Starting phenix.real_space_refine
on Sun Apr  5 02:40:31 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9vbx_64935/04_2026/9vbx_64935.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9vbx_64935/04_2026/9vbx_64935.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.4
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/9vbx_64935/04_2026/9vbx_64935.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9vbx_64935/04_2026/9vbx_64935.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/9vbx_64935/04_2026/9vbx_64935.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9vbx_64935/04_2026/9vbx_64935.map"
  }
  resolution = 2.4
  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: 5
    Type Number    sf(0)   Gaussians
     Ca      4      9.91       5
     Mn      4      7.51       5
     C    4712      2.51       5
     N    1200      2.21       5
     O    1533      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 4 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc1-6017/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 7453
  Number of models: 1
  Model: ""
    Number of chains: 16
    Chain: "A"
      Number of atoms: 1805
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 231, 1805
          Classifications: {'peptide': 231}
          Link IDs: {'CIS': 1, 'PTRANS': 12, 'TRANS': 217}
          Chain breaks: 1
    Chain: "B"
      Number of atoms: 1805
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 231, 1805
          Classifications: {'peptide': 231}
          Link IDs: {'CIS': 1, 'PTRANS': 12, 'TRANS': 217}
          Chain breaks: 1
    Chain: "C"
      Number of atoms: 1805
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 231, 1805
          Classifications: {'peptide': 231}
          Link IDs: {'CIS': 1, 'PTRANS': 12, 'TRANS': 217}
          Chain breaks: 1
    Chain: "D"
      Number of atoms: 1805
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 231, 1805
          Classifications: {'peptide': 231}
          Link IDs: {'CIS': 1, 'PTRANS': 12, 'TRANS': 217}
          Chain breaks: 1
    Chain: "b"
      Number of atoms: 47
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 4, 47
          Unusual residues: {'FUC': 1, 'GAL': 1, 'MAN': 1, 'NAG': 1}
          Classifications: {'undetermined': 4}
          Link IDs: {None: 3}
          Unresolved non-hydrogen bonds: 3
          Unresolved non-hydrogen angles: 6
          Unresolved non-hydrogen dihedrals: 9
          Unresolved non-hydrogen chiralities: 3
    Chain: "c"
      Number of atoms: 47
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 4, 47
          Unusual residues: {'FUC': 1, 'GAL': 1, 'MAN': 1, 'NAG': 1}
          Classifications: {'undetermined': 4}
          Link IDs: {None: 3}
          Unresolved non-hydrogen bonds: 3
          Unresolved non-hydrogen angles: 6
          Unresolved non-hydrogen dihedrals: 9
          Unresolved non-hydrogen chiralities: 3
    Chain: "d"
      Number of atoms: 47
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 4, 47
          Unusual residues: {'FUC': 1, 'GAL': 1, 'MAN': 1, 'NAG': 1}
          Classifications: {'undetermined': 4}
          Link IDs: {None: 3}
          Unresolved non-hydrogen bonds: 3
          Unresolved non-hydrogen angles: 6
          Unresolved non-hydrogen dihedrals: 9
          Unresolved non-hydrogen chiralities: 3
    Chain: "a"
      Number of atoms: 47
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 4, 47
          Unusual residues: {'FUC': 1, 'GAL': 1, 'MAN': 1, 'NAG': 1}
          Classifications: {'undetermined': 4}
          Link IDs: {None: 3}
          Unresolved non-hydrogen bonds: 3
          Unresolved non-hydrogen angles: 6
          Unresolved non-hydrogen dihedrals: 9
          Unresolved non-hydrogen chiralities: 3
    Chain: "A"
      Number of atoms: 2
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 2
          Unusual residues: {' CA': 1, ' MN': 1}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
    Chain: "B"
      Number of atoms: 2
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 2
          Unusual residues: {' CA': 1, ' MN': 1}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
    Chain: "C"
      Number of atoms: 2
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 2
          Unusual residues: {' CA': 1, ' MN': 1}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
    Chain: "D"
      Number of atoms: 2
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 2
          Unusual residues: {' CA': 1, ' MN': 1}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
    Chain: "A"
      Number of atoms: 12
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 12, 12
          Classifications: {'water': 12}
          Link IDs: {None: 11}
    Chain: "B"
      Number of atoms: 8
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 8, 8
          Classifications: {'water': 8}
          Link IDs: {None: 7}
    Chain: "C"
      Number of atoms: 10
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 10, 10
          Classifications: {'water': 10}
          Link IDs: {None: 9}
    Chain: "D"
      Number of atoms: 7
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 7, 7
          Classifications: {'water': 7}
          Link IDs: {None: 6}
  Time building chain proxies: 1.77, per 1000 atoms: 0.24
  Number of scatterers: 7453
  At special positions: 0
  Unit cell: (80.51, 88.81, 83.83, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     Mn      4     24.99
     Ca      4     19.99
     O    1533      8.00
     N    1200      7.00
     C    4712      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Links applied
    BETA1-2
      " MAN a   1 " - " NAG a   2 "
      " MAN b   1 " - " NAG b   2 "
      " MAN c   1 " - " NAG c   2 "
      " MAN d   1 " - " NAG d   2 "
    BETA1-3
      " NAG a   2 " - " FUC a   3 "
       ~> Even though FUC is an alpha isomer, a beta linkage is required...
      " NAG b   2 " - " FUC b   3 "
      " NAG c   2 " - " FUC c   3 "
      " NAG d   2 " - " FUC d   3 "
    BETA1-4
      " NAG a   2 " - " GAL a   4 "
      " NAG b   2 " - " GAL b   4 "
      " NAG c   2 " - " GAL c   4 "
      " NAG d   2 " - " GAL d   4 "
  Time building additional restraints: 0.89
  Conformation dependent library (CDL) restraints added in 263.8 milliseconds
  

  1816 Ramachandran restraints generated.
    908 Oldfield, 0 Emsley, 908 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1744

