Starting phenix.real_space_refine
on Thu Jul 24 00:41:46 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7q66_13853/07_2025/7q66_13853.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7q66_13853/07_2025/7q66_13853.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.79
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7q66_13853/07_2025/7q66_13853.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7q66_13853/07_2025/7q66_13853.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7q66_13853/07_2025/7q66_13853.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7q66_13853/07_2025/7q66_13853.cif"
  }
  resolution = 2.79
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.001 sd=   0.009
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 3
    Type Number    sf(0)   Gaussians
     C    2959      2.51       5
     N     814      2.21       5
     O    1034      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-5711/modules/chem_data/mon_lib"
  Total number of atoms: 4807
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "A"
      Number of atoms: 262
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 37, 262
          Classifications: {'peptide': 37}
          Link IDs: {'PTRANS': 1, 'TRANS': 35}
    Chain: "B"
      Number of atoms: 175
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 25, 175
          Classifications: {'peptide': 25}
          Link IDs: {'TRANS': 24}
  Restraints were copied for chains:
    C, E, G, I, K, M, O, Q, S, U, D, F, H, J, L, N, P, R, T, V
  Time building chain proxies: 1.75, per 1000 atoms: 0.36
  Number of scatterers: 4807
  At special positions: 0
  Unit cell: (66.15, 61.95, 72.45, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 3
    Type Number    sf(0)
     O    1034      8.00
     N     814      7.00
     C    2959      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  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
  Time building additional restraints: 1.34
  Conformation dependent library (CDL) restraints added in 616.6 milliseconds
  

  1276 Ramachandran restraints generated.
    638 Oldfield, 0 Emsley, 638 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1166

  Finding SS restraints...
    Secondary structure from input PDB file:
      0 helices and 7 sheets defined
      0.0% alpha, 53.2% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.90
  Creating SS restraints...
    Processing sheet with id=AA1, first strand: chain 'A' and resid 88 through 92
      removed outlier: 6.095A  pdb=" N   ALA A  88 " --> pdb=" O   ASN C  89 " (cutoff:3.500A)
      removed outlier: 8.054A  pdb=" N   LEU C  91 " --> pdb=" O   ALA A  88 " (cutoff:3.500A)
      removed outlier: 8.956A  pdb=" N   THR A  90 " --> pdb=" O   LEU C  91 " (cutoff:3.500A)
      removed outlier: 6.095A  pdb=" N   ALA C  88 " --> pdb=" O   ASN E  89 " (cutoff:3.500A)
      removed outlier: 8.055A  pdb=" N   LEU E  91 " --> pdb=" O   ALA C  88 " (cutoff:3.500A)
      removed outlier: 8.956A  pdb=" N   THR C  90 " --> pdb=" O   LEU E  91 " (cutoff:3.500A)
      removed outlier: 6.094A  pdb=" N   ALA E  88 " --> pdb=" O   ASN G  89 " (cutoff:3.500A)
      removed outlier: 8.054A  pdb=" N   LEU G  91 " --> pdb=" O   ALA E  88 " (cutoff:3.500A)
      removed outlier: 8.956A  pdb=" N   THR E  90 " --> pdb=" O   LEU G  91 " (cutoff:3.500A)
      removed outlier: 6.094A  pdb=" N   ALA G  88 " --> pdb=" O   ASN I  89 " (cutoff:3.500A)
      removed outlier: 8.054A  pdb=" N   LEU I  91 " --> pdb=" O   ALA G  88 " (cutoff:3.500A)
      removed outlier: 8.956A  pdb=" N   THR G  90 " --> pdb=" O   LEU I  91 " (cutoff:3.500A)
      removed outlier: 6.095A  pdb=" N   ALA I  88 " --> pdb=" O   ASN K  89 " (cutoff:3.500A)
      removed outlier: 8.054A  pdb=" N   LEU K  91 " --> pdb=" O   ALA I  88 " (cutoff:3.500A)
      removed outlier: 8.955A  pdb=" N   THR I  90 " --> pdb=" O   LEU K  91 " (cutoff:3.500A)
      removed outlier: 6.094A  pdb=" N   ALA K  88 " --> pdb=" O   ASN M  89 " (cutoff:3.500A)
      removed outlier: 8.054A  pdb=" N   LEU M  91 " --> pdb=" O   ALA K  88 " (cutoff:3.500A)
      removed outlier: 8.955A  pdb=" N   THR K  90 " --> pdb=" O   LEU M  91 " (cutoff:3.500A)
      removed outlier: 6.095A  pdb=" N   ALA M  88 " --> pdb=" O   ASN O  89 " (cutoff:3.500A)
      removed outlier: 8.055A  pdb=" N   LEU O  91 " --> pdb=" O   ALA M  88 " (cutoff:3.500A)
      removed outlier: 8.956A  pdb=" N   THR M  90 " --> pdb=" O   LEU O  91 " (cutoff:3.500A)
      removed outlier: 6.094A  pdb=" N   ALA O  88 " --> pdb=" O   ASN Q  89 " (cutoff:3.500A)
      removed outlier: 8.054A  pdb=" N   LEU Q  91 " --> pdb=" O   ALA O  88 " (cutoff:3.500A)
      removed outlier: 8.956A  pdb=" N   THR O  90 " --> pdb=" O   LEU Q  91 " (cutoff:3.500A)
      removed outlier: 6.094A  pdb=" N   ALA Q  88 " --> pdb=" O   ASN S  89 " (cutoff:3.500A)
      removed outlier: 8.054A  pdb=" N   LEU S  91 " --> pdb=" O   ALA Q  88 " (cutoff:3.500A)
      removed outlier: 8.956A  pdb=" N   THR Q  90 " --> pdb=" O   LEU S  91 " (cutoff:3.500A)
      removed outlier: 6.094A  pdb=" N   ALA S  88 " --> pdb=" O   ASN U  89 " (cutoff:3.500A)
      removed outlier: 8.054A  pdb=" N   LEU U  91 " --> pdb=" O   ALA S  88 " (cutoff:3.500A)
      removed outlier: 8.956A  pdb=" N   THR S  90 " --> pdb=" O   LEU U  91 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA1
    Processing sheet with id=AA2, first strand: chain 'A' and resid 95 through 96
      removed outlier: 6.382A  pdb=" N   ALA A  95 " --> pdb=" O   SER C  96 " (cutoff:3.500A)
      removed outlier: 6.382A  pdb=" N   ALA C  95 " --> pdb=" O   SER E  96 " (cutoff:3.500A)
      removed outlier: 6.383A  pdb=" N   ALA E  95 " --> pdb=" O   SER G  96 " (cutoff:3.500A)
      removed outlier: 6.382A  pdb=" N   ALA G  95 " --> pdb=" O   SER I  96 " (cutoff:3.500A)
      removed outlier: 6.382A  pdb=" N   ALA I  95 " --> pdb=" O   SER K  96 " (cutoff:3.500A)
      removed outlier: 6.383A  pdb=" N   ALA K  95 " --> pdb=" O   SER M  96 " (cutoff:3.500A)
      removed outlier: 6.383A  pdb=" N   ALA M  95 " --> pdb=" O   SER O  96 " (cutoff:3.500A)
      removed outlier: 6.383A  pdb=" N   ALA O  95 " --> pdb=" O   SER Q  96 " (cutoff:3.500A)
      removed outlier: 6.382A  pdb=" N   ALA Q  95 " --> pdb=" O   SER S  96 " (cutoff:3.500A)
      removed outlier: 6.382A  pdb=" N   ALA S  95 " --> pdb=" O   SER U  96 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA2
    Processing sheet with id=AA3, first strand: chain 'A' and resid 100 through 101
    Processing sheet with id=AA4, first strand: chain 'A' and resid 105 through 112
      removed outlier: 6.882A  pdb=" N   ASN A 106 " --> pdb=" O   ASN C 107 " (cutoff:3.500A)
      removed outlier: 7.833A  pdb=" N   PHE C 109 " --> pdb=" O   ASN A 106 " (cutoff:3.500A)
      removed outlier: 6.108A  pdb=" N   ALA A 108 " --> pdb=" O   PHE C 109 " (cutoff:3.500A)
      removed outlier: 7.346A  pdb=" N   GLN C 111 " --> pdb=" O   ALA A 108 " (cutoff:3.500A)
      removed outlier: 6.153A  pdb=" N   ALA A 110 " --> pdb=" O   GLN C 111 " (cutoff:3.500A)
      removed outlier: 6.882A  pdb=" N   ASN C 106 " --> pdb=" O   ASN E 107 " (cutoff:3.500A)
      removed outlier: 7.834A  pdb=" N   PHE E 109 " --> pdb=" O   ASN C 106 " (cutoff:3.500A)
      removed outlier: 6.108A  pdb=" N   ALA C 108 " --> pdb=" O   PHE E 109 " (cutoff:3.500A)
      removed outlier: 7.346A  pdb=" N   GLN E 111 " --> pdb=" O   ALA C 108 " (cutoff:3.500A)
      removed outlier: 6.153A  pdb=" N   ALA C 110 " --> pdb=" O   GLN E 111 " (cutoff:3.500A)
      removed outlier: 6.881A  pdb=" N   ASN E 106 " --> pdb=" O   ASN G 107 " (cutoff:3.500A)
      removed outlier: 7.833A  pdb=" N   PHE G 109 " --> pdb=" O   ASN E 106 " (cutoff:3.500A)
      removed outlier: 6.107A  pdb=" N   ALA E 108 " --> pdb=" O   PHE G 109 " (cutoff:3.500A)
      removed outlier: 7.346A  pdb=" N   GLN G 111 " --> pdb=" O   ALA E 108 " (cutoff:3.500A)
      removed outlier: 6.153A  pdb=" N   ALA E 110 " --> pdb=" O   GLN G 111 " (cutoff:3.500A)
      removed outlier: 6.882A  pdb=" N   ASN G 106 " --> pdb=" O   ASN I 107 " (cutoff:3.500A)
      removed outlier: 7.833A  pdb=" N   PHE I 109 " --> pdb=" O   ASN G 106 " (cutoff:3.500A)
      removed outlier: 6.108A  pdb=" N   ALA G 108 " --> pdb=" O   PHE I 109 " (cutoff:3.500A)
      removed outlier: 7.345A  pdb=" N   GLN I 111 " --> pdb=" O   ALA G 108 " (cutoff:3.500A)
      removed outlier: 6.153A  pdb=" N   ALA G 110 " --> pdb=" O   GLN I 111 " (cutoff:3.500A)
      removed outlier: 6.882A  pdb=" N   ASN I 106 " --> pdb=" O   ASN K 107 " (cutoff:3.500A)
      removed outlier: 7.833A  pdb=" N   PHE K 109 " --> pdb=" O   ASN I 106 " (cutoff:3.500A)
      removed outlier: 6.107A  pdb=" N   ALA I 108 " --> pdb=" O   PHE K 109 " (cutoff:3.500A)
      removed outlier: 7.346A  pdb=" N   GLN K 111 " --> pdb=" O   ALA I 108 " (cutoff:3.500A)
      removed outlier: 6.153A  pdb=" N   ALA I 110 " --> pdb=" O   GLN K 111 " (cutoff:3.500A)
      removed outlier: 6.881A  pdb=" N   ASN K 106 " --> pdb=" O   ASN M 107 " (cutoff:3.500A)
      removed outlier: 7.832A  pdb=" N   PHE M 109 " --> pdb=" O   ASN K 106 " (cutoff:3.500A)
      removed outlier: 6.107A  pdb=" N   ALA K 108 " --> pdb=" O   PHE M 109 " (cutoff:3.500A)
      removed outlier: 7.346A  pdb=" N   GLN M 111 " --> pdb=" O   ALA K 108 " (cutoff:3.500A)
      removed outlier: 6.152A  pdb=" N   ALA K 110 " --> pdb=" O   GLN M 111 " (cutoff:3.500A)
      removed outlier: 6.882A  pdb=" N   ASN M 106 " --> pdb=" O   ASN O 107 " (cutoff:3.500A)
      removed outlier: 7.834A  pdb=" N   PHE O 109 " --> pdb=" O   ASN M 106 " (cutoff:3.500A)
      removed outlier: 6.107A  pdb=" N   ALA M 108 " --> pdb=" O   PHE O 109 " (cutoff:3.500A)
      removed outlier: 7.346A  pdb=" N   GLN O 111 " --> pdb=" O   ALA M 108 " (cutoff:3.500A)
      removed outlier: 6.153A  pdb=" N   ALA M 110 " --> pdb=" O   GLN O 111 " (cutoff:3.500A)
      removed outlier: 6.882A  pdb=" N   ASN O 106 " --> pdb=" O   ASN Q 107 " (cutoff:3.500A)
      removed outlier: 7.833A  pdb=" N   PHE Q 109 " --> pdb=" O   ASN O 106 " (cutoff:3.500A)
      removed outlier: 6.107A  pdb=" N   ALA O 108 " --> pdb=" O   PHE Q 109 " (cutoff:3.500A)
      removed outlier: 7.346A  pdb=" N   GLN Q 111 " --> pdb=" O   ALA O 108 " (cutoff:3.500A)
      removed outlier: 6.152A  pdb=" N   ALA O 110 " --> pdb=" O   GLN Q 111 " (cutoff:3.500A)
      removed outlier: 6.882A  pdb=" N   ASN Q 106 " --> pdb=" O   ASN S 107 " (cutoff:3.500A)
      removed outlier: 7.833A  pdb=" N   PHE S 109 " --> pdb=" O   ASN Q 106 " (cutoff:3.500A)
      removed outlier: 6.107A  pdb=" N   ALA Q 108 " --> pdb=" O   PHE S 109 " (cutoff:3.500A)
      removed outlier: 7.346A  pdb=" N   GLN S 111 " --> pdb=" O   ALA Q 108 " (cutoff:3.500A)
      removed outlier: 6.153A  pdb=" N   ALA Q 110 " --> pdb=" O   GLN S 111 " (cutoff:3.500A)
      removed outlier: 6.881A  pdb=" N   ASN S 106 " --> pdb=" O   ASN U 107 " (cutoff:3.500A)
      removed outlier: 7.833A  pdb=" N   PHE U 109 " --> pdb=" O   ASN S 106 " (cutoff:3.500A)
      removed outlier: 6.107A  pdb=" N   ALA S 108 " --> pdb=" O   PHE U 109 " (cutoff:3.500A)
      removed outlier: 7.346A  pdb=" N   GLN U 111 " --> pdb=" O   ALA S 108 " (cutoff:3.500A)
      removed outlier: 6.152A  pdb=" N   ALA S 110 " --> pdb=" O   GLN U 111 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA4
    Processing sheet with id=AA5, first strand: chain 'A' and resid 115 through 120
      removed outlier: 6.517A  pdb=" N   THR A 115 " --> pdb=" O   GLY C 116 " (cutoff:3.500A)
      removed outlier: 7.893A  pdb=" N   GLY C 118 " --> pdb=" O   THR A 115 " (cutoff:3.500A)
      removed outlier: 6.410A  pdb=" N   PHE A 117 " --> pdb=" O   GLY C 118 " (cutoff:3.500A)
      removed outlier: 7.297A  pdb=" N   PHE C 120 " --> pdb=" O   PHE A 117 " (cutoff:3.500A)
      removed outlier: 6.018A  pdb=" N   ASN A 119 " --> pdb=" O   PHE C 120 " (cutoff:3.500A)
      removed outlier: 6.517A  pdb=" N   THR C 115 " --> pdb=" O   GLY E 116 " (cutoff:3.500A)
      removed outlier: 7.892A  pdb=" N   GLY E 118 " --> pdb=" O   THR C 115 " (cutoff:3.500A)
      removed outlier: 6.410A  pdb=" N   PHE C 117 " --> pdb=" O   GLY E 118 " (cutoff:3.500A)
      removed outlier: 7.298A  pdb=" N   PHE E 120 " --> pdb=" O   PHE C 117 " (cutoff:3.500A)
      removed outlier: 6.018A  pdb=" N   ASN C 119 " --> pdb=" O   PHE E 120 " (cutoff:3.500A)
      removed outlier: 6.517A  pdb=" N   THR E 115 " --> pdb=" O   GLY G 116 " (cutoff:3.500A)
      removed outlier: 7.893A  pdb=" N   GLY G 118 " --> pdb=" O   THR E 115 " (cutoff:3.500A)
      removed outlier: 6.410A  pdb=" N   PHE E 117 " --> pdb=" O   GLY G 118 " (cutoff:3.500A)
      removed outlier: 7.298A  pdb=" N   PHE G 120 " --> pdb=" O   PHE E 117 " (cutoff:3.500A)
      removed outlier: 6.018A  pdb=" N   ASN E 119 " --> pdb=" O   PHE G 120 " (cutoff:3.500A)
      removed outlier: 6.517A  pdb=" N   THR G 115 " --> pdb=" O   GLY I 116 " (cutoff:3.500A)
      removed outlier: 7.893A  pdb=" N   GLY I 118 " --> pdb=" O   THR G 115 " (cutoff:3.500A)
      removed outlier: 6.410A  pdb=" N   PHE G 117 " --> pdb=" O   GLY I 118 " (cutoff:3.500A)
      removed outlier: 7.298A  pdb=" N   PHE I 120 " --> pdb=" O   PHE G 117 " (cutoff:3.500A)
      removed outlier: 6.017A  pdb=" N   ASN G 119 " --> pdb=" O   PHE I 120 " (cutoff:3.500A)
      removed outlier: 6.517A  pdb=" N   THR I 115 " --> pdb=" O   GLY K 116 " (cutoff:3.500A)
      removed outlier: 7.893A  pdb=" N   GLY K 118 " --> pdb=" O   THR I 115 " (cutoff:3.500A)
      removed outlier: 6.410A  pdb=" N   PHE I 117 " --> pdb=" O   GLY K 118 " (cutoff:3.500A)
      removed outlier: 7.297A  pdb=" N   PHE K 120 " --> pdb=" O   PHE I 117 " (cutoff:3.500A)
      removed outlier: 6.017A  pdb=" N   ASN I 119 " --> pdb=" O   PHE K 120 " (cutoff:3.500A)
      removed outlier: 6.517A  pdb=" N   THR K 115 " --> pdb=" O   GLY M 116 " (cutoff:3.500A)
      removed outlier: 7.893A  pdb=" N   GLY M 118 " --> pdb=" O   THR K 115 " (cutoff:3.500A)
      removed outlier: 6.410A  pdb=" N   PHE K 117 " --> pdb=" O   GLY M 118 " (cutoff:3.500A)
      removed outlier: 7.298A  pdb=" N   PHE M 120 " --> pdb=" O   PHE K 117 " (cutoff:3.500A)
      removed outlier: 6.018A  pdb=" N   ASN K 119 " --> pdb=" O   PHE M 120 " (cutoff:3.500A)
      removed outlier: 6.517A  pdb=" N   THR M 115 " --> pdb=" O   GLY O 116 " (cutoff:3.500A)
      removed outlier: 7.893A  pdb=" N   GLY O 118 " --> pdb=" O   THR M 115 " (cutoff:3.500A)
      removed outlier: 6.411A  pdb=" N   PHE M 117 " --> pdb=" O   GLY O 118 " (cutoff:3.500A)
      removed outlier: 7.298A  pdb=" N   PHE O 120 " --> pdb=" O   PHE M 117 " (cutoff:3.500A)
      removed outlier: 6.018A  pdb=" N   ASN M 119 " --> pdb=" O   PHE O 120 " (cutoff:3.500A)
      removed outlier: 6.517A  pdb=" N   THR O 115 " --> pdb=" O   GLY Q 116 " (cutoff:3.500A)
      removed outlier: 7.894A  pdb=" N   GLY Q 118 " --> pdb=" O   THR O 115 " (cutoff:3.500A)
      removed outlier: 6.410A  pdb=" N   PHE O 117 " --> pdb=" O   GLY Q 118 " (cutoff:3.500A)
      removed outlier: 7.298A  pdb=" N   PHE Q 120 " --> pdb=" O   PHE O 117 " (cutoff:3.500A)
      removed outlier: 6.018A  pdb=" N   ASN O 119 " --> pdb=" O   PHE Q 120 " (cutoff:3.500A)
      removed outlier: 6.517A  pdb=" N   THR Q 115 " --> pdb=" O   GLY S 116 " (cutoff:3.500A)
      removed outlier: 7.893A  pdb=" N   GLY S 118 " --> pdb=" O   THR Q 115 " (cutoff:3.500A)
      removed outlier: 6.410A  pdb=" N   PHE Q 117 " --> pdb=" O   GLY S 118 " (cutoff:3.500A)
      removed outlier: 7.298A  pdb=" N   PHE S 120 " --> pdb=" O   PHE Q 117 " (cutoff:3.500A)
      removed outlier: 6.017A  pdb=" N   ASN Q 119 " --> pdb=" O   PHE S 120 " (cutoff:3.500A)
      removed outlier: 6.516A  pdb=" N   THR S 115 " --> pdb=" O   GLY U 116 " (cutoff:3.500A)
      removed outlier: 7.893A  pdb=" N   GLY U 118 " --> pdb=" O   THR S 115 " (cutoff:3.500A)
      removed outlier: 6.411A  pdb=" N   PHE S 117 " --> pdb=" O   GLY U 118 " (cutoff:3.500A)
      removed outlier: 7.298A  pdb=" N   PHE U 120 " --> pdb=" O   PHE S 117 " (cutoff:3.500A)
      removed outlier: 6.018A  pdb=" N   ASN S 119 " --> pdb=" O   PHE U 120 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA5
    Processing sheet with id=AA6, first strand: chain 'B' and resid 87 through 92
    Processing sheet with id=AA7, first strand: chain 'B' and resid 98 through 108

