Starting phenix.real_space_refine
on Wed Mar  4 06:41:11 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/6v6d_21071/03_2026/6v6d_21071.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/6v6d_21071/03_2026/6v6d_21071.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.77
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/6v6d_21071/03_2026/6v6d_21071.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/6v6d_21071/03_2026/6v6d_21071.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/6v6d_21071/03_2026/6v6d_21071.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/6v6d_21071/03_2026/6v6d_21071.map"
  }
  resolution = 3.77
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.004
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 4
    Type Number    sf(0)   Gaussians
     S      63      5.16       5
     C    7924      2.51       5
     N    1778      2.21       5
     O    1974      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 49 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 11739
  Number of models: 1
  Model: ""
    Number of chains: 1
    Chain: "A"
      Number of atoms: 1677
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 209, 1677
          Classifications: {'peptide': 209}
          Link IDs: {'PTRANS': 10, 'TRANS': 198}
          Chain breaks: 3
  Restraints were copied for chains:
    B, C, D, E, F, G
  Time building chain proxies: 1.58, per 1000 atoms: 0.13
  Number of scatterers: 11739
  At special positions: 0
  Unit cell: (110, 110, 94.6, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     S      63     16.00
     O    1974      8.00
     N    1778      7.00
     C    7924      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=14, symmetry=0
    Simple disulfide: pdb=" SG  CYS A  66 " - pdb=" SG  CYS A 265 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A  84 " - pdb=" SG  CYS A 246 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B  66 " - pdb=" SG  CYS B 265 " distance=2.03
    Simple disulfide: pdb=" SG  CYS C  66 " - pdb=" SG  CYS C 265 " distance=2.03
    Simple disulfide: pdb=" SG  CYS D  66 " - pdb=" SG  CYS D 265 " distance=2.03
    Simple disulfide: pdb=" SG  CYS E  66 " - pdb=" SG  CYS E 265 " distance=2.03
    Simple disulfide: pdb=" SG  CYS F  66 " - pdb=" SG  CYS F 265 " distance=2.03
    Simple disulfide: pdb=" SG  CYS G  66 " - pdb=" SG  CYS G 265 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B  84 " - pdb=" SG  CYS B 246 " distance=2.03
    Simple disulfide: pdb=" SG  CYS C  84 " - pdb=" SG  CYS C 246 " distance=2.03
    Simple disulfide: pdb=" SG  CYS D  84 " - pdb=" SG  CYS D 246 " distance=2.03
    Simple disulfide: pdb=" SG  CYS E  84 " - pdb=" SG  CYS E 246 " distance=2.03
    Simple disulfide: pdb=" SG  CYS F  84 " - pdb=" SG  CYS F 246 " distance=2.03
    Simple disulfide: pdb=" SG  CYS G  84 " - pdb=" SG  CYS G 246 " distance=2.03

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 0.96
  Conformation dependent library (CDL) restraints added in 532.7 milliseconds
  

  2814 Ramachandran restraints generated.
    1407 Oldfield, 0 Emsley, 1407 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2856

  Finding SS restraints...
    Secondary structure from input PDB file:
      56 helices and 7 sheets defined
      71.8% alpha, 4.3% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.32
  Creating SS restraints...
    Processing helix  chain 'A' and resid 32 through 54
      Proline residue:  A  46  - end of helix
      removed outlier: 3.800A  pdb=" N   PHE A  54 " --> pdb=" O   ILE A  50 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 73 through 86
    Processing helix  chain 'A' and resid 103 through 108
    Processing helix  chain 'A' and resid 108 through 139
      Proline residue:  A 123  - end of helix
      removed outlier: 3.754A  pdb=" N   PHE A 129 " --> pdb=" O   LEU A 125 " (cutoff:3.500A)
      removed outlier: 3.563A  pdb=" N   ALA A 130 " --> pdb=" O   PHE A 126 " (cutoff:3.500A)
      Proline residue:  A 133  - end of helix
    Processing helix  chain 'A' and resid 208 through 237
      removed outlier: 3.574A  pdb=" N   LEU A 237 " --> pdb=" O   TYR A 233 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 250 through 255
      removed outlier: 4.458A  pdb=" N   ASN A 255 " --> pdb=" O   ILE A 252 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 269 through 296
      removed outlier: 3.647A  pdb=" N   LEU A 286 " --> pdb=" O   VAL A 282 " (cutoff:3.500A)
      removed outlier: 3.690A  pdb=" N   ALA A 288 " --> pdb=" O   TYR A 284 " (cutoff:3.500A)
      Proline residue:  A 289  - end of helix
      removed outlier: 3.716A  pdb=" N   PHE A 296 " --> pdb=" O   VAL A 292 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 326 through 336
      removed outlier: 3.725A  pdb=" N   LEU A 330 " --> pdb=" O   ASN A 326 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 32 through 54
      Proline residue:  B  46  - end of helix
      removed outlier: 3.800A  pdb=" N   PHE B  54 " --> pdb=" O   ILE B  50 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 73 through 86
    Processing helix  chain 'B' and resid 103 through 108
    Processing helix  chain 'B' and resid 108 through 139
      Proline residue:  B 123  - end of helix
      removed outlier: 3.754A  pdb=" N   PHE B 129 " --> pdb=" O   LEU B 125 " (cutoff:3.500A)
      removed outlier: 3.563A  pdb=" N   ALA B 130 " --> pdb=" O   PHE B 126 " (cutoff:3.500A)
      Proline residue:  B 133  - end of helix
    Processing helix  chain 'B' and resid 208 through 237
      removed outlier: 3.575A  pdb=" N   LEU B 237 " --> pdb=" O   TYR B 233 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 250 through 255
      removed outlier: 4.459A  pdb=" N   ASN B 255 " --> pdb=" O   ILE B 252 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 269 through 296
      removed outlier: 3.647A  pdb=" N   LEU B 286 " --> pdb=" O   VAL B 282 " (cutoff:3.500A)
      removed outlier: 3.690A  pdb=" N   ALA B 288 " --> pdb=" O   TYR B 284 " (cutoff:3.500A)
      Proline residue:  B 289  - end of helix
      removed outlier: 3.716A  pdb=" N   PHE B 296 " --> pdb=" O   VAL B 292 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 326 through 336
      removed outlier: 3.725A  pdb=" N   LEU B 330 " --> pdb=" O   ASN B 326 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 32 through 54
      Proline residue:  C  46  - end of helix
      removed outlier: 3.799A  pdb=" N   PHE C  54 " --> pdb=" O   ILE C  50 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 73 through 86
    Processing helix  chain 'C' and resid 103 through 108
    Processing helix  chain 'C' and resid 108 through 139
      Proline residue:  C 123  - end of helix
      removed outlier: 3.754A  pdb=" N   PHE C 129 " --> pdb=" O   LEU C 125 " (cutoff:3.500A)
      removed outlier: 3.563A  pdb=" N   ALA C 130 " --> pdb=" O   PHE C 126 " (cutoff:3.500A)
      Proline residue:  C 133  - end of helix
    Processing helix  chain 'C' and resid 208 through 237
      removed outlier: 3.574A  pdb=" N   LEU C 237 " --> pdb=" O   TYR C 233 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 250 through 255
      removed outlier: 4.457A  pdb=" N   ASN C 255 " --> pdb=" O   ILE C 252 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 269 through 296
      removed outlier: 3.646A  pdb=" N   LEU C 286 " --> pdb=" O   VAL C 282 " (cutoff:3.500A)
      removed outlier: 3.690A  pdb=" N   ALA C 288 " --> pdb=" O   TYR C 284 " (cutoff:3.500A)
      Proline residue:  C 289  - end of helix
      removed outlier: 3.716A  pdb=" N   PHE C 296 " --> pdb=" O   VAL C 292 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 326 through 336
      removed outlier: 3.725A  pdb=" N   LEU C 330 " --> pdb=" O   ASN C 326 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 32 through 54
      Proline residue:  D  46  - end of helix
      removed outlier: 3.800A  pdb=" N   PHE D  54 " --> pdb=" O   ILE D  50 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 73 through 86
    Processing helix  chain 'D' and resid 103 through 108
    Processing helix  chain 'D' and resid 108 through 139
      Proline residue:  D 123  - end of helix
      removed outlier: 3.754A  pdb=" N   PHE D 129 " --> pdb=" O   LEU D 125 " (cutoff:3.500A)
      removed outlier: 3.563A  pdb=" N   ALA D 130 " --> pdb=" O   PHE D 126 " (cutoff:3.500A)
      Proline residue:  D 133  - end of helix
    Processing helix  chain 'D' and resid 208 through 237
      removed outlier: 3.575A  pdb=" N   LEU D 237 " --> pdb=" O   TYR D 233 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 250 through 255
      removed outlier: 4.458A  pdb=" N   ASN D 255 " --> pdb=" O   ILE D 252 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 269 through 296
      removed outlier: 3.647A  pdb=" N   LEU D 286 " --> pdb=" O   VAL D 282 " (cutoff:3.500A)
      removed outlier: 3.690A  pdb=" N   ALA D 288 " --> pdb=" O   TYR D 284 " (cutoff:3.500A)
      Proline residue:  D 289  - end of helix
      removed outlier: 3.716A  pdb=" N   PHE D 296 " --> pdb=" O   VAL D 292 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 326 through 336
      removed outlier: 3.725A  pdb=" N   LEU D 330 " --> pdb=" O   ASN D 326 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 32 through 54
      Proline residue:  E  46  - end of helix
      removed outlier: 3.800A  pdb=" N   PHE E  54 " --> pdb=" O   ILE E  50 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 73 through 86
    Processing helix  chain 'E' and resid 103 through 108
    Processing helix  chain 'E' and resid 108 through 139
      Proline residue:  E 123  - end of helix
      removed outlier: 3.754A  pdb=" N   PHE E 129 " --> pdb=" O   LEU E 125 " (cutoff:3.500A)
      removed outlier: 3.563A  pdb=" N   ALA E 130 " --> pdb=" O   PHE E 126 " (cutoff:3.500A)
      Proline residue:  E 133  - end of helix
    Processing helix  chain 'E' and resid 208 through 237
      removed outlier: 3.574A  pdb=" N   LEU E 237 " --> pdb=" O   TYR E 233 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 250 through 255
      removed outlier: 4.458A  pdb=" N   ASN E 255 " --> pdb=" O   ILE E 252 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 269 through 296
      removed outlier: 3.647A  pdb=" N   LEU E 286 " --> pdb=" O   VAL E 282 " (cutoff:3.500A)
      removed outlier: 3.691A  pdb=" N   ALA E 288 " --> pdb=" O   TYR E 284 " (cutoff:3.500A)
      Proline residue:  E 289  - end of helix
      removed outlier: 3.717A  pdb=" N   PHE E 296 " --> pdb=" O   VAL E 292 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 326 through 336
      removed outlier: 3.725A  pdb=" N   LEU E 330 " --> pdb=" O   ASN E 326 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 32 through 54
      Proline residue:  F  46  - end of helix
      removed outlier: 3.800A  pdb=" N   PHE F  54 " --> pdb=" O   ILE F  50 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 73 through 86
    Processing helix  chain 'F' and resid 103 through 108
    Processing helix  chain 'F' and resid 108 through 139
      Proline residue:  F 123  - end of helix
      removed outlier: 3.754A  pdb=" N   PHE F 129 " --> pdb=" O   LEU F 125 " (cutoff:3.500A)
      removed outlier: 3.563A  pdb=" N   ALA F 130 " --> pdb=" O   PHE F 126 " (cutoff:3.500A)
      Proline residue:  F 133  - end of helix
    Processing helix  chain 'F' and resid 208 through 237
      removed outlier: 3.574A  pdb=" N   LEU F 237 " --> pdb=" O   TYR F 233 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 250 through 255
      removed outlier: 4.459A  pdb=" N   ASN F 255 " --> pdb=" O   ILE F 252 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 269 through 296
      removed outlier: 3.647A  pdb=" N   LEU F 286 " --> pdb=" O   VAL F 282 " (cutoff:3.500A)
      removed outlier: 3.691A  pdb=" N   ALA F 288 " --> pdb=" O   TYR F 284 " (cutoff:3.500A)
      Proline residue:  F 289  - end of helix
      removed outlier: 3.716A  pdb=" N   PHE F 296 " --> pdb=" O   VAL F 292 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 326 through 336
      removed outlier: 3.726A  pdb=" N   LEU F 330 " --> pdb=" O   ASN F 326 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 32 through 54
      Proline residue:  G  46  - end of helix
      removed outlier: 3.800A  pdb=" N   PHE G  54 " --> pdb=" O   ILE G  50 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 73 through 86
    Processing helix  chain 'G' and resid 103 through 108
    Processing helix  chain 'G' and resid 108 through 139
      Proline residue:  G 123  - end of helix
      removed outlier: 3.754A  pdb=" N   PHE G 129 " --> pdb=" O   LEU G 125 " (cutoff:3.500A)
      removed outlier: 3.563A  pdb=" N   ALA G 130 " --> pdb=" O   PHE G 126 " (cutoff:3.500A)
      Proline residue:  G 133  - end of helix
    Processing helix  chain 'G' and resid 208 through 237
      removed outlier: 3.575A  pdb=" N   LEU G 237 " --> pdb=" O   TYR G 233 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 250 through 255
      removed outlier: 4.458A  pdb=" N   ASN G 255 " --> pdb=" O   ILE G 252 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 269 through 296
      removed outlier: 3.647A  pdb=" N   LEU G 286 " --> pdb=" O   VAL G 282 " (cutoff:3.500A)
      removed outlier: 3.690A  pdb=" N   ALA G 288 " --> pdb=" O   TYR G 284 " (cutoff:3.500A)
      Proline residue:  G 289  - end of helix
      removed outlier: 3.717A  pdb=" N   PHE G 296 " --> pdb=" O   VAL G 292 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 326 through 336
      removed outlier: 3.725A  pdb=" N   LEU G 330 " --> pdb=" O   ASN G 326 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 64 through 66
    Processing sheet with id=AA2, first strand: chain 'B' and resid 64 through 66
    Processing sheet with id=AA3, first strand: chain 'C' and resid 64 through 66
    Processing sheet with id=AA4, first strand: chain 'D' and resid 64 through 66
    Processing sheet with id=AA5, first strand: chain 'E' and resid 64 through 66
    Processing sheet with id=AA6, first strand: chain 'F' and resid 64 through 66
    Processing sheet with id=AA7, first strand: chain 'G' and resid 64 through 66