  Finding SS restraints...
    Secondary structure from input PDB file:
      12 helices and 12 sheets defined
      6.5% alpha, 58.4% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.33
  Creating SS restraints...
    Processing helix  chain 'A' and resid 102 through 106
      removed outlier: 3.697A  pdb=" N   PHE A 105 " --> pdb=" O   HIS A 102 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 144 through 148
    Processing helix  chain 'A' and resid 210 through 214
    Processing helix  chain 'B' and resid 102 through 106
      removed outlier: 3.697A  pdb=" N   PHE B 105 " --> pdb=" O   HIS B 102 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 144 through 148
    Processing helix  chain 'B' and resid 210 through 214
    Processing helix  chain 'C' and resid 102 through 106
      removed outlier: 3.696A  pdb=" N   PHE C 105 " --> pdb=" O   HIS C 102 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 144 through 148
    Processing helix  chain 'C' and resid 210 through 214
    Processing helix  chain 'D' and resid 102 through 106
      removed outlier: 3.697A  pdb=" N   PHE D 105 " --> pdb=" O   HIS D 102 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 144 through 148
    Processing helix  chain 'D' and resid 210 through 214
    Processing sheet with id=AA1, first strand: chain 'A' and resid 25 through 27
    Processing sheet with id=AA2, first strand: chain 'A' and resid 203 through 208
      removed outlier: 6.778A  pdb=" N   TRP A 246 " --> pdb=" O   VAL A  64 " (cutoff:3.500A)
      removed outlier: 4.389A  pdb=" N   THR A  66 " --> pdb=" O   SER A 244 " (cutoff:3.500A)
      removed outlier: 6.748A  pdb=" N   SER A 244 " --> pdb=" O   THR A  66 " (cutoff:3.500A)
      removed outlier: 4.395A  pdb=" N   PHE A  68 " --> pdb=" O   THR A 242 " (cutoff:3.500A)
      removed outlier: 6.753A  pdb=" N   THR A 242 " --> pdb=" O   PHE A  68 " (cutoff:3.500A)
      removed outlier: 4.478A  pdb=" N   THR A  70 " --> pdb=" O   SER A 240 " (cutoff:3.500A)
      removed outlier: 6.640A  pdb=" N   SER A 240 " --> pdb=" O   THR A  70 " (cutoff:3.500A)
      removed outlier: 4.472A  pdb=" N   ILE A  72 " --> pdb=" O   SER A 238 " (cutoff:3.500A)
      removed outlier: 6.485A  pdb=" N   SER A 238 " --> pdb=" O   ILE A  72 " (cutoff:3.500A)
      removed outlier: 6.444A  pdb=" N   PHE A  74 " --> pdb=" O   VAL A 236 " (cutoff:3.500A)
      removed outlier: 6.527A  pdb=" N   VAL A 236 " --> pdb=" O   PHE A  74 " (cutoff:3.500A)
      removed outlier: 6.954A  pdb=" N   ILE A  76 " --> pdb=" O   ASN A 234 " (cutoff:3.500A)
      removed outlier: 6.985A  pdb=" N   ASN A 234 " --> pdb=" O   ILE A  76 " (cutoff:3.500A)
      removed outlier: 6.984A  pdb=" N   ASN B 234 " --> pdb=" O   ILE B  76 " (cutoff:3.500A)
      removed outlier: 6.954A  pdb=" N   ILE B  76 " --> pdb=" O   ASN B 234 " (cutoff:3.500A)
      removed outlier: 6.526A  pdb=" N   VAL B 236 " --> pdb=" O   PHE B  74 " (cutoff:3.500A)
      removed outlier: 6.445A  pdb=" N   PHE B  74 " --> pdb=" O   VAL B 236 " (cutoff:3.500A)
      removed outlier: 6.485A  pdb=" N   SER B 238 " --> pdb=" O   ILE B  72 " (cutoff:3.500A)
      removed outlier: 4.472A  pdb=" N   ILE B  72 " --> pdb=" O   SER B 238 " (cutoff:3.500A)
      removed outlier: 6.639A  pdb=" N   SER B 240 " --> pdb=" O   THR B  70 " (cutoff:3.500A)
      removed outlier: 4.478A  pdb=" N   THR B  70 " --> pdb=" O   SER B 240 " (cutoff:3.500A)
      removed outlier: 6.752A  pdb=" N   THR B 242 " --> pdb=" O   PHE B  68 " (cutoff:3.500A)
      removed outlier: 4.395A  pdb=" N   PHE B  68 " --> pdb=" O   THR B 242 " (cutoff:3.500A)
      removed outlier: 6.749A  pdb=" N   SER B 244 " --> pdb=" O   THR B  66 " (cutoff:3.500A)
      removed outlier: 4.388A  pdb=" N   THR B  66 " --> pdb=" O   SER B 244 " (cutoff:3.500A)
      removed outlier: 6.778A  pdb=" N   TRP B 246 " --> pdb=" O   VAL B  64 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 18 through 22
      removed outlier: 5.101A  pdb=" N   VAL A 221 " --> pdb=" O   TYR A  52 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 18 through 22
      removed outlier: 5.101A  pdb=" N   VAL A 221 " --> pdb=" O   TYR A  52 " (cutoff:3.500A)
      removed outlier: 3.870A  pdb=" N   VAL A 166 " --> pdb=" O   ILE A 157 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'B' and resid 18 through 22
      removed outlier: 5.100A  pdb=" N   VAL B 221 " --> pdb=" O   TYR B  52 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'B' and resid 18 through 22
      removed outlier: 5.100A  pdb=" N   VAL B 221 " --> pdb=" O   TYR B  52 " (cutoff:3.500A)
      removed outlier: 3.870A  pdb=" N   VAL B 166 " --> pdb=" O   ILE B 157 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'C' and resid 25 through 27
    Processing sheet with id=AA8, first strand: chain 'C' and resid 203 through 208
      removed outlier: 6.778A  pdb=" N   TRP C 246 " --> pdb=" O   VAL C  64 " (cutoff:3.500A)
      removed outlier: 4.389A  pdb=" N   THR C  66 " --> pdb=" O   SER C 244 " (cutoff:3.500A)
      removed outlier: 6.749A  pdb=" N   SER C 244 " --> pdb=" O   THR C  66 " (cutoff:3.500A)
      removed outlier: 4.395A  pdb=" N   PHE C  68 " --> pdb=" O   THR C 242 " (cutoff:3.500A)
      removed outlier: 6.752A  pdb=" N   THR C 242 " --> pdb=" O   PHE C  68 " (cutoff:3.500A)
      removed outlier: 4.477A  pdb=" N   THR C  70 " --> pdb=" O   SER C 240 " (cutoff:3.500A)
      removed outlier: 6.639A  pdb=" N   SER C 240 " --> pdb=" O   THR C  70 " (cutoff:3.500A)
      removed outlier: 4.472A  pdb=" N   ILE C  72 " --> pdb=" O   SER C 238 " (cutoff:3.500A)
      removed outlier: 6.484A  pdb=" N   SER C 238 " --> pdb=" O   ILE C  72 " (cutoff:3.500A)
      removed outlier: 6.444A  pdb=" N   PHE C  74 " --> pdb=" O   VAL C 236 " (cutoff:3.500A)
      removed outlier: 6.526A  pdb=" N   VAL C 236 " --> pdb=" O   PHE C  74 " (cutoff:3.500A)
      removed outlier: 6.954A  pdb=" N   ILE C  76 " --> pdb=" O   ASN C 234 " (cutoff:3.500A)
      removed outlier: 6.984A  pdb=" N   ASN C 234 " --> pdb=" O   ILE C  76 " (cutoff:3.500A)
      removed outlier: 6.985A  pdb=" N   ASN D 234 " --> pdb=" O   ILE D  76 " (cutoff:3.500A)
      removed outlier: 6.954A  pdb=" N   ILE D  76 " --> pdb=" O   ASN D 234 " (cutoff:3.500A)
      removed outlier: 6.527A  pdb=" N   VAL D 236 " --> pdb=" O   PHE D  74 " (cutoff:3.500A)
      removed outlier: 6.445A  pdb=" N   PHE D  74 " --> pdb=" O   VAL D 236 " (cutoff:3.500A)
      removed outlier: 6.485A  pdb=" N   SER D 238 " --> pdb=" O   ILE D  72 " (cutoff:3.500A)
      removed outlier: 4.472A  pdb=" N   ILE D  72 " --> pdb=" O   SER D 238 " (cutoff:3.500A)
      removed outlier: 6.638A  pdb=" N   SER D 240 " --> pdb=" O   THR D  70 " (cutoff:3.500A)
      removed outlier: 4.478A  pdb=" N   THR D  70 " --> pdb=" O   SER D 240 " (cutoff:3.500A)
      removed outlier: 6.753A  pdb=" N   THR D 242 " --> pdb=" O   PHE D  68 " (cutoff:3.500A)
      removed outlier: 4.395A  pdb=" N   PHE D  68 " --> pdb=" O   THR D 242 " (cutoff:3.500A)
      removed outlier: 6.748A  pdb=" N   SER D 244 " --> pdb=" O   THR D  66 " (cutoff:3.500A)
      removed outlier: 4.389A  pdb=" N   THR D  66 " --> pdb=" O   SER D 244 " (cutoff:3.500A)
      removed outlier: 6.778A  pdb=" N   TRP D 246 " --> pdb=" O   VAL D  64 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'C' and resid 18 through 22
      removed outlier: 5.100A  pdb=" N   VAL C 221 " --> pdb=" O   TYR C  52 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'C' and resid 18 through 22
      removed outlier: 5.100A  pdb=" N   VAL C 221 " --> pdb=" O   TYR C  52 " (cutoff:3.500A)
      removed outlier: 3.871A  pdb=" N   VAL C 166 " --> pdb=" O   ILE C 157 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'D' and resid 18 through 22
      removed outlier: 5.100A  pdb=" N   VAL D 221 " --> pdb=" O   TYR D  52 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'D' and resid 18 through 22
      removed outlier: 5.100A  pdb=" N   VAL D 221 " --> pdb=" O   TYR D  52 " (cutoff:3.500A)
      removed outlier: 3.871A  pdb=" N   VAL D 166 " --> pdb=" O   ILE D 157 " (cutoff:3.500A)

    412 hydrogen bonds defined for protein.
    1032 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: 1.08

