Starting phenix.real_space_refine
on Sat Jul  4 10:24:19 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8flk_29281/07_2026/8flk_29281_trim.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8flk_29281/07_2026/8flk_29281.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=4.0
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8flk_29281/07_2026/8flk_29281.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8flk_29281/07_2026/8flk_29281.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8flk_29281/07_2026/8flk_29281_trim.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8flk_29281/07_2026/8flk_29281_trim.cif"
  }
  resolution = 4.0
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.001 sd=   0.002
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: 6
    Type Number    sf(0)   Gaussians
     P       4      5.49       5
     S      52      5.16       5
     C    6542      2.51       5
     N    1806      2.21       5
     O    1828      1.98       5
     H   10124      0.53       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 51 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib"
  Total number of atoms: 20356
  Number of models: 1
  Model: ""
    Number of chains: 6
    Chain: "A"
      Number of atoms: 5051
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 319, 5051
          Classifications: {'peptide': 319}
          Link IDs: {'PTRANS': 17, 'TRANS': 301}
          Chain breaks: 3
    Chain: "B"
      Number of atoms: 5051
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 319, 5051
          Classifications: {'peptide': 319}
          Link IDs: {'PTRANS': 17, 'TRANS': 301}
          Chain breaks: 3
    Chain: "C"
      Number of atoms: 5051
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 319, 5051
          Classifications: {'peptide': 319}
          Link IDs: {'PTRANS': 17, 'TRANS': 301}
          Chain breaks: 3
    Chain: "D"
      Number of atoms: 5051
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 319, 5051
          Classifications: {'peptide': 319}
          Link IDs: {'PTRANS': 17, 'TRANS': 301}
          Chain breaks: 3
    Chain: "A"
      Number of atoms: 76
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 76
          Unusual residues: {'1SY': 1, 'Y6H': 1}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
    Chain: "C"
      Number of atoms: 76
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 76
          Unusual residues: {'1SY': 1, 'Y6H': 1}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
  Time building chain proxies: 3.40, per 1000 atoms: 0.17
  Number of scatterers: 20356
  At special positions: 0
  Unit cell: (91.8, 100.44, 105.84, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 6
    Type Number    sf(0)
     S      52     16.00
     P       4     15.00
     O    1828      8.00
     N    1806      7.00
     C    6542      6.00
     H   10124      1.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=1, symmetry=0
  Number of additional bonds: simple=1, symmetry=0
  Coordination:
  Other bonds:
  Time building additional restraints: 1.64
  Conformation dependent library (CDL) restraints added in 443.6 milliseconds
  

  2488 Ramachandran restraints generated.
    1244 Oldfield, 0 Emsley, 1244 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2376

  Finding SS restraints...
    Secondary structure from input PDB file:
      52 helices and 6 sheets defined
      64.8% alpha, 8.3% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.24
  Creating SS restraints...
    Processing helix  chain 'A' and resid 16 through 37
    Processing helix  chain 'A' and resid 39 through 70
      removed outlier: 3.746A  pdb=" N   GLU A  68 " --> pdb=" O   CYS A  64 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 72 through 77
    Processing helix  chain 'A' and resid 80 through 90
    Processing helix  chain 'A' and resid 91 through 109
    Processing helix  chain 'A' and resid 117 through 135
    Processing helix  chain 'A' and resid 140 through 152
    Processing helix  chain 'A' and resid 154 through 166
      removed outlier: 3.586A  pdb=" N   GLY A 158 " --> pdb=" O   ASN A 154 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 167 through 186
      Proline residue:  A 173  - end of helix
      removed outlier: 4.409A  pdb=" N   GLN A 176 " --> pdb=" O   LEU A 172 " (cutoff:3.500A)
      removed outlier: 4.925A  pdb=" N   ALA A 177 " --> pdb=" O   PRO A 173 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 211 through 216
      removed outlier: 3.865A  pdb=" N   ALA A 215 " --> pdb=" O   ASN A 211 " (cutoff:3.500A)
      removed outlier: 3.933A  pdb=" N   ASP A 216 " --> pdb=" O   LEU A 212 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 211 through 216'
    Processing helix  chain 'A' and resid 262 through 274
      removed outlier: 4.144A  pdb=" N   GLN A 266 " --> pdb=" O   ALA A 262 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 280 through 302
    Processing helix  chain 'A' and resid 324 through 335
    Processing helix  chain 'B' and resid 16 through 37
    Processing helix  chain 'B' and resid 39 through 70
    Processing helix  chain 'B' and resid 72 through 77
    Processing helix  chain 'B' and resid 80 through 90
    Processing helix  chain 'B' and resid 91 through 109
    Processing helix  chain 'B' and resid 117 through 134
    Processing helix  chain 'B' and resid 140 through 151
    Processing helix  chain 'B' and resid 154 through 165
      removed outlier: 3.804A  pdb=" N   GLY B 158 " --> pdb=" O   ASN B 154 " (cutoff:3.500A)
      removed outlier: 3.567A  pdb=" N   LEU B 159 " --> pdb=" O   VAL B 155 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 167 through 186
      Proline residue:  B 173  - end of helix
      removed outlier: 4.280A  pdb=" N   GLN B 176 " --> pdb=" O   LEU B 172 " (cutoff:3.500A)
      removed outlier: 4.644A  pdb=" N   ALA B 177 " --> pdb=" O   PRO B 173 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 211 through 216
      removed outlier: 3.849A  pdb=" N   ALA B 215 " --> pdb=" O   ASN B 211 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 263 through 274
    Processing helix  chain 'B' and resid 280 through 302
    Processing helix  chain 'B' and resid 324 through 334
    Processing helix  chain 'C' and resid 16 through 37
    Processing helix  chain 'C' and resid 39 through 70
      removed outlier: 4.110A  pdb=" N   GLU C  68 " --> pdb=" O   CYS C  64 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 72 through 77
      removed outlier: 3.533A  pdb=" N   TYR C  77 " --> pdb=" O   ILE C  73 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 80 through 90
    Processing helix  chain 'C' and resid 91 through 109
    Processing helix  chain 'C' and resid 117 through 135
    Processing helix  chain 'C' and resid 140 through 152
    Processing helix  chain 'C' and resid 154 through 166
      removed outlier: 3.571A  pdb=" N   GLY C 158 " --> pdb=" O   ASN C 154 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 167 through 186
      Proline residue:  C 173  - end of helix
      removed outlier: 4.519A  pdb=" N   GLN C 176 " --> pdb=" O   LEU C 172 " (cutoff:3.500A)
      removed outlier: 5.073A  pdb=" N   ALA C 177 " --> pdb=" O   PRO C 173 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 211 through 216
      removed outlier: 3.846A  pdb=" N   ALA C 215 " --> pdb=" O   ASN C 211 " (cutoff:3.500A)
      removed outlier: 3.903A  pdb=" N   ASP C 216 " --> pdb=" O   LEU C 212 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'C' and resid 211 through 216'
    Processing helix  chain 'C' and resid 262 through 274
      removed outlier: 4.218A  pdb=" N   GLN C 266 " --> pdb=" O   ALA C 262 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 280 through 302
    Processing helix  chain 'C' and resid 324 through 335
    Processing helix  chain 'D' and resid 16 through 37
      removed outlier: 3.800A  pdb=" N   LYS D  20 " --> pdb=" O   HIS D  16 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 39 through 70
    Processing helix  chain 'D' and resid 72 through 77
    Processing helix  chain 'D' and resid 80 through 90
    Processing helix  chain 'D' and resid 91 through 109
    Processing helix  chain 'D' and resid 117 through 134
    Processing helix  chain 'D' and resid 140 through 151
    Processing helix  chain 'D' and resid 154 through 165
      removed outlier: 3.802A  pdb=" N   GLY D 158 " --> pdb=" O   ASN D 154 " (cutoff:3.500A)
      removed outlier: 3.560A  pdb=" N   LEU D 159 " --> pdb=" O   VAL D 155 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 167 through 186
      Proline residue:  D 173  - end of helix
      removed outlier: 4.315A  pdb=" N   GLN D 176 " --> pdb=" O   LEU D 172 " (cutoff:3.500A)
      removed outlier: 4.569A  pdb=" N   ALA D 177 " --> pdb=" O   PRO D 173 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 211 through 216
      removed outlier: 3.883A  pdb=" N   ALA D 215 " --> pdb=" O   ASN D 211 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 262 through 274
      removed outlier: 3.789A  pdb=" N   GLN D 266 " --> pdb=" O   ALA D 262 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 280 through 302
    Processing helix  chain 'D' and resid 324 through 334
    Processing sheet with id=AA1, first strand: chain 'A' and resid 260 through 261
      removed outlier: 3.634A  pdb=" N   ARG A 310 " --> pdb=" O   LEU A 198 " (cutoff:3.500A)
      removed outlier: 3.526A  pdb=" N   ILE A 200 " --> pdb=" O   ARG A 310 " (cutoff:3.500A)
      removed outlier: 3.567A  pdb=" N   TYR A 314 " --> pdb=" O   LEU A 202 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 219 through 224
      removed outlier: 5.442A  pdb=" N   ILE A 219 " --> pdb=" O   LEU A 248 " (cutoff:3.500A)
      removed outlier: 6.994A  pdb=" N   LEU A 248 " --> pdb=" O   ILE A 219 " (cutoff:3.500A)
      removed outlier: 5.059A  pdb=" N   PHE A 221 " --> pdb=" O   GLU A 246 " (cutoff:3.500A)
      removed outlier: 5.412A  pdb=" N   GLU A 246 " --> pdb=" O   PHE A 221 " (cutoff:3.500A)
      removed outlier: 3.517A  pdb=" N   ASP A 223 " --> pdb=" O   ILE A 244 " (cutoff:3.500A)
      removed outlier: 3.558A  pdb=" N   GLY A 255 " --> pdb=" O   LEU A 247 " (cutoff:3.500A)
      removed outlier: 6.234A  pdb=" N   GLU A 249 " --> pdb=" O   ARG A 253 " (cutoff:3.500A)
      removed outlier: 4.638A  pdb=" N   ARG A 253 " --> pdb=" O   GLU A 249 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'B' and resid 219 through 223
      removed outlier: 7.043A  pdb=" N   ILE B 244 " --> pdb=" O   LEU B 222 " (cutoff:3.500A)
      removed outlier: 3.705A  pdb=" N   CYS B 257 " --> pdb=" O   TYR B 245 " (cutoff:3.500A)
      removed outlier: 3.613A  pdb=" N   GLY B 255 " --> pdb=" O   LEU B 247 " (cutoff:3.500A)
      removed outlier: 6.034A  pdb=" N   GLU B 249 " --> pdb=" O   ARG B 253 " (cutoff:3.500A)
      removed outlier: 5.162A  pdb=" N   ARG B 253 " --> pdb=" O   GLU B 249 " (cutoff:3.500A)
      removed outlier: 6.125A  pdb=" N   LEU B 198 " --> pdb=" O   ARG B 310 " (cutoff:3.500A)
      removed outlier: 7.006A  pdb=" N   ILE B 312 " --> pdb=" O   LEU B 198 " (cutoff:3.500A)
      removed outlier: 6.197A  pdb=" N   ILE B 200 " --> pdb=" O   ILE B 312 " (cutoff:3.500A)
      removed outlier: 7.857A  pdb=" N   TYR B 314 " --> pdb=" O   ILE B 200 " (cutoff:3.500A)
      removed outlier: 6.430A  pdb=" N   LEU B 202 " --> pdb=" O   TYR B 314 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'C' and resid 260 through 261
      removed outlier: 6.491A  pdb=" N   LEU C 198 " --> pdb=" O   ARG C 310 " (cutoff:3.500A)
      removed outlier: 7.388A  pdb=" N   ILE C 312 " --> pdb=" O   LEU C 198 " (cutoff:3.500A)
      removed outlier: 6.346A  pdb=" N   ILE C 200 " --> pdb=" O   ILE C 312 " (cutoff:3.500A)
      removed outlier: 8.000A  pdb=" N   TYR C 314 " --> pdb=" O   ILE C 200 " (cutoff:3.500A)
      removed outlier: 6.745A  pdb=" N   LEU C 202 " --> pdb=" O   TYR C 314 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'C' and resid 219 through 224
      removed outlier: 5.434A  pdb=" N   ILE C 219 " --> pdb=" O   LEU C 248 " (cutoff:3.500A)
      removed outlier: 6.934A  pdb=" N   LEU C 248 " --> pdb=" O   ILE C 219 " (cutoff:3.500A)
      removed outlier: 5.134A  pdb=" N   PHE C 221 " --> pdb=" O   GLU C 246 " (cutoff:3.500A)
      removed outlier: 5.343A  pdb=" N   GLU C 246 " --> pdb=" O   PHE C 221 " (cutoff:3.500A)
      removed outlier: 3.516A  pdb=" N   ASP C 223 " --> pdb=" O   ILE C 244 " (cutoff:3.500A)
      removed outlier: 3.619A  pdb=" N   GLY C 255 " --> pdb=" O   LEU C 247 " (cutoff:3.500A)
      removed outlier: 6.251A  pdb=" N   GLU C 249 " --> pdb=" O   ARG C 253 " (cutoff:3.500A)
      removed outlier: 4.623A  pdb=" N   ARG C 253 " --> pdb=" O   GLU C 249 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'D' and resid 219 through 221
      removed outlier: 3.741A  pdb=" N   CYS D 257 " --> pdb=" O   TYR D 245 " (cutoff:3.500A)
      removed outlier: 3.669A  pdb=" N   GLY D 255 " --> pdb=" O   LEU D 247 " (cutoff:3.500A)
      removed outlier: 5.795A  pdb=" N   GLU D 249 " --> pdb=" O   ARG D 253 " (cutoff:3.500A)
      removed outlier: 5.194A  pdb=" N   ARG D 253 " --> pdb=" O   GLU D 249 " (cutoff:3.500A)
      removed outlier: 6.198A  pdb=" N   LEU D 198 " --> pdb=" O   ARG D 310 " (cutoff:3.500A)
      removed outlier: 7.110A  pdb=" N   ILE D 312 " --> pdb=" O   LEU D 198 " (cutoff:3.500A)
      removed outlier: 6.185A  pdb=" N   ILE D 200 " --> pdb=" O   ILE D 312 " (cutoff:3.500A)
      removed outlier: 7.841A  pdb=" N   TYR D 314 " --> pdb=" O   ILE D 200 " (cutoff:3.500A)
      removed outlier: 6.412A  pdb=" N   LEU D 202 " --> pdb=" O   TYR D 314 " (cutoff:3.500A)

