Starting phenix.real_space_refine
on Tue Mar  3 15:50:21 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7sqg_25384/03_2026/7sqg_25384.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7sqg_25384/03_2026/7sqg_25384.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.6
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7sqg_25384/03_2026/7sqg_25384.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7sqg_25384/03_2026/7sqg_25384.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7sqg_25384/03_2026/7sqg_25384.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7sqg_25384/03_2026/7sqg_25384.cif"
  }
  resolution = 2.6
  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=   0.016
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 4
    Type Number    sf(0)   Gaussians
     S      27      5.16       5
     C    4296      2.51       5
     N    1083      2.21       5
     O    1224      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 8 residue(s): 0.00s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 6630
  Number of models: 1
  Model: ""
    Number of chains: 6
    Chain: "A"
      Number of atoms: 2154
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 270, 2154
          Classifications: {'peptide': 270}
          Incomplete info: {'truncation_to_alanine': 10}
          Link IDs: {'PTRANS': 13, 'TRANS': 256}
          Unresolved non-hydrogen bonds: 37
          Unresolved non-hydrogen angles: 44
          Unresolved non-hydrogen dihedrals: 32
          Unresolved non-hydrogen chiralities: 5
          Planarities with less than four sites: {'PHE:plan': 1}
          Unresolved non-hydrogen planarities: 6
    Chain: "B"
      Number of atoms: 2154
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 270, 2154
          Classifications: {'peptide': 270}
          Incomplete info: {'truncation_to_alanine': 10}
          Link IDs: {'PTRANS': 13, 'TRANS': 256}
          Unresolved non-hydrogen bonds: 37
          Unresolved non-hydrogen angles: 44
          Unresolved non-hydrogen dihedrals: 32
          Unresolved non-hydrogen chiralities: 5
          Planarities with less than four sites: {'PHE:plan': 1}
          Unresolved non-hydrogen planarities: 6
    Chain: "C"
      Number of atoms: 2154
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 270, 2154
          Classifications: {'peptide': 270}
          Incomplete info: {'truncation_to_alanine': 10}
          Link IDs: {'PTRANS': 13, 'TRANS': 256}
          Unresolved non-hydrogen bonds: 37
          Unresolved non-hydrogen angles: 44
          Unresolved non-hydrogen dihedrals: 32
          Unresolved non-hydrogen chiralities: 5
          Planarities with less than four sites: {'PHE:plan': 1}
          Unresolved non-hydrogen planarities: 6
    Chain: "A"
      Number of atoms: 56
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 4, 56
          Unusual residues: {'NAG': 4}
          Classifications: {'undetermined': 4}
          Link IDs: {None: 3}
          Unresolved non-hydrogen bonds: 4
          Unresolved non-hydrogen angles: 8
          Unresolved non-hydrogen dihedrals: 12
          Unresolved non-hydrogen chiralities: 4
    Chain: "B"
      Number of atoms: 56
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 4, 56
          Unusual residues: {'NAG': 4}
          Classifications: {'undetermined': 4}
          Link IDs: {None: 3}
          Unresolved non-hydrogen bonds: 4
          Unresolved non-hydrogen angles: 8
          Unresolved non-hydrogen dihedrals: 12
          Unresolved non-hydrogen chiralities: 4
    Chain: "C"
      Number of atoms: 56
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 4, 56
          Unusual residues: {'NAG': 4}
          Classifications: {'undetermined': 4}
          Link IDs: {None: 3}
          Unresolved non-hydrogen bonds: 4
          Unresolved non-hydrogen angles: 8
          Unresolved non-hydrogen dihedrals: 12
          Unresolved non-hydrogen chiralities: 4
  Time building chain proxies: 1.24, per 1000 atoms: 0.19
  Number of scatterers: 6630
  At special positions: 0
  Unit cell: (83.426, 82.6, 125.552, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     S      27     16.00
     O    1224      8.00
     N    1083      7.00
     C    4296      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
    NAG-ASN
      " NAG A 401 " - " ASN A 148 "
      " NAG A 402 " - " ASN A 162 "
      " NAG A 403 " - " ASN A 190 "
      " NAG A 404 " - " ASN A 155 "
      " NAG B 401 " - " ASN B 148 "
      " NAG B 402 " - " ASN B 162 "
      " NAG B 403 " - " ASN B 190 "
      " NAG B 404 " - " ASN B 155 "
      " NAG C 401 " - " ASN C 148 "
      " NAG C 402 " - " ASN C 162 "
      " NAG C 403 " - " ASN C 190 "
      " NAG C 404 " - " ASN C 155 "
  Time building additional restraints: 0.63
  Conformation dependent library (CDL) restraints added in 241.4 milliseconds
  

  1608 Ramachandran restraints generated.
    804 Oldfield, 0 Emsley, 804 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1560

