Starting phenix.real_space_refine
on Sun Jan 19 01:22:14 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8yx8_39650/01_2025/8yx8_39650.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8yx8_39650/01_2025/8yx8_39650.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/8yx8_39650/01_2025/8yx8_39650.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8yx8_39650/01_2025/8yx8_39650.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8yx8_39650/01_2025/8yx8_39650.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8yx8_39650/01_2025/8yx8_39650.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-5571/modules/chem_data/mon_lib"
  Total number of atoms: 13070
  Number of models: 1
  Model: ""
    Number of chains: 15
    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: "B"
      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: "C"
      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: "D"
      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: "E"
      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: "F"
      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: "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: "H"
      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: "I"
      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: "J"
      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
    Chain: "B"
      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
    Chain: "C"
      Number of atoms: 14
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 14
          Unusual residues: {'NAG': 1}
          Classifications: {'undetermined': 1}
          Unresolved non-hydrogen bonds: 1
          Unresolved non-hydrogen angles: 2
          Unresolved non-hydrogen dihedrals: 3
          Unresolved non-hydrogen chiralities: 1
    Chain: "D"
      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
    Chain: "E"
      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
  Residues with excluded nonbonded symmetry interactions: 5
    residue:
      pdb=" C1  NAG F   2 " occ=0.60
      ... (12 atoms not shown)
      pdb=" O7  NAG F   2 " occ=0.60
    residue:
      pdb=" C1  NAG G   2 " occ=0.60
      ... (12 atoms not shown)
      pdb=" O7  NAG G   2 " occ=0.60
    residue:
      pdb=" C1  NAG H   2 " occ=0.60
      ... (12 atoms not shown)
      pdb=" O7  NAG H   2 " occ=0.60
    residue:
      pdb=" C1  NAG I   2 " occ=0.60
      ... (12 atoms not shown)
      pdb=" O7  NAG I   2 " occ=0.60
    residue:
      pdb=" C1  NAG J   2 " occ=0.60
      ... (12 atoms not shown)
      pdb=" O7  NAG J   2 " occ=0.60
  Time building chain proxies: 7.81, per 1000 atoms: 0.60
  Number of scatterers: 13070
  At special positions: 0
  Unit cell: (93, 93, 121.83, 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 B 157 " - pdb=" SG  CYS B 171 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 289 " - pdb=" SG  CYS B 394 " distance=2.03
    Simple disulfide: pdb=" SG  CYS C 157 " - pdb=" SG  CYS C 171 " distance=2.03
    Simple disulfide: pdb=" SG  CYS C 289 " - pdb=" SG  CYS C 394 " distance=2.03
    Simple disulfide: pdb=" SG  CYS D 157 " - pdb=" SG  CYS D 171 " distance=2.03
    Simple disulfide: pdb=" SG  CYS D 289 " - pdb=" SG  CYS D 394 " distance=2.03
    Simple disulfide: pdb=" SG  CYS E 157 " - pdb=" SG  CYS E 171 " distance=2.03
    Simple disulfide: pdb=" SG  CYS E 289 " - pdb=" SG  CYS E 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: 3.21
  Conformation dependent library (CDL) restraints added in 1.7 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:
      30 helices and 15 sheets defined
      36.7% alpha, 32.7% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 1.41
  Creating SS restraints...
    Processing helix  chain 'A' and resid 94 through 97
    Processing helix  chain 'A' and resid 231 through 252
      removed outlier: 4.465A  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 259 through 283
      removed outlier: 4.175A  pdb=" N   GLY A 263 " --> pdb=" O   ILE A 259 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 291 through 320
      removed outlier: 3.998A  pdb=" N   TYR A 295 " --> pdb=" O   PRO A 291 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 361 through 392
    Processing helix  chain 'A' and resid 399 through 404
    Processing helix  chain 'B' and resid 94 through 97
    Processing helix  chain 'B' and resid 231 through 252
      removed outlier: 4.463A  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 259 through 283
      removed outlier: 4.175A  pdb=" N   GLY B 263 " --> pdb=" O   ILE B 259 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 291 through 320
      removed outlier: 3.998A  pdb=" N   TYR B 295 " --> pdb=" O   PRO B 291 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 361 through 392
    Processing helix  chain 'B' and resid 399 through 404
    Processing helix  chain 'C' and resid 94 through 97
    Processing helix  chain 'C' and resid 231 through 252
      removed outlier: 4.463A  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 259 through 283
      removed outlier: 4.175A  pdb=" N   GLY C 263 " --> pdb=" O   ILE C 259 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 291 through 320
      removed outlier: 3.998A  pdb=" N   TYR C 295 " --> pdb=" O   PRO C 291 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 361 through 392
    Processing helix  chain 'C' and resid 399 through 404
    Processing helix  chain 'D' and resid 94 through 97
    Processing helix  chain 'D' and resid 231 through 252
      removed outlier: 4.465A  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 259 through 283
      removed outlier: 4.175A  pdb=" N   GLY D 263 " --> pdb=" O   ILE D 259 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 291 through 320
      removed outlier: 3.998A  pdb=" N   TYR D 295 " --> pdb=" O   PRO D 291 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 361 through 392
    Processing helix  chain 'D' and resid 399 through 404
    Processing helix  chain 'E' and resid 94 through 97
    Processing helix  chain 'E' and resid 231 through 252
      removed outlier: 4.464A  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 259 through 283
      removed outlier: 4.175A  pdb=" N   GLY E 263 " --> pdb=" O   ILE E 259 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 291 through 320
      removed outlier: 3.998A  pdb=" N   TYR E 295 " --> pdb=" O   PRO E 291 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 361 through 392
    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: 5.688A  pdb=" N   GLN A 136 " --> pdb=" O   ASN A 148 " (cutoff:3.500A)
      removed outlier: 4.913A  pdb=" N   ASN A 148 " --> pdb=" O   GLN A 136 " (cutoff:3.500A)
      removed outlier: 4.382A  pdb=" N   HIS A 144 " --> pdb=" O   ASP A 140 " (cutoff:3.500A)
      removed outlier: 7.117A  pdb=" N   ALA A 150 " --> pdb=" O   TRP A 130 " (cutoff:3.500A)
      removed outlier: 4.665A  pdb=" N   TRP A 130 " --> pdb=" O   ALA A 150 " (cutoff:3.500A)
      removed outlier: 6.564A  pdb=" N   ALA A 152 " --> pdb=" O   VAL A 128 " (cutoff:3.500A)
      removed outlier: 4.474A  pdb=" N   VAL A 128 " --> pdb=" O   ALA A 152 " (cutoff:3.500A)
      removed outlier: 6.649A  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: 5.688A  pdb=" N   GLN A 136 " --> pdb=" O   ASN A 148 " (cutoff:3.500A)
      removed outlier: 4.913A  pdb=" N   ASN A 148 " --> pdb=" O   GLN A 136 " (cutoff:3.500A)
      removed outlier: 4.382A  pdb=" N   HIS A 144 " --> pdb=" O   ASP A 140 " (cutoff:3.500A)
      removed outlier: 3.775A  pdb=" N   ASN A  73 " --> pdb=" O   SER A  82 " (cutoff:3.500A)
      removed outlier: 7.335A  pdb=" N   MET A  84 " --> pdb=" O   VAL A  71 " (cutoff:3.500A)
      removed outlier: 5.881A  pdb=" N   VAL A  71 " --> pdb=" O   MET A  84 " (cutoff:3.500A)
      removed outlier: 8.577A  pdb=" N   LEU A  86 " --> pdb=" O   SER A  69 " (cutoff:3.500A)
      removed outlier: 7.093A  pdb=" N   SER A  69 " --> pdb=" O   LEU A  86 " (cutoff:3.500A)
      removed outlier: 7.835A  pdb=" N   ARG A  88 " --> pdb=" O   PHE A  67 " (cutoff:3.500A)
      removed outlier: 7.926A  pdb=" N   PHE A  67 " --> pdb=" O   ARG A  88 " (cutoff:3.500A)
      removed outlier: 7.853A  pdb=" N   SER A  90 " --> pdb=" O   ARG A  65 " (cutoff:3.500A)
      removed outlier: 7.785A  pdb=" N   ARG A  65 " --> pdb=" O   SER A  90 " (cutoff:3.500A)
      removed outlier: 8.768A  pdb=" N   LEU A  92 " --> pdb=" O   ASP A  63 " (cutoff:3.500A)
      removed outlier: 9.645A  pdb=" N   ASP A  63 " --> pdb=" O   LEU A  92 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 121 through 122
      removed outlier: 4.115A  pdb=" N   ASP A 206 " --> pdb=" O   ARG A 225 " (cutoff:3.500A)
      removed outlier: 7.023A  pdb=" N   LYS A 227 " --> pdb=" O   VAL A 204 " (cutoff:3.500A)
      removed outlier: 5.484A  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: 5.687A  pdb=" N   GLN B 136 " --> pdb=" O   ASN B 148 " (cutoff:3.500A)
      removed outlier: 4.913A  pdb=" N   ASN B 148 " --> pdb=" O   GLN B 136 " (cutoff:3.500A)
      removed outlier: 4.381A  pdb=" N   HIS B 144 " --> pdb=" O   ASP B 140 " (cutoff:3.500A)
      removed outlier: 7.118A  pdb=" N   ALA B 150 " --> pdb=" O   TRP B 130 " (cutoff:3.500A)
      removed outlier: 4.667A  pdb=" N   TRP B 130 " --> pdb=" O   ALA B 150 " (cutoff:3.500A)
      removed outlier: 6.564A  pdb=" N   ALA B 152 " --> pdb=" O   VAL B 128 " (cutoff:3.500A)
      removed outlier: 4.475A  pdb=" N   VAL B 128 " --> pdb=" O   ALA B 152 " (cutoff:3.500A)
      removed outlier: 6.650A  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: 5.687A  pdb=" N   GLN B 136 " --> pdb=" O   ASN B 148 " (cutoff:3.500A)
      removed outlier: 4.913A  pdb=" N   ASN B 148 " --> pdb=" O   GLN B 136 " (cutoff:3.500A)
      removed outlier: 4.381A  pdb=" N   HIS B 144 " --> pdb=" O   ASP B 140 " (cutoff:3.500A)
      removed outlier: 3.775A  pdb=" N   ASN B  73 " --> pdb=" O   SER B  82 " (cutoff:3.500A)
      removed outlier: 7.335A  pdb=" N   MET B  84 " --> pdb=" O   VAL B  71 " (cutoff:3.500A)
      removed outlier: 5.881A  pdb=" N   VAL B  71 " --> pdb=" O   MET B  84 " (cutoff:3.500A)
      removed outlier: 8.578A  pdb=" N   LEU B  86 " --> pdb=" O   SER B  69 " (cutoff:3.500A)
      removed outlier: 7.093A  pdb=" N   SER B  69 " --> pdb=" O   LEU B  86 " (cutoff:3.500A)
      removed outlier: 7.835A  pdb=" N   ARG B  88 " --> pdb=" O   PHE B  67 " (cutoff:3.500A)
      removed outlier: 7.926A  pdb=" N   PHE B  67 " --> pdb=" O   ARG B  88 " (cutoff:3.500A)
      removed outlier: 7.853A  pdb=" N   SER B  90 " --> pdb=" O   ARG B  65 " (cutoff:3.500A)
      removed outlier: 7.784A  pdb=" N   ARG B  65 " --> pdb=" O   SER B  90 " (cutoff:3.500A)
      removed outlier: 8.768A  pdb=" N   LEU B  92 " --> pdb=" O   ASP B  63 " (cutoff:3.500A)
      removed outlier: 9.645A  pdb=" N   ASP B  63 " --> pdb=" O   LEU B  92 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'B' and resid 121 through 122
      removed outlier: 4.115A  pdb=" N   ASP B 206 " --> pdb=" O   ARG B 225 " (cutoff:3.500A)
      removed outlier: 7.024A  pdb=" N   LYS B 227 " --> pdb=" O   VAL B 204 " (cutoff:3.500A)
      removed outlier: 5.484A  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: 5.687A  pdb=" N   GLN C 136 " --> pdb=" O   ASN C 148 " (cutoff:3.500A)
      removed outlier: 4.913A  pdb=" N   ASN C 148 " --> pdb=" O   GLN C 136 " (cutoff:3.500A)
      removed outlier: 4.381A  pdb=" N   HIS C 144 " --> pdb=" O   ASP C 140 " (cutoff:3.500A)
      removed outlier: 7.117A  pdb=" N   ALA C 150 " --> pdb=" O   TRP C 130 " (cutoff:3.500A)
      removed outlier: 4.666A  pdb=" N   TRP C 130 " --> pdb=" O   ALA C 150 " (cutoff:3.500A)
      removed outlier: 6.564A  pdb=" N   ALA C 152 " --> pdb=" O   VAL C 128 " (cutoff:3.500A)
      removed outlier: 4.474A  pdb=" N   VAL C 128 " --> pdb=" O   ALA C 152 " (cutoff:3.500A)
      removed outlier: 6.649A  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: 5.687A  pdb=" N   GLN C 136 " --> pdb=" O   ASN C 148 " (cutoff:3.500A)
      removed outlier: 4.913A  pdb=" N   ASN C 148 " --> pdb=" O   GLN C 136 " (cutoff:3.500A)
      removed outlier: 4.381A  pdb=" N   HIS C 144 " --> pdb=" O   ASP C 140 " (cutoff:3.500A)
      removed outlier: 3.775A  pdb=" N   ASN C  73 " --> pdb=" O   SER C  82 " (cutoff:3.500A)
      removed outlier: 7.335A  pdb=" N   MET C  84 " --> pdb=" O   VAL C  71 " (cutoff:3.500A)
      removed outlier: 5.881A  pdb=" N   VAL C  71 " --> pdb=" O   MET C  84 " (cutoff:3.500A)
      removed outlier: 8.577A  pdb=" N   LEU C  86 " --> pdb=" O   SER C  69 " (cutoff:3.500A)
      removed outlier: 7.093A  pdb=" N   SER C  69 " --> pdb=" O   LEU C  86 " (cutoff:3.500A)
      removed outlier: 7.835A  pdb=" N   ARG C  88 " --> pdb=" O   PHE C  67 " (cutoff:3.500A)
      removed outlier: 7.926A  pdb=" N   PHE C  67 " --> pdb=" O   ARG C  88 " (cutoff:3.500A)
      removed outlier: 7.853A  pdb=" N   SER C  90 " --> pdb=" O   ARG C  65 " (cutoff:3.500A)
      removed outlier: 7.784A  pdb=" N   ARG C  65 " --> pdb=" O   SER C  90 " (cutoff:3.500A)
      removed outlier: 8.768A  pdb=" N   LEU C  92 " --> pdb=" O   ASP C  63 " (cutoff:3.500A)
      removed outlier: 9.645A  pdb=" N   ASP C  63 " --> pdb=" O   LEU C  92 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'C' and resid 121 through 122
      removed outlier: 4.114A  pdb=" N   ASP C 206 " --> pdb=" O   ARG C 225 " (cutoff:3.500A)
      removed outlier: 7.023A  pdb=" N   LYS C 227 " --> pdb=" O   VAL C 204 " (cutoff:3.500A)
      removed outlier: 5.484A  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: 5.688A  pdb=" N   GLN D 136 " --> pdb=" O   ASN D 148 " (cutoff:3.500A)
      removed outlier: 4.913A  pdb=" N   ASN D 148 " --> pdb=" O   GLN D 136 " (cutoff:3.500A)
      removed outlier: 4.382A  pdb=" N   HIS D 144 " --> pdb=" O   ASP D 140 " (cutoff:3.500A)
      removed outlier: 7.118A  pdb=" N   ALA D 150 " --> pdb=" O   TRP D 130 " (cutoff:3.500A)
      removed outlier: 4.667A  pdb=" N   TRP D 130 " --> pdb=" O   ALA D 150 " (cutoff:3.500A)
      removed outlier: 6.563A  pdb=" N   ALA D 152 " --> pdb=" O   VAL D 128 " (cutoff:3.500A)
      removed outlier: 4.475A  pdb=" N   VAL D 128 " --> pdb=" O   ALA D 152 " (cutoff:3.500A)
      removed outlier: 6.650A  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: 5.688A  pdb=" N   GLN D 136 " --> pdb=" O   ASN D 148 " (cutoff:3.500A)
      removed outlier: 4.913A  pdb=" N   ASN D 148 " --> pdb=" O   GLN D 136 " (cutoff:3.500A)
      removed outlier: 4.382A  pdb=" N   HIS D 144 " --> pdb=" O   ASP D 140 " (cutoff:3.500A)
      removed outlier: 3.775A  pdb=" N   ASN D  73 " --> pdb=" O   SER D  82 " (cutoff:3.500A)
      removed outlier: 7.335A  pdb=" N   MET D  84 " --> pdb=" O   VAL D  71 " (cutoff:3.500A)
      removed outlier: 5.881A  pdb=" N   VAL D  71 " --> pdb=" O   MET D  84 " (cutoff:3.500A)
      removed outlier: 8.578A  pdb=" N   LEU D  86 " --> pdb=" O   SER D  69 " (cutoff:3.500A)
      removed outlier: 7.093A  pdb=" N   SER D  69 " --> pdb=" O   LEU D  86 " (cutoff:3.500A)
      removed outlier: 7.835A  pdb=" N   ARG D  88 " --> pdb=" O   PHE D  67 " (cutoff:3.500A)
      removed outlier: 7.926A  pdb=" N   PHE D  67 " --> pdb=" O   ARG D  88 " (cutoff:3.500A)
      removed outlier: 7.853A  pdb=" N   SER D  90 " --> pdb=" O   ARG D  65 " (cutoff:3.500A)
      removed outlier: 7.785A  pdb=" N   ARG D  65 " --> pdb=" O   SER D  90 " (cutoff:3.500A)
      removed outlier: 8.768A  pdb=" N   LEU D  92 " --> pdb=" O   ASP D  63 " (cutoff:3.500A)
      removed outlier: 9.645A  pdb=" N   ASP D  63 " --> pdb=" O   LEU D  92 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'D' and resid 121 through 122
      removed outlier: 4.115A  pdb=" N   ASP D 206 " --> pdb=" O   ARG D 225 " (cutoff:3.500A)
      removed outlier: 7.023A  pdb=" N   LYS D 227 " --> pdb=" O   VAL D 204 " (cutoff:3.500A)
      removed outlier: 5.484A  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: 5.687A  pdb=" N   GLN E 136 " --> pdb=" O   ASN E 148 " (cutoff:3.500A)
      removed outlier: 4.913A  pdb=" N   ASN E 148 " --> pdb=" O   GLN E 136 " (cutoff:3.500A)
      removed outlier: 4.381A  pdb=" N   HIS E 144 " --> pdb=" O   ASP E 140 " (cutoff:3.500A)
      removed outlier: 7.118A  pdb=" N   ALA E 150 " --> pdb=" O   TRP E 130 " (cutoff:3.500A)
      removed outlier: 4.666A  pdb=" N   TRP E 130 " --> pdb=" O   ALA E 150 " (cutoff:3.500A)
      removed outlier: 6.564A  pdb=" N   ALA E 152 " --> pdb=" O   VAL E 128 " (cutoff:3.500A)
      removed outlier: 4.474A  pdb=" N   VAL E 128 " --> pdb=" O   ALA E 152 " (cutoff:3.500A)
      removed outlier: 6.649A  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: 5.687A  pdb=" N   GLN E 136 " --> pdb=" O   ASN E 148 " (cutoff:3.500A)
      removed outlier: 4.913A  pdb=" N   ASN E 148 " --> pdb=" O   GLN E 136 " (cutoff:3.500A)
      removed outlier: 4.381A  pdb=" N   HIS E 144 " --> pdb=" O   ASP E 140 " (cutoff:3.500A)
      removed outlier: 3.775A  pdb=" N   ASN E  73 " --> pdb=" O   SER E  82 " (cutoff:3.500A)
      removed outlier: 7.334A  pdb=" N   MET E  84 " --> pdb=" O   VAL E  71 " (cutoff:3.500A)
      removed outlier: 5.881A  pdb=" N   VAL E  71 " --> pdb=" O   MET E  84 " (cutoff:3.500A)
      removed outlier: 8.577A  pdb=" N   LEU E  86 " --> pdb=" O   SER E  69 " (cutoff:3.500A)
      removed outlier: 7.093A  pdb=" N   SER E  69 " --> pdb=" O   LEU E  86 " (cutoff:3.500A)
      removed outlier: 7.835A  pdb=" N   ARG E  88 " --> pdb=" O   PHE E  67 " (cutoff:3.500A)
      removed outlier: 7.926A  pdb=" N   PHE E  67 " --> pdb=" O   ARG E  88 " (cutoff:3.500A)
      removed outlier: 7.853A  pdb=" N   SER E  90 " --> pdb=" O   ARG E  65 " (cutoff:3.500A)
      removed outlier: 7.785A  pdb=" N   ARG E  65 " --> pdb=" O   SER E  90 " (cutoff:3.500A)
      removed outlier: 8.768A  pdb=" N   LEU E  92 " --> pdb=" O   ASP E  63 " (cutoff:3.500A)
      removed outlier: 9.645A  pdb=" N   ASP E  63 " --> pdb=" O   LEU E  92 " (cutoff:3.500A)
    Processing sheet with id=AB6, first strand: chain 'E' and resid 121 through 122
      removed outlier: 4.114A  pdb=" N   ASP E 206 " --> pdb=" O   ARG E 225 " (cutoff:3.500A)
      removed outlier: 7.023A  pdb=" N   LYS E 227 " --> pdb=" O   VAL E 204 " (cutoff:3.500A)
      removed outlier: 5.484A  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: 4.13