    605 hydrogen bonds defined for protein.
    1809 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 3.34

  Time building geometry restraints manager: 2.18 seconds

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

  Histogram of bond lengths:
        0.84 -     1.03: 10084
        1.03 -     1.23: 42
        1.23 -     1.42: 4422
        1.42 -     1.62: 5980
        1.62 -     1.81: 68
  Bond restraints: 20596
  Sorted by residual:
  bond pdb=" C40 1SY C 401 "
       pdb=" N39 1SY C 401 "
    ideal  model  delta    sigma   weight residual
    1.304  1.428 -0.124 2.00e-02 2.50e+03 3.82e+01
  bond pdb=" C40 1SY A 401 "
       pdb=" N39 1SY A 401 "
    ideal  model  delta    sigma   weight residual
    1.304  1.424 -0.120 2.00e-02 2.50e+03 3.62e+01
  bond pdb=" C36 1SY C 401 "
       pdb=" N42 1SY C 401 "
    ideal  model  delta    sigma   weight residual
    1.357  1.470 -0.113 2.00e-02 2.50e+03 3.21e+01
  bond pdb=" C36 1SY A 401 "
       pdb=" N42 1SY A 401 "
    ideal  model  delta    sigma   weight residual
    1.357  1.465 -0.108 2.00e-02 2.50e+03 2.89e+01
  bond pdb=" C3' 1SY C 401 "
       pdb=" C4' 1SY C 401 "
    ideal  model  delta    sigma   weight residual
    1.531  1.425  0.106 2.00e-02 2.50e+03 2.82e+01
  ... (remaining 20591 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     6.12: 37085
        6.12 -    12.23: 28
       12.23 -    18.35: 15
       18.35 -    24.46: 0
       24.46 -    30.58: 4
  Bond angle restraints: 37132
  Sorted by residual:
  angle pdb=" C18 Y6H A 402 "
        pdb=" C19 Y6H A 402 "
        pdb=" C21 Y6H A 402 "
      ideal   model   delta    sigma   weight residual
     111.16  141.74  -30.58 3.00e+00 1.11e-01 1.04e+02
  angle pdb=" C18 Y6H C 402 "
        pdb=" C19 Y6H C 402 "
        pdb=" C21 Y6H C 402 "
      ideal   model   delta    sigma   weight residual
     111.16  141.69  -30.53 3.00e+00 1.11e-01 1.04e+02
  angle pdb=" C20 Y6H C 402 "
        pdb=" C19 Y6H C 402 "
        pdb=" C22 Y6H C 402 "
      ideal   model   delta    sigma   weight residual
     108.62  139.00  -30.38 3.00e+00 1.11e-01 1.03e+02
  angle pdb=" C20 Y6H A 402 "
        pdb=" C19 Y6H A 402 "
        pdb=" C22 Y6H A 402 "
      ideal   model   delta    sigma   weight residual
     108.62  138.09  -29.47 3.00e+00 1.11e-01 9.65e+01
  angle pdb=" O19 1SY A 401 "
        pdb=" P18 1SY A 401 "
        pdb=" O44 1SY A 401 "
      ideal   model   delta    sigma   weight residual
     123.21  104.90   18.31 3.00e+00 1.11e-01 3.73e+01
  ... (remaining 37127 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    20.88: 8895
       20.88 -    41.76: 664
       41.76 -    62.64: 193
       62.64 -    83.52: 30
       83.52 -   104.39: 8
  Dihedral angle restraints: 9790
    sinusoidal: 5478
      harmonic: 4312
  Sorted by residual:
  dihedral pdb=" CA  GLU D 260 "
           pdb=" C   GLU D 260 "
           pdb=" N   TYR D 261 "
           pdb=" CA  TYR D 261 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  161.46   18.54     0      5.00e+00 4.00e-02 1.37e+01
  dihedral pdb=" C18 Y6H A 402 "
           pdb=" C24 Y6H A 402 "
           pdb=" O23 Y6H A 402 "
           pdb=" C25 Y6H A 402 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -58.10   46.29 -104.39     1      3.00e+01 1.11e-03 1.33e+01
  dihedral pdb=" C18 Y6H A 402 "
           pdb=" C28 Y6H A 402 "
           pdb=" O29 Y6H A 402 "
           pdb=" C25 Y6H A 402 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -58.49   40.70  -99.19     1      3.00e+01 1.11e-03 1.24e+01
  ... (remaining 9787 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.047: 1340
       0.047 -    0.093: 192
       0.093 -    0.140: 48
       0.140 -    0.187: 4
       0.187 -    0.234: 2
  Chirality restraints: 1586
  Sorted by residual:
  chirality pdb=" C2' 1SY C 401 "
            pdb=" C1' 1SY C 401 "
            pdb=" C3' 1SY C 401 "
            pdb=" O2' 1SY C 401 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.74   -2.51   -0.23 2.00e-01 2.50e+01 1.36e+00
  chirality pdb=" C2' 1SY A 401 "
            pdb=" C1' 1SY A 401 "
            pdb=" C3' 1SY A 401 "
            pdb=" O2' 1SY A 401 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.74   -2.52   -0.22 2.00e-01 2.50e+01 1.20e+00
  chirality pdb=" C22 1SY C 401 "
            pdb=" C21 1SY C 401 "
            pdb=" C24 1SY C 401 "
            pdb=" O23 1SY C 401 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.70   -2.53   -0.17 2.00e-01 2.50e+01 7.13e-01
  ... (remaining 1583 not shown)

