Starting phenix.real_space_refine
on Sun May 25 22:48:56 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8bhb_16051/05_2025/8bhb_16051_trim.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8bhb_16051/05_2025/8bhb_16051.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.54
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8bhb_16051/05_2025/8bhb_16051.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8bhb_16051/05_2025/8bhb_16051.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8bhb_16051/05_2025/8bhb_16051_trim.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8bhb_16051/05_2025/8bhb_16051_trim.cif"
  }
  resolution = 2.54
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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=   0.001 sd=   0.009
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 5
    Type Number    sf(0)   Gaussians
     S      85      5.16       5
     C    8910      2.51       5
     N    2290      2.21       5
     O    2550      1.98       5
     H   13415      0.53       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model
  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib"
  Total number of atoms: 27250
  Number of models: 1
  Model: ""
    Number of chains: 7
    Chain: "A"
      Number of atoms: 5399
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 336, 5399
          Classifications: {'peptide': 336}
          Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 13, 'TRANS': 320}
    Chain: "A"
      Number of atoms: 38
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 38
          Unusual residues: {'EIE': 1, 'NAG': 1}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
          Unresolved non-hydrogen bonds: 1
          Unresolved non-hydrogen angles: 2
          Unresolved non-hydrogen dihedrals: 3
          Unresolved non-hydrogen chiralities: 1
    Chain: "A"
      Number of atoms: 13
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 13, 13
          Classifications: {'water': 13}
          Link IDs: {None: 12}
    Chain: "B"
      Number of atoms: 13
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 13, 13
          Classifications: {'water': 13}
          Link IDs: {None: 12}
    Chain: "C"
      Number of atoms: 13
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 13, 13
          Classifications: {'water': 13}
          Link IDs: {None: 12}
    Chain: "D"
      Number of atoms: 13
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 13, 13
          Classifications: {'water': 13}
          Link IDs: {None: 12}
    Chain: "E"
      Number of atoms: 13
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 13, 13
          Classifications: {'water': 13}
          Link IDs: {None: 12}
  Restraints were copied for chains:
    C, B, E, D
  Time building chain proxies: 15.79, per 1000 atoms: 0.58
  Number of scatterers: 27250
  At special positions: 0
  Unit cell: (90.628, 93.888, 123.228, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S      85     16.00
     O    2550      8.00
     N    2290      7.00
     C    8910      6.00
     H   13415      1.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=5, symmetry=0
    Simple disulfide: pdb=" SG  CYS A 142 " - pdb=" SG  CYS A 156 " distance=2.03
    Simple disulfide: pdb=" SG  CYS C 142 " - pdb=" SG  CYS C 156 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 142 " - pdb=" SG  CYS B 156 " distance=2.03
    Simple disulfide: pdb=" SG  CYS E 142 " - pdb=" SG  CYS E 156 " distance=2.03
    Simple disulfide: pdb=" SG  CYS D 142 " - pdb=" SG  CYS D 156 " 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
    NAG-ASN
      " NAG A 501 " - " ASN A 205 "
      " NAG B 501 " - " ASN B 205 "
      " NAG C 501 " - " ASN C 205 "
      " NAG D 501 " - " ASN D 205 "
      " NAG E 501 " - " ASN E 205 "
  Time building additional restraints: 7.56
  Conformation dependent library (CDL) restraints added in 2.2 seconds
  

  3340 Ramachandran restraints generated.
    1670 Oldfield, 0 Emsley, 1670 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  3190

