Starting phenix.real_space_refine
on Mon Jun 23 17:59:45 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8bhb_16051/06_2025/8bhb_16051_trim.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8bhb_16051/06_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_16051/06_2025/8bhb_16051.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8bhb_16051/06_2025/8bhb_16051.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8bhb_16051/06_2025/8bhb_16051_trim.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8bhb_16051/06_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-5710/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: 15.40, per 1000 atoms: 0.57
  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: 7.44
  Conformation dependent library (CDL) restraints added in 1.9 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: 2.24
  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: 10.00

  Time building geometry restraints manager: 8.93 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: 0.12
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:             7.910
  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:             0.530
  Extract box with map and model:          1.140
  Check model and map are aligned:         0.200
  Set scattering table:                    0.270
  Process input model:                     59.730
  Find NCS groups from input model:        0.400
  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:             0.010
  Load rotamer database and sin/cos tables:11.030
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   81.280
-------------------------------------------------------------------------------
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  : 1.899 
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: 3.1944
  time to fit residues: 914.9915
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  : 1.993 
-------------------------------------------------------------------------------
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 = 35)----------------|
| r_work = 0.2971 r_free = 0.2971 target = 0.070422 restraints weight = 73222.493|
|-----------------------------------------------------------------------------|
r_work (start): 0.2951 rms_B_bonded: 2.34
r_work: 0.2853 rms_B_bonded: 2.51 restraints_weight: 0.5000
r_work: 0.2734 rms_B_bonded: 4.19 restraints_weight: 0.2500
r_work (final): 0.2734
-------------------------------------------------------------------------------
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       4.73793 ( 2430)
  SS BOND              : bond        0.00404 (    5)
  SS BOND              : angle       0.47956 (   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  : 2.177 
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: 0.8285 (pt0) cc_final: 0.7826 (pm20)
REVERT: A  277 ARG cc_start: 0.8042 (OUTLIER) cc_final: 0.7662 (mmt180)
REVERT: B   84 MET cc_start: 0.7978 (ttm) cc_final: 0.7776 (ttm)
REVERT: B  109 LYS cc_start: 0.8682 (tttt) cc_final: 0.8166 (tptp)
REVERT: B  115 MET cc_start: 0.8502 (mmp) cc_final: 0.7957 (mmp)
REVERT: B  193 GLN cc_start: 0.8355 (pt0) cc_final: 0.7947 (pm20)
REVERT: B  251 ASN cc_start: 0.7749 (OUTLIER) cc_final: 0.7378 (t0)
REVERT: C   60 GLU cc_start: 0.8797 (mt-10) cc_final: 0.8591 (mt-10)
REVERT: C  109 LYS cc_start: 0.8668 (tttt) cc_final: 0.8142 (tptp)
REVERT: D  109 LYS cc_start: 0.8713 (tttt) cc_final: 0.8199 (tptp)
REVERT: D  193 GLN cc_start: 0.8302 (pt0) cc_final: 0.7908 (pm20)
REVERT: D  251 ASN cc_start: 0.8057 (t0) cc_final: 0.7732 (t0)
REVERT: E  109 LYS cc_start: 0.8694 (tttt) cc_final: 0.8185 (tptp)
REVERT: E  193 GLN cc_start: 0.8257 (pt0) cc_final: 0.7886 (pm20)
  outliers start: 21
  outliers final: 9
  residues processed: 163
  average time/residue: 2.5328
  time to fit residues: 457.3812
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  : 1.969 
-------------------------------------------------------------------------------
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:    0.9980
   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:    1.9990
   overall best weight:    1.2584

-------------------------------------------------------------------------------
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 = 0.3138 r_free = 0.3138 target = 0.080536 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.2905 r_free = 0.2905 target = 0.067009 restraints weight = 74410.631|
|-----------------------------------------------------------------------------|
r_work (start): 0.2866 rms_B_bonded: 2.33
r_work: 0.2767 rms_B_bonded: 2.48 restraints_weight: 0.5000
r_work: 0.2650 rms_B_bonded: 4.11 restraints_weight: 0.2500
r_work (final): 0.2650
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8741
moved from start:          0.2679

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.039  14150  Z= 0.177
  Angle     :  0.487   6.742  19270  Z= 0.258
  Chirality :  0.041   0.130   2160
  Planarity :  0.004   0.038   2395
  Dihedral  :  3.886  18.353   2030
  Min Nonbonded Distance : 2.316

Molprobity Statistics.
  All-atom Clashscore : 1.80
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.16 %
    Favored  : 97.84 %
  Rotamer:
    Outliers :  1.81 %
    Allowed  :  7.45 %
    Favored  : 90.74 %
  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:  3.23 (0.20), residues: 610
  sheet:  0.29 (0.24), residues: 455
  loop :  0.20 (0.24), residues: 605