  Time building geometry restraints manager: 3.72 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 -     1.44: 3605
        1.44 -     1.56: 7685
        1.56 -     1.69: 0
        1.69 -     1.81: 75
  Bond restraints: 13385
  Sorted by residual:
  bond pdb=" C7  NAG J   1 "
       pdb=" N2  NAG J   1 "
    ideal  model  delta    sigma   weight residual
    1.346  1.463 -0.117 2.00e-02 2.50e+03 3.42e+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 H   1 "
       pdb=" N2  NAG H   1 "
    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 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
  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
  ... (remaining 13380 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.10: 17547
        1.10 -     2.20: 461
        2.20 -     3.30: 169
        3.30 -     4.40: 81
        4.40 -     5.50: 47
  Bond angle restraints: 18305
  Sorted by residual:
  angle pdb=" C4  NAG H   2 "
        pdb=" C5  NAG H   2 "
        pdb=" C6  NAG H   2 "
      ideal   model   delta    sigma   weight residual
     113.89  108.79    5.10 3.00e+00 1.11e-01 2.89e+00
  angle pdb=" C4  NAG G   2 "
        pdb=" C5  NAG G   2 "
        pdb=" C6  NAG G   2 "
      ideal   model   delta    sigma   weight residual
     113.89  108.81    5.08 3.00e+00 1.11e-01 2.87e+00
  angle pdb=" C4  NAG F   2 "
        pdb=" C5  NAG F   2 "
        pdb=" C6  NAG F   2 "
      ideal   model   delta    sigma   weight residual
     113.89  108.81    5.08 3.00e+00 1.11e-01 2.87e+00
  angle pdb=" C4  NAG I   2 "
        pdb=" C5  NAG I   2 "
        pdb=" C6  NAG I   2 "
      ideal   model   delta    sigma   weight residual
     113.89  108.82    5.07 3.00e+00 1.11e-01 2.86e+00
  angle pdb=" C4  NAG J   2 "
        pdb=" C5  NAG J   2 "
        pdb=" C6  NAG J   2 "
      ideal   model   delta    sigma   weight residual
     113.89  108.84    5.05 3.00e+00 1.11e-01 2.84e+00
  ... (remaining 18300 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.97: 7582
       17.97 -    35.94: 523
       35.94 -    53.91: 60
       53.91 -    71.87: 5
       71.87 -    89.84: 10
  Dihedral angle restraints: 8180
    sinusoidal: 3385
      harmonic: 4795
  Sorted by residual:
  dihedral pdb=" CA  VAL B  71 "
           pdb=" C   VAL B  71 "
           pdb=" N   PHE B  72 "
           pdb=" CA  PHE B  72 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -165.58  -14.42     0      5.00e+00 4.00e-02 8.31e+00
  dihedral pdb=" CA  VAL D  71 "
           pdb=" C   VAL D  71 "
           pdb=" N   PHE D  72 "
           pdb=" CA  PHE D  72 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -165.60  -14.40     0      5.00e+00 4.00e-02 8.29e+00
  dihedral pdb=" CA  VAL A  71 "
           pdb=" C   VAL A  71 "
           pdb=" N   PHE A  72 "
           pdb=" CA  PHE A  72 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -165.62  -14.38     0      5.00e+00 4.00e-02 8.27e+00
  ... (remaining 8177 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.031: 1462
       0.031 -    0.063: 539
       0.063 -    0.094: 129
       0.094 -    0.126: 80
       0.126 -    0.157: 25
  Chirality restraints: 2235
  Sorted by residual:
  chirality pdb=" CA  PHE A  72 "
            pdb=" N   PHE A  72 "
            pdb=" C   PHE A  72 "
            pdb=" CB  PHE A  72 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.35    0.16 2.00e-01 2.50e+01 6.16e-01
  chirality pdb=" CA  PHE E  72 "
            pdb=" N   PHE E  72 "
            pdb=" C   PHE E  72 "
            pdb=" CB  PHE E  72 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.36    0.16 2.00e-01 2.50e+01 6.01e-01
  chirality pdb=" CA  PHE B  72 "
            pdb=" N   PHE B  72 "
            pdb=" C   PHE B  72 "
            pdb=" CB  PHE B  72 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.36    0.15 2.00e-01 2.50e+01 5.96e-01
  ... (remaining 2232 not shown)

  Planarity restraints: 2260
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  PHE B  72 "   -0.010 2.00e-02 2.50e+03   8.91e-03 1.39e+00
        pdb=" CG  PHE B  72 "    0.021 2.00e-02 2.50e+03
        pdb=" CD1 PHE B  72 "   -0.004 2.00e-02 2.50e+03
        pdb=" CD2 PHE B  72 "   -0.002 2.00e-02 2.50e+03
        pdb=" CE1 PHE B  72 "    0.000 2.00e-02 2.50e+03
        pdb=" CE2 PHE B  72 "   -0.002 2.00e-02 2.50e+03
        pdb=" CZ  PHE B  72 "   -0.003 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  PHE C  72 "    0.010 2.00e-02 2.50e+03   8.88e-03 1.38e+00
        pdb=" CG  PHE C  72 "   -0.021 2.00e-02 2.50e+03
        pdb=" CD1 PHE C  72 "    0.004 2.00e-02 2.50e+03
        pdb=" CD2 PHE C  72 "    0.002 2.00e-02 2.50e+03
        pdb=" CE1 PHE C  72 "    0.000 2.00e-02 2.50e+03
        pdb=" CE2 PHE C  72 "    0.002 2.00e-02 2.50e+03
        pdb=" CZ  PHE C  72 "    0.002 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  PHE D  72 "    0.010 2.00e-02 2.50e+03   8.72e-03 1.33e+00
        pdb=" CG  PHE D  72 "   -0.020 2.00e-02 2.50e+03
        pdb=" CD1 PHE D  72 "    0.004 2.00e-02 2.50e+03
        pdb=" CD2 PHE D  72 "    0.002 2.00e-02 2.50e+03
        pdb=" CE1 PHE D  72 "   -0.000 2.00e-02 2.50e+03
        pdb=" CE2 PHE D  72 "    0.002 2.00e-02 2.50e+03
        pdb=" CZ  PHE D  72 "    0.003 2.00e-02 2.50e+03
  ... (remaining 2257 not shown)

  Histogram of nonbonded interaction distances:
        2.28 -     2.80: 2871
        2.80 -     3.33: 11982
        3.33 -     3.85: 22222
        3.85 -     4.38: 25474
        4.38 -     4.90: 44314
  Nonbonded interactions: 106863
  Sorted by model distance:
  nonbonded pdb=" OE2 GLU D 242 "
            pdb=" OH  TYR D 296 "
     model   vdw
     2.281 3.040
  nonbonded pdb=" OE2 GLU B 242 "
            pdb=" OH  TYR B 296 "
     model   vdw
     2.281 3.040
  nonbonded pdb=" OE2 GLU A 242 "
            pdb=" OH  TYR A 296 "
     model   vdw
     2.281 3.040
  nonbonded pdb=" OE2 GLU C 242 "
            pdb=" OH  TYR C 296 "
     model   vdw
     2.281 3.040
  nonbonded pdb=" NE1 TRP B 127 "
            pdb=" OE1 GLU B 154 "
     model   vdw
     2.282 3.120
  ... (remaining 106858 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=0.60 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:             1.280
  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:          0.520
  Check model and map are aligned:         0.110
  Set scattering table:                    0.140
  Process input model:                     30.690
  Find NCS groups from input model:        0.250
  Set up NCS constraints:                  0.060
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:12.330
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   45.390
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7932
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  13385  Z= 0.429
  Angle     :  0.578   5.495  18305  Z= 0.265
  Chirality :  0.040   0.157   2235
  Planarity :  0.003   0.029   2250
  Dihedral  : 12.018  89.842   5010
  Min Nonbonded Distance : 2.281

Molprobity Statistics.
  All-atom Clashscore : 8.00
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.00 %
    Favored  : 100.00 %
  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:  2.24 (0.21), residues: 1600
  helix:  3.04 (0.20), residues: 530
  sheet:  1.44 (0.25), residues: 495
  loop :  0.04 (0.26), residues: 575

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP D  91 
 HIS   0.001   0.000   HIS B 276 
 PHE   0.021   0.001   PHE C  72 
 TYR   0.009   0.001   TYR A 272 
 ARG   0.002   0.000   ARG A 200 

*********************** 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
  491 residues out of total 1430 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 491
  time to evaluate  : 1.484 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  124 GLU cc_start: 0.8389 (mp0) cc_final: 0.8073 (mp0)
REVERT: A  176 TYR cc_start: 0.8727 (m-80) cc_final: 0.8425 (m-80)
REVERT: A  184 GLU cc_start: 0.8121 (mt-10) cc_final: 0.7873 (mt-10)
REVERT: A  206 ASP cc_start: 0.8188 (t0) cc_final: 0.7831 (t0)
REVERT: A  208 LYS cc_start: 0.8308 (ptpt) cc_final: 0.8039 (mtmm)
REVERT: A  259 ILE cc_start: 0.9299 (pt) cc_final: 0.9050 (pp)
REVERT: A  272 TYR cc_start: 0.8625 (t80) cc_final: 0.8103 (t80)
REVERT: A  283 LEU cc_start: 0.8421 (mt) cc_final: 0.7824 (mp)
REVERT: A  297 PHE cc_start: 0.8570 (m-80) cc_final: 0.8119 (m-80)
REVERT: A  364 GLU cc_start: 0.7934 (mt-10) cc_final: 0.7640 (mt-10)
REVERT: B   75 ASP cc_start: 0.7925 (t0) cc_final: 0.7045 (t0)
REVERT: B  129 ASP cc_start: 0.8050 (t0) cc_final: 0.7833 (t0)
REVERT: B  206 ASP cc_start: 0.8133 (t0) cc_final: 0.7629 (t0)
REVERT: B  208 LYS cc_start: 0.8348 (ptpt) cc_final: 0.8081 (mtmm)
REVERT: B  259 ILE cc_start: 0.9220 (pt) cc_final: 0.8798 (pp)
REVERT: B  281 GLN cc_start: 0.8557 (mm110) cc_final: 0.8330 (pt0)
REVERT: B  283 LEU cc_start: 0.8378 (mt) cc_final: 0.7797 (mp)
REVERT: B  310 GLU cc_start: 0.8661 (tm-30) cc_final: 0.8341 (pp20)
REVERT: B  361 SER cc_start: 0.8191 (m) cc_final: 0.7662 (p)
REVERT: C   75 ASP cc_start: 0.8016 (t0) cc_final: 0.7206 (t0)
REVERT: C   77 LEU cc_start: 0.9344 (mt) cc_final: 0.9128 (mm)
REVERT: C  124 GLU cc_start: 0.8371 (mp0) cc_final: 0.7991 (mp0)
REVERT: C  129 ASP cc_start: 0.8026 (t0) cc_final: 0.7814 (t0)
REVERT: C  208 LYS cc_start: 0.8453 (ptpt) cc_final: 0.8157 (mtmm)
REVERT: C  279 LEU cc_start: 0.8964 (tp) cc_final: 0.8611 (tp)
REVERT: C  281 GLN cc_start: 0.8559 (mm110) cc_final: 0.8328 (tt0)
REVERT: C  283 LEU cc_start: 0.8597 (mt) cc_final: 0.8058 (mp)
REVERT: C  297 PHE cc_start: 0.8595 (m-80) cc_final: 0.8258 (m-10)
REVERT: C  361 SER cc_start: 0.8129 (m) cc_final: 0.7926 (p)
REVERT: D   75 ASP cc_start: 0.8025 (t0) cc_final: 0.7304 (t0)
REVERT: D   77 LEU cc_start: 0.9336 (mt) cc_final: 0.9082 (mm)
REVERT: D  124 GLU cc_start: 0.8357 (mp0) cc_final: 0.8040 (mp0)
REVERT: D  206 ASP cc_start: 0.8104 (t0) cc_final: 0.7884 (t0)
REVERT: D  259 ILE cc_start: 0.9437 (pt) cc_final: 0.9156 (pp)
REVERT: D  272 TYR cc_start: 0.8495 (t80) cc_final: 0.7830 (t80)
REVERT: D  279 LEU cc_start: 0.9006 (tp) cc_final: 0.8733 (tp)
REVERT: D  283 LEU cc_start: 0.8620 (mt) cc_final: 0.8066 (mp)
REVERT: D  297 PHE cc_start: 0.8572 (m-80) cc_final: 0.7882 (m-10)
REVERT: E   75 ASP cc_start: 0.8068 (t0) cc_final: 0.7406 (t0)
REVERT: E   77 LEU cc_start: 0.9319 (mt) cc_final: 0.9075 (mm)
REVERT: E  206 ASP cc_start: 0.8133 (t0) cc_final: 0.7782 (t0)
REVERT: E  208 LYS cc_start: 0.8310 (ptpt) cc_final: 0.7910 (mtmm)
REVERT: E  227 LYS cc_start: 0.8278 (ptmt) cc_final: 0.8042 (ptmt)
REVERT: E  272 TYR cc_start: 0.8636 (t80) cc_final: 0.8185 (t80)
REVERT: E  283 LEU cc_start: 0.8482 (mt) cc_final: 0.7935 (mp)
REVERT: E  297 PHE cc_start: 0.8564 (m-80) cc_final: 0.7960 (m-10)
  outliers start: 0
  outliers final: 1
  residues processed: 491
  average time/residue: 1.0779
  time to fit residues: 583.3206
Evaluate side-chains
  353 residues out of total 1430 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 352
  time to evaluate  : 1.624 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain E residue  142 ASP
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 160
   random chunks:
   chunk 135 optimal weight:    0.0870
   chunk 121 optimal weight:    1.9990
   chunk 67 optimal weight:    3.9990
   chunk 41 optimal weight:    6.9990
   chunk 81 optimal weight:    0.6980
   chunk 64 optimal weight:    0.6980
   chunk 125 optimal weight:    0.8980
   chunk 48 optimal weight:    5.9990
   chunk 76 optimal weight:    2.9990
   chunk 93 optimal weight:    0.6980
   chunk 145 optimal weight:    0.8980
   overall best weight:    0.6158