    160 hydrogen bonds defined for protein.
    480 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: 1.40

  Time building geometry restraints manager: 1.59 seconds

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

  Histogram of bond lengths:
        1.21 -     1.27: 803
        1.27 -     1.34: 803
        1.34 -     1.41: 594
        1.41 -     1.47: 979
        1.47 -     1.54: 1705
  Bond restraints: 4884
  Sorted by residual:
  bond pdb=" CB  THR A  90 "
       pdb=" CG2 THR A  90 "
    ideal  model  delta    sigma   weight residual
    1.521  1.354  0.167 3.30e-02 9.18e+02 2.57e+01
  bond pdb=" CB  THR C  90 "
       pdb=" CG2 THR C  90 "
    ideal  model  delta    sigma   weight residual
    1.521  1.354  0.167 3.30e-02 9.18e+02 2.56e+01
  bond pdb=" CB  THR K  90 "
       pdb=" CG2 THR K  90 "
    ideal  model  delta    sigma   weight residual
    1.521  1.354  0.167 3.30e-02 9.18e+02 2.56e+01
  bond pdb=" CB  THR O  90 "
       pdb=" CG2 THR O  90 "
    ideal  model  delta    sigma   weight residual
    1.521  1.354  0.167 3.30e-02 9.18e+02 2.56e+01
  bond pdb=" CB  THR M  90 "
       pdb=" CG2 THR M  90 "
    ideal  model  delta    sigma   weight residual
    1.521  1.354  0.167 3.30e-02 9.18e+02 2.56e+01
  ... (remaining 4879 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.89: 5817
        1.89 -     3.78: 563
        3.78 -     5.67: 176
        5.67 -     7.56: 33
        7.56 -     9.45: 22
  Bond angle restraints: 6611
  Sorted by residual:
  angle pdb=" N   LYS A 113 "
        pdb=" CA  LYS A 113 "
        pdb=" C   LYS A 113 "
      ideal   model   delta    sigma   weight residual
     111.53  119.09   -7.56 2.18e+00 2.10e-01 1.20e+01
  angle pdb=" N   LYS G 113 "
        pdb=" CA  LYS G 113 "
        pdb=" C   LYS G 113 "
      ideal   model   delta    sigma   weight residual
     111.53  119.08   -7.55 2.18e+00 2.10e-01 1.20e+01
  angle pdb=" N   LYS U 113 "
        pdb=" CA  LYS U 113 "
        pdb=" C   LYS U 113 "
      ideal   model   delta    sigma   weight residual
     111.53  119.08   -7.55 2.18e+00 2.10e-01 1.20e+01
  angle pdb=" N   LYS K 113 "
        pdb=" CA  LYS K 113 "
        pdb=" C   LYS K 113 "
      ideal   model   delta    sigma   weight residual
     111.53  119.08   -7.55 2.18e+00 2.10e-01 1.20e+01
  angle pdb=" N   LYS O 113 "
        pdb=" CA  LYS O 113 "
        pdb=" C   LYS O 113 "
      ideal   model   delta    sigma   weight residual
     111.53  119.07   -7.54 2.18e+00 2.10e-01 1.20e+01
  ... (remaining 6606 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    12.71: 2376
       12.71 -    25.42: 209
       25.42 -    38.13: 66
       38.13 -    50.84: 11
       50.84 -    63.55: 11
  Dihedral angle restraints: 2673
    sinusoidal: 847
      harmonic: 1826
  Sorted by residual:
  dihedral pdb=" C   LYS K 113 "
           pdb=" N   LYS K 113 "
           pdb=" CA  LYS K 113 "
           pdb=" CB  LYS K 113 "
      ideal   model   delta  harmonic     sigma   weight residual
    -122.60 -131.58    8.98     0      2.50e+00 1.60e-01 1.29e+01
  dihedral pdb=" C   LYS M 113 "
           pdb=" N   LYS M 113 "
           pdb=" CA  LYS M 113 "
           pdb=" CB  LYS M 113 "
      ideal   model   delta  harmonic     sigma   weight residual
    -122.60 -131.54    8.94     0      2.50e+00 1.60e-01 1.28e+01
  dihedral pdb=" C   LYS I 113 "
           pdb=" N   LYS I 113 "
           pdb=" CA  LYS I 113 "
           pdb=" CB  LYS I 113 "
      ideal   model   delta  harmonic     sigma   weight residual
    -122.60 -131.54    8.94     0      2.50e+00 1.60e-01 1.28e+01
  ... (remaining 2670 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.096: 638
       0.096 -    0.191: 66
       0.191 -    0.287: 33
       0.287 -    0.383: 11
       0.383 -    0.478: 22
  Chirality restraints: 770
  Sorted by residual:
  chirality pdb=" CG  LEU B 101 "
            pdb=" CB  LEU B 101 "
            pdb=" CD1 LEU B 101 "
            pdb=" CD2 LEU B 101 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.59   -2.11   -0.48 2.00e-01 2.50e+01 5.72e+00
  chirality pdb=" CG  LEU T 101 "
            pdb=" CB  LEU T 101 "
            pdb=" CD1 LEU T 101 "
            pdb=" CD2 LEU T 101 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.59   -2.11   -0.48 2.00e-01 2.50e+01 5.71e+00
  chirality pdb=" CG  LEU F 101 "
            pdb=" CB  LEU F 101 "
            pdb=" CD1 LEU F 101 "
            pdb=" CD2 LEU F 101 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.59   -2.11   -0.48 2.00e-01 2.50e+01 5.71e+00
  ... (remaining 767 not shown)