  Time building geometry restraints manager: 1.09 seconds

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

  Histogram of bond lengths:
        1.21 -     1.28: 1180
        1.28 -     1.35: 1139
        1.35 -     1.42: 965
        1.42 -     1.48: 1292
        1.48 -     1.55: 3032
  Bond restraints: 7608
  Sorted by residual:
  bond pdb=" N   TYR B 147 "
       pdb=" CA  TYR B 147 "
    ideal  model  delta    sigma   weight residual
    1.456  1.492 -0.036 1.26e-02 6.30e+03 8.21e+00
  bond pdb=" N   TYR D 147 "
       pdb=" CA  TYR D 147 "
    ideal  model  delta    sigma   weight residual
    1.456  1.491 -0.036 1.26e-02 6.30e+03 8.01e+00
  bond pdb=" N   TYR C 147 "
       pdb=" CA  TYR C 147 "
    ideal  model  delta    sigma   weight residual
    1.456  1.490 -0.035 1.26e-02 6.30e+03 7.71e+00
  bond pdb=" N   SER C 200 "
       pdb=" CA  SER C 200 "
    ideal  model  delta    sigma   weight residual
    1.455  1.488 -0.033 1.27e-02 6.20e+03 6.64e+00
  bond pdb=" N   TYR A 147 "
       pdb=" CA  TYR A 147 "
    ideal  model  delta    sigma   weight residual
    1.456  1.488 -0.032 1.26e-02 6.30e+03 6.59e+00
  ... (remaining 7603 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.75: 9749
        1.75 -     3.50: 588
        3.50 -     5.25: 41
        5.25 -     7.01: 26
        7.01 -     8.76: 4
  Bond angle restraints: 10408
  Sorted by residual:
  angle pdb=" N   GLU D  60 "
        pdb=" CA  GLU D  60 "
        pdb=" C   GLU D  60 "
      ideal   model   delta    sigma   weight residual
     109.07  103.19    5.88 1.52e+00 4.33e-01 1.50e+01
  angle pdb=" N   GLU B  60 "
        pdb=" CA  GLU B  60 "
        pdb=" C   GLU B  60 "
      ideal   model   delta    sigma   weight residual
     109.07  103.23    5.84 1.52e+00 4.33e-01 1.47e+01
  angle pdb=" N   GLU A  60 "
        pdb=" CA  GLU A  60 "
        pdb=" C   GLU A  60 "
      ideal   model   delta    sigma   weight residual
     109.07  103.25    5.82 1.52e+00 4.33e-01 1.47e+01
  angle pdb=" N   GLU C  60 "
        pdb=" CA  GLU C  60 "
        pdb=" C   GLU C  60 "
      ideal   model   delta    sigma   weight residual
     109.07  103.26    5.81 1.52e+00 4.33e-01 1.46e+01
  angle pdb=" N   GLY B  87 "
        pdb=" CA  GLY B  87 "
        pdb=" C   GLY B  87 "
      ideal   model   delta    sigma   weight residual
     110.38  115.68   -5.30 1.42e+00 4.96e-01 1.39e+01
  ... (remaining 10403 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    16.13: 4199
       16.13 -    32.25: 310
       32.25 -    48.38: 83
       48.38 -    64.51: 12
       64.51 -    80.63: 12
  Dihedral angle restraints: 4616
    sinusoidal: 1916
      harmonic: 2700
  Sorted by residual:
  dihedral pdb=" CA  ALA D  89 "
           pdb=" C   ALA D  89 "
           pdb=" N   PHE D  90 "
           pdb=" CA  PHE D  90 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  161.40   18.60     0      5.00e+00 4.00e-02 1.38e+01
  dihedral pdb=" CA  ALA A  89 "
           pdb=" C   ALA A  89 "
           pdb=" N   PHE A  90 "
           pdb=" CA  PHE A  90 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  161.40   18.60     0      5.00e+00 4.00e-02 1.38e+01
  dihedral pdb=" CA  ALA B  89 "
           pdb=" C   ALA B  89 "
           pdb=" N   PHE B  90 "
           pdb=" CA  PHE B  90 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  161.43   18.57     0      5.00e+00 4.00e-02 1.38e+01
  ... (remaining 4613 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.047: 679
       0.047 -    0.093: 392
       0.093 -    0.140: 115
       0.140 -    0.186: 33
       0.186 -    0.233: 5
  Chirality restraints: 1224
  Sorted by residual:
  chirality pdb=" C1  NAG d   2 "
            pdb=" O2  MAN d   1 "
            pdb=" C2  NAG d   2 "
            pdb=" O5  NAG d   2 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.40   -2.25   -0.15 2.00e-02 2.50e+03 5.81e+01
  chirality pdb=" C1  NAG a   2 "
            pdb=" O2  MAN a   1 "
            pdb=" C2  NAG a   2 "
            pdb=" O5  NAG a   2 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.40   -2.25   -0.15 2.00e-02 2.50e+03 5.79e+01
  chirality pdb=" C1  NAG b   2 "
            pdb=" O2  MAN b   1 "
            pdb=" C2  NAG b   2 "
            pdb=" O5  NAG b   2 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.40   -2.25   -0.15 2.00e-02 2.50e+03 5.59e+01
  ... (remaining 1221 not shown)

  Planarity restraints: 1300
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C2  NAG b   2 "    0.038 2.00e-02 2.50e+03   3.13e-02 1.22e+01
        pdb=" C7  NAG b   2 "   -0.009 2.00e-02 2.50e+03
        pdb=" C8  NAG b   2 "    0.029 2.00e-02 2.50e+03
        pdb=" N2  NAG b   2 "   -0.050 2.00e-02 2.50e+03
        pdb=" O7  NAG b   2 "   -0.008 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C2  NAG a   2 "    0.037 2.00e-02 2.50e+03   3.07e-02 1.18e+01
        pdb=" C7  NAG a   2 "   -0.009 2.00e-02 2.50e+03
        pdb=" C8  NAG a   2 "    0.028 2.00e-02 2.50e+03
        pdb=" N2  NAG a   2 "   -0.049 2.00e-02 2.50e+03
        pdb=" O7  NAG a   2 "   -0.008 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C2  NAG c   2 "   -0.037 2.00e-02 2.50e+03   3.06e-02 1.17e+01
        pdb=" C7  NAG c   2 "    0.009 2.00e-02 2.50e+03
        pdb=" C8  NAG c   2 "   -0.028 2.00e-02 2.50e+03
        pdb=" N2  NAG c   2 "    0.049 2.00e-02 2.50e+03
        pdb=" O7  NAG c   2 "    0.008 2.00e-02 2.50e+03
  ... (remaining 1297 not shown)

  Histogram of nonbonded interaction distances:
        1.86 -     2.47: 72
        2.47 -     3.08: 4957
        3.08 -     3.69: 12198
        3.69 -     4.29: 19117
        4.29 -     4.90: 31434
  Nonbonded interactions: 67778
  Sorted by model distance:
  nonbonded pdb=" OD1 ASP A 149 "
            pdb="MN    MN A 302 "
     model   vdw
     1.864 2.320
  nonbonded pdb=" OD1 ASP C 149 "
            pdb="MN    MN C 302 "
     model   vdw
     1.865 2.320
  nonbonded pdb=" OD1 ASP D 149 "
            pdb="MN    MN D 302 "
     model   vdw
     1.865 2.320
  nonbonded pdb=" OD1 ASP B 149 "
            pdb="MN    MN B 302 "
     model   vdw
     1.866 2.320
  nonbonded pdb=" OD2 ASP C 140 "
            pdb="MN    MN C 302 "
     model   vdw
     1.903 2.320
  ... (remaining 67773 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: 0.02
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'B'
  selection = chain 'C'
  selection = chain 'D'
}
ncs_group {
  reference = chain 'b'
  selection = chain 'c'
  selection = chain 'd'
  selection = chain 'a'
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             1.110
  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:          0.120
  Check model and map are aligned:         0.020
  Set scattering table:                    0.020
  Process input model:                     8.860
  Find NCS groups from input model:        0.060
  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:7.080
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   17.280
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8308
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.009   0.058   7620  Z= 0.415
  Angle     :  0.927   8.758  10444  Z= 0.528
  Chirality :  0.062   0.233   1224
  Planarity :  0.005   0.042   1300
  Dihedral  : 13.418  80.634   2872
  Min Nonbonded Distance : 1.864

Molprobity Statistics.
  All-atom Clashscore : 11.51
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.20 %
    Favored  : 97.80 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  : 15.22 %
    Favored  : 84.78 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.46 %
    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: -0.74 (0.25), residues: 908
  helix:  None (None), residues: 0
  sheet:  0.12 (0.24), residues: 420
  loop : -1.03 (0.25), residues: 488

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B  83 
 TYR   0.012   0.002   TYR A 147 
 PHE   0.020   0.004   PHE C   6 
 TRP   0.012   0.003   TRP A 246 
 HIS   0.005   0.002   HIS A  23 

Details of bonding type rmsd
  covalent geometry    : bond        0.00860 ( 7608)
  covalent geometry    : angle       0.92830 (10408)
  hydrogen bonds       : bond        0.09977 (  324)
  hydrogen bonds       : angle       6.60827 ( 1032)
  link_BETA1-2         : bond        0.00034 (    4)
  link_BETA1-2         : angle       0.73827 (   12)
  link_BETA1-3         : bond        0.00212 (    4)
  link_BETA1-3         : angle       0.74986 (   12)
  link_BETA1-4         : bond        0.00077 (    4)
  link_BETA1-4         : angle       0.36410 (   12)

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

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

  1816 Ramachandran restraints generated.
    908 Oldfield, 0 Emsley, 908 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1816 Ramachandran restraints generated.
    908 Oldfield, 0 Emsley, 908 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  203 residues out of total 808 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 203
  time to evaluate  : 0.291 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
  outliers start: 0
  outliers final: 0
  residues processed: 203
  average time/residue: 0.4848
  time to fit residues: 104.7293
Evaluate side-chains
  168 residues out of total 808 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 168
  time to evaluate  : 0.280 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 92
   random chunks:
   chunk 49 optimal weight:    0.7980
   chunk 53 optimal weight:    0.6980
   chunk 5 optimal weight:    1.9990
   chunk 33 optimal weight:    1.9990
   chunk 65 optimal weight:    0.9980
   chunk 62 optimal weight:    2.9990
   chunk 51 optimal weight:    0.8980
   chunk 38 optimal weight:    5.9990
   chunk 61 optimal weight:    2.9990
   chunk 45 optimal weight:    2.9990
   chunk 74 optimal weight:    0.8980
   overall best weight:    0.8580

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

Flipped N/Q/H residues before XYZ refinement:
A  23 HIS
A  73 ASN
A 102 HIS
A 133 ASN
A 160 ASN
A 173 GLN
A 174 ASN
B  23 HIS
B  73 ASN
B 102 HIS
B 133 ASN
B 160 ASN
B 173 GLN
B 174 ASN
C  23 HIS
C  73 ASN
C 102 HIS
C 133 ASN
C 160 ASN
C 173 GLN
C 174 ASN
D  23 HIS
D  73 ASN
D 102 HIS
D 133 ASN
D 160 ASN
D 173 GLN
D 174 ASN