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

Flipped N/Q/H residues before XYZ refinement:
A 221 GLN
B 215 GLN
B 221 GLN
C 214 GLN
C 221 GLN
D 221 GLN
E 221 GLN

Total number of N/Q/H flips: 7

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3241 r_free = 0.3241 target = 0.097080 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3042 r_free = 0.3042 target = 0.084023 restraints weight = 20225.952|
|-----------------------------------------------------------------------------|
r_work (start): 0.3042 rms_B_bonded: 2.50
r_work: 0.2905 rms_B_bonded: 2.87 restraints_weight: 0.5000
r_work: 0.2758 rms_B_bonded: 4.82 restraints_weight: 0.2500
r_work (final): 0.2758
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2783
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2783 r_free = 0.2783    target_work(ls_wunit_k1) = 0.069         |
| occupancies: max = 1.00  min = 0.60   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2779 r_free = 0.2779    target_work(ls_wunit_k1) = 0.068         |
| occupancies: max = 1.00  min = 0.80   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2779
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8198
moved from start:          0.1720

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.025  13385  Z= 0.178
  Angle     :  0.514   7.656  18305  Z= 0.253
  Chirality :  0.039   0.142   2235
  Planarity :  0.004   0.031   2250
  Dihedral  :  5.852  59.449   2062
  Min Nonbonded Distance : 2.462

Molprobity Statistics.
  All-atom Clashscore : 8.84
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.69 %
    Favored  : 99.31 %
  Rotamer:
    Outliers :  2.52 %
    Allowed  : 14.20 %
    Favored  : 83.29 %
  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:  2.28 (0.21), residues: 1600
  helix:  3.21 (0.20), residues: 530
  sheet:  1.35 (0.24), residues: 465
  loop :  0.10 (0.26), residues: 605

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP E  91 
 HIS   0.002   0.000   HIS C 276 
 PHE   0.020   0.002   PHE A  72 
 TYR   0.019   0.002   TYR D 176 
 ARG   0.007   0.001   ARG C 257 

*********************** 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
  407 residues out of total 1430 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 371
  time to evaluate  : 1.610 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   48 GLU cc_start: 0.8478 (tp30) cc_final: 0.8058 (mm-30)
REVERT: A   75 ASP cc_start: 0.8382 (t0) cc_final: 0.8053 (t0)
REVERT: A   78 ARG cc_start: 0.8789 (mtp85) cc_final: 0.8568 (mtp85)
REVERT: A  160 GLU cc_start: 0.8536 (tt0) cc_final: 0.7778 (tm-30)
REVERT: A  176 TYR cc_start: 0.8805 (m-80) cc_final: 0.8529 (m-80)
REVERT: A  201 GLU cc_start: 0.8699 (mt-10) cc_final: 0.8307 (mp0)
REVERT: A  206 ASP cc_start: 0.8461 (t0) cc_final: 0.8088 (t0)
REVERT: A  208 LYS cc_start: 0.8479 (ptpt) cc_final: 0.8247 (mtmm)
REVERT: A  221 GLN cc_start: 0.8721 (tt0) cc_final: 0.8404 (tt0)
REVERT: A  272 TYR cc_start: 0.8852 (t80) cc_final: 0.8319 (t80)
REVERT: A  283 LEU cc_start: 0.8531 (mt) cc_final: 0.8029 (mp)
REVERT: A  297 PHE cc_start: 0.8772 (m-80) cc_final: 0.8404 (m-10)
REVERT: A  364 GLU cc_start: 0.8435 (mt-10) cc_final: 0.8121 (mt-10)
REVERT: B   48 GLU cc_start: 0.8539 (tp30) cc_final: 0.8234 (mm-30)
REVERT: B   54 ASN cc_start: 0.9000 (OUTLIER) cc_final: 0.8493 (m-40)
REVERT: B   75 ASP cc_start: 0.8231 (t0) cc_final: 0.7682 (t0)
REVERT: B  113 GLU cc_start: 0.8470 (OUTLIER) cc_final: 0.8013 (mp0)
REVERT: B  129 ASP cc_start: 0.8567 (t0) cc_final: 0.8217 (t0)
REVERT: B  154 GLU cc_start: 0.8670 (tt0) cc_final: 0.8412 (tt0)
REVERT: B  160 GLU cc_start: 0.8587 (tt0) cc_final: 0.7927 (tm-30)
REVERT: B  201 GLU cc_start: 0.8593 (mt-10) cc_final: 0.8242 (mp0)
REVERT: B  206 ASP cc_start: 0.8360 (t0) cc_final: 0.7816 (t0)
REVERT: B  259 ILE cc_start: 0.9351 (pt) cc_final: 0.9018 (mt)
REVERT: B  281 GLN cc_start: 0.8720 (mm110) cc_final: 0.8286 (pt0)
REVERT: B  283 LEU cc_start: 0.8450 (mt) cc_final: 0.8067 (mp)
REVERT: B  310 GLU cc_start: 0.8957 (tm-30) cc_final: 0.8660 (pp20)
REVERT: C   48 GLU cc_start: 0.8383 (tp30) cc_final: 0.8098 (mm-30)
REVERT: C   75 ASP cc_start: 0.8267 (t0) cc_final: 0.7707 (t0)
REVERT: C   77 LEU cc_start: 0.9267 (mt) cc_final: 0.9050 (mm)
REVERT: C  124 GLU cc_start: 0.8976 (mp0) cc_final: 0.8695 (mp0)
REVERT: C  129 ASP cc_start: 0.8568 (t0) cc_final: 0.8236 (t0)
REVERT: C  160 GLU cc_start: 0.8589 (tt0) cc_final: 0.7982 (tp30)
REVERT: C  201 GLU cc_start: 0.8586 (mt-10) cc_final: 0.8273 (mp0)
REVERT: C  208 LYS cc_start: 0.8598 (ptpt) cc_final: 0.8299 (mtmm)
REVERT: C  281 GLN cc_start: 0.8751 (mm110) cc_final: 0.8267 (pt0)
REVERT: C  283 LEU cc_start: 0.8711 (mt) cc_final: 0.8310 (mp)
REVERT: C  402 GLU cc_start: 0.8635 (mm-30) cc_final: 0.8373 (mt-10)
REVERT: D   75 ASP cc_start: 0.8394 (t0) cc_final: 0.7866 (t0)
REVERT: D   77 LEU cc_start: 0.9267 (mt) cc_final: 0.9036 (mm)
REVERT: D  124 GLU cc_start: 0.8847 (mp0) cc_final: 0.8342 (mp0)
REVERT: D  141 GLN cc_start: 0.8661 (OUTLIER) cc_final: 0.8060 (pm20)
REVERT: D  160 GLU cc_start: 0.8717 (tt0) cc_final: 0.8179 (tp30)
REVERT: D  188 GLN cc_start: 0.8323 (mt0) cc_final: 0.8115 (tt0)
REVERT: D  201 GLU cc_start: 0.8587 (mt-10) cc_final: 0.8346 (mp0)
REVERT: D  206 ASP cc_start: 0.8376 (t0) cc_final: 0.8083 (t0)
REVERT: D  208 LYS cc_start: 0.8661 (mtmm) cc_final: 0.8441 (mtmm)
REVERT: D  283 LEU cc_start: 0.8654 (mt) cc_final: 0.8235 (mp)
REVERT: D  402 GLU cc_start: 0.8535 (mm-30) cc_final: 0.8238 (mt-10)
REVERT: E   75 ASP cc_start: 0.8352 (t0) cc_final: 0.7893 (t0)
REVERT: E   77 LEU cc_start: 0.9219 (mt) cc_final: 0.8988 (mm)
REVERT: E   78 ARG cc_start: 0.8842 (mtp85) cc_final: 0.8625 (mtm110)
REVERT: E  113 GLU cc_start: 0.8578 (OUTLIER) cc_final: 0.8186 (mp0)
REVERT: E  160 GLU cc_start: 0.8741 (tt0) cc_final: 0.7894 (tm-30)
REVERT: E  201 GLU cc_start: 0.8626 (mt-10) cc_final: 0.8288 (mp0)
REVERT: E  206 ASP cc_start: 0.8392 (t0) cc_final: 0.8027 (t0)
REVERT: E  208 LYS cc_start: 0.8546 (ptpt) cc_final: 0.8190 (mtmm)
REVERT: E  272 TYR cc_start: 0.8862 (t80) cc_final: 0.8362 (t80)
REVERT: E  283 LEU cc_start: 0.8550 (mt) cc_final: 0.8077 (mp)
REVERT: E  297 PHE cc_start: 0.8818 (m-80) cc_final: 0.8382 (m-10)
REVERT: E  370 PHE cc_start: 0.8726 (t80) cc_final: 0.8500 (t80)
REVERT: E  390 MET cc_start: 0.8043 (mmt) cc_final: 0.7825 (mmt)
REVERT: E  402 GLU cc_start: 0.8487 (mm-30) cc_final: 0.8247 (mt-10)
  outliers start: 36
  outliers final: 14
  residues processed: 388
  average time/residue: 1.2167
  time to fit residues: 516.6186
Evaluate side-chains
  355 residues out of total 1430 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 337
  time to evaluate  : 1.479 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  117 THR
Chi-restraints excluded: chain A residue  179 SER
Chi-restraints excluded: chain A residue  183 MET
Chi-restraints excluded: chain A residue  211 VAL
Chi-restraints excluded: chain A residue  302 LEU
Chi-restraints excluded: chain B residue   54 ASN
Chi-restraints excluded: chain B residue  113 GLU
Chi-restraints excluded: chain B residue  179 SER
Chi-restraints excluded: chain B residue  235 ILE
Chi-restraints excluded: chain C residue  179 SER
Chi-restraints excluded: chain C residue  304 LEU
Chi-restraints excluded: chain D residue  141 GLN
Chi-restraints excluded: chain D residue  153 THR
Chi-restraints excluded: chain D residue  179 SER
Chi-restraints excluded: chain D residue  304 LEU
Chi-restraints excluded: chain E residue  113 GLU
Chi-restraints excluded: chain E residue  142 ASP
Chi-restraints excluded: chain E residue  198 VAL
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 160
   random chunks:
   chunk 107 optimal weight:    0.9990
   chunk 88 optimal weight:    3.9990
   chunk 65 optimal weight:    7.9990
   chunk 98 optimal weight:    4.9990
   chunk 63 optimal weight:    9.9990
   chunk 114 optimal weight:    0.9980
   chunk 42 optimal weight:    0.9980
   chunk 53 optimal weight:    2.9990
   chunk 105 optimal weight:    4.9990
   chunk 92 optimal weight:    4.9990
   chunk 102 optimal weight:    2.9990
   overall best weight:    1.7986

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

Flipped N/Q/H residues before XYZ refinement:
A 156 ASN
B 221 GLN
** C 156 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 221 GLN
** D 156 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
D 221 GLN
E 156 ASN
E 382 GLN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3190 r_free = 0.3190 target = 0.094348 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.2985 r_free = 0.2985 target = 0.080267 restraints weight = 20461.817|
|-----------------------------------------------------------------------------|
r_work (start): 0.2974 rms_B_bonded: 2.79
r_work: 0.2808 rms_B_bonded: 3.20 restraints_weight: 0.5000
r_work (final): 0.2808
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2804
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2804 r_free = 0.2804    target_work(ls_wunit_k1) = 0.070         |
| occupancies: max = 1.00  min = 0.80   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2803 r_free = 0.2803    target_work(ls_wunit_k1) = 0.070         |
| occupancies: max = 1.00  min = 0.86   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2803
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8048
moved from start:          0.2385

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.031  13385  Z= 0.326
  Angle     :  0.555   8.406  18305  Z= 0.273
  Chirality :  0.041   0.217   2235
  Planarity :  0.004   0.036   2250
  Dihedral  :  5.556  55.683   2062
  Min Nonbonded Distance : 2.426

Molprobity Statistics.
  All-atom Clashscore : 8.99
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.88 %
    Favored  : 99.12 %
  Rotamer:
    Outliers :  3.71 %
    Allowed  : 14.90 %
    Favored  : 81.40 %
  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:  1.90 (0.21), residues: 1600
  helix:  2.85 (0.20), residues: 530
  sheet:  1.28 (0.25), residues: 430
  loop : -0.12 (0.25), residues: 640

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP A 112 
 HIS   0.003   0.001   HIS E 103 
 PHE   0.021   0.002   PHE A  72 
 TYR   0.019   0.002   TYR E 176 
 ARG   0.007   0.001   ARG B  78 