  Planarity restraints: 2992
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CD  ARG C 281 "    0.172 9.50e-02 1.11e+02   5.75e-02 4.14e+00
        pdb=" NE  ARG C 281 "   -0.014 2.00e-02 2.50e+03
        pdb=" CZ  ARG C 281 "    0.012 2.00e-02 2.50e+03
        pdb=" NH1 ARG C 281 "   -0.002 2.00e-02 2.50e+03
        pdb=" NH2 ARG C 281 "    0.000 2.00e-02 2.50e+03
        pdb="HH11 ARG C 281 "   -0.004 2.00e-02 2.50e+03
        pdb="HH12 ARG C 281 "    0.001 2.00e-02 2.50e+03
        pdb="HH21 ARG C 281 "    0.000 2.00e-02 2.50e+03
        pdb="HH22 ARG C 281 "   -0.000 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ILE A  10 "    0.031 5.00e-02 4.00e+02   4.65e-02 3.45e+00
        pdb=" N   PRO A  11 "   -0.080 5.00e-02 4.00e+02
        pdb=" CA  PRO A  11 "    0.024 5.00e-02 4.00e+02
        pdb=" CD  PRO A  11 "    0.026 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ALA C 156 "   -0.007 2.00e-02 2.50e+03   1.34e-02 1.79e+00
        pdb=" C   ALA C 156 "    0.023 2.00e-02 2.50e+03
        pdb=" O   ALA C 156 "   -0.009 2.00e-02 2.50e+03
        pdb=" N   HIS C 157 "   -0.008 2.00e-02 2.50e+03
  ... (remaining 2989 not shown)

  Histogram of nonbonded interaction distances:
        1.61 -     2.21: 1582
        2.21 -     2.81: 42612
        2.81 -     3.40: 56688
        3.40 -     4.00: 71086
        4.00 -     4.60: 109547
  Nonbonded interactions: 281515
  Sorted by model distance:
  nonbonded pdb=" O   GLY C 234 "
            pdb=" HH  TYR D 245 "
     model   vdw
     1.610 2.450
  nonbonded pdb=" O   GLY A 234 "
            pdb=" HH  TYR B 245 "
     model   vdw
     1.627 2.450
  nonbonded pdb=" OE1 GLN A 276 "
            pdb=" H   GLN A 276 "
     model   vdw
     1.627 2.450
  nonbonded pdb="HH21 ARG B 178 "
            pdb=" OD1 ASN B 242 "
     model   vdw
     1.634 2.450
  nonbonded pdb="HH21 ARG D 178 "
            pdb=" OD1 ASN D 242 "
     model   vdw
     1.642 2.450
  ... (remaining 281510 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.01
Found NCS groups:
ncs_group {
  reference = (chain 'A' and resid 3 through 335)
  selection = chain 'B'
  selection = (chain 'C' and resid 3 through 335)
  selection = chain 'D'
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             0.250
  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:             0.120
  Extract box with map and model:          0.300
  Check model and map are aligned:         0.060
  Set scattering table:                    0.030
  Process input model:                     16.420
  Find NCS groups from input model:        0.330
  Set up NCS constraints:                  0.030
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.090
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   18.630
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7949
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      :  0.009   0.638  10473  Z= 0.714
  Angle     :  1.034  30.578  14240  Z= 0.425
  Chirality :  0.037   0.234   1586
  Planarity :  0.004   0.076   1796
  Dihedral  : 15.951 104.394   4006
  Min Nonbonded Distance : 1.974

Molprobity Statistics.
  All-atom Clashscore : 10.18
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.34 %
    Favored  : 95.66 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.28 %
    Favored  : 99.72 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.51 (0.24), residues: 1244
  helix:  2.11 (0.18), residues: 744
  sheet: -1.11 (0.51), residues: 96
  loop : -0.55 (0.33), residues: 404

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.013   0.001   ARG C 281 
 TYR   0.016   0.001   TYR C 106 
 PHE   0.011   0.002   PHE D 279 
 TRP   0.011   0.001   TRP C 161 
 HIS   0.004   0.001   HIS D   7 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00703 /  0.35 (10472)
  covalent geometry    : angle       1.03429 /  0.43 (14240)
  hydrogen bonds       : bond        0.12663 /  8.57 (  605)
  hydrogen bonds       : angle       6.24804 /  4.51 ( 1809)
  Misc. bond           : bond        0.63760 / 33.56 (    1)

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

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

  2488 Ramachandran restraints generated.
    1244 Oldfield, 0 Emsley, 1244 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2488 Ramachandran restraints generated.
    1244 Oldfield, 0 Emsley, 1244 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  276 residues out of total 1080 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 276
  time to evaluate  : 0.450 
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: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A    4 SER cc_start: 0.8570 (t) cc_final: 0.8104 (m)
REVERT: A   29 CYS cc_start: 0.9307 (m) cc_final: 0.9054 (m)
REVERT: A  181 THR cc_start: 0.8427 (m) cc_final: 0.8137 (m)
REVERT: B  152 ASN cc_start: 0.9020 (m-40) cc_final: 0.8683 (t0)
REVERT: B  154 ASN cc_start: 0.9114 (m-40) cc_final: 0.8844 (m-40)
REVERT: B  271 MET cc_start: 0.9202 (ttm) cc_final: 0.8941 (ttm)
REVERT: C  181 THR cc_start: 0.8429 (m) cc_final: 0.8155 (m)
REVERT: C  223 ASP cc_start: 0.8355 (t70) cc_final: 0.8062 (t70)
REVERT: C  237 ASP cc_start: 0.8493 (m-30) cc_final: 0.8222 (m-30)
REVERT: C  296 GLU cc_start: 0.8610 (tm-30) cc_final: 0.8309 (tm-30)
REVERT: C  304 GLU cc_start: 0.8197 (mp0) cc_final: 0.7905 (mp0)
REVERT: C  305 SER cc_start: 0.9019 (t) cc_final: 0.8691 (p)
REVERT: D  154 ASN cc_start: 0.9142 (m110) cc_final: 0.8781 (m-40)
  outliers start: 0
  outliers final: 0
  residues processed: 276
  average time/residue: 0.1607
  time to fit residues: 67.1040
Evaluate side-chains
  214 residues out of total 1080 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 214
  time to evaluate  : 0.377 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 124
   random chunks:
   chunk 108 optimal weight:    0.9980
   chunk 49 optimal weight:   10.0000
   chunk 97 optimal weight:    0.8980
   chunk 113 optimal weight:    1.9990
   chunk 53 optimal weight:    5.9990
   chunk 5 optimal weight:    0.9990
   chunk 33 optimal weight:    7.9990
   chunk 123 optimal weight:    0.1980
   chunk 65 optimal weight:    0.9980
   chunk 62 optimal weight:    8.9990
   chunk 51 optimal weight:    0.9990
   overall best weight:    0.8182

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 327 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3254 r_free = 0.3254 target = 0.094696 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.2903 r_free = 0.2903 target = 0.075511 restraints weight = 70682.158|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.2981 r_free = 0.2981 target = 0.079555 restraints weight = 28325.571|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3032 r_free = 0.3032 target = 0.082271 restraints weight = 16320.198|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.3063 r_free = 0.3063 target = 0.083943 restraints weight = 11292.648|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 39)----------------|
| r_work = 0.3087 r_free = 0.3087 target = 0.085256 restraints weight = 8903.011|
|-----------------------------------------------------------------------------|
r_work (final): 0.3085
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7820
moved from start:          0.1445

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041  10473  Z= 0.119
  Angle     :  0.548   6.861  14240  Z= 0.271
  Chirality :  0.035   0.154   1586
  Planarity :  0.004   0.040   1796
  Dihedral  :  7.600  66.425   1626
  Min Nonbonded Distance : 2.165

Molprobity Statistics.
  All-atom Clashscore : 7.34
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.25 %
    Favored  : 97.75 %
  Rotamer:
    Outliers :  1.39 %
    Allowed  : 10.19 %
    Favored  : 88.43 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.87 (0.25), residues: 1244
  helix:  2.35 (0.19), residues: 756
  sheet: -1.18 (0.49), residues: 96
  loop : -0.32 (0.36), residues: 392

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG C 281 
 TYR   0.018   0.001   TYR D 106 
 PHE   0.017   0.001   PHE C 279 
 TRP   0.005   0.001   TRP B 119 
 HIS   0.007   0.001   HIS C 157 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00255 /  0.12 (10472)
  covalent geometry    : angle       0.54768 /  0.27 (14240)
  hydrogen bonds       : bond        0.04016 /  2.81 (  605)
  hydrogen bonds       : angle       4.72461 /  3.43 ( 1809)
  Misc. bond           : bond        0.00349 /  0.18 (    1)