    728 hydrogen bonds defined for protein.
    2121 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 1.55

  Time building geometry restraints manager: 1.33 seconds

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

  Histogram of bond lengths:
        1.23 -     1.34: 3374
        1.34 -     1.46: 2809
        1.46 -     1.58: 5787
        1.58 -     1.69: 0
        1.69 -     1.81: 70
  Bond restraints: 12040
  Sorted by residual:
  bond pdb=" N   ILE E  41 "
       pdb=" CA  ILE E  41 "
    ideal  model  delta    sigma   weight residual
    1.459  1.496 -0.037 1.21e-02 6.83e+03 9.11e+00
  bond pdb=" N   ILE B  41 "
       pdb=" CA  ILE B  41 "
    ideal  model  delta    sigma   weight residual
    1.459  1.496 -0.036 1.21e-02 6.83e+03 9.03e+00
  bond pdb=" N   ILE F  41 "
       pdb=" CA  ILE F  41 "
    ideal  model  delta    sigma   weight residual
    1.459  1.496 -0.036 1.21e-02 6.83e+03 9.03e+00
  bond pdb=" N   ILE D  41 "
       pdb=" CA  ILE D  41 "
    ideal  model  delta    sigma   weight residual
    1.459  1.495 -0.036 1.21e-02 6.83e+03 8.88e+00
  bond pdb=" N   ILE G  41 "
       pdb=" CA  ILE G  41 "
    ideal  model  delta    sigma   weight residual
    1.459  1.495 -0.036 1.21e-02 6.83e+03 8.85e+00
  ... (remaining 12035 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.43: 15923
        2.43 -     4.85: 391
        4.85 -     7.28: 66
        7.28 -     9.70: 35
        9.70 -    12.13: 7
  Bond angle restraints: 16422
  Sorted by residual:
  angle pdb=" N   GLY C  61 "
        pdb=" CA  GLY C  61 "
        pdb=" C   GLY C  61 "
      ideal   model   delta    sigma   weight residual
     112.73  124.86  -12.13 1.20e+00 6.94e-01 1.02e+02
  angle pdb=" N   GLY G  61 "
        pdb=" CA  GLY G  61 "
        pdb=" C   GLY G  61 "
      ideal   model   delta    sigma   weight residual
     112.73  124.86  -12.13 1.20e+00 6.94e-01 1.02e+02
  angle pdb=" N   GLY E  61 "
        pdb=" CA  GLY E  61 "
        pdb=" C   GLY E  61 "
      ideal   model   delta    sigma   weight residual
     112.73  124.85  -12.12 1.20e+00 6.94e-01 1.02e+02
  angle pdb=" N   GLY F  61 "
        pdb=" CA  GLY F  61 "
        pdb=" C   GLY F  61 "
      ideal   model   delta    sigma   weight residual
     112.73  124.83  -12.10 1.20e+00 6.94e-01 1.02e+02
  angle pdb=" N   GLY D  61 "
        pdb=" CA  GLY D  61 "
        pdb=" C   GLY D  61 "
      ideal   model   delta    sigma   weight residual
     112.73  124.83  -12.10 1.20e+00 6.94e-01 1.02e+02
  ... (remaining 16417 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.09: 6405
       17.09 -    34.18: 581
       34.18 -    51.27: 77
       51.27 -    68.36: 7
       68.36 -    85.45: 7
  Dihedral angle restraints: 7077
    sinusoidal: 2709
      harmonic: 4368
  Sorted by residual:
  dihedral pdb=" C   ASP B  35 "
           pdb=" N   ASP B  35 "
           pdb=" CA  ASP B  35 "
           pdb=" CB  ASP B  35 "
      ideal   model   delta  harmonic     sigma   weight residual
    -122.60 -131.85    9.25     0      2.50e+00 1.60e-01 1.37e+01
  dihedral pdb=" C   ASP F  35 "
           pdb=" N   ASP F  35 "
           pdb=" CA  ASP F  35 "
           pdb=" CB  ASP F  35 "
      ideal   model   delta  harmonic     sigma   weight residual
    -122.60 -131.84    9.24     0      2.50e+00 1.60e-01 1.37e+01
  dihedral pdb=" C   ASP A  35 "
           pdb=" N   ASP A  35 "
           pdb=" CA  ASP A  35 "
           pdb=" CB  ASP A  35 "
      ideal   model   delta  harmonic     sigma   weight residual
    -122.60 -131.82    9.22     0      2.50e+00 1.60e-01 1.36e+01
  ... (remaining 7074 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.057: 1559
       0.057 -    0.114: 308
       0.114 -    0.171: 107
       0.171 -    0.229: 7
       0.229 -    0.286: 14
  Chirality restraints: 1995
  Sorted by residual:
  chirality pdb=" CA  LEU D  32 "
            pdb=" N   LEU D  32 "
            pdb=" C   LEU D  32 "
            pdb=" CB  LEU D  32 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.80   -0.29 2.00e-01 2.50e+01 2.04e+00
  chirality pdb=" CA  LEU C  32 "
            pdb=" N   LEU C  32 "
            pdb=" C   LEU C  32 "
            pdb=" CB  LEU C  32 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.79   -0.28 2.00e-01 2.50e+01 2.02e+00
  chirality pdb=" CA  LEU B  32 "
            pdb=" N   LEU B  32 "
            pdb=" C   LEU B  32 "
            pdb=" CB  LEU B  32 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.79   -0.28 2.00e-01 2.50e+01 2.01e+00
  ... (remaining 1992 not shown)

  Planarity restraints: 1953
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ALA E 132 "   -0.041 5.00e-02 4.00e+02   6.14e-02 6.02e+00
        pdb=" N   PRO E 133 "    0.106 5.00e-02 4.00e+02
        pdb=" CA  PRO E 133 "   -0.031 5.00e-02 4.00e+02
        pdb=" CD  PRO E 133 "   -0.035 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ALA G 132 "    0.041 5.00e-02 4.00e+02   6.13e-02 6.01e+00
        pdb=" N   PRO G 133 "   -0.106 5.00e-02 4.00e+02
        pdb=" CA  PRO G 133 "    0.031 5.00e-02 4.00e+02
        pdb=" CD  PRO G 133 "    0.035 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ALA F 132 "   -0.041 5.00e-02 4.00e+02   6.13e-02 6.01e+00
        pdb=" N   PRO F 133 "    0.106 5.00e-02 4.00e+02
        pdb=" CA  PRO F 133 "   -0.031 5.00e-02 4.00e+02
        pdb=" CD  PRO F 133 "   -0.035 5.00e-02 4.00e+02
  ... (remaining 1950 not shown)

  Histogram of nonbonded interaction distances:
        2.28 -     2.80: 3326
        2.80 -     3.33: 11144
        3.33 -     3.85: 18671
        3.85 -     4.38: 20454
        4.38 -     4.90: 36759
  Nonbonded interactions: 90354
  Sorted by model distance:
  nonbonded pdb=" OH  TYR E 111 "
            pdb=" O   LEU F  52 "
     model   vdw
     2.280 3.040
  nonbonded pdb=" OH  TYR D 111 "
            pdb=" O   LEU E  52 "
     model   vdw
     2.307 3.040
  nonbonded pdb=" OH  TYR C 111 "
            pdb=" O   LEU D  52 "
     model   vdw
     2.323 3.040
  nonbonded pdb=" OH  TYR F 111 "
            pdb=" O   LEU G  52 "
     model   vdw
     2.325 3.040
  nonbonded pdb=" O   SER D 241 "
            pdb=" OG  SER D 241 "
     model   vdw
     2.350 3.040
  ... (remaining 90349 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: 0.03
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'B'
  selection = chain 'C'
  selection = chain 'D'
  selection = chain 'E'
  selection = chain 'F'
  selection = chain 'G'
}

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:             1.280
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.170
  Check model and map are aligned:         0.030
  Set scattering table:                    0.030
  Process input model:                     9.960
  Find NCS groups from input model:        0.100
  Set up NCS constraints:                  0.010
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.230
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   12.810
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8391
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      :  0.005   0.053  12054  Z= 0.307
  Angle     :  0.948  12.128  16450  Z= 0.571
  Chirality :  0.058   0.286   1995
  Planarity :  0.007   0.061   1953
  Dihedral  : 13.309  85.452   4179
  Min Nonbonded Distance : 2.280

Molprobity Statistics.
  All-atom Clashscore : 6.03
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.99 %
    Favored  : 98.01 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  6.20 %
    Favored  : 93.80 %
  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: -2.17 (0.20), residues: 1407
  helix: -0.43 (0.15), residues: 1001
  sheet: -2.75 (0.55), residues: 84
  loop : -4.03 (0.18), residues: 322

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG C 254 
 TYR   0.009   0.001   TYR E 230 
 PHE   0.010   0.001   PHE G 129 
 TRP   0.011   0.001   TRP B  74 
 HIS   0.001   0.000   HIS E 134 

Details of bonding type rmsd
  covalent geometry    : bond        0.00548 (12040)
  covalent geometry    : angle       0.94751 (16422)
  SS BOND              : bond        0.00104 (   14)
  SS BOND              : angle       1.11443 (   28)
  hydrogen bonds       : bond        0.14117 (  728)
  hydrogen bonds       : angle       5.25097 ( 2121)

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

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

  2814 Ramachandran restraints generated.
    1407 Oldfield, 0 Emsley, 1407 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2814 Ramachandran restraints generated.
    1407 Oldfield, 0 Emsley, 1407 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  347 residues out of total 1323 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 347
  time to evaluate  : 0.420 
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: A   36 LYS cc_start: 0.8764 (tptt) cc_final: 0.8538 (tttt)
REVERT: A   75 ARG cc_start: 0.8539 (mmm160) cc_final: 0.8292 (mmt180)
REVERT: A  212 LYS cc_start: 0.7283 (mttp) cc_final: 0.7010 (mttp)
REVERT: A  326 ASN cc_start: 0.6408 (p0) cc_final: 0.5651 (p0)
REVERT: B   36 LYS cc_start: 0.8908 (tptt) cc_final: 0.8494 (tttt)
REVERT: B  293 TYR cc_start: 0.9148 (t80) cc_final: 0.8889 (t80)
REVERT: B  326 ASN cc_start: 0.6799 (p0) cc_final: 0.5894 (p0)
REVERT: B  333 LEU cc_start: 0.8827 (pp) cc_final: 0.8497 (pp)
REVERT: C   36 LYS cc_start: 0.8986 (tptt) cc_final: 0.8586 (tttt)
REVERT: C  126 PHE cc_start: 0.8798 (t80) cc_final: 0.8498 (t80)
REVERT: C  275 LEU cc_start: 0.8998 (tt) cc_final: 0.8666 (tp)
REVERT: C  326 ASN cc_start: 0.6431 (p0) cc_final: 0.5564 (p0)
REVERT: C  327 ASP cc_start: 0.8750 (m-30) cc_final: 0.8495 (m-30)
REVERT: C  333 LEU cc_start: 0.8664 (pp) cc_final: 0.8384 (pp)
REVERT: D   36 LYS cc_start: 0.8900 (tptt) cc_final: 0.8631 (tttt)
REVERT: D   75 ARG cc_start: 0.8692 (mmm160) cc_final: 0.8270 (mmt180)
REVERT: D  326 ASN cc_start: 0.6895 (p0) cc_final: 0.6027 (p0)
REVERT: D  331 TYR cc_start: 0.8608 (m-80) cc_final: 0.8374 (m-80)
REVERT: D  333 LEU cc_start: 0.8780 (pp) cc_final: 0.8361 (pp)
REVERT: E   36 LYS cc_start: 0.8892 (tptt) cc_final: 0.8565 (tttt)
REVERT: E  327 ASP cc_start: 0.8831 (m-30) cc_final: 0.8505 (m-30)
REVERT: F   36 LYS cc_start: 0.9053 (tptt) cc_final: 0.8542 (tttt)
REVERT: F   75 ARG cc_start: 0.8616 (mmm160) cc_final: 0.8296 (mmt180)
REVERT: F  208 ASN cc_start: 0.8407 (p0) cc_final: 0.8170 (p0)
REVERT: F  212 LYS cc_start: 0.7540 (mttp) cc_final: 0.7195 (mttt)
REVERT: F  230 TYR cc_start: 0.9330 (t80) cc_final: 0.9076 (t80)
REVERT: F  293 TYR cc_start: 0.9129 (t80) cc_final: 0.8675 (t80)
REVERT: G   29 ARG cc_start: 0.8049 (ttm110) cc_final: 0.7837 (mtm180)
REVERT: G   36 LYS cc_start: 0.8877 (tptt) cc_final: 0.8609 (tttt)
REVERT: G  212 LYS cc_start: 0.7452 (mttp) cc_final: 0.7080 (mttp)
REVERT: G  326 ASN cc_start: 0.6795 (p0) cc_final: 0.5933 (p0)
  outliers start: 0
  outliers final: 0
  residues processed: 347
  average time/residue: 0.1284
  time to fit residues: 60.1179
Evaluate side-chains
  251 residues out of total 1323 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 251
  time to evaluate  : 0.447 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 140
   random chunks:
   chunk 98 optimal weight:   10.0000
   chunk 107 optimal weight:    0.9980
   chunk 10 optimal weight:    5.9990
   chunk 66 optimal weight:    4.9990
   chunk 130 optimal weight:    2.9990
   chunk 124 optimal weight:    1.9990
   chunk 103 optimal weight:    2.9990
   chunk 77 optimal weight:    2.9990
   chunk 122 optimal weight:    1.9990
   chunk 91 optimal weight:    6.9990
   chunk 55 optimal weight:   10.0000
   overall best weight:    2.1988

