Starting phenix.real_space_refine
on Tue Feb  3 18:54:00 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9pl9_71715/02_2026/9pl9_71715.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9pl9_71715/02_2026/9pl9_71715.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=4.18
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/9pl9_71715/02_2026/9pl9_71715.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9pl9_71715/02_2026/9pl9_71715.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9pl9_71715/02_2026/9pl9_71715.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9pl9_71715/02_2026/9pl9_71715.cif"
  }
  resolution = 4.18
  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=   0.014
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      48      5.16       5
     C    3850      2.51       5
     N    1050      2.21       5
     O    1212      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 10 residue(s): 0.00s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 6160
  Number of models: 1
  Model: ""
    Number of chains: 4
    Chain: "A"
      Number of atoms: 3030
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 401, 3030
          Classifications: {'peptide': 401}
          Link IDs: {'PCIS': 1, 'PTRANS': 14, 'TRANS': 385}
    Chain: "B"
      Number of atoms: 3030
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 401, 3030
          Classifications: {'peptide': 401}
          Link IDs: {'PCIS': 1, 'PTRANS': 14, 'TRANS': 385}
    Chain: "C"
      Number of atoms: 50
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 4, 50
          Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2}
          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: "G"
      Number of atoms: 50
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 4, 50
          Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2}
          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: 1.15, per 1000 atoms: 0.19
  Number of scatterers: 6160
  At special positions: 0
  Unit cell: (72.898, 168.91, 70.231, 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      48     16.00
     O    1212      8.00
     N    1050      7.00
     C    3850      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=14, symmetry=0
    Simple disulfide: pdb=" SG  CYS A   3 " - pdb=" SG  CYS A  30 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A   5 " - pdb=" SG  CYS B 102 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A  60 " - pdb=" SG  CYS A 121 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A  74 " - pdb=" SG  CYS A 105 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A  92 " - pdb=" SG  CYS A 116 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 102 " - pdb=" SG  CYS B   5 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 190 " - pdb=" SG  CYS A 287 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 304 " - pdb=" SG  CYS A 335 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B   3 " - pdb=" SG  CYS B  30 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B  60 " - pdb=" SG  CYS B 121 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B  74 " - pdb=" SG  CYS B 105 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B  92 " - pdb=" SG  CYS B 116 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 190 " - pdb=" SG  CYS B 287 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 304 " - pdb=" SG  CYS B 335 " distance=2.03

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Links applied
    ALPHA1-3
      " BMA C   3 " - " MAN C   4 "
      " BMA G   3 " - " MAN G   4 "
    BETA1-4
      " NAG C   1 " - " NAG C   2 "
      " NAG C   2 " - " BMA C   3 "
      " NAG G   1 " - " NAG G   2 "
      " NAG G   2 " - " BMA G   3 "
    NAG-ASN
      " NAG C   1 " - " ASN A 154 "
      " NAG G   1 " - " ASN B 154 "
  Time building additional restraints: 0.57
  Conformation dependent library (CDL) restraints added in 193.5 milliseconds
  

  1596 Ramachandran restraints generated.
    798 Oldfield, 0 Emsley, 798 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1456

