5.9990
   chunk 73 optimal weight:    2.9990
   chunk 42 optimal weight:    6.9990
   chunk 19 optimal weight:    0.0170
   chunk 48 optimal weight:    0.4980
   overall best weight:    1.0422

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

Flipped N/Q/H residues before XYZ refinement:
** A  57 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B  42 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B  66 ASN
C  40 HIS
** C 100 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4520 r_free = 0.4520 target = 0.134881 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 54)----------------|
| r_work = 0.4105 r_free = 0.4105 target = 0.109828 restraints weight = 15761.818|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.4155 r_free = 0.4155 target = 0.112662 restraints weight = 10188.279|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.4191 r_free = 0.4191 target = 0.114684 restraints weight = 7386.385|
|-----------------------------------------------------------------------------|
r_work (final): 0.4185
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6141
moved from start:          0.2854

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.039   6267  Z= 0.162
  Angle     :  0.598   9.231   8516  Z= 0.302
  Chirality :  0.045   0.137    932
  Planarity :  0.004   0.039   1093
  Dihedral  :  5.530  48.524    823
  Min Nonbonded Distance : 2.536

Molprobity Statistics.
  All-atom Clashscore : 10.39
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.43 %
    Favored  : 96.57 %
  Rotamer:
    Outliers :  3.86 %
    Allowed  : 10.30 %
    Favored  : 85.84 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.12 %
    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: -0.61 (0.30), residues: 759
  helix:  0.06 (0.49), residues: 106
  sheet: -0.56 (0.32), residues: 267
  loop : -0.27 (0.30), residues: 386

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP C 283 
 HIS   0.009   0.001   HIS D 102 
 PHE   0.012   0.001   PHE A  24 
 TYR   0.013   0.001   TYR B  50 
 ARG   0.004   0.000   ARG C 259 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03227 (  161)
  hydrogen bonds       : angle       5.82787 (  462)
  SS BOND              : bond        0.00428 (   23)
  SS BOND              : angle       0.95455 (   46)
  covalent geometry    : bond        0.00371 ( 6244)
  covalent geometry    : angle       0.59560 ( 8470)

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

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

  1518 Ramachandran restraints generated.
    759 Oldfield, 0 Emsley, 759 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1518 Ramachandran restraints generated.
    759 Oldfield, 0 Emsley, 759 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  126 residues out of total 699 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 99
  time to evaluate  : 0.761 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   35 GLU cc_start: 0.7558 (mm-30) cc_final: 0.7349 (mm-30)
REVERT: B   69 ASN cc_start: 0.8000 (t0) cc_final: 0.7708 (t0)
REVERT: D  102 HIS cc_start: 0.5363 (m-70) cc_final: 0.4945 (p-80)
REVERT: D  123 MET cc_start: 0.0853 (mmt) cc_final: 0.0196 (mmt)
REVERT: E   78 GLU cc_start: 0.7876 (tp30) cc_final: 0.7274 (pt0)
REVERT: E  123 MET cc_start: 0.7833 (mmt) cc_final: 0.7271 (tpt)
  outliers start: 27
  outliers final: 23
  residues processed: 116
  average time/residue: 0.1412
  time to fit residues: 23.4617
Evaluate side-chains
  114 residues out of total 699 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 91
  time to evaluate  : 0.740 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   17 VAL
Chi-restraints excluded: chain A residue   39 TYR
Chi-restraints excluded: chain A residue   42 ASN
Chi-restraints excluded: chain A residue  104 MET
Chi-restraints excluded: chain B residue    7 CYS
Chi-restraints excluded: chain B residue   17 VAL
Chi-restraints excluded: chain B residue   20 LEU
Chi-restraints excluded: chain B residue   59 SER
Chi-restraints excluded: chain B residue   77 CYS
Chi-restraints excluded: chain B residue   79 VAL
Chi-restraints excluded: chain B residue   89 VAL
Chi-restraints excluded: chain B residue  111 CYS
Chi-restraints excluded: chain D residue   85 VAL
Chi-restraints excluded: chain D residue  121 CYS
Chi-restraints excluded: chain E residue   74 THR
Chi-restraints excluded: chain E residue  121 CYS
Chi-restraints excluded: chain C residue  201 CYS
Chi-restraints excluded: chain C residue  204 ASP
Chi-restraints excluded: chain C residue  258 LEU
Chi-restraints excluded: chain C residue  271 VAL
Chi-restraints excluded: chain C residue  285 ILE
Chi-restraints excluded: chain C residue  291 MET
Chi-restraints excluded: chain C residue  355 LEU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 74
   random chunks:
   chunk 26 optimal weight:    7.9990
   chunk 13 optimal weight:    2.9990
   chunk 29 optimal weight:    6.9990
   chunk 19 optimal weight:    2.9990
   chunk 45 optimal weight:    0.9990
   chunk 11 optimal weight:    8.9990
   chunk 63 optimal weight:    2.9990
   chunk 69 optimal weight:    4.9990
   chunk 49 optimal weight:    0.4980
   chunk 23 optimal weight:   20.0000
   chunk 44 optimal weight:    6.9990
   overall best weight:    2.0988

