Starting phenix.real_space_refine
on Thu May 15 11:12:08 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8yx7_39649/05_2025/8yx7_39649.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8yx7_39649/05_2025/8yx7_39649.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.8
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8yx7_39649/05_2025/8yx7_39649.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8yx7_39649/05_2025/8yx7_39649.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8yx7_39649/05_2025/8yx7_39649.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8yx7_39649/05_2025/8yx7_39649.cif"
  }
  resolution = 2.8
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


Starting job
===============================================================================
-------------------------------------------------------------------------------
Citation:
*********
Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams
PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography.
Acta Cryst. D74:531-544.

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.001 sd=   0.024
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 4
    Type Number    sf(0)   Gaussians
     S      55      5.16       5
     C    8485      2.51       5
     N    2190      2.21       5
     O    2340      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model
  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib"
  Total number of atoms: 13070
  Number of models: 1
  Model: ""
    Number of chains: 3
    Chain: "A"
      Number of atoms: 2572
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 324, 2572
          Classifications: {'peptide': 324}
          Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 306}
          Chain breaks: 1
    Chain: "G"
      Number of atoms: 28
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 28
          Unusual residues: {'NAG': 2}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
          Unresolved non-hydrogen bonds: 2
          Unresolved non-hydrogen angles: 4
          Unresolved non-hydrogen dihedrals: 6
          Unresolved non-hydrogen chiralities: 2
    Chain: "A"
      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
  Restraints were copied for chains:
    C, B, E, D, F, I, H, J
  Residues with excluded nonbonded symmetry interactions: 5
    residue:
      pdb=" C1  NAG F   2 " occ=0.80
      ... (12 atoms not shown)
      pdb=" O7  NAG F   2 " occ=0.80
    residue:
      pdb=" C1  NAG G   2 " occ=0.80
      ... (12 atoms not shown)
      pdb=" O7  NAG G   2 " occ=0.80
    residue:
      pdb=" C1  NAG H   2 " occ=0.80
      ... (12 atoms not shown)
      pdb=" O7  NAG H   2 " occ=0.80
    residue:
      pdb=" C1  NAG I   2 " occ=0.80
      ... (12 atoms not shown)
      pdb=" O7  NAG I   2 " occ=0.80
    residue:
      pdb=" C1  NAG J   2 " occ=0.80
      ... (12 atoms not shown)
      pdb=" O7  NAG J   2 " occ=0.80
  Time building chain proxies: 5.57, per 1000 atoms: 0.43
  Number of scatterers: 13070
  At special positions: 0
  Unit cell: (93, 92.07, 122.76, 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      55     16.00
     O    2340      8.00
     N    2190      7.00
     C    8485      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=10, symmetry=0
    Simple disulfide: pdb=" SG  CYS A 157 " - pdb=" SG  CYS A 171 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 289 " - pdb=" SG  CYS A 394 " distance=2.03
    Simple disulfide: pdb=" SG  CYS C 157 " - pdb=" SG  CYS C 171 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 157 " - pdb=" SG  CYS B 171 " distance=2.03
    Simple disulfide: pdb=" SG  CYS E 157 " - pdb=" SG  CYS E 171 " distance=2.03
    Simple disulfide: pdb=" SG  CYS D 157 " - pdb=" SG  CYS D 171 " distance=2.03
    Simple disulfide: pdb=" SG  CYS C 289 " - pdb=" SG  CYS C 394 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 289 " - pdb=" SG  CYS B 394 " distance=2.03
    Simple disulfide: pdb=" SG  CYS E 289 " - pdb=" SG  CYS E 394 " distance=2.03
    Simple disulfide: pdb=" SG  CYS D 289 " - pdb=" SG  CYS D 394 " 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
    BETA1-4
      " NAG F   1 " - " NAG F   2 "
      " NAG G   1 " - " NAG G   2 "
      " NAG H   1 " - " NAG H   2 "
      " NAG I   1 " - " NAG I   2 "
      " NAG J   1 " - " NAG J   2 "
    NAG-ASN
      " NAG A 501 " - " ASN A 170 "
      " NAG B 501 " - " ASN B 170 "
      " NAG C 501 " - " ASN C 170 "
      " NAG D 501 " - " ASN D 170 "
      " NAG E 501 " - " ASN E 170 "
      " NAG F   1 " - " ASN A  55 "
      " NAG G   1 " - " ASN B  55 "
      " NAG H   1 " - " ASN C  55 "
      " NAG I   1 " - " ASN D  55 "
      " NAG J   1 " - " ASN E  55 "
  Time building additional restraints: 2.92
  Conformation dependent library (CDL) restraints added in 1.6 seconds
  

  3200 Ramachandran restraints generated.
    1600 Oldfield, 0 Emsley, 1600 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  3140