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP C 291 
 HIS   0.003   0.001   HIS D 221 
 PHE   0.013   0.002   PHE C  69 
 TYR   0.011   0.001   TYR A 132 
 ARG   0.003   0.000   ARG B 277 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00150 (    5)
  link_NAG-ASN         : angle       1.59929 (   15)
  hydrogen bonds       : bond        0.04411 (  735)
  hydrogen bonds       : angle       4.46124 ( 2430)
  SS BOND              : bond        0.00407 (    5)
  SS BOND              : angle       0.60314 (   10)
  covalent geometry    : bond        0.00396 (14140)
  covalent geometry    : angle       0.48499 (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
  169 residues out of total 1490 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 142
  time to evaluate  : 2.179 
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   60 GLU cc_start: 0.8786 (mt-10) cc_final: 0.8533 (mt-10)
REVERT: A  109 LYS cc_start: 0.8710 (tttt) cc_final: 0.8190 (tptp)
REVERT: A  151 MET cc_start: 0.9117 (mpt) cc_final: 0.8896 (mpt)
REVERT: A  193 GLN cc_start: 0.8331 (pt0) cc_final: 0.7900 (pm20)
REVERT: A  277 ARG cc_start: 0.7987 (OUTLIER) cc_final: 0.7682 (mmt180)
REVERT: B  109 LYS cc_start: 0.8641 (tttt) cc_final: 0.8119 (tptp)
REVERT: B  193 GLN cc_start: 0.8359 (pt0) cc_final: 0.7932 (pm20)
REVERT: B  251 ASN cc_start: 0.7714 (OUTLIER) cc_final: 0.7309 (t0)
REVERT: C   39 GLU cc_start: 0.8344 (OUTLIER) cc_final: 0.8038 (tp30)
REVERT: C   60 GLU cc_start: 0.8775 (mt-10) cc_final: 0.8536 (mt-10)
REVERT: C  109 LYS cc_start: 0.8645 (tttt) cc_final: 0.8134 (tptp)
REVERT: D  109 LYS cc_start: 0.8666 (tttt) cc_final: 0.8133 (tptp)
REVERT: D  151 MET cc_start: 0.9092 (mpt) cc_final: 0.8799 (mpt)
REVERT: D  193 GLN cc_start: 0.8364 (pt0) cc_final: 0.7936 (pm20)
REVERT: D  251 ASN cc_start: 0.8070 (t0) cc_final: 0.7734 (t0)
REVERT: E  109 LYS cc_start: 0.8662 (tttt) cc_final: 0.8150 (tptp)
REVERT: E  193 GLN cc_start: 0.8294 (pt0) cc_final: 0.7888 (pm20)
  outliers start: 27
  outliers final: 9
  residues processed: 151
  average time/residue: 2.4749
  time to fit residues: 415.0254
Evaluate side-chains
  140 residues out of total 1490 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 128
  time to evaluate  : 2.170 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   47 ASP
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  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=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 165
   random chunks:
   chunk 3 optimal weight:    2.9990
   chunk 20 optimal weight:    2.9990
   chunk 95 optimal weight:    2.9990
   chunk 109 optimal weight:    0.3980
   chunk 42 optimal weight:    1.9990
   chunk 83 optimal weight:    2.9990
   chunk 63 optimal weight:    1.9990
   chunk 22 optimal weight:    1.9990
   chunk 62 optimal weight:    0.9990
   chunk 147 optimal weight:    0.9990
   chunk 158 optimal weight:    2.9990
   overall best weight:    1.2788

-------------------------------------------------------------------------------
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 = 0.3126 r_free = 0.3126 target = 0.079859 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 28)----------------|
| r_work = 0.2889 r_free = 0.2889 target = 0.066245 restraints weight = 74982.957|
|-----------------------------------------------------------------------------|
r_work (start): 0.2887 rms_B_bonded: 2.34
r_work: 0.2791 rms_B_bonded: 2.47 restraints_weight: 0.5000
r_work: 0.2677 rms_B_bonded: 4.11 restraints_weight: 0.2500
r_work (final): 0.2677
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8755
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      :  0.004   0.042  14150  Z= 0.178
  Angle     :  0.482   6.703  19270  Z= 0.253
  Chirality :  0.040   0.126   2160
  Planarity :  0.004   0.038   2395
  Dihedral  :  3.978  19.341   2030
  Min Nonbonded Distance : 2.353

Molprobity Statistics.
  All-atom Clashscore : 1.65
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.86 %
    Favored  : 98.14 %
  Rotamer:
    Outliers :  2.35 %
    Allowed  :  7.32 %
    Favored  : 90.34 %
  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:  1.93 (0.21), residues: 1670
  helix:  3.28 (0.20), residues: 610
  sheet:  0.19 (0.24), residues: 455
  loop :  0.12 (0.24), residues: 605

