Starting phenix.real_space_refine
on Wed Jul 30 17:45:01 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8hc5_34652/07_2025/8hc5_34652.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8hc5_34652/07_2025/8hc5_34652.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.43
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8hc5_34652/07_2025/8hc5_34652.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8hc5_34652/07_2025/8hc5_34652.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8hc5_34652/07_2025/8hc5_34652.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8hc5_34652/07_2025/8hc5_34652.cif"
  }
  resolution = 3.43
  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=   0.002 sd=   0.058
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
  Anisotropic ADP refinement not supported. Converting 1488 atoms to isotropic.
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 4
    Type Number    sf(0)   Gaussians
     S      45      5.16       5
     C    7218      2.51       5
     N    1906      2.21       5
     O    2231      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 12 residue(s): 0.03s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib"
  Total number of atoms: 11400
  Number of models: 1
  Model: ""
    Number of chains: 6
    Chain: "C"
      Number of atoms: 4948
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 624, 4948
          Classifications: {'peptide': 624}
          Link IDs: {'PTRANS': 31, 'TRANS': 592}
          Chain breaks: 2
    Chain: "H"
      Number of atoms: 1588
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 214, 1588
          Classifications: {'peptide': 214}
          Link IDs: {'PCIS': 2, 'PTRANS': 9, 'TRANS': 202}
          Chain breaks: 1
    Chain: "L"
      Number of atoms: 1628
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 215, 1628
          Classifications: {'peptide': 215}
          Link IDs: {'PCIS': 1, 'PTRANS': 10, 'TRANS': 203}
    Chain: "D"
      Number of atoms: 1665
      Number of conformers: 2
      Conformer: "A"
        Number of residues, atoms: 227, 1661
          Classifications: {'peptide': 227}
          Incomplete info: {'truncation_to_alanine': 1}
          Link IDs: {'PTRANS': 12, 'TRANS': 214}
          Unresolved non-hydrogen bonds: 4
          Unresolved non-hydrogen angles: 4
          Unresolved non-hydrogen dihedrals: 4
      Conformer: "B"
        Number of residues, atoms: 227, 1661
          Classifications: {'peptide': 227}
          Incomplete info: {'truncation_to_alanine': 1}
          Link IDs: {'PTRANS': 12, 'TRANS': 214}
          Unresolved non-hydrogen bonds: 4
          Unresolved non-hydrogen angles: 4
          Unresolved non-hydrogen dihedrals: 4
          bond proxies already assigned to first conformer: 1690
    Chain: "E"
      Number of atoms: 1557
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 213, 1557
          Classifications: {'peptide': 213}
          Incomplete info: {'truncation_to_alanine': 2}
          Link IDs: {'PTRANS': 16, 'TRANS': 196}
          Unresolved non-hydrogen bonds: 8
          Unresolved non-hydrogen angles: 9
          Unresolved non-hydrogen dihedrals: 7
          Planarities with less than four sites: {'GLU:plan': 1}
          Unresolved non-hydrogen planarities: 4
    Chain: "C"
      Number of atoms: 14
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 14
          Unusual residues: {'NAG': 1}
          Classifications: {'undetermined': 1}
          Unresolved non-hydrogen bonds: 1
          Unresolved non-hydrogen angles: 2
          Unresolved non-hydrogen dihedrals: 3
          Unresolved non-hydrogen chiralities: 1
  Time building chain proxies: 7.04, per 1000 atoms: 0.62
  Number of scatterers: 11400
  At special positions: 0
  Unit cell: (99.552, 171.288, 161.04, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     S      45     16.00
     O    2231      8.00
     N    1906      7.00
     C    7218      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=18, symmetry=0
    Simple disulfide: pdb=" SG  CYS C 131 " - pdb=" SG  CYS C 166 " distance=2.03
    Simple disulfide: pdb=" SG  CYS C 291 " - pdb=" SG  CYS C 301 " distance=2.03
    Simple disulfide: pdb=" SG  CYS C 336 " - pdb=" SG  CYS C 361 " distance=2.03
    Simple disulfide: pdb=" SG  CYS C 379 " - pdb=" SG  CYS C 432 " distance=2.04
    Simple disulfide: pdb=" SG  CYS C 391 " - pdb=" SG  CYS C 525 " distance=2.04
    Simple disulfide: pdb=" SG  CYS C 480 " - pdb=" SG  CYS C 488 " distance=2.03
    Simple disulfide: pdb=" SG  CYS C 538 " - pdb=" SG  CYS C 590 " distance=2.03
    Simple disulfide: pdb=" SG  CYS C 617 " - pdb=" SG  CYS C 649 " distance=2.03
    Simple disulfide: pdb=" SG  CYS C 662 " - pdb=" SG  CYS C 671 " distance=2.03
    Simple disulfide: pdb=" SG  CYS H  22 " - pdb=" SG  CYS H  95 " distance=2.03
    Simple disulfide: pdb=" SG  CYS H 143 " - pdb=" SG  CYS H 199 " distance=2.03
    Simple disulfide: pdb=" SG  CYS H 219 " - pdb=" SG  CYS L 215 " distance=2.03
    Simple disulfide: pdb=" SG  CYS L  23 " - pdb=" SG  CYS L  88 " distance=2.03
    Simple disulfide: pdb=" SG  CYS L 135 " - pdb=" SG  CYS L 195 " distance=2.03
    Simple disulfide: pdb=" SG  CYS D  22 " - pdb=" SG  CYS D  96 " distance=2.03
    Simple disulfide: pdb=" SG  CYS D 151 " - pdb=" SG  CYS D 207 " distance=2.03
    Simple disulfide: pdb=" SG  CYS E  22 " - pdb=" SG  CYS E  90 " distance=2.03
    Simple disulfide: pdb=" SG  CYS E 139 " - pdb=" SG  CYS E 198 " 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 C 701 " - " ASN C 343 "
  Time building additional restraints: 2.36
  Conformation dependent library (CDL) restraints added in 1.7 seconds
  

  2958 Ramachandran restraints generated.
    1479 Oldfield, 0 Emsley, 1479 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2748

