Starting phenix.real_space_refine
on Sun Apr  5 02:29:50 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9vc0_64938/04_2026/9vc0_64938.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9vc0_64938/04_2026/9vc0_64938.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.48
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/9vc0_64938/04_2026/9vc0_64938.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9vc0_64938/04_2026/9vc0_64938.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/9vc0_64938/04_2026/9vc0_64938.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9vc0_64938/04_2026/9vc0_64938.map"
  }
  resolution = 2.48
  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=   0.094
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    4656      2.51       5
     N    1196      2.21       5
     O    1510      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 12 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: 7370
  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: "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: "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: "a"
      Number of atoms: 23
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 23
          Unusual residues: {'BMA': 1, 'MAN': 1}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
          Unresolved non-hydrogen bonds: 1
          Unresolved non-hydrogen angles: 2
          Unresolved non-hydrogen dihedrals: 3
          Unresolved non-hydrogen chiralities: 1
    Chain: "b"
      Number of atoms: 23
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 23
          Unusual residues: {'BMA': 1, 'MAN': 1}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
          Unresolved non-hydrogen bonds: 1
          Unresolved non-hydrogen angles: 2
          Unresolved non-hydrogen dihedrals: 3
          Unresolved non-hydrogen chiralities: 1
    Chain: "c"
      Number of atoms: 23
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 23
          Unusual residues: {'BMA': 1, 'MAN': 1}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
          Unresolved non-hydrogen bonds: 1
          Unresolved non-hydrogen angles: 2
          Unresolved non-hydrogen dihedrals: 3
          Unresolved non-hydrogen chiralities: 1
    Chain: "d"
      Number of atoms: 23
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 23
          Unusual residues: {'BMA': 1, 'MAN': 1}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
          Unresolved non-hydrogen bonds: 1
          Unresolved non-hydrogen angles: 2
          Unresolved non-hydrogen dihedrals: 3
          Unresolved non-hydrogen chiralities: 1
    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: "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: "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: "A"
      Number of atoms: 13
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 13, 13
          Classifications: {'water': 13}
          Link IDs: {None: 12}
    Chain: "B"
      Number of atoms: 12
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 12, 12
          Classifications: {'water': 12}
          Link IDs: {None: 11}
    Chain: "D"
      Number of atoms: 12
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 12, 12
          Classifications: {'water': 12}
          Link IDs: {None: 11}
    Chain: "C"
      Number of atoms: 13
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 13, 13
          Classifications: {'water': 13}
          Link IDs: {None: 12}
  Time building chain proxies: 1.73, per 1000 atoms: 0.23
  Number of scatterers: 7370
  At special positions: 0
  Unit cell: (87.48, 81, 79.704, 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    1510      8.00
     N    1196      7.00
     C    4656      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
    ALPHA1-3
      " BMA a   1 " - " MAN a   2 "
      " BMA b   1 " - " MAN b   2 "
      " BMA c   1 " - " MAN c   2 "
      " BMA d   1 " - " MAN d   2 "
  Time building additional restraints: 0.73
  Conformation dependent library (CDL) restraints added in 263.4 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:
      8 helices and 12 sheets defined
      4.3% alpha, 55.4% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.29
  Creating SS restraints...
    Processing helix  chain 'A' and resid 102 through 106
      removed outlier: 3.876A  pdb=" N   PHE A 105 " --> pdb=" O   HIS A 102 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 210 through 214
    Processing helix  chain 'B' and resid 102 through 106
      removed outlier: 3.875A  pdb=" N   PHE B 105 " --> pdb=" O   HIS B 102 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 210 through 214
    Processing helix  chain 'D' and resid 102 through 106
      removed outlier: 3.876A  pdb=" N   PHE D 105 " --> pdb=" O   HIS D 102 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 210 through 214
    Processing helix  chain 'C' and resid 102 through 106
      removed outlier: 3.876A  pdb=" N   PHE C 105 " --> pdb=" O   HIS C 102 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 210 through 214
    Processing sheet with id=AA1, first strand: chain 'A' and resid 31 through 32
    Processing sheet with id=AA2, first strand: chain 'A' and resid 203 through 208
      removed outlier: 6.335A  pdb=" N   ALA A  63 " --> pdb=" O   THR A 247 " (cutoff:3.500A)
      removed outlier: 6.334A  pdb=" N   THR A 247 " --> pdb=" O   ALA A  63 " (cutoff:3.500A)
      removed outlier: 6.923A  pdb=" N   LEU A  65 " --> pdb=" O   LEU A 245 " (cutoff:3.500A)
      removed outlier: 4.548A  pdb=" N   LEU A 245 " --> pdb=" O   LEU A  65 " (cutoff:3.500A)
      removed outlier: 6.900A  pdb=" N   SER A  67 " --> pdb=" O   SER A 243 " (cutoff:3.500A)
      removed outlier: 4.549A  pdb=" N   SER A 243 " --> pdb=" O   SER A  67 " (cutoff:3.500A)
      removed outlier: 6.921A  pdb=" N   ASP A  69 " --> pdb=" O   PHE A 241 " (cutoff:3.500A)
      removed outlier: 4.527A  pdb=" N   PHE A 241 " --> pdb=" O   ASP A  69 " (cutoff:3.500A)
      removed outlier: 6.665A  pdb=" N   ILE A  71 " --> pdb=" O   TRP A 239 " (cutoff:3.500A)
      removed outlier: 4.307A  pdb=" N   TRP A 239 " --> pdb=" O   ILE A  71 " (cutoff:3.500A)
      removed outlier: 6.615A  pdb=" N   ASN A  73 " --> pdb=" O   HIS A 237 " (cutoff:3.500A)
      removed outlier: 6.614A  pdb=" N   ASN B  73 " --> pdb=" O   HIS B 237 " (cutoff:3.500A)
      removed outlier: 4.307A  pdb=" N   TRP B 239 " --> pdb=" O   ILE B  71 " (cutoff:3.500A)
      removed outlier: 6.666A  pdb=" N   ILE B  71 " --> pdb=" O   TRP B 239 " (cutoff:3.500A)
      removed outlier: 4.527A  pdb=" N   PHE B 241 " --> pdb=" O   ASP B  69 " (cutoff:3.500A)
      removed outlier: 6.921A  pdb=" N   ASP B  69 " --> pdb=" O   PHE B 241 " (cutoff:3.500A)
      removed outlier: 4.549A  pdb=" N   SER B 243 " --> pdb=" O   SER B  67 " (cutoff:3.500A)
      removed outlier: 6.900A  pdb=" N   SER B  67 " --> pdb=" O   SER B 243 " (cutoff:3.500A)
      removed outlier: 4.549A  pdb=" N   LEU B 245 " --> pdb=" O   LEU B  65 " (cutoff:3.500A)
      removed outlier: 6.923A  pdb=" N   LEU B  65 " --> pdb=" O   LEU B 245 " (cutoff:3.500A)
      removed outlier: 6.335A  pdb=" N   THR B 247 " --> pdb=" O   ALA B  63 " (cutoff:3.500A)
      removed outlier: 6.335A  pdb=" N   ALA B  63 " --> pdb=" O   THR B 247 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 18 through 22
      removed outlier: 5.239A  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: 5.239A  pdb=" N   VAL A 221 " --> pdb=" O   TYR A  52 " (cutoff:3.500A)
      removed outlier: 3.636A  pdb=" N   GLY A  87 " --> pdb=" O   SER A 226 " (cutoff:3.500A)
      removed outlier: 4.220A  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: 5.238A  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: 5.238A  pdb=" N   VAL B 221 " --> pdb=" O   TYR B  52 " (cutoff:3.500A)
      removed outlier: 3.637A  pdb=" N   GLY B  87 " --> pdb=" O   SER B 226 " (cutoff:3.500A)
      removed outlier: 4.220A  pdb=" N   VAL B 166 " --> pdb=" O   ILE B 157 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'D' and resid 31 through 32
    Processing sheet with id=AA8, first strand: chain 'D' and resid 203 through 208
      removed outlier: 6.334A  pdb=" N   ALA D  63 " --> pdb=" O   THR D 247 " (cutoff:3.500A)
      removed outlier: 6.334A  pdb=" N   THR D 247 " --> pdb=" O   ALA D  63 " (cutoff:3.500A)
      removed outlier: 6.922A  pdb=" N   LEU D  65 " --> pdb=" O   LEU D 245 " (cutoff:3.500A)
      removed outlier: 4.548A  pdb=" N   LEU D 245 " --> pdb=" O   LEU D  65 " (cutoff:3.500A)
      removed outlier: 6.899A  pdb=" N   SER D  67 " --> pdb=" O   SER D 243 " (cutoff:3.500A)
      removed outlier: 4.548A  pdb=" N   SER D 243 " --> pdb=" O   SER D  67 " (cutoff:3.500A)
      removed outlier: 6.921A  pdb=" N   ASP D  69 " --> pdb=" O   PHE D 241 " (cutoff:3.500A)
      removed outlier: 4.526A  pdb=" N   PHE D 241 " --> pdb=" O   ASP D  69 " (cutoff:3.500A)
      removed outlier: 6.666A  pdb=" N   ILE D  71 " --> pdb=" O   TRP D 239 " (cutoff:3.500A)
      removed outlier: 4.306A  pdb=" N   TRP D 239 " --> pdb=" O   ILE D  71 " (cutoff:3.500A)
      removed outlier: 6.615A  pdb=" N   ASN D  73 " --> pdb=" O   HIS D 237 " (cutoff:3.500A)
      removed outlier: 6.615A  pdb=" N   ASN C  73 " --> pdb=" O   HIS C 237 " (cutoff:3.500A)
      removed outlier: 4.306A  pdb=" N   TRP C 239 " --> pdb=" O   ILE C  71 " (cutoff:3.500A)
      removed outlier: 6.665A  pdb=" N   ILE C  71 " --> pdb=" O   TRP C 239 " (cutoff:3.500A)
      removed outlier: 4.526A  pdb=" N   PHE C 241 " --> pdb=" O   ASP C  69 " (cutoff:3.500A)
      removed outlier: 6.922A  pdb=" N   ASP C  69 " --> pdb=" O   PHE C 241 " (cutoff:3.500A)
      removed outlier: 4.549A  pdb=" N   SER C 243 " --> pdb=" O   SER C  67 " (cutoff:3.500A)
      removed outlier: 6.900A  pdb=" N   SER C  67 " --> pdb=" O   SER C 243 " (cutoff:3.500A)
      removed outlier: 4.549A  pdb=" N   LEU C 245 " --> pdb=" O   LEU C  65 " (cutoff:3.500A)
      removed outlier: 6.923A  pdb=" N   LEU C  65 " --> pdb=" O   LEU C 245 " (cutoff:3.500A)
      removed outlier: 6.334A  pdb=" N   THR C 247 " --> pdb=" O   ALA C  63 " (cutoff:3.500A)
      removed outlier: 6.333A  pdb=" N   ALA C  63 " --> pdb=" O   THR C 247 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'D' and resid 18 through 22
      removed outlier: 5.239A  pdb=" N   VAL D 221 " --> pdb=" O   TYR D  52 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'D' and resid 18 through 22
      removed outlier: 5.239A  pdb=" N   VAL D 221 " --> pdb=" O   TYR D  52 " (cutoff:3.500A)
      removed outlier: 3.637A  pdb=" N   GLY D  87 " --> pdb=" O   SER D 226 " (cutoff:3.500A)
      removed outlier: 4.220A  pdb=" N   VAL D 166 " --> pdb=" O   ILE D 157 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'C' and resid 18 through 22
      removed outlier: 5.238A  pdb=" N   VAL C 221 " --> pdb=" O   TYR C  52 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'C' and resid 18 through 22
      removed outlier: 5.238A  pdb=" N   VAL C 221 " --> pdb=" O   TYR C  52 " (cutoff:3.500A)
      removed outlier: 3.636A  pdb=" N   GLY C  87 " --> pdb=" O   SER C 226 " (cutoff:3.500A)
      removed outlier: 4.221A  pdb=" N   VAL C 166 " --> pdb=" O   ILE C 157 " (cutoff:3.500A)