  Finding SS restraints...
    Secondary structure from input PDB file:
      15 helices and 9 sheets defined
      34.6% alpha, 43.0% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.23
  Creating SS restraints...
    Processing helix  chain 'A' and resid 65 through 98
      removed outlier: 3.563A  pdb=" N   LEU A  69 " --> pdb=" O   VAL A  65 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 206 through 212
      removed outlier: 3.516A  pdb=" N   PHE A 210 " --> pdb=" O   SER A 206 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 215 through 227
      removed outlier: 3.691A  pdb=" N   SER A 225 " --> pdb=" O   GLN A 221 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 272 through 278
      removed outlier: 3.810A  pdb=" N   SER A 277 " --> pdb=" O   ALA A 274 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 302 through 334
    Processing helix  chain 'B' and resid 66 through 98
    Processing helix  chain 'B' and resid 206 through 212
      removed outlier: 3.516A  pdb=" N   PHE B 210 " --> pdb=" O   SER B 206 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 215 through 227
      removed outlier: 3.691A  pdb=" N   SER B 225 " --> pdb=" O   GLN B 221 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 272 through 278
      removed outlier: 3.810A  pdb=" N   SER B 277 " --> pdb=" O   ALA B 274 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 302 through 334
    Processing helix  chain 'C' and resid 66 through 98
    Processing helix  chain 'C' and resid 206 through 212
      removed outlier: 3.516A  pdb=" N   PHE C 210 " --> pdb=" O   SER C 206 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 215 through 227
      removed outlier: 3.691A  pdb=" N   SER C 225 " --> pdb=" O   GLN C 221 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 272 through 278
      removed outlier: 3.810A  pdb=" N   SER C 277 " --> pdb=" O   ALA C 274 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 302 through 334
    Processing sheet with id=AA1, first strand: chain 'A' and resid 100 through 107
      removed outlier: 13.537A  pdb=" N   PHE A 291 " --> pdb=" O   VAL A 240 " (cutoff:3.500A)
      removed outlier: 9.278A  pdb=" N   MET A 242 " --> pdb=" O   PHE A 291 " (cutoff:3.500A)
      removed outlier: 9.162A  pdb=" N   GLN A 293 " --> pdb=" O   MET A 242 " (cutoff:3.500A)
      removed outlier: 6.610A  pdb=" N   LEU A 244 " --> pdb=" O   GLN A 293 " (cutoff:3.500A)
      removed outlier: 7.767A  pdb=" N   VAL A 295 " --> pdb=" O   LEU A 244 " (cutoff:3.500A)
      removed outlier: 6.369A  pdb=" N   LYS A 246 " --> pdb=" O   VAL A 295 " (cutoff:3.500A)
      removed outlier: 8.109A  pdb=" N   ASP A 297 " --> pdb=" O   LYS A 246 " (cutoff:3.500A)
      removed outlier: 7.924A  pdb=" N   LYS A 248 " --> pdb=" O   ASP A 297 " (cutoff:3.500A)
      removed outlier: 4.437A  pdb=" N   PHE A 236 " --> pdb=" O   LEU A 280 " (cutoff:3.500A)
      removed outlier: 4.598A  pdb=" N   TRP A 287 " --> pdb=" O   GLU A 181 " (cutoff:3.500A)
      removed outlier: 6.981A  pdb=" N   GLU A 181 " --> pdb=" O   TRP A 287 " (cutoff:3.500A)
      removed outlier: 6.488A  pdb=" N   ARG A 188 " --> pdb=" O   LEU A 125 " (cutoff:3.500A)
      removed outlier: 5.547A  pdb=" N   LEU A 125 " --> pdb=" O   ARG A 188 " (cutoff:3.500A)
      removed outlier: 7.721A  pdb=" N   ASN A 148 " --> pdb=" O   LEU A 126 " (cutoff:3.500A)
      removed outlier: 6.420A  pdb=" N   CYS A 128 " --> pdb=" O   ASN A 148 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 100 through 107
      removed outlier: 13.537A  pdb=" N   PHE A 291 " --> pdb=" O   VAL A 240 " (cutoff:3.500A)
      removed outlier: 9.278A  pdb=" N   MET A 242 " --> pdb=" O   PHE A 291 " (cutoff:3.500A)
      removed outlier: 9.162A  pdb=" N   GLN A 293 " --> pdb=" O   MET A 242 " (cutoff:3.500A)
      removed outlier: 6.610A  pdb=" N   LEU A 244 " --> pdb=" O   GLN A 293 " (cutoff:3.500A)
      removed outlier: 7.767A  pdb=" N   VAL A 295 " --> pdb=" O   LEU A 244 " (cutoff:3.500A)
      removed outlier: 6.369A  pdb=" N   LYS A 246 " --> pdb=" O   VAL A 295 " (cutoff:3.500A)
      removed outlier: 8.109A  pdb=" N   ASP A 297 " --> pdb=" O   LYS A 246 " (cutoff:3.500A)
      removed outlier: 7.924A  pdb=" N   LYS A 248 " --> pdb=" O   ASP A 297 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 151 through 157
      removed outlier: 3.743A  pdb=" N   ASP A 200 " --> pdb=" O   TYR A 119 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'B' and resid 100 through 107
      removed outlier: 13.537A  pdb=" N   PHE B 291 " --> pdb=" O   VAL B 240 " (cutoff:3.500A)
      removed outlier: 9.278A  pdb=" N   MET B 242 " --> pdb=" O   PHE B 291 " (cutoff:3.500A)
      removed outlier: 9.162A  pdb=" N   GLN B 293 " --> pdb=" O   MET B 242 " (cutoff:3.500A)
      removed outlier: 6.610A  pdb=" N   LEU B 244 " --> pdb=" O   GLN B 293 " (cutoff:3.500A)
      removed outlier: 7.767A  pdb=" N   VAL B 295 " --> pdb=" O   LEU B 244 " (cutoff:3.500A)
      removed outlier: 6.368A  pdb=" N   LYS B 246 " --> pdb=" O   VAL B 295 " (cutoff:3.500A)
      removed outlier: 8.109A  pdb=" N   ASP B 297 " --> pdb=" O   LYS B 246 " (cutoff:3.500A)
      removed outlier: 7.924A  pdb=" N   LYS B 248 " --> pdb=" O   ASP B 297 " (cutoff:3.500A)
      removed outlier: 4.437A  pdb=" N   PHE B 236 " --> pdb=" O   LEU B 280 " (cutoff:3.500A)
      removed outlier: 4.598A  pdb=" N   TRP B 287 " --> pdb=" O   GLU B 181 " (cutoff:3.500A)
      removed outlier: 6.981A  pdb=" N   GLU B 181 " --> pdb=" O   TRP B 287 " (cutoff:3.500A)
      removed outlier: 6.488A  pdb=" N   ARG B 188 " --> pdb=" O   LEU B 125 " (cutoff:3.500A)
      removed outlier: 5.547A  pdb=" N   LEU B 125 " --> pdb=" O   ARG B 188 " (cutoff:3.500A)
      removed outlier: 7.721A  pdb=" N   ASN B 148 " --> pdb=" O   LEU B 126 " (cutoff:3.500A)
      removed outlier: 6.419A  pdb=" N   CYS B 128 " --> pdb=" O   ASN B 148 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'B' and resid 100 through 107
      removed outlier: 13.537A  pdb=" N   PHE B 291 " --> pdb=" O   VAL B 240 " (cutoff:3.500A)
      removed outlier: 9.278A  pdb=" N   MET B 242 " --> pdb=" O   PHE B 291 " (cutoff:3.500A)
      removed outlier: 9.162A  pdb=" N   GLN B 293 " --> pdb=" O   MET B 242 " (cutoff:3.500A)
      removed outlier: 6.610A  pdb=" N   LEU B 244 " --> pdb=" O   GLN B 293 " (cutoff:3.500A)
      removed outlier: 7.767A  pdb=" N   VAL B 295 " --> pdb=" O   LEU B 244 " (cutoff:3.500A)
      removed outlier: 6.368A  pdb=" N   LYS B 246 " --> pdb=" O   VAL B 295 " (cutoff:3.500A)
      removed outlier: 8.109A  pdb=" N   ASP B 297 " --> pdb=" O   LYS B 246 " (cutoff:3.500A)
      removed outlier: 7.924A  pdb=" N   LYS B 248 " --> pdb=" O   ASP B 297 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'B' and resid 151 through 157
      removed outlier: 3.741A  pdb=" N   ASP B 200 " --> pdb=" O   TYR B 119 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'C' and resid 100 through 107
      removed outlier: 13.537A  pdb=" N   PHE C 291 " --> pdb=" O   VAL C 240 " (cutoff:3.500A)
      removed outlier: 9.278A  pdb=" N   MET C 242 " --> pdb=" O   PHE C 291 " (cutoff:3.500A)
      removed outlier: 9.162A  pdb=" N   GLN C 293 " --> pdb=" O   MET C 242 " (cutoff:3.500A)
      removed outlier: 6.611A  pdb=" N   LEU C 244 " --> pdb=" O   GLN C 293 " (cutoff:3.500A)
      removed outlier: 7.767A  pdb=" N   VAL C 295 " --> pdb=" O   LEU C 244 " (cutoff:3.500A)
      removed outlier: 6.368A  pdb=" N   LYS C 246 " --> pdb=" O   VAL C 295 " (cutoff:3.500A)
      removed outlier: 8.109A  pdb=" N   ASP C 297 " --> pdb=" O   LYS C 246 " (cutoff:3.500A)
      removed outlier: 7.924A  pdb=" N   LYS C 248 " --> pdb=" O   ASP C 297 " (cutoff:3.500A)
      removed outlier: 4.437A  pdb=" N   PHE C 236 " --> pdb=" O   LEU C 280 " (cutoff:3.500A)
      removed outlier: 4.598A  pdb=" N   TRP C 287 " --> pdb=" O   GLU C 181 " (cutoff:3.500A)
      removed outlier: 6.980A  pdb=" N   GLU C 181 " --> pdb=" O   TRP C 287 " (cutoff:3.500A)
      removed outlier: 6.488A  pdb=" N   ARG C 188 " --> pdb=" O   LEU C 125 " (cutoff:3.500A)
      removed outlier: 5.546A  pdb=" N   LEU C 125 " --> pdb=" O   ARG C 188 " (cutoff:3.500A)
      removed outlier: 7.721A  pdb=" N   ASN C 148 " --> pdb=" O   LEU C 126 " (cutoff:3.500A)
      removed outlier: 6.420A  pdb=" N   CYS C 128 " --> pdb=" O   ASN C 148 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'C' and resid 100 through 107
      removed outlier: 13.537A  pdb=" N   PHE C 291 " --> pdb=" O   VAL C 240 " (cutoff:3.500A)
      removed outlier: 9.278A  pdb=" N   MET C 242 " --> pdb=" O   PHE C 291 " (cutoff:3.500A)
      removed outlier: 9.162A  pdb=" N   GLN C 293 " --> pdb=" O   MET C 242 " (cutoff:3.500A)
      removed outlier: 6.611A  pdb=" N   LEU C 244 " --> pdb=" O   GLN C 293 " (cutoff:3.500A)
      removed outlier: 7.767A  pdb=" N   VAL C 295 " --> pdb=" O   LEU C 244 " (cutoff:3.500A)
      removed outlier: 6.368A  pdb=" N   LYS C 246 " --> pdb=" O   VAL C 295 " (cutoff:3.500A)
      removed outlier: 8.109A  pdb=" N   ASP C 297 " --> pdb=" O   LYS C 246 " (cutoff:3.500A)
      removed outlier: 7.924A  pdb=" N   LYS C 248 " --> pdb=" O   ASP C 297 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'C' and resid 151 through 157
      removed outlier: 3.733A  pdb=" N   ASP C 200 " --> pdb=" O   TYR C 119 " (cutoff:3.500A)

    414 hydrogen bonds defined for protein.
    1179 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: 1.07

  Time building geometry restraints manager: 0.76 seconds

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

  Histogram of bond lengths:
        1.22 -     1.34: 2049
        1.34 -     1.46: 1202
        1.46 -     1.57: 3505
        1.57 -     1.69: 0
        1.69 -     1.81: 42
  Bond restraints: 6798
  Sorted by residual:
  bond pdb=" N   GLU A 224 "
       pdb=" CA  GLU A 224 "
    ideal  model  delta    sigma   weight residual
    1.459  1.490 -0.032 1.25e-02 6.40e+03 6.43e+00
  bond pdb=" N   ARG C  93 "
       pdb=" CA  ARG C  93 "
    ideal  model  delta    sigma   weight residual
    1.459  1.489 -0.030 1.19e-02 7.06e+03 6.36e+00
  bond pdb=" N   GLU C 224 "
       pdb=" CA  GLU C 224 "
    ideal  model  delta    sigma   weight residual
    1.459  1.490 -0.031 1.25e-02 6.40e+03 6.15e+00
  bond pdb=" N   ARG B  93 "
       pdb=" CA  ARG B  93 "
    ideal  model  delta    sigma   weight residual
    1.459  1.489 -0.030 1.19e-02 7.06e+03 6.15e+00
  bond pdb=" N   GLU B 224 "
       pdb=" CA  GLU B 224 "
    ideal  model  delta    sigma   weight residual
    1.459  1.490 -0.031 1.25e-02 6.40e+03 6.14e+00
  ... (remaining 6793 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     0.97: 8460
        0.97 -     1.94: 559
        1.94 -     2.91: 161
        2.91 -     3.88: 32
        3.88 -     4.84: 10
  Bond angle restraints: 9222
  Sorted by residual:
  angle pdb=" C   ARG A 259 "
        pdb=" N   GLN A 260 "
        pdb=" CA  GLN A 260 "
      ideal   model   delta    sigma   weight residual
     122.99  118.15    4.84 1.41e+00 5.03e-01 1.18e+01
  angle pdb=" C   ARG C 259 "
        pdb=" N   GLN C 260 "
        pdb=" CA  GLN C 260 "
      ideal   model   delta    sigma   weight residual
     122.99  118.15    4.84 1.41e+00 5.03e-01 1.18e+01
  angle pdb=" C   ARG B 259 "
        pdb=" N   GLN B 260 "
        pdb=" CA  GLN B 260 "
      ideal   model   delta    sigma   weight residual
     122.99  118.23    4.76 1.41e+00 5.03e-01 1.14e+01
  angle pdb=" CA  ARG B  93 "
        pdb=" C   ARG B  93 "
        pdb=" O   ARG B  93 "
      ideal   model   delta    sigma   weight residual
     120.82  117.99    2.83 1.05e+00 9.07e-01 7.29e+00
  angle pdb=" CA  ARG C  93 "
        pdb=" C   ARG C  93 "
        pdb=" O   ARG C  93 "
      ideal   model   delta    sigma   weight residual
     120.82  118.00    2.82 1.05e+00 9.07e-01 7.22e+00
  ... (remaining 9217 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    21.51: 3910
       21.51 -    43.02: 199
       43.02 -    64.53: 63
       64.53 -    86.03: 7
       86.03 -   107.54: 24
  Dihedral angle restraints: 4203
    sinusoidal: 1806
      harmonic: 2397
  Sorted by residual:
  dihedral pdb=" CA  PHE A 236 "
           pdb=" C   PHE A 236 "
           pdb=" N   ARG A 237 "
           pdb=" CA  ARG A 237 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  155.89   24.11     0      5.00e+00 4.00e-02 2.33e+01
  dihedral pdb=" CA  PHE B 236 "
           pdb=" C   PHE B 236 "
           pdb=" N   ARG B 237 "
           pdb=" CA  ARG B 237 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  155.89   24.11     0      5.00e+00 4.00e-02 2.33e+01
  dihedral pdb=" CA  PHE C 236 "
           pdb=" C   PHE C 236 "
           pdb=" N   ARG C 237 "
           pdb=" CA  ARG C 237 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  155.94   24.06     0      5.00e+00 4.00e-02 2.31e+01
  ... (remaining 4200 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.041: 721
       0.041 -    0.083: 231
       0.083 -    0.124: 86
       0.124 -    0.166: 8
       0.166 -    0.207: 4
  Chirality restraints: 1050
  Sorted by residual:
  chirality pdb=" CA  LEU A 169 "
            pdb=" N   LEU A 169 "
            pdb=" C   LEU A 169 "
            pdb=" CB  LEU A 169 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.72   -0.21 2.00e-01 2.50e+01 1.07e+00
  chirality pdb=" CA  LEU B 169 "
            pdb=" N   LEU B 169 "
            pdb=" C   LEU B 169 "
            pdb=" CB  LEU B 169 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.72   -0.21 2.00e-01 2.50e+01 1.07e+00
  chirality pdb=" CA  LEU C 169 "
            pdb=" N   LEU C 169 "
            pdb=" C   LEU C 169 "
            pdb=" CB  LEU C 169 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.72   -0.21 2.00e-01 2.50e+01 1.05e+00
  ... (remaining 1047 not shown)