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

Flipped N/Q/H residues before XYZ refinement:
A 106 HIS
A 332 ASN
B 106 HIS
B 332 ASN
C 106 HIS
D 106 HIS
D 332 ASN
E 106 HIS
** E 332 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
F 106 HIS
G 106 HIS
** G 332 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 10

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3272 r_free = 0.3272 target = 0.112033 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.2871 r_free = 0.2871 target = 0.085836 restraints weight = 20057.955|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.2906 r_free = 0.2906 target = 0.088163 restraints weight = 10889.864|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 47)----------------|
| r_work = 0.2930 r_free = 0.2930 target = 0.089613 restraints weight = 7742.333|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 26)----------------|
| r_work = 0.2939 r_free = 0.2939 target = 0.090225 restraints weight = 6420.080|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 31)----------------|
| r_work = 0.2946 r_free = 0.2946 target = 0.090694 restraints weight = 5891.278|
|-----------------------------------------------------------------------------|
r_work (final): 0.2943
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8457
moved from start:          0.2140

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.033  12054  Z= 0.194
  Angle     :  0.684   8.683  16450  Z= 0.342
  Chirality :  0.042   0.136   1995
  Planarity :  0.005   0.048   1953
  Dihedral  :  4.269  17.502   1554
  Min Nonbonded Distance : 2.520

Molprobity Statistics.
  All-atom Clashscore : 3.48
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.63 %
    Favored  : 97.37 %
  Rotamer:
    Outliers :  2.12 %
    Allowed  : 15.95 %
    Favored  : 81.93 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.33 (0.22), residues: 1407
  helix:  0.90 (0.16), residues: 1008
  sheet: -2.42 (0.54), residues: 84
  loop : -3.24 (0.24), residues: 315

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG B  29 
 TYR   0.019   0.002   TYR E 213 
 PHE   0.018   0.001   PHE A 299 
 TRP   0.012   0.001   TRP G  74 
 HIS   0.002   0.001   HIS E 106 

Details of bonding type rmsd
  covalent geometry    : bond        0.00460 (12040)
  covalent geometry    : angle       0.68236 (16422)
  SS BOND              : bond        0.00170 (   14)
  SS BOND              : angle       1.21478 (   28)
  hydrogen bonds       : bond        0.03856 (  728)
  hydrogen bonds       : angle       4.15388 ( 2121)

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

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

  2814 Ramachandran restraints generated.
    1407 Oldfield, 0 Emsley, 1407 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2814 Ramachandran restraints generated.
    1407 Oldfield, 0 Emsley, 1407 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  331 residues out of total 1323 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 303
  time to evaluate  : 0.434 
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: A   36 LYS cc_start: 0.9042 (tptt) cc_final: 0.8623 (tttt)
REVERT: A   75 ARG cc_start: 0.8595 (mmm160) cc_final: 0.8377 (mmt180)
REVERT: A  326 ASN cc_start: 0.6472 (p0) cc_final: 0.5716 (p0)
REVERT: B   36 LYS cc_start: 0.9061 (tptt) cc_final: 0.8455 (tttt)
REVERT: B   63 GLN cc_start: 0.8044 (mt0) cc_final: 0.7741 (mp10)
REVERT: B  111 TYR cc_start: 0.8804 (m-10) cc_final: 0.8143 (m-10)
REVERT: B  326 ASN cc_start: 0.6812 (p0) cc_final: 0.6087 (p0)
REVERT: C   36 LYS cc_start: 0.9156 (tptt) cc_final: 0.8698 (tttt)
REVERT: C   75 ARG cc_start: 0.8673 (mmm160) cc_final: 0.8377 (mmt180)
REVERT: C  111 TYR cc_start: 0.8910 (m-10) cc_final: 0.8618 (m-10)
REVERT: C  212 LYS cc_start: 0.7948 (mttp) cc_final: 0.7483 (mttp)
REVERT: C  275 LEU cc_start: 0.9129 (tt) cc_final: 0.8720 (tp)
REVERT: C  326 ASN cc_start: 0.6533 (p0) cc_final: 0.5715 (p0)
REVERT: C  327 ASP cc_start: 0.8685 (m-30) cc_final: 0.8467 (m-30)
REVERT: D   36 LYS cc_start: 0.9120 (tptt) cc_final: 0.8651 (tttt)
REVERT: D   75 ARG cc_start: 0.8645 (mmm160) cc_final: 0.8235 (mmt180)
REVERT: D   83 TYR cc_start: 0.8683 (t80) cc_final: 0.8200 (t80)
REVERT: D  212 LYS cc_start: 0.7833 (mttp) cc_final: 0.7462 (mttp)
REVERT: D  276 LEU cc_start: 0.9313 (mt) cc_final: 0.9056 (mt)
REVERT: D  326 ASN cc_start: 0.6902 (p0) cc_final: 0.6110 (p0)
REVERT: E   36 LYS cc_start: 0.9118 (tptt) cc_final: 0.8603 (tttm)
REVERT: E  326 ASN cc_start: 0.6714 (p0) cc_final: 0.6051 (p0)
REVERT: E  333 LEU cc_start: 0.8829 (pp) cc_final: 0.8472 (pp)
REVERT: F   36 LYS cc_start: 0.9164 (tptt) cc_final: 0.8587 (tttt)
REVERT: F   75 ARG cc_start: 0.8698 (mmm160) cc_final: 0.8341 (mmt180)
REVERT: F  276 LEU cc_start: 0.9314 (mt) cc_final: 0.9090 (mt)
REVERT: F  333 LEU cc_start: 0.8702 (pp) cc_final: 0.8490 (pp)
REVERT: G   36 LYS cc_start: 0.9119 (tptt) cc_final: 0.8677 (tttt)
REVERT: G   75 ARG cc_start: 0.8498 (mmm160) cc_final: 0.8218 (mmt180)
REVERT: G  326 ASN cc_start: 0.6796 (p0) cc_final: 0.6053 (p0)
REVERT: G  334 PHE cc_start: 0.8670 (OUTLIER) cc_final: 0.7683 (t80)
  outliers start: 28
  outliers final: 16
  residues processed: 317
  average time/residue: 0.1286
  time to fit residues: 54.7608
Evaluate side-chains
  259 residues out of total 1323 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 242
  time to evaluate  : 0.285 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  218 LEU
Chi-restraints excluded: chain A residue  228 CYS
Chi-restraints excluded: chain A residue  292 VAL
Chi-restraints excluded: chain B residue  218 LEU
Chi-restraints excluded: chain B residue  252 ILE
Chi-restraints excluded: chain B residue  292 VAL
Chi-restraints excluded: chain C residue  218 LEU
Chi-restraints excluded: chain C residue  228 CYS
Chi-restraints excluded: chain D residue  252 ILE
Chi-restraints excluded: chain D residue  297 VAL
Chi-restraints excluded: chain E residue  218 LEU
Chi-restraints excluded: chain E residue  297 VAL
Chi-restraints excluded: chain F residue  228 CYS
Chi-restraints excluded: chain F residue  259 VAL
Chi-restraints excluded: chain F residue  261 ASP
Chi-restraints excluded: chain F residue  297 VAL
Chi-restraints excluded: chain G residue  334 PHE
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 140
   random chunks:
   chunk 72 optimal weight:    2.9990
   chunk 48 optimal weight:    2.9990
   chunk 7 optimal weight:    0.6980
   chunk 46 optimal weight:    4.9990
   chunk 110 optimal weight:    4.9990
   chunk 56 optimal weight:    1.9990
   chunk 95 optimal weight:    6.9990
   chunk 14 optimal weight:    0.9990
   chunk 36 optimal weight:    3.9990
   chunk 101 optimal weight:    1.9990
   chunk 116 optimal weight:    0.9990
   overall best weight:    1.3388

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

Flipped N/Q/H residues before XYZ refinement:
G 332 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3282 r_free = 0.3282 target = 0.113106 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.2888 r_free = 0.2888 target = 0.087160 restraints weight = 19733.974|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.2923 r_free = 0.2923 target = 0.089522 restraints weight = 10521.110|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 41)----------------|
| r_work = 0.2946 r_free = 0.2946 target = 0.091032 restraints weight = 7432.552|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.2956 r_free = 0.2956 target = 0.091685 restraints weight = 6154.666|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 18)----------------|
| r_work = 0.2964 r_free = 0.2964 target = 0.092219 restraints weight = 5638.627|
|-----------------------------------------------------------------------------|
r_work (final): 0.2954
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8420
moved from start:          0.2439

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029  12054  Z= 0.139
  Angle     :  0.626   6.636  16450  Z= 0.308
  Chirality :  0.040   0.135   1995
  Planarity :  0.005   0.042   1953
  Dihedral  :  3.971  12.991   1554
  Min Nonbonded Distance : 2.482

Molprobity Statistics.
  All-atom Clashscore : 3.60
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.99 %
    Favored  : 97.01 %
  Rotamer:
    Outliers :  2.12 %
    Allowed  : 19.20 %
    Favored  : 78.68 %
  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:  0.34 (0.23), residues: 1407
  helix:  1.45 (0.17), residues: 1008
  sheet: -2.57 (0.50), residues: 84
  loop : -3.06 (0.26), residues: 315

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B  29 
 TYR   0.019   0.002   TYR E 230 
 PHE   0.016   0.001   PHE A 299 
 TRP   0.010   0.001   TRP G  74 
 HIS   0.001   0.000   HIS E 106 

Details of bonding type rmsd
  covalent geometry    : bond        0.00326 (12040)
  covalent geometry    : angle       0.62551 (16422)
  SS BOND              : bond        0.00074 (   14)
  SS BOND              : angle       0.75869 (   28)
  hydrogen bonds       : bond        0.03284 (  728)
  hydrogen bonds       : angle       3.97691 ( 2121)