    384 hydrogen bonds defined for protein.
    1008 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: 1.17

  Time building geometry restraints manager: 0.95 seconds

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

  Histogram of bond lengths:
        1.22 -     1.29: 1176
        1.29 -     1.36: 1156
        1.36 -     1.42: 967
        1.42 -     1.49: 1214
        1.49 -     1.55: 2999
  Bond restraints: 7512
  Sorted by residual:
  bond pdb=" N   ILE A 162 "
       pdb=" CA  ILE A 162 "
    ideal  model  delta    sigma   weight residual
    1.462  1.492 -0.030 1.17e-02 7.31e+03 6.39e+00
  bond pdb=" N   SER B 164 "
       pdb=" CA  SER B 164 "
    ideal  model  delta    sigma   weight residual
    1.456  1.486 -0.030 1.23e-02 6.61e+03 5.93e+00
  bond pdb=" C1  BMA b   1 "
       pdb=" O1  BMA b   1 "
    ideal  model  delta    sigma   weight residual
    1.383  1.432 -0.049 2.00e-02 2.50e+03 5.92e+00
  bond pdb=" C1  BMA c   1 "
       pdb=" O1  BMA c   1 "
    ideal  model  delta    sigma   weight residual
    1.383  1.432 -0.049 2.00e-02 2.50e+03 5.90e+00
  bond pdb=" C1  BMA a   1 "
       pdb=" O1  BMA a   1 "
    ideal  model  delta    sigma   weight residual
    1.383  1.431 -0.048 2.00e-02 2.50e+03 5.76e+00
  ... (remaining 7507 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.36: 9548
        1.36 -     2.71: 562
        2.71 -     4.07: 117
        4.07 -     5.42: 33
        5.42 -     6.78: 16
  Bond angle restraints: 10276
  Sorted by residual:
  angle pdb=" N   ILE A 162 "
        pdb=" CA  ILE A 162 "
        pdb=" C   ILE A 162 "
      ideal   model   delta    sigma   weight residual
     113.07  107.98    5.09 1.36e+00 5.41e-01 1.40e+01
  angle pdb=" C   ALA B  85 "
        pdb=" N   ASP B  86 "
        pdb=" CA  ASP B  86 "
      ideal   model   delta    sigma   weight residual
     121.70  127.24   -5.54 1.80e+00 3.09e-01 9.48e+00
  angle pdb=" C   ALA A  85 "
        pdb=" N   ASP A  86 "
        pdb=" CA  ASP A  86 "
      ideal   model   delta    sigma   weight residual
     121.70  127.17   -5.47 1.80e+00 3.09e-01 9.24e+00
  angle pdb=" C   ALA D  85 "
        pdb=" N   ASP D  86 "
        pdb=" CA  ASP D  86 "
      ideal   model   delta    sigma   weight residual
     121.70  127.17   -5.47 1.80e+00 3.09e-01 9.23e+00
  angle pdb=" C   ALA C  85 "
        pdb=" N   ASP C  86 "
        pdb=" CA  ASP C  86 "
      ideal   model   delta    sigma   weight residual
     121.70  127.15   -5.45 1.80e+00 3.09e-01 9.17e+00
  ... (remaining 10271 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    21.55: 4176
       21.55 -    43.09: 215
       43.09 -    64.64: 25
       64.64 -    86.19: 32
       86.19 -   107.74: 16
  Dihedral angle restraints: 4464
    sinusoidal: 1764
      harmonic: 2700
  Sorted by residual:
  dihedral pdb=" CA  ALA C  89 "
           pdb=" C   ALA C  89 "
           pdb=" N   PHE C  90 "
           pdb=" CA  PHE C  90 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  160.84   19.16     0      5.00e+00 4.00e-02 1.47e+01
  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  160.85   19.15     0      5.00e+00 4.00e-02 1.47e+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  160.86   19.14     0      5.00e+00 4.00e-02 1.47e+01
  ... (remaining 4461 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.047: 743
       0.047 -    0.094: 306
       0.094 -    0.140: 108
       0.140 -    0.187: 18
       0.187 -    0.234: 9
  Chirality restraints: 1184
  Sorted by residual:
  chirality pdb=" C3  BMA d   1 "
            pdb=" C2  BMA d   1 "
            pdb=" C4  BMA d   1 "
            pdb=" O3  BMA d   1 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.41    2.64   -0.23 2.00e-01 2.50e+01 1.37e+00
  chirality pdb=" C3  BMA c   1 "
            pdb=" C2  BMA c   1 "
            pdb=" C4  BMA c   1 "
            pdb=" O3  BMA c   1 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.41    2.64   -0.23 2.00e-01 2.50e+01 1.34e+00
  chirality pdb=" C3  BMA a   1 "
            pdb=" C2  BMA a   1 "
            pdb=" C4  BMA a   1 "
            pdb=" O3  BMA a   1 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.41    2.64   -0.23 2.00e-01 2.50e+01 1.32e+00
  ... (remaining 1181 not shown)