  Finding SS restraints...
    Secondary structure from input PDB file:
      13 helices and 34 sheets defined
      4.8% alpha, 39.3% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 1.59
  Creating SS restraints...
    Processing helix  chain 'C' and resid 294 through 304
      removed outlier: 3.986A  pdb=" N   LYS C 300 " --> pdb=" O   LEU C 296 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 337 through 343
      removed outlier: 3.928A  pdb=" N   VAL C 341 " --> pdb=" O   PRO C 337 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 365 through 370
      removed outlier: 3.596A  pdb=" N   TYR C 369 " --> pdb=" O   TYR C 365 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 404 through 408
    Processing helix  chain 'C' and resid 409 through 411
      No H-bonds generated for 'chain 'C' and resid 409 through 411'
    Processing helix  chain 'H' and resid 86 through 90
      removed outlier: 4.049A  pdb=" N   THR H  90 " --> pdb=" O   ALA H  87 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 159 through 161
      No H-bonds generated for 'chain 'H' and resid 159 through 161'
    Processing helix  chain 'H' and resid 188 through 192
      removed outlier: 3.524A  pdb=" N   SER H 191 " --> pdb=" O   PRO H 188 " (cutoff:3.500A)
      removed outlier: 3.551A  pdb=" N   LEU H 192 " --> pdb=" O   SER H 189 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'H' and resid 188 through 192'
    Processing helix  chain 'L' and resid 122 through 127
      removed outlier: 3.612A  pdb=" N   LYS L 127 " --> pdb=" O   GLU L 124 " (cutoff:3.500A)
    Processing helix  chain 'L' and resid 184 through 188
      removed outlier: 3.566A  pdb=" N   GLU L 188 " --> pdb=" O   LYS L 184 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'L' and resid 184 through 188'
    Processing helix  chain 'D' and resid 198 through 200
      No H-bonds generated for 'chain 'D' and resid 198 through 200'
    Processing helix  chain 'E' and resid 81 through 85
      removed outlier: 3.962A  pdb=" N   GLU E  85 " --> pdb=" O   ALA E  82 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 126 through 133
      removed outlier: 3.872A  pdb=" N   GLN E 131 " --> pdb=" O   GLU E 128 " (cutoff:3.500A)
      removed outlier: 4.038A  pdb=" N   ASN E 133 " --> pdb=" O   LEU E 130 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'C' and resid 47 through 55
      removed outlier: 4.142A  pdb=" N   VAL C  47 " --> pdb=" O   TYR C 279 " (cutoff:3.500A)
      removed outlier: 3.975A  pdb=" N   TYR C 279 " --> pdb=" O   VAL C  47 " (cutoff:3.500A)
      removed outlier: 3.970A  pdb=" N   HIS C  49 " --> pdb=" O   LEU C 277 " (cutoff:3.500A)
      removed outlier: 3.608A  pdb=" N   LEU C 277 " --> pdb=" O   HIS C  49 " (cutoff:3.500A)
      removed outlier: 3.543A  pdb=" N   THR C  51 " --> pdb=" O   PHE C 275 " (cutoff:3.500A)
      removed outlier: 3.701A  pdb=" N   PHE C 275 " --> pdb=" O   THR C  51 " (cutoff:3.500A)
      removed outlier: 4.280A  pdb=" N   ASP C  53 " --> pdb=" O   ARG C 273 " (cutoff:3.500A)
      removed outlier: 3.556A  pdb=" N   ARG C 273 " --> pdb=" O   ASP C  53 " (cutoff:3.500A)
      removed outlier: 3.535A  pdb=" N   LYS C 278 " --> pdb=" O   ASP C 287 " (cutoff:3.500A)
      removed outlier: 5.009A  pdb=" N   ASP C 287 " --> pdb=" O   LYS C 278 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'C' and resid 63 through 67
      removed outlier: 3.509A  pdb=" N   VAL C 267 " --> pdb=" O   THR C  63 " (cutoff:3.500A)
      removed outlier: 3.975A  pdb=" N   ALA C 264 " --> pdb=" O   THR C  95 " (cutoff:3.500A)
      removed outlier: 3.808A  pdb=" N   VAL C  90 " --> pdb=" O   PHE C 194 " (cutoff:3.500A)
      removed outlier: 4.120A  pdb=" N   LYS C 187 " --> pdb=" O   ILE C 210 " (cutoff:3.500A)
      removed outlier: 3.763A  pdb=" N   GLU C 191 " --> pdb=" O   LYS C 206 " (cutoff:3.500A)
      removed outlier: 3.681A  pdb=" N   LYS C 206 " --> pdb=" O   GLU C 191 " (cutoff:3.500A)
      removed outlier: 3.977A  pdb=" N   VAL C 227 " --> pdb=" O   ILE C 203 " (cutoff:3.500A)
      removed outlier: 6.194A  pdb=" N   SER C 205 " --> pdb=" O   PRO C 225 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'C' and resid 83 through 85
      removed outlier: 3.504A  pdb=" N   GLY C 107 " --> pdb=" O   ARG C 237 " (cutoff:3.500A)
      removed outlier: 4.271A  pdb=" N   GLY C 103 " --> pdb=" O   LEU C 241 " (cutoff:3.500A)
      removed outlier: 3.896A  pdb=" N   PHE C 168 " --> pdb=" O   VAL C 130 " (cutoff:3.500A)
      removed outlier: 7.875A  pdb=" N   GLU C 132 " --> pdb=" O   CYS C 166 " (cutoff:3.500A)
      removed outlier: 7.620A  pdb=" N   CYS C 166 " --> pdb=" O   GLU C 132 " (cutoff:3.500A)
      removed outlier: 10.490A  pdb=" N   GLN C 134 " --> pdb=" O   ASN C 164 " (cutoff:3.500A)
      removed outlier: 9.682A  pdb=" N   ASN C 164 " --> pdb=" O   GLN C 134 " (cutoff:3.500A)
      removed outlier: 8.707A  pdb=" N   CYS C 136 " --> pdb=" O   SER C 162 " (cutoff:3.500A)
      removed outlier: 10.555A  pdb=" N   SER C 162 " --> pdb=" O   CYS C 136 " (cutoff:3.500A)
      removed outlier: 10.634A  pdb=" N   ASP C 138 " --> pdb=" O   TYR C 160 " (cutoff:3.500A)
      removed outlier: 8.366A  pdb=" N   TYR C 160 " --> pdb=" O   ASP C 138 " (cutoff:3.500A)
      removed outlier: 6.071A  pdb=" N   TYR C 144 " --> pdb=" O   GLU C 154 " (cutoff:3.500A)
      removed outlier: 5.659A  pdb=" N   GLU C 154 " --> pdb=" O   TYR C 144 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'C' and resid 83 through 85
      removed outlier: 3.504A  pdb=" N   GLY C 107 " --> pdb=" O   ARG C 237 " (cutoff:3.500A)
      removed outlier: 4.271A  pdb=" N   GLY C 103 " --> pdb=" O   LEU C 241 " (cutoff:3.500A)
      removed outlier: 8.110A  pdb=" N   LEU C 244 " --> pdb=" O   PRO C 139 " (cutoff:3.500A)
      removed outlier: 6.467A  pdb=" N   LEU C 141 " --> pdb=" O   LEU C 244 " (cutoff:3.500A)
      removed outlier: 7.576A  pdb=" N   ARG C 246 " --> pdb=" O   LEU C 141 " (cutoff:3.500A)
      removed outlier: 6.514A  pdb=" N   VAL C 143 " --> pdb=" O   ARG C 246 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'C' and resid 312 through 313
      removed outlier: 3.710A  pdb=" N   TYR C 313 " --> pdb=" O   VAL C 597 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'C' and resid 354 through 358
      removed outlier: 3.708A  pdb=" N   ASN C 354 " --> pdb=" O   SER C 399 " (cutoff:3.500A)
      removed outlier: 3.511A  pdb=" N   CYS C 432 " --> pdb=" O   LEU C 513 " (cutoff:3.500A)
      removed outlier: 6.348A  pdb=" N   ALA C 435 " --> pdb=" O   SER C 375 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'C' and resid 361 through 362
      removed outlier: 6.737A  pdb=" N   CYS C 361 " --> pdb=" O   CYS C 525 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA7
    Processing sheet with id=AA8, first strand: chain 'C' and resid 452 through 454
    Processing sheet with id=AA9, first strand: chain 'C' and resid 466 through 468
      removed outlier: 4.087A  pdb=" N   ARG C 466 " --> pdb=" O   GLY D 104 " (cutoff:3.500A)
      removed outlier: 4.452A  pdb=" N   GLY D 104 " --> pdb=" O   ARG C 466 " (cutoff:3.500A)
      removed outlier: 4.026A  pdb=" N   ILE C 468 " --> pdb=" O   TYR D 102 " (cutoff:3.500A)
      removed outlier: 3.630A  pdb=" N   TYR D 102 " --> pdb=" O   ILE C 468 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA9
    Processing sheet with id=AB1, first strand: chain 'C' and resid 473 through 474
    Processing sheet with id=AB2, first strand: chain 'C' and resid 538 through 543
      removed outlier: 3.750A  pdb=" N   THR C 553 " --> pdb=" O   ASP C 586 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'C' and resid 664 through 667
      removed outlier: 3.670A  pdb=" N   ILE C 664 " --> pdb=" O   ALA C 672 " (cutoff:3.500A)
      removed outlier: 3.874A  pdb=" N   ALA C 672 " --> pdb=" O   ILE C 664 " (cutoff:3.500A)
      removed outlier: 6.524A  pdb=" N   ILE C 670 " --> pdb=" O   ILE C 666 " (cutoff:3.500A)
    Processing sheet with id=AB4, first strand: chain 'H' and resid 3 through 7
    Processing sheet with id=AB5, first strand: chain 'H' and resid 11 through 12
      removed outlier: 4.189A  pdb=" N   TYR H  33 " --> pdb=" O   GLY H  98 " (cutoff:3.500A)
      removed outlier: 3.548A  pdb=" N   SER H  49 " --> pdb=" O   TRP H  36 " (cutoff:3.500A)
      removed outlier: 5.857A  pdb=" N   ARG H  38 " --> pdb=" O   TRP H  47 " (cutoff:3.500A)
      removed outlier: 4.823A  pdb=" N   TRP H  47 " --> pdb=" O   ARG H  38 " (cutoff:3.500A)
    Processing sheet with id=AB6, first strand: chain 'H' and resid 11 through 12
      removed outlier: 7.129A  pdb=" N   ARG H  97 " --> pdb=" O   ASP H 104 " (cutoff:3.500A)
    Processing sheet with id=AB7, first strand: chain 'H' and resid 123 through 127
      removed outlier: 4.202A  pdb=" N   GLY H 142 " --> pdb=" O   LEU H 127 " (cutoff:3.500A)
      removed outlier: 3.539A  pdb=" N   SER H 183 " --> pdb=" O   CYS H 143 " (cutoff:3.500A)
      removed outlier: 3.588A  pdb=" N   ASP H 147 " --> pdb=" O   TYR H 179 " (cutoff:3.500A)
      removed outlier: 6.610A  pdb=" N   TYR H 179 " --> pdb=" O   ASP H 147 " (cutoff:3.500A)
      removed outlier: 3.629A  pdb=" N   VAL H 184 " --> pdb=" O   HIS H 167 " (cutoff:3.500A)
    Processing sheet with id=AB8, first strand: chain 'H' and resid 123 through 127
      removed outlier: 4.202A  pdb=" N   GLY H 142 " --> pdb=" O   LEU H 127 " (cutoff:3.500A)
      removed outlier: 3.539A  pdb=" N   SER H 183 " --> pdb=" O   CYS H 143 " (cutoff:3.500A)
      removed outlier: 3.588A  pdb=" N   ASP H 147 " --> pdb=" O   TYR H 179 " (cutoff:3.500A)
      removed outlier: 6.610A  pdb=" N   TYR H 179 " --> pdb=" O   ASP H 147 " (cutoff:3.500A)
    Processing sheet with id=AB9, first strand: chain 'H' and resid 154 through 157
      removed outlier: 3.559A  pdb=" N   THR H 154 " --> pdb=" O   ASN H 202 " (cutoff:3.500A)
      removed outlier: 3.744A  pdb=" N   ASN H 202 " --> pdb=" O   THR H 154 " (cutoff:3.500A)
      removed outlier: 3.828A  pdb=" N   CYS H 199 " --> pdb=" O   LYS H 212 " (cutoff:3.500A)
      removed outlier: 4.152A  pdb=" N   LYS H 212 " --> pdb=" O   CYS H 199 " (cutoff:3.500A)
      removed outlier: 3.985A  pdb=" N   VAL H 201 " --> pdb=" O   VAL H 210 " (cutoff:3.500A)
      removed outlier: 3.803A  pdb=" N   VAL H 210 " --> pdb=" O   VAL H 201 " (cutoff:3.500A)
    Processing sheet with id=AC1, first strand: chain 'L' and resid 5 through 6
      removed outlier: 3.650A  pdb=" N   CYS L  23 " --> pdb=" O   PHE L  71 " (cutoff:3.500A)
      removed outlier: 3.743A  pdb=" N   PHE L  71 " --> pdb=" O   CYS L  23 " (cutoff:3.500A)
    Processing sheet with id=AC2, first strand: chain 'L' and resid 10 through 12
      removed outlier: 3.822A  pdb=" N   TYR L  87 " --> pdb=" O   TYR L  36 " (cutoff:3.500A)
      removed outlier: 6.674A  pdb=" N   TRP L  35 " --> pdb=" O   LEU L  47 " (cutoff:3.500A)
    Processing sheet with id=AC3, first strand: chain 'L' and resid 10 through 12
      removed outlier: 3.677A  pdb=" N   GLN L  90 " --> pdb=" O   THR L  98 " (cutoff:3.500A)
    Processing sheet with id=AC4, first strand: chain 'L' and resid 112 through 119
      removed outlier: 7.156A  pdb=" N   ALA L 113 " --> pdb=" O   PHE L 140 " (cutoff:3.500A)
      removed outlier: 4.492A  pdb=" N   PHE L 140 " --> pdb=" O   ALA L 113 " (cutoff:3.500A)
      removed outlier: 3.675A  pdb=" N   ASN L 138 " --> pdb=" O   SER L 115 " (cutoff:3.500A)
      removed outlier: 3.788A  pdb=" N   VAL L 134 " --> pdb=" O   PHE L 119 " (cutoff:3.500A)
      removed outlier: 3.535A  pdb=" N   VAL L 133 " --> pdb=" O   LEU L 180 " (cutoff:3.500A)
      removed outlier: 3.611A  pdb=" N   LEU L 180 " --> pdb=" O   VAL L 133 " (cutoff:3.500A)
      removed outlier: 4.172A  pdb=" N   CYS L 135 " --> pdb=" O   SER L 178 " (cutoff:3.500A)
      removed outlier: 4.118A  pdb=" N   SER L 178 " --> pdb=" O   CYS L 135 " (cutoff:3.500A)
      removed outlier: 6.745A  pdb=" N   TYR L 174 " --> pdb=" O   ASN L 139 " (cutoff:3.500A)
    Processing sheet with id=AC5, first strand: chain 'L' and resid 154 through 155
      removed outlier: 3.792A  pdb=" N   TYR L 193 " --> pdb=" O   PHE L 210 " (cutoff:3.500A)
      removed outlier: 3.697A  pdb=" N   PHE L 210 " --> pdb=" O   TYR L 193 " (cutoff:3.500A)
      removed outlier: 4.417A  pdb=" N   CYS L 195 " --> pdb=" O   LYS L 208 " (cutoff:3.500A)
      removed outlier: 4.313A  pdb=" N   LYS L 208 " --> pdb=" O   CYS L 195 " (cutoff:3.500A)
      removed outlier: 3.905A  pdb=" N   VAL L 197 " --> pdb=" O   VAL L 206 " (cutoff:3.500A)
      removed outlier: 4.037A  pdb=" N   VAL L 206 " --> pdb=" O   VAL L 197 " (cutoff:3.500A)
    Processing sheet with id=AC6, first strand: chain 'D' and resid 3 through 6
    Processing sheet with id=AC7, first strand: chain 'D' and resid 10 through 12
      removed outlier: 4.034A  pdb=" N   GLY D  49 " --> pdb=" O   TRP D  36 " (cutoff:3.500A)
      removed outlier: 7.160A  pdb=" N   ARG D  38 " --> pdb=" O   TRP D  47 " (cutoff:3.500A)
      removed outlier: 5.710A  pdb=" N   TRP D  47 " --> pdb=" O   ARG D  38 " (cutoff:3.500A)
    Processing sheet with id=AC8, first strand: chain 'D' and resid 10 through 12
      removed outlier: 6.670A  pdb=" N   ASN D 100 " --> pdb=" O   PHE D 111 " (cutoff:3.500A)
      removed outlier: 6.087A  pdb=" N   PHE D 111 " --> pdb=" O   ASN D 100 " (cutoff:3.500A)
    Processing sheet with id=AC9, first strand: chain 'D' and resid 68 through 69
    Processing sheet with id=AD1, first strand: chain 'D' and resid 131 through 135
      removed outlier: 3.675A  pdb=" N   LYS D 154 " --> pdb=" O   SER D 131 " (cutoff:3.500A)
      removed outlier: 4.323A  pdb=" N   PHE D 133 " --> pdb=" O   LEU D 152 " (cutoff:3.500A)
      removed outlier: 4.291A  pdb=" N   LEU D 152 " --> pdb=" O   PHE D 133 " (cutoff:3.500A)
      removed outlier: 3.665A  pdb=" N   GLY D 150 " --> pdb=" O   LEU D 135 " (cutoff:3.500A)
      removed outlier: 3.673A  pdb=" N   LEU D 149 " --> pdb=" O   VAL D 193 " (cutoff:3.500A)
    Processing sheet with id=AD2, first strand: chain 'D' and resid 163 through 165
      removed outlier: 3.690A  pdb=" N   SER D 164 " --> pdb=" O   ASN D 208 " (cutoff:3.500A)
      removed outlier: 3.582A  pdb=" N   ASN D 208 " --> pdb=" O   SER D 164 " (cutoff:3.500A)
      removed outlier: 4.614A  pdb=" N   TYR D 205 " --> pdb=" O   VAL D 222 " (cutoff:3.500A)
      removed outlier: 3.642A  pdb=" N   CYS D 207 " --> pdb=" O   LYS D 220 " (cutoff:3.500A)
      removed outlier: 4.015A  pdb=" N   LYS D 220 " --> pdb=" O   CYS D 207 " (cutoff:3.500A)
      removed outlier: 4.098A  pdb=" N   VAL D 209 " --> pdb=" O   VAL D 218 " (cutoff:3.500A)
      removed outlier: 3.818A  pdb=" N   VAL D 218 " --> pdb=" O   VAL D 209 " (cutoff:3.500A)
      removed outlier: 3.528A  pdb=" N   THR D 216 " --> pdb=" O   HIS D 211 " (cutoff:3.500A)
    Processing sheet with id=AD3, first strand: chain 'E' and resid 10 through 11
      removed outlier: 3.941A  pdb=" N   THR E 109 " --> pdb=" O   VAL E  10 " (cutoff:3.500A)
      removed outlier: 3.528A  pdb=" N   TYR E  88 " --> pdb=" O   THR E 106 " (cutoff:3.500A)
      removed outlier: 6.609A  pdb=" N   TRP E  37 " --> pdb=" O   LEU E  49 " (cutoff:3.500A)
    Processing sheet with id=AD4, first strand: chain 'E' and resid 10 through 11
      removed outlier: 3.941A  pdb=" N   THR E 109 " --> pdb=" O   VAL E  10 " (cutoff:3.500A)
      removed outlier: 3.528A  pdb=" N   TYR E  88 " --> pdb=" O   THR E 106 " (cutoff:3.500A)
    Processing sheet with id=AD5, first strand: chain 'E' and resid 17 through 22
      removed outlier: 4.166A  pdb=" N   VAL E  18 " --> pdb=" O   ILE E  77 " (cutoff:3.500A)
      removed outlier: 3.840A  pdb=" N   ILE E  77 " --> pdb=" O   VAL E  18 " (cutoff:3.500A)
      removed outlier: 3.589A  pdb=" N   ILE E  20 " --> pdb=" O   LEU E  75 " (cutoff:3.500A)
    Processing sheet with id=AD6, first strand: chain 'E' and resid 119 through 123
      removed outlier: 3.586A  pdb=" N   SER E 181 " --> pdb=" O   CYS E 139 " (cutoff:3.500A)
      removed outlier: 3.570A  pdb=" N   ILE E 141 " --> pdb=" O   ALA E 179 " (cutoff:3.500A)
      removed outlier: 3.789A  pdb=" N   ALA E 179 " --> pdb=" O   ILE E 141 " (cutoff:3.500A)
      removed outlier: 4.667A  pdb=" N   ASP E 143 " --> pdb=" O   TYR E 177 " (cutoff:3.500A)
      removed outlier: 7.808A  pdb=" N   TYR E 177 " --> pdb=" O   ASP E 143 " (cutoff:3.500A)
    Processing sheet with id=AD7, first strand: chain 'E' and resid 150 through 154
      removed outlier: 4.277A  pdb=" N   THR E 150 " --> pdb=" O   THR E 201 " (cutoff:3.500A)
      removed outlier: 3.542A  pdb=" N   THR E 201 " --> pdb=" O   THR E 150 " (cutoff:3.500A)
      removed outlier: 3.728A  pdb=" N   LYS E 154 " --> pdb=" O   SER E 197 " (cutoff:3.500A)
      removed outlier: 3.551A  pdb=" N   SER E 197 " --> pdb=" O   LYS E 154 " (cutoff:3.500A)
      removed outlier: 3.770A  pdb=" N   TYR E 196 " --> pdb=" O   VAL E 211 " (cutoff:3.500A)
      removed outlier: 3.788A  pdb=" N   CYS E 198 " --> pdb=" O   LYS E 209 " (cutoff:3.500A)
      removed outlier: 4.373A  pdb=" N   LYS E 209 " --> pdb=" O   CYS E 198 " (cutoff:3.500A)
      removed outlier: 4.250A  pdb=" N   VAL E 200 " --> pdb=" O   VAL E 207 " (cutoff:3.500A)
      removed outlier: 3.920A  pdb=" N   VAL E 207 " --> pdb=" O   VAL E 200 " (cutoff:3.500A)