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

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

  2814 Ramachandran restraints generated.
    1407 Oldfield, 0 Emsley, 1407 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2814 Ramachandran restraints generated.
    1407 Oldfield, 0 Emsley, 1407 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  316 residues out of total 1323 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 288
  time to evaluate  : 0.447 
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: A   36 LYS cc_start: 0.9037 (tptt) cc_final: 0.8610 (tttt)
REVERT: A   75 ARG cc_start: 0.8636 (mmm160) cc_final: 0.8401 (mmt180)
REVERT: A   76 GLN cc_start: 0.8276 (mt0) cc_final: 0.7921 (mt0)
REVERT: A  111 TYR cc_start: 0.8685 (m-10) cc_final: 0.8408 (m-10)
REVERT: A  326 ASN cc_start: 0.6543 (p0) cc_final: 0.5754 (p0)
REVERT: B   29 ARG cc_start: 0.7988 (ttm110) cc_final: 0.7569 (mtm110)
REVERT: B   36 LYS cc_start: 0.9054 (tptt) cc_final: 0.8553 (tttt)
REVERT: B  111 TYR cc_start: 0.8714 (m-10) cc_final: 0.7987 (m-10)
REVERT: B  212 LYS cc_start: 0.8130 (mttp) cc_final: 0.7586 (mttp)
REVERT: B  326 ASN cc_start: 0.6823 (p0) cc_final: 0.6070 (p0)
REVERT: B  333 LEU cc_start: 0.8637 (pp) cc_final: 0.8344 (pp)
REVERT: C   36 LYS cc_start: 0.9168 (tptt) cc_final: 0.8713 (tttt)
REVERT: C   75 ARG cc_start: 0.8626 (mmm160) cc_final: 0.8337 (mmt180)
REVERT: C  212 LYS cc_start: 0.8056 (mttp) cc_final: 0.7529 (mttp)
REVERT: C  275 LEU cc_start: 0.9045 (tt) cc_final: 0.8633 (tp)
REVERT: C  326 ASN cc_start: 0.6559 (p0) cc_final: 0.5896 (p0)
REVERT: D   36 LYS cc_start: 0.9136 (tptt) cc_final: 0.8663 (tttt)
REVERT: D   75 ARG cc_start: 0.8673 (mmm160) cc_final: 0.8245 (mmt180)
REVERT: D   83 TYR cc_start: 0.8662 (t80) cc_final: 0.8125 (t80)
REVERT: D  111 TYR cc_start: 0.8740 (m-10) cc_final: 0.7936 (m-10)
REVERT: D  212 LYS cc_start: 0.7884 (mttp) cc_final: 0.7428 (mttp)
REVERT: D  326 ASN cc_start: 0.6932 (p0) cc_final: 0.6130 (p0)
REVERT: E   36 LYS cc_start: 0.9142 (tptt) cc_final: 0.8635 (tttt)
REVERT: E  111 TYR cc_start: 0.8826 (m-10) cc_final: 0.7907 (m-10)
REVERT: E  276 LEU cc_start: 0.9269 (mt) cc_final: 0.9056 (mt)
REVERT: E  326 ASN cc_start: 0.6583 (p0) cc_final: 0.5929 (p0)
REVERT: F   36 LYS cc_start: 0.9167 (tptt) cc_final: 0.8566 (tttt)
REVERT: F   75 ARG cc_start: 0.8651 (mmm160) cc_final: 0.8269 (mmt180)
REVERT: G   36 LYS cc_start: 0.9112 (tptt) cc_final: 0.8672 (tttt)
REVERT: G   75 ARG cc_start: 0.8571 (mmm160) cc_final: 0.8271 (mmt180)
REVERT: G  111 TYR cc_start: 0.8769 (m-10) cc_final: 0.7997 (m-10)
REVERT: G  326 ASN cc_start: 0.6807 (p0) cc_final: 0.6021 (p0)
REVERT: G  334 PHE cc_start: 0.8631 (OUTLIER) cc_final: 0.7835 (t80)
  outliers start: 28
  outliers final: 20
  residues processed: 298
  average time/residue: 0.1255
  time to fit residues: 50.5836
Evaluate side-chains
  290 residues out of total 1323 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 269
  time to evaluate  : 0.340 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  218 LEU
Chi-restraints excluded: chain A residue  228 CYS
Chi-restraints excluded: chain A residue  292 VAL
Chi-restraints excluded: chain B residue  218 LEU
Chi-restraints excluded: chain B residue  252 ILE
Chi-restraints excluded: chain B residue  259 VAL
Chi-restraints excluded: chain B residue  292 VAL
Chi-restraints excluded: chain C residue  218 LEU
Chi-restraints excluded: chain C residue  228 CYS
Chi-restraints excluded: chain C residue  252 ILE
Chi-restraints excluded: chain C residue  297 VAL
Chi-restraints excluded: chain D residue  252 ILE
Chi-restraints excluded: chain D residue  297 VAL
Chi-restraints excluded: chain E residue  218 LEU
Chi-restraints excluded: chain E residue  297 VAL
Chi-restraints excluded: chain F residue  228 CYS
Chi-restraints excluded: chain F residue  259 VAL
Chi-restraints excluded: chain F residue  261 ASP
Chi-restraints excluded: chain F residue  297 VAL
Chi-restraints excluded: chain G residue  297 VAL
Chi-restraints excluded: chain G residue  334 PHE
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 140
   random chunks:
   chunk 25 optimal weight:    4.9990
   chunk 92 optimal weight:    0.9990
   chunk 28 optimal weight:    0.8980
   chunk 82 optimal weight:    2.9990
   chunk 93 optimal weight:    6.9990
   chunk 118 optimal weight:    3.9990
   chunk 110 optimal weight:    2.9990
   chunk 73 optimal weight:    6.9990
   chunk 44 optimal weight:    0.6980
   chunk 64 optimal weight:    0.6980
   chunk 10 optimal weight:    4.9990
   overall best weight:    1.2584

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3293 r_free = 0.3293 target = 0.113529 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.2900 r_free = 0.2900 target = 0.087526 restraints weight = 19890.411|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.2936 r_free = 0.2936 target = 0.089879 restraints weight = 10743.858|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.2955 r_free = 0.2955 target = 0.091205 restraints weight = 7623.998|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 42)----------------|
| r_work = 0.2971 r_free = 0.2971 target = 0.092136 restraints weight = 6397.340|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.2975 r_free = 0.2975 target = 0.092401 restraints weight = 5764.260|
|-----------------------------------------------------------------------------|
r_work (final): 0.2967
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8424
moved from start:          0.2690

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029  12054  Z= 0.133
  Angle     :  0.618   8.526  16450  Z= 0.299
  Chirality :  0.039   0.134   1995
  Planarity :  0.004   0.037   1953
  Dihedral  :  3.791  11.756   1554
  Min Nonbonded Distance : 2.502

Molprobity Statistics.
  All-atom Clashscore : 3.86
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.77 %
    Favored  : 97.23 %
  Rotamer:
    Outliers :  2.27 %
    Allowed  : 22.30 %
    Favored  : 75.43 %
  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:  0.69 (0.23), residues: 1407
  helix:  1.67 (0.17), residues: 1008
  sheet: -2.46 (0.49), residues: 84
  loop : -2.80 (0.28), residues: 315

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG F  29 
 TYR   0.019   0.001   TYR B 293 
 PHE   0.015   0.001   PHE C 126 
 TRP   0.009   0.001   TRP C  74 
 HIS   0.001   0.000   HIS E 106 

Details of bonding type rmsd
  covalent geometry    : bond        0.00313 (12040)
  covalent geometry    : angle       0.61817 (16422)
  SS BOND              : bond        0.00069 (   14)
  SS BOND              : angle       0.63262 (   28)
  hydrogen bonds       : bond        0.03115 (  728)
  hydrogen bonds       : angle       3.91931 ( 2121)

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

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

  2814 Ramachandran restraints generated.
    1407 Oldfield, 0 Emsley, 1407 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2814 Ramachandran restraints generated.
    1407 Oldfield, 0 Emsley, 1407 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  313 residues out of total 1323 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 283
  time to evaluate  : 0.437 
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   36 LYS cc_start: 0.9077 (tptt) cc_final: 0.8624 (tttt)
REVERT: A   75 ARG cc_start: 0.8646 (mmm160) cc_final: 0.8402 (mmt180)
REVERT: A   76 GLN cc_start: 0.8262 (mt0) cc_final: 0.7922 (mt0)
REVERT: A  111 TYR cc_start: 0.8681 (m-10) cc_final: 0.8283 (m-10)
REVERT: A  326 ASN cc_start: 0.6454 (p0) cc_final: 0.5683 (p0)
REVERT: B   29 ARG cc_start: 0.8058 (ttm110) cc_final: 0.7676 (mtm110)
REVERT: B   36 LYS cc_start: 0.9048 (tptt) cc_final: 0.8546 (tttt)
REVERT: B   58 ILE cc_start: 0.8893 (tp) cc_final: 0.8662 (tp)
REVERT: B   75 ARG cc_start: 0.8694 (mmm160) cc_final: 0.8421 (mmt180)
REVERT: B  111 TYR cc_start: 0.8750 (m-10) cc_final: 0.8025 (m-10)
REVERT: B  212 LYS cc_start: 0.8192 (mttp) cc_final: 0.7919 (mttp)
REVERT: B  213 TYR cc_start: 0.8939 (t80) cc_final: 0.8717 (t80)
REVERT: B  326 ASN cc_start: 0.6852 (p0) cc_final: 0.6157 (p0)
REVERT: C   36 LYS cc_start: 0.9126 (tptt) cc_final: 0.8748 (tttt)
REVERT: C   75 ARG cc_start: 0.8618 (mmm160) cc_final: 0.8344 (mmt180)
REVERT: C  111 TYR cc_start: 0.8774 (m-10) cc_final: 0.8230 (m-10)
REVERT: C  212 LYS cc_start: 0.8082 (mttp) cc_final: 0.7520 (mttp)
REVERT: C  243 GLU cc_start: 0.8443 (pt0) cc_final: 0.8201 (pt0)
REVERT: C  275 LEU cc_start: 0.9014 (tt) cc_final: 0.8591 (tp)
REVERT: C  326 ASN cc_start: 0.6598 (p0) cc_final: 0.5978 (p0)
REVERT: D   36 LYS cc_start: 0.9131 (tptt) cc_final: 0.8685 (tttt)
REVERT: D   75 ARG cc_start: 0.8715 (mmm160) cc_final: 0.8251 (mmt180)
REVERT: D   83 TYR cc_start: 0.8646 (t80) cc_final: 0.8025 (t80)
REVERT: D  111 TYR cc_start: 0.8749 (m-10) cc_final: 0.8021 (m-10)
REVERT: D  212 LYS cc_start: 0.7953 (mttp) cc_final: 0.7419 (mttp)
REVERT: D  326 ASN cc_start: 0.6943 (p0) cc_final: 0.6148 (p0)
REVERT: D  331 TYR cc_start: 0.8590 (m-80) cc_final: 0.8317 (m-80)
REVERT: E   36 LYS cc_start: 0.9082 (tptt) cc_final: 0.8634 (tttt)
REVERT: E   58 ILE cc_start: 0.9010 (OUTLIER) cc_final: 0.8755 (tp)
REVERT: E  111 TYR cc_start: 0.8761 (m-10) cc_final: 0.7910 (m-10)
REVERT: E  276 LEU cc_start: 0.9260 (mt) cc_final: 0.9033 (mt)
REVERT: E  326 ASN cc_start: 0.6657 (p0) cc_final: 0.6032 (p0)
REVERT: F   36 LYS cc_start: 0.9155 (tptt) cc_final: 0.8586 (tttt)
REVERT: F   75 ARG cc_start: 0.8673 (mmm160) cc_final: 0.8270 (mmt180)
REVERT: F  111 TYR cc_start: 0.8885 (m-10) cc_final: 0.7925 (m-10)
REVERT: F  276 LEU cc_start: 0.9179 (mt) cc_final: 0.8967 (mt)
REVERT: G   36 LYS cc_start: 0.9103 (tptt) cc_final: 0.8668 (tttt)
REVERT: G   75 ARG cc_start: 0.8594 (mmm160) cc_final: 0.8319 (mmt180)
REVERT: G  111 TYR cc_start: 0.8743 (m-10) cc_final: 0.8023 (m-10)
REVERT: G  326 ASN cc_start: 0.6833 (p0) cc_final: 0.6023 (p0)
REVERT: G  334 PHE cc_start: 0.8616 (OUTLIER) cc_final: 0.7941 (t80)
  outliers start: 30
  outliers final: 25
  residues processed: 295
  average time/residue: 0.1258
  time to fit residues: 50.2006
Evaluate side-chains
  298 residues out of total 1323 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 271
  time to evaluate  : 0.428 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   43 VAL
Chi-restraints excluded: chain A residue  218 LEU
Chi-restraints excluded: chain A residue  228 CYS
Chi-restraints excluded: chain A residue  292 VAL
Chi-restraints excluded: chain A residue  335 LEU
Chi-restraints excluded: chain B residue   43 VAL
Chi-restraints excluded: chain B residue  218 LEU
Chi-restraints excluded: chain B residue  252 ILE
Chi-restraints excluded: chain B residue  259 VAL
Chi-restraints excluded: chain B residue  292 VAL
Chi-restraints excluded: chain C residue  228 CYS
Chi-restraints excluded: chain C residue  252 ILE
Chi-restraints excluded: chain D residue  125 LEU
Chi-restraints excluded: chain D residue  252 ILE
Chi-restraints excluded: chain D residue  292 VAL
Chi-restraints excluded: chain D residue  297 VAL
Chi-restraints excluded: chain E residue   58 ILE
Chi-restraints excluded: chain E residue  218 LEU
Chi-restraints excluded: chain E residue  261 ASP
Chi-restraints excluded: chain E residue  297 VAL
Chi-restraints excluded: chain F residue   43 VAL
Chi-restraints excluded: chain F residue  228 CYS
Chi-restraints excluded: chain F residue  259 VAL
Chi-restraints excluded: chain F residue  261 ASP
Chi-restraints excluded: chain F residue  297 VAL
Chi-restraints excluded: chain G residue  297 VAL
Chi-restraints excluded: chain G residue  334 PHE
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 140
   random chunks:
   chunk 118 optimal weight:    5.9990
   chunk 90 optimal weight:    1.9990
   chunk 83 optimal weight:    0.6980
   chunk 3 optimal weight:    0.8980
   chunk 112 optimal weight:    3.9990
   chunk 49 optimal weight:    1.9990
   chunk 60 optimal weight:   10.0000
   chunk 26 optimal weight:    5.9990
   chunk 46 optimal weight:    0.7980
   chunk 19 optimal weight:    6.9990
   chunk 8 optimal weight:    2.9990
   overall best weight:    1.2784

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

Flipped N/Q/H residues before XYZ refinement:
G  76 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3286 r_free = 0.3286 target = 0.113262 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.2892 r_free = 0.2892 target = 0.087320 restraints weight = 19782.136|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.2929 r_free = 0.2929 target = 0.089745 restraints weight = 10394.498|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.2949 r_free = 0.2949 target = 0.091126 restraints weight = 7291.444|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 32)----------------|
| r_work = 0.2962 r_free = 0.2962 target = 0.092004 restraints weight = 6081.273|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.2966 r_free = 0.2966 target = 0.092287 restraints weight = 5522.319|
|-----------------------------------------------------------------------------|
r_work (final): 0.2960
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8415
moved from start:          0.2842

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029  12054  Z= 0.133
  Angle     :  0.603   7.376  16450  Z= 0.293
  Chirality :  0.039   0.131   1995
  Planarity :  0.004   0.036   1953
  Dihedral  :  3.675  11.734   1554
  Min Nonbonded Distance : 2.490

Molprobity Statistics.
  All-atom Clashscore : 3.94
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.42 %
    Favored  : 97.58 %
  Rotamer:
    Outliers :  2.65 %
    Allowed  : 23.05 %
    Favored  : 74.30 %
  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:  0.87 (0.23), residues: 1407
  helix:  1.79 (0.17), residues: 1008
  sheet: -2.35 (0.49), residues: 84
  loop : -2.68 (0.28), residues: 315

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG C 128 
 TYR   0.022   0.001   TYR B 293 
 PHE   0.028   0.001   PHE G 126 
 TRP   0.009   0.001   TRP F  74 
 HIS   0.001   0.000   HIS E 106 