  Planarity restraints: 880
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ALA Q 110 "    0.012 2.00e-02 2.50e+03   2.43e-02 5.90e+00
        pdb=" C   ALA Q 110 "   -0.042 2.00e-02 2.50e+03
        pdb=" O   ALA Q 110 "    0.016 2.00e-02 2.50e+03
        pdb=" N   GLN Q 111 "    0.014 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ALA U 110 "    0.012 2.00e-02 2.50e+03   2.43e-02 5.90e+00
        pdb=" C   ALA U 110 "   -0.042 2.00e-02 2.50e+03
        pdb=" O   ALA U 110 "    0.016 2.00e-02 2.50e+03
        pdb=" N   GLN U 111 "    0.014 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ALA S 110 "    0.012 2.00e-02 2.50e+03   2.43e-02 5.90e+00
        pdb=" C   ALA S 110 "   -0.042 2.00e-02 2.50e+03
        pdb=" O   ALA S 110 "    0.016 2.00e-02 2.50e+03
        pdb=" N   GLN S 111 "    0.014 2.00e-02 2.50e+03
  ... (remaining 877 not shown)

  Histogram of nonbonded interaction distances:
        2.28 -     2.80: 1632
        2.80 -     3.33: 4132
        3.33 -     3.85: 9177
        3.85 -     4.38: 11100
        4.38 -     4.90: 21252
  Nonbonded interactions: 47293
  Sorted by model distance:
  nonbonded pdb=" ND2 ASN A 106 "
            pdb=" OG  SER B 103 "
     model   vdw
     2.277 3.120
  nonbonded pdb=" ND2 ASN G 106 "
            pdb=" OG  SER H 103 "
     model   vdw
     2.277 3.120
  nonbonded pdb=" ND2 ASN S 106 "
            pdb=" OG  SER T 103 "
     model   vdw
     2.278 3.120
  nonbonded pdb=" ND2 ASN O 106 "
            pdb=" OG  SER P 103 "
     model   vdw
     2.278 3.120
  nonbonded pdb=" ND2 ASN U 106 "
            pdb=" OG  SER V 103 "
     model   vdw
     2.278 3.120
  ... (remaining 47288 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: 0.05
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'C'
  selection = chain 'E'
  selection = chain 'G'
  selection = chain 'I'
  selection = chain 'K'
  selection = chain 'M'
  selection = chain 'O'
  selection = chain 'Q'
  selection = chain 'S'
  selection = chain 'U'
}
ncs_group {
  reference = chain 'B'
  selection = chain 'D'
  selection = chain 'F'
  selection = chain 'H'
  selection = chain 'J'
  selection = chain 'L'
  selection = chain 'N'
  selection = chain 'P'
  selection = chain 'R'
  selection = chain 'T'
  selection = chain 'V'
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             1.420
  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:          0.190
  Check model and map are aligned:         0.040
  Set scattering table:                    0.040
  Process input model:                     15.250
  Find NCS groups from input model:        0.120
  Set up NCS constraints:                  0.010
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.010
  Load rotamer database and sin/cos tables:12.430
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   29.520
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8088
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      :  0.021   0.167   4884  Z= 0.896
  Angle     :  1.424   9.452   6611  Z= 0.782
  Chirality :  0.115   0.478    770
  Planarity :  0.007   0.024    880
  Dihedral  : 12.578  63.547   1507
  Min Nonbonded Distance : 2.277

Molprobity Statistics.
  All-atom Clashscore : 13.59
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.00 %
    Favored  : 100.00 %
  Rotamer:
    Outliers :  6.52 %
    Allowed  :  4.35 %
    Favored  : 89.13 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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: -4.18 (0.15), residues: 638
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -3.18 (0.11), residues: 638

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 PHE   0.034   0.006   PHE S 109 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.13764 (  160)
  hydrogen bonds       : angle       8.38790 (  480)
  covalent geometry    : bond        0.02061 ( 4884)
  covalent geometry    : angle       1.42395 ( 6611)

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

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

  1276 Ramachandran restraints generated.
    638 Oldfield, 0 Emsley, 638 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1276 Ramachandran restraints generated.
    638 Oldfield, 0 Emsley, 638 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  291 residues out of total 506 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 258
  time to evaluate  : 0.462 
Fit side-chains
REVERT: H  105 GLN cc_start: 0.8627 (tt0) cc_final: 0.8409 (tt0)
REVERT: K  107 ASN cc_start: 0.8585 (OUTLIER) cc_final: 0.8224 (p0)
REVERT: M  105 GLN cc_start: 0.8601 (tm130) cc_final: 0.8332 (tm-30)
REVERT: O  107 ASN cc_start: 0.8586 (OUTLIER) cc_final: 0.8261 (p0)
REVERT: P  105 GLN cc_start: 0.8903 (tt0) cc_final: 0.8616 (tt0)
REVERT: R   87 THR cc_start: 0.8477 (p) cc_final: 0.8115 (t)
REVERT: S  105 GLN cc_start: 0.8773 (tm130) cc_final: 0.8525 (tm130)
  outliers start: 33
  outliers final: 6
  residues processed: 269
  average time/residue: 0.4495
  time to fit residues: 131.7122
Evaluate side-chains
  184 residues out of total 506 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 176
  time to evaluate  : 0.470 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain D residue  101 LEU
Chi-restraints excluded: chain K residue  107 ASN
Chi-restraints excluded: chain L residue  101 LEU
Chi-restraints excluded: chain M residue  101 LEU
Chi-restraints excluded: chain N residue  101 LEU
Chi-restraints excluded: chain O residue  107 ASN
Chi-restraints excluded: chain P residue  101 LEU
Chi-restraints excluded: chain R residue  101 LEU
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 55
   random chunks:
   chunk 46 optimal weight:    0.9990
   chunk 41 optimal weight:    0.9990
   chunk 23 optimal weight:    3.9990
   chunk 14 optimal weight:    0.9990
   chunk 28 optimal weight:    0.8980
   chunk 22 optimal weight:    1.9990
   chunk 43 optimal weight:    2.9990
   chunk 16 optimal weight:    1.9990
   chunk 26 optimal weight:    0.9990
   chunk 32 optimal weight:    0.9990
   chunk 49 optimal weight:    0.9980
   overall best weight:    0.9786

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

Flipped N/Q/H residues before XYZ refinement:
A 107 ASN
B 105 GLN
** C 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
D 105 GLN
** E 106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
E 112 ASN
F 105 GLN
** G 106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
G 112 ASN
H 105 GLN
** I 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** I 106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
I 112 ASN
** K 106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
K 112 ASN
** M 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** M 106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** O 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
P 105 GLN
R 105 GLN
** S 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
S 112 ASN
T 105 GLN
** U 106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 13

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3241 r_free = 0.3241 target = 0.079965 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3108 r_free = 0.3108 target = 0.071777 restraints weight = 7566.064|
|-----------------------------------------------------------------------------|
r_work (start): 0.3106 rms_B_bonded: 1.63
r_work: 0.3021 rms_B_bonded: 1.83 restraints_weight: 0.5000
r_work: 0.2926 rms_B_bonded: 3.20 restraints_weight: 0.2500
r_work (final): 0.2926
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8487
moved from start:          0.2296

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.035   4884  Z= 0.193
  Angle     :  0.737   9.884   6611  Z= 0.349
  Chirality :  0.047   0.219    770
  Planarity :  0.003   0.019    880
  Dihedral  :  6.463  46.453    676
  Min Nonbonded Distance : 2.448

Molprobity Statistics.
  All-atom Clashscore : 15.77
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.78 %
    Favored  : 99.22 %
  Rotamer:
    Outliers : 17.39 %
    Allowed  : 16.60 %
    Favored  : 66.01 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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: -4.25 (0.15), residues: 638
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -3.23 (0.12), residues: 638

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 PHE   0.015   0.002   PHE G 109 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04727 (  160)
  hydrogen bonds       : angle       5.78582 (  480)
  covalent geometry    : bond        0.00405 ( 4884)
  covalent geometry    : angle       0.73735 ( 6611)

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

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

  1276 Ramachandran restraints generated.
    638 Oldfield, 0 Emsley, 638 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1276 Ramachandran restraints generated.
    638 Oldfield, 0 Emsley, 638 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  296 residues out of total 506 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 88
    poor density    : 208
  time to evaluate  : 0.519 
Fit side-chains
REVERT: B   91 LEU cc_start: 0.8611 (OUTLIER) cc_final: 0.8288 (tt)
REVERT: C  106 ASN cc_start: 0.9132 (OUTLIER) cc_final: 0.8452 (p0)
REVERT: D   91 LEU cc_start: 0.8534 (OUTLIER) cc_final: 0.8128 (tt)
REVERT: E  106 ASN cc_start: 0.8855 (OUTLIER) cc_final: 0.8636 (p0)
REVERT: H  105 GLN cc_start: 0.8916 (tt0) cc_final: 0.8713 (tt0)
REVERT: I  107 ASN cc_start: 0.8792 (p0) cc_final: 0.8316 (p0)
REVERT: K   99 THR cc_start: 0.9176 (p) cc_final: 0.8944 (t)
REVERT: K  107 ASN cc_start: 0.8583 (OUTLIER) cc_final: 0.8313 (p0)
REVERT: M  106 ASN cc_start: 0.8964 (OUTLIER) cc_final: 0.8130 (p0)
REVERT: M  107 ASN cc_start: 0.8919 (OUTLIER) cc_final: 0.8608 (p0)
REVERT: M  119 ASN cc_start: 0.8693 (m110) cc_final: 0.8407 (m-40)
REVERT: N   89 ASN cc_start: 0.8935 (m-40) cc_final: 0.8718 (m110)
REVERT: P  105 GLN cc_start: 0.8982 (tt0) cc_final: 0.8708 (tt0)
REVERT: T   91 LEU cc_start: 0.8633 (OUTLIER) cc_final: 0.8427 (mm)
  outliers start: 88
  outliers final: 51
  residues processed: 248
  average time/residue: 0.3432
  time to fit residues: 95.4777
Evaluate side-chains
  234 residues out of total 506 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 59
    poor density    : 175
  time to evaluate  : 0.511 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   99 THR
Chi-restraints excluded: chain B residue   87 THR
Chi-restraints excluded: chain B residue   91 LEU
Chi-restraints excluded: chain B residue   96 SER
Chi-restraints excluded: chain B residue  106 ASN
Chi-restraints excluded: chain C residue   87 THR
Chi-restraints excluded: chain C residue   94 THR
Chi-restraints excluded: chain C residue   99 THR
Chi-restraints excluded: chain C residue  100 SER
Chi-restraints excluded: chain C residue  106 ASN
Chi-restraints excluded: chain C residue  107 ASN
Chi-restraints excluded: chain D residue   91 LEU
Chi-restraints excluded: chain D residue  100 SER
Chi-restraints excluded: chain D residue  101 LEU
Chi-restraints excluded: chain E residue  106 ASN
Chi-restraints excluded: chain F residue   87 THR
Chi-restraints excluded: chain F residue   91 LEU
Chi-restraints excluded: chain F residue   96 SER
Chi-restraints excluded: chain F residue  104 SER
Chi-restraints excluded: chain G residue   94 THR
Chi-restraints excluded: chain G residue   99 THR
Chi-restraints excluded: chain G residue  106 ASN
Chi-restraints excluded: chain H residue   91 LEU
Chi-restraints excluded: chain H residue  100 SER
Chi-restraints excluded: chain I residue  106 ASN
Chi-restraints excluded: chain J residue   87 THR
Chi-restraints excluded: chain J residue   91 LEU
Chi-restraints excluded: chain J residue   96 SER
Chi-restraints excluded: chain J residue  101 LEU
Chi-restraints excluded: chain J residue  104 SER
Chi-restraints excluded: chain K residue   94 THR
Chi-restraints excluded: chain K residue  106 ASN
Chi-restraints excluded: chain K residue  107 ASN
Chi-restraints excluded: chain L residue  101 LEU
Chi-restraints excluded: chain L residue  104 SER
Chi-restraints excluded: chain M residue  106 ASN
Chi-restraints excluded: chain M residue  107 ASN
Chi-restraints excluded: chain N residue  101 LEU
Chi-restraints excluded: chain O residue   94 THR
Chi-restraints excluded: chain O residue   99 THR
Chi-restraints excluded: chain O residue  106 ASN
Chi-restraints excluded: chain P residue   91 LEU
Chi-restraints excluded: chain P residue   96 SER
Chi-restraints excluded: chain P residue  101 LEU
Chi-restraints excluded: chain Q residue   94 THR
Chi-restraints excluded: chain Q residue  100 SER
Chi-restraints excluded: chain Q residue  106 ASN
Chi-restraints excluded: chain Q residue  107 ASN
Chi-restraints excluded: chain R residue   91 LEU
Chi-restraints excluded: chain R residue  101 LEU
Chi-restraints excluded: chain S residue   94 THR
Chi-restraints excluded: chain S residue  100 SER
Chi-restraints excluded: chain S residue  106 ASN
Chi-restraints excluded: chain T residue   91 LEU
Chi-restraints excluded: chain T residue   96 SER
Chi-restraints excluded: chain T residue  101 LEU
Chi-restraints excluded: chain U residue  106 ASN
Chi-restraints excluded: chain V residue   91 LEU
Chi-restraints excluded: chain V residue  100 SER
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 55
   random chunks:
   chunk 29 optimal weight:    1.9990
   chunk 31 optimal weight:    4.9990
   chunk 51 optimal weight:    0.0980
   chunk 32 optimal weight:    1.9990
   chunk 25 optimal weight:    3.9990
   chunk 9 optimal weight:    9.9990
   chunk 10 optimal weight:    5.9990
   chunk 27 optimal weight:    2.9990
   chunk 2 optimal weight:    2.9990
   chunk 48 optimal weight:    7.9990
   chunk 21 optimal weight:    5.9990
   overall best weight:    2.0188