  Planarity restraints: 1170
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  LEU C 118 "   -0.008 2.00e-02 2.50e+03   1.55e-02 2.41e+00
        pdb=" C   LEU C 118 "    0.027 2.00e-02 2.50e+03
        pdb=" O   LEU C 118 "   -0.010 2.00e-02 2.50e+03
        pdb=" N   TYR C 119 "   -0.009 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  LEU B 118 "   -0.007 2.00e-02 2.50e+03   1.51e-02 2.27e+00
        pdb=" C   LEU B 118 "    0.026 2.00e-02 2.50e+03
        pdb=" O   LEU B 118 "   -0.010 2.00e-02 2.50e+03
        pdb=" N   TYR B 119 "   -0.009 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  LEU A 118 "   -0.007 2.00e-02 2.50e+03   1.50e-02 2.26e+00
        pdb=" C   LEU A 118 "    0.026 2.00e-02 2.50e+03
        pdb=" O   LEU A 118 "   -0.010 2.00e-02 2.50e+03
        pdb=" N   TYR A 119 "   -0.009 2.00e-02 2.50e+03
  ... (remaining 1167 not shown)

  Histogram of nonbonded interaction distances:
        2.42 -     2.92: 2643
        2.92 -     3.41: 5865
        3.41 -     3.91: 11062
        3.91 -     4.40: 11948
        4.40 -     4.90: 20624
  Nonbonded interactions: 52142
  Sorted by model distance:
  nonbonded pdb=" OG1 THR A 150 "
            pdb=" OE1 GLN A 172 "
     model   vdw
     2.423 3.040
  nonbonded pdb=" OG1 THR C 150 "
            pdb=" OE1 GLN C 172 "
     model   vdw
     2.423 3.040
  nonbonded pdb=" OG1 THR B 150 "
            pdb=" OE1 GLN B 172 "
     model   vdw
     2.423 3.040
  nonbonded pdb=" OG  SER C 197 "
            pdb=" OE1 GLN C 279 "
     model   vdw
     2.439 3.040
  nonbonded pdb=" OG  SER A 197 "
            pdb=" OE1 GLN A 279 "
     model   vdw
     2.440 3.040
  ... (remaining 52137 not shown)

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

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:             2.540
  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:          0.150
  Check model and map are aligned:         0.020
  Set scattering table:                    0.020
  Process input model:                     7.240
  Find NCS groups from input model:        0.050
  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:             0.010
  Load rotamer database and sin/cos tables:7.330
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   17.370
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7321
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      :  0.004   0.032   6810  Z= 0.223
  Angle     :  0.614   4.844   9258  Z= 0.342
  Chirality :  0.047   0.207   1050
  Planarity :  0.004   0.033   1158
  Dihedral  : 17.267 107.543   2643
  Min Nonbonded Distance : 2.423

Molprobity Statistics.
  All-atom Clashscore : 3.35
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.99 %
    Favored  : 97.01 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.74 %
    Favored  : 98.26 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.39 (0.30), residues: 804
  helix:  3.12 (0.28), residues: 273
  sheet:  0.75 (0.29), residues: 318
  loop : -1.86 (0.40), residues: 213

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 110 
 TYR   0.009   0.001   TYR A 201 
 PHE   0.020   0.002   PHE A 219 
 TRP   0.007   0.001   TRP B 304 
 HIS   0.001   0.001   HIS A  98 

Details of bonding type rmsd
  covalent geometry    : bond        0.00407 ( 6798)
  covalent geometry    : angle       0.60470 ( 9222)
  hydrogen bonds       : bond        0.09118 (  390)
  hydrogen bonds       : angle       4.91090 ( 1179)
  link_NAG-ASN         : bond        0.00252 (   12)
  link_NAG-ASN         : angle       1.85381 (   36)

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

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

  1608 Ramachandran restraints generated.
    804 Oldfield, 0 Emsley, 804 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1608 Ramachandran restraints generated.
    804 Oldfield, 0 Emsley, 804 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  261 residues out of total 720 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 261
  time to evaluate  : 0.256 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   78 MET cc_start: 0.7274 (ttt) cc_final: 0.6970 (ttt)
REVERT: A   94 GLU cc_start: 0.7009 (tp30) cc_final: 0.6807 (tp30)
REVERT: A  106 LYS cc_start: 0.7670 (tttp) cc_final: 0.7363 (tttp)
REVERT: A  143 GLN cc_start: 0.7727 (mm110) cc_final: 0.7497 (mm110)
REVERT: A  147 MET cc_start: 0.7523 (mtm) cc_final: 0.7285 (mtp)
REVERT: A  166 LYS cc_start: 0.7903 (mtpt) cc_final: 0.7694 (mttm)
REVERT: A  180 ARG cc_start: 0.7102 (mtp180) cc_final: 0.6806 (mtp180)
REVERT: A  294 LYS cc_start: 0.7529 (mttt) cc_final: 0.7281 (mttt)
REVERT: A  304 TRP cc_start: 0.7393 (m100) cc_final: 0.7012 (m100)
REVERT: B   94 GLU cc_start: 0.7036 (tp30) cc_final: 0.6790 (tp30)
REVERT: B   98 HIS cc_start: 0.8294 (m90) cc_final: 0.8075 (m-70)
REVERT: B  180 ARG cc_start: 0.7003 (mtp180) cc_final: 0.6686 (mtp180)
REVERT: B  197 SER cc_start: 0.8098 (p) cc_final: 0.7657 (p)
REVERT: B  219 PHE cc_start: 0.7931 (t80) cc_final: 0.7657 (t80)
REVERT: B  224 GLU cc_start: 0.7251 (mm-30) cc_final: 0.6878 (mm-30)
REVERT: B  247 THR cc_start: 0.7494 (m) cc_final: 0.7187 (t)
REVERT: B  275 LYS cc_start: 0.7412 (mmtt) cc_final: 0.6944 (mmmm)
REVERT: C   92 PHE cc_start: 0.7508 (t80) cc_final: 0.6960 (t80)
REVERT: C  124 GLN cc_start: 0.7490 (pt0) cc_final: 0.7262 (pt0)
REVERT: C  148 ASN cc_start: 0.6303 (t0) cc_final: 0.6057 (p0)
REVERT: C  176 GLU cc_start: 0.7333 (mp0) cc_final: 0.6829 (mp0)
REVERT: C  179 LYS cc_start: 0.8267 (mtpp) cc_final: 0.8010 (mtmt)
REVERT: C  188 ARG cc_start: 0.7500 (ttp-170) cc_final: 0.7048 (ttp-170)
REVERT: C  194 GLU cc_start: 0.6927 (tm-30) cc_final: 0.6424 (tm-30)
REVERT: C  197 SER cc_start: 0.8136 (p) cc_final: 0.7731 (p)
REVERT: C  219 PHE cc_start: 0.7989 (t80) cc_final: 0.7659 (t80)
REVERT: C  271 ARG cc_start: 0.7742 (mtm180) cc_final: 0.7444 (mtm-85)
REVERT: C  304 TRP cc_start: 0.7634 (m100) cc_final: 0.7103 (m100)
  outliers start: 0
  outliers final: 0
  residues processed: 261
  average time/residue: 0.7599
  time to fit residues: 205.0479
Evaluate side-chains
  236 residues out of total 720 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 236
  time to evaluate  : 0.225 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 81
   random chunks:
   chunk 49 optimal weight:    0.7980
   chunk 53 optimal weight:    0.6980
   chunk 5 optimal weight:    0.1980
   chunk 33 optimal weight:    0.0670
   chunk 65 optimal weight:    0.9980
   chunk 62 optimal weight:    0.9990
   chunk 51 optimal weight:    0.5980
   chunk 38 optimal weight:    0.4980
   chunk 61 optimal weight:    0.0030
   chunk 45 optimal weight:    0.6980
   chunk 74 optimal weight:    0.9990
   overall best weight:    0.2728

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

Flipped N/Q/H residues before XYZ refinement:
A 152 GLN
A 172 GLN
A 208 GLN
A 293 GLN
A 296 GLN
B 172 GLN
B 266 ASN
** B 279 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 293 GLN
B 296 GLN
C  98 HIS
C 186 GLN
** C 296 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 11