  Finding SS restraints...
    Secondary structure from input PDB file:
      50 helices and 15 sheets defined
      41.4% alpha, 39.3% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 2.94
  Creating SS restraints...
    Processing helix  chain 'A' and resid 15 through 27
      removed outlier: 3.573A  pdb=" N   THR A  19 " --> pdb=" O   ILE A  15 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 76 through 79
    Processing helix  chain 'A' and resid 90 through 94
      removed outlier: 3.577A  pdb=" N   LEU A  93 " --> pdb=" O   ASN A  90 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 177 through 181
    Processing helix  chain 'A' and resid 227 through 233
    Processing helix  chain 'A' and resid 233 through 246
    Processing helix  chain 'A' and resid 247 through 250
    Processing helix  chain 'A' and resid 254 through 280
      removed outlier: 4.147A  pdb=" N   SER A 279 " --> pdb=" O   SER A 275 " (cutoff:3.500A)
      removed outlier: 3.742A  pdb=" N   LEU A 280 " --> pdb=" O   ALA A 276 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 287 through 314
    Processing helix  chain 'A' and resid 317 through 418
      removed outlier: 4.033A  pdb=" N   ILE A 400 " --> pdb=" O   LYS A 396 " (cutoff:3.500A)
      Proline residue:  A 403  - end of helix
    Processing helix  chain 'B' and resid 15 through 27
      removed outlier: 3.573A  pdb=" N   THR B  19 " --> pdb=" O   ILE B  15 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 76 through 79
    Processing helix  chain 'B' and resid 90 through 94
      removed outlier: 3.576A  pdb=" N   LEU B  93 " --> pdb=" O   ASN B  90 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 177 through 181
    Processing helix  chain 'B' and resid 227 through 233
    Processing helix  chain 'B' and resid 233 through 246
    Processing helix  chain 'B' and resid 247 through 250
    Processing helix  chain 'B' and resid 254 through 280
      removed outlier: 4.147A  pdb=" N   SER B 279 " --> pdb=" O   SER B 275 " (cutoff:3.500A)
      removed outlier: 3.741A  pdb=" N   LEU B 280 " --> pdb=" O   ALA B 276 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 287 through 314
    Processing helix  chain 'B' and resid 317 through 418
      removed outlier: 4.033A  pdb=" N   ILE B 400 " --> pdb=" O   LYS B 396 " (cutoff:3.500A)
      Proline residue:  B 403  - end of helix
    Processing helix  chain 'C' and resid 15 through 27
      removed outlier: 3.574A  pdb=" N   THR C  19 " --> pdb=" O   ILE C  15 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 76 through 79
    Processing helix  chain 'C' and resid 90 through 94
      removed outlier: 3.577A  pdb=" N   LEU C  93 " --> pdb=" O   ASN C  90 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 177 through 181
    Processing helix  chain 'C' and resid 227 through 233
    Processing helix  chain 'C' and resid 233 through 246
    Processing helix  chain 'C' and resid 247 through 250
    Processing helix  chain 'C' and resid 254 through 280
      removed outlier: 4.148A  pdb=" N   SER C 279 " --> pdb=" O   SER C 275 " (cutoff:3.500A)
      removed outlier: 3.743A  pdb=" N   LEU C 280 " --> pdb=" O   ALA C 276 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 287 through 314
    Processing helix  chain 'C' and resid 317 through 418
      removed outlier: 4.033A  pdb=" N   ILE C 400 " --> pdb=" O   LYS C 396 " (cutoff:3.500A)
      Proline residue:  C 403  - end of helix
    Processing helix  chain 'D' and resid 15 through 27
      removed outlier: 3.573A  pdb=" N   THR D  19 " --> pdb=" O   ILE D  15 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 76 through 79
    Processing helix  chain 'D' and resid 90 through 94
      removed outlier: 3.577A  pdb=" N   LEU D  93 " --> pdb=" O   ASN D  90 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 177 through 181
    Processing helix  chain 'D' and resid 227 through 233
    Processing helix  chain 'D' and resid 233 through 246
    Processing helix  chain 'D' and resid 247 through 250
    Processing helix  chain 'D' and resid 254 through 280
      removed outlier: 4.147A  pdb=" N   SER D 279 " --> pdb=" O   SER D 275 " (cutoff:3.500A)
      removed outlier: 3.742A  pdb=" N   LEU D 280 " --> pdb=" O   ALA D 276 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 287 through 314
    Processing helix  chain 'D' and resid 317 through 418
      removed outlier: 4.034A  pdb=" N   ILE D 400 " --> pdb=" O   LYS D 396 " (cutoff:3.500A)
      Proline residue:  D 403  - end of helix
    Processing helix  chain 'E' and resid 15 through 27
      removed outlier: 3.573A  pdb=" N   THR E  19 " --> pdb=" O   ILE E  15 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 76 through 79
    Processing helix  chain 'E' and resid 90 through 94
      removed outlier: 3.577A  pdb=" N   LEU E  93 " --> pdb=" O   ASN E  90 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 177 through 181
    Processing helix  chain 'E' and resid 227 through 233
    Processing helix  chain 'E' and resid 233 through 246
    Processing helix  chain 'E' and resid 247 through 250
    Processing helix  chain 'E' and resid 254 through 280
      removed outlier: 4.147A  pdb=" N   SER E 279 " --> pdb=" O   SER E 275 " (cutoff:3.500A)
      removed outlier: 3.742A  pdb=" N   LEU E 280 " --> pdb=" O   ALA E 276 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 287 through 314
    Processing helix  chain 'E' and resid 317 through 418
      removed outlier: 4.033A  pdb=" N   ILE E 400 " --> pdb=" O   LYS E 396 " (cutoff:3.500A)
      Proline residue:  E 403  - end of helix
    Processing sheet with id=AA1, first strand: chain 'A' and resid 86 through 88
      removed outlier: 3.613A  pdb=" N   ILE A 124 " --> pdb=" O   LEU A  87 " (cutoff:3.500A)
      removed outlier: 4.367A  pdb=" N   ARG A 129 " --> pdb=" O   TRP A 125 " (cutoff:3.500A)
      removed outlier: 7.010A  pdb=" N   GLU A  62 " --> pdb=" O   PRO A  55 " (cutoff:3.500A)
      removed outlier: 6.637A  pdb=" N   THR A  64 " --> pdb=" O   PHE A  53 " (cutoff:3.500A)
      removed outlier: 5.171A  pdb=" N   PHE A  53 " --> pdb=" O   THR A  64 " (cutoff:3.500A)
      removed outlier: 6.901A  pdb=" N   ASP A  66 " --> pdb=" O   ASN A  51 " (cutoff:3.500A)
      removed outlier: 4.455A  pdb=" N   LYS A  74 " --> pdb=" O   GLN A  43 " (cutoff:3.500A)
      removed outlier: 6.437A  pdb=" N   GLN A  43 " --> pdb=" O   LYS A  74 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 107 through 112
      removed outlier: 7.067A  pdb=" N   SER A 139 " --> pdb=" O   LYS A 108 " (cutoff:3.500A)
      removed outlier: 4.664A  pdb=" N   SER A 110 " --> pdb=" O   THR A 137 " (cutoff:3.500A)
      removed outlier: 6.813A  pdb=" N   THR A 137 " --> pdb=" O   SER A 110 " (cutoff:3.500A)
      removed outlier: 5.273A  pdb=" N   ALA A 112 " --> pdb=" O   ARG A 135 " (cutoff:3.500A)
      removed outlier: 8.425A  pdb=" N   ARG A 135 " --> pdb=" O   ALA A 112 " (cutoff:3.500A)
      removed outlier: 7.010A  pdb=" N   GLU A  62 " --> pdb=" O   PRO A  55 " (cutoff:3.500A)
      removed outlier: 6.637A  pdb=" N   THR A  64 " --> pdb=" O   PHE A  53 " (cutoff:3.500A)
      removed outlier: 5.171A  pdb=" N   PHE A  53 " --> pdb=" O   THR A  64 " (cutoff:3.500A)
      removed outlier: 6.901A  pdb=" N   ASP A  66 " --> pdb=" O   ASN A  51 " (cutoff:3.500A)
      removed outlier: 4.455A  pdb=" N   LYS A  74 " --> pdb=" O   GLN A  43 " (cutoff:3.500A)
      removed outlier: 6.437A  pdb=" N   GLN A  43 " --> pdb=" O   LYS A  74 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 102 through 104
      removed outlier: 4.780A  pdb=" N   SER A 162 " --> pdb=" O   THR A 214 " (cutoff:3.500A)
      removed outlier: 6.614A  pdb=" N   THR A 214 " --> pdb=" O   SER A 162 " (cutoff:3.500A)
      removed outlier: 3.936A  pdb=" N   GLY A 198 " --> pdb=" O   HIS A 221 " (cutoff:3.500A)
      removed outlier: 7.006A  pdb=" N   LYS A 223 " --> pdb=" O   LEU A 196 " (cutoff:3.500A)
      removed outlier: 5.573A  pdb=" N   LEU A 196 " --> pdb=" O   LYS A 223 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'B' and resid 86 through 88
      removed outlier: 3.612A  pdb=" N   ILE B 124 " --> pdb=" O   LEU B  87 " (cutoff:3.500A)
      removed outlier: 4.369A  pdb=" N   ARG B 129 " --> pdb=" O   TRP B 125 " (cutoff:3.500A)
      removed outlier: 7.010A  pdb=" N   GLU B  62 " --> pdb=" O   PRO B  55 " (cutoff:3.500A)
      removed outlier: 6.637A  pdb=" N   THR B  64 " --> pdb=" O   PHE B  53 " (cutoff:3.500A)
      removed outlier: 5.170A  pdb=" N   PHE B  53 " --> pdb=" O   THR B  64 " (cutoff:3.500A)
      removed outlier: 6.901A  pdb=" N   ASP B  66 " --> pdb=" O   ASN B  51 " (cutoff:3.500A)
      removed outlier: 4.454A  pdb=" N   LYS B  74 " --> pdb=" O   GLN B  43 " (cutoff:3.500A)
      removed outlier: 6.438A  pdb=" N   GLN B  43 " --> pdb=" O   LYS B  74 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'B' and resid 107 through 112
      removed outlier: 7.067A  pdb=" N   SER B 139 " --> pdb=" O   LYS B 108 " (cutoff:3.500A)
      removed outlier: 4.665A  pdb=" N   SER B 110 " --> pdb=" O   THR B 137 " (cutoff:3.500A)
      removed outlier: 6.812A  pdb=" N   THR B 137 " --> pdb=" O   SER B 110 " (cutoff:3.500A)
      removed outlier: 5.273A  pdb=" N   ALA B 112 " --> pdb=" O   ARG B 135 " (cutoff:3.500A)
      removed outlier: 8.425A  pdb=" N   ARG B 135 " --> pdb=" O   ALA B 112 " (cutoff:3.500A)
      removed outlier: 7.010A  pdb=" N   GLU B  62 " --> pdb=" O   PRO B  55 " (cutoff:3.500A)
      removed outlier: 6.637A  pdb=" N   THR B  64 " --> pdb=" O   PHE B  53 " (cutoff:3.500A)
      removed outlier: 5.170A  pdb=" N   PHE B  53 " --> pdb=" O   THR B  64 " (cutoff:3.500A)
      removed outlier: 6.901A  pdb=" N   ASP B  66 " --> pdb=" O   ASN B  51 " (cutoff:3.500A)
      removed outlier: 4.454A  pdb=" N   LYS B  74 " --> pdb=" O   GLN B  43 " (cutoff:3.500A)
      removed outlier: 6.438A  pdb=" N   GLN B  43 " --> pdb=" O   LYS B  74 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'B' and resid 102 through 104
      removed outlier: 4.780A  pdb=" N   SER B 162 " --> pdb=" O   THR B 214 " (cutoff:3.500A)
      removed outlier: 6.615A  pdb=" N   THR B 214 " --> pdb=" O   SER B 162 " (cutoff:3.500A)
      removed outlier: 3.936A  pdb=" N   GLY B 198 " --> pdb=" O   HIS B 221 " (cutoff:3.500A)
      removed outlier: 7.006A  pdb=" N   LYS B 223 " --> pdb=" O   LEU B 196 " (cutoff:3.500A)
      removed outlier: 5.573A  pdb=" N   LEU B 196 " --> pdb=" O   LYS B 223 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'C' and resid 86 through 88
      removed outlier: 3.612A  pdb=" N   ILE C 124 " --> pdb=" O   LEU C  87 " (cutoff:3.500A)
      removed outlier: 4.369A  pdb=" N   ARG C 129 " --> pdb=" O   TRP C 125 " (cutoff:3.500A)
      removed outlier: 7.010A  pdb=" N   GLU C  62 " --> pdb=" O   PRO C  55 " (cutoff:3.500A)
      removed outlier: 6.637A  pdb=" N   THR C  64 " --> pdb=" O   PHE C  53 " (cutoff:3.500A)
      removed outlier: 5.170A  pdb=" N   PHE C  53 " --> pdb=" O   THR C  64 " (cutoff:3.500A)
      removed outlier: 6.902A  pdb=" N   ASP C  66 " --> pdb=" O   ASN C  51 " (cutoff:3.500A)
      removed outlier: 4.454A  pdb=" N   LYS C  74 " --> pdb=" O   GLN C  43 " (cutoff:3.500A)
      removed outlier: 6.437A  pdb=" N   GLN C  43 " --> pdb=" O   LYS C  74 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'C' and resid 107 through 112
      removed outlier: 7.068A  pdb=" N   SER C 139 " --> pdb=" O   LYS C 108 " (cutoff:3.500A)
      removed outlier: 4.665A  pdb=" N   SER C 110 " --> pdb=" O   THR C 137 " (cutoff:3.500A)
      removed outlier: 6.813A  pdb=" N   THR C 137 " --> pdb=" O   SER C 110 " (cutoff:3.500A)
      removed outlier: 5.273A  pdb=" N   ALA C 112 " --> pdb=" O   ARG C 135 " (cutoff:3.500A)
      removed outlier: 8.425A  pdb=" N   ARG C 135 " --> pdb=" O   ALA C 112 " (cutoff:3.500A)
      removed outlier: 7.010A  pdb=" N   GLU C  62 " --> pdb=" O   PRO C  55 " (cutoff:3.500A)
      removed outlier: 6.637A  pdb=" N   THR C  64 " --> pdb=" O   PHE C  53 " (cutoff:3.500A)
      removed outlier: 5.170A  pdb=" N   PHE C  53 " --> pdb=" O   THR C  64 " (cutoff:3.500A)
      removed outlier: 6.902A  pdb=" N   ASP C  66 " --> pdb=" O   ASN C  51 " (cutoff:3.500A)
      removed outlier: 4.454A  pdb=" N   LYS C  74 " --> pdb=" O   GLN C  43 " (cutoff:3.500A)
      removed outlier: 6.437A  pdb=" N   GLN C  43 " --> pdb=" O   LYS C  74 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'C' and resid 102 through 104
      removed outlier: 4.780A  pdb=" N   SER C 162 " --> pdb=" O   THR C 214 " (cutoff:3.500A)
      removed outlier: 6.614A  pdb=" N   THR C 214 " --> pdb=" O   SER C 162 " (cutoff:3.500A)
      removed outlier: 3.936A  pdb=" N   GLY C 198 " --> pdb=" O   HIS C 221 " (cutoff:3.500A)
      removed outlier: 7.007A  pdb=" N   LYS C 223 " --> pdb=" O   LEU C 196 " (cutoff:3.500A)
      removed outlier: 5.573A  pdb=" N   LEU C 196 " --> pdb=" O   LYS C 223 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'D' and resid 86 through 88
      removed outlier: 3.613A  pdb=" N   ILE D 124 " --> pdb=" O   LEU D  87 " (cutoff:3.500A)
      removed outlier: 4.368A  pdb=" N   ARG D 129 " --> pdb=" O   TRP D 125 " (cutoff:3.500A)
      removed outlier: 7.010A  pdb=" N   GLU D  62 " --> pdb=" O   PRO D  55 " (cutoff:3.500A)
      removed outlier: 6.637A  pdb=" N   THR D  64 " --> pdb=" O   PHE D  53 " (cutoff:3.500A)
      removed outlier: 5.171A  pdb=" N   PHE D  53 " --> pdb=" O   THR D  64 " (cutoff:3.500A)
      removed outlier: 6.902A  pdb=" N   ASP D  66 " --> pdb=" O   ASN D  51 " (cutoff:3.500A)
      removed outlier: 4.454A  pdb=" N   LYS D  74 " --> pdb=" O   GLN D  43 " (cutoff:3.500A)
      removed outlier: 6.438A  pdb=" N   GLN D  43 " --> pdb=" O   LYS D  74 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'D' and resid 107 through 112
      removed outlier: 7.068A  pdb=" N   SER D 139 " --> pdb=" O   LYS D 108 " (cutoff:3.500A)
      removed outlier: 4.665A  pdb=" N   SER D 110 " --> pdb=" O   THR D 137 " (cutoff:3.500A)
      removed outlier: 6.813A  pdb=" N   THR D 137 " --> pdb=" O   SER D 110 " (cutoff:3.500A)
      removed outlier: 5.274A  pdb=" N   ALA D 112 " --> pdb=" O   ARG D 135 " (cutoff:3.500A)
      removed outlier: 8.425A  pdb=" N   ARG D 135 " --> pdb=" O   ALA D 112 " (cutoff:3.500A)
      removed outlier: 7.010A  pdb=" N   GLU D  62 " --> pdb=" O   PRO D  55 " (cutoff:3.500A)
      removed outlier: 6.637A  pdb=" N   THR D  64 " --> pdb=" O   PHE D  53 " (cutoff:3.500A)
      removed outlier: 5.171A  pdb=" N   PHE D  53 " --> pdb=" O   THR D  64 " (cutoff:3.500A)
      removed outlier: 6.902A  pdb=" N   ASP D  66 " --> pdb=" O   ASN D  51 " (cutoff:3.500A)
      removed outlier: 4.454A  pdb=" N   LYS D  74 " --> pdb=" O   GLN D  43 " (cutoff:3.500A)
      removed outlier: 6.438A  pdb=" N   GLN D  43 " --> pdb=" O   LYS D  74 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'D' and resid 102 through 104
      removed outlier: 4.780A  pdb=" N   SER D 162 " --> pdb=" O   THR D 214 " (cutoff:3.500A)
      removed outlier: 6.614A  pdb=" N   THR D 214 " --> pdb=" O   SER D 162 " (cutoff:3.500A)
      removed outlier: 3.936A  pdb=" N   GLY D 198 " --> pdb=" O   HIS D 221 " (cutoff:3.500A)
      removed outlier: 7.006A  pdb=" N   LYS D 223 " --> pdb=" O   LEU D 196 " (cutoff:3.500A)
      removed outlier: 5.572A  pdb=" N   LEU D 196 " --> pdb=" O   LYS D 223 " (cutoff:3.500A)
    Processing sheet with id=AB4, first strand: chain 'E' and resid 86 through 88
      removed outlier: 3.612A  pdb=" N   ILE E 124 " --> pdb=" O   LEU E  87 " (cutoff:3.500A)
      removed outlier: 4.367A  pdb=" N   ARG E 129 " --> pdb=" O   TRP E 125 " (cutoff:3.500A)
      removed outlier: 7.010A  pdb=" N   GLU E  62 " --> pdb=" O   PRO E  55 " (cutoff:3.500A)
      removed outlier: 6.637A  pdb=" N   THR E  64 " --> pdb=" O   PHE E  53 " (cutoff:3.500A)
      removed outlier: 5.170A  pdb=" N   PHE E  53 " --> pdb=" O   THR E  64 " (cutoff:3.500A)
      removed outlier: 6.902A  pdb=" N   ASP E  66 " --> pdb=" O   ASN E  51 " (cutoff:3.500A)
      removed outlier: 4.455A  pdb=" N   LYS E  74 " --> pdb=" O   GLN E  43 " (cutoff:3.500A)
      removed outlier: 6.438A  pdb=" N   GLN E  43 " --> pdb=" O   LYS E  74 " (cutoff:3.500A)
    Processing sheet with id=AB5, first strand: chain 'E' and resid 107 through 112
      removed outlier: 7.067A  pdb=" N   SER E 139 " --> pdb=" O   LYS E 108 " (cutoff:3.500A)
      removed outlier: 4.666A  pdb=" N   SER E 110 " --> pdb=" O   THR E 137 " (cutoff:3.500A)
      removed outlier: 6.814A  pdb=" N   THR E 137 " --> pdb=" O   SER E 110 " (cutoff:3.500A)
      removed outlier: 5.274A  pdb=" N   ALA E 112 " --> pdb=" O   ARG E 135 " (cutoff:3.500A)
      removed outlier: 8.425A  pdb=" N   ARG E 135 " --> pdb=" O   ALA E 112 " (cutoff:3.500A)
      removed outlier: 7.010A  pdb=" N   GLU E  62 " --> pdb=" O   PRO E  55 " (cutoff:3.500A)
      removed outlier: 6.637A  pdb=" N   THR E  64 " --> pdb=" O   PHE E  53 " (cutoff:3.500A)
      removed outlier: 5.170A  pdb=" N   PHE E  53 " --> pdb=" O   THR E  64 " (cutoff:3.500A)
      removed outlier: 6.902A  pdb=" N   ASP E  66 " --> pdb=" O   ASN E  51 " (cutoff:3.500A)
      removed outlier: 4.455A  pdb=" N   LYS E  74 " --> pdb=" O   GLN E  43 " (cutoff:3.500A)
      removed outlier: 6.438A  pdb=" N   GLN E  43 " --> pdb=" O   LYS E  74 " (cutoff:3.500A)
    Processing sheet with id=AB6, first strand: chain 'E' and resid 102 through 104
      removed outlier: 4.780A  pdb=" N   SER E 162 " --> pdb=" O   THR E 214 " (cutoff:3.500A)
      removed outlier: 6.614A  pdb=" N   THR E 214 " --> pdb=" O   SER E 162 " (cutoff:3.500A)
      removed outlier: 3.936A  pdb=" N   GLY E 198 " --> pdb=" O   HIS E 221 " (cutoff:3.500A)
      removed outlier: 7.007A  pdb=" N   LYS E 223 " --> pdb=" O   LEU E 196 " (cutoff:3.500A)
      removed outlier: 5.573A  pdb=" N   LEU E 196 " --> pdb=" O   LYS E 223 " (cutoff:3.500A)