    319 hydrogen bonds defined for protein.
    768 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: 3.98

  Time building geometry restraints manager: 2.93 seconds

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

  Histogram of bond lengths:
        1.23 -     1.35: 3657
        1.35 -     1.46: 2889
        1.46 -     1.58: 5078
        1.58 -     1.70: 0
        1.70 -     1.82: 54
  Bond restraints: 11678
  Sorted by residual:
  bond pdb=" C1  NAG C 701 "
       pdb=" O5  NAG C 701 "
    ideal  model  delta    sigma   weight residual
    1.406  1.437 -0.031 2.00e-02 2.50e+03 2.33e+00
  bond pdb=" CB  GLU D  89 "
       pdb=" CG  GLU D  89 "
    ideal  model  delta    sigma   weight residual
    1.520  1.562 -0.042 3.00e-02 1.11e+03 1.93e+00
  bond pdb=" CA  PHE D 157 "
       pdb=" C   PHE D 157 "
    ideal  model  delta    sigma   weight residual
    1.524  1.540 -0.016 1.26e-02 6.30e+03 1.68e+00
  bond pdb=" C5  NAG C 701 "
       pdb=" O5  NAG C 701 "
    ideal  model  delta    sigma   weight residual
    1.413  1.437 -0.024 2.00e-02 2.50e+03 1.40e+00
  bond pdb=" CA  LYS H 213 "
       pdb=" C   LYS H 213 "
    ideal  model  delta    sigma   weight residual
    1.526  1.509  0.017 1.42e-02 4.96e+03 1.38e+00
  ... (remaining 11673 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.06: 15694
        2.06 -     4.11: 192
        4.11 -     6.17: 11
        6.17 -     8.23: 7
        8.23 -    10.28: 1
  Bond angle restraints: 15905
  Sorted by residual:
  angle pdb=" CA  GLU D  89 "
        pdb=" CB  GLU D  89 "
        pdb=" CG  GLU D  89 "
      ideal   model   delta    sigma   weight residual
     114.10  120.50   -6.40 2.00e+00 2.50e-01 1.02e+01
  angle pdb=" CA  GLU D 159 "
        pdb=" C   GLU D 159 "
        pdb=" N   PRO D 160 "
      ideal   model   delta    sigma   weight residual
     120.79  117.78    3.01 9.70e-01 1.06e+00 9.65e+00
  angle pdb=" CA  LEU H 181 "
        pdb=" CB  LEU H 181 "
        pdb=" CG  LEU H 181 "
      ideal   model   delta    sigma   weight residual
     116.30  126.58  -10.28 3.50e+00 8.16e-02 8.63e+00
  angle pdb=" N   LYS H 204 "
        pdb=" CA  LYS H 204 "
        pdb=" C   LYS H 204 "
      ideal   model   delta    sigma   weight residual
     109.81  116.20   -6.39 2.21e+00 2.05e-01 8.35e+00
  angle pdb=" CB  GLU D  89 "
        pdb=" CG  GLU D  89 "
        pdb=" CD  GLU D  89 "
      ideal   model   delta    sigma   weight residual
     112.60  117.50   -4.90 1.70e+00 3.46e-01 8.31e+00
  ... (remaining 15900 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.58: 6093
       17.58 -    35.17: 656
       35.17 -    52.75: 177
       52.75 -    70.33: 21
       70.33 -    87.91: 14
  Dihedral angle restraints: 6961
    sinusoidal: 2652
      harmonic: 4309
  Sorted by residual:
  dihedral pdb=" CB  CYS H 143 "
           pdb=" SG  CYS H 143 "
           pdb=" SG  CYS H 199 "
           pdb=" CB  CYS H 199 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00  165.28  -72.28     1      1.00e+01 1.00e-02 6.68e+01
  dihedral pdb=" CB  CYS C 480 "
           pdb=" SG  CYS C 480 "
           pdb=" SG  CYS C 488 "
           pdb=" CB  CYS C 488 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00  145.44  -52.44     1      1.00e+01 1.00e-02 3.75e+01
  dihedral pdb=" CB  CYS L  23 "
           pdb=" SG  CYS L  23 "
           pdb=" SG  CYS L  88 "
           pdb=" CB  CYS L  88 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00   63.78   29.22     1      1.00e+01 1.00e-02 1.22e+01
  ... (remaining 6958 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.043: 1360
       0.043 -    0.086: 278
       0.086 -    0.130: 147
       0.130 -    0.173: 4
       0.173 -    0.216: 1
  Chirality restraints: 1790
  Sorted by residual:
  chirality pdb=" CB  THR H  90 "
            pdb=" CA  THR H  90 "
            pdb=" OG1 THR H  90 "
            pdb=" CG2 THR H  90 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.55    2.34    0.22 2.00e-01 2.50e+01 1.16e+00
  chirality pdb=" CB  VAL L 147 "
            pdb=" CA  VAL L 147 "
            pdb=" CG1 VAL L 147 "
            pdb=" CG2 VAL L 147 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -2.47   -0.16 2.00e-01 2.50e+01 6.09e-01
  chirality pdb=" CA  VAL D 161 "
            pdb=" N   VAL D 161 "
            pdb=" C   VAL D 161 "
            pdb=" CB  VAL D 161 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.58   -0.14 2.00e-01 2.50e+01 4.75e-01
  ... (remaining 1787 not shown)