*********************** 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
  399 residues out of total 1430 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 53
    poor density    : 346
  time to evaluate  : 1.530 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   48 GLU cc_start: 0.8375 (tp30) cc_final: 0.7938 (mm-30)
REVERT: A   75 ASP cc_start: 0.8169 (t0) cc_final: 0.7777 (t0)
REVERT: A   78 ARG cc_start: 0.8700 (mtp85) cc_final: 0.8454 (mtp85)
REVERT: A  132 ASP cc_start: 0.8230 (m-30) cc_final: 0.7954 (t0)
REVERT: A  160 GLU cc_start: 0.8403 (tt0) cc_final: 0.7553 (tm-30)
REVERT: A  176 TYR cc_start: 0.8741 (m-80) cc_final: 0.8227 (m-80)
REVERT: A  201 GLU cc_start: 0.8662 (mt-10) cc_final: 0.8330 (mp0)
REVERT: A  206 ASP cc_start: 0.8339 (t0) cc_final: 0.7892 (t0)
REVERT: A  208 LYS cc_start: 0.8448 (ptpt) cc_final: 0.8125 (mtmm)
REVERT: A  272 TYR cc_start: 0.8782 (t80) cc_final: 0.8167 (t80)
REVERT: A  281 GLN cc_start: 0.8703 (mm110) cc_final: 0.8279 (pt0)
REVERT: A  283 LEU cc_start: 0.8682 (mt) cc_final: 0.8270 (mp)
REVERT: A  297 PHE cc_start: 0.8688 (m-80) cc_final: 0.8302 (m-10)
REVERT: A  364 GLU cc_start: 0.8247 (mt-10) cc_final: 0.7767 (mt-10)
REVERT: B   75 ASP cc_start: 0.7913 (t0) cc_final: 0.7394 (t0)
REVERT: B  129 ASP cc_start: 0.8529 (t0) cc_final: 0.8047 (t0)
REVERT: B  146 LYS cc_start: 0.8451 (OUTLIER) cc_final: 0.7639 (mttp)
REVERT: B  199 LYS cc_start: 0.8185 (ptpt) cc_final: 0.7742 (ptmm)
REVERT: B  201 GLU cc_start: 0.8512 (mt-10) cc_final: 0.8163 (mp0)
REVERT: B  206 ASP cc_start: 0.8288 (t0) cc_final: 0.7648 (t0)
REVERT: B  208 LYS cc_start: 0.8422 (mtmm) cc_final: 0.8149 (mtmm)
REVERT: B  233 SER cc_start: 0.8669 (OUTLIER) cc_final: 0.8469 (p)
REVERT: B  281 GLN cc_start: 0.8731 (mm110) cc_final: 0.8324 (pt0)
REVERT: B  283 LEU cc_start: 0.8566 (mt) cc_final: 0.8155 (mp)
REVERT: C   75 ASP cc_start: 0.8070 (t0) cc_final: 0.7419 (t0)
REVERT: C  113 GLU cc_start: 0.8997 (mp0) cc_final: 0.8734 (mp0)
REVERT: C  129 ASP cc_start: 0.8623 (t0) cc_final: 0.8180 (t0)
REVERT: C  146 LYS cc_start: 0.8431 (mtpt) cc_final: 0.7741 (mtmp)
REVERT: C  160 GLU cc_start: 0.8536 (tt0) cc_final: 0.7986 (mm-30)
REVERT: C  184 GLU cc_start: 0.8417 (mt-10) cc_final: 0.7907 (pt0)
REVERT: C  201 GLU cc_start: 0.8631 (mt-10) cc_final: 0.8334 (mp0)
REVERT: C  208 LYS cc_start: 0.8460 (ptpt) cc_final: 0.8179 (mtmm)
REVERT: C  232 LYS cc_start: 0.8623 (ttmt) cc_final: 0.8347 (ttmt)
REVERT: C  233 SER cc_start: 0.8712 (m) cc_final: 0.8485 (p)
REVERT: C  281 GLN cc_start: 0.8803 (mm110) cc_final: 0.8265 (pt0)
REVERT: C  283 LEU cc_start: 0.8764 (mt) cc_final: 0.8376 (mp)
REVERT: C  402 GLU cc_start: 0.8531 (mm-30) cc_final: 0.8278 (mt-10)
REVERT: D   48 GLU cc_start: 0.8312 (tp30) cc_final: 0.8028 (mm-30)
REVERT: D   75 ASP cc_start: 0.8164 (t0) cc_final: 0.7530 (t0)
REVERT: D   77 LEU cc_start: 0.9243 (mt) cc_final: 0.9004 (mm)
REVERT: D  124 GLU cc_start: 0.8723 (mp0) cc_final: 0.8326 (mp0)
REVERT: D  154 GLU cc_start: 0.8860 (tt0) cc_final: 0.8632 (tt0)
REVERT: D  184 GLU cc_start: 0.8298 (mt-10) cc_final: 0.7769 (pt0)
REVERT: D  201 GLU cc_start: 0.8491 (mt-10) cc_final: 0.8262 (mp0)
REVERT: D  206 ASP cc_start: 0.8272 (t0) cc_final: 0.7849 (t0)
REVERT: D  208 LYS cc_start: 0.8493 (mtmm) cc_final: 0.8182 (mtmm)
REVERT: D  214 GLN cc_start: 0.8189 (mm-40) cc_final: 0.7989 (mm-40)
REVERT: D  272 TYR cc_start: 0.8786 (t80) cc_final: 0.7828 (t80)
REVERT: D  281 GLN cc_start: 0.8688 (mm110) cc_final: 0.8385 (mm-40)
REVERT: D  283 LEU cc_start: 0.8734 (mt) cc_final: 0.8364 (mp)
REVERT: D  402 GLU cc_start: 0.8445 (mm-30) cc_final: 0.8169 (mt-10)
REVERT: E   75 ASP cc_start: 0.8124 (t0) cc_final: 0.7544 (t0)
REVERT: E   77 LEU cc_start: 0.9198 (mt) cc_final: 0.8915 (mm)
REVERT: E   78 ARG cc_start: 0.8733 (mtp85) cc_final: 0.8487 (mtp85)
REVERT: E  146 LYS cc_start: 0.8482 (mtpt) cc_final: 0.7732 (mtmp)
REVERT: E  160 GLU cc_start: 0.8653 (tt0) cc_final: 0.8167 (mm-30)
REVERT: E  198 VAL cc_start: 0.9302 (OUTLIER) cc_final: 0.9002 (m)
REVERT: E  201 GLU cc_start: 0.8579 (mt-10) cc_final: 0.8259 (mp0)
REVERT: E  206 ASP cc_start: 0.8264 (t0) cc_final: 0.7827 (t0)
REVERT: E  208 LYS cc_start: 0.8369 (ptpt) cc_final: 0.7962 (mtmm)
REVERT: E  283 LEU cc_start: 0.8660 (mt) cc_final: 0.8322 (mp)
  outliers start: 53
  outliers final: 20
  residues processed: 370
  average time/residue: 1.1006
  time to fit residues: 449.1876
Evaluate side-chains
  344 residues out of total 1430 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 321
  time to evaluate  : 1.660 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  117 THR
Chi-restraints excluded: chain A residue  179 SER
Chi-restraints excluded: chain A residue  211 VAL
Chi-restraints excluded: chain A residue  302 LEU
Chi-restraints excluded: chain A residue  372 LEU
Chi-restraints excluded: chain B residue   54 ASN
Chi-restraints excluded: chain B residue  113 GLU
Chi-restraints excluded: chain B residue  146 LYS
Chi-restraints excluded: chain B residue  179 SER
Chi-restraints excluded: chain B residue  210 GLN
Chi-restraints excluded: chain B residue  233 SER
Chi-restraints excluded: chain B residue  253 LEU
Chi-restraints excluded: chain C residue  179 SER
Chi-restraints excluded: chain C residue  198 VAL
Chi-restraints excluded: chain C residue  235 ILE
Chi-restraints excluded: chain D residue  153 THR
Chi-restraints excluded: chain D residue  179 SER
Chi-restraints excluded: chain D residue  183 MET
Chi-restraints excluded: chain D residue  235 ILE
Chi-restraints excluded: chain E residue  142 ASP
Chi-restraints excluded: chain E residue  198 VAL
Chi-restraints excluded: chain E residue  237 LEU
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:    3.9990
   chunk 83 optimal weight:    0.0970
   chunk 135 optimal weight:    0.9980
   chunk 5 optimal weight:    0.0870
   chunk 138 optimal weight:    0.9980
   chunk 15 optimal weight:    0.9990
   chunk 106 optimal weight:    0.9980
   chunk 113 optimal weight:    0.9990
   chunk 46 optimal weight:    0.9990
   chunk 148 optimal weight:    4.9990
   chunk 98 optimal weight:    1.9990
   overall best weight:    0.6356

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

Flipped N/Q/H residues before XYZ refinement:
** A 156 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 221 GLN
** C 156 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 221 GLN
** D 156 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
E 156 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3219 r_free = 0.3219 target = 0.096203 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3005 r_free = 0.3005 target = 0.081618 restraints weight = 20037.920|
|-----------------------------------------------------------------------------|
r_work (start): 0.3024 rms_B_bonded: 2.89
r_work: 0.2863 rms_B_bonded: 3.27 restraints_weight: 0.5000
r_work (final): 0.2863
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2839
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2839 r_free = 0.2839    target_work(ls_wunit_k1) = 0.072         |
| occupancies: max = 1.00  min = 0.86   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2839 r_free = 0.2839    target_work(ls_wunit_k1) = 0.072         |
| occupancies: max = 1.00  min = 0.88   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2839
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7937
moved from start:          0.2436

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.026  13385  Z= 0.167
  Angle     :  0.510   8.431  18305  Z= 0.249
  Chirality :  0.039   0.180   2235
  Planarity :  0.004   0.030   2250
  Dihedral  :  5.414  55.686   2062
  Min Nonbonded Distance : 2.448

Molprobity Statistics.
  All-atom Clashscore : 8.19
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.94 %
    Favored  : 99.06 %
  Rotamer:
    Outliers :  3.15 %
    Allowed  : 16.99 %
    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:  1.97 (0.21), residues: 1600
  helix:  2.95 (0.20), residues: 530
  sheet:  0.84 (0.24), residues: 475
  loop :  0.25 (0.27), residues: 595

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP E 112 
 HIS   0.001   0.000   HIS C 276 
 PHE   0.017   0.002   PHE B 385 
 TYR   0.015   0.002   TYR E 176 
 ARG   0.008   0.000   ARG C 257 

*********************** 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
  378 residues out of total 1430 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 45
    poor density    : 333
  time to evaluate  : 1.519 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   75 ASP cc_start: 0.8093 (t0) cc_final: 0.7645 (t0)
REVERT: A   78 ARG cc_start: 0.8573 (mtp85) cc_final: 0.8332 (mtp85)
REVERT: A  141 GLN cc_start: 0.8501 (OUTLIER) cc_final: 0.7927 (pm20)
REVERT: A  153 THR cc_start: 0.9120 (p) cc_final: 0.8861 (t)
REVERT: A  201 GLU cc_start: 0.8546 (mt-10) cc_final: 0.8174 (mp0)
REVERT: A  206 ASP cc_start: 0.8289 (t0) cc_final: 0.7850 (t0)
REVERT: A  208 LYS cc_start: 0.8340 (ptpt) cc_final: 0.8034 (mtmm)
REVERT: A  232 LYS cc_start: 0.8485 (ttmt) cc_final: 0.8063 (ttmm)
REVERT: A  272 TYR cc_start: 0.8686 (t80) cc_final: 0.8033 (t80)
REVERT: A  281 GLN cc_start: 0.8679 (mm110) cc_final: 0.8258 (pt0)
REVERT: A  283 LEU cc_start: 0.8496 (mt) cc_final: 0.8167 (mp)
REVERT: A  297 PHE cc_start: 0.8544 (m-80) cc_final: 0.8136 (m-10)
REVERT: A  364 GLU cc_start: 0.8175 (mt-10) cc_final: 0.7685 (mt-10)
REVERT: B   75 ASP cc_start: 0.7825 (t0) cc_final: 0.7272 (t0)
REVERT: B  129 ASP cc_start: 0.8542 (t0) cc_final: 0.8027 (t0)
REVERT: B  146 LYS cc_start: 0.8398 (mtmt) cc_final: 0.7583 (mttp)
REVERT: B  160 GLU cc_start: 0.8389 (mm-30) cc_final: 0.8041 (mm-30)
REVERT: B  199 LYS cc_start: 0.8011 (ptpt) cc_final: 0.7762 (ptmt)
REVERT: B  201 GLU cc_start: 0.8395 (mt-10) cc_final: 0.8060 (mp0)
REVERT: B  206 ASP cc_start: 0.8246 (t0) cc_final: 0.7649 (t0)
REVERT: B  279 LEU cc_start: 0.8922 (tp) cc_final: 0.8690 (tt)
REVERT: B  281 GLN cc_start: 0.8722 (mm110) cc_final: 0.8332 (pt0)
REVERT: B  283 LEU cc_start: 0.8525 (mt) cc_final: 0.8153 (mp)
REVERT: B  296 TYR cc_start: 0.8317 (t80) cc_final: 0.8076 (t80)
REVERT: C   75 ASP cc_start: 0.7972 (t0) cc_final: 0.7283 (t0)
REVERT: C   77 LEU cc_start: 0.9185 (mt) cc_final: 0.8949 (mm)
REVERT: C  113 GLU cc_start: 0.9046 (mp0) cc_final: 0.8583 (mp0)
REVERT: C  129 ASP cc_start: 0.8588 (t0) cc_final: 0.8110 (t0)
REVERT: C  146 LYS cc_start: 0.8372 (mtpt) cc_final: 0.7685 (mtmp)
REVERT: C  160 GLU cc_start: 0.8509 (tt0) cc_final: 0.7912 (mm-30)
REVERT: C  184 GLU cc_start: 0.8301 (mt-10) cc_final: 0.7713 (pt0)
REVERT: C  201 GLU cc_start: 0.8574 (mt-10) cc_final: 0.8262 (mp0)
REVERT: C  208 LYS cc_start: 0.8372 (ptpt) cc_final: 0.8087 (mtmm)
REVERT: C  232 LYS cc_start: 0.8544 (ttmt) cc_final: 0.8311 (ttmt)
REVERT: C  233 SER cc_start: 0.8682 (m) cc_final: 0.8388 (p)
REVERT: C  281 GLN cc_start: 0.8711 (mm110) cc_final: 0.8162 (pt0)
REVERT: C  283 LEU cc_start: 0.8688 (mt) cc_final: 0.8369 (mp)
REVERT: C  402 GLU cc_start: 0.8486 (mm-30) cc_final: 0.8237 (mt-10)
REVERT: D   75 ASP cc_start: 0.8090 (t0) cc_final: 0.7387 (t0)
REVERT: D   77 LEU cc_start: 0.9167 (mt) cc_final: 0.8925 (mm)
REVERT: D   78 ARG cc_start: 0.8763 (mtp85) cc_final: 0.8452 (mtp85)
REVERT: D  160 GLU cc_start: 0.8690 (OUTLIER) cc_final: 0.8318 (mm-30)
REVERT: D  184 GLU cc_start: 0.8284 (mt-10) cc_final: 0.7723 (pt0)
REVERT: D  201 GLU cc_start: 0.8441 (mt-10) cc_final: 0.8178 (mp0)
REVERT: D  206 ASP cc_start: 0.8224 (t0) cc_final: 0.7821 (t0)
REVERT: D  208 LYS cc_start: 0.8458 (mtmm) cc_final: 0.8128 (mtmm)
REVERT: D  281 GLN cc_start: 0.8644 (mm110) cc_final: 0.8109 (pt0)
REVERT: D  283 LEU cc_start: 0.8628 (mt) cc_final: 0.8065 (mp)
REVERT: D  402 GLU cc_start: 0.8436 (mm-30) cc_final: 0.8144 (mt-10)
REVERT: E   75 ASP cc_start: 0.8034 (t0) cc_final: 0.7392 (t0)
REVERT: E   77 LEU cc_start: 0.9071 (mt) cc_final: 0.8836 (mm)
REVERT: E   78 ARG cc_start: 0.8646 (mtp85) cc_final: 0.8428 (mtp85)
REVERT: E  113 GLU cc_start: 0.9010 (mp0) cc_final: 0.8557 (mp0)
REVERT: E  146 LYS cc_start: 0.8385 (mtpt) cc_final: 0.7646 (mtmp)
REVERT: E  160 GLU cc_start: 0.8621 (tt0) cc_final: 0.8125 (mm-30)
REVERT: E  184 GLU cc_start: 0.8116 (mt-10) cc_final: 0.7902 (mt-10)
REVERT: E  188 GLN cc_start: 0.7994 (mt0) cc_final: 0.7683 (tt0)
REVERT: E  198 VAL cc_start: 0.9255 (OUTLIER) cc_final: 0.8950 (m)
REVERT: E  201 GLU cc_start: 0.8502 (mt-10) cc_final: 0.8158 (mp0)
REVERT: E  206 ASP cc_start: 0.8209 (t0) cc_final: 0.7772 (t0)
REVERT: E  208 LYS cc_start: 0.8289 (ptpt) cc_final: 0.7852 (mtmm)
REVERT: E  279 LEU cc_start: 0.8904 (tp) cc_final: 0.8692 (tt)
REVERT: E  283 LEU cc_start: 0.8510 (mt) cc_final: 0.8060 (mp)
  outliers start: 45
  outliers final: 20
  residues processed: 356
  average time/residue: 1.0504
  time to fit residues: 413.7145
Evaluate side-chains
  343 residues out of total 1430 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 320
  time to evaluate  : 1.546 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  141 GLN
Chi-restraints excluded: chain A residue  179 SER
Chi-restraints excluded: chain A residue  211 VAL
Chi-restraints excluded: chain A residue  253 LEU
Chi-restraints excluded: chain A residue  302 LEU
Chi-restraints excluded: chain B residue   54 ASN
Chi-restraints excluded: chain B residue  179 SER
Chi-restraints excluded: chain B residue  246 LEU
Chi-restraints excluded: chain B residue  253 LEU
Chi-restraints excluded: chain B residue  277 SER
Chi-restraints excluded: chain C residue   54 ASN
Chi-restraints excluded: chain C residue  179 SER
Chi-restraints excluded: chain C residue  198 VAL
Chi-restraints excluded: chain C residue  304 LEU
Chi-restraints excluded: chain D residue  153 THR
Chi-restraints excluded: chain D residue  160 GLU
Chi-restraints excluded: chain D residue  179 SER
Chi-restraints excluded: chain D residue  235 ILE
Chi-restraints excluded: chain E residue  156 ASN
Chi-restraints excluded: chain E residue  198 VAL
Chi-restraints excluded: chain E residue  233 SER
Chi-restraints excluded: chain E residue  237 LEU
Chi-restraints excluded: chain E residue  277 SER
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:    5.9990
   chunk 98 optimal weight:    0.7980
   chunk 151 optimal weight:    6.9990
   chunk 114 optimal weight:    1.9990
   chunk 122 optimal weight:    2.9990
   chunk 34 optimal weight:    0.5980
   chunk 111 optimal weight:    0.7980
   chunk 35 optimal weight:    5.9990
   chunk 102 optimal weight:    3.9990
   chunk 127 optimal weight:   10.0000
   overall best weight:    1.4384

