Starting phenix.real_space_refine
on Thu Jul  2 03:26:32 2026 by dcliebschner
===============================================================================

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

  Found model, restraint, /net/cci-nas-00/data/ceres_data/7qa8_13880/07_2026/7qa8_13880.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7qa8_13880/07_2026/7qa8_13880.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.7
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    restraint_files = "/net/cci-nas-00/data/ceres_data/7qa8_13880/07_2026/7qa8_13880.cif"
    default_restraint = "/net/cci-nas-00/data/ceres_data/7qa8_13880/07_2026/7qa8_13880.cif"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7qa8_13880/07_2026/7qa8_13880.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7qa8_13880/07_2026/7qa8_13880.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/7qa8_13880/07_2026/7qa8_13880.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7qa8_13880/07_2026/7qa8_13880.map"
  }
  resolution = 2.7
  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=   0.005
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      20      5.16       5
     C    4235      2.51       5
     N     769      2.21       5
     O    1087      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 6 residue(s): 0.00s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib"
  Total number of atoms: 6111
  Number of models: 1
  Model: ""
    Number of chains: 11
    Chain: "A"
      Number of atoms: 2299
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 299, 2299
          Classifications: {'peptide': 299}
          Incomplete info: {'truncation_to_alanine': 4}
          Link IDs: {'PTRANS': 8, 'TRANS': 290}
          Unresolved non-hydrogen bonds: 12
          Unresolved non-hydrogen angles: 15
          Unresolved non-hydrogen dihedrals: 9
          Planarities with less than four sites: {'ASP:plan': 2, 'ASN:plan1': 1}
          Unresolved non-hydrogen planarities: 9
    Chain: "K"
      Number of atoms: 97
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 12, 97
          Classifications: {'peptide': 12}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 2, 'TRANS': 9}
          Unresolved non-hydrogen bonds: 1
          Unresolved non-hydrogen angles: 2
          Planarities with less than four sites: {'NLE:plan-1': 1}
          Unresolved non-hydrogen planarities: 1
    Chain: "I"
      Number of atoms: 97
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 12, 97
          Classifications: {'peptide': 12}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 2, 'TRANS': 9}
          Unresolved non-hydrogen bonds: 1
          Unresolved non-hydrogen angles: 2
          Planarities with less than four sites: {'NLE:plan-1': 1}
          Unresolved non-hydrogen planarities: 1
    Chain: "B"
      Number of atoms: 2302
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 299, 2302
          Classifications: {'peptide': 299}
          Incomplete info: {'truncation_to_alanine': 3}
          Link IDs: {'PTRANS': 8, 'TRANS': 290}
          Unresolved non-hydrogen bonds: 9
          Unresolved non-hydrogen angles: 11
          Unresolved non-hydrogen dihedrals: 7
          Planarities with less than four sites: {'ASP:plan': 2}
          Unresolved non-hydrogen planarities: 6
    Chain: "A"
      Number of atoms: 588
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 18, 588
          Unusual residues: {'NAG': 2, 'Y01': 16}
          Classifications: {'undetermined': 18}
          Link IDs: {None: 17}
          Unresolved non-hydrogen bonds: 2
          Unresolved non-hydrogen angles: 4
          Unresolved non-hydrogen chiralities: 2
    Chain: "I"
      Number of atoms: 35
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 35
          Unusual residues: {'Y01': 1}
          Classifications: {'undetermined': 1}
    Chain: "B"
      Number of atoms: 623
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 19, 623
          Unusual residues: {'NAG': 2, 'Y01': 17}
          Classifications: {'undetermined': 19}
          Link IDs: {None: 18}
          Unresolved non-hydrogen bonds: 2
          Unresolved non-hydrogen angles: 4
          Unresolved non-hydrogen chiralities: 2
    Chain: "A"
      Number of atoms: 32
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 32, 32
          Classifications: {'water': 32}
          Link IDs: {None: 31}
    Chain: "K"
      Number of atoms: 4
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 4, 4
          Classifications: {'water': 4}
          Link IDs: {None: 3}
    Chain: "I"
      Number of atoms: 4
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 4, 4
          Classifications: {'water': 4}
          Link IDs: {None: 3}
    Chain: "B"
      Number of atoms: 30
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 30, 30
          Classifications: {'water': 30}
          Link IDs: {None: 29}
  Time building chain proxies: 1.28, per 1000 atoms: 0.21
  Number of scatterers: 6111
  At special positions: 0
  Unit cell: (80.84, 93.74, 98.9, 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      20     16.00
     O    1087      8.00
     N     769      7.00
     C    4235      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Links applied
    NAG-ASN
      " NAG A 501 " - " ASN A  25 "
      " NAG A 502 " - " ASN A  32 "
      " NAG B 501 " - " ASN B  32 "
      " NAG B 502 " - " ASN B  25 "
  Time building additional restraints: 0.46
  Conformation dependent library (CDL) restraints added in 185.2 milliseconds
  

  1220 Ramachandran restraints generated.
    610 Oldfield, 0 Emsley, 610 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1180