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3871 r_free = 0.3871 target = 0.140394 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3626 r_free = 0.3626 target = 0.122348 restraints weight = 9815.391|
|-----------------------------------------------------------------------------|
r_work (start): 0.3623 rms_B_bonded: 2.31
r_work: 0.3484 rms_B_bonded: 2.75 restraints_weight: 0.5000
r_work: 0.3315 rms_B_bonded: 4.72 restraints_weight: 0.2500
r_work (final): 0.3315
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7869
moved from start:          0.1491

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.056   6810  Z= 0.136
  Angle     :  0.600   9.135   9258  Z= 0.293
  Chirality :  0.044   0.198   1050
  Planarity :  0.003   0.029   1158
  Dihedral  : 13.079  82.369   1125
  Min Nonbonded Distance : 2.510

Molprobity Statistics.
  All-atom Clashscore : 5.34
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.87 %
    Favored  : 98.13 %
  Rotamer:
    Outliers :  2.75 %
    Allowed  : 14.35 %
    Favored  : 82.90 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.77 (0.29), residues: 804
  helix:  3.33 (0.28), residues: 258
  sheet:  1.15 (0.29), residues: 300
  loop : -1.28 (0.39), residues: 246

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG B 110 
 TYR   0.008   0.001   TYR B 119 
 PHE   0.021   0.002   PHE A 219 
 TRP   0.008   0.001   TRP A 304 
 HIS   0.009   0.002   HIS C  98 

Details of bonding type rmsd
  covalent geometry    : bond        0.00313 ( 6798)
  covalent geometry    : angle       0.58095 ( 9222)
  hydrogen bonds       : bond        0.03128 (  390)
  hydrogen bonds       : angle       4.14602 ( 1179)
  link_NAG-ASN         : bond        0.00296 (   12)
  link_NAG-ASN         : angle       2.47521 (   36)

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

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

  1608 Ramachandran restraints generated.
    804 Oldfield, 0 Emsley, 804 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1608 Ramachandran restraints generated.
    804 Oldfield, 0 Emsley, 804 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  243 residues out of total 720 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 224
  time to evaluate  : 0.224 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  106 LYS cc_start: 0.8432 (tttp) cc_final: 0.8205 (ttmm)
REVERT: A  147 MET cc_start: 0.7783 (mtm) cc_final: 0.7545 (mtp)
REVERT: A  176 GLU cc_start: 0.8040 (mp0) cc_final: 0.7280 (mp0)
REVERT: A  180 ARG cc_start: 0.7932 (mtp180) cc_final: 0.7688 (mtp180)
REVERT: A  181 GLU cc_start: 0.8080 (tt0) cc_final: 0.7595 (tt0)
REVERT: A  206 SER cc_start: 0.8576 (m) cc_final: 0.8367 (t)
REVERT: A  304 TRP cc_start: 0.8377 (m100) cc_final: 0.8168 (m100)
REVERT: B  219 PHE cc_start: 0.8289 (t80) cc_final: 0.7804 (t80)
REVERT: B  271 ARG cc_start: 0.8729 (mtm180) cc_final: 0.8495 (mtm180)
REVERT: C   92 PHE cc_start: 0.8660 (t80) cc_final: 0.8367 (t80)
REVERT: C  148 ASN cc_start: 0.7034 (t0) cc_final: 0.6628 (p0)
REVERT: C  176 GLU cc_start: 0.8133 (mp0) cc_final: 0.7258 (mp0)
REVERT: C  181 GLU cc_start: 0.8046 (tt0) cc_final: 0.7637 (tt0)
REVERT: C  188 ARG cc_start: 0.8277 (ttp-170) cc_final: 0.8010 (ttp-170)
REVERT: C  194 GLU cc_start: 0.6936 (tm-30) cc_final: 0.6616 (tm-30)
REVERT: C  219 PHE cc_start: 0.8381 (t80) cc_final: 0.8001 (t80)
REVERT: C  271 ARG cc_start: 0.8685 (mtm180) cc_final: 0.8259 (mtm-85)
REVERT: C  304 TRP cc_start: 0.8475 (m100) cc_final: 0.8187 (m100)
  outliers start: 19
  outliers final: 10
  residues processed: 227
  average time/residue: 0.7446
  time to fit residues: 174.9063
Evaluate side-chains
  232 residues out of total 720 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 222
  time to evaluate  : 0.258 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  202 LEU
Chi-restraints excluded: chain A residue  264 VAL
Chi-restraints excluded: chain A residue  322 GLU
Chi-restraints excluded: chain B residue  186 GLN
Chi-restraints excluded: chain B residue  200 ASP
Chi-restraints excluded: chain B residue  315 LEU
Chi-restraints excluded: chain B residue  322 GLU
Chi-restraints excluded: chain C residue  165 VAL
Chi-restraints excluded: chain C residue  277 SER
Chi-restraints excluded: chain C residue  315 LEU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 81
   random chunks:
   chunk 5 optimal weight:    0.0570
   chunk 28 optimal weight:    0.5980
   chunk 56 optimal weight:    0.7980
   chunk 80 optimal weight:    0.9980
   chunk 64 optimal weight:    0.9980
   chunk 52 optimal weight:    0.5980
   chunk 17 optimal weight:    0.9990
   chunk 70 optimal weight:    1.9990
   chunk 69 optimal weight:    0.7980
   chunk 4 optimal weight:    0.9980
   chunk 25 optimal weight:    0.0970
   overall best weight:    0.4296

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

Flipped N/Q/H residues before XYZ refinement:
A 152 GLN
A 208 GLN
A 293 GLN
B 172 GLN
** B 279 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 293 GLN
C  98 HIS
C 124 GLN

Total number of N/Q/H flips: 7

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3864 r_free = 0.3864 target = 0.139832 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3600 r_free = 0.3600 target = 0.120492 restraints weight = 9433.498|
|-----------------------------------------------------------------------------|
r_work (start): 0.3603 rms_B_bonded: 2.41
r_work: 0.3459 rms_B_bonded: 2.82 restraints_weight: 0.5000
r_work: 0.3284 rms_B_bonded: 4.81 restraints_weight: 0.2500
r_work (final): 0.3284
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7916
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      :  0.004   0.045   6810  Z= 0.176
  Angle     :  0.603   8.588   9258  Z= 0.296
  Chirality :  0.044   0.151   1050
  Planarity :  0.004   0.030   1158
  Dihedral  :  9.509  58.722   1125
  Min Nonbonded Distance : 2.542

Molprobity Statistics.
  All-atom Clashscore : 5.18
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.74 %
    Favored  : 97.26 %
  Rotamer:
    Outliers :  3.19 %
    Allowed  : 19.71 %
    Favored  : 77.10 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.52 (0.29), residues: 804
  helix:  2.83 (0.29), residues: 279
  sheet:  0.93 (0.27), residues: 318
  loop : -1.51 (0.41), residues: 207

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG A 175 
 TYR   0.010   0.001   TYR B 119 
 PHE   0.019   0.002   PHE B 204 
 TRP   0.009   0.001   TRP C 239 
 HIS   0.009   0.001   HIS C  98 

Details of bonding type rmsd
  covalent geometry    : bond        0.00417 ( 6798)
  covalent geometry    : angle       0.59271 ( 9222)
  hydrogen bonds       : bond        0.03398 (  390)
  hydrogen bonds       : angle       4.13685 ( 1179)
  link_NAG-ASN         : bond        0.00449 (   12)
  link_NAG-ASN         : angle       1.83974 (   36)

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

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

  1608 Ramachandran restraints generated.
    804 Oldfield, 0 Emsley, 804 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1608 Ramachandran restraints generated.
    804 Oldfield, 0 Emsley, 804 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  250 residues out of total 720 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 228
  time to evaluate  : 0.260 
Fit side-chains
   revert: symmetry clash
REVERT: A  129 LYS cc_start: 0.8561 (mtpt) cc_final: 0.8325 (mttt)
REVERT: A  147 MET cc_start: 0.7876 (mtm) cc_final: 0.7616 (mtp)
REVERT: A  175 ARG cc_start: 0.7852 (mtp85) cc_final: 0.7492 (mtp85)
REVERT: A  176 GLU cc_start: 0.8141 (mp0) cc_final: 0.7111 (mp0)
REVERT: A  181 GLU cc_start: 0.8119 (tt0) cc_final: 0.7761 (tt0)
REVERT: A  194 GLU cc_start: 0.6601 (tm-30) cc_final: 0.6265 (tm-30)
REVERT: A  206 SER cc_start: 0.8655 (m) cc_final: 0.8441 (t)
REVERT: B  180 ARG cc_start: 0.8070 (mtp180) cc_final: 0.7808 (mtp180)
REVERT: C   92 PHE cc_start: 0.8669 (t80) cc_final: 0.8454 (t80)
REVERT: C   93 ARG cc_start: 0.7793 (mtt180) cc_final: 0.7533 (mtm110)
REVERT: C  148 ASN cc_start: 0.7133 (t0) cc_final: 0.6717 (p0)
REVERT: C  176 GLU cc_start: 0.8198 (mp0) cc_final: 0.7376 (mp0)
REVERT: C  181 GLU cc_start: 0.8080 (tt0) cc_final: 0.7733 (tt0)
REVERT: C  188 ARG cc_start: 0.8364 (ttp-170) cc_final: 0.8112 (ttp-170)
REVERT: C  194 GLU cc_start: 0.6968 (tm-30) cc_final: 0.6627 (tm-30)
REVERT: C  212 GLN cc_start: 0.7263 (mp10) cc_final: 0.6894 (mp10)
REVERT: C  271 ARG cc_start: 0.8682 (mtm180) cc_final: 0.8241 (mtm-85)
REVERT: C  304 TRP cc_start: 0.8507 (m100) cc_final: 0.8157 (m100)
  outliers start: 22
  outliers final: 11
  residues processed: 232
  average time/residue: 0.7132
  time to fit residues: 171.4436
Evaluate side-chains
  236 residues out of total 720 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 225
  time to evaluate  : 0.245 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   73 ILE
Chi-restraints excluded: chain A residue  197 SER
Chi-restraints excluded: chain A residue  202 LEU
Chi-restraints excluded: chain A residue  315 LEU
Chi-restraints excluded: chain A residue  322 GLU
Chi-restraints excluded: chain B residue  186 GLN
Chi-restraints excluded: chain B residue  200 ASP
Chi-restraints excluded: chain B residue  322 GLU
Chi-restraints excluded: chain C residue   73 ILE
Chi-restraints excluded: chain C residue  257 GLU
Chi-restraints excluded: chain C residue  315 LEU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 81
   random chunks:
   chunk 43 optimal weight:    0.5980
   chunk 5 optimal weight:    0.0870
   chunk 36 optimal weight:    0.8980
   chunk 79 optimal weight:    0.9980
   chunk 26 optimal weight:    0.2980
   chunk 24 optimal weight:    0.0570
   chunk 28 optimal weight:    1.9990
   chunk 11 optimal weight:    0.9990
   chunk 35 optimal weight:    1.9990
   chunk 68 optimal weight:    0.0870
   chunk 2 optimal weight:    0.0970
   overall best weight:    0.1252

