Starting phenix.real_space_refine
on Tue Feb  3 14:20:18 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9rbd_53891/02_2026/9rbd_53891.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9rbd_53891/02_2026/9rbd_53891.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.96
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/9rbd_53891/02_2026/9rbd_53891.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9rbd_53891/02_2026/9rbd_53891.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9rbd_53891/02_2026/9rbd_53891.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9rbd_53891/02_2026/9rbd_53891.cif"
  }
  resolution = 2.96
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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=   0.000 sd=   0.001
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 4
    Type Number    sf(0)   Gaussians
     S      60      5.16       5
     C    2120      2.51       5
     N     700      2.21       5
     O     680      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 9 residue(s): 0.00s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 3560
  Number of models: 1
  Model: ""
    Number of chains: 20
    Chain: "J"
      Number of atoms: 178
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 24, 178
          Classifications: {'peptide': 24}
          Modifications used: {'COO': 1}
          Link IDs: {'TRANS': 23}
    Chain: "L"
      Number of atoms: 178
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 24, 178
          Classifications: {'peptide': 24}
          Modifications used: {'COO': 1}
          Link IDs: {'TRANS': 23}
    Chain: "g"
      Number of atoms: 178
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 24, 178
          Classifications: {'peptide': 24}
          Modifications used: {'COO': 1}
          Link IDs: {'TRANS': 23}
    Chain: "i"
      Number of atoms: 178
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 24, 178
          Classifications: {'peptide': 24}
          Modifications used: {'COO': 1}
          Link IDs: {'TRANS': 23}
    Chain: "A"
      Number of atoms: 178
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 24, 178
          Classifications: {'peptide': 24}
          Modifications used: {'COO': 1}
          Link IDs: {'TRANS': 23}
    Chain: "B"
      Number of atoms: 178
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 24, 178
          Classifications: {'peptide': 24}
          Modifications used: {'COO': 1}
          Link IDs: {'TRANS': 23}
    Chain: "C"
      Number of atoms: 178
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 24, 178
          Classifications: {'peptide': 24}
          Modifications used: {'COO': 1}
          Link IDs: {'TRANS': 23}
    Chain: "D"
      Number of atoms: 178
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 24, 178
          Classifications: {'peptide': 24}
          Modifications used: {'COO': 1}
          Link IDs: {'TRANS': 23}
    Chain: "E"
      Number of atoms: 178
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 24, 178
          Classifications: {'peptide': 24}
          Modifications used: {'COO': 1}
          Link IDs: {'TRANS': 23}
    Chain: "F"
      Number of atoms: 178
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 24, 178
          Classifications: {'peptide': 24}
          Modifications used: {'COO': 1}
          Link IDs: {'TRANS': 23}
    Chain: "G"
      Number of atoms: 178
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 24, 178
          Classifications: {'peptide': 24}
          Modifications used: {'COO': 1}
          Link IDs: {'TRANS': 23}
    Chain: "H"
      Number of atoms: 178
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 24, 178
          Classifications: {'peptide': 24}
          Modifications used: {'COO': 1}
          Link IDs: {'TRANS': 23}
    Chain: "I"
      Number of atoms: 178
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 24, 178
          Classifications: {'peptide': 24}
          Modifications used: {'COO': 1}
          Link IDs: {'TRANS': 23}
    Chain: "K"
      Number of atoms: 178
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 24, 178
          Classifications: {'peptide': 24}
          Modifications used: {'COO': 1}
          Link IDs: {'TRANS': 23}
    Chain: "M"
      Number of atoms: 178
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 24, 178
          Classifications: {'peptide': 24}
          Modifications used: {'COO': 1}
          Link IDs: {'TRANS': 23}
    Chain: "N"
      Number of atoms: 178
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 24, 178
          Classifications: {'peptide': 24}
          Modifications used: {'COO': 1}
          Link IDs: {'TRANS': 23}
    Chain: "O"
      Number of atoms: 178
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 24, 178
          Classifications: {'peptide': 24}
          Modifications used: {'COO': 1}
          Link IDs: {'TRANS': 23}
    Chain: "P"
      Number of atoms: 178
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 24, 178
          Classifications: {'peptide': 24}
          Modifications used: {'COO': 1}
          Link IDs: {'TRANS': 23}
    Chain: "Q"
      Number of atoms: 178
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 24, 178
          Classifications: {'peptide': 24}
          Modifications used: {'COO': 1}
          Link IDs: {'TRANS': 23}
    Chain: "R"
      Number of atoms: 178
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 24, 178
          Classifications: {'peptide': 24}
          Modifications used: {'COO': 1}
          Link IDs: {'TRANS': 23}
  Time building chain proxies: 0.99, per 1000 atoms: 0.28
  Number of scatterers: 3560
  At special positions: 0
  Unit cell: (94.7707, 62.0622, 44.45, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     S      60     16.00
     O     680      8.00
     N     700      7.00
     C    2120      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=10, symmetry=0
    Simple disulfide: pdb=" SG  CYS J 105 " - pdb=" SG  CYS g 121 " distance=2.13
    Simple disulfide: pdb=" SG  CYS L 105 " - pdb=" SG  CYS i 121 " distance=2.11
    Simple disulfide: pdb=" SG  CYS A 105 " - pdb=" SG  CYS C 121 " distance=2.15
    Simple disulfide: pdb=" SG  CYS B 105 " - pdb=" SG  CYS D 121 " distance=1.91
    Simple disulfide: pdb=" SG  CYS E 105 " - pdb=" SG  CYS G 121 " distance=2.11
    Simple disulfide: pdb=" SG  CYS F 105 " - pdb=" SG  CYS H 121 " distance=1.94
    Simple disulfide: pdb=" SG  CYS I 105 " - pdb=" SG  CYS M 121 " distance=1.95
    Simple disulfide: pdb=" SG  CYS K 105 " - pdb=" SG  CYS N 121 " distance=2.21
    Simple disulfide: pdb=" SG  CYS O 105 " - pdb=" SG  CYS Q 121 " distance=1.80
    Simple disulfide: pdb=" SG  CYS P 105 " - pdb=" SG  CYS R 121 " distance=2.00

  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: 0.26
  Conformation dependent library (CDL) restraints added in 134.2 milliseconds
  

  880 Ramachandran restraints generated.
    440 Oldfield, 0 Emsley, 440 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  760