  Finding SS restraints...
    Secondary structure from input PDB file:
      40 helices and 15 sheets defined
      39.2% alpha, 33.3% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 1.28
  Creating SS restraints...
    Processing helix  chain 'A' and resid 94 through 97
    Processing helix  chain 'A' and resid 113 through 115
      No H-bonds generated for 'chain 'A' and resid 113 through 115'
    Processing helix  chain 'A' and resid 160 through 164
      removed outlier: 4.224A  pdb=" N   HIS A 163 " --> pdb=" O   GLU A 160 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 231 through 252
      removed outlier: 4.692A  pdb=" N   VAL A 239 " --> pdb=" O   ILE A 235 " (cutoff:3.500A)
      Proline residue:  A 240  - end of helix
    Processing helix  chain 'A' and resid 258 through 283
      removed outlier: 4.400A  pdb=" N   ILE A 262 " --> pdb=" O   ALA A 258 " (cutoff:3.500A)
      removed outlier: 3.989A  pdb=" N   GLY A 263 " --> pdb=" O   ILE A 259 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 291 through 320
      removed outlier: 3.859A  pdb=" N   TYR A 295 " --> pdb=" O   PRO A 291 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 361 through 391
    Processing helix  chain 'A' and resid 399 through 404
    Processing helix  chain 'B' and resid 94 through 97
    Processing helix  chain 'B' and resid 113 through 115
      No H-bonds generated for 'chain 'B' and resid 113 through 115'
    Processing helix  chain 'B' and resid 160 through 164
      removed outlier: 4.224A  pdb=" N   HIS B 163 " --> pdb=" O   GLU B 160 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 231 through 252
      removed outlier: 4.692A  pdb=" N   VAL B 239 " --> pdb=" O   ILE B 235 " (cutoff:3.500A)
      Proline residue:  B 240  - end of helix
    Processing helix  chain 'B' and resid 258 through 283
      removed outlier: 4.400A  pdb=" N   ILE B 262 " --> pdb=" O   ALA B 258 " (cutoff:3.500A)
      removed outlier: 3.989A  pdb=" N   GLY B 263 " --> pdb=" O   ILE B 259 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 291 through 320
      removed outlier: 3.859A  pdb=" N   TYR B 295 " --> pdb=" O   PRO B 291 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 361 through 391
    Processing helix  chain 'B' and resid 399 through 404
    Processing helix  chain 'C' and resid 94 through 97
    Processing helix  chain 'C' and resid 113 through 115
      No H-bonds generated for 'chain 'C' and resid 113 through 115'
    Processing helix  chain 'C' and resid 160 through 164
      removed outlier: 4.224A  pdb=" N   HIS C 163 " --> pdb=" O   GLU C 160 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 231 through 252
      removed outlier: 4.693A  pdb=" N   VAL C 239 " --> pdb=" O   ILE C 235 " (cutoff:3.500A)
      Proline residue:  C 240  - end of helix
    Processing helix  chain 'C' and resid 258 through 283
      removed outlier: 4.400A  pdb=" N   ILE C 262 " --> pdb=" O   ALA C 258 " (cutoff:3.500A)
      removed outlier: 3.989A  pdb=" N   GLY C 263 " --> pdb=" O   ILE C 259 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 291 through 320
      removed outlier: 3.858A  pdb=" N   TYR C 295 " --> pdb=" O   PRO C 291 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 361 through 391
    Processing helix  chain 'C' and resid 399 through 404
    Processing helix  chain 'D' and resid 94 through 97
    Processing helix  chain 'D' and resid 113 through 115
      No H-bonds generated for 'chain 'D' and resid 113 through 115'
    Processing helix  chain 'D' and resid 160 through 164
      removed outlier: 4.224A  pdb=" N   HIS D 163 " --> pdb=" O   GLU D 160 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 231 through 252
      removed outlier: 4.692A  pdb=" N   VAL D 239 " --> pdb=" O   ILE D 235 " (cutoff:3.500A)
      Proline residue:  D 240  - end of helix
    Processing helix  chain 'D' and resid 258 through 283
      removed outlier: 4.400A  pdb=" N   ILE D 262 " --> pdb=" O   ALA D 258 " (cutoff:3.500A)
      removed outlier: 3.989A  pdb=" N   GLY D 263 " --> pdb=" O   ILE D 259 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 291 through 320
      removed outlier: 3.859A  pdb=" N   TYR D 295 " --> pdb=" O   PRO D 291 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 361 through 391
    Processing helix  chain 'D' and resid 399 through 404
    Processing helix  chain 'E' and resid 94 through 97
    Processing helix  chain 'E' and resid 113 through 115
      No H-bonds generated for 'chain 'E' and resid 113 through 115'
    Processing helix  chain 'E' and resid 160 through 164
      removed outlier: 4.224A  pdb=" N   HIS E 163 " --> pdb=" O   GLU E 160 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 231 through 252
      removed outlier: 4.692A  pdb=" N   VAL E 239 " --> pdb=" O   ILE E 235 " (cutoff:3.500A)
      Proline residue:  E 240  - end of helix
    Processing helix  chain 'E' and resid 258 through 283
      removed outlier: 4.400A  pdb=" N   ILE E 262 " --> pdb=" O   ALA E 258 " (cutoff:3.500A)
      removed outlier: 3.989A  pdb=" N   GLY E 263 " --> pdb=" O   ILE E 259 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 291 through 320
      removed outlier: 3.859A  pdb=" N   TYR E 295 " --> pdb=" O   PRO E 291 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 361 through 391
    Processing helix  chain 'E' and resid 399 through 404
    Processing sheet with id=AA1, first strand: chain 'A' and resid 107 through 111
      removed outlier: 5.773A  pdb=" N   GLN A 136 " --> pdb=" O   ASN A 148 " (cutoff:3.500A)
      removed outlier: 4.999A  pdb=" N   ASN A 148 " --> pdb=" O   GLN A 136 " (cutoff:3.500A)
      removed outlier: 4.440A  pdb=" N   HIS A 144 " --> pdb=" O   ASP A 140 " (cutoff:3.500A)
      removed outlier: 7.217A  pdb=" N   ALA A 150 " --> pdb=" O   TRP A 130 " (cutoff:3.500A)
      removed outlier: 4.785A  pdb=" N   TRP A 130 " --> pdb=" O   ALA A 150 " (cutoff:3.500A)
      removed outlier: 6.589A  pdb=" N   ALA A 152 " --> pdb=" O   VAL A 128 " (cutoff:3.500A)
      removed outlier: 4.542A  pdb=" N   VAL A 128 " --> pdb=" O   ALA A 152 " (cutoff:3.500A)
      removed outlier: 6.651A  pdb=" N   GLU A 154 " --> pdb=" O   LEU A 126 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 107 through 111
      removed outlier: 5.773A  pdb=" N   GLN A 136 " --> pdb=" O   ASN A 148 " (cutoff:3.500A)
      removed outlier: 4.999A  pdb=" N   ASN A 148 " --> pdb=" O   GLN A 136 " (cutoff:3.500A)
      removed outlier: 4.440A  pdb=" N   HIS A 144 " --> pdb=" O   ASP A 140 " (cutoff:3.500A)
      removed outlier: 3.837A  pdb=" N   ASN A  73 " --> pdb=" O   SER A  82 " (cutoff:3.500A)
      removed outlier: 7.366A  pdb=" N   MET A  84 " --> pdb=" O   VAL A  71 " (cutoff:3.500A)
      removed outlier: 5.890A  pdb=" N   VAL A  71 " --> pdb=" O   MET A  84 " (cutoff:3.500A)
      removed outlier: 8.601A  pdb=" N   LEU A  86 " --> pdb=" O   SER A  69 " (cutoff:3.500A)
      removed outlier: 7.122A  pdb=" N   SER A  69 " --> pdb=" O   LEU A  86 " (cutoff:3.500A)
      removed outlier: 7.855A  pdb=" N   ARG A  88 " --> pdb=" O   PHE A  67 " (cutoff:3.500A)
      removed outlier: 7.893A  pdb=" N   PHE A  67 " --> pdb=" O   ARG A  88 " (cutoff:3.500A)
      removed outlier: 7.859A  pdb=" N   SER A  90 " --> pdb=" O   ARG A  65 " (cutoff:3.500A)
      removed outlier: 7.797A  pdb=" N   ARG A  65 " --> pdb=" O   SER A  90 " (cutoff:3.500A)
      removed outlier: 8.760A  pdb=" N   LEU A  92 " --> pdb=" O   ASP A  63 " (cutoff:3.500A)
      removed outlier: 9.665A  pdb=" N   ASP A  63 " --> pdb=" O   LEU A  92 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 120 through 122
      removed outlier: 4.072A  pdb=" N   ASP A 206 " --> pdb=" O   ARG A 225 " (cutoff:3.500A)
      removed outlier: 7.102A  pdb=" N   LYS A 227 " --> pdb=" O   VAL A 204 " (cutoff:3.500A)
      removed outlier: 5.500A  pdb=" N   VAL A 204 " --> pdb=" O   LYS A 227 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'B' and resid 107 through 111
      removed outlier: 5.773A  pdb=" N   GLN B 136 " --> pdb=" O   ASN B 148 " (cutoff:3.500A)
      removed outlier: 4.998A  pdb=" N   ASN B 148 " --> pdb=" O   GLN B 136 " (cutoff:3.500A)
      removed outlier: 4.439A  pdb=" N   HIS B 144 " --> pdb=" O   ASP B 140 " (cutoff:3.500A)
      removed outlier: 7.217A  pdb=" N   ALA B 150 " --> pdb=" O   TRP B 130 " (cutoff:3.500A)
      removed outlier: 4.786A  pdb=" N   TRP B 130 " --> pdb=" O   ALA B 150 " (cutoff:3.500A)
      removed outlier: 6.589A  pdb=" N   ALA B 152 " --> pdb=" O   VAL B 128 " (cutoff:3.500A)
      removed outlier: 4.543A  pdb=" N   VAL B 128 " --> pdb=" O   ALA B 152 " (cutoff:3.500A)
      removed outlier: 6.652A  pdb=" N   GLU B 154 " --> pdb=" O   LEU B 126 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'B' and resid 107 through 111
      removed outlier: 5.773A  pdb=" N   GLN B 136 " --> pdb=" O   ASN B 148 " (cutoff:3.500A)
      removed outlier: 4.998A  pdb=" N   ASN B 148 " --> pdb=" O   GLN B 136 " (cutoff:3.500A)
      removed outlier: 4.439A  pdb=" N   HIS B 144 " --> pdb=" O   ASP B 140 " (cutoff:3.500A)
      removed outlier: 3.838A  pdb=" N   ASN B  73 " --> pdb=" O   SER B  82 " (cutoff:3.500A)
      removed outlier: 7.366A  pdb=" N   MET B  84 " --> pdb=" O   VAL B  71 " (cutoff:3.500A)
      removed outlier: 5.890A  pdb=" N   VAL B  71 " --> pdb=" O   MET B  84 " (cutoff:3.500A)
      removed outlier: 8.601A  pdb=" N   LEU B  86 " --> pdb=" O   SER B  69 " (cutoff:3.500A)
      removed outlier: 7.123A  pdb=" N   SER B  69 " --> pdb=" O   LEU B  86 " (cutoff:3.500A)
      removed outlier: 7.855A  pdb=" N   ARG B  88 " --> pdb=" O   PHE B  67 " (cutoff:3.500A)
      removed outlier: 7.893A  pdb=" N   PHE B  67 " --> pdb=" O   ARG B  88 " (cutoff:3.500A)
      removed outlier: 7.859A  pdb=" N   SER B  90 " --> pdb=" O   ARG B  65 " (cutoff:3.500A)
      removed outlier: 7.797A  pdb=" N   ARG B  65 " --> pdb=" O   SER B  90 " (cutoff:3.500A)
      removed outlier: 8.759A  pdb=" N   LEU B  92 " --> pdb=" O   ASP B  63 " (cutoff:3.500A)
      removed outlier: 9.665A  pdb=" N   ASP B  63 " --> pdb=" O   LEU B  92 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'B' and resid 120 through 122
      removed outlier: 4.073A  pdb=" N   ASP B 206 " --> pdb=" O   ARG B 225 " (cutoff:3.500A)
      removed outlier: 7.102A  pdb=" N   LYS B 227 " --> pdb=" O   VAL B 204 " (cutoff:3.500A)
      removed outlier: 5.500A  pdb=" N   VAL B 204 " --> pdb=" O   LYS B 227 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'C' and resid 107 through 111
      removed outlier: 5.772A  pdb=" N   GLN C 136 " --> pdb=" O   ASN C 148 " (cutoff:3.500A)
      removed outlier: 4.999A  pdb=" N   ASN C 148 " --> pdb=" O   GLN C 136 " (cutoff:3.500A)
      removed outlier: 4.440A  pdb=" N   HIS C 144 " --> pdb=" O   ASP C 140 " (cutoff:3.500A)
      removed outlier: 7.217A  pdb=" N   ALA C 150 " --> pdb=" O   TRP C 130 " (cutoff:3.500A)
      removed outlier: 4.786A  pdb=" N   TRP C 130 " --> pdb=" O   ALA C 150 " (cutoff:3.500A)
      removed outlier: 6.588A  pdb=" N   ALA C 152 " --> pdb=" O   VAL C 128 " (cutoff:3.500A)
      removed outlier: 4.543A  pdb=" N   VAL C 128 " --> pdb=" O   ALA C 152 " (cutoff:3.500A)
      removed outlier: 6.652A  pdb=" N   GLU C 154 " --> pdb=" O   LEU C 126 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'C' and resid 107 through 111
      removed outlier: 5.772A  pdb=" N   GLN C 136 " --> pdb=" O   ASN C 148 " (cutoff:3.500A)
      removed outlier: 4.999A  pdb=" N   ASN C 148 " --> pdb=" O   GLN C 136 " (cutoff:3.500A)
      removed outlier: 4.440A  pdb=" N   HIS C 144 " --> pdb=" O   ASP C 140 " (cutoff:3.500A)
      removed outlier: 3.837A  pdb=" N   ASN C  73 " --> pdb=" O   SER C  82 " (cutoff:3.500A)
      removed outlier: 7.366A  pdb=" N   MET C  84 " --> pdb=" O   VAL C  71 " (cutoff:3.500A)
      removed outlier: 5.890A  pdb=" N   VAL C  71 " --> pdb=" O   MET C  84 " (cutoff:3.500A)
      removed outlier: 8.601A  pdb=" N   LEU C  86 " --> pdb=" O   SER C  69 " (cutoff:3.500A)
      removed outlier: 7.122A  pdb=" N   SER C  69 " --> pdb=" O   LEU C  86 " (cutoff:3.500A)
      removed outlier: 7.854A  pdb=" N   ARG C  88 " --> pdb=" O   PHE C  67 " (cutoff:3.500A)
      removed outlier: 7.893A  pdb=" N   PHE C  67 " --> pdb=" O   ARG C  88 " (cutoff:3.500A)
      removed outlier: 7.859A  pdb=" N   SER C  90 " --> pdb=" O   ARG C  65 " (cutoff:3.500A)
      removed outlier: 7.796A  pdb=" N   ARG C  65 " --> pdb=" O   SER C  90 " (cutoff:3.500A)
      removed outlier: 8.760A  pdb=" N   LEU C  92 " --> pdb=" O   ASP C  63 " (cutoff:3.500A)
      removed outlier: 9.665A  pdb=" N   ASP C  63 " --> pdb=" O   LEU C  92 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'C' and resid 120 through 122
      removed outlier: 4.072A  pdb=" N   ASP C 206 " --> pdb=" O   ARG C 225 " (cutoff:3.500A)
      removed outlier: 7.103A  pdb=" N   LYS C 227 " --> pdb=" O   VAL C 204 " (cutoff:3.500A)
      removed outlier: 5.500A  pdb=" N   VAL C 204 " --> pdb=" O   LYS C 227 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'D' and resid 107 through 111
      removed outlier: 5.773A  pdb=" N   GLN D 136 " --> pdb=" O   ASN D 148 " (cutoff:3.500A)
      removed outlier: 4.999A  pdb=" N   ASN D 148 " --> pdb=" O   GLN D 136 " (cutoff:3.500A)
      removed outlier: 4.439A  pdb=" N   HIS D 144 " --> pdb=" O   ASP D 140 " (cutoff:3.500A)
      removed outlier: 7.217A  pdb=" N   ALA D 150 " --> pdb=" O   TRP D 130 " (cutoff:3.500A)
      removed outlier: 4.786A  pdb=" N   TRP D 130 " --> pdb=" O   ALA D 150 " (cutoff:3.500A)
      removed outlier: 6.589A  pdb=" N   ALA D 152 " --> pdb=" O   VAL D 128 " (cutoff:3.500A)
      removed outlier: 4.543A  pdb=" N   VAL D 128 " --> pdb=" O   ALA D 152 " (cutoff:3.500A)
      removed outlier: 6.652A  pdb=" N   GLU D 154 " --> pdb=" O   LEU D 126 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'D' and resid 107 through 111
      removed outlier: 5.773A  pdb=" N   GLN D 136 " --> pdb=" O   ASN D 148 " (cutoff:3.500A)
      removed outlier: 4.999A  pdb=" N   ASN D 148 " --> pdb=" O   GLN D 136 " (cutoff:3.500A)
      removed outlier: 4.439A  pdb=" N   HIS D 144 " --> pdb=" O   ASP D 140 " (cutoff:3.500A)
      removed outlier: 3.837A  pdb=" N   ASN D  73 " --> pdb=" O   SER D  82 " (cutoff:3.500A)
      removed outlier: 7.366A  pdb=" N   MET D  84 " --> pdb=" O   VAL D  71 " (cutoff:3.500A)
      removed outlier: 5.890A  pdb=" N   VAL D  71 " --> pdb=" O   MET D  84 " (cutoff:3.500A)
      removed outlier: 8.601A  pdb=" N   LEU D  86 " --> pdb=" O   SER D  69 " (cutoff:3.500A)
      removed outlier: 7.123A  pdb=" N   SER D  69 " --> pdb=" O   LEU D  86 " (cutoff:3.500A)
      removed outlier: 7.855A  pdb=" N   ARG D  88 " --> pdb=" O   PHE D  67 " (cutoff:3.500A)
      removed outlier: 7.893A  pdb=" N   PHE D  67 " --> pdb=" O   ARG D  88 " (cutoff:3.500A)
      removed outlier: 7.859A  pdb=" N   SER D  90 " --> pdb=" O   ARG D  65 " (cutoff:3.500A)
      removed outlier: 7.796A  pdb=" N   ARG D  65 " --> pdb=" O   SER D  90 " (cutoff:3.500A)
      removed outlier: 8.760A  pdb=" N   LEU D  92 " --> pdb=" O   ASP D  63 " (cutoff:3.500A)
      removed outlier: 9.664A  pdb=" N   ASP D  63 " --> pdb=" O   LEU D  92 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'D' and resid 120 through 122
      removed outlier: 4.073A  pdb=" N   ASP D 206 " --> pdb=" O   ARG D 225 " (cutoff:3.500A)
      removed outlier: 7.102A  pdb=" N   LYS D 227 " --> pdb=" O   VAL D 204 " (cutoff:3.500A)
      removed outlier: 5.500A  pdb=" N   VAL D 204 " --> pdb=" O   LYS D 227 " (cutoff:3.500A)
    Processing sheet with id=AB4, first strand: chain 'E' and resid 107 through 111
      removed outlier: 5.772A  pdb=" N   GLN E 136 " --> pdb=" O   ASN E 148 " (cutoff:3.500A)
      removed outlier: 4.998A  pdb=" N   ASN E 148 " --> pdb=" O   GLN E 136 " (cutoff:3.500A)
      removed outlier: 4.439A  pdb=" N   HIS E 144 " --> pdb=" O   ASP E 140 " (cutoff:3.500A)
      removed outlier: 7.217A  pdb=" N   ALA E 150 " --> pdb=" O   TRP E 130 " (cutoff:3.500A)
      removed outlier: 4.785A  pdb=" N   TRP E 130 " --> pdb=" O   ALA E 150 " (cutoff:3.500A)
      removed outlier: 6.588A  pdb=" N   ALA E 152 " --> pdb=" O   VAL E 128 " (cutoff:3.500A)
      removed outlier: 4.543A  pdb=" N   VAL E 128 " --> pdb=" O   ALA E 152 " (cutoff:3.500A)
      removed outlier: 6.652A  pdb=" N   GLU E 154 " --> pdb=" O   LEU E 126 " (cutoff:3.500A)
    Processing sheet with id=AB5, first strand: chain 'E' and resid 107 through 111
      removed outlier: 5.772A  pdb=" N   GLN E 136 " --> pdb=" O   ASN E 148 " (cutoff:3.500A)
      removed outlier: 4.998A  pdb=" N   ASN E 148 " --> pdb=" O   GLN E 136 " (cutoff:3.500A)
      removed outlier: 4.439A  pdb=" N   HIS E 144 " --> pdb=" O   ASP E 140 " (cutoff:3.500A)
      removed outlier: 3.838A  pdb=" N   ASN E  73 " --> pdb=" O   SER E  82 " (cutoff:3.500A)
      removed outlier: 7.366A  pdb=" N   MET E  84 " --> pdb=" O   VAL E  71 " (cutoff:3.500A)
      removed outlier: 5.890A  pdb=" N   VAL E  71 " --> pdb=" O   MET E  84 " (cutoff:3.500A)
      removed outlier: 8.601A  pdb=" N   LEU E  86 " --> pdb=" O   SER E  69 " (cutoff:3.500A)
      removed outlier: 7.123A  pdb=" N   SER E  69 " --> pdb=" O   LEU E  86 " (cutoff:3.500A)
      removed outlier: 7.855A  pdb=" N   ARG E  88 " --> pdb=" O   PHE E  67 " (cutoff:3.500A)
      removed outlier: 7.893A  pdb=" N   PHE E  67 " --> pdb=" O   ARG E  88 " (cutoff:3.500A)
      removed outlier: 7.859A  pdb=" N   SER E  90 " --> pdb=" O   ARG E  65 " (cutoff:3.500A)
      removed outlier: 7.797A  pdb=" N   ARG E  65 " --> pdb=" O   SER E  90 " (cutoff:3.500A)
      removed outlier: 8.760A  pdb=" N   LEU E  92 " --> pdb=" O   ASP E  63 " (cutoff:3.500A)
      removed outlier: 9.665A  pdb=" N   ASP E  63 " --> pdb=" O   LEU E  92 " (cutoff:3.500A)
    Processing sheet with id=AB6, first strand: chain 'E' and resid 120 through 122
      removed outlier: 4.073A  pdb=" N   ASP E 206 " --> pdb=" O   ARG E 225 " (cutoff:3.500A)
      removed outlier: 7.102A  pdb=" N   LYS E 227 " --> pdb=" O   VAL E 204 " (cutoff:3.500A)
      removed outlier: 5.500A  pdb=" N   VAL E 204 " --> pdb=" O   LYS E 227 " (cutoff:3.500A)

    715 hydrogen bonds defined for protein.
    2100 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: 3.49 seconds

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

  Histogram of bond lengths:
        1.18 -     1.31: 2020
        1.31 -     1.43: 3605
        1.43 -     1.56: 7685
        1.56 -     1.68: 0
        1.68 -     1.81: 75
  Bond restraints: 13385
  Sorted by residual:
  bond pdb=" C7  NAG I   2 "
       pdb=" N2  NAG I   2 "
    ideal  model  delta    sigma   weight residual
    1.346  1.463 -0.117 2.00e-02 2.50e+03 3.40e+01
  bond pdb=" C7  NAG G   2 "
       pdb=" N2  NAG G   2 "
    ideal  model  delta    sigma   weight residual
    1.346  1.463 -0.117 2.00e-02 2.50e+03 3.40e+01
  bond pdb=" C7  NAG H   2 "
       pdb=" N2  NAG H   2 "
    ideal  model  delta    sigma   weight residual
    1.346  1.463 -0.117 2.00e-02 2.50e+03 3.40e+01
  bond pdb=" C7  NAG F   2 "
       pdb=" N2  NAG F   2 "
    ideal  model  delta    sigma   weight residual
    1.346  1.462 -0.116 2.00e-02 2.50e+03 3.39e+01
  bond pdb=" C7  NAG J   2 "
       pdb=" N2  NAG J   2 "
    ideal  model  delta    sigma   weight residual
    1.346  1.462 -0.116 2.00e-02 2.50e+03 3.39e+01
  ... (remaining 13380 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.19: 17651
        1.19 -     2.37: 391
        2.37 -     3.56: 178
        3.56 -     4.74: 38
        4.74 -     5.93: 47
  Bond angle restraints: 18305
  Sorted by residual:
  angle pdb=" N   LEU B 237 "
        pdb=" CA  LEU B 237 "
        pdb=" C   LEU B 237 "
      ideal   model   delta    sigma   weight residual
     113.18  115.61   -2.43 1.33e+00 5.65e-01 3.35e+00
  angle pdb=" N   LEU D 237 "
        pdb=" CA  LEU D 237 "
        pdb=" C   LEU D 237 "
      ideal   model   delta    sigma   weight residual
     113.18  115.61   -2.43 1.33e+00 5.65e-01 3.34e+00
  angle pdb=" N   LEU C 237 "
        pdb=" CA  LEU C 237 "
        pdb=" C   LEU C 237 "
      ideal   model   delta    sigma   weight residual
     113.18  115.60   -2.42 1.33e+00 5.65e-01 3.31e+00
  angle pdb=" N   LEU E 237 "
        pdb=" CA  LEU E 237 "
        pdb=" C   LEU E 237 "
      ideal   model   delta    sigma   weight residual
     113.18  115.58   -2.40 1.33e+00 5.65e-01 3.25e+00
  angle pdb=" N   LEU A 237 "
        pdb=" CA  LEU A 237 "
        pdb=" C   LEU A 237 "
      ideal   model   delta    sigma   weight residual
     113.18  115.57   -2.39 1.33e+00 5.65e-01 3.24e+00
  ... (remaining 18300 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    11.22: 7030
       11.22 -    22.45: 795
       22.45 -    33.67: 270
       33.67 -    44.90: 65
       44.90 -    56.12: 20
  Dihedral angle restraints: 8180
    sinusoidal: 3385
      harmonic: 4795
  Sorted by residual:
  dihedral pdb=" CB  CYS D 289 "
           pdb=" SG  CYS D 289 "
           pdb=" SG  CYS D 394 "
           pdb=" CB  CYS D 394 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -86.00 -117.09   31.09     1      1.00e+01 1.00e-02 1.38e+01
  dihedral pdb=" CB  CYS A 289 "
           pdb=" SG  CYS A 289 "
           pdb=" SG  CYS A 394 "
           pdb=" CB  CYS A 394 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -86.00 -117.09   31.09     1      1.00e+01 1.00e-02 1.38e+01
  dihedral pdb=" CB  CYS C 289 "
           pdb=" SG  CYS C 289 "
           pdb=" SG  CYS C 394 "
           pdb=" CB  CYS C 394 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -86.00 -117.08   31.08     1      1.00e+01 1.00e-02 1.38e+01
  ... (remaining 8177 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.030: 1432
       0.030 -    0.059: 544
       0.059 -    0.088: 124
       0.088 -    0.118: 76
       0.118 -    0.147: 59
  Chirality restraints: 2235
  Sorted by residual:
  chirality pdb=" C5  NAG B 501 "
            pdb=" C4  NAG B 501 "
            pdb=" C6  NAG B 501 "
            pdb=" O5  NAG B 501 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.41   -2.56    0.15 2.00e-01 2.50e+01 5.44e-01
  chirality pdb=" C5  NAG E 501 "
            pdb=" C4  NAG E 501 "
            pdb=" C6  NAG E 501 "
            pdb=" O5  NAG E 501 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.41   -2.56    0.15 2.00e-01 2.50e+01 5.29e-01
  chirality pdb=" CA  TRP E 362 "
            pdb=" N   TRP E 362 "
            pdb=" C   TRP E 362 "
            pdb=" CB  TRP E 362 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.37    0.14 2.00e-01 2.50e+01 5.19e-01
  ... (remaining 2232 not shown)