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP C  73 
 HIS   0.003   0.001   HIS C 221 
 PHE   0.011   0.001   PHE B  69 
 TYR   0.010   0.001   TYR A 132 
 ARG   0.003   0.000   ARG B 277 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00147 (    5)
  link_NAG-ASN         : angle       1.67654 (   15)
  hydrogen bonds       : bond        0.04046 (  735)
  hydrogen bonds       : angle       4.32872 ( 2430)
  SS BOND              : bond        0.00435 (    5)
  SS BOND              : angle       0.71153 (   10)
  covalent geometry    : bond        0.00402 (14140)
  covalent geometry    : angle       0.47953 (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
  177 residues out of total 1490 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 142
  time to evaluate  : 2.310 
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: symmetry clash
REVERT: A   60 GLU cc_start: 0.8773 (mt-10) cc_final: 0.8494 (mt-10)
REVERT: A  109 LYS cc_start: 0.8712 (tttt) cc_final: 0.8188 (tptp)
REVERT: A  193 GLN cc_start: 0.8329 (pt0) cc_final: 0.7905 (pm20)
REVERT: B  109 LYS cc_start: 0.8651 (tttt) cc_final: 0.8136 (tptp)
REVERT: B  193 GLN cc_start: 0.8377 (pt0) cc_final: 0.8010 (pm20)
REVERT: B  251 ASN cc_start: 0.7743 (OUTLIER) cc_final: 0.7360 (t0)
REVERT: C   60 GLU cc_start: 0.8793 (mt-10) cc_final: 0.8538 (mt-10)
REVERT: C  109 LYS cc_start: 0.8651 (tttt) cc_final: 0.8134 (tptp)
REVERT: D  109 LYS cc_start: 0.8690 (tttt) cc_final: 0.8169 (tptp)
REVERT: D  193 GLN cc_start: 0.8383 (pt0) cc_final: 0.7929 (pm20)
REVERT: D  251 ASN cc_start: 0.8076 (t0) cc_final: 0.7751 (t0)
REVERT: E  109 LYS cc_start: 0.8680 (tttt) cc_final: 0.8163 (tptp)
REVERT: E  193 GLN cc_start: 0.8310 (pt0) cc_final: 0.7925 (pm20)
  outliers start: 35
  outliers final: 13
  residues processed: 155
  average time/residue: 2.3670
  time to fit residues: 409.1261
Evaluate side-chains
  147 residues out of total 1490 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 133
  time to evaluate  : 1.949 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   47 ASP
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  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 C residue  397 MET
Chi-restraints excluded: chain D residue   47 ASP
Chi-restraints excluded: chain D residue  280 LEU
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=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 165
   random chunks:
   chunk 149 optimal weight:    2.9990
   chunk 88 optimal weight:    1.9990
   chunk 152 optimal weight:    1.9990
   chunk 9 optimal weight:    1.9990
   chunk 100 optimal weight:    3.9990
   chunk 129 optimal weight:    1.9990
   chunk 39 optimal weight:    1.9990
   chunk 121 optimal weight:    0.9990
   chunk 87 optimal weight:    1.9990
   chunk 38 optimal weight:    1.9990
   chunk 73 optimal weight:    0.2980
   overall best weight:    1.4588

-------------------------------------------------------------------------------
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 = 0.3097 r_free = 0.3097 target = 0.077880 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.2861 r_free = 0.2861 target = 0.064316 restraints weight = 74903.648|
|-----------------------------------------------------------------------------|
r_work (start): 0.2826 rms_B_bonded: 2.32
r_work: 0.2727 rms_B_bonded: 2.46 restraints_weight: 0.5000
r_work: 0.2608 rms_B_bonded: 4.06 restraints_weight: 0.2500
r_work (final): 0.2608
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8733
moved from start:          0.3148

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= 0.200
  Angle     :  0.493   6.674  19270  Z= 0.259
  Chirality :  0.041   0.127   2160
  Planarity :  0.004   0.040   2395
  Dihedral  :  4.155  19.976   2030
  Min Nonbonded Distance : 2.361