  Finding SS restraints...
    Secondary structure from input PDB file:
      0 helices and 9 sheets defined
      0.0% alpha, 35.2% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.15
  Creating SS restraints...
    Processing sheet with id=AA1, first strand: chain 'J' and resid 105 through 106
      removed outlier: 6.846A  pdb=" N   CYS J 105 " --> pdb=" O   PHE A 106 " (cutoff:3.500A)
      removed outlier: 6.443A  pdb=" N   CYS A 105 " --> pdb=" O   PHE E 106 " (cutoff:3.500A)
      removed outlier: 6.266A  pdb=" N   CYS E 105 " --> pdb=" O   PHE I 106 " (cutoff:3.500A)
      removed outlier: 6.949A  pdb=" N   CYS I 105 " --> pdb=" O   PHE O 106 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA1
    Processing sheet with id=AA2, first strand: chain 'J' and resid 109 through 110
    Processing sheet with id=AA3, first strand: chain 'J' and resid 114 through 119
      removed outlier: 6.541A  pdb=" N   ALA J 115 " --> pdb=" O   GLN A 116 " (cutoff:3.500A)
      removed outlier: 8.111A  pdb=" N   GLY A 118 " --> pdb=" O   ALA J 115 " (cutoff:3.500A)
      removed outlier: 5.812A  pdb=" N   SER J 117 " --> pdb=" O   GLY A 118 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'L' and resid 105 through 106
      removed outlier: 7.113A  pdb=" N   CYS L 105 " --> pdb=" O   PHE B 106 " (cutoff:3.500A)
      removed outlier: 6.585A  pdb=" N   CYS B 105 " --> pdb=" O   PHE F 106 " (cutoff:3.500A)
      removed outlier: 6.874A  pdb=" N   CYS F 105 " --> pdb=" O   PHE K 106 " (cutoff:3.500A)
      removed outlier: 6.893A  pdb=" N   CYS K 105 " --> pdb=" O   PHE P 106 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA4
    Processing sheet with id=AA5, first strand: chain 'L' and resid 109 through 119
      removed outlier: 3.507A  pdb=" N   ASP B 111 " --> pdb=" O   MET L 110 " (cutoff:3.500A)
      removed outlier: 7.287A  pdb=" N   ARG L 112 " --> pdb=" O   ASP B 111 " (cutoff:3.500A)
      removed outlier: 7.229A  pdb=" N   ILE B 113 " --> pdb=" O   ARG L 112 " (cutoff:3.500A)
      removed outlier: 7.314A  pdb=" N   GLY L 114 " --> pdb=" O   ILE B 113 " (cutoff:3.500A)
      removed outlier: 7.307A  pdb=" N   ALA B 115 " --> pdb=" O   GLY L 114 " (cutoff:3.500A)
      removed outlier: 7.344A  pdb=" N   GLN L 116 " --> pdb=" O   ALA B 115 " (cutoff:3.500A)
      removed outlier: 7.342A  pdb=" N   SER B 117 " --> pdb=" O   GLN L 116 " (cutoff:3.500A)
      removed outlier: 7.414A  pdb=" N   GLY L 118 " --> pdb=" O   SER B 117 " (cutoff:3.500A)
      removed outlier: 7.376A  pdb=" N   LEU B 119 " --> pdb=" O   GLY L 118 " (cutoff:3.500A)
      removed outlier: 7.097A  pdb=" N   MET F 110 " --> pdb=" O   ARG B 109 " (cutoff:3.500A)
      removed outlier: 6.928A  pdb=" N   ASP B 111 " --> pdb=" O   MET F 110 " (cutoff:3.500A)
      removed outlier: 6.946A  pdb=" N   ARG F 112 " --> pdb=" O   ASP K 111 " (cutoff:3.500A)
      removed outlier: 6.931A  pdb=" N   ILE K 113 " --> pdb=" O   ARG F 112 " (cutoff:3.500A)
      removed outlier: 7.007A  pdb=" N   GLY F 114 " --> pdb=" O   ILE K 113 " (cutoff:3.500A)
      removed outlier: 7.016A  pdb=" N   ALA K 115 " --> pdb=" O   GLY F 114 " (cutoff:3.500A)
      removed outlier: 7.073A  pdb=" N   GLN F 116 " --> pdb=" O   ALA K 115 " (cutoff:3.500A)
      removed outlier: 7.072A  pdb=" N   SER K 117 " --> pdb=" O   GLN F 116 " (cutoff:3.500A)
      removed outlier: 7.150A  pdb=" N   GLY F 118 " --> pdb=" O   SER K 117 " (cutoff:3.500A)
      removed outlier: 7.075A  pdb=" N   LEU K 119 " --> pdb=" O   GLY F 118 " (cutoff:3.500A)
      removed outlier: 7.015A  pdb=" N   ARG K 112 " --> pdb=" O   ASP P 111 " (cutoff:3.500A)
      removed outlier: 6.979A  pdb=" N   ILE P 113 " --> pdb=" O   ARG K 112 " (cutoff:3.500A)
      removed outlier: 7.039A  pdb=" N   GLY K 114 " --> pdb=" O   ILE P 113 " (cutoff:3.500A)
      removed outlier: 7.062A  pdb=" N   ALA P 115 " --> pdb=" O   GLY K 114 " (cutoff:3.500A)
      removed outlier: 7.077A  pdb=" N   GLN K 116 " --> pdb=" O   ALA P 115 " (cutoff:3.500A)
      removed outlier: 7.105A  pdb=" N   SER P 117 " --> pdb=" O   GLN K 116 " (cutoff:3.500A)
      removed outlier: 7.148A  pdb=" N   GLY K 118 " --> pdb=" O   SER P 117 " (cutoff:3.500A)
      removed outlier: 7.142A  pdb=" N   LEU P 119 " --> pdb=" O   GLY K 118 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'g' and resid 104 through 105
    Processing sheet with id=AA7, first strand: chain 'g' and resid 110 through 119
      removed outlier: 7.239A  pdb=" N   ASP g 111 " --> pdb=" O   MET C 110 " (cutoff:3.500A)
      removed outlier: 5.563A  pdb=" N   ASP C 111 " --> pdb=" O   ARG G 112 " (cutoff:3.500A)
      removed outlier: 7.081A  pdb=" N   GLY G 114 " --> pdb=" O   ASP C 111 " (cutoff:3.500A)
      removed outlier: 6.500A  pdb=" N   ILE C 113 " --> pdb=" O   GLY G 114 " (cutoff:3.500A)
      removed outlier: 7.851A  pdb=" N   GLN G 116 " --> pdb=" O   ILE C 113 " (cutoff:3.500A)
      removed outlier: 6.306A  pdb=" N   ALA C 115 " --> pdb=" O   GLN G 116 " (cutoff:3.500A)
      removed outlier: 7.731A  pdb=" N   GLY G 118 " --> pdb=" O   ALA C 115 " (cutoff:3.500A)
      removed outlier: 5.919A  pdb=" N   SER C 117 " --> pdb=" O   GLY G 118 " (cutoff:3.500A)
      removed outlier: 7.036A  pdb=" N   ASP G 111 " --> pdb=" O   MET M 110 " (cutoff:3.500A)
      removed outlier: 5.560A  pdb=" N   ASP M 111 " --> pdb=" O   ARG Q 112 " (cutoff:3.500A)
      removed outlier: 7.204A  pdb=" N   GLY Q 114 " --> pdb=" O   ASP M 111 " (cutoff:3.500A)
      removed outlier: 6.616A  pdb=" N   ILE M 113 " --> pdb=" O   GLY Q 114 " (cutoff:3.500A)
      removed outlier: 7.947A  pdb=" N   GLN Q 116 " --> pdb=" O   ILE M 113 " (cutoff:3.500A)
      removed outlier: 6.403A  pdb=" N   ALA M 115 " --> pdb=" O   GLN Q 116 " (cutoff:3.500A)
      removed outlier: 7.829A  pdb=" N   GLY Q 118 " --> pdb=" O   ALA M 115 " (cutoff:3.500A)
      removed outlier: 6.004A  pdb=" N   SER M 117 " --> pdb=" O   GLY Q 118 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'i' and resid 109 through 110
    Processing sheet with id=AA9, first strand: chain 'i' and resid 114 through 119
      removed outlier: 6.412A  pdb=" N   ALA D 115 " --> pdb=" O   GLN H 116 " (cutoff:3.500A)
      removed outlier: 7.938A  pdb=" N   GLY H 118 " --> pdb=" O   ALA D 115 " (cutoff:3.500A)
      removed outlier: 5.795A  pdb=" N   SER D 117 " --> pdb=" O   GLY H 118 " (cutoff:3.500A)
      removed outlier: 6.338A  pdb=" N   ALA H 115 " --> pdb=" O   GLN N 116 " (cutoff:3.500A)
      removed outlier: 7.877A  pdb=" N   GLY N 118 " --> pdb=" O   ALA H 115 " (cutoff:3.500A)
      removed outlier: 5.742A  pdb=" N   SER H 117 " --> pdb=" O   GLY N 118 " (cutoff:3.500A)

    65 hydrogen bonds defined for protein.
    195 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: 0.47

  Time building geometry restraints manager: 0.36 seconds

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

  Histogram of bond lengths:
        1.23 -     1.34: 1255
        1.34 -     1.46: 919
        1.46 -     1.58: 1346
        1.58 -     1.69: 0
        1.69 -     1.81: 80
  Bond restraints: 3600
  Sorted by residual:
  bond pdb=" C   SER G 104 "
       pdb=" N   CYS G 105 "
    ideal  model  delta    sigma   weight residual
    1.330  1.346 -0.016 1.76e-02 3.23e+03 8.04e-01
  bond pdb=" C   SER C 104 "
       pdb=" N   CYS C 105 "
    ideal  model  delta    sigma   weight residual
    1.330  1.345 -0.015 1.76e-02 3.23e+03 7.57e-01
  bond pdb=" C   SER g 104 "
       pdb=" N   CYS g 105 "
    ideal  model  delta    sigma   weight residual
    1.330  1.345 -0.015 1.76e-02 3.23e+03 7.45e-01
  bond pdb=" C   SER Q 104 "
       pdb=" N   CYS Q 105 "
    ideal  model  delta    sigma   weight residual
    1.330  1.345 -0.015 1.76e-02 3.23e+03 7.42e-01
  bond pdb=" C   SER M 104 "
       pdb=" N   CYS M 105 "
    ideal  model  delta    sigma   weight residual
    1.330  1.345 -0.015 1.76e-02 3.23e+03 6.92e-01
  ... (remaining 3595 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.04: 4484
        1.04 -     2.07: 228
        2.07 -     3.11: 23
        3.11 -     4.14: 0
        4.14 -     5.18: 5
  Bond angle restraints: 4740
  Sorted by residual:
  angle pdb=" CA  CYS I 105 "
        pdb=" CB  CYS I 105 "
        pdb=" SG  CYS I 105 "
      ideal   model   delta    sigma   weight residual
     114.40  109.22    5.18 2.30e+00 1.89e-01 5.07e+00
  angle pdb=" CA  CYS J 105 "
        pdb=" CB  CYS J 105 "
        pdb=" SG  CYS J 105 "
      ideal   model   delta    sigma   weight residual
     114.40  109.24    5.16 2.30e+00 1.89e-01 5.04e+00
  angle pdb=" CA  CYS O 105 "
        pdb=" CB  CYS O 105 "
        pdb=" SG  CYS O 105 "
      ideal   model   delta    sigma   weight residual
     114.40  109.24    5.16 2.30e+00 1.89e-01 5.03e+00
  angle pdb=" CA  CYS E 105 "
        pdb=" CB  CYS E 105 "
        pdb=" SG  CYS E 105 "
      ideal   model   delta    sigma   weight residual
     114.40  109.25    5.15 2.30e+00 1.89e-01 5.01e+00
  angle pdb=" CA  CYS A 105 "
        pdb=" CB  CYS A 105 "
        pdb=" SG  CYS A 105 "
      ideal   model   delta    sigma   weight residual
     114.40  109.26    5.14 2.30e+00 1.89e-01 4.99e+00
  ... (remaining 4735 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    11.35: 1819
       11.35 -    22.70: 199
       22.70 -    34.04: 41
       34.04 -    45.39: 46
       45.39 -    56.74: 5
  Dihedral angle restraints: 2110
    sinusoidal: 870
      harmonic: 1240
  Sorted by residual:
  dihedral pdb=" CA  ARG i 125 "
           pdb=" CB  ARG i 125 "
           pdb=" CG  ARG i 125 "
           pdb=" CD  ARG i 125 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -60.00 -116.74   56.74     3      1.50e+01 4.44e-03 9.41e+00
  dihedral pdb=" CA  ARG R 125 "
           pdb=" CB  ARG R 125 "
           pdb=" CG  ARG R 125 "
           pdb=" CD  ARG R 125 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -60.00 -116.72   56.72     3      1.50e+01 4.44e-03 9.41e+00
  dihedral pdb=" CA  ARG D 125 "
           pdb=" CB  ARG D 125 "
           pdb=" CG  ARG D 125 "
           pdb=" CD  ARG D 125 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -60.00 -116.69   56.69     3      1.50e+01 4.44e-03 9.41e+00
  ... (remaining 2107 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.021: 220
       0.021 -    0.041: 87
       0.041 -    0.062: 57
       0.062 -    0.082: 41
       0.082 -    0.102: 15
  Chirality restraints: 420
  Sorted by residual:
  chirality pdb=" CA  ILE R 113 "
            pdb=" N   ILE R 113 "
            pdb=" C   ILE R 113 "
            pdb=" CB  ILE R 113 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.54   -0.10 2.00e-01 2.50e+01 2.62e-01
  chirality pdb=" CA  ILE i 113 "
            pdb=" N   ILE i 113 "
            pdb=" C   ILE i 113 "
            pdb=" CB  ILE i 113 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.53   -0.10 2.00e-01 2.50e+01 2.57e-01
  chirality pdb=" CA  ILE N 113 "
            pdb=" N   ILE N 113 "
            pdb=" C   ILE N 113 "
            pdb=" CB  ILE N 113 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.53   -0.10 2.00e-01 2.50e+01 2.54e-01
  ... (remaining 417 not shown)

  Planarity restraints: 660
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  GLN D 116 "   -0.002 2.00e-02 2.50e+03   3.97e-03 1.58e-01
        pdb=" C   GLN D 116 "    0.007 2.00e-02 2.50e+03
        pdb=" O   GLN D 116 "   -0.003 2.00e-02 2.50e+03
        pdb=" N   SER D 117 "   -0.002 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  GLN N 116 "   -0.002 2.00e-02 2.50e+03   3.80e-03 1.44e-01
        pdb=" C   GLN N 116 "    0.007 2.00e-02 2.50e+03
        pdb=" O   GLN N 116 "   -0.002 2.00e-02 2.50e+03
        pdb=" N   SER N 117 "   -0.002 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  GLN R 116 "   -0.002 2.00e-02 2.50e+03   3.57e-03 1.28e-01
        pdb=" C   GLN R 116 "    0.006 2.00e-02 2.50e+03
        pdb=" O   GLN R 116 "   -0.002 2.00e-02 2.50e+03
        pdb=" N   SER R 117 "   -0.002 2.00e-02 2.50e+03
  ... (remaining 657 not shown)