  Planarity restraints: 2260
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ILE B 234 "    0.005 2.00e-02 2.50e+03   1.08e-02 1.17e+00
        pdb=" C   ILE B 234 "   -0.019 2.00e-02 2.50e+03
        pdb=" O   ILE B 234 "    0.007 2.00e-02 2.50e+03
        pdb=" N   ILE B 235 "    0.006 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ILE C 234 "    0.005 2.00e-02 2.50e+03   1.08e-02 1.16e+00
        pdb=" C   ILE C 234 "   -0.019 2.00e-02 2.50e+03
        pdb=" O   ILE C 234 "    0.007 2.00e-02 2.50e+03
        pdb=" N   ILE C 235 "    0.006 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ILE D 234 "    0.005 2.00e-02 2.50e+03   1.07e-02 1.15e+00
        pdb=" C   ILE D 234 "   -0.019 2.00e-02 2.50e+03
        pdb=" O   ILE D 234 "    0.007 2.00e-02 2.50e+03
        pdb=" N   ILE D 235 "    0.006 2.00e-02 2.50e+03
  ... (remaining 2257 not shown)

  Histogram of nonbonded interaction distances:
        2.23 -     2.76: 1814
        2.76 -     3.30: 12090
        3.30 -     3.83: 22021
        3.83 -     4.37: 25754
        4.37 -     4.90: 45159
  Nonbonded interactions: 106838
  Sorted by model distance:
  nonbonded pdb=" O   ALA B 247 "
            pdb=" OH  TYR B 264 "
     model   vdw
     2.227 3.040
  nonbonded pdb=" O   ALA C 247 "
            pdb=" OH  TYR C 264 "
     model   vdw
     2.227 3.040
  nonbonded pdb=" O   ALA D 247 "
            pdb=" OH  TYR D 264 "
     model   vdw
     2.227 3.040
  nonbonded pdb=" O   ALA A 247 "
            pdb=" OH  TYR A 264 "
     model   vdw
     2.227 3.040
  nonbonded pdb=" O   ALA E 247 "
            pdb=" OH  TYR E 264 "
     model   vdw
     2.227 3.040
  ... (remaining 106833 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: 0.10
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'C'
  selection = chain 'B'
  selection = chain 'E'
  selection = chain 'D'
}
ncs_group {
  reference = chain 'G'
  selection = chain 'F'
  selection = chain 'I'
  selection = chain 'H'
  selection = chain 'J'
}

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=0.80 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             1.520
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.540
  Check model and map are aligned:         0.100
  Set scattering table:                    0.130
  Process input model:                     27.310
  Find NCS groups from input model:        0.260
  Set up NCS constraints:                  0.040
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:11.980
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   41.890
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8031
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      :  0.007   0.117  13410  Z= 0.346
  Angle     :  0.581   5.926  18370  Z= 0.264
  Chirality :  0.041   0.147   2235
  Planarity :  0.003   0.024   2250
  Dihedral  : 10.872  56.122   5010
  Min Nonbonded Distance : 2.227

Molprobity Statistics.
  All-atom Clashscore : 7.55
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.94 %
    Favored  : 99.06 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.00 %
    Favored  : 100.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.88 %
    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:  2.69 (0.21), residues: 1600
  helix:  3.39 (0.20), residues: 545
  sheet:  1.80 (0.24), residues: 405
  loop :  0.38 (0.26), residues: 650

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP A 116 
 HIS   0.001   0.000   HIS A 276 
 PHE   0.016   0.001   PHE A  72 
 TYR   0.013   0.001   TYR E 264 
 ARG   0.002   0.000   ARG A 138 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00101 (   10)
  link_NAG-ASN         : angle       1.01321 (   30)
  link_BETA1-4         : bond        0.00084 (    5)
  link_BETA1-4         : angle       0.47366 (   15)
  hydrogen bonds       : bond        0.11820 (  680)
  hydrogen bonds       : angle       4.49157 ( 2100)
  SS BOND              : bond        0.00077 (   10)
  SS BOND              : angle       1.05905 (   20)
  covalent geometry    : bond        0.00701 (13385)
  covalent geometry    : angle       0.57898 (18305)

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

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

  3200 Ramachandran restraints generated.
    1600 Oldfield, 0 Emsley, 1600 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3200 Ramachandran restraints generated.
    1600 Oldfield, 0 Emsley, 1600 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  428 residues out of total 1430 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 428
  time to evaluate  : 1.554 
Fit side-chains
REVERT: A   75 ASP cc_start: 0.8373 (t0) cc_final: 0.7986 (t0)
REVERT: A  124 GLU cc_start: 0.8208 (mp0) cc_final: 0.7921 (pm20)
REVERT: A  221 GLN cc_start: 0.8634 (pt0) cc_final: 0.8187 (pt0)
REVERT: A  259 ILE cc_start: 0.9352 (pt) cc_final: 0.9139 (pt)
REVERT: A  391 TRP cc_start: 0.8159 (m-90) cc_final: 0.7825 (m-90)
REVERT: B  124 GLU cc_start: 0.8189 (mp0) cc_final: 0.7985 (mp0)
REVERT: B  259 ILE cc_start: 0.9409 (pt) cc_final: 0.9192 (pt)
REVERT: B  391 TRP cc_start: 0.8253 (m-90) cc_final: 0.7967 (m-90)
REVERT: C  124 GLU cc_start: 0.8134 (mp0) cc_final: 0.7791 (pm20)
REVERT: C  210 GLN cc_start: 0.8137 (pt0) cc_final: 0.7922 (pt0)
REVERT: C  221 GLN cc_start: 0.8665 (pt0) cc_final: 0.8148 (pt0)
REVERT: C  364 GLU cc_start: 0.7627 (mt-10) cc_final: 0.7405 (mt-10)
REVERT: D  124 GLU cc_start: 0.8114 (mp0) cc_final: 0.7801 (pm20)
REVERT: D  364 GLU cc_start: 0.7805 (mt-10) cc_final: 0.7501 (mt-10)
REVERT: D  391 TRP cc_start: 0.8195 (m-90) cc_final: 0.7946 (m-90)
REVERT: E  221 GLN cc_start: 0.8614 (pt0) cc_final: 0.8293 (pt0)
REVERT: E  391 TRP cc_start: 0.8111 (m-90) cc_final: 0.7818 (m-10)
  outliers start: 0
  outliers final: 1
  residues processed: 428
  average time/residue: 1.0637
  time to fit residues: 500.5242
Evaluate side-chains
  290 residues out of total 1430 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 289
  time to evaluate  : 1.479 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue  259 ILE
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 160
   random chunks:
   chunk 135 optimal weight:    4.9990
   chunk 121 optimal weight:    4.9990
   chunk 67 optimal weight:    2.9990
   chunk 41 optimal weight:    6.9990
   chunk 81 optimal weight:    0.7980
   chunk 64 optimal weight:    0.6980
   chunk 125 optimal weight:    3.9990
   chunk 48 optimal weight:    5.9990
   chunk 76 optimal weight:    4.9990
   chunk 93 optimal weight:    4.9990
   chunk 145 optimal weight:    0.0470
   overall best weight:    1.7082

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

Flipped N/Q/H residues before XYZ refinement:
A 188 GLN
B 188 GLN
C 156 ASN
C 382 GLN
D 188 GLN
E 188 GLN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3216 r_free = 0.3216 target = 0.095689 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.2967 r_free = 0.2967 target = 0.079183 restraints weight = 20701.639|
|-----------------------------------------------------------------------------|
r_work (start): 0.2962 rms_B_bonded: 3.04
r_work: 0.2800 rms_B_bonded: 3.45 restraints_weight: 0.5000
r_work (final): 0.2800
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2784
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2784 r_free = 0.2784    target_work(ls_wunit_k1) = 0.069         |
| occupancies: max = 1.00  min = 0.80   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2784 r_free = 0.2784    target_work(ls_wunit_k1) = 0.069         |
| occupancies: max = 1.00  min = 0.85   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2784
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7690
moved from start:          0.1939

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.036  13410  Z= 0.206
  Angle     :  0.599   6.591  18370  Z= 0.292
  Chirality :  0.042   0.147   2235
  Planarity :  0.004   0.048   2250
  Dihedral  :  4.433  30.450   2062
  Min Nonbonded Distance : 2.589

Molprobity Statistics.
  All-atom Clashscore : 7.59
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.94 %
    Favored  : 98.06 %
  Rotamer:
    Outliers :  3.64 %
    Allowed  : 10.70 %
    Favored  : 85.66 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.88 %
    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:  2.34 (0.21), residues: 1600
  helix:  3.55 (0.20), residues: 515
  sheet:  1.26 (0.24), residues: 430
  loop :  0.13 (0.25), residues: 655

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.001   TRP A 112 
 HIS   0.002   0.001   HIS B 276 
 PHE   0.021   0.002   PHE C  72 
 TYR   0.015   0.002   TYR D 176 
 ARG   0.007   0.001   ARG B 257 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00421 (   10)
  link_NAG-ASN         : angle       1.86242 (   30)
  link_BETA1-4         : bond        0.00391 (    5)
  link_BETA1-4         : angle       0.81250 (   15)
  hydrogen bonds       : bond        0.04142 (  680)
  hydrogen bonds       : angle       3.93203 ( 2100)
  SS BOND              : bond        0.00807 (   10)
  SS BOND              : angle       1.53254 (   20)
  covalent geometry    : bond        0.00473 (13385)
  covalent geometry    : angle       0.59254 (18305)

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

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

  3200 Ramachandran restraints generated.
    1600 Oldfield, 0 Emsley, 1600 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3200 Ramachandran restraints generated.
    1600 Oldfield, 0 Emsley, 1600 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  346 residues out of total 1430 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 52
    poor density    : 294
  time to evaluate  : 1.521 
Fit side-chains
REVERT: A   75 ASP cc_start: 0.7816 (t0) cc_final: 0.7472 (t0)
REVERT: A  201 GLU cc_start: 0.8558 (mt-10) cc_final: 0.7949 (mp0)
REVERT: A  260 GLU cc_start: 0.8760 (OUTLIER) cc_final: 0.8392 (pm20)
REVERT: A  391 TRP cc_start: 0.8067 (m-90) cc_final: 0.7845 (m-90)
REVERT: A  402 GLU cc_start: 0.8204 (mm-30) cc_final: 0.8003 (mt-10)
REVERT: B   48 GLU cc_start: 0.7851 (tp30) cc_final: 0.7561 (tp30)
REVERT: B  112 TRP cc_start: 0.8046 (OUTLIER) cc_final: 0.7543 (t-100)
REVERT: B  124 GLU cc_start: 0.8475 (mp0) cc_final: 0.8133 (mp0)
REVERT: B  154 GLU cc_start: 0.8743 (tt0) cc_final: 0.8539 (tt0)
REVERT: B  201 GLU cc_start: 0.8493 (mt-10) cc_final: 0.8004 (mp0)
REVERT: B  391 TRP cc_start: 0.8152 (m-90) cc_final: 0.7836 (m-90)
REVERT: C  124 GLU cc_start: 0.8428 (mp0) cc_final: 0.8120 (mp0)
REVERT: C  154 GLU cc_start: 0.8804 (tt0) cc_final: 0.8592 (tt0)
REVERT: C  201 GLU cc_start: 0.8597 (mt-10) cc_final: 0.8056 (mp0)
REVERT: C  221 GLN cc_start: 0.8497 (pt0) cc_final: 0.7877 (pt0)
REVERT: D   78 ARG cc_start: 0.8556 (OUTLIER) cc_final: 0.8264 (mtp85)
REVERT: D  113 GLU cc_start: 0.8549 (mp0) cc_final: 0.8223 (mp0)
REVERT: D  124 GLU cc_start: 0.8360 (mp0) cc_final: 0.7978 (mp0)
REVERT: D  160 GLU cc_start: 0.8207 (OUTLIER) cc_final: 0.8001 (mt-10)
REVERT: D  364 GLU cc_start: 0.7849 (mt-10) cc_final: 0.7429 (mt-10)
REVERT: D  372 LEU cc_start: 0.8090 (OUTLIER) cc_final: 0.7862 (tt)
REVERT: D  391 TRP cc_start: 0.8206 (m-90) cc_final: 0.7913 (m-10)
REVERT: E  113 GLU cc_start: 0.8568 (mp0) cc_final: 0.8338 (mp0)
REVERT: E  124 GLU cc_start: 0.8365 (mp0) cc_final: 0.8072 (mp0)
REVERT: E  214 GLN cc_start: 0.8103 (mm-40) cc_final: 0.7840 (pt0)
REVERT: E  221 GLN cc_start: 0.8497 (pt0) cc_final: 0.8093 (pt0)
REVERT: E  257 ARG cc_start: 0.8933 (ptp90) cc_final: 0.8281 (ptp-110)
REVERT: E  391 TRP cc_start: 0.8147 (m-90) cc_final: 0.7866 (m-10)
  outliers start: 52
  outliers final: 22
  residues processed: 325
  average time/residue: 1.1209
  time to fit residues: 399.1799
Evaluate side-chains
  285 residues out of total 1430 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 258
  time to evaluate  : 1.532 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  198 VAL
Chi-restraints excluded: chain A residue  260 GLU
Chi-restraints excluded: chain A residue  275 LEU
Chi-restraints excluded: chain A residue  373 VAL
Chi-restraints excluded: chain B residue  112 TRP
Chi-restraints excluded: chain B residue  245 LEU
Chi-restraints excluded: chain B residue  275 LEU
Chi-restraints excluded: chain B residue  372 LEU
Chi-restraints excluded: chain B residue  373 VAL
Chi-restraints excluded: chain C residue  198 VAL
Chi-restraints excluded: chain C residue  259 ILE
Chi-restraints excluded: chain C residue  275 LEU
Chi-restraints excluded: chain C residue  372 LEU
Chi-restraints excluded: chain C residue  373 VAL
Chi-restraints excluded: chain D residue   78 ARG
Chi-restraints excluded: chain D residue  160 GLU
Chi-restraints excluded: chain D residue  191 VAL
Chi-restraints excluded: chain D residue  198 VAL
Chi-restraints excluded: chain D residue  275 LEU
Chi-restraints excluded: chain D residue  372 LEU
Chi-restraints excluded: chain D residue  373 VAL
Chi-restraints excluded: chain E residue  198 VAL
Chi-restraints excluded: chain E residue  210 GLN
Chi-restraints excluded: chain E residue  293 LEU
Chi-restraints excluded: chain E residue  299 ILE
Chi-restraints excluded: chain E residue  372 LEU
Chi-restraints excluded: chain E residue  373 VAL
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 160
   random chunks:
   chunk 107 optimal weight:    0.6980
   chunk 88 optimal weight:    3.9990
   chunk 65 optimal weight:    3.9990
   chunk 98 optimal weight:    0.9990
   chunk 63 optimal weight:    0.7980
   chunk 114 optimal weight:    3.9990
   chunk 42 optimal weight:    4.9990
   chunk 53 optimal weight:    0.9990
   chunk 105 optimal weight:    2.9990
   chunk 92 optimal weight:    4.9990
   chunk 102 optimal weight:    0.8980
   overall best weight:    0.8784