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

Flipped N/Q/H residues before XYZ refinement:
** A  57 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B  42 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
C  68 HIS
C 100 HIS
** C 251 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4461 r_free = 0.4461 target = 0.130706 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.4040 r_free = 0.4040 target = 0.105678 restraints weight = 16061.635|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 43)----------------|
| r_work = 0.4088 r_free = 0.4088 target = 0.108324 restraints weight = 10515.495|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.4122 r_free = 0.4122 target = 0.110216 restraints weight = 7720.127|
|-----------------------------------------------------------------------------|
r_work (final): 0.4118
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6304
moved from start:          0.3451

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.047   6267  Z= 0.272
  Angle     :  0.686   7.921   8516  Z= 0.352
  Chirality :  0.047   0.162    932
  Planarity :  0.005   0.044   1093
  Dihedral  :  6.157  52.222    823
  Min Nonbonded Distance : 2.452

Molprobity Statistics.
  All-atom Clashscore : 16.95
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.27 %
    Favored  : 94.73 %
  Rotamer:
    Outliers :  4.58 %
    Allowed  : 11.73 %
    Favored  : 83.69 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.12 %
    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: -1.03 (0.29), residues: 759
  helix: -0.99 (0.44), residues: 111
  sheet: -0.49 (0.33), residues: 236
  loop : -0.61 (0.29), residues: 412

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.002   TRP C 283 
 HIS   0.005   0.001   HIS C 237 
 PHE   0.018   0.002   PHE A  24 
 TYR   0.020   0.002   TYR B  50 
 ARG   0.003   0.000   ARG C 259 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03940 (  161)
  hydrogen bonds       : angle       6.48960 (  462)
  SS BOND              : bond        0.00622 (   23)
  SS BOND              : angle       1.19172 (   46)
  covalent geometry    : bond        0.00613 ( 6244)
  covalent geometry    : angle       0.68251 ( 8470)

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

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

  1518 Ramachandran restraints generated.
    759 Oldfield, 0 Emsley, 759 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1518 Ramachandran restraints generated.
    759 Oldfield, 0 Emsley, 759 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  121 residues out of total 699 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 89
  time to evaluate  : 0.725 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   35 GLU cc_start: 0.7599 (mm-30) cc_final: 0.7371 (mm-30)
REVERT: B   69 ASN cc_start: 0.8012 (t0) cc_final: 0.7706 (t0)
REVERT: D  102 HIS cc_start: 0.5532 (m-70) cc_final: 0.5197 (m90)
REVERT: D  123 MET cc_start: 0.0768 (mmt) cc_final: 0.0088 (mmt)
REVERT: E   68 MET cc_start: 0.5931 (ppp) cc_final: 0.5634 (ppp)
  outliers start: 32
  outliers final: 25
  residues processed: 110
  average time/residue: 0.1284
  time to fit residues: 20.5703
Evaluate side-chains
  106 residues out of total 699 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 81
  time to evaluate  : 0.715 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   17 VAL
Chi-restraints excluded: chain A residue   39 TYR
Chi-restraints excluded: chain A residue   42 ASN
Chi-restraints excluded: chain B residue    7 CYS
Chi-restraints excluded: chain B residue   20 LEU
Chi-restraints excluded: chain B residue   77 CYS
Chi-restraints excluded: chain B residue   79 VAL
Chi-restraints excluded: chain B residue   89 VAL
Chi-restraints excluded: chain B residue  104 MET
Chi-restraints excluded: chain B residue  111 CYS
Chi-restraints excluded: chain D residue   74 THR
Chi-restraints excluded: chain D residue   85 VAL
Chi-restraints excluded: chain D residue  121 CYS
Chi-restraints excluded: chain D residue  133 PHE
Chi-restraints excluded: chain E residue   74 THR
Chi-restraints excluded: chain E residue   77 CYS
Chi-restraints excluded: chain C residue   99 VAL
Chi-restraints excluded: chain C residue  159 HIS
Chi-restraints excluded: chain C residue  201 CYS
Chi-restraints excluded: chain C residue  204 ASP
Chi-restraints excluded: chain C residue  258 LEU
Chi-restraints excluded: chain C residue  271 VAL
Chi-restraints excluded: chain C residue  285 ILE
Chi-restraints excluded: chain C residue  291 MET
Chi-restraints excluded: chain C residue  355 LEU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 74
   random chunks:
   chunk 14 optimal weight:    0.9990
   chunk 25 optimal weight:    7.9990
   chunk 11 optimal weight:    8.9990
   chunk 59 optimal weight:    3.9990
   chunk 47 optimal weight:    0.7980
   chunk 46 optimal weight:    0.4980
   chunk 60 optimal weight:    1.9990
   chunk 41 optimal weight:    0.4980
   chunk 5 optimal weight:    0.9990
   chunk 32 optimal weight:    1.9990
   chunk 40 optimal weight:    0.9990
   overall best weight:    0.7584

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

Flipped N/Q/H residues before XYZ refinement:
** A  57 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B  42 ASN
** C 242 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4499 r_free = 0.4499 target = 0.133871 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.4080 r_free = 0.4080 target = 0.108457 restraints weight = 15562.946|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.4132 r_free = 0.4132 target = 0.111378 restraints weight = 9835.925|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.4170 r_free = 0.4170 target = 0.113500 restraints weight = 6991.735|
|-----------------------------------------------------------------------------|
r_work (final): 0.4164
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6183
moved from start:          0.3556

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.043   6267  Z= 0.136
  Angle     :  0.571   8.481   8516  Z= 0.288
  Chirality :  0.044   0.150    932
  Planarity :  0.004   0.038   1093
  Dihedral  :  5.739  48.763    823
  Min Nonbonded Distance : 2.590