Molprobity Statistics.
  All-atom Clashscore : 1.87
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.10 %
    Favored  : 97.90 %
  Rotamer:
    Outliers :  2.82 %
    Allowed  :  7.85 %
    Favored  : 89.33 %
  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:  1.88 (0.21), residues: 1670
  helix:  3.31 (0.20), residues: 610
  sheet:  0.04 (0.24), residues: 465
  loop :  0.12 (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 221 
 PHE   0.012   0.002   PHE A 104 
 TYR   0.009   0.001   TYR A 132 
 ARG   0.002   0.000   ARG B 277 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00213 (    5)
  link_NAG-ASN         : angle       1.78884 (   15)
  hydrogen bonds       : bond        0.04072 (  735)
  hydrogen bonds       : angle       4.31588 ( 2430)
  SS BOND              : bond        0.00471 (    5)
  SS BOND              : angle       0.80512 (   10)
  covalent geometry    : bond        0.00450 (14140)
  covalent geometry    : angle       0.49027 (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
  174 residues out of total 1490 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 42
    poor density    : 132
  time to evaluate  : 2.047 
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: A   47 ASP cc_start: 0.8290 (OUTLIER) cc_final: 0.8066 (p0)
REVERT: A  147 GLU cc_start: 0.8338 (OUTLIER) cc_final: 0.8101 (tp30)
REVERT: A  193 GLN cc_start: 0.8348 (pt0) cc_final: 0.7852 (pm20)
REVERT: B   84 MET cc_start: 0.8017 (ttm) cc_final: 0.7807 (ttm)
REVERT: B  109 LYS cc_start: 0.8628 (tttt) cc_final: 0.8093 (tptp)
REVERT: B  193 GLN cc_start: 0.8378 (pt0) cc_final: 0.7952 (pm20)
REVERT: B  251 ASN cc_start: 0.7759 (OUTLIER) cc_final: 0.7365 (t0)
REVERT: C   60 GLU cc_start: 0.8784 (mt-10) cc_final: 0.8522 (mt-10)
REVERT: C  109 LYS cc_start: 0.8646 (tttt) cc_final: 0.8100 (tptp)
REVERT: D   60 GLU cc_start: 0.8743 (mt-10) cc_final: 0.8490 (mt-10)
REVERT: D  109 LYS cc_start: 0.8656 (tttt) cc_final: 0.8109 (tptp)
REVERT: D  193 GLN cc_start: 0.8355 (pt0) cc_final: 0.7876 (pm20)
REVERT: E  193 GLN cc_start: 0.8305 (pt0) cc_final: 0.7848 (pm20)
REVERT: E  251 ASN cc_start: 0.8015 (t0) cc_final: 0.7784 (t0)
  outliers start: 42
  outliers final: 18
  residues processed: 148
  average time/residue: 2.4411
  time to fit residues: 401.3511
Evaluate side-chains
  145 residues out of total 1490 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 124
  time to evaluate  : 2.156 
-------------------------------------------------------------------------------
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  141 GLU
Chi-restraints excluded: chain A residue  147 GLU
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  117 THR
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  280 LEU
Chi-restraints excluded: chain C residue  395 ASP
Chi-restraints excluded: chain D residue  117 THR
Chi-restraints excluded: chain D residue  280 LEU
Chi-restraints excluded: chain E residue  117 THR
Chi-restraints excluded: chain E residue  121 MET
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:    2.9990
   chunk 127 optimal weight:    1.9990
   chunk 43 optimal weight:    2.9990
   chunk 16 optimal weight:    0.6980
   chunk 162 optimal weight:    0.4980
   chunk 5 optimal weight:    0.6980
   chunk 85 optimal weight:    0.9980
   chunk 59 optimal weight:    2.9990
   overall best weight:    0.9782

-------------------------------------------------------------------------------
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 = 0.3118 r_free = 0.3118 target = 0.079234 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 24)----------------|
| r_work = 0.2892 r_free = 0.2892 target = 0.065838 restraints weight = 75590.411|
|-----------------------------------------------------------------------------|
r_work (start): 0.2860 rms_B_bonded: 2.28
r_work: 0.2766 rms_B_bonded: 2.43 restraints_weight: 0.5000
r_work: 0.2650 rms_B_bonded: 4.03 restraints_weight: 0.2500
r_work (final): 0.2650
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8714
moved from start:          0.3202

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031  14150  Z= 0.147
  Angle     :  0.470   6.909  19270  Z= 0.244
  Chirality :  0.040   0.121   2160
  Planarity :  0.004   0.039   2395
  Dihedral  :  3.997  19.858   2030
  Min Nonbonded Distance : 2.380

Molprobity Statistics.
  All-atom Clashscore : 1.80
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.04 %
    Favored  : 97.96 %
  Rotamer:
    Outliers :  1.74 %
    Allowed  :  8.72 %
    Favored  : 89.53 %
  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:  1.93 (0.21), residues: 1670
  helix:  3.37 (0.20), residues: 610
  sheet:  0.09 (0.25), residues: 460
  loop :  0.10 (0.24), residues: 600