  Finding SS restraints...
    Secondary structure from input PDB file:
      14 helices and 16 sheets defined
      10.6% alpha, 40.0% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.24
  Creating SS restraints...
    Processing helix  chain 'A' and resid 82 through 86
      removed outlier: 3.775A  pdb=" N   ARG A  85 " --> pdb=" O   ASN A  82 " (cutoff:3.500A)
      removed outlier: 4.039A  pdb=" N   ALA A  86 " --> pdb=" O   GLU A  83 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 82 through 86'
    Processing helix  chain 'A' and resid 154 through 161
    Processing helix  chain 'A' and resid 191 through 195
      removed outlier: 3.537A  pdb=" N   SER A 194 " --> pdb=" O   GLU A 191 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 214 through 220
      removed outlier: 3.517A  pdb=" N   ASP A 220 " --> pdb=" O   GLU A 216 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 235 through 238
    Processing helix  chain 'A' and resid 258 through 266
      removed outlier: 3.602A  pdb=" N   LEU A 262 " --> pdb=" O   GLN A 258 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 387 through 391
      removed outlier: 3.643A  pdb=" N   GLN A 391 " --> pdb=" O   GLY A 388 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 82 through 87
      removed outlier: 3.534A  pdb=" N   ARG B  85 " --> pdb=" O   ASN B  82 " (cutoff:3.500A)
      removed outlier: 3.701A  pdb=" N   ALA B  86 " --> pdb=" O   GLU B  83 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 100 through 104
      removed outlier: 3.564A  pdb=" N   GLY B 104 " --> pdb=" O   TRP B 101 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 154 through 161
    Processing helix  chain 'B' and resid 191 through 195
      removed outlier: 3.727A  pdb=" N   SER B 194 " --> pdb=" O   GLU B 191 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 215 through 220
      removed outlier: 3.679A  pdb=" N   ASP B 220 " --> pdb=" O   GLU B 216 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 235 through 238
    Processing helix  chain 'B' and resid 259 through 266
    Processing sheet with id=AA1, first strand: chain 'A' and resid 9 through 13
      removed outlier: 3.804A  pdb=" N   VAL A  43 " --> pdb=" O   LEU A  31 " (cutoff:3.500A)
      removed outlier: 5.321A  pdb=" N   VAL A  43 " --> pdb=" O   PHE A 142 " (cutoff:3.500A)
      removed outlier: 7.541A  pdb=" N   PHE A 142 " --> pdb=" O   VAL A  43 " (cutoff:3.500A)
      removed outlier: 5.543A  pdb=" N   MET A  45 " --> pdb=" O   GLY A 140 " (cutoff:3.500A)
      removed outlier: 6.783A  pdb=" N   GLY A 140 " --> pdb=" O   MET A  45 " (cutoff:3.500A)
      removed outlier: 4.021A  pdb=" N   ASN A  47 " --> pdb=" O   LYS A 138 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 9 through 13
      removed outlier: 3.804A  pdb=" N   VAL A  43 " --> pdb=" O   LEU A  31 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 20 through 26
      removed outlier: 3.793A  pdb=" N   ARG A 288 " --> pdb=" O   ASP A 189 " (cutoff:3.500A)
      removed outlier: 3.556A  pdb=" N   ASP A 189 " --> pdb=" O   ARG A 288 " (cutoff:3.500A)
      removed outlier: 3.808A  pdb=" N   LYS A 290 " --> pdb=" O   THR A 187 " (cutoff:3.500A)
      removed outlier: 4.203A  pdb=" N   THR A 187 " --> pdb=" O   LYS A 290 " (cutoff:3.500A)
      removed outlier: 3.953A  pdb=" N   VAL A 186 " --> pdb=" O   LEU A 178 " (cutoff:3.500A)
      removed outlier: 3.730A  pdb=" N   LEU A 178 " --> pdb=" O   VAL A 186 " (cutoff:3.500A)
      removed outlier: 3.503A  pdb=" N   VAL A 176 " --> pdb=" O   LEU A 188 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 230 through 234
      removed outlier: 3.796A  pdb=" N   SER A 227 " --> pdb=" O   SER A 230 " (cutoff:3.500A)
      removed outlier: 7.307A  pdb=" N   ALA A 232 " --> pdb=" O   TRP A 225 " (cutoff:3.500A)
      removed outlier: 7.179A  pdb=" N   TRP A 225 " --> pdb=" O   ALA A 232 " (cutoff:3.500A)
      removed outlier: 7.419A  pdb=" N   GLY A 127 " --> pdb=" O   VAL A  56 " (cutoff:3.500A)
      removed outlier: 4.693A  pdb=" N   SER A  58 " --> pdb=" O   ALA A 125 " (cutoff:3.500A)
      removed outlier: 6.234A  pdb=" N   ALA A 125 " --> pdb=" O   SER A  58 " (cutoff:3.500A)
      removed outlier: 5.348A  pdb=" N   CYS A  60 " --> pdb=" O   SER A 123 " (cutoff:3.500A)
      removed outlier: 8.042A  pdb=" N   SER A 123 " --> pdb=" O   CYS A  60 " (cutoff:3.500A)
      removed outlier: 7.549A  pdb=" N   HIS A  62 " --> pdb=" O   CYS A 121 " (cutoff:3.500A)
      removed outlier: 5.157A  pdb=" N   CYS A 121 " --> pdb=" O   HIS A  62 " (cutoff:3.500A)
      removed outlier: 3.665A  pdb=" N   ILE A 126 " --> pdb=" O   THR A 205 " (cutoff:3.500A)
      removed outlier: 3.961A  pdb=" N   SER A 210 " --> pdb=" O   VAL A 272 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'A' and resid 69 through 72
      removed outlier: 3.561A  pdb=" N   ILE A 113 " --> pdb=" O   GLY A  95 " (cutoff:3.500A)
      removed outlier: 3.720A  pdb=" N   GLY A  95 " --> pdb=" O   ILE A 113 " (cutoff:3.500A)
      removed outlier: 3.507A  pdb=" N   THR A 115 " --> pdb=" O   LYS A  93 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'A' and resid 240 through 246
      removed outlier: 5.183A  pdb=" N   PHE A 242 " --> pdb=" O   VAL A 253 " (cutoff:3.500A)
      removed outlier: 7.358A  pdb=" N   VAL A 253 " --> pdb=" O   PHE A 242 " (cutoff:3.500A)
      removed outlier: 5.105A  pdb=" N   GLY A 244 " --> pdb=" O   SER A 251 " (cutoff:3.500A)
      removed outlier: 4.308A  pdb=" N   SER A 251 " --> pdb=" O   GLY A 244 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'A' and resid 308 through 316
      removed outlier: 3.799A  pdb=" N   ALA A 311 " --> pdb=" O   GLU A 325 " (cutoff:3.500A)
      removed outlier: 7.614A  pdb=" N   GLU A 325 " --> pdb=" O   ALA A 311 " (cutoff:3.500A)
      removed outlier: 7.334A  pdb=" N   ASN A 313 " --> pdb=" O   VAL A 323 " (cutoff:3.500A)
      removed outlier: 7.602A  pdb=" N   VAL A 323 " --> pdb=" O   ASN A 313 " (cutoff:3.500A)
      removed outlier: 3.507A  pdb=" N   VAL A 370 " --> pdb=" O   LEU A 326 " (cutoff:3.500A)
      removed outlier: 3.599A  pdb=" N   SER A 368 " --> pdb=" O   TYR A 328 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'A' and resid 339 through 342
      removed outlier: 3.960A  pdb=" N   VAL A 340 " --> pdb=" O   VAL A 384 " (cutoff:3.500A)
      removed outlier: 3.619A  pdb=" N   VAL A 384 " --> pdb=" O   VAL A 340 " (cutoff:3.500A)
      removed outlier: 3.628A  pdb=" N   VAL A 342 " --> pdb=" O   TYR A 382 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'B' and resid 10 through 13
      removed outlier: 3.592A  pdb=" N   VAL B  43 " --> pdb=" O   LEU B  31 " (cutoff:3.500A)
      removed outlier: 5.335A  pdb=" N   VAL B  43 " --> pdb=" O   PHE B 142 " (cutoff:3.500A)
      removed outlier: 7.501A  pdb=" N   PHE B 142 " --> pdb=" O   VAL B  43 " (cutoff:3.500A)
      removed outlier: 5.689A  pdb=" N   MET B  45 " --> pdb=" O   GLY B 140 " (cutoff:3.500A)
      removed outlier: 6.561A  pdb=" N   GLY B 140 " --> pdb=" O   MET B  45 " (cutoff:3.500A)
      removed outlier: 4.092A  pdb=" N   ASN B  47 " --> pdb=" O   LYS B 138 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'B' and resid 10 through 13
      removed outlier: 3.592A  pdb=" N   VAL B  43 " --> pdb=" O   LEU B  31 " (cutoff:3.500A)
      removed outlier: 4.341A  pdb=" N   GLU B 273 " --> pdb=" O   MET B 279 " (cutoff:3.500A)
      removed outlier: 3.972A  pdb=" N   ILE B 270 " --> pdb=" O   LEU B 212 " (cutoff:3.500A)
      removed outlier: 3.891A  pdb=" N   SER B 210 " --> pdb=" O   VAL B 272 " (cutoff:3.500A)
      removed outlier: 7.544A  pdb=" N   PHE B 201 " --> pdb=" O   ILE B 130 " (cutoff:3.500A)
      removed outlier: 5.105A  pdb=" N   ILE B 130 " --> pdb=" O   PHE B 201 " (cutoff:3.500A)
      removed outlier: 3.951A  pdb=" N   ARG B  57 " --> pdb=" O   GLY B 127 " (cutoff:3.500A)
      removed outlier: 6.141A  pdb=" N   THR B 129 " --> pdb=" O   GLU B  55 " (cutoff:3.500A)
      removed outlier: 5.934A  pdb=" N   GLU B  55 " --> pdb=" O   THR B 129 " (cutoff:3.500A)
      removed outlier: 3.653A  pdb=" N   SER B  58 " --> pdb=" O   THR B 226 " (cutoff:3.500A)
      removed outlier: 6.884A  pdb=" N   TRP B 225 " --> pdb=" O   ALA B 232 " (cutoff:3.500A)
      removed outlier: 6.856A  pdb=" N   ALA B 232 " --> pdb=" O   TRP B 225 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'B' and resid 20 through 26
    Processing sheet with id=AB3, first strand: chain 'B' and resid 69 through 72
      removed outlier: 4.306A  pdb=" N   GLY B 109 " --> pdb=" O   ARG B  99 " (cutoff:3.500A)
      removed outlier: 3.918A  pdb=" N   GLY B  95 " --> pdb=" O   ILE B 113 " (cutoff:3.500A)
    Processing sheet with id=AB4, first strand: chain 'B' and resid 175 through 179
      removed outlier: 3.612A  pdb=" N   LEU B 178 " --> pdb=" O   VAL B 186 " (cutoff:3.500A)
      removed outlier: 3.631A  pdb=" N   VAL B 186 " --> pdb=" O   LEU B 178 " (cutoff:3.500A)
    Processing sheet with id=AB5, first strand: chain 'B' and resid 240 through 246
      removed outlier: 5.280A  pdb=" N   PHE B 242 " --> pdb=" O   VAL B 253 " (cutoff:3.500A)
      removed outlier: 7.131A  pdb=" N   VAL B 253 " --> pdb=" O   PHE B 242 " (cutoff:3.500A)
      removed outlier: 4.975A  pdb=" N   GLY B 244 " --> pdb=" O   SER B 251 " (cutoff:3.500A)
      removed outlier: 4.182A  pdb=" N   SER B 251 " --> pdb=" O   GLY B 244 " (cutoff:3.500A)
    Processing sheet with id=AB6, first strand: chain 'B' and resid 308 through 316
      removed outlier: 6.251A  pdb=" N   ALA B 311 " --> pdb=" O   SER B 327 " (cutoff:3.500A)
      removed outlier: 7.613A  pdb=" N   SER B 327 " --> pdb=" O   ALA B 311 " (cutoff:3.500A)
      removed outlier: 5.678A  pdb=" N   ASN B 313 " --> pdb=" O   GLU B 325 " (cutoff:3.500A)
      removed outlier: 5.272A  pdb=" N   GLU B 325 " --> pdb=" O   ASN B 313 " (cutoff:3.500A)
      removed outlier: 3.592A  pdb=" N   SER B 368 " --> pdb=" O   TYR B 328 " (cutoff:3.500A)
    Processing sheet with id=AB7, first strand: chain 'B' and resid 339 through 342
      removed outlier: 3.788A  pdb=" N   VAL B 340 " --> pdb=" O   VAL B 384 " (cutoff:3.500A)