Details of bonding type rmsd
  covalent geometry    : bond        0.00314 (12040)
  covalent geometry    : angle       0.60325 (16422)
  SS BOND              : bond        0.00066 (   14)
  SS BOND              : angle       0.51968 (   28)
  hydrogen bonds       : bond        0.03038 (  728)
  hydrogen bonds       : angle       3.87803 ( 2121)

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

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

  2814 Ramachandran restraints generated.
    1407 Oldfield, 0 Emsley, 1407 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2814 Ramachandran restraints generated.
    1407 Oldfield, 0 Emsley, 1407 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  323 residues out of total 1323 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 288
  time to evaluate  : 0.439 
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   36 LYS cc_start: 0.9098 (tptt) cc_final: 0.8657 (tttt)
REVERT: A   75 ARG cc_start: 0.8685 (mmm160) cc_final: 0.8457 (mmt180)
REVERT: A   76 GLN cc_start: 0.8250 (mt0) cc_final: 0.7929 (mt0)
REVERT: A  111 TYR cc_start: 0.8703 (m-10) cc_final: 0.7883 (m-10)
REVERT: A  326 ASN cc_start: 0.6585 (p0) cc_final: 0.5762 (p0)
REVERT: B   29 ARG cc_start: 0.8135 (ttm110) cc_final: 0.7761 (mtm110)
REVERT: B   36 LYS cc_start: 0.9044 (tptt) cc_final: 0.8562 (tttt)
REVERT: B   58 ILE cc_start: 0.8960 (tp) cc_final: 0.8725 (tp)
REVERT: B   75 ARG cc_start: 0.8678 (mmm160) cc_final: 0.8407 (mmt180)
REVERT: B  111 TYR cc_start: 0.8758 (m-10) cc_final: 0.8096 (m-10)
REVERT: B  212 LYS cc_start: 0.8194 (mttp) cc_final: 0.7860 (mtmm)
REVERT: B  213 TYR cc_start: 0.8950 (t80) cc_final: 0.8725 (t80)
REVERT: B  326 ASN cc_start: 0.6864 (p0) cc_final: 0.6155 (p0)
REVERT: C   36 LYS cc_start: 0.9123 (tptt) cc_final: 0.8760 (tttt)
REVERT: C   75 ARG cc_start: 0.8658 (mmm160) cc_final: 0.8387 (mmt180)
REVERT: C  111 TYR cc_start: 0.8794 (m-10) cc_final: 0.8270 (m-10)
REVERT: C  212 LYS cc_start: 0.8082 (mttp) cc_final: 0.7518 (mttp)
REVERT: C  243 GLU cc_start: 0.8471 (pt0) cc_final: 0.8230 (pt0)
REVERT: C  275 LEU cc_start: 0.8992 (tt) cc_final: 0.8575 (tp)
REVERT: D   36 LYS cc_start: 0.9143 (tptt) cc_final: 0.8707 (tttt)
REVERT: D   75 ARG cc_start: 0.8728 (mmm160) cc_final: 0.8274 (mmt180)
REVERT: D   83 TYR cc_start: 0.8651 (t80) cc_final: 0.8026 (t80)
REVERT: D  111 TYR cc_start: 0.8746 (m-10) cc_final: 0.8066 (m-10)
REVERT: D  213 TYR cc_start: 0.9046 (t80) cc_final: 0.8833 (t80)
REVERT: D  326 ASN cc_start: 0.6837 (p0) cc_final: 0.6067 (p0)
REVERT: E   36 LYS cc_start: 0.9078 (tptt) cc_final: 0.8612 (tttt)
REVERT: E  111 TYR cc_start: 0.8769 (m-10) cc_final: 0.8013 (m-10)
REVERT: E  326 ASN cc_start: 0.6648 (p0) cc_final: 0.5998 (p0)
REVERT: F   35 ASP cc_start: 0.8589 (p0) cc_final: 0.8381 (p0)
REVERT: F   36 LYS cc_start: 0.9163 (tptt) cc_final: 0.8552 (tttt)
REVERT: F   75 ARG cc_start: 0.8681 (mmm160) cc_final: 0.8293 (mmt180)
REVERT: F  111 TYR cc_start: 0.8819 (m-10) cc_final: 0.7918 (m-10)
REVERT: F  276 LEU cc_start: 0.9153 (mt) cc_final: 0.8951 (mt)
REVERT: G   36 LYS cc_start: 0.9081 (tptt) cc_final: 0.8658 (tttt)
REVERT: G   75 ARG cc_start: 0.8631 (mmm160) cc_final: 0.8308 (mmt180)
REVERT: G  111 TYR cc_start: 0.8696 (m-10) cc_final: 0.7926 (m-10)
REVERT: G  212 LYS cc_start: 0.7951 (mttp) cc_final: 0.7609 (mttp)
REVERT: G  301 GLN cc_start: 0.7718 (pp30) cc_final: 0.7459 (pp30)
REVERT: G  326 ASN cc_start: 0.6977 (p0) cc_final: 0.6580 (p0)
REVERT: G  334 PHE cc_start: 0.8581 (OUTLIER) cc_final: 0.7949 (t80)
  outliers start: 35
  outliers final: 30
  residues processed: 303
  average time/residue: 0.1245
  time to fit residues: 51.2083
Evaluate side-chains
  305 residues out of total 1323 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 274
  time to evaluate  : 0.274 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   43 VAL
Chi-restraints excluded: chain A residue  218 LEU
Chi-restraints excluded: chain A residue  228 CYS
Chi-restraints excluded: chain A residue  292 VAL
Chi-restraints excluded: chain A residue  297 VAL
Chi-restraints excluded: chain A residue  335 LEU
Chi-restraints excluded: chain B residue   43 VAL
Chi-restraints excluded: chain B residue  218 LEU
Chi-restraints excluded: chain B residue  228 CYS
Chi-restraints excluded: chain B residue  252 ILE
Chi-restraints excluded: chain B residue  259 VAL
Chi-restraints excluded: chain B residue  292 VAL
Chi-restraints excluded: chain C residue  218 LEU
Chi-restraints excluded: chain C residue  228 CYS
Chi-restraints excluded: chain C residue  252 ILE
Chi-restraints excluded: chain D residue   43 VAL
Chi-restraints excluded: chain D residue  252 ILE
Chi-restraints excluded: chain D residue  292 VAL
Chi-restraints excluded: chain D residue  297 VAL
Chi-restraints excluded: chain E residue   43 VAL
Chi-restraints excluded: chain E residue  218 LEU
Chi-restraints excluded: chain E residue  261 ASP
Chi-restraints excluded: chain E residue  292 VAL
Chi-restraints excluded: chain E residue  297 VAL
Chi-restraints excluded: chain F residue   43 VAL
Chi-restraints excluded: chain F residue  228 CYS
Chi-restraints excluded: chain F residue  259 VAL
Chi-restraints excluded: chain F residue  261 ASP
Chi-restraints excluded: chain G residue   43 VAL
Chi-restraints excluded: chain G residue  297 VAL
Chi-restraints excluded: chain G residue  334 PHE
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 140
   random chunks:
   chunk 111 optimal weight:    1.9990
   chunk 27 optimal weight:    0.9990
   chunk 44 optimal weight:    0.8980
   chunk 67 optimal weight:    0.6980
   chunk 119 optimal weight:    0.5980
   chunk 2 optimal weight:    0.8980
   chunk 132 optimal weight:    1.9990
   chunk 43 optimal weight:    0.0770
   chunk 14 optimal weight:    0.9990
   chunk 127 optimal weight:    1.9990
   chunk 61 optimal weight:    0.0980
   overall best weight:    0.4738

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3322 r_free = 0.3322 target = 0.115597 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.2945 r_free = 0.2945 target = 0.090330 restraints weight = 19608.766|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.2981 r_free = 0.2981 target = 0.092759 restraints weight = 10393.694|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3000 r_free = 0.3000 target = 0.094089 restraints weight = 7273.890|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 43)----------------|
| r_work = 0.3016 r_free = 0.3016 target = 0.095065 restraints weight = 6064.133|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 25)----------------|
| r_work = 0.3019 r_free = 0.3019 target = 0.095294 restraints weight = 5431.134|
|-----------------------------------------------------------------------------|
r_work (final): 0.3013
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8374
moved from start:          0.3044

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.026  12054  Z= 0.109
  Angle     :  0.591   6.726  16450  Z= 0.285
  Chirality :  0.038   0.129   1995
  Planarity :  0.004   0.037   1953
  Dihedral  :  3.527  11.978   1554
  Min Nonbonded Distance : 2.499

Molprobity Statistics.
  All-atom Clashscore : 4.19
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.85 %
    Favored  : 98.15 %
  Rotamer:
    Outliers :  2.27 %
    Allowed  : 23.66 %
    Favored  : 74.07 %
  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:  1.11 (0.23), residues: 1407
  helix:  1.97 (0.17), residues: 1008
  sheet: -2.28 (0.47), residues: 84
  loop : -2.61 (0.29), residues: 315

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG C  29 
 TYR   0.023   0.001   TYR B 293 
 PHE   0.016   0.001   PHE E 299 
 TRP   0.009   0.001   TRP F  74 
 HIS   0.001   0.000   HIS E 106 

Details of bonding type rmsd
  covalent geometry    : bond        0.00237 (12040)
  covalent geometry    : angle       0.59100 (16422)
  SS BOND              : bond        0.00120 (   14)
  SS BOND              : angle       0.78769 (   28)
  hydrogen bonds       : bond        0.02581 (  728)
  hydrogen bonds       : angle       3.66436 ( 2121)

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

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

  2814 Ramachandran restraints generated.
    1407 Oldfield, 0 Emsley, 1407 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2814 Ramachandran restraints generated.
    1407 Oldfield, 0 Emsley, 1407 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  327 residues out of total 1323 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 297
  time to evaluate  : 0.365 
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   36 LYS cc_start: 0.9093 (tptt) cc_final: 0.8680 (tttt)
REVERT: A   75 ARG cc_start: 0.8607 (mmm160) cc_final: 0.8377 (mmt180)
REVERT: A  111 TYR cc_start: 0.8605 (m-10) cc_final: 0.7899 (m-10)
REVERT: A  326 ASN cc_start: 0.6584 (p0) cc_final: 0.5802 (p0)
REVERT: B   29 ARG cc_start: 0.8110 (ttm110) cc_final: 0.7810 (mtm110)
REVERT: B   36 LYS cc_start: 0.9033 (tptt) cc_final: 0.8575 (tttt)
REVERT: B   58 ILE cc_start: 0.8940 (tp) cc_final: 0.8717 (tp)
REVERT: B   75 ARG cc_start: 0.8611 (mmm160) cc_final: 0.8321 (mmt180)
REVERT: B  111 TYR cc_start: 0.8665 (m-10) cc_final: 0.7998 (m-10)
REVERT: B  212 LYS cc_start: 0.8213 (mttp) cc_final: 0.7812 (mtmm)
REVERT: B  326 ASN cc_start: 0.6684 (p0) cc_final: 0.6003 (p0)
REVERT: C   36 LYS cc_start: 0.9103 (tptt) cc_final: 0.8745 (tttt)
REVERT: C   75 ARG cc_start: 0.8619 (mmm160) cc_final: 0.8358 (mmt180)
REVERT: C  111 TYR cc_start: 0.8656 (m-10) cc_final: 0.8149 (m-10)
REVERT: C  126 PHE cc_start: 0.8799 (t80) cc_final: 0.8511 (t80)
REVERT: C  326 ASN cc_start: 0.6587 (p0) cc_final: 0.6018 (p0)
REVERT: D   36 LYS cc_start: 0.9129 (tptt) cc_final: 0.8718 (tttt)
REVERT: D   75 ARG cc_start: 0.8693 (mmm160) cc_final: 0.8219 (mmt180)
REVERT: D   83 TYR cc_start: 0.8684 (t80) cc_final: 0.8106 (t80)
REVERT: D  111 TYR cc_start: 0.8614 (m-10) cc_final: 0.8015 (m-10)
REVERT: D  276 LEU cc_start: 0.9166 (mt) cc_final: 0.8949 (mt)
REVERT: D  326 ASN cc_start: 0.6726 (p0) cc_final: 0.5986 (p0)
REVERT: D  331 TYR cc_start: 0.8499 (m-80) cc_final: 0.8287 (m-80)
REVERT: E   36 LYS cc_start: 0.9085 (tptt) cc_final: 0.8633 (tttt)
REVERT: E   58 ILE cc_start: 0.8972 (OUTLIER) cc_final: 0.8672 (tp)
REVERT: E  111 TYR cc_start: 0.8642 (m-10) cc_final: 0.7899 (m-10)
REVERT: E  326 ASN cc_start: 0.6585 (p0) cc_final: 0.5972 (p0)
REVERT: F   36 LYS cc_start: 0.9152 (tptt) cc_final: 0.8610 (tttt)
REVERT: F   75 ARG cc_start: 0.8659 (mmm160) cc_final: 0.8230 (mmt180)
REVERT: F  111 TYR cc_start: 0.8719 (m-10) cc_final: 0.7910 (m-10)
REVERT: G   36 LYS cc_start: 0.9090 (tptt) cc_final: 0.8684 (tttt)
REVERT: G   75 ARG cc_start: 0.8570 (mmm160) cc_final: 0.8219 (mmt180)
REVERT: G  111 TYR cc_start: 0.8640 (m-10) cc_final: 0.8025 (m-10)
REVERT: G  212 LYS cc_start: 0.7816 (mttp) cc_final: 0.7599 (mttp)
REVERT: G  301 GLN cc_start: 0.7841 (pp30) cc_final: 0.7554 (tm-30)
  outliers start: 30
  outliers final: 26
  residues processed: 309
  average time/residue: 0.1125
  time to fit residues: 47.5921
Evaluate side-chains
  303 residues out of total 1323 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 276
  time to evaluate  : 0.471 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  218 LEU
Chi-restraints excluded: chain A residue  225 LEU
Chi-restraints excluded: chain A residue  228 CYS
Chi-restraints excluded: chain A residue  292 VAL
Chi-restraints excluded: chain A residue  297 VAL
Chi-restraints excluded: chain A residue  335 LEU
Chi-restraints excluded: chain B residue  228 CYS
Chi-restraints excluded: chain B residue  252 ILE
Chi-restraints excluded: chain B residue  259 VAL
Chi-restraints excluded: chain B residue  292 VAL
Chi-restraints excluded: chain C residue  228 CYS
Chi-restraints excluded: chain D residue   43 VAL
Chi-restraints excluded: chain D residue  252 ILE
Chi-restraints excluded: chain D residue  292 VAL
Chi-restraints excluded: chain D residue  297 VAL
Chi-restraints excluded: chain E residue   43 VAL
Chi-restraints excluded: chain E residue   58 ILE
Chi-restraints excluded: chain E residue  261 ASP
Chi-restraints excluded: chain E residue  297 VAL
Chi-restraints excluded: chain F residue  228 CYS
Chi-restraints excluded: chain F residue  259 VAL
Chi-restraints excluded: chain F residue  261 ASP
Chi-restraints excluded: chain F residue  292 VAL
Chi-restraints excluded: chain F residue  297 VAL
Chi-restraints excluded: chain G residue   43 VAL
Chi-restraints excluded: chain G residue  292 VAL
Chi-restraints excluded: chain G residue  297 VAL
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 140
   random chunks:
   chunk 58 optimal weight:    6.9990
   chunk 7 optimal weight:    0.6980
   chunk 99 optimal weight:    4.9990
   chunk 132 optimal weight:    0.8980
   chunk 47 optimal weight:    0.8980
   chunk 129 optimal weight:    7.9990
   chunk 6 optimal weight:    1.9990
   chunk 116 optimal weight:    0.8980
   chunk 131 optimal weight:    1.9990
   chunk 29 optimal weight:    3.9990
   chunk 53 optimal weight:    1.9990
   overall best weight:    1.0782