  Histogram of nonbonded interaction distances:
        2.26 -     2.79: 742
        2.79 -     3.31: 2935
        3.31 -     3.84: 5745
        3.84 -     4.37: 7124
        4.37 -     4.90: 12023
  Nonbonded interactions: 28569
  Sorted by model distance:
  nonbonded pdb=" O   GLY P 120 "
            pdb=" OG  SER P 123 "
     model   vdw
     2.257 3.040
  nonbonded pdb=" O   GLY F 120 "
            pdb=" OG  SER F 123 "
     model   vdw
     2.257 3.040
  nonbonded pdb=" O   GLY L 120 "
            pdb=" OG  SER L 123 "
     model   vdw
     2.257 3.040
  nonbonded pdb=" O   GLY K 120 "
            pdb=" OG  SER K 123 "
     model   vdw
     2.257 3.040
  nonbonded pdb=" O   GLY B 120 "
            pdb=" OG  SER B 123 "
     model   vdw
     2.258 3.040
  ... (remaining 28564 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.00
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'B'
  selection = chain 'C'
  selection = chain 'D'
  selection = chain 'E'
  selection = chain 'F'
  selection = chain 'G'
  selection = chain 'H'
  selection = chain 'I'
  selection = chain 'J'
  selection = chain 'K'
  selection = chain 'L'
  selection = chain 'M'
  selection = chain 'N'
  selection = chain 'O'
  selection = chain 'P'
  selection = chain 'Q'
  selection = chain 'R'
  selection = chain 'g'
  selection = chain 'i'
}

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:             4.420
  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:          0.060
  Check model and map are aligned:         0.010
  Set scattering table:                    0.010
  Process input model:                     5.740
  Find NCS groups from input model:        0.070
  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:             0.000
  Load rotamer database and sin/cos tables:6.750
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   17.080
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7687
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.007   0.231   3610  Z= 0.370
  Angle     :  0.705  18.142   4760  Z= 0.373
  Chirality :  0.038   0.102    420
  Planarity :  0.002   0.008    660
  Dihedral  : 11.643  56.739   1320
  Min Nonbonded Distance : 2.257

Molprobity Statistics.
  All-atom Clashscore : 6.30
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.09 %
    Favored  : 95.91 %
  Rotamer:
    Outliers :  1.39 %
    Allowed  : 15.00 %
    Favored  : 83.61 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -3.46 (0.34), residues: 440
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.63 (0.26), residues: 440

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG J 109 
 TYR   0.003   0.001   TYR E 126 
 PHE   0.005   0.001   PHE D 106 

Details of bonding type rmsd
  covalent geometry    : bond        0.00366 ( 3600)
  covalent geometry    : angle       0.52432 ( 4740)
  SS BOND              : bond        0.12304 (   10)
  SS BOND              : angle       7.28751 (   20)
  hydrogen bonds       : bond        0.20179 (   65)
  hydrogen bonds       : angle      10.12313 (  195)

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

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

  880 Ramachandran restraints generated.
    440 Oldfield, 0 Emsley, 440 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  880 Ramachandran restraints generated.
    440 Oldfield, 0 Emsley, 440 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  149 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 144
  time to evaluate  : 0.191 
Fit side-chains
   revert: symmetry clash
REVERT: J  122 ASN cc_start: 0.7949 (t0) cc_final: 0.7744 (t0)
REVERT: J  125 ARG cc_start: 0.7581 (mtp180) cc_final: 0.6802 (mmm160)
REVERT: L  122 ASN cc_start: 0.8166 (t0) cc_final: 0.7827 (t0)
REVERT: L  125 ARG cc_start: 0.7583 (mtp-110) cc_final: 0.6946 (mmm160)
REVERT: i  125 ARG cc_start: 0.7295 (mmm160) cc_final: 0.7058 (mmp-170)
REVERT: A  122 ASN cc_start: 0.7930 (t0) cc_final: 0.7558 (t0)
REVERT: B  122 ASN cc_start: 0.8061 (t0) cc_final: 0.7770 (t0)
REVERT: B  125 ARG cc_start: 0.7529 (mtp-110) cc_final: 0.6937 (mtm-85)
REVERT: E  122 ASN cc_start: 0.7917 (t0) cc_final: 0.7586 (t0)
REVERT: E  125 ARG cc_start: 0.7523 (mtp180) cc_final: 0.6831 (mtm180)
REVERT: F  125 ARG cc_start: 0.7423 (mtp-110) cc_final: 0.7186 (mtp-110)
REVERT: H  106 PHE cc_start: 0.7194 (m-80) cc_final: 0.6976 (m-80)
REVERT: I  125 ARG cc_start: 0.7475 (mtp180) cc_final: 0.6867 (mtm110)
REVERT: O  112 ARG cc_start: 0.8243 (mtm180) cc_final: 0.5698 (mtp180)
REVERT: P  112 ARG cc_start: 0.7986 (mtm180) cc_final: 0.5564 (mtp180)
REVERT: Q  112 ARG cc_start: 0.8088 (mtt180) cc_final: 0.6956 (mtp180)
REVERT: R  112 ARG cc_start: 0.6830 (mtm-85) cc_final: 0.5885 (tpt-90)
  outliers start: 5
  outliers final: 0
  residues processed: 147
  average time/residue: 0.6334
  time to fit residues: 95.2557
Evaluate side-chains
  112 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 112
  time to evaluate  : 0.141 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 40
   random chunks:
   chunk 24 optimal weight:    0.9990
   chunk 26 optimal weight:    2.9990
   chunk 2 optimal weight:    2.9990
   chunk 16 optimal weight:    2.9990
   chunk 32 optimal weight:    2.9990
   chunk 31 optimal weight:    0.6980
   chunk 25 optimal weight:    2.9990
   chunk 19 optimal weight:    2.9990
   chunk 30 optimal weight:    4.9990
   chunk 22 optimal weight:    0.9980
   chunk 37 optimal weight:    0.9980
   overall best weight:    1.3384

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

Flipped N/Q/H residues before XYZ refinement:
** J 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
F 122 ASN
H 122 ASN
** I 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
P 122 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4350 r_free = 0.4350 target = 0.155754 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3999 r_free = 0.3999 target = 0.123547 restraints weight = 4152.323|
|-----------------------------------------------------------------------------|
r_work (start): 0.4004 rms_B_bonded: 2.25
r_work: 0.3870 rms_B_bonded: 3.01 restraints_weight: 0.5000
r_work: 0.3732 rms_B_bonded: 4.77 restraints_weight: 0.2500
r_work (final): 0.3732
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8227
moved from start:          0.3953

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.037   3610  Z= 0.263
  Angle     :  0.664   4.916   4760  Z= 0.363
  Chirality :  0.047   0.127    420
  Planarity :  0.004   0.033    660
  Dihedral  :  4.455  27.019    560
  Min Nonbonded Distance : 2.477

Molprobity Statistics.
  All-atom Clashscore : 10.70
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.95 %
    Favored  : 92.05 %
  Rotamer:
    Outliers :  3.33 %
    Allowed  : 23.06 %
    Favored  : 73.61 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -3.69 (0.31), residues: 440
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.80 (0.24), residues: 440

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG P 109 
 TYR   0.005   0.001   TYR J 126 
 PHE   0.018   0.002   PHE I 106 

Details of bonding type rmsd
  covalent geometry    : bond        0.00581 ( 3600)
  covalent geometry    : angle       0.65853 ( 4740)
  SS BOND              : bond        0.00611 (   10)
  SS BOND              : angle       1.46133 (   20)
  hydrogen bonds       : bond        0.02925 (   65)
  hydrogen bonds       : angle       6.43293 (  195)

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

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

  880 Ramachandran restraints generated.
    440 Oldfield, 0 Emsley, 440 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  880 Ramachandran restraints generated.
    440 Oldfield, 0 Emsley, 440 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  142 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 130
  time to evaluate  : 0.146 
Fit side-chains
REVERT: J  122 ASN cc_start: 0.8376 (t0) cc_final: 0.8156 (t0)
REVERT: J  125 ARG cc_start: 0.8264 (mtp180) cc_final: 0.7460 (mmm160)
REVERT: L  122 ASN cc_start: 0.8417 (t0) cc_final: 0.8082 (t160)
REVERT: L  125 ARG cc_start: 0.7953 (mtp-110) cc_final: 0.7247 (mmm160)
REVERT: g  125 ARG cc_start: 0.5952 (mmp-170) cc_final: 0.5667 (mmm160)
REVERT: i  112 ARG cc_start: 0.8455 (mtm-85) cc_final: 0.6508 (ppt90)
REVERT: i  125 ARG cc_start: 0.7869 (mmm160) cc_final: 0.7013 (mmp-170)
REVERT: A  122 ASN cc_start: 0.8474 (t0) cc_final: 0.8046 (t0)
REVERT: A  125 ARG cc_start: 0.8314 (mtp180) cc_final: 0.7897 (mtm110)
REVERT: B  125 ARG cc_start: 0.7977 (mtp-110) cc_final: 0.7500 (mtm-85)
REVERT: G  122 ASN cc_start: 0.8829 (m-40) cc_final: 0.8434 (m-40)
REVERT: H  106 PHE cc_start: 0.7306 (m-80) cc_final: 0.6665 (t80)
REVERT: I  125 ARG cc_start: 0.8028 (mtp180) cc_final: 0.7502 (mtm110)
REVERT: K  121 CYS cc_start: 0.8674 (p) cc_final: 0.8248 (m)
REVERT: K  122 ASN cc_start: 0.8450 (t0) cc_final: 0.8174 (t160)
REVERT: N  122 ASN cc_start: 0.8721 (m110) cc_final: 0.8374 (m110)
REVERT: Q  112 ARG cc_start: 0.8122 (mtt180) cc_final: 0.6593 (mtp180)
REVERT: R  112 ARG cc_start: 0.7975 (mtm-85) cc_final: 0.6452 (mtp180)
REVERT: R  125 ARG cc_start: 0.8047 (mmm160) cc_final: 0.6902 (pmt-80)
  outliers start: 12
  outliers final: 4
  residues processed: 134
  average time/residue: 0.7011
  time to fit residues: 96.1068
Evaluate side-chains
  124 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 120
  time to evaluate  : 0.147 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain L residue  121 CYS
Chi-restraints excluded: chain A residue  105 CYS
Chi-restraints excluded: chain H residue  104 SER
Chi-restraints excluded: chain H residue  105 CYS
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 40
   random chunks:
   chunk 32 optimal weight:    4.9990
   chunk 8 optimal weight:    0.5980
   chunk 38 optimal weight:    3.9990
   chunk 12 optimal weight:    4.9990
   chunk 35 optimal weight:    0.0040
   chunk 36 optimal weight:    0.0870
   chunk 33 optimal weight:    2.9990
   chunk 39 optimal weight:    1.9990
   chunk 27 optimal weight:    0.7980
   chunk 25 optimal weight:    2.9990
   chunk 16 optimal weight:    0.7980
   overall best weight:    0.4570