Molprobity Statistics.
  All-atom Clashscore : 11.14
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.29 %
    Favored  : 96.71 %
  Rotamer:
    Outliers :  4.29 %
    Allowed  : 11.59 %
    Favored  : 84.12 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.12 %
    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: -0.98 (0.29), residues: 759
  helix: -0.69 (0.47), residues: 111
  sheet: -0.65 (0.33), residues: 249
  loop : -0.51 (0.30), residues: 399

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP C 167 
 HIS   0.004   0.001   HIS C 237 
 PHE   0.007   0.001   PHE D 133 
 TYR   0.018   0.001   TYR B  50 
 ARG   0.003   0.000   ARG C 259 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03063 (  161)
  hydrogen bonds       : angle       5.97581 (  462)
  SS BOND              : bond        0.00348 (   23)
  SS BOND              : angle       0.87559 (   46)
  covalent geometry    : bond        0.00313 ( 6244)
  covalent geometry    : angle       0.56913 ( 8470)

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

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

  1518 Ramachandran restraints generated.
    759 Oldfield, 0 Emsley, 759 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1518 Ramachandran restraints generated.
    759 Oldfield, 0 Emsley, 759 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  126 residues out of total 699 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 96
  time to evaluate  : 0.658 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   69 ASN cc_start: 0.8255 (t0) cc_final: 0.7977 (t0)
REVERT: D  123 MET cc_start: 0.0614 (mmt) cc_final: -0.0015 (mmt)
REVERT: E   68 MET cc_start: 0.5897 (ppp) cc_final: 0.5616 (ppp)
REVERT: E   78 GLU cc_start: 0.7919 (tp30) cc_final: 0.7426 (tp30)
REVERT: E  123 MET cc_start: 0.7664 (mmt) cc_final: 0.6841 (tpt)
REVERT: C  297 MET cc_start: 0.5754 (tpp) cc_final: 0.5239 (tpp)
  outliers start: 30
  outliers final: 28
  residues processed: 113
  average time/residue: 0.1379
  time to fit residues: 22.4864
Evaluate side-chains
  116 residues out of total 699 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 88
  time to evaluate  : 0.720 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   17 VAL
Chi-restraints excluded: chain A residue   39 TYR
Chi-restraints excluded: chain A residue   42 ASN
Chi-restraints excluded: chain B residue    7 CYS
Chi-restraints excluded: chain B residue   17 VAL
Chi-restraints excluded: chain B residue   20 LEU
Chi-restraints excluded: chain B residue   59 SER
Chi-restraints excluded: chain B residue   77 CYS
Chi-restraints excluded: chain B residue   79 VAL
Chi-restraints excluded: chain B residue   89 VAL
Chi-restraints excluded: chain B residue  104 MET
Chi-restraints excluded: chain B residue  111 CYS
Chi-restraints excluded: chain D residue   74 THR
Chi-restraints excluded: chain D residue   85 VAL
Chi-restraints excluded: chain D residue  121 CYS
Chi-restraints excluded: chain D residue  133 PHE
Chi-restraints excluded: chain E residue   74 THR
Chi-restraints excluded: chain E residue  121 CYS
Chi-restraints excluded: chain C residue   99 VAL
Chi-restraints excluded: chain C residue  159 HIS
Chi-restraints excluded: chain C residue  196 VAL
Chi-restraints excluded: chain C residue  201 CYS
Chi-restraints excluded: chain C residue  204 ASP
Chi-restraints excluded: chain C residue  258 LEU
Chi-restraints excluded: chain C residue  271 VAL
Chi-restraints excluded: chain C residue  285 ILE
Chi-restraints excluded: chain C residue  291 MET
Chi-restraints excluded: chain C residue  355 LEU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 74
   random chunks:
   chunk 36 optimal weight:    3.9990
   chunk 15 optimal weight:    3.9990
   chunk 18 optimal weight:    0.9980
   chunk 54 optimal weight:    1.9990
   chunk 72 optimal weight:    0.9980
   chunk 69 optimal weight:    0.8980
   chunk 37 optimal weight:    2.9990
   chunk 20 optimal weight:    1.9990
   chunk 70 optimal weight:    0.7980
   chunk 62 optimal weight:    5.9990
   chunk 16 optimal weight:    0.5980
   overall best weight:    0.8580

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

Flipped N/Q/H residues before XYZ refinement:
** C 242 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 351 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4495 r_free = 0.4495 target = 0.133562 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.4089 r_free = 0.4089 target = 0.108952 restraints weight = 15235.901|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.4138 r_free = 0.4138 target = 0.111672 restraints weight = 9791.403|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.4172 r_free = 0.4172 target = 0.113558 restraints weight = 7089.374|
|-----------------------------------------------------------------------------|
r_work (final): 0.4168
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6175
moved from start:          0.3718

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.043   6267  Z= 0.142
  Angle     :  0.575   8.222   8516  Z= 0.290
  Chirality :  0.044   0.142    932
  Planarity :  0.004   0.037   1093
  Dihedral  :  5.785  58.900    823
  Min Nonbonded Distance : 2.529

Molprobity Statistics.
  All-atom Clashscore : 11.14
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.95 %
    Favored  : 96.05 %
  Rotamer:
    Outliers :  4.01 %
    Allowed  : 13.45 %
    Favored  : 82.55 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.12 %
    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: -0.98 (0.30), residues: 759
  helix: -0.65 (0.47), residues: 111
  sheet: -0.67 (0.32), residues: 258
  loop : -0.50 (0.31), residues: 390