  Finding SS restraints...
    Secondary structure from input PDB file:
      24 helices and 2 sheets defined
      75.2% alpha, 3.5% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.11
  Creating SS restraints...
    Processing helix  chain 'A' and resid 9 through 14
      removed outlier: 3.504A  pdb=" N   ASP A  14 " --> pdb=" O   LEU A  11 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 38 through 72
      removed outlier: 3.712A  pdb=" N   SER A  47 " --> pdb=" O   GLY A  43 " (cutoff:3.500A)
      removed outlier: 3.818A  pdb=" N   THR A  48 " --> pdb=" O   LEU A  44 " (cutoff:3.500A)
      removed outlier: 3.746A  pdb=" N   ILE A  53 " --> pdb=" O   VAL A  49 " (cutoff:3.500A)
      removed outlier: 3.950A  pdb=" N   MET A  54 " --> pdb=" O   THR A  50 " (cutoff:3.500A)
      removed outlier: 4.100A  pdb=" N   PHE A  55 " --> pdb=" O   GLN A  51 " (cutoff:3.500A)
      removed outlier: 3.712A  pdb=" N   VAL A  68 " --> pdb=" O   LEU A  64 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 78 through 103
      removed outlier: 3.708A  pdb=" N   LEU A  88 " --> pdb=" O   ASN A  84 " (cutoff:3.500A)
      removed outlier: 3.905A  pdb=" N   PHE A  89 " --> pdb=" O   GLN A  85 " (cutoff:3.500A)
      removed outlier: 3.547A  pdb=" N   ILE A  92 " --> pdb=" O   LEU A  88 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 108 through 114
    Processing helix  chain 'A' and resid 116 through 120
      removed outlier: 3.584A  pdb=" N   ILE A 120 " --> pdb=" O   PRO A 117 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 123 through 154
      removed outlier: 3.697A  pdb=" N   VAL A 127 " --> pdb=" O   GLY A 123 " (cutoff:3.500A)
      removed outlier: 3.685A  pdb=" N   TYR A 128 " --> pdb=" O   ASP A 124 " (cutoff:3.500A)
      removed outlier: 3.811A  pdb=" N   VAL A 136 " --> pdb=" O   ASN A 132 " (cutoff:3.500A)
      removed outlier: 3.826A  pdb=" N   SER A 141 " --> pdb=" O   LEU A 137 " (cutoff:3.500A)
      removed outlier: 3.771A  pdb=" N   PHE A 154 " --> pdb=" O   ILE A 150 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 159 through 195
      removed outlier: 3.867A  pdb=" N   GLY A 163 " --> pdb=" O   PHE A 159 " (cutoff:3.500A)
      removed outlier: 3.543A  pdb=" N   LEU A 164 " --> pdb=" O   LYS A 160 " (cutoff:3.500A)
      removed outlier: 3.577A  pdb=" N   MET A 165 " --> pdb=" O   ARG A 161 " (cutoff:3.500A)
      removed outlier: 3.581A  pdb=" N   THR A 167 " --> pdb=" O   GLY A 163 " (cutoff:3.500A)
      removed outlier: 3.707A  pdb=" N   SER A 168 " --> pdb=" O   LEU A 164 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 203 through 236
      removed outlier: 3.775A  pdb=" N   SER A 207 " --> pdb=" O   TYR A 203 " (cutoff:3.500A)
      removed outlier: 4.554A  pdb=" N   ILE A 209 " --> pdb=" O   ASN A 205 " (cutoff:3.500A)
      removed outlier: 3.925A  pdb=" N   ARG A 233 " --> pdb=" O   ALA A 229 " (cutoff:3.500A)
      removed outlier: 3.931A  pdb=" N   ARG A 234 " --> pdb=" O   ILE A 230 " (cutoff:3.500A)
      removed outlier: 3.758A  pdb=" N   PHE A 235 " --> pdb=" O   ARG A 231 " (cutoff:3.500A)
      removed outlier: 3.537A  pdb=" N   LEU A 236 " --> pdb=" O   SER A 232 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 243 through 251
      removed outlier: 4.182A  pdb=" N   LEU A 247 " --> pdb=" O   SER A 243 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 255 through 268
      removed outlier: 3.618A  pdb=" N   TYR A 266 " --> pdb=" O   PHE A 262 " (cutoff:3.500A)
      removed outlier: 3.672A  pdb=" N   SER A 267 " --> pdb=" O   ILE A 263 " (cutoff:3.500A)
      removed outlier: 3.766A  pdb=" N   LEU A 268 " --> pdb=" O   LEU A 264 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 269 through 272
    Processing helix  chain 'A' and resid 273 through 297
      removed outlier: 3.514A  pdb=" N   LEU A 277 " --> pdb=" O   GLY A 273 " (cutoff:3.500A)
      removed outlier: 3.667A  pdb=" N   THR A 278 " --> pdb=" O   THR A 274 " (cutoff:3.500A)
      removed outlier: 3.872A  pdb=" N   THR A 279 " --> pdb=" O   ASP A 275 " (cutoff:3.500A)
      removed outlier: 3.703A  pdb=" N   VAL A 280 " --> pdb=" O   VAL A 276 " (cutoff:3.500A)
      removed outlier: 3.525A  pdb=" N   LEU A 283 " --> pdb=" O   THR A 279 " (cutoff:3.500A)
      Proline residue:  A 290  - end of helix
      removed outlier: 3.683A  pdb=" N   MET A 294 " --> pdb=" O   PRO A 290 " (cutoff:3.500A)
      removed outlier: 3.917A  pdb=" N   TRP A 295 " --> pdb=" O   LEU A 291 " (cutoff:3.500A)
      removed outlier: 3.777A  pdb=" N   THR A 297 " --> pdb=" O   SER A 293 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 9 through 14
      removed outlier: 3.504A  pdb=" N   ASP B  14 " --> pdb=" O   LEU B  11 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 38 through 72
      removed outlier: 3.712A  pdb=" N   SER B  47 " --> pdb=" O   GLY B  43 " (cutoff:3.500A)
      removed outlier: 3.819A  pdb=" N   THR B  48 " --> pdb=" O   LEU B  44 " (cutoff:3.500A)
      removed outlier: 3.746A  pdb=" N   ILE B  53 " --> pdb=" O   VAL B  49 " (cutoff:3.500A)
      removed outlier: 3.951A  pdb=" N   MET B  54 " --> pdb=" O   THR B  50 " (cutoff:3.500A)
      removed outlier: 4.101A  pdb=" N   PHE B  55 " --> pdb=" O   GLN B  51 " (cutoff:3.500A)
      removed outlier: 3.712A  pdb=" N   VAL B  68 " --> pdb=" O   LEU B  64 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 78 through 103
      removed outlier: 3.708A  pdb=" N   LEU B  88 " --> pdb=" O   ASN B  84 " (cutoff:3.500A)
      removed outlier: 3.905A  pdb=" N   PHE B  89 " --> pdb=" O   GLN B  85 " (cutoff:3.500A)
      removed outlier: 3.546A  pdb=" N   ILE B  92 " --> pdb=" O   LEU B  88 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 108 through 114
    Processing helix  chain 'B' and resid 116 through 120
      removed outlier: 3.584A  pdb=" N   ILE B 120 " --> pdb=" O   PRO B 117 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 123 through 154
      removed outlier: 3.698A  pdb=" N   VAL B 127 " --> pdb=" O   GLY B 123 " (cutoff:3.500A)
      removed outlier: 3.686A  pdb=" N   TYR B 128 " --> pdb=" O   ASP B 124 " (cutoff:3.500A)
      removed outlier: 3.810A  pdb=" N   VAL B 136 " --> pdb=" O   ASN B 132 " (cutoff:3.500A)
      removed outlier: 3.826A  pdb=" N   SER B 141 " --> pdb=" O   LEU B 137 " (cutoff:3.500A)
      removed outlier: 3.770A  pdb=" N   PHE B 154 " --> pdb=" O   ILE B 150 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 159 through 195
      removed outlier: 3.866A  pdb=" N   GLY B 163 " --> pdb=" O   PHE B 159 " (cutoff:3.500A)
      removed outlier: 3.542A  pdb=" N   LEU B 164 " --> pdb=" O   LYS B 160 " (cutoff:3.500A)
      removed outlier: 3.577A  pdb=" N   MET B 165 " --> pdb=" O   ARG B 161 " (cutoff:3.500A)
      removed outlier: 3.582A  pdb=" N   THR B 167 " --> pdb=" O   GLY B 163 " (cutoff:3.500A)
      removed outlier: 3.708A  pdb=" N   SER B 168 " --> pdb=" O   LEU B 164 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 203 through 236
      removed outlier: 3.696A  pdb=" N   SER B 207 " --> pdb=" O   TYR B 203 " (cutoff:3.500A)
      removed outlier: 4.555A  pdb=" N   ILE B 209 " --> pdb=" O   ASN B 205 " (cutoff:3.500A)
      removed outlier: 3.925A  pdb=" N   ARG B 233 " --> pdb=" O   ALA B 229 " (cutoff:3.500A)
      removed outlier: 3.932A  pdb=" N   ARG B 234 " --> pdb=" O   ILE B 230 " (cutoff:3.500A)
      removed outlier: 3.758A  pdb=" N   PHE B 235 " --> pdb=" O   ARG B 231 " (cutoff:3.500A)
      removed outlier: 3.536A  pdb=" N   LEU B 236 " --> pdb=" O   SER B 232 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 243 through 251
      removed outlier: 4.182A  pdb=" N   LEU B 247 " --> pdb=" O   SER B 243 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 255 through 268
      removed outlier: 3.617A  pdb=" N   TYR B 266 " --> pdb=" O   PHE B 262 " (cutoff:3.500A)
      removed outlier: 3.672A  pdb=" N   SER B 267 " --> pdb=" O   ILE B 263 " (cutoff:3.500A)
      removed outlier: 3.768A  pdb=" N   LEU B 268 " --> pdb=" O   LEU B 264 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 269 through 272
    Processing helix  chain 'B' and resid 273 through 297
      removed outlier: 3.514A  pdb=" N   LEU B 277 " --> pdb=" O   GLY B 273 " (cutoff:3.500A)
      removed outlier: 3.689A  pdb=" N   THR B 278 " --> pdb=" O   THR B 274 " (cutoff:3.500A)
      removed outlier: 3.864A  pdb=" N   THR B 279 " --> pdb=" O   ASP B 275 " (cutoff:3.500A)
      removed outlier: 3.760A  pdb=" N   VAL B 280 " --> pdb=" O   VAL B 276 " (cutoff:3.500A)
      removed outlier: 3.524A  pdb=" N   LEU B 283 " --> pdb=" O   THR B 279 " (cutoff:3.500A)
      Proline residue:  B 290  - end of helix
      removed outlier: 3.683A  pdb=" N   MET B 294 " --> pdb=" O   PRO B 290 " (cutoff:3.500A)
      removed outlier: 3.917A  pdb=" N   TRP B 295 " --> pdb=" O   LEU B 291 " (cutoff:3.500A)
      removed outlier: 3.778A  pdb=" N   THR B 297 " --> pdb=" O   SER B 293 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 23 through 28
      removed outlier: 6.477A  pdb=" N   ILE A  24 " --> pdb=" O   THR A  35 " (cutoff:3.500A)
      removed outlier: 4.227A  pdb=" N   THR A  35 " --> pdb=" O   ILE A  24 " (cutoff:3.500A)
      removed outlier: 5.869A  pdb=" N   TYR A  26 " --> pdb=" O   GLY A  33 " (cutoff:3.500A)
      removed outlier: 3.654A  pdb=" N   GLY A  33 " --> pdb=" O   TYR A  26 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'B' and resid 23 through 28
      removed outlier: 6.478A  pdb=" N   ILE B  24 " --> pdb=" O   THR B  35 " (cutoff:3.500A)
      removed outlier: 4.227A  pdb=" N   THR B  35 " --> pdb=" O   ILE B  24 " (cutoff:3.500A)
      removed outlier: 5.869A  pdb=" N   TYR B  26 " --> pdb=" O   GLY B  33 " (cutoff:3.500A)
      removed outlier: 3.655A  pdb=" N   GLY B  33 " --> pdb=" O   TYR B  26 " (cutoff:3.500A)