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

Flipped N/Q/H residues before XYZ refinement:
B  89 ASN
B 105 GLN
D  89 ASN
** E 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
F  89 ASN
F 105 GLN
H  89 ASN
H 105 GLN
** I 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
K 112 ASN
L  89 ASN
** M 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
M 112 ASN
** O 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
P 105 GLN
R  89 ASN
R 105 GLN
T 105 GLN
** U 106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
V 105 GLN

Total number of N/Q/H flips: 15

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3185 r_free = 0.3185 target = 0.076508 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3048 r_free = 0.3048 target = 0.068110 restraints weight = 7603.414|
|-----------------------------------------------------------------------------|
r_work (start): 0.3054 rms_B_bonded: 1.64
r_work: 0.2974 rms_B_bonded: 1.81 restraints_weight: 0.5000
r_work: 0.2878 rms_B_bonded: 3.13 restraints_weight: 0.2500
r_work (final): 0.2878
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8539
moved from start:          0.2823

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.047   4884  Z= 0.250
  Angle     :  0.734   9.494   6611  Z= 0.338
  Chirality :  0.047   0.248    770
  Planarity :  0.003   0.015    880
  Dihedral  :  6.004  56.458    672
  Min Nonbonded Distance : 2.500

Molprobity Statistics.
  All-atom Clashscore : 13.59
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.25 %
    Favored  : 98.75 %
  Rotamer:
    Outliers : 15.81 %
    Allowed  : 22.33 %
    Favored  : 61.86 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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: -4.22 (0.15), residues: 638
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -3.21 (0.11), residues: 638

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 PHE   0.016   0.002   PHE U 109 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03387 (  160)
  hydrogen bonds       : angle       4.95580 (  480)
  covalent geometry    : bond        0.00554 ( 4884)
  covalent geometry    : angle       0.73384 ( 6611)

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

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

  1276 Ramachandran restraints generated.
    638 Oldfield, 0 Emsley, 638 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1276 Ramachandran restraints generated.
    638 Oldfield, 0 Emsley, 638 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  271 residues out of total 506 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 80
    poor density    : 191
  time to evaluate  : 0.591 
Fit side-chains
REVERT: B   91 LEU cc_start: 0.8650 (OUTLIER) cc_final: 0.8357 (tt)
REVERT: C  106 ASN cc_start: 0.9107 (OUTLIER) cc_final: 0.8552 (p0)
REVERT: D   91 LEU cc_start: 0.8560 (OUTLIER) cc_final: 0.8202 (tt)
REVERT: D  106 ASN cc_start: 0.8703 (OUTLIER) cc_final: 0.8352 (m-40)
REVERT: E  101 LEU cc_start: 0.9347 (tt) cc_final: 0.9087 (tm)
REVERT: I   96 SER cc_start: 0.9120 (t) cc_final: 0.8872 (p)
REVERT: I   99 THR cc_start: 0.9334 (OUTLIER) cc_final: 0.8934 (p)
REVERT: M  106 ASN cc_start: 0.9149 (OUTLIER) cc_final: 0.8356 (p0)
REVERT: N  106 ASN cc_start: 0.8611 (OUTLIER) cc_final: 0.8175 (m110)
REVERT: O  107 ASN cc_start: 0.8943 (OUTLIER) cc_final: 0.8653 (p0)
REVERT: P   91 LEU cc_start: 0.8427 (OUTLIER) cc_final: 0.8213 (mm)
REVERT: R   91 LEU cc_start: 0.8501 (OUTLIER) cc_final: 0.8128 (tt)
REVERT: T   91 LEU cc_start: 0.8670 (OUTLIER) cc_final: 0.8453 (mm)
  outliers start: 80
  outliers final: 54
  residues processed: 225
  average time/residue: 0.3219
  time to fit residues: 81.8065
Evaluate side-chains
  236 residues out of total 506 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 65
    poor density    : 171
  time to evaluate  : 0.515 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   99 THR
Chi-restraints excluded: chain A residue  107 ASN
Chi-restraints excluded: chain B residue   87 THR
Chi-restraints excluded: chain B residue   91 LEU
Chi-restraints excluded: chain B residue   96 SER
Chi-restraints excluded: chain C residue   87 THR
Chi-restraints excluded: chain C residue   96 SER
Chi-restraints excluded: chain C residue  106 ASN
Chi-restraints excluded: chain C residue  107 ASN
Chi-restraints excluded: chain D residue   91 LEU
Chi-restraints excluded: chain D residue  101 LEU
Chi-restraints excluded: chain D residue  106 ASN
Chi-restraints excluded: chain E residue   99 THR
Chi-restraints excluded: chain E residue  106 ASN
Chi-restraints excluded: chain F residue   87 THR
Chi-restraints excluded: chain F residue   91 LEU
Chi-restraints excluded: chain F residue   96 SER
Chi-restraints excluded: chain F residue  101 LEU
Chi-restraints excluded: chain G residue   94 THR
Chi-restraints excluded: chain G residue   99 THR
Chi-restraints excluded: chain G residue  106 ASN
Chi-restraints excluded: chain H residue   91 LEU
Chi-restraints excluded: chain H residue  100 SER
Chi-restraints excluded: chain I residue   99 THR
Chi-restraints excluded: chain I residue  100 SER
Chi-restraints excluded: chain I residue  106 ASN
Chi-restraints excluded: chain J residue   87 THR
Chi-restraints excluded: chain J residue   91 LEU
Chi-restraints excluded: chain J residue   96 SER
Chi-restraints excluded: chain J residue  106 ASN
Chi-restraints excluded: chain K residue   94 THR
Chi-restraints excluded: chain K residue  106 ASN
Chi-restraints excluded: chain L residue   87 THR
Chi-restraints excluded: chain L residue  100 SER
Chi-restraints excluded: chain L residue  101 LEU
Chi-restraints excluded: chain M residue   96 SER
Chi-restraints excluded: chain M residue  106 ASN
Chi-restraints excluded: chain M residue  107 ASN
Chi-restraints excluded: chain N residue   91 LEU
Chi-restraints excluded: chain N residue  101 LEU
Chi-restraints excluded: chain N residue  106 ASN
Chi-restraints excluded: chain O residue   94 THR
Chi-restraints excluded: chain O residue   99 THR
Chi-restraints excluded: chain O residue  106 ASN
Chi-restraints excluded: chain O residue  107 ASN
Chi-restraints excluded: chain P residue   91 LEU
Chi-restraints excluded: chain P residue   96 SER
Chi-restraints excluded: chain P residue  101 LEU
Chi-restraints excluded: chain Q residue   94 THR
Chi-restraints excluded: chain Q residue   96 SER
Chi-restraints excluded: chain Q residue   99 THR
Chi-restraints excluded: chain Q residue  100 SER
Chi-restraints excluded: chain Q residue  106 ASN
Chi-restraints excluded: chain Q residue  107 ASN
Chi-restraints excluded: chain R residue   91 LEU
Chi-restraints excluded: chain R residue  101 LEU
Chi-restraints excluded: chain S residue   99 THR
Chi-restraints excluded: chain S residue  104 SER
Chi-restraints excluded: chain S residue  106 ASN
Chi-restraints excluded: chain T residue   91 LEU
Chi-restraints excluded: chain T residue  101 LEU
Chi-restraints excluded: chain U residue   96 SER
Chi-restraints excluded: chain U residue   99 THR
Chi-restraints excluded: chain V residue   91 LEU
Chi-restraints excluded: chain V residue  100 SER
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 55
   random chunks:
   chunk 2 optimal weight:    1.9990
   chunk 43 optimal weight:   10.0000
   chunk 49 optimal weight:    0.9990
   chunk 46 optimal weight:    6.9990
   chunk 15 optimal weight:    6.9990
   chunk 32 optimal weight:    4.9990
   chunk 47 optimal weight:    0.9990
   chunk 48 optimal weight:    2.9990
   chunk 39 optimal weight:    6.9990
   chunk 51 optimal weight:    3.9990
   chunk 50 optimal weight:    0.9990
   overall best weight:    1.5990

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

Flipped N/Q/H residues before XYZ refinement:
** A 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 107 ASN
** C 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
F 105 GLN
I 112 ASN
J  89 ASN
J 105 GLN
K 112 ASN
** M 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** M 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
M 112 ASN
N  89 ASN
** O 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
P  89 ASN
R 105 GLN
S 112 ASN
T 105 GLN
** U 106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 12

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3173 r_free = 0.3173 target = 0.075900 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3032 r_free = 0.3032 target = 0.067548 restraints weight = 7695.616|
|-----------------------------------------------------------------------------|
r_work (start): 0.3043 rms_B_bonded: 1.66
r_work: 0.2956 rms_B_bonded: 1.82 restraints_weight: 0.5000
r_work: 0.2861 rms_B_bonded: 3.14 restraints_weight: 0.2500
r_work (final): 0.2861
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8562
moved from start:          0.3150

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.038   4884  Z= 0.208
  Angle     :  0.684   8.833   6611  Z= 0.310
  Chirality :  0.044   0.232    770
  Planarity :  0.002   0.014    880
  Dihedral  :  5.410  26.112    670
  Min Nonbonded Distance : 2.584

Molprobity Statistics.
  All-atom Clashscore : 12.72
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.78 %
    Favored  : 99.22 %
  Rotamer:
    Outliers : 14.62 %
    Allowed  : 25.30 %
    Favored  : 60.08 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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: -4.24 (0.14), residues: 638
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -3.23 (0.11), residues: 638

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 PHE   0.017   0.001   PHE Q 109 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02803 (  160)
  hydrogen bonds       : angle       4.82222 (  480)
  covalent geometry    : bond        0.00462 ( 4884)
  covalent geometry    : angle       0.68417 ( 6611)