Total number of N/Q/H flips: 28

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3940 r_free = 0.3940 target = 0.166431 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3625 r_free = 0.3625 target = 0.139310 restraints weight = 7370.131|
|-----------------------------------------------------------------------------|
r_work (start): 0.3516 rms_B_bonded: 1.65
r_work: 0.3390 rms_B_bonded: 2.30 restraints_weight: 0.5000
r_work: 0.3260 rms_B_bonded: 3.82 restraints_weight: 0.2500
r_work (final): 0.3260
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8668
moved from start:          0.1802

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.022   7620  Z= 0.150
  Angle     :  0.606   4.201  10444  Z= 0.340
  Chirality :  0.047   0.166   1224
  Planarity :  0.005   0.037   1300
  Dihedral  :  5.235  17.864   1300
  Min Nonbonded Distance : 2.137

Molprobity Statistics.
  All-atom Clashscore : 5.38
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.20 %
    Favored  : 97.80 %
  Rotamer:
    Outliers :  3.22 %
    Allowed  : 15.35 %
    Favored  : 81.44 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.46 %
    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: -0.25 (0.27), residues: 908
  helix:  None (None), residues: 0
  sheet:  0.43 (0.25), residues: 404
  loop : -0.65 (0.26), residues: 504

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.001   ARG C  57 
 TYR   0.007   0.001   TYR A 184 
 PHE   0.015   0.002   PHE D  68 
 TRP   0.007   0.001   TRP D 246 
 HIS   0.004   0.001   HIS D 181 

Details of bonding type rmsd
  covalent geometry    : bond        0.00303 ( 7608)
  covalent geometry    : angle       0.60153 (10408)
  hydrogen bonds       : bond        0.04416 (  324)
  hydrogen bonds       : angle       5.04830 ( 1032)
  link_BETA1-2         : bond        0.00518 (    4)
  link_BETA1-2         : angle       1.13834 (   12)
  link_BETA1-3         : bond        0.01145 (    4)
  link_BETA1-3         : angle       1.28821 (   12)
  link_BETA1-4         : bond        0.00618 (    4)
  link_BETA1-4         : angle       1.55552 (   12)

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

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

  1816 Ramachandran restraints generated.
    908 Oldfield, 0 Emsley, 908 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1816 Ramachandran restraints generated.
    908 Oldfield, 0 Emsley, 908 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  206 residues out of total 808 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 180
  time to evaluate  : 0.288 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  176 LYS cc_start: 0.7724 (mptp) cc_final: 0.7033 (mtpt)
REVERT: B  176 LYS cc_start: 0.7730 (mptp) cc_final: 0.7019 (mtpt)
REVERT: C  176 LYS cc_start: 0.7706 (mptp) cc_final: 0.7018 (mtpt)
REVERT: D  176 LYS cc_start: 0.7732 (mptp) cc_final: 0.7044 (mtpt)
  outliers start: 26
  outliers final: 18
  residues processed: 195
  average time/residue: 0.5285
  time to fit residues: 109.0049
Evaluate side-chains
  186 residues out of total 808 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 168
  time to evaluate  : 0.268 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    5 SER
Chi-restraints excluded: chain A residue   62 SER
Chi-restraints excluded: chain A residue   86 ASP
Chi-restraints excluded: chain A residue  100 SER
Chi-restraints excluded: chain A residue  204 THR
Chi-restraints excluded: chain B residue    5 SER
Chi-restraints excluded: chain B residue   62 SER
Chi-restraints excluded: chain B residue   86 ASP
Chi-restraints excluded: chain B residue  100 SER
Chi-restraints excluded: chain B residue  204 THR
Chi-restraints excluded: chain C residue  100 SER
Chi-restraints excluded: chain C residue  166 VAL
Chi-restraints excluded: chain C residue  204 THR
Chi-restraints excluded: chain D residue    5 SER
Chi-restraints excluded: chain D residue   86 ASP
Chi-restraints excluded: chain D residue  100 SER
Chi-restraints excluded: chain D residue  166 VAL
Chi-restraints excluded: chain D residue  204 THR
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 92
   random chunks:
   chunk 31 optimal weight:    5.9990
   chunk 25 optimal weight:    5.9990
   chunk 62 optimal weight:    8.9990
   chunk 34 optimal weight:    6.9990
   chunk 44 optimal weight:    0.7980
   chunk 24 optimal weight:    0.7980
   chunk 73 optimal weight:   10.0000
   chunk 91 optimal weight:    1.9990
   chunk 41 optimal weight:    2.9990
   chunk 19 optimal weight:    5.9990
   chunk 8 optimal weight:    0.8980
   overall best weight:    1.4984

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

Flipped N/Q/H residues before XYZ refinement:
B 212 HIS
C 212 HIS
D 212 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3926 r_free = 0.3926 target = 0.164464 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3610 r_free = 0.3610 target = 0.137407 restraints weight = 7424.409|
|-----------------------------------------------------------------------------|
r_work (start): 0.3468 rms_B_bonded: 1.64
r_work: 0.3349 rms_B_bonded: 2.22 restraints_weight: 0.5000
r_work: 0.3222 rms_B_bonded: 3.67 restraints_weight: 0.2500
r_work (final): 0.3222
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8685
moved from start:          0.2085

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.024   7620  Z= 0.185
  Angle     :  0.592   4.553  10444  Z= 0.334
  Chirality :  0.048   0.157   1224
  Planarity :  0.004   0.038   1300
  Dihedral  :  5.056  16.979   1300
  Min Nonbonded Distance : 2.014

Molprobity Statistics.
  All-atom Clashscore : 4.90
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.09 %
    Favored  : 97.91 %
  Rotamer:
    Outliers :  4.33 %
    Allowed  : 15.22 %
    Favored  : 80.45 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.46 %
    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:  0.00 (0.27), residues: 908
  helix:  None (None), residues: 0
  sheet:  0.58 (0.26), residues: 404
  loop : -0.45 (0.27), residues: 504

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG D  57 
 TYR   0.007   0.001   TYR A 184 
 PHE   0.014   0.002   PHE A  68 
 TRP   0.004   0.001   TRP D 218 
 HIS   0.005   0.001   HIS B 181 

Details of bonding type rmsd
  covalent geometry    : bond        0.00393 ( 7608)
  covalent geometry    : angle       0.58905 (10408)
  hydrogen bonds       : bond        0.04480 (  324)
  hydrogen bonds       : angle       4.86819 ( 1032)
  link_BETA1-2         : bond        0.00397 (    4)
  link_BETA1-2         : angle       0.92033 (   12)
  link_BETA1-3         : bond        0.00908 (    4)
  link_BETA1-3         : angle       1.46239 (   12)
  link_BETA1-4         : bond        0.00558 (    4)
  link_BETA1-4         : angle       1.19089 (   12)

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

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

  1816 Ramachandran restraints generated.
    908 Oldfield, 0 Emsley, 908 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1816 Ramachandran restraints generated.
    908 Oldfield, 0 Emsley, 908 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  196 residues out of total 808 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 161
  time to evaluate  : 0.218 
Fit side-chains
REVERT: A  138 GLU cc_start: 0.8894 (OUTLIER) cc_final: 0.8594 (pt0)
REVERT: A  176 LYS cc_start: 0.7813 (mptp) cc_final: 0.7093 (mtpt)
REVERT: B  138 GLU cc_start: 0.8867 (OUTLIER) cc_final: 0.8574 (pt0)
REVERT: B  176 LYS cc_start: 0.7806 (mptp) cc_final: 0.7098 (mtpt)
REVERT: B  189 LYS cc_start: 0.8926 (mtmm) cc_final: 0.8616 (mtmm)
REVERT: C  138 GLU cc_start: 0.8889 (OUTLIER) cc_final: 0.8573 (pt0)
REVERT: C  176 LYS cc_start: 0.7818 (mptp) cc_final: 0.7098 (mtpt)
REVERT: D  138 GLU cc_start: 0.8877 (OUTLIER) cc_final: 0.8584 (pt0)
REVERT: D  176 LYS cc_start: 0.7818 (mptp) cc_final: 0.7101 (mtpt)
REVERT: D  189 LYS cc_start: 0.8931 (mtmm) cc_final: 0.8626 (mtmm)
  outliers start: 35
  outliers final: 23
  residues processed: 178
  average time/residue: 0.5616
  time to fit residues: 105.3553
Evaluate side-chains
  183 residues out of total 808 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 156
  time to evaluate  : 0.265 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    5 SER
Chi-restraints excluded: chain A residue   56 LEU
Chi-restraints excluded: chain A residue   62 SER
Chi-restraints excluded: chain A residue   82 SER
Chi-restraints excluded: chain A residue   86 ASP
Chi-restraints excluded: chain A residue  100 SER
Chi-restraints excluded: chain A residue  138 GLU
Chi-restraints excluded: chain A residue  166 VAL
Chi-restraints excluded: chain B residue    5 SER
Chi-restraints excluded: chain B residue   56 LEU
Chi-restraints excluded: chain B residue   62 SER
Chi-restraints excluded: chain B residue   82 SER
Chi-restraints excluded: chain B residue   86 ASP
Chi-restraints excluded: chain B residue  100 SER
Chi-restraints excluded: chain B residue  138 GLU
Chi-restraints excluded: chain C residue    5 SER
Chi-restraints excluded: chain C residue   62 SER
Chi-restraints excluded: chain C residue   82 SER
Chi-restraints excluded: chain C residue  100 SER
Chi-restraints excluded: chain C residue  138 GLU
Chi-restraints excluded: chain D residue    5 SER
Chi-restraints excluded: chain D residue   56 LEU
Chi-restraints excluded: chain D residue   62 SER
Chi-restraints excluded: chain D residue   82 SER
Chi-restraints excluded: chain D residue   86 ASP
Chi-restraints excluded: chain D residue  100 SER
Chi-restraints excluded: chain D residue  138 GLU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 92
   random chunks:
   chunk 30 optimal weight:    0.9990
   chunk 88 optimal weight:    0.6980
   chunk 37 optimal weight:    6.9990
   chunk 26 optimal weight:    7.9990
   chunk 90 optimal weight:    1.9990
   chunk 15 optimal weight:    8.9990
   chunk 78 optimal weight:    2.9990
   chunk 1 optimal weight:    0.8980
   chunk 60 optimal weight:    7.9990
   chunk 59 optimal weight:    6.9990
   chunk 33 optimal weight:    2.9990
   overall best weight:    1.5186