    298 hydrogen bonds defined for protein.
    864 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: 0.52

  Time building geometry restraints manager: 0.65 seconds

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

  Histogram of bond lengths:
        1.18 -     1.31: 819
        1.31 -     1.43: 1417
        1.43 -     1.56: 3916
        1.56 -     1.68: 55
        1.68 -     1.80: 36
  Bond restraints: 6243
  Sorted by residual:
  bond pdb=" C7  NAG B 501 "
       pdb=" N2  NAG B 501 "
    ideal  model  delta    sigma   weight residual
    1.346  1.461 -0.115 2.00e-02 2.50e+03 3.31e+01
  bond pdb=" C7  NAG A 502 "
       pdb=" N2  NAG A 502 "
    ideal  model  delta    sigma   weight residual
    1.346  1.461 -0.115 2.00e-02 2.50e+03 3.29e+01
  bond pdb=" C7  NAG B 502 "
       pdb=" N2  NAG B 502 "
    ideal  model  delta    sigma   weight residual
    1.346  1.460 -0.114 2.00e-02 2.50e+03 3.23e+01
  bond pdb=" C7  NAG A 501 "
       pdb=" N2  NAG A 501 "
    ideal  model  delta    sigma   weight residual
    1.346  1.458 -0.112 2.00e-02 2.50e+03 3.12e+01
  bond pdb=" C1  NAG A 501 "
       pdb=" O5  NAG A 501 "
    ideal  model  delta    sigma   weight residual
    1.406  1.516 -0.110 2.00e-02 2.50e+03 3.05e+01
  ... (remaining 6238 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.60: 7731
        1.60 -     3.20: 737
        3.20 -     4.80: 149
        4.80 -     6.40: 58
        6.40 -     8.00: 7
  Bond angle restraints: 8682
  Sorted by residual:
  angle pdb=" N   PHE A  99 "
        pdb=" CA  PHE A  99 "
        pdb=" C   PHE A  99 "
      ideal   model   delta    sigma   weight residual
     111.36  105.46    5.90 1.09e+00 8.42e-01 2.93e+01
  angle pdb=" N   PHE B  99 "
        pdb=" CA  PHE B  99 "
        pdb=" C   PHE B  99 "
      ideal   model   delta    sigma   weight residual
     111.36  105.63    5.73 1.09e+00 8.42e-01 2.76e+01
  angle pdb=" N   PHE A 204 "
        pdb=" CA  PHE A 204 "
        pdb=" C   PHE A 204 "
      ideal   model   delta    sigma   weight residual
     113.41  107.33    6.08 1.22e+00 6.72e-01 2.48e+01
  angle pdb=" N   LYS B 202 "
        pdb=" CA  LYS B 202 "
        pdb=" C   LYS B 202 "
      ideal   model   delta    sigma   weight residual
     113.97  107.77    6.20 1.28e+00 6.10e-01 2.35e+01
  angle pdb=" N   TYR B 106 "
        pdb=" CA  TYR B 106 "
        pdb=" C   TYR B 106 "
      ideal   model   delta    sigma   weight residual
     113.28  107.50    5.78 1.22e+00 6.72e-01 2.24e+01
  ... (remaining 8677 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.74: 3035
       17.74 -    35.49: 204
       35.49 -    53.23: 56
       53.23 -    70.97: 23
       70.97 -    88.72: 6
  Dihedral angle restraints: 3324
    sinusoidal: 1498
      harmonic: 1826
  Sorted by residual:
  dihedral pdb=" C   ASP B 275 "
           pdb=" N   ASP B 275 "
           pdb=" CA  ASP B 275 "
           pdb=" CB  ASP B 275 "
      ideal   model   delta  harmonic     sigma   weight residual
    -122.60 -113.06   -9.54     0      2.50e+00 1.60e-01 1.46e+01
  dihedral pdb=" CA  CYS A 252 "
           pdb=" C   CYS A 252 "
           pdb=" N   GLN A 253 "
           pdb=" CA  GLN A 253 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  162.14   17.86     0      5.00e+00 4.00e-02 1.28e+01
  dihedral pdb=" CA  CYS B 252 "
           pdb=" C   CYS B 252 "
           pdb=" N   GLN B 253 "
           pdb=" CA  GLN B 253 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  162.15   17.85     0      5.00e+00 4.00e-02 1.27e+01
  ... (remaining 3321 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.062: 890
       0.062 -    0.124: 172
       0.124 -    0.186: 46
       0.186 -    0.248: 10
       0.248 -    0.310: 4
  Chirality restraints: 1122
  Sorted by residual:
  chirality pdb=" CBC Y01 A 518 "
            pdb=" CAR Y01 A 518 "
            pdb=" CAV Y01 A 518 "
            pdb=" OAW Y01 A 518 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.54   -2.23   -0.31 2.00e-01 2.50e+01 2.40e+00
  chirality pdb=" C1  NAG A 501 "
            pdb=" ND2 ASN A  25 "
            pdb=" C2  NAG A 501 "
            pdb=" O5  NAG A 501 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.40   -2.10   -0.30 2.00e-01 2.50e+01 2.26e+00
  chirality pdb=" CBC Y01 A 514 "
            pdb=" CAR Y01 A 514 "
            pdb=" CAV Y01 A 514 "
            pdb=" OAW Y01 A 514 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.54   -2.27   -0.28 2.00e-01 2.50e+01 1.90e+00
  ... (remaining 1119 not shown)

  Planarity restraints: 883
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  SER A 104 "   -0.021 2.00e-02 2.50e+03   4.36e-02 1.90e+01
        pdb=" C   SER A 104 "    0.075 2.00e-02 2.50e+03
        pdb=" O   SER A 104 "   -0.029 2.00e-02 2.50e+03
        pdb=" N   ASN A 105 "   -0.025 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  SER B 104 "    0.020 2.00e-02 2.50e+03   4.10e-02 1.68e+01
        pdb=" C   SER B 104 "   -0.071 2.00e-02 2.50e+03
        pdb=" O   SER B 104 "    0.028 2.00e-02 2.50e+03
        pdb=" N   ASN B 105 "    0.023 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  VAL B 186 "   -0.018 2.00e-02 2.50e+03   3.63e-02 1.32e+01
        pdb=" C   VAL B 186 "    0.063 2.00e-02 2.50e+03
        pdb=" O   VAL B 186 "   -0.023 2.00e-02 2.50e+03
        pdb=" N   LYS B 187 "   -0.021 2.00e-02 2.50e+03
  ... (remaining 880 not shown)

  Histogram of nonbonded interaction distances:
        2.32 -     2.84: 1617
        2.84 -     3.35: 5592
        3.35 -     3.87: 9104
        3.87 -     4.38: 10853
        4.38 -     4.90: 18087
  Nonbonded interactions: 45253
  Sorted by model distance:
  nonbonded pdb=" O   ASN A  46 "
            pdb=" OG1 THR A  50 "
     model   vdw
     2.323 3.040
  nonbonded pdb=" O   ASN B  46 "
            pdb=" OG1 THR B  50 "
     model   vdw
     2.324 3.040
  nonbonded pdb=" OXT TYR K  13 "
            pdb=" O   HOH K 101 "
     model   vdw
     2.338 3.040
  nonbonded pdb=" O   LYS B 151 "
            pdb=" OG1 THR B 155 "
     model   vdw
     2.338 3.040
  nonbonded pdb=" O   LYS A 151 "
            pdb=" OG1 THR A 155 "
     model   vdw
     2.339 3.040
  ... (remaining 45248 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: 0.00
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = (chain 'B' and (resid 5 through 157 or (resid 158 and (name N or name CA or name \ 
 C or name O or name CB )) or resid 159 through 518))
}
ncs_group {
  reference = (chain 'I' and resid 2 through 13)
  selection = chain 'K'
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             1.030
  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:          0.110
  Check model and map are aligned:         0.020
  Set scattering table:                    0.010
  Process input model:                     5.820
  Find NCS groups from input model:        0.060
  Set up NCS constraints:                  0.010
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:6.210
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   13.280
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7889
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.009   0.115   6247  Z= 0.474
  Angle     :  1.119   8.003   8694  Z= 0.598
  Chirality :  0.059   0.310   1122
  Planarity :  0.009   0.055    879
  Dihedral  : 14.610  88.718   2144
  Min Nonbonded Distance : 2.323