  Planarity restraints: 1296
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ALA D  93 "   -0.031 5.00e-02 4.00e+02   4.69e-02 3.51e+00
        pdb=" N   PRO D  94 "    0.081 5.00e-02 4.00e+02
        pdb=" CA  PRO D  94 "   -0.024 5.00e-02 4.00e+02
        pdb=" CD  PRO D  94 "   -0.026 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ALA A  93 "    0.031 5.00e-02 4.00e+02   4.69e-02 3.51e+00
        pdb=" N   PRO A  94 "   -0.081 5.00e-02 4.00e+02
        pdb=" CA  PRO A  94 "    0.024 5.00e-02 4.00e+02
        pdb=" CD  PRO A  94 "    0.026 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ALA C  93 "    0.031 5.00e-02 4.00e+02   4.67e-02 3.48e+00
        pdb=" N   PRO C  94 "   -0.081 5.00e-02 4.00e+02
        pdb=" CA  PRO C  94 "    0.024 5.00e-02 4.00e+02
        pdb=" CD  PRO C  94 "    0.026 5.00e-02 4.00e+02
  ... (remaining 1293 not shown)

  Histogram of nonbonded interaction distances:
        2.01 -     2.59: 76
        2.59 -     3.17: 5629
        3.17 -     3.74: 12079
        3.74 -     4.32: 18596
        4.32 -     4.90: 30138
  Nonbonded interactions: 66518
  Sorted by model distance:
  nonbonded pdb=" OE2 GLU C 138 "
            pdb="MN    MN C 302 "
     model   vdw
     2.012 2.320
  nonbonded pdb=" OE2 GLU B 138 "
            pdb="MN    MN B 302 "
     model   vdw
     2.022 2.320
  nonbonded pdb=" OE2 GLU A 138 "
            pdb="MN    MN A 302 "
     model   vdw
     2.024 2.320
  nonbonded pdb=" OE2 GLU D 138 "
            pdb="MN    MN D 302 "
     model   vdw
     2.069 2.320
  nonbonded pdb=" NE2 HIS A 154 "
            pdb="MN    MN A 302 "
     model   vdw
     2.215 2.400
  ... (remaining 66513 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 'D'
  selection = chain 'C'
}
ncs_group {
  reference = chain 'a'
  selection = chain 'b'
  selection = chain 'c'
  selection = chain 'd'
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as 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:             2.170
  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:          0.130
  Check model and map are aligned:         0.020
  Set scattering table:                    0.030
  Process input model:                     8.390
  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:6.830
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   17.640
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8495
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.049   7516  Z= 0.238
  Angle     :  0.794   6.778  10288  Z= 0.431
  Chirality :  0.057   0.234   1184
  Planarity :  0.007   0.047   1296
  Dihedral  : 16.953 107.736   2720
  Min Nonbonded Distance : 2.012

Molprobity Statistics.
  All-atom Clashscore : 3.98
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.20 %
    Favored  : 97.80 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.10 %
    Favored  : 97.90 %
  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: -0.92 (0.25), residues: 908
  helix:  None (None), residues: 0
  sheet:  0.39 (0.25), residues: 372
  loop : -1.41 (0.22), residues: 536

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B 220 
 TYR   0.008   0.002   TYR A  52 
 PHE   0.020   0.003   PHE A 241 
 TRP   0.008   0.001   TRP D  59 
 HIS   0.004   0.001   HIS C 212 

Details of bonding type rmsd
  covalent geometry    : bond        0.00482 ( 7512)
  covalent geometry    : angle       0.79399 (10276)
  hydrogen bonds       : bond        0.23229 (  304)
  hydrogen bonds       : angle       9.02724 ( 1008)
  link_ALPHA1-3        : bond        0.00482 (    4)
  link_ALPHA1-3        : angle       0.98932 (   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
  139 residues out of total 808 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 139
  time to evaluate  : 0.282 
Fit side-chains
REVERT: A   41 ASN cc_start: 0.8557 (m-40) cc_final: 0.8320 (m-40)
REVERT: A  231 LYS cc_start: 0.8243 (ptpp) cc_final: 0.8005 (pttt)
REVERT: B   41 ASN cc_start: 0.8594 (m-40) cc_final: 0.8334 (m-40)
REVERT: B  231 LYS cc_start: 0.8260 (ptpp) cc_final: 0.8026 (pttt)
REVERT: D   41 ASN cc_start: 0.8700 (m-40) cc_final: 0.8421 (m-40)
REVERT: D  231 LYS cc_start: 0.8239 (ptpp) cc_final: 0.7977 (pttt)
REVERT: C   41 ASN cc_start: 0.8508 (m-40) cc_final: 0.8275 (m-40)
REVERT: C  231 LYS cc_start: 0.8171 (ptpp) cc_final: 0.7868 (pttt)
  outliers start: 0
  outliers final: 1
  residues processed: 139
  average time/residue: 0.6769
  time to fit residues: 98.4596
Evaluate side-chains
  125 residues out of total 808 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 124
  time to evaluate  : 0.270 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   86 ASP
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 92
   random chunks:
   chunk 49 optimal weight:    4.9990
   chunk 53 optimal weight:    0.8980
   chunk 5 optimal weight:    3.9990
   chunk 33 optimal weight:    0.0370
   chunk 65 optimal weight:    4.9990
   chunk 62 optimal weight:    2.9990
   chunk 51 optimal weight:    4.9990
   chunk 38 optimal weight:    2.9990
   chunk 61 optimal weight:    0.6980
   chunk 45 optimal weight:    1.9990
   chunk 74 optimal weight:    0.0670
   overall best weight:    0.7398

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

Flipped N/Q/H residues before XYZ refinement:
A  14 ASN
A  23 HIS
A  73 ASN
A 113 ASN
A 160 ASN
A 173 GLN
A 234 ASN
B  14 ASN
B  23 HIS
B  73 ASN
B 113 ASN
B 160 ASN
B 173 GLN
B 234 ASN
D  14 ASN
D  23 HIS
D  73 ASN
D 113 ASN
D 160 ASN
D 173 GLN
D 234 ASN
C  14 ASN
C  23 HIS
C  73 ASN
C 113 ASN
C 160 ASN
C 173 GLN

Total number of N/Q/H flips: 27

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3662 r_free = 0.3662 target = 0.134213 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3440 r_free = 0.3440 target = 0.115768 restraints weight = 8196.198|
|-----------------------------------------------------------------------------|
r_work (start): 0.3446 rms_B_bonded: 1.67
r_work: 0.3362 rms_B_bonded: 2.08 restraints_weight: 0.5000
r_work: 0.3266 rms_B_bonded: 3.47 restraints_weight: 0.2500
r_work (final): 0.3266
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8741
moved from start:          0.1533

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.019   7516  Z= 0.141
  Angle     :  0.585   4.452  10288  Z= 0.325
  Chirality :  0.047   0.166   1184
  Planarity :  0.005   0.040   1296
  Dihedral  : 13.148  72.237   1150
  Min Nonbonded Distance : 2.162

Molprobity Statistics.
  All-atom Clashscore : 6.42
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.10 %
    Favored  : 98.90 %
  Rotamer:
    Outliers :  0.50 %
    Allowed  :  7.67 %
    Favored  : 91.83 %
  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: -0.40 (0.26), residues: 908
  helix:  None (None), residues: 0
  sheet:  0.59 (0.29), residues: 336
  loop : -0.82 (0.24), residues: 572

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG A 190 
 TYR   0.008   0.001   TYR C 184 
 PHE   0.015   0.002   PHE C  68 
 TRP   0.004   0.001   TRP D  59 
 HIS   0.002   0.000   HIS B 212 