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.001   TRP C 167 
 HIS   0.003   0.001   HIS C 237 
 PHE   0.006   0.001   PHE A  43 
 TYR   0.017   0.001   TYR B  50 
 ARG   0.003   0.000   ARG C 259 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03079 (  161)
  hydrogen bonds       : angle       5.94614 (  462)
  SS BOND              : bond        0.00350 (   23)
  SS BOND              : angle       0.83394 (   46)
  covalent geometry    : bond        0.00326 ( 6244)
  covalent geometry    : angle       0.57375 ( 8470)

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

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

  1518 Ramachandran restraints generated.
    759 Oldfield, 0 Emsley, 759 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1518 Ramachandran restraints generated.
    759 Oldfield, 0 Emsley, 759 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  122 residues out of total 699 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 94
  time to evaluate  : 0.796 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   65 TYR cc_start: 0.7363 (t80) cc_final: 0.7110 (t80)
REVERT: D  102 HIS cc_start: 0.5723 (m90) cc_final: 0.5158 (p-80)
REVERT: D  123 MET cc_start: 0.0517 (mmt) cc_final: -0.0115 (mmt)
REVERT: E   68 MET cc_start: 0.5856 (ppp) cc_final: 0.5563 (ppp)
REVERT: E   78 GLU cc_start: 0.7862 (tp30) cc_final: 0.7430 (tp30)
REVERT: E  123 MET cc_start: 0.7658 (mmt) cc_final: 0.6967 (tpt)
REVERT: C   45 MET cc_start: 0.4584 (ttm) cc_final: 0.3920 (ttm)
REVERT: C  205 ASN cc_start: 0.7736 (m-40) cc_final: 0.7022 (t0)
REVERT: C  206 LYS cc_start: 0.6689 (mttt) cc_final: 0.6316 (mttm)
REVERT: C  297 MET cc_start: 0.5735 (tpp) cc_final: 0.5300 (tpp)
  outliers start: 28
  outliers final: 28
  residues processed: 109
  average time/residue: 0.1366
  time to fit residues: 22.0538
Evaluate side-chains
  120 residues out of total 699 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 92
  time to evaluate  : 0.667 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   17 VAL
Chi-restraints excluded: chain A residue   39 TYR
Chi-restraints excluded: chain A residue   42 ASN
Chi-restraints excluded: chain B residue    7 CYS
Chi-restraints excluded: chain B residue   17 VAL
Chi-restraints excluded: chain B residue   20 LEU
Chi-restraints excluded: chain B residue   59 SER
Chi-restraints excluded: chain B residue   77 CYS
Chi-restraints excluded: chain B residue   79 VAL
Chi-restraints excluded: chain B residue   89 VAL
Chi-restraints excluded: chain B residue  104 MET
Chi-restraints excluded: chain B residue  111 CYS
Chi-restraints excluded: chain D residue   74 THR
Chi-restraints excluded: chain D residue   85 VAL
Chi-restraints excluded: chain D residue  121 CYS
Chi-restraints excluded: chain D residue  133 PHE
Chi-restraints excluded: chain E residue   74 THR
Chi-restraints excluded: chain E residue  121 CYS
Chi-restraints excluded: chain C residue   99 VAL
Chi-restraints excluded: chain C residue  159 HIS
Chi-restraints excluded: chain C residue  196 VAL
Chi-restraints excluded: chain C residue  201 CYS
Chi-restraints excluded: chain C residue  204 ASP
Chi-restraints excluded: chain C residue  258 LEU
Chi-restraints excluded: chain C residue  271 VAL
Chi-restraints excluded: chain C residue  285 ILE
Chi-restraints excluded: chain C residue  291 MET
Chi-restraints excluded: chain C residue  355 LEU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 74
   random chunks:
   chunk 55 optimal weight:    3.9990
   chunk 63 optimal weight:    0.0040
   chunk 30 optimal weight:    8.9990
   chunk 23 optimal weight:   20.0000
   chunk 12 optimal weight:    7.9990
   chunk 6 optimal weight:    0.7980
   chunk 3 optimal weight:    0.9990
   chunk 10 optimal weight:    0.7980
   chunk 54 optimal weight:    0.5980
   chunk 66 optimal weight:    0.8980
   chunk 21 optimal weight:    1.9990
   overall best weight:    0.6192

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

Flipped N/Q/H residues before XYZ refinement:
** B  42 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 242 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4533 r_free = 0.4533 target = 0.135688 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.4112 r_free = 0.4112 target = 0.110281 restraints weight = 15284.585|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.4158 r_free = 0.4158 target = 0.112974 restraints weight = 9875.204|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.4195 r_free = 0.4195 target = 0.115020 restraints weight = 7252.142|
|-----------------------------------------------------------------------------|
r_work (final): 0.4191
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6145
moved from start:          0.3865

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.044   6267  Z= 0.121
  Angle     :  0.561   8.874   8516  Z= 0.283
  Chirality :  0.044   0.145    932
  Planarity :  0.004   0.037   1093
  Dihedral  :  5.652  59.960    823
  Min Nonbonded Distance : 2.552

Molprobity Statistics.
  All-atom Clashscore : 10.39
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.90 %
    Favored  : 97.10 %
  Rotamer:
    Outliers :  3.86 %
    Allowed  : 13.30 %
    Favored  : 82.83 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.12 %
    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: -0.90 (0.29), residues: 759
  helix: -0.48 (0.49), residues: 105
  sheet: -0.78 (0.32), residues: 241
  loop : -0.38 (0.30), residues: 413