-------------------------------------------------------------------------------
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 = 0.3927 r_free = 0.3927 target = 0.164379 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3611 r_free = 0.3611 target = 0.137384 restraints weight = 7507.210|
|-----------------------------------------------------------------------------|
r_work (start): 0.3509 rms_B_bonded: 1.65
r_work: 0.3390 rms_B_bonded: 2.26 restraints_weight: 0.5000
r_work: 0.3265 rms_B_bonded: 3.75 restraints_weight: 0.2500
r_work (final): 0.3265
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8705
moved from start:          0.2309

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.022   7620  Z= 0.179
  Angle     :  0.576   4.454  10444  Z= 0.324
  Chirality :  0.046   0.152   1224
  Planarity :  0.004   0.038   1300
  Dihedral  :  5.000  16.646   1300
  Min Nonbonded Distance : 2.076

Molprobity Statistics.
  All-atom Clashscore : 5.38
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.42 %
    Favored  : 97.58 %
  Rotamer:
    Outliers :  3.59 %
    Allowed  : 16.71 %
    Favored  : 79.70 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.46 %
    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:  0.10 (0.28), residues: 908
  helix:  None (None), residues: 0
  sheet:  0.73 (0.26), residues: 396
  loop : -0.44 (0.27), residues: 512

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG B  57 
 TYR   0.008   0.001   TYR A  52 
 PHE   0.015   0.002   PHE D  68 
 TRP   0.004   0.001   TRP D 246 
 HIS   0.004   0.001   HIS D 181 

Details of bonding type rmsd
  covalent geometry    : bond        0.00382 ( 7608)
  covalent geometry    : angle       0.57221 (10408)
  hydrogen bonds       : bond        0.04336 (  324)
  hydrogen bonds       : angle       4.82413 ( 1032)
  link_BETA1-2         : bond        0.00393 (    4)
  link_BETA1-2         : angle       0.91859 (   12)
  link_BETA1-3         : bond        0.00952 (    4)
  link_BETA1-3         : angle       1.46536 (   12)
  link_BETA1-4         : bond        0.00466 (    4)
  link_BETA1-4         : angle       1.35444 (   12)

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

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

  1816 Ramachandran restraints generated.
    908 Oldfield, 0 Emsley, 908 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1816 Ramachandran restraints generated.
    908 Oldfield, 0 Emsley, 908 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  193 residues out of total 808 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 164
  time to evaluate  : 0.331 
Fit side-chains
REVERT: A  176 LYS cc_start: 0.7875 (mptp) cc_final: 0.7202 (mtpt)
REVERT: B  176 LYS cc_start: 0.7866 (mptp) cc_final: 0.7208 (mtpt)
REVERT: C  176 LYS cc_start: 0.7885 (mptp) cc_final: 0.7208 (mtpt)
REVERT: D  176 LYS cc_start: 0.7883 (mptp) cc_final: 0.7221 (mtpt)
REVERT: D  189 LYS cc_start: 0.8957 (OUTLIER) cc_final: 0.8750 (mttp)
  outliers start: 29
  outliers final: 24
  residues processed: 180
  average time/residue: 0.5651
  time to fit residues: 107.3745
Evaluate side-chains
  187 residues out of total 808 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 162
  time to evaluate  : 0.274 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    5 SER
Chi-restraints excluded: chain A residue   56 LEU
Chi-restraints excluded: chain A residue   62 SER
Chi-restraints excluded: chain A residue   82 SER
Chi-restraints excluded: chain A residue  100 SER
Chi-restraints excluded: chain A residue  166 VAL
Chi-restraints excluded: chain B residue    5 SER
Chi-restraints excluded: chain B residue   56 LEU
Chi-restraints excluded: chain B residue   62 SER
Chi-restraints excluded: chain B residue   82 SER
Chi-restraints excluded: chain B residue  100 SER
Chi-restraints excluded: chain B residue  166 VAL
Chi-restraints excluded: chain C residue    5 SER
Chi-restraints excluded: chain C residue   56 LEU
Chi-restraints excluded: chain C residue   62 SER
Chi-restraints excluded: chain C residue   82 SER
Chi-restraints excluded: chain C residue  100 SER
Chi-restraints excluded: chain C residue  166 VAL
Chi-restraints excluded: chain D residue    5 SER
Chi-restraints excluded: chain D residue   56 LEU
Chi-restraints excluded: chain D residue   62 SER
Chi-restraints excluded: chain D residue   82 SER
Chi-restraints excluded: chain D residue  100 SER
Chi-restraints excluded: chain D residue  166 VAL
Chi-restraints excluded: chain D residue  189 LYS
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 92
   random chunks:
   chunk 10 optimal weight:    0.6980
   chunk 75 optimal weight:    0.9990
   chunk 6 optimal weight:    0.8980
   chunk 72 optimal weight:    7.9990
   chunk 45 optimal weight:    4.9990
   chunk 40 optimal weight:    3.9990
   chunk 62 optimal weight:    3.9990
   chunk 67 optimal weight:    3.9990
   chunk 46 optimal weight:    4.9990
   chunk 68 optimal weight:    1.9990
   chunk 84 optimal weight:    7.9990
   overall best weight:    1.7186

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

Flipped N/Q/H residues before XYZ refinement:
B  28 ASN
D  28 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3923 r_free = 0.3923 target = 0.163757 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3607 r_free = 0.3607 target = 0.136927 restraints weight = 7569.296|
|-----------------------------------------------------------------------------|
r_work (start): 0.3472 rms_B_bonded: 1.65
r_work: 0.3353 rms_B_bonded: 2.24 restraints_weight: 0.5000
r_work: 0.3227 rms_B_bonded: 3.71 restraints_weight: 0.2500
r_work (final): 0.3227
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8700
moved from start:          0.2409

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.024   7620  Z= 0.195
  Angle     :  0.592   4.338  10444  Z= 0.331
  Chirality :  0.047   0.152   1224
  Planarity :  0.005   0.039   1300
  Dihedral  :  5.065  16.342   1300
  Min Nonbonded Distance : 2.051

Molprobity Statistics.
  All-atom Clashscore : 5.52
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.08 %
    Favored  : 96.92 %
  Rotamer:
    Outliers :  4.95 %
    Allowed  : 16.71 %
    Favored  : 78.34 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.46 %
    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:  0.21 (0.28), residues: 908
  helix:  None (None), residues: 0
  sheet:  0.80 (0.26), residues: 396
  loop : -0.36 (0.28), residues: 512

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG A  57 
 TYR   0.008   0.001   TYR A  52 
 PHE   0.015   0.002   PHE B   6 
 TRP   0.004   0.001   TRP D 246 
 HIS   0.005   0.001   HIS C 181 

Details of bonding type rmsd
  covalent geometry    : bond        0.00418 ( 7608)
  covalent geometry    : angle       0.58795 (10408)
  hydrogen bonds       : bond        0.04400 (  324)
  hydrogen bonds       : angle       4.84705 ( 1032)
  link_BETA1-2         : bond        0.00339 (    4)
  link_BETA1-2         : angle       0.85350 (   12)
  link_BETA1-3         : bond        0.00926 (    4)
  link_BETA1-3         : angle       1.59491 (   12)
  link_BETA1-4         : bond        0.00521 (    4)
  link_BETA1-4         : angle       1.34905 (   12)