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

Flipped N/Q/H residues before XYZ refinement:
B 188 GLN
D 188 GLN
E 382 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3235 r_free = 0.3235 target = 0.096735 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.2991 r_free = 0.2991 target = 0.080468 restraints weight = 20743.495|
|-----------------------------------------------------------------------------|
r_work (start): 0.2976 rms_B_bonded: 3.01
r_work: 0.2813 rms_B_bonded: 3.44 restraints_weight: 0.5000
r_work (final): 0.2813
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2801
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2801 r_free = 0.2801    target_work(ls_wunit_k1) = 0.070         |
| occupancies: max = 1.00  min = 0.85   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2801 r_free = 0.2801    target_work(ls_wunit_k1) = 0.070         |
| occupancies: max = 1.00  min = 0.88   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2801
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7664
moved from start:          0.2118

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030  13410  Z= 0.130
  Angle     :  0.538   7.529  18370  Z= 0.260
  Chirality :  0.040   0.144   2235
  Planarity :  0.004   0.033   2250
  Dihedral  :  4.082  29.772   2062
  Min Nonbonded Distance : 2.607

Molprobity Statistics.
  All-atom Clashscore : 7.09
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.56 %
    Favored  : 98.44 %
  Rotamer:
    Outliers :  2.94 %
    Allowed  : 13.99 %
    Favored  : 83.08 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.88 %
    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:  2.21 (0.21), residues: 1600
  helix:  3.49 (0.20), residues: 515
  sheet:  1.14 (0.24), residues: 420
  loop :  0.06 (0.25), residues: 665

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.001   TRP C 112 
 HIS   0.002   0.000   HIS D 276 
 PHE   0.017   0.001   PHE E  72 
 TYR   0.015   0.002   TYR A 272 
 ARG   0.006   0.001   ARG E  78 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00198 (   10)
  link_NAG-ASN         : angle       1.24041 (   30)
  link_BETA1-4         : bond        0.00131 (    5)
  link_BETA1-4         : angle       0.83475 (   15)
  hydrogen bonds       : bond        0.03902 (  680)
  hydrogen bonds       : angle       3.81720 ( 2100)
  SS BOND              : bond        0.00259 (   10)
  SS BOND              : angle       1.26621 (   20)
  covalent geometry    : bond        0.00295 (13385)
  covalent geometry    : angle       0.53398 (18305)

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

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

  3200 Ramachandran restraints generated.
    1600 Oldfield, 0 Emsley, 1600 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3200 Ramachandran restraints generated.
    1600 Oldfield, 0 Emsley, 1600 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  327 residues out of total 1430 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 42
    poor density    : 285
  time to evaluate  : 1.451 
Fit side-chains
REVERT: A   75 ASP cc_start: 0.7783 (t0) cc_final: 0.7415 (t0)
REVERT: A  201 GLU cc_start: 0.8558 (mt-10) cc_final: 0.7939 (mp0)
REVERT: A  221 GLN cc_start: 0.8558 (pt0) cc_final: 0.8070 (pt0)
REVERT: A  260 GLU cc_start: 0.8712 (pt0) cc_final: 0.8420 (pm20)
REVERT: A  391 TRP cc_start: 0.7992 (m-90) cc_final: 0.7746 (m-90)
REVERT: B   48 GLU cc_start: 0.7854 (tp30) cc_final: 0.7498 (tp30)
REVERT: B   75 ASP cc_start: 0.7566 (t0) cc_final: 0.7185 (t0)
REVERT: B  113 GLU cc_start: 0.8748 (mp0) cc_final: 0.8393 (mp0)
REVERT: B  124 GLU cc_start: 0.8411 (mp0) cc_final: 0.8026 (mp0)
REVERT: B  154 GLU cc_start: 0.8772 (tt0) cc_final: 0.8551 (tt0)
REVERT: B  201 GLU cc_start: 0.8501 (mt-10) cc_final: 0.8003 (mp0)
REVERT: B  260 GLU cc_start: 0.8598 (pm20) cc_final: 0.8338 (pm20)
REVERT: B  391 TRP cc_start: 0.8091 (m-90) cc_final: 0.7791 (m-90)
REVERT: C  132 ASP cc_start: 0.8046 (p0) cc_final: 0.7621 (t0)
REVERT: C  176 TYR cc_start: 0.8371 (m-80) cc_final: 0.8076 (m-80)
REVERT: C  188 GLN cc_start: 0.8084 (tt0) cc_final: 0.7489 (tt0)
REVERT: C  201 GLU cc_start: 0.8603 (mt-10) cc_final: 0.8043 (mp0)
REVERT: D  113 GLU cc_start: 0.8501 (mp0) cc_final: 0.8220 (mp0)
REVERT: D  160 GLU cc_start: 0.8206 (OUTLIER) cc_final: 0.7926 (mt-10)
REVERT: D  364 GLU cc_start: 0.7832 (mt-10) cc_final: 0.7614 (mt-10)
REVERT: D  372 LEU cc_start: 0.8041 (OUTLIER) cc_final: 0.7830 (tt)
REVERT: D  391 TRP cc_start: 0.8167 (m-90) cc_final: 0.7884 (m-90)
REVERT: E  132 ASP cc_start: 0.8010 (OUTLIER) cc_final: 0.7599 (t0)
REVERT: E  214 GLN cc_start: 0.8099 (mm-40) cc_final: 0.7871 (pt0)
REVERT: E  221 GLN cc_start: 0.8422 (pt0) cc_final: 0.8041 (pt0)
REVERT: E  257 ARG cc_start: 0.8920 (ptp90) cc_final: 0.8249 (ptp-110)
REVERT: E  259 ILE cc_start: 0.9396 (pt) cc_final: 0.9194 (mp)
REVERT: E  260 GLU cc_start: 0.8850 (pm20) cc_final: 0.8307 (pm20)
REVERT: E  391 TRP cc_start: 0.8109 (m-90) cc_final: 0.7800 (m-10)
  outliers start: 42
  outliers final: 15
  residues processed: 311
  average time/residue: 1.0163
  time to fit residues: 349.1221
Evaluate side-chains
  287 residues out of total 1430 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 269
  time to evaluate  : 1.542 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  198 VAL
Chi-restraints excluded: chain A residue  275 LEU
Chi-restraints excluded: chain B residue  245 LEU
Chi-restraints excluded: chain B residue  364 GLU
Chi-restraints excluded: chain B residue  372 LEU
Chi-restraints excluded: chain C residue  179 SER
Chi-restraints excluded: chain C residue  198 VAL
Chi-restraints excluded: chain C residue  259 ILE
Chi-restraints excluded: chain C residue  275 LEU
Chi-restraints excluded: chain D residue  146 LYS
Chi-restraints excluded: chain D residue  160 GLU
Chi-restraints excluded: chain D residue  372 LEU
Chi-restraints excluded: chain E residue  132 ASP
Chi-restraints excluded: chain E residue  198 VAL
Chi-restraints excluded: chain E residue  210 GLN
Chi-restraints excluded: chain E residue  275 LEU
Chi-restraints excluded: chain E residue  299 ILE
Chi-restraints excluded: chain E residue  372 LEU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 160
   random chunks:
   chunk 88 optimal weight:    0.7980
   chunk 83 optimal weight:    0.4980
   chunk 135 optimal weight:    2.9990
   chunk 5 optimal weight:    0.8980
   chunk 138 optimal weight:    4.9990
   chunk 15 optimal weight:    6.9990
   chunk 106 optimal weight:    3.9990
   chunk 113 optimal weight:    3.9990
   chunk 46 optimal weight:    5.9990
   chunk 148 optimal weight:    2.9990
   chunk 98 optimal weight:    2.9990
   overall best weight:    1.6384

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

Flipped N/Q/H residues before XYZ refinement:
A 276 HIS
B 276 HIS
C 276 HIS
D 276 HIS
E 382 GLN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3188 r_free = 0.3188 target = 0.093810 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.2939 r_free = 0.2939 target = 0.077573 restraints weight = 20687.042|
|-----------------------------------------------------------------------------|
r_work (start): 0.2934 rms_B_bonded: 2.99
r_work: 0.2773 rms_B_bonded: 3.38 restraints_weight: 0.5000
r_work (final): 0.2773
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2755
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2755 r_free = 0.2755    target_work(ls_wunit_k1) = 0.068         |
| occupancies: max = 1.00  min = 0.88   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2755 r_free = 0.2755    target_work(ls_wunit_k1) = 0.068         |
| occupancies: max = 1.00  min = 0.89   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2755
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7700
moved from start:          0.2458

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.036  13410  Z= 0.193
  Angle     :  0.556   6.545  18370  Z= 0.273
  Chirality :  0.041   0.148   2235
  Planarity :  0.004   0.035   2250
  Dihedral  :  4.043  31.202   2062
  Min Nonbonded Distance : 2.591

Molprobity Statistics.
  All-atom Clashscore : 7.44
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.25 %
    Favored  : 97.75 %
  Rotamer:
    Outliers :  4.34 %
    Allowed  : 13.78 %
    Favored  : 81.89 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.88 %
    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:  2.06 (0.21), residues: 1600
  helix:  3.35 (0.20), residues: 515
  sheet:  0.88 (0.23), residues: 420
  loop :  0.11 (0.25), residues: 665

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.022   0.001   TRP B 112 
 HIS   0.003   0.001   HIS D 276 
 PHE   0.022   0.002   PHE C  72 
 TYR   0.011   0.002   TYR A 272 
 ARG   0.006   0.000   ARG C  78 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00274 (   10)
  link_NAG-ASN         : angle       1.32973 (   30)
  link_BETA1-4         : bond        0.00078 (    5)
  link_BETA1-4         : angle       0.94060 (   15)
  hydrogen bonds       : bond        0.03988 (  680)
  hydrogen bonds       : angle       3.84534 ( 2100)
  SS BOND              : bond        0.00568 (   10)
  SS BOND              : angle       1.19256 (   20)
  covalent geometry    : bond        0.00446 (13385)
  covalent geometry    : angle       0.55255 (18305)

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

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

  3200 Ramachandran restraints generated.
    1600 Oldfield, 0 Emsley, 1600 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3200 Ramachandran restraints generated.
    1600 Oldfield, 0 Emsley, 1600 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  321 residues out of total 1430 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 62
    poor density    : 259
  time to evaluate  : 1.367 
Fit side-chains
REVERT: A  112 TRP cc_start: 0.8228 (OUTLIER) cc_final: 0.7566 (t-100)
REVERT: A  124 GLU cc_start: 0.8338 (mp0) cc_final: 0.7876 (mp0)
REVERT: A  132 ASP cc_start: 0.7297 (t0) cc_final: 0.7069 (p0)
REVERT: A  154 GLU cc_start: 0.8659 (tt0) cc_final: 0.8404 (tt0)
REVERT: A  184 GLU cc_start: 0.8330 (pt0) cc_final: 0.8116 (pt0)
REVERT: A  201 GLU cc_start: 0.8619 (mt-10) cc_final: 0.7984 (mp0)
REVERT: A  214 GLN cc_start: 0.8194 (mm-40) cc_final: 0.7850 (pt0)
REVERT: A  221 GLN cc_start: 0.8629 (pt0) cc_final: 0.8195 (pt0)
REVERT: A  260 GLU cc_start: 0.8723 (pt0) cc_final: 0.8405 (pm20)
REVERT: A  391 TRP cc_start: 0.8068 (m-90) cc_final: 0.7854 (m-90)
REVERT: B   48 GLU cc_start: 0.7931 (tp30) cc_final: 0.7574 (tp30)
REVERT: B   75 ASP cc_start: 0.7672 (t0) cc_final: 0.7061 (t0)
REVERT: B  112 TRP cc_start: 0.8117 (OUTLIER) cc_final: 0.7349 (t-100)
REVERT: B  124 GLU cc_start: 0.8435 (mp0) cc_final: 0.7903 (mp0)
REVERT: B  132 ASP cc_start: 0.7393 (t0) cc_final: 0.7096 (p0)
REVERT: B  154 GLU cc_start: 0.8780 (tt0) cc_final: 0.8558 (tt0)
REVERT: B  201 GLU cc_start: 0.8538 (mt-10) cc_final: 0.8040 (mp0)
REVERT: B  214 GLN cc_start: 0.8273 (mm-40) cc_final: 0.8044 (pt0)
REVERT: B  260 GLU cc_start: 0.8662 (pm20) cc_final: 0.8364 (pm20)
REVERT: B  391 TRP cc_start: 0.8158 (m-90) cc_final: 0.7857 (m-90)
REVERT: C  112 TRP cc_start: 0.8187 (OUTLIER) cc_final: 0.7424 (t-100)
REVERT: C  132 ASP cc_start: 0.7938 (OUTLIER) cc_final: 0.7587 (t0)
REVERT: C  146 LYS cc_start: 0.8063 (OUTLIER) cc_final: 0.7663 (mtpp)
REVERT: C  176 TYR cc_start: 0.8451 (m-80) cc_final: 0.8061 (m-80)
REVERT: C  188 GLN cc_start: 0.8082 (tt0) cc_final: 0.7519 (tt0)
REVERT: C  201 GLU cc_start: 0.8626 (mt-10) cc_final: 0.8046 (mp0)
REVERT: D  112 TRP cc_start: 0.8255 (OUTLIER) cc_final: 0.7495 (t-100)
REVERT: D  364 GLU cc_start: 0.7836 (mt-10) cc_final: 0.7429 (mt-10)
REVERT: D  372 LEU cc_start: 0.8070 (OUTLIER) cc_final: 0.7846 (tt)
REVERT: D  391 TRP cc_start: 0.8192 (m-90) cc_final: 0.7901 (m-90)
REVERT: E   81 MET cc_start: 0.8742 (ttp) cc_final: 0.8412 (ptt)
REVERT: E  112 TRP cc_start: 0.8087 (OUTLIER) cc_final: 0.7027 (t-100)
REVERT: E  132 ASP cc_start: 0.8044 (OUTLIER) cc_final: 0.7629 (t0)
REVERT: E  214 GLN cc_start: 0.8138 (mm-40) cc_final: 0.7887 (pt0)
REVERT: E  221 GLN cc_start: 0.8468 (pt0) cc_final: 0.8121 (pt0)
REVERT: E  246 LEU cc_start: 0.8263 (tp) cc_final: 0.8055 (tp)
REVERT: E  257 ARG cc_start: 0.8926 (ptp90) cc_final: 0.8262 (ptp-110)
REVERT: E  260 GLU cc_start: 0.8863 (pm20) cc_final: 0.8374 (pm20)
REVERT: E  382 GLN cc_start: 0.8359 (mm110) cc_final: 0.8103 (mm-40)
REVERT: E  391 TRP cc_start: 0.8187 (m-90) cc_final: 0.7913 (m-10)
  outliers start: 62
  outliers final: 27
  residues processed: 289
  average time/residue: 1.1254
  time to fit residues: 356.4118
Evaluate side-chains
  285 residues out of total 1430 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 249
  time to evaluate  : 1.341 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   84 MET
Chi-restraints excluded: chain A residue  112 TRP
Chi-restraints excluded: chain A residue  123 LEU
Chi-restraints excluded: chain A residue  210 GLN
Chi-restraints excluded: chain A residue  275 LEU
Chi-restraints excluded: chain A residue  372 LEU
Chi-restraints excluded: chain A residue  373 VAL
Chi-restraints excluded: chain B residue  112 TRP
Chi-restraints excluded: chain B residue  210 GLN
Chi-restraints excluded: chain B residue  245 LEU
Chi-restraints excluded: chain B residue  275 LEU
Chi-restraints excluded: chain B residue  372 LEU
Chi-restraints excluded: chain B residue  373 VAL
Chi-restraints excluded: chain C residue  112 TRP
Chi-restraints excluded: chain C residue  132 ASP
Chi-restraints excluded: chain C residue  146 LYS
Chi-restraints excluded: chain C residue  179 SER
Chi-restraints excluded: chain C residue  198 VAL
Chi-restraints excluded: chain C residue  259 ILE
Chi-restraints excluded: chain C residue  275 LEU
Chi-restraints excluded: chain C residue  372 LEU
Chi-restraints excluded: chain C residue  373 VAL
Chi-restraints excluded: chain D residue  112 TRP
Chi-restraints excluded: chain D residue  198 VAL
Chi-restraints excluded: chain D residue  299 ILE
Chi-restraints excluded: chain D residue  372 LEU
Chi-restraints excluded: chain D residue  373 VAL
Chi-restraints excluded: chain E residue  112 TRP
Chi-restraints excluded: chain E residue  132 ASP
Chi-restraints excluded: chain E residue  198 VAL
Chi-restraints excluded: chain E residue  210 GLN
Chi-restraints excluded: chain E residue  237 LEU
Chi-restraints excluded: chain E residue  275 LEU
Chi-restraints excluded: chain E residue  299 ILE
Chi-restraints excluded: chain E residue  372 LEU
Chi-restraints excluded: chain E residue  373 VAL
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 160
   random chunks:
   chunk 124 optimal weight:    4.9990
   chunk 0 optimal weight:    6.9990
   chunk 98 optimal weight:    0.8980
   chunk 151 optimal weight:    0.6980
   chunk 114 optimal weight:    3.9990
   chunk 122 optimal weight:    0.9990
   chunk 34 optimal weight:    3.9990
   chunk 111 optimal weight:    0.8980
   chunk 35 optimal weight:    0.8980
   chunk 102 optimal weight:    4.9990
   chunk 127 optimal weight:    0.9980
   overall best weight:    0.8780