  Planarity restraints: 2049
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  GLY E 112 "   -0.014 2.00e-02 2.50e+03   2.73e-02 7.45e+00
        pdb=" C   GLY E 112 "    0.047 2.00e-02 2.50e+03
        pdb=" O   GLY E 112 "   -0.018 2.00e-02 2.50e+03
        pdb=" N   GLN E 113 "   -0.016 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   LYS H 204 "   -0.045 5.00e-02 4.00e+02   6.81e-02 7.42e+00
        pdb=" N   PRO H 205 "    0.118 5.00e-02 4.00e+02
        pdb=" CA  PRO H 205 "   -0.034 5.00e-02 4.00e+02
        pdb=" CD  PRO H 205 "   -0.038 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  PHE D 133 "   -0.010 2.00e-02 2.50e+03   1.46e-02 3.71e+00
        pdb=" CG  PHE D 133 "    0.033 2.00e-02 2.50e+03
        pdb=" CD1 PHE D 133 "   -0.012 2.00e-02 2.50e+03
        pdb=" CD2 PHE D 133 "   -0.012 2.00e-02 2.50e+03
        pdb=" CE1 PHE D 133 "    0.000 2.00e-02 2.50e+03
        pdb=" CE2 PHE D 133 "    0.000 2.00e-02 2.50e+03
        pdb=" CZ  PHE D 133 "    0.000 2.00e-02 2.50e+03
  ... (remaining 2046 not shown)

  Histogram of nonbonded interaction distances:
        2.25 -     2.78: 2089
        2.78 -     3.31: 9272
        3.31 -     3.84: 18298
        3.84 -     4.37: 19741
        4.37 -     4.90: 35658
  Nonbonded interactions: 85058
  Sorted by model distance:
  nonbonded pdb=" OD1 ASN L  92 "
            pdb=" N   SER L  93 "
     model   vdw
     2.249 3.120
  nonbonded pdb=" O   LEU C 455 "
            pdb=" OH  TYR H  33 "
     model   vdw
     2.258 3.040
  nonbonded pdb=" OH  TYR C  37 "
            pdb=" O   LEU C  54 "
     model   vdw
     2.300 3.040
  nonbonded pdb=" O   CYS D 151 "
            pdb=" OG  SER D 191 "
     model   vdw
     2.313 3.040
  nonbonded pdb=" OH  TYR E  33 "
            pdb=" OG  SER E  95 "
     model   vdw
     2.337 3.040
  ... (remaining 85053 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.00
========== WARNING! ============

  No NCS relation were found !!!

================================

Found NCS groups:
  found none.
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=0.00 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:             0.610
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.070
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.460
  Check model and map are aligned:         0.100
  Set scattering table:                    0.130
  Process input model:                     29.150
  Find NCS groups from input model:        0.210
  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:3.030
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   33.840
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5695
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      :  0.002   0.042  11697  Z= 0.112
  Angle     :  0.527  10.282  15946  Z= 0.275
  Chirality :  0.043   0.216   1790
  Planarity :  0.004   0.068   2048
  Dihedral  : 15.559  87.915   4156
  Min Nonbonded Distance : 2.249

Molprobity Statistics.
  All-atom Clashscore : 5.34
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.99 %
    Favored  : 96.01 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  : 23.19 %
    Favored  : 76.81 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.70 %
    Cis-general     : 0.00 %
    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: -0.79 (0.21), residues: 1479
  helix: -3.27 (0.45), residues: 57
  sheet:  0.50 (0.25), residues: 460
  loop : -0.89 (0.19), residues: 962

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.001   TRP C 104 
 HIS   0.003   0.000   HIS H 203 
 PHE   0.033   0.001   PHE D 133 
 TYR   0.027   0.001   TYR L 141 
 ARG   0.002   0.000   ARG D  87 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00152 (    1)
  link_NAG-ASN         : angle       0.84712 (    3)
  hydrogen bonds       : bond        0.31730 (  275)
  hydrogen bonds       : angle      10.81994 (  768)
  SS BOND              : bond        0.00177 (   18)
  SS BOND              : angle       0.45530 (   38)
  covalent geometry    : bond        0.00216 (11678)
  covalent geometry    : angle       0.52694 (15905)

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

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

  2958 Ramachandran restraints generated.
    1479 Oldfield, 0 Emsley, 1479 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2958 Ramachandran restraints generated.
    1479 Oldfield, 0 Emsley, 1479 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  74 residues out of total 1271 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 74
  time to evaluate  : 1.142 
Fit side-chains
   revert: symmetry clash
REVERT: D   89 GLU cc_start: 0.8110 (tm-30) cc_final: 0.7870 (tm-30)
  outliers start: 0
  outliers final: 0
  residues processed: 74
  average time/residue: 0.1768
  time to fit residues: 21.5039
Evaluate side-chains
  65 residues out of total 1271 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 65
  time to evaluate  : 1.120 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 147
   random chunks:
   chunk 124 optimal weight:   40.0000
   chunk 111 optimal weight:    4.9990
   chunk 61 optimal weight:    6.9990
   chunk 38 optimal weight:    1.9990
   chunk 75 optimal weight:   20.0000
   chunk 59 optimal weight:    3.9990
   chunk 115 optimal weight:    0.9980
   chunk 44 optimal weight:    0.8980
   chunk 70 optimal weight:    0.6980
   chunk 85 optimal weight:    0.4980
   chunk 133 optimal weight:    5.9990
   overall best weight:    1.0182

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

Flipped N/Q/H residues before XYZ refinement:
H  72 ASN
** L  38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
D 210 ASN
E  81 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4834 r_free = 0.4834 target = 0.259960 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.4554 r_free = 0.4554 target = 0.231830 restraints weight = 14667.021|
|-----------------------------------------------------------------------------|
r_work (start): 0.4541 rms_B_bonded: 3.44
r_work: 0.4302 rms_B_bonded: 2.59 restraints_weight: 0.5000
r_work (final): 0.4302
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.4315
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.4315 r_free = 0.4315    target_work(ls_wunit_k1) = 0.200         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.4315 r_free = 0.4315    target_work(ls_wunit_k1) = 0.200         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|
r_final: 0.4315
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6396
moved from start:          0.1622

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.044  11697  Z= 0.150
  Angle     :  0.549   7.913  15946  Z= 0.285
  Chirality :  0.044   0.166   1790
  Planarity :  0.005   0.066   2048
  Dihedral  :  3.422  22.868   1628
  Min Nonbonded Distance : 2.530

Molprobity Statistics.
  All-atom Clashscore : 5.66
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.39 %
    Favored  : 96.61 %
  Rotamer:
    Outliers :  1.97 %
    Allowed  : 21.31 %
    Favored  : 76.73 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.70 %
    Cis-general     : 0.00 %
    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: -0.58 (0.22), residues: 1479
  helix: -2.74 (0.56), residues: 56
  sheet:  0.38 (0.24), residues: 502
  loop : -0.66 (0.20), residues: 921

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP D 114 
 HIS   0.003   0.001   HIS H  35 
 PHE   0.016   0.001   PHE C 429 
 TYR   0.013   0.001   TYR D  95 
 ARG   0.006   0.001   ARG D  98 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00034 (    1)
  link_NAG-ASN         : angle       1.16147 (    3)
  hydrogen bonds       : bond        0.03865 (  275)
  hydrogen bonds       : angle       6.96237 (  768)
  SS BOND              : bond        0.00392 (   18)
  SS BOND              : angle       0.78025 (   38)
  covalent geometry    : bond        0.00343 (11678)
  covalent geometry    : angle       0.54857 (15905)

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

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

  2958 Ramachandran restraints generated.
    1479 Oldfield, 0 Emsley, 1479 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2958 Ramachandran restraints generated.
    1479 Oldfield, 0 Emsley, 1479 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  98 residues out of total 1271 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 73
  time to evaluate  : 1.282 
Fit side-chains
   revert: symmetry clash
REVERT: D   51 ILE cc_start: 0.8002 (OUTLIER) cc_final: 0.7750 (tt)
  outliers start: 25
  outliers final: 13
  residues processed: 94
  average time/residue: 0.2211
  time to fit residues: 31.8269
Evaluate side-chains
  79 residues out of total 1271 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 65
  time to evaluate  : 1.436 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue  433 VAL
Chi-restraints excluded: chain C residue  506 GLN
Chi-restraints excluded: chain C residue  638 THR
Chi-restraints excluded: chain H residue  110 THR
Chi-restraints excluded: chain H residue  115 SER
Chi-restraints excluded: chain L residue   85 SER
Chi-restraints excluded: chain D residue   51 ILE
Chi-restraints excluded: chain D residue   68 VAL
Chi-restraints excluded: chain D residue   69 THR
Chi-restraints excluded: chain D residue   70 ILE
Chi-restraints excluded: chain E residue   55 ASN
Chi-restraints excluded: chain E residue   58 SER
Chi-restraints excluded: chain E residue   97 LEU
Chi-restraints excluded: chain E residue  138 VAL
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 147
   random chunks:
   chunk 10 optimal weight:    9.9990
   chunk 36 optimal weight:    2.9990
   chunk 104 optimal weight:    0.5980
   chunk 70 optimal weight:    0.6980
   chunk 51 optimal weight:    6.9990
   chunk 13 optimal weight:   10.0000
   chunk 89 optimal weight:    4.9990
   chunk 20 optimal weight:    8.9990
   chunk 78 optimal weight:    7.9990
   chunk 82 optimal weight:    9.9990
   chunk 72 optimal weight:    0.9990
   overall best weight:    2.0586

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

Flipped N/Q/H residues before XYZ refinement:
H  39 GLN
H 203 HIS
L  38 GLN
E  39 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4740 r_free = 0.4740 target = 0.248486 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 28)----------------|
| r_work = 0.4397 r_free = 0.4397 target = 0.214087 restraints weight = 24511.783|
|-----------------------------------------------------------------------------|
r_work (start): 0.4375 rms_B_bonded: 4.79
r_work: 0.4118 rms_B_bonded: 3.28 restraints_weight: 0.5000
r_work: 0.4054 rms_B_bonded: 4.18 restraints_weight: 0.2500
r_work (final): 0.4054
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.4067
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.4067 r_free = 0.4067    target_work(ls_wunit_k1) = 0.175         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.4067 r_free = 0.4067    target_work(ls_wunit_k1) = 0.175         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|
r_final: 0.4067
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6823
moved from start:          0.3031

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.052  11697  Z= 0.235
  Angle     :  0.630   7.583  15946  Z= 0.326
  Chirality :  0.047   0.166   1790
  Planarity :  0.005   0.050   2048
  Dihedral  :  4.184  27.856   1628
  Min Nonbonded Distance : 2.509