Details of bonding type rmsd
  covalent geometry    : bond        0.00285 ( 7512)
  covalent geometry    : angle       0.58267 (10276)
  hydrogen bonds       : bond        0.05513 (  304)
  hydrogen bonds       : angle       5.70166 ( 1008)
  link_ALPHA1-3        : bond        0.00454 (    4)
  link_ALPHA1-3        : angle       1.77457 (   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
  129 residues out of total 808 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 125
  time to evaluate  : 0.279 
Fit side-chains
REVERT: A   41 ASN cc_start: 0.8691 (m-40) cc_final: 0.8408 (m-40)
REVERT: A  149 ASP cc_start: 0.8313 (m-30) cc_final: 0.8048 (m-30)
REVERT: A  231 LYS cc_start: 0.8379 (ptpp) cc_final: 0.8171 (pttt)
REVERT: B   41 ASN cc_start: 0.8689 (m-40) cc_final: 0.8389 (m-40)
REVERT: B   86 ASP cc_start: 0.8753 (OUTLIER) cc_final: 0.8427 (m-30)
REVERT: B  149 ASP cc_start: 0.8325 (m-30) cc_final: 0.8028 (m-30)
REVERT: B  231 LYS cc_start: 0.8403 (ptpp) cc_final: 0.8192 (pttt)
REVERT: D   41 ASN cc_start: 0.8733 (m-40) cc_final: 0.8394 (m-40)
REVERT: D  149 ASP cc_start: 0.8353 (m-30) cc_final: 0.7991 (m-30)
REVERT: D  231 LYS cc_start: 0.8440 (ptpp) cc_final: 0.8182 (pttt)
REVERT: C   41 ASN cc_start: 0.8586 (m-40) cc_final: 0.8333 (m-40)
REVERT: C   86 ASP cc_start: 0.8715 (OUTLIER) cc_final: 0.8469 (m-30)
REVERT: C  231 LYS cc_start: 0.8374 (ptpp) cc_final: 0.8115 (pttt)
  outliers start: 4
  outliers final: 1
  residues processed: 127
  average time/residue: 0.7454
  time to fit residues: 98.6956
Evaluate side-chains
  121 residues out of total 808 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 118
  time to evaluate  : 0.213 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  100 SER
Chi-restraints excluded: chain B residue   86 ASP
Chi-restraints excluded: chain C residue   86 ASP
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 92
   random chunks:
   chunk 41 optimal weight:    0.9990
   chunk 63 optimal weight:    4.9990
   chunk 46 optimal weight:    6.9990
   chunk 82 optimal weight:    6.9990
   chunk 80 optimal weight:    0.4980
   chunk 56 optimal weight:    2.9990
   chunk 8 optimal weight:    9.9990
   chunk 11 optimal weight:    6.9990
   chunk 68 optimal weight:    0.9980
   chunk 36 optimal weight:    0.9980
   chunk 83 optimal weight:    1.9990
   overall best weight:    1.0984

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

Flipped N/Q/H residues before XYZ refinement:
A 133 ASN
B 133 ASN
D 133 ASN
C  28 ASN
C 133 ASN
C 234 ASN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3645 r_free = 0.3645 target = 0.133050 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 28)----------------|
| r_work = 0.3418 r_free = 0.3418 target = 0.114419 restraints weight = 8157.264|
|-----------------------------------------------------------------------------|
r_work (start): 0.3427 rms_B_bonded: 1.68
r_work: 0.3342 rms_B_bonded: 2.08 restraints_weight: 0.5000
r_work: 0.3245 rms_B_bonded: 3.47 restraints_weight: 0.2500
r_work (final): 0.3245
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8757
moved from start:          0.1860

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.023   7516  Z= 0.157
  Angle     :  0.576   4.830  10288  Z= 0.311
  Chirality :  0.047   0.156   1184
  Planarity :  0.005   0.054   1296
  Dihedral  :  9.775  47.820   1148
  Min Nonbonded Distance : 2.141

Molprobity Statistics.
  All-atom Clashscore : 5.93
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.09 %
    Favored  : 97.91 %
  Rotamer:
    Outliers :  1.73 %
    Allowed  :  9.03 %
    Favored  : 89.23 %
  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: -0.17 (0.27), residues: 908
  helix:  None (None), residues: 0
  sheet:  0.54 (0.27), residues: 376
  loop : -0.59 (0.26), residues: 532

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG A 190 
 TYR   0.011   0.001   TYR D  52 
 PHE   0.015   0.002   PHE D  68 
 TRP   0.004   0.001   TRP D  59 
 HIS   0.003   0.001   HIS B 212 

Details of bonding type rmsd
  covalent geometry    : bond        0.00341 ( 7512)
  covalent geometry    : angle       0.57260 (10276)
  hydrogen bonds       : bond        0.04576 (  304)
  hydrogen bonds       : angle       5.22291 ( 1008)
  link_ALPHA1-3        : bond        0.00716 (    4)
  link_ALPHA1-3        : angle       1.81174 (   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
  134 residues out of total 808 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 120
  time to evaluate  : 0.206 
Fit side-chains
REVERT: A   41 ASN cc_start: 0.8802 (m-40) cc_final: 0.8459 (m-40)
REVERT: A  231 LYS cc_start: 0.8422 (ptpp) cc_final: 0.8208 (pttt)
REVERT: B   41 ASN cc_start: 0.8796 (m-40) cc_final: 0.8475 (m-40)
REVERT: B   86 ASP cc_start: 0.8773 (OUTLIER) cc_final: 0.8505 (m-30)
REVERT: B  231 LYS cc_start: 0.8451 (ptpp) cc_final: 0.8228 (pttt)
REVERT: D   41 ASN cc_start: 0.8812 (m-40) cc_final: 0.8452 (m-40)
REVERT: D   86 ASP cc_start: 0.8769 (OUTLIER) cc_final: 0.8496 (m-30)
REVERT: D  231 LYS cc_start: 0.8466 (ptpp) cc_final: 0.8211 (pttt)
REVERT: C   41 ASN cc_start: 0.8685 (m-40) cc_final: 0.8314 (m-40)
REVERT: C   86 ASP cc_start: 0.8759 (OUTLIER) cc_final: 0.8472 (m-30)
REVERT: C  231 LYS cc_start: 0.8417 (ptpp) cc_final: 0.8158 (pttt)
  outliers start: 14
  outliers final: 8
  residues processed: 129
  average time/residue: 0.7462
  time to fit residues: 100.4130
Evaluate side-chains
  122 residues out of total 808 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 111
  time to evaluate  : 0.292 
-------------------------------------------------------------------------------
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   86 ASP
Chi-restraints excluded: chain B residue   88 LEU
Chi-restraints excluded: chain B residue  100 SER
Chi-restraints excluded: chain D residue   86 ASP
Chi-restraints excluded: chain D residue   88 LEU
Chi-restraints excluded: chain D residue  100 SER
Chi-restraints excluded: chain C residue   86 ASP
Chi-restraints excluded: chain C residue   88 LEU
Chi-restraints excluded: chain C residue  100 SER
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 92
   random chunks:
   chunk 66 optimal weight:    7.9990
   chunk 23 optimal weight:    5.9990
   chunk 35 optimal weight:    0.5980
   chunk 60 optimal weight:    3.9990
   chunk 54 optimal weight:    5.9990
   chunk 26 optimal weight:    4.9990
   chunk 91 optimal weight:    6.9990
   chunk 63 optimal weight:    4.9990
   chunk 72 optimal weight:    5.9990
   chunk 85 optimal weight:    6.9990
   chunk 56 optimal weight:    1.9990
   overall best weight:    3.3188

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

Flipped N/Q/H residues before XYZ refinement:
A 234 ASN
B 234 ASN
D 234 ASN
C  28 ASN
C 234 ASN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3587 r_free = 0.3587 target = 0.129671 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3357 r_free = 0.3357 target = 0.109522 restraints weight = 8586.671|
|-----------------------------------------------------------------------------|
r_work (start): 0.3355 rms_B_bonded: 1.73
r_work: 0.3270 rms_B_bonded: 2.09 restraints_weight: 0.5000
r_work: 0.3174 rms_B_bonded: 3.47 restraints_weight: 0.2500
r_work (final): 0.3174
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8833
moved from start:          0.2031