-------------------------------------------------------------------------------
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 = 0.3225 r_free = 0.3225 target = 0.096081 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.2981 r_free = 0.2981 target = 0.079794 restraints weight = 20871.655|
|-----------------------------------------------------------------------------|
r_work (start): 0.2934 rms_B_bonded: 3.05
r_work: 0.2770 rms_B_bonded: 3.43 restraints_weight: 0.5000
r_work (final): 0.2770
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2798
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2798 r_free = 0.2798    target_work(ls_wunit_k1) = 0.069         |
| occupancies: max = 1.00  min = 0.89   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2798 r_free = 0.2798    target_work(ls_wunit_k1) = 0.069         |
| occupancies: max = 1.00  min = 0.88   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2798
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7662
moved from start:          0.2543

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031  13410  Z= 0.128
  Angle     :  0.528   6.989  18370  Z= 0.257
  Chirality :  0.039   0.144   2235
  Planarity :  0.004   0.041   2250
  Dihedral  :  3.933  31.416   2062
  Min Nonbonded Distance : 2.618

Molprobity Statistics.
  All-atom Clashscore : 7.70
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.88 %
    Favored  : 98.12 %
  Rotamer:
    Outliers :  2.94 %
    Allowed  : 15.24 %
    Favored  : 81.82 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.88 %
    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:  2.04 (0.21), residues: 1600
  helix:  3.08 (0.20), residues: 545
  sheet:  0.82 (0.24), residues: 420
  loop :  0.23 (0.26), residues: 635

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.022   0.001   TRP A 112 
 HIS   0.001   0.000   HIS E 276 
 PHE   0.018   0.001   PHE D  72 
 TYR   0.014   0.002   TYR B 176 
 ARG   0.009   0.000   ARG D 257 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00094 (   10)
  link_NAG-ASN         : angle       1.21911 (   30)
  link_BETA1-4         : bond        0.00077 (    5)
  link_BETA1-4         : angle       0.90544 (   15)
  hydrogen bonds       : bond        0.03789 (  680)
  hydrogen bonds       : angle       3.72935 ( 2100)
  SS BOND              : bond        0.00378 (   10)
  SS BOND              : angle       0.85624 (   20)
  covalent geometry    : bond        0.00289 (13385)
  covalent geometry    : angle       0.52558 (18305)

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

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

  3200 Ramachandran restraints generated.
    1600 Oldfield, 0 Emsley, 1600 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3200 Ramachandran restraints generated.
    1600 Oldfield, 0 Emsley, 1600 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  306 residues out of total 1430 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 42
    poor density    : 264
  time to evaluate  : 1.419 
Fit side-chains
REVERT: A  124 GLU cc_start: 0.8327 (mp0) cc_final: 0.7885 (mp0)
REVERT: A  132 ASP cc_start: 0.7319 (t0) cc_final: 0.7047 (p0)
REVERT: A  184 GLU cc_start: 0.8328 (pt0) cc_final: 0.8118 (pt0)
REVERT: A  201 GLU cc_start: 0.8609 (mt-10) cc_final: 0.7981 (mp0)
REVERT: A  214 GLN cc_start: 0.8233 (mm-40) cc_final: 0.7879 (pt0)
REVERT: A  260 GLU cc_start: 0.8705 (pt0) cc_final: 0.8439 (pm20)
REVERT: A  391 TRP cc_start: 0.8014 (m-90) cc_final: 0.7762 (m-90)
REVERT: B   48 GLU cc_start: 0.7946 (tp30) cc_final: 0.7584 (tp30)
REVERT: B   75 ASP cc_start: 0.7594 (t0) cc_final: 0.7054 (t0)
REVERT: B  124 GLU cc_start: 0.8429 (mp0) cc_final: 0.7891 (mp0)
REVERT: B  132 ASP cc_start: 0.7492 (t0) cc_final: 0.7053 (p0)
REVERT: B  146 LYS cc_start: 0.8246 (mtmm) cc_final: 0.7942 (mtpp)
REVERT: B  154 GLU cc_start: 0.8745 (tt0) cc_final: 0.8537 (tt0)
REVERT: B  201 GLU cc_start: 0.8538 (mt-10) cc_final: 0.8008 (mp0)
REVERT: B  214 GLN cc_start: 0.8262 (mm-40) cc_final: 0.8034 (pt0)
REVERT: B  260 GLU cc_start: 0.8668 (pm20) cc_final: 0.8325 (pm20)
REVERT: B  391 TRP cc_start: 0.8123 (m-90) cc_final: 0.7866 (m-90)
REVERT: C  112 TRP cc_start: 0.8058 (OUTLIER) cc_final: 0.7272 (t-100)
REVERT: C  176 TYR cc_start: 0.8300 (m-80) cc_final: 0.7882 (m-80)
REVERT: C  188 GLN cc_start: 0.8051 (tt0) cc_final: 0.7477 (tt0)
REVERT: C  201 GLU cc_start: 0.8617 (mt-10) cc_final: 0.8040 (mp0)
REVERT: D  129 ASP cc_start: 0.8334 (t0) cc_final: 0.8065 (OUTLIER)
REVERT: D  160 GLU cc_start: 0.8415 (mt-10) cc_final: 0.8051 (mt-10)
REVERT: D  364 GLU cc_start: 0.7845 (mt-10) cc_final: 0.7410 (mt-10)
REVERT: D  372 LEU cc_start: 0.8015 (OUTLIER) cc_final: 0.7807 (tt)
REVERT: D  391 TRP cc_start: 0.8157 (m-90) cc_final: 0.7878 (m-90)
REVERT: E  214 GLN cc_start: 0.8147 (mm-40) cc_final: 0.7924 (pt0)
REVERT: E  221 GLN cc_start: 0.8381 (pt0) cc_final: 0.8040 (pt0)
REVERT: E  246 LEU cc_start: 0.8238 (tp) cc_final: 0.8018 (tp)
REVERT: E  257 ARG cc_start: 0.8902 (ptp90) cc_final: 0.8271 (ptp-110)
REVERT: E  260 GLU cc_start: 0.8901 (pm20) cc_final: 0.8344 (pm20)
REVERT: E  391 TRP cc_start: 0.8023 (m-90) cc_final: 0.7758 (m-10)
  outliers start: 42
  outliers final: 17
  residues processed: 289
  average time/residue: 1.1156
  time to fit residues: 353.7211
Evaluate side-chains
  277 residues out of total 1430 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 259
  time to evaluate  : 1.396 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  275 LEU
Chi-restraints excluded: chain B residue  245 LEU
Chi-restraints excluded: chain B residue  275 LEU
Chi-restraints excluded: chain B residue  372 LEU
Chi-restraints excluded: chain C residue  112 TRP
Chi-restraints excluded: chain C residue  198 VAL
Chi-restraints excluded: chain C residue  259 ILE
Chi-restraints excluded: chain C residue  275 LEU
Chi-restraints excluded: chain C residue  306 LEU
Chi-restraints excluded: chain C residue  373 VAL
Chi-restraints excluded: chain D residue   50 ILE
Chi-restraints excluded: chain D residue  146 LYS
Chi-restraints excluded: chain D residue  237 LEU
Chi-restraints excluded: chain D residue  299 ILE
Chi-restraints excluded: chain D residue  372 LEU
Chi-restraints excluded: chain E residue  198 VAL
Chi-restraints excluded: chain E residue  299 ILE
Chi-restraints excluded: chain E residue  372 LEU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 160
   random chunks:
   chunk 107 optimal weight:    4.9990
   chunk 72 optimal weight:    4.9990
   chunk 125 optimal weight:    4.9990
   chunk 39 optimal weight:    2.9990
   chunk 151 optimal weight:    0.9990
   chunk 101 optimal weight:    7.9990
   chunk 89 optimal weight:    4.9990
   chunk 124 optimal weight:    3.9990
   chunk 20 optimal weight:    0.9990
   chunk 155 optimal weight:    0.8980
   chunk 75 optimal weight:    0.9980
   overall best weight:    1.3786

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

Flipped N/Q/H residues before XYZ refinement:
E  73 ASN
E 382 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3204 r_free = 0.3204 target = 0.094531 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.2959 r_free = 0.2959 target = 0.078345 restraints weight = 21011.043|
|-----------------------------------------------------------------------------|
r_work (start): 0.2914 rms_B_bonded: 3.03
r_work: 0.2749 rms_B_bonded: 3.41 restraints_weight: 0.5000
r_work (final): 0.2749
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2758
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2758 r_free = 0.2758    target_work(ls_wunit_k1) = 0.068         |
| occupancies: max = 1.00  min = 0.88   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2758 r_free = 0.2758    target_work(ls_wunit_k1) = 0.068         |
| occupancies: max = 1.00  min = 0.88   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2758
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7678
moved from start:          0.2644

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.038  13410  Z= 0.171
  Angle     :  0.549   8.060  18370  Z= 0.267
  Chirality :  0.040   0.148   2235
  Planarity :  0.004   0.043   2250
  Dihedral  :  3.935  30.798   2062
  Min Nonbonded Distance : 2.585

Molprobity Statistics.
  All-atom Clashscore : 7.74
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.06 %
    Favored  : 97.94 %
  Rotamer:
    Outliers :  3.92 %
    Allowed  : 15.10 %
    Favored  : 80.98 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.88 %
    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:  2.00 (0.21), residues: 1600
  helix:  3.04 (0.20), residues: 545
  sheet:  0.76 (0.23), residues: 420
  loop :  0.25 (0.26), residues: 635

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.022   0.001   TRP B 112 
 HIS   0.002   0.000   HIS E 276 
 PHE   0.019   0.002   PHE C  72 
 TYR   0.017   0.002   TYR B 176 
 ARG   0.010   0.000   ARG D 257 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00184 (   10)
  link_NAG-ASN         : angle       1.27618 (   30)
  link_BETA1-4         : bond        0.00023 (    5)
  link_BETA1-4         : angle       0.93248 (   15)
  hydrogen bonds       : bond        0.03877 (  680)
  hydrogen bonds       : angle       3.74725 ( 2100)
  SS BOND              : bond        0.00454 (   10)
  SS BOND              : angle       0.96147 (   20)
  covalent geometry    : bond        0.00395 (13385)
  covalent geometry    : angle       0.54586 (18305)