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

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

  1276 Ramachandran restraints generated.
    638 Oldfield, 0 Emsley, 638 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1276 Ramachandran restraints generated.
    638 Oldfield, 0 Emsley, 638 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  256 residues out of total 506 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 74
    poor density    : 182
  time to evaluate  : 0.508 
Fit side-chains
REVERT: B   91 LEU cc_start: 0.8644 (OUTLIER) cc_final: 0.8414 (tt)
REVERT: C  106 ASN cc_start: 0.9117 (OUTLIER) cc_final: 0.8591 (p0)
REVERT: D   91 LEU cc_start: 0.8534 (OUTLIER) cc_final: 0.8249 (tt)
REVERT: D  106 ASN cc_start: 0.8702 (OUTLIER) cc_final: 0.8376 (m-40)
REVERT: E  101 LEU cc_start: 0.9384 (tt) cc_final: 0.9125 (tm)
REVERT: F   91 LEU cc_start: 0.8549 (OUTLIER) cc_final: 0.8290 (tt)
REVERT: I   96 SER cc_start: 0.9113 (t) cc_final: 0.8844 (p)
REVERT: I   99 THR cc_start: 0.9286 (OUTLIER) cc_final: 0.8940 (p)
REVERT: J   91 LEU cc_start: 0.8578 (OUTLIER) cc_final: 0.8316 (tt)
REVERT: M  106 ASN cc_start: 0.9163 (OUTLIER) cc_final: 0.8524 (p0)
REVERT: N  106 ASN cc_start: 0.8575 (OUTLIER) cc_final: 0.8240 (m110)
REVERT: O  107 ASN cc_start: 0.8864 (OUTLIER) cc_final: 0.8458 (p0)
REVERT: P   91 LEU cc_start: 0.8510 (OUTLIER) cc_final: 0.8283 (tt)
REVERT: R   91 LEU cc_start: 0.8528 (OUTLIER) cc_final: 0.8202 (tt)
REVERT: R  106 ASN cc_start: 0.8717 (OUTLIER) cc_final: 0.8409 (m110)
REVERT: S  107 ASN cc_start: 0.8847 (OUTLIER) cc_final: 0.8385 (p0)
REVERT: T   91 LEU cc_start: 0.8667 (OUTLIER) cc_final: 0.8403 (mm)
  outliers start: 74
  outliers final: 45
  residues processed: 212
  average time/residue: 0.3100
  time to fit residues: 75.2311
Evaluate side-chains
  228 residues out of total 506 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 60
    poor density    : 168
  time to evaluate  : 0.680 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   99 THR
Chi-restraints excluded: chain A residue  107 ASN
Chi-restraints excluded: chain B residue   87 THR
Chi-restraints excluded: chain B residue   91 LEU
Chi-restraints excluded: chain B residue   96 SER
Chi-restraints excluded: chain C residue   87 THR
Chi-restraints excluded: chain C residue  106 ASN
Chi-restraints excluded: chain C residue  107 ASN
Chi-restraints excluded: chain D residue   91 LEU
Chi-restraints excluded: chain D residue   96 SER
Chi-restraints excluded: chain D residue  101 LEU
Chi-restraints excluded: chain D residue  106 ASN
Chi-restraints excluded: chain E residue   99 THR
Chi-restraints excluded: chain E residue  107 ASN
Chi-restraints excluded: chain F residue   87 THR
Chi-restraints excluded: chain F residue   91 LEU
Chi-restraints excluded: chain F residue   96 SER
Chi-restraints excluded: chain G residue   94 THR
Chi-restraints excluded: chain G residue   96 SER
Chi-restraints excluded: chain G residue   99 THR
Chi-restraints excluded: chain G residue  106 ASN
Chi-restraints excluded: chain H residue   91 LEU
Chi-restraints excluded: chain H residue  101 LEU
Chi-restraints excluded: chain I residue   99 THR
Chi-restraints excluded: chain I residue  106 ASN
Chi-restraints excluded: chain J residue   87 THR
Chi-restraints excluded: chain J residue   91 LEU
Chi-restraints excluded: chain J residue   96 SER
Chi-restraints excluded: chain K residue   94 THR
Chi-restraints excluded: chain K residue   99 THR
Chi-restraints excluded: chain K residue  106 ASN
Chi-restraints excluded: chain L residue   87 THR
Chi-restraints excluded: chain L residue  101 LEU
Chi-restraints excluded: chain L residue  104 SER
Chi-restraints excluded: chain M residue   96 SER
Chi-restraints excluded: chain M residue  106 ASN
Chi-restraints excluded: chain N residue  101 LEU
Chi-restraints excluded: chain N residue  106 ASN
Chi-restraints excluded: chain O residue   94 THR
Chi-restraints excluded: chain O residue   99 THR
Chi-restraints excluded: chain O residue  106 ASN
Chi-restraints excluded: chain O residue  107 ASN
Chi-restraints excluded: chain P residue   91 LEU
Chi-restraints excluded: chain P residue   96 SER
Chi-restraints excluded: chain P residue  101 LEU
Chi-restraints excluded: chain Q residue   94 THR
Chi-restraints excluded: chain Q residue   99 THR
Chi-restraints excluded: chain Q residue  106 ASN
Chi-restraints excluded: chain Q residue  107 ASN
Chi-restraints excluded: chain R residue   91 LEU
Chi-restraints excluded: chain R residue  101 LEU
Chi-restraints excluded: chain R residue  106 ASN
Chi-restraints excluded: chain S residue   99 THR
Chi-restraints excluded: chain S residue  106 ASN
Chi-restraints excluded: chain S residue  107 ASN
Chi-restraints excluded: chain T residue   91 LEU
Chi-restraints excluded: chain T residue   96 SER
Chi-restraints excluded: chain T residue  101 LEU
Chi-restraints excluded: chain U residue   96 SER
Chi-restraints excluded: chain V residue   91 LEU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 55
   random chunks:
   chunk 10 optimal weight:    2.9990
   chunk 48 optimal weight:    8.9990
   chunk 40 optimal weight:    6.9990
   chunk 15 optimal weight:    0.8980
   chunk 43 optimal weight:    4.9990
   chunk 49 optimal weight:    0.9990
   chunk 33 optimal weight:    9.9990
   chunk 44 optimal weight:    0.8980
   chunk 32 optimal weight:    5.9990
   chunk 54 optimal weight:    0.8980
   chunk 24 optimal weight:   10.0000
   overall best weight:    1.3384

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

Flipped N/Q/H residues before XYZ refinement:
** A 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
F 105 GLN
J 105 GLN
J 107 ASN
** K 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
K 112 ASN
** M 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** M 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
M 112 ASN
N 105 GLN
N 107 ASN
P  89 ASN
S 112 ASN
** U 106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 9

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3200 r_free = 0.3200 target = 0.077157 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3063 r_free = 0.3063 target = 0.069032 restraints weight = 7747.055|
|-----------------------------------------------------------------------------|
r_work (start): 0.3068 rms_B_bonded: 1.64
r_work: 0.2984 rms_B_bonded: 1.81 restraints_weight: 0.5000
r_work: 0.2890 rms_B_bonded: 3.12 restraints_weight: 0.2500
r_work (final): 0.2890
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8534
moved from start:          0.3359

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.038   4884  Z= 0.185
  Angle     :  0.670   9.064   6611  Z= 0.301
  Chirality :  0.043   0.226    770
  Planarity :  0.002   0.016    880
  Dihedral  :  5.259  27.509    670
  Min Nonbonded Distance : 2.578

Molprobity Statistics.
  All-atom Clashscore : 11.96
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.94 %
    Favored  : 99.06 %
  Rotamer:
    Outliers : 15.61 %
    Allowed  : 22.53 %
    Favored  : 61.86 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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: -4.21 (0.15), residues: 638
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -3.20 (0.11), residues: 638

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 PHE   0.013   0.001   PHE Q 109 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02542 (  160)
  hydrogen bonds       : angle       4.71594 (  480)
  covalent geometry    : bond        0.00414 ( 4884)
  covalent geometry    : angle       0.67032 ( 6611)

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

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

  1276 Ramachandran restraints generated.
    638 Oldfield, 0 Emsley, 638 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1276 Ramachandran restraints generated.
    638 Oldfield, 0 Emsley, 638 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  251 residues out of total 506 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 79
    poor density    : 172
  time to evaluate  : 0.945 
Fit side-chains
REVERT: C  106 ASN cc_start: 0.9099 (OUTLIER) cc_final: 0.8555 (p0)
REVERT: D   91 LEU cc_start: 0.8523 (OUTLIER) cc_final: 0.8258 (tt)
REVERT: D  106 ASN cc_start: 0.8652 (OUTLIER) cc_final: 0.8323 (m-40)
REVERT: F   91 LEU cc_start: 0.8550 (OUTLIER) cc_final: 0.8272 (tt)
REVERT: I   99 THR cc_start: 0.9272 (OUTLIER) cc_final: 0.8958 (p)
REVERT: J   91 LEU cc_start: 0.8576 (OUTLIER) cc_final: 0.8318 (tt)
REVERT: M  101 LEU cc_start: 0.9302 (tt) cc_final: 0.8986 (tm)
REVERT: M  106 ASN cc_start: 0.9227 (OUTLIER) cc_final: 0.8817 (p0)
REVERT: N  106 ASN cc_start: 0.8646 (OUTLIER) cc_final: 0.8185 (m110)
REVERT: O  107 ASN cc_start: 0.8844 (OUTLIER) cc_final: 0.8446 (p0)
REVERT: P   91 LEU cc_start: 0.8499 (OUTLIER) cc_final: 0.8289 (tt)
REVERT: R   91 LEU cc_start: 0.8493 (OUTLIER) cc_final: 0.8205 (tt)
REVERT: R  106 ASN cc_start: 0.8675 (OUTLIER) cc_final: 0.8364 (m110)
REVERT: S  107 ASN cc_start: 0.8869 (OUTLIER) cc_final: 0.8419 (p0)
REVERT: T   91 LEU cc_start: 0.8568 (OUTLIER) cc_final: 0.8159 (tt)
REVERT: U   96 SER cc_start: 0.9248 (OUTLIER) cc_final: 0.9046 (p)
  outliers start: 79
  outliers final: 49
  residues processed: 207
  average time/residue: 0.3428
  time to fit residues: 80.2031
Evaluate side-chains
  227 residues out of total 506 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 64
    poor density    : 163
  time to evaluate  : 0.580 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   99 THR
Chi-restraints excluded: chain A residue  107 ASN
Chi-restraints excluded: chain B residue   87 THR
Chi-restraints excluded: chain B residue   96 SER
Chi-restraints excluded: chain C residue  106 ASN
Chi-restraints excluded: chain C residue  107 ASN
Chi-restraints excluded: chain D residue   91 LEU
Chi-restraints excluded: chain D residue   96 SER
Chi-restraints excluded: chain D residue  101 LEU
Chi-restraints excluded: chain D residue  106 ASN
Chi-restraints excluded: chain E residue   99 THR
Chi-restraints excluded: chain F residue   87 THR
Chi-restraints excluded: chain F residue   91 LEU
Chi-restraints excluded: chain F residue   96 SER
Chi-restraints excluded: chain G residue   94 THR
Chi-restraints excluded: chain G residue   96 SER
Chi-restraints excluded: chain G residue   99 THR
Chi-restraints excluded: chain G residue  106 ASN
Chi-restraints excluded: chain H residue   91 LEU
Chi-restraints excluded: chain H residue  100 SER
Chi-restraints excluded: chain I residue   96 SER
Chi-restraints excluded: chain I residue   99 THR
Chi-restraints excluded: chain I residue  106 ASN
Chi-restraints excluded: chain J residue   87 THR
Chi-restraints excluded: chain J residue   91 LEU
Chi-restraints excluded: chain J residue   96 SER
Chi-restraints excluded: chain J residue  101 LEU
Chi-restraints excluded: chain K residue   94 THR
Chi-restraints excluded: chain K residue   99 THR
Chi-restraints excluded: chain K residue  106 ASN
Chi-restraints excluded: chain L residue   87 THR
Chi-restraints excluded: chain L residue  100 SER
Chi-restraints excluded: chain L residue  101 LEU
Chi-restraints excluded: chain M residue   96 SER
Chi-restraints excluded: chain M residue   99 THR
Chi-restraints excluded: chain M residue  103 SER
Chi-restraints excluded: chain M residue  106 ASN
Chi-restraints excluded: chain N residue   91 LEU
Chi-restraints excluded: chain N residue  101 LEU
Chi-restraints excluded: chain N residue  106 ASN
Chi-restraints excluded: chain O residue   94 THR
Chi-restraints excluded: chain O residue   99 THR
Chi-restraints excluded: chain O residue  106 ASN
Chi-restraints excluded: chain O residue  107 ASN
Chi-restraints excluded: chain P residue   91 LEU
Chi-restraints excluded: chain P residue  101 LEU
Chi-restraints excluded: chain Q residue   94 THR
Chi-restraints excluded: chain Q residue   96 SER
Chi-restraints excluded: chain Q residue   99 THR
Chi-restraints excluded: chain Q residue  103 SER
Chi-restraints excluded: chain Q residue  106 ASN
Chi-restraints excluded: chain Q residue  107 ASN
Chi-restraints excluded: chain R residue   90 THR
Chi-restraints excluded: chain R residue   91 LEU
Chi-restraints excluded: chain R residue  106 ASN
Chi-restraints excluded: chain S residue   99 THR
Chi-restraints excluded: chain S residue  106 ASN
Chi-restraints excluded: chain S residue  107 ASN
Chi-restraints excluded: chain T residue   91 LEU
Chi-restraints excluded: chain T residue   96 SER
Chi-restraints excluded: chain T residue  101 LEU
Chi-restraints excluded: chain U residue   96 SER
Chi-restraints excluded: chain U residue   99 THR
Chi-restraints excluded: chain V residue   91 LEU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 55
   random chunks:
   chunk 25 optimal weight:    8.9990
   chunk 0 optimal weight:    5.9990
   chunk 42 optimal weight:    4.9990
   chunk 30 optimal weight:    0.9980
   chunk 32 optimal weight:    0.0670
   chunk 35 optimal weight:    1.9990
   chunk 6 optimal weight:    6.9990
   chunk 9 optimal weight:    8.9990
   chunk 11 optimal weight:    0.9990
   chunk 4 optimal weight:    0.9980
   chunk 39 optimal weight:    5.9990
   overall best weight:    1.0122

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

Flipped N/Q/H residues before XYZ refinement:
** A 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 107 ASN
** E 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
F 105 GLN
** G 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** K 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
K 112 ASN
L 107 ASN
** M 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
M 112 ASN
P  89 ASN
S 112 ASN

Total number of N/Q/H flips: 7

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3230 r_free = 0.3230 target = 0.077947 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 28)----------------|
| r_work = 0.3098 r_free = 0.3098 target = 0.069973 restraints weight = 7860.306|
|-----------------------------------------------------------------------------|
r_work (start): 0.3097 rms_B_bonded: 1.68
r_work: 0.3011 rms_B_bonded: 1.85 restraints_weight: 0.5000
r_work: 0.2912 rms_B_bonded: 3.22 restraints_weight: 0.2500
r_work (final): 0.2912
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8540
moved from start:          0.3503