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

Flipped N/Q/H residues before XYZ refinement:
A 172 GLN
B 186 GLN
C 186 GLN
C 266 ASN
** C 279 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3885 r_free = 0.3885 target = 0.141305 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3631 r_free = 0.3631 target = 0.122667 restraints weight = 9598.192|
|-----------------------------------------------------------------------------|
r_work (start): 0.3636 rms_B_bonded: 2.34
r_work: 0.3499 rms_B_bonded: 2.74 restraints_weight: 0.5000
r_work: 0.3328 rms_B_bonded: 4.73 restraints_weight: 0.2500
r_work (final): 0.3328
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7870
moved from start:          0.2222

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.034   6810  Z= 0.098
  Angle     :  0.537   7.069   9258  Z= 0.266
  Chirality :  0.043   0.150   1050
  Planarity :  0.003   0.027   1158
  Dihedral  :  7.537  56.596   1125
  Min Nonbonded Distance : 2.550

Molprobity Statistics.
  All-atom Clashscore : 5.41
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.99 %
    Favored  : 98.01 %
  Rotamer:
    Outliers :  2.61 %
    Allowed  : 21.59 %
    Favored  : 75.80 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.87 (0.29), residues: 804
  helix:  3.36 (0.28), residues: 258
  sheet:  1.14 (0.27), residues: 306
  loop : -1.10 (0.39), residues: 240

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 175 
 TYR   0.007   0.001   TYR B 111 
 PHE   0.014   0.001   PHE C 204 
 TRP   0.007   0.001   TRP A 304 
 HIS   0.002   0.000   HIS C  98 

Details of bonding type rmsd
  covalent geometry    : bond        0.00215 ( 6798)
  covalent geometry    : angle       0.52620 ( 9222)
  hydrogen bonds       : bond        0.02801 (  390)
  hydrogen bonds       : angle       3.98753 ( 1179)
  link_NAG-ASN         : bond        0.00442 (   12)
  link_NAG-ASN         : angle       1.80090 (   36)

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

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

  1608 Ramachandran restraints generated.
    804 Oldfield, 0 Emsley, 804 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1608 Ramachandran restraints generated.
    804 Oldfield, 0 Emsley, 804 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  229 residues out of total 720 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 211
  time to evaluate  : 0.280 
Fit side-chains
   revert: symmetry clash
REVERT: A  129 LYS cc_start: 0.8549 (mtpt) cc_final: 0.8334 (mttt)
REVERT: A  147 MET cc_start: 0.7864 (mtm) cc_final: 0.7642 (mtp)
REVERT: A  175 ARG cc_start: 0.7767 (mtp85) cc_final: 0.7492 (mtp85)
REVERT: A  176 GLU cc_start: 0.8095 (mp0) cc_final: 0.7194 (mp0)
REVERT: A  181 GLU cc_start: 0.8073 (tt0) cc_final: 0.7744 (tt0)
REVERT: A  206 SER cc_start: 0.8622 (m) cc_final: 0.8419 (t)
REVERT: B  180 ARG cc_start: 0.8041 (mtp180) cc_final: 0.7769 (mtp180)
REVERT: B  186 GLN cc_start: 0.8148 (OUTLIER) cc_final: 0.7871 (mt0)
REVERT: C  148 ASN cc_start: 0.7093 (t0) cc_final: 0.6756 (p0)
REVERT: C  176 GLU cc_start: 0.8143 (mp0) cc_final: 0.7235 (mp0)
REVERT: C  181 GLU cc_start: 0.8043 (tt0) cc_final: 0.7638 (tt0)
REVERT: C  188 ARG cc_start: 0.8352 (ttp-170) cc_final: 0.8082 (ttp-170)
REVERT: C  194 GLU cc_start: 0.6997 (tm-30) cc_final: 0.6670 (tm-30)
REVERT: C  206 SER cc_start: 0.8636 (m) cc_final: 0.8410 (t)
REVERT: C  212 GLN cc_start: 0.7209 (mp10) cc_final: 0.6879 (mp10)
REVERT: C  219 PHE cc_start: 0.8164 (t80) cc_final: 0.7949 (t80)
REVERT: C  271 ARG cc_start: 0.8688 (mtm180) cc_final: 0.8251 (mtm-85)
REVERT: C  304 TRP cc_start: 0.8439 (m100) cc_final: 0.8124 (m100)
  outliers start: 18
  outliers final: 7
  residues processed: 216
  average time/residue: 0.7754
  time to fit residues: 173.0933
Evaluate side-chains
  216 residues out of total 720 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 208
  time to evaluate  : 0.156 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   78 MET
Chi-restraints excluded: chain A residue  322 GLU
Chi-restraints excluded: chain B residue  186 GLN
Chi-restraints excluded: chain B residue  200 ASP
Chi-restraints excluded: chain B residue  211 LEU
Chi-restraints excluded: chain B residue  322 GLU
Chi-restraints excluded: chain C residue  165 VAL
Chi-restraints excluded: chain C residue  315 LEU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 81
   random chunks:
   chunk 68 optimal weight:    0.1980
   chunk 1 optimal weight:    0.8980
   chunk 24 optimal weight:    0.5980
   chunk 41 optimal weight:    0.0970
   chunk 21 optimal weight:    0.4980
   chunk 7 optimal weight:    4.9990
   chunk 11 optimal weight:    0.9990
   chunk 50 optimal weight:    1.9990
   chunk 66 optimal weight:    0.8980
   chunk 5 optimal weight:    0.0980
   chunk 46 optimal weight:    0.6980
   overall best weight:    0.2978

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

Flipped N/Q/H residues before XYZ refinement:
** A 279 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 293 GLN
B 293 GLN
C 186 GLN
C 293 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3867 r_free = 0.3867 target = 0.139956 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3606 r_free = 0.3606 target = 0.120913 restraints weight = 9645.088|
|-----------------------------------------------------------------------------|
r_work (start): 0.3616 rms_B_bonded: 2.37
r_work: 0.3477 rms_B_bonded: 2.79 restraints_weight: 0.5000
r_work: 0.3303 rms_B_bonded: 4.79 restraints_weight: 0.2500
r_work (final): 0.3303
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7901
moved from start:          0.2350

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040   6810  Z= 0.139
  Angle     :  0.553   6.891   9258  Z= 0.275
  Chirality :  0.043   0.146   1050
  Planarity :  0.003   0.028   1158
  Dihedral  :  6.666  55.312   1125
  Min Nonbonded Distance : 2.549

Molprobity Statistics.
  All-atom Clashscore : 5.79
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.11 %
    Favored  : 97.89 %
  Rotamer:
    Outliers :  2.03 %
    Allowed  : 22.03 %
    Favored  : 75.94 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.92 (0.29), residues: 804
  helix:  3.38 (0.29), residues: 258
  sheet:  0.96 (0.26), residues: 333
  loop : -0.94 (0.43), residues: 213

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG C  93 
 TYR   0.007   0.001   TYR B 111 
 PHE   0.017   0.002   PHE B 204 
 TRP   0.006   0.001   TRP B 239 
 HIS   0.002   0.001   HIS C 130 

Details of bonding type rmsd
  covalent geometry    : bond        0.00328 ( 6798)
  covalent geometry    : angle       0.54277 ( 9222)
  hydrogen bonds       : bond        0.03043 (  390)
  hydrogen bonds       : angle       3.98724 ( 1179)
  link_NAG-ASN         : bond        0.00386 (   12)
  link_NAG-ASN         : angle       1.82144 (   36)