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

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

  3200 Ramachandran restraints generated.
    1600 Oldfield, 0 Emsley, 1600 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3200 Ramachandran restraints generated.
    1600 Oldfield, 0 Emsley, 1600 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  321 residues out of total 1430 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 56
    poor density    : 265
  time to evaluate  : 1.490 
Fit side-chains
REVERT: A  124 GLU cc_start: 0.8358 (mp0) cc_final: 0.7847 (mp0)
REVERT: A  132 ASP cc_start: 0.7468 (t0) cc_final: 0.7020 (t0)
REVERT: A  154 GLU cc_start: 0.8663 (tt0) cc_final: 0.8165 (tt0)
REVERT: A  184 GLU cc_start: 0.8328 (pt0) cc_final: 0.8113 (pt0)
REVERT: A  201 GLU cc_start: 0.8594 (mt-10) cc_final: 0.7960 (mp0)
REVERT: A  214 GLN cc_start: 0.8230 (mm-40) cc_final: 0.7951 (pt0)
REVERT: A  260 GLU cc_start: 0.8687 (pt0) cc_final: 0.8378 (pm20)
REVERT: A  364 GLU cc_start: 0.8063 (mt-10) cc_final: 0.7595 (mt-10)
REVERT: A  391 TRP cc_start: 0.8060 (m-90) cc_final: 0.7805 (m-90)
REVERT: B   48 GLU cc_start: 0.7986 (tp30) cc_final: 0.7734 (tp30)
REVERT: B   75 ASP cc_start: 0.7584 (t0) cc_final: 0.7227 (t0)
REVERT: B  124 GLU cc_start: 0.8421 (mp0) cc_final: 0.7929 (mp0)
REVERT: B  132 ASP cc_start: 0.7294 (t0) cc_final: 0.6787 (p0)
REVERT: B  146 LYS cc_start: 0.8242 (mtmm) cc_final: 0.7952 (mtpp)
REVERT: B  154 GLU cc_start: 0.8757 (tt0) cc_final: 0.8540 (tt0)
REVERT: B  201 GLU cc_start: 0.8512 (mt-10) cc_final: 0.7992 (mp0)
REVERT: B  214 GLN cc_start: 0.8289 (mm-40) cc_final: 0.8013 (pt0)
REVERT: B  260 GLU cc_start: 0.8677 (pm20) cc_final: 0.8304 (pm20)
REVERT: B  391 TRP cc_start: 0.8159 (m-90) cc_final: 0.7888 (m-90)
REVERT: C   75 ASP cc_start: 0.7513 (t0) cc_final: 0.6930 (t0)
REVERT: C  112 TRP cc_start: 0.8168 (OUTLIER) cc_final: 0.7738 (t-100)
REVERT: C  132 ASP cc_start: 0.7891 (OUTLIER) cc_final: 0.7570 (t0)
REVERT: C  188 GLN cc_start: 0.8052 (tt0) cc_final: 0.7495 (tt0)
REVERT: C  201 GLU cc_start: 0.8624 (mt-10) cc_final: 0.8041 (mp0)
REVERT: D  113 GLU cc_start: 0.8728 (mp0) cc_final: 0.8526 (mp0)
REVERT: D  364 GLU cc_start: 0.7875 (mt-10) cc_final: 0.7448 (mt-10)
REVERT: D  372 LEU cc_start: 0.8011 (OUTLIER) cc_final: 0.7800 (tt)
REVERT: D  391 TRP cc_start: 0.8173 (m-90) cc_final: 0.7940 (m-90)
REVERT: D  402 GLU cc_start: 0.8309 (mt-10) cc_final: 0.8019 (mm-30)
REVERT: E   81 MET cc_start: 0.8753 (ttp) cc_final: 0.8411 (ptt)
REVERT: E  112 TRP cc_start: 0.8124 (OUTLIER) cc_final: 0.6952 (t-100)
REVERT: E  132 ASP cc_start: 0.7944 (OUTLIER) cc_final: 0.7600 (t0)
REVERT: E  221 GLN cc_start: 0.8425 (pt0) cc_final: 0.8065 (pt0)
REVERT: E  246 LEU cc_start: 0.8313 (tp) cc_final: 0.8059 (tp)
REVERT: E  257 ARG cc_start: 0.8906 (ptp90) cc_final: 0.8258 (ptp-110)
REVERT: E  260 GLU cc_start: 0.8910 (pm20) cc_final: 0.8432 (pm20)
REVERT: E  382 GLN cc_start: 0.8379 (mm110) cc_final: 0.8107 (mm-40)
REVERT: E  391 TRP cc_start: 0.8158 (m-90) cc_final: 0.7928 (m-10)
  outliers start: 56
  outliers final: 24
  residues processed: 298
  average time/residue: 1.1579
  time to fit residues: 377.7189
Evaluate side-chains
  288 residues out of total 1430 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 259
  time to evaluate  : 1.368 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  123 LEU
Chi-restraints excluded: chain A residue  275 LEU
Chi-restraints excluded: chain A residue  372 LEU
Chi-restraints excluded: chain A residue  373 VAL
Chi-restraints excluded: chain B residue  245 LEU
Chi-restraints excluded: chain B residue  275 LEU
Chi-restraints excluded: chain B residue  364 GLU
Chi-restraints excluded: chain B residue  372 LEU
Chi-restraints excluded: chain B residue  373 VAL
Chi-restraints excluded: chain B residue  394 CYS
Chi-restraints excluded: chain C residue  112 TRP
Chi-restraints excluded: chain C residue  132 ASP
Chi-restraints excluded: chain C residue  198 VAL
Chi-restraints excluded: chain C residue  275 LEU
Chi-restraints excluded: chain C residue  306 LEU
Chi-restraints excluded: chain C residue  372 LEU
Chi-restraints excluded: chain C residue  373 VAL
Chi-restraints excluded: chain D residue  146 LYS
Chi-restraints excluded: chain D residue  153 THR
Chi-restraints excluded: chain D residue  198 VAL
Chi-restraints excluded: chain D residue  275 LEU
Chi-restraints excluded: chain D residue  372 LEU
Chi-restraints excluded: chain D residue  373 VAL
Chi-restraints excluded: chain E residue  112 TRP
Chi-restraints excluded: chain E residue  132 ASP
Chi-restraints excluded: chain E residue  198 VAL
Chi-restraints excluded: chain E residue  275 LEU
Chi-restraints excluded: chain E residue  372 LEU
Chi-restraints excluded: chain E residue  373 VAL
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 160
   random chunks:
   chunk 95 optimal weight:    0.6980
   chunk 28 optimal weight:    4.9990
   chunk 122 optimal weight:    3.9990
   chunk 136 optimal weight:    4.9990
   chunk 157 optimal weight:    4.9990
   chunk 135 optimal weight:    2.9990
   chunk 3 optimal weight:    1.9990
   chunk 71 optimal weight:    2.9990
   chunk 100 optimal weight:    0.8980
   chunk 105 optimal weight:    0.8980
   chunk 108 optimal weight:    5.9990
   overall best weight:    1.4984

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

Flipped N/Q/H residues before XYZ refinement:
A 382 GLN
E  73 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3199 r_free = 0.3199 target = 0.094114 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 28)----------------|
| r_work = 0.2954 r_free = 0.2954 target = 0.077984 restraints weight = 20801.173|
|-----------------------------------------------------------------------------|
r_work (start): 0.2909 rms_B_bonded: 3.01
r_work: 0.2744 rms_B_bonded: 3.40 restraints_weight: 0.5000
r_work (final): 0.2744
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2756
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2756 r_free = 0.2756    target_work(ls_wunit_k1) = 0.068         |
| occupancies: max = 1.00  min = 0.88   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2756 r_free = 0.2756    target_work(ls_wunit_k1) = 0.068         |
| occupancies: max = 1.00  min = 0.88   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2756
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7683
moved from start:          0.2729

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.038  13410  Z= 0.182
  Angle     :  0.556   8.690  18370  Z= 0.270
  Chirality :  0.040   0.149   2235
  Planarity :  0.003   0.030   2250
  Dihedral  :  3.877  16.055   2060
  Min Nonbonded Distance : 2.594

Molprobity Statistics.
  All-atom Clashscore : 7.81
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.19 %
    Favored  : 97.81 %
  Rotamer:
    Outliers :  3.92 %
    Allowed  : 15.24 %
    Favored  : 80.84 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.88 %
    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:  1.99 (0.21), residues: 1600
  helix:  3.02 (0.20), residues: 545
  sheet:  0.70 (0.23), residues: 440
  loop :  0.29 (0.27), residues: 615

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.025   0.001   TRP B 112 
 HIS   0.002   0.000   HIS E 276 
 PHE   0.034   0.002   PHE D 385 
 TYR   0.018   0.002   TYR B 176 
 ARG   0.008   0.000   ARG D 257 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00174 (   10)
  link_NAG-ASN         : angle       1.33413 (   30)
  link_BETA1-4         : bond        0.00046 (    5)
  link_BETA1-4         : angle       0.91456 (   15)
  hydrogen bonds       : bond        0.03909 (  680)
  hydrogen bonds       : angle       3.75234 ( 2100)
  SS BOND              : bond        0.00547 (   10)
  SS BOND              : angle       0.95601 (   20)
  covalent geometry    : bond        0.00421 (13385)
  covalent geometry    : angle       0.55254 (18305)

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

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

  3200 Ramachandran restraints generated.
    1600 Oldfield, 0 Emsley, 1600 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3200 Ramachandran restraints generated.
    1600 Oldfield, 0 Emsley, 1600 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  321 residues out of total 1430 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 56
    poor density    : 265
  time to evaluate  : 1.345 
Fit side-chains
REVERT: A  124 GLU cc_start: 0.8354 (mp0) cc_final: 0.7928 (mp0)
REVERT: A  132 ASP cc_start: 0.7503 (t0) cc_final: 0.7041 (t0)
REVERT: A  184 GLU cc_start: 0.8353 (pt0) cc_final: 0.8082 (pt0)
REVERT: A  201 GLU cc_start: 0.8593 (mt-10) cc_final: 0.7964 (mp0)
REVERT: A  214 GLN cc_start: 0.8244 (mm-40) cc_final: 0.7939 (pt0)
REVERT: A  260 GLU cc_start: 0.8699 (pt0) cc_final: 0.8390 (pm20)
REVERT: A  364 GLU cc_start: 0.8068 (mt-10) cc_final: 0.7606 (mt-10)
REVERT: A  391 TRP cc_start: 0.8052 (m-90) cc_final: 0.7817 (m-90)
REVERT: B   48 GLU cc_start: 0.8018 (tp30) cc_final: 0.7765 (tp30)
REVERT: B   75 ASP cc_start: 0.7611 (t0) cc_final: 0.7251 (t0)
REVERT: B  112 TRP cc_start: 0.7912 (OUTLIER) cc_final: 0.7292 (t-100)
REVERT: B  124 GLU cc_start: 0.8420 (mp0) cc_final: 0.7914 (mp0)
REVERT: B  132 ASP cc_start: 0.7365 (t0) cc_final: 0.7042 (t0)
REVERT: B  146 LYS cc_start: 0.8254 (mtmm) cc_final: 0.7979 (mtpp)
REVERT: B  154 GLU cc_start: 0.8761 (tt0) cc_final: 0.8533 (tt0)
REVERT: B  201 GLU cc_start: 0.8522 (mt-10) cc_final: 0.7989 (mp0)
REVERT: B  214 GLN cc_start: 0.8331 (mm-40) cc_final: 0.8064 (pt0)
REVERT: B  260 GLU cc_start: 0.8689 (pm20) cc_final: 0.8308 (pm20)
REVERT: B  272 TYR cc_start: 0.8568 (t80) cc_final: 0.8300 (t80)
REVERT: B  364 GLU cc_start: 0.7704 (OUTLIER) cc_final: 0.7501 (mp0)
REVERT: B  391 TRP cc_start: 0.8146 (m-90) cc_final: 0.7905 (m-90)
REVERT: C   75 ASP cc_start: 0.7587 (t0) cc_final: 0.7099 (t0)
REVERT: C  112 TRP cc_start: 0.8236 (OUTLIER) cc_final: 0.7896 (t-100)
REVERT: C  132 ASP cc_start: 0.7856 (OUTLIER) cc_final: 0.7521 (t0)
REVERT: C  146 LYS cc_start: 0.8118 (OUTLIER) cc_final: 0.7682 (mtpp)
REVERT: C  176 TYR cc_start: 0.8315 (m-80) cc_final: 0.7963 (m-80)
REVERT: C  188 GLN cc_start: 0.8052 (tt0) cc_final: 0.7434 (tt0)
REVERT: C  201 GLU cc_start: 0.8668 (mt-10) cc_final: 0.8048 (mp0)
REVERT: D   63 ASP cc_start: 0.8334 (t70) cc_final: 0.8031 (t0)
REVERT: D   75 ASP cc_start: 0.7597 (t0) cc_final: 0.7393 (t0)
REVERT: D  112 TRP cc_start: 0.7988 (OUTLIER) cc_final: 0.7732 (t-100)
REVERT: D  113 GLU cc_start: 0.8749 (mp0) cc_final: 0.8226 (mp0)
REVERT: D  129 ASP cc_start: 0.8445 (t0) cc_final: 0.8056 (t0)
REVERT: D  132 ASP cc_start: 0.7825 (p0) cc_final: 0.7489 (t0)
REVERT: D  160 GLU cc_start: 0.8452 (mt-10) cc_final: 0.8070 (mt-10)
REVERT: D  364 GLU cc_start: 0.7932 (mt-10) cc_final: 0.7532 (mt-10)
REVERT: D  372 LEU cc_start: 0.8020 (OUTLIER) cc_final: 0.7806 (tt)
REVERT: D  391 TRP cc_start: 0.8155 (m-90) cc_final: 0.7918 (m-90)
REVERT: D  402 GLU cc_start: 0.8312 (mt-10) cc_final: 0.8037 (mm-30)
REVERT: E   81 MET cc_start: 0.8747 (ttp) cc_final: 0.8421 (ptt)
REVERT: E  112 TRP cc_start: 0.8167 (OUTLIER) cc_final: 0.7011 (t-100)
REVERT: E  132 ASP cc_start: 0.7918 (OUTLIER) cc_final: 0.7625 (t0)
REVERT: E  221 GLN cc_start: 0.8453 (pt0) cc_final: 0.8098 (pt0)
REVERT: E  246 LEU cc_start: 0.8318 (tp) cc_final: 0.8053 (tp)
REVERT: E  257 ARG cc_start: 0.8903 (ptp90) cc_final: 0.8262 (ptp-110)
REVERT: E  260 GLU cc_start: 0.8909 (pm20) cc_final: 0.8409 (pm20)
REVERT: E  391 TRP cc_start: 0.8118 (m-90) cc_final: 0.7885 (m-10)
  outliers start: 56
  outliers final: 30
  residues processed: 294
  average time/residue: 1.1218
  time to fit residues: 361.3737
Evaluate side-chains
  287 residues out of total 1430 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 39
    poor density    : 248
  time to evaluate  : 1.547 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  123 LEU
Chi-restraints excluded: chain A residue  275 LEU
Chi-restraints excluded: chain A residue  285 SER
Chi-restraints excluded: chain A residue  372 LEU
Chi-restraints excluded: chain A residue  373 VAL
Chi-restraints excluded: chain A residue  394 CYS
Chi-restraints excluded: chain B residue  112 TRP
Chi-restraints excluded: chain B residue  210 GLN
Chi-restraints excluded: chain B residue  245 LEU
Chi-restraints excluded: chain B residue  275 LEU
Chi-restraints excluded: chain B residue  364 GLU
Chi-restraints excluded: chain B residue  372 LEU
Chi-restraints excluded: chain B residue  373 VAL
Chi-restraints excluded: chain B residue  394 CYS
Chi-restraints excluded: chain C residue   81 MET
Chi-restraints excluded: chain C residue  112 TRP
Chi-restraints excluded: chain C residue  129 ASP
Chi-restraints excluded: chain C residue  132 ASP
Chi-restraints excluded: chain C residue  146 LYS
Chi-restraints excluded: chain C residue  179 SER
Chi-restraints excluded: chain C residue  198 VAL
Chi-restraints excluded: chain C residue  275 LEU
Chi-restraints excluded: chain C residue  306 LEU
Chi-restraints excluded: chain C residue  372 LEU
Chi-restraints excluded: chain C residue  373 VAL
Chi-restraints excluded: chain D residue  112 TRP
Chi-restraints excluded: chain D residue  146 LYS
Chi-restraints excluded: chain D residue  153 THR
Chi-restraints excluded: chain D residue  198 VAL
Chi-restraints excluded: chain D residue  275 LEU
Chi-restraints excluded: chain D residue  299 ILE
Chi-restraints excluded: chain D residue  372 LEU
Chi-restraints excluded: chain D residue  373 VAL
Chi-restraints excluded: chain E residue  112 TRP
Chi-restraints excluded: chain E residue  132 ASP
Chi-restraints excluded: chain E residue  198 VAL
Chi-restraints excluded: chain E residue  275 LEU
Chi-restraints excluded: chain E residue  372 LEU
Chi-restraints excluded: chain E residue  373 VAL
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 160
   random chunks:
   chunk 32 optimal weight:    5.9990
   chunk 10 optimal weight:    0.7980
   chunk 153 optimal weight:    2.9990
   chunk 89 optimal weight:    3.9990
   chunk 101 optimal weight:    0.9990
   chunk 27 optimal weight:    0.9980
   chunk 28 optimal weight:    2.9990
   chunk 8 optimal weight:    0.8980
   chunk 116 optimal weight:    3.9990
   chunk 50 optimal weight:    1.9990
   chunk 71 optimal weight:    0.9990
   overall best weight:    0.9384