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

Flipped N/Q/H residues before XYZ refinement:
** J 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
E 122 ASN
F 122 ASN
** I 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
M 122 ASN
R 116 GLN
R 122 ASN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4398 r_free = 0.4398 target = 0.160625 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.4063 r_free = 0.4063 target = 0.128742 restraints weight = 4029.590|
|-----------------------------------------------------------------------------|
r_work (start): 0.4066 rms_B_bonded: 2.29
r_work: 0.3935 rms_B_bonded: 3.03 restraints_weight: 0.5000
r_work: 0.3800 rms_B_bonded: 4.84 restraints_weight: 0.2500
r_work (final): 0.3800
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8164
moved from start:          0.3965

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.027   3610  Z= 0.118
  Angle     :  0.500   4.196   4760  Z= 0.271
  Chirality :  0.040   0.117    420
  Planarity :  0.003   0.037    660
  Dihedral  :  3.720  20.541    560
  Min Nonbonded Distance : 2.508

Molprobity Statistics.
  All-atom Clashscore : 8.21
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.09 %
    Favored  : 95.91 %
  Rotamer:
    Outliers :  2.78 %
    Allowed  : 25.83 %
    Favored  : 71.39 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -3.61 (0.32), residues: 440
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.75 (0.24), residues: 440

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.000   ARG K 109 
 TYR   0.004   0.001   TYR J 126 
 PHE   0.012   0.001   PHE E 106 

Details of bonding type rmsd
  covalent geometry    : bond        0.00261 ( 3600)
  covalent geometry    : angle       0.49654 ( 4740)
  SS BOND              : bond        0.00315 (   10)
  SS BOND              : angle       1.00649 (   20)
  hydrogen bonds       : bond        0.01672 (   65)
  hydrogen bonds       : angle       5.66215 (  195)

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

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

  880 Ramachandran restraints generated.
    440 Oldfield, 0 Emsley, 440 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  880 Ramachandran restraints generated.
    440 Oldfield, 0 Emsley, 440 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  142 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 132
  time to evaluate  : 0.146 
Fit side-chains
REVERT: J  122 ASN cc_start: 0.8243 (t0) cc_final: 0.8029 (t0)
REVERT: J  125 ARG cc_start: 0.8210 (mtp180) cc_final: 0.7396 (mmm160)
REVERT: L  122 ASN cc_start: 0.8299 (t0) cc_final: 0.7872 (t0)
REVERT: L  125 ARG cc_start: 0.7928 (mtp-110) cc_final: 0.7192 (mmm160)
REVERT: g  105 CYS cc_start: 0.6479 (m) cc_final: 0.5166 (m)
REVERT: i  110 MET cc_start: 0.8794 (mtm) cc_final: 0.8256 (mtt)
REVERT: i  125 ARG cc_start: 0.7890 (mmm160) cc_final: 0.6982 (mmp-170)
REVERT: A  122 ASN cc_start: 0.8270 (t0) cc_final: 0.7920 (t0)
REVERT: A  125 ARG cc_start: 0.8195 (mtp180) cc_final: 0.7811 (mtm110)
REVERT: B  125 ARG cc_start: 0.7965 (mtp-110) cc_final: 0.7495 (mtm-85)
REVERT: D  125 ARG cc_start: 0.8163 (mtp180) cc_final: 0.7882 (mmt180)
REVERT: G  122 ASN cc_start: 0.8692 (m-40) cc_final: 0.8367 (m-40)
REVERT: G  125 ARG cc_start: 0.7769 (mtt180) cc_final: 0.7397 (mmm-85)
REVERT: H  106 PHE cc_start: 0.7307 (m-80) cc_final: 0.6706 (t80)
REVERT: H  119 LEU cc_start: 0.8879 (OUTLIER) cc_final: 0.8548 (mt)
REVERT: H  125 ARG cc_start: 0.7639 (mtt-85) cc_final: 0.7376 (mtt90)
REVERT: I  125 ARG cc_start: 0.7974 (mtp180) cc_final: 0.7439 (mtm110)
REVERT: K  121 CYS cc_start: 0.8647 (p) cc_final: 0.8325 (m)
REVERT: M  106 PHE cc_start: 0.7636 (m-10) cc_final: 0.7400 (m-10)
REVERT: N  122 ASN cc_start: 0.8621 (m110) cc_final: 0.8293 (m110)
REVERT: Q  112 ARG cc_start: 0.8145 (mtt180) cc_final: 0.6546 (mtp180)
REVERT: R  112 ARG cc_start: 0.7877 (mtm-85) cc_final: 0.6197 (tpt90)
REVERT: R  125 ARG cc_start: 0.8008 (mmm160) cc_final: 0.6822 (pmt-80)
  outliers start: 10
  outliers final: 3
  residues processed: 136
  average time/residue: 0.6910
  time to fit residues: 96.0300
Evaluate side-chains
  123 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 119
  time to evaluate  : 0.086 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain L residue  121 CYS
Chi-restraints excluded: chain H residue  104 SER
Chi-restraints excluded: chain H residue  119 LEU
Chi-restraints excluded: chain R residue  117 SER
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 40
   random chunks:
   chunk 13 optimal weight:    2.9990
   chunk 38 optimal weight:    5.9990
   chunk 12 optimal weight:    5.9990
   chunk 22 optimal weight:    0.8980
   chunk 23 optimal weight:    2.9990
   chunk 0 optimal weight:    4.9990
   chunk 19 optimal weight:    1.9990
   chunk 17 optimal weight:    1.9990
   chunk 21 optimal weight:    0.6980
   chunk 39 optimal weight:    0.1980
   chunk 3 optimal weight:    3.9990
   overall best weight:    1.1584

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

Flipped N/Q/H residues before XYZ refinement:
** J 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** I 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4329 r_free = 0.4329 target = 0.154255 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.4003 r_free = 0.4003 target = 0.122731 restraints weight = 4104.794|
|-----------------------------------------------------------------------------|
r_work (start): 0.4008 rms_B_bonded: 2.31
r_work: 0.3861 rms_B_bonded: 3.08 restraints_weight: 0.5000
r_work: 0.3721 rms_B_bonded: 4.86 restraints_weight: 0.2500
r_work (final): 0.3721
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8250
moved from start:          0.4399

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.044   3610  Z= 0.234
  Angle     :  0.602   5.059   4760  Z= 0.328
  Chirality :  0.044   0.119    420
  Planarity :  0.004   0.041    660
  Dihedral  :  4.354  25.553    560
  Min Nonbonded Distance : 2.569

Molprobity Statistics.
  All-atom Clashscore : 10.41
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.27 %
    Favored  : 92.73 %
  Rotamer:
    Outliers :  2.78 %
    Allowed  : 28.61 %
    Favored  : 68.61 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -3.79 (0.30), residues: 440
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.88 (0.23), residues: 440

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.001   ARG F 125 
 TYR   0.015   0.001   TYR K 126 
 PHE   0.012   0.001   PHE E 106 

Details of bonding type rmsd
  covalent geometry    : bond        0.00519 ( 3600)
  covalent geometry    : angle       0.59777 ( 4740)
  SS BOND              : bond        0.00505 (   10)
  SS BOND              : angle       1.19415 (   20)
  hydrogen bonds       : bond        0.02304 (   65)
  hydrogen bonds       : angle       5.55719 (  195)

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

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

  880 Ramachandran restraints generated.
    440 Oldfield, 0 Emsley, 440 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  880 Ramachandran restraints generated.
    440 Oldfield, 0 Emsley, 440 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  137 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 127
  time to evaluate  : 0.091 
Fit side-chains
   revert: symmetry clash
REVERT: J  122 ASN cc_start: 0.8223 (t0) cc_final: 0.7963 (t0)
REVERT: J  125 ARG cc_start: 0.8252 (mtp180) cc_final: 0.7457 (mmm160)
REVERT: L  122 ASN cc_start: 0.8389 (t0) cc_final: 0.8064 (t160)
REVERT: L  125 ARG cc_start: 0.8020 (mtp-110) cc_final: 0.7249 (mmm160)
REVERT: i  125 ARG cc_start: 0.7974 (mmm160) cc_final: 0.7039 (mmp-170)
REVERT: B  125 ARG cc_start: 0.7994 (mtp-110) cc_final: 0.7564 (mtm-85)
REVERT: C  125 ARG cc_start: 0.8245 (mtp180) cc_final: 0.7928 (mtt180)
REVERT: E  125 ARG cc_start: 0.7975 (mtp85) cc_final: 0.7400 (mtm180)
REVERT: F  125 ARG cc_start: 0.7903 (mtp-110) cc_final: 0.7142 (mtm180)
REVERT: G  105 CYS cc_start: 0.7051 (m) cc_final: 0.5988 (m)
REVERT: G  122 ASN cc_start: 0.8730 (m-40) cc_final: 0.8369 (m-40)
REVERT: H  106 PHE cc_start: 0.7476 (m-80) cc_final: 0.6769 (t80)
REVERT: H  119 LEU cc_start: 0.8908 (OUTLIER) cc_final: 0.8627 (mt)
REVERT: H  125 ARG cc_start: 0.7612 (mtt-85) cc_final: 0.7172 (mtt90)
REVERT: I  121 CYS cc_start: 0.8374 (p) cc_final: 0.7998 (m)
REVERT: I  125 ARG cc_start: 0.7996 (mtp180) cc_final: 0.7493 (mtm110)
REVERT: K  122 ASN cc_start: 0.8448 (t0) cc_final: 0.8107 (t160)
REVERT: M  106 PHE cc_start: 0.7914 (m-10) cc_final: 0.7643 (m-10)
REVERT: M  116 GLN cc_start: 0.8682 (tm-30) cc_final: 0.8340 (tm-30)
REVERT: N  122 ASN cc_start: 0.8741 (m110) cc_final: 0.8418 (m110)
REVERT: O  110 MET cc_start: 0.8807 (OUTLIER) cc_final: 0.8421 (mtp)
REVERT: P  110 MET cc_start: 0.9016 (OUTLIER) cc_final: 0.8662 (mtp)
REVERT: Q  112 ARG cc_start: 0.8177 (mtt180) cc_final: 0.6550 (mtp180)
REVERT: R  109 ARG cc_start: 0.7568 (ttm110) cc_final: 0.6425 (mmp-170)
REVERT: R  112 ARG cc_start: 0.8083 (mtm-85) cc_final: 0.6509 (mtp180)
REVERT: R  125 ARG cc_start: 0.7980 (mmm160) cc_final: 0.6833 (pmt-80)
  outliers start: 10
  outliers final: 4
  residues processed: 133
  average time/residue: 0.4933
  time to fit residues: 67.2328
Evaluate side-chains
  125 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 118
  time to evaluate  : 0.139 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  105 CYS
Chi-restraints excluded: chain C residue  105 CYS
Chi-restraints excluded: chain H residue  104 SER
Chi-restraints excluded: chain H residue  119 LEU
Chi-restraints excluded: chain O residue  110 MET
Chi-restraints excluded: chain P residue  110 MET
Chi-restraints excluded: chain R residue  117 SER
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 40
   random chunks:
   chunk 26 optimal weight:    2.9990
   chunk 32 optimal weight:    4.9990
   chunk 2 optimal weight:    3.9990
   chunk 8 optimal weight:    5.9990
   chunk 9 optimal weight:    0.4980
   chunk 14 optimal weight:    7.9990
   chunk 31 optimal weight:    2.9990
   chunk 4 optimal weight:    5.9990
   chunk 34 optimal weight:    0.6980
   chunk 1 optimal weight:    0.8980
   chunk 0 optimal weight:    0.5980
   overall best weight:    1.1382