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

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

  2488 Ramachandran restraints generated.
    1244 Oldfield, 0 Emsley, 1244 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2488 Ramachandran restraints generated.
    1244 Oldfield, 0 Emsley, 1244 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  252 residues out of total 1080 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 237
  time to evaluate  : 0.523 
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: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A    4 SER cc_start: 0.8545 (t) cc_final: 0.8129 (m)
REVERT: A   29 CYS cc_start: 0.9147 (m) cc_final: 0.8941 (m)
REVERT: B  152 ASN cc_start: 0.9035 (m-40) cc_final: 0.8581 (t0)
REVERT: B  271 MET cc_start: 0.9240 (ttm) cc_final: 0.8957 (ttm)
REVERT: C  143 GLU cc_start: 0.8538 (mp0) cc_final: 0.8121 (mp0)
REVERT: C  223 ASP cc_start: 0.8191 (t70) cc_final: 0.7859 (t70)
REVERT: C  237 ASP cc_start: 0.8580 (m-30) cc_final: 0.8336 (m-30)
REVERT: C  263 THR cc_start: 0.9146 (m) cc_final: 0.8940 (m)
REVERT: C  296 GLU cc_start: 0.8640 (tm-30) cc_final: 0.8355 (tm-30)
REVERT: D   51 LEU cc_start: 0.9420 (mt) cc_final: 0.9194 (mp)
  outliers start: 15
  outliers final: 15
  residues processed: 241
  average time/residue: 0.1704
  time to fit residues: 61.7333
Evaluate side-chains
  227 residues out of total 1080 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 212
  time to evaluate  : 0.534 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   64 CYS
Chi-restraints excluded: chain A residue  103 ILE
Chi-restraints excluded: chain A residue  332 HIS
Chi-restraints excluded: chain B residue   64 CYS
Chi-restraints excluded: chain B residue   66 LEU
Chi-restraints excluded: chain B residue  147 VAL
Chi-restraints excluded: chain C residue   64 CYS
Chi-restraints excluded: chain C residue  103 ILE
Chi-restraints excluded: chain C residue  299 LEU
Chi-restraints excluded: chain C residue  332 HIS
Chi-restraints excluded: chain D residue    6 LEU
Chi-restraints excluded: chain D residue   64 CYS
Chi-restraints excluded: chain D residue   66 LEU
Chi-restraints excluded: chain D residue  147 VAL
Chi-restraints excluded: chain D residue  205 ASP
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 124
   random chunks:
   chunk 39 optimal weight:    2.9990
   chunk 106 optimal weight:    0.8980
   chunk 20 optimal weight:   10.0000
   chunk 38 optimal weight:    1.9990
   chunk 92 optimal weight:    5.9990
   chunk 16 optimal weight:    6.9990
   chunk 91 optimal weight:    6.9990
   chunk 84 optimal weight:    0.7980
   chunk 112 optimal weight:    4.9990
   chunk 67 optimal weight:    6.9990
   chunk 19 optimal weight:    7.9990
   overall best weight:    2.3386

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 184 GLN
A 327 GLN
C 184 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3230 r_free = 0.3230 target = 0.093243 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.2876 r_free = 0.2876 target = 0.074021 restraints weight = 71547.589|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.2954 r_free = 0.2954 target = 0.078038 restraints weight = 29124.758|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3006 r_free = 0.3006 target = 0.080723 restraints weight = 16776.242|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 41)----------------|
| r_work = 0.3039 r_free = 0.3039 target = 0.082479 restraints weight = 11606.259|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 41)----------------|
| r_work = 0.3061 r_free = 0.3061 target = 0.083696 restraints weight = 9049.941|
|-----------------------------------------------------------------------------|
r_work (final): 0.3059
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7858
moved from start:          0.1789

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035  10473  Z= 0.139
  Angle     :  0.529   6.455  14240  Z= 0.262
  Chirality :  0.034   0.142   1586
  Planarity :  0.004   0.040   1796
  Dihedral  :  5.565  40.545   1626
  Min Nonbonded Distance : 2.162

Molprobity Statistics.
  All-atom Clashscore : 7.39
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.89 %
    Favored  : 97.11 %
  Rotamer:
    Outliers :  2.41 %
    Allowed  : 12.31 %
    Favored  : 85.28 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.87 (0.25), residues: 1244
  helix:  2.38 (0.19), residues: 756
  sheet: -1.29 (0.49), residues: 96
  loop : -0.35 (0.36), residues: 392

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 284 
 TYR   0.014   0.001   TYR D 106 
 PHE   0.014   0.001   PHE C 279 
 TRP   0.006   0.001   TRP A 161 
 HIS   0.006   0.001   HIS B   3 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00298 /  0.14 (10472)
  covalent geometry    : angle       0.52857 /  0.26 (14240)
  hydrogen bonds       : bond        0.03702 /  2.57 (  605)
  hydrogen bonds       : angle       4.46137 /  3.24 ( 1809)
  Misc. bond           : bond        0.00443 /  0.23 (    1)

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

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

  2488 Ramachandran restraints generated.
    1244 Oldfield, 0 Emsley, 1244 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2488 Ramachandran restraints generated.
    1244 Oldfield, 0 Emsley, 1244 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  250 residues out of total 1080 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 224
  time to evaluate  : 0.581 
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: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A    4 SER cc_start: 0.8597 (t) cc_final: 0.8129 (m)
REVERT: A   25 LEU cc_start: 0.9402 (tt) cc_final: 0.8870 (tt)
REVERT: A   29 CYS cc_start: 0.9157 (m) cc_final: 0.8843 (m)
REVERT: B  152 ASN cc_start: 0.9055 (m-40) cc_final: 0.8583 (t0)
REVERT: B  271 MET cc_start: 0.9278 (ttm) cc_final: 0.9016 (ttm)
REVERT: C  143 GLU cc_start: 0.8443 (mp0) cc_final: 0.8077 (mp0)
REVERT: C  152 ASN cc_start: 0.9128 (m-40) cc_final: 0.8835 (t0)
REVERT: C  223 ASP cc_start: 0.8179 (t70) cc_final: 0.7847 (t70)
REVERT: C  237 ASP cc_start: 0.8603 (m-30) cc_final: 0.8365 (m-30)
REVERT: D  223 ASP cc_start: 0.8236 (OUTLIER) cc_final: 0.7664 (m-30)
  outliers start: 26
  outliers final: 22
  residues processed: 236
  average time/residue: 0.1754
  time to fit residues: 62.5844
Evaluate side-chains
  230 residues out of total 1080 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 207
  time to evaluate  : 0.546 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   64 CYS
Chi-restraints excluded: chain A residue  103 ILE
Chi-restraints excluded: chain A residue  184 GLN
Chi-restraints excluded: chain A residue  332 HIS
Chi-restraints excluded: chain B residue   43 THR
Chi-restraints excluded: chain B residue   64 CYS
Chi-restraints excluded: chain B residue   66 LEU
Chi-restraints excluded: chain B residue  205 ASP
Chi-restraints excluded: chain C residue    4 SER
Chi-restraints excluded: chain C residue  103 ILE
Chi-restraints excluded: chain C residue  184 GLN
Chi-restraints excluded: chain C residue  299 LEU
Chi-restraints excluded: chain C residue  332 HIS
Chi-restraints excluded: chain D residue    6 LEU
Chi-restraints excluded: chain D residue   43 THR
Chi-restraints excluded: chain D residue   49 LEU
Chi-restraints excluded: chain D residue   64 CYS
Chi-restraints excluded: chain D residue   66 LEU
Chi-restraints excluded: chain D residue  147 VAL
Chi-restraints excluded: chain D residue  205 ASP
Chi-restraints excluded: chain D residue  223 ASP
Chi-restraints excluded: chain D residue  261 TYR
Chi-restraints excluded: chain D residue  263 THR
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 124
   random chunks:
   chunk 37 optimal weight:    5.9990
   chunk 53 optimal weight:    5.9990
   chunk 48 optimal weight:   10.0000
   chunk 109 optimal weight:    4.9990
   chunk 63 optimal weight:    9.9990
   chunk 118 optimal weight:    0.9980
   chunk 38 optimal weight:    2.9990
   chunk 50 optimal weight:    8.9990
   chunk 62 optimal weight:    7.9990
   chunk 33 optimal weight:    8.9990
   chunk 67 optimal weight:    6.9990
   overall best weight:    4.1988

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 327 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3188 r_free = 0.3188 target = 0.090568 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.2834 r_free = 0.2834 target = 0.071640 restraints weight = 71750.010|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.2909 r_free = 0.2909 target = 0.075474 restraints weight = 29284.387|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 43)----------------|
| r_work = 0.2959 r_free = 0.2959 target = 0.078030 restraints weight = 16998.993|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 39)----------------|
| r_work = 0.2992 r_free = 0.2992 target = 0.079766 restraints weight = 11876.738|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 25)----------------|
| r_work = 0.3013 r_free = 0.3013 target = 0.080873 restraints weight = 9262.386|
|-----------------------------------------------------------------------------|
r_work (final): 0.3014
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7904
moved from start:          0.1998

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.037  10473  Z= 0.206
  Angle     :  0.553   6.275  14240  Z= 0.280
  Chirality :  0.035   0.140   1586
  Planarity :  0.004   0.041   1796
  Dihedral  :  5.758  44.662   1626
  Min Nonbonded Distance : 2.168