    180 hydrogen bonds defined for protein.
    444 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: 0.86

  Time building geometry restraints manager: 0.69 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: 1982
        1.34 -     1.46: 1315
        1.46 -     1.58: 2925
        1.58 -     1.70: 2
        1.70 -     1.82: 68
  Bond restraints: 6292
  Sorted by residual:
  bond pdb=" C1  BMA G   3 "
       pdb=" C2  BMA G   3 "
    ideal  model  delta    sigma   weight residual
    1.519  1.579 -0.060 2.00e-02 2.50e+03 8.95e+00
  bond pdb=" C1  MAN C   4 "
       pdb=" C2  MAN C   4 "
    ideal  model  delta    sigma   weight residual
    1.526  1.582 -0.056 2.00e-02 2.50e+03 7.79e+00
  bond pdb=" C1  MAN G   4 "
       pdb=" O5  MAN G   4 "
    ideal  model  delta    sigma   weight residual
    1.399  1.454 -0.055 2.00e-02 2.50e+03 7.52e+00
  bond pdb=" C1  MAN C   4 "
       pdb=" O5  MAN C   4 "
    ideal  model  delta    sigma   weight residual
    1.399  1.452 -0.053 2.00e-02 2.50e+03 7.02e+00
  bond pdb=" C5  MAN C   4 "
       pdb=" O5  MAN C   4 "
    ideal  model  delta    sigma   weight residual
    1.418  1.467 -0.049 2.00e-02 2.50e+03 5.95e+00
  ... (remaining 6287 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.14: 8334
        2.14 -     4.28: 159
        4.28 -     6.42: 29
        6.42 -     8.55: 8
        8.55 -    10.69: 2
  Bond angle restraints: 8532
  Sorted by residual:
  angle pdb=" N   SER A 276 "
        pdb=" CA  SER A 276 "
        pdb=" C   SER A 276 "
      ideal   model   delta    sigma   weight residual
     114.56  108.74    5.82 1.27e+00 6.20e-01 2.10e+01
  angle pdb=" C   PRO A  75 "
        pdb=" N   THR A  76 "
        pdb=" CA  THR A  76 "
      ideal   model   delta    sigma   weight residual
     121.54  129.54   -8.00 1.91e+00 2.74e-01 1.75e+01
  angle pdb=" CB  MET A 279 "
        pdb=" CG  MET A 279 "
        pdb=" SD  MET A 279 "
      ideal   model   delta    sigma   weight residual
     112.70  123.39  -10.69 3.00e+00 1.11e-01 1.27e+01
  angle pdb=" N   VAL B 351 "
        pdb=" CA  VAL B 351 "
        pdb=" C   VAL B 351 "
      ideal   model   delta    sigma   weight residual
     113.42  109.32    4.10 1.17e+00 7.31e-01 1.23e+01
  angle pdb=" C   PRO B  75 "
        pdb=" N   THR B  76 "
        pdb=" CA  THR B  76 "
      ideal   model   delta    sigma   weight residual
     121.54  127.96   -6.42 1.91e+00 2.74e-01 1.13e+01
  ... (remaining 8527 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    24.16: 3605
       24.16 -    48.32: 189
       48.32 -    72.48: 32
       72.48 -    96.64: 22
       96.64 -   120.80: 10
  Dihedral angle restraints: 3858
    sinusoidal: 1580
      harmonic: 2278
  Sorted by residual:
  dihedral pdb=" CB  CYS A   5 "
           pdb=" SG  CYS A   5 "
           pdb=" SG  CYS B 102 "
           pdb=" CB  CYS B 102 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00  175.55  -82.55     1      1.00e+01 1.00e-02 8.36e+01
  dihedral pdb=" CB  CYS A 102 "
           pdb=" SG  CYS A 102 "
           pdb=" SG  CYS B   5 "
           pdb=" CB  CYS B   5 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00  174.80  -81.80     1      1.00e+01 1.00e-02 8.23e+01
  dihedral pdb=" CB  CYS A  74 "
           pdb=" SG  CYS A  74 "
           pdb=" SG  CYS A 105 "
           pdb=" CB  CYS A 105 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00  167.32  -74.32     1      1.00e+01 1.00e-02 7.01e+01
  ... (remaining 3855 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.084: 882
       0.084 -    0.167: 96
       0.167 -    0.251: 5
       0.251 -    0.334: 2
       0.334 -    0.418: 1
  Chirality restraints: 986
  Sorted by residual:
  chirality pdb=" CB  ILE A 339 "
            pdb=" CA  ILE A 339 "
            pdb=" CG1 ILE A 339 "
            pdb=" CG2 ILE A 339 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.23    0.42 2.00e-01 2.50e+01 4.36e+00
  chirality pdb=" C5  BMA C   3 "
            pdb=" C4  BMA C   3 "
            pdb=" C6  BMA C   3 "
            pdb=" O5  BMA C   3 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.27   -2.55    0.28 2.00e-01 2.50e+01 1.91e+00
  chirality pdb=" C5  BMA G   3 "
            pdb=" C4  BMA G   3 "
            pdb=" C6  BMA G   3 "
            pdb=" O5  BMA G   3 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.27   -2.54    0.26 2.00e-01 2.50e+01 1.74e+00
  ... (remaining 983 not shown)

  Planarity restraints: 1086
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   CYS B  74 "    0.044 5.00e-02 4.00e+02   6.68e-02 7.14e+00
        pdb=" N   PRO B  75 "   -0.116 5.00e-02 4.00e+02
        pdb=" CA  PRO B  75 "    0.035 5.00e-02 4.00e+02
        pdb=" CD  PRO B  75 "    0.036 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ALA A 173 "    0.043 5.00e-02 4.00e+02   6.51e-02 6.77e+00
        pdb=" N   PRO A 174 "   -0.113 5.00e-02 4.00e+02
        pdb=" CA  PRO A 174 "    0.034 5.00e-02 4.00e+02
        pdb=" CD  PRO A 174 "    0.036 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   SER A 227 "   -0.040 5.00e-02 4.00e+02   6.10e-02 5.95e+00
        pdb=" N   PRO A 228 "    0.105 5.00e-02 4.00e+02
        pdb=" CA  PRO A 228 "   -0.031 5.00e-02 4.00e+02
        pdb=" CD  PRO A 228 "   -0.034 5.00e-02 4.00e+02
  ... (remaining 1083 not shown)