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

Flipped N/Q/H residues before XYZ refinement:
** J 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
F 122 ASN
** I 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
P 122 ASN
R 122 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4311 r_free = 0.4311 target = 0.153881 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.4005 r_free = 0.4005 target = 0.122953 restraints weight = 4131.388|
|-----------------------------------------------------------------------------|
r_work (start): 0.4009 rms_B_bonded: 2.29
r_work: 0.3862 rms_B_bonded: 3.05 restraints_weight: 0.5000
r_work: 0.3717 rms_B_bonded: 4.86 restraints_weight: 0.2500
r_work (final): 0.3717
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8281
moved from start:          0.4686

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.071   3610  Z= 0.232
  Angle     :  0.615   5.564   4760  Z= 0.331
  Chirality :  0.043   0.120    420
  Planarity :  0.004   0.038    660
  Dihedral  :  4.535  25.925    560
  Min Nonbonded Distance : 2.472

Molprobity Statistics.
  All-atom Clashscore : 10.85
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.91 %
    Favored  : 94.09 %
  Rotamer:
    Outliers :  5.00 %
    Allowed  : 26.94 %
    Favored  : 68.06 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -3.79 (0.30), residues: 440
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.88 (0.23), residues: 440

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.001   ARG O 109 
 TYR   0.012   0.001   TYR K 126 
 PHE   0.011   0.001   PHE H 106 

Details of bonding type rmsd
  covalent geometry    : bond        0.00525 ( 3600)
  covalent geometry    : angle       0.61157 ( 4740)
  SS BOND              : bond        0.00495 (   10)
  SS BOND              : angle       1.17687 (   20)
  hydrogen bonds       : bond        0.02144 (   65)
  hydrogen bonds       : angle       5.51082 (  195)

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

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

  880 Ramachandran restraints generated.
    440 Oldfield, 0 Emsley, 440 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  880 Ramachandran restraints generated.
    440 Oldfield, 0 Emsley, 440 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  146 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 128
  time to evaluate  : 0.087 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: J  122 ASN cc_start: 0.8078 (t0) cc_final: 0.7857 (t0)
REVERT: J  125 ARG cc_start: 0.8333 (mtp180) cc_final: 0.7582 (mmm160)
REVERT: L  122 ASN cc_start: 0.8399 (t0) cc_final: 0.8092 (t160)
REVERT: L  125 ARG cc_start: 0.8043 (mtp-110) cc_final: 0.7313 (mmm160)
REVERT: g  109 ARG cc_start: 0.6735 (mtt180) cc_final: 0.6397 (pmt-80)
REVERT: i  110 MET cc_start: 0.8868 (mtm) cc_final: 0.8550 (mtm)
REVERT: i  125 ARG cc_start: 0.8028 (mmm160) cc_final: 0.7137 (mmp-170)
REVERT: B  125 ARG cc_start: 0.7994 (mtp-110) cc_final: 0.7586 (mtm-85)
REVERT: C  125 ARG cc_start: 0.8244 (mtp180) cc_final: 0.7932 (mtt-85)
REVERT: D  125 ARG cc_start: 0.8127 (mtp180) cc_final: 0.7878 (mmt180)
REVERT: E  122 ASN cc_start: 0.8531 (t0) cc_final: 0.8103 (t0)
REVERT: E  125 ARG cc_start: 0.7991 (mtp85) cc_final: 0.7386 (mtm180)
REVERT: F  125 ARG cc_start: 0.7852 (mtp-110) cc_final: 0.7148 (mtt180)
REVERT: G  105 CYS cc_start: 0.7483 (OUTLIER) cc_final: 0.7228 (m)
REVERT: G  122 ASN cc_start: 0.8783 (m-40) cc_final: 0.8349 (m-40)
REVERT: H  106 PHE cc_start: 0.7496 (m-80) cc_final: 0.6821 (t80)
REVERT: H  125 ARG cc_start: 0.7649 (OUTLIER) cc_final: 0.7225 (mtt90)
REVERT: I  119 LEU cc_start: 0.8654 (OUTLIER) cc_final: 0.8453 (mp)
REVERT: I  122 ASN cc_start: 0.8253 (t0) cc_final: 0.7887 (t160)
REVERT: I  125 ARG cc_start: 0.8038 (mtp180) cc_final: 0.7539 (mtm110)
REVERT: K  110 MET cc_start: 0.8831 (mtt) cc_final: 0.8570 (mtt)
REVERT: K  122 ASN cc_start: 0.8460 (t0) cc_final: 0.8099 (t160)
REVERT: M  106 PHE cc_start: 0.8054 (m-10) cc_final: 0.7803 (m-10)
REVERT: M  116 GLN cc_start: 0.8703 (tm-30) cc_final: 0.8385 (tm-30)
REVERT: M  125 ARG cc_start: 0.7651 (mmt90) cc_final: 0.7173 (mmm-85)
REVERT: N  110 MET cc_start: 0.9044 (OUTLIER) cc_final: 0.8752 (mtm)
REVERT: O  110 MET cc_start: 0.8814 (OUTLIER) cc_final: 0.8380 (mtp)
REVERT: P  110 MET cc_start: 0.9010 (OUTLIER) cc_final: 0.8277 (mpp)
REVERT: Q  112 ARG cc_start: 0.8230 (mtt180) cc_final: 0.6628 (mtp180)
REVERT: R  109 ARG cc_start: 0.7486 (ttm110) cc_final: 0.6434 (mmp-170)
REVERT: R  112 ARG cc_start: 0.8079 (mtm-85) cc_final: 0.6543 (mtp180)
REVERT: R  125 ARG cc_start: 0.8010 (mmm160) cc_final: 0.6879 (pmt-80)
  outliers start: 18
  outliers final: 6
  residues processed: 140
  average time/residue: 0.6692
  time to fit residues: 95.8020
Evaluate side-chains
  130 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 118
  time to evaluate  : 0.146 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain J residue  121 CYS
Chi-restraints excluded: chain L residue  121 CYS
Chi-restraints excluded: chain A residue  105 CYS
Chi-restraints excluded: chain G residue  105 CYS
Chi-restraints excluded: chain H residue  104 SER
Chi-restraints excluded: chain H residue  119 LEU
Chi-restraints excluded: chain H residue  125 ARG
Chi-restraints excluded: chain I residue  119 LEU
Chi-restraints excluded: chain N residue  110 MET
Chi-restraints excluded: chain O residue  110 MET
Chi-restraints excluded: chain P residue  110 MET
Chi-restraints excluded: chain R residue  117 SER
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 40
   random chunks:
   chunk 6 optimal weight:    6.9990
   chunk 11 optimal weight:    1.9990
   chunk 14 optimal weight:    1.9990
   chunk 31 optimal weight:    1.9990
   chunk 27 optimal weight:    1.9990
   chunk 24 optimal weight:    3.9990
   chunk 1 optimal weight:    0.6980
   chunk 16 optimal weight:    0.8980
   chunk 10 optimal weight:    3.9990
   chunk 26 optimal weight:    0.8980
   chunk 34 optimal weight:    2.9990
   overall best weight:    1.2984

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

Flipped N/Q/H residues before XYZ refinement:
** J 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** I 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
M 122 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4284 r_free = 0.4284 target = 0.152784 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3972 r_free = 0.3972 target = 0.121290 restraints weight = 4088.959|
|-----------------------------------------------------------------------------|
r_work (start): 0.3970 rms_B_bonded: 2.27
r_work: 0.3826 rms_B_bonded: 3.06 restraints_weight: 0.5000
r_work: 0.3687 rms_B_bonded: 4.81 restraints_weight: 0.2500
r_work (final): 0.3687
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8275
moved from start:          0.4864

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.065   3610  Z= 0.257
  Angle     :  0.651   5.792   4760  Z= 0.351
  Chirality :  0.045   0.121    420
  Planarity :  0.004   0.045    660
  Dihedral  :  4.835  27.215    560
  Min Nonbonded Distance : 2.570

Molprobity Statistics.
  All-atom Clashscore : 10.85
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.18 %
    Favored  : 91.82 %
  Rotamer:
    Outliers :  3.89 %
    Allowed  : 30.28 %
    Favored  : 65.83 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -3.79 (0.29), residues: 440
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.88 (0.22), residues: 440

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.011   0.001   ARG P 109 
 TYR   0.011   0.001   TYR K 126 
 PHE   0.010   0.001   PHE I 106 

Details of bonding type rmsd
  covalent geometry    : bond        0.00576 ( 3600)
  covalent geometry    : angle       0.64692 ( 4740)
  SS BOND              : bond        0.00567 (   10)
  SS BOND              : angle       1.30002 (   20)
  hydrogen bonds       : bond        0.02525 (   65)
  hydrogen bonds       : angle       5.55787 (  195)