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP C  73 
 HIS   0.003   0.001   HIS C 195 
 PHE   0.009   0.001   PHE A 104 
 TYR   0.007   0.001   TYR A 132 
 ARG   0.002   0.000   ARG B 277 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00102 (    5)
  link_NAG-ASN         : angle       1.77676 (   15)
  hydrogen bonds       : bond        0.03695 (  735)
  hydrogen bonds       : angle       4.20151 ( 2430)
  SS BOND              : bond        0.00378 (    5)
  SS BOND              : angle       0.71521 (   10)
  covalent geometry    : bond        0.00325 (14140)
  covalent geometry    : angle       0.46773 (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
  152 residues out of total 1490 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 126
  time to evaluate  : 1.991 
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: 0.8350 (pt0) cc_final: 0.7868 (pm20)
REVERT: B   84 MET cc_start: 0.7949 (ttm) cc_final: 0.7708 (ttm)
REVERT: B  109 LYS cc_start: 0.8636 (tttt) cc_final: 0.8101 (tptp)
REVERT: B  134 LEU cc_start: 0.9178 (OUTLIER) cc_final: 0.8911 (pt)
REVERT: B  193 GLN cc_start: 0.8351 (pt0) cc_final: 0.7950 (pm20)
REVERT: B  251 ASN cc_start: 0.7758 (OUTLIER) cc_final: 0.7376 (t0)
REVERT: C   60 GLU cc_start: 0.8769 (mt-10) cc_final: 0.8482 (mt-10)
REVERT: D   60 GLU cc_start: 0.8760 (mt-10) cc_final: 0.8503 (mt-10)
REVERT: D  193 GLN cc_start: 0.8355 (pt0) cc_final: 0.7888 (pm20)
REVERT: E  193 GLN cc_start: 0.8288 (pt0) cc_final: 0.7842 (pm20)
  outliers start: 26
  outliers final: 15
  residues processed: 131
  average time/residue: 2.3064
  time to fit residues: 340.9585
Evaluate side-chains
  135 residues out of total 1490 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 118
  time to evaluate  : 2.007 
-------------------------------------------------------------------------------
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  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  280 LEU
Chi-restraints excluded: chain D residue  117 THR
Chi-restraints excluded: chain D residue  280 LEU
Chi-restraints excluded: chain E residue  117 THR
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=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 165
   random chunks:
   chunk 16 optimal weight:    0.0970
   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:    0.5980
   chunk 32 optimal weight:    0.7980
   chunk 26 optimal weight:    1.9990
   chunk 114 optimal weight:    1.9990
   chunk 42 optimal weight:    1.9990
   overall best weight:    1.0982

-------------------------------------------------------------------------------
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 = 0.3104 r_free = 0.3104 target = 0.078273 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.2871 r_free = 0.2871 target = 0.064757 restraints weight = 75303.288|
|-----------------------------------------------------------------------------|
r_work (start): 0.2885 rms_B_bonded: 2.32
r_work: 0.2794 rms_B_bonded: 2.44 restraints_weight: 0.5000
r_work: 0.2682 rms_B_bonded: 4.07 restraints_weight: 0.2500
r_work (final): 0.2682
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8722
moved from start:          0.3257

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.032  14150  Z= 0.160
  Angle     :  0.473   6.168  19270  Z= 0.246
  Chirality :  0.040   0.120   2160
  Planarity :  0.004   0.039   2395
  Dihedral  :  4.035  19.957   2030
  Min Nonbonded Distance : 2.384

Molprobity Statistics.
  All-atom Clashscore : 1.76
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.16 %
    Favored  : 97.84 %
  Rotamer:
    Outliers :  2.55 %
    Allowed  :  8.39 %
    Favored  : 89.06 %
  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:  1.93 (0.21), residues: 1670
  helix:  3.40 (0.20), residues: 610
  sheet:  0.06 (0.24), residues: 460
  loop :  0.09 (0.24), residues: 600

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP E 414 
 HIS   0.003   0.001   HIS C 195 
 PHE   0.010   0.001   PHE A 104 
 TYR   0.008   0.001   TYR E 413 
 ARG   0.002   0.000   ARG B 277 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00145 (    5)
  link_NAG-ASN         : angle       1.78949 (   15)
  hydrogen bonds       : bond        0.03696 (  735)
  hydrogen bonds       : angle       4.18895 ( 2430)
  SS BOND              : bond        0.00400 (    5)
  SS BOND              : angle       0.75628 (   10)
  covalent geometry    : bond        0.00359 (14140)
  covalent geometry    : angle       0.47051 (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
  158 residues out of total 1490 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 38
    poor density    : 120
  time to evaluate  : 2.260 
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: 0.8363 (pt0) cc_final: 0.7880 (pm20)
REVERT: B   84 MET cc_start: 0.7963 (ttm) cc_final: 0.7713 (ttm)
REVERT: B  134 LEU cc_start: 0.9165 (OUTLIER) cc_final: 0.8944 (pt)
REVERT: B  193 GLN cc_start: 0.8348 (pt0) cc_final: 0.7948 (pm20)
REVERT: B  251 ASN cc_start: 0.7759 (OUTLIER) cc_final: 0.7389 (t0)
REVERT: C   60 GLU cc_start: 0.8769 (mt-10) cc_final: 0.8500 (mt-10)
REVERT: C  245 GLN cc_start: 0.9190 (OUTLIER) cc_final: 0.8846 (mt0)
REVERT: D  193 GLN cc_start: 0.8368 (pt0) cc_final: 0.7906 (pm20)
REVERT: E  193 GLN cc_start: 0.8302 (pt0) cc_final: 0.7858 (pm20)
  outliers start: 38
  outliers final: 18
  residues processed: 135
  average time/residue: 2.3040
  time to fit residues: 348.4563
Evaluate side-chains
  135 residues out of total 1490 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 114
  time to evaluate  : 2.172 
-------------------------------------------------------------------------------
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  280 LEU
Chi-restraints excluded: chain A residue  397 MET
Chi-restraints excluded: chain B residue  116 THR
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  280 LEU
Chi-restraints excluded: chain E residue  117 THR
Chi-restraints excluded: chain E residue  121 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=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 165
   random chunks:
   chunk 158 optimal weight:    0.9980
   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:    1.9990
   chunk 87 optimal weight:    1.9990
   chunk 82 optimal weight:    1.9990
   chunk 46 optimal weight:    0.9990
   chunk 141 optimal weight:    2.9990
   chunk 2 optimal weight:    0.4980
   overall best weight:    1.0984