    830 hydrogen bonds defined for protein.
    2430 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: 11.01

  Time building geometry restraints manager: 9.09 seconds

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

  Histogram of bond lengths:
        0.84 -     1.03: 13415
        1.03 -     1.23: 18
        1.23 -     1.42: 6102
        1.42 -     1.62: 7870
        1.62 -     1.81: 150
  Bond restraints: 27555
  Sorted by residual:
  bond pdb=" N   ASN B  14 "
       pdb=" H   ASN B  14 "
    ideal  model  delta    sigma   weight residual
    0.860  0.960 -0.100 2.00e-02 2.50e+03 2.49e+01
  bond pdb=" N   ASN D  14 "
       pdb=" H   ASN D  14 "
    ideal  model  delta    sigma   weight residual
    0.860  0.960 -0.100 2.00e-02 2.50e+03 2.48e+01
  bond pdb=" N   ASN E  14 "
       pdb=" H   ASN E  14 "
    ideal  model  delta    sigma   weight residual
    0.860  0.960 -0.100 2.00e-02 2.50e+03 2.48e+01
  bond pdb=" N   ASN C  14 "
       pdb=" H   ASN C  14 "
    ideal  model  delta    sigma   weight residual
    0.860  0.960 -0.100 2.00e-02 2.50e+03 2.48e+01
  bond pdb=" N   ASN A  14 "
       pdb=" H   ASN A  14 "
    ideal  model  delta    sigma   weight residual
    0.860  0.959 -0.099 2.00e-02 2.50e+03 2.47e+01
  ... (remaining 27550 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.25: 48531
        1.25 -     2.51: 856
        2.51 -     3.76: 89
        3.76 -     5.02: 34
        5.02 -     6.27: 10
  Bond angle restraints: 49520
  Sorted by residual:
  angle pdb=" C   MET D 115 "
        pdb=" N   THR D 116 "
        pdb=" CA  THR D 116 "
      ideal   model   delta    sigma   weight residual
     121.70  126.91   -5.21 1.80e+00 3.09e-01 8.37e+00
  angle pdb=" C   MET C 115 "
        pdb=" N   THR C 116 "
        pdb=" CA  THR C 116 "
      ideal   model   delta    sigma   weight residual
     121.70  126.87   -5.17 1.80e+00 3.09e-01 8.26e+00
  angle pdb=" C   MET B 115 "
        pdb=" N   THR B 116 "
        pdb=" CA  THR B 116 "
      ideal   model   delta    sigma   weight residual
     121.70  126.86   -5.16 1.80e+00 3.09e-01 8.22e+00
  angle pdb=" C   MET E 115 "
        pdb=" N   THR E 116 "
        pdb=" CA  THR E 116 "
      ideal   model   delta    sigma   weight residual
     121.70  126.85   -5.15 1.80e+00 3.09e-01 8.20e+00
  angle pdb=" C   MET A 115 "
        pdb=" N   THR A 116 "
        pdb=" CA  THR A 116 "
      ideal   model   delta    sigma   weight residual
     121.70  126.83   -5.13 1.80e+00 3.09e-01 8.12e+00
  ... (remaining 49515 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    15.91: 12603
       15.91 -    31.82: 382
       31.82 -    47.73: 90
       47.73 -    63.63: 95
       63.63 -    79.54: 5
  Dihedral angle restraints: 13175
    sinusoidal: 7045
      harmonic: 6130
  Sorted by residual:
  dihedral pdb=" CB  MET E 115 "
           pdb=" CG  MET E 115 "
           pdb=" SD  MET E 115 "
           pdb=" CE  MET E 115 "
      ideal   model   delta sinusoidal    sigma   weight residual
      60.00  103.42  -43.42     3      1.50e+01 4.44e-03 7.80e+00
  dihedral pdb=" CB  MET D 115 "
           pdb=" CG  MET D 115 "
           pdb=" SD  MET D 115 "
           pdb=" CE  MET D 115 "
      ideal   model   delta sinusoidal    sigma   weight residual
      60.00  103.41  -43.41     3      1.50e+01 4.44e-03 7.80e+00
  dihedral pdb=" CB  MET A 115 "
           pdb=" CG  MET A 115 "
           pdb=" SD  MET A 115 "
           pdb=" CE  MET A 115 "
      ideal   model   delta sinusoidal    sigma   weight residual
      60.00  103.40  -43.40     3      1.50e+01 4.44e-03 7.80e+00
  ... (remaining 13172 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.024: 1225
       0.024 -    0.047: 607
       0.047 -    0.071: 173
       0.071 -    0.095: 71
       0.095 -    0.119: 84
  Chirality restraints: 2160
  Sorted by residual:
  chirality pdb=" CA  ILE D 124 "
            pdb=" N   ILE D 124 "
            pdb=" C   ILE D 124 "
            pdb=" CB  ILE D 124 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.55   -0.12 2.00e-01 2.50e+01 3.52e-01
  chirality pdb=" CA  ILE C 124 "
            pdb=" N   ILE C 124 "
            pdb=" C   ILE C 124 "
            pdb=" CB  ILE C 124 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.55   -0.12 2.00e-01 2.50e+01 3.45e-01
  chirality pdb=" CA  ILE E 124 "
            pdb=" N   ILE E 124 "
            pdb=" C   ILE E 124 "
            pdb=" CB  ILE E 124 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.55   -0.12 2.00e-01 2.50e+01 3.45e-01
  ... (remaining 2157 not shown)

  Planarity restraints: 4000
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C10 EIE E 502 "    0.482 2.00e-02 2.50e+03   4.61e-01 5.84e+03
        pdb=" C11 EIE E 502 "    0.364 2.00e-02 2.50e+03
        pdb=" C12 EIE E 502 "    0.062 2.00e-02 2.50e+03
        pdb=" C13 EIE E 502 "   -0.130 2.00e-02 2.50e+03
        pdb=" C7  EIE E 502 "   -0.210 2.00e-02 2.50e+03
        pdb=" C8  EIE E 502 "   -0.015 2.00e-02 2.50e+03
        pdb=" C9  EIE E 502 "    0.294 2.00e-02 2.50e+03
        pdb=" N1  EIE E 502 "    0.787 2.00e-02 2.50e+03
        pdb=" N2  EIE E 502 "   -0.210 2.00e-02 2.50e+03
        pdb=" N3  EIE E 502 "   -0.978 2.00e-02 2.50e+03
        pdb=" N4  EIE E 502 "   -0.445 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C10 EIE D 502 "   -0.482 2.00e-02 2.50e+03   4.61e-01 5.84e+03
        pdb=" C11 EIE D 502 "   -0.364 2.00e-02 2.50e+03
        pdb=" C12 EIE D 502 "   -0.062 2.00e-02 2.50e+03
        pdb=" C13 EIE D 502 "    0.131 2.00e-02 2.50e+03
        pdb=" C7  EIE D 502 "    0.210 2.00e-02 2.50e+03
        pdb=" C8  EIE D 502 "    0.014 2.00e-02 2.50e+03
        pdb=" C9  EIE D 502 "   -0.294 2.00e-02 2.50e+03
        pdb=" N1  EIE D 502 "   -0.787 2.00e-02 2.50e+03
        pdb=" N2  EIE D 502 "    0.211 2.00e-02 2.50e+03
        pdb=" N3  EIE D 502 "    0.978 2.00e-02 2.50e+03
        pdb=" N4  EIE D 502 "    0.445 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C10 EIE B 502 "   -0.482 2.00e-02 2.50e+03   4.61e-01 5.83e+03
        pdb=" C11 EIE B 502 "   -0.365 2.00e-02 2.50e+03
        pdb=" C12 EIE B 502 "   -0.062 2.00e-02 2.50e+03
        pdb=" C13 EIE B 502 "    0.130 2.00e-02 2.50e+03
        pdb=" C7  EIE B 502 "    0.209 2.00e-02 2.50e+03
        pdb=" C8  EIE B 502 "    0.015 2.00e-02 2.50e+03
        pdb=" C9  EIE B 502 "   -0.294 2.00e-02 2.50e+03
        pdb=" N1  EIE B 502 "   -0.787 2.00e-02 2.50e+03
        pdb=" N2  EIE B 502 "    0.211 2.00e-02 2.50e+03
        pdb=" N3  EIE B 502 "    0.978 2.00e-02 2.50e+03
        pdb=" N4  EIE B 502 "    0.445 2.00e-02 2.50e+03
  ... (remaining 3997 not shown)