Molprobity Statistics.
  All-atom Clashscore : 8.22
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.62 %
    Favored  : 96.38 %
  Rotamer:
    Outliers :  2.59 %
    Allowed  : 13.52 %
    Favored  : 83.89 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.70 (0.25), residues: 1244
  helix:  2.28 (0.19), residues: 756
  sheet: -1.34 (0.49), residues: 96
  loop : -0.50 (0.35), residues: 392

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 281 
 TYR   0.014   0.001   TYR D 106 
 PHE   0.013   0.002   PHE C 279 
 TRP   0.007   0.001   TRP C 161 
 HIS   0.009   0.001   HIS B   3 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00430 /  0.21 (10472)
  covalent geometry    : angle       0.55294 /  0.28 (14240)
  hydrogen bonds       : bond        0.03739 /  2.60 (  605)
  hydrogen bonds       : angle       4.52972 /  3.28 ( 1809)
  Misc. bond           : bond        0.00411 /  0.22 (    1)

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

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

  2488 Ramachandran restraints generated.
    1244 Oldfield, 0 Emsley, 1244 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2488 Ramachandran restraints generated.
    1244 Oldfield, 0 Emsley, 1244 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  239 residues out of total 1080 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 211
  time to evaluate  : 0.401 
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: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A    4 SER cc_start: 0.8558 (t) cc_final: 0.7964 (m)
REVERT: A   29 CYS cc_start: 0.9165 (m) cc_final: 0.8962 (m)
REVERT: A  143 GLU cc_start: 0.8481 (mp0) cc_final: 0.8209 (mp0)
REVERT: B   69 GLU cc_start: 0.9193 (mm-30) cc_final: 0.8948 (mm-30)
REVERT: B  152 ASN cc_start: 0.9055 (m-40) cc_final: 0.8729 (m-40)
REVERT: B  260 GLU cc_start: 0.8153 (tp30) cc_final: 0.7948 (tp30)
REVERT: B  271 MET cc_start: 0.9300 (ttm) cc_final: 0.9067 (ttm)
REVERT: C  143 GLU cc_start: 0.8445 (mp0) cc_final: 0.8087 (mp0)
REVERT: C  152 ASN cc_start: 0.9225 (m-40) cc_final: 0.8919 (t0)
REVERT: C  223 ASP cc_start: 0.8240 (t70) cc_final: 0.7914 (t70)
REVERT: C  237 ASP cc_start: 0.8644 (m-30) cc_final: 0.8388 (m-30)
REVERT: D  223 ASP cc_start: 0.8270 (OUTLIER) cc_final: 0.7813 (m-30)
  outliers start: 28
  outliers final: 24
  residues processed: 223
  average time/residue: 0.1780
  time to fit residues: 59.7837
Evaluate side-chains
  225 residues out of total 1080 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 200
  time to evaluate  : 0.529 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   64 CYS
Chi-restraints excluded: chain A residue  103 ILE
Chi-restraints excluded: chain A residue  172 LEU
Chi-restraints excluded: chain A residue  206 CYS
Chi-restraints excluded: chain A residue  332 HIS
Chi-restraints excluded: chain B residue   43 THR
Chi-restraints excluded: chain B residue   64 CYS
Chi-restraints excluded: chain B residue   66 LEU
Chi-restraints excluded: chain B residue   99 LEU
Chi-restraints excluded: chain B residue  205 ASP
Chi-restraints excluded: chain C residue    4 SER
Chi-restraints excluded: chain C residue  103 ILE
Chi-restraints excluded: chain C residue  206 CYS
Chi-restraints excluded: chain C residue  299 LEU
Chi-restraints excluded: chain C residue  332 HIS
Chi-restraints excluded: chain D residue    6 LEU
Chi-restraints excluded: chain D residue   43 THR
Chi-restraints excluded: chain D residue   49 LEU
Chi-restraints excluded: chain D residue   64 CYS
Chi-restraints excluded: chain D residue   66 LEU
Chi-restraints excluded: chain D residue   99 LEU
Chi-restraints excluded: chain D residue  205 ASP
Chi-restraints excluded: chain D residue  223 ASP
Chi-restraints excluded: chain D residue  261 TYR
Chi-restraints excluded: chain D residue  263 THR
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 124
   random chunks:
   chunk 29 optimal weight:    2.9990
   chunk 75 optimal weight:    8.9990
   chunk 35 optimal weight:    8.9990
   chunk 97 optimal weight:    3.9990
   chunk 73 optimal weight:    8.9990
   chunk 63 optimal weight:    8.9990
   chunk 41 optimal weight:    4.9990
   chunk 22 optimal weight:    9.9990
   chunk 27 optimal weight:    4.9990
   chunk 94 optimal weight:    8.9990
   chunk 12 optimal weight:    7.9990
   overall best weight:    4.9990

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
D 327 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3160 r_free = 0.3160 target = 0.088914 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.2801 r_free = 0.2801 target = 0.070010 restraints weight = 72459.636|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.2876 r_free = 0.2876 target = 0.073755 restraints weight = 29722.738|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.2926 r_free = 0.2926 target = 0.076283 restraints weight = 17429.409|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 33)----------------|
| r_work = 0.2958 r_free = 0.2958 target = 0.077955 restraints weight = 12258.843|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 38)----------------|
| r_work = 0.2980 r_free = 0.2980 target = 0.079076 restraints weight = 9635.607|
|-----------------------------------------------------------------------------|
r_work (final): 0.2977
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7942
moved from start:          0.2270

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.039  10473  Z= 0.238
  Angle     :  0.582   5.906  14240  Z= 0.296
  Chirality :  0.035   0.140   1586
  Planarity :  0.004   0.042   1796
  Dihedral  :  5.920  45.981   1626
  Min Nonbonded Distance : 2.054

Molprobity Statistics.
  All-atom Clashscore : 8.90
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.10 %
    Favored  : 95.90 %
  Rotamer:
    Outliers :  3.15 %
    Allowed  : 15.37 %
    Favored  : 81.48 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.44 (0.25), residues: 1244
  helix:  2.12 (0.19), residues: 756
  sheet: -1.36 (0.50), residues: 96
  loop : -0.77 (0.33), residues: 392

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG C 232 
 TYR   0.014   0.001   TYR D 106 
 PHE   0.016   0.002   PHE C 279 
 TRP   0.009   0.001   TRP A 161 
 HIS   0.010   0.001   HIS B   3 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00496 /  0.24 (10472)
  covalent geometry    : angle       0.58206 /  0.30 (14240)
  hydrogen bonds       : bond        0.03879 /  2.70 (  605)
  hydrogen bonds       : angle       4.60504 /  3.32 ( 1809)
  Misc. bond           : bond        0.00473 /  0.25 (    1)

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

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

  2488 Ramachandran restraints generated.
    1244 Oldfield, 0 Emsley, 1244 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2488 Ramachandran restraints generated.
    1244 Oldfield, 0 Emsley, 1244 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  237 residues out of total 1080 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 203
  time to evaluate  : 0.333 
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: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A    4 SER cc_start: 0.8523 (t) cc_final: 0.8109 (m)
REVERT: A   29 CYS cc_start: 0.9213 (m) cc_final: 0.9008 (m)
REVERT: A  143 GLU cc_start: 0.8500 (mp0) cc_final: 0.8219 (mp0)
REVERT: B   69 GLU cc_start: 0.9182 (mm-30) cc_final: 0.8897 (mm-30)
REVERT: B  223 ASP cc_start: 0.8456 (m-30) cc_final: 0.8046 (m-30)
REVERT: B  271 MET cc_start: 0.9329 (ttm) cc_final: 0.9101 (ttm)
REVERT: C  143 GLU cc_start: 0.8439 (mp0) cc_final: 0.8105 (mp0)
REVERT: C  152 ASN cc_start: 0.9187 (m-40) cc_final: 0.8864 (t0)
REVERT: C  223 ASP cc_start: 0.8349 (t70) cc_final: 0.8010 (t70)
REVERT: D    6 LEU cc_start: 0.9535 (OUTLIER) cc_final: 0.9304 (tt)
REVERT: D  223 ASP cc_start: 0.8331 (OUTLIER) cc_final: 0.7995 (m-30)
  outliers start: 34
  outliers final: 29
  residues processed: 215
  average time/residue: 0.1576
  time to fit residues: 51.1114
Evaluate side-chains
  224 residues out of total 1080 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 193
  time to evaluate  : 0.379 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   64 CYS
Chi-restraints excluded: chain A residue  103 ILE
Chi-restraints excluded: chain A residue  181 THR
Chi-restraints excluded: chain A residue  206 CYS
Chi-restraints excluded: chain A residue  259 LEU
Chi-restraints excluded: chain A residue  307 ASN
Chi-restraints excluded: chain A residue  332 HIS
Chi-restraints excluded: chain B residue   43 THR
Chi-restraints excluded: chain B residue   64 CYS
Chi-restraints excluded: chain B residue   66 LEU
Chi-restraints excluded: chain B residue   99 LEU
Chi-restraints excluded: chain B residue  148 CYS
Chi-restraints excluded: chain B residue  205 ASP
Chi-restraints excluded: chain C residue    4 SER
Chi-restraints excluded: chain C residue   64 CYS
Chi-restraints excluded: chain C residue  103 ILE
Chi-restraints excluded: chain C residue  181 THR
Chi-restraints excluded: chain C residue  184 GLN
Chi-restraints excluded: chain C residue  206 CYS
Chi-restraints excluded: chain C residue  307 ASN
Chi-restraints excluded: chain C residue  332 HIS
Chi-restraints excluded: chain D residue    6 LEU
Chi-restraints excluded: chain D residue   43 THR
Chi-restraints excluded: chain D residue   64 CYS
Chi-restraints excluded: chain D residue   66 LEU
Chi-restraints excluded: chain D residue   99 LEU
Chi-restraints excluded: chain D residue  148 CYS
Chi-restraints excluded: chain D residue  205 ASP
Chi-restraints excluded: chain D residue  223 ASP
Chi-restraints excluded: chain D residue  261 TYR
Chi-restraints excluded: chain D residue  263 THR
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 124
   random chunks:
   chunk 96 optimal weight:   10.0000
   chunk 77 optimal weight:    7.9990
   chunk 74 optimal weight:    7.9990
   chunk 84 optimal weight:    6.9990
   chunk 56 optimal weight:    5.9990
   chunk 70 optimal weight:    1.9990
   chunk 21 optimal weight:   10.0000
   chunk 8 optimal weight:    0.9980
   chunk 52 optimal weight:   10.0000
   chunk 120 optimal weight:    5.9990
   chunk 98 optimal weight:    6.9990
   overall best weight:    4.3988