-------------------------------------------------------------------------------
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 = 0.3104 r_free = 0.3104 target = 0.078293 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.2870 r_free = 0.2870 target = 0.064842 restraints weight = 75056.543|
|-----------------------------------------------------------------------------|
r_work (start): 0.2845 rms_B_bonded: 2.31
r_work: 0.2748 rms_B_bonded: 2.46 restraints_weight: 0.5000
r_work: 0.2633 rms_B_bonded: 4.07 restraints_weight: 0.2500
r_work (final): 0.2633
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8723
moved from start:          0.3320

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.033  14150  Z= 0.160
  Angle     :  0.474   6.112  19270  Z= 0.246
  Chirality :  0.040   0.120   2160
  Planarity :  0.004   0.039   2395
  Dihedral  :  4.030  19.942   2030
  Min Nonbonded Distance : 2.389

Molprobity Statistics.
  All-atom Clashscore : 1.80
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.10 %
    Favored  : 97.90 %
  Rotamer:
    Outliers :  2.01 %
    Allowed  :  8.99 %
    Favored  : 88.99 %
  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:  1.96 (0.21), residues: 1670
  helix:  3.45 (0.20), residues: 610
  sheet:  0.07 (0.25), residues: 460
  loop :  0.07 (0.24), residues: 600

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP E 414 
 HIS   0.003   0.001   HIS C 195 
 PHE   0.010   0.001   PHE A 104 
 TYR   0.007   0.001   TYR E 413 
 ARG   0.002   0.000   ARG B 277 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00144 (    5)
  link_NAG-ASN         : angle       1.79931 (   15)
  hydrogen bonds       : bond        0.03630 (  735)
  hydrogen bonds       : angle       4.16463 ( 2430)
  SS BOND              : bond        0.00391 (    5)
  SS BOND              : angle       0.75369 (   10)
  covalent geometry    : bond        0.00358 (14140)
  covalent geometry    : angle       0.47091 (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
  149 residues out of total 1490 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 119
  time to evaluate  : 2.473 
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: 0.8381 (pt0) cc_final: 0.7889 (pm20)
REVERT: B   84 MET cc_start: 0.7957 (ttm) cc_final: 0.7701 (ttm)
REVERT: B  193 GLN cc_start: 0.8381 (pt0) cc_final: 0.7957 (pm20)
REVERT: B  251 ASN cc_start: 0.7755 (OUTLIER) cc_final: 0.7379 (t0)
REVERT: C   60 GLU cc_start: 0.8779 (mt-10) cc_final: 0.8512 (mt-10)
REVERT: C  134 LEU cc_start: 0.9199 (OUTLIER) cc_final: 0.8849 (pt)
REVERT: C  245 GLN cc_start: 0.9184 (OUTLIER) cc_final: 0.8830 (mt0)
REVERT: D   60 GLU cc_start: 0.8771 (mt-10) cc_final: 0.8566 (mt-10)
REVERT: D  193 GLN cc_start: 0.8383 (pt0) cc_final: 0.7912 (pm20)
REVERT: E  193 GLN cc_start: 0.8332 (pt0) cc_final: 0.7868 (pm20)
  outliers start: 30
  outliers final: 19
  residues processed: 128
  average time/residue: 2.2671
  time to fit residues: 326.3908
Evaluate side-chains
  142 residues out of total 1490 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 120
  time to evaluate  : 2.201 
-------------------------------------------------------------------------------
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  280 LEU
Chi-restraints excluded: chain A residue  397 MET
Chi-restraints excluded: chain B residue  116 THR
Chi-restraints excluded: chain B residue  117 THR
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  121 MET
Chi-restraints excluded: chain C residue  134 LEU
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  280 LEU
Chi-restraints excluded: chain E residue  117 THR
Chi-restraints excluded: chain E residue  121 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=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 165
   random chunks:
   chunk 18 optimal weight:    1.9990
   chunk 137 optimal weight:    1.9990
   chunk 91 optimal weight:    1.9990
   chunk 65 optimal weight:    1.9990
   chunk 120 optimal weight:    1.9990
   chunk 90 optimal weight:    0.4980
   chunk 24 optimal weight:    1.9990
   chunk 126 optimal weight:    2.9990
   chunk 125 optimal weight:    2.9990
   chunk 87 optimal weight:    0.8980
   chunk 147 optimal weight:    0.7980
   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 = 0.3103 r_free = 0.3103 target = 0.078328 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.2876 r_free = 0.2876 target = 0.064997 restraints weight = 75175.339|
|-----------------------------------------------------------------------------|
r_work (start): 0.2854 rms_B_bonded: 2.27
r_work: 0.2758 rms_B_bonded: 2.42 restraints_weight: 0.5000
r_work: 0.2642 rms_B_bonded: 4.01 restraints_weight: 0.2500
r_work (final): 0.2642
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8719
moved from start:          0.3390