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

Flipped N/Q/H residues before XYZ refinement:
A  76 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3291 r_free = 0.3291 target = 0.113522 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.2911 r_free = 0.2911 target = 0.088192 restraints weight = 19880.026|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 43)----------------|
| r_work = 0.2946 r_free = 0.2946 target = 0.090497 restraints weight = 10586.519|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.2967 r_free = 0.2967 target = 0.091906 restraints weight = 7493.165|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.2977 r_free = 0.2977 target = 0.092589 restraints weight = 6236.680|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 32)----------------|
| r_work = 0.2984 r_free = 0.2984 target = 0.093078 restraints weight = 5692.435|
|-----------------------------------------------------------------------------|
r_work (final): 0.2979
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8410
moved from start:          0.3153

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028  12054  Z= 0.127
  Angle     :  0.611   7.087  16450  Z= 0.294
  Chirality :  0.039   0.130   1995
  Planarity :  0.004   0.036   1953
  Dihedral  :  3.538  11.192   1554
  Min Nonbonded Distance : 2.482

Molprobity Statistics.
  All-atom Clashscore : 4.99
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.35 %
    Favored  : 97.65 %
  Rotamer:
    Outliers :  2.72 %
    Allowed  : 24.04 %
    Favored  : 73.24 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z 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:  1.13 (0.23), residues: 1407
  helix:  1.92 (0.17), residues: 1008
  sheet: -1.95 (0.50), residues: 84
  loop : -2.46 (0.29), residues: 315

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG F 128 
 TYR   0.024   0.001   TYR B 293 
 PHE   0.022   0.001   PHE G 126 
 TRP   0.012   0.001   TRP E  85 
 HIS   0.001   0.000   HIS E 106 

Details of bonding type rmsd
  covalent geometry    : bond        0.00303 (12040)
  covalent geometry    : angle       0.60929 (16422)
  SS BOND              : bond        0.00168 (   14)
  SS BOND              : angle       1.32992 (   28)
  hydrogen bonds       : bond        0.02734 (  728)
  hydrogen bonds       : angle       3.73606 ( 2121)

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

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

  2814 Ramachandran restraints generated.
    1407 Oldfield, 0 Emsley, 1407 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2814 Ramachandran restraints generated.
    1407 Oldfield, 0 Emsley, 1407 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  315 residues out of total 1323 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 279
  time to evaluate  : 0.310 
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: A   36 LYS cc_start: 0.9097 (tptt) cc_final: 0.8671 (tttt)
REVERT: A   75 ARG cc_start: 0.8674 (mmm160) cc_final: 0.8454 (mmt180)
REVERT: A  111 TYR cc_start: 0.8650 (m-10) cc_final: 0.7935 (m-10)
REVERT: A  326 ASN cc_start: 0.6687 (p0) cc_final: 0.5875 (p0)
REVERT: B   29 ARG cc_start: 0.8023 (ttm110) cc_final: 0.7718 (mtm110)
REVERT: B   36 LYS cc_start: 0.9045 (tptt) cc_final: 0.8582 (tttt)
REVERT: B   58 ILE cc_start: 0.8973 (tp) cc_final: 0.8760 (tp)
REVERT: B   75 ARG cc_start: 0.8635 (mmm160) cc_final: 0.8368 (mmt180)
REVERT: B  111 TYR cc_start: 0.8729 (m-10) cc_final: 0.8029 (m-10)
REVERT: B  212 LYS cc_start: 0.8230 (mttp) cc_final: 0.7806 (mtmm)
REVERT: B  326 ASN cc_start: 0.6803 (p0) cc_final: 0.6159 (p0)
REVERT: C   36 LYS cc_start: 0.9094 (tptt) cc_final: 0.8764 (tttt)
REVERT: C   75 ARG cc_start: 0.8670 (mmm160) cc_final: 0.8417 (mmt180)
REVERT: C  111 TYR cc_start: 0.8706 (m-10) cc_final: 0.8225 (m-10)
REVERT: C  126 PHE cc_start: 0.8802 (t80) cc_final: 0.8487 (t80)
REVERT: C  243 GLU cc_start: 0.8487 (pt0) cc_final: 0.8213 (pt0)
REVERT: C  326 ASN cc_start: 0.6717 (p0) cc_final: 0.6119 (p0)
REVERT: D   36 LYS cc_start: 0.9152 (tptt) cc_final: 0.8719 (tttt)
REVERT: D   75 ARG cc_start: 0.8743 (mmm160) cc_final: 0.8307 (mmt180)
REVERT: D  111 TYR cc_start: 0.8691 (m-10) cc_final: 0.8054 (m-10)
REVERT: D  212 LYS cc_start: 0.7921 (mttp) cc_final: 0.7448 (mttp)
REVERT: D  326 ASN cc_start: 0.6874 (p0) cc_final: 0.6094 (p0)
REVERT: E   36 LYS cc_start: 0.9062 (tptt) cc_final: 0.8610 (tttt)
REVERT: E   58 ILE cc_start: 0.8992 (OUTLIER) cc_final: 0.8696 (tp)
REVERT: E  111 TYR cc_start: 0.8730 (m-10) cc_final: 0.8016 (m-10)
REVERT: E  326 ASN cc_start: 0.6685 (p0) cc_final: 0.6040 (p0)
REVERT: F   36 LYS cc_start: 0.9157 (tptt) cc_final: 0.8588 (tttt)
REVERT: F   75 ARG cc_start: 0.8700 (mmm160) cc_final: 0.8285 (mmt180)
REVERT: F  111 TYR cc_start: 0.8746 (m-10) cc_final: 0.7937 (m-10)
REVERT: F  326 ASN cc_start: 0.7086 (p0) cc_final: 0.6371 (p0)
REVERT: G   36 LYS cc_start: 0.9096 (tptt) cc_final: 0.8694 (tttt)
REVERT: G   75 ARG cc_start: 0.8645 (mmm160) cc_final: 0.8345 (mmt180)
REVERT: G  111 TYR cc_start: 0.8680 (m-10) cc_final: 0.8065 (m-10)
REVERT: G  212 LYS cc_start: 0.7852 (mttp) cc_final: 0.7559 (mttp)
REVERT: G  301 GLN cc_start: 0.7880 (pp30) cc_final: 0.7548 (pp30)
REVERT: G  326 ASN cc_start: 0.6707 (p0) cc_final: 0.6346 (p0)
  outliers start: 36
  outliers final: 30
  residues processed: 296
  average time/residue: 0.1246
  time to fit residues: 49.9695
Evaluate side-chains
  301 residues out of total 1323 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 270
  time to evaluate  : 0.443 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   43 VAL
Chi-restraints excluded: chain A residue  218 LEU
Chi-restraints excluded: chain A residue  228 CYS
Chi-restraints excluded: chain A residue  292 VAL
Chi-restraints excluded: chain A residue  297 VAL
Chi-restraints excluded: chain B residue   43 VAL
Chi-restraints excluded: chain B residue  228 CYS
Chi-restraints excluded: chain B residue  252 ILE
Chi-restraints excluded: chain B residue  259 VAL
Chi-restraints excluded: chain B residue  292 VAL
Chi-restraints excluded: chain B residue  335 LEU
Chi-restraints excluded: chain C residue  228 CYS
Chi-restraints excluded: chain C residue  252 ILE
Chi-restraints excluded: chain D residue  252 ILE
Chi-restraints excluded: chain D residue  292 VAL
Chi-restraints excluded: chain D residue  297 VAL
Chi-restraints excluded: chain E residue   43 VAL
Chi-restraints excluded: chain E residue   58 ILE
Chi-restraints excluded: chain E residue  218 LEU
Chi-restraints excluded: chain E residue  261 ASP
Chi-restraints excluded: chain E residue  297 VAL
Chi-restraints excluded: chain F residue   43 VAL
Chi-restraints excluded: chain F residue  228 CYS
Chi-restraints excluded: chain F residue  259 VAL
Chi-restraints excluded: chain F residue  261 ASP
Chi-restraints excluded: chain F residue  292 VAL
Chi-restraints excluded: chain F residue  297 VAL
Chi-restraints excluded: chain G residue   43 VAL
Chi-restraints excluded: chain G residue  218 LEU
Chi-restraints excluded: chain G residue  292 VAL
Chi-restraints excluded: chain G residue  297 VAL
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 140
   random chunks:
   chunk 18 optimal weight:    0.9990
   chunk 123 optimal weight:    0.7980
   chunk 122 optimal weight:    0.9980
   chunk 46 optimal weight:    0.8980
   chunk 62 optimal weight:    0.9990
   chunk 51 optimal weight:    5.9990
   chunk 107 optimal weight:    0.9980
   chunk 71 optimal weight:    5.9990
   chunk 112 optimal weight:    0.9980
   chunk 43 optimal weight:    0.7980
   chunk 83 optimal weight:    0.0000
   overall best weight:    0.6984

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3299 r_free = 0.3299 target = 0.114241 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.2921 r_free = 0.2921 target = 0.089046 restraints weight = 19587.554|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.2956 r_free = 0.2956 target = 0.091387 restraints weight = 10240.609|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 47)----------------|
| r_work = 0.2980 r_free = 0.2980 target = 0.092925 restraints weight = 7146.988|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.2990 r_free = 0.2990 target = 0.093640 restraints weight = 5897.913|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 20)----------------|
| r_work = 0.2993 r_free = 0.2993 target = 0.093882 restraints weight = 5370.405|
|-----------------------------------------------------------------------------|
r_work (final): 0.2987
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8385
moved from start:          0.3287

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028  12054  Z= 0.114
  Angle     :  0.603   7.087  16450  Z= 0.290
  Chirality :  0.039   0.128   1995
  Planarity :  0.004   0.037   1953
  Dihedral  :  3.467  11.079   1554
  Min Nonbonded Distance : 2.483

Molprobity Statistics.
  All-atom Clashscore : 5.36
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.49 %
    Favored  : 98.51 %
  Rotamer:
    Outliers :  3.02 %
    Allowed  : 24.49 %
    Favored  : 72.49 %
  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:  1.22 (0.23), residues: 1407
  helix:  2.01 (0.17), residues: 1001
  sheet: -1.78 (0.50), residues: 84
  loop : -2.46 (0.29), residues: 322

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.001   ARG D  29 
 TYR   0.025   0.001   TYR B 293 
 PHE   0.019   0.001   PHE G 299 
 TRP   0.009   0.001   TRP E  85 
 HIS   0.001   0.000   HIS E 106 

Details of bonding type rmsd
  covalent geometry    : bond        0.00262 (12040)
  covalent geometry    : angle       0.60169 (16422)
  SS BOND              : bond        0.00157 (   14)
  SS BOND              : angle       1.25186 (   28)
  hydrogen bonds       : bond        0.02510 (  728)
  hydrogen bonds       : angle       3.65065 ( 2121)