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   4884  Z= 0.155
  Angle     :  0.664   9.653   6611  Z= 0.295
  Chirality :  0.042   0.215    770
  Planarity :  0.002   0.014    880
  Dihedral  :  5.004  28.891    668
  Min Nonbonded Distance : 2.516

Molprobity Statistics.
  All-atom Clashscore : 11.64
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.31 %
    Favored  : 99.69 %
  Rotamer:
    Outliers : 14.23 %
    Allowed  : 23.91 %
    Favored  : 61.86 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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: -4.21 (0.15), residues: 638
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -3.20 (0.11), residues: 638

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 PHE   0.012   0.001   PHE Q 109 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02326 (  160)
  hydrogen bonds       : angle       4.65025 (  480)
  covalent geometry    : bond        0.00347 ( 4884)
  covalent geometry    : angle       0.66444 ( 6611)

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

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

  1276 Ramachandran restraints generated.
    638 Oldfield, 0 Emsley, 638 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1276 Ramachandran restraints generated.
    638 Oldfield, 0 Emsley, 638 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  241 residues out of total 506 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 72
    poor density    : 169
  time to evaluate  : 1.542 
Fit side-chains
REVERT: C  106 ASN cc_start: 0.9090 (OUTLIER) cc_final: 0.8610 (p0)
REVERT: D   91 LEU cc_start: 0.8549 (OUTLIER) cc_final: 0.8302 (tt)
REVERT: E  101 LEU cc_start: 0.9363 (tt) cc_final: 0.9131 (tm)
REVERT: F   91 LEU cc_start: 0.8556 (OUTLIER) cc_final: 0.8300 (tt)
REVERT: G   94 THR cc_start: 0.9173 (OUTLIER) cc_final: 0.8938 (m)
REVERT: I   99 THR cc_start: 0.9288 (OUTLIER) cc_final: 0.8988 (p)
REVERT: J   91 LEU cc_start: 0.8593 (OUTLIER) cc_final: 0.8343 (tt)
REVERT: K  107 ASN cc_start: 0.8846 (m110) cc_final: 0.8599 (m110)
REVERT: M  101 LEU cc_start: 0.9278 (tt) cc_final: 0.8992 (tm)
REVERT: M  106 ASN cc_start: 0.9186 (OUTLIER) cc_final: 0.8706 (p0)
REVERT: N   87 THR cc_start: 0.9155 (t) cc_final: 0.8944 (m)
REVERT: N   91 LEU cc_start: 0.8549 (OUTLIER) cc_final: 0.8305 (tt)
REVERT: N  106 ASN cc_start: 0.8619 (OUTLIER) cc_final: 0.8215 (m110)
REVERT: O  107 ASN cc_start: 0.8857 (OUTLIER) cc_final: 0.8352 (p0)
REVERT: R   91 LEU cc_start: 0.8491 (OUTLIER) cc_final: 0.8209 (tt)
REVERT: R  106 ASN cc_start: 0.8671 (OUTLIER) cc_final: 0.8391 (m110)
REVERT: T   91 LEU cc_start: 0.8565 (OUTLIER) cc_final: 0.8173 (tt)
  outliers start: 72
  outliers final: 46
  residues processed: 202
  average time/residue: 0.5819
  time to fit residues: 133.2758
Evaluate side-chains
  220 residues out of total 506 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 59
    poor density    : 161
  time to evaluate  : 0.777 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   99 THR
Chi-restraints excluded: chain B residue   87 THR
Chi-restraints excluded: chain B residue   96 SER
Chi-restraints excluded: chain C residue   87 THR
Chi-restraints excluded: chain C residue  106 ASN
Chi-restraints excluded: chain C residue  107 ASN
Chi-restraints excluded: chain D residue   91 LEU
Chi-restraints excluded: chain D residue   96 SER
Chi-restraints excluded: chain D residue  101 LEU
Chi-restraints excluded: chain E residue   99 THR
Chi-restraints excluded: chain E residue  107 ASN
Chi-restraints excluded: chain F residue   87 THR
Chi-restraints excluded: chain F residue   91 LEU
Chi-restraints excluded: chain F residue   96 SER
Chi-restraints excluded: chain F residue  101 LEU
Chi-restraints excluded: chain G residue   94 THR
Chi-restraints excluded: chain G residue   96 SER
Chi-restraints excluded: chain G residue   99 THR
Chi-restraints excluded: chain G residue  106 ASN
Chi-restraints excluded: chain H residue   91 LEU
Chi-restraints excluded: chain I residue   96 SER
Chi-restraints excluded: chain I residue   99 THR
Chi-restraints excluded: chain I residue  106 ASN
Chi-restraints excluded: chain J residue   87 THR
Chi-restraints excluded: chain J residue   91 LEU
Chi-restraints excluded: chain J residue   96 SER
Chi-restraints excluded: chain J residue  101 LEU
Chi-restraints excluded: chain J residue  106 ASN
Chi-restraints excluded: chain K residue   94 THR
Chi-restraints excluded: chain K residue   99 THR
Chi-restraints excluded: chain K residue  106 ASN
Chi-restraints excluded: chain L residue   87 THR
Chi-restraints excluded: chain L residue  101 LEU
Chi-restraints excluded: chain M residue   96 SER
Chi-restraints excluded: chain M residue   99 THR
Chi-restraints excluded: chain M residue  103 SER
Chi-restraints excluded: chain M residue  106 ASN
Chi-restraints excluded: chain N residue   91 LEU
Chi-restraints excluded: chain N residue  101 LEU
Chi-restraints excluded: chain N residue  106 ASN
Chi-restraints excluded: chain O residue   94 THR
Chi-restraints excluded: chain O residue   99 THR
Chi-restraints excluded: chain O residue  106 ASN
Chi-restraints excluded: chain O residue  107 ASN
Chi-restraints excluded: chain Q residue   94 THR
Chi-restraints excluded: chain Q residue   99 THR
Chi-restraints excluded: chain Q residue  103 SER
Chi-restraints excluded: chain Q residue  106 ASN
Chi-restraints excluded: chain R residue   90 THR
Chi-restraints excluded: chain R residue   91 LEU
Chi-restraints excluded: chain R residue  106 ASN
Chi-restraints excluded: chain S residue   99 THR
Chi-restraints excluded: chain S residue  106 ASN
Chi-restraints excluded: chain T residue   91 LEU
Chi-restraints excluded: chain T residue   96 SER
Chi-restraints excluded: chain T residue  101 LEU
Chi-restraints excluded: chain U residue   99 THR
Chi-restraints excluded: chain V residue   91 LEU
Chi-restraints excluded: chain V residue  101 LEU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 55
   random chunks:
   chunk 22 optimal weight:    0.9980
   chunk 37 optimal weight:    2.9990
   chunk 31 optimal weight:    4.9990
   chunk 2 optimal weight:    4.9990
   chunk 42 optimal weight:    0.6980
   chunk 17 optimal weight:    0.8980
   chunk 29 optimal weight:    2.9990
   chunk 15 optimal weight:    5.9990
   chunk 44 optimal weight:   10.0000
   chunk 43 optimal weight:    4.9990
   chunk 26 optimal weight:    3.9990
   overall best weight:    1.7184

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

Flipped N/Q/H residues before XYZ refinement:
** A 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 105 GLN
C 111 GLN
** E 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
F 105 GLN
** G 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
G 112 ASN
I 112 ASN
J 105 GLN
J 107 ASN
** K 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
K 112 ASN
M 112 ASN
N 105 GLN
** O 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
S 112 ASN

Total number of N/Q/H flips: 11

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3183 r_free = 0.3183 target = 0.075620 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.3050 r_free = 0.3050 target = 0.067594 restraints weight = 7856.540|
|-----------------------------------------------------------------------------|
r_work (start): 0.3056 rms_B_bonded: 1.70
r_work: 0.2966 rms_B_bonded: 1.86 restraints_weight: 0.5000
r_work: 0.2867 rms_B_bonded: 3.21 restraints_weight: 0.2500
r_work (final): 0.2867
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8577
moved from start:          0.3550

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.041   4884  Z= 0.215
  Angle     :  0.687   9.821   6611  Z= 0.309
  Chirality :  0.045   0.248    770
  Planarity :  0.002   0.015    880
  Dihedral  :  4.927  28.888    666
  Min Nonbonded Distance : 2.589

Molprobity Statistics.
  All-atom Clashscore : 12.29
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.94 %
    Favored  : 99.06 %
  Rotamer:
    Outliers : 13.83 %
    Allowed  : 24.31 %
    Favored  : 61.86 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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: -4.16 (0.15), residues: 638
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -3.16 (0.11), residues: 638

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 PHE   0.013   0.001   PHE Q 109 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02445 (  160)
  hydrogen bonds       : angle       4.60355 (  480)
  covalent geometry    : bond        0.00484 ( 4884)
  covalent geometry    : angle       0.68667 ( 6611)

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

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

  1276 Ramachandran restraints generated.
    638 Oldfield, 0 Emsley, 638 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1276 Ramachandran restraints generated.
    638 Oldfield, 0 Emsley, 638 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  232 residues out of total 506 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 70
    poor density    : 162
  time to evaluate  : 1.689 
Fit side-chains
REVERT: C  106 ASN cc_start: 0.9089 (OUTLIER) cc_final: 0.8653 (p0)
REVERT: D   91 LEU cc_start: 0.8551 (OUTLIER) cc_final: 0.8317 (tt)
REVERT: E   94 THR cc_start: 0.9176 (t) cc_final: 0.8958 (m)
REVERT: E  101 LEU cc_start: 0.9383 (tt) cc_final: 0.9155 (tm)
REVERT: F   91 LEU cc_start: 0.8572 (OUTLIER) cc_final: 0.8324 (tt)
REVERT: G   94 THR cc_start: 0.9179 (OUTLIER) cc_final: 0.8937 (m)
REVERT: I   99 THR cc_start: 0.9310 (OUTLIER) cc_final: 0.9019 (p)
REVERT: J   91 LEU cc_start: 0.8607 (OUTLIER) cc_final: 0.8321 (tt)
REVERT: J  105 GLN cc_start: 0.8724 (tt0) cc_final: 0.8438 (tt0)
REVERT: K  107 ASN cc_start: 0.8929 (m110) cc_final: 0.8651 (m110)
REVERT: N   87 THR cc_start: 0.9143 (t) cc_final: 0.8932 (m)
REVERT: N   91 LEU cc_start: 0.8577 (OUTLIER) cc_final: 0.8294 (tt)
REVERT: N  106 ASN cc_start: 0.8593 (OUTLIER) cc_final: 0.8145 (m110)
REVERT: O  107 ASN cc_start: 0.8823 (OUTLIER) cc_final: 0.8337 (p0)
REVERT: R   91 LEU cc_start: 0.8521 (OUTLIER) cc_final: 0.8238 (tt)
REVERT: R  106 ASN cc_start: 0.8690 (OUTLIER) cc_final: 0.8401 (m110)
REVERT: T   91 LEU cc_start: 0.8573 (OUTLIER) cc_final: 0.8155 (tt)
  outliers start: 70
  outliers final: 48
  residues processed: 192
  average time/residue: 0.3526
  time to fit residues: 76.7285
Evaluate side-chains
  220 residues out of total 506 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 60
    poor density    : 160
  time to evaluate  : 0.493 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   90 THR
Chi-restraints excluded: chain A residue   99 THR
Chi-restraints excluded: chain B residue   87 THR
Chi-restraints excluded: chain B residue   96 SER
Chi-restraints excluded: chain C residue   87 THR
Chi-restraints excluded: chain C residue   99 THR
Chi-restraints excluded: chain C residue  106 ASN
Chi-restraints excluded: chain C residue  107 ASN
Chi-restraints excluded: chain D residue   91 LEU
Chi-restraints excluded: chain D residue   96 SER
Chi-restraints excluded: chain D residue  101 LEU
Chi-restraints excluded: chain E residue   99 THR
Chi-restraints excluded: chain E residue  106 ASN
Chi-restraints excluded: chain E residue  107 ASN
Chi-restraints excluded: chain F residue   87 THR
Chi-restraints excluded: chain F residue   91 LEU
Chi-restraints excluded: chain F residue   96 SER
Chi-restraints excluded: chain F residue  101 LEU
Chi-restraints excluded: chain G residue   94 THR
Chi-restraints excluded: chain G residue   96 SER
Chi-restraints excluded: chain G residue   99 THR
Chi-restraints excluded: chain G residue  106 ASN
Chi-restraints excluded: chain H residue   91 LEU
Chi-restraints excluded: chain I residue   96 SER
Chi-restraints excluded: chain I residue   99 THR
Chi-restraints excluded: chain I residue  106 ASN
Chi-restraints excluded: chain J residue   87 THR
Chi-restraints excluded: chain J residue   91 LEU
Chi-restraints excluded: chain J residue   96 SER
Chi-restraints excluded: chain J residue  101 LEU
Chi-restraints excluded: chain K residue   99 THR
Chi-restraints excluded: chain K residue  106 ASN
Chi-restraints excluded: chain L residue   87 THR
Chi-restraints excluded: chain L residue  101 LEU
Chi-restraints excluded: chain M residue   96 SER
Chi-restraints excluded: chain M residue   99 THR
Chi-restraints excluded: chain M residue  106 ASN
Chi-restraints excluded: chain N residue   91 LEU
Chi-restraints excluded: chain N residue  106 ASN
Chi-restraints excluded: chain O residue   94 THR
Chi-restraints excluded: chain O residue   99 THR
Chi-restraints excluded: chain O residue  106 ASN
Chi-restraints excluded: chain O residue  107 ASN
Chi-restraints excluded: chain P residue  101 LEU
Chi-restraints excluded: chain Q residue   94 THR
Chi-restraints excluded: chain Q residue   96 SER
Chi-restraints excluded: chain Q residue   99 THR
Chi-restraints excluded: chain Q residue  103 SER
Chi-restraints excluded: chain Q residue  106 ASN
Chi-restraints excluded: chain R residue   90 THR
Chi-restraints excluded: chain R residue   91 LEU
Chi-restraints excluded: chain R residue  101 LEU
Chi-restraints excluded: chain R residue  106 ASN
Chi-restraints excluded: chain S residue   99 THR
Chi-restraints excluded: chain S residue  106 ASN
Chi-restraints excluded: chain T residue   91 LEU
Chi-restraints excluded: chain T residue   96 SER
Chi-restraints excluded: chain T residue  101 LEU
Chi-restraints excluded: chain U residue   99 THR
Chi-restraints excluded: chain V residue   91 LEU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 55
   random chunks:
   chunk 21 optimal weight:    7.9990
   chunk 38 optimal weight:   10.0000
   chunk 18 optimal weight:   10.0000
   chunk 7 optimal weight:    1.9990
   chunk 29 optimal weight:    7.9990
   chunk 22 optimal weight:    0.9990
   chunk 46 optimal weight:    4.9990
   chunk 10 optimal weight:    5.9990
   chunk 51 optimal weight:    0.9990
   chunk 3 optimal weight:    6.9990
   chunk 35 optimal weight:    2.9990
   overall best weight:    2.3990