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

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

  880 Ramachandran restraints generated.
    440 Oldfield, 0 Emsley, 440 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  880 Ramachandran restraints generated.
    440 Oldfield, 0 Emsley, 440 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  133 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 119
  time to evaluate  : 0.151 
Fit side-chains
REVERT: J  122 ASN cc_start: 0.8286 (t0) cc_final: 0.8014 (t0)
REVERT: J  125 ARG cc_start: 0.8366 (mtp180) cc_final: 0.7520 (mmm160)
REVERT: L  106 PHE cc_start: 0.7268 (m-80) cc_final: 0.6782 (p90)
REVERT: L  122 ASN cc_start: 0.8439 (t0) cc_final: 0.8102 (t160)
REVERT: L  125 ARG cc_start: 0.8014 (mtp-110) cc_final: 0.7240 (mmm160)
REVERT: i  125 ARG cc_start: 0.7984 (mmm160) cc_final: 0.7060 (mmp-170)
REVERT: B  125 ARG cc_start: 0.8020 (mtp-110) cc_final: 0.7582 (mtm-85)
REVERT: C  125 ARG cc_start: 0.8195 (mtp180) cc_final: 0.7908 (mtt-85)
REVERT: D  125 ARG cc_start: 0.8168 (OUTLIER) cc_final: 0.7944 (mtp180)
REVERT: E  125 ARG cc_start: 0.7913 (mtp85) cc_final: 0.7336 (mtm180)
REVERT: F  125 ARG cc_start: 0.7885 (mtp-110) cc_final: 0.7169 (mtt180)
REVERT: G  122 ASN cc_start: 0.8691 (m-40) cc_final: 0.8314 (m-40)
REVERT: H  106 PHE cc_start: 0.7468 (m-80) cc_final: 0.6839 (t80)
REVERT: I  119 LEU cc_start: 0.8658 (OUTLIER) cc_final: 0.8436 (mp)
REVERT: I  121 CYS cc_start: 0.8432 (p) cc_final: 0.8178 (m)
REVERT: I  122 ASN cc_start: 0.8258 (t0) cc_final: 0.7882 (t160)
REVERT: I  125 ARG cc_start: 0.8113 (mtp180) cc_final: 0.7538 (mtm110)
REVERT: K  110 MET cc_start: 0.8854 (mtt) cc_final: 0.8570 (mtt)
REVERT: K  121 CYS cc_start: 0.8655 (p) cc_final: 0.8249 (m)
REVERT: K  122 ASN cc_start: 0.8420 (t0) cc_final: 0.7987 (t160)
REVERT: M  106 PHE cc_start: 0.8058 (m-10) cc_final: 0.7829 (m-10)
REVERT: M  116 GLN cc_start: 0.8727 (tm-30) cc_final: 0.8421 (tm-30)
REVERT: M  125 ARG cc_start: 0.7667 (mmt90) cc_final: 0.7052 (mmm-85)
REVERT: N  110 MET cc_start: 0.9047 (OUTLIER) cc_final: 0.8629 (mtm)
REVERT: N  122 ASN cc_start: 0.8733 (m110) cc_final: 0.8416 (m110)
REVERT: O  110 MET cc_start: 0.8820 (OUTLIER) cc_final: 0.8425 (mtp)
REVERT: P  110 MET cc_start: 0.9051 (OUTLIER) cc_final: 0.8753 (mtp)
REVERT: Q  112 ARG cc_start: 0.8257 (mtt180) cc_final: 0.6639 (mtp180)
REVERT: R  109 ARG cc_start: 0.7454 (ttm110) cc_final: 0.6309 (tpm170)
REVERT: R  112 ARG cc_start: 0.8097 (mtm-85) cc_final: 0.6502 (mtp180)
REVERT: R  116 GLN cc_start: 0.8687 (OUTLIER) cc_final: 0.7815 (tt0)
REVERT: R  125 ARG cc_start: 0.8015 (mmm160) cc_final: 0.6783 (pmt-80)
  outliers start: 14
  outliers final: 5
  residues processed: 127
  average time/residue: 0.6975
  time to fit residues: 90.5556
Evaluate side-chains
  123 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 112
  time to evaluate  : 0.147 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain L residue  103 SER
Chi-restraints excluded: chain L residue  121 CYS
Chi-restraints excluded: chain D residue  125 ARG
Chi-restraints excluded: chain H residue  104 SER
Chi-restraints excluded: chain H residue  119 LEU
Chi-restraints excluded: chain I residue  119 LEU
Chi-restraints excluded: chain N residue  110 MET
Chi-restraints excluded: chain O residue  110 MET
Chi-restraints excluded: chain P residue  110 MET
Chi-restraints excluded: chain R residue  116 GLN
Chi-restraints excluded: chain R residue  117 SER
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 40
   random chunks:
   chunk 22 optimal weight:    2.9990
   chunk 14 optimal weight:    0.9990
   chunk 3 optimal weight:    2.9990
   chunk 7 optimal weight:    0.0870
   chunk 36 optimal weight:    3.9990
   chunk 1 optimal weight:    0.5980
   chunk 9 optimal weight:    0.5980
   chunk 23 optimal weight:    0.6980
   chunk 34 optimal weight:    2.9990
   chunk 35 optimal weight:    0.9990
   chunk 18 optimal weight:    1.9990
   overall best weight:    0.5960

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

Flipped N/Q/H residues before XYZ refinement:
** J 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** I 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
M 122 ASN
R 122 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4368 r_free = 0.4368 target = 0.160939 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.4053 r_free = 0.4053 target = 0.128977 restraints weight = 4005.122|
|-----------------------------------------------------------------------------|
r_work (start): 0.4044 rms_B_bonded: 2.28
r_work: 0.3907 rms_B_bonded: 3.03 restraints_weight: 0.5000
r_work: 0.3768 rms_B_bonded: 4.81 restraints_weight: 0.2500
r_work (final): 0.3768
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8226
moved from start:          0.4947

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   3610  Z= 0.144
  Angle     :  0.567   5.948   4760  Z= 0.303
  Chirality :  0.040   0.117    420
  Planarity :  0.004   0.048    660
  Dihedral  :  4.248  22.556    560
  Min Nonbonded Distance : 2.590

Molprobity Statistics.
  All-atom Clashscore : 9.09
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.00 %
    Favored  : 95.00 %
  Rotamer:
    Outliers :  3.33 %
    Allowed  : 30.56 %
    Favored  : 66.11 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -3.63 (0.31), residues: 440
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.76 (0.23), residues: 440

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.011   0.001   ARG K 109 
 TYR   0.010   0.001   TYR K 126 
 PHE   0.010   0.001   PHE O 106 

Details of bonding type rmsd
  covalent geometry    : bond        0.00326 ( 3600)
  covalent geometry    : angle       0.56553 ( 4740)
  SS BOND              : bond        0.00311 (   10)
  SS BOND              : angle       0.90373 (   20)
  hydrogen bonds       : bond        0.02069 (   65)
  hydrogen bonds       : angle       5.31322 (  195)

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

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

  880 Ramachandran restraints generated.
    440 Oldfield, 0 Emsley, 440 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  880 Ramachandran restraints generated.
    440 Oldfield, 0 Emsley, 440 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  134 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 122
  time to evaluate  : 0.150 
Fit side-chains
   revert: symmetry clash
REVERT: J  122 ASN cc_start: 0.8312 (t0) cc_final: 0.8042 (t0)
REVERT: J  125 ARG cc_start: 0.8256 (mtp180) cc_final: 0.7440 (mmm160)
REVERT: L  106 PHE cc_start: 0.6758 (m-80) cc_final: 0.6550 (p90)
REVERT: L  122 ASN cc_start: 0.8331 (t0) cc_final: 0.7916 (t0)
REVERT: L  125 ARG cc_start: 0.7958 (mtp-110) cc_final: 0.7176 (mmm160)
REVERT: i  110 MET cc_start: 0.8888 (mtm) cc_final: 0.8588 (mtm)
REVERT: i  125 ARG cc_start: 0.7962 (mmm160) cc_final: 0.6998 (mmp-170)
REVERT: B  125 ARG cc_start: 0.7941 (mtp-110) cc_final: 0.7528 (mtm-85)
REVERT: C  125 ARG cc_start: 0.8283 (mtp180) cc_final: 0.7975 (mtt-85)
REVERT: E  125 ARG cc_start: 0.7899 (mtp85) cc_final: 0.7399 (mtm180)
REVERT: F  125 ARG cc_start: 0.7793 (mtp-110) cc_final: 0.7132 (mtt180)
REVERT: G  105 CYS cc_start: 0.7590 (OUTLIER) cc_final: 0.7338 (m)
REVERT: G  122 ASN cc_start: 0.8683 (m-40) cc_final: 0.8278 (m-40)
REVERT: H  106 PHE cc_start: 0.7274 (m-80) cc_final: 0.6783 (t80)
REVERT: H  125 ARG cc_start: 0.7541 (mtt-85) cc_final: 0.7291 (mtt90)
REVERT: I  122 ASN cc_start: 0.8204 (t0) cc_final: 0.7833 (t160)
REVERT: I  125 ARG cc_start: 0.8083 (mtp180) cc_final: 0.7511 (mtm110)
REVERT: K  110 MET cc_start: 0.8786 (mtt) cc_final: 0.8504 (mtt)
REVERT: K  121 CYS cc_start: 0.8602 (p) cc_final: 0.8292 (m)
REVERT: M  116 GLN cc_start: 0.8672 (tm-30) cc_final: 0.8373 (tm-30)
REVERT: M  125 ARG cc_start: 0.7653 (mmt90) cc_final: 0.7115 (mmt180)
REVERT: N  122 ASN cc_start: 0.8694 (m110) cc_final: 0.8358 (m110)
REVERT: Q  112 ARG cc_start: 0.8259 (mtt180) cc_final: 0.6612 (mtp180)
REVERT: R  112 ARG cc_start: 0.8068 (mtm-85) cc_final: 0.6545 (mtp180)
REVERT: R  116 GLN cc_start: 0.8641 (OUTLIER) cc_final: 0.7772 (tt0)
REVERT: R  125 ARG cc_start: 0.7989 (mmm160) cc_final: 0.6799 (pmt-80)
  outliers start: 12
  outliers final: 6
  residues processed: 128
  average time/residue: 0.6819
  time to fit residues: 89.3149
Evaluate side-chains
  119 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 111
  time to evaluate  : 0.148 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain L residue  103 SER
Chi-restraints excluded: chain L residue  121 CYS
Chi-restraints excluded: chain F residue  117 SER
Chi-restraints excluded: chain G residue  105 CYS
Chi-restraints excluded: chain H residue  104 SER
Chi-restraints excluded: chain H residue  119 LEU
Chi-restraints excluded: chain R residue  116 GLN
Chi-restraints excluded: chain R residue  117 SER
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 40
   random chunks:
   chunk 17 optimal weight:    0.9990
   chunk 28 optimal weight:    3.9990
   chunk 23 optimal weight:    4.9990
   chunk 13 optimal weight:    1.9990
   chunk 29 optimal weight:    0.8980
   chunk 31 optimal weight:    0.8980
   chunk 2 optimal weight:    3.9990
   chunk 5 optimal weight:    0.8980
   chunk 32 optimal weight:    0.6980
   chunk 11 optimal weight:    2.9990
   chunk 0 optimal weight:    3.9990
   overall best weight:    0.8782