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.008   0.058   7516  Z= 0.348
  Angle     :  0.699   7.379  10288  Z= 0.377
  Chirality :  0.053   0.170   1184
  Planarity :  0.006   0.048   1296
  Dihedral  :  9.252  39.311   1148
  Min Nonbonded Distance : 2.135

Molprobity Statistics.
  All-atom Clashscore : 6.00
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.98 %
    Favored  : 98.02 %
  Rotamer:
    Outliers :  2.60 %
    Allowed  :  9.16 %
    Favored  : 88.24 %
  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: -0.02 (0.27), residues: 908
  helix:  None (None), residues: 0
  sheet:  0.77 (0.27), residues: 376
  loop : -0.60 (0.25), residues: 532

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.001   ARG B 163 
 TYR   0.014   0.002   TYR D  52 
 PHE   0.017   0.003   PHE D  68 
 TRP   0.006   0.002   TRP A 246 
 HIS   0.004   0.001   HIS B 212 

Details of bonding type rmsd
  covalent geometry    : bond        0.00814 ( 7512)
  covalent geometry    : angle       0.69586 (10276)
  hydrogen bonds       : bond        0.05458 (  304)
  hydrogen bonds       : angle       5.73745 ( 1008)
  link_ALPHA1-3        : bond        0.00300 (    4)
  link_ALPHA1-3        : angle       1.94959 (   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
  129 residues out of total 808 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 108
  time to evaluate  : 0.439 
Fit side-chains
REVERT: A  231 LYS cc_start: 0.8526 (ptpp) cc_final: 0.8282 (pttt)
REVERT: B   86 ASP cc_start: 0.8927 (OUTLIER) cc_final: 0.8566 (m-30)
REVERT: B  138 GLU cc_start: 0.8984 (OUTLIER) cc_final: 0.8685 (pt0)
REVERT: B  231 LYS cc_start: 0.8562 (ptpp) cc_final: 0.8317 (pttt)
REVERT: D   86 ASP cc_start: 0.8915 (OUTLIER) cc_final: 0.8551 (m-30)
REVERT: D  138 GLU cc_start: 0.8972 (OUTLIER) cc_final: 0.8672 (pt0)
REVERT: D  231 LYS cc_start: 0.8569 (ptpp) cc_final: 0.8323 (pttt)
REVERT: C   86 ASP cc_start: 0.8941 (OUTLIER) cc_final: 0.8584 (m-30)
REVERT: C  138 GLU cc_start: 0.8977 (OUTLIER) cc_final: 0.8668 (pt0)
REVERT: C  231 LYS cc_start: 0.8544 (ptpp) cc_final: 0.8289 (pttt)
  outliers start: 21
  outliers final: 9
  residues processed: 125
  average time/residue: 0.7614
  time to fit residues: 99.2201
Evaluate side-chains
  120 residues out of total 808 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 105
  time to evaluate  : 0.274 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   43 VAL
Chi-restraints excluded: chain A residue  100 SER
Chi-restraints excluded: chain A residue  138 GLU
Chi-restraints excluded: chain B residue   43 VAL
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 D residue   43 VAL
Chi-restraints excluded: chain D residue   86 ASP
Chi-restraints excluded: chain D residue  100 SER
Chi-restraints excluded: chain D residue  138 GLU
Chi-restraints excluded: chain C residue   43 VAL
Chi-restraints excluded: chain C residue   86 ASP
Chi-restraints excluded: chain C residue  100 SER
Chi-restraints excluded: chain C residue  138 GLU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 92
   random chunks:
   chunk 27 optimal weight:    5.9990
   chunk 36 optimal weight:    4.9990
   chunk 7 optimal weight:    2.9990
   chunk 33 optimal weight:    2.9990
   chunk 45 optimal weight:    1.9990
   chunk 44 optimal weight:    0.8980
   chunk 91 optimal weight:    1.9990
   chunk 20 optimal weight:    4.9990
   chunk 12 optimal weight:    1.9990
   chunk 57 optimal weight:    4.9990
   chunk 73 optimal weight:    5.9990
   overall best weight:    1.9788

-------------------------------------------------------------------------------
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 = 0.3599 r_free = 0.3599 target = 0.129530 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3350 r_free = 0.3350 target = 0.110034 restraints weight = 8274.087|
|-----------------------------------------------------------------------------|
r_work (start): 0.3373 rms_B_bonded: 1.72
r_work: 0.3293 rms_B_bonded: 2.07 restraints_weight: 0.5000
r_work: 0.3196 rms_B_bonded: 3.45 restraints_weight: 0.2500
r_work (final): 0.3196
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8798
moved from start:          0.2091

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.036   7516  Z= 0.230
  Angle     :  0.617   6.002  10288  Z= 0.336
  Chirality :  0.048   0.162   1184
  Planarity :  0.006   0.069   1296
  Dihedral  :  8.136  41.063   1148
  Min Nonbonded Distance : 2.219

Molprobity Statistics.
  All-atom Clashscore : 5.52
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.20 %
    Favored  : 97.80 %
  Rotamer:
    Outliers :  2.35 %
    Allowed  :  9.78 %
    Favored  : 87.87 %
  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:  0.01 (0.27), residues: 908
  helix:  None (None), residues: 0
  sheet:  0.77 (0.27), residues: 376
  loop : -0.55 (0.25), residues: 532

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG C 190 
 TYR   0.011   0.002   TYR A  52 
 PHE   0.016   0.003   PHE B  68 
 TRP   0.004   0.001   TRP B 246 
 HIS   0.003   0.001   HIS A 212 

Details of bonding type rmsd
  covalent geometry    : bond        0.00518 ( 7512)
  covalent geometry    : angle       0.61402 (10276)
  hydrogen bonds       : bond        0.04872 (  304)
  hydrogen bonds       : angle       5.51739 ( 1008)
  link_ALPHA1-3        : bond        0.00397 (    4)
  link_ALPHA1-3        : angle       1.88706 (   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
  136 residues out of total 808 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 117
  time to evaluate  : 0.271 
Fit side-chains
REVERT: A   88 LEU cc_start: 0.8816 (OUTLIER) cc_final: 0.8404 (tt)
REVERT: A  138 GLU cc_start: 0.8944 (OUTLIER) cc_final: 0.8633 (pt0)
REVERT: A  231 LYS cc_start: 0.8503 (ptpp) cc_final: 0.8253 (pttt)
REVERT: B   86 ASP cc_start: 0.8861 (OUTLIER) cc_final: 0.8538 (m-30)
REVERT: B   88 LEU cc_start: 0.8810 (OUTLIER) cc_final: 0.8476 (tt)
REVERT: B  138 GLU cc_start: 0.8943 (OUTLIER) cc_final: 0.8625 (pt0)
REVERT: B  231 LYS cc_start: 0.8519 (ptpp) cc_final: 0.8270 (pttt)
REVERT: D   86 ASP cc_start: 0.8862 (OUTLIER) cc_final: 0.8533 (m-30)
REVERT: D   88 LEU cc_start: 0.8806 (OUTLIER) cc_final: 0.8452 (tt)
REVERT: D  138 GLU cc_start: 0.8931 (OUTLIER) cc_final: 0.8611 (pt0)
REVERT: D  231 LYS cc_start: 0.8533 (ptpp) cc_final: 0.8291 (pttt)
REVERT: C   86 ASP cc_start: 0.8876 (OUTLIER) cc_final: 0.8550 (m-30)
REVERT: C   88 LEU cc_start: 0.8816 (OUTLIER) cc_final: 0.8435 (tt)
REVERT: C  138 GLU cc_start: 0.8932 (OUTLIER) cc_final: 0.8609 (pt0)
REVERT: C  231 LYS cc_start: 0.8502 (ptpp) cc_final: 0.8251 (pttt)
  outliers start: 19
  outliers final: 6
  residues processed: 131
  average time/residue: 0.7250
  time to fit residues: 99.2648
Evaluate side-chains
  129 residues out of total 808 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 112
  time to evaluate  : 0.288 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   43 VAL
Chi-restraints excluded: chain A residue   88 LEU
Chi-restraints excluded: chain A residue  100 SER
Chi-restraints excluded: chain A residue  138 GLU
Chi-restraints excluded: chain B residue   43 VAL
Chi-restraints excluded: chain B residue   86 ASP
Chi-restraints excluded: chain B residue   88 LEU
Chi-restraints excluded: chain B residue  100 SER
Chi-restraints excluded: chain B residue  138 GLU
Chi-restraints excluded: chain D residue   86 ASP
Chi-restraints excluded: chain D residue   88 LEU
Chi-restraints excluded: chain D residue  100 SER
Chi-restraints excluded: chain D residue  138 GLU
Chi-restraints excluded: chain C residue   86 ASP
Chi-restraints excluded: chain C residue   88 LEU
Chi-restraints excluded: chain C residue  100 SER
Chi-restraints excluded: chain C residue  138 GLU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 92
   random chunks:
   chunk 78 optimal weight:    0.0070
   chunk 35 optimal weight:    0.6980
   chunk 34 optimal weight:    0.0870
   chunk 66 optimal weight:    0.9990
   chunk 55 optimal weight:    0.9990
   chunk 41 optimal weight:    0.5980
   chunk 49 optimal weight:    0.9990
   chunk 5 optimal weight:    3.9990
   chunk 20 optimal weight:    0.7980
   chunk 9 optimal weight:    0.3980
   chunk 10 optimal weight:    0.4980
   overall best weight:    0.3176