Molprobity Statistics.
  All-atom Clashscore : 1.73
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.28 %
    Favored  : 96.72 %
  Rotamer:
    Outliers :  0.75 %
    Allowed  :  1.50 %
    Favored  : 97.76 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.98 (0.28), residues: 610
  helix: -1.93 (0.22), residues: 396
  sheet:  None (None), residues: 0
  loop : -1.71 (0.33), residues: 214

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.001   ARG B 231 
 TYR   0.022   0.003   TYR B  26 
 PHE   0.031   0.003   PHE A  55 
 TRP   0.014   0.002   TRP A 295 
 HIS   0.006   0.003   HIS A  94 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00862 /  0.47 ( 6243)
  covalent geometry    : angle       1.11364 /  0.60 ( 8682)
  hydrogen bonds       : bond        0.16321 / 10.15 (  298)
  hydrogen bonds       : angle       5.32187 /  3.84 (  864)
  link_NAG-ASN         : bond        0.00545 /  0.24 (    4)
  link_NAG-ASN         : angle       3.15994 /  2.05 (   12)

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

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

  1220 Ramachandran restraints generated.
    610 Oldfield, 0 Emsley, 610 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1220 Ramachandran restraints generated.
    610 Oldfield, 0 Emsley, 610 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  71 residues out of total 542 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 67
  time to evaluate  : 0.117 
Fit side-chains
REVERT: A  165 MET cc_start: 0.6585 (ptm) cc_final: 0.6242 (ptm)
REVERT: B  165 MET cc_start: 0.6597 (ptm) cc_final: 0.6325 (ptm)
  outliers start: 4
  outliers final: 3
  residues processed: 71
  average time/residue: 0.3601
  time to fit residues: 27.1899
Evaluate side-chains
  52 residues out of total 542 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 49
  time to evaluate  : 0.126 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  106 TYR
Chi-restraints excluded: chain B residue  106 TYR
Chi-restraints excluded: chain B residue  274 THR
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 60
   random chunks:
   chunk 54 optimal weight:    0.2980
   chunk 24 optimal weight:    0.6980
   chunk 48 optimal weight:    0.8980
   chunk 56 optimal weight:    0.9980
   chunk 26 optimal weight:    0.9990
   chunk 2 optimal weight:    0.7980
   chunk 16 optimal weight:    3.9990
   chunk 32 optimal weight:    0.0870
   chunk 31 optimal weight:    0.9980
   chunk 25 optimal weight:    0.2980
   chunk 58 optimal weight:    2.9990
   overall best weight:    0.4358

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A  51 GLN
A  94 HIS
A 118 GLN
A 135 GLN
B  51 GLN
B  94 HIS
B 118 GLN
B 135 GLN

Total number of N/Q/H flips: 8

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4047 r_free = 0.4047 target = 0.177075 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3512 r_free = 0.3512 target = 0.128383 restraints weight = 7103.304|
|-----------------------------------------------------------------------------|
r_work (start): 0.3425 rms_B_bonded: 1.91
r_work: 0.3267 rms_B_bonded: 3.40 restraints_weight: 0.5000
r_work (final): 0.3267
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8008
moved from start:          0.1195

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.030   6247  Z= 0.116
  Angle     :  0.517   6.541   8694  Z= 0.256
  Chirality :  0.035   0.269   1122
  Planarity :  0.004   0.035    879
  Dihedral  : 11.064  59.382   1115
  Min Nonbonded Distance : 2.571

Molprobity Statistics.
  All-atom Clashscore : 2.75
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.46 %
    Favored  : 97.54 %
  Rotamer:
    Outliers :  2.62 %
    Allowed  :  6.54 %
    Favored  : 90.84 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.01 (0.33), residues: 610
  helix:  0.63 (0.26), residues: 410
  sheet:  None (None), residues: 0
  loop : -1.25 (0.37), residues: 200

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A 122 
 TYR   0.008   0.001   TYR A 266 
 PHE   0.014   0.001   PHE A 204 
 TRP   0.005   0.001   TRP A 295 
 HIS   0.004   0.001   HIS A  94 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00221 /  0.12 ( 6243)
  covalent geometry    : angle       0.51226 /  0.25 ( 8682)
  hydrogen bonds       : bond        0.06173 /  3.84 (  298)
  hydrogen bonds       : angle       3.68282 /  2.64 (  864)
  link_NAG-ASN         : bond        0.00323 /  0.16 (    4)
  link_NAG-ASN         : angle       1.96907 /  1.44 (   12)

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

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

  1220 Ramachandran restraints generated.
    610 Oldfield, 0 Emsley, 610 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1220 Ramachandran restraints generated.
    610 Oldfield, 0 Emsley, 610 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  77 residues out of total 542 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 63
  time to evaluate  : 0.199 
Fit side-chains
   revert: symmetry clash
REVERT: A  165 MET cc_start: 0.6592 (ptm) cc_final: 0.6350 (ptm)
REVERT: B  197 SER cc_start: 0.7012 (m) cc_final: 0.6609 (p)
  outliers start: 14
  outliers final: 7
  residues processed: 73
  average time/residue: 0.3859
  time to fit residues: 30.0512
Evaluate side-chains
  62 residues out of total 542 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 55
  time to evaluate  : 0.164 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   64 LEU
Chi-restraints excluded: chain A residue  106 TYR
Chi-restraints excluded: chain A residue  150 ILE
Chi-restraints excluded: chain A residue  164 LEU
Chi-restraints excluded: chain B residue   64 LEU
Chi-restraints excluded: chain B residue  106 TYR
Chi-restraints excluded: chain B residue  164 LEU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 60
   random chunks:
   chunk 51 optimal weight:    5.9990
   chunk 21 optimal weight:    1.9990
   chunk 33 optimal weight:    0.9990
   chunk 37 optimal weight:    3.9990
   chunk 58 optimal weight:    5.9990
   chunk 53 optimal weight:    1.9990
   chunk 25 optimal weight:    0.9990
   chunk 34 optimal weight:    2.9990
   chunk 45 optimal weight:    2.9990
   chunk 7 optimal weight:    4.9990
   chunk 6 optimal weight:    1.9990
   overall best weight:    1.5990

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 118 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3943 r_free = 0.3943 target = 0.167707 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3374 r_free = 0.3374 target = 0.118348 restraints weight = 7005.231|
|-----------------------------------------------------------------------------|
r_work (start): 0.3333 rms_B_bonded: 1.90
r_work: 0.3177 rms_B_bonded: 3.35 restraints_weight: 0.5000
r_work (final): 0.3177
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8158
moved from start:          0.2043

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.044   6247  Z= 0.178
  Angle     :  0.696   5.938   8694  Z= 0.321
  Chirality :  0.041   0.229   1122
  Planarity :  0.004   0.034    879
  Dihedral  : 12.086  59.388   1114
  Min Nonbonded Distance : 2.564

Molprobity Statistics.
  All-atom Clashscore : 4.48
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.26 %
    Favored  : 95.74 %
  Rotamer:
    Outliers :  4.11 %
    Allowed  : 10.09 %
    Favored  : 85.79 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.76 (0.33), residues: 610
  helix:  1.39 (0.26), residues: 412
  sheet:  None (None), residues: 0
  loop : -1.40 (0.37), residues: 198

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.001   ARG A  74 
 TYR   0.009   0.002   TYR B  17 
 PHE   0.016   0.002   PHE B 262 
 TRP   0.006   0.001   TRP B 295 
 HIS   0.007   0.002   HIS A  94 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00390 /  0.18 ( 6243)
  covalent geometry    : angle       0.69096 /  0.32 ( 8682)
  hydrogen bonds       : bond        0.08514 /  5.32 (  298)
  hydrogen bonds       : angle       4.04064 /  2.90 (  864)
  link_NAG-ASN         : bond        0.00110 /  0.04 (    4)
  link_NAG-ASN         : angle       2.29045 /  1.44 (   12)