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

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

  1816 Ramachandran restraints generated.
    908 Oldfield, 0 Emsley, 908 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1816 Ramachandran restraints generated.
    908 Oldfield, 0 Emsley, 908 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  202 residues out of total 808 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 40
    poor density    : 162
  time to evaluate  : 0.264 
Fit side-chains
REVERT: A  138 GLU cc_start: 0.8888 (OUTLIER) cc_final: 0.8584 (pt0)
REVERT: A  176 LYS cc_start: 0.7857 (mptp) cc_final: 0.7153 (mtpt)
REVERT: B  138 GLU cc_start: 0.8880 (OUTLIER) cc_final: 0.8577 (pt0)
REVERT: B  176 LYS cc_start: 0.7861 (mptp) cc_final: 0.7173 (mtpt)
REVERT: C  138 GLU cc_start: 0.8887 (OUTLIER) cc_final: 0.8584 (pt0)
REVERT: C  176 LYS cc_start: 0.7869 (mptp) cc_final: 0.7166 (mtpt)
REVERT: D  138 GLU cc_start: 0.8886 (OUTLIER) cc_final: 0.8587 (pt0)
REVERT: D  176 LYS cc_start: 0.7870 (mptp) cc_final: 0.7170 (mtpt)
  outliers start: 40
  outliers final: 24
  residues processed: 186
  average time/residue: 0.5699
  time to fit residues: 111.7903
Evaluate side-chains
  189 residues out of total 808 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 161
  time to evaluate  : 0.317 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    5 SER
Chi-restraints excluded: chain A residue   56 LEU
Chi-restraints excluded: chain A residue   62 SER
Chi-restraints excluded: chain A residue   82 SER
Chi-restraints excluded: chain A residue  100 SER
Chi-restraints excluded: chain A residue  138 GLU
Chi-restraints excluded: chain A residue  166 VAL
Chi-restraints excluded: chain B residue    5 SER
Chi-restraints excluded: chain B residue   56 LEU
Chi-restraints excluded: chain B residue   62 SER
Chi-restraints excluded: chain B residue   82 SER
Chi-restraints excluded: chain B residue  100 SER
Chi-restraints excluded: chain B residue  138 GLU
Chi-restraints excluded: chain B residue  166 VAL
Chi-restraints excluded: chain C residue    5 SER
Chi-restraints excluded: chain C residue   56 LEU
Chi-restraints excluded: chain C residue   62 SER
Chi-restraints excluded: chain C residue   82 SER
Chi-restraints excluded: chain C residue  100 SER
Chi-restraints excluded: chain C residue  138 GLU
Chi-restraints excluded: chain C residue  166 VAL
Chi-restraints excluded: chain D residue    5 SER
Chi-restraints excluded: chain D residue   56 LEU
Chi-restraints excluded: chain D residue   62 SER
Chi-restraints excluded: chain D residue   82 SER
Chi-restraints excluded: chain D residue  100 SER
Chi-restraints excluded: chain D residue  138 GLU
Chi-restraints excluded: chain D residue  166 VAL
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 92
   random chunks:
   chunk 37 optimal weight:    0.0030
   chunk 33 optimal weight:    1.9990
   chunk 75 optimal weight:    0.9990
   chunk 44 optimal weight:    0.7980
   chunk 22 optimal weight:    3.9990
   chunk 54 optimal weight:    0.0020
   chunk 38 optimal weight:    5.9990
   chunk 4 optimal weight:    7.9990
   chunk 83 optimal weight:    3.9990
   chunk 45 optimal weight:    0.9980
   chunk 29 optimal weight:    4.9990
   overall best weight:    0.5600

-------------------------------------------------------------------------------
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 = 0.3967 r_free = 0.3967 target = 0.167950 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3665 r_free = 0.3665 target = 0.141538 restraints weight = 7578.208|
|-----------------------------------------------------------------------------|
r_work (start): 0.3613 rms_B_bonded: 1.67
r_work: 0.3498 rms_B_bonded: 2.30 restraints_weight: 0.5000
r_work: 0.3379 rms_B_bonded: 3.83 restraints_weight: 0.2500
r_work (final): 0.3379
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8668
moved from start:          0.2639

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.026   7620  Z= 0.115
  Angle     :  0.531   4.426  10444  Z= 0.295
  Chirality :  0.045   0.147   1224
  Planarity :  0.004   0.040   1300
  Dihedral  :  4.706  16.143   1300
  Min Nonbonded Distance : 2.143

Molprobity Statistics.
  All-atom Clashscore : 5.17
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.76 %
    Favored  : 98.24 %
  Rotamer:
    Outliers :  2.60 %
    Allowed  : 18.69 %
    Favored  : 78.71 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.46 %
    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:  0.25 (0.28), residues: 908
  helix:  None (None), residues: 0
  sheet:  0.85 (0.28), residues: 356
  loop : -0.26 (0.27), residues: 552

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG C  57 
 TYR   0.007   0.001   TYR B 147 
 PHE   0.015   0.002   PHE D  68 
 TRP   0.004   0.001   TRP C 246 
 HIS   0.002   0.001   HIS A 212 

Details of bonding type rmsd
  covalent geometry    : bond        0.00229 ( 7608)
  covalent geometry    : angle       0.52755 (10408)
  hydrogen bonds       : bond        0.03598 (  324)
  hydrogen bonds       : angle       4.60926 ( 1032)
  link_BETA1-2         : bond        0.00369 (    4)
  link_BETA1-2         : angle       0.79988 (   12)
  link_BETA1-3         : bond        0.01000 (    4)
  link_BETA1-3         : angle       1.35653 (   12)
  link_BETA1-4         : bond        0.00553 (    4)
  link_BETA1-4         : angle       1.29512 (   12)

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

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

  1816 Ramachandran restraints generated.
    908 Oldfield, 0 Emsley, 908 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1816 Ramachandran restraints generated.
    908 Oldfield, 0 Emsley, 908 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  190 residues out of total 808 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 169
  time to evaluate  : 0.286 
Fit side-chains
REVERT: A  138 GLU cc_start: 0.8840 (OUTLIER) cc_final: 0.8538 (pt0)
REVERT: B  138 GLU cc_start: 0.8837 (OUTLIER) cc_final: 0.8539 (pt0)
REVERT: C  138 GLU cc_start: 0.8845 (OUTLIER) cc_final: 0.8552 (pt0)
REVERT: D  138 GLU cc_start: 0.8851 (OUTLIER) cc_final: 0.8559 (pt0)
  outliers start: 21
  outliers final: 8
  residues processed: 173
  average time/residue: 0.5796
  time to fit residues: 105.6034
Evaluate side-chains
  179 residues out of total 808 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 167
  time to evaluate  : 0.215 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   56 LEU
Chi-restraints excluded: chain A residue  100 SER
Chi-restraints excluded: chain A residue  138 GLU
Chi-restraints excluded: chain B residue   56 LEU
Chi-restraints excluded: chain B residue  100 SER
Chi-restraints excluded: chain B residue  138 GLU
Chi-restraints excluded: chain C residue   56 LEU
Chi-restraints excluded: chain C residue  100 SER
Chi-restraints excluded: chain C residue  138 GLU
Chi-restraints excluded: chain D residue   56 LEU
Chi-restraints excluded: chain D residue  100 SER
Chi-restraints excluded: chain D residue  138 GLU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 92
   random chunks:
   chunk 88 optimal weight:    5.9990
   chunk 74 optimal weight:    0.9990
   chunk 4 optimal weight:    0.7980
   chunk 76 optimal weight:    2.9990
   chunk 48 optimal weight:    0.9990
   chunk 14 optimal weight:    0.4980
   chunk 82 optimal weight:    6.9990
   chunk 12 optimal weight:    1.9990
   chunk 49 optimal weight:    0.7980
   chunk 58 optimal weight:    0.8980
   chunk 79 optimal weight:    2.9990
   overall best weight:    0.7982

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

Flipped N/Q/H residues before XYZ refinement:
A 133 ASN
C 133 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3965 r_free = 0.3965 target = 0.167657 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3661 r_free = 0.3661 target = 0.141123 restraints weight = 7608.799|
|-----------------------------------------------------------------------------|
r_work (start): 0.3527 rms_B_bonded: 1.67
r_work: 0.3402 rms_B_bonded: 2.31 restraints_weight: 0.5000
r_work: 0.3274 rms_B_bonded: 3.80 restraints_weight: 0.2500
r_work (final): 0.3274
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8660
moved from start:          0.2729

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   7620  Z= 0.127
  Angle     :  0.540   4.717  10444  Z= 0.298
  Chirality :  0.045   0.147   1224
  Planarity :  0.004   0.041   1300
  Dihedral  :  4.690  16.056   1300
  Min Nonbonded Distance : 2.092

Molprobity Statistics.
  All-atom Clashscore : 5.52
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.43 %
    Favored  : 98.57 %
  Rotamer:
    Outliers :  2.48 %
    Allowed  : 19.06 %
    Favored  : 78.47 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.46 %
    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:  0.27 (0.28), residues: 908
  helix:  None (None), residues: 0
  sheet:  0.84 (0.27), residues: 356
  loop : -0.24 (0.27), residues: 552

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG B  57 
 TYR   0.008   0.001   TYR D  52 
 PHE   0.015   0.002   PHE A  68 
 TRP   0.003   0.001   TRP C 218 
 HIS   0.003   0.001   HIS C 181 