  Histogram of nonbonded interaction distances:
        2.23 -     2.77: 891
        2.77 -     3.30: 5267
        3.30 -     3.83: 9774
        3.83 -     4.37: 10287
        4.37 -     4.90: 18557
  Nonbonded interactions: 44776
  Sorted by model distance:
  nonbonded pdb=" OG  SER B 257 "
            pdb=" OE1 GLU B 259 "
     model   vdw
     2.232 3.040
  nonbonded pdb=" O   CYS B  74 "
            pdb=" OG1 THR B  77 "
     model   vdw
     2.260 3.040
  nonbonded pdb=" OG1 THR A 321 "
            pdb=" O   MET A 374 "
     model   vdw
     2.290 3.040
  nonbonded pdb=" OG1 THR B 148 "
            pdb=" OD1 ASN B 151 "
     model   vdw
     2.299 3.040
  nonbonded pdb=" O   CYS A  74 "
            pdb=" OG1 THR A  77 "
     model   vdw
     2.301 3.040
  ... (remaining 44771 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'
}
ncs_group {
  reference = chain 'C'
  selection = chain 'G'
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             1.820
  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:             0.010
  Extract box with map and model:          0.100
  Check model and map are aligned:         0.010
  Set scattering table:                    0.010
  Process input model:                     6.310
  Find NCS groups from input model:        0.080
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.100
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:    9.460
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7116
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   0.060   6314  Z= 0.193
  Angle     :  0.789  10.692   8584  Z= 0.392
  Chirality :  0.052   0.418    986
  Planarity :  0.006   0.067   1084
  Dihedral  : 17.206 120.804   2360
  Min Nonbonded Distance : 2.232

Molprobity Statistics.
  All-atom Clashscore : 5.11
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.01 %
    Favored  : 97.99 %
  Rotamer:
    Outliers :  0.15 %
    Allowed  :  0.30 %
    Favored  : 99.55 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.67 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.22 (0.27), residues: 798
  helix: -2.63 (0.49), residues: 60
  sheet:  0.34 (0.33), residues: 252
  loop : -1.24 (0.24), residues: 486

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG A  44 
 TYR   0.027   0.002   TYR A 274 
 PHE   0.012   0.002   PHE A   1 
 TRP   0.027   0.001   TRP B  20 
 HIS   0.003   0.001   HIS B 263 

Details of bonding type rmsd
  covalent geometry    : bond        0.00403 ( 6292)
  covalent geometry    : angle       0.76251 ( 8532)
  SS BOND              : bond        0.00210 (   14)
  SS BOND              : angle       1.74275 (   28)
  hydrogen bonds       : bond        0.30119 (  167)
  hydrogen bonds       : angle       9.95057 (  444)
  link_ALPHA1-3        : bond        0.01531 (    2)
  link_ALPHA1-3        : angle       3.78129 (    6)
  link_BETA1-4         : bond        0.00731 (    4)
  link_BETA1-4         : angle       4.19836 (   12)
  link_NAG-ASN         : bond        0.00215 (    2)
  link_NAG-ASN         : angle       0.50530 (    6)

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

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

  1596 Ramachandran restraints generated.
    798 Oldfield, 0 Emsley, 798 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1596 Ramachandran restraints generated.
    798 Oldfield, 0 Emsley, 798 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  84 residues out of total 666 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 83
  time to evaluate  : 0.158 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  204 MET cc_start: 0.6014 (tpp) cc_final: 0.5760 (tpp)
REVERT: B   74 CYS cc_start: 0.5441 (t) cc_final: 0.5176 (t)
REVERT: B  274 TYR cc_start: 0.7403 (t80) cc_final: 0.7103 (t80)
  outliers start: 1
  outliers final: 0
  residues processed: 83
  average time/residue: 0.0386
  time to fit residues: 4.9079
Evaluate side-chains
  58 residues out of total 666 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 58
  time to evaluate  : 0.224 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 80
   random chunks:
   chunk 49 optimal weight:    1.9990
   chunk 53 optimal weight:    3.9990
   chunk 5 optimal weight:    5.9990
   chunk 33 optimal weight:    0.6980
   chunk 65 optimal weight:    8.9990
   chunk 62 optimal weight:    0.0370
   chunk 51 optimal weight:    0.6980
   chunk 38 optimal weight:    5.9990
   chunk 61 optimal weight:    2.9990
   chunk 45 optimal weight:    0.9990
   chunk 74 optimal weight:   10.0000
   overall best weight:    0.8862

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

Flipped N/Q/H residues before XYZ refinement:
A 158 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4144 r_free = 0.4144 target = 0.138062 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3753 r_free = 0.3753 target = 0.111925 restraints weight = 14622.693|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3790 r_free = 0.3790 target = 0.114224 restraints weight = 10901.751|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3818 r_free = 0.3818 target = 0.116047 restraints weight = 8792.902|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 38)----------------|
| r_work = 0.3840 r_free = 0.3840 target = 0.117392 restraints weight = 7479.047|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3850 r_free = 0.3850 target = 0.118124 restraints weight = 6635.849|
|-----------------------------------------------------------------------------|
r_work (final): 0.3851
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7338
moved from start:          0.1368

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.027   6314  Z= 0.136
  Angle     :  0.634   8.093   8584  Z= 0.313
  Chirality :  0.045   0.181    986
  Planarity :  0.005   0.061   1084
  Dihedral  : 13.602  85.913   1010
  Min Nonbonded Distance : 2.387

Molprobity Statistics.
  All-atom Clashscore : 7.09
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.63 %
    Favored  : 98.37 %
  Rotamer:
    Outliers :  0.30 %
    Allowed  :  5.71 %
    Favored  : 93.99 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.67 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.99 (0.28), residues: 798
  helix: -1.96 (0.63), residues: 64
  sheet:  0.47 (0.32), residues: 256
  loop : -1.14 (0.26), residues: 478

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 236 
 TYR   0.008   0.001   TYR B  90 
 PHE   0.021   0.001   PHE B  11 
 TRP   0.011   0.001   TRP B  20 
 HIS   0.004   0.001   HIS A 144 

Details of bonding type rmsd
  covalent geometry    : bond        0.00295 ( 6292)
  covalent geometry    : angle       0.60229 ( 8532)
  SS BOND              : bond        0.00197 (   14)
  SS BOND              : angle       1.78524 (   28)
  hydrogen bonds       : bond        0.04877 (  167)
  hydrogen bonds       : angle       6.93593 (  444)
  link_ALPHA1-3        : bond        0.02402 (    2)
  link_ALPHA1-3        : angle       3.99379 (    6)
  link_BETA1-4         : bond        0.01107 (    4)
  link_BETA1-4         : angle       3.72159 (   12)
  link_NAG-ASN         : bond        0.00740 (    2)
  link_NAG-ASN         : angle       0.93457 (    6)

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

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

  1596 Ramachandran restraints generated.
    798 Oldfield, 0 Emsley, 798 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1596 Ramachandran restraints generated.
    798 Oldfield, 0 Emsley, 798 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  75 residues out of total 666 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 73
  time to evaluate  : 0.150 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  210 SER cc_start: 0.8122 (m) cc_final: 0.7498 (p)
REVERT: B  274 TYR cc_start: 0.7366 (t80) cc_final: 0.7118 (t80)
  outliers start: 2
  outliers final: 0
  residues processed: 74
  average time/residue: 0.0415
  time to fit residues: 4.6570
Evaluate side-chains
  55 residues out of total 666 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 55
  time to evaluate  : 0.225 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 80
   random chunks:
   chunk 13 optimal weight:    3.9990
   chunk 78 optimal weight:    5.9990
   chunk 46 optimal weight:    0.9990
   chunk 42 optimal weight:    2.9990
   chunk 32 optimal weight:    3.9990
   chunk 65 optimal weight:    0.9980
   chunk 29 optimal weight:    5.9990
   chunk 63 optimal weight:    0.9990
   chunk 74 optimal weight:    0.8980
   chunk 27 optimal weight:    5.9990
   chunk 72 optimal weight:    4.9990
   overall best weight:    1.3786