Molprobity Statistics.
  All-atom Clashscore : 7.92
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.74 %
    Favored  : 95.26 %
  Rotamer:
    Outliers :  3.62 %
    Allowed  : 19.97 %
    Favored  : 76.42 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.70 %
    Cis-general     : 0.00 %
    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: -0.83 (0.21), residues: 1479
  helix: -2.51 (0.63), residues: 48
  sheet:  0.07 (0.23), residues: 530
  loop : -0.81 (0.20), residues: 901

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.002   TRP H  36 
 HIS   0.006   0.001   HIS H  35 
 PHE   0.028   0.002   PHE H  67 
 TYR   0.026   0.002   TYR C 423 
 ARG   0.010   0.001   ARG L 212 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00126 (    1)
  link_NAG-ASN         : angle       1.96679 (    3)
  hydrogen bonds       : bond        0.04429 (  275)
  hydrogen bonds       : angle       6.57710 (  768)
  SS BOND              : bond        0.00477 (   18)
  SS BOND              : angle       1.08158 (   38)
  covalent geometry    : bond        0.00551 (11678)
  covalent geometry    : angle       0.62839 (15905)

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

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

  2958 Ramachandran restraints generated.
    1479 Oldfield, 0 Emsley, 1479 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2958 Ramachandran restraints generated.
    1479 Oldfield, 0 Emsley, 1479 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  117 residues out of total 1271 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 46
    poor density    : 71
  time to evaluate  : 1.238 
Fit side-chains
   revert: symmetry clash
REVERT: C  377 PHE cc_start: 0.8394 (OUTLIER) cc_final: 0.7811 (m-80)
REVERT: C  433 VAL cc_start: 0.8809 (OUTLIER) cc_final: 0.8497 (t)
REVERT: H   19 ARG cc_start: 0.7950 (tpp80) cc_final: 0.7745 (ttt90)
REVERT: H  111 LEU cc_start: 0.8382 (mt) cc_final: 0.8122 (tp)
REVERT: L   77 SER cc_start: 0.6990 (OUTLIER) cc_final: 0.6726 (p)
REVERT: L  193 TYR cc_start: 0.5682 (p90) cc_final: 0.5466 (p90)
REVERT: E   55 ASN cc_start: 0.6441 (OUTLIER) cc_final: 0.6015 (m-40)
REVERT: E   81 GLN cc_start: 0.7547 (OUTLIER) cc_final: 0.6203 (mm110)
  outliers start: 46
  outliers final: 27
  residues processed: 113
  average time/residue: 0.2017
  time to fit residues: 35.0343
Evaluate side-chains
  93 residues out of total 1271 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 61
  time to evaluate  : 1.199 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue  296 LEU
Chi-restraints excluded: chain C residue  350 VAL
Chi-restraints excluded: chain C residue  377 PHE
Chi-restraints excluded: chain C residue  402 ILE
Chi-restraints excluded: chain C residue  420 ASP
Chi-restraints excluded: chain C residue  433 VAL
Chi-restraints excluded: chain C residue  470 THR
Chi-restraints excluded: chain C residue  506 GLN
Chi-restraints excluded: chain C residue  547 THR
Chi-restraints excluded: chain H residue   22 CYS
Chi-restraints excluded: chain H residue   68 THR
Chi-restraints excluded: chain H residue   69 ILE
Chi-restraints excluded: chain H residue  110 THR
Chi-restraints excluded: chain H residue  115 SER
Chi-restraints excluded: chain H residue  143 CYS
Chi-restraints excluded: chain H residue  144 LEU
Chi-restraints excluded: chain H residue  153 VAL
Chi-restraints excluded: chain L residue   22 THR
Chi-restraints excluded: chain L residue   77 SER
Chi-restraints excluded: chain L residue  116 VAL
Chi-restraints excluded: chain D residue   18 VAL
Chi-restraints excluded: chain D residue   25 SER
Chi-restraints excluded: chain D residue   69 THR
Chi-restraints excluded: chain D residue   70 ILE
Chi-restraints excluded: chain D residue   84 SER
Chi-restraints excluded: chain D residue  218 VAL
Chi-restraints excluded: chain E residue   55 ASN
Chi-restraints excluded: chain E residue   58 SER
Chi-restraints excluded: chain E residue   81 GLN
Chi-restraints excluded: chain E residue  106 THR
Chi-restraints excluded: chain E residue  138 VAL
Chi-restraints excluded: chain E residue  149 VAL
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 147
   random chunks:
   chunk 70 optimal weight:    0.7980
   chunk 71 optimal weight:    1.9990
   chunk 117 optimal weight:   50.0000
   chunk 121 optimal weight:   40.0000
   chunk 59 optimal weight:   20.0000
   chunk 12 optimal weight:    2.9990
   chunk 80 optimal weight:    0.8980
   chunk 24 optimal weight:    6.9990
   chunk 78 optimal weight:    5.9990
   chunk 40 optimal weight:    0.8980
   chunk 135 optimal weight:    0.7980
   overall best weight:    1.0782

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

Flipped N/Q/H residues before XYZ refinement:
H  83 ASN
L 161 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4758 r_free = 0.4758 target = 0.250714 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 29)----------------|
| r_work = 0.4309 r_free = 0.4309 target = 0.207641 restraints weight = 14740.933|
|-----------------------------------------------------------------------------|
r_work (start): 0.4261 rms_B_bonded: 5.18
r_work: 0.3821 rms_B_bonded: 4.96 restraints_weight: 0.5000
r_work (final): 0.3821
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3579
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3579 r_free = 0.3579    target_work(ls_wunit_k1) = 0.133         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3579 r_free = 0.3579    target_work(ls_wunit_k1) = 0.133         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|
r_final: 0.3579
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7229
moved from start:          0.3207

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040  11697  Z= 0.137
  Angle     :  0.527   7.166  15946  Z= 0.270
  Chirality :  0.044   0.153   1790
  Planarity :  0.004   0.049   2048
  Dihedral  :  3.829  26.274   1628
  Min Nonbonded Distance : 2.569

Molprobity Statistics.
  All-atom Clashscore : 7.03
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.06 %
    Favored  : 95.94 %
  Rotamer:
    Outliers :  2.67 %
    Allowed  : 20.83 %
    Favored  : 76.49 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.70 %
    Cis-general     : 0.00 %
    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: -0.73 (0.22), residues: 1479
  helix: -2.29 (0.66), residues: 48
  sheet:  0.01 (0.23), residues: 524
  loop : -0.65 (0.20), residues: 907

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.001   TRP D  36 
 HIS   0.004   0.001   HIS H  35 
 PHE   0.012   0.001   PHE C 562 
 TYR   0.015   0.001   TYR C 423 
 ARG   0.002   0.000   ARG C 509 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00024 (    1)
  link_NAG-ASN         : angle       1.76799 (    3)
  hydrogen bonds       : bond        0.03196 (  275)
  hydrogen bonds       : angle       6.06963 (  768)
  SS BOND              : bond        0.00558 (   18)
  SS BOND              : angle       1.31922 (   38)
  covalent geometry    : bond        0.00319 (11678)
  covalent geometry    : angle       0.52321 (15905)

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

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

  2958 Ramachandran restraints generated.
    1479 Oldfield, 0 Emsley, 1479 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2958 Ramachandran restraints generated.
    1479 Oldfield, 0 Emsley, 1479 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  111 residues out of total 1271 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 77
  time to evaluate  : 1.283 
Fit side-chains
   revert: symmetry clash
REVERT: C  377 PHE cc_start: 0.7753 (OUTLIER) cc_final: 0.7337 (m-80)
REVERT: C  405 ASP cc_start: 0.6893 (t70) cc_final: 0.6557 (t0)
REVERT: H   19 ARG cc_start: 0.8011 (tpp80) cc_final: 0.7804 (ttt90)
REVERT: H   83 ASN cc_start: 0.5907 (m110) cc_final: 0.5606 (m-40)
REVERT: H  190 SER cc_start: 0.4789 (OUTLIER) cc_final: 0.4248 (p)
REVERT: L   77 SER cc_start: 0.7629 (OUTLIER) cc_final: 0.7387 (p)
REVERT: E   55 ASN cc_start: 0.6757 (OUTLIER) cc_final: 0.6417 (m-40)
  outliers start: 34
  outliers final: 21
  residues processed: 109
  average time/residue: 0.2226
  time to fit residues: 36.9255
Evaluate side-chains
  93 residues out of total 1271 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 68
  time to evaluate  : 1.200 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue  233 ILE
Chi-restraints excluded: chain C residue  345 THR
Chi-restraints excluded: chain C residue  377 PHE
Chi-restraints excluded: chain C residue  402 ILE
Chi-restraints excluded: chain C residue  420 ASP
Chi-restraints excluded: chain C residue  433 VAL
Chi-restraints excluded: chain C residue  506 GLN
Chi-restraints excluded: chain C residue  539 VAL
Chi-restraints excluded: chain H residue   69 ILE
Chi-restraints excluded: chain H residue  115 SER
Chi-restraints excluded: chain H residue  143 CYS
Chi-restraints excluded: chain H residue  144 LEU
Chi-restraints excluded: chain H residue  190 SER
Chi-restraints excluded: chain H residue  218 SER
Chi-restraints excluded: chain L residue   77 SER
Chi-restraints excluded: chain L residue  107 ILE
Chi-restraints excluded: chain D residue   25 SER
Chi-restraints excluded: chain D residue   68 VAL
Chi-restraints excluded: chain D residue  218 VAL
Chi-restraints excluded: chain E residue   55 ASN
Chi-restraints excluded: chain E residue   58 SER
Chi-restraints excluded: chain E residue   97 LEU
Chi-restraints excluded: chain E residue  106 THR
Chi-restraints excluded: chain E residue  138 VAL
Chi-restraints excluded: chain E residue  149 VAL
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 147
   random chunks:
   chunk 36 optimal weight:    0.9980
   chunk 99 optimal weight:   10.0000
   chunk 83 optimal weight:    5.9990
   chunk 106 optimal weight:    5.9990
   chunk 19 optimal weight:   50.0000
   chunk 7 optimal weight:    9.9990
   chunk 31 optimal weight:    0.8980
   chunk 132 optimal weight:    0.0980
   chunk 16 optimal weight:    9.9990
   chunk 89 optimal weight:    3.9990
   chunk 57 optimal weight:    0.8980
   overall best weight:    1.3782

-------------------------------------------------------------------------------
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 = 0.4742 r_free = 0.4742 target = 0.248622 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 28)----------------|
| r_work = 0.4357 r_free = 0.4357 target = 0.210584 restraints weight = 20795.980|
|-----------------------------------------------------------------------------|
r_work (start): 0.4323 rms_B_bonded: 4.94
r_work: 0.4064 rms_B_bonded: 3.44 restraints_weight: 0.5000
r_work (final): 0.4064
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.4030
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.4030 r_free = 0.4030    target_work(ls_wunit_k1) = 0.171         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.4030 r_free = 0.4030    target_work(ls_wunit_k1) = 0.171         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|
r_final: 0.4030
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6854
moved from start:          0.3550