Details of bonding type rmsd
  covalent geometry    : bond        0.00258 ( 7608)
  covalent geometry    : angle       0.53600 (10408)
  hydrogen bonds       : bond        0.03630 (  324)
  hydrogen bonds       : angle       4.56185 ( 1032)
  link_BETA1-2         : bond        0.00369 (    4)
  link_BETA1-2         : angle       0.87988 (   12)
  link_BETA1-3         : bond        0.00962 (    4)
  link_BETA1-3         : angle       1.48179 (   12)
  link_BETA1-4         : bond        0.00524 (    4)
  link_BETA1-4         : angle       1.30239 (   12)

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

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

  1816 Ramachandran restraints generated.
    908 Oldfield, 0 Emsley, 908 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1816 Ramachandran restraints generated.
    908 Oldfield, 0 Emsley, 908 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  190 residues out of total 808 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 170
  time to evaluate  : 0.339 
Fit side-chains
REVERT: A  138 GLU cc_start: 0.8872 (OUTLIER) cc_final: 0.8560 (pt0)
REVERT: B  138 GLU cc_start: 0.8872 (OUTLIER) cc_final: 0.8573 (pt0)
REVERT: C  138 GLU cc_start: 0.8881 (OUTLIER) cc_final: 0.8582 (pt0)
REVERT: D  138 GLU cc_start: 0.8880 (OUTLIER) cc_final: 0.8580 (pt0)
  outliers start: 20
  outliers final: 14
  residues processed: 182
  average time/residue: 0.5423
  time to fit residues: 104.3434
Evaluate side-chains
  186 residues out of total 808 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 168
  time to evaluate  : 0.281 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    5 SER
Chi-restraints excluded: chain A residue   82 SER
Chi-restraints excluded: chain A residue  100 SER
Chi-restraints excluded: chain A residue  138 GLU
Chi-restraints excluded: chain B residue    5 SER
Chi-restraints excluded: chain B residue   82 SER
Chi-restraints excluded: chain B residue  100 SER
Chi-restraints excluded: chain B residue  138 GLU
Chi-restraints excluded: chain C residue    5 SER
Chi-restraints excluded: chain C residue   56 LEU
Chi-restraints excluded: chain C residue   82 SER
Chi-restraints excluded: chain C residue  100 SER
Chi-restraints excluded: chain C residue  138 GLU
Chi-restraints excluded: chain D residue    5 SER
Chi-restraints excluded: chain D residue   56 LEU
Chi-restraints excluded: chain D residue   82 SER
Chi-restraints excluded: chain D residue  100 SER
Chi-restraints excluded: chain D residue  138 GLU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 92
   random chunks:
   chunk 56 optimal weight:    7.9990
   chunk 52 optimal weight:    0.2980
   chunk 51 optimal weight:    3.9990
   chunk 80 optimal weight:    2.9990
   chunk 63 optimal weight:    3.9990
   chunk 83 optimal weight:    1.9990
   chunk 58 optimal weight:    2.9990
   chunk 64 optimal weight:    0.7980
   chunk 27 optimal weight:    5.9990
   chunk 21 optimal weight:    0.9980
   chunk 3 optimal weight:    3.9990
   overall best weight:    1.4184

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

Flipped N/Q/H residues before XYZ refinement:
B 212 HIS
C 212 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3930 r_free = 0.3930 target = 0.164698 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3611 r_free = 0.3611 target = 0.137479 restraints weight = 7650.999|
|-----------------------------------------------------------------------------|
r_work (start): 0.3493 rms_B_bonded: 1.68
r_work: 0.3373 rms_B_bonded: 2.27 restraints_weight: 0.5000
r_work: 0.3247 rms_B_bonded: 3.74 restraints_weight: 0.2500
r_work (final): 0.3247
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8682
moved from start:          0.2710

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.027   7620  Z= 0.169
  Angle     :  0.576   4.890  10444  Z= 0.319
  Chirality :  0.046   0.156   1224
  Planarity :  0.004   0.040   1300
  Dihedral  :  4.869  15.999   1300
  Min Nonbonded Distance : 2.071

Molprobity Statistics.
  All-atom Clashscore : 5.58
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.54 %
    Favored  : 98.46 %
  Rotamer:
    Outliers :  2.23 %
    Allowed  : 19.68 %
    Favored  : 78.09 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.46 %
    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:  0.28 (0.28), residues: 908
  helix:  None (None), residues: 0
  sheet:  0.86 (0.27), residues: 356
  loop : -0.24 (0.27), residues: 552

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG C  57 
 TYR   0.008   0.001   TYR A  52 
 PHE   0.015   0.002   PHE A   6 
 TRP   0.004   0.001   TRP A 218 
 HIS   0.004   0.001   HIS A 181 

Details of bonding type rmsd
  covalent geometry    : bond        0.00355 ( 7608)
  covalent geometry    : angle       0.57121 (10408)
  hydrogen bonds       : bond        0.04019 (  324)
  hydrogen bonds       : angle       4.69347 ( 1032)
  link_BETA1-2         : bond        0.00265 (    4)
  link_BETA1-2         : angle       0.90429 (   12)
  link_BETA1-3         : bond        0.00970 (    4)
  link_BETA1-3         : angle       1.60256 (   12)
  link_BETA1-4         : bond        0.00476 (    4)
  link_BETA1-4         : angle       1.37871 (   12)

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

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

  1816 Ramachandran restraints generated.
    908 Oldfield, 0 Emsley, 908 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1816 Ramachandran restraints generated.
    908 Oldfield, 0 Emsley, 908 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  188 residues out of total 808 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 170
  time to evaluate  : 0.267 
Fit side-chains
REVERT: B  176 LYS cc_start: 0.7888 (mptp) cc_final: 0.7210 (mtpt)
REVERT: C  138 GLU cc_start: 0.8900 (OUTLIER) cc_final: 0.8595 (pt0)
REVERT: D  138 GLU cc_start: 0.8905 (OUTLIER) cc_final: 0.8605 (pt0)
  outliers start: 18
  outliers final: 14
  residues processed: 182
  average time/residue: 0.5555
  time to fit residues: 106.7703
Evaluate side-chains
  181 residues out of total 808 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 165
  time to evaluate  : 0.294 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    5 SER
Chi-restraints excluded: chain A residue   82 SER
Chi-restraints excluded: chain A residue  100 SER
Chi-restraints excluded: chain B residue    5 SER
Chi-restraints excluded: chain B residue   82 SER
Chi-restraints excluded: chain B residue  100 SER
Chi-restraints excluded: chain C residue    5 SER
Chi-restraints excluded: chain C residue   56 LEU
Chi-restraints excluded: chain C residue   82 SER
Chi-restraints excluded: chain C residue  100 SER
Chi-restraints excluded: chain C residue  138 GLU
Chi-restraints excluded: chain D residue    5 SER
Chi-restraints excluded: chain D residue   56 LEU
Chi-restraints excluded: chain D residue   82 SER
Chi-restraints excluded: chain D residue  100 SER
Chi-restraints excluded: chain D residue  138 GLU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 92
   random chunks:
   chunk 65 optimal weight:    5.9990
   chunk 62 optimal weight:    6.9990
   chunk 8 optimal weight:    6.9990
   chunk 2 optimal weight:    0.2980
   chunk 39 optimal weight:    5.9990
   chunk 76 optimal weight:    0.9990
   chunk 30 optimal weight:    0.8980
   chunk 38 optimal weight:    0.9980
   chunk 47 optimal weight:    0.4980
   chunk 64 optimal weight:    0.0030
   chunk 20 optimal weight:    7.9990
   overall best weight:    0.5390

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

Flipped N/Q/H residues before XYZ refinement:
B 133 ASN
B 212 HIS
C 212 HIS
D 133 ASN
D 212 HIS

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3984 r_free = 0.3984 target = 0.168744 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3682 r_free = 0.3682 target = 0.142436 restraints weight = 7578.135|
|-----------------------------------------------------------------------------|
r_work (start): 0.3542 rms_B_bonded: 1.66
r_work: 0.3417 rms_B_bonded: 2.30 restraints_weight: 0.5000
r_work: 0.3287 rms_B_bonded: 3.79 restraints_weight: 0.2500
r_work (final): 0.3287
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8633
moved from start:          0.2882

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.030   7620  Z= 0.113
  Angle     :  0.532   5.157  10444  Z= 0.292
  Chirality :  0.044   0.146   1224
  Planarity :  0.004   0.040   1300
  Dihedral  :  4.631  15.960   1300
  Min Nonbonded Distance : 2.146

Molprobity Statistics.
  All-atom Clashscore : 5.38
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.87 %
    Favored  : 98.13 %
  Rotamer:
    Outliers :  1.61 %
    Allowed  : 20.92 %
    Favored  : 77.48 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.46 %
    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 (0.28), residues: 908
  helix:  None (None), residues: 0
  sheet:  0.95 (0.28), residues: 356
  loop : -0.26 (0.27), residues: 552

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG D  57 
 TYR   0.007   0.001   TYR A 147 
 PHE   0.015   0.002   PHE A  68 
 TRP   0.004   0.001   TRP B 246 
 HIS   0.002   0.001   HIS A 181 