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

Flipped N/Q/H residues before XYZ refinement:
** A 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 105 GLN
B 107 ASN
** C 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 111 GLN
** E 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
F 105 GLN
** K 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
K 112 ASN
L 107 ASN
M 112 ASN
N 105 GLN
** O 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
P 105 GLN
S 112 ASN

Total number of N/Q/H flips: 10

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3145 r_free = 0.3145 target = 0.073709 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 24)----------------|
| r_work = 0.3010 r_free = 0.3010 target = 0.065603 restraints weight = 7969.088|
|-----------------------------------------------------------------------------|
r_work (start): 0.3018 rms_B_bonded: 1.72
r_work: 0.2926 rms_B_bonded: 1.86 restraints_weight: 0.5000
r_work: 0.2826 rms_B_bonded: 3.21 restraints_weight: 0.2500
r_work (final): 0.2826
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8607
moved from start:          0.3555

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.050   4884  Z= 0.278
  Angle     :  0.726   9.995   6611  Z= 0.328
  Chirality :  0.048   0.328    770
  Planarity :  0.003   0.018    880
  Dihedral  :  4.948  38.990    664
  Min Nonbonded Distance : 2.451

Molprobity Statistics.
  All-atom Clashscore : 12.18
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.10 %
    Favored  : 98.90 %
  Rotamer:
    Outliers : 14.43 %
    Allowed  : 23.72 %
    Favored  : 61.86 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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: -4.11 (0.15), residues: 638
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -3.13 (0.11), residues: 638

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 PHE   0.015   0.001   PHE Q 109 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02638 (  160)
  hydrogen bonds       : angle       4.59837 (  480)
  covalent geometry    : bond        0.00623 ( 4884)
  covalent geometry    : angle       0.72609 ( 6611)

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

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

  1276 Ramachandran restraints generated.
    638 Oldfield, 0 Emsley, 638 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1276 Ramachandran restraints generated.
    638 Oldfield, 0 Emsley, 638 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  240 residues out of total 506 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 73
    poor density    : 167
  time to evaluate  : 1.097 
Fit side-chains
REVERT: C  106 ASN cc_start: 0.9156 (OUTLIER) cc_final: 0.8712 (p0)
REVERT: D   91 LEU cc_start: 0.8536 (OUTLIER) cc_final: 0.8285 (tt)
REVERT: D  106 ASN cc_start: 0.8648 (OUTLIER) cc_final: 0.8367 (m110)
REVERT: E   94 THR cc_start: 0.9189 (t) cc_final: 0.8962 (m)
REVERT: E  101 LEU cc_start: 0.9402 (tt) cc_final: 0.9163 (tm)
REVERT: G   94 THR cc_start: 0.9182 (OUTLIER) cc_final: 0.8954 (m)
REVERT: I   99 THR cc_start: 0.9336 (OUTLIER) cc_final: 0.9063 (p)
REVERT: K  107 ASN cc_start: 0.8931 (m110) cc_final: 0.8674 (m110)
REVERT: M   99 THR cc_start: 0.9264 (OUTLIER) cc_final: 0.9042 (p)
REVERT: N   87 THR cc_start: 0.9149 (t) cc_final: 0.8936 (m)
REVERT: N  106 ASN cc_start: 0.8558 (OUTLIER) cc_final: 0.8162 (m110)
REVERT: O  107 ASN cc_start: 0.8801 (OUTLIER) cc_final: 0.8235 (p0)
REVERT: P  105 GLN cc_start: 0.9035 (tt0) cc_final: 0.8833 (tt0)
REVERT: R   91 LEU cc_start: 0.8562 (OUTLIER) cc_final: 0.8255 (tt)
REVERT: R  106 ASN cc_start: 0.8676 (OUTLIER) cc_final: 0.8375 (m110)
REVERT: T   91 LEU cc_start: 0.8705 (OUTLIER) cc_final: 0.8451 (mm)
  outliers start: 73
  outliers final: 51
  residues processed: 198
  average time/residue: 0.6320
  time to fit residues: 141.5597
Evaluate side-chains
  228 residues out of total 506 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 62
    poor density    : 166
  time to evaluate  : 0.690 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   90 THR
Chi-restraints excluded: chain A residue   99 THR
Chi-restraints excluded: chain B residue   87 THR
Chi-restraints excluded: chain B residue   96 SER
Chi-restraints excluded: chain C residue   87 THR
Chi-restraints excluded: chain C residue   96 SER
Chi-restraints excluded: chain C residue   99 THR
Chi-restraints excluded: chain C residue  106 ASN
Chi-restraints excluded: chain C residue  107 ASN
Chi-restraints excluded: chain D residue   91 LEU
Chi-restraints excluded: chain D residue   96 SER
Chi-restraints excluded: chain D residue  101 LEU
Chi-restraints excluded: chain D residue  106 ASN
Chi-restraints excluded: chain E residue   99 THR
Chi-restraints excluded: chain E residue  107 ASN
Chi-restraints excluded: chain F residue   87 THR
Chi-restraints excluded: chain F residue   91 LEU
Chi-restraints excluded: chain F residue   96 SER
Chi-restraints excluded: chain F residue  101 LEU
Chi-restraints excluded: chain G residue   94 THR
Chi-restraints excluded: chain G residue   96 SER
Chi-restraints excluded: chain G residue   99 THR
Chi-restraints excluded: chain G residue  106 ASN
Chi-restraints excluded: chain H residue   91 LEU
Chi-restraints excluded: chain I residue   96 SER
Chi-restraints excluded: chain I residue   99 THR
Chi-restraints excluded: chain I residue  106 ASN
Chi-restraints excluded: chain J residue   87 THR
Chi-restraints excluded: chain J residue   96 SER
Chi-restraints excluded: chain K residue   94 THR
Chi-restraints excluded: chain K residue   99 THR
Chi-restraints excluded: chain K residue  106 ASN
Chi-restraints excluded: chain L residue   87 THR
Chi-restraints excluded: chain L residue  104 SER
Chi-restraints excluded: chain M residue   96 SER
Chi-restraints excluded: chain M residue   99 THR
Chi-restraints excluded: chain M residue  106 ASN
Chi-restraints excluded: chain N residue   91 LEU
Chi-restraints excluded: chain N residue  106 ASN
Chi-restraints excluded: chain O residue   94 THR
Chi-restraints excluded: chain O residue   99 THR
Chi-restraints excluded: chain O residue  106 ASN
Chi-restraints excluded: chain O residue  107 ASN
Chi-restraints excluded: chain P residue  101 LEU
Chi-restraints excluded: chain Q residue   94 THR
Chi-restraints excluded: chain Q residue   96 SER
Chi-restraints excluded: chain Q residue   99 THR
Chi-restraints excluded: chain Q residue  103 SER
Chi-restraints excluded: chain Q residue  106 ASN
Chi-restraints excluded: chain R residue   90 THR
Chi-restraints excluded: chain R residue   91 LEU
Chi-restraints excluded: chain R residue  101 LEU
Chi-restraints excluded: chain R residue  106 ASN
Chi-restraints excluded: chain S residue   99 THR
Chi-restraints excluded: chain S residue  103 SER
Chi-restraints excluded: chain S residue  106 ASN
Chi-restraints excluded: chain T residue   90 THR
Chi-restraints excluded: chain T residue   91 LEU
Chi-restraints excluded: chain T residue   96 SER
Chi-restraints excluded: chain T residue  101 LEU
Chi-restraints excluded: chain U residue   99 THR
Chi-restraints excluded: chain V residue   91 LEU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 55
   random chunks:
   chunk 7 optimal weight:    0.8980
   chunk 37 optimal weight:    0.3980
   chunk 29 optimal weight:    8.9990
   chunk 14 optimal weight:    5.9990
   chunk 43 optimal weight:    5.9990
   chunk 31 optimal weight:    0.9990
   chunk 50 optimal weight:    5.9990
   chunk 10 optimal weight:    1.9990
   chunk 24 optimal weight:    0.8980
   chunk 5 optimal weight:    0.6980
   chunk 46 optimal weight:    1.9990
   overall best weight:    0.7782

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

Flipped N/Q/H residues before XYZ refinement:
** A 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 105 GLN
C 111 GLN
** E 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
F 105 GLN
** G 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
J 105 GLN
J 107 ASN
** K 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
K 112 ASN
M 112 ASN
** O 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
P 105 GLN
R 105 GLN
S 112 ASN

Total number of N/Q/H flips: 10

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3234 r_free = 0.3234 target = 0.077927 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3106 r_free = 0.3106 target = 0.069982 restraints weight = 7757.788|
|-----------------------------------------------------------------------------|
r_work (start): 0.3109 rms_B_bonded: 1.69
r_work: 0.3020 rms_B_bonded: 1.86 restraints_weight: 0.5000
r_work: 0.2922 rms_B_bonded: 3.22 restraints_weight: 0.2500
r_work (final): 0.2922
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8546
moved from start:          0.3769

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   4884  Z= 0.140
  Angle     :  0.655   9.450   6611  Z= 0.292
  Chirality :  0.041   0.241    770
  Planarity :  0.002   0.015    880
  Dihedral  :  4.413  19.265    662
  Min Nonbonded Distance : 2.599

Molprobity Statistics.
  All-atom Clashscore : 12.07
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.47 %
    Favored  : 99.53 %
  Rotamer:
    Outliers : 12.06 %
    Allowed  : 26.68 %
    Favored  : 61.26 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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: -4.21 (0.15), residues: 638
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -3.20 (0.11), residues: 638

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 PHE   0.007   0.001   PHE H  92 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02205 (  160)
  hydrogen bonds       : angle       4.54202 (  480)
  covalent geometry    : bond        0.00310 ( 4884)
  covalent geometry    : angle       0.65479 ( 6611)