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

Flipped N/Q/H residues before XYZ refinement:
D 382 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3211 r_free = 0.3211 target = 0.095004 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.2969 r_free = 0.2969 target = 0.078881 restraints weight = 20877.792|
|-----------------------------------------------------------------------------|
r_work (start): 0.2922 rms_B_bonded: 3.02
r_work: 0.2758 rms_B_bonded: 3.40 restraints_weight: 0.5000
r_work (final): 0.2758
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2786
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2786 r_free = 0.2786    target_work(ls_wunit_k1) = 0.069         |
| occupancies: max = 1.00  min = 0.88   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2786 r_free = 0.2786    target_work(ls_wunit_k1) = 0.069         |
| occupancies: max = 1.00  min = 0.86   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2786
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7666
moved from start:          0.2766

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033  13410  Z= 0.137
  Angle     :  0.544   9.759  18370  Z= 0.262
  Chirality :  0.040   0.154   2235
  Planarity :  0.003   0.032   2250
  Dihedral  :  3.825  15.480   2060
  Min Nonbonded Distance : 2.621

Molprobity Statistics.
  All-atom Clashscore : 8.00
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.31 %
    Favored  : 97.69 %
  Rotamer:
    Outliers :  2.73 %
    Allowed  : 16.92 %
    Favored  : 80.35 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.88 %
    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:  2.02 (0.21), residues: 1600
  helix:  3.08 (0.20), residues: 545
  sheet:  0.69 (0.23), residues: 440
  loop :  0.30 (0.27), residues: 615

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.023   0.001   TRP B 112 
 HIS   0.002   0.000   HIS E 276 
 PHE   0.025   0.002   PHE D 385 
 TYR   0.022   0.002   TYR B 176 
 ARG   0.007   0.000   ARG D 257 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00086 (   10)
  link_NAG-ASN         : angle       1.25079 (   30)
  link_BETA1-4         : bond        0.00054 (    5)
  link_BETA1-4         : angle       0.92299 (   15)
  hydrogen bonds       : bond        0.03809 (  680)
  hydrogen bonds       : angle       3.70853 ( 2100)
  SS BOND              : bond        0.00394 (   10)
  SS BOND              : angle       0.84899 (   20)
  covalent geometry    : bond        0.00312 (13385)
  covalent geometry    : angle       0.54079 (18305)

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

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

  3200 Ramachandran restraints generated.
    1600 Oldfield, 0 Emsley, 1600 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3200 Ramachandran restraints generated.
    1600 Oldfield, 0 Emsley, 1600 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  287 residues out of total 1430 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 39
    poor density    : 248
  time to evaluate  : 1.353 
Fit side-chains
REVERT: A  124 GLU cc_start: 0.8354 (mp0) cc_final: 0.7791 (mp0)
REVERT: A  132 ASP cc_start: 0.7397 (t0) cc_final: 0.6911 (t0)
REVERT: A  184 GLU cc_start: 0.8366 (pt0) cc_final: 0.8092 (pt0)
REVERT: A  201 GLU cc_start: 0.8586 (mt-10) cc_final: 0.7959 (mp0)
REVERT: A  214 GLN cc_start: 0.8228 (mm-40) cc_final: 0.7915 (pt0)
REVERT: A  260 GLU cc_start: 0.8683 (pt0) cc_final: 0.8378 (pm20)
REVERT: A  364 GLU cc_start: 0.8037 (mt-10) cc_final: 0.7575 (mt-10)
REVERT: A  391 TRP cc_start: 0.8048 (m-90) cc_final: 0.7803 (m-90)
REVERT: B   48 GLU cc_start: 0.8011 (tp30) cc_final: 0.7746 (tp30)
REVERT: B   75 ASP cc_start: 0.7580 (t0) cc_final: 0.6998 (t0)
REVERT: B  124 GLU cc_start: 0.8347 (mp0) cc_final: 0.7838 (mp0)
REVERT: B  132 ASP cc_start: 0.7402 (t0) cc_final: 0.7074 (t0)
REVERT: B  146 LYS cc_start: 0.8260 (mtmm) cc_final: 0.7982 (mtpp)
REVERT: B  201 GLU cc_start: 0.8515 (mt-10) cc_final: 0.7984 (mp0)
REVERT: B  214 GLN cc_start: 0.8311 (mm-40) cc_final: 0.8044 (pt0)
REVERT: B  260 GLU cc_start: 0.8728 (pm20) cc_final: 0.8343 (pm20)
REVERT: B  272 TYR cc_start: 0.8536 (t80) cc_final: 0.8299 (t80)
REVERT: B  364 GLU cc_start: 0.7625 (mt-10) cc_final: 0.6676 (mp0)
REVERT: B  391 TRP cc_start: 0.8122 (m-90) cc_final: 0.7877 (m-90)
REVERT: C   75 ASP cc_start: 0.7554 (t0) cc_final: 0.7059 (t0)
REVERT: C  112 TRP cc_start: 0.8153 (OUTLIER) cc_final: 0.7798 (t-100)
REVERT: C  132 ASP cc_start: 0.7847 (OUTLIER) cc_final: 0.7438 (t0)
REVERT: C  146 LYS cc_start: 0.8105 (OUTLIER) cc_final: 0.7665 (mtpp)
REVERT: C  188 GLN cc_start: 0.8045 (tt0) cc_final: 0.7414 (tt0)
REVERT: C  201 GLU cc_start: 0.8665 (mt-10) cc_final: 0.8046 (mp0)
REVERT: D  112 TRP cc_start: 0.7903 (t-100) cc_final: 0.7641 (t-100)
REVERT: D  113 GLU cc_start: 0.8760 (mp0) cc_final: 0.8162 (mp0)
REVERT: D  201 GLU cc_start: 0.8689 (mt-10) cc_final: 0.8028 (mp0)
REVERT: D  260 GLU cc_start: 0.8827 (pm20) cc_final: 0.8281 (pm20)
REVERT: D  364 GLU cc_start: 0.7911 (mt-10) cc_final: 0.7501 (mt-10)
REVERT: D  372 LEU cc_start: 0.8008 (OUTLIER) cc_final: 0.7801 (tt)
REVERT: D  391 TRP cc_start: 0.8116 (m-90) cc_final: 0.7874 (m-90)
REVERT: D  402 GLU cc_start: 0.8298 (mt-10) cc_final: 0.8033 (mm-30)
REVERT: E  112 TRP cc_start: 0.8107 (OUTLIER) cc_final: 0.6891 (t-100)
REVERT: E  132 ASP cc_start: 0.7844 (OUTLIER) cc_final: 0.7568 (t0)
REVERT: E  221 GLN cc_start: 0.8428 (pt0) cc_final: 0.8121 (pt0)
REVERT: E  246 LEU cc_start: 0.8314 (tp) cc_final: 0.8055 (tp)
REVERT: E  257 ARG cc_start: 0.8888 (ptp90) cc_final: 0.8252 (ptp-110)
REVERT: E  260 GLU cc_start: 0.8906 (pm20) cc_final: 0.8430 (pm20)
  outliers start: 39
  outliers final: 21
  residues processed: 268
  average time/residue: 1.1773
  time to fit residues: 345.5778
Evaluate side-chains
  278 residues out of total 1430 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 251
  time to evaluate  : 1.421 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  123 LEU
Chi-restraints excluded: chain A residue  275 LEU
Chi-restraints excluded: chain A residue  285 SER
Chi-restraints excluded: chain A residue  394 CYS
Chi-restraints excluded: chain B residue  245 LEU
Chi-restraints excluded: chain B residue  372 LEU
Chi-restraints excluded: chain B residue  394 CYS
Chi-restraints excluded: chain C residue   81 MET
Chi-restraints excluded: chain C residue  112 TRP
Chi-restraints excluded: chain C residue  132 ASP
Chi-restraints excluded: chain C residue  146 LYS
Chi-restraints excluded: chain C residue  179 SER
Chi-restraints excluded: chain C residue  198 VAL
Chi-restraints excluded: chain C residue  210 GLN
Chi-restraints excluded: chain C residue  275 LEU
Chi-restraints excluded: chain C residue  306 LEU
Chi-restraints excluded: chain C residue  372 LEU
Chi-restraints excluded: chain C residue  373 VAL
Chi-restraints excluded: chain D residue  146 LYS
Chi-restraints excluded: chain D residue  153 THR
Chi-restraints excluded: chain D residue  299 ILE
Chi-restraints excluded: chain D residue  372 LEU
Chi-restraints excluded: chain E residue  112 TRP
Chi-restraints excluded: chain E residue  132 ASP
Chi-restraints excluded: chain E residue  198 VAL
Chi-restraints excluded: chain E residue  275 LEU
Chi-restraints excluded: chain E residue  372 LEU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 160
   random chunks:
   chunk 92 optimal weight:    4.9990
   chunk 23 optimal weight:    4.9990
   chunk 128 optimal weight:    5.9990
   chunk 81 optimal weight:    2.9990
   chunk 25 optimal weight:    2.9990
   chunk 43 optimal weight:    2.9990
   chunk 106 optimal weight:    4.9990
   chunk 112 optimal weight:    0.9980
   chunk 75 optimal weight:    0.6980
   chunk 137 optimal weight:    6.9990
   chunk 13 optimal weight:    4.9990
   overall best weight:    2.1386

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

Flipped N/Q/H residues before XYZ refinement:
E 276 HIS
E 382 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3178 r_free = 0.3178 target = 0.092639 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.2931 r_free = 0.2931 target = 0.076524 restraints weight = 20920.734|
|-----------------------------------------------------------------------------|
r_work (start): 0.2908 rms_B_bonded: 3.00
r_work: 0.2747 rms_B_bonded: 3.37 restraints_weight: 0.5000
r_work (final): 0.2747
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2747
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2747 r_free = 0.2747    target_work(ls_wunit_k1) = 0.067         |
| occupancies: max = 1.00  min = 0.86   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2747 r_free = 0.2747    target_work(ls_wunit_k1) = 0.067         |
| occupancies: max = 1.00  min = 0.86   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2747
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7781
moved from start:          0.2887

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.043  13410  Z= 0.240
  Angle     :  0.601  10.534  18370  Z= 0.291
  Chirality :  0.042   0.156   2235
  Planarity :  0.004   0.029   2250
  Dihedral  :  4.009  16.409   2060
  Min Nonbonded Distance : 2.604

Molprobity Statistics.
  All-atom Clashscore : 8.12
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.38 %
    Favored  : 97.62 %
  Rotamer:
    Outliers :  3.22 %
    Allowed  : 16.92 %
    Favored  : 79.86 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.88 %
    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:  1.85 (0.21), residues: 1600
  helix:  2.95 (0.20), residues: 545
  sheet:  0.59 (0.23), residues: 450
  loop :  0.19 (0.27), residues: 605

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.026   0.001   TRP B 112 
 HIS   0.003   0.000   HIS E 276 
 PHE   0.030   0.002   PHE D 385 
 TYR   0.022   0.002   TYR B 176 
 ARG   0.007   0.001   ARG D 257 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00336 (   10)
  link_NAG-ASN         : angle       1.44283 (   30)
  link_BETA1-4         : bond        0.00113 (    5)
  link_BETA1-4         : angle       0.93209 (   15)
  hydrogen bonds       : bond        0.04062 (  680)
  hydrogen bonds       : angle       3.83416 ( 2100)
  SS BOND              : bond        0.00527 (   10)
  SS BOND              : angle       1.05294 (   20)
  covalent geometry    : bond        0.00555 (13385)
  covalent geometry    : angle       0.59779 (18305)