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.033  14150  Z= 0.175
  Angle     :  0.482   6.215  19270  Z= 0.251
  Chirality :  0.040   0.121   2160
  Planarity :  0.004   0.040   2395
  Dihedral  :  4.112  20.175   2030
  Min Nonbonded Distance : 2.392

Molprobity Statistics.
  All-atom Clashscore : 1.69
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.46 %
    Favored  : 97.54 %
  Rotamer:
    Outliers :  1.61 %
    Allowed  :  9.60 %
    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:  1.96 (0.21), residues: 1670
  helix:  3.47 (0.20), residues: 610
  sheet:  0.07 (0.24), residues: 460
  loop :  0.05 (0.24), residues: 600

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 B 277 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00169 (    5)
  link_NAG-ASN         : angle       1.84091 (   15)
  hydrogen bonds       : bond        0.03735 (  735)
  hydrogen bonds       : angle       4.19867 ( 2430)
  SS BOND              : bond        0.00416 (    5)
  SS BOND              : angle       0.77700 (   10)
  covalent geometry    : bond        0.00395 (14140)
  covalent geometry    : angle       0.47895 (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
  144 residues out of total 1490 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 120
  time to evaluate  : 2.012 
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: 0.8249 (OUTLIER) cc_final: 0.8034 (p0)
REVERT: A  193 GLN cc_start: 0.8365 (pt0) cc_final: 0.7864 (pm20)
REVERT: B   84 MET cc_start: 0.7944 (ttm) cc_final: 0.7737 (ttm)
REVERT: B  193 GLN cc_start: 0.8354 (pt0) cc_final: 0.7941 (pm20)
REVERT: B  251 ASN cc_start: 0.7744 (OUTLIER) cc_final: 0.7377 (t0)
REVERT: C   60 GLU cc_start: 0.8744 (mt-10) cc_final: 0.8467 (mt-10)
REVERT: C  134 LEU cc_start: 0.9199 (OUTLIER) cc_final: 0.8877 (pt)
REVERT: D  193 GLN cc_start: 0.8377 (pt0) cc_final: 0.7904 (pm20)
REVERT: E  193 GLN cc_start: 0.8336 (pt0) cc_final: 0.7847 (pm20)
  outliers start: 24
  outliers final: 18
  residues processed: 125
  average time/residue: 2.2033
  time to fit residues: 309.6374
Evaluate side-chains
  139 residues out of total 1490 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 118
  time to evaluate  : 2.060 
-------------------------------------------------------------------------------
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  280 LEU
Chi-restraints excluded: chain A residue  397 MET
Chi-restraints excluded: chain B residue  116 THR
Chi-restraints excluded: chain B residue  117 THR
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  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  187 ASP
Chi-restraints excluded: chain D residue  280 LEU
Chi-restraints excluded: chain E residue  117 THR
Chi-restraints excluded: chain E residue  121 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=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:    1.9990
   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:    1.7990

-------------------------------------------------------------------------------
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 = 0.3082 r_free = 0.3082 target = 0.077054 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.2853 r_free = 0.2853 target = 0.063757 restraints weight = 75889.381|
|-----------------------------------------------------------------------------|
r_work (start): 0.2825 rms_B_bonded: 2.26
r_work: 0.2730 rms_B_bonded: 2.39 restraints_weight: 0.5000
r_work: 0.2614 rms_B_bonded: 3.96 restraints_weight: 0.2500
r_work (final): 0.2614
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8728
moved from start:          0.3427

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.045  14150  Z= 0.238
  Angle     :  0.520   6.716  19270  Z= 0.273
  Chirality :  0.042   0.131   2160
  Planarity :  0.004   0.039   2395
  Dihedral  :  4.411  23.069   2030
  Min Nonbonded Distance : 2.344

Molprobity Statistics.
  All-atom Clashscore : 1.91
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.46 %
    Favored  : 97.54 %
  Rotamer:
    Outliers :  1.88 %
    Allowed  :  9.33 %
    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:  1.83 (0.21), residues: 1670
  helix:  3.40 (0.20), residues: 610
  sheet: -0.06 (0.24), residues: 470
  loop : -0.00 (0.24), residues: 590