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

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

  2814 Ramachandran restraints generated.
    1407 Oldfield, 0 Emsley, 1407 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2814 Ramachandran restraints generated.
    1407 Oldfield, 0 Emsley, 1407 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  327 residues out of total 1323 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 40
    poor density    : 287
  time to evaluate  : 0.418 
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   36 LYS cc_start: 0.9111 (tptt) cc_final: 0.8703 (tttt)
REVERT: A   75 ARG cc_start: 0.8673 (mmm160) cc_final: 0.8465 (mmt180)
REVERT: A  111 TYR cc_start: 0.8616 (m-10) cc_final: 0.7942 (m-10)
REVERT: A  326 ASN cc_start: 0.6698 (p0) cc_final: 0.5973 (p0)
REVERT: B   29 ARG cc_start: 0.8013 (ttm110) cc_final: 0.7732 (mtm110)
REVERT: B   36 LYS cc_start: 0.9013 (tptt) cc_final: 0.8571 (tttt)
REVERT: B   58 ILE cc_start: 0.8988 (tp) cc_final: 0.8747 (tp)
REVERT: B   75 ARG cc_start: 0.8613 (mmm160) cc_final: 0.8360 (mmt180)
REVERT: B  111 TYR cc_start: 0.8681 (m-10) cc_final: 0.8024 (m-10)
REVERT: B  301 GLN cc_start: 0.7699 (pp30) cc_final: 0.7489 (pp30)
REVERT: B  326 ASN cc_start: 0.6679 (p0) cc_final: 0.5974 (p0)
REVERT: C   36 LYS cc_start: 0.9078 (tptt) cc_final: 0.8745 (tttt)
REVERT: C   75 ARG cc_start: 0.8655 (mmm160) cc_final: 0.8400 (mmt180)
REVERT: C  111 TYR cc_start: 0.8647 (m-10) cc_final: 0.8136 (m-10)
REVERT: C  126 PHE cc_start: 0.8774 (t80) cc_final: 0.8467 (t80)
REVERT: C  326 ASN cc_start: 0.6634 (p0) cc_final: 0.5974 (p0)
REVERT: D   36 LYS cc_start: 0.9138 (tptt) cc_final: 0.8710 (tttt)
REVERT: D   75 ARG cc_start: 0.8718 (mmm160) cc_final: 0.8170 (mmt180)
REVERT: D  111 TYR cc_start: 0.8619 (m-10) cc_final: 0.8079 (m-10)
REVERT: D  212 LYS cc_start: 0.7928 (mttp) cc_final: 0.7505 (mttp)
REVERT: D  276 LEU cc_start: 0.9160 (mt) cc_final: 0.8931 (mt)
REVERT: D  326 ASN cc_start: 0.6730 (p0) cc_final: 0.5974 (p0)
REVERT: E   36 LYS cc_start: 0.9061 (tptt) cc_final: 0.8628 (tttt)
REVERT: E   58 ILE cc_start: 0.8949 (OUTLIER) cc_final: 0.8568 (tp)
REVERT: E   81 ASP cc_start: 0.7667 (m-30) cc_final: 0.7124 (m-30)
REVERT: E  111 TYR cc_start: 0.8663 (m-10) cc_final: 0.7928 (m-10)
REVERT: E  276 LEU cc_start: 0.9170 (mt) cc_final: 0.8940 (mt)
REVERT: E  326 ASN cc_start: 0.6652 (p0) cc_final: 0.6014 (p0)
REVERT: F   36 LYS cc_start: 0.9119 (tptt) cc_final: 0.8596 (tttt)
REVERT: F   75 ARG cc_start: 0.8684 (mmm160) cc_final: 0.8189 (mmt180)
REVERT: F  111 TYR cc_start: 0.8692 (m-10) cc_final: 0.7965 (m-10)
REVERT: F  326 ASN cc_start: 0.6959 (p0) cc_final: 0.6181 (p0)
REVERT: G   36 LYS cc_start: 0.9104 (tptt) cc_final: 0.8683 (tttt)
REVERT: G   75 ARG cc_start: 0.8644 (mmm160) cc_final: 0.8291 (mmt180)
REVERT: G   81 ASP cc_start: 0.7619 (m-30) cc_final: 0.6976 (m-30)
REVERT: G  111 TYR cc_start: 0.8610 (m-10) cc_final: 0.8048 (m-10)
REVERT: G  212 LYS cc_start: 0.7852 (mttp) cc_final: 0.7596 (mttp)
REVERT: G  301 GLN cc_start: 0.7777 (pp30) cc_final: 0.7420 (pp30)
  outliers start: 40
  outliers final: 33
  residues processed: 307
  average time/residue: 0.1227
  time to fit residues: 51.3962
Evaluate side-chains
  312 residues out of total 1323 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 278
  time to evaluate  : 0.471 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   43 VAL
Chi-restraints excluded: chain A residue  218 LEU
Chi-restraints excluded: chain A residue  228 CYS
Chi-restraints excluded: chain A residue  292 VAL
Chi-restraints excluded: chain A residue  297 VAL
Chi-restraints excluded: chain B residue   43 VAL
Chi-restraints excluded: chain B residue  228 CYS
Chi-restraints excluded: chain B residue  252 ILE
Chi-restraints excluded: chain B residue  259 VAL
Chi-restraints excluded: chain B residue  292 VAL
Chi-restraints excluded: chain B residue  335 LEU
Chi-restraints excluded: chain C residue  228 CYS
Chi-restraints excluded: chain C residue  246 CYS
Chi-restraints excluded: chain C residue  292 VAL
Chi-restraints excluded: chain D residue  218 LEU
Chi-restraints excluded: chain D residue  252 ILE
Chi-restraints excluded: chain D residue  292 VAL
Chi-restraints excluded: chain D residue  297 VAL
Chi-restraints excluded: chain E residue   43 VAL
Chi-restraints excluded: chain E residue   58 ILE
Chi-restraints excluded: chain E residue  218 LEU
Chi-restraints excluded: chain E residue  246 CYS
Chi-restraints excluded: chain E residue  292 VAL
Chi-restraints excluded: chain E residue  297 VAL
Chi-restraints excluded: chain F residue   43 VAL
Chi-restraints excluded: chain F residue  228 CYS
Chi-restraints excluded: chain F residue  259 VAL
Chi-restraints excluded: chain F residue  261 ASP
Chi-restraints excluded: chain F residue  292 VAL
Chi-restraints excluded: chain F residue  297 VAL
Chi-restraints excluded: chain G residue   43 VAL
Chi-restraints excluded: chain G residue  218 LEU
Chi-restraints excluded: chain G residue  292 VAL
Chi-restraints excluded: chain G residue  297 VAL
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 140
   random chunks:
   chunk 77 optimal weight:    0.5980
   chunk 111 optimal weight:    0.9980
   chunk 88 optimal weight:    1.9990
   chunk 47 optimal weight:    0.7980
   chunk 24 optimal weight:    1.9990
   chunk 81 optimal weight:    2.9990
   chunk 21 optimal weight:    0.0470
   chunk 0 optimal weight:   10.0000
   chunk 55 optimal weight:    0.9990
   chunk 46 optimal weight:    0.8980
   chunk 113 optimal weight:    0.0070
   overall best weight:    0.4696

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3317 r_free = 0.3317 target = 0.115487 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.2942 r_free = 0.2942 target = 0.090251 restraints weight = 19579.661|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 43)----------------|
| r_work = 0.2978 r_free = 0.2978 target = 0.092666 restraints weight = 10288.561|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 41)----------------|
| r_work = 0.3000 r_free = 0.3000 target = 0.094168 restraints weight = 7193.376|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.3011 r_free = 0.3011 target = 0.094910 restraints weight = 5933.781|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.3014 r_free = 0.3014 target = 0.095159 restraints weight = 5393.710|
|-----------------------------------------------------------------------------|
r_work (final): 0.3008
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8365
moved from start:          0.3406

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.031  12054  Z= 0.110
  Angle     :  0.606   7.001  16450  Z= 0.291
  Chirality :  0.038   0.128   1995
  Planarity :  0.004   0.036   1953
  Dihedral  :  3.381  11.041   1554
  Min Nonbonded Distance : 2.488

Molprobity Statistics.
  All-atom Clashscore : 5.03
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.71 %
    Favored  : 98.29 %
  Rotamer:
    Outliers :  2.42 %
    Allowed  : 25.70 %
    Favored  : 71.88 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z 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:  1.32 (0.23), residues: 1407
  helix:  2.06 (0.17), residues: 1001
  sheet: -1.61 (0.51), residues: 84
  loop : -2.36 (0.29), residues: 322

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG C  29 
 TYR   0.026   0.001   TYR B 293 
 PHE   0.028   0.001   PHE G 126 
 TRP   0.010   0.001   TRP E  85 
 HIS   0.000   0.000   HIS E 106 

Details of bonding type rmsd
  covalent geometry    : bond        0.00247 (12040)
  covalent geometry    : angle       0.60461 (16422)
  SS BOND              : bond        0.00190 (   14)
  SS BOND              : angle       1.19216 (   28)
  hydrogen bonds       : bond        0.02356 (  728)
  hydrogen bonds       : angle       3.60179 ( 2121)

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

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

  2814 Ramachandran restraints generated.
    1407 Oldfield, 0 Emsley, 1407 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2814 Ramachandran restraints generated.
    1407 Oldfield, 0 Emsley, 1407 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  321 residues out of total 1323 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 289
  time to evaluate  : 0.497 
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: A   36 LYS cc_start: 0.9101 (tptt) cc_final: 0.8723 (tttt)
REVERT: A   75 ARG cc_start: 0.8659 (mmm160) cc_final: 0.8429 (mmt180)
REVERT: A  111 TYR cc_start: 0.8560 (m-10) cc_final: 0.7930 (m-10)
REVERT: A  212 LYS cc_start: 0.7978 (mttp) cc_final: 0.7572 (mptt)
REVERT: A  326 ASN cc_start: 0.6706 (p0) cc_final: 0.5980 (p0)
REVERT: B   29 ARG cc_start: 0.7961 (ttm110) cc_final: 0.7697 (mtm110)
REVERT: B   36 LYS cc_start: 0.9009 (tptt) cc_final: 0.8555 (tttt)
REVERT: B   58 ILE cc_start: 0.8985 (tp) cc_final: 0.8760 (tp)
REVERT: B   75 ARG cc_start: 0.8610 (mmm160) cc_final: 0.8348 (mmt180)
REVERT: B  111 TYR cc_start: 0.8645 (m-10) cc_final: 0.8006 (m-10)
REVERT: B  301 GLN cc_start: 0.7856 (pp30) cc_final: 0.7613 (pp30)
REVERT: B  326 ASN cc_start: 0.6587 (p0) cc_final: 0.5907 (p0)
REVERT: C   36 LYS cc_start: 0.9077 (tptt) cc_final: 0.8737 (tttt)
REVERT: C   75 ARG cc_start: 0.8683 (mmm160) cc_final: 0.8424 (mmt180)
REVERT: C  111 TYR cc_start: 0.8573 (m-10) cc_final: 0.8052 (m-10)
REVERT: C  126 PHE cc_start: 0.8716 (t80) cc_final: 0.8458 (t80)
REVERT: C  248 ILE cc_start: 0.9011 (pt) cc_final: 0.8692 (tp)
REVERT: C  326 ASN cc_start: 0.6626 (p0) cc_final: 0.5998 (p0)
REVERT: D   36 LYS cc_start: 0.9107 (tptt) cc_final: 0.8704 (tttt)
REVERT: D   75 ARG cc_start: 0.8765 (mmm160) cc_final: 0.8231 (mmt180)
REVERT: D  111 TYR cc_start: 0.8530 (m-10) cc_final: 0.8039 (m-10)
REVERT: D  212 LYS cc_start: 0.7920 (mttp) cc_final: 0.7541 (mttp)
REVERT: D  276 LEU cc_start: 0.9154 (mt) cc_final: 0.8933 (mt)
REVERT: D  326 ASN cc_start: 0.6689 (p0) cc_final: 0.6020 (p0)
REVERT: E   36 LYS cc_start: 0.9043 (tptt) cc_final: 0.8627 (tttt)
REVERT: E   58 ILE cc_start: 0.8909 (OUTLIER) cc_final: 0.8621 (tp)
REVERT: E   81 ASP cc_start: 0.7601 (m-30) cc_final: 0.7009 (m-30)
REVERT: E  111 TYR cc_start: 0.8618 (m-10) cc_final: 0.7962 (m-10)
REVERT: E  268 ILE cc_start: 0.9099 (mm) cc_final: 0.8892 (mm)
REVERT: E  276 LEU cc_start: 0.9145 (mt) cc_final: 0.8937 (mt)
REVERT: E  326 ASN cc_start: 0.6631 (p0) cc_final: 0.6011 (p0)
REVERT: F   36 LYS cc_start: 0.9108 (tptt) cc_final: 0.8591 (tttt)
REVERT: F   75 ARG cc_start: 0.8667 (mmm160) cc_final: 0.8266 (mmt180)
REVERT: F  111 TYR cc_start: 0.8691 (m-10) cc_final: 0.7975 (m-10)
REVERT: F  248 ILE cc_start: 0.9114 (pt) cc_final: 0.8870 (tp)
REVERT: F  326 ASN cc_start: 0.6830 (p0) cc_final: 0.6048 (p0)
REVERT: G   36 LYS cc_start: 0.9085 (tptt) cc_final: 0.8679 (tttt)
REVERT: G   75 ARG cc_start: 0.8666 (mmm160) cc_final: 0.8334 (mmt180)
REVERT: G  111 TYR cc_start: 0.8537 (m-10) cc_final: 0.7969 (m-10)
REVERT: G  212 LYS cc_start: 0.7834 (mttp) cc_final: 0.7610 (mttp)
REVERT: G  301 GLN cc_start: 0.7681 (pp30) cc_final: 0.7452 (tm-30)
  outliers start: 32
  outliers final: 29
  residues processed: 300
  average time/residue: 0.1246
  time to fit residues: 50.8574
Evaluate side-chains
  304 residues out of total 1323 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 274
  time to evaluate  : 0.428 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   43 VAL
Chi-restraints excluded: chain A residue  218 LEU
Chi-restraints excluded: chain A residue  225 LEU
Chi-restraints excluded: chain A residue  228 CYS
Chi-restraints excluded: chain A residue  292 VAL
Chi-restraints excluded: chain A residue  297 VAL
Chi-restraints excluded: chain B residue   43 VAL
Chi-restraints excluded: chain B residue  228 CYS
Chi-restraints excluded: chain B residue  259 VAL
Chi-restraints excluded: chain B residue  292 VAL
Chi-restraints excluded: chain C residue  228 CYS
Chi-restraints excluded: chain C residue  292 VAL
Chi-restraints excluded: chain D residue  218 LEU
Chi-restraints excluded: chain D residue  252 ILE
Chi-restraints excluded: chain D residue  292 VAL
Chi-restraints excluded: chain D residue  297 VAL
Chi-restraints excluded: chain E residue   43 VAL
Chi-restraints excluded: chain E residue   58 ILE
Chi-restraints excluded: chain E residue  218 LEU
Chi-restraints excluded: chain E residue  246 CYS
Chi-restraints excluded: chain E residue  297 VAL
Chi-restraints excluded: chain F residue   43 VAL
Chi-restraints excluded: chain F residue  228 CYS
Chi-restraints excluded: chain F residue  259 VAL
Chi-restraints excluded: chain F residue  261 ASP
Chi-restraints excluded: chain F residue  292 VAL
Chi-restraints excluded: chain G residue   43 VAL
Chi-restraints excluded: chain G residue  218 LEU
Chi-restraints excluded: chain G residue  292 VAL
Chi-restraints excluded: chain G residue  297 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 140
   random chunks:
   chunk 97 optimal weight:    0.9980
   chunk 116 optimal weight:    1.9990
   chunk 6 optimal weight:    1.9990
   chunk 46 optimal weight:    0.5980
   chunk 33 optimal weight:    2.9990
   chunk 85 optimal weight:    0.6980
   chunk 18 optimal weight:    2.9990
   chunk 44 optimal weight:    0.0770
   chunk 30 optimal weight:    0.9980
   chunk 103 optimal weight:    4.9990
   chunk 74 optimal weight:    1.9990
   overall best weight:    0.6738