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.049  11697  Z= 0.162
  Angle     :  0.545   9.581  15946  Z= 0.281
  Chirality :  0.045   0.187   1790
  Planarity :  0.004   0.049   2048
  Dihedral  :  3.885  26.606   1628
  Min Nonbonded Distance : 2.562

Molprobity Statistics.
  All-atom Clashscore : 6.99
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.01 %
    Favored  : 94.99 %
  Rotamer:
    Outliers :  3.69 %
    Allowed  : 20.28 %
    Favored  : 76.02 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.70 %
    Cis-general     : 0.00 %
    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: -0.68 (0.22), residues: 1479
  helix: -2.09 (0.71), residues: 48
  sheet:  0.12 (0.24), residues: 520
  loop : -0.68 (0.20), residues: 911

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP C 436 
 HIS   0.005   0.001   HIS H  35 
 PHE   0.014   0.001   PHE C 429 
 TYR   0.019   0.001   TYR C 396 
 ARG   0.004   0.000   ARG L 212 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00076 (    1)
  link_NAG-ASN         : angle       1.88650 (    3)
  hydrogen bonds       : bond        0.03233 (  275)
  hydrogen bonds       : angle       5.88303 (  768)
  SS BOND              : bond        0.00558 (   18)
  SS BOND              : angle       1.17374 (   38)
  covalent geometry    : bond        0.00383 (11678)
  covalent geometry    : angle       0.54223 (15905)

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

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

  2958 Ramachandran restraints generated.
    1479 Oldfield, 0 Emsley, 1479 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2958 Ramachandran restraints generated.
    1479 Oldfield, 0 Emsley, 1479 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  118 residues out of total 1271 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 47
    poor density    : 71
  time to evaluate  : 1.673 
Fit side-chains
   revert: symmetry clash
REVERT: H   83 ASN cc_start: 0.6022 (m110) cc_final: 0.5685 (m-40)
REVERT: H  190 SER cc_start: 0.4374 (OUTLIER) cc_final: 0.3973 (p)
REVERT: E   55 ASN cc_start: 0.7169 (OUTLIER) cc_final: 0.6836 (m-40)
REVERT: E   81 GLN cc_start: 0.7602 (OUTLIER) cc_final: 0.6234 (mm110)
  outliers start: 47
  outliers final: 28
  residues processed: 115
  average time/residue: 0.2071
  time to fit residues: 36.6842
Evaluate side-chains
  96 residues out of total 1271 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 65
  time to evaluate  : 1.199 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue  233 ILE
Chi-restraints excluded: chain C residue  238 PHE
Chi-restraints excluded: chain C residue  296 LEU
Chi-restraints excluded: chain C residue  345 THR
Chi-restraints excluded: chain C residue  350 VAL
Chi-restraints excluded: chain C residue  368 LEU
Chi-restraints excluded: chain C residue  402 ILE
Chi-restraints excluded: chain C residue  500 THR
Chi-restraints excluded: chain C residue  506 GLN
Chi-restraints excluded: chain C residue  539 VAL
Chi-restraints excluded: chain H residue   69 ILE
Chi-restraints excluded: chain H residue  143 CYS
Chi-restraints excluded: chain H residue  153 VAL
Chi-restraints excluded: chain H residue  173 LEU
Chi-restraints excluded: chain H residue  190 SER
Chi-restraints excluded: chain L residue   22 THR
Chi-restraints excluded: chain L residue   33 LEU
Chi-restraints excluded: chain L residue   54 LEU
Chi-restraints excluded: chain L residue  107 ILE
Chi-restraints excluded: chain D residue   18 VAL
Chi-restraints excluded: chain D residue   25 SER
Chi-restraints excluded: chain D residue   68 VAL
Chi-restraints excluded: chain D residue   69 THR
Chi-restraints excluded: chain D residue  218 VAL
Chi-restraints excluded: chain E residue   55 ASN
Chi-restraints excluded: chain E residue   58 SER
Chi-restraints excluded: chain E residue   75 LEU
Chi-restraints excluded: chain E residue   81 GLN
Chi-restraints excluded: chain E residue  106 THR
Chi-restraints excluded: chain E residue  138 VAL
Chi-restraints excluded: chain E residue  149 VAL
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 147
   random chunks:
   chunk 145 optimal weight:   40.0000
   chunk 109 optimal weight:    0.1980
   chunk 23 optimal weight:   20.0000
   chunk 134 optimal weight:    1.9990
   chunk 65 optimal weight:    1.9990
   chunk 51 optimal weight:    6.9990
   chunk 50 optimal weight:    0.8980
   chunk 45 optimal weight:    1.9990
   chunk 24 optimal weight:    5.9990
   chunk 49 optimal weight:    3.9990
   chunk 63 optimal weight:    0.8980
   overall best weight:    1.1984

-------------------------------------------------------------------------------
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 = 0.4730 r_free = 0.4730 target = 0.247323 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 24)----------------|
| r_work = 0.4669 r_free = 0.4669 target = 0.240038 restraints weight = 12645.559|
|-----------------------------------------------------------------------------|
r_work (start): 0.4670 rms_B_bonded: 0.63
r_work: 0.4568 rms_B_bonded: 1.21 restraints_weight: 0.5000
r_work: 0.4527 rms_B_bonded: 1.96 restraints_weight: 0.2500
r_work (final): 0.4527
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.4532
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.4532 r_free = 0.4532    target_work(ls_wunit_k1) = 0.224         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.4532 r_free = 0.4532    target_work(ls_wunit_k1) = 0.224         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|
r_final: 0.4532
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6008
moved from start:          0.3726

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.046  11697  Z= 0.146
  Angle     :  0.527   7.643  15946  Z= 0.271
  Chirality :  0.044   0.154   1790
  Planarity :  0.004   0.046   2048
  Dihedral  :  3.807  25.465   1628
  Min Nonbonded Distance : 2.569

Molprobity Statistics.
  All-atom Clashscore : 7.35
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.60 %
    Favored  : 95.40 %
  Rotamer:
    Outliers :  3.14 %
    Allowed  : 20.91 %
    Favored  : 75.94 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.70 %
    Cis-general     : 0.00 %
    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: -0.65 (0.22), residues: 1479
  helix: -2.00 (0.72), residues: 48
  sheet:  0.05 (0.23), residues: 539
  loop : -0.60 (0.21), residues: 892

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP C 436 
 HIS   0.004   0.001   HIS H  35 
 PHE   0.012   0.001   PHE D 157 
 TYR   0.016   0.001   TYR C 396 
 ARG   0.002   0.000   ARG H  19 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00044 (    1)
  link_NAG-ASN         : angle       1.88519 (    3)
  hydrogen bonds       : bond        0.03050 (  275)
  hydrogen bonds       : angle       5.71825 (  768)
  SS BOND              : bond        0.00438 (   18)
  SS BOND              : angle       1.08429 (   38)
  covalent geometry    : bond        0.00345 (11678)
  covalent geometry    : angle       0.52397 (15905)

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

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

  2958 Ramachandran restraints generated.
    1479 Oldfield, 0 Emsley, 1479 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2958 Ramachandran restraints generated.
    1479 Oldfield, 0 Emsley, 1479 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  110 residues out of total 1271 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 40
    poor density    : 70
  time to evaluate  : 1.344 
Fit side-chains
   revert: symmetry clash
REVERT: H   83 ASN cc_start: 0.5832 (m110) cc_final: 0.5561 (m-40)
REVERT: E   55 ASN cc_start: 0.7658 (OUTLIER) cc_final: 0.7277 (m-40)
REVERT: E   81 GLN cc_start: 0.7561 (OUTLIER) cc_final: 0.6201 (mm110)
  outliers start: 40
  outliers final: 30
  residues processed: 107
  average time/residue: 0.2093
  time to fit residues: 34.5504
Evaluate side-chains
  98 residues out of total 1271 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 66
  time to evaluate  : 1.237 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue  233 ILE
Chi-restraints excluded: chain C residue  238 PHE
Chi-restraints excluded: chain C residue  345 THR
Chi-restraints excluded: chain C residue  350 VAL
Chi-restraints excluded: chain C residue  368 LEU
Chi-restraints excluded: chain C residue  390 LEU
Chi-restraints excluded: chain C residue  402 ILE
Chi-restraints excluded: chain C residue  433 VAL
Chi-restraints excluded: chain C residue  500 THR
Chi-restraints excluded: chain C residue  506 GLN
Chi-restraints excluded: chain H residue   69 ILE
Chi-restraints excluded: chain H residue  143 CYS
Chi-restraints excluded: chain H residue  144 LEU
Chi-restraints excluded: chain H residue  153 VAL
Chi-restraints excluded: chain L residue   22 THR
Chi-restraints excluded: chain L residue   33 LEU
Chi-restraints excluded: chain L residue   53 THR
Chi-restraints excluded: chain L residue   54 LEU
Chi-restraints excluded: chain L residue  107 ILE
Chi-restraints excluded: chain L residue  210 PHE
Chi-restraints excluded: chain D residue   18 VAL
Chi-restraints excluded: chain D residue   25 SER
Chi-restraints excluded: chain D residue   68 VAL
Chi-restraints excluded: chain D residue   69 THR
Chi-restraints excluded: chain D residue  218 VAL
Chi-restraints excluded: chain E residue   55 ASN
Chi-restraints excluded: chain E residue   58 SER
Chi-restraints excluded: chain E residue   75 LEU
Chi-restraints excluded: chain E residue   81 GLN
Chi-restraints excluded: chain E residue  106 THR
Chi-restraints excluded: chain E residue  138 VAL
Chi-restraints excluded: chain E residue  149 VAL
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 147
   random chunks:
   chunk 42 optimal weight:    0.6980
   chunk 139 optimal weight:   20.0000
   chunk 69 optimal weight:    0.9980
   chunk 29 optimal weight:    0.0170
   chunk 93 optimal weight:    2.9990
   chunk 20 optimal weight:    7.9990
   chunk 121 optimal weight:   30.0000
   chunk 47 optimal weight:    2.9990
   chunk 50 optimal weight:    4.9990
   chunk 111 optimal weight:    0.9980
   chunk 8 optimal weight:   50.0000
   overall best weight:    1.1420

-------------------------------------------------------------------------------
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 = 0.4741 r_free = 0.4741 target = 0.248630 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 29)----------------|
| r_work = 0.4319 r_free = 0.4319 target = 0.207931 restraints weight = 16432.116|
|-----------------------------------------------------------------------------|
r_work (start): 0.4276 rms_B_bonded: 4.96
r_work: 0.3937 rms_B_bonded: 3.75 restraints_weight: 0.5000
r_work (final): 0.3937
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3839
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3839 r_free = 0.3839    target_work(ls_wunit_k1) = 0.154         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3839 r_free = 0.3839    target_work(ls_wunit_k1) = 0.154         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|
r_final: 0.3839
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7060
moved from start:          0.3886

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.049  11697  Z= 0.140
  Angle     :  0.519   7.601  15946  Z= 0.267
  Chirality :  0.044   0.151   1790
  Planarity :  0.004   0.045   2048
  Dihedral  :  3.789  25.527   1628
  Min Nonbonded Distance : 2.580