Details of bonding type rmsd
  covalent geometry    : bond        0.00226 ( 7608)
  covalent geometry    : angle       0.52823 (10408)
  hydrogen bonds       : bond        0.03449 (  324)
  hydrogen bonds       : angle       4.53010 ( 1032)
  link_BETA1-2         : bond        0.00371 (    4)
  link_BETA1-2         : angle       0.76377 (   12)
  link_BETA1-3         : bond        0.00988 (    4)
  link_BETA1-3         : angle       1.33739 (   12)
  link_BETA1-4         : bond        0.00521 (    4)
  link_BETA1-4         : angle       1.39180 (   12)

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

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

  1816 Ramachandran restraints generated.
    908 Oldfield, 0 Emsley, 908 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1816 Ramachandran restraints generated.
    908 Oldfield, 0 Emsley, 908 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  198 residues out of total 808 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 185
  time to evaluate  : 0.271 
Fit side-chains
REVERT: A  138 GLU cc_start: 0.8858 (OUTLIER) cc_final: 0.8532 (pt0)
REVERT: B  138 GLU cc_start: 0.8863 (OUTLIER) cc_final: 0.8549 (pt0)
REVERT: C  138 GLU cc_start: 0.8878 (OUTLIER) cc_final: 0.8574 (pt0)
REVERT: D  138 GLU cc_start: 0.8876 (OUTLIER) cc_final: 0.8579 (pt0)
  outliers start: 13
  outliers final: 7
  residues processed: 192
  average time/residue: 0.5357
  time to fit residues: 108.8361
Evaluate side-chains
  184 residues out of total 808 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 173
  time to evaluate  : 0.321 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  100 SER
Chi-restraints excluded: chain A residue  138 GLU
Chi-restraints excluded: chain B residue   82 SER
Chi-restraints excluded: chain B residue  100 SER
Chi-restraints excluded: chain B residue  138 GLU
Chi-restraints excluded: chain C residue   82 SER
Chi-restraints excluded: chain C residue  100 SER
Chi-restraints excluded: chain C residue  138 GLU
Chi-restraints excluded: chain D residue   82 SER
Chi-restraints excluded: chain D residue  100 SER
Chi-restraints excluded: chain D residue  138 GLU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 92
   random chunks:
   chunk 43 optimal weight:    7.9990
   chunk 29 optimal weight:    0.7980
   chunk 42 optimal weight:    0.2980
   chunk 5 optimal weight:    2.9990
   chunk 13 optimal weight:    3.9990
   chunk 7 optimal weight:    3.9990
   chunk 4 optimal weight:    7.9990
   chunk 64 optimal weight:    3.9990
   chunk 62 optimal weight:    7.9990
   chunk 28 optimal weight:    0.9990
   chunk 83 optimal weight:    0.1980
   overall best weight:    1.0584

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

Flipped N/Q/H residues before XYZ refinement:
A  23 HIS
C  23 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3951 r_free = 0.3951 target = 0.166066 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 53)----------------|
| r_work = 0.3635 r_free = 0.3635 target = 0.139143 restraints weight = 7614.592|
|-----------------------------------------------------------------------------|
r_work (start): 0.3586 rms_B_bonded: 1.68
r_work: 0.3471 rms_B_bonded: 2.29 restraints_weight: 0.5000
r_work: 0.3351 rms_B_bonded: 3.81 restraints_weight: 0.2500
r_work (final): 0.3351
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8678
moved from start:          0.2860

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028   7620  Z= 0.142
  Angle     :  0.556   5.103  10444  Z= 0.306
  Chirality :  0.045   0.153   1224
  Planarity :  0.004   0.041   1300
  Dihedral  :  4.742  15.907   1300
  Min Nonbonded Distance : 2.078

Molprobity Statistics.
  All-atom Clashscore : 5.38
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.98 %
    Favored  : 98.02 %
  Rotamer:
    Outliers :  1.73 %
    Allowed  : 22.28 %
    Favored  : 75.99 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.46 %
    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:  0.31 (0.28), residues: 908
  helix:  None (None), residues: 0
  sheet:  0.95 (0.28), residues: 356
  loop : -0.27 (0.27), residues: 552

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG C  57 
 TYR   0.008   0.001   TYR D  52 
 PHE   0.014   0.002   PHE A  68 
 TRP   0.003   0.001   TRP A 218 
 HIS   0.003   0.001   HIS A 181 

Details of bonding type rmsd
  covalent geometry    : bond        0.00293 ( 7608)
  covalent geometry    : angle       0.55143 (10408)
  hydrogen bonds       : bond        0.03742 (  324)
  hydrogen bonds       : angle       4.58654 ( 1032)
  link_BETA1-2         : bond        0.00309 (    4)
  link_BETA1-2         : angle       0.88706 (   12)
  link_BETA1-3         : bond        0.01002 (    4)
  link_BETA1-3         : angle       1.51476 (   12)
  link_BETA1-4         : bond        0.00463 (    4)
  link_BETA1-4         : angle       1.37238 (   12)

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

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

  1816 Ramachandran restraints generated.
    908 Oldfield, 0 Emsley, 908 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1816 Ramachandran restraints generated.
    908 Oldfield, 0 Emsley, 908 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  188 residues out of total 808 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 174
  time to evaluate  : 0.280 
Fit side-chains
REVERT: A  138 GLU cc_start: 0.8914 (OUTLIER) cc_final: 0.8613 (pt0)
REVERT: B  138 GLU cc_start: 0.8895 (OUTLIER) cc_final: 0.8575 (pt0)
REVERT: C  138 GLU cc_start: 0.8893 (OUTLIER) cc_final: 0.8581 (pt0)
REVERT: D  138 GLU cc_start: 0.8898 (OUTLIER) cc_final: 0.8599 (pt0)
  outliers start: 14
  outliers final: 10
  residues processed: 184
  average time/residue: 0.5386
  time to fit residues: 104.7321
Evaluate side-chains
  188 residues out of total 808 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 174
  time to evaluate  : 0.272 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    5 SER
Chi-restraints excluded: chain A residue   82 SER
Chi-restraints excluded: chain A residue  100 SER
Chi-restraints excluded: chain A residue  138 GLU
Chi-restraints excluded: chain B residue   82 SER
Chi-restraints excluded: chain B residue  100 SER
Chi-restraints excluded: chain B residue  138 GLU
Chi-restraints excluded: chain C residue   82 SER
Chi-restraints excluded: chain C residue  100 SER
Chi-restraints excluded: chain C residue  138 GLU
Chi-restraints excluded: chain D residue    5 SER
Chi-restraints excluded: chain D residue   82 SER
Chi-restraints excluded: chain D residue  100 SER
Chi-restraints excluded: chain D residue  138 GLU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 92
   random chunks:
   chunk 50 optimal weight:    3.9990
   chunk 73 optimal weight:    4.9990
   chunk 23 optimal weight:    3.9990
   chunk 78 optimal weight:    0.6980
   chunk 79 optimal weight:    0.9990
   chunk 90 optimal weight:    0.8980
   chunk 29 optimal weight:    0.4980
   chunk 6 optimal weight:    2.9990
   chunk 69 optimal weight:    2.9990
   chunk 47 optimal weight:    1.9990
   chunk 85 optimal weight:    8.9990
   overall best weight:    1.0184

-------------------------------------------------------------------------------
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 = 0.3967 r_free = 0.3967 target = 0.167084 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3659 r_free = 0.3659 target = 0.140640 restraints weight = 7552.411|
|-----------------------------------------------------------------------------|
r_work (start): 0.3536 rms_B_bonded: 1.66
r_work: 0.3408 rms_B_bonded: 2.31 restraints_weight: 0.5000
r_work: 0.3279 rms_B_bonded: 3.81 restraints_weight: 0.2500
r_work (final): 0.3279
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8671
moved from start:          0.2863

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028   7620  Z= 0.139
  Angle     :  0.554   5.111  10444  Z= 0.305
  Chirality :  0.045   0.152   1224
  Planarity :  0.004   0.040   1300
  Dihedral  :  4.743  15.892   1300
  Min Nonbonded Distance : 2.099

Molprobity Statistics.
  All-atom Clashscore : 5.38
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.76 %
    Favored  : 98.24 %
  Rotamer:
    Outliers :  1.86 %
    Allowed  : 22.28 %
    Favored  : 75.87 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.46 %
    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 (0.28), residues: 908
  helix:  None (None), residues: 0
  sheet:  0.98 (0.28), residues: 356
  loop : -0.26 (0.27), residues: 552

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG C  57 
 TYR   0.008   0.001   TYR B  52 
 PHE   0.015   0.002   PHE A  68 
 TRP   0.003   0.001   TRP C 218 
 HIS   0.003   0.001   HIS D 181 

Details of bonding type rmsd
  covalent geometry    : bond        0.00288 ( 7608)
  covalent geometry    : angle       0.54962 (10408)
  hydrogen bonds       : bond        0.03724 (  324)
  hydrogen bonds       : angle       4.58895 ( 1032)
  link_BETA1-2         : bond        0.00267 (    4)
  link_BETA1-2         : angle       0.88007 (   12)
  link_BETA1-3         : bond        0.01002 (    4)
  link_BETA1-3         : angle       1.47837 (   12)
  link_BETA1-4         : bond        0.00432 (    4)
  link_BETA1-4         : angle       1.38325 (   12)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3377.03 seconds
wall clock time: 58 minutes 12.17 seconds (3492.17 seconds total)