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP C 167 
 HIS   0.003   0.001   HIS C 237 
 PHE   0.009   0.001   PHE E 111 
 TYR   0.015   0.001   TYR B  50 
 ARG   0.003   0.000   ARG C 259 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02932 (  161)
  hydrogen bonds       : angle       5.69007 (  462)
  SS BOND              : bond        0.00292 (   23)
  SS BOND              : angle       0.77586 (   46)
  covalent geometry    : bond        0.00282 ( 6244)
  covalent geometry    : angle       0.55960 ( 8470)

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

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

  1518 Ramachandran restraints generated.
    759 Oldfield, 0 Emsley, 759 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1518 Ramachandran restraints generated.
    759 Oldfield, 0 Emsley, 759 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  126 residues out of total 699 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 99
  time to evaluate  : 0.738 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   65 TYR cc_start: 0.7468 (t80) cc_final: 0.7249 (t80)
REVERT: D  123 MET cc_start: 0.0569 (mmt) cc_final: -0.0030 (mmt)
REVERT: E   68 MET cc_start: 0.5898 (ppp) cc_final: 0.5584 (ppp)
REVERT: E   78 GLU cc_start: 0.7901 (tp30) cc_final: 0.7450 (tp30)
REVERT: E  123 MET cc_start: 0.7589 (mmt) cc_final: 0.7009 (tpt)
REVERT: C   45 MET cc_start: 0.4854 (ttm) cc_final: 0.4265 (ttm)
REVERT: C  205 ASN cc_start: 0.7730 (m-40) cc_final: 0.7038 (t0)
REVERT: C  206 LYS cc_start: 0.6643 (mttt) cc_final: 0.6297 (mttm)
REVERT: C  297 MET cc_start: 0.5738 (tpp) cc_final: 0.5269 (tpp)
  outliers start: 27
  outliers final: 25
  residues processed: 113
  average time/residue: 0.1393
  time to fit residues: 23.0620
Evaluate side-chains
  119 residues out of total 699 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 94
  time to evaluate  : 0.755 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   17 VAL
Chi-restraints excluded: chain A residue   39 TYR
Chi-restraints excluded: chain A residue   42 ASN
Chi-restraints excluded: chain B residue    7 CYS
Chi-restraints excluded: chain B residue   17 VAL
Chi-restraints excluded: chain B residue   20 LEU
Chi-restraints excluded: chain B residue   77 CYS
Chi-restraints excluded: chain B residue   79 VAL
Chi-restraints excluded: chain B residue   89 VAL
Chi-restraints excluded: chain B residue  104 MET
Chi-restraints excluded: chain B residue  111 CYS
Chi-restraints excluded: chain D residue   74 THR
Chi-restraints excluded: chain D residue   85 VAL
Chi-restraints excluded: chain D residue  121 CYS
Chi-restraints excluded: chain D residue  133 PHE
Chi-restraints excluded: chain E residue   74 THR
Chi-restraints excluded: chain E residue  121 CYS
Chi-restraints excluded: chain C residue   99 VAL
Chi-restraints excluded: chain C residue  159 HIS
Chi-restraints excluded: chain C residue  196 VAL
Chi-restraints excluded: chain C residue  201 CYS
Chi-restraints excluded: chain C residue  204 ASP
Chi-restraints excluded: chain C residue  258 LEU
Chi-restraints excluded: chain C residue  271 VAL
Chi-restraints excluded: chain C residue  291 MET
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 74
   random chunks:
   chunk 62 optimal weight:    4.9990
   chunk 10 optimal weight:    2.9990
   chunk 3 optimal weight:    0.7980
   chunk 69 optimal weight:    6.9990
   chunk 54 optimal weight:    0.0970
   chunk 2 optimal weight:    0.0970
   chunk 32 optimal weight:    0.7980
   chunk 29 optimal weight:    9.9990
   chunk 7 optimal weight:    0.9990
   chunk 16 optimal weight:    0.8980
   chunk 49 optimal weight:    1.9990
   overall best weight:    0.5376

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

Flipped N/Q/H residues before XYZ refinement:
** C 242 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 251 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4542 r_free = 0.4542 target = 0.136163 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.4119 r_free = 0.4119 target = 0.110675 restraints weight = 15181.922|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.4171 r_free = 0.4171 target = 0.113563 restraints weight = 9579.499|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 47)----------------|
| r_work = 0.4207 r_free = 0.4207 target = 0.115654 restraints weight = 6871.029|
|-----------------------------------------------------------------------------|
r_work (final): 0.4203
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6112
moved from start:          0.4032

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042   6267  Z= 0.118
  Angle     :  0.572  10.355   8516  Z= 0.286
  Chirality :  0.045   0.209    932
  Planarity :  0.004   0.037   1093
  Dihedral  :  5.606  59.787    823
  Min Nonbonded Distance : 2.562

Molprobity Statistics.
  All-atom Clashscore : 10.80
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.03 %
    Favored  : 96.97 %
  Rotamer:
    Outliers :  3.72 %
    Allowed  : 14.45 %
    Favored  : 81.83 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.12 %
    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: -0.82 (0.29), residues: 759
  helix: -0.39 (0.49), residues: 105
  sheet: -0.66 (0.34), residues: 220
  loop : -0.41 (0.29), residues: 434