  Histogram of nonbonded interaction distances:
        1.66 -     2.25: 2393
        2.25 -     2.83: 62032
        2.83 -     3.42: 69894
        3.42 -     4.01: 100558
        4.01 -     4.60: 155147
  Nonbonded interactions: 390024
  Sorted by model distance:
  nonbonded pdb=" H   ASN A 167 "
            pdb=" O   GLU A 212 "
     model   vdw
     1.657 2.450
  nonbonded pdb=" H   ASN E 167 "
            pdb=" O   GLU E 212 "
     model   vdw
     1.657 2.450
  nonbonded pdb=" H   ASN B 167 "
            pdb=" O   GLU B 212 "
     model   vdw
     1.658 2.450
  nonbonded pdb=" H   ASN C 167 "
            pdb=" O   GLU C 212 "
     model   vdw
     1.658 2.450
  nonbonded pdb=" H   ASN D 167 "
            pdb=" O   GLU D 212 "
     model   vdw
     1.658 2.450
  ... (remaining 390019 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: 0.13
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'C'
  selection = chain 'B'
  selection = chain 'E'
  selection = chain 'D'
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             9.510
  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:             0.490
  Extract box with map and model:          1.110
  Check model and map are aligned:         0.210
  Set scattering table:                    0.270
  Process input model:                     63.470
  Find NCS groups from input model:        0.410
  Set up NCS constraints:                  0.060
  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:11.340
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   86.870
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8693
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      :  0.003   0.050  14150  Z= 0.119
  Angle     :  0.418   6.270  19270  Z= 0.194
  Chirality :  0.037   0.119   2160
  Planarity :  0.021   0.461   2395
  Dihedral  :  7.198  79.543   5165
  Min Nonbonded Distance : 2.149

Molprobity Statistics.
  All-atom Clashscore : 2.09
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.90 %
    Favored  : 99.10 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.01 %
    Favored  : 98.99 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 7.14 %
    Cis-general     : 0.31 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.13 (0.21), residues: 1670
  helix:  2.96 (0.22), residues: 585
  sheet:  0.65 (0.27), residues: 435
  loop :  0.61 (0.25), residues: 650

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.004   0.000   TRP B 414 
 HIS   0.003   0.001   HIS B 195 
 PHE   0.005   0.001   PHE E 104 
 TYR   0.005   0.001   TYR B 285 
 ARG   0.001   0.000   ARG A 320 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00061 (    5)
  link_NAG-ASN         : angle       1.76874 (   15)
  hydrogen bonds       : bond        0.21737 (  735)
  hydrogen bonds       : angle       7.40739 ( 2430)
  SS BOND              : bond        0.00064 (    5)
  SS BOND              : angle       0.15322 (   10)
  covalent geometry    : bond        0.00261 (14140)
  covalent geometry    : angle       0.41514 (19245)

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

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

  3340 Ramachandran restraints generated.
    1670 Oldfield, 0 Emsley, 1670 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3340 Ramachandran restraints generated.
    1670 Oldfield, 0 Emsley, 1670 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  265 residues out of total 1490 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 265
  time to evaluate  : 1.997 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  109 LYS cc_start: 0.8597 (tttt) cc_final: 0.8284 (tptp)
REVERT: A  193 GLN cc_start: 0.8146 (pt0) cc_final: 0.7829 (pm20)
REVERT: B  109 LYS cc_start: 0.8583 (tttt) cc_final: 0.8245 (tptp)
REVERT: B  193 GLN cc_start: 0.8164 (pt0) cc_final: 0.7957 (pm20)
REVERT: B  253 GLU cc_start: 0.8677 (pm20) cc_final: 0.7852 (pm20)
REVERT: C  109 LYS cc_start: 0.8597 (tttt) cc_final: 0.8272 (tptp)
REVERT: D  109 LYS cc_start: 0.8619 (tttt) cc_final: 0.8304 (tptp)
REVERT: D  193 GLN cc_start: 0.8169 (pt0) cc_final: 0.7950 (pm20)
REVERT: E  109 LYS cc_start: 0.8603 (tttt) cc_final: 0.8289 (tptp)
REVERT: E  193 GLN cc_start: 0.8149 (pt0) cc_final: 0.7898 (pm20)
  outliers start: 0
  outliers final: 0
  residues processed: 265
  average time/residue: 3.1200
  time to fit residues: 895.5409
Evaluate side-chains
  135 residues out of total 1490 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 135
  time to evaluate  : 2.140 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 165
   random chunks:
   chunk 139 optimal weight:    0.0980
   chunk 125 optimal weight:    3.9990
   chunk 69 optimal weight:    1.9990
   chunk 42 optimal weight:    1.9990
   chunk 84 optimal weight:    2.9990
   chunk 66 optimal weight:    3.9990
   chunk 129 optimal weight:    0.0670
   chunk 50 optimal weight:    3.9990
   chunk 78 optimal weight:    0.8980
   chunk 96 optimal weight:    0.9990
   chunk 149 optimal weight:    3.9990
   overall best weight:    0.8122

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

Flipped N/Q/H residues before XYZ refinement:
A 155 ASN
B 155 ASN
C 155 ASN
D 155 ASN
E 155 ASN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3197 r_free = 0.3197 target = 0.083821 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.2971 r_free = 0.2971 target = 0.070449 restraints weight = 73222.393|
|-----------------------------------------------------------------------------|
r_work (start): 0.2952 rms_B_bonded: 2.34
r_work: 0.2854 rms_B_bonded: 2.51 restraints_weight: 0.5000
r_work: 0.2735 rms_B_bonded: 4.18 restraints_weight: 0.2500
r_work (final): 0.2735
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8690
moved from start:          0.2134

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.026  14150  Z= 0.146
  Angle     :  0.491   6.907  19270  Z= 0.261
  Chirality :  0.040   0.133   2160
  Planarity :  0.004   0.032   2395
  Dihedral  :  3.507  18.159   2030
  Min Nonbonded Distance : 2.253

Molprobity Statistics.
  All-atom Clashscore : 1.94
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.92 %
    Favored  : 98.08 %
  Rotamer:
    Outliers :  1.41 %
    Allowed  :  7.11 %
    Favored  : 91.48 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 7.14 %
    Cis-general     : 0.31 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.15 (0.21), residues: 1670
  helix:  3.20 (0.20), residues: 615
  sheet:  0.50 (0.25), residues: 455
  loop :  0.36 (0.25), residues: 600

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP E  73 
 HIS   0.002   0.001   HIS C 221 
 PHE   0.010   0.001   PHE C  68 
 TYR   0.008   0.001   TYR E 194 
 ARG   0.003   0.000   ARG E 277 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00018 (    5)
  link_NAG-ASN         : angle       1.35391 (   15)
  hydrogen bonds       : bond        0.04886 (  735)
  hydrogen bonds       : angle       4.73792 ( 2430)
  SS BOND              : bond        0.00404 (    5)
  SS BOND              : angle       0.47957 (   10)
  covalent geometry    : bond        0.00313 (14140)
  covalent geometry    : angle       0.48946 (19245)

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

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

  3340 Ramachandran restraints generated.
    1670 Oldfield, 0 Emsley, 1670 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3340 Ramachandran restraints generated.
    1670 Oldfield, 0 Emsley, 1670 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  180 residues out of total 1490 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 159
  time to evaluate  : 2.184 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  109 LYS cc_start: 0.8707 (tttt) cc_final: 0.8200 (tptp)
REVERT: A  193 GLN cc_start: 0.8284 (pt0) cc_final: 0.7826 (pm20)
REVERT: A  277 ARG cc_start: 0.8042 (OUTLIER) cc_final: 0.7661 (mmt180)
REVERT: B   84 MET cc_start: 0.7976 (ttm) cc_final: 0.7775 (ttm)
REVERT: B  109 LYS cc_start: 0.8682 (tttt) cc_final: 0.8166 (tptp)
REVERT: B  115 MET cc_start: 0.8500 (mmp) cc_final: 0.7955 (mmp)
REVERT: B  193 GLN cc_start: 0.8354 (pt0) cc_final: 0.7948 (pm20)
REVERT: B  251 ASN cc_start: 0.7747 (OUTLIER) cc_final: 0.7376 (t0)
REVERT: C   60 GLU cc_start: 0.8796 (mt-10) cc_final: 0.8591 (mt-10)
REVERT: C  109 LYS cc_start: 0.8669 (tttt) cc_final: 0.8143 (tptp)
REVERT: D  109 LYS cc_start: 0.8715 (tttt) cc_final: 0.8199 (tptp)
REVERT: D  193 GLN cc_start: 0.8301 (pt0) cc_final: 0.7909 (pm20)
REVERT: D  251 ASN cc_start: 0.8057 (t0) cc_final: 0.7732 (t0)
REVERT: E  109 LYS cc_start: 0.8695 (tttt) cc_final: 0.8185 (tptp)
REVERT: E  193 GLN cc_start: 0.8256 (pt0) cc_final: 0.7887 (pm20)
  outliers start: 21
  outliers final: 9
  residues processed: 163
  average time/residue: 2.5035
  time to fit residues: 453.7574
Evaluate side-chains
  149 residues out of total 1490 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 138
  time to evaluate  : 2.165 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  277 ARG
Chi-restraints excluded: chain A residue  280 LEU
Chi-restraints excluded: chain B residue  251 ASN
Chi-restraints excluded: chain B residue  280 LEU
Chi-restraints excluded: chain B residue  397 MET
Chi-restraints excluded: chain C residue  280 LEU
Chi-restraints excluded: chain D residue  280 LEU
Chi-restraints excluded: chain D residue  397 MET
Chi-restraints excluded: chain E residue   47 ASP
Chi-restraints excluded: chain E residue  280 LEU
Chi-restraints excluded: chain E residue  397 MET
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 165
   random chunks:
   chunk 135 optimal weight:    2.9990
   chunk 14 optimal weight:    1.9990
   chunk 25 optimal weight:    1.9990
   chunk 88 optimal weight:    0.8980
   chunk 153 optimal weight:    1.9990
   chunk 30 optimal weight:    0.6980
   chunk 127 optimal weight:    1.9990
   chunk 33 optimal weight:    3.9990
   chunk 26 optimal weight:    0.5980
   chunk 90 optimal weight:    1.9990
   chunk 62 optimal weight:    2.9990
   overall best weight:    1.2384