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4104 r_free = 0.4104 target = 0.135294 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 28)----------------|
| r_work = 0.3790 r_free = 0.3790 target = 0.113157 restraints weight = 14544.867|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3802 r_free = 0.3802 target = 0.114685 restraints weight = 12241.391|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3811 r_free = 0.3811 target = 0.115480 restraints weight = 9800.037|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3821 r_free = 0.3821 target = 0.116139 restraints weight = 8336.634|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3822 r_free = 0.3822 target = 0.116242 restraints weight = 8402.120|
|-----------------------------------------------------------------------------|
r_work (final): 0.3823
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7390
moved from start:          0.2018

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.028   6314  Z= 0.171
  Angle     :  0.657   7.042   8584  Z= 0.323
  Chirality :  0.046   0.157    986
  Planarity :  0.005   0.070   1084
  Dihedral  : 11.216  89.082   1010
  Min Nonbonded Distance : 2.400

Molprobity Statistics.
  All-atom Clashscore : 8.82
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.88 %
    Favored  : 98.12 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  4.65 %
    Favored  : 95.35 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.67 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.96 (0.29), residues: 798
  helix: -1.51 (0.65), residues: 64
  sheet:  0.09 (0.30), residues: 290
  loop : -0.99 (0.29), residues: 444

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG A  44 
 TYR   0.017   0.002   TYR B  90 
 PHE   0.015   0.002   PHE B  11 
 TRP   0.006   0.001   TRP B 233 
 HIS   0.004   0.001   HIS A 144 

Details of bonding type rmsd
  covalent geometry    : bond        0.00389 ( 6292)
  covalent geometry    : angle       0.63169 ( 8532)
  SS BOND              : bond        0.00320 (   14)
  SS BOND              : angle       1.41578 (   28)
  hydrogen bonds       : bond        0.04274 (  167)
  hydrogen bonds       : angle       6.01392 (  444)
  link_ALPHA1-3        : bond        0.02005 (    2)
  link_ALPHA1-3        : angle       3.55240 (    6)
  link_BETA1-4         : bond        0.00619 (    4)
  link_BETA1-4         : angle       3.73844 (   12)
  link_NAG-ASN         : bond        0.00650 (    2)
  link_NAG-ASN         : angle       0.49148 (    6)

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

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

  1596 Ramachandran restraints generated.
    798 Oldfield, 0 Emsley, 798 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1596 Ramachandran restraints generated.
    798 Oldfield, 0 Emsley, 798 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  67 residues out of total 666 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 67
  time to evaluate  : 0.150 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   74 CYS cc_start: 0.5587 (t) cc_final: 0.5324 (t)
REVERT: B  274 TYR cc_start: 0.7497 (t80) cc_final: 0.7264 (t80)
  outliers start: 0
  outliers final: 0
  residues processed: 67
  average time/residue: 0.0422
  time to fit residues: 4.3098
Evaluate side-chains
  52 residues out of total 666 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 52
  time to evaluate  : 0.227 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 80
   random chunks:
   chunk 21 optimal weight:    7.9990
   chunk 71 optimal weight:    0.8980
   chunk 17 optimal weight:    0.7980
   chunk 73 optimal weight:    0.8980
   chunk 58 optimal weight:    1.9990
   chunk 52 optimal weight:    8.9990
   chunk 49 optimal weight:    0.9980
   chunk 53 optimal weight:    1.9990
   chunk 29 optimal weight:    5.9990
   chunk 10 optimal weight:    0.8980
   chunk 11 optimal weight:    0.1980
   overall best weight:    0.7380

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4127 r_free = 0.4127 target = 0.136956 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3771 r_free = 0.3771 target = 0.112571 restraints weight = 14726.309|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3779 r_free = 0.3779 target = 0.113896 restraints weight = 12774.755|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.3798 r_free = 0.3798 target = 0.115077 restraints weight = 10094.625|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.3806 r_free = 0.3806 target = 0.115675 restraints weight = 8465.862|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3810 r_free = 0.3810 target = 0.115933 restraints weight = 8300.665|
|-----------------------------------------------------------------------------|
r_work (final): 0.3812
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7416
moved from start:          0.2243

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.027   6314  Z= 0.117
  Angle     :  0.617   7.278   8584  Z= 0.296
  Chirality :  0.045   0.182    986
  Planarity :  0.004   0.060   1084
  Dihedral  :  9.754  81.537   1010
  Min Nonbonded Distance : 2.421

Molprobity Statistics.
  All-atom Clashscore : 6.59
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.13 %
    Favored  : 98.87 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.70 %
    Favored  : 97.30 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.67 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.83 (0.30), residues: 798
  helix: -1.17 (0.68), residues: 64
  sheet:  0.11 (0.30), residues: 290
  loop : -0.88 (0.29), residues: 444

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG B 387 
 TYR   0.015   0.001   TYR B  90 
 PHE   0.015   0.001   PHE B 108 
 TRP   0.009   0.001   TRP B 101 
 HIS   0.003   0.001   HIS A 394 

Details of bonding type rmsd
  covalent geometry    : bond        0.00262 ( 6292)
  covalent geometry    : angle       0.58225 ( 8532)
  SS BOND              : bond        0.00196 (   14)
  SS BOND              : angle       2.04385 (   28)
  hydrogen bonds       : bond        0.03366 (  167)
  hydrogen bonds       : angle       5.70248 (  444)
  link_ALPHA1-3        : bond        0.02264 (    2)
  link_ALPHA1-3        : angle       4.12970 (    6)
  link_BETA1-4         : bond        0.00845 (    4)
  link_BETA1-4         : angle       3.56646 (   12)
  link_NAG-ASN         : bond        0.00455 (    2)
  link_NAG-ASN         : angle       0.65789 (    6)

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

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

  1596 Ramachandran restraints generated.
    798 Oldfield, 0 Emsley, 798 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1596 Ramachandran restraints generated.
    798 Oldfield, 0 Emsley, 798 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  71 residues out of total 666 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 71
  time to evaluate  : 0.143 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  274 TYR cc_start: 0.7532 (t80) cc_final: 0.7296 (t80)
REVERT: B  293 LYS cc_start: 0.7982 (mmtm) cc_final: 0.7717 (mmtt)
REVERT: B  321 THR cc_start: 0.8493 (t) cc_final: 0.8255 (p)
  outliers start: 0
  outliers final: 0
  residues processed: 71
  average time/residue: 0.0447
  time to fit residues: 4.6907
Evaluate side-chains
  54 residues out of total 666 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 54
  time to evaluate  : 0.206 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 80
   random chunks:
   chunk 10 optimal weight:    0.0270
   chunk 35 optimal weight:    0.1980
   chunk 55 optimal weight:    5.9990
   chunk 20 optimal weight:    1.9990
   chunk 16 optimal weight:    3.9990
   chunk 22 optimal weight:    0.0470
   chunk 75 optimal weight:    2.9990
   chunk 21 optimal weight:    0.9990
   chunk 32 optimal weight:    4.9990
   chunk 34 optimal weight:    7.9990
   chunk 41 optimal weight:    8.9990
   overall best weight:    0.6540