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

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

  1220 Ramachandran restraints generated.
    610 Oldfield, 0 Emsley, 610 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1220 Ramachandran restraints generated.
    610 Oldfield, 0 Emsley, 610 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  71 residues out of total 542 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 49
  time to evaluate  : 0.119 
Fit side-chains
REVERT: A  197 SER cc_start: 0.7506 (m) cc_final: 0.7184 (p)
REVERT: A  264 LEU cc_start: 0.8042 (OUTLIER) cc_final: 0.7784 (mt)
REVERT: B   98 TYR cc_start: 0.8966 (OUTLIER) cc_final: 0.8759 (t80)
REVERT: B  197 SER cc_start: 0.7440 (m) cc_final: 0.7185 (p)
  outliers start: 22
  outliers final: 12
  residues processed: 66
  average time/residue: 0.3248
  time to fit residues: 23.1387
Evaluate side-chains
  63 residues out of total 542 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 49
  time to evaluate  : 0.174 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   64 LEU
Chi-restraints excluded: chain A residue  106 TYR
Chi-restraints excluded: chain A residue  150 ILE
Chi-restraints excluded: chain A residue  164 LEU
Chi-restraints excluded: chain A residue  191 VAL
Chi-restraints excluded: chain A residue  264 LEU
Chi-restraints excluded: chain A residue  297 THR
Chi-restraints excluded: chain B residue   64 LEU
Chi-restraints excluded: chain B residue   98 TYR
Chi-restraints excluded: chain B residue  106 TYR
Chi-restraints excluded: chain B residue  150 ILE
Chi-restraints excluded: chain B residue  164 LEU
Chi-restraints excluded: chain B residue  191 VAL
Chi-restraints excluded: chain B residue  297 THR
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 60
   random chunks:
   chunk 0 optimal weight:   10.0000
   chunk 31 optimal weight:    6.9990
   chunk 26 optimal weight:    2.9990
   chunk 34 optimal weight:    3.9990
   chunk 8 optimal weight:    1.9990
   chunk 38 optimal weight:    1.9990
   chunk 40 optimal weight:    2.9990
   chunk 1 optimal weight:    5.9990
   chunk 46 optimal weight:    8.9990
   chunk 59 optimal weight:    0.7980
   chunk 44 optimal weight:    0.8980
   overall best weight:    1.7386

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 118 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3932 r_free = 0.3932 target = 0.166704 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3374 r_free = 0.3374 target = 0.118298 restraints weight = 7045.546|
|-----------------------------------------------------------------------------|
r_work (start): 0.3261 rms_B_bonded: 1.88
r_work: 0.3095 rms_B_bonded: 3.33 restraints_weight: 0.5000
r_work (final): 0.3095
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8167
moved from start:          0.2475

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.039   6247  Z= 0.177
  Angle     :  0.696   7.358   8694  Z= 0.319
  Chirality :  0.041   0.238   1122
  Planarity :  0.004   0.035    879
  Dihedral  : 13.033  58.622   1114
  Min Nonbonded Distance : 2.580

Molprobity Statistics.
  All-atom Clashscore : 4.88
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.61 %
    Favored  : 96.39 %
  Rotamer:
    Outliers :  3.93 %
    Allowed  : 11.21 %
    Favored  : 84.86 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.22 (0.33), residues: 610
  helix:  1.88 (0.26), residues: 414
  sheet:  None (None), residues: 0
  loop : -1.62 (0.36), residues: 196

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG A 161 
 TYR   0.007   0.002   TYR B 266 
 PHE   0.019   0.002   PHE A 244 
 TRP   0.007   0.002   TRP B  70 
 HIS   0.006   0.001   HIS A  94 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00387 /  0.18 ( 6243)
  covalent geometry    : angle       0.69196 /  0.32 ( 8682)
  hydrogen bonds       : bond        0.08403 /  5.27 (  298)
  hydrogen bonds       : angle       4.00001 /  2.89 (  864)
  link_NAG-ASN         : bond        0.00141 /  0.07 (    4)
  link_NAG-ASN         : angle       2.14107 /  1.31 (   12)

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

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

  1220 Ramachandran restraints generated.
    610 Oldfield, 0 Emsley, 610 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1220 Ramachandran restraints generated.
    610 Oldfield, 0 Emsley, 610 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  69 residues out of total 542 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 48
  time to evaluate  : 0.209 
Fit side-chains
REVERT: A   98 TYR cc_start: 0.8996 (OUTLIER) cc_final: 0.8694 (t80)
REVERT: A  197 SER cc_start: 0.7487 (m) cc_final: 0.7285 (p)
REVERT: B   98 TYR cc_start: 0.8958 (OUTLIER) cc_final: 0.8738 (t80)
  outliers start: 21
  outliers final: 13
  residues processed: 65
  average time/residue: 0.3310
  time to fit residues: 23.0799
Evaluate side-chains
  62 residues out of total 542 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 47
  time to evaluate  : 0.138 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   64 LEU
Chi-restraints excluded: chain A residue   98 TYR
Chi-restraints excluded: chain A residue  106 TYR
Chi-restraints excluded: chain A residue  136 VAL
Chi-restraints excluded: chain A residue  150 ILE
Chi-restraints excluded: chain A residue  164 LEU
Chi-restraints excluded: chain A residue  264 LEU
Chi-restraints excluded: chain A residue  297 THR
Chi-restraints excluded: chain B residue   64 LEU
Chi-restraints excluded: chain B residue   98 TYR
Chi-restraints excluded: chain B residue  106 TYR
Chi-restraints excluded: chain B residue  136 VAL
Chi-restraints excluded: chain B residue  150 ILE
Chi-restraints excluded: chain B residue  164 LEU
Chi-restraints excluded: chain B residue  297 THR
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 60
   random chunks:
   chunk 13 optimal weight:    3.9990
   chunk 54 optimal weight:    3.9990
   chunk 42 optimal weight:    4.9990
   chunk 50 optimal weight:    5.9990
   chunk 4 optimal weight:    0.6980
   chunk 44 optimal weight:    1.9990
   chunk 3 optimal weight:    0.6980
   chunk 12 optimal weight:    2.9990
   chunk 1 optimal weight:    0.8980
   chunk 31 optimal weight:    6.9990
   chunk 38 optimal weight:    3.9990
   overall best weight:    1.4584

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 118 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3934 r_free = 0.3934 target = 0.166942 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3381 r_free = 0.3381 target = 0.118868 restraints weight = 7124.610|
|-----------------------------------------------------------------------------|
r_work (start): 0.3267 rms_B_bonded: 1.86
r_work: 0.3104 rms_B_bonded: 3.28 restraints_weight: 0.5000
r_work (final): 0.3104
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8144
moved from start:          0.2661

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.038   6247  Z= 0.162
  Angle     :  0.662   8.329   8694  Z= 0.303
  Chirality :  0.040   0.230   1122
  Planarity :  0.004   0.034    879
  Dihedral  : 13.000  59.987   1114
  Min Nonbonded Distance : 2.596

Molprobity Statistics.
  All-atom Clashscore : 4.88
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.10 %
    Favored  : 95.90 %
  Rotamer:
    Outliers :  4.11 %
    Allowed  : 12.15 %
    Favored  : 83.74 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.55 (0.33), residues: 610
  helix:  2.19 (0.25), residues: 414
  sheet:  None (None), residues: 0
  loop : -1.65 (0.36), residues: 196

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.001   ARG A  74 
 TYR   0.007   0.001   TYR B  17 
 PHE   0.014   0.002   PHE B 244 
 TRP   0.005   0.001   TRP A 295 
 HIS   0.004   0.001   HIS A  94 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00350 /  0.16 ( 6243)
  covalent geometry    : angle       0.65803 /  0.30 ( 8682)
  hydrogen bonds       : bond        0.07931 /  4.97 (  298)
  hydrogen bonds       : angle       3.88533 /  2.82 (  864)
  link_NAG-ASN         : bond        0.00099 /  0.05 (    4)
  link_NAG-ASN         : angle       2.00927 /  1.25 (   12)