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

Flipped N/Q/H residues before XYZ refinement:
** J 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** I 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
M 122 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4317 r_free = 0.4317 target = 0.154697 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3999 r_free = 0.3999 target = 0.123020 restraints weight = 4142.890|
|-----------------------------------------------------------------------------|
r_work (start): 0.4007 rms_B_bonded: 2.32
r_work: 0.3864 rms_B_bonded: 3.10 restraints_weight: 0.5000
r_work: 0.3723 rms_B_bonded: 4.90 restraints_weight: 0.2500
r_work (final): 0.3723
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8252
moved from start:          0.5066

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.033   3610  Z= 0.188
  Angle     :  0.622   6.756   4760  Z= 0.332
  Chirality :  0.043   0.127    420
  Planarity :  0.004   0.054    660
  Dihedral  :  4.409  23.638    560
  Min Nonbonded Distance : 2.568

Molprobity Statistics.
  All-atom Clashscore : 11.00
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.50 %
    Favored  : 92.50 %
  Rotamer:
    Outliers :  3.06 %
    Allowed  : 33.06 %
    Favored  : 63.89 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -3.66 (0.31), residues: 440
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.78 (0.23), residues: 440

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.012   0.001   ARG K 109 
 TYR   0.009   0.001   TYR K 126 
 PHE   0.011   0.001   PHE G 106 

Details of bonding type rmsd
  covalent geometry    : bond        0.00423 ( 3600)
  covalent geometry    : angle       0.62041 ( 4740)
  SS BOND              : bond        0.00428 (   10)
  SS BOND              : angle       0.99089 (   20)
  hydrogen bonds       : bond        0.02183 (   65)
  hydrogen bonds       : angle       5.37752 (  195)

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

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

  880 Ramachandran restraints generated.
    440 Oldfield, 0 Emsley, 440 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  880 Ramachandran restraints generated.
    440 Oldfield, 0 Emsley, 440 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  130 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 119
  time to evaluate  : 0.087 
Fit side-chains
REVERT: J  122 ASN cc_start: 0.8392 (t0) cc_final: 0.8128 (t0)
REVERT: J  125 ARG cc_start: 0.8328 (mtp180) cc_final: 0.7433 (mmm160)
REVERT: L  106 PHE cc_start: 0.7163 (m-80) cc_final: 0.6712 (p90)
REVERT: L  122 ASN cc_start: 0.8321 (t0) cc_final: 0.7903 (t0)
REVERT: L  125 ARG cc_start: 0.7990 (mtp-110) cc_final: 0.7197 (mmm160)
REVERT: i  125 ARG cc_start: 0.7892 (mmm160) cc_final: 0.6904 (mmp-170)
REVERT: B  125 ARG cc_start: 0.7968 (mtp-110) cc_final: 0.7449 (mtm-85)
REVERT: C  125 ARG cc_start: 0.8291 (mtp180) cc_final: 0.7951 (mtt-85)
REVERT: E  125 ARG cc_start: 0.7920 (mtp85) cc_final: 0.7370 (mtm180)
REVERT: G  122 ASN cc_start: 0.8694 (m-40) cc_final: 0.8227 (m-40)
REVERT: H  106 PHE cc_start: 0.7227 (m-80) cc_final: 0.6718 (t80)
REVERT: I  110 MET cc_start: 0.8747 (mtm) cc_final: 0.8279 (mtt)
REVERT: I  119 LEU cc_start: 0.8601 (OUTLIER) cc_final: 0.8333 (mp)
REVERT: I  121 CYS cc_start: 0.8434 (p) cc_final: 0.7977 (m)
REVERT: I  122 ASN cc_start: 0.8269 (t0) cc_final: 0.7822 (t160)
REVERT: I  125 ARG cc_start: 0.8075 (mtp180) cc_final: 0.7476 (mtm110)
REVERT: K  110 MET cc_start: 0.8826 (mtt) cc_final: 0.8529 (mtt)
REVERT: K  121 CYS cc_start: 0.8654 (p) cc_final: 0.8310 (m)
REVERT: M  125 ARG cc_start: 0.7640 (mmt90) cc_final: 0.7093 (mmt180)
REVERT: N  122 ASN cc_start: 0.8717 (m110) cc_final: 0.8421 (m110)
REVERT: P  110 MET cc_start: 0.8976 (OUTLIER) cc_final: 0.8594 (mtp)
REVERT: Q  112 ARG cc_start: 0.8264 (mtt180) cc_final: 0.6652 (mtp180)
REVERT: R  109 ARG cc_start: 0.7406 (ttm110) cc_final: 0.6262 (tpm170)
REVERT: R  112 ARG cc_start: 0.8105 (mtm-85) cc_final: 0.6537 (mtp180)
REVERT: R  116 GLN cc_start: 0.8668 (OUTLIER) cc_final: 0.7813 (tt0)
REVERT: R  125 ARG cc_start: 0.7998 (mmm160) cc_final: 0.6731 (pmt-80)
  outliers start: 11
  outliers final: 6
  residues processed: 125
  average time/residue: 0.4792
  time to fit residues: 61.2745
Evaluate side-chains
  122 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 113
  time to evaluate  : 0.086 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain L residue  103 SER
Chi-restraints excluded: chain L residue  121 CYS
Chi-restraints excluded: chain F residue  117 SER
Chi-restraints excluded: chain H residue  104 SER
Chi-restraints excluded: chain H residue  119 LEU
Chi-restraints excluded: chain I residue  119 LEU
Chi-restraints excluded: chain P residue  110 MET
Chi-restraints excluded: chain R residue  116 GLN
Chi-restraints excluded: chain R residue  117 SER
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 40
   random chunks:
   chunk 29 optimal weight:    2.9990
   chunk 26 optimal weight:    2.9990
   chunk 2 optimal weight:    3.9990
   chunk 14 optimal weight:    7.9990
   chunk 36 optimal weight:    0.0030
   chunk 17 optimal weight:    1.9990
   chunk 19 optimal weight:    0.5980
   chunk 37 optimal weight:    3.9990
   chunk 35 optimal weight:    0.9980
   chunk 9 optimal weight:    0.6980
   chunk 6 optimal weight:    2.9990
   overall best weight:    0.8592

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

Flipped N/Q/H residues before XYZ refinement:
** J 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** I 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** M 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
M 122 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4338 r_free = 0.4338 target = 0.158032 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 25)----------------|
| r_work = 0.4017 r_free = 0.4017 target = 0.126114 restraints weight = 4002.526|
|-----------------------------------------------------------------------------|
r_work (start): 0.4010 rms_B_bonded: 2.27
r_work: 0.3865 rms_B_bonded: 3.05 restraints_weight: 0.5000
r_work: 0.3720 rms_B_bonded: 4.83 restraints_weight: 0.2500
r_work (final): 0.3720
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8268
moved from start:          0.5160

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.035   3610  Z= 0.188
  Angle     :  0.641   7.349   4760  Z= 0.344
  Chirality :  0.042   0.140    420
  Planarity :  0.005   0.057    660
  Dihedral  :  4.434  23.533    560
  Min Nonbonded Distance : 2.563

Molprobity Statistics.
  All-atom Clashscore : 11.88
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.36 %
    Favored  : 93.64 %
  Rotamer:
    Outliers :  2.50 %
    Allowed  : 34.72 %
    Favored  : 62.78 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -3.72 (0.31), residues: 440
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.83 (0.23), residues: 440

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.014   0.001   ARG K 109 
 TYR   0.009   0.001   TYR K 126 
 PHE   0.010   0.001   PHE O 106 

Details of bonding type rmsd
  covalent geometry    : bond        0.00427 ( 3600)
  covalent geometry    : angle       0.63887 ( 4740)
  SS BOND              : bond        0.00399 (   10)
  SS BOND              : angle       0.99945 (   20)
  hydrogen bonds       : bond        0.02194 (   65)
  hydrogen bonds       : angle       5.31468 (  195)