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

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

  3200 Ramachandran restraints generated.
    1600 Oldfield, 0 Emsley, 1600 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3200 Ramachandran restraints generated.
    1600 Oldfield, 0 Emsley, 1600 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  305 residues out of total 1430 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 46
    poor density    : 259
  time to evaluate  : 1.478 
Fit side-chains
REVERT: A  112 TRP cc_start: 0.8219 (OUTLIER) cc_final: 0.7975 (t-100)
REVERT: A  124 GLU cc_start: 0.8411 (mp0) cc_final: 0.7958 (mp0)
REVERT: A  201 GLU cc_start: 0.8684 (mt-10) cc_final: 0.8062 (mp0)
REVERT: A  260 GLU cc_start: 0.8733 (pt0) cc_final: 0.8401 (pm20)
REVERT: A  364 GLU cc_start: 0.8113 (mt-10) cc_final: 0.7667 (mt-10)
REVERT: A  391 TRP cc_start: 0.8146 (m-90) cc_final: 0.7915 (m-90)
REVERT: B   48 GLU cc_start: 0.8109 (tp30) cc_final: 0.7844 (tp30)
REVERT: B   75 ASP cc_start: 0.7701 (t0) cc_final: 0.7335 (t0)
REVERT: B  112 TRP cc_start: 0.8097 (OUTLIER) cc_final: 0.7446 (t-100)
REVERT: B  124 GLU cc_start: 0.8463 (mp0) cc_final: 0.7940 (mp0)
REVERT: B  132 ASP cc_start: 0.7498 (t0) cc_final: 0.7151 (t0)
REVERT: B  146 LYS cc_start: 0.8348 (mtmm) cc_final: 0.8082 (mtpp)
REVERT: B  201 GLU cc_start: 0.8580 (mt-10) cc_final: 0.8041 (mp0)
REVERT: B  214 GLN cc_start: 0.8325 (mm-40) cc_final: 0.8069 (pt0)
REVERT: B  260 GLU cc_start: 0.8785 (pm20) cc_final: 0.8397 (pm20)
REVERT: B  272 TYR cc_start: 0.8600 (t80) cc_final: 0.8318 (t80)
REVERT: B  364 GLU cc_start: 0.7732 (OUTLIER) cc_final: 0.6740 (mp0)
REVERT: B  391 TRP cc_start: 0.8242 (m-90) cc_final: 0.8017 (m-10)
REVERT: C   75 ASP cc_start: 0.7664 (t0) cc_final: 0.7137 (t0)
REVERT: C  112 TRP cc_start: 0.8375 (OUTLIER) cc_final: 0.7962 (t-100)
REVERT: C  132 ASP cc_start: 0.7845 (OUTLIER) cc_final: 0.7500 (t0)
REVERT: C  146 LYS cc_start: 0.8201 (OUTLIER) cc_final: 0.7745 (mtpp)
REVERT: C  188 GLN cc_start: 0.8097 (tt0) cc_final: 0.7867 (tt0)
REVERT: C  201 GLU cc_start: 0.8702 (mt-10) cc_final: 0.8049 (mp0)
REVERT: C  260 GLU cc_start: 0.8955 (pm20) cc_final: 0.8568 (pm20)
REVERT: D   63 ASP cc_start: 0.8438 (t70) cc_final: 0.8127 (t0)
REVERT: D   75 ASP cc_start: 0.7751 (t0) cc_final: 0.7545 (t0)
REVERT: D  112 TRP cc_start: 0.8165 (OUTLIER) cc_final: 0.7910 (t-100)
REVERT: D  113 GLU cc_start: 0.8790 (mp0) cc_final: 0.8277 (mp0)
REVERT: D  129 ASP cc_start: 0.8451 (t0) cc_final: 0.8052 (t0)
REVERT: D  132 ASP cc_start: 0.7716 (p0) cc_final: 0.7456 (t0)
REVERT: D  201 GLU cc_start: 0.8745 (mt-10) cc_final: 0.8103 (mp0)
REVERT: D  364 GLU cc_start: 0.7998 (mt-10) cc_final: 0.7589 (mt-10)
REVERT: D  372 LEU cc_start: 0.8101 (OUTLIER) cc_final: 0.7870 (tt)
REVERT: D  391 TRP cc_start: 0.8168 (m-90) cc_final: 0.7924 (m-90)
REVERT: D  402 GLU cc_start: 0.8307 (mt-10) cc_final: 0.8057 (mm-30)
REVERT: E   81 MET cc_start: 0.8763 (ttp) cc_final: 0.8429 (ptt)
REVERT: E  112 TRP cc_start: 0.8361 (OUTLIER) cc_final: 0.7233 (t-100)
REVERT: E  132 ASP cc_start: 0.7929 (OUTLIER) cc_final: 0.7621 (t0)
REVERT: E  221 GLN cc_start: 0.8598 (pt0) cc_final: 0.8224 (pt0)
REVERT: E  257 ARG cc_start: 0.8915 (ptp90) cc_final: 0.8294 (ptp-110)
REVERT: E  260 GLU cc_start: 0.8952 (pm20) cc_final: 0.8513 (pm20)
REVERT: E  285 SER cc_start: 0.8808 (t) cc_final: 0.8454 (t)
  outliers start: 46
  outliers final: 26
  residues processed: 279
  average time/residue: 1.0741
  time to fit residues: 330.0362
Evaluate side-chains
  292 residues out of total 1430 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 256
  time to evaluate  : 1.519 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  112 TRP
Chi-restraints excluded: chain A residue  123 LEU
Chi-restraints excluded: chain A residue  275 LEU
Chi-restraints excluded: chain A residue  285 SER
Chi-restraints excluded: chain A residue  372 LEU
Chi-restraints excluded: chain A residue  373 VAL
Chi-restraints excluded: chain A residue  394 CYS
Chi-restraints excluded: chain B residue  112 TRP
Chi-restraints excluded: chain B residue  123 LEU
Chi-restraints excluded: chain B residue  245 LEU
Chi-restraints excluded: chain B residue  364 GLU
Chi-restraints excluded: chain B residue  372 LEU
Chi-restraints excluded: chain B residue  373 VAL
Chi-restraints excluded: chain B residue  394 CYS
Chi-restraints excluded: chain C residue  112 TRP
Chi-restraints excluded: chain C residue  129 ASP
Chi-restraints excluded: chain C residue  132 ASP
Chi-restraints excluded: chain C residue  146 LYS
Chi-restraints excluded: chain C residue  179 SER
Chi-restraints excluded: chain C residue  198 VAL
Chi-restraints excluded: chain C residue  210 GLN
Chi-restraints excluded: chain C residue  275 LEU
Chi-restraints excluded: chain C residue  372 LEU
Chi-restraints excluded: chain C residue  373 VAL
Chi-restraints excluded: chain C residue  394 CYS
Chi-restraints excluded: chain D residue  112 TRP
Chi-restraints excluded: chain D residue  123 LEU
Chi-restraints excluded: chain D residue  153 THR
Chi-restraints excluded: chain D residue  372 LEU
Chi-restraints excluded: chain D residue  373 VAL
Chi-restraints excluded: chain E residue  112 TRP
Chi-restraints excluded: chain E residue  132 ASP
Chi-restraints excluded: chain E residue  198 VAL
Chi-restraints excluded: chain E residue  275 LEU
Chi-restraints excluded: chain E residue  372 LEU
Chi-restraints excluded: chain E residue  373 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 160
   random chunks:
   chunk 49 optimal weight:    2.9990
   chunk 23 optimal weight:    1.9990
   chunk 85 optimal weight:    0.9980
   chunk 1 optimal weight:    1.9990
   chunk 127 optimal weight:    0.1980
   chunk 73 optimal weight:    5.9990
   chunk 106 optimal weight:    0.9980
   chunk 136 optimal weight:    1.9990
   chunk 81 optimal weight:    1.9990
   chunk 22 optimal weight:    0.6980
   chunk 8 optimal weight:    0.9980
   overall best weight:    0.7780

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

Flipped N/Q/H residues before XYZ refinement:
D 382 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3212 r_free = 0.3212 target = 0.094930 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.2969 r_free = 0.2969 target = 0.078934 restraints weight = 20677.840|
|-----------------------------------------------------------------------------|
r_work (start): 0.2952 rms_B_bonded: 3.00
r_work: 0.2792 rms_B_bonded: 3.38 restraints_weight: 0.5000
r_work (final): 0.2792
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2793
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2793 r_free = 0.2793    target_work(ls_wunit_k1) = 0.069         |
| occupancies: max = 1.00  min = 0.86   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2793 r_free = 0.2793    target_work(ls_wunit_k1) = 0.069         |
| occupancies: max = 1.00  min = 0.86   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2793
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7739
moved from start:          0.2909

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041  13410  Z= 0.129
  Angle     :  0.571  10.889  18370  Z= 0.272
  Chirality :  0.040   0.179   2235
  Planarity :  0.003   0.029   2250
  Dihedral  :  3.910  15.265   2060
  Min Nonbonded Distance : 2.586

Molprobity Statistics.
  All-atom Clashscore : 8.12
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.25 %
    Favored  : 97.75 %
  Rotamer:
    Outliers :  1.96 %
    Allowed  : 18.81 %
    Favored  : 79.23 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.88 %
    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:  1.96 (0.21), residues: 1600
  helix:  3.07 (0.20), residues: 545
  sheet:  0.70 (0.24), residues: 420
  loop :  0.21 (0.26), residues: 635

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.023   0.001   TRP B 112 
 HIS   0.001   0.000   HIS E 276 
 PHE   0.022   0.002   PHE D 385 
 TYR   0.034   0.002   TYR E 176 
 ARG   0.007   0.000   ARG D 257 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00107 (   10)
  link_NAG-ASN         : angle       1.24669 (   30)
  link_BETA1-4         : bond        0.00114 (    5)
  link_BETA1-4         : angle       0.89269 (   15)
  hydrogen bonds       : bond        0.03865 (  680)
  hydrogen bonds       : angle       3.72824 ( 2100)
  SS BOND              : bond        0.00352 (   10)
  SS BOND              : angle       0.81725 (   20)
  covalent geometry    : bond        0.00292 (13385)
  covalent geometry    : angle       0.56845 (18305)

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

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

  3200 Ramachandran restraints generated.
    1600 Oldfield, 0 Emsley, 1600 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3200 Ramachandran restraints generated.
    1600 Oldfield, 0 Emsley, 1600 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  286 residues out of total 1430 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 258
  time to evaluate  : 1.478 
Fit side-chains
REVERT: A   81 MET cc_start: 0.8788 (ttp) cc_final: 0.8584 (ptm)
REVERT: A  124 GLU cc_start: 0.8423 (mp0) cc_final: 0.7847 (mp0)
REVERT: A  201 GLU cc_start: 0.8612 (mt-10) cc_final: 0.7990 (mp0)
REVERT: A  260 GLU cc_start: 0.8707 (pt0) cc_final: 0.8406 (pm20)
REVERT: A  364 GLU cc_start: 0.8094 (mt-10) cc_final: 0.7666 (mt-10)
REVERT: A  391 TRP cc_start: 0.8072 (m-90) cc_final: 0.7829 (m-90)
REVERT: B   48 GLU cc_start: 0.8108 (tp30) cc_final: 0.7834 (tp30)
REVERT: B   75 ASP cc_start: 0.7665 (t0) cc_final: 0.7113 (t0)
REVERT: B  124 GLU cc_start: 0.8399 (mp0) cc_final: 0.7888 (mp0)
REVERT: B  132 ASP cc_start: 0.7140 (t0) cc_final: 0.6773 (t0)
REVERT: B  146 LYS cc_start: 0.8330 (mtmm) cc_final: 0.8055 (mtpp)
REVERT: B  184 GLU cc_start: 0.8582 (pt0) cc_final: 0.8382 (pt0)
REVERT: B  201 GLU cc_start: 0.8566 (mt-10) cc_final: 0.8033 (mp0)
REVERT: B  214 GLN cc_start: 0.8329 (mm-40) cc_final: 0.8079 (pt0)
REVERT: B  260 GLU cc_start: 0.8782 (pm20) cc_final: 0.8399 (pm20)
REVERT: B  272 TYR cc_start: 0.8584 (t80) cc_final: 0.8337 (t80)
REVERT: B  364 GLU cc_start: 0.7670 (OUTLIER) cc_final: 0.6710 (mp0)
REVERT: B  391 TRP cc_start: 0.8145 (m-90) cc_final: 0.7911 (m-90)
REVERT: B  402 GLU cc_start: 0.8301 (mm-30) cc_final: 0.8003 (mm-30)
REVERT: C   75 ASP cc_start: 0.7619 (t0) cc_final: 0.7106 (t0)
REVERT: C  112 TRP cc_start: 0.8185 (OUTLIER) cc_final: 0.7849 (t-100)
REVERT: C  129 ASP cc_start: 0.8552 (t0) cc_final: 0.8293 (t0)
REVERT: C  132 ASP cc_start: 0.7796 (OUTLIER) cc_final: 0.7456 (t0)
REVERT: C  201 GLU cc_start: 0.8673 (mt-10) cc_final: 0.8045 (mp0)
REVERT: C  260 GLU cc_start: 0.8965 (pm20) cc_final: 0.8591 (pm20)
REVERT: D  112 TRP cc_start: 0.7934 (OUTLIER) cc_final: 0.7639 (t-100)
REVERT: D  113 GLU cc_start: 0.8762 (mp0) cc_final: 0.8229 (mp0)
REVERT: D  160 GLU cc_start: 0.8428 (mt-10) cc_final: 0.8062 (mt-10)
REVERT: D  201 GLU cc_start: 0.8723 (mt-10) cc_final: 0.8092 (mp0)
REVERT: D  364 GLU cc_start: 0.8007 (mt-10) cc_final: 0.7584 (mt-10)
REVERT: D  372 LEU cc_start: 0.8077 (OUTLIER) cc_final: 0.7720 (tp)
REVERT: D  391 TRP cc_start: 0.8091 (m-90) cc_final: 0.7848 (m-90)
REVERT: D  402 GLU cc_start: 0.8313 (mt-10) cc_final: 0.8044 (mm-30)
REVERT: E   81 MET cc_start: 0.8748 (ttp) cc_final: 0.8450 (ptt)
REVERT: E  112 TRP cc_start: 0.8150 (OUTLIER) cc_final: 0.6964 (t-100)
REVERT: E  132 ASP cc_start: 0.7860 (OUTLIER) cc_final: 0.7592 (t0)
REVERT: E  140 ASP cc_start: 0.8238 (m-30) cc_final: 0.7973 (t70)
REVERT: E  221 GLN cc_start: 0.8521 (pt0) cc_final: 0.8172 (pt0)
REVERT: E  257 ARG cc_start: 0.8908 (ptp90) cc_final: 0.8278 (ptp-110)
REVERT: E  260 GLU cc_start: 0.8933 (pm20) cc_final: 0.8487 (pm20)
REVERT: E  285 SER cc_start: 0.8676 (t) cc_final: 0.8363 (t)
  outliers start: 28
  outliers final: 15
  residues processed: 269
  average time/residue: 1.1587
  time to fit residues: 342.0848
Evaluate side-chains
  280 residues out of total 1430 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 258
  time to evaluate  : 1.370 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  123 LEU
Chi-restraints excluded: chain A residue  275 LEU
Chi-restraints excluded: chain A residue  394 CYS
Chi-restraints excluded: chain B residue  245 LEU
Chi-restraints excluded: chain B residue  364 GLU
Chi-restraints excluded: chain B residue  372 LEU
Chi-restraints excluded: chain B residue  394 CYS
Chi-restraints excluded: chain C residue   81 MET
Chi-restraints excluded: chain C residue  112 TRP
Chi-restraints excluded: chain C residue  132 ASP
Chi-restraints excluded: chain C residue  179 SER
Chi-restraints excluded: chain C residue  198 VAL
Chi-restraints excluded: chain C residue  210 GLN
Chi-restraints excluded: chain C residue  275 LEU
Chi-restraints excluded: chain C residue  373 VAL
Chi-restraints excluded: chain D residue  112 TRP
Chi-restraints excluded: chain D residue  123 LEU
Chi-restraints excluded: chain D residue  372 LEU
Chi-restraints excluded: chain E residue  112 TRP
Chi-restraints excluded: chain E residue  132 ASP
Chi-restraints excluded: chain E residue  198 VAL
Chi-restraints excluded: chain E residue  372 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 160
   random chunks:
   chunk 74 optimal weight:    0.2980
   chunk 1 optimal weight:    7.9990
   chunk 88 optimal weight:    3.9990
   chunk 126 optimal weight:    0.9980
   chunk 111 optimal weight:    5.9990
   chunk 10 optimal weight:    5.9990
   chunk 56 optimal weight:    1.9990
   chunk 154 optimal weight:    3.9990
   chunk 36 optimal weight:    0.9980
   chunk 83 optimal weight:    0.8980
   chunk 127 optimal weight:    0.0570
   overall best weight:    0.6498

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

Flipped N/Q/H residues before XYZ refinement:
E 382 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3224 r_free = 0.3224 target = 0.095762 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.2983 r_free = 0.2983 target = 0.079844 restraints weight = 20642.186|
|-----------------------------------------------------------------------------|
r_work (start): 0.2961 rms_B_bonded: 3.00
r_work: 0.2802 rms_B_bonded: 3.39 restraints_weight: 0.5000
r_work (final): 0.2802
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2817
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2817 r_free = 0.2817    target_work(ls_wunit_k1) = 0.071         |
| occupancies: max = 1.00  min = 0.86   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2817 r_free = 0.2817    target_work(ls_wunit_k1) = 0.071         |
| occupancies: max = 1.00  min = 0.86   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2817
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7671
moved from start:          0.2918

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033  13410  Z= 0.117
  Angle     :  0.551  10.404  18370  Z= 0.262
  Chirality :  0.039   0.148   2235
  Planarity :  0.003   0.032   2250
  Dihedral  :  3.794  15.102   2060
  Min Nonbonded Distance : 2.613

Molprobity Statistics.
  All-atom Clashscore : 7.63
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.88 %
    Favored  : 98.12 %
  Rotamer:
    Outliers :  1.82 %
    Allowed  : 18.81 %
    Favored  : 79.37 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.88 %
    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:  2.01 (0.21), residues: 1600
  helix:  3.21 (0.20), residues: 540
  sheet:  0.73 (0.24), residues: 420
  loop :  0.16 (0.26), residues: 640

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.023   0.001   TRP B 112 
 HIS   0.001   0.000   HIS B 276 
 PHE   0.020   0.001   PHE D 385 
 TYR   0.028   0.002   TYR E 176 
 ARG   0.009   0.000   ARG D 257 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00046 (   10)
  link_NAG-ASN         : angle       1.21429 (   30)
  link_BETA1-4         : bond        0.00169 (    5)
  link_BETA1-4         : angle       0.91312 (   15)
  hydrogen bonds       : bond        0.03778 (  680)
  hydrogen bonds       : angle       3.64944 ( 2100)
  SS BOND              : bond        0.00327 (   10)
  SS BOND              : angle       0.76974 (   20)
  covalent geometry    : bond        0.00263 (13385)
  covalent geometry    : angle       0.54901 (18305)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 8061.04 seconds
wall clock time: 139 minutes 34.52 seconds (8374.52 seconds total)