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
B 327 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3160 r_free = 0.3160 target = 0.088829 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.2800 r_free = 0.2800 target = 0.069888 restraints weight = 72782.005|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.2876 r_free = 0.2876 target = 0.073654 restraints weight = 29880.514|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 41)----------------|
| r_work = 0.2926 r_free = 0.2926 target = 0.076161 restraints weight = 17469.594|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 31)----------------|
| r_work = 0.2956 r_free = 0.2956 target = 0.077755 restraints weight = 12303.604|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 43)----------------|
| r_work = 0.2979 r_free = 0.2979 target = 0.078935 restraints weight = 9781.884|
|-----------------------------------------------------------------------------|
r_work (final): 0.2974
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7940
moved from start:          0.2479

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.037  10473  Z= 0.213
  Angle     :  0.561   5.663  14240  Z= 0.283
  Chirality :  0.035   0.139   1586
  Planarity :  0.004   0.040   1796
  Dihedral  :  5.737  43.945   1626
  Min Nonbonded Distance : 2.320

Molprobity Statistics.
  All-atom Clashscore : 8.81
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.70 %
    Favored  : 96.30 %
  Rotamer:
    Outliers :  3.06 %
    Allowed  : 16.94 %
    Favored  : 80.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.45 (0.25), residues: 1244
  helix:  2.16 (0.19), residues: 756
  sheet: -1.36 (0.51), residues: 96
  loop : -0.80 (0.33), residues: 392

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG C  71 
 TYR   0.013   0.001   TYR D 106 
 PHE   0.014   0.002   PHE C 279 
 TRP   0.008   0.001   TRP C 119 
 HIS   0.008   0.001   HIS B   3 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00445 /  0.21 (10472)
  covalent geometry    : angle       0.56135 /  0.28 (14240)
  hydrogen bonds       : bond        0.03758 /  2.61 (  605)
  hydrogen bonds       : angle       4.51706 /  3.26 ( 1809)
  Misc. bond           : bond        0.00410 /  0.22 (    1)

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

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

  2488 Ramachandran restraints generated.
    1244 Oldfield, 0 Emsley, 1244 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2488 Ramachandran restraints generated.
    1244 Oldfield, 0 Emsley, 1244 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  232 residues out of total 1080 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 199
  time to evaluate  : 0.542 
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: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   29 CYS cc_start: 0.9211 (m) cc_final: 0.9010 (m)
REVERT: A  143 GLU cc_start: 0.8480 (mp0) cc_final: 0.8201 (mp0)
REVERT: B   69 GLU cc_start: 0.9185 (mm-30) cc_final: 0.8872 (mm-30)
REVERT: B  223 ASP cc_start: 0.8487 (m-30) cc_final: 0.8145 (m-30)
REVERT: B  271 MET cc_start: 0.9336 (ttm) cc_final: 0.9125 (ttm)
REVERT: C  143 GLU cc_start: 0.8463 (mp0) cc_final: 0.8071 (mp0)
REVERT: C  152 ASN cc_start: 0.9211 (m-40) cc_final: 0.8867 (t0)
REVERT: C  223 ASP cc_start: 0.8330 (t70) cc_final: 0.7989 (t70)
REVERT: D   69 GLU cc_start: 0.9217 (mm-30) cc_final: 0.8939 (mm-30)
  outliers start: 33
  outliers final: 27
  residues processed: 212
  average time/residue: 0.1757
  time to fit residues: 55.7768
Evaluate side-chains
  217 residues out of total 1080 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 190
  time to evaluate  : 0.452 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   64 CYS
Chi-restraints excluded: chain A residue  103 ILE
Chi-restraints excluded: chain A residue  206 CYS
Chi-restraints excluded: chain A residue  307 ASN
Chi-restraints excluded: chain A residue  332 HIS
Chi-restraints excluded: chain B residue   43 THR
Chi-restraints excluded: chain B residue   64 CYS
Chi-restraints excluded: chain B residue   66 LEU
Chi-restraints excluded: chain B residue   99 LEU
Chi-restraints excluded: chain B residue  148 CYS
Chi-restraints excluded: chain B residue  205 ASP
Chi-restraints excluded: chain C residue    4 SER
Chi-restraints excluded: chain C residue   64 CYS
Chi-restraints excluded: chain C residue  103 ILE
Chi-restraints excluded: chain C residue  181 THR
Chi-restraints excluded: chain C residue  206 CYS
Chi-restraints excluded: chain C residue  299 LEU
Chi-restraints excluded: chain C residue  332 HIS
Chi-restraints excluded: chain D residue    6 LEU
Chi-restraints excluded: chain D residue   43 THR
Chi-restraints excluded: chain D residue   49 LEU
Chi-restraints excluded: chain D residue   64 CYS
Chi-restraints excluded: chain D residue   66 LEU
Chi-restraints excluded: chain D residue   99 LEU
Chi-restraints excluded: chain D residue  205 ASP
Chi-restraints excluded: chain D residue  261 TYR
Chi-restraints excluded: chain D residue  263 THR
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 124
   random chunks:
   chunk 46 optimal weight:    6.9990
   chunk 112 optimal weight:    3.9990
   chunk 102 optimal weight:    6.9990
   chunk 105 optimal weight:    3.9990
   chunk 97 optimal weight:    3.9990
   chunk 117 optimal weight:   10.0000
   chunk 25 optimal weight:    1.9990
   chunk 62 optimal weight:    8.9990
   chunk 60 optimal weight:    4.9990
   chunk 106 optimal weight:    0.6980
   chunk 81 optimal weight:    3.9990
   overall best weight:    2.9388

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

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3182 r_free = 0.3182 target = 0.090016 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.2827 r_free = 0.2827 target = 0.071163 restraints weight = 71680.124|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.2902 r_free = 0.2902 target = 0.074925 restraints weight = 29049.766|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.2952 r_free = 0.2952 target = 0.077479 restraints weight = 16978.784|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 43)----------------|
| r_work = 0.2985 r_free = 0.2985 target = 0.079168 restraints weight = 11877.216|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 42)----------------|
| r_work = 0.3007 r_free = 0.3007 target = 0.080321 restraints weight = 9308.236|
|-----------------------------------------------------------------------------|
r_work (final): 0.2998
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7908
moved from start:          0.2641

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035  10473  Z= 0.157
  Angle     :  0.534   5.289  14240  Z= 0.267
  Chirality :  0.034   0.141   1586
  Planarity :  0.004   0.041   1796
  Dihedral  :  5.526  42.623   1626
  Min Nonbonded Distance : 2.315

Molprobity Statistics.
  All-atom Clashscore : 7.73
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.14 %
    Favored  : 96.86 %
  Rotamer:
    Outliers :  2.41 %
    Allowed  : 18.06 %
    Favored  : 79.54 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.74 (0.25), residues: 1244
  helix:  2.40 (0.19), residues: 756
  sheet: -1.29 (0.51), residues: 96
  loop : -0.70 (0.33), residues: 392

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B 238 
 TYR   0.013   0.001   TYR D 106 
 PHE   0.011   0.002   PHE A 279 
 TRP   0.007   0.001   TRP C 119 
 HIS   0.008   0.001   HIS B   3 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00335 /  0.16 (10472)
  covalent geometry    : angle       0.53442 /  0.27 (14240)
  hydrogen bonds       : bond        0.03568 /  2.48 (  605)
  hydrogen bonds       : angle       4.31383 /  3.13 ( 1809)
  Misc. bond           : bond        0.00251 /  0.13 (    1)