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

Flipped N/Q/H residues before XYZ refinement:
** A 156 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 221 GLN
B 221 GLN
C 156 ASN
C 221 GLN
D 156 ASN
D 221 GLN
D 382 GLN
E 156 ASN

Total number of N/Q/H flips: 8

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3152 r_free = 0.3152 target = 0.091204 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 29)----------------|
| r_work = 0.2945 r_free = 0.2945 target = 0.078105 restraints weight = 20677.675|
|-----------------------------------------------------------------------------|
r_work (start): 0.2934 rms_B_bonded: 2.45
r_work: 0.2793 rms_B_bonded: 2.82 restraints_weight: 0.5000
r_work: 0.2644 rms_B_bonded: 4.69 restraints_weight: 0.2500
r_work (final): 0.2644
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2667
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2667 r_free = 0.2667    target_work(ls_wunit_k1) = 0.063         |
| occupancies: max = 1.00  min = 0.88   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2667 r_free = 0.2667    target_work(ls_wunit_k1) = 0.063         |
| occupancies: max = 1.00  min = 0.90   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2667
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8342
moved from start:          0.2667

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.029  13385  Z= 0.265
  Angle     :  0.528   8.791  18305  Z= 0.257
  Chirality :  0.040   0.139   2235
  Planarity :  0.004   0.034   2250
  Dihedral  :  5.124  52.376   2060
  Min Nonbonded Distance : 2.441

Molprobity Statistics.
  All-atom Clashscore : 8.23
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.00 %
    Favored  : 99.00 %
  Rotamer:
    Outliers :  3.36 %
    Allowed  : 17.69 %
    Favored  : 78.95 %
  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:  2.87 (0.20), residues: 530
  sheet:  0.72 (0.24), residues: 475
  loop :  0.20 (0.27), residues: 595

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP E 112 
 HIS   0.002   0.000   HIS E 103 
 PHE   0.019   0.002   PHE D  72 
 TYR   0.019   0.002   TYR D 176 
 ARG   0.011   0.000   ARG C 257 

*********************** 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
  390 residues out of total 1430 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 48
    poor density    : 342
  time to evaluate  : 1.641 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   75 ASP cc_start: 0.8449 (t0) cc_final: 0.8079 (t0)
REVERT: A  201 GLU cc_start: 0.8809 (mt-10) cc_final: 0.8473 (mp0)
REVERT: A  206 ASP cc_start: 0.8475 (t0) cc_final: 0.8113 (t0)
REVERT: A  207 LEU cc_start: 0.9341 (OUTLIER) cc_final: 0.9140 (mp)
REVERT: A  208 LYS cc_start: 0.8616 (ptpt) cc_final: 0.8334 (mtmm)
REVERT: A  272 TYR cc_start: 0.8970 (t80) cc_final: 0.8417 (t80)
REVERT: A  281 GLN cc_start: 0.8727 (mm110) cc_final: 0.8328 (pt0)
REVERT: A  283 LEU cc_start: 0.8590 (mt) cc_final: 0.8254 (mp)
REVERT: A  297 PHE cc_start: 0.8913 (m-80) cc_final: 0.8580 (m-10)
REVERT: A  364 GLU cc_start: 0.8512 (mt-10) cc_final: 0.8118 (mt-10)
REVERT: B   75 ASP cc_start: 0.8292 (t0) cc_final: 0.7802 (t0)
REVERT: B  129 ASP cc_start: 0.8824 (t0) cc_final: 0.8334 (t0)
REVERT: B  146 LYS cc_start: 0.8791 (mtmt) cc_final: 0.8092 (mttp)
REVERT: B  160 GLU cc_start: 0.8769 (mm-30) cc_final: 0.8381 (mm-30)
REVERT: B  201 GLU cc_start: 0.8671 (mt-10) cc_final: 0.8332 (mp0)
REVERT: B  206 ASP cc_start: 0.8414 (t0) cc_final: 0.7918 (t0)
REVERT: B  279 LEU cc_start: 0.9057 (tp) cc_final: 0.8788 (tt)
REVERT: B  281 GLN cc_start: 0.8777 (mm110) cc_final: 0.8390 (pt0)
REVERT: B  283 LEU cc_start: 0.8546 (mt) cc_final: 0.8209 (mp)
REVERT: B  296 TYR cc_start: 0.8615 (t80) cc_final: 0.8400 (t80)
REVERT: C   75 ASP cc_start: 0.8392 (t0) cc_final: 0.7790 (t0)
REVERT: C   77 LEU cc_start: 0.9409 (mt) cc_final: 0.9204 (mm)
REVERT: C  113 GLU cc_start: 0.9073 (mp0) cc_final: 0.8702 (mp0)
REVERT: C  129 ASP cc_start: 0.8825 (t0) cc_final: 0.8350 (t0)
REVERT: C  146 LYS cc_start: 0.8709 (mtpt) cc_final: 0.8108 (mtmp)
REVERT: C  160 GLU cc_start: 0.8580 (tt0) cc_final: 0.8159 (mm-30)
REVERT: C  184 GLU cc_start: 0.8644 (mt-10) cc_final: 0.8171 (pt0)
REVERT: C  199 LYS cc_start: 0.8339 (OUTLIER) cc_final: 0.7631 (ptmm)
REVERT: C  201 GLU cc_start: 0.8806 (mt-10) cc_final: 0.8514 (mp0)
REVERT: C  233 SER cc_start: 0.8837 (m) cc_final: 0.8623 (p)
REVERT: C  281 GLN cc_start: 0.8750 (mm110) cc_final: 0.8252 (pt0)
REVERT: C  283 LEU cc_start: 0.8671 (mt) cc_final: 0.8359 (mp)
REVERT: C  402 GLU cc_start: 0.8653 (mm-30) cc_final: 0.8413 (mt-10)
REVERT: D   48 GLU cc_start: 0.8575 (tp30) cc_final: 0.8289 (mm-30)
REVERT: D   75 ASP cc_start: 0.8451 (t0) cc_final: 0.7821 (t0)
REVERT: D   78 ARG cc_start: 0.8994 (mtp85) cc_final: 0.8625 (mtp85)
REVERT: D  124 GLU cc_start: 0.8949 (mp0) cc_final: 0.8593 (mp0)
REVERT: D  146 LYS cc_start: 0.8664 (OUTLIER) cc_final: 0.8075 (mttp)
REVERT: D  160 GLU cc_start: 0.8803 (OUTLIER) cc_final: 0.8309 (tp30)
REVERT: D  199 LYS cc_start: 0.8413 (ptpt) cc_final: 0.8142 (ptmm)
REVERT: D  201 GLU cc_start: 0.8734 (mt-10) cc_final: 0.8469 (mp0)
REVERT: D  206 ASP cc_start: 0.8465 (t0) cc_final: 0.8133 (t0)
REVERT: D  208 LYS cc_start: 0.8744 (mtmm) cc_final: 0.8525 (mtmm)
REVERT: D  272 TYR cc_start: 0.8952 (t80) cc_final: 0.8101 (t80)
REVERT: D  281 GLN cc_start: 0.8663 (mm110) cc_final: 0.8184 (pt0)
REVERT: D  283 LEU cc_start: 0.8727 (mt) cc_final: 0.8419 (mp)
REVERT: D  402 GLU cc_start: 0.8572 (mm-30) cc_final: 0.8333 (mt-10)
REVERT: E   75 ASP cc_start: 0.8414 (t0) cc_final: 0.7810 (t0)
REVERT: E   77 LEU cc_start: 0.9323 (mt) cc_final: 0.9106 (mm)
REVERT: E   78 ARG cc_start: 0.8885 (mtp85) cc_final: 0.8680 (mtp85)
REVERT: E  113 GLU cc_start: 0.9107 (mp0) cc_final: 0.8677 (mp0)
REVERT: E  146 LYS cc_start: 0.8742 (mtpt) cc_final: 0.8080 (mtmp)
REVERT: E  160 GLU cc_start: 0.8722 (OUTLIER) cc_final: 0.8345 (mm-30)
REVERT: E  198 VAL cc_start: 0.9357 (OUTLIER) cc_final: 0.9045 (m)
REVERT: E  201 GLU cc_start: 0.8738 (mt-10) cc_final: 0.8420 (mp0)
REVERT: E  206 ASP cc_start: 0.8435 (t0) cc_final: 0.8097 (t0)
REVERT: E  208 LYS cc_start: 0.8610 (ptpt) cc_final: 0.8187 (mtmm)
REVERT: E  279 LEU cc_start: 0.9089 (tp) cc_final: 0.8873 (tt)
REVERT: E  283 LEU cc_start: 0.8649 (mt) cc_final: 0.8318 (mp)
  outliers start: 48
  outliers final: 27
  residues processed: 372
  average time/residue: 1.1139
  time to fit residues: 457.9235
Evaluate side-chains
  364 residues out of total 1430 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 331
  time to evaluate  : 1.636 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  179 SER
Chi-restraints excluded: chain A residue  207 LEU
Chi-restraints excluded: chain A residue  211 VAL
Chi-restraints excluded: chain A residue  253 LEU
Chi-restraints excluded: chain A residue  302 LEU
Chi-restraints excluded: chain A residue  372 LEU
Chi-restraints excluded: chain B residue   54 ASN
Chi-restraints excluded: chain B residue  179 SER
Chi-restraints excluded: chain B residue  246 LEU
Chi-restraints excluded: chain B residue  253 LEU
Chi-restraints excluded: chain C residue   54 ASN
Chi-restraints excluded: chain C residue  179 SER
Chi-restraints excluded: chain C residue  198 VAL
Chi-restraints excluded: chain C residue  199 LYS
Chi-restraints excluded: chain C residue  235 ILE
Chi-restraints excluded: chain C residue  237 LEU
Chi-restraints excluded: chain C residue  304 LEU
Chi-restraints excluded: chain D residue  146 LYS
Chi-restraints excluded: chain D residue  153 THR
Chi-restraints excluded: chain D residue  160 GLU
Chi-restraints excluded: chain D residue  179 SER
Chi-restraints excluded: chain D residue  235 ILE
Chi-restraints excluded: chain D residue  277 SER
Chi-restraints excluded: chain D residue  304 LEU
Chi-restraints excluded: chain E residue  123 LEU
Chi-restraints excluded: chain E residue  155 THR
Chi-restraints excluded: chain E residue  160 GLU
Chi-restraints excluded: chain E residue  198 VAL
Chi-restraints excluded: chain E residue  233 SER
Chi-restraints excluded: chain E residue  237 LEU
Chi-restraints excluded: chain E residue  253 LEU
Chi-restraints excluded: chain E residue  277 SER
Chi-restraints excluded: chain E residue  379 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:    1.9990
   chunk 125 optimal weight:    1.9990
   chunk 39 optimal weight:    3.9990
   chunk 151 optimal weight:    2.9990
   chunk 101 optimal weight:    2.9990
   chunk 89 optimal weight:    3.9990
   chunk 124 optimal weight:    2.9990
   chunk 20 optimal weight:    0.5980
   chunk 155 optimal weight:    2.9990
   chunk 75 optimal weight:    4.9990
   overall best weight:    2.1188

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

Flipped N/Q/H residues before XYZ refinement:
A 156 ASN
A 221 GLN
C 156 ASN
** D 156 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
D 221 GLN
** E 156 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3120 r_free = 0.3120 target = 0.089233 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.2908 r_free = 0.2908 target = 0.075928 restraints weight = 20910.256|
|-----------------------------------------------------------------------------|
r_work (start): 0.2901 rms_B_bonded: 2.50
r_work: 0.2755 rms_B_bonded: 2.86 restraints_weight: 0.5000
r_work: 0.2605 rms_B_bonded: 4.73 restraints_weight: 0.2500
r_work (final): 0.2605
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2626
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2626 r_free = 0.2626    target_work(ls_wunit_k1) = 0.061         |
| occupancies: max = 1.00  min = 0.90   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2626 r_free = 0.2626    target_work(ls_wunit_k1) = 0.061         |
| occupancies: max = 1.00  min = 0.90   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2626
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8292
moved from start:          0.2844

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.042  13385  Z= 0.360
  Angle     :  0.569   8.963  18305  Z= 0.278
  Chirality :  0.041   0.144   2235
  Planarity :  0.004   0.033   2250
  Dihedral  :  5.024  48.926   2060
  Min Nonbonded Distance : 2.444

Molprobity Statistics.
  All-atom Clashscore : 8.95
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.31 %
    Favored  : 98.69 %
  Rotamer:
    Outliers :  3.64 %
    Allowed  : 18.53 %
    Favored  : 77.83 %
  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:  1.66 (0.21), residues: 1600
  helix:  2.71 (0.20), residues: 530
  sheet:  0.58 (0.24), residues: 475
  loop :  0.13 (0.26), residues: 595

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP E 112 
 HIS   0.002   0.001   HIS E 103 
 PHE   0.022   0.002   PHE A  72 
 TYR   0.021   0.002   TYR D 176 
 ARG   0.009   0.000   ARG C 257 