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.032   0.001   TRP C 167 
 HIS   0.003   0.000   HIS C 237 
 PHE   0.017   0.001   PHE E 111 
 TYR   0.014   0.001   TYR B  50 
 ARG   0.004   0.000   ARG C 259 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02882 (  161)
  hydrogen bonds       : angle       5.60060 (  462)
  SS BOND              : bond        0.00279 (   23)
  SS BOND              : angle       0.74426 (   46)
  covalent geometry    : bond        0.00274 ( 6244)
  covalent geometry    : angle       0.57111 ( 8470)

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

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

  1518 Ramachandran restraints generated.
    759 Oldfield, 0 Emsley, 759 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1518 Ramachandran restraints generated.
    759 Oldfield, 0 Emsley, 759 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  122 residues out of total 699 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 96
  time to evaluate  : 0.735 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   65 TYR cc_start: 0.7506 (t80) cc_final: 0.7268 (t80)
REVERT: D  102 HIS cc_start: 0.5919 (m90) cc_final: 0.5587 (p90)
REVERT: D  123 MET cc_start: 0.0424 (mmt) cc_final: -0.0151 (mmt)
REVERT: E   68 MET cc_start: 0.5961 (ppp) cc_final: 0.5628 (ppp)
REVERT: E   78 GLU cc_start: 0.7918 (tp30) cc_final: 0.7712 (tp30)
REVERT: E  123 MET cc_start: 0.7712 (mmt) cc_final: 0.7201 (tpt)
REVERT: C  205 ASN cc_start: 0.7765 (m-40) cc_final: 0.7041 (t0)
REVERT: C  206 LYS cc_start: 0.6621 (mttt) cc_final: 0.6355 (mttm)
REVERT: C  297 MET cc_start: 0.5823 (tpp) cc_final: 0.5329 (tpp)
  outliers start: 26
  outliers final: 26
  residues processed: 110
  average time/residue: 0.1310
  time to fit residues: 21.4956
Evaluate side-chains
  115 residues out of total 699 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 89
  time to evaluate  : 0.749 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   17 VAL
Chi-restraints excluded: chain A residue   39 TYR
Chi-restraints excluded: chain A residue   42 ASN
Chi-restraints excluded: chain B residue    7 CYS
Chi-restraints excluded: chain B residue   17 VAL
Chi-restraints excluded: chain B residue   59 SER
Chi-restraints excluded: chain B residue   77 CYS
Chi-restraints excluded: chain B residue   79 VAL
Chi-restraints excluded: chain B residue   89 VAL
Chi-restraints excluded: chain B residue  104 MET
Chi-restraints excluded: chain B residue  111 CYS
Chi-restraints excluded: chain D residue   74 THR
Chi-restraints excluded: chain D residue   85 VAL
Chi-restraints excluded: chain D residue  121 CYS
Chi-restraints excluded: chain D residue  133 PHE
Chi-restraints excluded: chain E residue   74 THR
Chi-restraints excluded: chain E residue  121 CYS
Chi-restraints excluded: chain C residue   99 VAL
Chi-restraints excluded: chain C residue  159 HIS
Chi-restraints excluded: chain C residue  196 VAL
Chi-restraints excluded: chain C residue  201 CYS
Chi-restraints excluded: chain C residue  204 ASP
Chi-restraints excluded: chain C residue  258 LEU
Chi-restraints excluded: chain C residue  271 VAL
Chi-restraints excluded: chain C residue  291 MET
Chi-restraints excluded: chain C residue  355 LEU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 74
   random chunks:
   chunk 66 optimal weight:    4.9990
   chunk 71 optimal weight:    0.9980
   chunk 57 optimal weight:    2.9990
   chunk 27 optimal weight:    7.9990
   chunk 44 optimal weight:    0.9990
   chunk 58 optimal weight:    2.9990
   chunk 54 optimal weight:    2.9990
   chunk 50 optimal weight:    0.0670
   chunk 3 optimal weight:    0.4980
   chunk 55 optimal weight:    2.9990
   chunk 42 optimal weight:    7.9990
   overall best weight:    1.1122

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

Flipped N/Q/H residues before XYZ refinement:
C  40 HIS
** C 242 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 251 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4509 r_free = 0.4509 target = 0.134083 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.4085 r_free = 0.4085 target = 0.108773 restraints weight = 15467.295|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.4135 r_free = 0.4135 target = 0.111490 restraints weight = 9925.986|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.4170 r_free = 0.4170 target = 0.113499 restraints weight = 7234.742|
|-----------------------------------------------------------------------------|
r_work (final): 0.4168
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6194
moved from start:          0.4177

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.042   6267  Z= 0.165
  Angle     :  0.603  10.109   8516  Z= 0.304
  Chirality :  0.045   0.256    932
  Planarity :  0.004   0.040   1093
  Dihedral  :  5.737  58.764    823
  Min Nonbonded Distance : 2.557

Molprobity Statistics.
  All-atom Clashscore : 13.38
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.48 %
    Favored  : 95.52 %
  Rotamer:
    Outliers :  4.01 %
    Allowed  : 14.31 %
    Favored  : 81.69 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.12 %
    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: -1.05 (0.29), residues: 759
  helix: -0.71 (0.47), residues: 111
  sheet: -0.80 (0.32), residues: 248
  loop : -0.49 (0.30), residues: 400