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

Flipped N/Q/H residues before XYZ refinement:
A 234 ASN
B 133 ASN
B 234 ASN
D 234 ASN
C 234 ASN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3672 r_free = 0.3672 target = 0.135399 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 25)----------------|
| r_work = 0.3439 r_free = 0.3439 target = 0.116618 restraints weight = 8159.688|
|-----------------------------------------------------------------------------|
r_work (start): 0.3452 rms_B_bonded: 1.69
r_work: 0.3375 rms_B_bonded: 2.06 restraints_weight: 0.5000
r_work: 0.3280 rms_B_bonded: 3.46 restraints_weight: 0.2500
r_work (final): 0.3280
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8718
moved from start:          0.2234

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.018   7516  Z= 0.102
  Angle     :  0.514   3.860  10288  Z= 0.281
  Chirality :  0.044   0.147   1184
  Planarity :  0.007   0.103   1296
  Dihedral  :  6.678  38.227   1148
  Min Nonbonded Distance : 2.310

Molprobity Statistics.
  All-atom Clashscore : 6.28
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.31 %
    Favored  : 97.69 %
  Rotamer:
    Outliers :  1.11 %
    Allowed  : 10.89 %
    Favored  : 88.00 %
  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 (0.28), residues: 908
  helix:  None (None), residues: 0
  sheet:  0.67 (0.27), residues: 376
  loop : -0.48 (0.26), residues: 532

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.001   ARG C 190 
 TYR   0.007   0.001   TYR B 184 
 PHE   0.014   0.002   PHE A  68 
 TRP   0.003   0.001   TRP B  59 
 HIS   0.002   0.001   HIS A 212 

Details of bonding type rmsd
  covalent geometry    : bond        0.00206 ( 7512)
  covalent geometry    : angle       0.51145 (10276)
  hydrogen bonds       : bond        0.03732 (  304)
  hydrogen bonds       : angle       5.01228 ( 1008)
  link_ALPHA1-3        : bond        0.00616 (    4)
  link_ALPHA1-3        : angle       1.54825 (   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
  133 residues out of total 808 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 124
  time to evaluate  : 0.322 
Fit side-chains
REVERT: A   41 ASN cc_start: 0.8820 (m-40) cc_final: 0.8518 (m-40)
REVERT: A  138 GLU cc_start: 0.8885 (OUTLIER) cc_final: 0.8547 (pt0)
REVERT: B   41 ASN cc_start: 0.8852 (m-40) cc_final: 0.8537 (m-40)
REVERT: B   86 ASP cc_start: 0.8660 (OUTLIER) cc_final: 0.8413 (m-30)
REVERT: B  149 ASP cc_start: 0.8208 (m-30) cc_final: 0.7926 (m-30)
REVERT: D   35 LYS cc_start: 0.8710 (ttmm) cc_final: 0.8313 (ttpp)
REVERT: D   41 ASN cc_start: 0.8837 (m-40) cc_final: 0.8509 (m-40)
REVERT: D  231 LYS cc_start: 0.8433 (ptpp) cc_final: 0.8226 (pttt)
REVERT: C   41 ASN cc_start: 0.8807 (m-40) cc_final: 0.8488 (m-40)
REVERT: C  231 LYS cc_start: 0.8401 (ptpp) cc_final: 0.8192 (pttt)
  outliers start: 9
  outliers final: 1
  residues processed: 130
  average time/residue: 0.6857
  time to fit residues: 93.3677
Evaluate side-chains
  120 residues out of total 808 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 117
  time to evaluate  : 0.280 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  138 GLU
Chi-restraints excluded: chain B residue   86 ASP
Chi-restraints excluded: chain B residue   88 LEU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 92
   random chunks:
   chunk 40 optimal weight:    2.9990
   chunk 86 optimal weight:    3.9990
   chunk 45 optimal weight:    5.9990
   chunk 76 optimal weight:    5.9990
   chunk 64 optimal weight:    0.0970
   chunk 78 optimal weight:    1.9990
   chunk 24 optimal weight:    0.0020
   chunk 28 optimal weight:    0.9980
   chunk 4 optimal weight:    0.1980
   chunk 63 optimal weight:    3.9990
   chunk 85 optimal weight:    0.7980
   overall best weight:    0.4186

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

Flipped N/Q/H residues before XYZ refinement:
A 133 ASN
D 144 ASN
C 133 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3682 r_free = 0.3682 target = 0.136296 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3446 r_free = 0.3446 target = 0.117437 restraints weight = 8188.433|
|-----------------------------------------------------------------------------|
r_work (start): 0.3458 rms_B_bonded: 1.70
r_work: 0.3380 rms_B_bonded: 2.09 restraints_weight: 0.5000
r_work: 0.3285 rms_B_bonded: 3.50 restraints_weight: 0.2500
r_work (final): 0.3285
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8708
moved from start:          0.2306

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.018   7516  Z= 0.101
  Angle     :  0.499   4.025  10288  Z= 0.272
  Chirality :  0.044   0.146   1184
  Planarity :  0.006   0.087   1296
  Dihedral  :  6.134  34.544   1148
  Min Nonbonded Distance : 2.288

Molprobity Statistics.
  All-atom Clashscore : 6.00
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.75 %
    Favored  : 97.25 %
  Rotamer:
    Outliers :  1.73 %
    Allowed  : 10.89 %
    Favored  : 87.38 %
  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:  0.05 (0.28), residues: 908
  helix:  None (None), residues: 0
  sheet:  0.70 (0.28), residues: 376
  loop : -0.45 (0.26), residues: 532

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG C 190 
 TYR   0.007   0.001   TYR B 142 
 PHE   0.014   0.002   PHE B  68 
 TRP   0.004   0.001   TRP A  59 
 HIS   0.002   0.001   HIS A 212 