Molprobity Statistics.
  All-atom Clashscore : 7.26
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.08 %
    Favored  : 94.92 %
  Rotamer:
    Outliers :  3.07 %
    Allowed  : 20.75 %
    Favored  : 76.18 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.70 %
    Cis-general     : 0.00 %
    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: -0.66 (0.22), residues: 1479
  helix: -1.91 (0.73), residues: 48
  sheet:  0.05 (0.23), residues: 538
  loop : -0.62 (0.21), residues: 893

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP C 436 
 HIS   0.004   0.001   HIS H  35 
 PHE   0.011   0.001   PHE D 157 
 TYR   0.015   0.001   TYR C 396 
 ARG   0.002   0.000   ARG C 454 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00045 (    1)
  link_NAG-ASN         : angle       1.91603 (    3)
  hydrogen bonds       : bond        0.03004 (  275)
  hydrogen bonds       : angle       5.64422 (  768)
  SS BOND              : bond        0.00474 (   18)
  SS BOND              : angle       1.06207 (   38)
  covalent geometry    : bond        0.00331 (11678)
  covalent geometry    : angle       0.51656 (15905)

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

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

  2958 Ramachandran restraints generated.
    1479 Oldfield, 0 Emsley, 1479 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2958 Ramachandran restraints generated.
    1479 Oldfield, 0 Emsley, 1479 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  107 residues out of total 1271 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 39
    poor density    : 68
  time to evaluate  : 1.272 
Fit side-chains
REVERT: H   83 ASN cc_start: 0.6058 (m110) cc_final: 0.5781 (m-40)
REVERT: E   81 GLN cc_start: 0.7684 (OUTLIER) cc_final: 0.6313 (mm110)
  outliers start: 39
  outliers final: 31
  residues processed: 105
  average time/residue: 0.2610
  time to fit residues: 43.6049
Evaluate side-chains
  94 residues out of total 1271 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 62
  time to evaluate  : 1.291 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue  233 ILE
Chi-restraints excluded: chain C residue  238 PHE
Chi-restraints excluded: chain C residue  296 LEU
Chi-restraints excluded: chain C residue  345 THR
Chi-restraints excluded: chain C residue  350 VAL
Chi-restraints excluded: chain C residue  368 LEU
Chi-restraints excluded: chain C residue  390 LEU
Chi-restraints excluded: chain C residue  402 ILE
Chi-restraints excluded: chain C residue  433 VAL
Chi-restraints excluded: chain C residue  506 GLN
Chi-restraints excluded: chain C residue  524 VAL
Chi-restraints excluded: chain C residue  539 VAL
Chi-restraints excluded: chain H residue   69 ILE
Chi-restraints excluded: chain H residue  143 CYS
Chi-restraints excluded: chain H residue  153 VAL
Chi-restraints excluded: chain H residue  173 LEU
Chi-restraints excluded: chain L residue   33 LEU
Chi-restraints excluded: chain L residue   53 THR
Chi-restraints excluded: chain L residue   54 LEU
Chi-restraints excluded: chain L residue   76 THR
Chi-restraints excluded: chain L residue  116 VAL
Chi-restraints excluded: chain D residue   18 VAL
Chi-restraints excluded: chain D residue   25 SER
Chi-restraints excluded: chain D residue   68 VAL
Chi-restraints excluded: chain D residue   69 THR
Chi-restraints excluded: chain D residue  218 VAL
Chi-restraints excluded: chain E residue   58 SER
Chi-restraints excluded: chain E residue   75 LEU
Chi-restraints excluded: chain E residue   81 GLN
Chi-restraints excluded: chain E residue  106 THR
Chi-restraints excluded: chain E residue  138 VAL
Chi-restraints excluded: chain E residue  149 VAL
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 147
   random chunks:
   chunk 31 optimal weight:    0.0670
   chunk 14 optimal weight:   50.0000
   chunk 101 optimal weight:   20.0000
   chunk 141 optimal weight:   30.0000
   chunk 21 optimal weight:   50.0000
   chunk 83 optimal weight:    5.9990
   chunk 137 optimal weight:    0.0970
   chunk 20 optimal weight:   10.0000
   chunk 132 optimal weight:    0.7980
   chunk 40 optimal weight:    3.9990
   chunk 70 optimal weight:    0.8980
   overall best weight:    1.1718

-------------------------------------------------------------------------------
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 = 0.4734 r_free = 0.4734 target = 0.247907 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 28)----------------|
| r_work = 0.4300 r_free = 0.4300 target = 0.205878 restraints weight = 20949.184|
|-----------------------------------------------------------------------------|
r_work (start): 0.4259 rms_B_bonded: 5.93
r_work: 0.3858 rms_B_bonded: 5.04 restraints_weight: 2.0000
r_work (final): 0.3858
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3791
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3791 r_free = 0.3791    target_work(ls_wunit_k1) = 0.149         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3791 r_free = 0.3791    target_work(ls_wunit_k1) = 0.149         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|
r_final: 0.3791
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7171
moved from start:          0.4059

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.049  11697  Z= 0.142
  Angle     :  0.526   7.384  15946  Z= 0.270
  Chirality :  0.044   0.151   1790
  Planarity :  0.004   0.045   2048
  Dihedral  :  3.832  25.348   1628
  Min Nonbonded Distance : 2.587

Molprobity Statistics.
  All-atom Clashscore : 7.39
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.15 %
    Favored  : 94.85 %
  Rotamer:
    Outliers :  3.14 %
    Allowed  : 21.23 %
    Favored  : 75.63 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.70 %
    Cis-general     : 0.00 %
    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: -0.66 (0.22), residues: 1479
  helix: -1.80 (0.74), residues: 48
  sheet:  0.01 (0.23), residues: 543
  loop : -0.60 (0.21), residues: 888

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP C 436 
 HIS   0.004   0.001   HIS H  35 
 PHE   0.010   0.001   PHE D 157 
 TYR   0.016   0.001   TYR L 193 
 ARG   0.004   0.000   ARG H  38 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00047 (    1)
  link_NAG-ASN         : angle       1.93196 (    3)
  hydrogen bonds       : bond        0.02977 (  275)
  hydrogen bonds       : angle       5.59109 (  768)
  SS BOND              : bond        0.00462 (   18)
  SS BOND              : angle       1.16988 (   38)
  covalent geometry    : bond        0.00337 (11678)
  covalent geometry    : angle       0.52240 (15905)

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

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

  2958 Ramachandran restraints generated.
    1479 Oldfield, 0 Emsley, 1479 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2958 Ramachandran restraints generated.
    1479 Oldfield, 0 Emsley, 1479 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  104 residues out of total 1271 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 40
    poor density    : 64
  time to evaluate  : 1.142 
Fit side-chains
REVERT: C  524 VAL cc_start: 0.8240 (OUTLIER) cc_final: 0.6938 (m)
REVERT: E   81 GLN cc_start: 0.7697 (OUTLIER) cc_final: 0.6320 (mm110)
  outliers start: 40
  outliers final: 31
  residues processed: 101
  average time/residue: 0.1904
  time to fit residues: 30.1953
Evaluate side-chains
  92 residues out of total 1271 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 59
  time to evaluate  : 1.153 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue  233 ILE
Chi-restraints excluded: chain C residue  238 PHE
Chi-restraints excluded: chain C residue  296 LEU
Chi-restraints excluded: chain C residue  345 THR
Chi-restraints excluded: chain C residue  350 VAL
Chi-restraints excluded: chain C residue  368 LEU
Chi-restraints excluded: chain C residue  390 LEU
Chi-restraints excluded: chain C residue  402 ILE
Chi-restraints excluded: chain C residue  433 VAL
Chi-restraints excluded: chain C residue  506 GLN
Chi-restraints excluded: chain C residue  524 VAL
Chi-restraints excluded: chain C residue  539 VAL
Chi-restraints excluded: chain H residue   69 ILE
Chi-restraints excluded: chain H residue  153 VAL
Chi-restraints excluded: chain H residue  173 LEU
Chi-restraints excluded: chain L residue   20 THR
Chi-restraints excluded: chain L residue   22 THR
Chi-restraints excluded: chain L residue   33 LEU
Chi-restraints excluded: chain L residue   53 THR
Chi-restraints excluded: chain L residue   54 LEU
Chi-restraints excluded: chain L residue   76 THR
Chi-restraints excluded: chain L residue  116 VAL
Chi-restraints excluded: chain D residue   18 VAL
Chi-restraints excluded: chain D residue   25 SER
Chi-restraints excluded: chain D residue   69 THR
Chi-restraints excluded: chain D residue  218 VAL
Chi-restraints excluded: chain E residue   58 SER
Chi-restraints excluded: chain E residue   75 LEU
Chi-restraints excluded: chain E residue   81 GLN
Chi-restraints excluded: chain E residue   97 LEU
Chi-restraints excluded: chain E residue  106 THR
Chi-restraints excluded: chain E residue  138 VAL
Chi-restraints excluded: chain E residue  149 VAL
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 147
   random chunks:
   chunk 21 optimal weight:   50.0000
   chunk 92 optimal weight:    0.0050
   chunk 138 optimal weight:   30.0000
   chunk 84 optimal weight:    3.9990
   chunk 86 optimal weight:    0.8980
   chunk 144 optimal weight:   40.0000
   chunk 34 optimal weight:    1.9990
   chunk 101 optimal weight:   20.0000
   chunk 8 optimal weight:   50.0000
   chunk 125 optimal weight:    2.9990
   chunk 121 optimal weight:    0.0870
   overall best weight:    1.1976

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

Flipped N/Q/H residues before XYZ refinement:
D 110 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4733 r_free = 0.4733 target = 0.247941 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.4305 r_free = 0.4305 target = 0.206609 restraints weight = 14393.820|
|-----------------------------------------------------------------------------|
r_work (start): 0.4261 rms_B_bonded: 4.54
r_work: 0.3974 rms_B_bonded: 3.15 restraints_weight: 0.5000
r_work (final): 0.3974
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3868
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3868 r_free = 0.3868    target_work(ls_wunit_k1) = 0.157         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3868 r_free = 0.3868    target_work(ls_wunit_k1) = 0.157         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|
r_final: 0.3868
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6999
moved from start:          0.4149

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.046  11697  Z= 0.144
  Angle     :  0.532   7.275  15946  Z= 0.272
  Chirality :  0.044   0.151   1790
  Planarity :  0.004   0.045   2048
  Dihedral  :  3.841  25.227   1628
  Min Nonbonded Distance : 2.569

Molprobity Statistics.
  All-atom Clashscore : 7.48
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.81 %
    Favored  : 95.19 %
  Rotamer:
    Outliers :  2.91 %
    Allowed  : 21.54 %
    Favored  : 75.55 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.70 %
    Cis-general     : 0.00 %
    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: -0.64 (0.22), residues: 1479
  helix: -1.17 (0.84), residues: 41
  sheet:  0.01 (0.23), residues: 543
  loop : -0.63 (0.21), residues: 895