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.021   0.001   TRP C 167 
 HIS   0.003   0.001   HIS C 352 
 PHE   0.012   0.001   PHE E 133 
 TYR   0.014   0.002   TYR A  58 
 ARG   0.003   0.000   ARG C 259 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03187 (  161)
  hydrogen bonds       : angle       5.94707 (  462)
  SS BOND              : bond        0.00376 (   23)
  SS BOND              : angle       0.80973 (   46)
  covalent geometry    : bond        0.00380 ( 6244)
  covalent geometry    : angle       0.60177 ( 8470)

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

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

  1518 Ramachandran restraints generated.
    759 Oldfield, 0 Emsley, 759 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1518 Ramachandran restraints generated.
    759 Oldfield, 0 Emsley, 759 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  117 residues out of total 699 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 89
  time to evaluate  : 0.774 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   65 TYR cc_start: 0.7448 (t80) cc_final: 0.7244 (t80)
REVERT: D  102 HIS cc_start: 0.6002 (m90) cc_final: 0.5594 (p90)
REVERT: D  123 MET cc_start: 0.0483 (mmt) cc_final: -0.0114 (mmt)
REVERT: E   68 MET cc_start: 0.5997 (ppp) cc_final: 0.5644 (ppp)
REVERT: E   78 GLU cc_start: 0.7938 (tp30) cc_final: 0.7448 (tp30)
REVERT: C  205 ASN cc_start: 0.7772 (m-40) cc_final: 0.7081 (t0)
REVERT: C  297 MET cc_start: 0.5834 (tpp) cc_final: 0.5347 (tpp)
  outliers start: 28
  outliers final: 27
  residues processed: 106
  average time/residue: 0.1158
  time to fit residues: 18.6792
Evaluate side-chains
  113 residues out of total 699 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 86
  time to evaluate  : 0.768 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   17 VAL
Chi-restraints excluded: chain A residue   39 TYR
Chi-restraints excluded: chain A residue   42 ASN
Chi-restraints excluded: chain B residue    7 CYS
Chi-restraints excluded: chain B residue   20 LEU
Chi-restraints excluded: chain B residue   59 SER
Chi-restraints excluded: chain B residue   77 CYS
Chi-restraints excluded: chain B residue   79 VAL
Chi-restraints excluded: chain B residue   89 VAL
Chi-restraints excluded: chain B residue  104 MET
Chi-restraints excluded: chain B residue  111 CYS
Chi-restraints excluded: chain D residue   74 THR
Chi-restraints excluded: chain D residue   85 VAL
Chi-restraints excluded: chain D residue  121 CYS
Chi-restraints excluded: chain D residue  133 PHE
Chi-restraints excluded: chain E residue   74 THR
Chi-restraints excluded: chain E residue   87 VAL
Chi-restraints excluded: chain E residue  121 CYS
Chi-restraints excluded: chain C residue   99 VAL
Chi-restraints excluded: chain C residue  159 HIS
Chi-restraints excluded: chain C residue  196 VAL
Chi-restraints excluded: chain C residue  201 CYS
Chi-restraints excluded: chain C residue  204 ASP
Chi-restraints excluded: chain C residue  258 LEU
Chi-restraints excluded: chain C residue  271 VAL
Chi-restraints excluded: chain C residue  291 MET
Chi-restraints excluded: chain C residue  355 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 74
   random chunks:
   chunk 62 optimal weight:    3.9990
   chunk 14 optimal weight:    0.5980
   chunk 70 optimal weight:    4.9990
   chunk 27 optimal weight:    2.9990
   chunk 65 optimal weight:    0.6980
   chunk 19 optimal weight:    0.8980
   chunk 46 optimal weight:    5.9990
   chunk 24 optimal weight:    9.9990
   chunk 12 optimal weight:    2.9990
   chunk 7 optimal weight:    3.9990
   chunk 30 optimal weight:    0.6980
   overall best weight:    1.1782

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

Flipped N/Q/H residues before XYZ refinement:
** C 242 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4505 r_free = 0.4505 target = 0.133838 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.4077 r_free = 0.4077 target = 0.108244 restraints weight = 15520.844|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.4127 r_free = 0.4127 target = 0.111068 restraints weight = 9792.569|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.4163 r_free = 0.4163 target = 0.113086 restraints weight = 7047.815|
|-----------------------------------------------------------------------------|
r_work (final): 0.4158
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6213
moved from start:          0.4286

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.042   6267  Z= 0.171
  Angle     :  0.617   9.932   8516  Z= 0.311
  Chirality :  0.046   0.248    932
  Planarity :  0.004   0.041   1093
  Dihedral  :  5.821  57.870    823
  Min Nonbonded Distance : 2.561

Molprobity Statistics.
  All-atom Clashscore : 14.13
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.08 %
    Favored  : 95.92 %
  Rotamer:
    Outliers :  3.86 %
    Allowed  : 14.74 %
    Favored  : 81.40 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.12 %
    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: -1.08 (0.29), residues: 759
  helix: -0.69 (0.47), residues: 109
  sheet: -0.76 (0.31), residues: 258
  loop : -0.55 (0.30), residues: 392

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.025   0.001   TRP C 167 
 HIS   0.003   0.001   HIS C 237 
 PHE   0.009   0.001   PHE A  24 
 TYR   0.014   0.002   TYR B  50 
 ARG   0.003   0.000   ARG C 259 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03335 (  161)
  hydrogen bonds       : angle       6.03841 (  462)
  SS BOND              : bond        0.00385 (   23)
  SS BOND              : angle       0.85741 (   46)
  covalent geometry    : bond        0.00391 ( 6244)
  covalent geometry    : angle       0.61506 ( 8470)