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

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

  1608 Ramachandran restraints generated.
    804 Oldfield, 0 Emsley, 804 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1608 Ramachandran restraints generated.
    804 Oldfield, 0 Emsley, 804 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  234 residues out of total 720 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 220
  time to evaluate  : 0.243 
Fit side-chains
   revert: symmetry clash
REVERT: A  106 LYS cc_start: 0.8446 (tttp) cc_final: 0.8211 (ttpp)
REVERT: A  147 MET cc_start: 0.7900 (mtm) cc_final: 0.7685 (mtp)
REVERT: A  175 ARG cc_start: 0.7802 (mtp85) cc_final: 0.7489 (mtp85)
REVERT: A  176 GLU cc_start: 0.8119 (mp0) cc_final: 0.7203 (mp0)
REVERT: A  181 GLU cc_start: 0.8121 (tt0) cc_final: 0.7838 (tt0)
REVERT: C   89 ILE cc_start: 0.8819 (mm) cc_final: 0.8539 (mt)
REVERT: C  148 ASN cc_start: 0.7179 (t0) cc_final: 0.6793 (p0)
REVERT: C  176 GLU cc_start: 0.8166 (mp0) cc_final: 0.7326 (mp0)
REVERT: C  181 GLU cc_start: 0.8093 (tt0) cc_final: 0.7710 (tt0)
REVERT: C  188 ARG cc_start: 0.8365 (ttp-170) cc_final: 0.8093 (ttp-170)
REVERT: C  194 GLU cc_start: 0.7022 (tm-30) cc_final: 0.6689 (tm-30)
REVERT: C  206 SER cc_start: 0.8617 (m) cc_final: 0.8407 (t)
REVERT: C  212 GLN cc_start: 0.7234 (mp10) cc_final: 0.6939 (mp10)
REVERT: C  219 PHE cc_start: 0.8163 (t80) cc_final: 0.7955 (t80)
REVERT: C  271 ARG cc_start: 0.8705 (mtm180) cc_final: 0.8234 (mtm-85)
REVERT: C  304 TRP cc_start: 0.8470 (m100) cc_final: 0.8126 (m100)
REVERT: C  319 LYS cc_start: 0.8106 (tppt) cc_final: 0.7895 (ttmm)
  outliers start: 14
  outliers final: 7
  residues processed: 222
  average time/residue: 0.7406
  time to fit residues: 170.1299
Evaluate side-chains
  222 residues out of total 720 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 215
  time to evaluate  : 0.237 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   78 MET
Chi-restraints excluded: chain A residue  322 GLU
Chi-restraints excluded: chain B residue  150 THR
Chi-restraints excluded: chain B residue  200 ASP
Chi-restraints excluded: chain B residue  322 GLU
Chi-restraints excluded: chain C residue  150 THR
Chi-restraints excluded: chain C residue  315 LEU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 81
   random chunks:
   chunk 44 optimal weight:    0.7980
   chunk 27 optimal weight:    3.9990
   chunk 45 optimal weight:    0.6980
   chunk 16 optimal weight:    1.9990
   chunk 47 optimal weight:    0.8980
   chunk 75 optimal weight:    0.2980
   chunk 8 optimal weight:    2.9990
   chunk 38 optimal weight:    0.6980
   chunk 70 optimal weight:    0.2980
   chunk 20 optimal weight:    0.0010
   chunk 61 optimal weight:    0.9990
   overall best weight:    0.3986

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

Flipped N/Q/H residues before XYZ refinement:
A 172 GLN
A 266 ASN
** A 279 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 293 GLN
B 293 GLN
C 186 GLN
C 293 GLN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3859 r_free = 0.3859 target = 0.139447 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3601 r_free = 0.3601 target = 0.120651 restraints weight = 9529.978|
|-----------------------------------------------------------------------------|
r_work (start): 0.3606 rms_B_bonded: 2.33
r_work: 0.3468 rms_B_bonded: 2.74 restraints_weight: 0.5000
r_work: 0.3294 rms_B_bonded: 4.71 restraints_weight: 0.2500
r_work (final): 0.3294
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7914
moved from start:          0.2526

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.029   6810  Z= 0.160
  Angle     :  0.561   7.058   9258  Z= 0.282
  Chirality :  0.044   0.176   1050
  Planarity :  0.004   0.030   1158
  Dihedral  :  5.738  39.787   1125
  Min Nonbonded Distance : 2.551

Molprobity Statistics.
  All-atom Clashscore : 6.17
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.86 %
    Favored  : 97.14 %
  Rotamer:
    Outliers :  2.32 %
    Allowed  : 22.90 %
    Favored  : 74.78 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.91 (0.29), residues: 804
  helix:  3.27 (0.29), residues: 258
  sheet:  1.02 (0.26), residues: 333
  loop : -0.94 (0.43), residues: 213

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG C  93 
 TYR   0.007   0.001   TYR B 111 
 PHE   0.018   0.002   PHE B 204 
 TRP   0.005   0.001   TRP C 239 
 HIS   0.002   0.001   HIS A 130 

Details of bonding type rmsd
  covalent geometry    : bond        0.00378 ( 6798)
  covalent geometry    : angle       0.55068 ( 9222)
  hydrogen bonds       : bond        0.03204 (  390)
  hydrogen bonds       : angle       4.06078 ( 1179)
  link_NAG-ASN         : bond        0.00345 (   12)
  link_NAG-ASN         : angle       1.81079 (   36)

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

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

  1608 Ramachandran restraints generated.
    804 Oldfield, 0 Emsley, 804 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1608 Ramachandran restraints generated.
    804 Oldfield, 0 Emsley, 804 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  240 residues out of total 720 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 224
  time to evaluate  : 0.250 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  106 LYS cc_start: 0.8476 (tttp) cc_final: 0.8254 (ttpp)
REVERT: A  147 MET cc_start: 0.7950 (mtm) cc_final: 0.7719 (mtp)
REVERT: A  175 ARG cc_start: 0.7828 (mtp85) cc_final: 0.7460 (mtp85)
REVERT: A  176 GLU cc_start: 0.8119 (mp0) cc_final: 0.7167 (mp0)
REVERT: A  181 GLU cc_start: 0.8146 (tt0) cc_final: 0.7801 (tt0)
REVERT: C   75 LEU cc_start: 0.7860 (mt) cc_final: 0.7643 (mt)
REVERT: C  148 ASN cc_start: 0.7235 (t0) cc_final: 0.6844 (p0)
REVERT: C  176 GLU cc_start: 0.8192 (mp0) cc_final: 0.7426 (mp0)
REVERT: C  181 GLU cc_start: 0.8113 (tt0) cc_final: 0.7780 (tt0)
REVERT: C  188 ARG cc_start: 0.8358 (ttp-170) cc_final: 0.8086 (ttp-170)
REVERT: C  194 GLU cc_start: 0.7022 (tm-30) cc_final: 0.6710 (tm-30)
REVERT: C  212 GLN cc_start: 0.7288 (mp10) cc_final: 0.7083 (mp10)
REVERT: C  248 LYS cc_start: 0.7514 (mmmm) cc_final: 0.7306 (ttmm)
REVERT: C  271 ARG cc_start: 0.8707 (mtm180) cc_final: 0.8227 (mtm-85)
REVERT: C  304 TRP cc_start: 0.8457 (m100) cc_final: 0.8125 (m100)
  outliers start: 16
  outliers final: 7
  residues processed: 226
  average time/residue: 0.7287
  time to fit residues: 170.4975
Evaluate side-chains
  215 residues out of total 720 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 208
  time to evaluate  : 0.249 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   73 ILE
Chi-restraints excluded: chain A residue  101 MET
Chi-restraints excluded: chain A residue  322 GLU
Chi-restraints excluded: chain B residue  150 THR
Chi-restraints excluded: chain B residue  322 GLU
Chi-restraints excluded: chain C residue  150 THR
Chi-restraints excluded: chain C residue  315 LEU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 81
   random chunks:
   chunk 48 optimal weight:    0.4980
   chunk 3 optimal weight:    0.9990
   chunk 78 optimal weight:    0.4980
   chunk 5 optimal weight:    0.4980
   chunk 66 optimal weight:    0.7980
   chunk 44 optimal weight:    0.7980
   chunk 79 optimal weight:    0.1980
   chunk 61 optimal weight:    1.9990
   chunk 77 optimal weight:    0.6980
   chunk 15 optimal weight:    0.0970
   chunk 33 optimal weight:    0.8980
   overall best weight:    0.3578

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

Flipped N/Q/H residues before XYZ refinement:
A 172 GLN
A 293 GLN
B 186 GLN
B 293 GLN
C 186 GLN
C 293 GLN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3851 r_free = 0.3851 target = 0.139620 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3601 r_free = 0.3601 target = 0.121240 restraints weight = 9590.201|
|-----------------------------------------------------------------------------|
r_work (start): 0.3602 rms_B_bonded: 2.30
r_work: 0.3467 rms_B_bonded: 2.72 restraints_weight: 0.5000
r_work: 0.3294 rms_B_bonded: 4.70 restraints_weight: 0.2500
r_work (final): 0.3294
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7911
moved from start:          0.2647

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.032   6810  Z= 0.149
  Angle     :  0.546   7.008   9258  Z= 0.278
  Chirality :  0.044   0.191   1050
  Planarity :  0.003   0.033   1158
  Dihedral  :  5.105  30.004   1125
  Min Nonbonded Distance : 2.531

Molprobity Statistics.
  All-atom Clashscore : 5.72
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.86 %
    Favored  : 97.14 %
  Rotamer:
    Outliers :  1.74 %
    Allowed  : 23.48 %
    Favored  : 74.78 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.93 (0.29), residues: 804
  helix:  3.28 (0.28), residues: 258
  sheet:  0.99 (0.26), residues: 336
  loop : -0.86 (0.43), residues: 210

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG C  93 
 TYR   0.007   0.001   TYR B 111 
 PHE   0.017   0.002   PHE B 204 
 TRP   0.006   0.001   TRP B 239 
 HIS   0.002   0.001   HIS C 130 

Details of bonding type rmsd
  covalent geometry    : bond        0.00350 ( 6798)
  covalent geometry    : angle       0.53584 ( 9222)
  hydrogen bonds       : bond        0.03184 (  390)
  hydrogen bonds       : angle       4.05518 ( 1179)
  link_NAG-ASN         : bond        0.00326 (   12)
  link_NAG-ASN         : angle       1.73891 (   36)