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

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

  1220 Ramachandran restraints generated.
    610 Oldfield, 0 Emsley, 610 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1220 Ramachandran restraints generated.
    610 Oldfield, 0 Emsley, 610 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  74 residues out of total 542 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 52
  time to evaluate  : 0.214 
Fit side-chains
REVERT: A  197 SER cc_start: 0.7419 (m) cc_final: 0.7214 (p)
REVERT: A  271 ASN cc_start: 0.5725 (m110) cc_final: 0.5425 (t0)
REVERT: B   98 TYR cc_start: 0.8932 (OUTLIER) cc_final: 0.8707 (t80)
REVERT: B  271 ASN cc_start: 0.5715 (m110) cc_final: 0.5452 (t0)
  outliers start: 22
  outliers final: 17
  residues processed: 70
  average time/residue: 0.3350
  time to fit residues: 25.1421
Evaluate side-chains
  66 residues out of total 542 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 48
  time to evaluate  : 0.141 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   64 LEU
Chi-restraints excluded: chain A residue  106 TYR
Chi-restraints excluded: chain A residue  136 VAL
Chi-restraints excluded: chain A residue  150 ILE
Chi-restraints excluded: chain A residue  164 LEU
Chi-restraints excluded: chain A residue  191 VAL
Chi-restraints excluded: chain A residue  252 CYS
Chi-restraints excluded: chain A residue  297 THR
Chi-restraints excluded: chain B residue   64 LEU
Chi-restraints excluded: chain B residue   98 TYR
Chi-restraints excluded: chain B residue  106 TYR
Chi-restraints excluded: chain B residue  136 VAL
Chi-restraints excluded: chain B residue  150 ILE
Chi-restraints excluded: chain B residue  164 LEU
Chi-restraints excluded: chain B residue  191 VAL
Chi-restraints excluded: chain B residue  252 CYS
Chi-restraints excluded: chain B residue  256 LEU
Chi-restraints excluded: chain B residue  297 THR
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 60
   random chunks:
   chunk 50 optimal weight:    0.2980
   chunk 15 optimal weight:    9.9990
   chunk 27 optimal weight:    0.5980
   chunk 59 optimal weight:    3.9990
   chunk 25 optimal weight:    1.9990
   chunk 7 optimal weight:    0.9990
   chunk 45 optimal weight:    0.9980
   chunk 35 optimal weight:    0.7980
   chunk 10 optimal weight:    4.9990
   chunk 4 optimal weight:    0.7980
   chunk 21 optimal weight:    0.8980
   overall best weight:    0.6780

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 118 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3983 r_free = 0.3983 target = 0.171476 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3452 r_free = 0.3452 target = 0.124149 restraints weight = 7083.591|
|-----------------------------------------------------------------------------|
r_work (start): 0.3380 rms_B_bonded: 1.86
r_work: 0.3226 rms_B_bonded: 3.30 restraints_weight: 0.5000
r_work (final): 0.3226
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8099
moved from start:          0.2646

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.033   6247  Z= 0.119
  Angle     :  0.555   8.716   8694  Z= 0.257
  Chirality :  0.036   0.251   1122
  Planarity :  0.003   0.032    879
  Dihedral  : 12.213  59.098   1114
  Min Nonbonded Distance : 2.616

Molprobity Statistics.
  All-atom Clashscore : 4.56
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.61 %
    Favored  : 96.39 %
  Rotamer:
    Outliers :  3.55 %
    Allowed  : 14.58 %
    Favored  : 81.87 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  2.13 (0.34), residues: 610
  helix:  2.60 (0.25), residues: 418
  sheet:  None (None), residues: 0
  loop : -1.43 (0.37), residues: 192

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B 161 
 TYR   0.007   0.001   TYR A 128 
 PHE   0.012   0.001   PHE A  81 
 TRP   0.004   0.001   TRP A 295 
 HIS   0.002   0.001   HIS B  94 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00233 /  0.12 ( 6243)
  covalent geometry    : angle       0.55212 /  0.26 ( 8682)
  hydrogen bonds       : bond        0.06195 /  3.87 (  298)
  hydrogen bonds       : angle       3.63154 /  2.66 (  864)
  link_NAG-ASN         : bond        0.00157 /  0.08 (    4)
  link_NAG-ASN         : angle       1.60137 /  0.98 (   12)

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

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

  1220 Ramachandran restraints generated.
    610 Oldfield, 0 Emsley, 610 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1220 Ramachandran restraints generated.
    610 Oldfield, 0 Emsley, 610 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  73 residues out of total 542 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 54
  time to evaluate  : 0.171 
Fit side-chains
REVERT: A  197 SER cc_start: 0.7382 (m) cc_final: 0.7068 (p)
REVERT: A  271 ASN cc_start: 0.5820 (m110) cc_final: 0.5472 (t0)
REVERT: B  271 ASN cc_start: 0.5760 (m110) cc_final: 0.5510 (t0)
  outliers start: 19
  outliers final: 14
  residues processed: 70
  average time/residue: 0.3423
  time to fit residues: 25.7957
Evaluate side-chains
  64 residues out of total 542 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 50
  time to evaluate  : 0.152 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   64 LEU
Chi-restraints excluded: chain A residue  106 TYR
Chi-restraints excluded: chain A residue  114 THR
Chi-restraints excluded: chain A residue  164 LEU
Chi-restraints excluded: chain A residue  252 CYS
Chi-restraints excluded: chain A residue  264 LEU
Chi-restraints excluded: chain A residue  297 THR
Chi-restraints excluded: chain B residue   64 LEU
Chi-restraints excluded: chain B residue  106 TYR
Chi-restraints excluded: chain B residue  114 THR
Chi-restraints excluded: chain B residue  164 LEU
Chi-restraints excluded: chain B residue  252 CYS
Chi-restraints excluded: chain B residue  256 LEU
Chi-restraints excluded: chain B residue  297 THR
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 60
   random chunks:
   chunk 39 optimal weight:    3.9990
   chunk 54 optimal weight:    6.9990
   chunk 41 optimal weight:    6.9990
   chunk 30 optimal weight:    0.5980
   chunk 25 optimal weight:    3.9990
   chunk 28 optimal weight:    0.7980
   chunk 16 optimal weight:    1.9990
   chunk 0 optimal weight:   10.0000
   chunk 59 optimal weight:    1.9990
   chunk 21 optimal weight:    0.9980
   chunk 13 optimal weight:    4.9990
   overall best weight:    1.2784

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 118 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3941 r_free = 0.3941 target = 0.167699 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3379 r_free = 0.3379 target = 0.119014 restraints weight = 7047.806|
|-----------------------------------------------------------------------------|
r_work (start): 0.3279 rms_B_bonded: 1.90
r_work: 0.3116 rms_B_bonded: 3.34 restraints_weight: 0.5000
r_work (final): 0.3116
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8142
moved from start:          0.2740

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   6247  Z= 0.151
  Angle     :  0.634   9.150   8694  Z= 0.289
  Chirality :  0.039   0.234   1122
  Planarity :  0.004   0.032    879
  Dihedral  : 12.439  59.843   1114
  Min Nonbonded Distance : 2.612

Molprobity Statistics.
  All-atom Clashscore : 5.27
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.93 %
    Favored  : 96.07 %
  Rotamer:
    Outliers :  4.11 %
    Allowed  : 14.95 %
    Favored  : 80.93 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  2.02 (0.33), residues: 610
  helix:  2.57 (0.25), residues: 414
  sheet:  None (None), residues: 0
  loop : -1.53 (0.36), residues: 196

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B 161 
 TYR   0.006   0.001   TYR B  17 
 PHE   0.011   0.002   PHE B 244 
 TRP   0.004   0.001   TRP A 295 
 HIS   0.004   0.001   HIS B  94 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00328 /  0.15 ( 6243)
  covalent geometry    : angle       0.63097 /  0.29 ( 8682)
  hydrogen bonds       : bond        0.07355 /  4.59 (  298)
  hydrogen bonds       : angle       3.80650 /  2.77 (  864)
  link_NAG-ASN         : bond        0.00049 /  0.02 (    4)
  link_NAG-ASN         : angle       1.86268 /  1.14 (   12)