*********************** 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
  375 residues out of total 1430 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 52
    poor density    : 323
  time to evaluate  : 1.604 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   48 GLU cc_start: 0.8569 (tp30) cc_final: 0.8144 (mm-30)
REVERT: A   75 ASP cc_start: 0.8393 (t0) cc_final: 0.7983 (t0)
REVERT: A  132 ASP cc_start: 0.8405 (m-30) cc_final: 0.8134 (t0)
REVERT: A  146 LYS cc_start: 0.8680 (mtpt) cc_final: 0.8092 (mttp)
REVERT: A  176 TYR cc_start: 0.9313 (m-80) cc_final: 0.8643 (m-80)
REVERT: A  201 GLU cc_start: 0.8792 (mt-10) cc_final: 0.8425 (mp0)
REVERT: A  206 ASP cc_start: 0.8516 (t0) cc_final: 0.8148 (t0)
REVERT: A  208 LYS cc_start: 0.8561 (ptpt) cc_final: 0.8246 (mtmm)
REVERT: A  232 LYS cc_start: 0.8651 (ttmt) cc_final: 0.8268 (ttmm)
REVERT: A  272 TYR cc_start: 0.8959 (t80) cc_final: 0.8291 (t80)
REVERT: A  281 GLN cc_start: 0.8797 (mm110) cc_final: 0.8352 (pt0)
REVERT: A  283 LEU cc_start: 0.8610 (mt) cc_final: 0.8294 (mp)
REVERT: A  297 PHE cc_start: 0.8877 (m-80) cc_final: 0.8506 (m-10)
REVERT: A  364 GLU cc_start: 0.8489 (mt-10) cc_final: 0.8064 (mt-10)
REVERT: B   75 ASP cc_start: 0.8239 (t0) cc_final: 0.7704 (t0)
REVERT: B  129 ASP cc_start: 0.8786 (t0) cc_final: 0.8258 (t0)
REVERT: B  146 LYS cc_start: 0.8727 (OUTLIER) cc_final: 0.8014 (mttp)
REVERT: B  201 GLU cc_start: 0.8708 (mt-10) cc_final: 0.8323 (mp0)
REVERT: B  206 ASP cc_start: 0.8406 (t0) cc_final: 0.7896 (t0)
REVERT: B  279 LEU cc_start: 0.9034 (tp) cc_final: 0.8765 (tt)
REVERT: B  281 GLN cc_start: 0.8759 (mm110) cc_final: 0.8318 (pt0)
REVERT: B  283 LEU cc_start: 0.8545 (mt) cc_final: 0.8201 (mp)
REVERT: C   75 ASP cc_start: 0.8336 (t0) cc_final: 0.7722 (t0)
REVERT: C   77 LEU cc_start: 0.9373 (mt) cc_final: 0.9117 (mm)
REVERT: C  113 GLU cc_start: 0.9125 (mp0) cc_final: 0.8731 (mp0)
REVERT: C  129 ASP cc_start: 0.8788 (t0) cc_final: 0.8253 (t0)
REVERT: C  146 LYS cc_start: 0.8656 (mtpt) cc_final: 0.8032 (mtmp)
REVERT: C  160 GLU cc_start: 0.8597 (tt0) cc_final: 0.8149 (mm-30)
REVERT: C  201 GLU cc_start: 0.8821 (mt-10) cc_final: 0.8489 (mp0)
REVERT: C  208 LYS cc_start: 0.8655 (mtmm) cc_final: 0.8375 (mtmm)
REVERT: C  281 GLN cc_start: 0.8763 (mm110) cc_final: 0.8278 (pt0)
REVERT: C  283 LEU cc_start: 0.8670 (mt) cc_final: 0.8335 (mp)
REVERT: C  402 GLU cc_start: 0.8647 (mm-30) cc_final: 0.8387 (mt-10)
REVERT: D   75 ASP cc_start: 0.8371 (t0) cc_final: 0.7746 (t0)
REVERT: D  146 LYS cc_start: 0.8591 (OUTLIER) cc_final: 0.7967 (mttp)
REVERT: D  160 GLU cc_start: 0.8824 (OUTLIER) cc_final: 0.8487 (mm-30)
REVERT: D  184 GLU cc_start: 0.8708 (mt-10) cc_final: 0.8244 (pt0)
REVERT: D  199 LYS cc_start: 0.8471 (ptpt) cc_final: 0.8137 (ptmm)
REVERT: D  201 GLU cc_start: 0.8737 (mt-10) cc_final: 0.8435 (mp0)
REVERT: D  206 ASP cc_start: 0.8487 (t0) cc_final: 0.8076 (t0)
REVERT: D  208 LYS cc_start: 0.8686 (mtmm) cc_final: 0.8438 (mtmm)
REVERT: D  272 TYR cc_start: 0.8971 (t80) cc_final: 0.8139 (t80)
REVERT: D  281 GLN cc_start: 0.8734 (mm110) cc_final: 0.8423 (mm-40)
REVERT: D  283 LEU cc_start: 0.8702 (mt) cc_final: 0.8319 (mp)
REVERT: D  402 GLU cc_start: 0.8546 (mm-30) cc_final: 0.8274 (mt-10)
REVERT: E   75 ASP cc_start: 0.8358 (t0) cc_final: 0.7695 (t0)
REVERT: E   77 LEU cc_start: 0.9285 (mt) cc_final: 0.9062 (mm)
REVERT: E  113 GLU cc_start: 0.9175 (mp0) cc_final: 0.8905 (mp0)
REVERT: E  132 ASP cc_start: 0.7913 (t0) cc_final: 0.7629 (t0)
REVERT: E  146 LYS cc_start: 0.8679 (mtpt) cc_final: 0.7996 (mtmp)
REVERT: E  160 GLU cc_start: 0.8777 (OUTLIER) cc_final: 0.8372 (mm-30)
REVERT: E  167 ASP cc_start: 0.9416 (p0) cc_final: 0.9059 (p0)
REVERT: E  201 GLU cc_start: 0.8724 (mt-10) cc_final: 0.8408 (mp0)
REVERT: E  206 ASP cc_start: 0.8439 (t0) cc_final: 0.8153 (t0)
REVERT: E  279 LEU cc_start: 0.9078 (tp) cc_final: 0.8864 (tt)
REVERT: E  283 LEU cc_start: 0.8694 (mt) cc_final: 0.8296 (mp)
  outliers start: 52
  outliers final: 24
  residues processed: 351
  average time/residue: 1.1170
  time to fit residues: 432.0866
Evaluate side-chains
  337 residues out of total 1430 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 309
  time to evaluate  : 1.535 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  179 SER
Chi-restraints excluded: chain A residue  253 LEU
Chi-restraints excluded: chain A residue  302 LEU
Chi-restraints excluded: chain A residue  372 LEU
Chi-restraints excluded: chain B residue   54 ASN
Chi-restraints excluded: chain B residue  146 LYS
Chi-restraints excluded: chain B residue  179 SER
Chi-restraints excluded: chain B residue  233 SER
Chi-restraints excluded: chain B residue  246 LEU
Chi-restraints excluded: chain B residue  253 LEU
Chi-restraints excluded: chain C residue  179 SER
Chi-restraints excluded: chain C residue  198 VAL
Chi-restraints excluded: chain C residue  235 ILE
Chi-restraints excluded: chain C residue  304 LEU
Chi-restraints excluded: chain D residue  146 LYS
Chi-restraints excluded: chain D residue  153 THR
Chi-restraints excluded: chain D residue  160 GLU
Chi-restraints excluded: chain D residue  179 SER
Chi-restraints excluded: chain D residue  235 ILE
Chi-restraints excluded: chain E residue  123 LEU
Chi-restraints excluded: chain E residue  155 THR
Chi-restraints excluded: chain E residue  160 GLU
Chi-restraints excluded: chain E residue  198 VAL
Chi-restraints excluded: chain E residue  233 SER
Chi-restraints excluded: chain E residue  237 LEU
Chi-restraints excluded: chain E residue  253 LEU
Chi-restraints excluded: chain E residue  372 LEU
Chi-restraints excluded: chain E residue  379 LEU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 160
   random chunks:
   chunk 95 optimal weight:    9.9990
   chunk 28 optimal weight:    3.9990
   chunk 122 optimal weight:    3.9990
   chunk 136 optimal weight:    4.9990
   chunk 157 optimal weight:    0.6980
   chunk 135 optimal weight:    0.6980
   chunk 3 optimal weight:    1.9990
   chunk 71 optimal weight:    0.9980
   chunk 100 optimal weight:    0.8980
   chunk 105 optimal weight:    0.9990
   chunk 108 optimal weight:    3.9990
   overall best weight:    0.8582

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

Flipped N/Q/H residues before XYZ refinement:
A 156 ASN
A 221 GLN
C 156 ASN
C 221 GLN
** D 156 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E 156 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3150 r_free = 0.3150 target = 0.091167 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.2942 r_free = 0.2942 target = 0.078044 restraints weight = 20544.680|
|-----------------------------------------------------------------------------|
r_work (start): 0.2937 rms_B_bonded: 2.43
r_work: 0.2796 rms_B_bonded: 2.81 restraints_weight: 0.5000
r_work: 0.2647 rms_B_bonded: 4.68 restraints_weight: 0.2500
r_work (final): 0.2647
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2685
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2685 r_free = 0.2685    target_work(ls_wunit_k1) = 0.064         |
| occupancies: max = 1.00  min = 0.90   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2685 r_free = 0.2685    target_work(ls_wunit_k1) = 0.064         |
| occupancies: max = 1.00  min = 0.90   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2685
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8333
moved from start:          0.2880

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029  13385  Z= 0.191
  Angle     :  0.533   9.299  18305  Z= 0.259
  Chirality :  0.039   0.186   2235
  Planarity :  0.004   0.027   2250
  Dihedral  :  4.734  44.639   2060
  Min Nonbonded Distance : 2.479

Molprobity Statistics.
  All-atom Clashscore : 7.97
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.12 %
    Favored  : 98.88 %
  Rotamer:
    Outliers :  2.80 %
    Allowed  : 20.00 %
    Favored  : 77.20 %
  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:  1.76 (0.21), residues: 1600
  helix:  2.85 (0.20), residues: 530
  sheet:  0.56 (0.24), residues: 475
  loop :  0.21 (0.27), residues: 595

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP A 112 
 HIS   0.001   0.000   HIS E 276 
 PHE   0.020   0.002   PHE A 385 
 TYR   0.020   0.002   TYR D 176 
 ARG   0.010   0.000   ARG C 257 

*********************** 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
  371 residues out of total 1430 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 40
    poor density    : 331
  time to evaluate  : 1.439 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   75 ASP cc_start: 0.8382 (t0) cc_final: 0.8034 (t0)
REVERT: A   81 MET cc_start: 0.9017 (ttp) cc_final: 0.8695 (ptt)
REVERT: A  132 ASP cc_start: 0.8331 (m-30) cc_final: 0.8117 (t0)
REVERT: A  153 THR cc_start: 0.9347 (p) cc_final: 0.9052 (t)
REVERT: A  201 GLU cc_start: 0.8764 (mt-10) cc_final: 0.8426 (mp0)
REVERT: A  206 ASP cc_start: 0.8475 (t0) cc_final: 0.8143 (t0)
REVERT: A  208 LYS cc_start: 0.8606 (ptpt) cc_final: 0.8265 (mtmm)
REVERT: A  232 LYS cc_start: 0.8709 (ttmt) cc_final: 0.8343 (ttmm)
REVERT: A  272 TYR cc_start: 0.8942 (t80) cc_final: 0.8289 (t80)
REVERT: A  281 GLN cc_start: 0.8728 (mm110) cc_final: 0.8327 (pt0)
REVERT: A  283 LEU cc_start: 0.8608 (mt) cc_final: 0.8200 (mp)
REVERT: A  296 TYR cc_start: 0.8454 (t80) cc_final: 0.8236 (t80)
REVERT: A  297 PHE cc_start: 0.8893 (m-80) cc_final: 0.8494 (m-10)
REVERT: A  364 GLU cc_start: 0.8530 (mt-10) cc_final: 0.8118 (mt-10)
REVERT: B   75 ASP cc_start: 0.8302 (t0) cc_final: 0.7789 (t0)
REVERT: B   78 ARG cc_start: 0.8767 (mtp85) cc_final: 0.8562 (mtp85)
REVERT: B  129 ASP cc_start: 0.8839 (t0) cc_final: 0.8341 (t0)
REVERT: B  146 LYS cc_start: 0.8794 (mtmt) cc_final: 0.8120 (mttp)
REVERT: B  201 GLU cc_start: 0.8647 (mt-10) cc_final: 0.8262 (mp0)
REVERT: B  206 ASP cc_start: 0.8377 (t0) cc_final: 0.7910 (t0)
REVERT: B  232 LYS cc_start: 0.8706 (ttmt) cc_final: 0.8386 (ttmm)
REVERT: B  260 GLU cc_start: 0.8927 (pm20) cc_final: 0.8397 (pm20)
REVERT: B  281 GLN cc_start: 0.8705 (mm110) cc_final: 0.8316 (pt0)
REVERT: B  283 LEU cc_start: 0.8555 (mt) cc_final: 0.8210 (mp)
REVERT: C   75 ASP cc_start: 0.8407 (t0) cc_final: 0.7970 (t0)
REVERT: C   77 LEU cc_start: 0.9374 (mt) cc_final: 0.9156 (mm)
REVERT: C  113 GLU cc_start: 0.9103 (mp0) cc_final: 0.8744 (mp0)
REVERT: C  129 ASP cc_start: 0.8833 (t0) cc_final: 0.8231 (t0)
REVERT: C  146 LYS cc_start: 0.8718 (mtpt) cc_final: 0.8128 (mtmp)
REVERT: C  160 GLU cc_start: 0.8572 (tt0) cc_final: 0.8148 (mm-30)
REVERT: C  184 GLU cc_start: 0.8736 (mt-10) cc_final: 0.8329 (pt0)
REVERT: C  201 GLU cc_start: 0.8773 (mt-10) cc_final: 0.8475 (mp0)
REVERT: C  208 LYS cc_start: 0.8727 (mtmm) cc_final: 0.8428 (mtmm)
REVERT: C  238 LEU cc_start: 0.8728 (OUTLIER) cc_final: 0.8486 (mm)
REVERT: C  281 GLN cc_start: 0.8717 (mm110) cc_final: 0.8218 (pt0)
REVERT: C  402 GLU cc_start: 0.8650 (mm-30) cc_final: 0.8437 (mt-10)
REVERT: D   75 ASP cc_start: 0.8438 (t0) cc_final: 0.7816 (t0)
REVERT: D  160 GLU cc_start: 0.8797 (OUTLIER) cc_final: 0.8546 (mm-30)
REVERT: D  184 GLU cc_start: 0.8647 (mt-10) cc_final: 0.8281 (pt0)
REVERT: D  199 LYS cc_start: 0.8416 (ptpt) cc_final: 0.8122 (ptmm)
REVERT: D  201 GLU cc_start: 0.8740 (mt-10) cc_final: 0.8458 (mp0)
REVERT: D  206 ASP cc_start: 0.8473 (t0) cc_final: 0.8113 (t0)
REVERT: D  208 LYS cc_start: 0.8727 (mtmm) cc_final: 0.8493 (mtmm)
REVERT: D  272 TYR cc_start: 0.8951 (t80) cc_final: 0.8056 (t80)
REVERT: D  281 GLN cc_start: 0.8664 (mm110) cc_final: 0.8247 (pt0)
REVERT: D  283 LEU cc_start: 0.8736 (mt) cc_final: 0.8237 (mp)
REVERT: D  402 GLU cc_start: 0.8580 (mm-30) cc_final: 0.8312 (mt-10)
REVERT: E   75 ASP cc_start: 0.8393 (t0) cc_final: 0.7937 (t0)
REVERT: E  113 GLU cc_start: 0.9140 (mp0) cc_final: 0.8912 (mp0)
REVERT: E  146 LYS cc_start: 0.8760 (mtpt) cc_final: 0.8085 (mttp)
REVERT: E  160 GLU cc_start: 0.8775 (OUTLIER) cc_final: 0.8411 (mm-30)
REVERT: E  167 ASP cc_start: 0.9425 (p0) cc_final: 0.9085 (p0)
REVERT: E  198 VAL cc_start: 0.9374 (OUTLIER) cc_final: 0.9011 (m)
REVERT: E  201 GLU cc_start: 0.8691 (mt-10) cc_final: 0.8371 (mp0)
REVERT: E  206 ASP cc_start: 0.8429 (t0) cc_final: 0.8078 (t0)
REVERT: E  208 LYS cc_start: 0.8750 (mtmm) cc_final: 0.8235 (mtmm)
REVERT: E  227 LYS cc_start: 0.8836 (ptmt) cc_final: 0.8530 (ptpp)
REVERT: E  232 LYS cc_start: 0.8797 (ttmt) cc_final: 0.8418 (ttmm)
REVERT: E  272 TYR cc_start: 0.8957 (t80) cc_final: 0.8222 (t80)
REVERT: E  283 LEU cc_start: 0.8637 (mt) cc_final: 0.8184 (mp)
  outliers start: 40
  outliers final: 20
  residues processed: 354
  average time/residue: 1.0805
  time to fit residues: 422.6135
Evaluate side-chains
  353 residues out of total 1430 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 329
  time to evaluate  : 1.393 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  179 SER
Chi-restraints excluded: chain A residue  253 LEU
Chi-restraints excluded: chain A residue  302 LEU
Chi-restraints excluded: chain B residue   54 ASN
Chi-restraints excluded: chain B residue  179 SER
Chi-restraints excluded: chain B residue  246 LEU
Chi-restraints excluded: chain B residue  253 LEU
Chi-restraints excluded: chain C residue  179 SER
Chi-restraints excluded: chain C residue  198 VAL
Chi-restraints excluded: chain C residue  238 LEU
Chi-restraints excluded: chain C residue  304 LEU
Chi-restraints excluded: chain D residue  153 THR
Chi-restraints excluded: chain D residue  160 GLU
Chi-restraints excluded: chain D residue  179 SER
Chi-restraints excluded: chain D residue  235 ILE
Chi-restraints excluded: chain D residue  253 LEU
Chi-restraints excluded: chain D residue  277 SER
Chi-restraints excluded: chain E residue  123 LEU
Chi-restraints excluded: chain E residue  142 ASP
Chi-restraints excluded: chain E residue  155 THR
Chi-restraints excluded: chain E residue  160 GLU
Chi-restraints excluded: chain E residue  198 VAL
Chi-restraints excluded: chain E residue  237 LEU
Chi-restraints excluded: chain E residue  253 LEU
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:    1.9990
   chunk 153 optimal weight:    4.9990
   chunk 89 optimal weight:    4.9990
   chunk 101 optimal weight:    0.0270
   chunk 27 optimal weight:    2.9990
   chunk 28 optimal weight:    2.9990
   chunk 8 optimal weight:    1.9990
   chunk 116 optimal weight:    2.9990
   chunk 50 optimal weight:    1.9990
   chunk 71 optimal weight:    4.9990
   overall best weight:    1.8046