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4131 r_free = 0.4131 target = 0.137579 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3769 r_free = 0.3769 target = 0.112173 restraints weight = 14641.850|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3775 r_free = 0.3775 target = 0.113346 restraints weight = 11964.627|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3797 r_free = 0.3797 target = 0.114800 restraints weight = 9599.521|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.3808 r_free = 0.3808 target = 0.115601 restraints weight = 7778.119|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.3811 r_free = 0.3811 target = 0.115802 restraints weight = 7724.158|
|-----------------------------------------------------------------------------|
r_work (final): 0.3811
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7439
moved from start:          0.2403

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   6314  Z= 0.112
  Angle     :  0.603   7.769   8584  Z= 0.288
  Chirality :  0.045   0.165    986
  Planarity :  0.004   0.061   1084
  Dihedral  :  8.742  78.528   1010
  Min Nonbonded Distance : 2.423

Molprobity Statistics.
  All-atom Clashscore : 6.43
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.50 %
    Favored  : 98.50 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.50 %
    Favored  : 98.50 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.67 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.83 (0.29), residues: 798
  helix: -1.03 (0.69), residues: 64
  sheet:  0.20 (0.32), residues: 262
  loop : -0.91 (0.28), residues: 472

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A  44 
 TYR   0.014   0.001   TYR B  90 
 PHE   0.013   0.001   PHE B 108 
 TRP   0.007   0.001   TRP B 101 
 HIS   0.002   0.000   HIS A 144 

Details of bonding type rmsd
  covalent geometry    : bond        0.00252 ( 6292)
  covalent geometry    : angle       0.56884 ( 8532)
  SS BOND              : bond        0.00198 (   14)
  SS BOND              : angle       1.83465 (   28)
  hydrogen bonds       : bond        0.03075 (  167)
  hydrogen bonds       : angle       5.40458 (  444)
  link_ALPHA1-3        : bond        0.02449 (    2)
  link_ALPHA1-3        : angle       4.51579 (    6)
  link_BETA1-4         : bond        0.00640 (    4)
  link_BETA1-4         : angle       3.42569 (   12)
  link_NAG-ASN         : bond        0.00417 (    2)
  link_NAG-ASN         : angle       0.68583 (    6)

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

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

  1596 Ramachandran restraints generated.
    798 Oldfield, 0 Emsley, 798 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1596 Ramachandran restraints generated.
    798 Oldfield, 0 Emsley, 798 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  68 residues out of total 666 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 68
  time to evaluate  : 0.143 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  204 MET cc_start: 0.6268 (tpp) cc_final: 0.6006 (tpp)
REVERT: B  293 LYS cc_start: 0.8002 (mmtm) cc_final: 0.7721 (mmtt)
  outliers start: 0
  outliers final: 0
  residues processed: 68
  average time/residue: 0.0436
  time to fit residues: 4.4102
Evaluate side-chains
  53 residues out of total 666 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 53
  time to evaluate  : 0.230 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 80
   random chunks:
   chunk 41 optimal weight:    7.9990
   chunk 17 optimal weight:    3.9990
   chunk 40 optimal weight:    3.9990
   chunk 28 optimal weight:    4.9990
   chunk 19 optimal weight:    0.2980
   chunk 36 optimal weight:    0.4980
   chunk 24 optimal weight:    3.9990
   chunk 9 optimal weight:    0.9980
   chunk 66 optimal weight:    6.9990
   chunk 31 optimal weight:    3.9990
   chunk 7 optimal weight:    0.9980
   overall best weight:    1.3582

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4096 r_free = 0.4096 target = 0.134840 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3736 r_free = 0.3736 target = 0.110252 restraints weight = 14629.420|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3742 r_free = 0.3742 target = 0.111318 restraints weight = 12565.483|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3760 r_free = 0.3760 target = 0.112517 restraints weight = 10208.364|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.3765 r_free = 0.3765 target = 0.112871 restraints weight = 8535.197|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 24)----------------|
| r_work = 0.3769 r_free = 0.3769 target = 0.113143 restraints weight = 8462.395|
|-----------------------------------------------------------------------------|
r_work (final): 0.3771
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7501
moved from start:          0.2708

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.030   6314  Z= 0.162
  Angle     :  0.634   7.719   8584  Z= 0.308
  Chirality :  0.045   0.161    986
  Planarity :  0.005   0.071   1084
  Dihedral  :  8.229  73.002   1010
  Min Nonbonded Distance : 2.412

Molprobity Statistics.
  All-atom Clashscore : 8.49
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.38 %
    Favored  : 97.62 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.80 %
    Favored  : 98.20 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.67 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.89 (0.30), residues: 798
  helix: -0.96 (0.70), residues: 64
  sheet:  0.04 (0.32), residues: 264
  loop : -0.89 (0.29), residues: 470

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A  44 
 TYR   0.015   0.001   TYR B  90 
 PHE   0.015   0.002   PHE A 142 
 TRP   0.005   0.001   TRP B  20 
 HIS   0.004   0.001   HIS B 144 

Details of bonding type rmsd
  covalent geometry    : bond        0.00372 ( 6292)
  covalent geometry    : angle       0.60240 ( 8532)
  SS BOND              : bond        0.00347 (   14)
  SS BOND              : angle       1.73308 (   28)
  hydrogen bonds       : bond        0.03393 (  167)
  hydrogen bonds       : angle       5.55776 (  444)
  link_ALPHA1-3        : bond        0.02504 (    2)
  link_ALPHA1-3        : angle       4.79476 (    6)
  link_BETA1-4         : bond        0.00493 (    4)
  link_BETA1-4         : angle       3.29355 (   12)
  link_NAG-ASN         : bond        0.00308 (    2)
  link_NAG-ASN         : angle       0.69461 (    6)

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

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

  1596 Ramachandran restraints generated.
    798 Oldfield, 0 Emsley, 798 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1596 Ramachandran restraints generated.
    798 Oldfield, 0 Emsley, 798 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  63 residues out of total 666 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 63
  time to evaluate  : 0.242 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   20 TRP cc_start: 0.7989 (p-90) cc_final: 0.7762 (p-90)
  outliers start: 0
  outliers final: 0
  residues processed: 63
  average time/residue: 0.0479
  time to fit residues: 4.5486
Evaluate side-chains
  50 residues out of total 666 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 50
  time to evaluate  : 0.232 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 80
   random chunks:
   chunk 0 optimal weight:    3.9990
   chunk 30 optimal weight:    0.9980
   chunk 55 optimal weight:    5.9990
   chunk 50 optimal weight:    0.5980
   chunk 40 optimal weight:    0.4980
   chunk 1 optimal weight:    5.9990
   chunk 27 optimal weight:    4.9990
   chunk 45 optimal weight:    6.9990
   chunk 64 optimal weight:    7.9990
   chunk 5 optimal weight:    0.9990
   chunk 18 optimal weight:    4.9990
   overall best weight:    1.4184

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4081 r_free = 0.4081 target = 0.133806 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3717 r_free = 0.3717 target = 0.109292 restraints weight = 14650.356|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3721 r_free = 0.3721 target = 0.110002 restraints weight = 12773.903|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3741 r_free = 0.3741 target = 0.111399 restraints weight = 10558.373|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.3744 r_free = 0.3744 target = 0.111683 restraints weight = 8756.420|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.3749 r_free = 0.3749 target = 0.111981 restraints weight = 8671.896|
|-----------------------------------------------------------------------------|
r_work (final): 0.3751
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7534
moved from start:          0.2959

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.037   6314  Z= 0.167
  Angle     :  0.645   8.871   8584  Z= 0.314
  Chirality :  0.045   0.225    986
  Planarity :  0.005   0.063   1084
  Dihedral  :  7.882  74.206   1010
  Min Nonbonded Distance : 2.398