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

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

  2488 Ramachandran restraints generated.
    1244 Oldfield, 0 Emsley, 1244 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2488 Ramachandran restraints generated.
    1244 Oldfield, 0 Emsley, 1244 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  226 residues out of total 1080 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 200
  time to evaluate  : 0.424 
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: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   25 LEU cc_start: 0.9367 (tt) cc_final: 0.8790 (tt)
REVERT: A   29 CYS cc_start: 0.9151 (m) cc_final: 0.8781 (m)
REVERT: A  143 GLU cc_start: 0.8535 (mp0) cc_final: 0.8248 (mp0)
REVERT: B   69 GLU cc_start: 0.9181 (mm-30) cc_final: 0.8874 (mm-30)
REVERT: B  271 MET cc_start: 0.9331 (ttm) cc_final: 0.9090 (ttm)
REVERT: C  143 GLU cc_start: 0.8489 (mp0) cc_final: 0.8140 (mp0)
REVERT: C  223 ASP cc_start: 0.8283 (t70) cc_final: 0.7936 (t70)
REVERT: D   69 GLU cc_start: 0.9194 (mm-30) cc_final: 0.8913 (mm-30)
  outliers start: 26
  outliers final: 22
  residues processed: 209
  average time/residue: 0.1737
  time to fit residues: 53.9077
Evaluate side-chains
  210 residues out of total 1080 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 188
  time to evaluate  : 0.370 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   64 CYS
Chi-restraints excluded: chain A residue  103 ILE
Chi-restraints excluded: chain A residue  206 CYS
Chi-restraints excluded: chain A residue  307 ASN
Chi-restraints excluded: chain A residue  332 HIS
Chi-restraints excluded: chain B residue   66 LEU
Chi-restraints excluded: chain B residue   99 LEU
Chi-restraints excluded: chain B residue  205 ASP
Chi-restraints excluded: chain C residue    4 SER
Chi-restraints excluded: chain C residue   64 CYS
Chi-restraints excluded: chain C residue  103 ILE
Chi-restraints excluded: chain C residue  149 GLU
Chi-restraints excluded: chain C residue  206 CYS
Chi-restraints excluded: chain C residue  332 HIS
Chi-restraints excluded: chain D residue    6 LEU
Chi-restraints excluded: chain D residue   49 LEU
Chi-restraints excluded: chain D residue   66 LEU
Chi-restraints excluded: chain D residue   99 LEU
Chi-restraints excluded: chain D residue  148 CYS
Chi-restraints excluded: chain D residue  205 ASP
Chi-restraints excluded: chain D residue  261 TYR
Chi-restraints excluded: chain D residue  263 THR
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 124
   random chunks:
   chunk 100 optimal weight:    9.9990
   chunk 46 optimal weight:    7.9990
   chunk 55 optimal weight:   10.0000
   chunk 0 optimal weight:    7.9990
   chunk 22 optimal weight:    4.9990
   chunk 14 optimal weight:    7.9990
   chunk 89 optimal weight:    6.9990
   chunk 50 optimal weight:    2.9990
   chunk 41 optimal weight:    0.9990
   chunk 44 optimal weight:    0.0870
   chunk 15 optimal weight:    5.9990
   overall best weight:    3.0166

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

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3181 r_free = 0.3181 target = 0.089919 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.2827 r_free = 0.2827 target = 0.071112 restraints weight = 71721.761|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.2901 r_free = 0.2901 target = 0.074874 restraints weight = 28899.305|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.2952 r_free = 0.2952 target = 0.077406 restraints weight = 16888.471|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 39)----------------|
| r_work = 0.2985 r_free = 0.2985 target = 0.079121 restraints weight = 11849.233|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 31)----------------|
| r_work = 0.3006 r_free = 0.3006 target = 0.080270 restraints weight = 9280.541|
|-----------------------------------------------------------------------------|
r_work (final): 0.3001
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7913
moved from start:          0.2794

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035  10473  Z= 0.161
  Angle     :  0.540   5.410  14240  Z= 0.269
  Chirality :  0.034   0.140   1586
  Planarity :  0.004   0.041   1796
  Dihedral  :  5.601  47.585   1626
  Min Nonbonded Distance : 2.318

Molprobity Statistics.
  All-atom Clashscore : 8.12
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.38 %
    Favored  : 96.62 %
  Rotamer:
    Outliers :  2.41 %
    Allowed  : 18.52 %
    Favored  : 79.07 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.74 (0.25), residues: 1244
  helix:  2.41 (0.19), residues: 760
  sheet: -1.32 (0.51), residues: 96
  loop : -0.76 (0.34), residues: 388

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG C  71 
 TYR   0.013   0.001   TYR D 106 
 PHE   0.013   0.001   PHE A 279 
 TRP   0.008   0.001   TRP C 119 
 HIS   0.006   0.001   HIS B   3 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00344 /  0.16 (10472)
  covalent geometry    : angle       0.54003 /  0.27 (14240)
  hydrogen bonds       : bond        0.03562 /  2.47 (  605)
  hydrogen bonds       : angle       4.28659 /  3.11 ( 1809)
  Misc. bond           : bond        0.00334 /  0.18 (    1)

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

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

  2488 Ramachandran restraints generated.
    1244 Oldfield, 0 Emsley, 1244 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2488 Ramachandran restraints generated.
    1244 Oldfield, 0 Emsley, 1244 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  217 residues out of total 1080 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 191
  time to evaluate  : 0.585 
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: symmetry clash
   revert: symmetry clash
REVERT: A   25 LEU cc_start: 0.9409 (tt) cc_final: 0.8817 (tt)
REVERT: A   29 CYS cc_start: 0.9183 (m) cc_final: 0.8835 (m)
REVERT: A  143 GLU cc_start: 0.8541 (mp0) cc_final: 0.8263 (mp0)
REVERT: B  271 MET cc_start: 0.9328 (ttm) cc_final: 0.9083 (ttm)
REVERT: C  143 GLU cc_start: 0.8508 (mp0) cc_final: 0.8171 (mp0)
REVERT: C  223 ASP cc_start: 0.8285 (t70) cc_final: 0.7938 (t70)
REVERT: D   69 GLU cc_start: 0.9189 (mm-30) cc_final: 0.8905 (mm-30)
  outliers start: 26
  outliers final: 25
  residues processed: 201
  average time/residue: 0.1669
  time to fit residues: 50.5959
Evaluate side-chains
  209 residues out of total 1080 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 184
  time to evaluate  : 0.366 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   64 CYS
Chi-restraints excluded: chain A residue  103 ILE
Chi-restraints excluded: chain A residue  206 CYS
Chi-restraints excluded: chain A residue  224 LYS
Chi-restraints excluded: chain A residue  307 ASN
Chi-restraints excluded: chain A residue  332 HIS
Chi-restraints excluded: chain B residue   43 THR
Chi-restraints excluded: chain B residue   66 LEU
Chi-restraints excluded: chain B residue   99 LEU
Chi-restraints excluded: chain B residue  205 ASP
Chi-restraints excluded: chain C residue    4 SER
Chi-restraints excluded: chain C residue   64 CYS
Chi-restraints excluded: chain C residue  103 ILE
Chi-restraints excluded: chain C residue  206 CYS
Chi-restraints excluded: chain C residue  332 HIS
Chi-restraints excluded: chain D residue    6 LEU
Chi-restraints excluded: chain D residue   43 THR
Chi-restraints excluded: chain D residue   49 LEU
Chi-restraints excluded: chain D residue   64 CYS
Chi-restraints excluded: chain D residue   66 LEU
Chi-restraints excluded: chain D residue   99 LEU
Chi-restraints excluded: chain D residue  148 CYS
Chi-restraints excluded: chain D residue  205 ASP
Chi-restraints excluded: chain D residue  261 TYR
Chi-restraints excluded: chain D residue  263 THR
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 124
   random chunks:
   chunk 14 optimal weight:    7.9990
   chunk 26 optimal weight:    9.9990
   chunk 44 optimal weight:    0.4980
   chunk 67 optimal weight:    6.9990
   chunk 7 optimal weight:    6.9990
   chunk 35 optimal weight:    7.9990
   chunk 55 optimal weight:    9.9990
   chunk 103 optimal weight:    9.9990
   chunk 96 optimal weight:    0.9980
   chunk 107 optimal weight:    8.9990
   chunk 59 optimal weight:    1.9990
   overall best weight:    3.4986

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

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3176 r_free = 0.3176 target = 0.089767 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.2816 r_free = 0.2816 target = 0.070777 restraints weight = 71969.140|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.2893 r_free = 0.2893 target = 0.074606 restraints weight = 29381.163|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.2943 r_free = 0.2943 target = 0.077131 restraints weight = 17176.503|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 49)----------------|
| r_work = 0.2976 r_free = 0.2976 target = 0.078817 restraints weight = 12097.617|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 32)----------------|
| r_work = 0.2996 r_free = 0.2996 target = 0.079933 restraints weight = 9532.205|
|-----------------------------------------------------------------------------|
r_work (final): 0.2986
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7929
moved from start:          0.2883

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.036  10473  Z= 0.179
  Angle     :  0.552   5.034  14240  Z= 0.276
  Chirality :  0.035   0.140   1586
  Planarity :  0.004   0.041   1796
  Dihedral  :  5.530  46.377   1626
  Min Nonbonded Distance : 2.316

Molprobity Statistics.
  All-atom Clashscore : 8.37
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.22 %
    Favored  : 96.78 %
  Rotamer:
    Outliers :  2.78 %
    Allowed  : 18.24 %
    Favored  : 78.98 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.70 (0.25), residues: 1244
  helix:  2.40 (0.19), residues: 760
  sheet: -1.30 (0.52), residues: 96
  loop : -0.83 (0.33), residues: 388

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG C  71 
 TYR   0.015   0.001   TYR A 106 
 PHE   0.014   0.002   PHE A 279 
 TRP   0.008   0.001   TRP A 161 
 HIS   0.006   0.001   HIS B   3 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00382 /  0.18 (10472)
  covalent geometry    : angle       0.55222 /  0.28 (14240)
  hydrogen bonds       : bond        0.03566 /  2.48 (  605)
  hydrogen bonds       : angle       4.30247 /  3.11 ( 1809)
  Misc. bond           : bond        0.00424 /  0.22 (    1)