-------------------------------------------------------------------------------
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 = 0.3133 r_free = 0.3133 target = 0.080372 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.2899 r_free = 0.2899 target = 0.066771 restraints weight = 74538.216|
|-----------------------------------------------------------------------------|
r_work (start): 0.2898 rms_B_bonded: 2.33
r_work: 0.2803 rms_B_bonded: 2.47 restraints_weight: 0.5000
r_work: 0.2690 rms_B_bonded: 4.08 restraints_weight: 0.2500
r_work (final): 0.2690
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8740
moved from start:          0.2790

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.044  14150  Z= 0.177
  Angle     :  0.494   6.675  19270  Z= 0.261
  Chirality :  0.041   0.130   2160
  Planarity :  0.004   0.038   2395
  Dihedral  :  3.976  18.789   2030
  Min Nonbonded Distance : 2.328

Molprobity Statistics.
  All-atom Clashscore : 1.65
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.16 %
    Favored  : 97.84 %
  Rotamer:
    Outliers :  1.95 %
    Allowed  :  7.38 %
    Favored  : 90.67 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 7.14 %
    Cis-general     : 0.31 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.97 (0.21), residues: 1670
  helix:  3.22 (0.20), residues: 610
  sheet:  0.27 (0.24), residues: 455
  loop :  0.19 (0.24), residues: 605

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP C 291 
 HIS   0.003   0.001   HIS D 221 
 PHE   0.014   0.002   PHE C  69 
 TYR   0.012   0.001   TYR E 132 
 ARG   0.004   0.000   ARG B 277 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00167 (    5)
  link_NAG-ASN         : angle       1.65332 (   15)
  hydrogen bonds       : bond        0.04315 (  735)
  hydrogen bonds       : angle       4.41534 ( 2430)
  SS BOND              : bond        0.00399 (    5)
  SS BOND              : angle       0.59967 (   10)
  covalent geometry    : bond        0.00397 (14140)
  covalent geometry    : angle       0.49205 (19245)

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

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

  3340 Ramachandran restraints generated.
    1670 Oldfield, 0 Emsley, 1670 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3340 Ramachandran restraints generated.
    1670 Oldfield, 0 Emsley, 1670 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  172 residues out of total 1490 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 143
  time to evaluate  : 2.032 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   60 GLU cc_start: 0.8787 (mt-10) cc_final: 0.8569 (mt-10)
REVERT: A  109 LYS cc_start: 0.8702 (tttt) cc_final: 0.8187 (tptp)
REVERT: A  151 MET cc_start: 0.9132 (mpt) cc_final: 0.8923 (mpt)
REVERT: A  193 GLN cc_start: 0.8330 (pt0) cc_final: 0.7915 (pm20)
REVERT: A  277 ARG cc_start: 0.7978 (OUTLIER) cc_final: 0.7686 (mmt180)
REVERT: B  109 LYS cc_start: 0.8645 (tttt) cc_final: 0.8131 (tptp)
REVERT: B  193 GLN cc_start: 0.8363 (pt0) cc_final: 0.7970 (pm20)
REVERT: B  251 ASN cc_start: 0.7730 (OUTLIER) cc_final: 0.7340 (t0)
REVERT: C   39 GLU cc_start: 0.8347 (OUTLIER) cc_final: 0.8086 (tp30)
REVERT: C   60 GLU cc_start: 0.8760 (mt-10) cc_final: 0.8520 (mt-10)
REVERT: C  109 LYS cc_start: 0.8638 (tttt) cc_final: 0.8125 (tptp)
REVERT: D  109 LYS cc_start: 0.8675 (tttt) cc_final: 0.8161 (tptp)
REVERT: D  193 GLN cc_start: 0.8365 (pt0) cc_final: 0.7934 (pm20)
REVERT: D  251 ASN cc_start: 0.8060 (t0) cc_final: 0.7729 (t0)
REVERT: E  109 LYS cc_start: 0.8667 (tttt) cc_final: 0.8156 (tptp)
REVERT: E  193 GLN cc_start: 0.8291 (pt0) cc_final: 0.7886 (pm20)
  outliers start: 29
  outliers final: 8
  residues processed: 153
  average time/residue: 2.4724
  time to fit residues: 421.0522
Evaluate side-chains
  141 residues out of total 1490 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 130
  time to evaluate  : 2.016 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   47 ASP
Chi-restraints excluded: chain A residue  141 GLU
Chi-restraints excluded: chain A residue  277 ARG
Chi-restraints excluded: chain A residue  280 LEU
Chi-restraints excluded: chain B residue  251 ASN
Chi-restraints excluded: chain B residue  280 LEU
Chi-restraints excluded: chain C residue   39 GLU
Chi-restraints excluded: chain C residue  280 LEU
Chi-restraints excluded: chain D residue  397 MET
Chi-restraints excluded: chain E residue  280 LEU
Chi-restraints excluded: chain E residue  397 MET
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 165
   random chunks:
   chunk 3 optimal weight:    2.9990
   chunk 20 optimal weight:    1.9990
   chunk 95 optimal weight:    0.9990
   chunk 109 optimal weight:    0.4980
   chunk 42 optimal weight:    2.9990
   chunk 83 optimal weight:    2.9990
   chunk 63 optimal weight:    1.9990
   chunk 22 optimal weight:    0.9980
   chunk 62 optimal weight:    1.9990
   chunk 147 optimal weight:    0.4980
   chunk 158 optimal weight:    1.9990
   overall best weight:    0.9984

-------------------------------------------------------------------------------
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 = 0.3141 r_free = 0.3141 target = 0.080741 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.2906 r_free = 0.2906 target = 0.067143 restraints weight = 74621.647|
|-----------------------------------------------------------------------------|
r_work (start): 0.2908 rms_B_bonded: 2.34
r_work: 0.2813 rms_B_bonded: 2.47 restraints_weight: 0.5000
r_work: 0.2701 rms_B_bonded: 4.09 restraints_weight: 0.2500
r_work (final): 0.2701
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8730
moved from start:          0.2947

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028  14150  Z= 0.147
  Angle     :  0.463   6.487  19270  Z= 0.241
  Chirality :  0.040   0.139   2160
  Planarity :  0.004   0.038   2395
  Dihedral  :  3.853  19.317   2030
  Min Nonbonded Distance : 2.357

Molprobity Statistics.
  All-atom Clashscore : 1.76
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.80 %
    Favored  : 98.20 %
  Rotamer:
    Outliers :  1.81 %
    Allowed  :  8.26 %
    Favored  : 89.93 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 7.14 %
    Cis-general     : 0.31 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.96 (0.21), residues: 1670
  helix:  3.31 (0.20), residues: 610
  sheet:  0.18 (0.24), residues: 455
  loop :  0.14 (0.24), residues: 605

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP E  73 
 HIS   0.003   0.001   HIS C 195 
 PHE   0.009   0.001   PHE E 307 
 TYR   0.008   0.001   TYR A 132 
 ARG   0.002   0.000   ARG B 277 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00074 (    5)
  link_NAG-ASN         : angle       1.65133 (   15)
  hydrogen bonds       : bond        0.03790 (  735)
  hydrogen bonds       : angle       4.23583 ( 2430)
  SS BOND              : bond        0.00388 (    5)
  SS BOND              : angle       0.65472 (   10)
  covalent geometry    : bond        0.00325 (14140)
  covalent geometry    : angle       0.46104 (19245)

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

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

  3340 Ramachandran restraints generated.
    1670 Oldfield, 0 Emsley, 1670 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3340 Ramachandran restraints generated.
    1670 Oldfield, 0 Emsley, 1670 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  163 residues out of total 1490 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 136
  time to evaluate  : 2.053 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   60 GLU cc_start: 0.8779 (mt-10) cc_final: 0.8492 (mt-10)
REVERT: A  109 LYS cc_start: 0.8703 (tttt) cc_final: 0.8188 (tptp)
REVERT: A  147 GLU cc_start: 0.8313 (OUTLIER) cc_final: 0.8110 (tp30)
REVERT: A  193 GLN cc_start: 0.8344 (pt0) cc_final: 0.7905 (pm20)
REVERT: B  109 LYS cc_start: 0.8650 (tttt) cc_final: 0.8141 (tptp)
REVERT: B  134 LEU cc_start: 0.9153 (OUTLIER) cc_final: 0.8918 (pt)
REVERT: B  193 GLN cc_start: 0.8362 (pt0) cc_final: 0.7958 (pm20)
REVERT: B  251 ASN cc_start: 0.7731 (OUTLIER) cc_final: 0.7333 (t0)
REVERT: C   60 GLU cc_start: 0.8782 (mt-10) cc_final: 0.8526 (mt-10)
REVERT: C  109 LYS cc_start: 0.8657 (tttt) cc_final: 0.8143 (tptp)
REVERT: D   60 GLU cc_start: 0.8735 (mt-10) cc_final: 0.8459 (mt-10)
REVERT: D  109 LYS cc_start: 0.8685 (tttt) cc_final: 0.8177 (tptp)
REVERT: D  193 GLN cc_start: 0.8364 (pt0) cc_final: 0.7918 (pm20)
REVERT: E  109 LYS cc_start: 0.8682 (tttt) cc_final: 0.8171 (tptp)
REVERT: E  193 GLN cc_start: 0.8297 (pt0) cc_final: 0.7866 (pm20)
  outliers start: 27
  outliers final: 12
  residues processed: 144
  average time/residue: 2.4276
  time to fit residues: 387.9936
Evaluate side-chains
  142 residues out of total 1490 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 127
  time to evaluate  : 2.165 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  147 GLU
Chi-restraints excluded: chain A residue  277 ARG
Chi-restraints excluded: chain A residue  280 LEU
Chi-restraints excluded: chain A residue  397 MET
Chi-restraints excluded: chain B residue  134 LEU
Chi-restraints excluded: chain B residue  251 ASN
Chi-restraints excluded: chain B residue  280 LEU
Chi-restraints excluded: chain B residue  397 MET
Chi-restraints excluded: chain C residue  280 LEU
Chi-restraints excluded: chain D residue   47 ASP
Chi-restraints excluded: chain D residue  280 LEU
Chi-restraints excluded: chain D residue  397 MET
Chi-restraints excluded: chain E residue  141 GLU
Chi-restraints excluded: chain E residue  280 LEU
Chi-restraints excluded: chain E residue  397 MET
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 165
   random chunks:
   chunk 149 optimal weight:    2.9990
   chunk 88 optimal weight:    0.5980
   chunk 152 optimal weight:    1.9990
   chunk 9 optimal weight:    1.9990
   chunk 100 optimal weight:    2.9990
   chunk 129 optimal weight:    1.9990
   chunk 39 optimal weight:    1.9990
   chunk 121 optimal weight:    0.7980
   chunk 87 optimal weight:    0.6980
   chunk 38 optimal weight:    1.9990
   chunk 73 optimal weight:    3.9990
   overall best weight:    1.2184