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

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

  1608 Ramachandran restraints generated.
    804 Oldfield, 0 Emsley, 804 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1608 Ramachandran restraints generated.
    804 Oldfield, 0 Emsley, 804 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  229 residues out of total 720 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 217
  time to evaluate  : 0.261 
Fit side-chains
   revert: symmetry clash
REVERT: A  106 LYS cc_start: 0.8433 (tttp) cc_final: 0.8200 (ttpp)
REVERT: A  147 MET cc_start: 0.7906 (mtm) cc_final: 0.7678 (mtp)
REVERT: A  175 ARG cc_start: 0.7790 (mtp85) cc_final: 0.7425 (mtp85)
REVERT: A  176 GLU cc_start: 0.8097 (mp0) cc_final: 0.7126 (mp0)
REVERT: A  180 ARG cc_start: 0.7948 (mtp180) cc_final: 0.7614 (mtp180)
REVERT: A  181 GLU cc_start: 0.8137 (tt0) cc_final: 0.7797 (tt0)
REVERT: A  248 LYS cc_start: 0.7502 (tppp) cc_final: 0.7286 (mtpt)
REVERT: B  268 ILE cc_start: 0.7872 (mm) cc_final: 0.7642 (mt)
REVERT: B  275 LYS cc_start: 0.8360 (mmmm) cc_final: 0.7989 (mtpp)
REVERT: C  148 ASN cc_start: 0.7201 (t0) cc_final: 0.6868 (p0)
REVERT: C  176 GLU cc_start: 0.8130 (mp0) cc_final: 0.7302 (mp0)
REVERT: C  180 ARG cc_start: 0.8121 (mtp180) cc_final: 0.7745 (mtp180)
REVERT: C  181 GLU cc_start: 0.8087 (tt0) cc_final: 0.7698 (tt0)
REVERT: C  188 ARG cc_start: 0.8360 (ttp-170) cc_final: 0.8109 (ttp-170)
REVERT: C  194 GLU cc_start: 0.7063 (tm-30) cc_final: 0.6755 (tm-30)
REVERT: C  248 LYS cc_start: 0.7532 (mmmm) cc_final: 0.7248 (mtpp)
REVERT: C  271 ARG cc_start: 0.8726 (mtm180) cc_final: 0.8275 (mtm-85)
REVERT: C  304 TRP cc_start: 0.8468 (m100) cc_final: 0.8136 (m100)
  outliers start: 12
  outliers final: 7
  residues processed: 219
  average time/residue: 0.7489
  time to fit residues: 169.6599
Evaluate side-chains
  213 residues out of total 720 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 206
  time to evaluate  : 0.239 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   73 ILE
Chi-restraints excluded: chain A residue  101 MET
Chi-restraints excluded: chain A residue  202 LEU
Chi-restraints excluded: chain A residue  322 GLU
Chi-restraints excluded: chain B residue  322 GLU
Chi-restraints excluded: chain C residue  150 THR
Chi-restraints excluded: chain C residue  315 LEU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 81
   random chunks:
   chunk 31 optimal weight:    0.9990
   chunk 68 optimal weight:    0.4980
   chunk 19 optimal weight:    0.8980
   chunk 30 optimal weight:    0.8980
   chunk 29 optimal weight:    0.9990
   chunk 4 optimal weight:    0.9990
   chunk 16 optimal weight:    0.6980
   chunk 69 optimal weight:    0.6980
   chunk 37 optimal weight:    0.6980
   chunk 46 optimal weight:    0.7980
   chunk 53 optimal weight:    0.8980
   overall best weight:    0.6780

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

Flipped N/Q/H residues before XYZ refinement:
A 172 GLN
A 293 GLN
B 293 GLN
C 186 GLN
C 279 GLN
C 293 GLN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3830 r_free = 0.3830 target = 0.138120 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3574 r_free = 0.3574 target = 0.119587 restraints weight = 9646.243|
|-----------------------------------------------------------------------------|
r_work (start): 0.3569 rms_B_bonded: 2.32
r_work: 0.3435 rms_B_bonded: 2.72 restraints_weight: 0.5000
r_work: 0.3264 rms_B_bonded: 4.66 restraints_weight: 0.2500
r_work (final): 0.3264
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7937
moved from start:          0.2845

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.047   6810  Z= 0.239
  Angle     :  0.600   7.649   9258  Z= 0.305
  Chirality :  0.046   0.208   1050
  Planarity :  0.004   0.034   1158
  Dihedral  :  4.906  29.570   1125
  Min Nonbonded Distance : 2.466

Molprobity Statistics.
  All-atom Clashscore : 6.48
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.61 %
    Favored  : 96.39 %
  Rotamer:
    Outliers :  2.17 %
    Allowed  : 23.77 %
    Favored  : 74.06 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.47 (0.29), residues: 804
  helix:  2.69 (0.30), residues: 279
  sheet:  0.97 (0.27), residues: 321
  loop : -1.55 (0.43), residues: 204

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG B 110 
 TYR   0.010   0.002   TYR B 119 
 PHE   0.022   0.002   PHE B 204 
 TRP   0.008   0.001   TRP B 230 
 HIS   0.004   0.001   HIS C 130 

Details of bonding type rmsd
  covalent geometry    : bond        0.00574 ( 6798)
  covalent geometry    : angle       0.59180 ( 9222)
  hydrogen bonds       : bond        0.03719 (  390)
  hydrogen bonds       : angle       4.23866 ( 1179)
  link_NAG-ASN         : bond        0.00321 (   12)
  link_NAG-ASN         : angle       1.72210 (   36)

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

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

  1608 Ramachandran restraints generated.
    804 Oldfield, 0 Emsley, 804 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1608 Ramachandran restraints generated.
    804 Oldfield, 0 Emsley, 804 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  234 residues out of total 720 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 219
  time to evaluate  : 0.153 
Fit side-chains
   revert: symmetry clash
REVERT: A  106 LYS cc_start: 0.8471 (tttp) cc_final: 0.8201 (ttpp)
REVERT: A  147 MET cc_start: 0.7951 (mtm) cc_final: 0.7709 (mtp)
REVERT: B  275 LYS cc_start: 0.8395 (mmmm) cc_final: 0.8020 (mtpp)
REVERT: C  148 ASN cc_start: 0.7193 (t0) cc_final: 0.6857 (p0)
REVERT: C  176 GLU cc_start: 0.8176 (mp0) cc_final: 0.7383 (mp0)
REVERT: C  181 GLU cc_start: 0.8143 (tt0) cc_final: 0.7773 (tt0)
REVERT: C  188 ARG cc_start: 0.8369 (ttp-170) cc_final: 0.8096 (ttp-170)
REVERT: C  194 GLU cc_start: 0.7087 (tm-30) cc_final: 0.6763 (tm-30)
REVERT: C  248 LYS cc_start: 0.7577 (mmmm) cc_final: 0.7316 (mtpp)
REVERT: C  304 TRP cc_start: 0.8492 (m100) cc_final: 0.8184 (m100)
REVERT: C  319 LYS cc_start: 0.8159 (tppt) cc_final: 0.7922 (ttmm)
  outliers start: 15
  outliers final: 9
  residues processed: 224
  average time/residue: 0.7419
  time to fit residues: 171.7191
Evaluate side-chains
  211 residues out of total 720 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 202
  time to evaluate  : 0.250 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   73 ILE
Chi-restraints excluded: chain A residue  194 GLU
Chi-restraints excluded: chain A residue  322 GLU
Chi-restraints excluded: chain B residue  150 THR
Chi-restraints excluded: chain B residue  257 GLU
Chi-restraints excluded: chain B residue  322 GLU
Chi-restraints excluded: chain C residue  150 THR
Chi-restraints excluded: chain C residue  257 GLU
Chi-restraints excluded: chain C residue  315 LEU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 81
   random chunks:
   chunk 56 optimal weight:    0.5980
   chunk 25 optimal weight:    0.9980
   chunk 54 optimal weight:    3.9990
   chunk 73 optimal weight:    0.6980
   chunk 12 optimal weight:    0.5980
   chunk 16 optimal weight:    0.5980
   chunk 3 optimal weight:    0.7980
   chunk 30 optimal weight:    0.3980
   chunk 71 optimal weight:    0.5980
   chunk 77 optimal weight:    0.0980
   chunk 68 optimal weight:    0.1980
   overall best weight:    0.3780

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

Flipped N/Q/H residues before XYZ refinement:
** A 279 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 293 GLN
B 186 GLN
B 293 GLN
C 186 GLN
C 293 GLN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3839 r_free = 0.3839 target = 0.138715 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3587 r_free = 0.3587 target = 0.120371 restraints weight = 9564.874|
|-----------------------------------------------------------------------------|
r_work (start): 0.3588 rms_B_bonded: 2.31
r_work: 0.3454 rms_B_bonded: 2.71 restraints_weight: 0.5000
r_work: 0.3283 rms_B_bonded: 4.67 restraints_weight: 0.2500
r_work (final): 0.3283
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7922
moved from start:          0.2873

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.032   6810  Z= 0.160
  Angle     :  0.553   7.279   9258  Z= 0.284
  Chirality :  0.044   0.201   1050
  Planarity :  0.004   0.035   1158
  Dihedral  :  4.612  28.867   1125
  Min Nonbonded Distance : 2.555

Molprobity Statistics.
  All-atom Clashscore : 6.56
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.36 %
    Favored  : 96.64 %
  Rotamer:
    Outliers :  1.88 %
    Allowed  : 24.35 %
    Favored  : 73.77 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.51 (0.29), residues: 804
  helix:  2.76 (0.29), residues: 279
  sheet:  0.91 (0.27), residues: 324
  loop : -1.48 (0.42), residues: 201

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG B 110 
 TYR   0.007   0.001   TYR B 111 
 PHE   0.018   0.002   PHE A 204 
 TRP   0.007   0.001   TRP B 230 
 HIS   0.002   0.001   HIS B  98 

Details of bonding type rmsd
  covalent geometry    : bond        0.00374 ( 6798)
  covalent geometry    : angle       0.54466 ( 9222)
  hydrogen bonds       : bond        0.03353 (  390)
  hydrogen bonds       : angle       4.16103 ( 1179)
  link_NAG-ASN         : bond        0.00301 (   12)
  link_NAG-ASN         : angle       1.61985 (   36)