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

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

  1220 Ramachandran restraints generated.
    610 Oldfield, 0 Emsley, 610 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1220 Ramachandran restraints generated.
    610 Oldfield, 0 Emsley, 610 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  75 residues out of total 542 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 53
  time to evaluate  : 0.122 
Fit side-chains
REVERT: A  197 SER cc_start: 0.7415 (m) cc_final: 0.7198 (p)
REVERT: A  271 ASN cc_start: 0.5764 (m110) cc_final: 0.5433 (t0)
REVERT: B  271 ASN cc_start: 0.5763 (m110) cc_final: 0.5484 (t0)
  outliers start: 22
  outliers final: 18
  residues processed: 70
  average time/residue: 0.3096
  time to fit residues: 23.3539
Evaluate side-chains
  69 residues out of total 542 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 51
  time to evaluate  : 0.325 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   64 LEU
Chi-restraints excluded: chain A residue  106 TYR
Chi-restraints excluded: chain A residue  114 THR
Chi-restraints excluded: chain A residue  136 VAL
Chi-restraints excluded: chain A residue  164 LEU
Chi-restraints excluded: chain A residue  191 VAL
Chi-restraints excluded: chain A residue  252 CYS
Chi-restraints excluded: chain A residue  264 LEU
Chi-restraints excluded: chain A residue  297 THR
Chi-restraints excluded: chain B residue   64 LEU
Chi-restraints excluded: chain B residue  106 TYR
Chi-restraints excluded: chain B residue  114 THR
Chi-restraints excluded: chain B residue  136 VAL
Chi-restraints excluded: chain B residue  164 LEU
Chi-restraints excluded: chain B residue  191 VAL
Chi-restraints excluded: chain B residue  252 CYS
Chi-restraints excluded: chain B residue  256 LEU
Chi-restraints excluded: chain B residue  297 THR
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 60
   random chunks:
   chunk 33 optimal weight:    0.7980
   chunk 26 optimal weight:    1.9990
   chunk 9 optimal weight:    3.9990
   chunk 13 optimal weight:    0.7980
   chunk 14 optimal weight:    2.9990
   chunk 16 optimal weight:    1.9990
   chunk 18 optimal weight:    2.9990
   chunk 22 optimal weight:    4.9990
   chunk 54 optimal weight:    5.9990
   chunk 30 optimal weight:    4.9990
   chunk 51 optimal weight:    2.9990
   overall best weight:    1.7186

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** A 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3916 r_free = 0.3916 target = 0.165269 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3346 r_free = 0.3346 target = 0.116392 restraints weight = 6978.923|
|-----------------------------------------------------------------------------|
r_work (start): 0.3329 rms_B_bonded: 1.89
r_work: 0.3173 rms_B_bonded: 3.32 restraints_weight: 0.5000
r_work (final): 0.3173
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8175
moved from start:          0.2966

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.039   6247  Z= 0.179
  Angle     :  0.716   9.838   8694  Z= 0.323
  Chirality :  0.042   0.241   1122
  Planarity :  0.004   0.035    879
  Dihedral  : 13.061  59.721   1114
  Min Nonbonded Distance : 2.597

Molprobity Statistics.
  All-atom Clashscore : 5.58
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.61 %
    Favored  : 96.39 %
  Rotamer:
    Outliers :  4.30 %
    Allowed  : 15.70 %
    Favored  : 80.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.82 (0.33), residues: 610
  helix:  2.47 (0.25), residues: 412
  sheet:  None (None), residues: 0
  loop : -1.70 (0.35), residues: 198

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG A  74 
 TYR   0.007   0.001   TYR B  17 
 PHE   0.011   0.002   PHE B  55 
 TRP   0.005   0.001   TRP B 295 
 HIS   0.004   0.001   HIS A  94 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00398 /  0.18 ( 6243)
  covalent geometry    : angle       0.71255 /  0.32 ( 8682)
  hydrogen bonds       : bond        0.08331 /  5.22 (  298)
  hydrogen bonds       : angle       3.98215 /  2.89 (  864)
  link_NAG-ASN         : bond        0.00118 /  0.06 (    4)
  link_NAG-ASN         : angle       2.11085 /  1.29 (   12)

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

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

  1220 Ramachandran restraints generated.
    610 Oldfield, 0 Emsley, 610 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1220 Ramachandran restraints generated.
    610 Oldfield, 0 Emsley, 610 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  69 residues out of total 542 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 46
  time to evaluate  : 0.233 
Fit side-chains
REVERT: A  197 SER cc_start: 0.7503 (m) cc_final: 0.7302 (p)
REVERT: A  271 ASN cc_start: 0.5847 (m110) cc_final: 0.5466 (t0)
REVERT: B  271 ASN cc_start: 0.5823 (m110) cc_final: 0.5491 (t0)
  outliers start: 23
  outliers final: 21
  residues processed: 67
  average time/residue: 0.2855
  time to fit residues: 20.6706
Evaluate side-chains
  66 residues out of total 542 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 45
  time to evaluate  : 0.134 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   23 THR
Chi-restraints excluded: chain A residue   64 LEU
Chi-restraints excluded: chain A residue  106 TYR
Chi-restraints excluded: chain A residue  114 THR
Chi-restraints excluded: chain A residue  136 VAL
Chi-restraints excluded: chain A residue  164 LEU
Chi-restraints excluded: chain A residue  191 VAL
Chi-restraints excluded: chain A residue  252 CYS
Chi-restraints excluded: chain A residue  264 LEU
Chi-restraints excluded: chain A residue  267 SER
Chi-restraints excluded: chain A residue  297 THR
Chi-restraints excluded: chain B residue   23 THR
Chi-restraints excluded: chain B residue   64 LEU
Chi-restraints excluded: chain B residue  106 TYR
Chi-restraints excluded: chain B residue  114 THR
Chi-restraints excluded: chain B residue  136 VAL
Chi-restraints excluded: chain B residue  164 LEU
Chi-restraints excluded: chain B residue  191 VAL
Chi-restraints excluded: chain B residue  252 CYS
Chi-restraints excluded: chain B residue  267 SER
Chi-restraints excluded: chain B residue  297 THR
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 60
   random chunks:
   chunk 56 optimal weight:    1.9990
   chunk 10 optimal weight:    4.9990
   chunk 54 optimal weight:    7.9990
   chunk 37 optimal weight:    3.9990
   chunk 15 optimal weight:   10.0000
   chunk 43 optimal weight:    0.9990
   chunk 11 optimal weight:    3.9990
   chunk 17 optimal weight:    1.9990
   chunk 57 optimal weight:    0.7980
   chunk 35 optimal weight:    0.9990
   chunk 33 optimal weight:    0.7980
   overall best weight:    1.1186

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** A 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3934 r_free = 0.3934 target = 0.167057 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3372 r_free = 0.3372 target = 0.118377 restraints weight = 7034.227|
|-----------------------------------------------------------------------------|
r_work (start): 0.3280 rms_B_bonded: 1.89
r_work: 0.3119 rms_B_bonded: 3.33 restraints_weight: 0.5000
r_work (final): 0.3119
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8136
moved from start:          0.2928

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   6247  Z= 0.141
  Angle     :  0.623   9.978   8694  Z= 0.283
  Chirality :  0.038   0.233   1122
  Planarity :  0.004   0.033    879
  Dihedral  : 12.706  59.289   1114
  Min Nonbonded Distance : 2.611

Molprobity Statistics.
  All-atom Clashscore : 5.35
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.44 %
    Favored  : 96.56 %
  Rotamer:
    Outliers :  4.86 %
    Allowed  : 15.14 %
    Favored  : 80.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  2.11 (0.33), residues: 610
  helix:  2.69 (0.25), residues: 414
  sheet:  None (None), residues: 0
  loop : -1.62 (0.36), residues: 196

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A  74 
 TYR   0.007   0.001   TYR B 128 
 PHE   0.012   0.001   PHE B  81 
 TRP   0.005   0.001   TRP A 295 
 HIS   0.003   0.001   HIS B  94 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00294 /  0.14 ( 6243)
  covalent geometry    : angle       0.62001 /  0.28 ( 8682)
  hydrogen bonds       : bond        0.07081 /  4.42 (  298)
  hydrogen bonds       : angle       3.79945 /  2.77 (  864)
  link_NAG-ASN         : bond        0.00043 /  0.02 (    4)
  link_NAG-ASN         : angle       1.85567 /  1.15 (   12)