-------------------------------------------------------------------------------
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 = 0.3127 r_free = 0.3127 target = 0.079855 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.2889 r_free = 0.2889 target = 0.066226 restraints weight = 74355.331|
|-----------------------------------------------------------------------------|
r_work (start): 0.2843 rms_B_bonded: 2.33
r_work: 0.2743 rms_B_bonded: 2.47 restraints_weight: 0.5000
r_work: 0.2627 rms_B_bonded: 4.08 restraints_weight: 0.2500
r_work (final): 0.2627
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8745
moved from start:          0.3089

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.030  14150  Z= 0.172
  Angle     :  0.476   7.384  19270  Z= 0.248
  Chirality :  0.040   0.168   2160
  Planarity :  0.004   0.039   2395
  Dihedral  :  3.998  19.829   2030
  Min Nonbonded Distance : 2.368

Molprobity Statistics.
  All-atom Clashscore : 1.83
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.28 %
    Favored  : 97.72 %
  Rotamer:
    Outliers :  2.42 %
    Allowed  :  7.72 %
    Favored  : 89.87 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 7.14 %
    Cis-general     : 0.31 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.94 (0.21), residues: 1670
  helix:  3.33 (0.20), residues: 610
  sheet:  0.16 (0.24), residues: 455
  loop :  0.10 (0.24), residues: 605

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.004   0.001   TRP C  73 
 HIS   0.003   0.001   HIS C 195 
 PHE   0.011   0.001   PHE A 104 
 TYR   0.009   0.001   TYR E 132 
 ARG   0.001   0.000   ARG B 277 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00161 (    5)
  link_NAG-ASN         : angle       1.74080 (   15)
  hydrogen bonds       : bond        0.03873 (  735)
  hydrogen bonds       : angle       4.23742 ( 2430)
  SS BOND              : bond        0.00423 (    5)
  SS BOND              : angle       0.74834 (   10)
  covalent geometry    : bond        0.00386 (14140)
  covalent geometry    : angle       0.47349 (19245)

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

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

  3340 Ramachandran restraints generated.
    1670 Oldfield, 0 Emsley, 1670 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3340 Ramachandran restraints generated.
    1670 Oldfield, 0 Emsley, 1670 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  167 residues out of total 1490 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 131
  time to evaluate  : 2.282 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  147 GLU cc_start: 0.8355 (OUTLIER) cc_final: 0.8131 (tp30)
REVERT: A  193 GLN cc_start: 0.8351 (pt0) cc_final: 0.7896 (pm20)
REVERT: B   84 MET cc_start: 0.7937 (ttm) cc_final: 0.7726 (ttm)
REVERT: B  109 LYS cc_start: 0.8624 (tttt) cc_final: 0.8109 (tptp)
REVERT: B  134 LEU cc_start: 0.9186 (OUTLIER) cc_final: 0.8953 (pt)
REVERT: B  193 GLN cc_start: 0.8390 (pt0) cc_final: 0.7998 (pm20)
REVERT: B  251 ASN cc_start: 0.7754 (OUTLIER) cc_final: 0.7375 (t0)
REVERT: C   60 GLU cc_start: 0.8789 (mt-10) cc_final: 0.8525 (mt-10)
REVERT: C  109 LYS cc_start: 0.8666 (tttt) cc_final: 0.8141 (tptp)
REVERT: D  109 LYS cc_start: 0.8678 (tttt) cc_final: 0.8152 (tptp)
REVERT: D  193 GLN cc_start: 0.8385 (pt0) cc_final: 0.7913 (pm20)
REVERT: E  193 GLN cc_start: 0.8311 (pt0) cc_final: 0.7891 (pm20)
REVERT: E  251 ASN cc_start: 0.7993 (t0) cc_final: 0.7750 (t0)
  outliers start: 36
  outliers final: 15
  residues processed: 146
  average time/residue: 2.4169
  time to fit residues: 392.6308
Evaluate side-chains
  145 residues out of total 1490 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 127
  time to evaluate  : 2.030 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   47 ASP
Chi-restraints excluded: chain A residue  147 GLU
Chi-restraints excluded: chain A residue  277 ARG
Chi-restraints excluded: chain A residue  280 LEU
Chi-restraints excluded: chain A residue  397 MET
Chi-restraints excluded: chain B residue  116 THR
Chi-restraints excluded: chain B residue  134 LEU
Chi-restraints excluded: chain B residue  251 ASN
Chi-restraints excluded: chain B residue  280 LEU
Chi-restraints excluded: chain B residue  397 MET
Chi-restraints excluded: chain C residue  280 LEU
Chi-restraints excluded: chain D residue   47 ASP
Chi-restraints excluded: chain D residue  280 LEU
Chi-restraints excluded: chain D residue  397 MET
Chi-restraints excluded: chain E residue  117 THR
Chi-restraints excluded: chain E residue  253 GLU
Chi-restraints excluded: chain E residue  280 LEU
Chi-restraints excluded: chain E residue  397 MET
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 165
   random chunks:
   chunk 88 optimal weight:    1.9990
   chunk 3 optimal weight:    2.9990
   chunk 38 optimal weight:    1.9990
   chunk 120 optimal weight:    1.9990
   chunk 127 optimal weight:    1.9990
   chunk 43 optimal weight:    2.9990
   chunk 16 optimal weight:    0.8980
   chunk 162 optimal weight:    0.2980
   chunk 5 optimal weight:    0.5980
   chunk 85 optimal weight:    0.9990
   chunk 59 optimal weight:    3.9990
   overall best weight:    0.9584

-------------------------------------------------------------------------------
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 = 0.3133 r_free = 0.3133 target = 0.080224 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.2896 r_free = 0.2896 target = 0.066630 restraints weight = 74877.457|
|-----------------------------------------------------------------------------|
r_work (start): 0.2853 rms_B_bonded: 2.34
r_work: 0.2753 rms_B_bonded: 2.49 restraints_weight: 0.5000
r_work: 0.2634 rms_B_bonded: 4.13 restraints_weight: 0.2500
r_work (final): 0.2634
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8735
moved from start:          0.3182

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029  14150  Z= 0.144
  Angle     :  0.462   7.375  19270  Z= 0.239
  Chirality :  0.040   0.164   2160
  Planarity :  0.004   0.039   2395
  Dihedral  :  3.907  19.819   2030
  Min Nonbonded Distance : 2.382

Molprobity Statistics.
  All-atom Clashscore : 1.69
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.04 %
    Favored  : 97.96 %
  Rotamer:
    Outliers :  1.81 %
    Allowed  :  8.79 %
    Favored  : 89.40 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 7.14 %
    Cis-general     : 0.31 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.96 (0.21), residues: 1670
  helix:  3.41 (0.20), residues: 610
  sheet:  0.08 (0.24), residues: 460
  loop :  0.12 (0.24), residues: 600

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP E  73 
 HIS   0.003   0.001   HIS C 195 
 PHE   0.009   0.001   PHE A 104 
 TYR   0.007   0.001   TYR A 413 
 ARG   0.002   0.000   ARG B 277 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00093 (    5)
  link_NAG-ASN         : angle       1.73186 (   15)
  hydrogen bonds       : bond        0.03624 (  735)
  hydrogen bonds       : angle       4.15179 ( 2430)
  SS BOND              : bond        0.00370 (    5)
  SS BOND              : angle       0.70540 (   10)
  covalent geometry    : bond        0.00318 (14140)
  covalent geometry    : angle       0.45963 (19245)

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

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

  3340 Ramachandran restraints generated.
    1670 Oldfield, 0 Emsley, 1670 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3340 Ramachandran restraints generated.
    1670 Oldfield, 0 Emsley, 1670 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  155 residues out of total 1490 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 128
  time to evaluate  : 1.969 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  193 GLN cc_start: 0.8375 (pt0) cc_final: 0.7900 (pm20)
REVERT: B  109 LYS cc_start: 0.8646 (tttt) cc_final: 0.8129 (tptp)
REVERT: B  134 LEU cc_start: 0.9182 (OUTLIER) cc_final: 0.8942 (pt)
REVERT: B  193 GLN cc_start: 0.8390 (pt0) cc_final: 0.7981 (pm20)
REVERT: B  251 ASN cc_start: 0.7762 (OUTLIER) cc_final: 0.7384 (t0)
REVERT: C   60 GLU cc_start: 0.8792 (mt-10) cc_final: 0.8505 (mt-10)
REVERT: D  193 GLN cc_start: 0.8396 (pt0) cc_final: 0.7924 (pm20)
REVERT: E  193 GLN cc_start: 0.8323 (pt0) cc_final: 0.7883 (pm20)
  outliers start: 27
  outliers final: 17
  residues processed: 132
  average time/residue: 2.1465
  time to fit residues: 321.4937
Evaluate side-chains
  137 residues out of total 1490 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 118
  time to evaluate  : 2.323 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   47 ASP
Chi-restraints excluded: chain A residue  117 THR
Chi-restraints excluded: chain A residue  277 ARG
Chi-restraints excluded: chain A residue  280 LEU
Chi-restraints excluded: chain A residue  397 MET
Chi-restraints excluded: chain B residue  117 THR
Chi-restraints excluded: chain B residue  134 LEU
Chi-restraints excluded: chain B residue  251 ASN
Chi-restraints excluded: chain B residue  280 LEU
Chi-restraints excluded: chain C residue  117 THR
Chi-restraints excluded: chain C residue  280 LEU
Chi-restraints excluded: chain D residue   47 ASP
Chi-restraints excluded: chain D residue  117 THR
Chi-restraints excluded: chain D residue  280 LEU
Chi-restraints excluded: chain D residue  397 MET
Chi-restraints excluded: chain E residue  117 THR
Chi-restraints excluded: chain E residue  121 MET
Chi-restraints excluded: chain E residue  280 LEU
Chi-restraints excluded: chain E residue  397 MET
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 165
   random chunks:
   chunk 16 optimal weight:    0.5980
   chunk 27 optimal weight:    2.9990
   chunk 128 optimal weight:    1.9990
   chunk 24 optimal weight:    2.9990
   chunk 11 optimal weight:    1.9990
   chunk 0 optimal weight:    3.9990
   chunk 4 optimal weight:    0.0570
   chunk 32 optimal weight:    0.6980
   chunk 26 optimal weight:    0.6980
   chunk 114 optimal weight:    1.9990
   chunk 42 optimal weight:    1.9990
   overall best weight:    0.8100

-------------------------------------------------------------------------------
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 = 0.3140 r_free = 0.3140 target = 0.080650 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.2906 r_free = 0.2906 target = 0.067175 restraints weight = 74755.178|
|-----------------------------------------------------------------------------|
r_work (start): 0.2875 rms_B_bonded: 2.33
r_work: 0.2781 rms_B_bonded: 2.46 restraints_weight: 0.5000
r_work: 0.2667 rms_B_bonded: 4.10 restraints_weight: 0.2500
r_work (final): 0.2667
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8715
moved from start:          0.3226