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3320 r_free = 0.3320 target = 0.115537 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.2948 r_free = 0.2948 target = 0.090406 restraints weight = 19929.920|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.2983 r_free = 0.2983 target = 0.092754 restraints weight = 10586.706|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3003 r_free = 0.3003 target = 0.094165 restraints weight = 7458.836|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 46)----------------|
| r_work = 0.3017 r_free = 0.3017 target = 0.095032 restraints weight = 6203.268|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3022 r_free = 0.3022 target = 0.095367 restraints weight = 5584.622|
|-----------------------------------------------------------------------------|
r_work (final): 0.3020
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8371
moved from start:          0.3487

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031  12054  Z= 0.115
  Angle     :  0.616   7.272  16450  Z= 0.296
  Chirality :  0.039   0.132   1995
  Planarity :  0.004   0.036   1953
  Dihedral  :  3.364  10.405   1554
  Min Nonbonded Distance : 2.475

Molprobity Statistics.
  All-atom Clashscore : 5.24
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.63 %
    Favored  : 98.37 %
  Rotamer:
    Outliers :  2.49 %
    Allowed  : 25.77 %
    Favored  : 71.73 %
  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:  1.35 (0.23), residues: 1407
  helix:  2.03 (0.17), residues: 1001
  sheet: -1.36 (0.53), residues: 84
  loop : -2.25 (0.30), residues: 322

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG F 128 
 TYR   0.027   0.001   TYR B 293 
 PHE   0.021   0.001   PHE B 299 
 TRP   0.011   0.001   TRP E  85 
 HIS   0.001   0.000   HIS E 106 

Details of bonding type rmsd
  covalent geometry    : bond        0.00264 (12040)
  covalent geometry    : angle       0.61430 (16422)
  SS BOND              : bond        0.00125 (   14)
  SS BOND              : angle       1.24808 (   28)
  hydrogen bonds       : bond        0.02434 (  728)
  hydrogen bonds       : angle       3.65255 ( 2121)

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

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

  2814 Ramachandran restraints generated.
    1407 Oldfield, 0 Emsley, 1407 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2814 Ramachandran restraints generated.
    1407 Oldfield, 0 Emsley, 1407 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  316 residues out of total 1323 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 283
  time to evaluate  : 0.427 
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: A   36 LYS cc_start: 0.9113 (tptt) cc_final: 0.8711 (tttt)
REVERT: A   75 ARG cc_start: 0.8653 (mmm160) cc_final: 0.8430 (mmt180)
REVERT: A  111 TYR cc_start: 0.8575 (m-10) cc_final: 0.7981 (m-10)
REVERT: A  212 LYS cc_start: 0.8020 (mttp) cc_final: 0.7610 (mptt)
REVERT: A  326 ASN cc_start: 0.6744 (p0) cc_final: 0.6016 (p0)
REVERT: B   29 ARG cc_start: 0.7986 (ttm110) cc_final: 0.7744 (mtm110)
REVERT: B   36 LYS cc_start: 0.8993 (tptt) cc_final: 0.8554 (tttt)
REVERT: B   58 ILE cc_start: 0.8985 (tp) cc_final: 0.8757 (tp)
REVERT: B   75 ARG cc_start: 0.8622 (mmm160) cc_final: 0.8363 (mmt180)
REVERT: B  111 TYR cc_start: 0.8656 (m-10) cc_final: 0.8015 (m-10)
REVERT: B  248 ILE cc_start: 0.9094 (pt) cc_final: 0.8890 (tp)
REVERT: B  301 GLN cc_start: 0.7840 (pp30) cc_final: 0.7598 (pp30)
REVERT: B  326 ASN cc_start: 0.6574 (p0) cc_final: 0.5902 (p0)
REVERT: C   36 LYS cc_start: 0.9083 (tptt) cc_final: 0.8735 (tttt)
REVERT: C   75 ARG cc_start: 0.8680 (mmm160) cc_final: 0.8428 (mmt180)
REVERT: C  111 TYR cc_start: 0.8606 (m-10) cc_final: 0.8095 (m-10)
REVERT: C  126 PHE cc_start: 0.8735 (t80) cc_final: 0.8487 (t80)
REVERT: C  326 ASN cc_start: 0.6660 (p0) cc_final: 0.6016 (p0)
REVERT: D   36 LYS cc_start: 0.9098 (tptt) cc_final: 0.8700 (tttt)
REVERT: D   75 ARG cc_start: 0.8742 (mmm160) cc_final: 0.8216 (mmt180)
REVERT: D  111 TYR cc_start: 0.8568 (m-10) cc_final: 0.8045 (m-10)
REVERT: D  212 LYS cc_start: 0.7915 (mttp) cc_final: 0.7546 (mttp)
REVERT: D  276 LEU cc_start: 0.9136 (mt) cc_final: 0.8906 (mt)
REVERT: D  326 ASN cc_start: 0.6657 (p0) cc_final: 0.6019 (p0)
REVERT: E   36 LYS cc_start: 0.9032 (tptt) cc_final: 0.8614 (tttt)
REVERT: E   58 ILE cc_start: 0.8891 (OUTLIER) cc_final: 0.8579 (tp)
REVERT: E   81 ASP cc_start: 0.7644 (m-30) cc_final: 0.7046 (m-30)
REVERT: E  111 TYR cc_start: 0.8636 (m-10) cc_final: 0.7978 (m-10)
REVERT: E  126 PHE cc_start: 0.8862 (t80) cc_final: 0.8657 (t80)
REVERT: E  326 ASN cc_start: 0.6654 (p0) cc_final: 0.6022 (p0)
REVERT: F   29 ARG cc_start: 0.7710 (ptp90) cc_final: 0.7496 (ptp90)
REVERT: F   36 LYS cc_start: 0.9101 (tptt) cc_final: 0.8649 (tttt)
REVERT: F   75 ARG cc_start: 0.8673 (mmm160) cc_final: 0.8297 (mmt180)
REVERT: F  111 TYR cc_start: 0.8674 (m-10) cc_final: 0.7963 (m-10)
REVERT: F  248 ILE cc_start: 0.9138 (pt) cc_final: 0.8880 (tp)
REVERT: F  326 ASN cc_start: 0.6876 (p0) cc_final: 0.6138 (p0)
REVERT: G   36 LYS cc_start: 0.9098 (tptt) cc_final: 0.8713 (tttt)
REVERT: G   75 ARG cc_start: 0.8677 (mmm160) cc_final: 0.8360 (mmt180)
REVERT: G  111 TYR cc_start: 0.8561 (m-10) cc_final: 0.7986 (m-10)
REVERT: G  212 LYS cc_start: 0.7853 (mttp) cc_final: 0.7611 (mttp)
  outliers start: 33
  outliers final: 30
  residues processed: 297
  average time/residue: 0.1211
  time to fit residues: 49.2219
Evaluate side-chains
  309 residues out of total 1323 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 278
  time to evaluate  : 0.409 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   43 VAL
Chi-restraints excluded: chain A residue  218 LEU
Chi-restraints excluded: chain A residue  225 LEU
Chi-restraints excluded: chain A residue  228 CYS
Chi-restraints excluded: chain A residue  252 ILE
Chi-restraints excluded: chain A residue  292 VAL
Chi-restraints excluded: chain A residue  297 VAL
Chi-restraints excluded: chain B residue   43 VAL
Chi-restraints excluded: chain B residue  228 CYS
Chi-restraints excluded: chain B residue  259 VAL
Chi-restraints excluded: chain B residue  292 VAL
Chi-restraints excluded: chain C residue  218 LEU
Chi-restraints excluded: chain C residue  228 CYS
Chi-restraints excluded: chain C residue  246 CYS
Chi-restraints excluded: chain C residue  292 VAL
Chi-restraints excluded: chain D residue  252 ILE
Chi-restraints excluded: chain D residue  292 VAL
Chi-restraints excluded: chain D residue  297 VAL
Chi-restraints excluded: chain E residue   43 VAL
Chi-restraints excluded: chain E residue   58 ILE
Chi-restraints excluded: chain E residue  218 LEU
Chi-restraints excluded: chain E residue  246 CYS
Chi-restraints excluded: chain E residue  297 VAL
Chi-restraints excluded: chain F residue   43 VAL
Chi-restraints excluded: chain F residue  259 VAL
Chi-restraints excluded: chain F residue  261 ASP
Chi-restraints excluded: chain F residue  292 VAL
Chi-restraints excluded: chain G residue   43 VAL
Chi-restraints excluded: chain G residue  218 LEU
Chi-restraints excluded: chain G residue  292 VAL
Chi-restraints excluded: chain G residue  297 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 140
   random chunks:
   chunk 110 optimal weight:    3.9990
   chunk 73 optimal weight:    3.9990
   chunk 65 optimal weight:    2.9990
   chunk 132 optimal weight:    0.8980
   chunk 114 optimal weight:    0.5980
   chunk 112 optimal weight:    2.9990
   chunk 86 optimal weight:    2.9990
   chunk 102 optimal weight:    4.9990
   chunk 75 optimal weight:    0.7980
   chunk 34 optimal weight:    3.9990
   chunk 60 optimal weight:   10.0000
   overall best weight:    1.6584

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3259 r_free = 0.3259 target = 0.111519 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.2867 r_free = 0.2867 target = 0.085872 restraints weight = 19825.180|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.2901 r_free = 0.2901 target = 0.088107 restraints weight = 10564.386|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 43)----------------|
| r_work = 0.2925 r_free = 0.2925 target = 0.089581 restraints weight = 7485.887|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.2935 r_free = 0.2935 target = 0.090221 restraints weight = 6223.570|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 22)----------------|
| r_work = 0.2935 r_free = 0.2935 target = 0.090221 restraints weight = 5706.650|
|-----------------------------------------------------------------------------|
r_work (final): 0.2932
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8439
moved from start:          0.3390

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.031  12054  Z= 0.158
  Angle     :  0.655   7.942  16450  Z= 0.316
  Chirality :  0.040   0.130   1995
  Planarity :  0.004   0.036   1953
  Dihedral  :  3.557  11.319   1554
  Min Nonbonded Distance : 2.463

Molprobity Statistics.
  All-atom Clashscore : 5.32
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.56 %
    Favored  : 97.44 %
  Rotamer:
    Outliers :  2.72 %
    Allowed  : 26.30 %
    Favored  : 70.98 %
  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:  1.20 (0.23), residues: 1407
  helix:  1.84 (0.17), residues: 1008
  sheet: -1.33 (0.54), residues: 84
  loop : -2.07 (0.30), residues: 315

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 128 
 TYR   0.028   0.001   TYR B 293 
 PHE   0.032   0.001   PHE G 126 
 TRP   0.013   0.001   TRP E  85 
 HIS   0.001   0.000   HIS E 106 

Details of bonding type rmsd
  covalent geometry    : bond        0.00383 (12040)
  covalent geometry    : angle       0.65298 (16422)
  SS BOND              : bond        0.00197 (   14)
  SS BOND              : angle       1.34067 (   28)
  hydrogen bonds       : bond        0.03014 (  728)
  hydrogen bonds       : angle       3.90409 ( 2121)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1788.69 seconds
wall clock time: 31 minutes 42.74 seconds (1902.74 seconds total)