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

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

  1518 Ramachandran restraints generated.
    759 Oldfield, 0 Emsley, 759 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1518 Ramachandran restraints generated.
    759 Oldfield, 0 Emsley, 759 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  119 residues out of total 699 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 92
  time to evaluate  : 0.674 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   65 TYR cc_start: 0.7553 (t80) cc_final: 0.7331 (t80)
REVERT: D  102 HIS cc_start: 0.5989 (m90) cc_final: 0.5538 (p90)
REVERT: D  123 MET cc_start: 0.0422 (mmt) cc_final: -0.0079 (mmt)
REVERT: E   68 MET cc_start: 0.6069 (ppp) cc_final: 0.5712 (ppp)
REVERT: E   78 GLU cc_start: 0.7959 (tp30) cc_final: 0.7398 (tp30)
REVERT: C  205 ASN cc_start: 0.7825 (m-40) cc_final: 0.7062 (t0)
REVERT: C  297 MET cc_start: 0.5865 (tpp) cc_final: 0.5379 (tpp)
  outliers start: 27
  outliers final: 27
  residues processed: 109
  average time/residue: 0.1147
  time to fit residues: 18.8215
Evaluate side-chains
  117 residues out of total 699 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 90
  time to evaluate  : 0.686 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   17 VAL
Chi-restraints excluded: chain A residue   39 TYR
Chi-restraints excluded: chain A residue   42 ASN
Chi-restraints excluded: chain B residue    7 CYS
Chi-restraints excluded: chain B residue   17 VAL
Chi-restraints excluded: chain B residue   20 LEU
Chi-restraints excluded: chain B residue   59 SER
Chi-restraints excluded: chain B residue   77 CYS
Chi-restraints excluded: chain B residue   79 VAL
Chi-restraints excluded: chain B residue   89 VAL
Chi-restraints excluded: chain B residue  104 MET
Chi-restraints excluded: chain B residue  111 CYS
Chi-restraints excluded: chain D residue   74 THR
Chi-restraints excluded: chain D residue   85 VAL
Chi-restraints excluded: chain D residue  121 CYS
Chi-restraints excluded: chain D residue  133 PHE
Chi-restraints excluded: chain E residue   74 THR
Chi-restraints excluded: chain E residue  121 CYS
Chi-restraints excluded: chain C residue   99 VAL
Chi-restraints excluded: chain C residue  159 HIS
Chi-restraints excluded: chain C residue  196 VAL
Chi-restraints excluded: chain C residue  201 CYS
Chi-restraints excluded: chain C residue  204 ASP
Chi-restraints excluded: chain C residue  258 LEU
Chi-restraints excluded: chain C residue  271 VAL
Chi-restraints excluded: chain C residue  291 MET
Chi-restraints excluded: chain C residue  355 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 74
   random chunks:
   chunk 44 optimal weight:    6.9990
   chunk 22 optimal weight:   10.0000
   chunk 17 optimal weight:    0.6980
   chunk 53 optimal weight:    1.9990
   chunk 14 optimal weight:    0.8980
   chunk 3 optimal weight:    0.9980
   chunk 27 optimal weight:    9.9990
   chunk 28 optimal weight:    9.9990
   chunk 9 optimal weight:    0.0770
   chunk 26 optimal weight:    0.9990
   chunk 19 optimal weight:    0.9990
   overall best weight:    0.7340

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

Flipped N/Q/H residues before XYZ refinement:
** B 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 242 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4519 r_free = 0.4519 target = 0.134911 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.4089 r_free = 0.4089 target = 0.109028 restraints weight = 15811.679|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.4143 r_free = 0.4143 target = 0.112048 restraints weight = 9810.637|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 41)----------------|
| r_work = 0.4180 r_free = 0.4180 target = 0.114240 restraints weight = 6945.930|
|-----------------------------------------------------------------------------|
r_work (final): 0.4178
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6165
moved from start:          0.4338

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.043   6267  Z= 0.136
  Angle     :  0.597   9.884   8516  Z= 0.304
  Chirality :  0.045   0.213    932
  Planarity :  0.004   0.059   1093
  Dihedral  :  5.747  58.827    823
  Min Nonbonded Distance : 2.452

Molprobity Statistics.
  All-atom Clashscore : 12.30
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.56 %
    Favored  : 96.44 %
  Rotamer:
    Outliers :  4.01 %
    Allowed  : 15.02 %
    Favored  : 80.97 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.12 %
    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: -1.03 (0.30), residues: 759
  helix: -0.64 (0.47), residues: 111
  sheet: -0.78 (0.32), residues: 258
  loop : -0.48 (0.31), residues: 390

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.027   0.001   TRP C 167 
 HIS   0.005   0.001   HIS E 109 
 PHE   0.012   0.001   PHE E 134 
 TYR   0.013   0.001   TYR B  50 
 ARG   0.003   0.000   ARG C 259 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03049 (  161)
  hydrogen bonds       : angle       5.93895 (  462)
  SS BOND              : bond        0.00294 (   23)
  SS BOND              : angle       0.76542 (   46)
  covalent geometry    : bond        0.00316 ( 6244)
  covalent geometry    : angle       0.59600 ( 8470)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2961.46 seconds
wall clock time: 52 minutes 25.59 seconds (3145.59 seconds total)