Details of bonding type rmsd
  covalent geometry    : bond        0.00211 ( 7512)
  covalent geometry    : angle       0.49653 (10276)
  hydrogen bonds       : bond        0.03531 (  304)
  hydrogen bonds       : angle       4.84980 ( 1008)
  link_ALPHA1-3        : bond        0.00615 (    4)
  link_ALPHA1-3        : angle       1.51853 (   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
  137 residues out of total 808 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 123
  time to evaluate  : 0.218 
Fit side-chains
REVERT: A   41 ASN cc_start: 0.8793 (m-40) cc_final: 0.8494 (m-40)
REVERT: A  138 GLU cc_start: 0.8879 (OUTLIER) cc_final: 0.8519 (pt0)
REVERT: B   34 THR cc_start: 0.8548 (p) cc_final: 0.8337 (p)
REVERT: B   41 ASN cc_start: 0.8827 (m-40) cc_final: 0.8527 (m-40)
REVERT: B   86 ASP cc_start: 0.8630 (OUTLIER) cc_final: 0.8405 (m-30)
REVERT: B  138 GLU cc_start: 0.8877 (OUTLIER) cc_final: 0.8525 (pt0)
REVERT: D   41 ASN cc_start: 0.8834 (m-40) cc_final: 0.8506 (m-40)
REVERT: D  138 GLU cc_start: 0.8877 (OUTLIER) cc_final: 0.8532 (pt0)
REVERT: D  231 LYS cc_start: 0.8368 (ptpp) cc_final: 0.8105 (pttt)
REVERT: C   41 ASN cc_start: 0.8809 (m-40) cc_final: 0.8501 (m-40)
REVERT: C  138 GLU cc_start: 0.8877 (OUTLIER) cc_final: 0.8525 (pt0)
  outliers start: 14
  outliers final: 4
  residues processed: 132
  average time/residue: 0.6896
  time to fit residues: 95.3288
Evaluate side-chains
  126 residues out of total 808 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 117
  time to evaluate  : 0.285 
-------------------------------------------------------------------------------
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   86 ASP
Chi-restraints excluded: chain B residue   88 LEU
Chi-restraints excluded: chain B residue  138 GLU
Chi-restraints excluded: chain B residue  231 LYS
Chi-restraints excluded: chain D residue  138 GLU
Chi-restraints excluded: chain C residue   12 ASP
Chi-restraints excluded: chain C residue  138 GLU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 92
   random chunks:
   chunk 52 optimal weight:    0.9980
   chunk 82 optimal weight:    3.9990
   chunk 0 optimal weight:    6.9990
   chunk 3 optimal weight:    0.1980
   chunk 62 optimal weight:    3.9990
   chunk 25 optimal weight:    0.1980
   chunk 41 optimal weight:    0.1980
   chunk 36 optimal weight:    6.9990
   chunk 38 optimal weight:    0.7980
   chunk 74 optimal weight:    3.9990
   chunk 6 optimal weight:    0.7980
   overall best weight:    0.4380

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

Flipped N/Q/H residues before XYZ refinement:
D 133 ASN
C  28 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3698 r_free = 0.3698 target = 0.137580 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 28)----------------|
| r_work = 0.3463 r_free = 0.3463 target = 0.118872 restraints weight = 8196.198|
|-----------------------------------------------------------------------------|
r_work (start): 0.3475 rms_B_bonded: 1.69
r_work: 0.3396 rms_B_bonded: 2.09 restraints_weight: 0.5000
r_work: 0.3303 rms_B_bonded: 3.49 restraints_weight: 0.2500
r_work (final): 0.3303
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8695
moved from start:          0.2465

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.021   7516  Z= 0.102
  Angle     :  0.494   3.916  10288  Z= 0.270
  Chirality :  0.044   0.146   1184
  Planarity :  0.006   0.093   1296
  Dihedral  :  5.665  27.477   1148
  Min Nonbonded Distance : 2.282

Molprobity Statistics.
  All-atom Clashscore : 6.14
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.42 %
    Favored  : 97.58 %
  Rotamer:
    Outliers :  1.61 %
    Allowed  : 11.14 %
    Favored  : 87.25 %
  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:  0.01 (0.28), residues: 908
  helix:  None (None), residues: 0
  sheet:  0.61 (0.29), residues: 336
  loop : -0.34 (0.25), residues: 572

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 190 
 TYR   0.007   0.001   TYR C 184 
 PHE   0.014   0.002   PHE B  68 
 TRP   0.004   0.001   TRP C  59 
 HIS   0.003   0.001   HIS B 212 

Details of bonding type rmsd
  covalent geometry    : bond        0.00216 ( 7512)
  covalent geometry    : angle       0.49234 (10276)
  hydrogen bonds       : bond        0.03413 (  304)
  hydrogen bonds       : angle       4.74729 ( 1008)
  link_ALPHA1-3        : bond        0.00507 (    4)
  link_ALPHA1-3        : angle       1.43343 (   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
  142 residues out of total 808 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 129
  time to evaluate  : 0.337 
Fit side-chains
REVERT: A   41 ASN cc_start: 0.8768 (m-40) cc_final: 0.8464 (m-40)
REVERT: A  138 GLU cc_start: 0.8884 (OUTLIER) cc_final: 0.8514 (pt0)
REVERT: B   41 ASN cc_start: 0.8755 (m-40) cc_final: 0.8460 (m-40)
REVERT: B   86 ASP cc_start: 0.8553 (OUTLIER) cc_final: 0.8300 (m-30)
REVERT: B  138 GLU cc_start: 0.8862 (OUTLIER) cc_final: 0.8493 (pt0)
REVERT: D   41 ASN cc_start: 0.8853 (m-40) cc_final: 0.8533 (m-40)
REVERT: D  138 GLU cc_start: 0.8874 (OUTLIER) cc_final: 0.8510 (pt0)
REVERT: D  231 LYS cc_start: 0.8319 (ptpp) cc_final: 0.8064 (pttt)
REVERT: C   41 ASN cc_start: 0.8792 (m-40) cc_final: 0.8488 (m-40)
REVERT: C  138 GLU cc_start: 0.8868 (OUTLIER) cc_final: 0.8504 (pt0)
  outliers start: 13
  outliers final: 4
  residues processed: 136
  average time/residue: 0.6908
  time to fit residues: 98.3591
Evaluate side-chains
  125 residues out of total 808 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 116
  time to evaluate  : 0.202 
-------------------------------------------------------------------------------
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   86 ASP
Chi-restraints excluded: chain B residue   88 LEU
Chi-restraints excluded: chain B residue  138 GLU
Chi-restraints excluded: chain D residue   12 ASP
Chi-restraints excluded: chain D residue  138 GLU
Chi-restraints excluded: chain C residue   12 ASP
Chi-restraints excluded: chain C residue  138 GLU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 92
   random chunks:
   chunk 23 optimal weight:    1.9990
   chunk 73 optimal weight:    0.0670
   chunk 43 optimal weight:    6.9990
   chunk 2 optimal weight:    3.9990
   chunk 25 optimal weight:    3.9990
   chunk 84 optimal weight:    6.9990
   chunk 89 optimal weight:    6.9990
   chunk 57 optimal weight:    7.9990
   chunk 17 optimal weight:    2.9990
   chunk 65 optimal weight:    0.9980
   chunk 64 optimal weight:    0.7980
   overall best weight:    1.3722

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

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

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3633 r_free = 0.3633 target = 0.132450 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3392 r_free = 0.3392 target = 0.113323 restraints weight = 8165.707|
|-----------------------------------------------------------------------------|
r_work (start): 0.3406 rms_B_bonded: 1.69
r_work: 0.3325 rms_B_bonded: 2.07 restraints_weight: 0.5000
r_work: 0.3229 rms_B_bonded: 3.48 restraints_weight: 0.2500
r_work (final): 0.3229
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8760
moved from start:          0.2368

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.025   7516  Z= 0.177
  Angle     :  0.556   5.308  10288  Z= 0.304
  Chirality :  0.046   0.155   1184
  Planarity :  0.006   0.096   1296
  Dihedral  :  5.807  22.580   1148
  Min Nonbonded Distance : 2.215

Molprobity Statistics.
  All-atom Clashscore : 6.00
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.42 %
    Favored  : 97.58 %
  Rotamer:
    Outliers :  2.23 %
    Allowed  : 11.51 %
    Favored  : 86.26 %
  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:  0.07 (0.27), residues: 908
  helix:  None (None), residues: 0
  sheet:  0.70 (0.29), residues: 336
  loop : -0.33 (0.25), residues: 572

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.013   0.001   ARG D 190 
 TYR   0.012   0.001   TYR A  52 
 PHE   0.016   0.002   PHE B  68 
 TRP   0.006   0.001   TRP B  59 
 HIS   0.003   0.001   HIS B 212 