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

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

  1276 Ramachandran restraints generated.
    638 Oldfield, 0 Emsley, 638 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1276 Ramachandran restraints generated.
    638 Oldfield, 0 Emsley, 638 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  225 residues out of total 506 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 61
    poor density    : 164
  time to evaluate  : 1.600 
Fit side-chains
REVERT: C  106 ASN cc_start: 0.9102 (OUTLIER) cc_final: 0.8707 (p0)
REVERT: D  106 ASN cc_start: 0.8614 (OUTLIER) cc_final: 0.8294 (m110)
REVERT: E  101 LEU cc_start: 0.9375 (tt) cc_final: 0.9146 (tm)
REVERT: F   91 LEU cc_start: 0.8548 (OUTLIER) cc_final: 0.8317 (tt)
REVERT: G   94 THR cc_start: 0.9173 (OUTLIER) cc_final: 0.8970 (m)
REVERT: J   91 LEU cc_start: 0.8594 (mm) cc_final: 0.8356 (tt)
REVERT: K   99 THR cc_start: 0.9297 (OUTLIER) cc_final: 0.9067 (p)
REVERT: N   87 THR cc_start: 0.9125 (t) cc_final: 0.8916 (m)
REVERT: N   91 LEU cc_start: 0.8506 (OUTLIER) cc_final: 0.8263 (tt)
REVERT: N  106 ASN cc_start: 0.8581 (OUTLIER) cc_final: 0.8130 (m110)
REVERT: O  107 ASN cc_start: 0.8523 (OUTLIER) cc_final: 0.8300 (p0)
REVERT: R   91 LEU cc_start: 0.8476 (OUTLIER) cc_final: 0.8271 (tt)
REVERT: R  106 ASN cc_start: 0.8644 (OUTLIER) cc_final: 0.8355 (m110)
REVERT: T   91 LEU cc_start: 0.8547 (OUTLIER) cc_final: 0.8177 (tt)
REVERT: V  106 ASN cc_start: 0.8564 (m110) cc_final: 0.8197 (t0)
  outliers start: 61
  outliers final: 40
  residues processed: 196
  average time/residue: 0.5793
  time to fit residues: 132.9069
Evaluate side-chains
  211 residues out of total 506 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 51
    poor density    : 160
  time to evaluate  : 0.577 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   99 THR
Chi-restraints excluded: chain B residue   87 THR
Chi-restraints excluded: chain C residue   87 THR
Chi-restraints excluded: chain C residue   99 THR
Chi-restraints excluded: chain C residue  106 ASN
Chi-restraints excluded: chain D residue   96 SER
Chi-restraints excluded: chain D residue  101 LEU
Chi-restraints excluded: chain D residue  106 ASN
Chi-restraints excluded: chain E residue   99 THR
Chi-restraints excluded: chain E residue  107 ASN
Chi-restraints excluded: chain F residue   87 THR
Chi-restraints excluded: chain F residue   91 LEU
Chi-restraints excluded: chain F residue   96 SER
Chi-restraints excluded: chain F residue  101 LEU
Chi-restraints excluded: chain G residue   94 THR
Chi-restraints excluded: chain G residue   96 SER
Chi-restraints excluded: chain G residue   99 THR
Chi-restraints excluded: chain G residue  106 ASN
Chi-restraints excluded: chain I residue   96 SER
Chi-restraints excluded: chain I residue  106 ASN
Chi-restraints excluded: chain J residue   87 THR
Chi-restraints excluded: chain J residue   96 SER
Chi-restraints excluded: chain K residue   94 THR
Chi-restraints excluded: chain K residue   99 THR
Chi-restraints excluded: chain K residue  106 ASN
Chi-restraints excluded: chain M residue   96 SER
Chi-restraints excluded: chain M residue   99 THR
Chi-restraints excluded: chain M residue  106 ASN
Chi-restraints excluded: chain N residue   91 LEU
Chi-restraints excluded: chain N residue  106 ASN
Chi-restraints excluded: chain O residue   94 THR
Chi-restraints excluded: chain O residue   99 THR
Chi-restraints excluded: chain O residue  106 ASN
Chi-restraints excluded: chain O residue  107 ASN
Chi-restraints excluded: chain P residue   96 SER
Chi-restraints excluded: chain P residue  101 LEU
Chi-restraints excluded: chain Q residue   99 THR
Chi-restraints excluded: chain Q residue  103 SER
Chi-restraints excluded: chain Q residue  106 ASN
Chi-restraints excluded: chain R residue   90 THR
Chi-restraints excluded: chain R residue   91 LEU
Chi-restraints excluded: chain R residue  101 LEU
Chi-restraints excluded: chain R residue  106 ASN
Chi-restraints excluded: chain S residue   99 THR
Chi-restraints excluded: chain S residue  103 SER
Chi-restraints excluded: chain T residue   91 LEU
Chi-restraints excluded: chain T residue   96 SER
Chi-restraints excluded: chain T residue  101 LEU
Chi-restraints excluded: chain U residue   99 THR
Chi-restraints excluded: chain V residue   91 LEU
Chi-restraints excluded: chain V residue  101 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 55
   random chunks:
   chunk 28 optimal weight:    9.9990
   chunk 4 optimal weight:    6.9990
   chunk 54 optimal weight:    1.9990
   chunk 8 optimal weight:   10.0000
   chunk 21 optimal weight:    0.9980
   chunk 6 optimal weight:    6.9990
   chunk 46 optimal weight:    8.9990
   chunk 13 optimal weight:    2.9990
   chunk 1 optimal weight:    0.7980
   chunk 16 optimal weight:    3.9990
   chunk 19 optimal weight:    1.9990
   overall best weight:    1.7586

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

Flipped N/Q/H residues before XYZ refinement:
** A 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 105 GLN
B 107 ASN
** E 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
F 105 GLN
** G 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
G 112 ASN
I 112 ASN
J 105 GLN
** K 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
L 107 ASN
** O 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
R 105 GLN
S 112 ASN

Total number of N/Q/H flips: 9

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3193 r_free = 0.3193 target = 0.075917 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3061 r_free = 0.3061 target = 0.067859 restraints weight = 7775.587|
|-----------------------------------------------------------------------------|
r_work (start): 0.3066 rms_B_bonded: 1.68
r_work: 0.2978 rms_B_bonded: 1.83 restraints_weight: 0.5000
r_work: 0.2879 rms_B_bonded: 3.16 restraints_weight: 0.2500
r_work (final): 0.2879
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8569
moved from start:          0.3763

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.038   4884  Z= 0.214
  Angle     :  0.697   9.628   6611  Z= 0.310
  Chirality :  0.044   0.277    770
  Planarity :  0.002   0.015    880
  Dihedral  :  4.486  18.281    662
  Min Nonbonded Distance : 2.447

Molprobity Statistics.
  All-atom Clashscore : 11.74
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.78 %
    Favored  : 99.22 %
  Rotamer:
    Outliers : 11.46 %
    Allowed  : 27.27 %
    Favored  : 61.26 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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: -4.18 (0.15), residues: 638
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -3.18 (0.11), residues: 638

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 PHE   0.012   0.001   PHE Q 109 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02422 (  160)
  hydrogen bonds       : angle       4.44836 (  480)
  covalent geometry    : bond        0.00481 ( 4884)
  covalent geometry    : angle       0.69666 ( 6611)

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

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

  1276 Ramachandran restraints generated.
    638 Oldfield, 0 Emsley, 638 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1276 Ramachandran restraints generated.
    638 Oldfield, 0 Emsley, 638 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  217 residues out of total 506 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 58
    poor density    : 159
  time to evaluate  : 0.541 
Fit side-chains
REVERT: C  106 ASN cc_start: 0.9050 (OUTLIER) cc_final: 0.8698 (p0)
REVERT: D  106 ASN cc_start: 0.8622 (OUTLIER) cc_final: 0.8338 (m110)
REVERT: E  101 LEU cc_start: 0.9391 (tt) cc_final: 0.9121 (tm)
REVERT: F   91 LEU cc_start: 0.8562 (OUTLIER) cc_final: 0.8358 (tt)
REVERT: J   91 LEU cc_start: 0.8641 (mm) cc_final: 0.8340 (tt)
REVERT: J  105 GLN cc_start: 0.8686 (tt0) cc_final: 0.8411 (tt0)
REVERT: K  107 ASN cc_start: 0.8980 (m110) cc_final: 0.8710 (m-40)
REVERT: N   87 THR cc_start: 0.9104 (t) cc_final: 0.8877 (m)
REVERT: N   91 LEU cc_start: 0.8584 (OUTLIER) cc_final: 0.8298 (tt)
REVERT: N  106 ASN cc_start: 0.8520 (OUTLIER) cc_final: 0.8104 (m110)
REVERT: O  107 ASN cc_start: 0.8623 (OUTLIER) cc_final: 0.8333 (p0)
REVERT: R   91 LEU cc_start: 0.8514 (OUTLIER) cc_final: 0.8287 (tt)
REVERT: R  106 ASN cc_start: 0.8651 (OUTLIER) cc_final: 0.8350 (m110)
REVERT: T   91 LEU cc_start: 0.8679 (OUTLIER) cc_final: 0.8264 (tt)
REVERT: V  106 ASN cc_start: 0.8526 (m110) cc_final: 0.8196 (t0)
  outliers start: 58
  outliers final: 40
  residues processed: 188
  average time/residue: 0.3600
  time to fit residues: 76.3085
Evaluate side-chains
  206 residues out of total 506 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 49
    poor density    : 157
  time to evaluate  : 0.560 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   99 THR
Chi-restraints excluded: chain B residue   87 THR
Chi-restraints excluded: chain B residue   96 SER
Chi-restraints excluded: chain C residue   87 THR
Chi-restraints excluded: chain C residue   99 THR
Chi-restraints excluded: chain C residue  106 ASN
Chi-restraints excluded: chain D residue   96 SER
Chi-restraints excluded: chain D residue  101 LEU
Chi-restraints excluded: chain D residue  106 ASN
Chi-restraints excluded: chain E residue   99 THR
Chi-restraints excluded: chain F residue   87 THR
Chi-restraints excluded: chain F residue   91 LEU
Chi-restraints excluded: chain F residue   96 SER
Chi-restraints excluded: chain F residue  101 LEU
Chi-restraints excluded: chain G residue   96 SER
Chi-restraints excluded: chain G residue   99 THR
Chi-restraints excluded: chain G residue  106 ASN
Chi-restraints excluded: chain I residue   96 SER
Chi-restraints excluded: chain I residue  106 ASN
Chi-restraints excluded: chain J residue   87 THR
Chi-restraints excluded: chain J residue   96 SER
Chi-restraints excluded: chain J residue  101 LEU
Chi-restraints excluded: chain J residue  106 ASN
Chi-restraints excluded: chain K residue   94 THR
Chi-restraints excluded: chain K residue  106 ASN
Chi-restraints excluded: chain M residue   96 SER
Chi-restraints excluded: chain M residue   99 THR
Chi-restraints excluded: chain M residue  106 ASN
Chi-restraints excluded: chain N residue   91 LEU
Chi-restraints excluded: chain N residue  106 ASN
Chi-restraints excluded: chain O residue   94 THR
Chi-restraints excluded: chain O residue   99 THR
Chi-restraints excluded: chain O residue  106 ASN
Chi-restraints excluded: chain O residue  107 ASN
Chi-restraints excluded: chain P residue  101 LEU
Chi-restraints excluded: chain Q residue   99 THR
Chi-restraints excluded: chain Q residue  103 SER
Chi-restraints excluded: chain Q residue  106 ASN
Chi-restraints excluded: chain R residue   90 THR
Chi-restraints excluded: chain R residue   91 LEU
Chi-restraints excluded: chain R residue  101 LEU
Chi-restraints excluded: chain R residue  106 ASN
Chi-restraints excluded: chain S residue   99 THR
Chi-restraints excluded: chain S residue  103 SER
Chi-restraints excluded: chain T residue   91 LEU
Chi-restraints excluded: chain T residue   96 SER
Chi-restraints excluded: chain T residue  101 LEU
Chi-restraints excluded: chain U residue   99 THR
Chi-restraints excluded: chain V residue   91 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 55
   random chunks:
   chunk 49 optimal weight:    6.9990
   chunk 43 optimal weight:    8.9990
   chunk 35 optimal weight:    5.9990
   chunk 5 optimal weight:    4.9990
   chunk 23 optimal weight:   10.0000
   chunk 10 optimal weight:    0.7980
   chunk 9 optimal weight:   10.0000
   chunk 29 optimal weight:    1.9990
   chunk 20 optimal weight:    4.9990
   chunk 21 optimal weight:    2.9990
   chunk 32 optimal weight:    1.9990
   overall best weight:    2.5588

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

Flipped N/Q/H residues before XYZ refinement:
** A 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 105 GLN
** E 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
F 105 GLN
** G 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
J 107 ASN
** K 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
K 112 ASN
M 112 ASN
** O 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
P 105 GLN
S 112 ASN

Total number of N/Q/H flips: 7

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3137 r_free = 0.3137 target = 0.073389 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3001 r_free = 0.3001 target = 0.065239 restraints weight = 7873.393|
|-----------------------------------------------------------------------------|
r_work (start): 0.3009 rms_B_bonded: 1.69
r_work: 0.2924 rms_B_bonded: 1.81 restraints_weight: 0.5000
r_work: 0.2827 rms_B_bonded: 3.12 restraints_weight: 0.2500
r_work (final): 0.2827
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8590
moved from start:          0.3731

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.007   0.048   4884  Z= 0.293
  Angle     :  0.743   9.760   6611  Z= 0.337
  Chirality :  0.048   0.306    770
  Planarity :  0.003   0.018    880
  Dihedral  :  4.744  16.558    662
  Min Nonbonded Distance : 2.554

Molprobity Statistics.
  All-atom Clashscore : 11.42
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.10 %
    Favored  : 98.90 %
  Rotamer:
    Outliers : 10.87 %
    Allowed  : 28.26 %
    Favored  : 60.87 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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: -4.13 (0.15), residues: 638
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -3.14 (0.11), residues: 638

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 PHE   0.015   0.002   PHE Q 109 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02722 (  160)
  hydrogen bonds       : angle       4.52039 (  480)
  covalent geometry    : bond        0.00652 ( 4884)
  covalent geometry    : angle       0.74284 ( 6611)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3887.32 seconds
wall clock time: 71 minutes 24.20 seconds (4284.20 seconds total)