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.004   0.001   TRP C 291 
 HIS   0.003   0.001   HIS C 195 
 PHE   0.014   0.002   PHE A 104 
 TYR   0.008   0.001   TYR E 228 
 ARG   0.002   0.000   ARG D 190 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00295 (    5)
  link_NAG-ASN         : angle       1.93689 (   15)
  hydrogen bonds       : bond        0.04105 (  735)
  hydrogen bonds       : angle       4.32385 ( 2430)
  SS BOND              : bond        0.00500 (    5)
  SS BOND              : angle       0.89856 (   10)
  covalent geometry    : bond        0.00542 (14140)
  covalent geometry    : angle       0.51744 (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
  148 residues out of total 1490 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 120
  time to evaluate  : 2.342 
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: A   47 ASP cc_start: 0.8376 (OUTLIER) cc_final: 0.8147 (p0)
REVERT: A  147 GLU cc_start: 0.8349 (OUTLIER) cc_final: 0.8090 (tp30)
REVERT: A  193 GLN cc_start: 0.8361 (pt0) cc_final: 0.7864 (pm20)
REVERT: B  193 GLN cc_start: 0.8353 (pt0) cc_final: 0.7886 (pm20)
REVERT: B  251 ASN cc_start: 0.7764 (OUTLIER) cc_final: 0.7381 (t0)
REVERT: C   60 GLU cc_start: 0.8730 (mt-10) cc_final: 0.8477 (mt-10)
REVERT: C  134 LEU cc_start: 0.9206 (OUTLIER) cc_final: 0.8844 (pt)
REVERT: D  193 GLN cc_start: 0.8374 (pt0) cc_final: 0.7899 (pm20)
REVERT: E  193 GLN cc_start: 0.8329 (pt0) cc_final: 0.7837 (pm20)
  outliers start: 28
  outliers final: 14
  residues processed: 131
  average time/residue: 2.2761
  time to fit residues: 339.7708
Evaluate side-chains
  136 residues out of total 1490 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 118
  time to evaluate  : 2.263 
-------------------------------------------------------------------------------
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  147 GLU
Chi-restraints excluded: chain A residue  397 MET
Chi-restraints excluded: chain B residue  116 THR
Chi-restraints excluded: chain B residue  117 THR
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  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  187 ASP
Chi-restraints excluded: chain D residue  280 LEU
Chi-restraints excluded: chain E residue  117 THR
Chi-restraints excluded: chain E residue  141 GLU
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:    0.0370
   chunk 113 optimal weight:    0.6980
   chunk 100 optimal weight:    0.6980
   chunk 53 optimal weight:    1.9990
   chunk 150 optimal weight:    0.9980
   chunk 162 optimal weight:    0.3980
   chunk 143 optimal weight:    0.9980
   chunk 67 optimal weight:    0.6980
   chunk 23 optimal weight:    1.9990
   chunk 70 optimal weight:    0.0980
   chunk 127 optimal weight:    1.9990
   overall best weight:    0.3858

-------------------------------------------------------------------------------
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 = 0.3150 r_free = 0.3150 target = 0.081234 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.2916 r_free = 0.2916 target = 0.067728 restraints weight = 74416.558|
|-----------------------------------------------------------------------------|
r_work (start): 0.2915 rms_B_bonded: 2.33
r_work: 0.2823 rms_B_bonded: 2.47 restraints_weight: 0.5000
r_work: 0.2710 rms_B_bonded: 4.11 restraints_weight: 0.2500
r_work (final): 0.2710
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8715
moved from start:          0.3418

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.031  14150  Z= 0.101
  Angle     :  0.450   6.493  19270  Z= 0.232
  Chirality :  0.039   0.207   2160
  Planarity :  0.004   0.040   2395
  Dihedral  :  3.828  19.729   2030
  Min Nonbonded Distance : 2.409

Molprobity Statistics.
  All-atom Clashscore : 2.42
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.16 %
    Favored  : 97.84 %
  Rotamer:
    Outliers :  1.28 %
    Allowed  :  9.93 %
    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:  2.03 (0.21), residues: 1670
  helix:  3.55 (0.20), residues: 610
  sheet:  0.10 (0.25), residues: 460
  loop :  0.08 (0.24), residues: 600

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 E 160 
 TYR   0.007   0.001   TYR D 297 
 ARG   0.003   0.000   ARG B 277 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00065 (    5)
  link_NAG-ASN         : angle       1.76375 (   15)
  hydrogen bonds       : bond        0.03214 (  735)
  hydrogen bonds       : angle       4.03697 ( 2430)
  SS BOND              : bond        0.00276 (    5)
  SS BOND              : angle       0.61573 (   10)
  covalent geometry    : bond        0.00219 (14140)
  covalent geometry    : angle       0.44737 (19245)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 17770.96 seconds
wall clock time: 306 minutes 47.05 seconds (18407.05 seconds total)