Molprobity Statistics.
  All-atom Clashscore : 8.32
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.63 %
    Favored  : 97.37 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.40 %
    Favored  : 97.60 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.67 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.93 (0.30), residues: 798
  helix: -0.85 (0.69), residues: 64
  sheet:  0.02 (0.32), residues: 264
  loop : -0.95 (0.28), residues: 470

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG B 387 
 TYR   0.016   0.002   TYR B  90 
 PHE   0.016   0.002   PHE A 142 
 TRP   0.010   0.001   TRP B 101 
 HIS   0.005   0.001   HIS B 144 

Details of bonding type rmsd
  covalent geometry    : bond        0.00384 ( 6292)
  covalent geometry    : angle       0.61099 ( 8532)
  SS BOND              : bond        0.00274 (   14)
  SS BOND              : angle       1.91311 (   28)
  hydrogen bonds       : bond        0.03400 (  167)
  hydrogen bonds       : angle       5.50876 (  444)
  link_ALPHA1-3        : bond        0.02659 (    2)
  link_ALPHA1-3        : angle       5.08183 (    6)
  link_BETA1-4         : bond        0.00680 (    4)
  link_BETA1-4         : angle       3.27499 (   12)
  link_NAG-ASN         : bond        0.00364 (    2)
  link_NAG-ASN         : angle       0.62463 (    6)

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

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

  1596 Ramachandran restraints generated.
    798 Oldfield, 0 Emsley, 798 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1596 Ramachandran restraints generated.
    798 Oldfield, 0 Emsley, 798 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  60 residues out of total 666 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 60
  time to evaluate  : 0.172 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   20 TRP cc_start: 0.7962 (p-90) cc_final: 0.7748 (p-90)
  outliers start: 0
  outliers final: 0
  residues processed: 60
  average time/residue: 0.0408
  time to fit residues: 3.7843
Evaluate side-chains
  48 residues out of total 666 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 48
  time to evaluate  : 0.179 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 80
   random chunks:
   chunk 57 optimal weight:    2.9990
   chunk 38 optimal weight:    2.9990
   chunk 72 optimal weight:    2.9990
   chunk 17 optimal weight:    3.9990
   chunk 59 optimal weight:    0.8980
   chunk 40 optimal weight:    1.9990
   chunk 6 optimal weight:    1.9990
   chunk 78 optimal weight:    2.9990
   chunk 74 optimal weight:    1.9990
   chunk 21 optimal weight:    0.7980
   chunk 26 optimal weight:    5.9990
   overall best weight:    1.5386

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4073 r_free = 0.4073 target = 0.133202 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3707 r_free = 0.3707 target = 0.108550 restraints weight = 14993.548|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3713 r_free = 0.3713 target = 0.109664 restraints weight = 12717.038|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.3728 r_free = 0.3728 target = 0.110615 restraints weight = 10302.366|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.3733 r_free = 0.3733 target = 0.111005 restraints weight = 8885.370|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 33)----------------|
| r_work = 0.3742 r_free = 0.3742 target = 0.111598 restraints weight = 8742.764|
|-----------------------------------------------------------------------------|
r_work (final): 0.3742
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7558
moved from start:          0.3181

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.033   6314  Z= 0.179
  Angle     :  0.659   7.766   8584  Z= 0.324
  Chirality :  0.045   0.224    986
  Planarity :  0.005   0.065   1084
  Dihedral  :  7.880  80.234   1010
  Min Nonbonded Distance : 2.396

Molprobity Statistics.
  All-atom Clashscore : 8.16
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.01 %
    Favored  : 96.99 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.90 %
    Favored  : 99.10 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.67 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.99 (0.30), residues: 798
  helix: -0.75 (0.70), residues: 64
  sheet: -0.13 (0.32), residues: 274
  loop : -0.96 (0.28), residues: 460

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG A  73 
 TYR   0.017   0.002   TYR B  90 
 PHE   0.017   0.002   PHE A 142 
 TRP   0.009   0.001   TRP B  20 
 HIS   0.005   0.001   HIS B 144 

Details of bonding type rmsd
  covalent geometry    : bond        0.00413 ( 6292)
  covalent geometry    : angle       0.62495 ( 8532)
  SS BOND              : bond        0.00326 (   14)
  SS BOND              : angle       2.01930 (   28)
  hydrogen bonds       : bond        0.03448 (  167)
  hydrogen bonds       : angle       5.54161 (  444)
  link_ALPHA1-3        : bond        0.02509 (    2)
  link_ALPHA1-3        : angle       5.07368 (    6)
  link_BETA1-4         : bond        0.00735 (    4)
  link_BETA1-4         : angle       3.15692 (   12)
  link_NAG-ASN         : bond        0.00397 (    2)
  link_NAG-ASN         : angle       0.62865 (    6)

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

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

  1596 Ramachandran restraints generated.
    798 Oldfield, 0 Emsley, 798 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1596 Ramachandran restraints generated.
    798 Oldfield, 0 Emsley, 798 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  60 residues out of total 666 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 60
  time to evaluate  : 0.140 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   20 TRP cc_start: 0.7991 (p-90) cc_final: 0.7746 (p-90)
  outliers start: 0
  outliers final: 0
  residues processed: 60
  average time/residue: 0.0360
  time to fit residues: 3.4424
Evaluate side-chains
  46 residues out of total 666 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 46
  time to evaluate  : 0.209 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 80
   random chunks:
   chunk 78 optimal weight:    7.9990
   chunk 44 optimal weight:    0.6980
   chunk 37 optimal weight:    2.9990
   chunk 49 optimal weight:    1.9990
   chunk 27 optimal weight:    0.9990
   chunk 51 optimal weight:    0.0570
   chunk 9 optimal weight:    1.9990
   chunk 42 optimal weight:    0.7980
   chunk 65 optimal weight:    0.0770
   chunk 18 optimal weight:    3.9990
   chunk 48 optimal weight:    5.9990
   overall best weight:    0.5258

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4104 r_free = 0.4104 target = 0.135739 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3749 r_free = 0.3749 target = 0.111239 restraints weight = 14552.346|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3751 r_free = 0.3751 target = 0.112140 restraints weight = 13030.167|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3767 r_free = 0.3767 target = 0.113191 restraints weight = 10648.109|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3776 r_free = 0.3776 target = 0.113858 restraints weight = 8635.615|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 24)----------------|
| r_work = 0.3780 r_free = 0.3780 target = 0.114096 restraints weight = 8556.249|
|-----------------------------------------------------------------------------|
r_work (final): 0.3780
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7486
moved from start:          0.3223

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.029   6314  Z= 0.106
  Angle     :  0.603  10.084   8584  Z= 0.291
  Chirality :  0.044   0.216    986
  Planarity :  0.004   0.067   1084
  Dihedral  :  7.403  83.817   1010
  Min Nonbonded Distance : 2.408

Molprobity Statistics.
  All-atom Clashscore : 6.18
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.38 %
    Favored  : 98.62 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.45 %
    Favored  : 99.55 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.67 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.81 (0.30), residues: 798
  helix: -0.66 (0.70), residues: 64
  sheet:  0.10 (0.32), residues: 272
  loop : -0.89 (0.29), residues: 462

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B 387 
 TYR   0.014   0.001   TYR B  90 
 PHE   0.009   0.001   PHE B 360 
 TRP   0.009   0.001   TRP B 233 
 HIS   0.002   0.000   HIS B 144 