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.027  14150  Z= 0.130
  Angle     :  0.454   7.386  19270  Z= 0.234
  Chirality :  0.039   0.161   2160
  Planarity :  0.004   0.039   2395
  Dihedral  :  3.846  19.717   2030
  Min Nonbonded Distance : 2.392

Molprobity Statistics.
  All-atom Clashscore : 1.76
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.16 %
    Favored  : 97.84 %
  Rotamer:
    Outliers :  2.01 %
    Allowed  :  8.72 %
    Favored  : 89.26 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 7.14 %
    Cis-general     : 0.31 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.02 (0.21), residues: 1670
  helix:  3.49 (0.20), residues: 610
  sheet:  0.09 (0.25), residues: 460
  loop :  0.14 (0.24), residues: 600

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP B  73 
 HIS   0.003   0.001   HIS C 195 
 PHE   0.008   0.001   PHE E 307 
 TYR   0.007   0.001   TYR D 413 
 ARG   0.002   0.000   ARG B 277 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00069 (    5)
  link_NAG-ASN         : angle       1.71373 (   15)
  hydrogen bonds       : bond        0.03479 (  735)
  hydrogen bonds       : angle       4.09876 ( 2430)
  SS BOND              : bond        0.00353 (    5)
  SS BOND              : angle       0.69007 (   10)
  covalent geometry    : bond        0.00286 (14140)
  covalent geometry    : angle       0.45111 (19245)

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

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

  3340 Ramachandran restraints generated.
    1670 Oldfield, 0 Emsley, 1670 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3340 Ramachandran restraints generated.
    1670 Oldfield, 0 Emsley, 1670 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  154 residues out of total 1490 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 124
  time to evaluate  : 2.129 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  193 GLN cc_start: 0.8365 (pt0) cc_final: 0.7895 (pm20)
REVERT: B   84 MET cc_start: 0.7809 (ttm) cc_final: 0.7582 (ttm)
REVERT: B  134 LEU cc_start: 0.9165 (OUTLIER) cc_final: 0.8941 (pt)
REVERT: B  193 GLN cc_start: 0.8389 (pt0) cc_final: 0.7971 (pm20)
REVERT: B  251 ASN cc_start: 0.7747 (OUTLIER) cc_final: 0.7380 (t0)
REVERT: C   60 GLU cc_start: 0.8764 (mt-10) cc_final: 0.8493 (mt-10)
REVERT: C  245 GLN cc_start: 0.9183 (OUTLIER) cc_final: 0.8844 (mt0)
REVERT: D  193 GLN cc_start: 0.8382 (pt0) cc_final: 0.7913 (pm20)
REVERT: E  193 GLN cc_start: 0.8313 (pt0) cc_final: 0.7876 (pm20)
  outliers start: 30
  outliers final: 19
  residues processed: 133
  average time/residue: 2.2601
  time to fit residues: 337.3171
Evaluate side-chains
  143 residues out of total 1490 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 121
  time to evaluate  : 1.997 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   47 ASP
Chi-restraints excluded: chain A residue  117 THR
Chi-restraints excluded: chain A residue  277 ARG
Chi-restraints excluded: chain A residue  280 LEU
Chi-restraints excluded: chain A residue  397 MET
Chi-restraints excluded: chain B residue  117 THR
Chi-restraints excluded: chain B residue  134 LEU
Chi-restraints excluded: chain B residue  251 ASN
Chi-restraints excluded: chain B residue  280 LEU
Chi-restraints excluded: chain C residue  117 THR
Chi-restraints excluded: chain C residue  245 GLN
Chi-restraints excluded: chain C residue  280 LEU
Chi-restraints excluded: chain C residue  395 ASP
Chi-restraints excluded: chain D residue   47 ASP
Chi-restraints excluded: chain D residue  117 THR
Chi-restraints excluded: chain D residue  121 MET
Chi-restraints excluded: chain D residue  280 LEU
Chi-restraints excluded: chain D residue  397 MET
Chi-restraints excluded: chain E residue  117 THR
Chi-restraints excluded: chain E residue  121 MET
Chi-restraints excluded: chain E residue  280 LEU
Chi-restraints excluded: chain E residue  397 MET
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 165
   random chunks:
   chunk 158 optimal weight:    2.9990
   chunk 9 optimal weight:    1.9990
   chunk 124 optimal weight:    1.9990
   chunk 44 optimal weight:    1.9990
   chunk 25 optimal weight:    0.9980
   chunk 142 optimal weight:    0.4980
   chunk 87 optimal weight:    2.9990
   chunk 82 optimal weight:    2.9990
   chunk 46 optimal weight:    0.9990
   chunk 141 optimal weight:    1.9990
   chunk 2 optimal weight:    0.4980
   overall best weight:    0.9984

-------------------------------------------------------------------------------
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 = 0.3131 r_free = 0.3131 target = 0.080117 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.2895 r_free = 0.2895 target = 0.066681 restraints weight = 74676.561|
|-----------------------------------------------------------------------------|
r_work (start): 0.2879 rms_B_bonded: 2.32
r_work: 0.2784 rms_B_bonded: 2.47 restraints_weight: 0.5000
r_work: 0.2669 rms_B_bonded: 4.10 restraints_weight: 0.2500
r_work (final): 0.2669
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8747
moved from start:          0.3287

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030  14150  Z= 0.148
  Angle     :  0.468   7.567  19270  Z= 0.242
  Chirality :  0.040   0.160   2160
  Planarity :  0.004   0.039   2395
  Dihedral  :  3.917  19.867   2030
  Min Nonbonded Distance : 2.394

Molprobity Statistics.
  All-atom Clashscore : 2.02
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.04 %
    Favored  : 97.96 %
  Rotamer:
    Outliers :  2.01 %
    Allowed  :  8.86 %
    Favored  : 89.13 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 7.14 %
    Cis-general     : 0.31 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.03 (0.21), residues: 1670
  helix:  3.47 (0.20), residues: 615
  sheet:  0.09 (0.25), residues: 460
  loop :  0.15 (0.24), residues: 595

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP D  73 
 HIS   0.003   0.001   HIS C 195 
 PHE   0.009   0.001   PHE E 104 
 TYR   0.007   0.001   TYR D 413 
 ARG   0.002   0.000   ARG B 277 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00127 (    5)
  link_NAG-ASN         : angle       1.74286 (   15)
  hydrogen bonds       : bond        0.03554 (  735)
  hydrogen bonds       : angle       4.11225 ( 2430)
  SS BOND              : bond        0.00379 (    5)
  SS BOND              : angle       0.72401 (   10)
  covalent geometry    : bond        0.00331 (14140)
  covalent geometry    : angle       0.46515 (19245)

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

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

  3340 Ramachandran restraints generated.
    1670 Oldfield, 0 Emsley, 1670 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3340 Ramachandran restraints generated.
    1670 Oldfield, 0 Emsley, 1670 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  152 residues out of total 1490 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 122
  time to evaluate  : 2.025 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  193 GLN cc_start: 0.8379 (pt0) cc_final: 0.7934 (pm20)
REVERT: B   84 MET cc_start: 0.7838 (ttm) cc_final: 0.7617 (ttm)
REVERT: B  134 LEU cc_start: 0.9186 (OUTLIER) cc_final: 0.8964 (pt)
REVERT: B  193 GLN cc_start: 0.8400 (pt0) cc_final: 0.8012 (pm20)
REVERT: B  251 ASN cc_start: 0.7763 (t0) cc_final: 0.7413 (t0)
REVERT: C   60 GLU cc_start: 0.8781 (mt-10) cc_final: 0.8512 (mt-10)
REVERT: C  134 LEU cc_start: 0.9214 (OUTLIER) cc_final: 0.8865 (pt)
REVERT: D  193 GLN cc_start: 0.8410 (pt0) cc_final: 0.7948 (pm20)
REVERT: E  193 GLN cc_start: 0.8350 (pt0) cc_final: 0.7925 (pm20)
  outliers start: 30
  outliers final: 18
  residues processed: 132
  average time/residue: 2.2171
  time to fit residues: 327.4388
Evaluate side-chains
  139 residues out of total 1490 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 119
  time to evaluate  : 1.985 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   47 ASP
Chi-restraints excluded: chain A residue  117 THR
Chi-restraints excluded: chain A residue  277 ARG
Chi-restraints excluded: chain A residue  280 LEU
Chi-restraints excluded: chain A residue  397 MET
Chi-restraints excluded: chain B residue  117 THR
Chi-restraints excluded: chain B residue  134 LEU
Chi-restraints excluded: chain B residue  280 LEU
Chi-restraints excluded: chain C residue  117 THR
Chi-restraints excluded: chain C residue  134 LEU
Chi-restraints excluded: chain C residue  280 LEU
Chi-restraints excluded: chain C residue  395 ASP
Chi-restraints excluded: chain D residue   47 ASP
Chi-restraints excluded: chain D residue  117 THR
Chi-restraints excluded: chain D residue  280 LEU
Chi-restraints excluded: chain D residue  397 MET
Chi-restraints excluded: chain E residue  117 THR
Chi-restraints excluded: chain E residue  121 MET
Chi-restraints excluded: chain E residue  280 LEU
Chi-restraints excluded: chain E residue  397 MET
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 165
   random chunks:
   chunk 18 optimal weight:    2.9990
   chunk 137 optimal weight:    0.5980
   chunk 91 optimal weight:    1.9990
   chunk 65 optimal weight:    1.9990
   chunk 120 optimal weight:    1.9990
   chunk 90 optimal weight:    0.7980
   chunk 24 optimal weight:    1.9990
   chunk 126 optimal weight:    2.9990
   chunk 125 optimal weight:    0.9980
   chunk 87 optimal weight:    1.9990
   chunk 147 optimal weight:    1.9990
   overall best weight:    1.2784

-------------------------------------------------------------------------------
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 = 0.3114 r_free = 0.3114 target = 0.079134 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.2878 r_free = 0.2878 target = 0.065658 restraints weight = 74694.162|
|-----------------------------------------------------------------------------|
r_work (start): 0.2841 rms_B_bonded: 2.32
r_work: 0.2743 rms_B_bonded: 2.47 restraints_weight: 0.5000
r_work: 0.2628 rms_B_bonded: 4.08 restraints_weight: 0.2500
r_work (final): 0.2628
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8755
moved from start:          0.3359

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.036  14150  Z= 0.179
  Angle     :  0.487   8.319  19270  Z= 0.253
  Chirality :  0.040   0.156   2160
  Planarity :  0.004   0.039   2395
  Dihedral  :  4.101  20.287   2030
  Min Nonbonded Distance : 2.387

Molprobity Statistics.
  All-atom Clashscore : 2.02
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.34 %
    Favored  : 97.66 %
  Rotamer:
    Outliers :  1.68 %
    Allowed  :  9.40 %
    Favored  : 88.93 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 7.14 %
    Cis-general     : 0.31 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.99 (0.21), residues: 1670
  helix:  3.45 (0.20), residues: 615
  sheet:  0.08 (0.24), residues: 460
  loop :  0.10 (0.24), residues: 595