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

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

  1220 Ramachandran restraints generated.
    610 Oldfield, 0 Emsley, 610 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1220 Ramachandran restraints generated.
    610 Oldfield, 0 Emsley, 610 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  75 residues out of total 542 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 49
  time to evaluate  : 0.140 
Fit side-chains
REVERT: A   98 TYR cc_start: 0.8980 (OUTLIER) cc_final: 0.8779 (t80)
REVERT: A  197 SER cc_start: 0.7461 (m) cc_final: 0.7234 (p)
REVERT: A  271 ASN cc_start: 0.5835 (m110) cc_final: 0.5452 (t0)
REVERT: B  271 ASN cc_start: 0.5842 (m110) cc_final: 0.5493 (t0)
  outliers start: 26
  outliers final: 19
  residues processed: 73
  average time/residue: 0.3032
  time to fit residues: 23.8934
Evaluate side-chains
  69 residues out of total 542 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 49
  time to evaluate  : 0.191 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   64 LEU
Chi-restraints excluded: chain A residue   98 TYR
Chi-restraints excluded: chain A residue  106 TYR
Chi-restraints excluded: chain A residue  114 THR
Chi-restraints excluded: chain A residue  136 VAL
Chi-restraints excluded: chain A residue  164 LEU
Chi-restraints excluded: chain A residue  191 VAL
Chi-restraints excluded: chain A residue  252 CYS
Chi-restraints excluded: chain A residue  264 LEU
Chi-restraints excluded: chain A residue  267 SER
Chi-restraints excluded: chain A residue  297 THR
Chi-restraints excluded: chain B residue   64 LEU
Chi-restraints excluded: chain B residue  106 TYR
Chi-restraints excluded: chain B residue  114 THR
Chi-restraints excluded: chain B residue  136 VAL
Chi-restraints excluded: chain B residue  164 LEU
Chi-restraints excluded: chain B residue  191 VAL
Chi-restraints excluded: chain B residue  252 CYS
Chi-restraints excluded: chain B residue  267 SER
Chi-restraints excluded: chain B residue  297 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 60
   random chunks:
   chunk 38 optimal weight:    0.7980
   chunk 28 optimal weight:    0.9980
   chunk 58 optimal weight:    3.9990
   chunk 29 optimal weight:    0.5980
   chunk 39 optimal weight:    2.9990
   chunk 41 optimal weight:    2.9990
   chunk 10 optimal weight:    4.9990
   chunk 27 optimal weight:    4.9990
   chunk 49 optimal weight:    0.9980
   chunk 3 optimal weight:    0.6980
   chunk 6 optimal weight:    0.9990
   overall best weight:    0.8180

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** A 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3967 r_free = 0.3967 target = 0.170348 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 53)----------------|
| r_work = 0.3432 r_free = 0.3432 target = 0.122789 restraints weight = 7057.116|
|-----------------------------------------------------------------------------|
r_work (start): 0.3314 rms_B_bonded: 1.86
r_work: 0.3153 rms_B_bonded: 3.31 restraints_weight: 0.5000
r_work (final): 0.3153
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8110
moved from start:          0.2944

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   6247  Z= 0.125
  Angle     :  0.586  10.851   8694  Z= 0.268
  Chirality :  0.037   0.239   1122
  Planarity :  0.004   0.033    879
  Dihedral  : 12.277  59.489   1114
  Min Nonbonded Distance : 2.617

Molprobity Statistics.
  All-atom Clashscore : 5.43
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.44 %
    Favored  : 96.56 %
  Rotamer:
    Outliers :  3.74 %
    Allowed  : 16.26 %
    Favored  : 80.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  2.48 (0.34), residues: 610
  helix:  2.98 (0.25), residues: 412
  sheet:  None (None), residues: 0
  loop : -1.45 (0.36), residues: 198

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B 161 
 TYR   0.007   0.001   TYR B 128 
 PHE   0.012   0.001   PHE A  81 
 TRP   0.006   0.001   TRP B  70 
 HIS   0.002   0.001   HIS A  94 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00255 /  0.13 ( 6243)
  covalent geometry    : angle       0.58311 /  0.27 ( 8682)
  hydrogen bonds       : bond        0.06361 /  3.97 (  298)
  hydrogen bonds       : angle       3.68657 /  2.69 (  864)
  link_NAG-ASN         : bond        0.00087 /  0.04 (    4)
  link_NAG-ASN         : angle       1.65415 /  1.00 (   12)

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

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

  1220 Ramachandran restraints generated.
    610 Oldfield, 0 Emsley, 610 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1220 Ramachandran restraints generated.
    610 Oldfield, 0 Emsley, 610 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  70 residues out of total 542 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 50
  time to evaluate  : 0.192 
Fit side-chains
REVERT: A  197 SER cc_start: 0.7301 (m) cc_final: 0.7098 (p)
REVERT: A  271 ASN cc_start: 0.5922 (m110) cc_final: 0.5576 (t0)
REVERT: B  271 ASN cc_start: 0.5920 (m110) cc_final: 0.5569 (t0)
  outliers start: 20
  outliers final: 19
  residues processed: 68
  average time/residue: 0.2712
  time to fit residues: 19.9848
Evaluate side-chains
  68 residues out of total 542 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 49
  time to evaluate  : 0.174 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   64 LEU
Chi-restraints excluded: chain A residue  106 TYR
Chi-restraints excluded: chain A residue  114 THR
Chi-restraints excluded: chain A residue  136 VAL
Chi-restraints excluded: chain A residue  164 LEU
Chi-restraints excluded: chain A residue  191 VAL
Chi-restraints excluded: chain A residue  252 CYS
Chi-restraints excluded: chain A residue  264 LEU
Chi-restraints excluded: chain A residue  267 SER
Chi-restraints excluded: chain A residue  297 THR
Chi-restraints excluded: chain B residue   64 LEU
Chi-restraints excluded: chain B residue  106 TYR
Chi-restraints excluded: chain B residue  114 THR
Chi-restraints excluded: chain B residue  136 VAL
Chi-restraints excluded: chain B residue  164 LEU
Chi-restraints excluded: chain B residue  191 VAL
Chi-restraints excluded: chain B residue  252 CYS
Chi-restraints excluded: chain B residue  267 SER
Chi-restraints excluded: chain B residue  297 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 60
   random chunks:
   chunk 20 optimal weight:    3.9990
   chunk 5 optimal weight:    3.9990
   chunk 49 optimal weight:    0.8980
   chunk 53 optimal weight:    2.9990
   chunk 32 optimal weight:    0.1980
   chunk 37 optimal weight:    3.9990
   chunk 41 optimal weight:    0.9980
   chunk 23 optimal weight:    6.9990
   chunk 39 optimal weight:    2.9990
   chunk 11 optimal weight:    4.9990
   chunk 44 optimal weight:    1.9990
   overall best weight:    1.4184

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** A 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3935 r_free = 0.3935 target = 0.167307 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3374 r_free = 0.3374 target = 0.118640 restraints weight = 6969.074|
|-----------------------------------------------------------------------------|
r_work (start): 0.3268 rms_B_bonded: 1.88
r_work: 0.3104 rms_B_bonded: 3.33 restraints_weight: 0.5000
r_work (final): 0.3104
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8154
moved from start:          0.3049

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.038   6247  Z= 0.160
  Angle     :  0.667  10.333   8694  Z= 0.301
  Chirality :  0.040   0.230   1122
  Planarity :  0.004   0.033    879
  Dihedral  : 12.806  59.799   1114
  Min Nonbonded Distance : 2.609

Molprobity Statistics.
  All-atom Clashscore : 5.35
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.77 %
    Favored  : 96.23 %
  Rotamer:
    Outliers :  3.93 %
    Allowed  : 16.26 %
    Favored  : 79.81 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  2.18 (0.33), residues: 610
  helix:  2.72 (0.25), residues: 414
  sheet:  None (None), residues: 0
  loop : -1.54 (0.36), residues: 196

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B 161 
 TYR   0.006   0.001   TYR B  26 
 PHE   0.011   0.002   PHE B  55 
 TRP   0.004   0.001   TRP A 295 
 HIS   0.003   0.001   HIS A  94 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00351 /  0.16 ( 6243)
  covalent geometry    : angle       0.66326 /  0.30 ( 8682)
  hydrogen bonds       : bond        0.07642 /  4.78 (  298)
  hydrogen bonds       : angle       3.89237 /  2.83 (  864)
  link_NAG-ASN         : bond        0.00049 /  0.03 (    4)
  link_NAG-ASN         : angle       1.94704 /  1.20 (   12)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1605.43 seconds
wall clock time: 28 minutes 10.08 seconds (1690.08 seconds total)