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

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

  1608 Ramachandran restraints generated.
    804 Oldfield, 0 Emsley, 804 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1608 Ramachandran restraints generated.
    804 Oldfield, 0 Emsley, 804 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  222 residues out of total 720 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 209
  time to evaluate  : 0.247 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  106 LYS cc_start: 0.8448 (tttp) cc_final: 0.8176 (ttpp)
REVERT: A  147 MET cc_start: 0.7967 (mtm) cc_final: 0.7728 (mtp)
REVERT: A  180 ARG cc_start: 0.7956 (mtp180) cc_final: 0.7617 (mtp180)
REVERT: B  197 SER cc_start: 0.8645 (p) cc_final: 0.8429 (m)
REVERT: C  148 ASN cc_start: 0.7207 (t0) cc_final: 0.6862 (p0)
REVERT: C  176 GLU cc_start: 0.8176 (mp0) cc_final: 0.7324 (mp0)
REVERT: C  181 GLU cc_start: 0.8085 (tt0) cc_final: 0.7670 (tt0)
REVERT: C  188 ARG cc_start: 0.8361 (ttp-170) cc_final: 0.8098 (ttp-170)
REVERT: C  194 GLU cc_start: 0.7103 (tm-30) cc_final: 0.6775 (tm-30)
REVERT: C  248 LYS cc_start: 0.7566 (mmmm) cc_final: 0.7293 (mtpp)
REVERT: C  271 ARG cc_start: 0.8717 (mtm180) cc_final: 0.8283 (mtm-85)
REVERT: C  304 TRP cc_start: 0.8466 (m100) cc_final: 0.8166 (m100)
REVERT: C  319 LYS cc_start: 0.8119 (tppt) cc_final: 0.7907 (ttmm)
  outliers start: 13
  outliers final: 8
  residues processed: 213
  average time/residue: 0.7093
  time to fit residues: 156.3766
Evaluate side-chains
  214 residues out of total 720 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 206
  time to evaluate  : 0.259 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   73 ILE
Chi-restraints excluded: chain A residue  194 GLU
Chi-restraints excluded: chain A residue  322 GLU
Chi-restraints excluded: chain B residue  150 THR
Chi-restraints excluded: chain B residue  200 ASP
Chi-restraints excluded: chain B residue  322 GLU
Chi-restraints excluded: chain C residue  197 SER
Chi-restraints excluded: chain C residue  315 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 81
   random chunks:
   chunk 69 optimal weight:    0.5980
   chunk 50 optimal weight:    0.7980
   chunk 28 optimal weight:    0.2980
   chunk 5 optimal weight:    0.2980
   chunk 27 optimal weight:    3.9990
   chunk 13 optimal weight:    0.9990
   chunk 7 optimal weight:    0.9990
   chunk 80 optimal weight:    0.0970
   chunk 8 optimal weight:    0.9980
   chunk 66 optimal weight:    0.6980
   chunk 20 optimal weight:    0.8980
   overall best weight:    0.3978

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

Flipped N/Q/H residues before XYZ refinement:
** A 279 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 293 GLN
B 293 GLN
C 293 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3841 r_free = 0.3841 target = 0.138877 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3589 r_free = 0.3589 target = 0.120530 restraints weight = 9548.792|
|-----------------------------------------------------------------------------|
r_work (start): 0.3590 rms_B_bonded: 2.29
r_work: 0.3457 rms_B_bonded: 2.70 restraints_weight: 0.5000
r_work: 0.3286 rms_B_bonded: 4.65 restraints_weight: 0.2500
r_work (final): 0.3286
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7921
moved from start:          0.2919

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.033   6810  Z= 0.164
  Angle     :  0.554   7.003   9258  Z= 0.286
  Chirality :  0.044   0.205   1050
  Planarity :  0.004   0.037   1158
  Dihedral  :  4.455  27.488   1125
  Min Nonbonded Distance : 2.557

Molprobity Statistics.
  All-atom Clashscore : 7.01
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.61 %
    Favored  : 96.39 %
  Rotamer:
    Outliers :  1.16 %
    Allowed  : 25.80 %
    Favored  : 73.04 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.51 (0.29), residues: 804
  helix:  2.79 (0.30), residues: 279
  sheet:  0.91 (0.27), residues: 324
  loop : -1.53 (0.42), residues: 201

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.000   ARG A 175 
 TYR   0.007   0.001   TYR C 201 
 PHE   0.031   0.002   PHE A 219 
 TRP   0.006   0.001   TRP B 230 
 HIS   0.004   0.001   HIS B  98 

Details of bonding type rmsd
  covalent geometry    : bond        0.00387 ( 6798)
  covalent geometry    : angle       0.54636 ( 9222)
  hydrogen bonds       : bond        0.03379 (  390)
  hydrogen bonds       : angle       4.15928 ( 1179)
  link_NAG-ASN         : bond        0.00274 (   12)
  link_NAG-ASN         : angle       1.55511 (   36)

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

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

  1608 Ramachandran restraints generated.
    804 Oldfield, 0 Emsley, 804 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1608 Ramachandran restraints generated.
    804 Oldfield, 0 Emsley, 804 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  214 residues out of total 720 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 206
  time to evaluate  : 0.204 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  106 LYS cc_start: 0.8453 (tttp) cc_final: 0.8190 (ttpp)
REVERT: A  122 GLN cc_start: 0.8155 (mm-40) cc_final: 0.7946 (mm-40)
REVERT: A  143 GLN cc_start: 0.8026 (mm110) cc_final: 0.7695 (mm110)
REVERT: A  147 MET cc_start: 0.7948 (mtm) cc_final: 0.7725 (mtp)
REVERT: A  180 ARG cc_start: 0.7964 (mtp180) cc_final: 0.7611 (mtp180)
REVERT: B  180 ARG cc_start: 0.8057 (mtp180) cc_final: 0.7731 (mtp180)
REVERT: B  197 SER cc_start: 0.8651 (p) cc_final: 0.8444 (m)
REVERT: B  271 ARG cc_start: 0.8811 (mtm180) cc_final: 0.8571 (mtm-85)
REVERT: C  148 ASN cc_start: 0.7181 (t0) cc_final: 0.6861 (p0)
REVERT: C  176 GLU cc_start: 0.8185 (mp0) cc_final: 0.7330 (mp0)
REVERT: C  181 GLU cc_start: 0.8101 (tt0) cc_final: 0.7676 (tt0)
REVERT: C  188 ARG cc_start: 0.8355 (ttp-170) cc_final: 0.8091 (ttp-170)
REVERT: C  194 GLU cc_start: 0.7092 (tm-30) cc_final: 0.6764 (tm-30)
REVERT: C  248 LYS cc_start: 0.7574 (mmmm) cc_final: 0.7302 (mtpp)
REVERT: C  271 ARG cc_start: 0.8727 (mtm180) cc_final: 0.8263 (mtm-85)
REVERT: C  304 TRP cc_start: 0.8467 (m100) cc_final: 0.8165 (m100)
REVERT: C  319 LYS cc_start: 0.8125 (tppt) cc_final: 0.7912 (ttmm)
  outliers start: 8
  outliers final: 7
  residues processed: 211
  average time/residue: 0.7597
  time to fit residues: 165.7399
Evaluate side-chains
  212 residues out of total 720 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 205
  time to evaluate  : 0.260 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  194 GLU
Chi-restraints excluded: chain A residue  322 GLU
Chi-restraints excluded: chain B residue  150 THR
Chi-restraints excluded: chain B residue  200 ASP
Chi-restraints excluded: chain B residue  322 GLU
Chi-restraints excluded: chain C residue  197 SER
Chi-restraints excluded: chain C residue  315 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 81
   random chunks:
   chunk 15 optimal weight:    0.1980
   chunk 29 optimal weight:    0.5980
   chunk 16 optimal weight:    0.7980
   chunk 1 optimal weight:    0.6980
   chunk 11 optimal weight:    0.7980
   chunk 54 optimal weight:    3.9990
   chunk 52 optimal weight:    0.4980
   chunk 70 optimal weight:    1.9990
   chunk 25 optimal weight:    0.2980
   chunk 12 optimal weight:    0.9980
   chunk 66 optimal weight:    0.9980
   overall best weight:    0.4580

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

Flipped N/Q/H residues before XYZ refinement:
** A 279 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 293 GLN
B 293 GLN
C 293 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3837 r_free = 0.3837 target = 0.138604 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3585 r_free = 0.3585 target = 0.120269 restraints weight = 9536.873|
|-----------------------------------------------------------------------------|
r_work (start): 0.3585 rms_B_bonded: 2.29
r_work: 0.3452 rms_B_bonded: 2.69 restraints_weight: 0.5000
r_work: 0.3282 rms_B_bonded: 4.63 restraints_weight: 0.2500
r_work (final): 0.3282
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7925
moved from start:          0.2986

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.035   6810  Z= 0.181
  Angle     :  0.566   7.167   9258  Z= 0.291
  Chirality :  0.045   0.208   1050
  Planarity :  0.004   0.038   1158
  Dihedral  :  4.383  25.918   1125
  Min Nonbonded Distance : 2.557

Molprobity Statistics.
  All-atom Clashscore : 7.47
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.61 %
    Favored  : 96.39 %
  Rotamer:
    Outliers :  1.45 %
    Allowed  : 25.51 %
    Favored  : 73.04 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.48 (0.29), residues: 804
  helix:  2.73 (0.30), residues: 279
  sheet:  0.91 (0.27), residues: 324
  loop : -1.49 (0.43), residues: 201

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG A 175 
 TYR   0.008   0.001   TYR B 111 
 PHE   0.029   0.002   PHE A 219 
 TRP   0.007   0.001   TRP B 230 
 HIS   0.006   0.001   HIS B  98 

Details of bonding type rmsd
  covalent geometry    : bond        0.00428 ( 6798)
  covalent geometry    : angle       0.55888 ( 9222)
  hydrogen bonds       : bond        0.03478 (  390)
  hydrogen bonds       : angle       4.18387 ( 1179)
  link_NAG-ASN         : bond        0.00271 (   12)
  link_NAG-ASN         : angle       1.49252 (   36)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3813.47 seconds
wall clock time: 65 minutes 17.55 seconds (3917.55 seconds total)