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

Flipped N/Q/H residues before XYZ refinement:
A 156 ASN
A 221 GLN
C 156 ASN
** D 156 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E 156 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3122 r_free = 0.3122 target = 0.089387 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.2908 r_free = 0.2908 target = 0.076043 restraints weight = 20856.863|
|-----------------------------------------------------------------------------|
r_work (start): 0.2914 rms_B_bonded: 2.49
r_work: 0.2773 rms_B_bonded: 2.84 restraints_weight: 0.5000
r_work: 0.2627 rms_B_bonded: 4.71 restraints_weight: 0.2500
r_work (final): 0.2627
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2628
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2628 r_free = 0.2628    target_work(ls_wunit_k1) = 0.061         |
| occupancies: max = 1.00  min = 0.90   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2628 r_free = 0.2628    target_work(ls_wunit_k1) = 0.061         |
| occupancies: max = 1.00  min = 0.90   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2628
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8288
moved from start:          0.3057

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.046  13385  Z= 0.322
  Angle     :  0.577   9.445  18305  Z= 0.281
  Chirality :  0.041   0.174   2235
  Planarity :  0.004   0.035   2250
  Dihedral  :  4.534  37.029   2060
  Min Nonbonded Distance : 2.501

Molprobity Statistics.
  All-atom Clashscore : 8.80
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.25 %
    Favored  : 98.75 %
  Rotamer:
    Outliers :  2.80 %
    Allowed  : 20.49 %
    Favored  : 76.71 %
  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:  1.58 (0.21), residues: 1600
  helix:  2.77 (0.20), residues: 525
  sheet:  0.73 (0.24), residues: 430
  loop : -0.14 (0.26), residues: 645

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP E 112 
 HIS   0.002   0.001   HIS E 103 
 PHE   0.025   0.002   PHE A 385 
 TYR   0.025   0.002   TYR B 176 
 ARG   0.014   0.000   ARG C 257 

*********************** 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
  374 residues out of total 1430 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 40
    poor density    : 334
  time to evaluate  : 1.644 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   48 GLU cc_start: 0.8584 (tp30) cc_final: 0.8155 (mm-30)
REVERT: A   75 ASP cc_start: 0.8367 (t0) cc_final: 0.7962 (t0)
REVERT: A   81 MET cc_start: 0.9062 (ttp) cc_final: 0.8773 (ptt)
REVERT: A  132 ASP cc_start: 0.8395 (m-30) cc_final: 0.8099 (t0)
REVERT: A  146 LYS cc_start: 0.8688 (mtpt) cc_final: 0.8103 (mttp)
REVERT: A  201 GLU cc_start: 0.8768 (mt-10) cc_final: 0.8405 (mp0)
REVERT: A  206 ASP cc_start: 0.8495 (t0) cc_final: 0.8142 (t0)
REVERT: A  208 LYS cc_start: 0.8567 (ptpt) cc_final: 0.8217 (mtmm)
REVERT: A  272 TYR cc_start: 0.8939 (t80) cc_final: 0.8278 (t80)
REVERT: A  281 GLN cc_start: 0.8792 (mm110) cc_final: 0.8330 (pt0)
REVERT: A  283 LEU cc_start: 0.8584 (mt) cc_final: 0.8266 (mp)
REVERT: A  296 TYR cc_start: 0.8439 (t80) cc_final: 0.8238 (t80)
REVERT: A  297 PHE cc_start: 0.8881 (m-80) cc_final: 0.8574 (m-80)
REVERT: A  364 GLU cc_start: 0.8517 (mt-10) cc_final: 0.8094 (mt-10)
REVERT: B   75 ASP cc_start: 0.8216 (t0) cc_final: 0.7686 (t0)
REVERT: B  129 ASP cc_start: 0.8776 (t0) cc_final: 0.8226 (t0)
REVERT: B  201 GLU cc_start: 0.8671 (mt-10) cc_final: 0.8267 (mp0)
REVERT: B  206 ASP cc_start: 0.8394 (t0) cc_final: 0.7944 (t0)
REVERT: B  260 GLU cc_start: 0.8909 (pm20) cc_final: 0.8361 (pm20)
REVERT: B  281 GLN cc_start: 0.8720 (mm110) cc_final: 0.8358 (pt0)
REVERT: C   48 GLU cc_start: 0.8493 (tp30) cc_final: 0.8229 (mm-30)
REVERT: C   75 ASP cc_start: 0.8342 (t0) cc_final: 0.8036 (t0)
REVERT: C   77 LEU cc_start: 0.9403 (mt) cc_final: 0.9176 (mm)
REVERT: C  113 GLU cc_start: 0.9130 (mp0) cc_final: 0.8785 (mp0)
REVERT: C  124 GLU cc_start: 0.8977 (mp0) cc_final: 0.8646 (mp0)
REVERT: C  129 ASP cc_start: 0.8771 (t0) cc_final: 0.8172 (t0)
REVERT: C  146 LYS cc_start: 0.8645 (mtpt) cc_final: 0.8014 (mtmp)
REVERT: C  160 GLU cc_start: 0.8589 (tt0) cc_final: 0.8062 (tp30)
REVERT: C  184 GLU cc_start: 0.8751 (mt-10) cc_final: 0.8283 (pt0)
REVERT: C  201 GLU cc_start: 0.8793 (mt-10) cc_final: 0.8446 (mp0)
REVERT: C  208 LYS cc_start: 0.8654 (mtmm) cc_final: 0.8400 (mtmm)
REVERT: C  232 LYS cc_start: 0.8632 (ttmt) cc_final: 0.8333 (tppp)
REVERT: C  281 GLN cc_start: 0.8770 (mm110) cc_final: 0.8282 (pt0)
REVERT: C  364 GLU cc_start: 0.8619 (mp0) cc_final: 0.8366 (mt-10)
REVERT: C  402 GLU cc_start: 0.8646 (mm-30) cc_final: 0.8408 (mt-10)
REVERT: D   48 GLU cc_start: 0.8542 (tp30) cc_final: 0.8253 (mm-30)
REVERT: D   75 ASP cc_start: 0.8383 (t0) cc_final: 0.7704 (t0)
REVERT: D  160 GLU cc_start: 0.8830 (OUTLIER) cc_final: 0.8297 (tp30)
REVERT: D  184 GLU cc_start: 0.8689 (mt-10) cc_final: 0.8218 (pt0)
REVERT: D  199 LYS cc_start: 0.8493 (ptpt) cc_final: 0.8196 (ptmm)
REVERT: D  201 GLU cc_start: 0.8747 (mt-10) cc_final: 0.8425 (mp0)
REVERT: D  206 ASP cc_start: 0.8481 (t0) cc_final: 0.8074 (t0)
REVERT: D  208 LYS cc_start: 0.8676 (mtmm) cc_final: 0.8421 (mtmm)
REVERT: D  272 TYR cc_start: 0.8961 (t80) cc_final: 0.8092 (t80)
REVERT: D  281 GLN cc_start: 0.8723 (mm110) cc_final: 0.8403 (mm-40)
REVERT: D  283 LEU cc_start: 0.8726 (mt) cc_final: 0.8310 (mp)
REVERT: D  402 GLU cc_start: 0.8572 (mm-30) cc_final: 0.8313 (mt-10)
REVERT: E   75 ASP cc_start: 0.8305 (t0) cc_final: 0.7963 (t0)
REVERT: E  113 GLU cc_start: 0.9178 (mp0) cc_final: 0.8930 (mp0)
REVERT: E  132 ASP cc_start: 0.7933 (t0) cc_final: 0.7626 (t0)
REVERT: E  146 LYS cc_start: 0.8664 (mtpt) cc_final: 0.7990 (mtmp)
REVERT: E  160 GLU cc_start: 0.8788 (OUTLIER) cc_final: 0.8397 (mm-30)
REVERT: E  167 ASP cc_start: 0.9426 (p0) cc_final: 0.9084 (p0)
REVERT: E  201 GLU cc_start: 0.8716 (mt-10) cc_final: 0.8410 (mp0)
REVERT: E  206 ASP cc_start: 0.8434 (t0) cc_final: 0.8062 (t0)
REVERT: E  208 LYS cc_start: 0.8757 (mtmm) cc_final: 0.8279 (mtmm)
REVERT: E  283 LEU cc_start: 0.8696 (mt) cc_final: 0.8469 (mp)
  outliers start: 40
  outliers final: 21
  residues processed: 357
  average time/residue: 1.2326
  time to fit residues: 482.0141
Evaluate side-chains
  344 residues out of total 1430 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 321
  time to evaluate  : 1.497 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  179 SER
Chi-restraints excluded: chain A residue  253 LEU
Chi-restraints excluded: chain A residue  302 LEU
Chi-restraints excluded: chain A residue  372 LEU
Chi-restraints excluded: chain B residue   54 ASN
Chi-restraints excluded: chain B residue  179 SER
Chi-restraints excluded: chain B residue  233 SER
Chi-restraints excluded: chain B residue  246 LEU
Chi-restraints excluded: chain B residue  253 LEU
Chi-restraints excluded: chain C residue  179 SER
Chi-restraints excluded: chain C residue  198 VAL
Chi-restraints excluded: chain C residue  235 ILE
Chi-restraints excluded: chain C residue  304 LEU
Chi-restraints excluded: chain D residue  153 THR
Chi-restraints excluded: chain D residue  160 GLU
Chi-restraints excluded: chain D residue  179 SER
Chi-restraints excluded: chain D residue  235 ILE
Chi-restraints excluded: chain E residue  123 LEU
Chi-restraints excluded: chain E residue  155 THR
Chi-restraints excluded: chain E residue  160 GLU
Chi-restraints excluded: chain E residue  237 LEU
Chi-restraints excluded: chain E residue  277 SER
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:    3.9990
   chunk 23 optimal weight:    4.9990
   chunk 128 optimal weight:    3.9990
   chunk 81 optimal weight:    0.9980
   chunk 25 optimal weight:    3.9990
   chunk 43 optimal weight:    0.8980
   chunk 106 optimal weight:    4.9990
   chunk 112 optimal weight:    3.9990
   chunk 75 optimal weight:    0.8980
   chunk 137 optimal weight:    3.9990
   chunk 13 optimal weight:    0.7980
   overall best weight:    1.5182

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

Flipped N/Q/H residues before XYZ refinement:
A 156 ASN
A 221 GLN
C 156 ASN
** D 156 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
D 382 GLN
** E 156 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3125 r_free = 0.3125 target = 0.089609 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.2910 r_free = 0.2910 target = 0.076341 restraints weight = 20486.806|
|-----------------------------------------------------------------------------|
r_work (start): 0.2912 rms_B_bonded: 2.43
r_work: 0.2770 rms_B_bonded: 2.80 restraints_weight: 0.5000
r_work: 0.2623 rms_B_bonded: 4.64 restraints_weight: 0.2500
r_work (final): 0.2623
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2658
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2658 r_free = 0.2658    target_work(ls_wunit_k1) = 0.062         |
| occupancies: max = 1.00  min = 0.90   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2658 r_free = 0.2658    target_work(ls_wunit_k1) = 0.062         |
| occupancies: max = 1.00  min = 0.91   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2658
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8353
moved from start:          0.3088

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.043  13385  Z= 0.280
  Angle     :  0.568   9.623  18305  Z= 0.277
  Chirality :  0.040   0.142   2235
  Planarity :  0.004   0.039   2250
  Dihedral  :  4.412  31.631   2060
  Min Nonbonded Distance : 2.543

Molprobity Statistics.
  All-atom Clashscore : 9.18
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.50 %
    Favored  : 98.50 %
  Rotamer:
    Outliers :  2.52 %
    Allowed  : 20.84 %
    Favored  : 76.64 %
  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:  1.59 (0.21), residues: 1600
  helix:  2.72 (0.20), residues: 530
  sheet:  0.68 (0.24), residues: 430
  loop : -0.06 (0.26), residues: 640

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP E 112 
 HIS   0.002   0.000   HIS E 276 
 PHE   0.022   0.002   PHE A 385 
 TYR   0.020   0.002   TYR D 176 
 ARG   0.017   0.001   ARG C 257 