Details of bonding type rmsd
  covalent geometry    : bond        0.00237 ( 6292)
  covalent geometry    : angle       0.56969 ( 8532)
  SS BOND              : bond        0.00202 (   14)
  SS BOND              : angle       1.84274 (   28)
  hydrogen bonds       : bond        0.02921 (  167)
  hydrogen bonds       : angle       5.25442 (  444)
  link_ALPHA1-3        : bond        0.02350 (    2)
  link_ALPHA1-3        : angle       4.91778 (    6)
  link_BETA1-4         : bond        0.00861 (    4)
  link_BETA1-4         : angle       2.96850 (   12)
  link_NAG-ASN         : bond        0.00526 (    2)
  link_NAG-ASN         : angle       0.49719 (    6)

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

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

  1596 Ramachandran restraints generated.
    798 Oldfield, 0 Emsley, 798 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1596 Ramachandran restraints generated.
    798 Oldfield, 0 Emsley, 798 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  65 residues out of total 666 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 65
  time to evaluate  : 0.251 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   20 TRP cc_start: 0.7957 (p-90) cc_final: 0.7707 (p-90)
  outliers start: 0
  outliers final: 0
  residues processed: 65
  average time/residue: 0.0551
  time to fit residues: 5.3721
Evaluate side-chains
  48 residues out of total 666 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 48
  time to evaluate  : 0.241 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 80
   random chunks:
   chunk 54 optimal weight:    0.6980
   chunk 0 optimal weight:    4.9990
   chunk 28 optimal weight:    4.9990
   chunk 79 optimal weight:    1.9990
   chunk 24 optimal weight:    4.9990
   chunk 15 optimal weight:    2.9990
   chunk 65 optimal weight:    0.0970
   chunk 35 optimal weight:    1.9990
   chunk 48 optimal weight:    0.5980
   chunk 10 optimal weight:    0.0030
   chunk 19 optimal weight:    0.0030
   overall best weight:    0.2798

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4131 r_free = 0.4131 target = 0.137669 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3790 r_free = 0.3790 target = 0.114156 restraints weight = 14539.143|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3790 r_free = 0.3790 target = 0.115470 restraints weight = 10600.490|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3812 r_free = 0.3812 target = 0.116748 restraints weight = 9141.575|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3821 r_free = 0.3821 target = 0.117242 restraints weight = 7376.157|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3823 r_free = 0.3823 target = 0.117408 restraints weight = 7126.134|
|-----------------------------------------------------------------------------|
r_work (final): 0.3826
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7422
moved from start:          0.3238

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.027   6314  Z= 0.095
  Angle     :  0.578   7.347   8584  Z= 0.279
  Chirality :  0.044   0.210    986
  Planarity :  0.004   0.071   1084
  Dihedral  :  7.165  86.546   1010
  Min Nonbonded Distance : 2.418

Molprobity Statistics.
  All-atom Clashscore : 5.52
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.25 %
    Favored  : 98.75 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.30 %
    Favored  : 99.70 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.67 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.71 (0.30), residues: 798
  helix: -0.66 (0.70), residues: 64
  sheet:  0.18 (0.32), residues: 272
  loop : -0.82 (0.29), residues: 462

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B 387 
 TYR   0.014   0.001   TYR A 137 
 PHE   0.009   0.001   PHE B 360 
 TRP   0.009   0.001   TRP B 233 
 HIS   0.002   0.000   HIS B 144 

Details of bonding type rmsd
  covalent geometry    : bond        0.00208 ( 6292)
  covalent geometry    : angle       0.54512 ( 8532)
  SS BOND              : bond        0.00111 (   14)
  SS BOND              : angle       1.94372 (   28)
  hydrogen bonds       : bond        0.02766 (  167)
  hydrogen bonds       : angle       5.03006 (  444)
  link_ALPHA1-3        : bond        0.02153 (    2)
  link_ALPHA1-3        : angle       4.74794 (    6)
  link_BETA1-4         : bond        0.00846 (    4)
  link_BETA1-4         : angle       2.77870 (   12)
  link_NAG-ASN         : bond        0.00508 (    2)
  link_NAG-ASN         : angle       0.50165 (    6)

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

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

  1596 Ramachandran restraints generated.
    798 Oldfield, 0 Emsley, 798 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1596 Ramachandran restraints generated.
    798 Oldfield, 0 Emsley, 798 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  62 residues out of total 666 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 62
  time to evaluate  : 0.218 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   20 TRP cc_start: 0.7903 (p-90) cc_final: 0.7676 (p-90)
  outliers start: 0
  outliers final: 0
  residues processed: 62
  average time/residue: 0.0540
  time to fit residues: 4.9736
Evaluate side-chains
  46 residues out of total 666 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 46
  time to evaluate  : 0.147 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 80
   random chunks:
   chunk 38 optimal weight:    3.9990
   chunk 36 optimal weight:   10.0000
   chunk 46 optimal weight:    0.5980
   chunk 73 optimal weight:    5.9990
   chunk 25 optimal weight:    6.9990
   chunk 54 optimal weight:    3.9990
   chunk 53 optimal weight:    0.8980
   chunk 49 optimal weight:    0.8980
   chunk 22 optimal weight:    5.9990
   chunk 21 optimal weight:    0.9990
   chunk 2 optimal weight:    0.0000
   overall best weight:    0.6786

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

Flipped N/Q/H residues before XYZ refinement:
A 144 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4124 r_free = 0.4124 target = 0.136951 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3766 r_free = 0.3766 target = 0.112330 restraints weight = 14562.449|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3765 r_free = 0.3765 target = 0.113025 restraints weight = 13261.579|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3781 r_free = 0.3781 target = 0.114148 restraints weight = 10866.186|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.3789 r_free = 0.3789 target = 0.114743 restraints weight = 8943.686|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 24)----------------|
| r_work = 0.3792 r_free = 0.3792 target = 0.114971 restraints weight = 8845.165|
|-----------------------------------------------------------------------------|
r_work (final): 0.3795
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7464
moved from start:          0.3343

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   6314  Z= 0.108
  Angle     :  0.570   8.498   8584  Z= 0.276
  Chirality :  0.044   0.206    986
  Planarity :  0.004   0.067   1084
  Dihedral  :  7.084  86.867   1010
  Min Nonbonded Distance : 2.417

Molprobity Statistics.
  All-atom Clashscore : 6.10
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.13 %
    Favored  : 97.87 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.00 %
    Favored  : 100.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.67 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.73 (0.30), residues: 798
  helix: -0.67 (0.70), residues: 64
  sheet: -0.03 (0.31), residues: 282
  loop : -0.71 (0.29), residues: 452

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B 387 
 TYR   0.016   0.001   TYR A 274 
 PHE   0.010   0.001   PHE B 142 
 TRP   0.006   0.001   TRP B  20 
 HIS   0.005   0.001   HIS A 144 

Details of bonding type rmsd
  covalent geometry    : bond        0.00250 ( 6292)
  covalent geometry    : angle       0.54059 ( 8532)
  SS BOND              : bond        0.00146 (   14)
  SS BOND              : angle       1.74953 (   28)
  hydrogen bonds       : bond        0.02846 (  167)
  hydrogen bonds       : angle       4.98237 (  444)
  link_ALPHA1-3        : bond        0.01987 (    2)
  link_ALPHA1-3        : angle       4.49836 (    6)
  link_BETA1-4         : bond        0.00745 (    4)
  link_BETA1-4         : angle       2.70315 (   12)
  link_NAG-ASN         : bond        0.00395 (    2)
  link_NAG-ASN         : angle       0.54303 (    6)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 872.20 seconds
wall clock time: 15 minutes 44.75 seconds (944.75 seconds total)