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.004   0.001   TRP E  73 
 HIS   0.003   0.001   HIS C 195 
 PHE   0.011   0.001   PHE A 104 
 TYR   0.009   0.001   TYR D 297 
 ARG   0.002   0.000   ARG C 277 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00185 (    5)
  link_NAG-ASN         : angle       1.82885 (   15)
  hydrogen bonds       : bond        0.03765 (  735)
  hydrogen bonds       : angle       4.19374 ( 2430)
  SS BOND              : bond        0.00433 (    5)
  SS BOND              : angle       0.77935 (   10)
  covalent geometry    : bond        0.00404 (14140)
  covalent geometry    : angle       0.48442 (19245)

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

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

  3340 Ramachandran restraints generated.
    1670 Oldfield, 0 Emsley, 1670 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3340 Ramachandran restraints generated.
    1670 Oldfield, 0 Emsley, 1670 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  145 residues out of total 1490 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 120
  time to evaluate  : 2.122 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  193 GLN cc_start: 0.8389 (pt0) cc_final: 0.7928 (pm20)
REVERT: B   84 MET cc_start: 0.7847 (ttm) cc_final: 0.7609 (ttm)
REVERT: B  134 LEU cc_start: 0.9186 (OUTLIER) cc_final: 0.8933 (pt)
REVERT: B  193 GLN cc_start: 0.8375 (pt0) cc_final: 0.7989 (pm20)
REVERT: B  251 ASN cc_start: 0.7769 (OUTLIER) cc_final: 0.7402 (t0)
REVERT: C   60 GLU cc_start: 0.8779 (mt-10) cc_final: 0.8505 (mt-10)
REVERT: C  134 LEU cc_start: 0.9201 (OUTLIER) cc_final: 0.8892 (pt)
REVERT: D  193 GLN cc_start: 0.8400 (pt0) cc_final: 0.7944 (pm20)
REVERT: E  193 GLN cc_start: 0.8338 (pt0) cc_final: 0.7906 (pm20)
  outliers start: 25
  outliers final: 16
  residues processed: 124
  average time/residue: 2.1730
  time to fit residues: 304.1215
Evaluate side-chains
  138 residues out of total 1490 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 119
  time to evaluate  : 2.256 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   47 ASP
Chi-restraints excluded: chain A residue  117 THR
Chi-restraints excluded: chain A residue  277 ARG
Chi-restraints excluded: chain A residue  280 LEU
Chi-restraints excluded: chain A residue  397 MET
Chi-restraints excluded: chain B residue  117 THR
Chi-restraints excluded: chain B residue  134 LEU
Chi-restraints excluded: chain B residue  251 ASN
Chi-restraints excluded: chain B residue  280 LEU
Chi-restraints excluded: chain B residue  397 MET
Chi-restraints excluded: chain C residue  117 THR
Chi-restraints excluded: chain C residue  134 LEU
Chi-restraints excluded: chain C residue  280 LEU
Chi-restraints excluded: chain C residue  395 ASP
Chi-restraints excluded: chain D residue  117 THR
Chi-restraints excluded: chain D residue  397 MET
Chi-restraints excluded: chain E residue  117 THR
Chi-restraints excluded: chain E residue  280 LEU
Chi-restraints excluded: chain E residue  397 MET
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 165
   random chunks:
   chunk 127 optimal weight:    1.9990
   chunk 114 optimal weight:    1.9990
   chunk 75 optimal weight:    1.9990
   chunk 163 optimal weight:    1.9990
   chunk 27 optimal weight:    2.9990
   chunk 10 optimal weight:    0.9990
   chunk 144 optimal weight:    0.8980
   chunk 117 optimal weight:    1.9990
   chunk 55 optimal weight:    1.9990
   chunk 140 optimal weight:    1.9990
   chunk 24 optimal weight:    1.9990
   overall best weight:    1.5788

-------------------------------------------------------------------------------
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 = 0.3090 r_free = 0.3090 target = 0.077523 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.2862 r_free = 0.2862 target = 0.064223 restraints weight = 75549.949|
|-----------------------------------------------------------------------------|
r_work (start): 0.2825 rms_B_bonded: 2.27
r_work: 0.2732 rms_B_bonded: 2.40 restraints_weight: 0.5000
r_work: 0.2617 rms_B_bonded: 3.98 restraints_weight: 0.2500
r_work (final): 0.2617
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8734
moved from start:          0.3388

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.040  14150  Z= 0.214
  Angle     :  0.508   8.646  19270  Z= 0.265
  Chirality :  0.041   0.155   2160
  Planarity :  0.004   0.039   2395
  Dihedral  :  4.281  20.741   2030
  Min Nonbonded Distance : 2.391

Molprobity Statistics.
  All-atom Clashscore : 1.98
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.40 %
    Favored  : 97.60 %
  Rotamer:
    Outliers :  1.61 %
    Allowed  :  9.53 %
    Favored  : 88.86 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 7.14 %
    Cis-general     : 0.31 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.90 (0.21), residues: 1670
  helix:  3.40 (0.20), residues: 615
  sheet: -0.03 (0.24), residues: 470
  loop :  0.08 (0.24), residues: 585

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.003   0.001   TRP B 291 
 HIS   0.003   0.001   HIS C 195 
 PHE   0.013   0.002   PHE A 104 
 TYR   0.007   0.001   TYR D 413 
 ARG   0.002   0.000   ARG E 190 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00244 (    5)
  link_NAG-ASN         : angle       1.90090 (   15)
  hydrogen bonds       : bond        0.03972 (  735)
  hydrogen bonds       : angle       4.26715 ( 2430)
  SS BOND              : bond        0.00476 (    5)
  SS BOND              : angle       0.85373 (   10)
  covalent geometry    : bond        0.00485 (14140)
  covalent geometry    : angle       0.50545 (19245)

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

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

  3340 Ramachandran restraints generated.
    1670 Oldfield, 0 Emsley, 1670 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3340 Ramachandran restraints generated.
    1670 Oldfield, 0 Emsley, 1670 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  141 residues out of total 1490 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 117
  time to evaluate  : 2.166 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   47 ASP cc_start: 0.8316 (OUTLIER) cc_final: 0.8096 (p0)
REVERT: A  193 GLN cc_start: 0.8388 (pt0) cc_final: 0.7892 (pm20)
REVERT: B   84 MET cc_start: 0.7821 (ttm) cc_final: 0.7571 (ttm)
REVERT: B  134 LEU cc_start: 0.9188 (OUTLIER) cc_final: 0.8885 (pt)
REVERT: B  193 GLN cc_start: 0.8344 (pt0) cc_final: 0.7935 (pm20)
REVERT: B  251 ASN cc_start: 0.7749 (OUTLIER) cc_final: 0.7367 (t0)
REVERT: C   60 GLU cc_start: 0.8749 (mt-10) cc_final: 0.8495 (mt-10)
REVERT: C  134 LEU cc_start: 0.9201 (OUTLIER) cc_final: 0.8839 (pt)
REVERT: D  193 GLN cc_start: 0.8387 (pt0) cc_final: 0.7916 (pm20)
REVERT: E  193 GLN cc_start: 0.8331 (pt0) cc_final: 0.7849 (pm20)
  outliers start: 24
  outliers final: 14
  residues processed: 120
  average time/residue: 2.3243
  time to fit residues: 316.9477
Evaluate side-chains
  133 residues out of total 1490 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 115
  time to evaluate  : 2.175 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   47 ASP
Chi-restraints excluded: chain A residue  117 THR
Chi-restraints excluded: chain A residue  277 ARG
Chi-restraints excluded: chain A residue  280 LEU
Chi-restraints excluded: chain A residue  397 MET
Chi-restraints excluded: chain B residue  117 THR
Chi-restraints excluded: chain B residue  134 LEU
Chi-restraints excluded: chain B residue  251 ASN
Chi-restraints excluded: chain B residue  280 LEU
Chi-restraints excluded: chain B residue  397 MET
Chi-restraints excluded: chain C residue  117 THR
Chi-restraints excluded: chain C residue  134 LEU
Chi-restraints excluded: chain C residue  280 LEU
Chi-restraints excluded: chain C residue  395 ASP
Chi-restraints excluded: chain D residue  117 THR
Chi-restraints excluded: chain D residue  397 MET
Chi-restraints excluded: chain E residue  117 THR
Chi-restraints excluded: chain E residue  397 MET
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 165
   random chunks:
   chunk 73 optimal weight:    0.5980
   chunk 113 optimal weight:    1.9990
   chunk 100 optimal weight:    1.9990
   chunk 53 optimal weight:    2.9990
   chunk 150 optimal weight:    0.0170
   chunk 162 optimal weight:    0.7980
   chunk 143 optimal weight:    0.7980
   chunk 67 optimal weight:    1.9990
   chunk 23 optimal weight:    0.3980
   chunk 70 optimal weight:    0.8980
   chunk 127 optimal weight:    1.9990
   overall best weight:    0.5218

-------------------------------------------------------------------------------
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 = 0.3147 r_free = 0.3147 target = 0.081143 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.2915 r_free = 0.2915 target = 0.067715 restraints weight = 74464.041|
|-----------------------------------------------------------------------------|
r_work (start): 0.2904 rms_B_bonded: 2.33
r_work: 0.2812 rms_B_bonded: 2.47 restraints_weight: 0.5000
r_work: 0.2698 rms_B_bonded: 4.11 restraints_weight: 0.2500
r_work (final): 0.2698
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8711
moved from start:          0.3379

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.030  14150  Z= 0.108
  Angle     :  0.450   7.355  19270  Z= 0.231
  Chirality :  0.039   0.182   2160
  Planarity :  0.004   0.040   2395
  Dihedral  :  3.801  19.648   2030
  Min Nonbonded Distance : 2.411

Molprobity Statistics.
  All-atom Clashscore : 2.38
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.28 %
    Favored  : 97.72 %
  Rotamer:
    Outliers :  1.14 %
    Allowed  : 10.07 %
    Favored  : 88.79 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 7.14 %
    Cis-general     : 0.31 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.07 (0.21), residues: 1670
  helix:  3.53 (0.20), residues: 615
  sheet:  0.13 (0.25), residues: 460
  loop :  0.13 (0.25), residues: 595

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP C  73 
 HIS   0.002   0.001   HIS C 195 
 PHE   0.007   0.001   PHE C 307 
 TYR   0.007   0.001   TYR D 413 
 ARG   0.002   0.000   ARG B 277 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00038 (    5)
  link_NAG-ASN         : angle       1.71211 (   15)
  hydrogen bonds       : bond        0.03223 (  735)
  hydrogen bonds       : angle       4.01630 ( 2430)
  SS BOND              : bond        0.00305 (    5)
  SS BOND              : angle       0.64290 (   10)
  covalent geometry    : bond        0.00238 (14140)
  covalent geometry    : angle       0.44706 (19245)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 16216.04 seconds
wall clock time: 278 minutes 31.08 seconds (16711.08 seconds total)