Details of bonding type rmsd
  covalent geometry    : bond        0.00396 ( 7512)
  covalent geometry    : angle       0.55420 (10276)
  hydrogen bonds       : bond        0.04088 (  304)
  hydrogen bonds       : angle       5.06586 ( 1008)
  link_ALPHA1-3        : bond        0.00400 (    4)
  link_ALPHA1-3        : angle       1.57194 (   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
  134 residues out of total 808 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 116
  time to evaluate  : 0.308 
Fit side-chains
REVERT: A  138 GLU cc_start: 0.8906 (OUTLIER) cc_final: 0.8539 (pt0)
REVERT: B   41 ASN cc_start: 0.8848 (m-40) cc_final: 0.8522 (m-40)
REVERT: B   86 ASP cc_start: 0.8741 (OUTLIER) cc_final: 0.8480 (m-30)
REVERT: B   88 LEU cc_start: 0.8765 (OUTLIER) cc_final: 0.8429 (tt)
REVERT: B  138 GLU cc_start: 0.8892 (OUTLIER) cc_final: 0.8535 (pt0)
REVERT: D  138 GLU cc_start: 0.8896 (OUTLIER) cc_final: 0.8540 (pt0)
REVERT: D  231 LYS cc_start: 0.8445 (ptpp) cc_final: 0.8244 (pttt)
REVERT: C  138 GLU cc_start: 0.8900 (OUTLIER) cc_final: 0.8545 (pt0)
  outliers start: 18
  outliers final: 8
  residues processed: 128
  average time/residue: 0.7046
  time to fit residues: 94.3256
Evaluate side-chains
  127 residues out of total 808 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 113
  time to evaluate  : 0.328 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   12 ASP
Chi-restraints excluded: chain A residue  100 SER
Chi-restraints excluded: chain A residue  138 GLU
Chi-restraints excluded: chain B residue   12 ASP
Chi-restraints excluded: chain B residue   86 ASP
Chi-restraints excluded: chain B residue   88 LEU
Chi-restraints excluded: chain B residue  100 SER
Chi-restraints excluded: chain B residue  138 GLU
Chi-restraints excluded: chain D residue   12 ASP
Chi-restraints excluded: chain D residue  100 SER
Chi-restraints excluded: chain D residue  138 GLU
Chi-restraints excluded: chain C residue   12 ASP
Chi-restraints excluded: chain C residue  100 SER
Chi-restraints excluded: chain C residue  138 GLU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 92
   random chunks:
   chunk 73 optimal weight:    0.1980
   chunk 30 optimal weight:    4.9990
   chunk 13 optimal weight:    1.9990
   chunk 40 optimal weight:    2.9990
   chunk 52 optimal weight:    1.9990
   chunk 69 optimal weight:    0.8980
   chunk 28 optimal weight:    2.9990
   chunk 35 optimal weight:    0.9980
   chunk 12 optimal weight:    0.2980
   chunk 9 optimal weight:    0.5980
   chunk 48 optimal weight:    3.9990
   overall best weight:    0.5980

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

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

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3670 r_free = 0.3670 target = 0.135262 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3434 r_free = 0.3434 target = 0.116454 restraints weight = 8178.347|
|-----------------------------------------------------------------------------|
r_work (start): 0.3448 rms_B_bonded: 1.69
r_work: 0.3368 rms_B_bonded: 2.09 restraints_weight: 0.5000
r_work: 0.3275 rms_B_bonded: 3.49 restraints_weight: 0.2500
r_work (final): 0.3275
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8717
moved from start:          0.2465

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.026   7516  Z= 0.116
  Angle     :  0.513   3.883  10288  Z= 0.282
  Chirality :  0.045   0.149   1184
  Planarity :  0.005   0.087   1296
  Dihedral  :  5.417  15.894   1148
  Min Nonbonded Distance : 2.272

Molprobity Statistics.
  All-atom Clashscore : 6.70
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.53 %
    Favored  : 97.47 %
  Rotamer:
    Outliers :  1.73 %
    Allowed  : 11.88 %
    Favored  : 86.39 %
  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:  0.05 (0.28), residues: 908
  helix:  None (None), residues: 0
  sheet:  0.66 (0.29), residues: 336
  loop : -0.33 (0.25), residues: 572

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.001   ARG D 190 
 TYR   0.008   0.001   TYR A  52 
 PHE   0.014   0.002   PHE B  68 
 TRP   0.004   0.001   TRP B  59 
 HIS   0.002   0.001   HIS A 212 

Details of bonding type rmsd
  covalent geometry    : bond        0.00247 ( 7512)
  covalent geometry    : angle       0.51046 (10276)
  hydrogen bonds       : bond        0.03668 (  304)
  hydrogen bonds       : angle       4.91007 ( 1008)
  link_ALPHA1-3        : bond        0.00381 (    4)
  link_ALPHA1-3        : angle       1.47380 (   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
  130 residues out of total 808 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 116
  time to evaluate  : 0.292 
Fit side-chains
REVERT: A  138 GLU cc_start: 0.8869 (OUTLIER) cc_final: 0.8492 (pt0)
REVERT: B   41 ASN cc_start: 0.8791 (m-40) cc_final: 0.8481 (m-40)
REVERT: B   86 ASP cc_start: 0.8602 (OUTLIER) cc_final: 0.8342 (m-30)
REVERT: B  138 GLU cc_start: 0.8875 (OUTLIER) cc_final: 0.8500 (pt0)
REVERT: D  138 GLU cc_start: 0.8869 (OUTLIER) cc_final: 0.8502 (pt0)
REVERT: D  231 LYS cc_start: 0.8308 (ptpp) cc_final: 0.8042 (pttt)
REVERT: C  138 GLU cc_start: 0.8862 (OUTLIER) cc_final: 0.8493 (pt0)
  outliers start: 14
  outliers final: 7
  residues processed: 125
  average time/residue: 0.6911
  time to fit residues: 90.3848
Evaluate side-chains
  128 residues out of total 808 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 116
  time to evaluate  : 0.285 
-------------------------------------------------------------------------------
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   12 ASP
Chi-restraints excluded: chain B residue   86 ASP
Chi-restraints excluded: chain B residue   88 LEU
Chi-restraints excluded: chain B residue  100 SER
Chi-restraints excluded: chain B residue  138 GLU
Chi-restraints excluded: chain D residue   12 ASP
Chi-restraints excluded: chain D residue  138 GLU
Chi-restraints excluded: chain C residue   12 ASP
Chi-restraints excluded: chain C residue  100 SER
Chi-restraints excluded: chain C residue  138 GLU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 92
   random chunks:
   chunk 47 optimal weight:    3.9990
   chunk 35 optimal weight:    0.9980
   chunk 63 optimal weight:    2.9990
   chunk 11 optimal weight:    4.9990
   chunk 59 optimal weight:    0.8980
   chunk 29 optimal weight:    0.6980
   chunk 31 optimal weight:    2.9990
   chunk 65 optimal weight:    0.9990
   chunk 32 optimal weight:    0.8980
   chunk 58 optimal weight:    0.5980
   chunk 40 optimal weight:    2.9990
   overall best weight:    0.8180

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

Flipped N/Q/H residues before XYZ refinement:
A  28 ASN
C  28 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3660 r_free = 0.3660 target = 0.134553 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3432 r_free = 0.3432 target = 0.116159 restraints weight = 8228.063|
|-----------------------------------------------------------------------------|
r_work (start): 0.3441 rms_B_bonded: 1.66
r_work: 0.3362 rms_B_bonded: 2.06 restraints_weight: 0.5000
r_work: 0.3268 rms_B_bonded: 3.45 restraints_weight: 0.2500
r_work (final): 0.3268
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8730
moved from start:          0.2465

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.027   7516  Z= 0.133
  Angle     :  0.524   4.399  10288  Z= 0.288
  Chirality :  0.045   0.151   1184
  Planarity :  0.006   0.092   1296
  Dihedral  :  5.342  15.557   1148
  Min Nonbonded Distance : 2.251

Molprobity Statistics.
  All-atom Clashscore : 6.63
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.31 %
    Favored  : 97.69 %
  Rotamer:
    Outliers :  1.86 %
    Allowed  : 11.39 %
    Favored  : 86.76 %
  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:  0.05 (0.28), residues: 908
  helix:  None (None), residues: 0
  sheet:  0.67 (0.29), residues: 336
  loop : -0.33 (0.25), residues: 572

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.014   0.001   ARG B 190 
 TYR   0.009   0.001   TYR B  52 
 PHE   0.015   0.002   PHE A  68 
 TRP   0.005   0.001   TRP C  59 
 HIS   0.003   0.001   HIS B 212 

Details of bonding type rmsd
  covalent geometry    : bond        0.00290 ( 7512)
  covalent geometry    : angle       0.52186 (10276)
  hydrogen bonds       : bond        0.03776 (  304)
  hydrogen bonds       : angle       4.90151 ( 1008)
  link_ALPHA1-3        : bond        0.00345 (    4)
  link_ALPHA1-3        : angle       1.48976 (   12)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2910.54 seconds
wall clock time: 50 minutes 21.62 seconds (3021.62 seconds total)