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

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

  880 Ramachandran restraints generated.
    440 Oldfield, 0 Emsley, 440 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  880 Ramachandran restraints generated.
    440 Oldfield, 0 Emsley, 440 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  127 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 118
  time to evaluate  : 0.088 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: J  122 ASN cc_start: 0.8407 (t0) cc_final: 0.8135 (t0)
REVERT: J  125 ARG cc_start: 0.8345 (mtp180) cc_final: 0.7492 (mmm160)
REVERT: L  106 PHE cc_start: 0.7159 (m-80) cc_final: 0.6731 (p90)
REVERT: L  122 ASN cc_start: 0.8331 (t0) cc_final: 0.7921 (t0)
REVERT: L  125 ARG cc_start: 0.7975 (mtp-110) cc_final: 0.7225 (mmm160)
REVERT: i  125 ARG cc_start: 0.7825 (mmm160) cc_final: 0.6839 (mmp-170)
REVERT: B  125 ARG cc_start: 0.7988 (mtp-110) cc_final: 0.7572 (mtm-85)
REVERT: C  125 ARG cc_start: 0.8302 (mtp180) cc_final: 0.8067 (mtt-85)
REVERT: E  125 ARG cc_start: 0.7927 (mtp85) cc_final: 0.7655 (mtp180)
REVERT: F  125 ARG cc_start: 0.7809 (mtp-110) cc_final: 0.7135 (mtt180)
REVERT: G  122 ASN cc_start: 0.8727 (m-40) cc_final: 0.8377 (m-40)
REVERT: H  106 PHE cc_start: 0.7245 (m-80) cc_final: 0.6704 (t80)
REVERT: I  110 MET cc_start: 0.8738 (mtm) cc_final: 0.8327 (mtt)
REVERT: I  122 ASN cc_start: 0.8229 (t0) cc_final: 0.7864 (t160)
REVERT: I  125 ARG cc_start: 0.8088 (mtp180) cc_final: 0.7518 (mtm110)
REVERT: K  109 ARG cc_start: 0.7907 (mtp-110) cc_final: 0.7374 (ttm110)
REVERT: K  110 MET cc_start: 0.8833 (mtt) cc_final: 0.8554 (mtt)
REVERT: M  125 ARG cc_start: 0.7602 (mmt90) cc_final: 0.7125 (mmt180)
REVERT: N  116 GLN cc_start: 0.8632 (tm-30) cc_final: 0.8420 (tp-100)
REVERT: N  122 ASN cc_start: 0.8725 (m110) cc_final: 0.8408 (m110)
REVERT: P  110 MET cc_start: 0.8943 (OUTLIER) cc_final: 0.8205 (mpp)
REVERT: Q  112 ARG cc_start: 0.8242 (mtt180) cc_final: 0.6688 (mtp180)
REVERT: R  109 ARG cc_start: 0.7397 (ttm110) cc_final: 0.6297 (tpm170)
REVERT: R  112 ARG cc_start: 0.8112 (mtm-85) cc_final: 0.6551 (mtp180)
REVERT: R  116 GLN cc_start: 0.8650 (OUTLIER) cc_final: 0.7709 (tt0)
REVERT: R  125 ARG cc_start: 0.8017 (mmm160) cc_final: 0.6759 (pmt-80)
  outliers start: 9
  outliers final: 5
  residues processed: 123
  average time/residue: 0.5478
  time to fit residues: 69.0362
Evaluate side-chains
  120 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 113
  time to evaluate  : 0.142 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain L residue  103 SER
Chi-restraints excluded: chain L residue  121 CYS
Chi-restraints excluded: chain F residue  117 SER
Chi-restraints excluded: chain H residue  104 SER
Chi-restraints excluded: chain P residue  110 MET
Chi-restraints excluded: chain R residue  116 GLN
Chi-restraints excluded: chain R residue  117 SER
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 40
   random chunks:
   chunk 6 optimal weight:    6.9990
   chunk 4 optimal weight:    2.9990
   chunk 35 optimal weight:    0.4980
   chunk 13 optimal weight:    3.9990
   chunk 10 optimal weight:    4.9990
   chunk 20 optimal weight:    4.9990
   chunk 18 optimal weight:    3.9990
   chunk 31 optimal weight:    3.9990
   chunk 36 optimal weight:    3.9990
   chunk 28 optimal weight:    1.9990
   chunk 17 optimal weight:    1.9990
   overall best weight:    2.2988

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

Flipped N/Q/H residues before XYZ refinement:
** J 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** I 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
M 116 GLN
M 122 ASN
R 122 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4264 r_free = 0.4264 target = 0.151392 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3941 r_free = 0.3941 target = 0.120021 restraints weight = 4098.696|
|-----------------------------------------------------------------------------|
r_work (start): 0.3928 rms_B_bonded: 2.24
r_work: 0.3779 rms_B_bonded: 3.02 restraints_weight: 0.5000
r_work: 0.3637 rms_B_bonded: 4.76 restraints_weight: 0.2500
r_work (final): 0.3637
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8339
moved from start:          0.5387

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.009   0.055   3610  Z= 0.418
  Angle     :  0.830   8.017   4760  Z= 0.445
  Chirality :  0.053   0.213    420
  Planarity :  0.006   0.052    660
  Dihedral  :  5.661  31.194    560
  Min Nonbonded Distance : 2.543

Molprobity Statistics.
  All-atom Clashscore : 12.61
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 11.82 %
    Favored  : 88.18 %
  Rotamer:
    Outliers :  2.78 %
    Allowed  : 33.89 %
    Favored  : 63.33 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -3.89 (0.29), residues: 440
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.96 (0.22), residues: 440

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.011   0.001   ARG K 109 
 TYR   0.008   0.002   TYR R 126 
 PHE   0.015   0.002   PHE I 106 

Details of bonding type rmsd
  covalent geometry    : bond        0.00923 ( 3600)
  covalent geometry    : angle       0.82410 ( 4740)
  SS BOND              : bond        0.00816 (   10)
  SS BOND              : angle       1.71736 (   20)
  hydrogen bonds       : bond        0.03253 (   65)
  hydrogen bonds       : angle       5.79934 (  195)

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

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

  880 Ramachandran restraints generated.
    440 Oldfield, 0 Emsley, 440 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  880 Ramachandran restraints generated.
    440 Oldfield, 0 Emsley, 440 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  136 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 126
  time to evaluate  : 0.147 
Fit side-chains
   revert: symmetry clash
REVERT: J  122 ASN cc_start: 0.8583 (t0) cc_final: 0.8276 (t0)
REVERT: J  125 ARG cc_start: 0.8377 (mtp180) cc_final: 0.7537 (mmm160)
REVERT: L  106 PHE cc_start: 0.7388 (m-80) cc_final: 0.7046 (p90)
REVERT: L  122 ASN cc_start: 0.8529 (t0) cc_final: 0.8174 (t160)
REVERT: L  125 ARG cc_start: 0.8066 (mtp-110) cc_final: 0.7284 (mmm160)
REVERT: i  125 ARG cc_start: 0.7979 (mmm160) cc_final: 0.6978 (mmp-170)
REVERT: B  125 ARG cc_start: 0.8045 (mtp-110) cc_final: 0.7625 (mtm-85)
REVERT: C  125 ARG cc_start: 0.8247 (mtp180) cc_final: 0.8019 (mtt-85)
REVERT: E  125 ARG cc_start: 0.8136 (mtp85) cc_final: 0.7551 (mtm180)
REVERT: F  125 ARG cc_start: 0.7922 (mtp-110) cc_final: 0.7191 (mtt180)
REVERT: G  105 CYS cc_start: 0.7566 (m) cc_final: 0.6868 (p)
REVERT: G  122 ASN cc_start: 0.8766 (m-40) cc_final: 0.8332 (m-40)
REVERT: H  106 PHE cc_start: 0.7538 (m-80) cc_final: 0.6883 (t80)
REVERT: I  110 MET cc_start: 0.8816 (mtm) cc_final: 0.8405 (mtt)
REVERT: I  119 LEU cc_start: 0.8760 (OUTLIER) cc_final: 0.8511 (mp)
REVERT: I  121 CYS cc_start: 0.8384 (p) cc_final: 0.8108 (m)
REVERT: I  122 ASN cc_start: 0.8257 (t0) cc_final: 0.7854 (t160)
REVERT: I  125 ARG cc_start: 0.8151 (mtp180) cc_final: 0.7594 (mtm110)
REVERT: K  122 ASN cc_start: 0.8417 (t0) cc_final: 0.8026 (t160)
REVERT: M  125 ARG cc_start: 0.7733 (mmt90) cc_final: 0.7214 (mmt180)
REVERT: N  122 ASN cc_start: 0.8780 (m110) cc_final: 0.8463 (m110)
REVERT: P  110 MET cc_start: 0.9068 (OUTLIER) cc_final: 0.8786 (mtp)
REVERT: Q  112 ARG cc_start: 0.8343 (mtt180) cc_final: 0.6735 (mtp180)
REVERT: R  109 ARG cc_start: 0.7476 (ttm110) cc_final: 0.6407 (mmp-170)
REVERT: R  112 ARG cc_start: 0.8106 (mtm-85) cc_final: 0.6547 (mtp180)
REVERT: R  116 GLN cc_start: 0.8707 (OUTLIER) cc_final: 0.7906 (tt0)
REVERT: R  125 ARG cc_start: 0.8051 (mmm160) cc_final: 0.6750 (pmt-80)
  outliers start: 10
  outliers final: 5
  residues processed: 133
  average time/residue: 0.6196
  time to fit residues: 84.3268
Evaluate side-chains
  128 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 120
  time to evaluate  : 0.143 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain L residue  103 SER
Chi-restraints excluded: chain L residue  121 CYS
Chi-restraints excluded: chain F residue  117 SER
Chi-restraints excluded: chain H residue  104 SER
Chi-restraints excluded: chain I residue  119 LEU
Chi-restraints excluded: chain P residue  110 MET
Chi-restraints excluded: chain R residue  116 GLN
Chi-restraints excluded: chain R residue  117 SER
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 40
   random chunks:
   chunk 30 optimal weight:    3.9990
   chunk 19 optimal weight:    0.6980
   chunk 0 optimal weight:    2.9990
   chunk 37 optimal weight:    0.3980
   chunk 18 optimal weight:    0.8980
   chunk 36 optimal weight:    0.4980
   chunk 25 optimal weight:    0.5980
   chunk 6 optimal weight:    4.9990
   chunk 21 optimal weight:    2.9990
   chunk 29 optimal weight:    0.9980
   chunk 4 optimal weight:    1.9990
   overall best weight:    0.6180

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

Flipped N/Q/H residues before XYZ refinement:
** J 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** I 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
M 116 GLN
M 122 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4351 r_free = 0.4351 target = 0.158000 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.4045 r_free = 0.4045 target = 0.126493 restraints weight = 3941.096|
|-----------------------------------------------------------------------------|
r_work (start): 0.4051 rms_B_bonded: 2.29
r_work: 0.3909 rms_B_bonded: 3.05 restraints_weight: 0.5000
r_work: 0.3770 rms_B_bonded: 4.83 restraints_weight: 0.2500
r_work (final): 0.3770
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8229
moved from start:          0.5370

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.041   3610  Z= 0.163
  Angle     :  0.656   7.393   4760  Z= 0.347
  Chirality :  0.042   0.121    420
  Planarity :  0.005   0.060    660
  Dihedral  :  4.652  24.775    560
  Min Nonbonded Distance : 2.580

Molprobity Statistics.
  All-atom Clashscore : 10.85
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.77 %
    Favored  : 95.23 %
  Rotamer:
    Outliers :  2.78 %
    Allowed  : 34.44 %
    Favored  : 62.78 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -3.73 (0.31), residues: 440
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.83 (0.23), residues: 440

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.014   0.001   ARG K 109 
 TYR   0.009   0.001   TYR K 126 
 PHE   0.011   0.001   PHE N 106 

Details of bonding type rmsd
  covalent geometry    : bond        0.00379 ( 3600)
  covalent geometry    : angle       0.65360 ( 4740)
  SS BOND              : bond        0.00307 (   10)
  SS BOND              : angle       1.02007 (   20)
  hydrogen bonds       : bond        0.02459 (   65)
  hydrogen bonds       : angle       5.53470 (  195)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1939.53 seconds
wall clock time: 33 minutes 52.80 seconds (2032.80 seconds total)