*********************** 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
  367 residues out of total 1430 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 331
  time to evaluate  : 1.557 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   75 ASP cc_start: 0.8382 (t0) cc_final: 0.7997 (t0)
REVERT: A   81 MET cc_start: 0.9041 (ttp) cc_final: 0.8754 (ptt)
REVERT: A  146 LYS cc_start: 0.8755 (mtpt) cc_final: 0.8191 (mttp)
REVERT: A  201 GLU cc_start: 0.8807 (mt-10) cc_final: 0.8440 (mp0)
REVERT: A  206 ASP cc_start: 0.8512 (t0) cc_final: 0.8192 (t0)
REVERT: A  232 LYS cc_start: 0.8706 (ttmt) cc_final: 0.8282 (ttmm)
REVERT: A  272 TYR cc_start: 0.8973 (t80) cc_final: 0.8335 (t80)
REVERT: A  281 GLN cc_start: 0.8795 (mm110) cc_final: 0.8395 (pt0)
REVERT: A  283 LEU cc_start: 0.8590 (mt) cc_final: 0.8200 (mp)
REVERT: A  297 PHE cc_start: 0.8930 (m-80) cc_final: 0.8571 (m-10)
REVERT: A  364 GLU cc_start: 0.8558 (mt-10) cc_final: 0.8118 (mt-10)
REVERT: B   48 GLU cc_start: 0.8652 (tp30) cc_final: 0.8421 (tp30)
REVERT: B   75 ASP cc_start: 0.8308 (t0) cc_final: 0.7795 (t0)
REVERT: B  129 ASP cc_start: 0.8807 (t0) cc_final: 0.8402 (t0)
REVERT: B  146 LYS cc_start: 0.8797 (mtmt) cc_final: 0.8132 (mttp)
REVERT: B  201 GLU cc_start: 0.8707 (mt-10) cc_final: 0.8312 (mp0)
REVERT: B  206 ASP cc_start: 0.8396 (t0) cc_final: 0.7979 (t0)
REVERT: B  232 LYS cc_start: 0.8708 (ttmt) cc_final: 0.8383 (ttmm)
REVERT: B  260 GLU cc_start: 0.8927 (pm20) cc_final: 0.8385 (pm20)
REVERT: B  281 GLN cc_start: 0.8717 (mm110) cc_final: 0.8358 (pt0)
REVERT: B  364 GLU cc_start: 0.8724 (mt-10) cc_final: 0.8473 (mt-10)
REVERT: C   48 GLU cc_start: 0.8544 (tp30) cc_final: 0.8284 (mm-30)
REVERT: C   75 ASP cc_start: 0.8414 (t0) cc_final: 0.7950 (t0)
REVERT: C   77 LEU cc_start: 0.9434 (mt) cc_final: 0.9221 (mm)
REVERT: C   81 MET cc_start: 0.9126 (ttp) cc_final: 0.8856 (ptm)
REVERT: C  113 GLU cc_start: 0.9123 (mp0) cc_final: 0.8815 (mp0)
REVERT: C  124 GLU cc_start: 0.8994 (mp0) cc_final: 0.8686 (mp0)
REVERT: C  129 ASP cc_start: 0.8827 (t0) cc_final: 0.8278 (t0)
REVERT: C  146 LYS cc_start: 0.8733 (mtpt) cc_final: 0.8140 (mtmp)
REVERT: C  160 GLU cc_start: 0.8572 (tt0) cc_final: 0.8091 (tp30)
REVERT: C  201 GLU cc_start: 0.8794 (mt-10) cc_final: 0.8466 (mp0)
REVERT: C  232 LYS cc_start: 0.8692 (ttmt) cc_final: 0.8365 (tppp)
REVERT: C  281 GLN cc_start: 0.8738 (mm110) cc_final: 0.8266 (pt0)
REVERT: C  364 GLU cc_start: 0.8668 (mp0) cc_final: 0.8435 (mt-10)
REVERT: C  402 GLU cc_start: 0.8666 (mm-30) cc_final: 0.8443 (mt-10)
REVERT: D   75 ASP cc_start: 0.8443 (t0) cc_final: 0.7789 (t0)
REVERT: D  146 LYS cc_start: 0.8700 (mtmt) cc_final: 0.8130 (mttp)
REVERT: D  160 GLU cc_start: 0.8833 (OUTLIER) cc_final: 0.8600 (mm-30)
REVERT: D  184 GLU cc_start: 0.8695 (mt-10) cc_final: 0.8266 (pt0)
REVERT: D  199 LYS cc_start: 0.8509 (ptpt) cc_final: 0.8221 (ptmm)
REVERT: D  201 GLU cc_start: 0.8768 (mt-10) cc_final: 0.8454 (mp0)
REVERT: D  206 ASP cc_start: 0.8492 (t0) cc_final: 0.8115 (t0)
REVERT: D  208 LYS cc_start: 0.8722 (mtmm) cc_final: 0.8465 (mtmm)
REVERT: D  232 LYS cc_start: 0.8563 (ttmt) cc_final: 0.8330 (tppp)
REVERT: D  281 GLN cc_start: 0.8772 (mm110) cc_final: 0.8473 (mm-40)
REVERT: D  283 LEU cc_start: 0.8693 (mt) cc_final: 0.8159 (mp)
REVERT: D  402 GLU cc_start: 0.8615 (mm-30) cc_final: 0.8368 (mt-10)
REVERT: E   75 ASP cc_start: 0.8397 (t0) cc_final: 0.7942 (t0)
REVERT: E  113 GLU cc_start: 0.9164 (mp0) cc_final: 0.8630 (mp0)
REVERT: E  132 ASP cc_start: 0.7922 (t0) cc_final: 0.7633 (t0)
REVERT: E  146 LYS cc_start: 0.8749 (mtpt) cc_final: 0.8093 (mtmp)
REVERT: E  160 GLU cc_start: 0.8785 (OUTLIER) cc_final: 0.8443 (mm-30)
REVERT: E  167 ASP cc_start: 0.9449 (p0) cc_final: 0.9097 (p0)
REVERT: E  201 GLU cc_start: 0.8721 (mt-10) cc_final: 0.8422 (mp0)
REVERT: E  206 ASP cc_start: 0.8454 (t0) cc_final: 0.8106 (t0)
REVERT: E  208 LYS cc_start: 0.8838 (mtmm) cc_final: 0.8395 (mtmm)
REVERT: E  232 LYS cc_start: 0.8784 (ttmt) cc_final: 0.8414 (ttmm)
REVERT: E  283 LEU cc_start: 0.8701 (mt) cc_final: 0.8360 (mp)
  outliers start: 36
  outliers final: 23
  residues processed: 355
  average time/residue: 1.1649
  time to fit residues: 454.1455
Evaluate side-chains
  334 residues out of total 1430 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 309
  time to evaluate  : 1.585 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  156 ASN
Chi-restraints excluded: chain A residue  179 SER
Chi-restraints excluded: chain A residue  253 LEU
Chi-restraints excluded: chain A residue  302 LEU
Chi-restraints excluded: chain A residue  372 LEU
Chi-restraints excluded: chain B residue   54 ASN
Chi-restraints excluded: chain B residue  179 SER
Chi-restraints excluded: chain B residue  246 LEU
Chi-restraints excluded: chain B residue  253 LEU
Chi-restraints excluded: chain C residue  179 SER
Chi-restraints excluded: chain C residue  198 VAL
Chi-restraints excluded: chain C residue  235 ILE
Chi-restraints excluded: chain C residue  304 LEU
Chi-restraints excluded: chain D residue  153 THR
Chi-restraints excluded: chain D residue  160 GLU
Chi-restraints excluded: chain D residue  179 SER
Chi-restraints excluded: chain D residue  235 ILE
Chi-restraints excluded: chain D residue  277 SER
Chi-restraints excluded: chain E residue  123 LEU
Chi-restraints excluded: chain E residue  155 THR
Chi-restraints excluded: chain E residue  160 GLU
Chi-restraints excluded: chain E residue  233 SER
Chi-restraints excluded: chain E residue  253 LEU
Chi-restraints excluded: chain E residue  277 SER
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 49 optimal weight:    0.5980
   chunk 23 optimal weight:    0.4980
   chunk 85 optimal weight:    2.9990
   chunk 1 optimal weight:    0.9980
   chunk 127 optimal weight:    4.9990
   chunk 73 optimal weight:    2.9990
   chunk 106 optimal weight:    4.9990
   chunk 136 optimal weight:    0.4980
   chunk 81 optimal weight:    0.5980
   chunk 22 optimal weight:    0.5980
   chunk 8 optimal weight:    2.9990
   overall best weight:    0.5580

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

Flipped N/Q/H residues before XYZ refinement:
A 156 ASN
A 221 GLN
C 156 ASN
C 221 GLN
** D 156 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
E 156 ASN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3161 r_free = 0.3161 target = 0.091845 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.2951 r_free = 0.2951 target = 0.078609 restraints weight = 20436.293|
|-----------------------------------------------------------------------------|
r_work (start): 0.2951 rms_B_bonded: 2.43
r_work: 0.2810 rms_B_bonded: 2.81 restraints_weight: 0.5000
r_work: 0.2663 rms_B_bonded: 4.68 restraints_weight: 0.2500
r_work (final): 0.2663
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2678
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2678 r_free = 0.2678    target_work(ls_wunit_k1) = 0.064         |
| occupancies: max = 1.00  min = 0.91   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2678 r_free = 0.2678    target_work(ls_wunit_k1) = 0.064         |
| occupancies: max = 1.00  min = 0.91   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2678
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8324
moved from start:          0.3064

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036  13385  Z= 0.176
  Angle     :  0.562   9.682  18305  Z= 0.271
  Chirality :  0.039   0.142   2235
  Planarity :  0.004   0.026   2250
  Dihedral  :  4.182  25.415   2060
  Min Nonbonded Distance : 2.599

Molprobity Statistics.
  All-atom Clashscore : 8.65
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.31 %
    Favored  : 98.69 %
  Rotamer:
    Outliers :  1.89 %
    Allowed  : 21.61 %
    Favored  : 76.50 %
  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:  1.75 (0.21), residues: 1600
  helix:  2.96 (0.20), residues: 525
  sheet:  0.72 (0.25), residues: 430
  loop : -0.02 (0.26), residues: 645

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP D 362 
 HIS   0.001   0.000   HIS A 276 
 PHE   0.020   0.002   PHE A 385 
 TYR   0.032   0.002   TYR D 176 
 ARG   0.011   0.000   ARG C 257 

********************** 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
  354 residues out of total 1430 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 327
  time to evaluate  : 1.645 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   48 GLU cc_start: 0.8647 (tp30) cc_final: 0.8220 (mm-30)
REVERT: A   75 ASP cc_start: 0.8381 (t0) cc_final: 0.8008 (t0)
REVERT: A   81 MET cc_start: 0.8973 (ttp) cc_final: 0.8668 (ptt)
REVERT: A  146 LYS cc_start: 0.8738 (mtpt) cc_final: 0.8177 (mttp)
REVERT: A  153 THR cc_start: 0.9341 (p) cc_final: 0.9038 (t)
REVERT: A  184 GLU cc_start: 0.8626 (mt-10) cc_final: 0.8425 (mt-10)
REVERT: A  201 GLU cc_start: 0.8763 (mt-10) cc_final: 0.8408 (mp0)
REVERT: A  206 ASP cc_start: 0.8433 (t0) cc_final: 0.8128 (t0)
REVERT: A  208 LYS cc_start: 0.8730 (ptpp) cc_final: 0.8209 (mtmm)
REVERT: A  232 LYS cc_start: 0.8696 (ttmt) cc_final: 0.8274 (ttmm)
REVERT: A  272 TYR cc_start: 0.8909 (t80) cc_final: 0.8271 (t80)
REVERT: A  283 LEU cc_start: 0.8641 (mt) cc_final: 0.8278 (mp)
REVERT: A  297 PHE cc_start: 0.8876 (m-80) cc_final: 0.8506 (m-10)
REVERT: A  364 GLU cc_start: 0.8543 (mt-10) cc_final: 0.8218 (mp0)
REVERT: B   75 ASP cc_start: 0.8257 (t0) cc_final: 0.7793 (t0)
REVERT: B  129 ASP cc_start: 0.8823 (t0) cc_final: 0.8415 (t0)
REVERT: B  146 LYS cc_start: 0.8786 (mtmt) cc_final: 0.8138 (mttp)
REVERT: B  160 GLU cc_start: 0.8938 (mm-30) cc_final: 0.8458 (mm-30)
REVERT: B  201 GLU cc_start: 0.8662 (mt-10) cc_final: 0.8274 (mp0)
REVERT: B  206 ASP cc_start: 0.8364 (t0) cc_final: 0.7916 (t0)
REVERT: B  232 LYS cc_start: 0.8706 (ttmt) cc_final: 0.8388 (ttmm)
REVERT: B  260 GLU cc_start: 0.8876 (pm20) cc_final: 0.8360 (pm20)
REVERT: C   75 ASP cc_start: 0.8407 (t0) cc_final: 0.7937 (t0)
REVERT: C   77 LEU cc_start: 0.9405 (mt) cc_final: 0.9204 (mm)
REVERT: C   81 MET cc_start: 0.9106 (ttp) cc_final: 0.8854 (ptm)
REVERT: C  129 ASP cc_start: 0.8834 (t0) cc_final: 0.8208 (t0)
REVERT: C  146 LYS cc_start: 0.8717 (mtpt) cc_final: 0.8128 (mtmp)
REVERT: C  160 GLU cc_start: 0.8574 (tt0) cc_final: 0.8147 (mm-30)
REVERT: C  184 GLU cc_start: 0.8720 (mt-10) cc_final: 0.8342 (pt0)
REVERT: C  201 GLU cc_start: 0.8728 (mt-10) cc_final: 0.8398 (mp0)
REVERT: C  232 LYS cc_start: 0.8714 (ttmt) cc_final: 0.8412 (tppp)
REVERT: C  260 GLU cc_start: 0.8882 (pm20) cc_final: 0.8400 (pm20)
REVERT: C  402 GLU cc_start: 0.8668 (mm-30) cc_final: 0.8458 (mt-10)
REVERT: D   75 ASP cc_start: 0.8460 (t0) cc_final: 0.7826 (t0)
REVERT: D  146 LYS cc_start: 0.8679 (mtmt) cc_final: 0.8104 (mttp)
REVERT: D  184 GLU cc_start: 0.8646 (mt-10) cc_final: 0.8280 (pt0)
REVERT: D  199 LYS cc_start: 0.8448 (ptpt) cc_final: 0.8127 (ptmm)
REVERT: D  201 GLU cc_start: 0.8744 (mt-10) cc_final: 0.8446 (mp0)
REVERT: D  206 ASP cc_start: 0.8462 (t0) cc_final: 0.8118 (t0)
REVERT: D  208 LYS cc_start: 0.8693 (mtmm) cc_final: 0.8446 (mtmm)
REVERT: D  232 LYS cc_start: 0.8533 (ttmt) cc_final: 0.8310 (tppp)
REVERT: D  272 TYR cc_start: 0.8952 (t80) cc_final: 0.8101 (t80)
REVERT: D  281 GLN cc_start: 0.8711 (mm110) cc_final: 0.8337 (pt0)
REVERT: D  283 LEU cc_start: 0.8682 (mt) cc_final: 0.8159 (mp)
REVERT: D  402 GLU cc_start: 0.8587 (mm-30) cc_final: 0.8338 (mt-10)
REVERT: E   75 ASP cc_start: 0.8381 (t0) cc_final: 0.7986 (t0)
REVERT: E  113 GLU cc_start: 0.9126 (mp0) cc_final: 0.8751 (mp0)
REVERT: E  132 ASP cc_start: 0.7815 (t0) cc_final: 0.7556 (t0)
REVERT: E  146 LYS cc_start: 0.8756 (mtpt) cc_final: 0.8080 (mttp)
REVERT: E  160 GLU cc_start: 0.8764 (OUTLIER) cc_final: 0.8435 (mm-30)
REVERT: E  167 ASP cc_start: 0.9440 (p0) cc_final: 0.9112 (p0)
REVERT: E  201 GLU cc_start: 0.8693 (mt-10) cc_final: 0.8405 (mp0)
REVERT: E  206 ASP cc_start: 0.8423 (t0) cc_final: 0.8100 (t0)
REVERT: E  208 LYS cc_start: 0.8805 (mtmm) cc_final: 0.8394 (mtmm)
REVERT: E  227 LYS cc_start: 0.8841 (ptmt) cc_final: 0.8533 (ptpp)
REVERT: E  232 LYS cc_start: 0.8780 (ttmt) cc_final: 0.8400 (ttmm)
REVERT: E  283 LEU cc_start: 0.8664 (mt) cc_final: 0.8349 (mp)
  outliers start: 27
  outliers final: 19
  residues processed: 345
  average time/residue: 1.1109
  time to fit residues: 422.9326
Evaluate side-chains
  336 residues out of total 1430 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 316
  time to evaluate  : 1.484 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  179 SER
Chi-restraints excluded: chain A residue  253 LEU
Chi-restraints excluded: chain A residue  302 LEU
Chi-restraints excluded: chain B residue   54 ASN
Chi-restraints excluded: chain B residue  179 SER
Chi-restraints excluded: chain B residue  246 LEU
Chi-restraints excluded: chain B residue  253 LEU
Chi-restraints excluded: chain C residue  179 SER
Chi-restraints excluded: chain C residue  198 VAL
Chi-restraints excluded: chain C residue  235 ILE
Chi-restraints excluded: chain C residue  304 LEU
Chi-restraints excluded: chain D residue  142 ASP
Chi-restraints excluded: chain D residue  153 THR
Chi-restraints excluded: chain D residue  179 SER
Chi-restraints excluded: chain D residue  235 ILE
Chi-restraints excluded: chain D residue  277 SER
Chi-restraints excluded: chain E residue  155 THR
Chi-restraints excluded: chain E residue  160 GLU
Chi-restraints excluded: chain E residue  277 SER
Chi-restraints excluded: chain E residue  305 PHE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 160
   random chunks:
   chunk 74 optimal weight:    5.9990
   chunk 1 optimal weight:    5.9990
   chunk 88 optimal weight:    0.8980
   chunk 126 optimal weight:    2.9990
   chunk 111 optimal weight:    2.9990
   chunk 10 optimal weight:    3.9990
   chunk 56 optimal weight:    0.2980
   chunk 154 optimal weight:    5.9990
   chunk 36 optimal weight:    3.9990
   chunk 83 optimal weight:    4.9990
   chunk 127 optimal weight:   10.0000
   overall best weight:    2.2386

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

Flipped N/Q/H residues before XYZ refinement:
A 156 ASN
A 221 GLN
C 156 ASN
C 382 GLN
** D 156 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
D 382 GLN
E 156 ASN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3118 r_free = 0.3118 target = 0.089105 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.2902 r_free = 0.2902 target = 0.075772 restraints weight = 20573.992|
|-----------------------------------------------------------------------------|
r_work (start): 0.2900 rms_B_bonded: 2.43
r_work: 0.2757 rms_B_bonded: 2.79 restraints_weight: 0.5000
r_work: 0.2610 rms_B_bonded: 4.62 restraints_weight: 0.2500
r_work (final): 0.2610
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2628
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2628 r_free = 0.2628    target_work(ls_wunit_k1) = 0.061         |
| occupancies: max = 1.00  min = 0.91   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2628 r_free = 0.2628    target_work(ls_wunit_k1) = 0.061         |
| occupancies: max = 1.00  min = 0.92   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2628
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8367
moved from start:          0.3225

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.062  13385  Z= 0.381
  Angle     :  0.608   9.724  18305  Z= 0.300
  Chirality :  0.042   0.248   2235
  Planarity :  0.004   0.027   2250
  Dihedral  :  4.278  23.308   2060
  Min Nonbonded Distance : 2.584

Molprobity Statistics.
  All-atom Clashscore : 10.20
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.50 %
    Favored  : 98.50 %
  Rotamer:
    Outliers :  2.24 %
    Allowed  : 21.12 %
    Favored  : 76.64 %
  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:  1.49 (0.21), residues: 1600
  helix:  2.68 (0.20), residues: 525
  sheet:  0.61 (0.24), residues: 430
  loop : -0.11 (0.26), residues: 645

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP E 112 
 HIS   0.002   0.001   HIS E 103 
 PHE   0.023   0.002   PHE A 385 
 TYR   0.059   0.003   TYR D 176 
 ARG   0.015   0.001   ARG C 257 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 9567.40 seconds
wall clock time: 170 minutes 21.58 seconds (10221.58 seconds total)