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

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

  2488 Ramachandran restraints generated.
    1244 Oldfield, 0 Emsley, 1244 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2488 Ramachandran restraints generated.
    1244 Oldfield, 0 Emsley, 1244 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  219 residues out of total 1080 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 189
  time to evaluate  : 0.546 
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: symmetry clash
REVERT: A   25 LEU cc_start: 0.9410 (tt) cc_final: 0.8816 (tt)
REVERT: A   29 CYS cc_start: 0.9181 (m) cc_final: 0.8836 (m)
REVERT: A  143 GLU cc_start: 0.8542 (mp0) cc_final: 0.8259 (mp0)
REVERT: B  271 MET cc_start: 0.9332 (ttm) cc_final: 0.9106 (ttm)
REVERT: C  143 GLU cc_start: 0.8532 (mp0) cc_final: 0.8315 (mp0)
REVERT: C  223 ASP cc_start: 0.8305 (t70) cc_final: 0.7962 (t70)
REVERT: D   69 GLU cc_start: 0.9200 (mm-30) cc_final: 0.8915 (mm-30)
  outliers start: 30
  outliers final: 28
  residues processed: 202
  average time/residue: 0.1738
  time to fit residues: 53.1947
Evaluate side-chains
  215 residues out of total 1080 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 187
  time to evaluate  : 0.375 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   49 LEU
Chi-restraints excluded: chain A residue   64 CYS
Chi-restraints excluded: chain A residue  103 ILE
Chi-restraints excluded: chain A residue  181 THR
Chi-restraints excluded: chain A residue  206 CYS
Chi-restraints excluded: chain A residue  224 LYS
Chi-restraints excluded: chain A residue  307 ASN
Chi-restraints excluded: chain A residue  332 HIS
Chi-restraints excluded: chain B residue   43 THR
Chi-restraints excluded: chain B residue   66 LEU
Chi-restraints excluded: chain B residue   99 LEU
Chi-restraints excluded: chain B residue  148 CYS
Chi-restraints excluded: chain B residue  205 ASP
Chi-restraints excluded: chain C residue    4 SER
Chi-restraints excluded: chain C residue   64 CYS
Chi-restraints excluded: chain C residue  103 ILE
Chi-restraints excluded: chain C residue  149 GLU
Chi-restraints excluded: chain C residue  206 CYS
Chi-restraints excluded: chain C residue  332 HIS
Chi-restraints excluded: chain D residue   43 THR
Chi-restraints excluded: chain D residue   49 LEU
Chi-restraints excluded: chain D residue   64 CYS
Chi-restraints excluded: chain D residue   66 LEU
Chi-restraints excluded: chain D residue   99 LEU
Chi-restraints excluded: chain D residue  148 CYS
Chi-restraints excluded: chain D residue  205 ASP
Chi-restraints excluded: chain D residue  261 TYR
Chi-restraints excluded: chain D residue  263 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 124
   random chunks:
   chunk 52 optimal weight:    5.9990
   chunk 93 optimal weight:    5.9990
   chunk 66 optimal weight:    4.9990
   chunk 30 optimal weight:    0.1980
   chunk 120 optimal weight:    3.9990
   chunk 60 optimal weight:    7.9990
   chunk 13 optimal weight:    0.2980
   chunk 29 optimal weight:    0.9990
   chunk 103 optimal weight:    8.9990
   chunk 45 optimal weight:    5.9990
   chunk 81 optimal weight:    0.0170
   overall best weight:    1.1022

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** B 185 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3215 r_free = 0.3215 target = 0.092122 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.2863 r_free = 0.2863 target = 0.073168 restraints weight = 70713.084|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.2941 r_free = 0.2941 target = 0.077132 restraints weight = 28480.383|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.2992 r_free = 0.2992 target = 0.079755 restraints weight = 16347.139|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 33)----------------|
| r_work = 0.3026 r_free = 0.3026 target = 0.081530 restraints weight = 11364.791|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 37)----------------|
| r_work = 0.3048 r_free = 0.3048 target = 0.082725 restraints weight = 8833.167|
|-----------------------------------------------------------------------------|
r_work (final): 0.3043
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7868
moved from start:          0.3026

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.030  10473  Z= 0.105
  Angle     :  0.516   5.009  14240  Z= 0.253
  Chirality :  0.034   0.143   1586
  Planarity :  0.004   0.042   1796
  Dihedral  :  5.216  43.117   1626
  Min Nonbonded Distance : 2.329

Molprobity Statistics.
  All-atom Clashscore : 7.49
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.49 %
    Favored  : 97.51 %
  Rotamer:
    Outliers :  1.48 %
    Allowed  : 19.72 %
    Favored  : 78.80 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  2.03 (0.25), residues: 1244
  helix:  2.66 (0.19), residues: 760
  sheet: -1.54 (0.47), residues: 116
  loop : -0.50 (0.36), residues: 368

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG C 284 
 TYR   0.017   0.001   TYR C 106 
 PHE   0.011   0.001   PHE A 279 
 TRP   0.005   0.001   TRP C 161 
 HIS   0.008   0.001   HIS B 185 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00237 /  0.11 (10472)
  covalent geometry    : angle       0.51559 /  0.25 (14240)
  hydrogen bonds       : bond        0.03320 /  2.31 (  605)
  hydrogen bonds       : angle       4.04321 /  2.93 ( 1809)
  Misc. bond           : bond        0.00256 /  0.13 (    1)

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

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

  2488 Ramachandran restraints generated.
    1244 Oldfield, 0 Emsley, 1244 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2488 Ramachandran restraints generated.
    1244 Oldfield, 0 Emsley, 1244 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  219 residues out of total 1080 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 203
  time to evaluate  : 0.406 
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: symmetry clash
REVERT: A   25 LEU cc_start: 0.9364 (tt) cc_final: 0.8770 (tt)
REVERT: A   29 CYS cc_start: 0.9113 (m) cc_final: 0.8765 (m)
REVERT: A  143 GLU cc_start: 0.8528 (mp0) cc_final: 0.8284 (mp0)
REVERT: B  271 MET cc_start: 0.9308 (ttm) cc_final: 0.9053 (ttm)
REVERT: C  143 GLU cc_start: 0.8479 (mp0) cc_final: 0.8260 (mp0)
REVERT: C  223 ASP cc_start: 0.8252 (t70) cc_final: 0.7906 (t70)
REVERT: D   69 GLU cc_start: 0.9153 (mm-30) cc_final: 0.8857 (mm-30)
  outliers start: 16
  outliers final: 14
  residues processed: 209
  average time/residue: 0.1655
  time to fit residues: 52.0509
Evaluate side-chains
  205 residues out of total 1080 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 191
  time to evaluate  : 0.441 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   64 CYS
Chi-restraints excluded: chain A residue  206 CYS
Chi-restraints excluded: chain A residue  224 LYS
Chi-restraints excluded: chain A residue  332 HIS
Chi-restraints excluded: chain B residue   66 LEU
Chi-restraints excluded: chain C residue   64 CYS
Chi-restraints excluded: chain C residue  206 CYS
Chi-restraints excluded: chain C residue  332 HIS
Chi-restraints excluded: chain D residue   49 LEU
Chi-restraints excluded: chain D residue   66 LEU
Chi-restraints excluded: chain D residue   99 LEU
Chi-restraints excluded: chain D residue  205 ASP
Chi-restraints excluded: chain D residue  261 TYR
Chi-restraints excluded: chain D residue  263 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 124
   random chunks:
   chunk 6 optimal weight:    5.9990
   chunk 96 optimal weight:    0.0970
   chunk 109 optimal weight:    0.0770
   chunk 62 optimal weight:    8.9990
   chunk 36 optimal weight:    5.9990
   chunk 79 optimal weight:   10.0000
   chunk 40 optimal weight:    2.9990
   chunk 26 optimal weight:    8.9990
   chunk 53 optimal weight:    6.9990
   chunk 43 optimal weight:    0.8980
   chunk 9 optimal weight:    4.9990
   overall best weight:    1.8140

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

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3213 r_free = 0.3213 target = 0.091885 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.2858 r_free = 0.2858 target = 0.072856 restraints weight = 71163.337|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.2934 r_free = 0.2934 target = 0.076749 restraints weight = 28818.444|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 41)----------------|
| r_work = 0.2985 r_free = 0.2985 target = 0.079353 restraints weight = 16698.523|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 35)----------------|
| r_work = 0.3017 r_free = 0.3017 target = 0.081021 restraints weight = 11645.219|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 37)----------------|
| r_work = 0.3040 r_free = 0.3040 target = 0.082234 restraints weight = 9165.789|
|-----------------------------------------------------------------------------|
r_work (final): 0.3039
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7883
moved from start:          0.3094

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030  10473  Z= 0.122
  Angle     :  0.529   6.462  14240  Z= 0.260
  Chirality :  0.034   0.142   1586
  Planarity :  0.004   0.042   1796
  Dihedral  :  5.265  44.117   1626
  Min Nonbonded Distance : 2.327

Molprobity Statistics.
  All-atom Clashscore : 7.29
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.65 %
    Favored  : 97.35 %
  Rotamer:
    Outliers :  1.20 %
    Allowed  : 20.28 %
    Favored  : 78.52 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  2.04 (0.26), residues: 1244
  helix:  2.66 (0.19), residues: 760
  sheet: -1.55 (0.47), residues: 116
  loop : -0.48 (0.36), residues: 368

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B 238 
 TYR   0.017   0.001   TYR C 106 
 PHE   0.013   0.001   PHE A 279 
 TRP   0.035   0.001   TRP B 119 
 HIS   0.006   0.001   HIS B   3 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00268 /  0.12 (10472)
  covalent geometry    : angle       0.52936 /  0.26 (14240)
  hydrogen bonds       : bond        0.03307 /  2.30 (  605)
  hydrogen bonds       : angle       4.03490 /  2.93 ( 1809)
  Misc. bond           : bond        0.00268 /  0.14 (    1)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2677.83 seconds
wall clock time: 46 minutes 24.11 seconds (2784.11 seconds total)