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP C 436 
 HIS   0.004   0.001   HIS H  35 
 PHE   0.010   0.001   PHE L  99 
 TYR   0.016   0.001   TYR L 141 
 ARG   0.008   0.000   ARG H  38 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00034 (    1)
  link_NAG-ASN         : angle       1.95148 (    3)
  hydrogen bonds       : bond        0.02965 (  275)
  hydrogen bonds       : angle       5.56833 (  768)
  SS BOND              : bond        0.00454 (   18)
  SS BOND              : angle       1.13051 (   38)
  covalent geometry    : bond        0.00343 (11678)
  covalent geometry    : angle       0.52870 (15905)

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

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

  2958 Ramachandran restraints generated.
    1479 Oldfield, 0 Emsley, 1479 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2958 Ramachandran restraints generated.
    1479 Oldfield, 0 Emsley, 1479 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  101 residues out of total 1271 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 37
    poor density    : 64
  time to evaluate  : 1.243 
Fit side-chains
REVERT: C  524 VAL cc_start: 0.8137 (OUTLIER) cc_final: 0.6826 (m)
REVERT: L  212 ARG cc_start: 0.6632 (ptp90) cc_final: 0.6278 (ptp90)
REVERT: E   81 GLN cc_start: 0.7666 (OUTLIER) cc_final: 0.6243 (mm110)
  outliers start: 37
  outliers final: 31
  residues processed: 101
  average time/residue: 0.2057
  time to fit residues: 32.2163
Evaluate side-chains
  95 residues out of total 1271 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 62
  time to evaluate  : 1.174 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue  233 ILE
Chi-restraints excluded: chain C residue  238 PHE
Chi-restraints excluded: chain C residue  296 LEU
Chi-restraints excluded: chain C residue  345 THR
Chi-restraints excluded: chain C residue  350 VAL
Chi-restraints excluded: chain C residue  368 LEU
Chi-restraints excluded: chain C residue  390 LEU
Chi-restraints excluded: chain C residue  402 ILE
Chi-restraints excluded: chain C residue  433 VAL
Chi-restraints excluded: chain C residue  506 GLN
Chi-restraints excluded: chain C residue  524 VAL
Chi-restraints excluded: chain C residue  539 VAL
Chi-restraints excluded: chain H residue   22 CYS
Chi-restraints excluded: chain H residue   46 GLU
Chi-restraints excluded: chain H residue   69 ILE
Chi-restraints excluded: chain H residue  153 VAL
Chi-restraints excluded: chain H residue  173 LEU
Chi-restraints excluded: chain L residue   22 THR
Chi-restraints excluded: chain L residue   33 LEU
Chi-restraints excluded: chain L residue   53 THR
Chi-restraints excluded: chain L residue   54 LEU
Chi-restraints excluded: chain L residue   76 THR
Chi-restraints excluded: chain D residue   18 VAL
Chi-restraints excluded: chain D residue   25 SER
Chi-restraints excluded: chain D residue   69 THR
Chi-restraints excluded: chain D residue  218 VAL
Chi-restraints excluded: chain E residue   58 SER
Chi-restraints excluded: chain E residue   75 LEU
Chi-restraints excluded: chain E residue   81 GLN
Chi-restraints excluded: chain E residue   97 LEU
Chi-restraints excluded: chain E residue  106 THR
Chi-restraints excluded: chain E residue  138 VAL
Chi-restraints excluded: chain E residue  149 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 147
   random chunks:
   chunk 94 optimal weight:    8.9990
   chunk 65 optimal weight:    1.9990
   chunk 22 optimal weight:   30.0000
   chunk 128 optimal weight:    0.8980
   chunk 87 optimal weight:    0.6980
   chunk 134 optimal weight:    0.6980
   chunk 16 optimal weight:    0.0270
   chunk 115 optimal weight:    0.9990
   chunk 72 optimal weight:    0.9980
   chunk 122 optimal weight:    8.9990
   chunk 129 optimal weight:    0.5980
   overall best weight:    0.5838

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

Flipped N/Q/H residues before XYZ refinement:
** E  36 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4752 r_free = 0.4752 target = 0.250084 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.4396 r_free = 0.4396 target = 0.214520 restraints weight = 20996.513|
|-----------------------------------------------------------------------------|
r_work (start): 0.4367 rms_B_bonded: 4.65
r_work: 0.4118 rms_B_bonded: 3.20 restraints_weight: 0.5000
r_work: 0.4025 rms_B_bonded: 4.47 restraints_weight: 0.2500
r_work (final): 0.4025
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3986
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3986 r_free = 0.3986    target_work(ls_wunit_k1) = 0.167         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3986 r_free = 0.3986    target_work(ls_wunit_k1) = 0.167         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|
r_final: 0.3986
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6870
moved from start:          0.4125

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.040  11697  Z= 0.102
  Angle     :  0.496   7.096  15946  Z= 0.253
  Chirality :  0.043   0.152   1790
  Planarity :  0.004   0.045   2048
  Dihedral  :  3.642  23.122   1628
  Min Nonbonded Distance : 2.570

Molprobity Statistics.
  All-atom Clashscore : 6.77
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.81 %
    Favored  : 95.19 %
  Rotamer:
    Outliers :  2.12 %
    Allowed  : 22.41 %
    Favored  : 75.47 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.70 %
    Cis-general     : 0.00 %
    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: -0.54 (0.22), residues: 1479
  helix: -1.14 (0.83), residues: 41
  sheet:  0.15 (0.23), residues: 547
  loop : -0.62 (0.21), residues: 891

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP C 436 
 HIS   0.004   0.001   HIS H  35 
 PHE   0.010   0.001   PHE D 157 
 TYR   0.017   0.001   TYR L 141 
 ARG   0.003   0.000   ARG H  38 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00043 (    1)
  link_NAG-ASN         : angle       1.85258 (    3)
  hydrogen bonds       : bond        0.02706 (  275)
  hydrogen bonds       : angle       5.33711 (  768)
  SS BOND              : bond        0.00386 (   18)
  SS BOND              : angle       0.99662 (   38)
  covalent geometry    : bond        0.00239 (11678)
  covalent geometry    : angle       0.49369 (15905)

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

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

  2958 Ramachandran restraints generated.
    1479 Oldfield, 0 Emsley, 1479 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2958 Ramachandran restraints generated.
    1479 Oldfield, 0 Emsley, 1479 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  97 residues out of total 1271 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 70
  time to evaluate  : 1.220 
Fit side-chains
REVERT: H   46 GLU cc_start: 0.8142 (OUTLIER) cc_final: 0.7647 (pt0)
REVERT: E   28 ASN cc_start: 0.8103 (p0) cc_final: 0.7578 (p0)
REVERT: E   83 GLU cc_start: 0.6133 (tt0) cc_final: 0.5884 (tt0)
  outliers start: 27
  outliers final: 24
  residues processed: 97
  average time/residue: 0.2064
  time to fit residues: 30.6874
Evaluate side-chains
  91 residues out of total 1271 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 66
  time to evaluate  : 1.259 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue  233 ILE
Chi-restraints excluded: chain C residue  238 PHE
Chi-restraints excluded: chain C residue  296 LEU
Chi-restraints excluded: chain C residue  350 VAL
Chi-restraints excluded: chain C residue  368 LEU
Chi-restraints excluded: chain C residue  390 LEU
Chi-restraints excluded: chain C residue  402 ILE
Chi-restraints excluded: chain C residue  433 VAL
Chi-restraints excluded: chain C residue  506 GLN
Chi-restraints excluded: chain C residue  524 VAL
Chi-restraints excluded: chain H residue   46 GLU
Chi-restraints excluded: chain L residue   22 THR
Chi-restraints excluded: chain L residue   33 LEU
Chi-restraints excluded: chain L residue   53 THR
Chi-restraints excluded: chain L residue   76 THR
Chi-restraints excluded: chain L residue  116 VAL
Chi-restraints excluded: chain D residue   18 VAL
Chi-restraints excluded: chain D residue   69 THR
Chi-restraints excluded: chain D residue  162 THR
Chi-restraints excluded: chain D residue  218 VAL
Chi-restraints excluded: chain E residue   58 SER
Chi-restraints excluded: chain E residue   75 LEU
Chi-restraints excluded: chain E residue  106 THR
Chi-restraints excluded: chain E residue  138 VAL
Chi-restraints excluded: chain E residue  149 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 147
   random chunks:
   chunk 64 optimal weight:    3.9990
   chunk 127 optimal weight:    0.0670
   chunk 138 optimal weight:   30.0000
   chunk 47 optimal weight:    1.9990
   chunk 22 optimal weight:    8.9990
   chunk 66 optimal weight:    0.9990
   chunk 20 optimal weight:    8.9990
   chunk 68 optimal weight:    1.9990
   chunk 11 optimal weight:   10.0000
   chunk 59 optimal weight:   50.0000
   chunk 124 optimal weight:   20.0000
   overall best weight:    1.8126

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

Flipped N/Q/H residues before XYZ refinement:
** E  36 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4702 r_free = 0.4702 target = 0.244227 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 23)----------------|
| r_work = 0.4652 r_free = 0.4652 target = 0.238260 restraints weight = 20647.154|
|-----------------------------------------------------------------------------|
r_work (start): 0.4651 rms_B_bonded: 0.55
r_work: 0.4545 rms_B_bonded: 1.10 restraints_weight: 0.5000
r_work: 0.4504 rms_B_bonded: 1.81 restraints_weight: 0.2500
r_work (final): 0.4504
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.4509
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.4509 r_free = 0.4509    target_work(ls_wunit_k1) = 0.222         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.4509 r_free = 0.4509    target_work(ls_wunit_k1) = 0.222         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|
r_final: 0.4509
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6075
moved from start:          0.4418

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.049  11697  Z= 0.196
  Angle     :  0.586   8.291  15946  Z= 0.303
  Chirality :  0.045   0.168   1790
  Planarity :  0.004   0.051   2048
  Dihedral  :  4.009  23.630   1628
  Min Nonbonded Distance : 2.367

Molprobity Statistics.
  All-atom Clashscore : 8.19
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.69 %
    Favored  : 94.31 %
  Rotamer:
    Outliers :  2.28 %
    Allowed  : 22.48 %
    Favored  : 75.24 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.70 %
    Cis-general     : 0.00 %
    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: -0.59 (0.22), residues: 1479
  helix: -1.73 (0.75), residues: 48
  sheet:  0.16 (0.23), residues: 542
  loop : -0.64 (0.21), residues: 889

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.001   TRP C 436 
 HIS   0.005   0.001   HIS L 199 
 PHE   0.013   0.001   PHE H  67 
 TYR   0.025   0.002   TYR C 396 
 ARG   0.004   0.000   ARG H  38 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00029 (    1)
  link_NAG-ASN         : angle       2.08549 (    3)
  hydrogen bonds       : bond        0.03223 (  275)
  hydrogen bonds       : angle       5.65044 (  768)
  SS BOND              : bond        0.00504 (   18)
  SS BOND              : angle       1.23605 (   38)
  covalent geometry    : bond        0.00468 (11678)
  covalent geometry    : angle       0.58268 (15905)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 5811.78 seconds
wall clock time: 100 minutes 23.20 seconds (6023.20 seconds total)